[ { "path": ".github/workflows/request-10GB-CI.yml", "content": "name: Request 10GB-CI\n\non:\n push:\n pull_request:\n\njobs:\n request-10GB-CI:\n runs-on: ubuntu-latest\n steps:\n - name: Request 10GB-CI\n run: |\n echo \"Event '${{ github.event.action }}' received from '${{ github.event.client_payload.repository }}'\"\n curl -X POST https://api.github.com/repos/webyrd/mediKanren-ops/dispatches \\\n -H 'Accept: application/vnd.github.everest-preview+json' \\\n -u ${{ secrets.GH_ACCESS_TOKEN }} \\\n --data '{\"event_type\": \"request-10GB-CI\", \"client_payload\": {\n \"repository\": \"'\"$GITHUB_REPOSITORY\"'\",\n \"github_sha1\": \"'$GITHUB_SHA1'\",\n \"github_ref\": \"'$GITHUB_REF'\",\n \"github_head_ref\": \"'$GITHUB_HEAD_REF'\",\n \"github_base_ref\": \"'$GITHUB_BASE_REF'\"\n }}'\n" }, { "path": ".gitignore", "content": ".DS_Store\n/ci_artifacts\n/code/semmed/publication-reference.scm\n/code/semmed/edge-by-object\n/code/semmed/edge-by-predicate\n/code/semmed/edge-by-subject\n/code/a.out\n/biolink/pieces-parts/etl_for_new_KGs/NCT000sample\n/biolink/pieces-parts/etl_for_new_KGs/NCT000sample/*.xml\nmedikanren/config.scm\nmedikanren2/config.scm\nmedikanren2/etc/config.scm\nmedikanren2/etc/config.installer.scm\n*.dep\n*.zo\n" }, { "path": "LICENSE", "content": "The MIT License (MIT)\n\nCopyright (c) 2017 William E. Byrd and Gregory Rosenblatt\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n" }, { "path": "Makefile", "content": "\nadirRepo := $(shell cd $(dir $(firstword $(MAKEFILE_LIST))) && pwd)\n# https://stackoverflow.com/questions/322936/common-gnu-makefile-directory-path\n\ndefault:\n\t@echo ***available targets***: prepare_ci, run_ci, install_pkgs\n\nprepare_ci:\n\t@echo about to setup_artifacts\n\t@mkdir -p $(adirRepo)/ci_artifacts\n\t@rm -rf $(adirRepo)/ci_artifacts/status\n\t@mkdir -p $(adirRepo)/ci_artifacts/status/pass\n\t@touch $(adirRepo)/ci_artifacts/status/pass/empty\n\t@mkdir -p $(adirRepo)/ci_artifacts/status/fail\n\t@touch $(adirRepo)/ci_artifacts/status/fail/empty\n\t@echo finished setup_artifacts\n\nrun_ci: prepare_ci\n\t-bash $(adirRepo)/medikanren/.run_ci.sh\n\t-bash $(adirRepo)/medikanren2/.run_ci.sh\n\ninstall_pkgs:\n\t-bash $(adirRepo)/medikanren/.install_pkgs.sh\n\t-bash $(adirRepo)/medikanren2/.install_pkgs.sh\n\n" }, { "path": "README.md", "content": "# mediKanren\n\n*** FOR RESEARCH PURPOSES ONLY ***\n\nProof-of-concept for reasoning over medical knowledge graphs, using miniKanren + heuristics + indexing.\n\nThere are several prototypes, each in its directory:\n\n- [`attic/code`](attic/code) is the original prototype.\n- [`medikanren`](medikanren) is the working prototype.\n- [`medikanren2`](medikanren2) is the next-generation prototype.\n\nContributed use cases, queries and applications are now located in a directory separate from medikanren itself:\n\n- [contrib/](contrib)\n\nIf you have previously contributed code applying medikanren and can't find yours, look there.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" }, { "path": "attic/code/README.md", "content": "# mediKanren\n\n*** FOR RESEARCH PURPOSES ONLY ***\n\nProof-of-concept for reasoning over the SemMedDB knowledge base, using miniKanren + heuristics + indexing.\n\n`./code/study-imatinib.rkt` contains the most iteresting examples currently.\n\nTODO: add SemMedDB files, along with terms of use information for SemMedDB.\n\nTODO: add simple instructions for running the queries.\n\n\n## Setup\n\n### Download and install Racket\n\nhttps://download.racket-lang.org/\n\n\n### Obtain a CSV dump of SemMed DB\n\nYou'll need to obtain the full data from: https://skr3.nlm.nih.gov/SemMedDB/\n\nA small sample, `code/sample_semmed.csv`, is provided to demonstrate the format expected for processing.\n\n\n### Index the data for consumption by mediKanren\n\nGiven `semmed.csv`, Run these commands from the `code` directory:\n\n```\nmkdir semmed\n\nracket csv-semmed-ordered-unique-enum.rkt semmed.csv semmed\n\nracket csv-semmed-simplify.rkt semmed.csv semmed\n\nracket semmed-index-predicate.rkt semmed\n```\n\nDepending on the size of the CSV you're using, these commands could take up to a few hours to process all records.\n\n\n## Use\n\n### Interact with the GUI\n\nThe GUI is a convenient way to express some forms of simple queries. For more power, see the section on running queries programmatically.\n\nFrom the `code` directory, run `racket gui-simple.rkt` to start the GUI.\n\nAs you interact, the console will display additional information in some cases.\n\n* When clicking on results, the corresponding PubMed URLs will be printed for your convenience. If you're running on OSX within iTerm2, you can CMD+click a URL to open it in the browser.\n* When querying with synthetic predicates such as `increases[*]/decreases[*]`, the results will not be displayed in the GUI, but will instead be continuously streamed to the console.\n\n\n### Run queries programmatically\n\nStart with `code/tacrine.rkt` `code/imatinib-query.rkt`, which includes queries taken from `code/study-imatinib.rkt`, and also includes a high-level description of the queries.\n\nTake a look at the various `study-*.rkt` files in the `code` directory for examples. You can run these from the command line, e.g., `racket study-imatinib.rkt`.\n\n\nTo write your own queries, either as a new `*.rkt` file or interactively, start with:\n\n```\n(require \"mk-db.rkt\")\n```\n\nto load the database and its indices (this will take several seconds, so be patient). Once loaded, you will have access to the full underlying miniKanren language, plus the new semmed-specific relations:\n\n```\n(concepto c)\n(fuzzy-concepto name c)\n(cuio c cui)\n(cui*o c cui*)\n(edgeo `(,subject-concept ,object-concept ,predicate ,subject-type ,object-type ,pubref))\n```\n\nwhich you can compose freely in queries. Being that mediKanren is an embedded DSL, you also have access to Racket for metaprogramming.\n" }, { "path": "attic/code/concept.rkt", "content": "#lang racket/base\n(provide\n concept-cui\n concept-name\n concept-type\n )\n\n(define (concept-cui concept) (vector-ref concept 0))\n(define (concept-name concept) (vector-ref concept 1))\n(define (concept-type concept) (vector-ref concept 2))\n" }, { "path": "attic/code/csv-semmed-ordered-unique-enum.rkt", "content": "#lang racket/base\n(require\n \"csv.rkt\"\n (except-in racket/control set)\n racket/set)\n\n;; This is the pre-normalization pass, which generates two files:\n\n;; * PREDICATE.scm\n;; * SEMTYPE.scm\n\n;; Each of these contains all unique string values for the corresponding\n;; field types, sorted. These are mapped to numeric indices during\n;; normalization.\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(IN_CSV OUT_DIR))\n\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n (error 'cmd-line-args (format \"expected ~s; given ~s\" argv-expected argv)))\n\n(define csv-file-name (vector-ref argv 0))\n(define out-dir (vector-ref argv 1))\n\n(define predicate-file-name (build-path out-dir \"PREDICATE.scm\"))\n(define semtype-file-name (build-path out-dir \"SEMTYPE.scm\"))\n\n(define (print-ordered-unique out-predicate out-semtype)\n (define (yield record)\n (define predicate (list-ref record 3))\n (define subject-semtype (list-ref record 6))\n (define object-semtype (list-ref record 10))\n (shift k (cons (list predicate subject-semtype object-semtype) k)))\n (lambda (in)\n (read-line in 'any) ;; Skip header.\n (let loop ((count 1)\n (seen-predicate (set))\n (seen-semtype (set))\n (next (reset (and ((csv-records yield) in) #f))))\n (when (= 0 (remainder count 100000))\n (printf \"processed ~s rows\\n\" count)\n (flush-output out-predicate)\n (flush-output out-semtype))\n (if next\n (let* ((data (car next))\n (predicate (list-ref data 0))\n (subject-semtype (list-ref data 1))\n (object-semtype (list-ref data 2))\n (k (cdr next))\n (seen-predicate2\n (if (set-member? seen-predicate predicate)\n seen-predicate\n (begin\n (printf \"~s\\n\" `(new predicate: ,predicate))\n (set-add seen-predicate predicate))))\n (seen-semtype2\n (if (set-member? seen-semtype subject-semtype)\n seen-semtype\n (begin\n (printf \"~s\\n\" `(new semtype: ,subject-semtype))\n (set-add seen-semtype subject-semtype))))\n (seen-semtype3\n (if (set-member? seen-semtype2 object-semtype)\n seen-semtype2\n (begin\n (printf \"~s\\n\" `(new semtype: ,object-semtype))\n (set-add seen-semtype2 object-semtype)))))\n (loop (+ 1 count) seen-predicate2 seen-semtype3 (k #t)))\n (begin\n (printf \"writing files:\\n~s\\n~s\\n\"\n (expand-user-path predicate-file-name)\n (expand-user-path semtype-file-name))\n (for ((predicate (sort (set->list seen-predicate) stringlist seen-semtype) string 0 i) (proc vports)\n (cw?f (build-path base-path (number->string i))\n (lambda (port) (vector-set! vports i port) (loop (- i 1)))))))\n(define (call-with-output-file-vector base-path n proc)\n (call-with-?-file-vector call-with-output-file base-path n proc))\n(define (call-with-input-file-vector base-path n proc)\n (call-with-?-file-vector call-with-input-file base-path n proc))\n(define (call-with-?-files cw?f paths proc)\n (let loop ((paths paths) (ports '()))\n (if (null? paths) (apply proc (reverse ports))\n (cw?f (car paths)\n (lambda (port) (loop (cdr paths) (cons port ports)))))))\n(define (call-with-output-files paths proc)\n (call-with-?-files call-with-output-file paths proc))\n\n(define edge-by-subject-dir\n (expand-user-path (build-path out-dir \"edge-by-subject/partitioned\")))\n(define edge-by-object-dir\n (expand-user-path (build-path out-dir \"edge-by-object/partitioned\")))\n(make-directories* (list edge-by-subject-dir edge-by-object-dir))\n\n;; Use these to build enumeration mappings.\n(define predicate-file-name (build-path out-dir \"PREDICATE.scm\"))\n(define semtype-file-name (build-path out-dir \"SEMTYPE.scm\"))\n\n(define (strings->string=>nat ss)\n (make-immutable-hash (map cons ss (range (length ss)))))\n\n(define predicate=>id\n (strings->string=>nat (read-all-from-file predicate-file-name)))\n(define semtype=>id\n (strings->string=>nat (read-all-from-file semtype-file-name)))\n\n(pretty-print `(predicate=>id ,predicate=>id))\n(pretty-print `(semtype=>id ,semtype=>id))\n\n;; Generate these.\n(define out-file-paths\n (map (lambda (p) (expand-user-path (build-path out-dir p)))\n '(\"publication-reference.scm\"\n \"concept.scm\"\n \"cui-by-semtype.scm\"\n )))\n\n(define out-edge-paths\n (map (lambda (p) (expand-user-path (build-path out-dir p)))\n '(\"edge-by-subject/index.scm\"\n \"edge-by-subject/detail.bin\"\n \"edge-by-object/index.scm\"\n \"edge-by-object/detail.bin\")))\n\n(define set-empty (set))\n(define (concept-add concept-by-cui concept)\n (define key (vector-ref concept 0))\n (define subdata0 (hash-ref concept-by-cui key set-empty))\n (define subdata1 (set-add subdata0 concept))\n (if (eq? subdata0 subdata1) concept-by-cui\n (hash-set concept-by-cui key subdata1)))\n(define (concept-sty concept) (vector-ref concept 2))\n(define (sty-novelty datum) (vector (concept-sty datum) (vector-ref datum 3)))\n(define (write-cui-by-semtype out concept-by-cui)\n (define cui-by-semtype\n (for*/fold ((cui-by-semtype (hash)))\n ((kv (in-hash-pairs concept-by-cui))\n (sty (in-list (map concept-sty (set->list (cdr kv))))))\n (hash-set cui-by-semtype sty\n (cons (car kv) (hash-ref cui-by-semtype sty '())))))\n (for ((sty (in-list (sort (hash-keys cui-by-semtype) <))))\n (fprintf out \"~s\\n\"\n (cons sty (sort (hash-ref cui-by-semtype sty) <)))))\n\n(define edge-cui-buckets 10)\n(define (edge-partition-add vout edge)\n (define cui (edge-src edge))\n (define key (cond ((< 1000000 cui) 9)\n ((< 400000 cui) 8)\n ((< 200000 cui) 7)\n ((< 50000 cui) 6)\n ((< 40000 cui) 5)\n ((< 30000 cui) 4)\n ((< 20000 cui) 3)\n ((< 10000 cui) 2)\n ((< 5000 cui) 1)\n (else 0)))\n (write-bytes (edge->bytes edge) (vector-ref vout key)))\n\n;; At least one PUBMED_ID is corrupted: PREDICATION_ID=57715160: \"20126278 [3]\"\n(define (robust-string->number s)\n (or (string->number s) (string->number (car (string-split s)))))\n\n(define (print-pubref/concept/edge\n vebs-out vebo-out out-pubref out-concept out-cui-by-semtype)\n (define (yield record)\n (define pubref (list->vector (map robust-string->number (take record 3))))\n (define (concept xs) ;; CUI, NAME, SEMTYPE, NOVELTY\n (define cui (string->number (substring (car xs) 1)))\n (define semtype (hash-ref semtype=>id (caddr xs)))\n (vector cui (cadr xs) semtype (string->number (cadddr xs))))\n (define concepts (drop record 4))\n (define subject (concept (take concepts 4)))\n (define object (concept (drop concepts 4)))\n (define edge (vector (vector-ref subject 0)\n (vector-ref object 0)\n (hash-ref predicate=>id (car (drop record 3)))\n (vector-ref subject 2)\n (vector-ref object 2)\n (vector-ref pubref 2)))\n (shift k (cons (list pubref subject object edge) k)))\n (lambda (in)\n (read-line in 'any) ;; Skip header.\n (let loop ((count 1)\n (concept-by-cui (hash))\n (next (reset (and ((csv-records yield) in) #f))))\n (when (= 0 (remainder count 100000))\n (printf \"processed ~s rows\\n\" count)\n (flush-output out-pubref))\n (if next\n (let* ((data (car next))\n (pubref (list-ref data 0))\n (subject (list-ref data 1))\n (object (list-ref data 2))\n (edge (list-ref data 3))\n (k (cdr next)))\n (fprintf out-pubref \"~s\\n\" pubref)\n (edge-partition-add vebs-out edge)\n (edge-partition-add vebo-out (edge-reverse edge))\n (loop (+ 1 count)\n (concept-add (concept-add concept-by-cui subject) object)\n (k #t)))\n (begin\n (printf \"Found ~s concepts\\n\" (hash-count concept-by-cui))\n (for ((key (in-list (sort (hash-keys concept-by-cui) <))))\n (define kdata (set->list (hash-ref concept-by-cui key)))\n (define kdata0 (car kdata))\n (fprintf out-concept \"~s\\n\" (vector (vector-ref kdata0 0)\n (vector-ref kdata0 1)\n (map sty-novelty kdata))))\n (flush-output out-concept)\n (write-cui-by-semtype out-cui-by-semtype concept-by-cui)\n (flush-output out-cui-by-semtype))))))\n\n(time (call-with-output-files\n out-file-paths\n (lambda out*\n (call-with-output-file-vector\n edge-by-subject-dir edge-cui-buckets\n (lambda (vebs-out)\n (call-with-output-file-vector\n edge-by-object-dir edge-cui-buckets\n (lambda (vebo-out)\n (call-with-input-file\n (expand-user-path csv-file-name)\n (apply print-pubref/concept/edge\n vebs-out vebo-out out*)))))))))\n\n(define (edge-add edges edge)\n (define key (edge-src (bytes->edge edge)))\n (hash-set edges key (cons edge (hash-ref edges key '()))))\n\n(define (write-edges offset edges out-index out-detail)\n (for/fold ((offset offset))\n ((key (in-list (sort (hash-keys edges) <))))\n (define es (hash-ref edges key))\n (for ((e (in-list (sort es bytesstring\n (let field ()\n (cond ((end-of-field?! in) '())\n ((field-quoted-begin?! in)\n (let field-quoted ()\n (if (field-quoted-end?! in) (field)\n (cons (read-char in) (field-quoted)))))\n (else (cons (read-char in) (field))))))\n (record)))))\n (record-stream)))))\n\n;; Test using:\n;; (call-with-input-file PATH\n;; (csv-records (lambda (record) (printf \"~s\\n\" `(record: ,record)))))\n" }, { "path": "attic/code/db.rkt", "content": "#lang racket/base\n(provide\n id=>predicate\n predicate=>id\n id=>semtype\n semtype=>id\n semtype-id=>cui*\n concept*\n cui=>concept\n fuzzy-name->concept*\n fuzzy-name*->concept*\n subject->edge*\n object->edge*\n subject&object->edge*\n subject*->edge*\n object*->edge*\n subject*&object*->edge*\n subject->edge*/stream\n object->edge*/stream\n predicate->edge*/stream\n edge*/stream\n concept-pretty\n edge-pretty\n direct-edge*\n count-ISA\n )\n\n(require\n \"concept.rkt\"\n \"edge.rkt\"\n \"read.rkt\"\n racket/list\n racket/stream\n racket/string\n )\n\n(define (file->hash path) (make-immutable-hash (read-all-from-file path)))\n(define (file->id=>name path)\n (define x* (read-all-from-file path))\n (make-immutable-hash (map cons (range (length x*)) x*)))\n(define (file->name=>id path)\n (define x* (read-all-from-file path))\n (make-immutable-hash (map cons x* (range (length x*)))))\n\n(define id=>predicate (file->id=>name \"semmed/PREDICATE.scm\"))\n(define predicate=>id (file->name=>id \"semmed/PREDICATE.scm\"))\n\n(define id=>semtype (file->id=>name \"semmed/SEMTYPE.scm\"))\n(define semtype=>id (file->name=>id \"semmed/SEMTYPE.scm\"))\n\n(define semtype-id=>cui* (file->hash \"semmed/cui-by-semtype.scm\"))\n\n(define concept* (read-all-from-file \"semmed/concept.scm\"))\n(define cui=>concept\n (make-immutable-hash (map (lambda (c) (cons (concept-cui c) c)) concept*)))\n\n(define (fuzzy-name->concept* concept* name case-insensitive?)\n (define needle (if case-insensitive? (string-downcase name) name))\n (define c->name (if case-insensitive?\n (lambda (c) (string-downcase (concept-name c)))\n concept-name))\n (filter (lambda (c) (string-contains? (c->name c) needle)) concept*))\n(define (fuzzy-name*->concept* concept* names case-insensitive?)\n (foldl (lambda (n c*) (fuzzy-name->concept* c* n case-insensitive?))\n concept* names))\n\n(define subject=>pos (file->hash \"semmed/edge-by-subject/index.scm\"))\n(define in-detail-ebs (open-input-file \"semmed/edge-by-subject/detail.bin\"))\n(define object=>pos (file->hash \"semmed/edge-by-object/index.scm\"))\n(define in-detail-ebo (open-input-file \"semmed/edge-by-object/detail.bin\"))\n(define predicate=>pos (file->hash \"semmed/edge-by-predicate/index.scm\"))\n(define in-detail-ebp (open-input-file \"semmed/edge-by-predicate/detail.bin\"))\n\n(define (maybe-bytes->edge bs) (if (eof-object? bs) bs (bytes->edge bs)))\n\n(define (edge*-contiguous pos in-detail continue? p?)\n (file-position in-detail pos)\n (let loop ((edge (maybe-bytes->edge (read-edge-bytes in-detail))))\n (if (and (not (eof-object? edge)) (continue? edge))\n (if (p? edge)\n (let build-edge ((pubs (list (edge-pub-info edge))))\n (define e-next (maybe-bytes->edge (read-edge-bytes in-detail)))\n (if (edge-meaning=? edge e-next)\n (build-edge (cons (edge-pub-info e-next) pubs))\n (cons (edge-pubrefs-set edge pubs) (loop e-next))))\n (loop (maybe-bytes->edge (read-edge-bytes in-detail))))\n '())))\n\n(define (cui->edge* cui=>pos in-detail cui p?)\n (define (cui-matches? e) (= cui (edge-src e)))\n (define pos (hash-ref cui=>pos cui #f))\n (if pos (edge*-contiguous pos in-detail cui-matches? p?) '()))\n\n(define (subject->edge* cui p?)\n (cui->edge* subject=>pos in-detail-ebs cui p?))\n(define (object->edge* cui p?)\n (cui->edge* object=>pos in-detail-ebo cui p?))\n(define (subject&object->edge* cui-s cui-o p?)\n (subject->edge* cui-s (lambda (e) (and (= cui-o (edge-dst e)) (p? e)))))\n(define (subject*->edge* cui* p?)\n (for/fold ((edge* '())) ((cui cui*)) (append (subject->edge* cui p?) edge*)))\n(define (object*->edge* cui* p?)\n (for/fold ((edge* '())) ((cui cui*)) (append (object->edge* cui p?) edge*)))\n(define (subject*&object*->edge* cui-s* cui-o* p?)\n (for*/fold ((edge* '()))\n ((cui-s cui-s*) (cui-o cui-o*))\n (append (subject&object->edge* cui-s cui-o p?) edge*)))\n\n(define (edge*-contiguous/stream pos in-detail continue? p?)\n (let loop ((pos pos) (set-pos? #t))\n (define edge (begin (when set-pos? (file-position in-detail pos))\n (maybe-bytes->edge (read-edge-bytes in-detail))))\n (define pos-next (+ pos edge-byte-size))\n (if (and (not (eof-object? edge)) (continue? edge))\n (if (p? edge)\n (let build-edge ((pos pos-next) (pubs (list (edge-pub-info edge))))\n (define e-next (maybe-bytes->edge (read-edge-bytes in-detail)))\n (if (edge-meaning=? edge e-next)\n (build-edge (+ pos edge-byte-size)\n (cons (edge-pub-info e-next) pubs))\n (stream-cons (edge-pubrefs-set edge pubs) (loop pos #t))))\n (loop pos-next #f))\n '())))\n\n(define (cui->edge*/stream cui=>pos in-detail cui p?)\n (define (cui-matches? e) (= cui (edge-src e)))\n (define pos (hash-ref cui=>pos cui #f))\n (if pos (edge*-contiguous/stream pos in-detail cui-matches? p?) '()))\n\n(define (subject->edge*/stream cui p?)\n (cui->edge*/stream subject=>pos in-detail-ebs cui p?))\n(define (object->edge*/stream cui p?)\n (cui->edge*/stream object=>pos in-detail-ebo cui p?))\n(define (predicate->edge*/stream predicate subject-type object-type p?)\n (define (edge*/stream pos set-pos?)\n (define edge (begin (when set-pos? (file-position in-detail-ebp pos))\n (maybe-bytes->edge (read-edge-bytes in-detail-ebp))))\n (define pos-next (+ pos edge-byte-size))\n (if (and (not (eof-object? edge))\n (= predicate (edge-predicate edge))\n (= subject-type (edge-src-type edge))\n (= object-type (edge-dst-type edge)))\n (if (p? edge)\n (stream-cons edge (edge*/stream pos-next #t))\n (edge*/stream pos-next #f))\n '()))\n (define pos (hash-ref predicate=>pos\n (vector predicate subject-type object-type) #f))\n (if pos (edge*/stream pos #t) '()))\n\n(define (edge*/stream p?)\n (edge*-contiguous/stream 0 in-detail-ebs (lambda (_) #t) p?))\n\n(define (concept-pretty c)\n (vector (concept-cui c) (concept-name c)\n (map (lambda (tn) (vector (hash-ref id=>semtype (vector-ref tn 0))\n (vector-ref tn 1)))\n (concept-type c))))\n\n(define (edge-pretty e)\n (vector (concept-pretty (hash-ref cui=>concept (edge-src e)))\n (concept-pretty (hash-ref cui=>concept (edge-dst e)))\n (hash-ref id=>predicate (edge-predicate e))\n (hash-ref id=>semtype (edge-src-type e))\n (hash-ref id=>semtype (edge-dst-type e))\n (edge-pub-info e)))\n\n(define (direct-edge* c*1 c*2)\n (map edge-pretty (subject*&object*->edge* (map concept-cui c*1)\n (map concept-cui c*2)\n (lambda (e) #t))))\n\n(define predicate-id-ISA (hash-ref predicate=>id \"ISA\"))\n\n(define (count-ISA cui)\n (define (edge-ISA? e) (= predicate-id-ISA (edge-predicate e)))\n (length (cui->edge* object=>pos in-detail-ebo cui edge-ISA?)))\n" }, { "path": "attic/code/edge.rkt", "content": "#lang racket/base\n(provide\n bytes->edge\n edge->bytes\n edge-byte-size\n edge-dst\n edge-src\n edge-predicate\n edge-src-type\n edge-dst-type\n edge-pub-info\n edge-meaning=?\n edge-pubrefs-set\n edge-reverse\n read-edge-bytes\n read-edge-bytes-all/stream\n )\n\n(require\n \"read.rkt\"\n racket/stream\n )\n\n;; 2 * 3-byte CUI + 1-byte predicate + 2 * 1-byte semtypes + 4-byte pubref\n(define edge-byte-size (+ (* 2 3) 1 2 4))\n\n(define (byte-at offset n) (bitwise-and 255 (arithmetic-shift n offset)))\n\n(define (edge->bytes e)\n (define c0 (vector-ref e 0))\n (define c1 (vector-ref e 1))\n (define pid (vector-ref e 5))\n (bytes (byte-at -16 c0) (byte-at -8 c0) (byte-at 0 c0)\n (byte-at -16 c1) (byte-at -8 c1) (byte-at 0 c1)\n (vector-ref e 2) (vector-ref e 3) (vector-ref e 4)\n (byte-at -24 pid) (byte-at -16 pid) (byte-at -8 pid) (byte-at 0 pid)))\n\n(define (bytes->edge bs)\n (define (bref pos) (bytes-ref bs pos))\n (define (bref-to pos offset) (arithmetic-shift (bref pos) offset))\n (define (bcui pos)\n (+ (bref-to pos 16) (bref-to (+ 1 pos) 8) (bref-to (+ 2 pos) 0)))\n (vector (bcui 0) (bcui 3) (bref 6) (bref 7) (bref 8)\n (+ (bref-to 9 24) (bref-to 10 16) (bref-to 11 8) (bref-to 12 0))))\n\n(define (edge-src edge) (vector-ref edge 0))\n(define (edge-dst edge) (vector-ref edge 1))\n(define (edge-predicate edge) (vector-ref edge 2))\n(define (edge-src-type edge) (vector-ref edge 3))\n(define (edge-dst-type edge) (vector-ref edge 4))\n(define (edge-pub-info edge) (vector-ref edge 5))\n(define (edge-meaning=? e1 e2)\n (and (= (edge-src e1) (edge-src e2))\n (= (edge-dst e1) (edge-dst e2))\n (= (edge-predicate e1) (edge-predicate e2))\n (= (edge-src-type e1) (edge-src-type e2))\n (= (edge-dst-type e1) (edge-dst-type e2))))\n(define (edge-pubrefs-set edge pubrefs)\n (vector (edge-src edge)\n (edge-dst edge)\n (edge-predicate edge)\n (edge-src-type edge)\n (edge-dst-type edge)\n pubrefs))\n\n(define (edge-reverse edge)\n (vector (edge-dst edge) (edge-src edge) (edge-predicate edge)\n (edge-dst-type edge) (edge-src-type edge) (edge-pub-info edge)))\n\n(define (read-edge-bytes in) (read-bytes edge-byte-size in))\n(define (read-edge-bytes-all/stream in)\n (define ebs (read-edge-bytes in))\n (if (eof-object? ebs) '() (stream-cons ebs (read-edge-bytes-all/stream in))))\n" }, { "path": "attic/code/gui-simple.rkt", "content": "#lang racket\n\n(require\n racket/sandbox\n racket/gui/base\n racket/engine\n racket/date\n \"db.rkt\"\n \"mk-db.rkt\"\n \"concept.rkt\"\n \"edge.rkt\"\n \"programmatically-defined-relations.rkt\"\n )\n\n(provide\n launch-gui)\n\n(displayln \"Starting mediKanren...\")\n(newline)\n(displayln \"************************************************\")\n(displayln \"*** mediKanren is for research purposes only ***\")\n(displayln \"************************************************\")\n(newline)\n\n(displayln\n \"Finished loading mk-db.rkt\")\n\n;; Add https://www.ncbi.nlm.nih.gov/pubmed/ in front of a PubMed ID to get a working URL. For example,\n;;\n;; ((1429928\n;; \"erythrocyte membrane protein 1, Plasmodium falciparum\"\n;; (\"gngm\" \"aapp\" \"imft\"))\n;; (1368474 \"rosetting\" (\"celf\"))\n;; \"AFFECTS\"\n;; \"aapp\"\n;; \"celf\"\n;; (25482886 19546191 10828049))\n;;\n;; corresponds to the URLs\n;;\n;; https://www.ncbi.nlm.nih.gov/pubmed/25482886\n;; https://www.ncbi.nlm.nih.gov/pubmed/19546191\n;; https://www.ncbi.nlm.nih.gov/pubmed/10828049\n\n\n(define *verbose* #t)\n\n;;; window size\n(define HORIZ-SIZE 800)\n(define VERT-SIZE 400)\n\n(define input-response-latency 50)\n\n(define MAX-CHAR-WIDTH 100)\n\n(define DECREASES_PREDICATE_STRING \"decreases [synthetic]\")\n(define INCREASES_PREDICATE_STRING \"increases [synthetic]\")\n(define DECREASES_STAR_PREDICATE_STRING \"decreases* [synthetic]\")\n(define INCREASES_STAR_PREDICATE_STRING \"increases* [synthetic]\")\n\n(define synthetic-relations\n `((,DECREASES_PREDICATE_STRING . ,decreases)\n (,INCREASES_PREDICATE_STRING . ,increases)\n (,DECREASES_STAR_PREDICATE_STRING . ,decreases*)\n (,INCREASES_STAR_PREDICATE_STRING . ,increases*)))\n\n(define SYNTHETIC_PREDICATE_STRINGS (list DECREASES_PREDICATE_STRING\n INCREASES_PREDICATE_STRING\n DECREASES_STAR_PREDICATE_STRING\n INCREASES_STAR_PREDICATE_STRING))\n\n(define *concept-1-name-string* (box \"\"))\n(define *concept-2-name-string* (box \"\"))\n(define *concept-1-isa-flag* (box #f))\n(define *concept-2-isa-flag* (box #f))\n(define *concept-1-choices* (box '()))\n(define *concept-2-choices* (box '()))\n(define *concept-X-choices* (box '()))\n(define *predicate-1-choices* (box '()))\n(define *predicate-2-choices* (box '()))\n(define *full-path-choices* (box '()))\n\n;; saved choices used to generate\n;; paths when clicking on a concept in the X list box.\n(define *solution-concept-1-name-string* (box \"\"))\n(define *solution-concept-2-name-string* (box \"\"))\n(define *solution-concept-1-isa-flag* (box #f))\n(define *solution-concept-2-isa-flag* (box #f))\n(define *solution-concept-1-choices* (box '()))\n(define *solution-concept-2-choices* (box '()))\n(define *solution-predicate-1-choices* (box '()))\n(define *solution-predicate-2-choices* (box '()))\n\n(define (path-confidence p)\n (define (weight-linear+1 n) (+ 1 n))\n (define (weight-exponential n) (expt 2 n))\n ;; To experiment with sorting, try to only change the weight calculation\n ;; being used. Leave everything else the same.\n (define weight weight-exponential)\n (define (pubmed-count e)\n (match e\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n ;; (printf \"p1 x: ~s unique pubmed length: ~s\\n\" x (remove-duplicates pubmed*))\n (length (remove-duplicates pubmed*))]))\n (define (confidence/edge e) (- 1 (/ 1.0 (weight (pubmed-count e)))))\n (foldl * 1 (map confidence/edge p)))\n(define (path-confidence Predicate 1 -> [X] -> Predicate 2 -> Concept 2\")))\n (define concept-2-search/isa-panel (new horizontal-panel%\n (parent frame)\n (alignment '(left center))\n (stretchable-height #f)))\n (define concept-2-list-boxes-panel (new horizontal-panel%\n (parent frame)\n (alignment '(left center))))\n (define predicate-2-list-box (new list-box%\n (label \"Predicate 2\")\n (choices (unbox *predicate-2-choices*))\n (columns '(\"Name\"))\n (parent concept-2-list-boxes-panel)\n (style '(extended))\n (callback (lambda (button event)\n (void)))))\n (define concept-2-list-box (concept-list frame concept-2-search/isa-panel concept-2-list-boxes-panel \"Concept 2\" *concept-2-name-string* *concept-2-isa-flag* *concept-2-choices* (lambda () predicate-2-list-box) *predicate-2-choices* 'in-edge))\n\n (define go-button (new button%\n (parent frame)\n (label \"go!\")\n (callback (lambda (button event)\n (send running-status-description set-label \"Running...\")\n\n (define concept-1-selections (send concept-1-list-box get-selections))\n (define concept-2-selections (send concept-2-list-box get-selections))\n\n (define concept-1-selected-concepts (foldr (lambda (i l) (cons (list-ref (unbox *concept-1-choices*) i) l)) '() concept-1-selections))\n (define concept-2-selected-concepts (foldr (lambda (i l) (cons (list-ref (unbox *concept-2-choices*) i) l)) '() concept-2-selections))\n\n #|\n (printf \"concept-1-selections: ~s\\n\" concept-1-selections)\n (displayln concept-1-selected-concepts)\n (printf \"---------------------------------\\n\")\n (printf \"concept-2-selections: ~s\\n\" concept-2-selections)\n (displayln concept-2-selected-concepts)\n (printf \"---------------------------------\\n\")\n |#\n\n (define predicate-1-selections (send predicate-1-list-box get-selections))\n (define predicate-2-selections (send predicate-2-list-box get-selections))\n\n (define predicate-1-selected-predicates (foldr (lambda (i l) (cons (list-ref (unbox *predicate-1-choices*) i) l)) '() predicate-1-selections))\n (define predicate-2-selected-predicates (foldr (lambda (i l) (cons (list-ref (unbox *predicate-2-choices*) i) l)) '() predicate-2-selections))\n\n #|\n (printf \"predicate-1-selections: ~s\\n\" predicate-1-selections)\n (displayln predicate-1-selected-predicates)\n (printf \"---------------------------------\\n\")\n (printf \"predicate-2-selections: ~s\\n\" predicate-2-selections)\n (displayln predicate-2-selected-predicates)\n (printf \"---------------------------------\\n\")\n |#\n\n (find-X-concepts concept-1-selected-concepts\n concept-2-selected-concepts\n predicate-1-selected-predicates\n predicate-2-selected-predicates\n concept-X-list-box\n running-status-description\n full-path-list-box)))))\n (define running-status-description (new message%\n (parent frame)\n (label \" \")))\n (define concept-X-list-box (new list-box%\n (label \"X\")\n (choices (unbox *concept-X-choices*))\n (columns '(\"CUI\" \"Concept Type*\" \"Name\"))\n (parent frame)\n (style '(column-headers single))\n (callback (lambda (button event)\n (let ((sel* (send concept-X-list-box get-selections)))\n (when (= (length sel*) 1)\n (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n ;; (printf \"selected ~s\\n\" selected-X)\n (define concept-1* (unbox *solution-concept-1-choices*))\n (define concept-2* (unbox *solution-concept-2-choices*))\n ;; (printf \"concept-1* ~s\\n\" concept-1*)\n ;; (printf \"concept-2* ~s\\n\" concept-2*)\n (define predicate-1* (unbox *solution-predicate-1-choices*))\n (define predicate-2* (unbox *solution-predicate-2-choices*))\n ;; (printf \"predicate-1* ~s\\n\" predicate-1*)\n ;; (printf \"predicate-2* ~s\\n\" predicate-2*)\n\n\n (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates predicate-1*))\n (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates predicate-2*))\n\n (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n\n (define paths '())\n\n (cond\n [(and (equal? (unbox *solution-concept-1-name-string*) \"\")\n (equal? (unbox *solution-concept-2-name-string*) \"\"))\n (set! paths '())]\n [(equal? (unbox *solution-concept-1-name-string*) \"\")\n (set! paths '())\n ;; run synthetic queries here\n (set! paths\n (remove-duplicates\n (append paths\n (run* (q)\n (fresh (e2\n x\n o p2 t2 t3 r2)\n (== (list e2) q)\n (== selected-X x)\n (== e2 `(,x ,o ,p2 ,t2 ,t3 ,r2))\n (membero o concept-2*)\n (membero p2 atomic-predicate-2*)\n (edgeo e2)\n )))))]\n [(equal? (unbox *solution-concept-2-name-string*) \"\")\n (set! paths '())\n ;; run synthetic queries here\n (set! paths\n (remove-duplicates\n (append paths\n (run* (q)\n (fresh (e1\n x\n s\n p1 ts t1 r1)\n (== (list e1) q)\n (== selected-X x)\n (== e1 `(,s ,x ,p1 ,ts ,t1 ,r1))\n (membero s concept-1*)\n (membero p1 atomic-predicate-1*)\n (edgeo e1)\n )))))]\n [else\n (set! paths '())\n ;; run synthetic queries here\n (set! paths\n (remove-duplicates\n (append paths\n (run* (e1 e2)\n (fresh (x\n s\n o p1 p2 ts t1 t2 t3 r1 r2)\n (== selected-X x)\n (== e1 `(,s ,x ,p1 ,ts ,t1 ,r1))\n (== e2 `(,x ,o ,p2 ,t2 ,t3 ,r2))\n (membero s concept-1*)\n (membero o concept-2*)\n (membero p1 atomic-predicate-1*)\n (membero p2 atomic-predicate-2*)\n (edgeo e1)\n (edgeo e2)\n )))))])\n\n ;; (printf \"sorting paths: ~s\\n\" paths)\n\n ;; This sorting affects the order of the \"Path\" list for the selected concept.\n (set! paths (map remove-duplicate-pubrefs/path (sort-paths paths)))\n\n ;; (printf \"sorted paths: ~s\\n\" paths)\n\n (define flattened-paths\n (let ((ls (foldr\n (lambda (p l)\n (cons\n (list \"----\" \"----\" \"----\" \"----\" \"----\" \"----\")\n (append (reverse p) l)))\n '()\n paths)))\n (if (null? ls)\n ;; ls should never be null!\n '()\n (reverse (cdr ls)))))\n\n (define full-path-subj-list\n (map (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (~a subj #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-obj-list\n (map (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (~a obj #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-pred-list\n (map (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (~a pred #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-subj-type-list\n (map (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (~a subj-type #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-obj-type-list\n (map (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (~a obj-type #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-pubmed*-list\n (map (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (~a pubmed* #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (send full-path-list-box\n set\n full-path-subj-list\n full-path-obj-list\n full-path-pred-list\n full-path-subj-type-list\n full-path-obj-type-list\n full-path-pubmed*-list)\n\n (set-box! *full-path-choices* flattened-paths)\n\n ;; unselect all items\n (for ([i (length flattened-paths)])\n (send full-path-list-box select i #f))\n\n ))\n (void))))))\n (define full-path-list-box (new list-box%\n (label \"Paths\")\n (choices (unbox *full-path-choices*))\n (columns '(\"Subject\" \"Object\" \"Predicate\" \"Subj Type\" \"Obj Type\" \"PubMed IDs\"))\n (parent frame)\n (style '(column-headers extended))\n (callback (lambda (self event)\n ;; (when *verbose*\n ;; (printf \"(unbox *full-path-choices*):\\n~s\\n\" (unbox *full-path-choices*)))\n (define selections (send self get-selections))\n (when *verbose*\n (printf \"selection for full path:\\n~s\\n\" selections))\n (define selected-full-paths (foldr (lambda (i l) (cons (list-ref (unbox *full-path-choices*) i) l)) '() selections))\n (when *verbose*\n (printf \"selected full path:\\n\")\n (for-each\n (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (let ((pubmed* (if (list? pubmed*)\n (map (lambda (pubmed-id) (string-append \"https://www.ncbi.nlm.nih.gov/pubmed/\" (~a pubmed-id)))\n pubmed*)\n pubmed*)))\n (pretty-print `(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)))]))\n selected-full-paths))\n))))\n\n\n (send frame show #t)\n ))\n\n(define (split-atomic/synthetic-predicates predicate*)\n\n (define atomic-predicate* predicate*)\n (define synthetic-predicate* '())\n\n (set! synthetic-predicate* (filter (lambda (pred) (member pred SYNTHETIC_PREDICATE_STRINGS))\n atomic-predicate*))\n\n (when (member DECREASES_PREDICATE_STRING atomic-predicate*)\n (set! atomic-predicate* (cons \"INHIBITS\" (cons \"PREVENTS\" (cons \"TREATS\" atomic-predicate*))))\n (set! synthetic-predicate* (remove DECREASES_PREDICATE_STRING synthetic-predicate*)))\n\n (when (member INCREASES_PREDICATE_STRING atomic-predicate*)\n (set! atomic-predicate* (cons \"STIMULATES\" (cons \"AUGMENTS\" (cons \"CAUSES\" atomic-predicate*))))\n (set! synthetic-predicate* (remove INCREASES_PREDICATE_STRING synthetic-predicate*)))\n\n (set! atomic-predicate* (filter (lambda (pred) (not (member pred SYNTHETIC_PREDICATE_STRINGS)))\n atomic-predicate*))\n\n (set! atomic-predicate* (remove-duplicates atomic-predicate*))\n\n (printf \"atomic-predicate*: ~s\\n\" atomic-predicate*)\n (printf \"synthetic-predicate*: ~s\\n\" synthetic-predicate*)\n\n (list atomic-predicate* synthetic-predicate*)\n )\n\n(define streaming-thread #f)\n\n(define (stop-streaming)\n (and streaming-thread (kill-thread streaming-thread))\n (set! streaming-thread #f))\n\n(define (print-stream ss)\n (when (not (stream-empty? ss))\n (pretty-print (stream-first ss))\n (displayln \"====================================\")\n (print-stream (stream-rest ss))))\n\n(define (start-streaming ss)\n (stop-streaming)\n (thread (lambda () (print-stream ss))))\n\n(define (find-X-concepts concept-1* concept-2* predicate-1* predicate-2* concept-X-list-box running-status-description full-path-list-box)\n\n (define start-time (current-milliseconds))\n\n #|\n (printf \"\\nfinding concepts X for which\\n[C1] -> P1 -> [X] -> P2 -> [C2]\\n\")\n (printf \"=============================\\n\")\n |#\n\n (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates predicate-1*))\n (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates predicate-2*))\n\n (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n (define all-X-concepts-with-edges '())\n\n (define (stream-query/predicate/trust predicate&nedges&ntrusted->ss)\n (start-streaming\n (foldr\n (lambda (pname ss)\n (define predicate (cdr (assoc pname synthetic-relations)))\n (define (run/ranked nedges ntrusted)\n (stream-cons\n (begin\n (displayln \"***************************************\")\n (printf \"Path length: ~s, Trusted edge count: ~s\\n\" nedges ntrusted)\n (displayln \"***************************************\")\n (flush-output))\n (predicate&nedges&ntrusted->ss predicate nedges ntrusted)))\n (stream-append\n (stream-cons\n (printf \"Streaming synthetic predicate ~s\\n\" pname)\n (stream-append\n (run/ranked 1 1)\n (stream-append\n (run/ranked 1 0)\n (let loop ((nedges 2) (ntrusted 2))\n (if (< 4 nedges)\n '()\n (stream-append\n (run/ranked nedges ntrusted)\n (loop (+ nedges 1) (+ ntrusted 1))))))))\n (stream-cons\n (printf \"Finished streaming synthetic predicate ~s\\n\" pname)\n ss)))\n (stream-cons (begin (displayln \"Finished all streaming.\")\n (flush-output))\n '())\n synthetic-predicate-2*)))\n\n (cond\n [(and (equal? (unbox *concept-1-name-string*) \"\")\n (equal? (unbox *concept-2-name-string*) \"\"))\n (set! all-X-concepts-with-edges '())]\n [(equal? (unbox *concept-1-name-string*) \"\")\n (set! all-X-concepts-with-edges '())\n ;; run synthetic queries here\n (stream-query/predicate/trust\n (lambda (predicate nedges ntrusted)\n (run-stream\n (path-url)\n (fresh (m o path)\n (path-length-trustedo path nedges ntrusted)\n (membero o concept-2*)\n (predicate m o path)\n (path/urlo path path-url)\n ;(== path path-url)\n ))))\n (set! all-X-concepts-with-edges\n (remove-duplicates\n (append all-X-concepts-with-edges\n (run* (q)\n (fresh (m\n e2\n o p2 t2 t3 r2)\n (== (list m (list r2) (list e2)) q)\n (== e2 `(,m ,o ,p2 ,t2 ,t3 ,r2))\n (membero o concept-2*)\n (membero p2 atomic-predicate-2*)\n (edgeo e2)\n )))))]\n [(equal? (unbox *concept-2-name-string*) \"\")\n (set! all-X-concepts-with-edges '())\n ;; run synthetic queries here\n (set! all-X-concepts-with-edges\n (remove-duplicates\n (append all-X-concepts-with-edges\n (run* (q)\n (fresh (m\n e1 e2\n s\n p1 ts t1 r1)\n (== (list m (list r1) (list e1)) q)\n (== e1 `(,s ,m ,p1 ,ts ,t1 ,r1))\n (membero s concept-1*)\n (membero p1 atomic-predicate-1*)\n (edgeo e1)\n )))))]\n [else\n (set! all-X-concepts-with-edges '())\n ;; run synthetic queries here\n (set! all-X-concepts-with-edges\n (remove-duplicates\n (append all-X-concepts-with-edges\n (run* (q)\n (fresh (m\n e1 e2\n s\n o p1 p2 ts t1 t2 t3 r1 r2)\n (== (list m (list r1 r2) (list e1 e2)) q)\n (== e1 `(,s ,m ,p1 ,ts ,t1 ,r1))\n (== e2 `(,m ,o ,p2 ,t2 ,t3 ,r2))\n (membero s concept-1*)\n (membero o concept-2*)\n (membero p1 atomic-predicate-1*)\n (membero p2 atomic-predicate-2*)\n (edgeo e1)\n (edgeo e2)\n )))))])\n\n (define end-time (current-milliseconds))\n\n (define elapsed-time (- end-time start-time))\n\n ;;(printf \"elapsed query time: ~s seconds\\n\" (/ elapsed-time 1000.0))\n ;;(printf \"=============================\\n\")\n\n ;; This sorting affects order of appearance in the \"X\" concept list\n (set! all-X-concepts-with-edges\n (sort\n all-X-concepts-with-edges\n (lambda (c1 c2)\n (match (list c1 c2)\n [`((,_ ,_ ,e1*) (,_ ,_ ,e2*))\n (not (path-confidencestring (seconds->date (current-seconds)) #t))\n (newline)\n\n (define number-Xs-found (length all-X-concepts))\n (define query-seconds (/ elapsed-time 1000.0))\n (define query-time-format-string \"Found ~s X's after ~s seconds\")\n (send running-status-description set-label (format query-time-format-string number-Xs-found query-seconds))\n (printf query-time-format-string number-Xs-found query-seconds)\n (newline)\n (newline)\n\n (set-box! *concept-X-choices* all-X-concepts)\n\n (set-box! *solution-concept-1-name-string* (unbox *concept-1-name-string*))\n (set-box! *solution-concept-2-name-string* (unbox *concept-2-name-string*))\n\n (set-box! *solution-concept-1-isa-flag* (unbox *concept-1-isa-flag*))\n (set-box! *solution-concept-2-isa-flag* (unbox *concept-2-isa-flag*))\n\n (set-box! *solution-concept-1-choices* concept-1*)\n (set-box! *solution-concept-2-choices* concept-2*)\n (set-box! *solution-predicate-1-choices* predicate-1*)\n (set-box! *solution-predicate-2-choices* predicate-2*)\n\n (printf \"*solution-concept-1-name-string*:\\n~s\\n\" (unbox *solution-concept-1-name-string*))\n (printf \"*solution-concept-1-isa-flag*:\\n~s\\n\" (unbox *solution-concept-1-isa-flag*))\n (printf \"*solution-concept-1-choices*:\\n\")\n (pretty-print (unbox *solution-concept-1-choices*))\n (printf \"*solution-predicate-1-choices*:\\n\")\n (pretty-print (unbox *solution-predicate-1-choices*))\n (newline)\n\n (printf \"*solution-concept-2-name-string*:\\n~s\\n\" (unbox *solution-concept-2-name-string*))\n (printf \"*solution-concept-2-isa-flag*:\\n~s\\n\" (unbox *solution-concept-2-isa-flag*))\n (printf \"*solution-concept-2-choices*:\\n\")\n (pretty-print (unbox *solution-concept-2-choices*))\n (printf \"*solution-predicate-2-choices*:\\n\")\n (pretty-print (unbox *solution-predicate-2-choices*))\n (newline)\n\n (define pretty-print-X-concepts-with-edges\n (lambda (X-concepts-with-edges)\n (with-output-to-file\n \"a.out\"\n (lambda ()\n (printf \"'(\\n\")\n (let loop ([ls X-concepts-with-edges])\n (cond\n [(null? ls)\n (printf \")\\n\")\n (newline)]\n [else\n (match (car ls)\n [`((,cui ,name ,concept-type*) ,pubmed** ,edge*)\n ;; (printf \"-----------------------------------------------\\n\")\n (for-each\n (lambda (x)\n (match x\n [`(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*)\n (let ((pubmed* (if (list? pubmed*)\n (map (lambda (pubmed-id) (string-append \"https://www.ncbi.nlm.nih.gov/pubmed/\" (~a pubmed-id)))\n pubmed*)\n pubmed*)))\n (pretty-print `(,subj ,obj ,pred ,subj-type ,obj-type ,pubmed*) (current-output-port) 1))]))\n edge*)\n (loop (cdr ls))])])))\n #:mode 'text\n #:exists 'append)))\n\n ;; (printf \"all-X-concepts-with-edges:\\n\")\n (pretty-print-X-concepts-with-edges all-X-concepts-with-edges)\n\n (printf \"========== end query results =============\\n\")\n\n (send concept-X-list-box\n set\n (map (lambda (x)\n (match x\n [`(,cui ,name ,concept-type*)\n (format \"~a\" cui)]))\n all-X-concepts)\n (map (lambda (x)\n (match x\n [`(,cui ,name ,concept-type*)\n (let ((concept-type*\n (sort concept-type* string\n;; 286\n\n\n;; Once we have decided that asthma is a disease of interest, we might\n;; want to see the paths between the 47 genes of interest (including\n;; KIT and C-KIT) and the asthma.\n;;\n;; Query takes 2 minutes on a laptop, single-threaded. We should be\n;; able to speed this up.\n;;\n;; The only specifc gene that is indirectly linked to asthma through\n;; mast cell activation (as opposed to signal transduction, which\n;; seems less specific) is KIT, through this chain:\n;;\n;; (((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; (1155074 \"mast cell activation\" (\"celf\"))\n;; \"CAUSES\"\n;; \"gngm\"\n;; \"celf\"\n;; (12373338))\n;; ((1155074 \"mast cell activation\" (\"celf\"))\n;; (4096 \"Asthma\" (\"dsyn\"))\n;; \"AFFECTS\"\n;; \"celf\"\n;; \"dsyn\"\n;; (18209484 10352758))\n;; ((4096 \"Asthma\" (\"dsyn\"))\n;; (1155074 \"mast cell activation\" (\"celf\"))\n;; \"MANIFESTATION_OF\"\n;; \"dsyn\"\n;; \"celf\"\n;; (2741114)))\n;;\n;; The numbers 12373338, 18209484, 10352758, 2741114 can be turned\n;; into PubMed URLs. For example, the URL for 12373338 is:\n;;\n;; https://www.ncbi.nlm.nih.gov/pubmed/12373338\n;;\n;; We can then focus on KIT to get the full chain from Gleevec/imatinib\n;; and asthma. Obviously thi can be automated, and composing the queries\n;; (or the cached answers from sub-queries) is straight-forward.\n;;\n;; Run this by calling (paths-of-interest)\n;;\n(define (paths-of-interest)\n (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 e3 celf disorder disorder-type rest1 rest2 rest3)\n (== (list e1 e2 e3) q)\n (fuzzy-concepto \"asthma\" disorder)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e1)\n (edgeo e3)\n (edgeo e2)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))))\n;; =>\n;; cpu time: 127629 real time: 128505 gc time: 1446\n#|\n'(()\n ((((919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (24564241 1281217))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (26467500))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (24188406\n 24188406\n 22841885\n 22841885\n 21978835\n 21978835\n 20597478\n 20597478\n 18256384\n 12176746\n 12176746))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23340802 23340802))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ()\n ()\n ((((915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (16789903 11409908 7835966))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (26758977 25633229))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22262845\n 19170657\n 19048108\n 17503113\n 15163542\n 14620151\n 14580993\n 12949238\n 12482196\n 12482196\n 12324469\n 9450748))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (25539676 16461989))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ((((33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22357971 19290922 18492778 16790031 16790031 16415076))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (17426060 12035499 7882988))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23222563))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (26023679\n 24850739\n 23682925\n 23660250\n 22498774\n 22319212\n 21601104\n 20036637\n 17203870\n 15180972\n 15180972\n 15053611\n 12670482\n 12477288\n 12194978\n 12112690\n 11175815\n 11073315\n 9676989\n 8616803\n 7902881))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (12393403))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ((((246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22095643 16883913 16557224 8619925))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (15650217 15590688 9916027))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23222563 14505491 12960248))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ()\n ()\n ()\n ()\n ()\n ()\n ()\n ()\n ((((1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (9517496))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (27224507))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23103565 19711112 19458196 17956356 7802667 2783138))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (24743893\n 20806817\n 17118962\n 16727886\n 15176971\n 13678963\n 11916364\n 11912280\n 11802165\n 9627110\n 9047384\n 7784069\n 7537742))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ()\n ((((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22885698 15887041 15494014 15494014 11406357 11406357))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (27904762\n 27479325\n 27194789\n 26748340\n 26283964\n 26198787\n 26001588\n 25954136\n 25522385\n 25457352\n 25250214\n 24987288\n 24847082\n 24404331\n 24098092\n 23380704\n 22310710\n 22132325\n 22014238\n 21824992\n 21291419\n 21050922\n 20505987\n 20003820\n 19888967\n 19465516\n 19348466\n 19203114\n 19001047\n 18952824\n 18380671\n 18367502\n 17920519\n 17632123\n 17485341\n 17466390\n 17373355\n 17355284\n 17303405\n 17254012\n 16956790\n 16956790\n 16371473\n 15827888\n 15795223\n 15583862\n 15356058\n 14731813\n 14731813\n 12919066\n 12110144\n 11544033\n 10917832\n 10859220\n 10762594\n 10629036\n 10533704\n 10374695\n 9842573\n 9380811\n 9136757\n 8875430\n 7669492\n 7532590\n 7512770\n 1326354\n 1323348))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (27994757\n 26852687\n 25367076\n 24931696\n 23979726\n 23862981\n 22002603\n 21848862\n 21629734\n 20159963\n 19636563\n 17408432\n 12881713\n 11896598\n 11491654\n 11280802\n 11049052\n 1840317\n 1838150))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (20956018))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ()\n ()\n ()\n ((((79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (17230190 15735964))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (25534229 20926645 19717519 10347231))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (18538998))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (12373338))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114)))))\n|#\n\n(displayln\n \"Finished loading paths-of-interest\")\n\n\n;; Genes inhibited by Gleevec\n;;\n;; Of the 52 results, at least a few appear to be classes of genes\n;; rather than specific genes:\n;;\n;; (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n;; (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n;; (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n;; (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n;; (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n;; (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n;; (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n;; (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n;; (80298 \"v-src Oncogenes\" (\"gngm\" \"aapp\" \"enzy\" \"aapp\" \"gngm\" \"bacs\"))\n;; (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n;; (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n;;\n;; Of course, is something like (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n;; even considered a gene class?\n;;\n;; Oh wow--I had missed the first one of the c-kit names before!\n;; So there are actually three synonyms, not two.\n;;\n;; (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n;; (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n;; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;;\n;; So, of the 52 results, ~10 are actually categories rather\n;; than specific genes. Of the remaining ~40 specific genes, 3 of\n;; them are synonyms/aliases for KIT.\n;; \n(time (rem-dups\n (run* (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== '(935987 \"Gleevec\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n;; =>\n#|\n'((2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (65344\n \"Lymphocyte Specific Protein Tyrosine Kinase p56(lck)\"\n (\"aapp\" \"gngm\" \"enzy\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (80298 \"v-src Oncogenes\" (\"gngm\" \"aapp\" \"enzy\" \"aapp\" \"gngm\" \"bacs\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (138965 \"protein-tyrosine kinase c-src\" (\"gngm\" \"aapp\" \"enzy\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (287666 \"Rad51 Recombinase\" (\"gngm\" \"aapp\" \"enzy\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (390431 \"PDGF receptor tyrosine kinase\" (\"aapp\" \"gngm\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\")))\n|#\n\n;; interesting! A direct *causal* link between KIT/C-KIT and asthma\n;; seems unknown. So we are not just trying to connect a drug and\n;; disease, but also KIT and the disease.\n;;\n;; This does make sense, in that if such a direct connection were\n;; known, SemMedDB would probably have a direct link between imatinib\n;; and asthma.\n(map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 celf disorder pred disorder-type rest0)\n (== e0 q)\n (fuzzy-concepto \"asthma\" disorder)\n (== `(,gene ,disorder ,pred \"gngm\" ,disorder-type . ,rest0) e0)\n (edgeo e0)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))))\n;; =>\n#|\n'(()\n (((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n \"ASSOCIATED_WITH\"\n \"gngm\"\n \"dsyn\"\n (25337192 22505052)))\n ())\n|#\n\n(displayln\n \"Finished loading no causal relationship\")\n\n\n;; Here is a first attempt at pruning down the number of candidate\n;; diseases, removing only those diseases known to be treated by our\n;; specific drug of interest (Gleevec) rather than all forms of\n;; imatinib.\n;;\n;; We found not only asthma, but a strong suggestion that Gleevec\n;; might treat diabetes (something the query writer didn't know before\n;; looking at these answers). It turns out that the connection\n;; between Gleevec and diabetes *is* known, but without using an\n;; ontology or other ways to connect concepts, not all\n;; diabetes-related entries were automatically removed. Still, we\n;; think this is interesting, since the connection to diabletes that\n;; was discovered is *indirect*, and simulates the sort of discovery\n;; we would hope for in practice.\n;;\n;;\n;; Original comments follow:\n;;\n;;\n;; remove from the 154 disorders (no neoplasms or pathologic functions)\n;; of interest those 53 disorders, neoplasms, or pathologic functions\n;; directly treated by Gleevec\n;;\n;; result is 151 diseases, including the useless \"Disease\" and \"Syndrome\" and \"Degenerative disorder\",\n;; and including:\n;; * at least 4 entries for epilepsy\n;; * approximately 7 entries related to kidney/renal disease\n;; * approximately 9 entries related to diabetes\n;; etc.\n;;\n;; Seems like there are a number of groups of diseases within the 151\n;; diseases. For example, diabetes is probably worth a look.\n;;\n;; And, of course, there is the 1 entry for asthma\n;;\n;; Wow!\n;;\n;; https://www.nbcnews.com/health/health-news/cancer-drug-gleevec-might-slow-type-1-diabetes-n771241\n;;\n;; https://www.medscape.com/viewarticle/882089\n;;\n;; http://www.ajmc.com/newsroom/scientists-find-accidental-cure-for-type-2-diabetes-imatinib\n;;\n;; March 29, 2016\n;;\n;; \"The cancer drug imatinib—marketed as Gleevec and known as a game-changer for conditions like chronic myeloid leukemia—may prove the same in type 2 diabetes (T2D), according to a study published recently in Diabetes.\"\n;;\n;;\n;; The article:\n;;\n;; http://diabetes.diabetesjournals.org/content/65/4/829\n;;\n;; Oh, SemMedDB does contain this information! The list of diseases Gleevec treats includes:\n;;\n;; (11847 \"Diabetes\" (\"dsyn\"))\n;; (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n;;\n;; The problem, of course, is that without doing more reasoning using\n;; an ontology or external information, or maybe getting lucky with\n;; the ISA predicate, the query has no way of knowing that those 9\n;; diabetes-related entries are actually related to the entry\n;; (11847 \"Diabetes\" (\"dsyn\")).\n;;\n;; Still, I was pleased that *I* learned something from the query, and\n;; that the signal was quite strong after all of that filtering.\n;;\n;; So, with more resoning, perhaps using an ontology, we should be\n;; able to reduce the ~150 answers by removing (or at least ranking\n;; lower) answers related to the diseases we know Gleevec treats.\n;;\n;; Seems that the full story is a bit complicated. There are papers\n;; indicating that imatinib/Gleevec treats diabetes in mouse models.\n;; At least one clinical trial on humans didn't seem to show\n;; improvement.\n(set-subtraction\n '((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n '((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n;; =>\n#|\n'((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n|#\n\n;; Check that the gene (such as KIT) that causes a celf that affects a\n;; disorder is also know to directly cause that disorder? Seems like\n;; this is a basic check we should do, to both increase confidence and\n;; perhaps reduce answers.\n;;\n;; Restrict the disease to \"dsyn\" or \"patf\", but not \"neop\" (since in\n;; the case of imatinib/Gleevec, we already know it treats cancer).\n;;\n;; Try across all 47 genes of interest.\n;;\n;; cpu time: 18586 real time: 18595 gc time: 286\n;;\n;; 93 answers\n;;\n;; includes (4096 \"Asthma\" (\"dsyn\")) and (11847 \"Diabetes\" (\"dsyn\"))\n;;\n;; run by typing (gene-causes-celf-affects-disorder)\n;;\n(define (gene-causes-celf-affects-disorder)\n (apply\n union*\n (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 e1 e2 e3 celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n ; [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e1)\n (edgeo e2)))))\n (rem-dups disorders)))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))))))\n;; =>\n#|\n'((7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (15376 \"Extravasation\" (\"patf\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (28778 \"Obstruction\" (\"patf\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\")))\n|#\n\n;; Now, remove all the diseases that imatinib variants are known to treat.\n;;\n;; 52 left, including asthma\n(set-subtraction\n '((7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (15376 \"Extravasation\" (\"patf\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (28778 \"Obstruction\" (\"patf\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\")))\n '((2871 \"Anemia\" (\"dsyn\"))\n (2874 \"Aplastic Anemia\" (\"dsyn\"))\n (2895 \"Sickle Cell Anemia\" (\"dsyn\"))\n (3047 \"Animal Diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (5940 \"Bone Diseases\" (\"dsyn\"))\n (18944 \"Hematoma\" (\"patf\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7682 \"CNS disorder\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6118 \"Brain Neoplasms\" (\"neop\"))\n (21368 \"Inflammation\" (\"patf\"))\n (8728 \"Churg-Strauss Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (10403 \"Cryoglobulinemia\" (\"dsyn\"))\n (11644 \"Scleroderma\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (29435 \"Osteolysis\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36429 \"Sclerosis\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (86565 \"Liver Dysfunction\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (151654 \"Myocardial fibrosis\" (\"patf\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (15624 \"Fanconi Syndrome\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (7114 \"Malignant neoplasm of skin\" (\"neop\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (231178 \"Chronic failure\" (\"patf\"))\n (19196 \"Hepatitis C\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (21141 \"Inappropriate ADH Syndrome\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (23890 \"Liver Cirrhosis\" (\"dsyn\"))\n (9404 \"Colorectal Neoplasms\" (\"neop\"))\n (24115 \"Lung diseases\" (\"dsyn\"))\n (333606 \"Dystrophy\" (\"patf\"))\n (24440 \"Macular Edema, Cystoid\" (\"dsyn\"))\n (443146 \"Autoimmune\" (\"patf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27697 \"Nephritis\" (\"dsyn\"))\n (549593 \"kidney functional\" (\"patf\"))\n (27947 \"Neutropenia\" (\"dsyn\"))\n (16048 \"Fibromatosis\" (\"neop\"))\n (33838 \"Kimura Disease\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (34063 \"Pulmonary Edema\" (\"dsyn\"))\n (744813 \"Hepatic embolisation\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (35920 \"Rubella\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (18923 \"Hemangiosarcoma\" (\"neop\"))\n (36992 \"Short Bowel Syndrome\" (\"dsyn\"))\n (1265815 \"Multiple ulcers\" (\"patf\"))\n (38013 \"Ankylosing spondylitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (1608322 \"Leak NOS\" (\"patf\"))\n (39103 \"Synovitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (85786 \"Hamman-Rich syndrome\" (\"dsyn\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (86438 \"Hypogammaglobulinemia\" (\"dsyn\"))\n (151859 \"Polyserositis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (158168 \"Villonodular synovitis\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206062 \"Lung Diseases, Interstitial\" (\"dsyn\"))\n (206143 \"Loeffler's Endocarditis\" (\"dsyn\"))\n (236178 \"Intraabdominal hemorrhage\" (\"dsyn\"))\n (238644 \"anemia; profound\" (\"dsyn\"))\n (238790 \"destruction; bone\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (263664 \"Generalized morphea\" (\"dsyn\"))\n (264939 \"Systemic vasculitis\" (\"dsyn\"))\n (23475 \"Leukemia, Myeloid, Philadelphia-Negative\" (\"neop\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n (276653 \"Invasive pulmonary aspergillosis\" (\"dsyn\"))\n (277554 \"Primary disease\" (\"dsyn\"))\n (277556 \"Recurrent disease\" (\"dsyn\"))\n (334102 \"Lymphangiomatosis\" (\"dsyn\"))\n (23484 \"Leukemia, Plasmacytic\" (\"neop\"))\n (340548 \"Pulmonary capillary hemangiomatosis\" (\"dsyn\"))\n (23601 \"Leydig Cell Tumor\" (\"neop\"))\n (341213 \"External gastric fistula\" (\"dsyn\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (341439 \"Chronic liver disease NOS\" (\"dsyn\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (442867 \"Malignant disease\" (\"dsyn\"))\n (549567 \"Pigmentation Disorders\" (\"dsyn\"))\n (678236 \"Rare Diseases\" (\"dsyn\"))\n (743496 \"END ORGAN DAMAGE\" (\"dsyn\"))\n (25286 \"meningioma\" (\"neop\"))\n (25500 \"Mesothelioma\" (\"neop\"))\n (854467 \"Myelosuppression\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (855227 \"Purging\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (920627 \"Orphan Diseases\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (948908 \"Nephrotoxic serum nephritis\" (\"dsyn\"))\n (1273070 \"Left ventricular diastolic dysfunction\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (27832 \"Neurofibromatosis 2\" (\"neop\"))\n (1299884 \"Eosinophilic myositis\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1332309 \"Anti-Basement Membrane Glomerulonephritis\" (\"dsyn\"))\n (1533022 \"Histiocytic proliferation\" (\"dsyn\"))\n (1565489 \"Renal Insufficiency\" (\"dsyn\"))\n (36221 \"Mast-Cell Sarcoma\" (\"neop\"))\n (41341 \"Tuberous Sclerosis\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (79772 \"T-Cell Lymphoma\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (162678 \"Neurofibromatoses\" (\"neop\"))\n (205853 \"Neoplasms, Epithelial\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206657 \"Sarcoma, Alveolar Soft Part\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (220650 \"Metastatic malignant neoplasm to brain\" (\"neop\"))\n (238463 \"Papillary thyroid carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (278517 \"Non-small cell lung cancer recurrent\" (\"neop\"))\n (278695 \"recurrent neuroblastoma\" (\"neop\"))\n (278704 \"Malignant Childhood Neoplasm\" (\"neop\"))\n (278727 \"Small cell lung cancer recurrent\" (\"neop\"))\n (279068 \"childhood solid tumor\" (\"neop\"))\n (279087 \"recurrent Kaposi's sarcoma\" (\"neop\"))\n (281361 \"Adenocarcinoma pancreas\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (334410 \"Leydig cell tumor, malignant\" (\"neop\"))\n (334695 \"Endometrial Stromal Tumors\" (\"neop\"))\n (349636 \"Pre B-cell acute lymphoblastic leukemia\" (\"neop\"))\n (553580 \"Ewings sarcoma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (685938 \"Malignant neoplasm of gastrointestinal tract\" (\"neop\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (854850 \"Mycosis fungoides refractory\" (\"neop\"))\n (855054 \"Fibrosarcoma metastatic\" (\"neop\"))\n (855211 \"Seminoma of testis\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (1266042 \"Chromophobe Renal Cell Carcinoma\" (\"neop\"))\n (1266101 \"Thymic epithelial neoplasm\" (\"neop\"))\n (1266119 \"Solitary fibrous tumor\" (\"neop\"))\n (1266120 \"Solitary fibrous tumor, malignant\" (\"neop\"))\n (1300127 \"Perivascular epithelial cell tumor\" (\"neop\"))\n (1306837 \"Papillary Renal Cell Carcinoma\" (\"neop\"))\n (1318543 \"Tenosynovial giant cell tumor\" (\"neop\"))\n (1319185 \"Chiasmal glioma\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1332884 \"Central Nervous System Leukemia\" (\"neop\"))\n (1333614 \"Fibrosarcomatous Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (1334432 \"Low Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1335996 \"Small Intestinal Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1378050 \"Oncocytic Neoplasm\" (\"neop\"))\n (1411997 \"Acute biphenotypic leukemia\" (\"neop\"))\n (1512409 \"Hepatocarcinogenesis\" (\"neop\"))\n (1524028 \"Intraepithelial Neoplasia of the Mouse Mammary Gland\" (\"neop\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (6272 \"Bronchiolitis Obliterans\" (\"dsyn\"))\n (9782 \"Connective Tissue Diseases\" (\"dsyn\"))\n (10828 \"Cytopenia\" (\"patf\"))\n (11603 \"Dermatitis\" (\"dsyn\"))\n (11633 \"Dermatomyositis\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (7102 \"Malignant tumor of colon\" (\"neop\"))\n (19618 \"Histiocytosis\" (\"dsyn\"))\n (243083 \"associated disease\" (\"patf\"))\n (19621 \"Histiocytosis, Langerhans-Cell\" (\"dsyn\"))\n (7115 \"Malignant neoplasm of thyroid\" (\"neop\"))\n (19624 \"Histiocytosis, Non-Langerhans-Cell\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (19625 \"Sinus histiocytosis\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (399498 \"Oral lichenoid reaction\" (\"patf\"))\n (24901 \"Mastocytosis, Diffuse Cutaneous\" (\"dsyn\"))\n (26272 \"Mixed Connective Tissue Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (31154 \"Peritonitis\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (7140 \"Carcinosarcoma\" (\"neop\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (33687 \"Proteinuria\" (\"dsyn\"))\n (7847 \"Malignant neoplasm of cervix uteri\" (\"neop\"))\n (34069 \"Pulmonary Fibrosis\" (\"dsyn\"))\n (34155 \"Purpura, Thrombotic Thrombocytopenic\" (\"dsyn\"))\n (8479 \"Chondrosarcoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (39106 \"Pigmented villonodular synovitis\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (42384 \"Vasculitis\" (\"dsyn\"))\n (18206 \"granulosa cell tumor\" (\"neop\"))\n (152171 \"Primary pulmonary hypertension\" (\"dsyn\"))\n (162835 \"Hypopigmentation\" (\"dsyn\"))\n (206061 \"Pneumonitis, Interstitial\" (\"dsyn\"))\n (23435 \"Leukemia, B-Cell, Acute\" (\"neop\"))\n (267437 \"Allergic diarrhea\" (\"dsyn\"))\n (282548 \"Leukostasis\" (\"dsyn\"))\n (339143 \"Thyroid associated opthalmopathies\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (341697 \"Renal impairment\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (745283 \"INFECTIOUS PROCESS\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (748159 \"PULMONARY INVOLVEMENT\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (836924 \"thrombocytosis\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (949690 \"Spondylarthritis\" (\"dsyn\"))\n (1112486 \"Aggressive Systemic Mastocytosis\" (\"dsyn\"))\n (1136033 \"Cutaneous Mastocytosis\" (\"dsyn\"))\n (1142420 \"Hepatitis B reactivation\" (\"dsyn\"))\n (1261469 \"End stage renal failure\" (\"dsyn\"))\n (23479 \"Leukemia, Myelomonocytic, Acute\" (\"neop\"))\n (1279945 \"Acute interstitial pneumonia\" (\"dsyn\"))\n (1368107 \"Aplastic bone marrow\" (\"dsyn\"))\n (1619734 \"Pulmonary arterial hypertension\" (\"dsyn\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23494 \"Leukemia, T-Cell, Chronic\" (\"neop\"))\n (23827 \"liposarcoma\" (\"neop\"))\n (26987 \"Myelofibrosis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (35412 \"Rhabdomyosarcoma\" (\"neop\"))\n (36220 \"Kaposi Sarcoma\" (\"neop\"))\n (36631 \"Seminoma\" (\"neop\"))\n (39101 \"synovial sarcoma\" (\"neop\"))\n (40100 \"Thymoma\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (151779 \"[X]Malignant melanoma of skin, unspecified\" (\"neop\"))\n (205851 \"Germ cell tumor\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (206630 \"Endometrial Stromal Sarcoma\" (\"neop\"))\n (206693 \"Medullary carcinoma\" (\"neop\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (276535 \"AIDS with Kaposi's sarcoma\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278678 \"Metastatic renal cell carcinoma\" (\"neop\"))\n (278694 \"Disseminated neuroblastoma\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (279549\n \"Philadelphia chromosome negative chronic myelogenous leukemia\"\n (\"neop\"))\n (280449 \"secondary acute myeloid leukemia\" (\"neop\"))\n (334664 \"Mast Cell Neoplasm\" (\"neop\"))\n (338113 \"Uterine Corpus Sarcoma\" (\"neop\"))\n (341823 \"Epithelial tumor of ovary\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (346421 \"Chronic eosinophilic leukemia\" (\"neop\"))\n (346976 \"Secondary malignant neoplasm of pancreas\" (\"neop\"))\n (349640 \"[M]Subacute myeloid leukemia\" (\"neop\"))\n (431109 \"Choroid Plexus Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (521158 \"Recurrent tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (549379 \"Recurrent Carcinoma\" (\"neop\"))\n (598798 \"Lymphoid neoplasm\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (677936 \"Refractory Carcinoma\" (\"neop\"))\n (699889 \"Female reproductive neoplasm malignant NOS\" (\"neop\"))\n (740267 \"Ocular melanomas\" (\"neop\"))\n (740277 \"Bile duct carcinoma\" (\"neop\"))\n (743535 \"EOSINOPHILIC GRANULOMATOSIS\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (812413 \"Malignant Pleural Mesothelioma\" (\"neop\"))\n (855013 \"Chondrosarcoma recurrent\" (\"neop\"))\n (936223 \"Prostate cancer metastatic\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1327920 \"childhood chronic myelogenous leukemia\" (\"neop\"))\n (1333768 \"Gastric Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334699 \"Mesenchymal Cell Neoplasm\" (\"neop\"))\n (1335711 \"Recurrent Mature T- and NK-Cell Non-Hodgkin's Lymphoma\" (\"neop\"))\n (1335713 \"Recurrent Meningioma\" (\"neop\"))\n (1335729 \"Refractory Neoplasm\" (\"neop\"))\n (1336746 \"Thymus Carcinoid Tumor\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (235063 \"Respiratory Depression\" (\"patf\"))\n (679222 \"functional insufficiency\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (1815 \"Primary Myelofibrosis\" (\"neop\"))\n (12634 \"Disease\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (24228 \"Lymphatic Diseases\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (37354 \"Smallpox\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (221013 \"Mastocytosis, Systemic\" (\"dsyn\"))\n (1318485 \"Liver regeneration disorder\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (456070 \"Growth delay\" (\"patf\"))\n (17638 \"Glioma\" (\"neop\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23453 \"Leukemia, Lymphocytic, Acute, L2\" (\"neop\"))\n (23476 \"Leukemia, Myeloid, Philadelphia-Positive\" (\"neop\"))\n (23480 \"Leukemia, Myelomonocytic, Chronic\" (\"neop\"))\n (23481 \"Leukemia, Neutrophilic, Chronic\" (\"neop\"))\n (27022 \"Myeloproliferative disease\" (\"neop\"))\n (27819 \"Neuroblastoma\" (\"neop\"))\n (29463 \"osteosarcoma\" (\"neop\"))\n (85136 \"Central Nervous System Neoplasms\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (152018 \"Esophageal carcinoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (206093 \"Neuroectodermal Tumors\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (238461 \"Anaplastic thyroid carcinoma\" (\"neop\"))\n (238462 \"Medullary carcinoma of thyroid\" (\"neop\"))\n (278726 \"Small cell lung cancer extensive stage\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (555198 \"Malignant Glioma\" (\"neop\"))\n (677930 \"Primary Neoplasm\" (\"neop\"))\n (699791 \"Stomach Carcinoma\" (\"neop\"))\n (750952 \"Biliary Tract Cancer\" (\"neop\"))\n (751606 \"Adult Acute Lymphocytic Leukemia\" (\"neop\"))\n (860582 \"Peritoneal metastases\" (\"neop\"))\n (877373 \"Advanced cancer\" (\"neop\"))\n (879615 \"Stromal Neoplasm\" (\"neop\"))\n (887833 \"Carcinoma, Pancreatic Ductal\" (\"neop\"))\n (920028 \"Leukaemia recurrent\" (\"neop\"))\n (1266137 \"Gastrointestinal stromal sarcoma\" (\"neop\"))\n (1279296 \"Chronic leukemia (category)\" (\"neop\"))\n (1370868 \"refractory CML\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n;; =>\n#|\n'((19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\")))\n|#\n\n\n;; let's test the individual parts of the query\n\n;; compare\n;;\n;; (32 (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")))\n;;\n;; and\n;;\n;; (35 (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))\n;;\n;; which cause 32 and 35 diseases, respectively, with these monstrosities:\n;;\n;; (291 (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\")))\n;; (296 (1823619 \"VEGFA gene\" (\"bacs\" \"phsu\" \"rcpt\" \"gngm\" \"imft\" \"enzy\" \"aapp\")))\n;; (418 (1456820 \"Tumor Necrosis Factor-alpha\" (\"imft\" \"gngm\" \"aapp\")))\n;; (506 (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\")))\n;; (579 (79189 \"cytokine\" (\"aapp\" \"imft\" \"gngm\")))\n;; (1171 (17337 \"Genes\" (\"aapp\" \"gngm\"))))\n;;\n;; Could either just drop entries like (1171 (17337 \"Genes\" (\"aapp\" \"gngm\")))\n;; and (506 (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))), or prioritize search\n;; to start with smallest number of diseases (or both).\n;;\n;; Also, should make sure to remove duplicate diseases in the results!\n;; And remove ridiculous entries like (12634 \"Disease\" (\"dsyn\"))\n;;\n;; Also, should take the union of diseases caused by C-KIT and KIT,\n;; rather than trying them both separately (and getting duplicate\n;; answers).\n;;\n;; Should also consider taking the union of all diseases produced by\n;; all genes, to avoid duplicate work, or do caching/memoization/tabling.\n;;\n(let ((genes-inhibited-by-imatinib\n (run* (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== gene q)\n\n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (edgeo e-drug/gene)\n\n ))))\n (let ((genes-inhibited-by-imatinib (rem-dups genes-inhibited-by-imatinib)))\n (sort\n (map (lambda (gene)\n (let ((num-diseases-caused-by-gene\n (length\n (run* (q)\n (fresh (drug known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== e-gene/known-disease q)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease \"CAUSES\" ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease))))))\n (list num-diseases-caused-by-gene gene)))\n genes-inhibited-by-imatinib)\n (lambda (l1 l2) (< (car l1) (car l2))))))\n\n(displayln\n \"Finished loading 'lets test the individual parts of the query'\")\n\n\n;; how many genes are inhibited by imatinib?\n;;\n;; cpu time: 10 real time: 10 gc time: 0\n;; 213 genes inhibited by imatinib\n;;\n;; some of these genes are dups! why?\n;; 206 unique genes\n;;\n;; one of these answers is (17337 \"Genes\" (\"aapp\" \"gngm\")), as opposed to a specific gene--does this result in a degenerate blowup? This seems fishy!!\n(time\n (length\n (run* (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== gene q)\n\n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (edgeo e-drug/gene)\n\n ))))\n\n(displayln\n \"done\")\n" }, { "path": "attic/code/microKanren/README.md", "content": "Kanren\n==========\n\nCopyright (C) 2013 Jason Hemann and Daniel P. Friedman\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n\n\n\n" }, { "path": "attic/code/microKanren/microKanren-test-programs.scm", "content": "\n(define-syntax test-check\n (syntax-rules ()\n ((_ title tested-expression expected-result)\n (begin\n (printf \"Testing ~s\\n\" title)\n (let* ((expected expected-result)\n (produced tested-expression))\n (or (equal? expected produced)\n (errorf 'test-check\n \"Failed: ~a~%Expected: ~a~%Computed: ~a~%\"\n 'tested-expression expected produced)))))))\n\n(define a-and-b\n (conj \n (call/fresh (lambda (a) (== a 7)))\n (call/fresh \n (lambda (b) \n (disj\n (== b 5)\n (== b 6))))))\n\n(define fives\n (lambda (x)\n (disj\n (== x 5) \n (lambda (a/c)\n (lambda ()\n ((fives x) a/c))))))\n\n(define appendo\n (lambda (l s out)\n (disj\n (conj (== '() l) (== s out))\n (call/fresh\n (lambda (a)\n (call/fresh\n (lambda (d)\n (conj\n (== `(,a . ,d) l)\n (call/fresh\n (lambda (res)\n (conj\n (== `(,a . ,res) out)\n (lambda (s/c)\n (lambda ()\n ((appendo d s res) s/c))))))))))))))\n\n(define appendo2\n (lambda (l s out)\n (disj\n (conj (== '() l) (== s out))\n (call/fresh\n (lambda (a)\n (call/fresh\n (lambda (d)\n (conj\n (== `(,a . ,d) l)\n (call/fresh\n (lambda (res)\n (conj\n (lambda (s/c)\n (lambda ()\n ((appendo2 d s res) s/c)))\n (== `(,a . ,res) out))))))))))))\n\n(define call-appendo\n (call/fresh\n (lambda (q)\n (call/fresh\n (lambda (l)\n (call/fresh\n (lambda (s)\n (call/fresh\n (lambda (out)\n (conj\n (appendo l s out)\n (== `(,l ,s ,out) q)))))))))))\n\n(define call-appendo2\n (call/fresh\n (lambda (q)\n (call/fresh\n (lambda (l)\n (call/fresh\n (lambda (s)\n (call/fresh\n (lambda (out)\n (conj\n (appendo2 l s out)\n (== `(,l ,s ,out) q)))))))))))\n\n(define call-appendo3\n (call/fresh\n (lambda (q)\n (call/fresh\n (lambda (l)\n (call/fresh\n (lambda (s)\n (call/fresh\n (lambda (out)\n (conj\n (== `(,l ,s ,out) q)\n (appendo l s out)))))))))))\n\n(define ground-appendo (appendo '(a) '(b) '(a b)))\n\n(define ground-appendo2 (appendo2 '(a) '(b) '(a b)))\n\n(define relo\n (lambda (x)\n (call/fresh\n (lambda (x1)\n (call/fresh\n (lambda (x2)\n (conj\n (== x `(,x1 . ,x2))\n (disj\n (== x1 x2)\n (lambda (s/c)\n (lambda () ((relo x) s/c)))))))))))\n\n(define many-non-ans\n (call/fresh\n (lambda (x)\n (disj\n (relo `(5 . 6))\n (== x 3)))))\n\n" }, { "path": "attic/code/microKanren/microKanren-test.scm", "content": "(load \"microKanren-test-programs.scm\")\n\n(test-check \"second-set t1\"\n (let (($ ((call/fresh (lambda (q) (== q 5))) empty-state)))\n (car $))\n '(((#(0) . 5)) . 1))\n\n(test-check \"second-set t2\"\n (let (($ ((call/fresh (lambda (q) (== q 5))) empty-state)))\n (cdr $))\n '())\n\n(test-check \"second-set t3\"\n (let (($ (a-and-b empty-state)))\n (car $))\n '(((#(1) . 5) (#(0) . 7)) . 2))\n\n(test-check \"second-set t3, take\"\n (let (($ (a-and-b empty-state)))\n (take 1 $))\n '((((#(1) . 5) (#(0) . 7)) . 2)))\n\n(test-check \"second-set t4\"\n (let (($ (a-and-b empty-state)))\n (car (cdr $)))\n '(((#(1) . 6) (#(0) . 7)) . 2))\n\n(test-check \"second-set t5\"\n (let (($ (a-and-b empty-state)))\n (cdr (cdr $)))\n '())\n\n(test-check \"who cares\"\n (let (($ ((call/fresh (lambda (q) (fives q))) empty-state)))\n (take 1 $))\n '((((#(0) . 5)) . 1)))\n\n(test-check \"take 2 a-and-b stream\"\n (let (($ (a-and-b empty-state)))\n (take 2 $))\n '((((#(1) . 5) (#(0) . 7)) . 2)\n (((#(1) . 6) (#(0) . 7)) . 2)))\n\n(test-check \"take-all a-and-b stream\"\n (let (($ (a-and-b empty-state)))\n (take-all $))\n '((((#(1) . 5) (#(0) . 7)) . 2)\n (((#(1) . 6) (#(0) . 7)) . 2)))\n\n(test-check \"ground appendo\"\n (car ((ground-appendo empty-state)))\n '(((#(2) b) (#(1)) (#(0) . a)) . 3))\n\n(test-check \"ground appendo2\"\n (car ((ground-appendo2 empty-state)))\n '(((#(2) b) (#(1)) (#(0) . a)) . 3))\n\n(test-check \"appendo\"\n (take 2 (call-appendo empty-state))\n '((((#(0) #(1) #(2) #(3)) (#(2) . #(3)) (#(1))) . 4)\n (((#(0) #(1) #(2) #(3)) (#(2) . #(6)) (#(5)) (#(3) #(4) . #(6)) (#(1) #(4) . #(5))) . 7)))\n\n(test-check \"appendo2\"\n (take 2 (call-appendo2 empty-state))\n '((((#(0) #(1) #(2) #(3)) (#(2) . #(3)) (#(1))) . 4) (((#(0) #(1) #(2) #(3)) (#(3) #(4) . #(6)) (#(2) . #(6)) (#(5)) (#(1) #(4) . #(5))) . 7)))\n\n(test-check \"reify-1st across appendo\"\n (map reify-1st (take 2 (call-appendo empty-state)))\n '((() _.0 _.0) ((_.0) _.1 (_.0 . _.1))))\n\n(test-check \"reify-1st across appendo2\"\n (map reify-1st (take 2 (call-appendo2 empty-state)))\n '((() _.0 _.0) ((_.0) _.1 (_.0 . _.1))))\n\n(test-check \"many non-ans\"\n (take 1 (many-non-ans empty-state))\n '((((#(0) . 3)) . 1)))" }, { "path": "attic/code/microKanren/microKanren.scm", "content": ";; Jason Hemann and Dan Friedman\n;; microKanren, final implementation from paper\n\n(define (var c) (vector c))\n(define (var? x) (vector? x))\n(define (var=? x1 x2) (= (vector-ref x1 0) (vector-ref x2 0)))\n\n(define (walk u s)\n (let ((pr (and (var? u) (assp (lambda (v) (var=? u v)) s))))\n (if pr (walk (cdr pr) s) u)))\n\n(define (ext-s x v s) `((,x . ,v) . ,s))\n\n(define (== u v)\n (lambda (s/c)\n (let ((s (unify u v (car s/c))))\n (if s (unit `(,s . ,(cdr s/c))) mzero))))\n\n(define (unit s/c) (cons s/c mzero))\n(define mzero '())\n\n(define (unify u v s)\n (let ((u (walk u s)) (v (walk v s)))\n (cond\n ((and (var? u) (var? v) (var=? u v)) s)\n ((var? u) (ext-s u v s))\n ((var? v) (ext-s v u s))\n ((and (pair? u) (pair? v))\n (let ((s (unify (car u) (car v) s)))\n (and s (unify (cdr u) (cdr v) s))))\n (else\n ;; WEB -- vanilla microKanren uses eqv? rather than equal?\n (and (equal? u v) s)))))\n\n(define (call/fresh f)\n (lambda (s/c)\n (let ((c (cdr s/c)))\n ((f (var c)) `(,(car s/c) . ,(+ c 1))))))\n\n(define (disj g1 g2) (lambda (s/c) (mplus (g1 s/c) (g2 s/c))))\n(define (conj g1 g2) (lambda (s/c) (bind (g1 s/c) g2)))\n\n(define (mplus $1 $2)\n (cond\n ((null? $1) $2)\n ((procedure? $1) (lambda () (mplus $2 ($1))))\n (else (cons (car $1) (mplus (cdr $1) $2)))))\n\n(define (bind $ g)\n (cond\n ((null? $) mzero)\n ((procedure? $) (lambda () (bind ($) g)))\n (else (mplus (g (car $)) (bind (cdr $) g)))))\n" }, { "path": "attic/code/microKanren/miniKanren-wrappers.scm", "content": "\n;;;; How to make a simple miniKanren (substitution only)\n\n(define-syntax Zzz\n (syntax-rules ()\n ((_ g) (lambda (s/c) (lambda () (g s/c))))))\n\n(define-syntax conj+\n (syntax-rules ()\n ((_ g) (Zzz g))\n ((_ g0 g ...) (conj (Zzz g0) (conj+ g ...)))))\n\n(define-syntax disj+\n (syntax-rules ()\n ((_ g) (Zzz g))\n ((_ g0 g ...) (disj (Zzz g0) (disj+ g ...)))))\n\n(define-syntax fresh\n (syntax-rules ()\n ((_ () g0 g ...) (conj+ g0 g ...))\n ((_ (x0 x ...) g0 g ...)\n (call/fresh\n (lambda (x0)\n (fresh (x ...) g0 g ...))))))\n\n(define-syntax conde\n (syntax-rules ()\n ((_ (g0 g ...) ...) (disj+ (conj+ g0 g ...) ...))))\n\n(define-syntax run\n (syntax-rules ()\n ((_ n (x ...) g0 g ...)\n (map reify-1st (take n (call/goal (fresh (x ...) g0 g ...)))))))\n\n(define-syntax run*\n (syntax-rules ()\n ((_ (x ...) g0 g ...)\n (map reify-1st (take-all (call/goal (fresh (x ...) g0 g ...)))))))\n\n(define empty-state '(() . 0))\n\n(define (call/goal g) (g empty-state))\n\n(define (pull $)\n (if (procedure? $) (pull ($)) $))\n\n(define (take-all $)\n (let (($ (pull $)))\n (if (null? $) '() (cons (car $) (take-all (cdr $))))))\n\n(define (take n $)\n (if (zero? n) '()\n (let (($ (pull $)))\n (if (null? $) '() (cons (car $) (take (- n 1) (cdr $)))))))\n\n(define (reify-1st s/c)\n (let ((v (walk* (var 0) (car s/c))))\n (walk* v (reify-s v '()))))\n\n(define (walk* v s)\n (let ((v (walk v s)))\n (cond\n ((var? v) v)\n ((pair? v) (cons (walk* (car v) s)\n (walk* (cdr v) s)))\n (else v))))\n\n(define (reify-s v s)\n (let ((v (walk v s)))\n (cond\n ((var? v)\n (let ((n (reify-name (length s))))\n (cons `(,v . ,n) s)))\n ((pair? v) (reify-s (cdr v) (reify-s (car v) s)))\n (else s))))\n\n(define (reify-name n)\n (string->symbol\n (string-append \"_\" \".\" (number->string n))))\n\n(define (fresh/nf n f)\n (letrec\n ((app-f/v*\n (lambda (n v*)\n (cond\n ((zero? n) (apply f (reverse v*)))\n (else (call/fresh\n (lambda (x)\n (app-f/v* (- n 1) (cons x v*)))))))))\n (app-f/v* n '())))\n\n;;; Test programs\n\n(define-syntax test-check\n (syntax-rules ()\n ((_ title tested-expression expected-result)\n (begin\n (printf \"Testing ~s\\n\" title)\n (let* ((expected expected-result)\n (produced tested-expression))\n (or (equal? expected produced)\n (errorf 'test-check\n \"Failed: ~a~%Expected: ~a~%Computed: ~a~%\"\n 'tested-expression expected produced)))))))\n\n(define (appendo l s out)\n (conde\n ((== '() l) (== s out))\n ((fresh (a d res)\n (== `(,a . ,d) l)\n (== `(,a . ,res) out)\n (appendo d s res)))))\n\n(test-check 'run*\n (run* (q) (fresh (x y) (== `(,x ,y) q) (appendo x y '(1 2 3 4 5))))\n '((() (1 2 3 4 5))\n ((1) (2 3 4 5))\n ((1 2) (3 4 5))\n ((1 2 3) (4 5))\n ((1 2 3 4) (5))\n ((1 2 3 4 5) ())))\n\n(test-check 'run*2\n (run* (q x y) (== `(,x ,y) q) (appendo x y '(1 2 3 4 5)))\n '((() (1 2 3 4 5))\n ((1) (2 3 4 5))\n ((1 2) (3 4 5))\n ((1 2 3) (4 5))\n ((1 2 3 4) (5))\n ((1 2 3 4 5) ())))\n \n(test-check 'rember*o\n (letrec\n ((rember*o (lambda (tr o)\n (conde\n ((== '() tr) (== '() o))\n ((fresh (a d)\n (== `(,a . ,d) tr)\n (conde\n ((fresh (aa da)\n (== `(,aa . ,da) a)\n (fresh (a^ d^)\n (rember*o a a^)\n (rember*o d d^)\n (== `(,a^ . ,d^) o))))\n ((== a 8) (rember*o d o))\n ((fresh (d^)\n (rember*o d d^)\n (== `(,a . ,d^) o))))))))))\n (run 8 (q) (rember*o q '(1 2 8 3 4 5))))\n '((1 2 8 3 4 5)\n (1 2 8 3 4 5 8)\n (1 2 8 3 4 8 5)\n (1 2 8 3 8 4 5)\n (1 2 8 8 3 4 5)\n (1 2 8 8 3 4 5)\n (1 8 2 8 3 4 5)\n (8 1 2 8 3 4 5)))\n\n(test-check 'rember*o\n (letrec\n ((rember*o (lambda (tr o)\n (conde\n ((== '() tr) (== '() o))\n ((fresh (a d)\n (== `(,a . ,d) tr)\n (conde\n ((fresh (aa da)\n (== `(,aa . ,da) a)\n (fresh (a^ d^)\n (== `(,a^ . ,d^) o)\n (rember*o d d^)\n (rember*o a a^))))\n ((== a 8) (rember*o d o))\n ((fresh (d^)\n (== `(,a . ,d^) o)\n (rember*o d d^))))))))))\n (run 9 (q) (rember*o q '(1 (2 8 3 4) 5))))\n '((1 (2 8 3 4) 5)\n (1 (2 8 3 4) 5 8)\n (1 (2 8 3 4) 5 8 8)\n (1 (2 8 3 4) 8 5)\n (1 8 (2 8 3 4) 5)\n (8 1 (2 8 3 4) 5)\n (1 (2 8 3 4) 5 8 8 8)\n (1 (2 8 3 4) 5 8 8 8 8)\n (1 (2 8 3 4) 5 8 8 8 8 8)))\n\n\n\n\n" }, { "path": "attic/code/mk/LICENSE", "content": "The MIT License (MIT)\n\nOriginal work Copyright (c) 2015 William E. Byrd and Michael Ballantyne\nModified work Copyright (c) 2017 Gregory Rosenblatt\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n\n" }, { "path": "attic/code/mk/README.md", "content": "# miniKanren-with-symbolic-constraints\n\nA revision of https://github.com/webyrd/miniKanren-with-symbolic-constraints/ for better performance. Up to 10x faster for large queries involving heavy use of constraints.\n\nIncludes `==`, `=/=`, `symbolo`, and `numbero`. `absento` is included, but the argument is required to be an eqv-comparable ground atom.\n\nEigen was removed.\n\n\n## Using miniKanren\n\nRun `scheme`, then load miniKanren with a path relative to your current directory. From this directory, run:\n\n```\n(load \"mk.scm\")\n```\n\n\n## Running Tests\n\nRun `scheme --script test-all.scm` from this directory.\n\nTo interact with relational arithmetic, type inferencer, and interpreter, run `scheme` from this directory and load the appropriate files.\n\nFor example, to load the interpreter and generate three quines, run the following in `scheme`:\n\n```\n(load \"evalo.scm\")\n(run 3 (q) (evalo q q))\n```\n" }, { "path": "attic/code/mk/arithmetic.scm", "content": "(load \"mk.scm\")\n;; Relational arithmetic\n\n(define appendo\n (lambda (l s out)\n (conde\n [(== '() l) (== s out)]\n [(fresh (a d res)\n (== `(,a . ,d) l)\n (== `(,a . ,res) out)\n (appendo d s res))])))\n\n(define build-num\n (lambda (n)\n (cond\n ((odd? n)\n (cons 1\n (build-num (quotient (- n 1) 2))))\n ((and (not (zero? n)) (even? n))\n (cons 0\n (build-num (quotient n 2))))\n ((zero? n) '()))))\n\n(define zeroo\n (lambda (n)\n (== '() n)))\n\n(define poso\n (lambda (n)\n (fresh (a d)\n (== `(,a . ,d) n))))\n\n(define >1o\n (lambda (n)\n (fresh (a ad dd)\n (== `(,a ,ad . ,dd) n))))\n\n(define full-addero\n (lambda (b x y r c)\n (conde\n ((== 0 b) (== 0 x) (== 0 y) (== 0 r) (== 0 c))\n ((== 1 b) (== 0 x) (== 0 y) (== 1 r) (== 0 c))\n ((== 0 b) (== 1 x) (== 0 y) (== 1 r) (== 0 c))\n ((== 1 b) (== 1 x) (== 0 y) (== 0 r) (== 1 c))\n ((== 0 b) (== 0 x) (== 1 y) (== 1 r) (== 0 c))\n ((== 1 b) (== 0 x) (== 1 y) (== 0 r) (== 1 c))\n ((== 0 b) (== 1 x) (== 1 y) (== 0 r) (== 1 c))\n ((== 1 b) (== 1 x) (== 1 y) (== 1 r) (== 1 c)))))\n\n(define addero\n (lambda (d n m r)\n (conde\n ((== 0 d) (== '() m) (== n r))\n ((== 0 d) (== '() n) (== m r)\n (poso m))\n ((== 1 d) (== '() m)\n (addero 0 n '(1) r))\n ((== 1 d) (== '() n) (poso m)\n (addero 0 '(1) m r))\n ((== '(1) n) (== '(1) m)\n (fresh (a c)\n (== `(,a ,c) r)\n (full-addero d 1 1 a c)))\n ((== '(1) n) (gen-addero d n m r))\n ((== '(1) m) (>1o n) (>1o r)\n (addero d '(1) n r))\n ((>1o n) (gen-addero d n m r)))))\n\n(define gen-addero\n (lambda (d n m r)\n (fresh (a b c e x y z)\n (== `(,a . ,x) n)\n (== `(,b . ,y) m) (poso y)\n (== `(,c . ,z) r) (poso z)\n (full-addero d a b c e)\n (addero e x y z))))\n\n(define pluso\n (lambda (n m k)\n (addero 0 n m k)))\n\n(define minuso\n (lambda (n m k)\n (pluso m k n)))\n\n(define *o\n (lambda (n m p)\n (conde\n ((== '() n) (== '() p))\n ((poso n) (== '() m) (== '() p))\n ((== '(1) n) (poso m) (== m p))\n ((>1o n) (== '(1) m) (== n p))\n ((fresh (x z)\n (== `(0 . ,x) n) (poso x)\n (== `(0 . ,z) p) (poso z)\n (>1o m)\n (*o x m z)))\n ((fresh (x y)\n (== `(1 . ,x) n) (poso x)\n (== `(0 . ,y) m) (poso y)\n (*o m n p)))\n ((fresh (x y)\n (== `(1 . ,x) n) (poso x)\n (== `(1 . ,y) m) (poso y)\n (odd-*o x n m p))))))\n\n(define odd-*o\n (lambda (x n m p)\n (fresh (q)\n (bound-*o q p n m)\n (*o x m q)\n (pluso `(0 . ,q) m p))))\n\n(define bound-*o\n (lambda (q p n m)\n (conde\n ((== '() q) (poso p))\n ((fresh (a0 a1 a2 a3 x y z)\n (== `(,a0 . ,x) q)\n (== `(,a1 . ,y) p)\n (conde\n ((== '() n)\n (== `(,a2 . ,z) m)\n (bound-*o x y z '()))\n ((== `(,a3 . ,z) n)\n (bound-*o x y z m))))))))\n\n(define =lo\n (lambda (n m)\n (conde\n ((== '() n) (== '() m))\n ((== '(1) n) (== '(1) m))\n ((fresh (a x b y)\n (== `(,a . ,x) n) (poso x)\n (== `(,b . ,y) m) (poso y)\n (=lo x y))))))\n\n(define 1o m))\n ((fresh (a x b y)\n (== `(,a . ,x) n) (poso x)\n (== `(,b . ,y) m) (poso y)\n (1o b) (=lo n b) (pluso r b n))\n ((== '(1) b) (poso q) (pluso r '(1) n))\n ((== '() b) (poso q) (== r n))\n ((== '(0 1) b)\n (fresh (a ad dd)\n (poso dd)\n (== `(,a ,ad . ,dd) n)\n (exp2 n '() q)\n (fresh (s)\n (splito n dd r s))))\n ((fresh (a ad add ddd)\n (conde\n ((== '(1 1) b))\n ((== `(,a ,ad ,add . ,ddd) b))))\n (1o n) (== '(1) q)\n (fresh (s)\n (splito n b s '(1))))\n ((fresh (q1 b2)\n (== `(0 . ,q1) q)\n (poso q1)\n (1o q)\n (fresh (q1 nq1)\n (pluso q1 '(1) q)\n (repeated-mul n q1 nq1)\n (*o nq1 n nq))))))\n\n(define expo\n (lambda (b q n)\n (logo n b q '())))\n\n" }, { "path": "attic/code/mk/evalo.scm", "content": "(load \"mk.scm\")\n\n(define evalo\n (lambda (exp val)\n (eval-expo exp '() val)))\n\n(define eval-expo\n (lambda (exp env val)\n (conde\n ((fresh (v)\n (== `(quote ,v) exp)\n (not-in-envo 'quote env)\n (absento 'closure v)\n (== v val)))\n ((fresh (a*)\n (== `(list . ,a*) exp)\n (not-in-envo 'list env)\n (absento 'closure a*)\n (proper-listo a* env val)))\n ((symbolo exp) (lookupo exp env val))\n ((fresh (rator rand x body env^ a)\n (== `(,rator ,rand) exp)\n (eval-expo rator env `(closure ,x ,body ,env^))\n (eval-expo rand env a)\n (eval-expo body `((,x . ,a) . ,env^) val)))\n ((fresh (x body)\n (== `(lambda (,x) ,body) exp)\n (symbolo x)\n (not-in-envo 'lambda env)\n (== `(closure ,x ,body ,env) val))))))\n\n(define not-in-envo\n (lambda (x env)\n (conde\n ((fresh (y v rest)\n (== `((,y . ,v) . ,rest) env)\n (=/= y x)\n (not-in-envo x rest)))\n ((== '() env)))))\n\n(define proper-listo\n (lambda (exp env val)\n (conde\n ((== '() exp)\n (== '() val))\n ((fresh (a d t-a t-d)\n (== `(,a . ,d) exp)\n (== `(,t-a . ,t-d) val)\n (eval-expo a env t-a)\n (proper-listo d env t-d))))))\n\n(define lookupo\n (lambda (x env t)\n (fresh (rest y v)\n (== `((,y . ,v) . ,rest) env)\n (conde\n ((== y x) (== v t))\n ((=/= y x) (lookupo x rest t))))))\n" }, { "path": "attic/code/mk/mk.scm", "content": "; Old trie implementation, due to Abdulaziz Ghuloum. Used for substitution\n; and constraint store.\n\n ;;; subst ::= (empty)\n ;;; | (node even odd)\n ;;; | (data idx val)\n\n(define-record-type node (fields e o))\n\n(define-record-type data (fields idx val))\n\n(define shift (lambda (n) (fxsra n 1)))\n\n(define unshift (lambda (n i) (fx+ (fxsll n 1) i)))\n\n\n;; Switched to N-way Trie implementation to reduce depth\n\n(define shift-size 4)\n(define node-size (fxsll 1 shift-size))\n(define local-mask (fx- node-size 1))\n(define (shift-n xi) (fxsra xi shift-size))\n(define (local-n xi) (fxand xi local-mask))\n(define node-n? vector?)\n(define (node-n-new i0 v0)\n (define result (make-vector (fx+ i0 1) '()))\n (vector-set! result i0 v0)\n result)\n(define (node-n-get nd idx)\n (if (fx= xi 0))\n (error 't:bind \"index must be a fixnum, got ~s\" xi))\n (nwt:bind s xi v)))\n\n(define t:lookup\n (lambda (xi s)\n (unless (and (fixnum? xi) (>= xi 0))\n (error 't:lookup \"index must be a fixnum, got ~s\" xi))\n (nwt:lookup s xi)))\n\n;;; old interface\n\n;(define t:size\n ;(lambda (x) (t:aux:size x)))\n\n;(define t:bind\n ;(lambda (xi v s)\n ;(unless (and (fixnum? xi) (>= xi 0))\n ;(error 't:bind \"index must be a fixnum, got ~s\" xi))\n ;(t:aux:bind xi v s)))\n\n;(define t:unbind\n ;(lambda (xi s)\n ;(unless (and (fixnum? xi) (>= xi 0))\n ;(error 't:unbind \"index must be a fixnum, got ~s\" xi))\n ;(t:aux:unbind xi s)))\n\n;(define t:lookup\n ;(lambda (xi s)\n ;(unless (and (fixnum? xi) (>= xi 0))\n ;(error 't:lookup \"index must be a fixnum, got ~s\" xi))\n ;(t:aux:lookup xi s)))\n\n;;; interface\n\n(define t:binding-value\n (lambda (s)\n (unless (data? s)\n (error 't:binding-value \"not a binding ~s\" s))\n (data-val s)))\n\n;;; helpers\n\n(define t:aux:push\n (lambda (xi vi xj vj)\n (if (fxeven? xi)\n (if (fxeven? xj)\n (make-node (t:aux:push (shift xi) vi (shift xj) vj) '())\n (make-node (make-data (shift xi) vi) (make-data (shift xj) vj)))\n (if (fxeven? xj)\n (make-node (make-data (shift xj) vj) (make-data (shift xi) vi))\n (make-node '() (t:aux:push (shift xi) vi (shift xj) vj))))))\n\n(define t:aux:bind\n (lambda (xi vi s*)\n (cond\n [(node? s*)\n (if (fxeven? xi)\n (make-node (t:aux:bind (shift xi) vi (node-e s*)) (node-o s*))\n (make-node (node-e s*) (t:aux:bind (shift xi) vi (node-o s*))))]\n [(data? s*)\n (let ([xj (data-idx s*)] [vj (data-val s*)])\n (if (fx= xi xj)\n (make-data xi vi)\n (t:aux:push xi vi xj vj)))]\n [else (make-data xi vi)])))\n\n(define t:aux:lookup\n (lambda (xi s*)\n (cond\n [(node? s*)\n (if (fxeven? xi)\n (t:aux:lookup (shift xi) (node-e s*))\n (t:aux:lookup (shift xi) (node-o s*)))]\n [(data? s*)\n (if (fx= (data-idx s*) xi)\n s*\n #f)]\n [else #f])))\n\n(define t:aux:size\n (lambda (s*)\n (cond\n [(node? s*) (fx+ (t:aux:size (node-e s*)) (t:aux:size (node-o s*)))]\n [(data? s*) 1]\n [else 0])))\n\n(define t:aux:cons^\n (lambda (e o)\n (cond\n [(or (node? e) (node? o)) (make-node e o)]\n [(data? e)\n (make-data (unshift (data-idx e) 0) (data-val e))]\n [(data? o)\n (make-data (unshift (data-idx o) 1) (data-val o))]\n [else '()])))\n\n(define t:aux:unbind\n (lambda (xi s*)\n (cond\n [(node? s*)\n (if (fxeven? xi)\n (t:aux:cons^ (t:aux:unbind (shift xi) (node-e s*)) (node-o s*))\n (t:aux:cons^ (node-e s*) (t:aux:unbind (shift xi) (node-o s*))))]\n [(and (data? s*) (fx= (data-idx s*) xi)) '()]\n [else s*])))\n\n\n; Substitution representation\n\n(define empty-subst-map '())\n\n(define subst-map-length t:size)\n\n; Returns #f if not found, or a pair of u and the result of the lookup.\n; This distinguishes between #f indicating absence and being the result.\n(define subst-map-lookup\n (lambda (u S)\n (let ((res (t:lookup (var-idx u) S)))\n (if res\n (data-val res)\n unbound))))\n\n(define (subst-map-add S var val)\n (t:bind (var-idx var) val S))\n\n(define subst-map-eq? eq?)\n\n\n; Alternative (unused) substitution representation, using alists.\n; Performance with the tries is usually about the same and\n; can be much better for huge substitutions.\n\n#|\n(define empty-subst-map '())\n\n(define subst-map-length length)\n\n; Returns #f if not found, or a pair of u and the result of the lookup.\n; This distinguishes between #f indicating absence and being the result.\n(define subst-map-lookup\n (lambda (u S)\n (let ((res (assq u S)))\n (if res\n (cdr res)\n unbound))))\n\n(define (subst-map-add S var val)\n (cons (cons var val) S))\n\n(define subst-map-eq? eq?)\n|#\n\n\n; Constraint store representation\n\n(define empty-C '())\n\n(define set-c\n (lambda (v c st)\n (state (state-S st)\n (t:bind (var-idx v) c (state-C st))\n (state-depth st)\n (state-deferred st))))\n\n(define lookup-c\n (lambda (v st)\n (let ((res (t:lookup (var-idx v) (state-C st))))\n (if res\n (data-val res)\n empty-c))))\n\n; t:unbind either is buggy or doesn't do what I would expect, so\n; I implement remove by setting the value to the empty constraint record.\n(define remove-c\n (lambda (v st)\n (let ((res (t:bind (var-idx v) empty-c (state-C st))))\n (state (state-S st) res (state-depth st) (state-deferred st)))))\n\n\n; Misc. missing functions\n\n(define (remove-duplicates l)\n (cond ((null? l)\n '())\n ((member (car l) (cdr l))\n (remove-duplicates (cdr l)))\n (else\n (cons (car l) (remove-duplicates (cdr l))))))\n\n(define (foldl f init seq)\n (if (null? seq)\n init\n (foldl f\n (f (car seq) init)\n (cdr seq))))\n\n\n; Scope object.\n; Used to determine whether a branch has occured between variable creation\n; and unification to allow the set-var-val! optimization in subst-add. Both variables\n; and substitutions will contain a scope. When a substitution flows through a\n; conde it is assigned a new scope.\n\n;; To allow use of optimizations that sacrifice completeness, set this to #t.\n(define allow-incomplete-search? #f)\n\n;; To allow use of experimental `conde1` optimization, set this to #t.\n(define enable-conde1? #t)\n\n; Creates a new scope that is not scope-eq? to any other scope\n(define new-scope\n (lambda ()\n (list 'scope)))\n\n; Scope used when variable bindings should always be made in the substitution,\n; as in disequality solving and reification. We don't want to set-var-val! a\n; variable when checking if a disequality constraint holds!\n(define nonlocal-scope\n (list 'non-local-scope))\n\n(define scope-eq? eq?)\n\n\n; Logic variable object.\n; Contains:\n; val - value for variable assigned by unification using set-var-val! optimization.\n; unbound if not yet set or stored in substitution.\n; scope - scope that the variable was created in.\n; idx - unique numeric index for the variable. Used by the trie substitution representation.\n; Variable objects are compared by object identity.\n\n; The unique val for variables that have not yet been bound to a value\n; or are bound in the substitution\n(define unbound (list 'unbound))\n\n(define var\n (let ((counter -1))\n (lambda (scope)\n (set! counter (+ 1 counter))\n (vector unbound scope counter))))\n\n; Vectors are not allowed as terms, so terms that are vectors are variables.\n(define var?\n (lambda (x)\n (vector? x)))\n\n(define var-eq? eq?)\n\n(define var-val\n (lambda (x)\n (vector-ref x 0)))\n\n(define set-var-val!\n (lambda (x v)\n (vector-set! x 0 v)))\n\n(define var-scope\n (lambda (x)\n (vector-ref x 1)))\n\n(define var-idx\n (lambda (x)\n (vector-ref x 2)))\n\n\n; Substitution object.\n; Contains:\n; map - mapping of variables to values\n; scope - scope at current program point, for set-var-val! optimization. Updated at conde.\n; Included in the substitution because it is required to fully define the substitution\n; and how it is to be extended.\n;\n; Implementation of the substitution map depends on the Scheme used, as we need a map.\n\n(define subst\n (lambda (mapping scope)\n (cons mapping scope)))\n\n(define subst-map car)\n\n(define subst-scope cdr)\n\n(define subst-length\n (lambda (S)\n (subst-map-length (subst-map S))))\n\n(define subst-with-scope\n (lambda (S new-scope)\n (subst (subst-map S) new-scope)))\n\n(define empty-subst (subst empty-subst-map (new-scope)))\n\n(define subst-add\n (lambda (S x v)\n ; set-var-val! optimization: set the value directly on the variable\n ; object if we haven't branched since its creation\n ; (the scope of the variable and the substitution are the same).\n ; Otherwise extend the substitution mapping.\n (if (scope-eq? (var-scope x) (subst-scope S))\n (begin\n (set-var-val! x v)\n S)\n (subst (subst-map-add (subst-map S) x v) (subst-scope S)))))\n\n(define subst-lookup\n (lambda (u S)\n ; set-var-val! optimization.\n ; Tried checking the scope here to avoid a subst-map-lookup\n ; if it was definitely unbound, but that was slower.\n (if (not (eq? (var-val u) unbound))\n (var-val u)\n (subst-map-lookup u (subst-map S)))))\n\n; Association object.\n; Describes an association mapping the lhs to the rhs. Returned by unification\n; to describe the associations that were added to the substitution (whose representation\n; is opaque) and used to represent disequality constraints.\n\n(define lhs car)\n\n(define rhs cdr)\n\n; Constraint record object.\n;\n; Describes the constraints attached to a single variable.\n;\n; Contains:\n; T - type constraint. 'symbolo 'numbero or #f to indicate no constraint\n; D - list of disequality constraints. Each disequality is a list of associations.\n; The constraint is violated if all associated variables are equal in the\n; substitution simultaneously. D could contain duplicate constraints (created\n; by distinct =/= calls). A given disequality constraint is only attached to\n; one of the variables involved, as all components of the constraint must be\n; violated to cause failure.\n; A - list of absento constraints. Each constraint is a ground atom. The list contains\n; no duplicates.\n\n(define empty-c `(#f () ()))\n\n(define c-T\n (lambda (c)\n (car c)))\n\n(define c-D\n (lambda (c)\n (cadr c)))\n\n(define c-A\n (lambda (c)\n (caddr c)))\n\n(define c-with-T\n (lambda (c T)\n (list T (c-D c) (c-A c))))\n\n(define c-with-D\n (lambda (c D)\n (list (c-T c) D (c-A c))))\n\n(define c-with-A\n (lambda (c A)\n (list (c-T c) (c-D c) A)))\n\n; Constraint store object.\n; Mapping of representative variable to constraint record. Constraints are\n; always on the representative element and must be moved / merged when that\n; element changes.\n\n; Implementation depends on the Scheme used, as we need a map.\n\n; State object.\n; The state is the value that is monadically passed through the search.\n; Contains:\n; S - the substitution\n; C - the constraint store\n; depth - the current search depth in terms of `conde` nesting\n; deferred - expensive goals that will be tried later\n\n; TODO: use set! to choose appropriate max-search-depth per-run?\n(define max-search-depth\n ;#f ; unlimited depth\n ; Is this a reasonable depth for typical Barliman problems?\n 100)\n\n(define state\n (lambda (S C depth deferred)\n (list S C depth deferred)))\n\n(define state-S (lambda (st) (car st)))\n(define state-C (lambda (st) (cadr st)))\n(define state-depth (lambda (st) (caddr st)))\n(define state-deferred (lambda (st) (cadddr st)))\n(define state-depth-set\n (lambda (st depth)\n (state (state-S st) (state-C st) depth (state-deferred st))))\n(define state-depth-deepen\n (lambda (st)\n (let ((next-depth (+ 1 (state-depth st))))\n (if (and allow-incomplete-search?\n max-search-depth (< max-search-depth next-depth))\n (mzero)\n (state (state-S st) (state-C st) next-depth (state-deferred st))))))\n(define state-deferred-defer\n (lambda (st goal)\n (let ((deferred (state-deferred st)))\n (if deferred\n (state (state-S st)\n (state-C st)\n (state-depth st)\n (cons goal (state-deferred st)))\n (goal st)))))\n(define state-deferred-resume\n (lambda (st)\n (let ((deferred (state-deferred st)))\n (if (and deferred (pair? deferred))\n ((fold-left (lambda (g1 g0)\n (lambda (st)\n (bind (g0 st) g1)))\n unit\n deferred)\n (state (state-S st) (state-C st) (state-depth st) #f))\n st))))\n\n(define (empty-state) (state empty-subst empty-C 0 (and enable-conde1? '())))\n\n(define state-with-scope\n (lambda (st new-scope)\n (state (subst-with-scope (state-S st) new-scope)\n (state-C st)\n (state-depth st)\n (state-deferred st))))\n\n; Unification\n\n(define walk\n (lambda (u S)\n (if (var? u)\n (let ((val (subst-lookup u S)))\n (if (eq? val unbound)\n u\n (walk val S)))\n u)))\n\n(define occurs-check\n (lambda (x v S)\n (let ((v (walk v S)))\n (cond\n ((var? v) (var-eq? v x))\n ((pair? v)\n (or\n (occurs-check x (car v) S)\n (occurs-check x (cdr v) S)))\n (else #f)))))\n\n(define ext-s-check\n (lambda (x v S)\n (cond\n ((occurs-check x v S) (values #f #f))\n (else (values (subst-add S x v) `((,x . ,v)))))))\n\n; Returns as values the extended substitution and a list of associations added\n; during the unification, or (values #f #f) if the unification failed.\n;\n; Right now appends the list of added values from sub-unifications. Alternatively\n; could be threaded monadically, which could be faster or slower.\n(define unify\n (lambda (u v s)\n (let ((u (walk u s))\n (v (walk v s)))\n (cond\n ((eq? u v) (values s '()))\n ((var? u) (ext-s-check u v s))\n ((var? v) (ext-s-check v u s))\n ((and (pair? u) (pair? v))\n (let-values (((s added-car) (unify (car u) (car v) s)))\n (if s\n (let-values (((s added-cdr) (unify (cdr u) (cdr v) s)))\n (values s (append added-car added-cdr)))\n (values #f #f))))\n ((equal? u v) (values s '()))\n (else (values #f #f))))))\n\n(define unify*\n (lambda (S+ S)\n (unify (map lhs S+) (map rhs S+) S)))\n\n\n; Search\n\n; Search result types. Names inspired by the plus monad?\n(define mzero (lambda () #f))\n(define unit (lambda (c) c))\n(define choice (lambda (c f) (cons c f)))\n\n(define-syntax inc\n (syntax-rules ()\n ((_ e) (lambda () e))))\n\n(define empty-f (inc (mzero)))\n(define pause (lambda (c) (inc c)))\n\n(define-syntax lambdag@\n (syntax-rules ()\n ((_ (st) e) (lambda (st) e))))\n\n(define-syntax case-inf\n (syntax-rules ()\n ((_ e (() e0) ((f^) e1) ((c^) e2) ((c f) e3))\n (let ((c-inf e))\n (cond\n ((not c-inf) e0)\n ((procedure? c-inf) (let ((f^ c-inf)) e1))\n ((not (and (pair? c-inf)\n (procedure? (cdr c-inf))))\n (let ((c^ c-inf)) e2))\n (else (let ((c (car c-inf)) (f (cdr c-inf)))\n e3)))))))\n\n(define-syntax let/vars\n (syntax-rules ()\n ((_ _ () body) body)\n ((_ _ () body ...) (begin body ...))\n ((_ st (qvar ...) body ...)\n (let ((scope (subst-scope (state-S st))))\n (let ((qvar (var scope)) ...)\n body ...)))))\n\n(define-syntax with-depth\n (syntax-rules ()\n ((_ dst g) (lambdag@ (st) (g (state-depth-set st (state-depth dst)))))))\n\n(define-syntax bind*-depth\n (syntax-rules ()\n ((_ st0 g0 g ...) (bind* (g0 st0) (with-depth st0 g) ...))))\n\n(define-syntax fresh\n (syntax-rules ()\n ((_ (x ...) g0 g ...)\n (lambdag@ (st)\n (inc\n (let ((scope (subst-scope (state-S st))))\n (let ((x (var scope)) ...)\n (bind*-depth st g0 g ...))))))))\n\n(define-syntax bind*\n (syntax-rules ()\n ((_ e) e)\n ((_ e g0 g ...) (bind* (bind e g0) g ...))))\n\n(define bind\n (lambda (c-inf g)\n (case-inf c-inf\n (() (mzero))\n ((f) (inc (bind (f) g)))\n ((c) (g c))\n ((c f) (mplus (g c) (inc (bind (f) g)))))))\n\n(define-syntax run\n (syntax-rules ()\n ((_ n (q) g0 g ...)\n (take n\n (inc\n ((fresh (q) g0 g ... state-deferred-resume\n (lambdag@ (st)\n (let ((st (state-with-scope st nonlocal-scope)))\n (let ((z ((reify q) st)))\n (choice z empty-f)))))\n (empty-state)))))\n ((_ n (q0 q1 q ...) g0 g ...)\n (run n (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n(define-syntax run*\n (syntax-rules ()\n ((_ (q0 q ...) g0 g ...) (run #f (q0 q ...) g0 g ...))))\n\n(define take\n (lambda (n f)\n (cond\n ((and n (zero? n)) '())\n (else\n (case-inf (f)\n (() '())\n ((f) (take n f))\n ((c) (cons c '()))\n ((c f) (cons c\n (take (and n (- n 1)) f))))))))\n\n(define-syntax conde\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n (inc (bind (state-depth-deepen (state-with-scope st (new-scope)))\n (lambdag@ (st)\n (mplus* (bind*-depth st g0 g ...)\n (bind*-depth st g1 g^ ...) ...))))))))\n(define-syntax conde-dfs\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n (inc (bind (state-depth-deepen (state-with-scope st (new-scope)))\n (lambdag@ (st)\n (mplus*-dfs (bind*-depth st g0 g ...)\n (bind*-depth st g1 g^ ...) ...))))))))\n(define-syntax conde-weighted\n (syntax-rules ()\n ((_ (w0 c0 g0 g ...) (w1 c1 g1 g^ ...) ...)\n (lambdag@ (st)\n (inc (bind (state-depth-deepen (state-with-scope st (new-scope)))\n (lambdag@ (st)\n (mplus*-weighted\n (w0 c0 (bind*-depth st g0 g ...))\n (w1 c1 (bind*-depth st g1 g^ ...)) ...))))))))\n\n(define-syntax conde$\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n (let ((st (state-with-scope st (new-scope))))\n (mplus*\n (bind*-depth st g0 g ...)\n (bind*-depth st g1 g^ ...) ...))))))\n(define-syntax conde$-dfs\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n (let ((st (state-with-scope st (new-scope))))\n (mplus*-dfs\n (bind*-depth st g0 g ...)\n (bind*-depth st g1 g^ ...) ...))))))\n(define-syntax conde$-weighted\n (syntax-rules ()\n ((_ (w0 c0 g0 g ...) (w1 c1 g1 g^ ...) ...)\n (lambdag@ (st)\n (let ((st (state-with-scope st (new-scope))))\n (mplus*-weighted\n (w0 c0 (bind*-depth st g0 g ...))\n (w1 c1 (bind*-depth st g1 g^ ...)) ...))))))\n\n(define-syntax case0\n (syntax-rules ()\n ((_ expr zero ((cs) more))\n (let ((result expr)) (if result (let ((cs result)) more) zero)))))\n\n(define-syntax mplus1*\n (syntax-rules ()\n ((_ e) e)\n ((_ e0 e ...)\n (case0 e0\n (mplus1* e ...)\n ((c0) (mplus0* c0 e ...))))))\n\n(define-syntax mplus0*\n (syntax-rules ()\n ((_ unpruned) (if (procedure? unpruned) (unpruned) unpruned))\n ((_ unpruned e0 e ...)\n (case0 e0\n (mplus0* unpruned e ...)\n ((c0) (inc (mplus unpruned (inc (mplus* c0 e ...)))))))))\n\n(define-syntax let**\n (syntax-rules ()\n ((_ () body) body)\n ((_ (((name val) ...) ... ((name1 val1) ...)) body ...)\n (let** (((name val) ...) ...) (let* ((name1 val1) ...) body ...)))))\n\n(define-syntax conde1^\n (syntax-rules ()\n ((_ conde^ (((name lvar) ...) ...) (g0 g ...) ...)\n (lambdag@ (st)\n (let** (((name (walk lvar (state-S st))) ...) ...\n ((depth (state-depth st))\n (goal (lambdag@ (st) ((conde^ (g0 g ...) ...)\n (state-depth-set st depth))))\n (goal-deterministic\n (lambdag@ (st) ((conde$ (g0 g ...) ...)\n (state-depth-set st depth))))))\n (if (and (ormap var? (list name ...)) ...)\n (state-deferred-defer st goal)\n (goal-deterministic st)))))))\n(define-syntax conde1\n (syntax-rules () ((_ body ...) (conde1^ conde body ...))))\n(define-syntax conde1$\n (syntax-rules () ((_ body ...) (conde1^ conde$ body ...))))\n\n(define-syntax mplus*\n (syntax-rules ()\n ((_ e) e)\n ((_ e0 e ...) (mplus e0\n (inc (mplus* e ...))))))\n(define-syntax mplus*-dfs\n (syntax-rules ()\n ((_ e) e)\n ((_ e0 e ...) (mplus-dfs e0\n (inc (mplus*-dfs e ...))))))\n(define-syntax mplus*-weighted\n (syntax-rules ()\n ((_ (_ _ e)) e)\n ((_ (w0 c0 e0) e ...)\n (mplus-weighted w0 w0 1 c0 e0 (inc (mplus*-weighted e ...))))))\n\n(define mplus\n (lambda (c-inf f)\n (case-inf c-inf\n (() (f))\n ((f^) (inc (mplus (f) f^)))\n ((c) (choice c f))\n ((c f^) (choice c (inc (mplus (f) f^)))))))\n\n(define mplus-dfs\n (lambda (c-inf f)\n (case-inf c-inf\n (() (f))\n ((f^) (inc (mplus-dfs (f^) f)))\n ((c) (choice c f))\n ((c f^) (choice c (inc (mplus-dfs (f^) f)))))))\n\n(define (mplus-weighted-next remaining weight other cycles f^ f)\n (inc (let ((weight-next (and remaining (- remaining 1))))\n (if (and weight-next (<= weight-next 0))\n (let ((cycles (and cycles (- cycles 1))))\n (if (and cycles (<= cycles 0))\n (mplus (f) f^)\n (mplus-weighted other other weight cycles (f) f^)))\n (mplus-weighted weight-next weight other cycles (f^) f)))))\n(define mplus-weighted\n (lambda (remaining weight other-weight cycles c-inf f)\n (case-inf c-inf\n (() (f))\n ((f^) (inc (mplus-weighted-next\n remaining weight other-weight cycles f^ f)))\n ((c) (choice c f))\n ((c f^) (choice c (inc (mplus-weighted-next\n remaining weight other-weight cycles f^ f)))))))\n\n; Constraints\n; C refers to the constraint store map\n; c refers to an individual constraint record\n\n\n; Requirements for type constraints:\n; 1. Must be positive, not negative. not-pairo wouldn't work.\n; 2. Each type must have infinitely many possible values to avoid\n; incorrectness in combination with disequality constraints, like:\n; (fresh (x) (booleano x) (=/= x #t) (=/= x #f))\n(define type-constraint\n (lambda (type-pred type-id)\n (lambda (u)\n (lambdag@ (st)\n (let ((term (walk u (state-S st))))\n (cond\n ((type-pred term) (unit st))\n ((var? term)\n (let* ((c (lookup-c term st))\n (T (c-T c)))\n (cond\n ((eq? T type-id) (unit st))\n ((not T) (unit (set-c term (c-with-T c type-id) st)))\n (else (mzero)))))\n (else (mzero))))))))\n\n(define symbolo (type-constraint symbol? 'symbolo))\n(define numbero (type-constraint number? 'numbero))\n\n(define (add-to-D st v d)\n (let* ((c (lookup-c v st))\n (c^ (c-with-D c (cons d (c-D c)))))\n (set-c v c^ st)))\n\n(define =/=*\n (lambda (S+)\n (lambdag@ (st)\n (let-values (((S added) (unify* S+ (subst-with-scope (state-S st) nonlocal-scope))))\n (cond\n ((not S) (unit st))\n ((null? added) (mzero))\n (else\n ; Choose one of the disequality elements (el) to attach the constraint to. Only\n ; need to choose one because all must fail to cause the constraint to fail.\n (let ((el (car added)))\n (let ((st (add-to-D st (car el) added)))\n (if (var? (cdr el))\n (add-to-D st (cdr el) added)\n st)))))))))\n\n(define =/=\n (lambda (u v)\n (=/=* `((,u . ,v)))))\n\n(define absento\n (lambda (ground-atom term)\n (lambdag@ (st)\n (let ((term (walk term (state-S st))))\n (cond\n ((pair? term)\n (let ((st^ ((absento ground-atom (car term)) st)))\n (and st^ ((absento ground-atom (cdr term)) st^))))\n ((eqv? term ground-atom) (mzero))\n ((var? term)\n (let* ((c (lookup-c term st))\n (A (c-A c)))\n (if (memv ground-atom A)\n (unit st)\n (let ((c^ (c-with-A c (cons ground-atom A))))\n (unit (set-c term c^ st))))))\n (else (unit st)))))))\n\n; Fold lst with proc and initial value init. If proc ever returns #f,\n; return with #f immediately. Used for applying a series of constraints\n; to a state, failing if any operation fails.\n(define (and-foldl proc init lst)\n (if (null? lst)\n init\n (let ([res (proc (car lst) init)])\n (and res (and-foldl proc res (cdr lst))))))\n\n(define ==\n (lambda (u v)\n (lambdag@ (st)\n (let-values (((S added) (unify u v (state-S st))))\n (if S\n (and-foldl\n update-constraints\n (state S (state-C st) (state-depth st) (state-deferred st)) added)\n (mzero))))))\n\n\n; Not fully optimized. Could do absento update with fewer hash-refs / hash-sets.\n(define update-constraints\n (lambda (a st)\n (let ([old-c (lookup-c (lhs a) st)])\n (if (eq? old-c empty-c)\n st\n (let ((st (remove-c (lhs a) st)))\n (and-foldl (lambda (op st) (op st)) st\n (append\n (if (eq? (c-T old-c) 'symbolo)\n (list (symbolo (rhs a)))\n '())\n (if (eq? (c-T old-c) 'numbero)\n (list (numbero (rhs a)))\n '())\n (map (lambda (atom) (absento atom (rhs a))) (c-A old-c))\n (map (lambda (d) (=/=* d)) (c-D old-c)))))))))\n\n\n; Reification\n\n(define walk*\n (lambda (v S)\n (let ((v (walk v S)))\n (cond\n ((var? v) v)\n ((pair? v)\n (cons (walk* (car v) S) (walk* (cdr v) S)))\n (else v)))))\n\n(define vars\n (lambda (term acc)\n (cond\n ((var? term) (cons term acc))\n ((pair? term)\n (vars (cdr term) (vars (car term) acc)))\n (else acc))))\n\n(define-syntax project\n (syntax-rules ()\n ((_ (x ...) g g* ...)\n (lambdag@ (st)\n (let ((x (walk* x (state-S st))) ...)\n ((fresh () g g* ...) st))))))\n\n(define-syntax project0\n (syntax-rules ()\n ((_ (x ...) g g* ...)\n (lambdag@ (st)\n (let ((x (walk x (state-S st))) ...)\n ((fresh () g g* ...) st))))))\n\n; Create a constraint store of the old representation from a state object,\n; so that we can use the old reifier. Only accumulates constraints related\n; to the variable being reified which makes things a bit faster.\n(define c-from-st\n (lambda (st x)\n (let ((vs (vars (walk* x (state-S st)) '())))\n (foldl\n (lambda (v c-store)\n (let ((c (lookup-c v st)))\n (let ((S (state-S st))\n (D (c->D c-store))\n (Y (c->Y c-store))\n (N (c->N c-store))\n (T (c->T c-store))\n (T^ (c-T c))\n (D^ (c-D c))\n (A^ (c-A c)))\n `(,S\n ,(append D^ D)\n ,(if (eq? T^ 'symbolo)\n (cons v Y)\n Y)\n ,(if (eq? T^ 'numbero)\n (cons v N)\n N)\n ,(append\n (map (lambda (atom) (cons atom v)) A^)\n T)))))\n `(,(state-S st) () () () ())\n (remove-duplicates vs)))))\n\n(define reify\n (lambda (x)\n (lambda (st)\n (let ((c (c-from-st st x)))\n (let ((c (cycle c)))\n (let* ((S (c->S c))\n (D (walk* (c->D c) S))\n (Y (walk* (c->Y c) S))\n (N (walk* (c->N c) S))\n (T (walk* (c->T c) S)))\n (let ((v (walk* x S)))\n (let ((R (reify-S v (subst empty-subst-map nonlocal-scope))))\n (reify+ v R\n (let ((D (remp\n (lambda (d)\n (let ((dw (walk* d S)))\n (anyvar? dw R)))\n (rem-xx-from-d c))))\n (rem-subsumed D))\n (remp\n (lambda (y) (var? (walk y R)))\n Y)\n (remp\n (lambda (n) (var? (walk n R)))\n N)\n (remp (lambda (t)\n (anyvar? t R)) T))))))))))\n\n\n; Bits from the old constraint implementation, still used for reification.\n\n; In this part of the code, c refers to the\n; old constraint store with components:\n; S - substitution\n; D - disequality constraints\n; Y - symbolo\n; N - numbero\n; T - absento\n\n(define c->S (lambda (c) (car c)))\n(define c->D (lambda (c) (cadr c)))\n(define c->Y (lambda (c) (caddr c)))\n(define c->N (lambda (c) (cadddr c)))\n(define c->T (lambda (c) (cadddr (cdr c))))\n\n(define-syntax conda\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n ;; is 'state-with-scope' required here, as it is with conde?\n ;; I don't think so.\n (inc\n (ifa ((g0 st) g ...)\n ((g1 st) g^ ...) ...))))))\n\n(define-syntax ifa\n (syntax-rules ()\n ((_) (mzero))\n ((_ (e g ...) b ...)\n (let loop ((c-inf e))\n (case-inf c-inf\n (() (ifa b ...))\n ((f) (inc (loop (f))))\n ((a) (bind* c-inf g ...))\n ((a f) (bind* c-inf g ...)))))))\n\n(define-syntax condu\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n ;; is 'state-with-scope' required here, as it is with conde?\n ;; I don't think so.\n (inc\n (ifu ((g0 st) g ...)\n ((g1 st) g^ ...) ...))))))\n\n(define-syntax ifu\n (syntax-rules ()\n ((_) (mzero))\n ((_ (e g ...) b ...)\n (let loop ((c-inf e))\n (case-inf c-inf\n (() (ifu b ...))\n ((f) (inc (loop (f))))\n ((c) (bind* c-inf g ...))\n ((c f) (bind* (unit c) g ...)))))))\n\n; Syntax for reification goal objects using the old constraint store\n(define-syntax lambdar@\n (syntax-rules (:)\n ((_ (c) e) (lambda (c) e))\n ((_ (c : S D Y N T) e)\n (lambda (c)\n (let ((S (c->S c)) (D (c->D c)) (Y (c->Y c)) (N (c->N c)) (T (c->T c)))\n e)))))\n\n(define tagged?\n (lambda (S Y y^)\n (exists (lambda (y) (eqv? (walk y S) y^)) Y)))\n\n(define untyped-var?\n (lambda (S Y N t^)\n (let ((in-type? (lambda (y) (var-eq? (walk y S) t^))))\n (and (var? t^)\n (not (exists in-type? Y))\n (not (exists in-type? N))))))\n\n(define reify-S\n (lambda (v S)\n (let ((v (walk v S)))\n (cond\n ((var? v)\n (let ((n (subst-length S)))\n (let ((name (reify-name n)))\n (subst-add S v name))))\n ((pair? v)\n (let ((S (reify-S (car v) S)))\n (reify-S (cdr v) S)))\n (else S)))))\n\n(define reify-name\n (lambda (n)\n (string->symbol\n (string-append \"_\" \".\" (number->string n)))))\n\n(define drop-dot\n (lambda (X)\n (map (lambda (t)\n (let ((a (lhs t))\n (d (rhs t)))\n `(,a ,d)))\n X)))\n\n(define sorter\n (lambda (ls)\n (list-sort lex<=? ls)))\n\n(define lex<=?\n (lambda (x y)\n (string<=? (datum->string x) (datum->string y))))\n\n(define datum->string\n (lambda (x)\n (call-with-string-output-port\n (lambda (p) (display x p)))))\n\n;;; WEB -- 28 June 2016 -- return #t if walk*'d term t contains a gensym\n;;; (Barliman hack to make the reified answers more readable.)\n(define anygen?\n (lambda (t)\n (cond\n ((pair? t)\n (or (anygen? (car t))\n (anygen? (cdr t))))\n (else (gensym? t)))))\n\n(define anyvar?\n (lambda (u r)\n (cond\n ((pair? u)\n (or (anyvar? (car u) r)\n (anyvar? (cdr u) r)))\n (else (var? (walk u r))))))\n\n(define member*\n (lambda (u v)\n (cond\n ((equal? u v) #t)\n ((pair? v)\n (or (member* u (car v)) (member* u (cdr v))))\n (else #f))))\n\n(define drop-N-b/c-const\n (lambdar@ (c : S D Y N T)\n (let ((const? (lambda (n)\n (not (var? (walk n S))))))\n (cond\n ((find const? N) =>\n (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n (else c)))))\n\n(define drop-Y-b/c-const\n (lambdar@ (c : S D Y N T)\n (let ((const? (lambda (y)\n (not (var? (walk y S))))))\n (cond\n ((find const? Y) =>\n (lambda (y) `(,S ,D ,(remq1 y Y) ,N ,T)))\n (else c)))))\n\n(define remq1\n (lambda (elem ls)\n (cond\n ((null? ls) '())\n ((eq? (car ls) elem) (cdr ls))\n (else (cons (car ls) (remq1 elem (cdr ls)))))))\n\n(define same-var?\n (lambda (v)\n (lambda (v^)\n (and (var? v) (var? v^) (var-eq? v v^)))))\n\n(define find-dup\n (lambda (f S)\n (lambda (set)\n (let loop ((set^ set))\n (cond\n ((null? set^) #f)\n (else\n (let ((elem (car set^)))\n (let ((elem^ (walk elem S)))\n (cond\n ((find (lambda (elem^^)\n ((f elem^) (walk elem^^ S)))\n (cdr set^))\n elem)\n (else (loop (cdr set^))))))))))))\n\n(define drop-N-b/c-dup-var\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-dup same-var? S) N) =>\n (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n (else c))))\n\n(define drop-Y-b/c-dup-var\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-dup same-var? S) Y) =>\n (lambda (y)\n `(,S ,D ,(remq1 y Y) ,N ,T)))\n (else c))))\n\n(define var-type-mismatch?\n (lambda (S Y N t1^ t2^)\n (cond\n ((num? S N t1^) (not (num? S N t2^)))\n ((sym? S Y t1^) (not (sym? S Y t2^)))\n (else #f))))\n\n(define term-ununifiable?\n (lambda (S Y N t1 t2)\n (let ((t1^ (walk t1 S))\n (t2^ (walk t2 S)))\n (cond\n ((or (untyped-var? S Y N t1^) (untyped-var? S Y N t2^)) #f)\n ((var? t1^) (var-type-mismatch? S Y N t1^ t2^))\n ((var? t2^) (var-type-mismatch? S Y N t2^ t1^))\n ((and (pair? t1^) (pair? t2^))\n (or (term-ununifiable? S Y N (car t1^) (car t2^))\n (term-ununifiable? S Y N (cdr t1^) (cdr t2^))))\n (else (not (eqv? t1^ t2^)))))))\n\n(define T-term-ununifiable?\n (lambda (S Y N)\n (lambda (t1)\n (let ((t1^ (walk t1 S)))\n (letrec\n ((t2-check\n (lambda (t2)\n (let ((t2^ (walk t2 S)))\n (if (pair? t2^)\n (and\n (term-ununifiable? S Y N t1^ t2^)\n (t2-check (car t2^))\n (t2-check (cdr t2^)))\n (term-ununifiable? S Y N t1^ t2^))))))\n t2-check)))))\n\n(define num?\n (lambda (S N n)\n (let ((n (walk n S)))\n (cond\n ((var? n) (tagged? S N n))\n (else (number? n))))))\n\n(define sym?\n (lambda (S Y y)\n (let ((y (walk y S)))\n (cond\n ((var? y) (tagged? S Y y))\n (else (symbol? y))))))\n\n(define drop-T-b/c-Y-and-N\n (lambdar@ (c : S D Y N T)\n (let ((drop-t? (T-term-ununifiable? S Y N)))\n (cond\n ((find (lambda (t) ((drop-t? (lhs t)) (rhs t))) T) =>\n (lambda (t) `(,S ,D ,Y ,N ,(remq1 t T))))\n (else c)))))\n\n(define move-T-to-D-b/c-t2-atom\n (lambdar@ (c : S D Y N T)\n (cond\n ((exists (lambda (t)\n (let ((t2^ (walk (rhs t) S)))\n (cond\n ((and (not (untyped-var? S Y N t2^))\n (not (pair? t2^)))\n (let ((T (remq1 t T)))\n `(,S ((,t) . ,D) ,Y ,N ,T)))\n (else #f))))\n T))\n (else c))))\n\n(define terms-pairwise=?\n (lambda (pr-a^ pr-d^ t-a^ t-d^ S)\n (or\n (and (term=? pr-a^ t-a^ S)\n (term=? pr-d^ t-a^ S))\n (and (term=? pr-a^ t-d^ S)\n (term=? pr-d^ t-a^ S)))))\n\n(define T-superfluous-pr?\n (lambda (S Y N T)\n (lambda (pr)\n (let ((pr-a^ (walk (lhs pr) S))\n (pr-d^ (walk (rhs pr) S)))\n (cond\n ((exists\n (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S)))\n T)\n (for-all\n (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (or\n (not (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S))\n (untyped-var? S Y N t-d^)\n (pair? t-d^))))\n T))\n (else #f))))))\n\n(define drop-from-D-b/c-T\n (lambdar@ (c : S D Y N T)\n (cond\n ((find\n (lambda (d)\n (exists\n (T-superfluous-pr? S Y N T)\n d))\n D) =>\n (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n (else c))))\n\n(define drop-t-b/c-t2-occurs-t1\n (lambdar@ (c : S D Y N T)\n (cond\n ((find (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (mem-check t-d^ t-a^ S)))\n T) =>\n (lambda (t)\n `(,S ,D ,Y ,N ,(remq1 t T))))\n (else c))))\n\n(define split-t-move-to-d-b/c-pair\n (lambdar@ (c : S D Y N T)\n (cond\n ((exists\n (lambda (t)\n (let ((t2^ (walk (rhs t) S)))\n (cond\n ((pair? t2^) (let ((ta `(,(lhs t) . ,(car t2^)))\n (td `(,(lhs t) . ,(cdr t2^))))\n (let ((T `(,ta ,td . ,(remq1 t T))))\n `(,S ((,t) . ,D) ,Y ,N ,T))))\n (else #f))))\n T))\n (else c))))\n\n(define find-d-conflict\n (lambda (S Y N)\n (lambda (D)\n (find\n (lambda (d)\n\t (exists (lambda (pr)\n\t\t (term-ununifiable? S Y N (lhs pr) (rhs pr)))\n\t\t d))\n D))))\n\n(define drop-D-b/c-Y-or-N\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-d-conflict S Y N) D) =>\n (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n (else c))))\n\n(define cycle\n (lambdar@ (c)\n (let loop ((c^ c)\n (fns^ (LOF))\n (n (length (LOF))))\n (cond\n ((zero? n) c^)\n ((null? fns^) (loop c^ (LOF) n))\n (else\n (let ((c^^ ((car fns^) c^)))\n (cond\n ((not (eq? c^^ c^))\n (loop c^^ (cdr fns^) (length (LOF))))\n (else (loop c^ (cdr fns^) (sub1 n))))))))))\n\n(define mem-check\n (lambda (u t S)\n (let ((t (walk t S)))\n (cond\n ((pair? t)\n (or (term=? u t S)\n (mem-check u (car t) S)\n (mem-check u (cdr t) S)))\n (else (term=? u t S))))))\n\n(define term=?\n (lambda (u t S)\n (let-values (((S added) (unify u t (subst-with-scope S nonlocal-scope))))\n (and S (null? added)))))\n\n(define ground-non-?\n (lambda (pred)\n (lambda (u S)\n (let ((u (walk u S)))\n (cond\n ((var? u) #f)\n (else (not (pred u))))))))\n\n(define ground-non-symbol?\n (ground-non-? symbol?))\n\n(define ground-non-number?\n (ground-non-? number?))\n\n(define succeed (== #f #f))\n\n(define fail (== #f #t))\n\n(define (onceo g)\n (condu\n (g succeed)))\n\n(define ==fail-check\n (lambda (S0 D Y N T)\n (let ([S0 (subst-with-scope S0 nonlocal-scope)])\n (cond\n ((atomic-fail-check S0 Y ground-non-symbol?) #t)\n ((atomic-fail-check S0 N ground-non-number?) #t)\n ((symbolo-numbero-fail-check S0 Y N) #t)\n ((=/=-fail-check S0 D) #t)\n ((absento-fail-check S0 T) #t)\n (else #f)))))\n\n(define atomic-fail-check\n (lambda (S A pred)\n (exists (lambda (a) (pred (walk a S) S)) A)))\n\n(define symbolo-numbero-fail-check\n (lambda (S A N)\n (let ((N (map (lambda (n) (walk n S)) N)))\n (exists (lambda (a) (exists (same-var? (walk a S)) N))\n A))))\n\n(define absento-fail-check\n (lambda (S T)\n (exists (lambda (t) (mem-check (lhs t) (rhs t) S)) T)))\n\n(define =/=-fail-check\n (lambda (S D)\n (exists (d-fail-check S) D)))\n\n(define d-fail-check\n (lambda (S)\n (lambda (d)\n (let-values (((S added) (unify* d S)))\n (and S (null? added))))))\n\n(define reify+\n (lambda (v R D Y N T)\n (form (walk* v R)\n (walk* D R)\n (walk* Y R)\n (walk* N R)\n (rem-subsumed-T (walk* T R)))))\n\n;;; WEB -- 28 June 2016 -- ensure reified value is always a list of\n;;; term followed by (potentially empty) list of constraints\n(define form\n (lambda (v D Y N T)\n (let ((fd (sort-D D))\n (fy (sorter Y))\n (fn (sorter N))\n (ft (sorter T)))\n (let ((fd (if (null? fd) fd\n (let ((fd (drop-dot-D fd)))\n `((=/= . ,fd)))))\n (fy (if (null? fy) fy `((sym . ,fy))))\n (fn (if (null? fn) fn `((num . ,fn))))\n (ft (if (null? ft) ft\n (let ((ft (drop-dot ft)))\n `((absento . ,ft))))))\n (append `(,v) (filter-gensyms (append fd fn fy ft)))))))\n\n;;; WEB -- 27 Oct 2016 -- (hopefully) fixed code that removes constraints containing gensyms\n;;; Must make sure we only remove those portions of a constraint that actually contain gensyms!\n;;; We don't need to worry about symbolo or numbero constraints, since gensyms are symbols!\n(define filter-gensyms\n (lambda (loc)\n (cond\n ((null? loc) '())\n ((or (eqv? (caar loc) '=/=)\n (eqv? (caar loc) 'absento))\n (let ((fc (filter (lambda (c) (not (anygen? c))) (cdar loc))))\n (if (null? fc)\n (filter-gensyms (cdr loc))\n (cons (cons (caar loc) fc)\n (filter-gensyms (cdr loc))))))\n (else (cons (car loc) (filter-gensyms (cdr loc)))))))\n\n#|\n(define form\n (lambda (v D Y N T)\n (let ((fd (sort-D D))\n (fy (sorter Y))\n (fn (sorter N))\n (ft (sorter T)))\n (let ((fd (if (null? fd) fd\n (let ((fd (drop-dot-D fd)))\n `((=/= . ,fd)))))\n (fy (if (null? fy) fy `((sym . ,fy))))\n (fn (if (null? fn) fn `((num . ,fn))))\n (ft (if (null? ft) ft\n (let ((ft (drop-dot ft)))\n `((absento . ,ft))))))\n (cond\n ((and (null? fd) (null? fy)\n (null? fn) (null? ft))\n v)\n (else (append `(,v) fd fn fy ft)))))))\n|#\n\n(define sort-D\n (lambda (D)\n (sorter\n (map sort-d D))))\n\n(define sort-d\n (lambda (d)\n (list-sort\n (lambda (x y)\n (lex<=? (car x) (car y)))\n (map sort-pr d))))\n\n(define drop-dot-D\n (lambda (D)\n (map drop-dot D)))\n\n(define lex<-reified-name?\n (lambda (r)\n (charstring r) 0)\n #\\_)))\n\n(define sort-pr\n (lambda (pr)\n (let ((l (lhs pr))\n (r (rhs pr)))\n (cond\n ((lex<-reified-name? r) pr)\n ((lex<=? r l) `(,r . ,l))\n (else pr)))))\n\n(define rem-subsumed\n (lambda (D)\n (let rem-subsumed ((D D) (d^* '()))\n (cond\n ((null? D) d^*)\n ((or (subsumed? (car D) (cdr D))\n (subsumed? (car D) d^*))\n (rem-subsumed (cdr D) d^*))\n (else (rem-subsumed (cdr D)\n (cons (car D) d^*)))))))\n\n(define subsumed?\n (lambda (d d*)\n (cond\n ((null? d*) #f)\n (else\n (let-values (((S ignore) (unify* d (subst empty-subst-map nonlocal-scope))))\n (let-values (((S+ added) (unify* (car d*) S)))\n (or\n (and S+ (null? added))\n (subsumed? d (cdr d*)))))))))\n\n\n\n(define rem-xx-from-d\n (lambdar@ (c : S D Y N T)\n (let ((D (walk* D S)))\n (remp not\n (map (lambda (d)\n (let-values (((S0 ignore) (unify* d S)))\n (cond\n ((not S0) #f)\n ((==fail-check S0 '() Y N T) #f)\n (else\n (let-values (((S added) (unify* d (subst empty-subst-map nonlocal-scope))))\n added)))))\n D)))))\n\n(define rem-subsumed-T\n (lambda (T)\n (let rem-subsumed ((T T) (T^ '()))\n (cond\n ((null? T) T^)\n (else\n (let ((lit (lhs (car T)))\n (big (rhs (car T))))\n (cond\n ((or (subsumed-T? lit big (cdr T))\n (subsumed-T? lit big T^))\n (rem-subsumed (cdr T) T^))\n (else (rem-subsumed (cdr T)\n (cons (car T) T^))))))))))\n\n(define subsumed-T?\n (lambda (lit big T)\n (cond\n ((null? T) #f)\n (else\n (let ((lit^ (lhs (car T)))\n (big^ (rhs (car T))))\n (or\n (and (eq? big big^) (member* lit^ lit))\n (subsumed-T? lit big (cdr T))))))))\n\n(define LOF\n (lambda ()\n `(,drop-N-b/c-const ,drop-Y-b/c-const ,drop-Y-b/c-dup-var\n ,drop-N-b/c-dup-var ,drop-D-b/c-Y-or-N ,drop-T-b/c-Y-and-N\n ,move-T-to-D-b/c-t2-atom ,split-t-move-to-d-b/c-pair\n ,drop-from-D-b/c-T ,drop-t-b/c-t2-occurs-t1)))\n\n" }, { "path": "attic/code/mk/test-all.scm", "content": "(printf \"test-type-infer\\n\")\n(load \"test-type-infer.scm\")\n\n(printf \"test-interp\\n\")\n(load \"test-interp.scm\")\n\n(printf \"test-quines\\n\")\n(load \"test-quines.scm\")\n\n(printf \"test-arithmetic\\n\")\n(load \"test-arithmetic.scm\")\n" }, { "path": "attic/code/mk/test-arithmetic.scm", "content": "(load \"test-check.scm\")\n(load \"arithmetic.scm\")\n\n(test \"test 1\"\n (run* (q) (*o (build-num 2) (build-num 3) q))\n '(((0 1 1))))\n\n(test \"test 2\"\n (run* (q)\n (fresh (n m)\n (*o n m (build-num 6))\n (== `(,n ,m) q)))\n '((((1) (0 1 1))) (((0 1 1) (1))) (((0 1) (1 1))) (((1 1) (0 1)))))\n\n(test \"sums\"\n (run 5 (q)\n (fresh (x y z)\n (pluso x y z)\n (== `(,x ,y ,z) q)))\n '(((_.0 () _.0))\n ((() (_.0 . _.1) (_.0 . _.1)))\n (((1) (1) (0 1)))\n (((1) (0 _.0 . _.1) (1 _.0 . _.1)))\n (((1) (1 1) (0 0 1)))))\n\n(test \"factors\"\n (run* (q)\n (fresh (x y)\n (*o x y (build-num 24))\n (== `(,x ,y ,(build-num 24)) q)))\n '((((1) (0 0 0 1 1) (0 0 0 1 1)))\n (((0 0 0 1 1) (1) (0 0 0 1 1)))\n (((0 1) (0 0 1 1) (0 0 0 1 1)))\n (((0 0 1) (0 1 1) (0 0 0 1 1)))\n (((0 0 0 1) (1 1) (0 0 0 1 1)))\n (((1 1) (0 0 0 1) (0 0 0 1 1)))\n (((0 1 1) (0 0 1) (0 0 0 1 1)))\n (((0 0 1 1) (0 1) (0 0 0 1 1)))))\n\n(define number-primo\n (lambda (exp env val)\n (fresh (n)\n (== `(intexp ,n) exp)\n (== `(intval ,n) val)\n (not-in-envo 'numo env))))\n\n(define sub1-primo\n (lambda (exp env val)\n (fresh (e n n-1)\n (== `(sub1 ,e) exp)\n (== `(intval ,n-1) val)\n (not-in-envo 'sub1 env)\n (eval-expo e env `(intval ,n))\n (minuso n '(1) n-1))))\n\n(define zero?-primo\n (lambda (exp env val)\n (fresh (e n)\n (== `(zero? ,e) exp)\n (conde\n ((zeroo n) (== #t val))\n ((poso n) (== #f val)))\n (not-in-envo 'zero? env)\n (eval-expo e env `(intval ,n)))))\n\n(define *-primo\n (lambda (exp env val)\n (fresh (e1 e2 n1 n2 n3)\n (== `(* ,e1 ,e2) exp)\n (== `(intval ,n3) val)\n (not-in-envo '* env)\n (eval-expo e1 env `(intval ,n1))\n (eval-expo e2 env `(intval ,n2))\n (*o n1 n2 n3))))\n\n(define if-primo\n (lambda (exp env val)\n (fresh (e1 e2 e3 t)\n (== `(if ,e1 ,e2 ,e3) exp)\n (not-in-envo 'if env)\n (eval-expo e1 env t)\n (conde\n ((== #t t) (eval-expo e2 env val))\n ((== #f t) (eval-expo e3 env val))))))\n\n(define boolean-primo\n (lambda (exp env val)\n (conde\n ((== #t exp) (== #t val))\n ((== #f exp) (== #f val)))))\n\n(define eval-expo\n (lambda (exp env val)\n (conde\n ((boolean-primo exp env val))\n ((number-primo exp env val))\n ((sub1-primo exp env val))\n ((zero?-primo exp env val))\n ((*-primo exp env val))\n ((if-primo exp env val))\n ((symbolo exp) (lookupo exp env val))\n ((fresh (rator rand x body env^ a)\n (== `(,rator ,rand) exp)\n (eval-expo rator env `(closure ,x ,body ,env^))\n (eval-expo rand env a)\n (eval-expo body `((,x . ,a) . ,env^) val)))\n ((fresh (x body)\n (== `(lambda (,x) ,body) exp)\n (symbolo x)\n (== `(closure ,x ,body ,env) val)\n (not-in-envo 'lambda env))))))\n\n(define not-in-envo\n (lambda (x env)\n (conde\n ((fresh (y v rest)\n (== `((,y . ,v) . ,rest) env)\n (=/= y x)\n (not-in-envo x rest)))\n ((== '() env)))))\n\n(define lookupo\n (lambda (x env t)\n (fresh (rest y v)\n (== `((,y . ,v) . ,rest) env)\n (conde\n ((== y x) (== v t))\n ((=/= y x) (lookupo x rest t))))))\n\n(test \"push-down problems 2\"\n (run* (q)\n (fresh (x a d)\n (absento 'intval x)\n (== 'intval a)\n (== `(,a . ,d) x)))\n '())\n\n(test \"push-down problems 3\"\n (run* (q)\n (fresh (x a d)\n (== `(,a . ,d) x)\n (absento 'intval x)\n (== 'intval a)))\n '())\n\n(test \"push-down problems 4\"\n (run* (q)\n (fresh (x a d)\n (== `(,a . ,d) x)\n (== 'intval a)\n (absento 'intval x)))\n '())\n\n(test \"push-down problems 6\"\n (run* (q)\n (fresh (x a d)\n (== 'intval a)\n (== `(,a . ,d) x)\n (absento 'intval x)))\n '())\n\n(test \"push-down problems 1\"\n (run* (q)\n (fresh (x a d)\n (absento 'intval x)\n (== `(,a . ,d) x)\n (== 'intval a)))\n '())\n\n(test \"push-down problems 5\"\n (run* (q)\n (fresh (x a d)\n (== 'intval a)\n (absento 'intval x)\n (== `(,a . ,d) x)))\n '())\n\n(test \"zero?\"\n (run 1 (q)\n (eval-expo `(zero? (sub1 (intexp ,(build-num 1)))) '() q))\n '((#t)))\n\n(test \"*\"\n (run 1 (q)\n (eval-expo `(* (intexp ,(build-num 3)) (intexp ,(build-num 2))) '() `(intval ,(build-num 6))))\n '((_.0)))\n\n(test \"sub1\"\n (run 1 (q)\n (eval-expo q '() `(intval ,(build-num 6))) (== `(sub1 (intexp ,(build-num 7))) q))\n '(((sub1 (intexp (1 1 1))))))\n\n(test \"sub1 bigger WAIT a minute\"\n (run 1 (q)\n (eval-expo q '() `(intval ,(build-num 6)))\n (== `(sub1 (sub1 (intexp ,(build-num 8)))) q))\n '(((sub1 (sub1 (intexp (0 0 0 1)))))))\n\n(test \"sub1 biggest WAIT a minute\"\n (run 1 (q)\n (eval-expo q '() `(intval ,(build-num 6)))\n (== `(sub1 (sub1 (sub1 (intexp ,(build-num 9))))) q))\n '(((sub1 (sub1 (sub1 (intexp (1 0 0 1))))))))\n\n(test \"lots of programs to make a 6\"\n (run 12 (q) (eval-expo q '() `(intval ,(build-num 6))))\n '(((intexp (0 1 1)))\n ((sub1 (intexp (1 1 1))))\n ((* (intexp (1)) (intexp (0 1 1))))\n ((* (intexp (0 1 1)) (intexp (1))))\n ((if #t (intexp (0 1 1)) _.0))\n ((* (intexp (0 1)) (intexp (1 1))))\n ((if #f _.0 (intexp (0 1 1))))\n ((sub1 (* (intexp (1)) (intexp (1 1 1)))))\n (((lambda (_.0) (intexp (0 1 1))) #t)\n (=/= ((_.0 numo)))\n (sym _.0))\n ((sub1 (* (intexp (1 1 1)) (intexp (1)))))\n ((sub1 (sub1 (intexp (0 0 0 1)))))\n ((sub1 (if #t (intexp (1 1 1)) _.0)))))\n\n(define rel-fact5\n `((lambda (f)\n ((f f) (intexp ,(build-num 5))))\n (lambda (f)\n (lambda (n)\n (if (zero? n)\n (intexp ,(build-num 1))\n (* n ((f f) (sub1 n))))))))\n\n(test \"rel-fact5\"\n (run* (q) (eval-expo rel-fact5 '() q))\n `(((intval ,(build-num 120)))))\n\n(test \"rel-fact5-backwards\"\n (run 1 (q)\n (eval-expo\n `((lambda (f)\n ((f ,q) (intexp ,(build-num 5))))\n (lambda (f)\n (lambda (n)\n (if (zero? n)\n (intexp ,(build-num 1))\n (* n ((f f) (sub1 n)))))))\n '()\n `(intval ,(build-num 120))))\n `((f)))\n" }, { "path": "attic/code/mk/test-check.scm", "content": "(define-syntax test\n (syntax-rules ()\n ((_ title tested-expression expected-result)\n (begin\n (printf \"Testing ~s\\n\" title)\n (let* ((expected expected-result)\n (produced tested-expression))\n (or (equal? expected produced)\n (printf \"Failed: ~s\\nExpected: ~s\\nComputed: ~s\\n\"\n 'tested-expression expected produced)))))))\n" }, { "path": "attic/code/mk/test-interp.scm", "content": "(load \"test-check.scm\")\n(load \"mk.scm\")\n\n(define eval-expo\n (lambda (exp env val)\n (conde\n ((fresh (rator rand x body env^ a)\n (== `(,rator ,rand) exp)\n (eval-expo rator env `(closure ,x ,body ,env^))\n (eval-expo rand env a)\n (eval-expo body `((,x . ,a) . ,env^) val)))\n ((fresh (x body)\n (== `(lambda (,x) ,body) exp)\n (symbolo x)\n (== `(closure ,x ,body ,env) val)\n (not-in-envo 'lambda env)))\n ((symbolo exp) (lookupo exp env val)))))\n\n(define not-in-envo\n (lambda (x env)\n (conde\n ((== '() env))\n ((fresh (y v rest)\n (== `((,y . ,v) . ,rest) env)\n (=/= y x)\n (not-in-envo x rest))))))\n\n(define lookupo\n (lambda (x env t)\n (conde\n ((fresh (y v rest)\n (== `((,y . ,v) . ,rest) env) (== y x)\n (== v t)))\n ((fresh (y v rest)\n (== `((,y . ,v) . ,rest) env) (=/= y x)\n (lookupo x rest t))))))\n\n(test \"running backwards\"\n (run 5 (q) (eval-expo q '() '(closure y x ((x . (closure z z ()))))))\n '((((lambda (x) (lambda (y) x)) (lambda (z) z)))\n (((lambda (x) (x (lambda (y) x))) (lambda (z) z)))\n (((lambda (x) (lambda (y) x))\n ((lambda (_.0) _.0) (lambda (z) z)))\n (sym _.0))\n (((lambda (_.0) _.0)\n ((lambda (x) (lambda (y) x)) (lambda (z) z)))\n (sym _.0))\n ((((lambda (_.0) _.0) (lambda (x) (lambda (y) x)))\n (lambda (z) z))\n (sym _.0))))\n\n(define lookupo\n (lambda (x env t)\n (fresh (rest y v)\n (== `((,y . ,v) . ,rest) env)\n (conde\n ((== y x) (== v t))\n ((=/= y x) (lookupo x rest t))))))\n\n(test \"eval-exp-lc 1\"\n (run* (q) (eval-expo '(((lambda (x) (lambda (y) x)) (lambda (z) z)) (lambda (a) a)) '() q))\n '(((closure z z ()))))\n\n(test \"eval-exp-lc 2\"\n (run* (q) (eval-expo '((lambda (x) (lambda (y) x)) (lambda (z) z)) '() q))\n '(((closure y x ((x . (closure z z ())))))))\n\n(test \"running backwards\"\n (run 5 (q) (eval-expo q '() '(closure y x ((x . (closure z z ()))))))\n '((((lambda (x) (lambda (y) x)) (lambda (z) z)))\n (((lambda (x) (x (lambda (y) x))) (lambda (z) z)))\n (((lambda (x) (lambda (y) x))\n ((lambda (_.0) _.0) (lambda (z) z)))\n (sym _.0))\n ((((lambda (_.0) _.0) (lambda (x) (lambda (y) x)))\n (lambda (z) z))\n (sym _.0))\n (((lambda (_.0) _.0)\n ((lambda (x) (lambda (y) x)) (lambda (z) z)))\n (sym _.0))))\n\n(test \"fully-running-backwards\"\n (run 5 (q)\n (fresh (e v)\n (eval-expo e '() v)\n (== `(,e ==> ,v) q)))\n '((((lambda (_.0) _.1)\n ==> (closure _.0 _.1 ())) (sym _.0))\n ((((lambda (_.0) _.0) (lambda (_.1) _.2))\n ==>\n (closure _.1 _.2 ()))\n (sym _.0 _.1))\n ((((lambda (_.0) (lambda (_.1) _.2)) (lambda (_.3) _.4))\n ==>\n (closure _.1 _.2 ((_.0 . (closure _.3 _.4 ())))))\n (=/= ((_.0 lambda)))\n (sym _.0 _.1 _.3))\n ((((lambda (_.0) (_.0 _.0)) (lambda (_.1) _.1))\n ==>\n (closure _.1 _.1 ()))\n (sym _.0 _.1))\n ((((lambda (_.0) (_.0 _.0))\n (lambda (_.1) (lambda (_.2) _.3)))\n ==>\n (closure _.2 _.3 ((_.1 . (closure _.1 (lambda (_.2) _.3) ())))))\n (=/= ((_.1 lambda)))\n (sym _.0 _.1 _.2))))\n" }, { "path": "attic/code/mk/test-quines.scm", "content": "(load \"test-check.scm\")\n(load \"evalo.scm\")\n\n(test \"1 quine\"\n (run 1 (q) (evalo q q))\n '((((lambda (_.0) (list _.0 (list 'quote _.0)))\n '(lambda (_.0) (list _.0 (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))))\n\n(test \"2 quines\"\n (run 2 (q) (evalo q q))\n '((((lambda (_.0) (list _.0 (list 'quote _.0)))\n '(lambda (_.0) (list _.0 (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))))\n\n(test \"3 quines\"\n (run 3 (q) (evalo q q))\n '((((lambda (_.0) (list _.0 (list 'quote _.0)))\n '(lambda (_.0) (list _.0 (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))))\n\n(test \"5 quines\"\n (run 5 (q) (evalo q q))\n '((((lambda (_.0) (list _.0 (list 'quote _.0)))\n '(lambda (_.0) (list _.0 (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list (list 'lambda '(_.0) _.0) (list 'quote _.0)))\n '(list (list 'lambda '(_.0) _.0) (list 'quote _.0)))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) _.1) 'quote) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) _.1) 'quote) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))))\n\n(test \"10 quines\"\n (run 10 (q) (evalo q q))\n '((((lambda (_.0) (list _.0 (list 'quote _.0)))\n '(lambda (_.0) (list _.0 (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list (list 'lambda '(_.0) _.0) (list 'quote _.0)))\n '(list (list 'lambda '(_.0) _.0) (list 'quote _.0)))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) _.1) 'quote) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) _.1) 'quote) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) '_.2))\n '(lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) '_.2)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) '_.2)))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) '_.2))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) '_.2))))\n '(lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) '_.2)))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n ((lambda (_.1) (list _.1 (list 'quote _.1))) _.0))\n '(lambda (_.0)\n ((lambda (_.1) (list _.1 (list 'quote _.1))) _.0)))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.1)) _.0)))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.1)) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))))\n\n(test \"40 quines\"\n (run 40 (q) (evalo q q))\n '((((lambda (_.0) (list _.0 (list 'quote _.0)))\n '(lambda (_.0) (list _.0 (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) '_.2) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list (list 'lambda '(_.0) _.0) (list 'quote _.0)))\n '(list (list 'lambda '(_.0) _.0) (list 'quote _.0)))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) _.1) 'quote) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) _.1) 'quote) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) '_.2))\n '(lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) '_.2)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) '_.2)))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) '_.2))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) '_.2))))\n '(lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) '_.2)))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n ((lambda (_.1) (list _.1 (list 'quote _.1))) _.0))\n '(lambda (_.0)\n ((lambda (_.1) (list _.1 (list 'quote _.1))) _.0)))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.1)) _.0)))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.1)) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n ((lambda (_.1) (list _.0 (list _.1 _.0))) 'quote))\n '(lambda (_.0)\n ((lambda (_.1) (list _.0 (list _.1 _.0))) 'quote)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list _.1 _.0)) 'quote)))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list _.1 _.0)) 'quote))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.1) _.0))))\n '(lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.1) _.0)))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list ((lambda (_.3) 'quote) '_.4) _.0)))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list ((lambda (_.3) 'quote) '_.4) _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.3 closure)) ((_.3 quote)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2) (closure _.4)))\n (((lambda (_.0)\n (list ((lambda (_.1) _.1) _.0) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.1) _.0) (list 'quote _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) _.0))))\n '(lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) _.0)))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) _.0)))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n ((lambda (_.1) (list _.1 (list 'quote _.0))) _.0))\n '(lambda (_.0)\n ((lambda (_.1) (list _.1 (list 'quote _.0))) _.0)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) _.0) _.0)))\n '(lambda (_.0)\n (list _.0 (list ((lambda (_.1) 'quote) _.0) _.0))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list ((lambda (_.3) _.3) 'quote) _.0)))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list ((lambda (_.3) _.3) 'quote) _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.3 closure)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list 'quote _.0)) '_.4)))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list 'quote _.0)) '_.4))))\n (=/= ((_.0 _.1)) ((_.0 _.3)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.3 closure))\n ((_.3 list)) ((_.3 quote)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2) (closure _.4)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list 'quote ((lambda (_.3) _.0) '_.4))))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list 'quote ((lambda (_.3) _.0) '_.4)))))\n (=/= ((_.0 _.1)) ((_.0 _.3)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.3 closure)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2) (closure _.4)))\n (((lambda (_.0)\n (list\n _.0\n (list\n ((lambda (_.1) 'quote) '_.2)\n ((lambda (_.3) _.0) '_.4))))\n '(lambda (_.0)\n (list\n _.0\n (list\n ((lambda (_.1) 'quote) '_.2)\n ((lambda (_.3) _.0) '_.4)))))\n (=/= ((_.0 _.3)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)) ((_.3 closure)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2) (closure _.4)))\n (((lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.1))) _.0))\n '(lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.1))) _.0)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) (list)))))\n '(lambda (_.0)\n (list _.0 (list 'quote ((lambda (_.1) _.0) (list))))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list\n (list 'lambda '(_.0) _.0)\n (list ((lambda (_.1) 'quote) '_.2) _.0)))\n '(list\n (list 'lambda '(_.0) _.0)\n (list ((lambda (_.1) 'quote) '_.2) _.0)))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n ((lambda (_.1)\n (list ((lambda (_.2) _.0) '_.3) (list 'quote _.0)))\n '_.4))\n '(lambda (_.0)\n ((lambda (_.1)\n (list ((lambda (_.2) _.0) '_.3) (list 'quote _.0)))\n '_.4)))\n (=/= ((_.0 _.1)) ((_.0 _.2)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.1 lambda))\n ((_.1 list)) ((_.1 quote)) ((_.2 closure)))\n (sym _.0 _.1 _.2)\n (absento (closure _.3) (closure _.4)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list 'quote _.3)) _.0)))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list 'quote _.3)) _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.3 closure)) ((_.3 list))\n ((_.3 quote)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list _.3 _.0)) 'quote)))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list _.3 _.0)) 'quote))))\n (=/= ((_.0 _.1)) ((_.0 _.3)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.3 closure))\n ((_.3 list)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list 'quote ((lambda (_.3) _.3) _.0))))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list 'quote ((lambda (_.3) _.3) _.0)))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.3 closure)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) (list))))\n '(lambda (_.0)\n (list _.0 ((lambda (_.1) (list 'quote _.0)) (list)))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list\n _.0\n (list\n ((lambda (_.1) 'quote) '_.2)\n ((lambda (_.3) _.3) _.0))))\n '(lambda (_.0)\n (list\n _.0\n (list\n ((lambda (_.1) 'quote) '_.2)\n ((lambda (_.3) _.3) _.0)))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)) ((_.3 closure)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) (list)))\n '(lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) (list))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list ((lambda (_.1) _.0) _.0) (list 'quote _.0)))\n '(lambda (_.0)\n (list ((lambda (_.1) _.0) _.0) (list 'quote _.0))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list\n (list 'lambda '(_.0) _.0)\n (list ((lambda (_.1) _.1) 'quote) _.0)))\n '(list\n (list 'lambda '(_.0) _.0)\n (list ((lambda (_.1) _.1) 'quote) _.0)))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1))\n (((lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) _.0))\n '(lambda (_.0)\n ((lambda (_.1) (list _.0 (list 'quote _.0))) _.0)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1))\n (((lambda (_.0)\n (list\n (list 'lambda '(_.0) _.0)\n ((lambda (_.1) (list 'quote _.0)) '_.2)))\n '(list\n (list 'lambda '(_.0) _.0)\n ((lambda (_.1) (list 'quote _.0)) '_.2)))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 list)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list 'quote ((lambda (_.3) _.0) _.0))))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n (list 'quote ((lambda (_.3) _.0) _.0)))))\n (=/= ((_.0 _.1)) ((_.0 _.3)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.3 closure)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list 'quote _.0)) _.0)))\n '(lambda (_.0)\n (list\n ((lambda (_.1) _.0) '_.2)\n ((lambda (_.3) (list 'quote _.0)) _.0))))\n (=/= ((_.0 _.1)) ((_.0 _.3)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.3 closure))\n ((_.3 list)) ((_.3 quote)))\n (sym _.0 _.1 _.3)\n (absento (closure _.2)))\n (((lambda (_.0)\n ((lambda (_.1)\n (list ((lambda (_.2) _.0) '_.3) (list _.1 _.0)))\n 'quote))\n '(lambda (_.0)\n ((lambda (_.1)\n (list ((lambda (_.2) _.0) '_.3) (list _.1 _.0)))\n 'quote)))\n (=/= ((_.0 _.1)) ((_.0 _.2)) ((_.0 closure)) ((_.0 lambda))\n ((_.0 list)) ((_.0 quote)) ((_.1 closure)) ((_.1 lambda))\n ((_.1 list)) ((_.1 quote)) ((_.2 closure)))\n (sym _.0 _.1 _.2)\n (absento (closure _.3)))))\n\n(test \"2 twines\"\n (run 2 (x) (fresh (p q)\n (=/= p q)\n (evalo p q)\n (evalo q p)\n (== `(,p ,q) x)))\n '((('((lambda (_.0)\n (list 'quote (list _.0 (list 'quote _.0))))\n '(lambda (_.0) (list 'quote (list _.0 (list 'quote _.0)))))\n ((lambda (_.0) (list 'quote (list _.0 (list 'quote _.0))))\n '(lambda (_.0) (list 'quote (list _.0 (list 'quote _.0))))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n (('((lambda (_.0)\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n '(lambda (_.0)\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))))\n ((lambda (_.0)\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))\n '(lambda (_.0)\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))))\n\n(test \"4 thrines\"\n (run 4 (x)\n (fresh (p q r)\n (=/= p q)\n (=/= q r)\n (=/= r p)\n (evalo p q)\n (evalo q r)\n (evalo r p)\n (== `(,p ,q ,r) x)))\n '(((''((lambda (_.0)\n (list 'quote (list 'quote (list _.0 (list 'quote _.0)))))\n '(lambda (_.0)\n (list 'quote (list 'quote (list _.0 (list 'quote _.0))))))\n '((lambda (_.0)\n (list 'quote (list 'quote (list _.0 (list 'quote _.0)))))\n '(lambda (_.0)\n (list 'quote (list 'quote (list _.0 (list 'quote _.0))))))\n ((lambda (_.0)\n (list 'quote (list 'quote (list _.0 (list 'quote _.0)))))\n '(lambda (_.0)\n (list 'quote (list 'quote (list _.0 (list 'quote _.0)))))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n ((''((lambda (_.0)\n (list\n 'quote\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))))\n '(lambda (_.0)\n (list\n 'quote\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))))\n '((lambda (_.0)\n (list\n 'quote\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))))\n '(lambda (_.0)\n (list\n 'quote\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0))))))\n ((lambda (_.0)\n (list\n 'quote\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))))\n '(lambda (_.0)\n (list\n 'quote\n (list\n 'quote\n (list ((lambda (_.1) _.0) '_.2) (list 'quote _.0)))))))\n (=/= ((_.0 _.1)) ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)))\n (sym _.0 _.1)\n (absento (closure _.2)))\n (('(list\n '(lambda (_.0)\n (list\n 'quote\n (list 'list _.0 (list 'quote (list 'quote _.0)))))\n '''(lambda (_.0)\n (list\n 'quote\n (list 'list _.0 (list 'quote (list 'quote _.0))))))\n (list\n '(lambda (_.0)\n (list\n 'quote\n (list 'list _.0 (list 'quote (list 'quote _.0)))))\n '''(lambda (_.0)\n (list\n 'quote\n (list 'list _.0 (list 'quote (list 'quote _.0))))))\n ((lambda (_.0)\n (list\n 'quote\n (list 'list _.0 (list 'quote (list 'quote _.0)))))\n ''(lambda (_.0)\n (list\n 'quote\n (list 'list _.0 (list 'quote (list 'quote _.0)))))))\n (=/= ((_.0 closure)) ((_.0 list)) ((_.0 quote)))\n (sym _.0))\n ((''((lambda (_.0)\n (list\n ((lambda (_.1) 'quote) '_.2)\n (list 'quote (list _.0 (list 'quote _.0)))))\n '(lambda (_.0)\n (list\n ((lambda (_.1) 'quote) '_.2)\n (list 'quote (list _.0 (list 'quote _.0))))))\n '((lambda (_.0)\n (list\n ((lambda (_.1) 'quote) '_.2)\n (list 'quote (list _.0 (list 'quote _.0)))))\n '(lambda (_.0)\n (list\n ((lambda (_.1) 'quote) '_.2)\n (list 'quote (list _.0 (list 'quote _.0))))))\n ((lambda (_.0)\n (list\n ((lambda (_.1) 'quote) '_.2)\n (list 'quote (list _.0 (list 'quote _.0)))))\n '(lambda (_.0)\n (list\n ((lambda (_.1) 'quote) '_.2)\n (list 'quote (list _.0 (list 'quote _.0)))))))\n (=/= ((_.0 closure)) ((_.0 lambda)) ((_.0 list))\n ((_.0 quote)) ((_.1 closure)) ((_.1 quote)))\n (sym _.0 _.1)\n (absento (closure _.2)))))\n" }, { "path": "attic/code/mk/test-type-infer.scm", "content": "(load \"test-check.scm\")\n(load \"type-infer.scm\")\n\n(test \"types\"\n (run 10 (q) (fresh (t exp) (!- exp '() t) (== `(,exp => ,t) q)))\n '((((lambda (_.0) _.0) => (-> _.1 _.1)) (sym _.0))\n (((lambda (_.0) (lambda (_.1) _.1))\n =>\n (-> _.2 (-> _.3 _.3)))\n (=/= ((_.0 lambda)))\n (sym _.0 _.1))\n (((lambda (_.0) (lambda (_.1) _.0))\n =>\n (-> _.2 (-> _.3 _.2)))\n (=/= ((_.0 _.1)) ((_.0 lambda)))\n (sym _.0 _.1))\n ((((lambda (_.0) _.0) (lambda (_.1) _.1)) => (-> _.2 _.2))\n (sym _.0 _.1))\n (((lambda (_.0) (lambda (_.1) (lambda (_.2) _.2)))\n =>\n (-> _.3 (-> _.4 (-> _.5 _.5))))\n (=/= ((_.0 lambda)) ((_.1 lambda)))\n (sym _.0 _.1 _.2))\n (((lambda (_.0) (lambda (_.1) (lambda (_.2) _.1)))\n =>\n (-> _.3 (-> _.4 (-> _.5 _.4))))\n (=/= ((_.0 lambda)) ((_.1 _.2)) ((_.1 lambda)))\n (sym _.0 _.1 _.2))\n (((lambda (_.0) (_.0 (lambda (_.1) _.1)))\n =>\n (-> (-> (-> _.2 _.2) _.3) _.3))\n (=/= ((_.0 lambda)))\n (sym _.0 _.1))\n (((lambda (_.0) (lambda (_.1) (lambda (_.2) _.0)))\n =>\n (-> _.3 (-> _.4 (-> _.5 _.3))))\n (=/= ((_.0 _.1)) ((_.0 _.2)) ((_.0 lambda)) ((_.1 lambda)))\n (sym _.0 _.1 _.2))\n (((lambda (_.0) (lambda (_.1) (_.1 _.0)))\n =>\n (-> _.2 (-> (-> _.2 _.3) _.3)))\n (=/= ((_.0 _.1)) ((_.0 lambda)))\n (sym _.0 _.1))\n ((((lambda (_.0) _.0) (lambda (_.1) (lambda (_.2) _.2)))\n =>\n (-> _.3 (-> _.4 _.4)))\n (=/= ((_.1 lambda)))\n (sym _.0 _.1 _.2))))\n" }, { "path": "attic/code/mk/type-infer.scm", "content": "(load \"mk.scm\")\n\n(define !-\n (lambda (exp env t)\n (conde\n [(symbolo exp) (lookupo exp env t)]\n [(fresh (x e t-x t-e)\n (== `(lambda (,x) ,e) exp)\n (symbolo x)\n (not-in-envo 'lambda env)\n (== `(-> ,t-x ,t-e) t)\n (!- e `((,x . ,t-x) . ,env) t-e))]\n [(fresh (rator rand t-x)\n (== `(,rator ,rand) exp)\n (!- rator env `(-> ,t-x ,t))\n (!- rand env t-x))])))\n\n(define lookupo\n (lambda (x env t)\n (fresh (rest y v)\n (== `((,y . ,v) . ,rest) env)\n (conde\n ((== y x) (== v t))\n ((=/= y x) (lookupo x rest t))))))\n\n(define not-in-envo\n (lambda (x env)\n (conde\n ((== '() env))\n ((fresh (y v rest)\n (== `((,y . ,v) . ,rest) env)\n (=/= y x)\n (not-in-envo x rest))))))\n" }, { "path": "attic/code/mk-db.rkt", "content": "#lang racket/base\n(provide\n (all-from-out \"mk.rkt\")\n concepto\n fuzzy-concepto\n concept-semtypeo\n cuio\n cui*o\n edgeo\n membero\n not-membero\n edge-subjecto\n edge-objecto\n concept-not-too-generalo\n edge-not-too-generalo\n path-not-too-generalo\n )\n\n(require\n \"db.rkt\"\n \"edge.rkt\"\n \"mk.rkt\"\n racket/stream\n )\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; list non-membership\n(define not-membero\n (lambda (x ls)\n (conde\n [(== '() ls)]\n [(fresh (y rest)\n (== `(,y . ,rest) ls)\n (=/= x y)\n (not-membero x rest))])))\n\n(define (ground-cui c) (and (pair? c) (number? (car c)) (car c)))\n\n(define (concept->list c) (vector->list (concept-pretty c)))\n\n(define (edge->list e)\n (list (concept->list (hash-ref cui=>concept (edge-src e)))\n (concept->list (hash-ref cui=>concept (edge-dst e)))\n (hash-ref id=>predicate (edge-predicate e))\n (hash-ref id=>semtype (edge-src-type e))\n (hash-ref id=>semtype (edge-dst-type e))\n (edge-pub-info e)))\n\n;; f and xs must be ground.\n(define (mapo f xs x)\n (if (null? xs) fail\n (conde\n ((== (f (car xs)) x))\n ((mapo f (cdr xs) x)))))\n\n(define (concepto c)\n (project (c)\n (if (ground-cui c)\n (== (concept->list (hash-ref cui=>concept (car c))) c)\n (mapo concept->list concept* c))))\n\n(define (fuzzy-concepto name c)\n (mapo concept->list (fuzzy-name->concept* concept* name #t) c))\n\n(define (concept-semtypeo c semtype)\n (fresh (cui name semtype*)\n (== `(,cui ,name ,semtype*) c)\n (membero semtype semtype*)))\n\n(define (cuio c cui) (fresh (c-rest) (== `(,cui . ,c-rest) c)))\n\n(define (cui*o c cui*)\n (fresh (cui a d)\n (== `(,a . ,d) cui*)\n (cuio c cui)\n (conde\n ((== cui a))\n ((=/= cui a) (cui*o c d)))))\n\n(define (edgeo edge)\n (fresh (subject object predicate subject-type object-type pubref)\n (== `(,subject ,object ,predicate ,subject-type ,object-type ,pubref) edge)\n (project (subject object predicate subject-type object-type pubref)\n (let* ((subject-cui (ground-cui subject))\n (object-cui (ground-cui object))\n (predicate-id (and (not (var? predicate))\n (hash-ref predicate=>id predicate)))\n (subject-stid (and (not (var? subject-type))\n (hash-ref semtype=>id subject-type)))\n (object-stid (and (not (var? object-type))\n (hash-ref semtype=>id object-type)))\n (p? (lambda (src dst src-type dst-type)\n (lambda (e)\n (and (or (not src) (= src (edge-src e)))\n (or (not dst) (= dst (edge-dst e)))\n (or (not predicate-id)\n (= predicate-id (edge-predicate e)))\n (or (not src-type) (= src-type (edge-src-type e)))\n (or (not dst-type)\n (= dst-type (edge-dst-type e))))))))\n (cond\n (subject-cui\n (let loop\n ((e* (subject->edge*/stream\n subject-cui\n (p? subject-cui object-cui subject-stid object-stid))))\n (if (stream-empty? e*) fail\n (conde\n ((== (edge->list (stream-first e*)) edge))\n ((loop (stream-rest e*)))))))\n (object-cui\n (let loop\n ((e* (object->edge*/stream\n object-cui\n (p? object-cui subject-cui object-stid subject-stid))))\n (if (stream-empty? e*) fail\n (conde\n ((== (edge->list (edge-reverse (stream-first e*))) edge))\n ((loop (stream-rest e*)))))))\n ((and predicate-id subject-stid object-stid)\n (let loop\n ((e* (predicate->edge*/stream\n predicate-id subject-stid object-stid (lambda (_) #t))))\n (if (stream-empty? e*) fail\n (conde\n ((== (edge->list (stream-first e*)) edge))\n ((loop (stream-rest e*)))))))\n (else\n (let loop\n ((e* (edge*/stream\n (p? subject-cui object-cui subject-stid object-stid))))\n (if (stream-empty? e*) fail\n (conde\n ((== (edge->list (stream-first e*)) edge))\n ((loop (stream-rest e*))))))))))))\n\n(define (edge-subjecto e s)\n (fresh (o p sty oty rs)\n (== `(,s ,o ,p ,sty ,oty ,rs) e)))\n\n(define (edge-objecto e o)\n (fresh (s p sty oty rs)\n (== `(,s ,o ,p ,sty ,oty ,rs) e)))\n\n(define (concept-not-too-generalo c)\n (project (c)\n (if (<= 1000 (count-ISA (ground-cui c)))\n fail\n succeed)))\n\n(define (edge-not-too-generalo e)\n (fresh (s o p sty oty rs)\n (== `(,s ,o ,p ,sty ,oty ,rs) e)\n (project (s o)\n (fresh ()\n (concept-not-too-generalo s)\n (concept-not-too-generalo o)))))\n\n(define (path-not-too-generalo p)\n (conde\n ((== '() p))\n ((fresh (a d)\n (== `(,a . ,d) p)\n (edge-not-too-generalo a)\n (path-not-too-generalo d)))))\n" }, { "path": "attic/code/mk.rkt", "content": "#lang racket/base\n\n(require racket/list\n racket/include\n racket/stream\n )\n\n(provide\n run run* run-stream\n == =/=\n fresh\n conde\n symbolo numbero\n absento\n project\n var?\n fail\n succeed\n choice\n inc\n unify\n walk\n walk*\n mplus\n mplus*\n bind\n bind*\n take take-stream\n reify\n )\n\n;; extra stuff for racket\n;; due mostly to samth\n(define (list-sort f l) (sort l f))\n\n(define (remp f l) (filter-not f l))\n\n(define (call-with-string-output-port f)\n (define p (open-output-string))\n (f p)\n (get-output-string p))\n\n(define (exists f l) (ormap f l))\n\n(define for-all andmap)\n\n(define (find f l)\n (cond [(memf f l) => car] [else #f]))\n\n(define memp memf)\n\n(define (var*? v) (var? (car v)))\n\n\n; Substitution representation\n\n(define empty-subst-map (hasheq))\n\n(define subst-map-length hash-count)\n\n; Returns #f if not found, or a pair of u and the result of the lookup.\n; This distinguishes between #f indicating absence and being the result.\n(define subst-map-lookup\n (lambda (u S)\n (hash-ref S u unbound)))\n\n(define (subst-map-add S var val)\n (hash-set S var val))\n\n(define subst-map-eq? eq?)\n\n\n; Constraint store representation\n\n(define empty-C (hasheq))\n\n(define set-c\n (lambda (v c st)\n (state (state-S st) (hash-set (state-C st) v c))))\n\n(define lookup-c\n (lambda (v st)\n (hash-ref (state-C st) v empty-c)))\n\n(define remove-c\n (lambda (v st)\n (state (state-S st) (hash-remove (state-C st) v))))\n\n\n; Scope object.\n; Used to determine whether a branch has occured between variable creation\n; and unification to allow the set-var-val! optimization in subst-add. Both variables\n; and substitutions will contain a scope. When a substitution flows through a\n; conde it is assigned a new scope.\n\n; Creates a new scope that is not scope-eq? to any other scope\n(define new-scope\n (lambda ()\n (list 'scope)))\n\n; Scope used when variable bindings should always be made in the substitution,\n; as in disequality solving and reification. We don't want to set-var-val! a\n; variable when checking if a disequality constraint holds!\n(define nonlocal-scope\n (list 'non-local-scope))\n\n(define scope-eq? eq?)\n\n\n; Logic variable object.\n; Contains:\n; val - value for variable assigned by unification using set-var-val! optimization.\n; unbound if not yet set or stored in substitution.\n; scope - scope that the variable was created in.\n; idx - unique numeric index for the variable. Used by the trie substitution representation.\n; Variable objects are compared by object identity.\n\n; The unique val for variables that have not yet been bound to a value\n; or are bound in the substitution\n(define unbound (list 'unbound))\n\n(define var\n (let ((counter -1))\n (lambda (scope)\n (set! counter (+ 1 counter))\n (vector unbound scope counter))))\n\n; Vectors are not allowed as terms, so terms that are vectors are variables.\n(define var?\n (lambda (x)\n (vector? x)))\n\n(define var-eq? eq?)\n\n(define var-val\n (lambda (x)\n (vector-ref x 0)))\n\n(define set-var-val!\n (lambda (x v)\n (vector-set! x 0 v)))\n\n(define var-scope\n (lambda (x)\n (vector-ref x 1)))\n\n(define var-idx\n (lambda (x)\n (vector-ref x 2)))\n\n\n; Substitution object.\n; Contains:\n; map - mapping of variables to values\n; scope - scope at current program point, for set-var-val! optimization. Updated at conde.\n; Included in the substitution because it is required to fully define the substitution\n; and how it is to be extended.\n;\n; Implementation of the substitution map depends on the Scheme used, as we need a map. See mk.rkt\n; and mk-vicare.scm.\n\n(define subst\n (lambda (mapping scope)\n (cons mapping scope)))\n\n(define subst-map car)\n\n(define subst-scope cdr)\n\n(define subst-length\n (lambda (S)\n (subst-map-length (subst-map S))))\n\n(define subst-with-scope\n (lambda (S new-scope)\n (subst (subst-map S) new-scope)))\n\n(define empty-subst (subst empty-subst-map (new-scope)))\n\n(define subst-add\n (lambda (S x v)\n ; set-var-val! optimization: set the value directly on the variable\n ; object if we haven't branched since its creation\n ; (the scope of the variable and the substitution are the same).\n ; Otherwise extend the substitution mapping.\n (if (scope-eq? (var-scope x) (subst-scope S))\n (begin\n (set-var-val! x v)\n S)\n (subst (subst-map-add (subst-map S) x v) (subst-scope S)))))\n\n(define subst-lookup\n (lambda (u S)\n ; set-var-val! optimization.\n ; Tried checking the scope here to avoid a subst-map-lookup\n ; if it was definitely unbound, but that was slower.\n (if (not (eq? (var-val u) unbound))\n (var-val u)\n (subst-map-lookup u (subst-map S)))))\n\n; Association object.\n; Describes an association mapping the lhs to the rhs. Returned by unification\n; to describe the associations that were added to the substitution (whose representation\n; is opaque) and used to represent disequality constraints.\n\n(define lhs car)\n\n(define rhs cdr)\n\n; Constraint record object.\n;\n; Describes the constraints attached to a single variable.\n;\n; Contains:\n; T - type constraint. 'symbolo 'numbero or #f to indicate no constraint\n; D - list of disequality constraints. Each disequality is a list of associations.\n; The constraint is violated if all associated variables are equal in the\n; substitution simultaneously. D could contain duplicate constraints (created\n; by distinct =/= calls). A given disequality constraint is only attached to\n; one of the variables involved, as all components of the constraint must be\n; violated to cause failure.\n; A - list of absento constraints. Each constraint is a ground atom. The list contains\n; no duplicates.\n\n(define empty-c `(#f () ()))\n\n(define c-T\n (lambda (c)\n (car c)))\n\n(define c-D\n (lambda (c)\n (cadr c)))\n\n(define c-A\n (lambda (c)\n (caddr c)))\n\n(define c-with-T\n (lambda (c T)\n (list T (c-D c) (c-A c))))\n\n(define c-with-D\n (lambda (c D)\n (list (c-T c) D (c-A c))))\n\n(define c-with-A\n (lambda (c A)\n (list (c-T c) (c-D c) A)))\n\n; Constraint store object.\n; Mapping of representative variable to constraint record. Constraints are\n; always on the representative element and must be moved / merged when that\n; element changes.\n\n; Implementation depends on the Scheme used, as we need a map. See mk.rkt\n; and mk-vicare.scm.\n\n; State object.\n; The state is the value that is monadically passed through the search.\n; Contains:\n; S - the substitution\n; C - the constraint store\n\n(define state\n (lambda (S C)\n (cons S C)))\n\n(define state-S (lambda (st) (car st)))\n(define state-C (lambda (st) (cdr st)))\n\n(define empty-state (state empty-subst empty-C))\n\n(define state-with-scope\n (lambda (st new-scope)\n (state (subst-with-scope (state-S st) new-scope) (state-C st))))\n\n; Unification\n\n(define walk\n (lambda (u S)\n (if (var? u)\n (let ((val (subst-lookup u S)))\n (if (eq? val unbound)\n u\n (walk val S)))\n u)))\n\n(define occurs-check\n (lambda (x v S)\n (let ((v (walk v S)))\n (cond\n ((var? v) (var-eq? v x))\n ((pair? v)\n (or\n (occurs-check x (car v) S)\n (occurs-check x (cdr v) S)))\n (else #f)))))\n\n(define ext-s-check\n (lambda (x v S)\n (cond\n ((occurs-check x v S) (values #f #f))\n (else (values (subst-add S x v) `((,x . ,v)))))))\n\n; Returns as values the extended substitution and a list of associations added\n; during the unification, or (values #f #f) if the unification failed.\n;\n; Right now appends the list of added values from sub-unifications. Alternatively\n; could be threaded monadically, which could be faster or slower.\n(define unify\n (lambda (u v s)\n (let ((u (walk u s))\n (v (walk v s)))\n (cond\n ((eq? u v) (values s '()))\n ((var? u) (ext-s-check u v s))\n ((var? v) (ext-s-check v u s))\n ((and (pair? u) (pair? v))\n (let-values (((s added-car) (unify (car u) (car v) s)))\n (if s\n (let-values (((s added-cdr) (unify (cdr u) (cdr v) s)))\n (values s (append added-car added-cdr)))\n (values #f #f))))\n ((equal? u v) (values s '()))\n (else (values #f #f))))))\n\n(define unify*\n (lambda (S+ S)\n (unify (map lhs S+) (map rhs S+) S)))\n\n\n; Search\n\n; SearchStream: #f | Procedure | State | (Pair State (-> SearchStream))\n\n; SearchStream constructor types. Names inspired by the plus monad?\n\n; -> SearchStream\n(define mzero (lambda () #f))\n\n; c: State\n; -> SearchStream\n(define unit (lambda (c) c))\n\n; c: State\n; f: (-> SearchStream)\n; -> SearchStream\n;\n; f is a thunk to avoid unnecessary computation in the case that c is the\n; last answer needed to satisfy the query.\n(define choice (lambda (c f) (cons c f)))\n\n; e: SearchStream\n; -> (-> SearchStream)\n(define-syntax inc\n (syntax-rules ()\n ((_ e) (lambda () e))))\n\n; Goal: (State -> SearchStream)\n\n; e: SearchStream\n; -> Goal\n(define-syntax lambdag@\n (syntax-rules ()\n ((_ (st) e) (lambda (st) e))))\n\n; Match on search streams. The state type must not be a pair with a procedure\n; in its cdr.\n;\n; (() e0) failure\n; ((f) e1) inc for interleaving. separate from success or failure to ensure\n; it goes all the way to the top of the tree.\n; ((c) e2) single result. Used rather than (choice c (inc (mzero))) to avoid\n; returning to search a part of the tree that will inevitably fail.\n; ((c f) e3) multiple results.\n(define-syntax case-inf\n (syntax-rules ()\n ((_ e (() e0) ((f^) e1) ((c^) e2) ((c f) e3))\n (let ((c-inf e))\n (cond\n ((not c-inf) e0)\n ((procedure? c-inf) (let ((f^ c-inf)) e1))\n ((not (and (pair? c-inf)\n (procedure? (cdr c-inf))))\n (let ((c^ c-inf)) e2))\n (else (let ((c (car c-inf)) (f (cdr c-inf)))\n e3)))))))\n\n; c-inf: SearchStream\n; f: (-> SearchStream)\n; -> SearchStream\n;\n; f is a thunk to avoid unnecesarry computation in the case that the first\n; answer produced by c-inf is enough to satisfy the query.\n(define mplus\n (lambda (c-inf f)\n (case-inf c-inf\n (() (f))\n ((f^) (inc (mplus (f) f^)))\n ((c) (choice c f))\n ((c f^) (choice c (inc (mplus (f) f^)))))))\n\n; c-inf: SearchStream\n; g: Goal\n; -> SearchStream\n(define bind\n (lambda (c-inf g)\n (case-inf c-inf\n (() (mzero))\n ((f) (inc (bind (f) g)))\n ((c) (g c))\n ((c f) (mplus (g c) (inc (bind (f) g)))))))\n\n; Int, SearchStream -> (ListOf SearchResult)\n(define take\n (lambda (n f)\n (cond\n ((and n (zero? n)) '())\n (else\n (case-inf (f)\n (() '())\n ((f) (take n f))\n ((c) (cons c '()))\n ((c f) (cons c\n (take (and n (- n 1)) f))))))))\n\n(define take-stream\n (lambda (f)\n (case-inf (f)\n (() '())\n ((f) (take-stream f))\n ((c) (stream-cons c '()))\n ((c f) (stream-cons c (take-stream f))))))\n\n; -> SearchStream\n(define-syntax bind*\n (syntax-rules ()\n ((_ e) e)\n ((_ e g0 g ...) (bind* (bind e g0) g ...))))\n\n; -> SearchStream\n(define-syntax mplus*\n (syntax-rules ()\n ((_ e) e)\n ((_ e0 e ...) (mplus e0\n (inc (mplus* e ...))))))\n\n; -> Goal\n(define-syntax fresh\n (syntax-rules ()\n ((_ (x ...) g0 g ...)\n (lambdag@ (st)\n ; this inc triggers interleaving\n (inc\n (let ((scope (subst-scope (state-S st))))\n (let ((x (var scope)) ...)\n (bind* (g0 st) g ...))))))))\n\n\n; -> Goal\n(define-syntax conde\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n ; this inc triggers interleaving\n (inc\n (let ((st (state-with-scope st (new-scope))))\n (mplus*\n (bind* (g0 st) g ...)\n (bind* (g1 st) g^ ...) ...)))))))\n\n(define-syntax run\n (syntax-rules ()\n ((_ n (q) g0 g ...)\n (take n\n (inc\n ((fresh (q) g0 g ...\n (lambdag@ (st)\n (let ((st (state-with-scope st nonlocal-scope)))\n (let ((z ((reify q) st)))\n (choice z (lambda () (lambda () #f)))))))\n empty-state))))\n ((_ n (q0 q1 q ...) g0 g ...)\n (run n (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n(define-syntax run*\n (syntax-rules ()\n ((_ (q0 q ...) g0 g ...) (run #f (q0 q ...) g0 g ...))))\n\n(define-syntax run-stream\n (syntax-rules ()\n ((_ (q) g0 g ...)\n (take-stream\n (inc\n ((fresh (q) g0 g ...\n (lambdag@ (st)\n (let ((st (state-with-scope st nonlocal-scope)))\n (let ((z ((reify q) st)))\n (choice z (lambda () (lambda () #f)))))))\n empty-state))))\n ((_ (q0 q1 q ...) g0 g ...)\n (run-stream (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n; Constraints\n; C refers to the constraint store map\n; c refers to an individual constraint record\n\n; Constraint: State -> #f | State\n;\n; (note that a Constraint is a Goal but a Goal is not a Constraint.\n; Constraint implementations currently use this more restrained type. See `and-foldl`\n; and `update-constraints`.)\n\n; Requirements for type constraints:\n; 1. Must be positive, not negative. not-pairo wouldn't work.\n; 2. Each type must have infinitely many possible values to avoid\n; incorrectness in combination with disequality constraints, like:\n; (fresh (x) (booleano x) (=/= x #t) (=/= x #f))\n(define type-constraint\n (lambda (type-pred type-id)\n (lambda (u)\n (lambdag@ (st)\n (let ((term (walk u (state-S st))))\n (cond\n ((type-pred term) st)\n ((var? term)\n (let* ((c (lookup-c term st))\n (T (c-T c)))\n (cond\n ((eq? T type-id) st)\n ((not T) (set-c term (c-with-T c type-id) st))\n (else #f))))\n (else #f)))))))\n\n(define symbolo (type-constraint symbol? 'symbolo))\n(define numbero (type-constraint number? 'numbero))\n\n(define (add-to-D st v d)\n (let* ((c (lookup-c v st))\n (c^ (c-with-D c (cons d (c-D c)))))\n (set-c v c^ st)))\n\n(define =/=*\n (lambda (S+)\n (lambdag@ (st)\n (let-values (((S added) (unify* S+ (subst-with-scope (state-S st) nonlocal-scope))))\n (cond\n ((not S) st)\n ((null? added) #f)\n (else\n ; Choose one of the disequality elements (el) to attach the constraint to. Only\n ; need to choose one because all must fail to cause the constraint to fail.\n (let ((el (car added)))\n (let ((st (add-to-D st (car el) added)))\n (if (var? (cdr el))\n (add-to-D st (cdr el) added)\n st)))))))))\n\n(define =/=\n (lambda (u v)\n (=/=* `((,u . ,v)))))\n\n(define absento\n (lambda (ground-atom term)\n (lambdag@ (st)\n (let ((term (walk term (state-S st))))\n (cond\n ((pair? term)\n (let ((st^ ((absento ground-atom (car term)) st)))\n (and st^ ((absento ground-atom (cdr term)) st^))))\n ((eqv? term ground-atom) #f)\n ((var? term)\n (let* ((c (lookup-c term st))\n (A (c-A c)))\n (if (memv ground-atom A)\n st\n (let ((c^ (c-with-A c (cons ground-atom A))))\n (set-c term c^ st)))))\n (else st))))))\n\n; Fold lst with proc and initial value init. If proc ever returns #f,\n; return with #f immediately. Used for applying a series of constraints\n; to a state, failing if any operation fails.\n(define (and-foldl proc init lst)\n (if (null? lst)\n init\n (let ([res (proc (car lst) init)])\n (and res (and-foldl proc res (cdr lst))))))\n\n(define ==\n (lambda (u v)\n (lambdag@ (st)\n (let-values (((S added) (unify u v (state-S st))))\n (if S\n (and-foldl update-constraints (state S (state-C st)) added)\n #f)))))\n\n\n; Not fully optimized. Could do absento update with fewer hash-refs / hash-sets.\n(define update-constraints\n (lambda (a st)\n (let ([old-c (lookup-c (lhs a) st)])\n (if (eq? old-c empty-c)\n st\n (let ((st (remove-c (lhs a) st)))\n (and-foldl (lambda (op st) (op st)) st\n (append\n (if (eq? (c-T old-c) 'symbolo)\n (list (symbolo (rhs a)))\n '())\n (if (eq? (c-T old-c) 'numbero)\n (list (numbero (rhs a)))\n '())\n (map (lambda (atom) (absento atom (rhs a))) (c-A old-c))\n (map (lambda (d) (=/=* d)) (c-D old-c)))))))))\n\n\n; Reification\n\n(define walk*\n (lambda (v S)\n (let ((v (walk v S)))\n (cond\n ((var? v) v)\n ((pair? v)\n (cons (walk* (car v) S) (walk* (cdr v) S)))\n (else v)))))\n\n(define vars\n (lambda (term acc)\n (cond\n ((var? term) (cons term acc))\n ((pair? term)\n (vars (cdr term) (vars (car term) acc)))\n (else acc))))\n\n(define-syntax project\n (syntax-rules ()\n ((_ (x ...) g g* ...)\n (lambdag@ (st)\n (let ((x (walk* x (state-S st))) ...)\n ((fresh () g g* ...) st))))))\n\n\n; Create a constraint store of the old representation from a state object,\n; so that we can use the old reifier. Only accumulates constraints related\n; to the variable being reified which makes things a bit faster.\n(define c-from-st\n (lambda (st x)\n (let ((vs (vars (walk* x (state-S st)) '())))\n (foldl\n (lambda (v c-store)\n (let ((c (lookup-c v st)))\n (let ((S (state-S st))\n (D (c->D c-store))\n (Y (c->Y c-store))\n (N (c->N c-store))\n (T (c->T c-store))\n (T^ (c-T c))\n (D^ (c-D c))\n (A^ (c-A c)))\n `(,S\n ,(append D^ D)\n ,(if (eq? T^ 'symbolo)\n (cons v Y)\n Y)\n ,(if (eq? T^ 'numbero)\n (cons v N)\n N)\n ,(append\n (map (lambda (atom) (cons atom v)) A^)\n T)))))\n `(,(state-S st) () () () ())\n (remove-duplicates vs)))))\n\n(define reify\n (lambda (x)\n (lambda (st)\n (let ((c (c-from-st st x)))\n (let ((c (cycle c)))\n (let* ((S (c->S c))\n (D (walk* (c->D c) S))\n (Y (walk* (c->Y c) S))\n (N (walk* (c->N c) S))\n (T (walk* (c->T c) S)))\n (let ((v (walk* x S)))\n (let ((R (reify-S v (subst empty-subst-map nonlocal-scope))))\n (reify+ v R\n (let ((D (remp\n (lambda (d)\n (let ((dw (walk* d S)))\n (anyvar? dw R)))\n (rem-xx-from-d c))))\n (rem-subsumed D))\n (remp\n (lambda (y) (var? (walk y R)))\n Y)\n (remp\n (lambda (n) (var? (walk n R)))\n N)\n (remp (lambda (t)\n (anyvar? t R)) T))))))))))\n\n\n; Bits from the old constraint implementation, still used for reification.\n\n; In this part of the code, c refers to the\n; old constraint store with components:\n; S - substitution\n; D - disequality constraints\n; Y - symbolo\n; N - numbero\n; T - absento\n\n(define c->S (lambda (c) (car c)))\n(define c->D (lambda (c) (cadr c)))\n(define c->Y (lambda (c) (caddr c)))\n(define c->N (lambda (c) (cadddr c)))\n(define c->T (lambda (c) (cadddr (cdr c))))\n\n; Syntax for reification goal objects using the old constraint store\n(define-syntax lambdar@\n (syntax-rules (:)\n ((_ (c) e) (lambda (c) e))\n ((_ (c : S D Y N T) e)\n (lambda (c)\n (let ((S (c->S c)) (D (c->D c)) (Y (c->Y c)) (N (c->N c)) (T (c->T c)))\n e)))))\n\n(define tagged?\n (lambda (S Y y^)\n (exists (lambda (y) (eqv? (walk y S) y^)) Y)))\n\n(define untyped-var?\n (lambda (S Y N t^)\n (let ((in-type? (lambda (y) (var-eq? (walk y S) t^))))\n (and (var? t^)\n (not (exists in-type? Y))\n (not (exists in-type? N))))))\n\n(define reify-S\n (lambda (v S)\n (let ((v (walk v S)))\n (cond\n ((var? v)\n (let ((n (subst-length S)))\n (let ((name (reify-name n)))\n (subst-add S v name))))\n ((pair? v)\n (let ((S (reify-S (car v) S)))\n (reify-S (cdr v) S)))\n (else S)))))\n\n(define reify-name\n (lambda (n)\n (string->symbol\n (string-append \"_\" \".\" (number->string n)))))\n\n(define drop-dot\n (lambda (X)\n (map (lambda (t)\n (let ((a (lhs t))\n (d (rhs t)))\n `(,a ,d)))\n X)))\n\n(define sorter\n (lambda (ls)\n (list-sort lex<=? ls)))\n\n(define lex<=?\n (lambda (x y)\n (string<=? (datum->string x) (datum->string y))))\n\n(define datum->string\n (lambda (x)\n (call-with-string-output-port\n (lambda (p) (display x p)))))\n\n(define anyvar?\n (lambda (u r)\n (cond\n ((pair? u)\n (or (anyvar? (car u) r)\n (anyvar? (cdr u) r)))\n (else (var? (walk u r))))))\n\n(define member*\n (lambda (u v)\n (cond\n ((equal? u v) #t)\n ((pair? v)\n (or (member* u (car v)) (member* u (cdr v))))\n (else #f))))\n\n(define drop-N-b/c-const\n (lambdar@ (c : S D Y N T)\n (let ((const? (lambda (n)\n (not (var? (walk n S))))))\n (cond\n ((find const? N) =>\n (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n (else c)))))\n\n(define drop-Y-b/c-const\n (lambdar@ (c : S D Y N T)\n (let ((const? (lambda (y)\n (not (var? (walk y S))))))\n (cond\n ((find const? Y) =>\n (lambda (y) `(,S ,D ,(remq1 y Y) ,N ,T)))\n (else c)))))\n\n(define remq1\n (lambda (elem ls)\n (cond\n ((null? ls) '())\n ((eq? (car ls) elem) (cdr ls))\n (else (cons (car ls) (remq1 elem (cdr ls)))))))\n\n(define same-var?\n (lambda (v)\n (lambda (v^)\n (and (var? v) (var? v^) (var-eq? v v^)))))\n\n(define find-dup\n (lambda (f S)\n (lambda (set)\n (let loop ((set^ set))\n (cond\n ((null? set^) #f)\n (else\n (let ((elem (car set^)))\n (let ((elem^ (walk elem S)))\n (cond\n ((find (lambda (elem^^)\n ((f elem^) (walk elem^^ S)))\n (cdr set^))\n elem)\n (else (loop (cdr set^))))))))))))\n\n(define drop-N-b/c-dup-var\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-dup same-var? S) N) =>\n (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n (else c))))\n\n(define drop-Y-b/c-dup-var\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-dup same-var? S) Y) =>\n (lambda (y)\n `(,S ,D ,(remq1 y Y) ,N ,T)))\n (else c))))\n\n(define var-type-mismatch?\n (lambda (S Y N t1^ t2^)\n (cond\n ((num? S N t1^) (not (num? S N t2^)))\n ((sym? S Y t1^) (not (sym? S Y t2^)))\n (else #f))))\n\n(define term-ununifiable?\n (lambda (S Y N t1 t2)\n (let ((t1^ (walk t1 S))\n (t2^ (walk t2 S)))\n (cond\n ((or (untyped-var? S Y N t1^) (untyped-var? S Y N t2^)) #f)\n ((var? t1^) (var-type-mismatch? S Y N t1^ t2^))\n ((var? t2^) (var-type-mismatch? S Y N t2^ t1^))\n ((and (pair? t1^) (pair? t2^))\n (or (term-ununifiable? S Y N (car t1^) (car t2^))\n (term-ununifiable? S Y N (cdr t1^) (cdr t2^))))\n (else (not (eqv? t1^ t2^)))))))\n\n(define T-term-ununifiable?\n (lambda (S Y N)\n (lambda (t1)\n (let ((t1^ (walk t1 S)))\n (letrec\n ((t2-check\n (lambda (t2)\n (let ((t2^ (walk t2 S)))\n (if (pair? t2^)\n (and\n (term-ununifiable? S Y N t1^ t2^)\n (t2-check (car t2^))\n (t2-check (cdr t2^)))\n (term-ununifiable? S Y N t1^ t2^))))))\n t2-check)))))\n\n(define num?\n (lambda (S N n)\n (let ((n (walk n S)))\n (cond\n ((var? n) (tagged? S N n))\n (else (number? n))))))\n\n(define sym?\n (lambda (S Y y)\n (let ((y (walk y S)))\n (cond\n ((var? y) (tagged? S Y y))\n (else (symbol? y))))))\n\n(define drop-T-b/c-Y-and-N\n (lambdar@ (c : S D Y N T)\n (let ((drop-t? (T-term-ununifiable? S Y N)))\n (cond\n ((find (lambda (t) ((drop-t? (lhs t)) (rhs t))) T) =>\n (lambda (t) `(,S ,D ,Y ,N ,(remq1 t T))))\n (else c)))))\n\n(define move-T-to-D-b/c-t2-atom\n (lambdar@ (c : S D Y N T)\n (cond\n ((exists (lambda (t)\n (let ((t2^ (walk (rhs t) S)))\n (cond\n ((and (not (untyped-var? S Y N t2^))\n (not (pair? t2^)))\n (let ((T (remq1 t T)))\n `(,S ((,t) . ,D) ,Y ,N ,T)))\n (else #f))))\n T))\n (else c))))\n\n(define terms-pairwise=?\n (lambda (pr-a^ pr-d^ t-a^ t-d^ S)\n (or\n (and (term=? pr-a^ t-a^ S)\n (term=? pr-d^ t-a^ S))\n (and (term=? pr-a^ t-d^ S)\n (term=? pr-d^ t-a^ S)))))\n\n(define T-superfluous-pr?\n (lambda (S Y N T)\n (lambda (pr)\n (let ((pr-a^ (walk (lhs pr) S))\n (pr-d^ (walk (rhs pr) S)))\n (cond\n ((exists\n (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S)))\n T)\n (for-all\n (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (or\n (not (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S))\n (untyped-var? S Y N t-d^)\n (pair? t-d^))))\n T))\n (else #f))))))\n\n(define drop-from-D-b/c-T\n (lambdar@ (c : S D Y N T)\n (cond\n ((find\n (lambda (d)\n (exists\n (T-superfluous-pr? S Y N T)\n d))\n D) =>\n (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n (else c))))\n\n(define drop-t-b/c-t2-occurs-t1\n (lambdar@ (c : S D Y N T)\n (cond\n ((find (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (mem-check t-d^ t-a^ S)))\n T) =>\n (lambda (t)\n `(,S ,D ,Y ,N ,(remq1 t T))))\n (else c))))\n\n(define split-t-move-to-d-b/c-pair\n (lambdar@ (c : S D Y N T)\n (cond\n ((exists\n (lambda (t)\n (let ((t2^ (walk (rhs t) S)))\n (cond\n ((pair? t2^) (let ((ta `(,(lhs t) . ,(car t2^)))\n (td `(,(lhs t) . ,(cdr t2^))))\n (let ((T `(,ta ,td . ,(remq1 t T))))\n `(,S ((,t) . ,D) ,Y ,N ,T))))\n (else #f))))\n T))\n (else c))))\n\n(define find-d-conflict\n (lambda (S Y N)\n (lambda (D)\n (find\n (lambda (d)\n (exists (lambda (pr)\n (term-ununifiable? S Y N (lhs pr) (rhs pr)))\n d))\n D))))\n\n(define drop-D-b/c-Y-or-N\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-d-conflict S Y N) D) =>\n (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n (else c))))\n\n(define cycle\n (lambdar@ (c)\n (let loop ((c^ c)\n (fns^ (LOF))\n (n (length (LOF))))\n (cond\n ((zero? n) c^)\n ((null? fns^) (loop c^ (LOF) n))\n (else\n (let ((c^^ ((car fns^) c^)))\n (cond\n ((not (eq? c^^ c^))\n (loop c^^ (cdr fns^) (length (LOF))))\n (else (loop c^ (cdr fns^) (sub1 n))))))))))\n\n(define mem-check\n (lambda (u t S)\n (let ((t (walk t S)))\n (cond\n ((pair? t)\n (or (term=? u t S)\n (mem-check u (car t) S)\n (mem-check u (cdr t) S)))\n (else (term=? u t S))))))\n\n(define term=?\n (lambda (u t S)\n (let-values (((S added) (unify u t (subst-with-scope S nonlocal-scope))))\n (and S (null? added)))))\n\n(define ground-non-?\n (lambda (pred)\n (lambda (u S)\n (let ((u (walk u S)))\n (cond\n ((var? u) #f)\n (else (not (pred u))))))))\n\n(define ground-non-symbol?\n (ground-non-? symbol?))\n\n(define ground-non-number?\n (ground-non-? number?))\n\n(define succeed (== #f #f))\n\n(define fail (== #f #t))\n\n(define ==fail-check\n (lambda (S0 D Y N T)\n (let ([S0 (subst-with-scope S0 nonlocal-scope)])\n (cond\n ((atomic-fail-check S0 Y ground-non-symbol?) #t)\n ((atomic-fail-check S0 N ground-non-number?) #t)\n ((symbolo-numbero-fail-check S0 Y N) #t)\n ((=/=-fail-check S0 D) #t)\n ((absento-fail-check S0 T) #t)\n (else #f)))))\n\n(define atomic-fail-check\n (lambda (S A pred)\n (exists (lambda (a) (pred (walk a S) S)) A)))\n\n(define symbolo-numbero-fail-check\n (lambda (S A N)\n (let ((N (map (lambda (n) (walk n S)) N)))\n (exists (lambda (a) (exists (same-var? (walk a S)) N))\n A))))\n\n(define absento-fail-check\n (lambda (S T)\n (exists (lambda (t) (mem-check (lhs t) (rhs t) S)) T)))\n\n(define =/=-fail-check\n (lambda (S D)\n (exists (d-fail-check S) D)))\n\n(define d-fail-check\n (lambda (S)\n (lambda (d)\n (let-values (((S added) (unify* d S)))\n (and S (null? added))))))\n\n(define reify+\n (lambda (v R D Y N T)\n (form (walk* v R)\n (walk* D R)\n (walk* Y R)\n (walk* N R)\n (rem-subsumed-T (walk* T R)))))\n\n(define form\n (lambda (v D Y N T)\n (let ((fd (sort-D D))\n (fy (sorter Y))\n (fn (sorter N))\n (ft (sorter T)))\n (let ((fd (if (null? fd) fd\n (let ((fd (drop-dot-D fd)))\n `((=/= . ,fd)))))\n (fy (if (null? fy) fy `((sym . ,fy))))\n (fn (if (null? fn) fn `((num . ,fn))))\n (ft (if (null? ft) ft\n (let ((ft (drop-dot ft)))\n `((absento . ,ft))))))\n (cond\n ((and (null? fd) (null? fy)\n (null? fn) (null? ft))\n v)\n (else (append `(,v) fd fn fy ft)))))))\n\n(define sort-D\n (lambda (D)\n (sorter\n (map sort-d D))))\n\n(define sort-d\n (lambda (d)\n (list-sort\n (lambda (x y)\n (lex<=? (car x) (car y)))\n (map sort-pr d))))\n\n(define drop-dot-D\n (lambda (D)\n (map drop-dot D)))\n\n(define lex<-reified-name?\n (lambda (r)\n (charstring r) 0)\n #\\_)))\n\n(define sort-pr\n (lambda (pr)\n (let ((l (lhs pr))\n (r (rhs pr)))\n (cond\n ((lex<-reified-name? r) pr)\n ((lex<=? r l) `(,r . ,l))\n (else pr)))))\n\n(define rem-subsumed\n (lambda (D)\n (let rem-subsumed ((D D) (d^* '()))\n (cond\n ((null? D) d^*)\n ((or (subsumed? (car D) (cdr D))\n (subsumed? (car D) d^*))\n (rem-subsumed (cdr D) d^*))\n (else (rem-subsumed (cdr D)\n (cons (car D) d^*)))))))\n\n(define subsumed?\n (lambda (d d*)\n (cond\n ((null? d*) #f)\n (else\n (let-values (((S ignore) (unify* d (subst empty-subst-map nonlocal-scope))))\n (let-values (((S+ added) (unify* (car d*) S)))\n (or\n (and S+ (null? added))\n (subsumed? d (cdr d*)))))))))\n\n\n\n(define rem-xx-from-d\n (lambdar@ (c : S D Y N T)\n (let ((D (walk* D S)))\n (remp not\n (map (lambda (d)\n (let-values (((S0 ignore) (unify* d S)))\n (cond\n ((not S0) #f)\n ((==fail-check S0 '() Y N T) #f)\n (else\n (let-values (((S added) (unify* d (subst empty-subst-map nonlocal-scope))))\n added)))))\n D)))))\n\n(define rem-subsumed-T\n (lambda (T)\n (let rem-subsumed ((T T) (T^ '()))\n (cond\n ((null? T) T^)\n (else\n (let ((lit (lhs (car T)))\n (big (rhs (car T))))\n (cond\n ((or (subsumed-T? lit big (cdr T))\n (subsumed-T? lit big T^))\n (rem-subsumed (cdr T) T^))\n (else (rem-subsumed (cdr T)\n (cons (car T) T^))))))))))\n\n(define subsumed-T?\n (lambda (lit big T)\n (cond\n ((null? T) #f)\n (else\n (let ((lit^ (lhs (car T)))\n (big^ (rhs (car T))))\n (or\n (and (eq? big big^) (member* lit^ lit))\n (subsumed-T? lit big (cdr T))))))))\n\n(define LOF\n (lambda ()\n `(,drop-N-b/c-const ,drop-Y-b/c-const ,drop-Y-b/c-dup-var\n ,drop-N-b/c-dup-var ,drop-D-b/c-Y-or-N ,drop-T-b/c-Y-and-N\n ,move-T-to-D-b/c-t2-atom ,split-t-move-to-d-b/c-pair\n ,drop-from-D-b/c-T ,drop-t-b/c-t2-occurs-t1)))\n\n" }, { "path": "attic/code/process-db.rkt", "content": "#lang racket\n\n;; Racket code to process the osteoporosis database, turning it into classy (but unnormalized) s-expressions using Racket.\n\n;; https://docs.racket-lang.org/csv-reading/index.html\n\n;; http://www.neilvandyke.org/racket/csv-reading/\n\n;; https://stackoverflow.com/questions/10883426/how-to-download-and-parse-a-csv-file-in-racket\n\n(require (planet neil/csv:2:0) net/url)\n\n;; change me to point to your ncats directory!\n(define ncats_proposal-location \"/Users/webyrd/github/\")\n\n(define iver-url \n (string->url\n (string-append \"file://\" ncats_proposal-location \"ncats_proposal/ncats-proof-of-concept/raw-data/semmedVER30_A_clean.C0029456_osteoporosis.csv\")))\n\n(define data (csv->list (get-pure-port iver-url)))\n\n(define symbolic-data\n (map (lambda (d)\n (list\n (string->number (list-ref d 0))\n (string->number (list-ref d 1))\n (string->number (list-ref d 2))\n (string->symbol (list-ref d 3))\n (string->symbol (list-ref d 4))\n (list-ref d 5)\n (string->symbol (list-ref d 6))\n (string->number (list-ref d 7))\n (string->symbol (list-ref d 8))\n (list-ref d 9)\n (string->symbol (list-ref d 10))\n (string->number (list-ref d 11))))\n data))\n\n(call-with-output-file (string-append ncats_proposal-location \"ncats_proposal/ncats-proof-of-concept/code/osteoporosis-data.scm\")\n (lambda (output-port)\n (fprintf output-port \"(define data '(\\n\")\n (let loop ([ls symbolic-data])\n (cond\n [(null? ls) (fprintf output-port \"))\\n\" )]\n [else\n (fprintf output-port \"~s\\n\" (car ls))\n (loop (cdr ls))]))))\n" }, { "path": "attic/code/programmatically-defined-relations.rkt", "content": "#lang racket\n(provide\n appendo\n decreases\n decreases*\n increases\n increases*\n lengtho\n length>=o\n not-nilo\n path-last-edgeo\n edge-subject-typeo\n edge-object-typeo\n edge-trustedo\n edge-untrustedo\n path-length-trustedo\n isa-counto\n may-treat\n gene-causes-disease\n pubmed->url\n edge/urlo\n path/urlo\n )\n\n(require\n racket/sandbox\n racket/gui/base\n racket/engine\n \"db.rkt\"\n \"mk-db.rkt\"\n \"concept.rkt\"\n \"edge.rkt\"\n )\n\n(displayln\n \"Finished loading mk-db.rkt\")\n\n(define (pubmed->url pubmed-id)\n (string-append \"https://www.ncbi.nlm.nih.gov/pubmed/\" (~a pubmed-id)))\n\n;; Warning: not relational in e\n(define (edge/urlo e e-url)\n (fresh (s o p sty oty r* url*)\n (== `(,s ,o ,p ,sty ,oty ,r*) e)\n (project (r*)\n (== (map pubmed->url r*) url*))\n (== `(,s ,o ,p ,sty ,oty ,url*) e-url)))\n\n;; Warning: not relational in p\n(define (path/urlo p p-url)\n (conde\n ((== '() p) (== '() p-url))\n ((fresh (e d e-url d-url)\n (== (cons e d) p)\n (== (cons e-url d-url) p-url)\n (edge/urlo e e-url)\n (path/urlo d d-url)))))\n\n(define (appendo l s out)\n (conde\n [(== '() l) (== s out)]\n [(fresh (a d res)\n (== (cons a d) l)\n (== (cons a res) out)\n (appendo d s res))]))\n\n;; Warning: not relational in n (length)\n(define (lengtho path n)\n (conde\n ((== 0 n) (== '() path))\n ((=/= 0 n)\n (fresh (a d)\n (== `(,a . ,d) path)\n (lengtho d (- n 1))))))\n\n;; Warning: not relational in n (length)\n(define (length>=o path n)\n (conde\n ((== 0 n))\n ((=/= 0 n)\n (fresh (a d)\n (== `(,a . ,d) path)\n (length>=o d (- n 1))))))\n\n(define (not-nilo l) (fresh (a d) (== `(,a . ,d) l)))\n\n;; Warning: path must be length-instantiated.\n(define (path-last-edgeo path last)\n (project (path)\n (== (car (reverse path)) last)))\n\n(define (edge-subject-typeo e sty)\n (fresh (s o pred oty ps)\n (== `(,s ,o ,pred ,sty ,oty ,ps) e)))\n\n(define (edge-object-typeo e oty)\n (fresh (s o pred sty ps)\n (== `(,s ,o ,pred ,sty ,oty ,ps) e)))\n\n(define (edge-trustedo edge)\n (fresh (s o p st ot pubrefs)\n (== `(,s ,o ,p ,st ,ot ,pubrefs) edge)\n (length>=o pubrefs 2)))\n\n(define (edge-untrustedo edge)\n (fresh (s o p st ot pubrefs)\n (== `(,s ,o ,p ,st ,ot ,pubrefs) edge)\n (lengtho pubrefs 1)))\n\n;; Warning: not relational in nlen or ntrusted\n(define (path-length-trustedo path len trusted)\n (conde\n ((== 0 len) (== '() path))\n ((=/= 0 len)\n (fresh (a d)\n (== `(,a . ,d) path)\n (cond\n ((= 0 trusted) (fresh ()\n (edge-untrustedo a)\n (path-length-trustedo d (- len 1) trusted)))\n ((= len trusted) (fresh ()\n (edge-trustedo a)\n (path-length-trustedo d (- len 1) (- trusted 1))))\n (else (conde\n ((edge-trustedo a)\n (path-length-trustedo d (- len 1) (- trusted 1)))\n ((edge-untrustedo a)\n (path-length-trustedo d (- len 1) trusted)))))))))\n\n;; Warning: not relational in o\n(define (isa-counto o n)\n (project (o)\n (== (length (run* (_)\n (fresh (s sty oty rs)\n (edgeo `(,s ,o \"ISA\" ,sty ,oty ,rs))))) n)))\n\n;; I’m having some fun defining relations that find that “a ultimately decreases b” and “a ultimately increases b” since you can have many ups and downs in the intermediate path.\n;; It’s inspired by this generic example:\n;; may_treat(drug,disease) iff\n;; causes(gene,disease) and\n;; increases(disease,gene) and\n;; decreases*(drug,gene)\n;; I had to define decreases* mutually recursively with increases*:\n;; decreases*(a,b) iff\n;; decreases(a,b)\n;; or there exists c such that\n;; increases*(a,c) and\n;; decreases*(c,b)\n;; increases*(a,b) iff\n;; increases(a,b)\n;; or there exists c such that\n;; decreases*(a,c) and\n;; increases*(c,b)\n;; I’m trying to emphasize the power of programmatically-defined relations.\n\n(define (may-treat drug disease explanation)\n (fresh (gene e1 e2 p1)\n (gene-causes-disease gene disease e1)\n (increases disease gene e2)\n (decreases* drug gene p1)\n (== `((drug: ,drug)\n (gene: ,gene)\n (disease: ,disease)\n (gene-causes-disease: ,e1)\n (increases-disease/gene: ,e2)\n (decreases*-drug/gene: . ,p1))\n explanation)))\n\n(define (gene-causes-disease gene disease edge)\n (fresh (t-gene t-disease pub)\n (== `(,gene ,disease \"CAUSES\" ,t-gene ,t-disease ,pub) edge)\n (edgeo edge)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) disease)\n (membero \"dsyn\" concept-type*))))\n\n(define (decreases a b edge)\n (fresh (pred ta tb pub)\n (== `(,a ,b ,pred ,ta ,tb ,pub) edge)\n (== \"INHIBITS\" pred)\n (edgeo edge)))\n\n(define (increases a b edge)\n (fresh (pred ta tb pub)\n (== `(,a ,b ,pred ,ta ,tb ,pub) edge)\n (== \"STIMULATES\" pred)\n (edgeo edge)))\n\n;; decrease, increase decreasers, decrease increasers\n(define (decreases* a b path)\n (conde\n [(fresh (e)\n (== `(,e) path)\n (decreases a b e))]\n [(fresh (c e p2)\n (== `(,e . ,p2) path)\n (not-nilo p2)\n (increases a c e)\n (decreases* c b p2))]\n [(fresh (c e p2)\n (== `(,e . ,p2) path)\n (not-nilo p2)\n (decreases a c e)\n (increases* c b p2))]))\n\n;; increase, increase increasers, decrease decreasers\n(define (increases* a b path)\n (conde\n [(fresh (e)\n (== `(,e) path)\n (increases a b e))]\n [(fresh (c e p2)\n (== `(,e . ,p2) path)\n (not-nilo p2)\n (increases a c e)\n (increases* c b p2))]\n [(fresh (c e p2)\n (== `(,e . ,p2) path)\n (not-nilo p2)\n (decreases a c e)\n (decreases* c b p2))]))\n" }, { "path": "attic/code/read.rkt", "content": "#lang racket/base\n(provide\n read-all\n read-all/stream\n read-all-from-file\n )\n\n(require\n racket/stream\n )\n\n(define (read-all in)\n (define datum (read in))\n (if (eof-object? datum) '() (cons datum (read-all in))))\n\n(define (read-all/stream in)\n (define datum (read in))\n (if (eof-object? datum) '() (stream-cons datum (read-all/stream in))))\n\n(define (read-all-from-file path)\n (call-with-input-file (expand-user-path path) read-all))\n" }, { "path": "attic/code/sample_semmed.csv", "content": "PREDICATION_ID,SENTENCE_ID,PMID,PREDICATE,SUBJECT_CUI,SUBJECT_NAME,SUBJECT_SEMTYPE,SUBJECT_NOVELTY,OBJECT_CUI,OBJECT_NAME,OBJECT_SEMTYPE,OBJECT_NOVELTY\n61,128,14420371,ISA,C0026879,Mutagens,hops,1,C0220806,Chemicals,chem,1\n62,116,5659339,PART_OF,C0017725,Glucose,bacs,1,C0022378,jejunum,bpoc,1\n63,146,12255310,PROCESS_OF,C0006147,Breast Feeding,orgf,1,C0020114,Human,humn,1\n64,170,12305488,TREATS,C0279494,Oestrogen therapy,topp,1,C0043210,Woman,popg,1\n65,116,5659339,PROCESS_OF,C0232338,Blood flow,orgf,1,C0012984,Canis familiaris,mamm,1\n66,120,14185243,LOCATION_OF,C0006104,Brain,bpoc,1,C0041249,Tryptophan,aapp,1\n67,134,13670501,PROCESS_OF,C0006434,Burn injury,inpo,1,C0728836,Young child,humn,1\n68,147,12305418,METHOD_OF,C0042387,Vasectomy,topp,1,C0038288,Sexual sterilization,topp,1\n69,167,14457919,TREATS,C0037766,Antispasmodics,phsu,1,C0002962,Angina Pectoris,sosy,1\n70,242,14934087,LOCATION_OF,C0036471,Scrotum,bpoc,1,C0016085,Filariasis,dsyn,1\n71,218,13930366,LOCATION_OF,C0037993,Spleen,bpoc,1,C0017086,Gangrene,dsyn,1\n72,136,5867984,PROCESS_OF,C0023290,\"Leishmaniasis, Visceral\",dsyn,1,C0020114,Human,humn,1\n73,221,6014351,LOCATION_OF,C1269901,Entire foramen magnum,bsoj,1,C0000768,Congenital Abnormality,cgab,1\n74,158,4966828,INTERACTS_WITH,C0024337,Lysine,aapp,1,C0038404,Enterococcus faecalis,bact,1\n75,127,13997680,LOCATION_OF,C0005767,Blood,tisu,1,C0007061,Carboxyhemoglobin,aapp,1\n76,163,13155021,LOCATION_OF,C0003483,Aorta,bpoc,1,C0332886,Coarctation,anab,1\n77,145,13974537,PART_OF,C0018563,Hand,bpoc,1,C0020114,Human,humn,1\n78,148,5776108,LOCATION_OF,C0022646,Kidney,bpoc,1,C0221198,Lesion,fndg,1\n79,181,13070168,ISA,C0025629,metharbital,orch,1,C0004743,Barbital,orch,1\n80,141,13738542,PROCESS_OF,C1457887,Symptoms,sosy,0,C0030705,Patients,humn,0\n81,256,13638644,LOCATION_OF,C0021853,Intestines,bpoc,1,C0010709,Cyst,anab,1\n82,216,5876094,LOCATION_OF,C0007806,Cerebrospinal Fluid,bdsu,1,C0022714,Kinins,aapp,1\n83,207,14812403,TREATS,C0396565,Lung excision,topp,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n84,223,13384308,PROCESS_OF,C0005778,Blood coagulation,ortf,1,C0030705,Patients,humn,0\n85,243,12275609,COEXISTS_WITH,C0009637,Conception,orgf,1,C0006147,Breast Feeding,orgf,1\n86,163,13155021,TREATS,C0011900,Diagnosis,hlca,1,C0008059,Child,humn,1\n87,254,13502773,LOCATION_OF,C0042036,Urine,bdsu,1,C0016581,Formiminoglutamic Acid,bacs,1\n88,148,5776108,DIAGNOSES,C0194073,Kidney biopsy,diap,1,C0032914,Pre-Eclampsia,dsyn,1\n89,213,11396507,PART_OF,C0221921,Stratum corneum,tisu,1,C0020114,Human,humn,1\n90,186,18856411,PROCESS_OF,C1458155,Mammary Neoplasms,neop,1,C0025920,\"Mice, Inbred C3H\",mamm,1\n91,174,12254865,PROCESS_OF,C0702166,Acne,dsyn,1,C0043210,Woman,humn,1\n92,163,13155021,TREATS,C1273870,Management procedure,hlca,1,C0008059,Child,humn,1\n93,285,14772444,LOCATION_OF,C0042149,Uterus,bpoc,1,C0036690,Septicemia,dsyn,1\n94,289,4958141,PART_OF,C0040291,Tissue Extracts,bacs,1,C0085979,Cavia,mamm,1\n95,212,13789574,ISA,C1010578,Spermophilus tridecemlineatus,mamm,1,C0037877,Susliks,mamm,1\n96,216,5876094,LOCATION_OF,C0007806,Cerebrospinal Fluid,bdsu,1,C0054012,bradykininogen,aapp,1\n97,234,11526826,PART_OF,C1304649,Tissue fiber,tisu,1,C0327011,Toad,amph,1\n98,148,5776108,COEXISTS_WITH,C0221198,Lesion,fndg,1,C0032914,Pre-Eclampsia,dsyn,1\n99,243,12275609,COEXISTS_WITH,C0025344,Menstruation,orgf,1,C0006147,Breast Feeding,orgf,1\n100,265,12264098,PROCESS_OF,C0027651,Neoplasm,neop,1,C0026809,Mus,mamm,1\n101,293,12332297,PART_OF,C0029974,Ovum,cell,1,C0020114,Human,humn,1\n102,313,14934088,LOCATION_OF,C0037925,Spinal Cord,bpoc,1,C0221198,Lesion,fndg,1\n103,278,12255535,TREATS,C0021587,Artificial Insemination,topp,1,C1522384,sex,orga,1\n104,348,14087163,LOCATION_OF,C0042036,Urine,bdsu,1,C0004965,Bence Jones Protein,aapp,1\n105,307,13930367,ISA,C0008059,Child,inpr,1,C0018684,Health,idcn,1\n106,310,5585326,PROCESS_OF,C0021311,Infection,dsyn,0,C0020114,Human,humn,1\n107,269,6029542,PROCESS_OF,C0018854,gamma-Chain Disease,dsyn,1,C0524824,Brassicaceae,plnt,1\n108,367,5933793,LOCATION_OF,C1269010,Entire aortic arch,bpoc,1,C0851256,Pseudocoarctation,anab,1\n109,323,14216905,PROCESS_OF,C0035435,Rheumatism,dsyn,1,C0030705,Patients,humn,0\n110,364,12334535,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0014180,Endometrium,bpoc,1\n111,320,13297195,CAUSES,C0003232,Antibiotics,antb,1,C0014356,Enterocolitis,dsyn,1\n112,338,14439951,PART_OF,C0025635,Methemoglobin,aapp,1,C0034693,Rattus norvegicus,mamm,1\n113,337,12233285,LOCATION_OF,C1280344,Entire vas deferens,bpoc,1,C0332853,Anastomosis,acab,1\n114,346,13582798,LOCATION_OF,C0227391,Sigmoid colon,bpoc,1,C1401877,vagina; artificial,fndg,1\n115,327,14055630,PROCESS_OF,C0151763,Liver damage,patf,1,C0741926,CARDIAC PATIENT,humn,1\n116,200,13867926,LOCATION_OF,C0022646,Kidney,bpoc,1,C0042036,Urine,bdsu,1\n117,294,14268251,AFFECTS,C0038425,Streptomycin,antb,1,C0178784,Organ,bpoc,1\n118,269,6029542,TREATS,C0450442,Agent,chvf,1,C0010709,Cyst,anab,1\n119,381,13384310,TREATS,C0008286,Chlorpromazine,orch,1,C0917816,Mental deficiency,mobd,1\n120,399,14772445,LOCATION_OF,C0227386,Transverse colon,bpoc,1,C0259974,\"Labor, Complicated\",dsyn,1\n121,345,12305487,ISA,C0039601,Testosterone,horm,1,C0087111,Therapeutic procedure,topp,0\n122,336,20285242,ASSOCIATED_WITH,C0005515,Biological Factors,bacs,0,C0596263,Carcinogenesis,neop,1\n123,200,13867926,PART_OF,C0022646,Kidney,bpoc,1,C0034493,Oryctolagus cuniculus,mamm,1\n124,305,12255534,PART_OF,C0037868,sperm cell,cell,1,C0020114,Human,humn,1\n125,284,12255446,TREATS,C0014912,Estradiol,horm,1,C0034693,Rattus norvegicus,mamm,1\n126,357,13070169,TREATS,C0012799,Mercurial diuretic,phsu,1,C0030705,Patients,podg,0\n127,269,6029542,TREATS,C0450442,Agent,chvf,1,C0018854,gamma-Chain Disease,dsyn,1\n128,208,16691646,ISA,C0008044,Chicago,geoa,1,C0020898,Illinois,geoa,1\n129,345,12305487,USES,C0087111,Therapeutic procedure,topp,0,C0039601,Testosterone,phsu,1\n130,452,12311486,PART_OF,C0024667,Animal Mammary Neoplasms,neop,1,C0939793,Bitch,mamm,1\n131,420,14934089,TREATS,C0011900,Diagnosis,hlca,1,C0008059,Child,humn,1\n132,374,6065069,LOCATION_OF,C0507816,Pulmonary capillary,bpoc,1,C0429627,Oxygen uptake,fndg,1\n133,398,12255008,METHOD_OF,C0042387,Vasectomy,topp,1,C0700589,Contraceptive methods,topp,1\n134,423,14880772,LOCATION_OF,C0005400,Bile duct structure,bpoc,1,C0175731,T-tube,medd,1\n135,284,12255446,TREATS,C0018061,Gonadotropins,horm,1,C0034693,Rattus norvegicus,mamm,1\n136,363,5659341,TREATS,C0001041,Acetylcholine,phsu,1,C0012984,Canis familiaris,mamm,1\n137,455,12255260,PRECEDES,C1148523,Childbirth,orgf,1,C0025344,Menstruation,orgf,1\n138,373,4159375,COEXISTS_WITH,C0032458,\"Polycyclic Hydrocarbons, Aromatic\",orch,1,C0043047,Water,inch,1\n139,306,14457921,LOCATION_OF,C0005767,Blood,tisu,1,C0036751,Serotonin,orch,1\n140,445,13551179,TREATS,C0543467,Operative Surgical Procedures,topp,1,C0267750,Acute peritonitis,dsyn,1\n141,306,14457921,PROCESS_OF,C0004153,Atherosclerosis,dsyn,1,C0325912,Columbidae,bird,1\n142,396,5729806,USES,C0087111,Therapeutic procedure,topp,0,C0008269,Chloroquine,phsu,1\n143,471,13582799,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0001575,Uterine adnexae structure,bpoc,1\n144,284,12255446,TREATS,C0039607,Testosterone Propionate,horm,1,C0034693,Rattus norvegicus,mamm,1\n145,483,13638647,PROCESS_OF,C0033931,Psychophysiologic Disorders,mobd,1,C0008059,Child,humn,1\n146,493,13670504,LOCATION_OF,C0013453,External Ear,bpoc,1,C0332952,Congenital invagination,cgab,1\n147,425,12305572,PROCESS_OF,C0025874,Metrorrhagia,patf,1,C0026447,Monkeys,mamm,1\n148,480,13155023,COEXISTS_WITH,C0010520,Cyanosis,sosy,1,C0243050,Cardiovascular Abnormalities,dsyn,1\n149,436,13930369,PROCESS_OF,C0240318,Mediastinal mass,dsyn,1,C0008059,Child,humn,1\n150,430,14812405,LOCATION_OF,C0229671,Serum,bdsu,1,C0008377,Cholesterol,bacs,1\n151,385,18856412,METHOD_OF,C0034618,Radiation therapy,topp,1,C0857127,Induction,topp,1\n152,475,13997693,COEXISTS_WITH,C0019147,Hepatic Coma,dsyn,1,C0019158,Hepatitis,dsyn,1\n153,454,13219190,PROCESS_OF,C0151798,Hepatic necrosis,dsyn,1,C0030705,Patients,humn,0\n154,469,12339641,LOCATION_OF,C0002424,Ambulatory Care Facilities,hcro,1,C0038951,Surveys,resa,1\n155,487,13384311,USES,C0087111,Therapeutic procedure,topp,0,C0008286,Chlorpromazine,phsu,1\n156,426,14847741,PART_OF,C0027809,Neurilemmoma,neop,1,C0038351,Stomach,bpoc,1\n157,430,14812405,PART_OF,C0008377,Cholesterol,bacs,1,C0085766,Aleuts,humn,1\n158,383,12279177,PROCESS_OF,C0006142,Malignant neoplasm of breast,neop,1,C0034693,Rattus norvegicus,mamm,1\n159,435,12255683,PROCESS_OF,C0032961,Pregnancy,orgf,1,C0034693,Rattus norvegicus,mamm,1\n160,436,13930369,PROCESS_OF,C0240318,Mediastinal mass,dsyn,1,C0021270,Infant,humn,1\n161,379,12275481,INTERACTS_WITH,C0770355,NORETHYNODREL-MESTRANOL,horm,1,C0013058,Dosage Forms,bodm,1\n162,451,13431634,TREATS,C0022209,isoniazid,phsu,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n163,402,11526826,PART_OF,C0018787,Heart,bpoc,1,C0327011,Toad,amph,1\n164,454,13219190,TREATS,C0041964,Urethane,orch,1,C0026764,Multiple Myeloma,neop,1\n165,509,13974540,LOCATION_OF,C0025066,Mediastinum,blor,1,C0010709,Cyst,anab,1\n166,383,12279177,CAUSES,C0025732,Methylcholanthrene,hops,1,C0006142,Malignant neoplasm of breast,neop,1\n167,426,14847741,COEXISTS_WITH,C0041582,Ulcer,patf,1,C0027809,Neurilemmoma,neop,1\n168,515,6029543,PROCESS_OF,C0678108,Sterility,patf,1,C0205653,Adolescent,humn,1\n169,454,13219190,PROCESS_OF,C0026764,Multiple Myeloma,neop,1,C0030705,Patients,humn,0\n170,439,12983060,PART_OF,C0040426,Tooth structure,bpoc,1,C0020114,Human,humn,1\n171,376,13502774,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0005682,Bladder,bpoc,1\n172,478,13292662,USES,C0087111,Therapeutic procedure,topp,0,C0282223,Lucanthone Hydrochloride,phsu,1\n173,549,4304789,PART_OF,C1334603,Malignant Mixed Mesodermal (Mullerian) Tumor,neop,1,C0042149,Uterus,bpoc,1\n174,467,12312852,PART_OF,C0042149,Uterus,bpoc,1,C0025914,House mice,mamm,1\n175,567,13155024,PROCESS_OF,C0003811,cardiac arrhythmia,patf,1,C0008059,Child,humn,1\n176,543,14774047,LOCATION_OF,C0014876,Esophagus,bpoc,1,C0243066,Atresia,cgab,1\n177,462,12255545,PROCESS_OF,C0006147,Breast Feeding,orgf,1,C0026591,Mothers,humn,1\n178,478,13292662,USES,C0087111,Therapeutic procedure,topp,0,C0301349,Sodium antimonyl gluconate,phsu,1\n179,376,13502774,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0023078,Larynx,bpoc,1\n180,560,14150908,PART_OF,C0025500,Mesothelioma,neop,1,C0032225,Pleura,bpoc,1\n181,467,12312852,CAUSES,C0014939,Estrogens,horm,1,C0027651,Neoplasm,neop,1\n182,567,13155024,PROCESS_OF,C0003811,cardiac arrhythmia,patf,1,C0021270,Infant,humn,1\n183,551,15394662,COEXISTS_WITH,C0015967,Fever,fndg,1,C0023891,\"Liver Cirrhosis, Alcoholic\",dsyn,1\n184,610,12304881,AFFECTS,C0019932,Hormones,horm,1,C1513094,Melanogenesis,moft,1\n185,512,5337389,PROCESS_OF,C0035203,Respiration,phsf,1,C0007450,Felis catus,mamm,1\n186,477,13789574,PROCESS_OF,C0003808,Arousal,menp,1,C0037877,Susliks,mamm,1\n187,612,14216908,COEXISTS_WITH,C0003892,Neurogenic arthropathy,dsyn,1,C0039144,Syringomyelia,dsyn,1\n188,467,12312852,PART_OF,C0027651,Neoplasm,neop,1,C0042149,Uterus,bpoc,1\n189,575,13997696,LOCATION_OF,C0734952,Wall of intestine,bpoc,1,C0025424,Mercury,elii,1\n190,376,13502774,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0024109,Lung,bpoc,1\n191,594,13737739,PROCESS_OF,C0013395,Dyspepsia,dsyn,1,C0021270,Infant,humn,1\n192,611,14877283,LOCATION_OF,C0003584,Apocrine Glands,bpoc,1,C0012634,Disease,dsyn,0\n193,581,12275695,PRECEDES,C0589113,Bilateral vasectomy,topp,1,C0332853,Anastomosis,acab,1\n194,612,14216908,ISA,C0003892,Neurogenic arthropathy,dsyn,1,C0263661,Disorder of skeletal system,dsyn,1\n195,570,14806329,LOCATION_OF,C0024109,Lung,bpoc,1,C0013421,Dystonia,sosy,1\n196,594,13737739,PROCESS_OF,C0029877,Otitis,dsyn,1,C0021270,Infant,humn,1\n197,376,13502774,PART_OF,C0006826,Malignant Neoplasms,neop,0,C1522730,CNS (MMHCC),tisu,1\n198,636,12332362,PART_OF,C0015965,Fetus,emst,1,C0020114,Human,humn,1\n199,474,14268252,LOCATION_OF,C0042606,Vestibule,bsoj,1,C0001969,Alcoholic Intoxication,mobd,1\n200,546,13189559,TREATS,C0042402,Vasodilator Agents,phsu,1,C0023223,Leg Ulcer,dsyn,1\n201,538,5659342,PART_OF,C0021853,Intestines,bpoc,1,C0034693,Rattus norvegicus,mamm,1\n202,584,14055632,PART_OF,C0031678,Phosphoric Monoester Hydrolases,aapp,1,C0227308,Jejunal mucous membrane,bpoc,1\n203,530,14185247,PROCESS_OF,C0015672,Fatigue,sosy,1,C0020114,Human,humn,1\n204,658,13347199,LOCATION_OF,C0014876,Esophagus,bpoc,1,C0006826,Malignant Neoplasms,neop,0\n205,662,14812408,TREATS,C0013804,Electrocoagulation,topp,1,C0263316,Pemphigus vegetans,dsyn,1\n206,404,5698836,PART_OF,C0737240,Somatic cell,cell,1,C0025914,House mice,mamm,1\n207,687,13292663,COEXISTS_WITH,C0018926,Hematemesis,patf,1,C0036330,Schistosoma mansonii infection,dsyn,1\n208,612,14216908,COEXISTS_WITH,C0263661,Disorder of skeletal system,dsyn,1,C0039144,Syringomyelia,dsyn,1\n209,581,12275695,LOCATION_OF,C1280344,Entire vas deferens,bpoc,1,C0332853,Anastomosis,acab,1\n210,482,4959380,LOCATION_OF,C0026927,Atypical Mycobacteria,bact,1,C0014964,Ethambutol,orch,1\n211,648,13930376,LOCATION_OF,C0022646,Kidney,bpoc,1,C0549453,Traumatic hematoma,inpo,1\n212,626,13384313,USES,C0013819,Electroencephalography,diap,1,C0004745,Barbiturates,phsu,1\n213,530,14185247,compared_with,C0053284,benzquinamide,orch,1,C0030883,Pentobarbital,orch,1\n214,621,12279177,PROCESS_OF,C0006142,Malignant neoplasm of breast,neop,1,C0034716,\"Rats, Wistar\",mamm,1\n215,404,5698836,COEXISTS_WITH,C0020687,Hypoxanthine Phosphoribosyltransferase,aapp,1,C0002583,Aminopterin,hops,1\n216,705,14847743,COEXISTS_WITH,C0012242,Digestive System Disorders,dsyn,0,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n217,724,5776110,LOCATION_OF,C0227391,Sigmoid colon,bpoc,1,C0032962,Pregnancy Complications,dsyn,1\n218,508,13867927,ASSOCIATED_WITH,C0005885,Body Composition,orga,1,C0028754,Obesity,dsyn,1\n219,658,13347199,LOCATION_OF,C0014876,Esophagus,bpoc,1,C0267085,Acquired supradiaphragmatic diverticulum of esophagus,acab,1\n220,588,12332367,LOCATION_OF,C1280344,Entire vas deferens,bpoc,1,C0332853,Anastomosis,acab,1\n221,474,14268252,AFFECTS,C0683208,oculomotor function,ortf,1,C0001969,Alcoholic Intoxication,mobd,1\n222,735,14934093,TREATS,C0700993,Resochin,phsu,1,C0024530,Malaria,dsyn,1\n223,725,5729809,PROCESS_OF,C0002871,Anemia,dsyn,1,C1265425,Hookworms,invt,1\n224,404,5698836,COEXISTS_WITH,C0020687,Hypoxanthine Phosphoribosyltransferase,aapp,1,C0020684,Hypoxanthine,bacs,1\n225,647,5933795,TREATS,C0001962,Ethanol,phsu,1,C0012984,Canis familiaris,mamm,1\n226,638,6065071,LOCATION_OF,C1281591,Entire face,bpoc,1,C0038561,Submersion,inpo,1\n227,626,13384313,USES,C0013819,Electroencephalography,diap,1,C0600062,Largactil,phsu,1\n228,633,14386674,LOCATION_OF,C0031066,Anogenital region,blor,1,C0043250,Injury wounds,inpo,1\n229,694,4961611,USES,C1510438,Assay,lbpr,1,C0040160,Thyrotropin,aapp,1\n230,482,4959380,LOCATION_OF,C0026927,Atypical Mycobacteria,bact,1,C0015021,Ethionamide,orch,1\n231,661,4865111,PART_OF,C0030274,Pancreas,bpoc,1,C0021270,Infant,humn,1\n232,617,14327662,PART_OF,C0021968,Iodine,bacs,1,C0007452,Cattle,mamm,1\n233,674,14457924,LOCATION_OF,C0015392,Eye,bpoc,1,C0043254,\"Wounds, Penetrating\",inpo,1\n234,647,5933795,TREATS,C0020268,Hydrocortisone,horm,1,C0012984,Canis familiaris,mamm,1\n235,733,16691885,PART_OF,C0027651,Neoplasm,neop,1,C0029130,Optic Nerve,bpoc,1\n236,404,5698836,COEXISTS_WITH,C0020687,Hypoxanthine Phosphoribosyltransferase,aapp,1,C0040077,Thymidine,bacs,1\n237,626,13384313,compared_with,C0600062,Largactil,orch,1,C0004745,Barbiturates,orch,1\n238,732,14251360,PROCESS_OF,C0597198,Performance,inbe,1,C0260267,School child,humn,1\n239,750,13189560,PROCESS_OF,C0011615,\"Dermatitis, Atopic\",dsyn,1,C0085979,Cavia,mamm,1\n240,789,13209178,TREATS,C0001632,Adrenalectomy,topp,1,C0006142,Malignant neoplasm of breast,neop,1\n241,699,15394663,ISA,C0025830,Methylthiouracil,nnon,1,C0040125,Antithyroid Agents,horm,1\n242,754,14055633,PART_OF,C0334108,Multiple polyps,neop,1,C0009368,Colon,bpoc,1\n243,674,14457924,PROCESS_OF,C0043254,\"Wounds, Penetrating\",inpo,1,C0008059,Child,humn,1\n244,721,6029544,PROCESS_OF,C1160618,molting cycle,orgf,1,C0023047,Larva,invt,1\n245,745,14087167,ISA,C0020114,Human,grup,1,C0029235,Organism,orgm,0\n246,482,4959380,TREATS,C0014964,Ethambutol,phsu,1,C0030705,Patients,podg,0\n247,734,14420386,ASSOCIATED_WITH,C0014563,Epinephrine,horm,1,C0020672,\"hypothermia, natural\",sosy,1\n248,696,5337390,PROCESS_OF,C0035203,Respiration,phsf,1,C0007450,Felis catus,mamm,1\n249,741,13737741,LOCATION_OF,C0025474,Mesentery,blor,1,C0497156,Enlargement of lymph nodes,fndg,1\n250,617,14327662,INTERACTS_WITH,C0001128,Acids,chem,1,C0021968,Iodine,bacs,1\n251,733,16691885,PART_OF,C0027651,Neoplasm,neop,1,C0035298,Retina,bpoc,1\n252,482,4959380,TREATS,C0015021,Ethionamide,phsu,1,C0030705,Patients,podg,0\n253,757,20241532,LOCATION_OF,C0205054,Hepatic,blor,1,C0009368,Colon,bpoc,1\n254,670,16691650,PART_OF,C0023317,\"Lens, Crystalline\",bpoc,1,C0015392,Eye,bpoc,1\n255,715,4974223,PART_OF,C0006104,Brain,bpoc,1,C0033147,Primates,mamm,1\n256,759,13100900,PART_OF,C0677930,Primary Neoplasm,neop,1,C0013303,Duodenum,bpoc,1\n257,741,13737741,PROCESS_OF,C0497156,Enlargement of lymph nodes,fndg,1,C0001675,Adult,humn,1\n258,762,13292664,ISA,C0012518,Dipetalonema perstans,invt,1,C0012516,Dipetalonema,invt,1\n259,757,20241532,PART_OF,C0007097,Carcinoma,neop,1,C0009368,Colon,bpoc,1\n260,617,14327662,INTERACTS_WITH,C0040165,Thyroxine,aapp,1,C0021968,Iodine,bacs,1\n261,670,16691650,LOCATION_OF,C0023317,\"Lens, Crystalline\",bpoc,1,C0016658,Fracture,inpo,1\n262,740,13738552,PART_OF,C0018787,Heart,bpoc,1,C0003459,Anura,amph,1\n263,786,13431637,TREATS,C0040071,Thymectomy,topp,1,C0026896,Myasthenia Gravis,dsyn,1\n264,819,12305503,TREATS,C0014942,Estrone,horm,1,C0006826,Malignant Neoplasms,neop,0\n265,715,4974223,LOCATION_OF,C0035804,Rodent,mamm,1,C0008429,Cholinesterases,aapp,1\n266,839,14150911,CAUSES,C0241669,Venous occlusion,patf,1,C0238261,Lymphedema praecox,dsyn,1\n267,740,13738552,LOCATION_OF,C0018787,Heart,bpoc,1,C0001041,Acetylcholine,orch,1\n268,778,13867928,PROCESS_OF,C0038435,Stress,fndg,1,C0021294,\"Infant, Premature\",humn,1\n269,749,5659343,PROCESS_OF,C0232750,Bile formation,ortf,1,C0085979,Cavia,mamm,1\n270,843,5933796,LOCATION_OF,C0459313,Left recurrent laryngeal nerve,bpoc,1,C0522224,Paralysed,fndg,1\n271,814,6065072,LOCATION_OF,C0011980,Diaphragm (Anatomy),bpoc,1,C0013839,Electromyography,diap,1\n272,819,12305503,TREATS,C0014942,Estrone,horm,1,C0034693,Rattus norvegicus,mamm,1\n273,847,14216910,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0024109,Lung,bpoc,1\n274,775,13026427,LOCATION_OF,C0332915,Congenital failure of fusion,cgab,1,C0039082,Syndrome,dsyn,0\n275,821,12336694,PROCESS_OF,C0011175,Dehydration,dsyn,1,C0021270,Infant,humn,1\n276,868,12275532,PRECEDES,C0042387,Vasectomy,topp,1,C0524865,Reconstructive Surgical Procedures,topp,1\n277,809,13997701,DIAGNOSES,C0040395,tomography,diap,1,C0543829,Clinical pneumonia,dsyn,1\n278,896,14880778,PART_OF,C0025202,melanoma,neop,1,C0028429,Nose,bpoc,1\n279,866,14055634,LOCATION_OF,C0016976,Gallbladder,bpoc,1,C0332907,Congenital absence,cgab,1\n280,819,12305503,PROCESS_OF,C0006826,Malignant Neoplasms,neop,0,C0034693,Rattus norvegicus,mamm,1\n281,875,13685015,PART_OF,C1280536,Entire placental membrane,emst,1,C0020114,Human,humn,1\n282,881,13155029,LOCATION_OF,C0021853,Intestines,bpoc,1,C0221198,Lesion,fndg,1\n283,870,13582804,LOCATION_OF,C0017421,Female genitalia,bpoc,1,C0013502,Echinococcosis,dsyn,1\n284,900,5988837,ASSOCIATED_WITH,C0037473,Sodium,bacs,1,C0018801,Heart failure,dsyn,1\n286,905,13219279,LOCATION_OF,C0037004,Shoulder,bpoc,1,C0158300,Adhesive Capsulitis,dsyn,1\n287,866,14055634,LOCATION_OF,C1280323,Entire cystic duct,bpoc,1,C0332907,Congenital absence,cgab,1\n288,879,14877286,TREATS,C0358490,Procaine hydrochloride,phsu,1,C0033774,Pruritus,sosy,1\n289,787,5214757,PREVENTS,C0185125,Application procedure,hlca,1,C0333519,Caries,dsyn,1\n290,875,13685015,LOCATION_OF,C1280536,Entire placental membrane,emst,1,C0030016,Oxidoreductase,aapp,1\n291,902,12255392,ASSOCIATED_WITH,C0028360,Norethynodrel,horm,1,C0040038,Thromboembolism,patf,1\n292,872,13551183,LOCATION_OF,C0022646,Kidney,bpoc,1,C0522562,Multilocular cyst,acab,1\n293,871,13464036,PROCESS_OF,C0241863,Diabetic,fndg,1,C0043210,Woman,humn,1\n294,881,13155029,PROCESS_OF,C0221198,Lesion,fndg,1,C0021289,\"Infant, Newborn\",humn,1\n295,855,13638652,TREATS,C0042313,Vancomycin,antb,1,C0038160,Staphylococcal Infections,dsyn,1\n296,890,5876096,PROCESS_OF,C0234222,Baresthesia,ortf,1,C0007450,Felis catus,mamm,1\n297,806,12983061,LOCATION_OF,C0026724,Mucous Membrane,tisu,1,C0012634,Disease,dsyn,0\n298,854,14782737,ASSOCIATED_WITH,C0010137,Cortisone,horm,1,C0021311,Infection,dsyn,0\n299,855,13638652,PROCESS_OF,C0038160,Staphylococcal Infections,dsyn,1,C0030705,Patients,humn,0\n300,822,14806332,TREATS,C0002696,Ampyrone,phsu,1,C0162323,Polyarthritis,dsyn,1\n301,878,14457926,PART_OF,C0007634,Cells,cell,1,C0003483,Aorta,bpoc,1\n302,920,14771461,LOCATION_OF,C0021853,Intestines,bpoc,1,C0030499,Parasitic Diseases,dsyn,1\n303,903,13737742,PROCESS_OF,C0743336,E COLI BACTEREMIA,dsyn,1,C0034493,Oryctolagus cuniculus,mamm,1\n304,933,16691887,PART_OF,C1261473,sarcoma,neop,1,C1278891,Entire iris,bpoc,1\n305,864,14087168,TREATS,C0038913,Urologic Surgical Procedures,topp,1,C0008059,Child,aggp,1\n306,943,5333709,ISA,C0026652,Moxibustion,topp,1,C0087111,Therapeutic procedure,topp,0\n307,936,13070175,PART_OF,C0001625,Adrenal Glands,bpoc,1,C0019944,Equus caballus,mamm,1\n308,806,12983061,LOCATION_OF,C1519551,Tooth Tissue,tisu,1,C0012634,Disease,dsyn,0\n309,964,12338435,COEXISTS_WITH,C0029965,Ovulation,ortf,1,C0006147,Breast Feeding,orgf,1\n310,914,13292665,PROCESS_OF,C0858318,Plasmodium falciparum infection,dsyn,1,C0322918,Anopheles quadrimaculatus,invt,1\n311,855,13638652,TREATS,C0042313,Vancomycin,antb,1,C0030705,Patients,podg,0\n313,878,14457926,PART_OF,C0007634,Cells,cell,1,C0027061,Myocardium,tisu,1\n314,920,14771461,PROCESS_OF,C0030499,Parasitic Diseases,dsyn,1,C0008059,Child,humn,1\n315,971,12255278,TREATS,C0520483,Tubal Ligation,topp,1,C0043210,Woman,popg,1\n316,895,4966828,NEG_INHIBITS,C0020366,Hydroxylysine,aapp,1,C0023689,Ligase,aapp,1\n317,898,14268254,LOCATION_OF,C0023078,Larynx,bpoc,1,C0040395,tomography,diap,1\n318,806,12983061,PROCESS_OF,C0012634,Disease,dsyn,0,C0920541,Guamanian,humn,1\n319,864,14087168,TREATS,C0038913,Urologic Surgical Procedures,topp,1,C0021270,Infant,aggp,1\n320,888,13930378,LOCATION_OF,C0016129,Fingers,blor,1,C1609508,Ligamentitis,dsyn,1\n321,936,13070175,PART_OF,C0001625,Adrenal Glands,bpoc,1,C0242372,Hares,mamm,1\n322,961,5305917,LOCATION_OF,C0019994,Hospitals,hcro,1,C0008972,Clinical Research,resa,1\n323,922,20241533,USES,C1292856,Stimulation procedure,topp,1,C0017725,Glucose,carb,1\n324,966,14216911,COEXISTS_WITH,C0153690,Secondary malignant neoplasm of bone,neop,1,C0006142,Malignant neoplasm of breast,neop,1\n325,878,14457926,AFFECTS,C0028040,Nicotine,hops,1,C0007634,Cells,cell,1\n326,946,15394665,TREATS,C0038425,Streptomycin,antb,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n327,913,16016715,ISA,C0015272,Exhibits,mnob,1,C0520510,Materials,sbst,1\n328,989,5988838,ASSOCIATED_WITH,C0032821,Potassium,bacs,1,C0018801,Heart failure,dsyn,1\n329,888,13930378,LOCATION_OF,C0018563,Hand,bpoc,1,C1609508,Ligamentitis,dsyn,1\n330,895,4966828,NEG_INHIBITS,C0024337,Lysine,aapp,1,C0023689,Ligase,aapp,1\n331,980,13789584,DIAGNOSES,C0019635,Histocytochemistry,lbpr,1,C0033860,Psoriasis,dsyn,1\n332,932,13297204,PART_OF,C0014876,Esophagus,bpoc,1,C0020114,Human,humn,1\n333,944,14150912,PROCESS_OF,C0002895,Sickle Cell Anemia,dsyn,1,C0008059,Child,humn,1\n334,947,5659344,LOCATION_OF,C0034693,Rattus norvegicus,mamm,1,C0003695,Arachidonic Acid,eico,1\n335,1017,12332147,METHOD_OF,C0007471,Cauterization - action,topp,1,C0015787,Female Sterilization,topp,1\n336,921,16691651,PART_OF,C0010031,Cornea,bpoc,1,C1278891,Entire iris,bpoc,1\n337,1030,16691888,PART_OF,C1261473,sarcoma,neop,1,C1278891,Entire iris,bpoc,1\n338,944,14150912,PROCESS_OF,C0002895,Sickle Cell Anemia,dsyn,1,C0238598,Young adult,humn,1\n339,980,13789584,TREATS,C0040864,Triamcinolone,phsu,1,C0033860,Psoriasis,dsyn,1\n340,910,12312852,COEXISTS_WITH,C0012203,Diethylstilbestrol,hops,1,C0028908,Oils,lipd,1\n341,932,13297204,LOCATION_OF,C0014876,Esophagus,bpoc,1,C0450432,Venous anastomosis,bsoj,1\n342,1042,13100904,USES,C0008327,Cholecystography,diap,1,C0795742,Telepaque,irda,1\n343,1009,5876097,CAUSES,C0441693,Hypothalamic stimulation,diap,1,C0748430,RIGHT VENTRICULAR HYPERTENSION,dsyn,1\n344,1020,14782738,TREATS,C1441129,Radioactive Iodine,hops,1,C0020550,Hyperthyroidism,dsyn,1\n345,856,5698836,ADMINISTERED_TO,C0040078,Thymidine Kinase,enzy,1,C0680022,member,humn,1\n346,921,16691651,PART_OF,C1304649,Tissue fiber,tisu,1,C1278891,Entire iris,bpoc,1\n347,986,20285250,LOCATION_OF,C0022417,Joints,bsoj,1,C0041296,Tuberculosis,dsyn,1\n348,991,13347203,CAUSES,C0600062,Largactil,orch,1,C0022346,Icterus,patf,1\n349,970,13997703,LOCATION_OF,C0023884,Liver,bpoc,1,C0017911,Glycogen,bacs,1\n350,992,14847745,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0227389,Descending colon,bpoc,1\n351,1024,13372584,USES,C0087111,Therapeutic procedure,topp,0,C0030054,Oxygen,phsu,1\n352,887,13502776,PART_OF,C0007634,Cells,cell,1,C0025914,House mice,mamm,1\n353,976,14880779,LOCATION_OF,C0030471,Sinus,bsoj,1,C0029443,Osteomyelitis,dsyn,1\n354,1031,14439961,PROCESS_OF,C0001811,Aging,orgf,1,C0870668,Hospitalized Patients,humn,1\n355,1012,13551184,PART_OF,C0023267,Fibroid Tumor,neop,1,C1280340,Entire transverse mesocolon,bpoc,1\n356,1056,5255106,PART_OF,C0029463,osteosarcoma,neop,1,C0009780,Connective Tissue,tisu,1\n357,1009,5876097,PROCESS_OF,C0748430,RIGHT VENTRICULAR HYPERTENSION,dsyn,1,C0007450,Felis catus,mamm,1\n358,856,5698836,PART_OF,C0008643,\"Chromosomes, Human\",celc,1,C0025914,House mice,mamm,1\n359,986,20285250,ISA,C0041296,Tuberculosis,dsyn,1,C0012634,Disease,dsyn,0\n360,970,13997703,LOCATION_OF,C0023884,Liver,bpoc,1,C0023779,Lipids,lipd,1\n361,1024,13372584,COEXISTS_WITH,C0028682,Care given by nurses,hlca,1,C0087111,Therapeutic procedure,topp,0\n362,976,14880779,LOCATION_OF,C0037303,Bone structure of cranium,bpoc,1,C0029443,Osteomyelitis,dsyn,1\n363,986,20285250,LOCATION_OF,C0262950,Skeletal bone,bpoc,1,C0041296,Tuberculosis,dsyn,1\n364,928,11526826,AFFECTS,C0023882,Little's Disease,dsyn,1,C0025251,Membrane Potentials,celf,1\n365,1043,13292666,ISA,C0026584,Culicidae,invt,1,C0322918,Anopheles quadrimaculatus,invt,1\n366,1033,5933797,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0003461,Anus,bpoc,1\n367,1047,13384315,AFFECTS,C0013819,Electroencephalography,diap,1,C0004936,Mental disorders,mobd,0\n368,1041,13638653,PROCESS_OF,C0039614,Tetanus,dsyn,1,C0443307,Plant spore,plnt,1\n369,986,20285250,LOCATION_OF,C0022417,Joints,bsoj,1,C0012634,Disease,dsyn,0\n370,1106,13100905,PART_OF,C0001430,adenoma,neop,1,C0032005,Pituitary Gland,bpoc,1\n371,1070,13209181,LOCATION_OF,C0003483,Aorta,bpoc,1,C0332886,Coarctation,anab,1\n372,1051,14771462,PROCESS_OF,C0041227,Trypanosomiasis,dsyn,1,C0020114,Human,humn,1\n373,1032,14327664,PART_OF,C0023607,Luteinizing Hormone,aapp,1,C0007452,Cattle,mamm,1\n374,1043,13292666,ISA,C0322918,Anopheles quadrimaculatus,invt,1,C0026584,Culicidae,invt,1\n375,1077,15394666,OCCURS_IN,C0011053,Deafness,dsyn,1,C0027362,Human Age Group,aggp,0\n376,1033,5933797,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0009368,Colon,bpoc,1\n377,1063,13670511,LOCATION_OF,C1278997,Entire scalp,bpoc,1,C0263442,Acne conglobata,dsyn,1\n378,973,12255649,PART_OF,C0014180,Endometrium,bpoc,1,C0020114,Human,humn,1\n379,1015,4176301,LOCATION_OF,C0229671,Serum,bdsu,1,C0021027,Immunoglobulins,aapp,1\n380,986,20285250,LOCATION_OF,C0262950,Skeletal bone,bpoc,1,C0012634,Disease,dsyn,0\n381,1070,13209181,LOCATION_OF,C0003483,Aorta,bpoc,1,C0497428,Question of pregnancy,fndg,1\n382,1072,14457928,TREATS,C0001617,Adrenal Cortex Hormones,horm,1,C0543974,Mucocutaneous ocular syndrome,dsyn,1\n383,1083,14770453,PROCESS_OF,C0003873,Rheumatoid Arthritis,dsyn,1,C0008059,Child,humn,1\n384,1033,5933797,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0034896,Rectum,bpoc,1\n385,1015,4176301,DIAGNOSES,C0231790,Thompson's test,diap,1,C0005830,Blood Protein Disorders,dsyn,1\n386,1083,14770453,PROCESS_OF,C0242154,Poisoning by vitamin D,inpo,1,C0008059,Child,humn,1\n387,1102,13789585,LOCATION_OF,C0521421,Entire ear,bpoc,1,C0039082,Syndrome,dsyn,0\n388,1147,10976199,PROCESS_OF,C0232976,Spermiogenesis,celf,1,C0524678,Lumbricus terrestris,invt,1\n389,1079,5988839,ASSOCIATED_WITH,C0014653,Equilibrium,orgf,1,C0018801,Heart failure,dsyn,1\n390,1095,5776114,ISA,C0012203,Diethylstilbestrol,hops,1,C0087111,Therapeutic procedure,topp,0\n391,1097,13974559,LOCATION_OF,C0728985,Cervical spine,bpoc,1,C0221198,Lesion,fndg,1\n392,1109,13685020,PROCESS_OF,C0042963,Vomiting,sosy,1,C0021270,Infant,humn,1\n393,1086,5659345,PROCESS_OF,C0221102,Excretory function,phsf,1,C0034693,Rattus norvegicus,mamm,1\n394,1104,12305404,ASSOCIATED_WITH,C0033308,Progesterone,horm,1,C0877373,Advanced cancer,neop,1\n395,1117,16691889,LOCATION_OF,C0230057,Orbital margin,bsoj,1,C0029463,osteosarcoma,neop,1\n396,1132,14847746,LOCATION_OF,C0022646,Kidney,bpoc,1,C0221198,Lesion,fndg,1\n397,1130,13551185,LOCATION_OF,C0014876,Esophagus,bpoc,1,C0243066,Atresia,cgab,1\n398,1078,12307964,LOCATION_OF,C0024400,Macaca mulatta,mamm,1,C0014939,Estrogens,strd,1\n399,1189,13670512,LOCATION_OF,C1278891,Entire iris,bpoc,1,C0009363,Coloboma,cgab,1\n400,1105,14386677,USES,C0021493,\"Injections, Intraperitoneal\",topp,1,C0030842,Penicillins,antb,1\n401,1061,5858957,PART_OF,C1517186,Filament,celc,1,C0002028,Algae,alga,1\n402,1095,5776114,TREATS,C0012203,Diethylstilbestrol,hops,1,C0014175,\"Endometriosis, site unspecified\",dsyn,1\n403,1198,14877290,TREATS,C0010137,Cortisone,horm,1,C0011606,\"Dermatitis, Exfoliative\",dsyn,1\n404,1193,15394667,USES,C0087111,Therapeutic procedure,topp,0,C0012799,Mercurial diuretic,phsu,1\n405,1113,13466835,PROCESS_OF,C0002875,Cooley's anemia,dsyn,1,C0008059,Child,humn,1\n406,1104,12305404,ASSOCIATED_WITH,C0167626,estradiol 3-benzoate,horm,1,C0877373,Advanced cancer,neop,1\n407,1205,14880781,LOCATION_OF,C0016734,frontal sinus,bsoj,1,C0206640,\"Fibroma, Ossifying\",neop,1\n408,1165,4869506,LOCATION_OF,C0445623,Microorganism,orgm,0,C0142281,Siderophores,orch,1\n409,1208,14770454,LOCATION_OF,C0030274,Pancreas,bpoc,1,C0221198,Lesion,fndg,1\n410,1195,13209182,COEXISTS_WITH,C0017086,Gangrene,dsyn,1,C0023434,Chronic Lymphocytic Leukemia,neop,1\n411,1152,13737748,PROCESS_OF,C0022680,Polycystic Kidney Diseases,dsyn,1,C0030705,Patients,humn,0\n412,1155,14087170,PART_OF,C0021853,Intestines,bpoc,1,C0005682,Bladder,bpoc,1\n413,1190,12233291,TREATS,C0857127,Induction,topp,1,C0001675,Adult,aggp,1\n414,1211,13789586,LOCATION_OF,C0521421,Entire ear,bpoc,1,C0175677,Injury,inpo,1\n415,1105,14386677,TREATS,C0030842,Penicillins,antb,1,C0031154,Peritonitis,dsyn,1\n416,1095,5776114,USES,C0087111,Therapeutic procedure,topp,0,C0012203,Diethylstilbestrol,phsu,1\n417,1113,13466835,LOCATION_OF,C0008059,Child,humn,1,C0003242,\"Antibodies, Anti-Idiotypic\",aapp,1\n418,1150,13347205,TREATS,C0001712,Aerosols,chvs,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n419,1219,14055638,PART_OF,C0001418,Adenocarcinoma,neop,1,C0009368,Colon,bpoc,1\n420,1211,13789586,PROCESS_OF,C0175677,Injury,inpo,1,C0403082,Diver,humn,1\n421,1085,14185253,COEXISTS_WITH,C0016412,Folic Acid Deficiency,dsyn,1,C0238644,anemia; profound,dsyn,1\n422,1155,14087170,PROCESS_OF,C0020564,Hypertrophy,patf,1,C0008059,Child,humn,1\n423,1202,5933798,PART_OF,C0007097,Carcinoma,neop,1,C0021851,Large Intestine,bpoc,1\n424,1170,16691653,USES,C0005971,Bone plates,medd,1,C0017596,Glass,mnob,1\n425,1292,14934100,PROCESS_OF,C0162429,Malnutrition,dsyn,1,C0008059,Child,humn,1\n426,1197,14782740,NEG_ADMINISTERED_TO,C0087111,Therapeutic procedure,topp,0,C0030705,Patients,humn,0\n427,1279,13502777,LOCATION_OF,C0002084,Structure of allantois,emst,1,C0086943,Rous sarcoma virus,virs,1\n428,1185,5914350,CAUSES,C0038379,Strabismus,dsyn,1,C0012569,Diplopia,dsyn,1\n429,1290,15394668,LOCATION_OF,C0021852,\"Intestines, Small\",bpoc,1,C0243066,Atresia,cgab,1\n430,1209,12332461,ASSOCIATED_WITH,C0065879,Megestrol Acetate,horm,1,C0017411,\"Genital Diseases, Female\",dsyn,1\n431,1287,14877291,USES,C0087111,Therapeutic procedure,topp,0,C0262967,Dihydrostreptomycin,antb,1\n432,1294,14770455,PART_OF,C1261473,sarcoma,neop,1,C0023884,Liver,bpoc,1\n433,1224,12334391,METHOD_OF,C1441717,RAPID TEST,lbpr,1,C1511790,Detection,topp,1\n434,1301,12259097,PART_OF,C0027651,Neoplasm,neop,1,C0032005,Pituitary Gland,bpoc,1\n435,1221,12312852,ISA,C0014939,Estrogens,horm,1,C0087111,Therapeutic procedure,topp,0\n436,1313,13551187,LOCATION_OF,C0037993,Spleen,bpoc,1,C0013502,Echinococcosis,dsyn,1\n437,1279,13502777,PART_OF,C0002084,Structure of allantois,emst,1,C0008046,Chick Embryo,emst,1\n438,1185,5914350,PROCESS_OF,C0012569,Diplopia,dsyn,1,C0001675,Adult,humn,1\n439,1270,5659346,INTERACTS_WITH,C0038187,Starvation,sosy,1,C0486616,Composition,clna,1\n440,1245,13974560,ASSOCIATED_WITH,C0005802,Blood Glucose,carb,1,C0394017,Alcoholic coma,patf,1\n441,1273,13638655,ASSOCIATED_WITH,C0085732,Ability,orga,1,C0022658,Kidney Diseases,dsyn,1\n442,1185,5914350,PROCESS_OF,C0012569,Diplopia,dsyn,1,C0205653,Adolescent,humn,1\n443,1301,12259097,CAUSES,C0720298,Estrogenic,horm,1,C0027651,Neoplasm,neop,1\n444,1221,12312852,USES,C0087111,Therapeutic procedure,topp,0,C0014939,Estrogens,phsu,1\n445,1253,16691890,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0008520,Choroid,bpoc,1\n446,1320,13347206,CAUSES,C0221386,Idiopathic hilar fibrosis,dsyn,1,C0039082,Syndrome,dsyn,0\n447,1221,12312852,PROCESS_OF,C0042138,Uterine Neoplasms,neop,1,C0026809,Mus,mamm,1\n448,1355,14185255,ISA,C0998427,Tribolium castaneum,invt,1,C0021585,Insecta,invt,1\n449,1235,5988840,ASSOCIATED_WITH,C0037494,Sodium Chloride,bacs,1,C0018801,Heart failure,dsyn,1\n450,1253,16691890,ISA,C0006826,Malignant Neoplasms,neop,0,C0027651,Neoplasm,neop,1\n451,1315,13789588,AFFECTS,C0017725,Glucose,bacs,1,C1158840,acetate metabolism,moft,1\n452,1282,13997705,ASSOCIATED_WITH,C0023823,Low-Density Lipoproteins,aapp,1,C0004153,Atherosclerosis,dsyn,1\n453,1234,10976199,COEXISTS_WITH,C0029385,Osmium Tetroxide,hops,1,C0052301,araldite,orch,1\n454,1321,5274921,LOCATION_OF,C0026367,Molar tooth,bpoc,1,C0549099,Perforation (observation),fndg,1\n455,1271,13670513,ADMINISTERED_TO,C0162476,Anatoxins,imft,1,C0019944,Equus caballus,mamm,1\n456,1253,16691890,PART_OF,C0027651,Neoplasm,neop,1,C0008520,Choroid,bpoc,1\n457,1282,13997705,PROCESS_OF,C0004153,Atherosclerosis,dsyn,1,C0034493,Oryctolagus cuniculus,mamm,1\n458,1236,4381579,LOCATION_OF,C0005767,Blood,tisu,1,C0019588,Histamine,orch,1\n459,1282,13997705,LOCATION_OF,C0229671,Serum,bdsu,1,C0023823,Low-Density Lipoproteins,aapp,1\n460,1317,13605273,PROCESS_OF,C0282607,Neoplasms in Vascular Tissue,neop,1,C0001675,Adult,humn,1\n461,1297,6029546,TREATS,C0038627,Succinylcholine,phsu,1,C0034493,Oryctolagus cuniculus,mamm,1\n462,1239,4966828,INTERACTS_WITH,C0020366,Hydroxylysine,aapp,1,C0024337,Lysine,aapp,1\n463,1347,13582811,METHOD_OF,C0199960,Transfusion - action,topp,1,C0199176,Prophylactic treatment,topp,1\n464,1441,13100911,PART_OF,C0027809,Neurilemmoma,neop,1,C0038351,Stomach,bpoc,1\n465,1377,5867990,LOCATION_OF,C0016504,Pes,bpoc,1,C0009081,Congenital clubfoot,cgab,1\n466,1381,13738561,CAUSES,C0018035,\"Gold, radioactive\",elii,1,C0009566,Complication,patf,0\n467,1367,14055639,LOCATION_OF,C0020026,\"Hospitals, State\",hcro,1,C0936012,Analysis,resa,1\n468,1428,5233223,LOCATION_OF,C1281562,Entire tooth,bpoc,1,C1289791,Plastic implant,medd,1\n469,1347,13582811,PROCESS_OF,C0272138,Erythroblastosis,dsyn,1,C0034493,Oryctolagus cuniculus,mamm,1\n470,1353,14934101,ASSOCIATED_WITH,C0027996,Nicotinic Acid,vita,1,C0011991,Diarrhea,sosy,1\n471,1406,13551188,LOCATION_OF,C0042425,Ampulla of Vater,bpoc,1,C0016542,Foreign Bodies,inpo,1\n472,1331,4171713,INTERACTS_WITH,C0005097,Benzpyrene,hops,1,C0020242,Hydrocarbons,orch,1\n473,1353,14934101,ASSOCIATED_WITH,C0027996,Nicotinic Acid,vita,1,C0027932,Neurotic Disorders,mobd,1\n474,1415,14880784,LOCATION_OF,C0005767,Blood,tisu,1,C0012634,Disease,dsyn,0\n475,1354,13464039,PROCESS_OF,C0241863,Diabetic,fndg,1,C0008059,Child,humn,1\n476,1427,12334491,PART_OF,C0027651,Neoplasm,neop,1,C0006141,Breast,bpoc,1\n477,1306,4162996,PROCESS_OF,C0003873,Rheumatoid Arthritis,dsyn,1,C0030705,Patients,humn,0\n478,1407,14877292,LOCATION_OF,C0229671,Serum,bdsu,1,C0023820,Lipoproteins,aapp,1\n479,1306,4162996,PART_OF,C0229671,Serum,bdsu,1,C0030705,Patients,humn,0\n480,1412,13867934,PART_OF,C0023884,Liver,bpoc,1,C0025914,House mice,mamm,1\n481,1354,13464039,PART_OF,C0030274,Pancreas,bpoc,1,C0008059,Child,humn,1\n482,1449,14770457,LOCATION_OF,C0036098,Salivary Glands,bpoc,1,C0275518,Acute infectious disease,dsyn,1\n483,1407,14877292,ASSOCIATED_WITH,C0023820,Lipoproteins,aapp,1,C0302314,Xanthoma,dsyn,1\n484,1434,12312852,PROCESS_OF,C0027651,Neoplasm,neop,1,C0026809,Mus,mamm,1\n485,1460,5776116,TREATS,C1511790,Detection,topp,1,C0152021,Congenital heart disease,dsyn,1\n486,1306,4162996,PART_OF,C0229671,Serum,bdsu,1,C0030705,Patients,humn,0\n487,1496,16691890,PART_OF,C1261473,sarcoma,neop,1,C0008520,Choroid,bpoc,1\n488,1394,12983065,LOCATION_OF,C0022122,Bone structure of ischium,bpoc,1,C1265664,Traumatic dislocation,inpo,1\n489,1397,5729812,TREATS,C0000163,17-Hydroxycorticosteroids,horm,1,C0034493,Oryctolagus cuniculus,mamm,1\n490,1306,4162996,LOCATION_OF,C0229671,Serum,bdsu,1,C0003242,\"Antibodies, Anti-Idiotypic\",aapp,1\n491,1460,5776116,PROCESS_OF,C0152021,Congenital heart disease,dsyn,1,C0008059,Child,humn,1\n492,1394,12983065,COEXISTS_WITH,C1265664,Traumatic dislocation,inpo,1,C0016658,Fracture,inpo,1\n493,1361,5339667,PART_OF,C0027651,Neoplasm,neop,1,C0015392,Eye,bpoc,1\n494,1511,14880785,PART_OF,C0086692,Benign Neoplasm,neop,0,C0014876,Esophagus,bpoc,1\n495,1402,13070180,METHOD_OF,C0260132,Flame photometry,lbpr,1,C0574032,Infusion procedures,topp,1\n496,1306,4162996,LOCATION_OF,C0229671,Serum,bdsu,1,C0003242,\"Antibodies, Anti-Idiotypic\",aapp,1\n497,1531,14847750,LOCATION_OF,C0009368,Colon,bpoc,1,C0012817,diverticulum,anab,1\n498,1394,12983065,LOCATION_OF,C0015811,Femur,bpoc,1,C0018670,Head,blor,1\n499,1472,5876098,LOCATION_OF,C0005767,Blood,tisu,1,C0019134,Heparin,carb,1\n500,1460,5776116,TREATS,C1511790,Detection,topp,1,C0008059,Child,aggp,1\n501,1361,5339667,PART_OF,C0034625,Radium,elii,1,C0015392,Eye,bpoc,1\n502,1310,13384317,USES,C0087111,Therapeutic procedure,topp,0,C0008286,Chlorpromazine,phsu,1\n503,1535,16691656,CAUSES,C0029385,Osmium Tetroxide,hops,1,C0002418,Amblyopia,dsyn,1\n504,1443,14268259,ISA,C1074887,Bufo stomaticus,amph,1,C0002668,Amphibia,amph,1\n505,1478,13974562,TREATS,C0041031,Trimeprazine,phsu,1,C0001957,Alcohol Withdrawal Delirium,dsyn,1\n506,1474,13997707,CAUSES,C0004611,Bacteria,bact,1,C0032285,Pneumonia,dsyn,1\n507,1419,4298172,LOCATION_OF,C0032105,Plasma,bdsu,1,C0003017,Angiotensinogen,aapp,1\n508,1491,13100912,PART_OF,C0006104,Brain,bpoc,1,C0020114,Human,humn,1\n509,1486,14386679,LOCATION_OF,C0230195,Linea alba,blor,1,C0019270,Hernia,anab,1\n510,1394,12983065,LOCATION_OF,C0018670,Head,blor,1,C0016658,Fracture,inpo,1\n511,1310,13384317,TREATS,C0087111,Therapeutic procedure,topp,0,C0013144,Drowsiness,sosy,1\n512,1491,13100912,LOCATION_OF,C0006104,Brain,bpoc,1,C0458360,Motor area,blor,1\n513,1475,20285299,PROCESS_OF,C0149781,Spontaneous pneumothorax NOS,dsyn,1,C0008059,Child,humn,1\n514,1424,13638656,PROCESS_OF,C0022658,Kidney Diseases,dsyn,1,C0030705,Patients,humn,0\n515,1491,13100912,LOCATION_OF,C0458360,Motor area,blor,1,C1280632,Entire trunk,bpoc,1\n516,1310,13384317,compared_with,C0087111,Therapeutic procedure,topp,0,C0087111,Therapeutic procedure,topp,0\n517,1534,13464040,PROCESS_OF,C0027059,Myocarditis,dsyn,1,C0023358,Leptospira,bact,1\n518,1424,13638656,PROCESS_OF,C0232827,Urinary concentration,ortf,1,C0030705,Patients,humn,0\n519,1541,14877293,COEXISTS_WITH,C0263367,Koebner phenomenon,dsyn,1,C0162849,Lichen Nitidus,dsyn,1\n520,1451,10976199,AFFECTS,C0007708,Centrioles,celc,1,C0026559,Morphogenesis,orgf,1\n521,1491,13100912,LOCATION_OF,C0458360,Motor area,blor,1,C1281592,Entire neck,bpoc,1\n522,1601,16691892,LOCATION_OF,C0009758,conjunctiva,bpoc,1,C0041296,Tuberculosis,dsyn,1\n523,1597,14934103,TREATS,C0038761,Sulfones,phsu,1,C0023343,Leprosy,dsyn,1\n524,1451,10976199,AFFECTS,C0007708,Centrioles,celc,1,C0029237,Physiologic Organization,phsf,1\n525,1468,14772458,LOCATION_OF,C0024109,Lung,bpoc,1,C0041321,\"Tuberculosis, Miliary\",dsyn,1\n526,1501,14185257,PROCESS_OF,C0221102,Excretory function,phsf,1,C0034693,Rattus norvegicus,mamm,1\n527,1545,13026597,LOCATION_OF,C0021853,Intestines,bpoc,1,C0012813,Diverticulitis,dsyn,0\n528,1497,13738563,PART_OF,C0230240,Falciform ligament,bpoc,1,C0023884,Liver,bpoc,1\n529,1468,14772458,PROCESS_OF,C0041321,\"Tuberculosis, Miliary\",dsyn,1,C0008059,Child,humn,1\n530,1506,13582812,CAUSES,C0036751,Serotonin,nsba,1,C0004096,Asthma,dsyn,1\n531,1545,13026597,LOCATION_OF,C0021853,Intestines,bpoc,1,C1510475,Diverticulosis,dsyn,1\n532,1572,13297211,LOCATION_OF,C0013303,Duodenum,bpoc,1,C0035955,Traumatic Rupture,inpo,1\n533,1553,5729813,ASSOCIATED_WITH,C0007412,Catecholamines,nsba,1,C1264527,Chronic poisoning,inpo,1\n534,1573,14216916,COEXISTS_WITH,C0031577,Phonation,ortf,1,C0035203,Respiration,phsf,1\n535,1590,13467017,PROCESS_OF,C0040921,Trichomonas Infections,dsyn,1,C0086582,Males,humn,1\n536,1514,13737754,CAUSES,C0026927,Atypical Mycobacteria,bact,1,C0021311,Infection,dsyn,0\n537,1552,5601121,TREATS,C0087111,Therapeutic procedure,topp,0,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n538,1574,13551190,TREATS,C0019144,Hepatectomy,topp,1,C0019204,Primary carcinoma of the liver cells,neop,1\n539,1510,13930394,PART_OF,C0178784,Organ,bpoc,1,C0034493,Oryctolagus cuniculus,mamm,1\n540,1553,5729813,PART_OF,C0007412,Catecholamines,nsba,1,C0027061,Myocardium,tisu,1\n541,1586,14847751,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0034896,Rectum,bpoc,1\n542,1596,5659347,LOCATION_OF,C0030518,Parathyroid gland,bpoc,1,C1565489,Renal Insufficiency,dsyn,1\n543,1604,13789593,COEXISTS_WITH,C0027051,Myocardial Infarction,dsyn,1,C0241863,Diabetic,fndg,1\n544,1635,5867991,PART_OF,C0032043,Placenta,emst,1,C0020114,Human,humn,1\n545,1669,13685032,PART_OF,C0007097,Carcinoma,neop,1,C0022646,Kidney,bpoc,1\n546,1599,14268260,PART_OF,C0007765,Cerebellum,bpoc,1,C0034693,Rattus norvegicus,mamm,1\n547,1542,12312852,PROCESS_OF,C0027651,Neoplasm,neop,1,C0026809,Mus,mamm,1\n548,1599,14268260,PART_OF,C0027750,Myelinated nerve fiber,celc,1,C0007765,Cerebellum,bpoc,1\n549,1621,6008280,USES,C1510438,Assay,lbpr,1,C0040160,Thyrotropin,aapp,1\n550,1539,15394671,TREATS,C0005841,Blood Transfusion,topp,1,C0023418,leukemia,neop,1\n551,1587,14880786,LOCATION_OF,C1116439,Posterior Fossa,bpoc,1,C0021311,Infection,dsyn,0\n552,1542,12312852,ADMINISTERED_TO,C0014939,Estrogens,horm,1,C0026809,Mus,mamm,1\n553,1526,12336540,METHOD_OF,C0441509,Coagulation procedure,topp,1,C0012002,Diathermy,topp,1\n554,1571,14770459,LOCATION_OF,C0506546,Wall of esophagus,bpoc,1,C0010709,Cyst,anab,1\n555,1587,14880786,LOCATION_OF,C1116439,Posterior Fossa,bpoc,1,C0270628,Cerebellar pyogenic abscess,acab,1\n556,1583,4290383,LOCATION_OF,C0042216,Vaccinia virus,virs,1,C0022209,isoniazid,orch,1\n557,1517,14782742,TREATS,C0030842,Penicillins,antb,1,C0014121,Bacterial Endocarditis,dsyn,1\n558,1677,14934105,TREATS,C0591251,Chloromycetin,phsu,1,C0041466,Typhoid Fever,dsyn,1\n559,1566,14806339,PROCESS_OF,C0039128,Syphilis,dsyn,1,C0699955,SUBCLASS SPIROCHETES,bact,1\n560,1693,4286771,LOCATION_OF,C1269041,Entire abdominal wall,bpoc,1,C0009062,Clostridium Infections,dsyn,1\n561,1592,13997710,LOCATION_OF,C0005767,Blood,tisu,1,C0014563,Epinephrine,orch,1\n562,1380,5698836,PART_OF,C0678933,genetic locus,gngm,1,C0020114,Human,humn,1\n563,1681,14457940,LOCATION_OF,C0262950,Skeletal bone,bpoc,1,C0034530,Radiation Injuries,inpo,1\n564,1587,14880786,PART_OF,C1116439,Posterior Fossa,bpoc,1,C0037303,Bone structure of cranium,bpoc,1\n565,1517,14782742,TREATS,C0728748,Aureomycin,antb,1,C0014121,Bacterial Endocarditis,dsyn,1\n566,1566,14806339,LOCATION_OF,C0699955,SUBCLASS SPIROCHETES,bact,1,C0030842,Penicillins,orch,1\n567,1592,13997710,LOCATION_OF,C0005767,Blood,tisu,1,C0019588,Histamine,orch,1\n568,1582,14055641,TREATS,C0034618,Radiation therapy,topp,1,C0006826,Malignant Neoplasms,neop,0\n569,1576,5955075,TREATS,C0441509,Coagulation procedure,topp,1,C0030705,Patients,podg,0\n570,1777,14087175,PROCESS_OF,C1261562,Detrusor instability,patf,1,C0043210,Woman,humn,1\n571,1665,14772459,INTERACTS_WITH,C0279516,Anti-Bacterial Agents,antb,1,C0038760,Sulfonamides,orch,1\n572,1736,13467019,LOCATION_OF,C0005682,Bladder,bpoc,1,C0041296,Tuberculosis,dsyn,1\n573,1724,14847753,LOCATION_OF,C0038351,Stomach,bpoc,1,C0012817,diverticulum,anab,1\n574,1707,14420409,AFFECTS,C0055819,Citric Acid,bacs,1,C0015852,Fermentation,moft,1\n575,1753,13026599,PROCESS_OF,C0016658,Fracture,inpo,1,C0008059,Child,humn,1\n576,1654,16691893,PART_OF,C1184740,Tubercle,bpoc,1,C1278891,Entire iris,bpoc,1\n577,1652,13372919,TREATS,C0013227,Pharmaceutical Preparations,phsu,0,C0277785,Functional disorder,patf,1\n578,1698,5601122,LOCATION_OF,C1266909,Entire bony skeleton,bdsy,1,C0087111,Therapeutic procedure,topp,0\n579,1784,5776118,DIAGNOSES,C0596473,Early Diagnosis,diap,1,C0018916,Hemangioma,neop,1\n580,1723,13502781,PART_OF,C0596707,histocompatibility gene,gngm,1,C0025914,House mice,mamm,1\n581,1747,16015914,LOCATION_OF,C0023625,\"Libraries, Medical\",hcro,1,C0043227,Work,ocac,1\n582,1641,12305492,PART_OF,C0018061,Gonadotropins,aapp,1,C0032005,Pituitary Gland,bpoc,1\n583,1756,5839808,LOCATION_OF,C0014876,Esophagus,bpoc,1,C0175677,Injury,inpo,1\n584,1730,20241545,USES,C0087111,Therapeutic procedure,topp,0,C0030842,Penicillins,antb,1\n585,1733,4294853,ASSOCIATED_WITH,C0013832,Electrolytes,inch,1,C0018802,Congestive heart failure,dsyn,1\n587,1697,13930398,LOCATION_OF,C1521714,Uterus - Cervix (MMHCC),tisu,1,C0027651,Neoplasm,neop,1\n588,1654,16691893,PART_OF,C1184740,Tubercle,bpoc,1,C1278891,Entire iris,bpoc,1\n589,1652,13372919,TREATS,C0450442,Agent,chvf,1,C0277785,Functional disorder,patf,1\n590,1718,13974566,LOCATION_OF,C0728985,Cervical spine,bpoc,1,C0221198,Lesion,fndg,1\n591,1719,5585336,TREATS,C0027996,Nicotinic Acid,phsu,1,C0034693,Rattus norvegicus,mamm,1\n592,1637,11712290,LOCATION_OF,C0036225,Sarcomeres,celc,1,C0233494,Tension,mobd,1\n593,1690,14327667,PART_OF,C0035946,Rumen,bpoc,1,C0007452,Cattle,mamm,1\n594,1641,12305492,TREATS,C0018061,Gonadotropins,phsu,1,C0043210,Woman,popg,1\n595,1697,13930398,PART_OF,C1521714,Uterus - Cervix (MMHCC),tisu,1,C0026809,Mus,mamm,1\n596,1659,14771467,ISA,C0020045,Musca domestica,invt,1,C0012578,Diptera,invt,1\n597,1784,5776118,DIAGNOSES,C0596473,Early Diagnosis,diap,1,C0038505,Sturge-Weber Syndrome,cgab,1\n598,1782,13867938,PROCESS_OF,C0006826,Malignant Neoplasms,neop,0,C0026809,Mus,mamm,1\n599,1733,4294853,ASSOCIATED_WITH,C0043047,Water,inch,1,C0018802,Congestive heart failure,dsyn,1\n600,1751,4966828,PART_OF,C0599104,mucopeptide,aapp,1,C0007623,Cell Wall,celc,1\n601,1799,14934107,LOCATION_OF,C0024109,Lung,bpoc,1,C0002438,Amebiasis,dsyn,1\n602,1814,14457943,PART_OF,C0027651,Neoplasm,neop,1,C0006655,Bone structure of calcaneum,bpoc,1\n603,1807,13070183,ISA,C0010980,Dapsone,orch,1,C0038761,Sulfones,orch,1\n604,1827,14770461,PART_OF,C0018915,Hemangioendothelioma,neop,1,C0023884,Liver,bpoc,1\n605,1400,12279177,CAUSES,C0025732,Methylcholanthrene,hops,1,C0006142,Malignant neoplasm of breast,neop,1\n606,1816,14055642,TREATS,C0003392,Antineoplastic Agents,phsu,1,C0029925,Ovarian Carcinoma,neop,1\n607,1845,15394674,DIAGNOSES,C0005560,Needle biopsy procedure,diap,1,C0024121,Lung Neoplasms,neop,1\n608,1700,5914353,LOCATION_OF,C0015392,Eye,bpoc,1,C0221198,Lesion,fndg,1\n609,1751,4966828,INTERACTS_WITH,C0243071,Analog,chvs,1,C0599104,mucopeptide,aapp,1\n610,1836,13209188,LOCATION_OF,C0004454,Axilla,blor,1,C0039259,Tail,bpoc,1\n611,1829,12305556,AFFECTS,C0175795,Oral medication,topp,1,C0015895,Fertility,orgf,1\n612,1803,20285372,TREATS,C0039957,Thiouracil,phsu,1,C0020550,Hyperthyroidism,dsyn,1\n613,1400,12279177,TREATS,C0039601,Testosterone,horm,1,C0006142,Malignant neoplasm of breast,neop,1\n614,1851,13738573,PROCESS_OF,C0006434,Burn injury,inpo,1,C0030705,Patients,humn,0\n615,1790,13100915,LOCATION_OF,C0005953,Bone Marrow,bpoc,1,C0002874,Aplastic Anemia,dsyn,1\n616,1838,16691659,LOCATION_OF,C0038925,Surgical Flaps,bpoc,1,C0038969,Surgical sutures,medd,1\n617,1831,13219295,TREATS,C0036075,salicylate,phsu,1,C0034693,Rattus norvegicus,mamm,1\n618,1836,13209188,PART_OF,C0039259,Tail,bpoc,1,C0006141,Breast,bpoc,1\n619,1774,13347212,TREATS,C0033972,\"Psychotherapy, Multiple\",topp,1,C0011608,Dermatitis Herpetiformis,dsyn,1\n620,1837,13384320,PROCESS_OF,C0014544,Epilepsy,dsyn,1,C0030705,Patients,humn,0\n621,1851,13738573,PART_OF,C0018563,Hand,bpoc,1,C0030705,Patients,humn,0\n622,1744,12279175,PROCESS_OF,C0001422,Adenofibroma,neop,1,C0034693,Rattus norvegicus,mamm,1\n623,1400,12279177,TREATS,C0014912,Estradiol,horm,1,C0032019,Pituitary Neoplasms,neop,1\n624,1757,13638658,PART_OF,C1514389,Pregnant Uterus,bpoc,1,C0020114,Human,humn,1\n625,1704,5659348,PART_OF,C0030016,Oxidoreductase,aapp,1,C0021289,\"Infant, Newborn\",humn,1\n626,1778,5933801,ASSOCIATED_WITH,C0011065,Cessation of life,orgf,1,C0031154,Peritonitis,dsyn,1\n627,1400,12279177,TREATS,C0014912,Estradiol,horm,1,C0032019,Pituitary Neoplasms,neop,1\n628,1826,5748939,STIMULATES,C0019878,homocysteine,aapp,1,C0015525,Factor XII,gngm,1\n629,1837,13384320,PROCESS_OF,C0027066,Myoclonus,sosy,1,C0030705,Patients,humn,0\n630,1821,13155043,LOCATION_OF,C0024109,Lung,bpoc,1,C0012634,Disease,dsyn,0\n631,1704,5659348,PART_OF,C0030016,Oxidoreductase,aapp,1,C0034693,Rattus norvegicus,mamm,1\n632,1757,13638658,LOCATION_OF,C1514389,Pregnant Uterus,bpoc,1,C0007343,Castor Oil,lipd,1\n633,1744,12279175,AFFECTS,C0036884,Gonadal Steroid Hormones,horm,1,C0018270,Growth,orgf,1\n634,1800,13464043,TREATS,C0547070,Ablation,topp,1,C0027627,Neoplasm Metastasis,neop,1\n635,1862,5877993,COEXISTS_WITH,C0012634,Disease,dsyn,0,C0027531,Neck Injuries,inpo,1\n636,1809,5955076,AFFECTS,C0038419,Streptolysins,bacs,1,C0003873,Rheumatoid Arthritis,dsyn,1\n637,1794,13605278,LOCATION_OF,C0596155,Basal Cell,cell,1,C0027960,Nevus,neop,1\n638,1800,13464043,PART_OF,C0027627,Neoplasm Metastasis,neop,1,C0006141,Breast,bpoc,1\n639,1907,14812427,LOCATION_OF,C0222603,Female breast,bpoc,1,C0080142,Self-Examination,diap,1\n640,1817,14386684,LOCATION_OF,C0025037,Meckel's Diverticulum,cgab,1,C0333291,Bleeding ulcer,dsyn,1\n641,1863,5839809,TREATS,C0035273,Resuscitation,topp,1,C0008059,Child,aggp,1\n642,1817,14386684,PROCESS_OF,C0025037,Meckel's Diverticulum,dsyn,1,C0021270,Infant,humn,1\n643,1892,5776119,ASSOCIATED_WITH,C0033452,Properdin,aapp,1,C0011847,Diabetes,dsyn,1\n644,1863,5839809,TREATS,C0035273,Resuscitation,topp,1,C0021270,Infant,aggp,1\n645,1894,13930399,PART_OF,C0596263,Carcinogenesis,neop,1,C0007874,Cervix Uteri,bpoc,1\n646,1842,5729815,PART_OF,C0022917,Lactate Dehydrogenase,aapp,1,C0014792,Erythrocytes,cell,1\n647,1840,4291298,LOCATION_OF,C0006104,Brain,bpoc,1,C0001617,Adrenal Cortex Hormones,strd,1\n648,1894,13930399,PART_OF,C0007874,Cervix Uteri,bpoc,1,C0026809,Mus,mamm,1\n649,1842,5729815,ASSOCIATED_WITH,C0022917,Lactate Dehydrogenase,aapp,1,C0002871,Anemia,dsyn,1\n651,1830,14772460,COEXISTS_WITH,C0027960,Nevus,neop,1,C0154653,Chronic meningitis,dsyn,1\n652,1894,13930399,ASSOCIATED_WITH,C0019932,Hormones,horm,1,C0596263,Carcinogenesis,neop,1\n653,1929,14420417,PROCESS_OF,C0006906,Capillary Permeability,ortf,1,C0008059,Child,humn,1\n654,1970,14268263,PART_OF,C0030518,Parathyroid gland,bpoc,1,C0023916,Lizards,rept,1\n655,1915,14877296,TREATS,C0454060,\"Superficial teletherapy procedure, Grenz type\",topp,1,C0235347,Black hairy tongue,dsyn,1\n656,1874,5585337,LOCATION_OF,C0227021,Enamel prisms,bpoc,1,C0009653,\"Condoms, Male\",medd,1\n657,1883,14327668,LOCATION_OF,C0026131,Milk,bdsu,1,C0021968,Iodine,bacs,1\n658,1929,14420417,PROCESS_OF,C0859036,Glomerulonephritis diffuse,dsyn,1,C0008059,Child,humn,1\n659,1957,5914355,LOCATION_OF,C1278891,Entire iris,bpoc,1,C0023794,Lipoidosis,dsyn,1\n660,1885,13372920,ISA,C1533685,Injection procedure,topp,1,C0087111,Therapeutic procedure,topp,0\n661,1969,20285399,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0006141,Breast,bpoc,1\n662,1935,12332438,METHOD_OF,C0279025,Endocrine therapy,topp,1,C0025335,Menstrual Regulation,topp,1\n663,1957,5914355,PROCESS_OF,C0023794,Lipoidosis,dsyn,1,C0034493,Oryctolagus cuniculus,mamm,1\n664,1776,13670517,CAUSES,C0033807,Pseudomonadaceae,bact,1,C0036690,Septicemia,dsyn,1\n665,1891,13189573,ASSOCIATED_WITH,C0017007,Gamma globulin,aapp,1,C0032371,Poliomyelitis,dsyn,1\n666,1883,14327668,LOCATION_OF,C0035946,Rumen,bpoc,1,C0021968,Iodine,bacs,1\n667,1990,13297274,compared_with,C0020700,\"Hysterectomy, Vaginal\",topp,1,C0404077,Abdominal hysterectomy,topp,1\n668,1885,13372920,TREATS,C1533685,Injection procedure,topp,1,C0019270,Hernia,anab,1\n669,1997,5971456,LOCATION_OF,C0037922,Spinal Canal,bsoj,1,C0027651,Neoplasm,neop,1\n670,1922,13026602,PART_OF,C0003842,Arteries,bpoc,1,C0006104,Brain,bpoc,1\n671,1957,5914355,DISRUPTS,C0024467,Magnesium,bacs,1,C0023794,Lipoidosis,dsyn,1\n672,1776,13670517,PROCESS_OF,C0012634,Disease,dsyn,0,C0016163,Fishes,fish,1\n673,1952,5748939,STIMULATES,C0019878,homocysteine,aapp,1,C0015525,Factor XII,gngm,1\n674,1928,16691660,PART_OF,C0282607,Neoplasms in Vascular Tissue,neop,1,C1278891,Entire iris,bpoc,1\n675,1922,13026602,PART_OF,C0003842,Arteries,bpoc,1,C0037925,Spinal Cord,bpoc,1\n676,1962,13347214,TREATS,C0028222,Nivaquine,phsu,1,C0011608,Dermatitis Herpetiformis,dsyn,1\n677,1917,14770462,PROCESS_OF,C0008925,Cleft Palate,dsyn,1,C0030705,Patients,humn,0\n678,1982,13638660,ISA,C0025029,Mecamylamine,orch,1,C0087111,Therapeutic procedure,topp,0\n679,1980,14386685,LOCATION_OF,C0025474,Mesentery,blor,1,C0010709,Cyst,anab,1\n680,1922,13026602,LOCATION_OF,C0003842,Arteries,bpoc,1,C0039082,Syndrome,dsyn,0\n681,1991,18856427,PART_OF,C0024296,Lymphoid Tissue,tisu,1,C0020114,Human,humn,1\n682,2000,14772461,TREATS,C0033218,Procaine,orch,1,C0018790,Heart Arrest,patf,1\n683,1941,12264095,ADMINISTERED_TO,C0720298,Estrogenic,horm,1,C0001792,Elderly,humn,1\n684,1857,12312852,TREATS,C0014939,Estrogens,horm,1,C0027651,Neoplasm,neop,1\n685,1949,12338137,PROCESS_OF,C0346156,Benign neoplasm of breast,neop,1,C0034693,Rattus norvegicus,mamm,1\n686,2006,5233232,PART_OF,C0015392,Eye,bpoc,1,C0031831,Physicians,humn,1\n687,1995,13737762,USES,C0087111,Therapeutic procedure,topp,0,C0018242,Griseofulvin,antb,1\n688,1982,13638660,USES,C0087111,Therapeutic procedure,topp,0,C0025029,Mecamylamine,phsu,1\n689,1983,13502783,PROCESS_OF,C0007125,\"Carcinoma, Ehrlich Tumor\",neop,1,C0026809,Mus,mamm,1\n690,1911,14087177,PRECEDES,C0038902,Gynecologic Surgical Procedures,topp,1,C0524865,Reconstructive Surgical Procedures,topp,1\n691,1941,12264095,PART_OF,C0014609,Epithelium,tisu,1,C0042232,Vagina,bpoc,1\n692,1937,11526827,LOCATION_OF,C0175996,Protoplasm,celc,1,C1185625,Compartments,bsoj,1\n693,1968,13605279,CAUSES,C0322496,Caterpillar,invt,1,C0011603,Dermatitis,dsyn,1\n694,1857,12312852,PROCESS_OF,C0027651,Neoplasm,neop,1,C0026809,Mus,mamm,1\n695,1931,13219296,LOCATION_OF,C0037949,Vertebral column,bpoc,1,C0000768,Congenital Abnormality,cgab,1\n696,2016,16691896,PART_OF,C1516384,Central Artery,bpoc,1,C0035298,Retina,bpoc,1\n697,1960,4968961,PROCESS_OF,C0042401,Vasodilation,phsf,1,C0006104,Brain,bpoc,1\n698,1991,18856427,PART_OF,C1333198,Cytoplasmic Protein,aapp,1,C0024296,Lymphoid Tissue,tisu,1\n699,2015,5323600,LOCATION_OF,C0229671,Serum,bdsu,1,C0023823,Low-Density Lipoproteins,aapp,1\n700,1985,5839810,TREATS,C0184661,Procedures,hlca,1,C0026266,Mitral Valve Insufficiency,dsyn,1\n701,1993,5729816,PROCESS_OF,C0000849,Absenteeism,inbe,1,C1527116,Workers,humn,1\n702,1931,13219296,LOCATION_OF,C0037949,Vertebral column,bpoc,1,C0265883,Double aortic arch,cgab,1\n703,2040,14268264,PART_OF,C0014609,Epithelium,tisu,1,C0014533,Epididymis,bpoc,1\n704,1901,5988843,AFFECTS,C0948575,Diuretic therapy,topp,1,C0001117,Acid-Base Equilibrium,ortf,1\n705,1959,15394676,LOCATION_OF,C1279075,Entire humerus,bpoc,1,C0027530,Neck,blor,1\n706,1857,12312852,TREATS,C0014939,Estrogens,horm,1,C0026809,Mus,mamm,1\n707,1951,13384321,USES,C0087111,Therapeutic procedure,topp,0,C0008286,Chlorpromazine,phsu,1\n708,2061,13372921,PART_OF,C0007095,Carcinoid Tumor,neop,1,C0034896,Rectum,bpoc,1\n709,2019,14055645,LOCATION_OF,C1279038,Entire diaphragm,bpoc,1,C0267195,Chronic gastric volvulus,dsyn,1\n710,1927,13100916,COEXISTS_WITH,C0035435,Rheumatism,dsyn,1,C0006826,Malignant Neoplasms,neop,0\n711,1942,13685041,TREATS,C0441587,Clinical act of insertion,hlca,1,C0008059,Child,humn,1\n712,2047,13680863,ISA,C0543467,Operative Surgical Procedures,topp,1,C0087111,Therapeutic procedure,topp,0\n713,2040,14268264,PART_OF,C0014609,Epithelium,tisu,1,C0012984,Canis familiaris,mamm,1\n714,2022,4965133,INTERACTS_WITH,C0178627,Ethylenediamine tetra-acetate,irda,1,C0033684,Proteins,aapp,1\n715,1994,13997718,PART_OF,C1516384,Central Artery,bpoc,1,C0035298,Retina,bpoc,1\n716,2079,20285401,PART_OF,C0007097,Carcinoma,neop,1,C0038351,Stomach,bpoc,1\n717,1959,15394676,LOCATION_OF,C0027530,Neck,blor,1,C0016658,Fracture,inpo,1\n718,2045,14457945,PART_OF,C0018920,\"Hemangioma, Cavernous\",neop,1,C0225317,soft tissue,tisu,1\n719,2047,13680863,LOCATION_OF,C0037004,Shoulder,bpoc,1,C0012691,Dislocations,inpo,1\n720,1822,13551193,PROCESS_OF,C0232478,Ingestion,biof,1,C0030705,Patients,humn,0\n721,2030,5601124,COEXISTS_WITH,C0022346,Icterus,patf,1,C0012634,Disease,dsyn,0\n722,2027,5187616,TREATS,C0013227,Pharmaceutical Preparations,phsu,0,C0022658,Kidney Diseases,dsyn,1\n723,1992,14812429,PART_OF,C0001418,Adenocarcinoma,neop,1,C0006141,Breast,bpoc,1\n724,2003,13467022,PART_OF,C0227391,Sigmoid colon,bpoc,1,C0005682,Bladder,bpoc,1\n725,2099,13155045,LOCATION_OF,C0024204,lymph nodes,bpoc,1,C0041296,Tuberculosis,dsyn,1\n726,2028,4179108,PROCESS_OF,C0025260,Memory,menp,1,C0026809,Mus,mamm,1\n727,1959,15394676,LOCATION_OF,C0027530,Neck,blor,1,C0221198,Lesion,fndg,1\n728,1994,13997718,LOCATION_OF,C1516384,Central Artery,bpoc,1,C0022116,Ischemia,dsyn,1\n729,2102,14772462,USES,C0087111,Therapeutic procedure,topp,0,C0145330,Tetraethylammonium Chloride,phsu,1\n730,2027,5187616,TREATS,C0035064,Renal Agents,phsu,1,C0022658,Kidney Diseases,dsyn,1\n731,2119,14782746,CAUSES,C0010137,Cortisone,horm,1,C0854110,Insulin resistant diabetes,dsyn,1\n732,2033,13738581,INTERACTS_WITH,C0074568,sinomenine,orch,1,C0030350,Papaverine,orch,1\n733,2103,5776121,TREATS,C0037995,Splenectomy,topp,1,C0018939,Hematological Disease,dsyn,1\n734,2101,13974576,LOCATION_OF,C0029939,Ovary,bpoc,1,C0010709,Cyst,anab,1\n735,2103,5776121,PROCESS_OF,C0018939,Hematological Disease,dsyn,1,C0008059,Child,humn,1\n736,2116,14439979,PART_OF,C0007097,Carcinoma,neop,1,C0009368,Colon,bpoc,1\n737,2107,12338106,LOCATION_OF,C0042149,Uterus,bpoc,1,C0720298,Estrogenic,orch,1\n738,2121,13605280,ASSOCIATED_WITH,C0443640,Specific antibody,aapp,1,C0019348,Herpes Simplex Infections,dsyn,1\n739,2143,14880793,LOCATION_OF,C0225565,Structure of ventricle of larynx,bsoj,1,C0010709,Cyst,anab,1\n740,2107,12338106,PART_OF,C0042149,Uterus,bpoc,1,C0025914,House mice,mamm,1\n741,2124,14087178,LOCATION_OF,C1280344,Entire vas deferens,bpoc,1,C0447577,Ureteric orifice,bsoj,1\n742,2189,14268266,LOCATION_OF,C0042149,Uterus,bpoc,1,C0232939,Primary physiologic amenorrhea,dsyn,1\n743,2195,14772463,PRECEDES,C0149781,Spontaneous pneumothorax NOS,dsyn,1,C0011071,\"Death, Sudden\",patf,1\n744,2167,13372922,CAUSES,C0025424,Mercury,elii,1,C0034884,Rectal Fistula,anab,1\n745,2136,13219297,LOCATION_OF,C0016976,Gallbladder,bpoc,1,C0267892,Aschoff-Rokitansky sinuses,dsyn,1\n746,1956,12279177,PROCESS_OF,C1458155,Mammary Neoplasms,neop,1,C0003062,Animals,anim,0\n747,2136,13219297,LOCATION_OF,C0016976,Gallbladder,bpoc,1,C0012813,Diverticulitis,dsyn,0\n748,2086,5748939,PROCESS_OF,C0019880,Homocystinuria,dsyn,1,C0030705,Patients,humn,0\n749,1956,12279177,ADMINISTERED_TO,C0014912,Estradiol,horm,1,C0003062,Animals,anim,0\n750,2086,5748939,PROCESS_OF,C0040053,Thrombosis,patf,1,C0030705,Patients,humn,0\n751,2146,5327093,AFFECTS,C0037995,Splenectomy,topp,1,C0020964,Immunity,phsf,1\n752,2187,5245632,TREATS,C0031705,Phosphorus,phsu,1,C0032463,Polycythemia Vera,neop,1\n753,1956,12279177,CAUSES,C0025732,Methylcholanthrene,hops,1,C1458155,Mammary Neoplasms,neop,1\n754,2133,13347216,LOCATION_OF,C0024204,lymph nodes,bpoc,1,C0333311,Sequestrum,anab,1\n755,2083,14251374,PROCESS_OF,C0870921,Motor Performance,orgf,1,C0021270,Infant,humn,1\n756,2214,5867996,ASSOCIATED_WITH,C0015667,\"Fat Emulsions, Intravenous\",lipd,1,C0043065,Water-Electrolyte Imbalance,patf,1\n757,1956,12279177,PROCESS_OF,C0032019,Pituitary Neoplasms,neop,1,C0003062,Animals,anim,0\n758,2185,14812430,PART_OF,C0003964,Peritoneal Fluid,bpoc,1,C0025914,House mice,mamm,1\n759,2133,13347216,PROCESS_OF,C0948192,Primary infection NOS,dsyn,1,C0001675,Adult,humn,1\n760,2187,5245632,PROCESS_OF,C0032463,Polycythemia Vera,neop,1,C0030705,Patients,humn,0\n761,2163,13189576,LOCATION_OF,C0036563,Seeds,plnt,1,C0007158,Cardiac Glycosides,carb,1\n762,2241,13670520,PART_OF,C0301838,Soluble antigen,imft,1,C0034497,Rabies virus,virs,1\n763,2153,14055646,LOCATION_OF,C1184808,Plexus,bpoc,1,C0278134,Lack of sensation,sosy,1\n764,2187,5245632,TREATS,C0031705,Phosphorus,phsu,1,C0030705,Patients,podg,0\n765,2177,5877996,TREATS,C0001617,Adrenal Cortex Hormones,horm,1,C0019357,\"Keratitis, Herpetic\",dsyn,1\n766,2194,12336800,TREATS,C0392535,\"Abortion, Induced\",topp,1,C0555047,Married,fndg,1\n767,2163,13189576,LOCATION_OF,C0036563,Seeds,plnt,1,C0304518,Aglycone,orch,1\n768,1956,12279177,ADMINISTERED_TO,C0014912,Estradiol,horm,1,C0003062,Animals,anim,0\n769,2223,5955079,PROCESS_OF,C0003873,Rheumatoid Arthritis,dsyn,1,C0030705,Patients,humn,0\n770,2153,14055646,LOCATION_OF,C1140618,Upper Extremity,bpoc,1,C0278134,Lack of sensation,sosy,1\n771,2194,12336800,PROCESS_OF,C0555047,Married,fndg,1,C0043210,Woman,humn,1\n772,2177,5877996,ISA,C0001617,Adrenal Cortex Hormones,horm,1,C0087111,Therapeutic procedure,topp,0\n773,2221,13974577,DIAGNOSES,C0203039,Hysterogram,diap,1,C0032987,\"Pregnancy, Ectopic\",dsyn,1\n774,2187,5245632,LOCATION_OF,C0030705,Patients,humn,0,C0005832,Blood Proteins,aapp,1\n775,1956,12279177,ADMINISTERED_TO,C0025732,Methylcholanthrene,hops,1,C0003062,Animals,anim,0\n776,2257,13464048,TREATS,C0015506,Factor VIII,phsu,1,C0019069,Hemophilia A,dsyn,1\n777,2096,14386686,LOCATION_OF,C0031066,Anogenital region,blor,1,C0175677,Injury,inpo,1\n778,2194,12336800,TREATS,C0392535,\"Abortion, Induced\",topp,1,C0043210,Woman,popg,1\n779,2177,5877996,USES,C0087111,Therapeutic procedure,topp,0,C0001617,Adrenal Cortex Hormones,phsu,1\n780,2096,14386686,TREATS,C0193200,Repair of anus NOS,topp,1,C0175677,Injury,inpo,1\n781,2257,13464048,PROCESS_OF,C0019069,Hemophilia A,dsyn,1,C0030705,Patients,humn,0\n782,2268,13372923,LOCATION_OF,C0009368,Colon,bpoc,1,C0012634,Disease,dsyn,0\n783,2089,5876103,PROCESS_OF,C0234222,Baresthesia,ortf,1,C0034493,Oryctolagus cuniculus,mamm,1\n784,2177,5877996,TREATS,C0087111,Therapeutic procedure,topp,0,C0019357,\"Keratitis, Herpetic\",dsyn,1\n785,2237,5914357,PROCESS_OF,C0392673,Adaptation,biof,1,C0034693,Rattus norvegicus,mamm,1\n786,2226,14439982,PART_OF,C0027651,Neoplasm,neop,1,C0242726,Plant Roots,plnt,1\n787,2268,13372923,LOCATION_OF,C0034896,Rectum,bpoc,1,C0012634,Disease,dsyn,0\n788,2229,13100918,ISA,C0025646,Methionine,aapp,1,C0087111,Therapeutic procedure,topp,0\n789,2257,13464048,TREATS,C0015506,Factor VIII,phsu,1,C0030705,Patients,podg,0\n790,2096,14386686,PROCESS_OF,C0175677,Injury,inpo,1,C0870221,Boys,humn,1\n791,2229,13100918,USES,C0087111,Therapeutic procedure,topp,0,C0025646,Methionine,aapp,1\n792,2171,4966828,PART_OF,C0599104,mucopeptide,aapp,1,C0007623,Cell Wall,celc,1\n793,2296,14251375,PROCESS_OF,C0814024,skin conductance,ortf,1,C0021289,\"Infant, Newborn\",humn,1\n794,2290,5933804,LOCATION_OF,C0025066,Mediastinum,blor,1,C0010626,Embryonic cyst,cgab,1\n795,2229,13100918,TREATS,C0025646,Methionine,aapp,1,C0003873,Rheumatoid Arthritis,dsyn,1\n796,2265,6029551,LOCATION_OF,C0817096,Chest,blor,1,C0028797,Occupational Diseases,dsyn,1\n797,2301,13297278,CAUSES,C0005806,Blood Group Incompatibility,dsyn,1,C1263988,Hemolytic disorder,dsyn,1\n798,2314,12983077,PART_OF,C0458459,Dorsal column,bpoc,1,C0012984,Canis familiaris,mamm,1\n799,2168,14327670,PART_OF,C0034595,Radioisotopes,elii,1,C0175925,Dairy cattle,mamm,1\n800,2203,14420425,ISA,C0000677,\"9,10-Dimethyl-1,2-benzanthracene\",hops,1,C0005032,Benzanthracenes,hops,1\n801,2184,5707416,PART_OF,C0006104,Brain,bpoc,1,C0034693,Rattus norvegicus,mamm,1\n802,2215,14216922,ISA,C0591817,Moditen,orch,1,C0016368,Fluphenazine,orch,1\n803,2151,12312852,PROCESS_OF,C0042138,Uterine Neoplasms,neop,1,C0026809,Mus,mamm,1\n804,2350,13997723,PROCESS_OF,C0042386,\"Vasculitis, Hemorrhagic\",dsyn,1,C0008059,Child,humn,1\n805,2210,14934120,AFFECTS,C0014695,Vitamin D2,phsu,1,C0007097,Carcinoma,neop,1\n806,2199,14847757,COEXISTS_WITH,C1510420,Cavitation,anab,1,C0333292,Perforated ulcer,acab,1\n807,2260,14087179,PROCESS_OF,C0012634,Disease,dsyn,0,C0022566,Keratinization,ortf,1\n808,2330,14185266,PROCESS_OF,C1291706,Psychogenic factor,fndg,1,C0008059,Child,humn,1\n809,2252,5971457,ISA,C0751495,\"Seizures, Focal\",sosy,1,C0014544,Epilepsy,dsyn,1\n810,2286,16691900,ASSOCIATED_WITH,C0025424,Mercury,elii,1,C0008526,Choroiditis,dsyn,1\n811,2377,14806346,TREATS,C1517925,Local Therapy,topp,1,C0030100,Oxyuriasis,dsyn,1\n812,2322,13155048,DIAGNOSES,C0006290,Bronchoscopy,diap,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n813,2203,14420425,ASSOCIATED_WITH,C0017973,Glycosaminoglycans,bacs,1,C0018188,Granuloma,patf,1\n814,2270,14268267,TREATS,C0033306,Progestins,horm,1,C0235873,Pelvic inflammation,patf,1\n815,2367,20285409,METHOD_OF,C0441509,Coagulation procedure,topp,1,C0728940,Excision,topp,1\n816,2313,13670521,LOCATION_OF,C0026927,Atypical Mycobacteria,bact,1,C0001962,Ethanol,orch,1\n817,2210,14934120,PART_OF,C0007097,Carcinoma,neop,1,C0026809,Mus,mamm,1\n818,2269,12338142,PART_OF,C0014609,Epithelium,tisu,1,C0042149,Uterus,bpoc,1\n819,2366,5914358,AFFECTS,C0032120,Plasma Proteins,aapp,1,C0302113,Fragility,comd,1\n820,2251,13737765,PART_OF,C0005962,Bone Matrix,tisu,1,C0015811,Femur,bpoc,1\n821,2302,13789602,LOCATION_OF,C0026447,Monkeys,mamm,1,C0028215,Nitrous Oxide,inch,1\n822,2370,5839813,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0009368,Colon,bpoc,1\n823,2199,14847757,LOCATION_OF,C0028977,Omentum,bpoc,1,C1510420,Cavitation,anab,1\n824,2360,13480921,USES,C0039593,Testing,resa,1,C0005971,Bone plates,medd,1\n825,2374,13738588,TREATS,C0543467,Operative Surgical Procedures,topp,1,C0001675,Adult,aggp,1\n826,2269,12338142,PROCESS_OF,C0025568,Metaplasia,comd,1,C0034693,Rattus norvegicus,mamm,1\n827,2398,13605283,TREATS,C0087111,Therapeutic procedure,topp,0,C0023048,Larva Migrans,dsyn,1\n828,2260,14087179,PROCESS_OF,C0012634,Disease,dsyn,0,C0030705,Patients,humn,0\n829,2322,13155048,PROCESS_OF,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1,C0008059,Child,humn,1\n830,2368,13372924,PROCESS_OF,C0039082,Syndrome,dsyn,0,C0021270,Infant,humn,1\n831,2260,14087179,PART_OF,C0005767,Blood,tisu,1,C0030705,Patients,humn,0\n832,2216,13502785,ISA,C0024398,Macaca,mamm,1,C0026447,Monkeys,mamm,1\n833,2384,13384325,USES,C0087111,Therapeutic procedure,topp,0,C0600062,Largactil,phsu,1\n834,2351,12279177,PROCESS_OF,C0006142,Malignant neoplasm of breast,neop,1,C0034693,Rattus norvegicus,mamm,1\n835,2347,5187619,PROCESS_OF,C0022658,Kidney Diseases,dsyn,1,C0008059,Child,humn,1\n836,2389,13026607,CAUSES,C0017601,Glaucoma,dsyn,1,C0456909,Blind Vision,dsyn,1\n837,2260,14087179,AFFECTS,C0042839,Vitamin A,orch,1,C0005767,Blood,tisu,1\n838,2216,13502785,PART_OF,C0032005,Pituitary Gland,bpoc,1,C0024398,Macaca,mamm,1\n839,2400,13100919,PROCESS_OF,C0028754,Obesity,dsyn,1,C0026591,Mothers,humn,1\n840,2365,5876104,PROCESS_OF,C0009348,Collateral Circulation,phsf,1,C0006104,Brain,bpoc,1\n841,2442,5339452,TREATS,C0700087,Tegretol,phsu,1,C0040997,Trigeminal Neuralgia,dsyn,1\n842,2435,16691901,LOCATION_OF,C0029127,Optic Disk,bpoc,1,C0010709,Cyst,anab,1\n843,2216,13502785,PART_OF,C0032005,Pituitary Gland,bpoc,1,C0026447,Monkeys,mamm,1\n844,2336,5955080,PROCESS_OF,C0035436,Rheumatic Fever,dsyn,1,C0008059,Child,humn,1\n845,2365,5876104,PROCESS_OF,C0009348,Collateral Circulation,phsf,1,C0034493,Oryctolagus cuniculus,mamm,1\n846,2385,13347218,COEXISTS_WITH,C0006902,Capillaritis,dsyn,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n847,2417,5707417,COEXISTS_WITH,C0014544,Epilepsy,dsyn,1,C0009951,Convulsions,dsyn,1\n848,2426,4967409,PART_OF,C0037303,Bone structure of cranium,bpoc,1,C0026447,Monkeys,mamm,1\n849,2395,5933805,TREATS,C0396565,Lung excision,topp,1,C1306038,Pulmonary histoplasmosis,dsyn,1\n850,2454,13974579,METHOD_OF,C0031006,In situ perfusion,topp,1,C0920425,Cancer Treatment,topp,1\n851,2423,14457951,CAUSES,C0023355,Leptomeningitis,dsyn,1,C0041296,Tuberculosis,dsyn,1\n852,2495,5187620,PROCESS_OF,C0022658,Kidney Diseases,dsyn,1,C0008059,Child,humn,1\n853,2481,5867998,PART_OF,C0027149,Myxoma,neop,1,C0225860,Left atrial structure,bpoc,1\n854,2403,5877998,ISA,C0185026,Plication,topp,1,C0543467,Operative Surgical Procedures,topp,1\n855,2471,5839814,PROCESS_OF,C0028778,Obstruction,patf,1,C0021289,\"Infant, Newborn\",humn,1\n856,2492,14772469,PART_OF,C0007097,Carcinoma,neop,1,C0024109,Lung,bpoc,1\n857,2466,12264118,PART_OF,C0024659,\"Mammary Glands, Animal\",bpoc,1,C0007097,Carcinoma,neop,1\n858,2403,5877998,TREATS,C0185026,Plication,topp,1,C0035305,Retinal Detachment,dsyn,1\n859,2491,5182923,PROCESS_OF,C0476273,Respiratory distress,sosy,1,C0008059,Child,humn,1\n860,2502,14087180,PROCESS_OF,C0042998,Vulvovaginitis,dsyn,1,C0008059,Child,humn,1\n861,2319,11850911,ISA,C0022594,Keratosis Blennorrhagica,dsyn,1,C0037284,Skin lesion,acab,1\n862,2488,13297280,TREATS,C0012002,Diathermy,topp,1,C0269062,Chronic cervicitis,dsyn,1\n863,2474,13605284,LOCATION_OF,C0005847,Blood Vessels,bpoc,1,C0019080,Hemorrhage,fndg,1\n864,2471,5839814,CAUSES,C0021828,Intestinal Atresia,dsyn,1,C0028778,Obstruction,patf,1\n865,2553,14771475,COEXISTS_WITH,C0020517,Hypersensitivity,patf,1,C0026946,Mycoses,dsyn,1\n866,2477,14150930,TREATS,C1293107,Expulsion,topp,1,C0426686,Liver finding,fndg,1\n867,2502,14087180,PROCESS_OF,C0276683,Candidiasis of vulva,dsyn,1,C0008059,Child,humn,1\n868,2483,13997727,COEXISTS_WITH,C0023530,Leukopenia,dsyn,1,C0036974,Shock,patf,1\n869,2530,14185268,TREATS,C0020699,Hysterectomy,topp,1,C0006826,Malignant Neoplasms,neop,0\n870,2496,6029553,LOCATION_OF,C0027361,Persons,humn,0,C0003818,Arsenic,elii,1\n871,2469,5914359,INTERACTS_WITH,C0002006,Aldosterone,horm,1,C0037494,Sodium Chloride,bacs,1\n872,2519,12259174,LOCATION_OF,C0026140,\"Milk, Human\",bdsu,1,C0028040,Nicotine,orch,1\n873,2520,13551199,PROCESS_OF,C0021400,Influenza,dsyn,1,C0008059,Child,humn,1\n874,2475,13155049,COEXISTS_WITH,C0699748,Pathogenesis,patf,0,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n875,2547,13372926,LOCATION_OF,C1275631,Perianal region structure,blor,1,C0006826,Malignant Neoplasms,neop,0\n876,2530,14185268,PART_OF,C0006826,Malignant Neoplasms,neop,0,C1521714,Uterus - Cervix (MMHCC),tisu,1\n877,2551,13347219,TREATS,C0351302,Sodium salts,phsu,1,C0023348,\"Leprosy, Lepromatous\",dsyn,1\n878,2516,4301646,USES,C0087111,Therapeutic procedure,topp,0,C0086123,Deoxycholate,phsu,1\n879,2450,5729819,LOCATION_OF,C0030274,Pancreas,bpoc,1,C0011847,Diabetes,dsyn,1\n880,2528,11712290,PROCESS_OF,C0012634,Disease,dsyn,0,C0080309,Ventricular Function,ortf,1\n881,2546,14439993,PART_OF,C0206674,\"Adenoma, Villous\",neop,1,C0034896,Rectum,bpoc,1\n882,2469,5914359,INTERACTS_WITH,C0003779,Argipressin,horm,1,C0037494,Sodium Chloride,bacs,1\n883,2519,12259174,LOCATION_OF,C0042036,Urine,bdsu,1,C0028040,Nicotine,orch,1\n884,2582,13974580,TREATS,C0031006,In situ perfusion,topp,1,C1261473,sarcoma,neop,1\n885,2575,13680870,TREATS,C0279025,Endocrine therapy,topp,1,C0334897,Obstetrician,humn,1\n886,2547,13372926,LOCATION_OF,C1275631,Perianal region structure,blor,1,C0877510,Precancerous skin lesion,dsyn,1\n887,2450,5729819,PROCESS_OF,C0011847,Diabetes,dsyn,1,C0001675,Adult,humn,1\n888,2443,12312852,PROCESS_OF,C0178554,cocarcinogen,patf,1,C0026809,Mus,mamm,1\n889,2536,13502786,PART_OF,C0006104,Brain,bpoc,1,C0024398,Macaca,mamm,1\n890,2557,5776126,COEXISTS_WITH,C1510428,Cerebral Abscess,dsyn,1,C0036117,Salmonella infections,dsyn,1\n891,2469,5914359,INTERACTS_WITH,C0010124,Corticosterone,horm,1,C0037494,Sodium Chloride,bacs,1\n892,2570,5707418,LOCATION_OF,C0006104,Brain,bpoc,1,C0017911,Glycogen,bacs,1\n893,2543,14847759,PART_OF,C0006826,Malignant Neoplasms,neop,0,C1305392,Entire common bile duct,bpoc,1\n894,2571,13685052,PART_OF,C0023779,Lipids,lipd,1,C0040934,Trichophyton mentagrophytes,fngs,1\n895,2594,5955083,LOCATION_OF,C0262950,Skeletal bone,bpoc,1,C0036202,Sarcoidosis,dsyn,1\n896,2450,5729819,PROCESS_OF,C0011847,Diabetes,dsyn,1,C0030705,Patients,humn,0\n897,2475,13155049,PROCESS_OF,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1,C0008059,Child,humn,1\n898,2515,4966829,PART_OF,C0017526,Giant Cells,cell,1,C0004595,Bacillus subtilis,bact,1\n899,2443,12312852,CAUSES,C0025732,Methylcholanthrene,hops,1,C0042138,Uterine Neoplasms,neop,1\n900,2612,14877306,PART_OF,C0007097,Carcinoma,neop,1,C1280388,Entire upper lip,bpoc,1\n901,2554,14812432,PART_OF,C0023884,Liver,bpoc,1,C0025914,House mice,mamm,1\n902,2524,13103847,ISA,C0699935,Terramycin,antb,1,C0030092,Oxytetracycline,antb,1\n903,2622,13464053,PROCESS_OF,C0027819,Neuroblastoma,neop,1,C0021270,Infant,humn,1\n904,2579,14268271,TREATS,C0034618,Radiation therapy,topp,1,C0036631,Seminoma,neop,1\n905,2430,13582820,TREATS,C0009574,Compound 48-80,phsu,1,C0034693,Rattus norvegicus,mamm,1\n906,2557,5776126,PROCESS_OF,C0036117,Salmonella infections,dsyn,1,C0021270,Infant,humn,1\n907,2536,13502786,LOCATION_OF,C0006104,Brain,bpoc,1,C0002059,Alkaline Phosphatase,aapp,1\n908,2443,12312852,STIMULATES,C0857127,Induction,topp,1,C0018270,Growth,orgf,1\n909,2524,13103847,ISA,C0728748,Aureomycin,antb,1,C0008293,Chlortetracycline,antb,1\n910,2633,13384327,TREATS,C0008286,Chlorpromazine,phsu,1,C0030705,Patients,podg,0\n911,2636,20241554,PART_OF,C1267211,Entire duct,bpoc,1,C1550312,Submaxillary,bpoc,1\n912,2569,13789604,PART_OF,C0334294,Multiple adenomatous polyps,neop,1,C0038351,Stomach,bpoc,1\n913,2681,16016739,LOCATION_OF,C0023625,\"Libraries, Medical\",hcro,1,C0007371,Cataloging,ocac,1\n914,2569,13789604,COEXISTS_WITH,C0153188,\"[X]Late syphilis, unspecified\",dsyn,1,C0334294,Multiple adenomatous polyps,neop,1\n915,2476,4878919,TREATS,C0013227,Pharmaceutical Preparations,phsu,0,C0019829,Hodgkin Disease,neop,1\n916,2576,4286772,PART_OF,C1368019,Paget's Disease,neop,1,C0006141,Breast,bpoc,1\n917,2690,14782769,PROCESS_OF,C0036341,Schizophrenia,mobd,1,C0205653,Adolescent,humn,1\n918,2703,13605286,TREATS,C0001712,Aerosols,chvs,1,C0037274,skin disorder,dsyn,0\n919,2626,14055650,ISA,C0036861,Sewage,eehu,1,C0392355,Pollution,eehu,1\n920,2644,14386691,TREATS,C0728940,Excision,topp,1,C0014009,Empyema,dsyn,1\n921,2588,10976199,PART_OF,C1167331,outer membrane,celc,1,C0037851,Sperm Tail,celc,1\n922,2645,4300082,LOCATION_OF,C0022646,Kidney,bpoc,1,C0151864,Disorder of pregnancy,dsyn,1\n923,2671,14185269,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0029939,Ovary,bpoc,1\n924,2599,5867999,ISA,C0027627,Neoplasm Metastasis,neop,1,C0006826,Malignant Neoplasms,neop,0\n925,2690,14782769,TREATS,C0009953,Convulsive therapy,topp,1,C0036341,Schizophrenia,mobd,1\n926,2576,4286772,ISA,C1368019,Paget's Disease,neop,1,C0006826,Malignant Neoplasms,neop,0\n927,2476,4878919,TREATS,C0013227,Pharmaceutical Preparations,phsu,0,C0162460,Reticulosis,neop,1\n928,2576,4286772,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0006141,Breast,bpoc,1\n929,2476,4878919,PROCESS_OF,C0019829,Hodgkin Disease,neop,1,C0030705,Patients,humn,0\n930,2706,16691905,METHOD_OF,C0038288,Sexual sterilization,topp,1,C0007389,Cataract Extraction,topp,1\n931,2739,12259050,PROCESS_OF,C0678108,Sterility,patf,1,C0025266,Male population group,humn,0\n932,2476,4878919,PROCESS_OF,C0162460,Reticulosis,neop,1,C0030705,Patients,humn,0\n933,2640,14150931,PART_OF,C0061241,germin,aapp,1,C0018067,Gonadal structure,bpoc,1\n934,2668,12308048,LOCATION_OF,C0036378,\"Schools, Medical\",hcro,1,C0039401,Educational process of instructing,edac,1\n935,2698,13431683,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0040132,Thyroid Gland,bpoc,1\n936,2685,13738592,PART_OF,C0005682,Bladder,bpoc,1,C0521377,Rectum and sigmoid colon,bpoc,1\n937,2718,13070195,PART_OF,C0006736,Calculi,bdsu,1,C0018494,hair,bpoc,1\n938,2676,13480924,TREATS,C0442936,Hemilaminectomy,topp,1,C0012984,Canis familiaris,mamm,1\n939,2728,13464054,COEXISTS_WITH,C0019066,Nontraumatic hemoperitoneum,patf,1,C0878751,Late pregnancy,dsyn,1\n940,2476,4878919,TREATS,C0013227,Pharmaceutical Preparations,phsu,0,C0030705,Patients,podg,0\n941,2689,12275493,PROCESS_OF,C0027497,Nausea,sosy,1,C0043210,Woman,humn,1\n942,2727,14877307,TREATS,C0020197,Hyaluronidase,aapp,1,C0027145,Myxedema,dsyn,1\n943,2747,13103848,USES,C0087111,Therapeutic procedure,topp,0,C1136254,Microbicides,phsu,1\n945,2649,13211298,TREATS,C0087111,Therapeutic procedure,topp,0,C0002962,Angina Pectoris,sosy,1\n946,2733,5839816,TREATS,C0543467,Operative Surgical Procedures,topp,1,C0522224,Paralysed,fndg,1\n947,2727,14877307,LOCATION_OF,C1280388,Entire upper lip,bpoc,1,C0027145,Myxedema,dsyn,1\n948,2748,14880803,TREATS,C0010137,Cortisone,horm,1,C0003873,Rheumatoid Arthritis,dsyn,1\n949,2743,13384328,USES,C0087111,Therapeutic procedure,topp,0,C0008286,Chlorpromazine,phsu,1\n950,2738,5776127,PROCESS_OF,C0546959,Atrial tachycardia,patf,1,C0870604,Girls,humn,1\n951,2649,13211298,PROCESS_OF,C0002962,Angina Pectoris,sosy,1,C0030705,Patients,humn,0\n952,2803,14772473,COEXISTS_WITH,C0871745,Family Crises,fndg,1,C0241953,Jaundice acholuric,dsyn,1\n953,2711,13026610,CAUSES,C0016470,Food Allergy,dsyn,1,C0013595,Eczema,dsyn,1\n954,2749,20241555,LOCATION_OF,C0027530,Neck,blor,1,C0017105,Gas Gangrene,dsyn,1\n955,2704,15394682,LOCATION_OF,C1305781,Supraspinatus tendon,bpoc,1,C0043246,Laceration,inpo,1\n956,2733,5839816,LOCATION_OF,C1278841,Entire brachial plexus,bpoc,1,C0522224,Paralysed,fndg,1\n957,2641,13997729,PART_OF,C0032005,Pituitary Gland,bpoc,1,C0003459,Anura,amph,1\n958,2743,13384328,TREATS,C0008286,Chlorpromazine,orch,1,C0033975,Psychotic Disorders,mobd,1\n959,2649,13211298,TREATS,C0087111,Therapeutic procedure,topp,0,C0030705,Patients,podg,0\n961,2746,14087182,PART_OF,C0178784,Organ,bpoc,1,C0230278,Minor pelvis,bpoc,1\n962,2711,13026610,LOCATION_OF,C0018563,Hand,bpoc,1,C0013595,Eczema,dsyn,1\n963,2641,13997729,PART_OF,C0796494,Lobe,bpoc,1,C0032005,Pituitary Gland,bpoc,1\n964,2649,13211298,TREATS,C1441129,Radioactive Iodine,phsu,1,C0741926,CARDIAC PATIENT,podg,1\n965,2790,13297282,PROCESS_OF,C0037864,Spermatogenesis,celf,1,C0020114,Human,humn,1\n966,2710,5914360,INTERACTS_WITH,C0002006,Aldosterone,horm,1,C0037494,Sodium Chloride,bacs,1\n967,2746,14087182,LOCATION_OF,C0178784,Organ,bpoc,1,C0042345,Varicosity,acab,1\n968,2693,13680883,PART_OF,C0035286,Reticulocytes,cell,1,C0034493,Oryctolagus cuniculus,mamm,1\n969,2819,14457955,CAUSES,C0034618,Radiation therapy,topp,1,C0022408,Arthropathies NOS,dsyn,1\n970,2833,5868001,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0029939,Ovary,bpoc,1\n971,2842,13551202,LOCATION_OF,C1278872,Entire sympathetic nerve,bpoc,1,C0270788,Paralytic syndrome,dsyn,1\n972,2860,5776128,COEXISTS_WITH,C0267956,Acute necrosis of pancreas,dsyn,1,C0027720,Nephrosis,dsyn,1\n973,2770,13789605,LOCATION_OF,C0024109,Lung,bpoc,1,C0038172,Staphylococcus aureus,bact,1\n974,2849,5878002,LOCATION_OF,C0015392,Eye,bpoc,1,C0221198,Lesion,fndg,1\n975,2725,14812433,PROCESS_OF,C0038356,Stomach Neoplasms,neop,1,C0026809,Mus,mamm,1\n976,2710,5914360,INTERACTS_WITH,C0003779,Argipressin,horm,1,C0037494,Sodium Chloride,bacs,1\n977,2856,14880804,USES,C0087111,Therapeutic procedure,topp,0,C0728748,Aureomycin,antb,1\n978,2825,13100924,ISA,C0022209,isoniazid,orch,1,C0087111,Therapeutic procedure,topp,0\n979,2693,13680883,INTERACTS_WITH,C0051395,alpha-ketoglutaric acid,orch,1,C0017797,Glutamine,aapp,1\n980,2726,13189580,PART_OF,C0023884,Liver,bpoc,1,C0003043,Animalia,anim,0\n982,2819,14457955,CAUSES,C0087111,Therapeutic procedure,topp,0,C0022408,Arthropathies NOS,dsyn,1\n983,2746,14087182,LOCATION_OF,C0042345,Varicosity,acab,1,C0236178,Intraabdominal hemorrhage,dsyn,1\n984,2875,14772474,COEXISTS_WITH,C1370824,Interstitial emphysema,dsyn,1,C0025007,Measles,dsyn,1\n985,2825,13100924,USES,C0087111,Therapeutic procedure,topp,0,C0022209,isoniazid,phsu,1\n986,2753,12264172,PROCESS_OF,C0024623,Malignant neoplasm of stomach,neop,1,C0034693,Rattus norvegicus,mamm,1\n987,2770,13789605,PART_OF,C0024109,Lung,bpoc,1,C0030705,Patients,humn,0\n988,2693,13680883,INTERACTS_WITH,C0061472,Glutamic Acid,aapp,1,C0017797,Glutamine,aapp,1\n989,2710,5914360,INTERACTS_WITH,C0010124,Corticosterone,horm,1,C0037494,Sodium Chloride,bacs,1\n990,2726,13189580,LOCATION_OF,C0023884,Liver,bpoc,1,C0042845,Vitamin B 12,orch,1\n991,2827,13431684,TREATS,C0010137,Cortisone,horm,1,C0264552,Serofibrinous pleurisy,dsyn,1\n992,2850,5955085,TREATS,C0040071,Thymectomy,topp,1,C0026896,Myasthenia Gravis,dsyn,1\n993,2815,13292704,PROCESS_OF,C0041296,Tuberculosis,dsyn,1,C0030705,Patients,humn,0\n994,2834,13347223,CAUSES,C0600062,Largactil,orch,1,C0022346,Icterus,patf,1\n995,2753,12264172,PROCESS_OF,C0153567,Uterine Cancer,neop,1,C0034693,Rattus norvegicus,mamm,1\n996,2825,13100924,TREATS,C0022209,isoniazid,phsu,1,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1\n997,2799,13685065,PART_OF,C0229671,Serum,bdsu,1,C0020114,Human,humn,1\n998,2824,5707419,PART_OF,C0023779,Lipids,lipd,1,C0027836,Neuroglia,cell,1\n999,2899,13070197,PART_OF,C0015801,Structure of femoral artery,bpoc,1,C0012984,Canis familiaris,mamm,1\n1000,2737,13582821,TREATS,C0019590,Histamine Antagonists,phsu,1,C0085979,Cavia,mamm,1\n1001,2912,13997730,PART_OF,C0796494,Lobe,bpoc,1,C0032005,Pituitary Gland,bpoc,1\n1002,2931,13551203,TREATS,C0025386,Meprobamate,phsu,1,C0700061,Obstetric Patient,podg,1\n1003,2824,5707419,PART_OF,C0682708,White Matter,tisu,1,C0007452,Cattle,mamm,1\n1004,2891,13219342,USES,C0087111,Therapeutic procedure,topp,0,C0012155,Diet,food,1\n1005,2899,13070197,PART_OF,C0741968,CAROTID,bpoc,1,C0012984,Canis familiaris,mamm,1\n1006,2949,16691908,LOCATION_OF,C0035298,Retina,bpoc,1,C0002982,Angioid Streaks,dsyn,1\n1007,2941,18856429,COEXISTS_WITH,C0238621,Aminoaciduria,dsyn,1,C0026850,Muscular Dystrophies,cgab,1\n1008,2824,5707419,LOCATION_OF,C0682708,White Matter,tisu,1,C0023779,Lipids,lipd,1\n1009,2944,13155053,PROCESS_OF,C0041327,\"Tuberculosis, Pulmonary\",dsyn,1,C0008059,Child,humn,1\n1010,2917,15394684,LOCATION_OF,C0003086,Ankle,blor,1,C0016658,Fracture,inpo,1\n1011,2906,14216928,PROCESS_OF,C0241856,Occupational deafness,dsyn,1,C0376706,Mechanics,npop,1\n1012,2963,16016747,METHOD_OF,C0220931,Training,edac,1,C0023620,Librarianship,ocdi,1\n1014,2873,14440000,LOCATION_OF,C0032105,Plasma,bdsu,1,C0040018,Thrombin,aapp,1\n1015,2942,13026612,PART_OF,C0018283,Epiphysial cartilage,tisu,1,C1279083,Entire radius,bpoc,1\n1016,2932,14934126,DIAGNOSES,C0037296,Hypersensitivity skin testing,diap,1,C0002994,Angioneurotic Edema,patf,1\n1017,2868,14386693,METHOD_OF,C0022100,Irrigation,topp,1,C0087111,Therapeutic procedure,topp,0\n1018,2855,4301646,NEG_INHIBITS,C0034145,Puromycin,antb,1,C0001480,Adenosine Triphosphate,bacs,1\n1019,2935,4300799,PROCESS_OF,C0023418,leukemia,neop,1,C0026809,Mus,mamm,1\n1020,2907,4892267,TREATS,C0040732,Transplantation,topp,1,C0020114,Human,humn,1\n1021,2870,20241556,COMPLICATES,C0017086,Gangrene,dsyn,1,C0864638,Cerebrospinal fever,dsyn,1\n1022,2979,13638675,TREATS,C0450442,Agent,chvf,1,C0027726,Nephrotic Syndrome,dsyn,1\n1023,2986,13930418,ASSOCIATED_WITH,C0232262,Diastolic murmur,sosy,1,C0003504,Aortic Valve Insufficiency,dsyn,1\n1024,2863,13372929,METHOD_OF,C0040597,Traction,topp,1,C0556666,Lumbar traction,topp,1\n1025,2966,14268284,DIAGNOSES,C0013798,Electrocardiogram,diap,1,C0023119,Lathyrism,inpo,1\n1026,2913,13502788,ISA,C0024398,Macaca,mamm,1,C0026447,Monkeys,mamm,1\n1027,2964,13431685,LOCATION_OF,C0038351,Stomach,bpoc,1,C0019291,\"Hernia, Hiatal\",anab,1\n1028,2965,12983088,METHOD_OF,C0042196,Vaccination,topp,1,C0199176,Prophylactic treatment,topp,1\n1029,2868,14386693,USES,C0087111,Therapeutic procedure,topp,0,C0030842,Penicillins,antb,1\n1030,2985,14847763,CAUSES,C0005036,Benzene,hops,1,C0023473,\"Myeloid Leukemia, Chronic\",neop,1\n1031,2980,13103850,TREATS,C0022678,\"Kidney, Artificial\",medd,1,C0022661,\"Kidney Failure, Chronic\",dsyn,1\n1032,2928,5878003,LOCATION_OF,C0016823,Structure of fundus of eye,blor,1,C0012634,Disease,dsyn,0\n1033,2970,12264172,PROCESS_OF,C0006826,Malignant Neoplasms,neop,0,C0034693,Rattus norvegicus,mamm,1\n1034,2932,14934126,DIAGNOSES,C0037296,Hypersensitivity skin testing,diap,1,C0042109,Urticaria,dsyn,1\n1035,3019,16691671,PART_OF,C0015392,Eye,bpoc,1,C0020114,Human,humn,1\n1036,2999,5585345,AFFECTS,C0040165,Thyroxine,aapp,1,C1149888,alkaline phosphatase activity,moft,1\n1037,2868,14386693,USES,C0087111,Therapeutic procedure,topp,0,C0771312,SULFATHIAZOLE SODIUM,phsu,1\n1038,2913,13502788,LOCATION_OF,C0927232,Neuraxis,bdsy,1,C0857127,Induction,topp,1\n1039,2863,13372929,ISA,C0040597,Traction,topp,1,C0087111,Therapeutic procedure,topp,0\n1040,2992,14782773,TREATS,C0185125,Application procedure,hlca,1,C0030193,Pain,sosy,1\n1041,3012,13384331,compared_with,C0008286,Chlorpromazine,orch,1,C0195775,Operation on brain,topp,1\n1042,2928,5878003,TREATS,C0023694,Light Coagulation,topp,1,C0012634,Disease,dsyn,0\n1043,2981,6065079,PART_OF,C0033679,Transglutaminases,aapp,1,C0023884,Liver,bpoc,1\n1044,2950,13867951,PART_OF,C0006826,Malignant Neoplasms,neop,0,C0032005,Pituitary Gland,bpoc,1\n1045,2952,11526828,compared_with,C0597277,Potassium Ions,bacs,1,C0022023,Ions,elii,1\n1047,2951,13280157,LOCATION_OF,C0038351,Stomach,bpoc,1,C0031746,Photofluorography,diap,1\n1048,2863,13372929,METHOD_OF,C0087111,Therapeutic procedure,topp,0,C0556666,Lumbar traction,topp,1\n1049,2952,11526828,higher_than,C0597277,Potassium Ions,bacs,1,C0022023,Ions,elii,1\n1051,2909,12275493,ADMINISTERED_TO,C0003297,Antiemetics,phsu,1,C0030705,Patients,humn,0\n1052,2919,12996023,PROCESS_OF,C0231178,Chronic failure,patf,1,C0008059,Child,humn,1\n1053,2967,5914361,TREATS,C0051066,alanosine,phsu,1,C0034693,Rattus norvegicus,mamm,1\n1054,3028,4236753,PART_OF,C0026237,Mitochondria,celc,1,C0006104,Brain,bpoc,1\n1055,2990,14770468,PROCESS_OF,C0027726,Nephrotic Syndrome,dsyn,1,C0008059,Child,humn,1\n1056,3038,15394685,CAUSES,C0034074,Pulmonary Infarction,dsyn,1,C0032326,Pneumothorax,dsyn,1\n1057,3030,13997734,PART_OF,C1519221,Secretory Cell,cell,1,C0796494,Lobe,bpoc,1\n1058,3020,14880806,METHOD_OF,C0011900,Diagnosis,hlca,1,C0543467,Operative Surgical Procedures,topp,1\n1059,3103,13867952,PROCESS_OF,C0017181,Gastrointestinal Hemorrhage,patf,1,C0021270,Infant,humn,1\n1060,3041,4960769,LOCATION_OF,C0003064,\"Animals, Laboratory\",anim,1,C0018062,Chorionic Gonadotropin,aapp,1\n1061,3077,13789614,TREATS,C0543467,Operative Surgical Procedures,topp,1,C0032994,\"Pregnancy, Tubal\",dsyn,1\n1062,3028,4236753,AFFECTS,C0005437,Bilirubin,bacs,1,C0014272,Energy Metabolism,phsf,1\n1063,2990,14770468,PROCESS_OF,C0221102,Excretory function,phsf,1,C0008059,Child,humn,1\n1064,3020,14880806,TREATS,C0543467,Operative Surgical Procedures,topp,1,C0747086,OTOMASTOIDITIS,dsyn,1\n1065,3030,13997734,PART_OF,C0796494,Lobe,bpoc,1,C0032005,Pituitary Gland,bpoc,1\n1066,2990,14770468,INTERACTS_WITH,C0001655,Corticotropin,aapp,1,C0037494,Sodium Chloride,bacs,1\n1067,2968,14327675,PROCESS_OF,C0006147,Breast Feeding,orgf,1,C0034715,\"Rats, Sprague-Dawley\",mamm,1\n1068,3081,4175348,COEXISTS_WITH,C0557034,Assisting,hlca,1,C0195775,Operation on brain,topp,1\n1069,3005,13582822,ISA,C0020268,Hydrocortisone,horm,1,C0087111,Therapeutic procedure,topp,0\n" }, { "path": "attic/code/semmed/PREDICATE.scm", "content": "\"1176\"\n\"ADMINISTERED_TO\"\n\"AFFECTS\"\n\"ASSOCIATED_WITH\"\n\"AUGMENTS\"\n\"CAUSES\"\n\"COEXISTS_WITH\"\n\"COMPLICATES\"\n\"CONVERTS_TO\"\n\"DIAGNOSES\"\n\"DISRUPTS\"\n\"INHIBITS\"\n\"INTERACTS_WITH\"\n\"ISA\"\n\"LOCATION_OF\"\n\"MANIFESTATION_OF\"\n\"METHOD_OF\"\n\"NEG_ADMINISTERED_TO\"\n\"NEG_AFFECTS\"\n\"NEG_ASSOCIATED_WITH\"\n\"NEG_AUGMENTS\"\n\"NEG_CAUSES\"\n\"NEG_COEXISTS_WITH\"\n\"NEG_COMPLICATES\"\n\"NEG_CONVERTS_TO\"\n\"NEG_DIAGNOSES\"\n\"NEG_DISRUPTS\"\n\"NEG_INHIBITS\"\n\"NEG_INTERACTS_WITH\"\n\"NEG_LOCATION_OF\"\n\"NEG_MANIFESTATION_OF\"\n\"NEG_METHOD_OF\"\n\"NEG_OCCURS_IN\"\n\"NEG_PART_OF\"\n\"NEG_PRECEDES\"\n\"NEG_PREDISPOSES\"\n\"NEG_PREVENTS\"\n\"NEG_PROCESS_OF\"\n\"NEG_PRODUCES\"\n\"NEG_STIMULATES\"\n\"NEG_TREATS\"\n\"NEG_USES\"\n\"NEG_higher_than\"\n\"NEG_lower_than\"\n\"OCCURS_IN\"\n\"PART_OF\"\n\"PRECEDES\"\n\"PREDISPOSES\"\n\"PREVENTS\"\n\"PROCESS_OF\"\n\"PRODUCES\"\n\"STIMULATES\"\n\"TREATS\"\n\"USES\"\n\"compared_with\"\n\"different_from\"\n\"different_than\"\n\"higher_from\"\n\"higher_than\"\n\"lower_than\"\n\"same_as\"\n\"than_as\"\n" }, { "path": "attic/code/semmed/PREDICATE_OCCURRENCE_ORDERED.scm", "content": "\"ISA\"\n\"PART_OF\"\n\"PROCESS_OF\"\n\"TREATS\"\n\"LOCATION_OF\"\n\"METHOD_OF\"\n\"INTERACTS_WITH\"\n\"COEXISTS_WITH\"\n\"DIAGNOSES\"\n\"CAUSES\"\n\"AFFECTS\"\n\"ASSOCIATED_WITH\"\n\"USES\"\n\"PRECEDES\"\n\"compared_with\"\n\"PREVENTS\"\n\"NEG_INHIBITS\"\n\"ADMINISTERED_TO\"\n\"OCCURS_IN\"\n\"NEG_ADMINISTERED_TO\"\n\"STIMULATES\"\n\"DISRUPTS\"\n\"COMPLICATES\"\n\"higher_than\"\n\"INHIBITS\"\n\"AUGMENTS\"\n\"MANIFESTATION_OF\"\n\"different_from\"\n\"NEG_AFFECTS\"\n\"PREDISPOSES\"\n\"NEG_higher_than\"\n\"same_as\"\n\"PRODUCES\"\n\"NEG_DISRUPTS\"\n\"NEG_CAUSES\"\n\"NEG_INTERACTS_WITH\"\n\"NEG_PROCESS_OF\"\n\"NEG_COEXISTS_WITH\"\n\"NEG_PART_OF\"\n\"NEG_USES\"\n\"lower_than\"\n\"NEG_PREVENTS\"\n\"NEG_LOCATION_OF\"\n\"NEG_METHOD_OF\"\n\"CONVERTS_TO\"\n\"NEG_DIAGNOSES\"\n\"NEG_AUGMENTS\"\n\"NEG_PREDISPOSES\"\n\"NEG_TREATS\"\n\"NEG_ASSOCIATED_WITH\"\n\"NEG_PRODUCES\"\n\"NEG_COMPLICATES\"\n\"NEG_STIMULATES\"\n\"NEG_OCCURS_IN\"\n\"different_than\"\n\"NEG_CONVERTS_TO\"\n\"NEG_lower_than\"\n\"NEG_MANIFESTATION_OF\"\n\"NEG_PRECEDES\"\n\"higher_from\"\n\"than_as\"\n\"1176\"\n" }, { "path": "attic/code/semmed/README.md", "content": "The data can be generated with these commands:\n\n```\nracket csv-semmed-ordered-unique-enum.rkt semmedVER30_A_clean.csv semmed\n\nracket csv-semmed-simplify.rkt semmedVER30_A_clean.csv semmed\n```\n\n\nNOTE:\n\nThe strange 1176 predicate might be legitimate, found in a couple records via:\n\n```\ntail -n 2318424 semmedVER30_A_clean.csv | head -n 118424 | grep 1176 | less\n78924979,136605831,11116842,1176,C0024485,Magnetic Resonance Imaging,diap,1,C3146964,COX5BP4 gene,0,1\n78924980,136605831,11116842,1176,C0024485,Magnetic Resonance Imaging,diap,1,C3146964,COX5BP4 gene,0,1\n```\n\nThe strange 0 semtype might be legitimate, found alongside predicate 1176.\n\n\nTODO:\n\nconcept ideas:\n cui-by-semtype\n\nedge ideas:\n edge, edge-reversed: #(cui cui detail-offset)\n Byte-level encode so that each record is at a predictable offset.\n Write this out in flattened search-tree form for fast lookup; store offset into edge-details.\n\n edge-details (and reversed cui version): #(cui cui (list-of #(predicate semtype semtype predication-id)))\n" }, { "path": "attic/code/semmed/SEMTYPE.scm", "content": "\"0\"\n\"aapp\"\n\"acab\"\n\"acty\"\n\"aggp\"\n\"alga\"\n\"amas\"\n\"amph\"\n\"anab\"\n\"anim\"\n\"anst\"\n\"antb\"\n\"arch\"\n\"bacs\"\n\"bact\"\n\"bdsu\"\n\"bdsy\"\n\"bhvr\"\n\"biof\"\n\"bird\"\n\"blor\"\n\"bmod\"\n\"bodm\"\n\"bpoc\"\n\"bsoj\"\n\"carb\"\n\"celc\"\n\"celf\"\n\"cell\"\n\"cgab\"\n\"chem\"\n\"chvf\"\n\"chvs\"\n\"clas\"\n\"clna\"\n\"clnd\"\n\"cnce\"\n\"comd\"\n\"diap\"\n\"dora\"\n\"drdd\"\n\"dsyn\"\n\"edac\"\n\"eehu\"\n\"eico\"\n\"elii\"\n\"emod\"\n\"emst\"\n\"enzy\"\n\"evnt\"\n\"famg\"\n\"ffas\"\n\"fish\"\n\"fndg\"\n\"fngs\"\n\"food\"\n\"ftcn\"\n\"genf\"\n\"geoa\"\n\"gngm\"\n\"gora\"\n\"grpa\"\n\"grup\"\n\"hcpp\"\n\"hcro\"\n\"hlca\"\n\"hops\"\n\"horm\"\n\"humn\"\n\"idcn\"\n\"imft\"\n\"inbe\"\n\"inch\"\n\"inpo\"\n\"inpr\"\n\"invt\"\n\"irda\"\n\"lang\"\n\"lbpr\"\n\"lbtr\"\n\"lipd\"\n\"mamm\"\n\"mbrt\"\n\"mcha\"\n\"medd\"\n\"menp\"\n\"mnob\"\n\"mobd\"\n\"moft\"\n\"mosq\"\n\"neop\"\n\"nnon\"\n\"npop\"\n\"nsba\"\n\"nusq\"\n\"ocac\"\n\"ocdi\"\n\"opco\"\n\"orch\"\n\"orga\"\n\"orgf\"\n\"orgm\"\n\"orgt\"\n\"ortf\"\n\"patf\"\n\"phob\"\n\"phpr\"\n\"phsf\"\n\"phsu\"\n\"plnt\"\n\"podg\"\n\"popg\"\n\"prog\"\n\"pros\"\n\"qlco\"\n\"qnco\"\n\"rcpt\"\n\"rept\"\n\"resa\"\n\"resd\"\n\"rich\"\n\"rnlw\"\n\"sbst\"\n\"shro\"\n\"socb\"\n\"sosy\"\n\"spco\"\n\"strd\"\n\"tisu\"\n\"tmco\"\n\"topp\"\n\"virs\"\n\"vita\"\n\"vtbt\"\n" }, { "path": "attic/code/semmed/cui-by-semtype.scm", "content": "(0 3146964)\n(1 52 84 107 132 152 165 184 189 246 254 257 291 324 340 359 366 378 392 404 412 413 435 490 500 507 530 578 608 644 656 829 977 997 999 1019 1021 1022 1024 1028 1044 1047 1053 1057 1060 1064 1067 1068 1098 1102 1109 1113 1115 1120 1136 1156 1214 1239 1245 1259 1271 1290 1291 1295 1345 1346 1347 1369 1388 1390 1412 1414 1451 1452 1457 1464 1471 1473 1475 1476 1477 1478 1479 1492 1497 1502 1503 1601 1638 1639 1642 1643 1655 1657 1694 1714 1897 1898 1899 1900 1904 1924 1942 1945 1954 1985 1986 1988 1990 1999 2000 2003 2004 2057 2059 2061 2085 2139 2142 2159 2189 2190 2191 2193 2195 2197 2198 2199 2202 2205 2210 2211 2215 2229 2230 2235 2240 2241 2242 2245 2248 2251 2255 2256 2257 2260 2261 2268 2269 2270 2272 2274 2278 2280 2287 2289 2290 2302 2308 2311 2313 2317 2318 2402 2484 2488 2492 2507 2512 2513 2515 2516 2517 2520 2521 2522 2523 2524 2525 2527 2529 2543 2545 2546 2559 2563 2564 2565 2570 2587 2594 2610 2651 2712 2716 2721 2722 2723 2791 2823 2843 3001 3006 3009 3011 3012 3013 3016 3017 3018 3039 3134 3168 3169 3241 3242 3243 3244 3245 3248 3250 3253 3313 3323 3327 3329 3343 3368 3369 3370 3371 3403 3410 3421 3436 3438 3440 3442 3450 3521 3589 3590 3591 3592 3593 3594 3595 3601 3607 3634 3641 3652 3691 3692 3693 3694 3731 3762 3763 3764 3765 3766 3768 3775 3776 3777 3778 3779 3805 3806 3927 3933 3938 3939 3940 3942 3967 3987 3993 3995 3997 3999 4002 4004 4006 4007 4008 4009 4010 4011 4012 4015 4018 4019 4020 4022 4025 4040 4149 4199 4203 4204 4218 4358 4371 4434 4480 4489 4525 4588 4596 4599 4609 4619 4625 4627 4641 4654 4891 4965 4967 5080 5091 5092 5105 5110 5148 5149 5151 5153 5157 5160 5161 5179 5186 5187 5194 5198 5200 5203 5204 5205 5210 5211 5213 5218 5220 5221 5223 5237 5238 5239 5244 5248 5249 5250 5251 5252 5253 5254 5255 5257 5261 5270 5281 5285 5286 5288 5289 5290 5294 5554 5651 5736 5738 5739 5740 5789 5832 5919 6051 6062 6070 6083 6100 6188 6217 6456 6529 6558 6560 6599 6631 6639 6668 6669 6671 6685 6710 6730 6732 6746 6772 6774 6776 6784 6785 6786 6787 6788 6825 6920 6938 6958 6961 6978 6992 6997 6998 7028 7033 7034 7035 7054 7061 7064 7067 7071 7072 7074 7075 7082 7258 7259 7261 7262 7267 7292 7331 7332 7364 7367 7369 7407 7420 7425 7427 7428 7507 7578 7579 7640 7641 7728 7743 7804 7810 7841 7913 7937 8142 8143 8145 8169 8202 8328 8356 8357 8380 8381 8385 8391 8396 8407 8415 8420 8429 8440 8455 8457 8459 8463 8468 8471 8473 8500 8514 8515 8516 8527 8546 8586 8600 8731 8736 8738 8741 8742 8744 8745 8746 8831 8844 8855 8864 8905 8988 8989 8991 9036 9053 9082 9083 9118 9147 9154 9165 9227 9228 9283 9284 9285 9286 9288 9289 9290 9291 9292 9293 9294 9295 9297 9298 9299 9300 9305 9306 9315 9316 9317 9318 9325 9331 9332 9333 9334 9335 9336 9337 9338 9339 9342 9343 9392 9412 9498 9499 9500 9502 9503 9504 9505 9506 9507 9508 9510 9511 9512 9514 9515 9516 9517 9518 9519 9521 9522 9523 9524 9525 9526 9543 9545 9552 9629 9630 9915 9976 9985 10007 10012 10132 10138 10192 10286 10287 10288 10289 10290 10291 10377 10404 10422 10434 10461 10531 10536 10575 10590 10592 10594 10640 10641 10642 10646 10652 10654 10656 10661 10662 10665 10682 10723 10744 10746 10749 10754 10755 10760 10762 10763 10772 10796 10797 10798 10803 10804 10805 10806 10807 10808 10809 10826 10852 10895 10906 10934 11176 11228 11243 11244 11353 11486 11491 11500 11513 11516 11518 11519 11522 11524 11525 11527 11696 11699 11701 11702 11732 11805 11824 11961 12020 12177 12274 12277 12312 12314 12343 12344 12408 12511 12512 12515 12524 12547 12550 12610 12750 12855 12863 12865 12873 12874 12875 12881 12882 12883 12888 12889 12890 12892 12906 12910 12920 12940 13023 13032 13035 13352 13355 13433 13508 13572 13588 13603 13662 13668 13700 13703 13705 13708 13728 13729 13733 13734 13735 13765 13877 14025 14026 14027 14063 14106 14110 14112 14114 14128 14143 14154 14155 14156 14158 14159 14162 14230 14240 14241 14242 14294 14295 14298 14314 14354 14360 14361 14366 14405 14436 14444 14559 14628 14640 14641 14642 14643 14684 14730 14764 14822 14894 14913 14914 14917 14933 14954 14978 14982 15023 15110 15145 15156 15278 15284 15290 15292 15296 15297 15301 15387 15416 15440 15491 15494 15498 15501 15502 15505 15506 15512 15513 15514 15518 15520 15522 15524 15525 15527 15528 15529 15533 15680 15683 15725 15775 15777 15785 15854 15856 15857 15858 15861 15874 15879 15880 15891 15933 15936 15950 15961 15980 15982 15996 16004 16006 16011 16013 16016 16023 16026 16042 16055 16061 16069 16186 16194 16217 16220 16223 16567 16570 16597 16744 16749 16755 16762 16764 16774 16787 16790 16799 16828 16829 16876 16890 16904 16924 16925 16937 16944 16947 16948 16953 16955 16957 16964 17007 17015 17017 17018 17019 17027 17029 17030 17032 17033 17037 17039 17040 17046 17048 17050 17052 17055 17056 17057 17058 17059 17132 17135 17151 17222 17237 17258 17272 17278 17279 17280 17281 17282 17283 17337 17338 17339 17340 17342 17343 17344 17345 17346 17347 17349 17350 17351 17351 17352 17354 17355 17356 17357 17359 17360 17361 17362 17363 17364 17365 17366 17367 17371 17372 17373 17374 17375 17376 17428 17429 17430 17519 17622 17626 17645 17649 17687 17700 17701 17713 17723 17724 17730 17735 17739 17742 17743 17755 17757 17759 17760 17764 17768 17772 17776 17781 17785 17786 17787 17789 17796 17797 17801 17811 17817 17822 17824 17829 17831 17832 17833 17834 17835 17836 17837 17842 17853 17857 17868 17874 17875 17890 17903 17915 17916 17932 17933 17953 17954 17955 17957 17958 17959 17960 17963 17966 17968 17976 17983 17984 18048 18061 18062 18064 18066 18157 18159 18160 18162 18164 18165 18296 18324 18358 18364 18437 18440 18446 18456 18594 18595 18664 18847 18850 18857 18887 18969 18974 18976 18999 19016 19018 19019 19020 19024 19026 19028 19030 19035 19042 19043 19046 19047 19067 19113 19137 19161 19353 19472 19475 19481 19484 19487 19492 19495 19534 19536 19573 19587 19596 19601 19602 19605 19609 19611 19629 19630 19643 19644 19646 19647 19648 19649 19651 19652 19683 19686 19691 19692 19701 19721 19733 19744 19746 19751 19754 19759 19761 19763 19764 19765 19774 19776 19780 19796 19797 19799 19800 19821 19822 19847 19877 19878 19879 19892 19895 19929 19941 19942 19943 20063 20135 20171 20172 20197 20199 20239 20284 20289 20331 20364 20366 20374 20375 20388 20390 20392 20398 20656 20660 20687 20731 20809 20814 20818 20835 20838 20840 20841 20843 20844 20845 20846 20852 20853 20854 20855 20856 20857 20858 20859 20860 20861 20862 20863 20884 20931 20960 21008 21010 21013 21016 21017 21018 21024 21027 21028 21029 21030 21031 21032 21033 21034 21035 21036 21037 21038 21040 21072 21088 21237 21404 21463 21557 21641 21642 21657 21658 21659 21662 21663 21665 21666 21669 21699 21701 21734 21735 21740 21741 21743 21745 21747 21753 21755 21756 21757 21758 21759 21760 21761 21762 21764 21769 21918 21965 21986 21989 21994 21995 21996 22009 22091 22095 22142 22143 22157 22159 22165 22173 22192 22194 22202 22204 22263 22453 22454 22457 22474 22478 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26832 26900 26900 26902 26906 26972 27015 27021 27047 27078 27096 27097 27098 27100 27101 27102 27103 27108 27111 27112 27113 27117 27118 27119 27120 27201 27203 27215 27228 27229 27260 27277 27280 27283 27293 27297 27298 27307 27310 27312 27318 27385 27481 27554 27597 27600 27642 27752 27753 27754 27758 27759 27768 27783 27803 27815 27847 27851 27875 27876 27893 27895 27898 27899 27900 27930 27937 27940 27943 28026 28115 28123 28135 28141 28174 28189 28195 28228 28291 28318 28375 28467 28567 28588 28589 28593 28608 28612 28613 28614 28615 28618 28623 28625 28626 28632 28833 28941 28954 29005 29007 29009 29014 29015 29016 29024 29073 29122 29276 29277 29278 29279 29282 29290 29297 29298 29303 29370 29419 29446 29912 29923 29960 29962 29992 30016 30017 30018 30065 30069 30095 30098 30114 30128 30135 30137 30156 30190 30191 30238 30242 30268 30292 30298 30304 30306 30342 30346 30466 30490 30520 30523 30616 30817 30825 30828 30841 30859 30897 30909 30910 30911 30913 30915 30918 30927 30933 30934 30935 30940 30943 30946 30947 30952 30953 30956 30957 30962 30966 31131 31165 31179 31304 31312 31397 31431 31453 31454 31456 31460 31515 31559 31561 31599 31602 31607 31622 31628 31634 31640 31643 31644 31646 31651 31653 31654 31656 31659 31662 31666 31667 31669 31670 31671 31678 31684 31686 31689 31691 31711 31713 31714 31721 31722 31724 31727 31728 31733 31788 31789 31798 31853 31857 31858 31861 32014 32015 32016 32017 32050 32052 32089 32120 32125 32140 32143 32144 32145 32168 32182 32183 32190 32191 32193 32195 32200 32350 32401 32405 32467 32491 32493 32496 32500 32518 32535 32538 32539 32545 32548 32549 32570 32583 32589 32593 32596 32693 32706 32823 32824 32834 32835 32923 32936 32974 32983 32999 33002 33024 33068 33069 33164 33186 33187 33195 33227 33232 33235 33237 33239 33240 33241 33243 33292 33310 33311 33321 33362 33371 33373 33374 33382 33384 33385 33417 33419 33436 33452 33453 33457 33503 33551 33553 33600 33602 33603 33608 33617 33621 33628 33631 33634 33638 33639 33640 33641 33649 33656 33660 33665 33679 33681 33684 33688 33691 33692 33693 33706 33712 33713 33714 33742 33791 33799 33801 33993 34135 34199 34204 34205 34208 34265 34270 34305 34307 34308 34311 34318 34330 34333 34340 34342 34343 34344 34346 34348 34349 34351 34361 34434 34481 34503 34504 34616 34677 34678 34684 34761 34767 34783 34784 34785 34786 34787 34788 34789 34790 34791 34792 34793 34794 34795 34796 34798 34799 34800 34801 34802 34803 34804 34805 34806 34807 34808 34809 34811 34812 34813 34814 34815 34816 34817 34818 34819 34821 34822 34823 34825 34826 34828 34830 34832 34833 34834 34835 34836 34838 34839 34840 34843 34844 34845 34847 34848 34857 34861 34862 34917 35018 35018 35031 35094 35100 35147 35158 35262 35285 35342 35379 35448 35478 35499 35531 35535 35539 35541 35542 35544 35545 35547 35551 35552 35565 35569 35571 35572 35654 35673 35678 35679 35680 35681 35685 35714 35727 35795 35899 35900 35903 35923 35938 36001 36002 36003 36027 36100 36107 36193 36199 36228 36425 36458 36461 36534 36538 36583 36584 36634 36639 36720 36723 36725 36734 36755 36757 36758 36763 36764 36773 36774 36775 36800 36825 36843 36883 36929 37027 37028 37039 37067 37131 37133 37143 37167 37183 37207 37336 37352 37483 37488 37492 37520 37550 37657 37659 37663 37668 37799 37875 37903 38022 38085 38156 38164 38180 38233 38296 38302 38304 38311 38312 38315 38415 38418 38429 38439 38512 38581 38585 38594 38597 38599 38601 38613 38615 38626 38634 38635 38652 38717 38719 38731 38733 38748 38749 38769 38790 38838 38858 39020 39064 39111 39115 39190 39213 39214 39216 39217 39218 39219 39241 39341 39346 39347 39350 39399 39415 39480 39534 39587 39602 39604 39615 39617 39659 39667 39676 39682 39718 39815 39816 39830 39847 39850 39852 39912 39938 39939 39941 39947 39949 40005 40008 40011 40018 40048 40052 40060 40073 40078 40083 40085 40103 40104 40105 40106 40123 40135 40139 40153 40160 40162 40164 40165 40168 40169 40174 40494 40495 40498 40626 40627 40632 40636 40639 40640 40641 40642 40643 40646 40648 40663 40664 40665 40676 40679 40688 40690 40691 40709 40814 40942 41014 41015 41016 41017 41078 41131 41193 41194 41195 41197 41199 41236 41239 41241 41243 41244 41247 41249 41252 41256 41258 41260 41261 41348 41350 41368 41378 41455 41457 41460 41481 41484 41485 41487 41490 41491 41493 41497 41499 41535 41538 41560 41562 41616 41931 41945 41950 41989 41990 42001 42006 42053 42071 42085 42089 42095 42145 42147 42172 42213 42285 42287 42301 42307 42313 42330 42395 42413 42418 42439 42456 42666 42697 42706 42711 42712 42713 42715 42716 42717 42720 42731 42736 42737 42738 42754 42773 42846 42872 42889 42892 42896 42897 42971 42988 43112 43316 43317 43376 43389 43391 43424 43458 43472 43483 43484 43485 43578 43583 43626 43627 43628 43636 43642 43653 43807 43897 44242 44245 44264 44267 44277 44278 44279 44280 44281 44288 44371 44422 44470 44498 44509 44528 44602 44620 44707 44726 44771 44894 44934 45065 45224 45231 45344 45356 45378 45756 45804 45836 45854 45858 45861 45869 45873 45877 45881 45888 45892 45895 45979 45993 46085 46123 46124 46125 46127 46131 46132 46137 46163 46167 46187 46209 46211 46212 46218 46227 46288 46293 46303 46321 46364 46375 46380 46392 46454 46471 46491 46493 46494 46495 46496 46497 46521 46546 46549 46567 46568 46592 46597 46697 46725 46795 46833 46834 46858 46859 46885 46886 47017 47145 47220 47226 47244 47280 47301 47338 47339 47341 47355 47383 47389 47392 47397 47421 47442 47444 47445 47446 47448 47449 47462 47468 47471 47481 47518 47519 47524 47526 47528 47532 47535 47542 47555 47557 47576 47600 47602 47620 47629 47645 47658 47659 47677 47678 47679 47680 47684 47692 47697 47708 47729 47738 48004 48040 48044 48052 48095 48137 48147 48156 48178 48184 48187 48201 48204 48209 48213 48264 48277 48281 48284 48298 48300 48307 48322 48331 48332 48351 48384 48387 48415 48431 48467 48469 48492 48495 48526 48527 48545 48555 48580 48589 48607 48616 48662 48663 48679 48704 48713 48744 48751 48766 48795 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158471 158473 158476 158477 158481 158489 158499 158503 158513 158516 161832 162280 162482 162810 178282 205204 205990 221245 221248 221369 221430 231557 231666 232183 235259 235346 235972 235990 236053 236058 237022 237048 237053 237054 237055 238047 238109 238268 238479 238965 239296 239942 240698 240821 241414 241653 241899 241970 242015 242621 259766 259768 262374 262537 262617 262622 263382 263486 263556 263568 263586 263616 263631 263861 263900 264132 264133 264134 264141 264145 264162 264167 264172 264173 264192 264355 264571 264969 265032 266106 267085 267087 267211 267229 267468 267471 267489 267493 267566 267594 267636 267681 267687 267741 267742 267767 267950 268873 268875 269126 269157 269161 269189 269196 270090 270628 271036 271055 271083 271160 271163 271166 271167 271331 271408 271413 271693 271759 272392 275828 276262 281814 281827 281961 281962 302148 302255 302859 302875 302887 311224 311242 311269 311270 311271 311277 332470 332603 332790 332791 332799 332836 332838 332840 332845 332853 332855 332859 333069 333077 333078 333092 333133 333145 333146 333148 333149 333150 333151 333152 333153 333154 333155 333156 333160 333161 333182 333183 333184 333185 333186 333189 333198 333199 333203 333204 333207 333208 333209 333210 333211 333212 333215 333216 333218 333221 333222 333223 333226 333227 333262 333263 333265 333266 333267 333292 333293 333294 333295 333296 333297 333298 333299 333301 333302 333303 333304 333305 333306 333307 333308 333309 333316 333317 333318 333319 333324 333325 333330 333331 333333 333334 333340 333440 333463 333468 333567 333568 333630 333972 334008 334070 334139 334156 334163 338593 339054 339133 339274 339287 339288 339366 339420 339441 339443 339444 339447 339448 339495 339502 339505 339543 339772 339781 339782 339863 340161 340217 340240 340533 340726 340763 340782 340911 341025 341047 341255 341406 341407 341539 341540 341698 341708 341722 341753 342117 342630 342653 343060 343062 343072 343292 344258 344271 344274 344287 344310 345370 348757 349070 349071 349789 375512 376154 392070 392394 392443 392454 392510 392530 393984 395807 395894 395905 396052 396063 398656 399495 400843 400850 400855 400856 400857 400858 400859 401074 401076 401097 401104 401112 401116 401122 401123 403654 403699 403703 403718 403766 403770 404445 404461 404463 404477 404541 406159 406161 406166 406168 406169 406170 406178 406180 406182 406183 406185 406193 406211 406560 406562 406564 406603 406607 410158 410329 410330 410337 410338 410343 410344 410440 410443 410549 410632 410706 410756 410783 423348 425852 425853 426551 426565 426571 426831 427252 428791 428870 428872 432525 438437 441253 442832 442833 442834 442839 442843 442846 442855 442872 442881 442887 444802 445243 448970 448971 450201 456084 457978 457981 459524 459683 472385 473122 473313 473565 474442 474983 474998 475321 475875 487852 489959 494710 520532 520571 520573 520724 520729 521172 521175 521478 521527 521617 521653 521681 521706 521707 521731 521732 521733 521735 522561 522562 522566 524541 541754 542107 544765 544769 544770 544771 544772 544777 544785 544812 544825 544827 544829 545033 545034 546242 546244 546255 546256 546261 546306 546324 546339 546340 546343 546395 546413 546958 549334 549357 553722 554019 559359 560240 563247 564758 566947 566951 577704 578448 581315 581357 581364 585103 587232 589361 595995 678127 700208 700588 729563 729731 730051 730053 740114 740406 740654 740787 741802 747489 747528 749079 749095 749098 749174 749730 750065 750099 751194 751533 751633 751634 751797 839218 849847 852869 854290 856346 856347 856485 858617 858699 859973 860018 860019 860200 860245 860250 865529 865818 865897 866036 866710 877081 877614 919665 919718 919937 936231 939959 939964 940041 940042 940043 941156 948226 948286 1096458 1112368 1112768 1142437 1142477 1168305 1258666 1260959 1262048 1262265 1265607 1265704 1265705 1265706 1265707 1265708 1265710 1265712 1265713 1265755 1265756 1265757 1265875 1269785 1274369 1274574 1274576 1278760 1278799 1281892 1281917 1282203 1282417 1282418 1282419 1282420 1282464 1285499 1290651 1297883 1299564 1299630 1299631 1302784 1302999 1304059 1304401 1306068 1314742 1314743 1328514 1328519 1328531 1331536 1385263 1390840 1391753 1392369 1398762 1398980 1399263 1400387 1401336 1401359 1401567 1404203 1405128 1405408 1405878 1406923 1407920 1408048 1410779 1410860 1444215 1444680 1450010 1455783 1515091 1519666 1527356 1531696 1532195 1533137 1536082 1536126 1608414 1610086)\n(3 1285 5530 7990 9476 15187 15189 15315 15922 16816 18582 19843 20115 20942 23844 26101 35187 35345 38952 43027 80115 206236 206244 242266 242267 242686 282116 441655 600210 871834 872021 872279 1449772 1510476 1565234)\n(4 1588 1589 1675 1792 1795 7667 8059 8100 21270 21289 21293 21294 27362 28296 28829 79377 87178 178694 205653 205847 238598 260267 392363 524337 524338 596727 596728 596947 597696 597772 598880 598967 678804 680085 682051 682052 682053 682054 683972 683973 699810 870102 870892 920381 1444711)\n(5 961 2028 2031 2032 2033 8155 8190 15154 15155 22980 29049 31864 32071 33734 34358 36500 85356 162769 175787 175807 320393 321020 331707 331709 331711 331713 331717 331721 331722 331723 446185 521088 524478 524479 524480 524481 524482 598157 599017 599224 696815 750898 750899 751493 996239 996241 996242 996243 996244 996245 996246 996247 996248 996249 996250 996251 996252 996253 996254 996255 996256 996257 996258 996259 996260 996261 996262 996263 996264 996265 996266 996267 996268 996269 996270 996272 996273 996274 996275 996276 996277 996278 996280 996283 996285 996286 996288 996294 996295 996296 996297 996298 996299 996309 996310 996311 996312 996333 996334 996338 996339 996340 996342 996344 996346 996349 996350 996351 996352 996353 996356 996357 996360 996361 996362 996364 996365 996367 996368 996371 996372 996373 996374 996375 996376 996377 996378 996379 996381 996389 996393 996396 996403 996405 996411 996437 996438 996485 996489 996509 997310 1000895 1000903 1001814 1001863 1001864 1001865 1002289 1002290 1002298 1002304 1002526 1002527 1002528 1002532 1002533 1002537 1002541 1002542 1002544 1002546 1002552 1002553 1002557 1002561 1003564 1003565 1003567 1003568 1003581 1003582 1003583 1003584 1003586 1003587 1003592 1003594 1003598 1003599 1003600 1003601 1003603 1003604 1003605 1003610 1003612 1003626 1003627 1003628 1003634 1003641 1003642 1003643 1003645 1003648 1003649 1003650 1003651 1003652 1003653 1003656 1003660 1003662 1003663 1003664 1003666 1003671 1003673 1003678 1003684 1003686 1004250 1004623 1004624 1004625 1004642 1004643 1004646 1004648 1004722 1004733 1004742 1004881 1005453 1005454 1005456 1005458 1005459 1005476 1005480 1005484 1005485 1005487 1005488 1005491 1005492 1005493 1005494 1005496 1005497 1005498 1005502 1005513 1005515 1005519 1005522 1005745 1005748 1005757 1005871 1006431 1006432 1006683 1006684 1006687 1006985 1007396 1007443 1007447 1007450 1007466 1007467 1007470 1007474 1007475 1007548 1007563 1007570 1007573 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1041445 1043404 1043405 1044801 1044804 1044805 1044810 1044811 1045934 1045937 1046472 1047066 1047894 1048122 1048167 1049033 1049035 1049704 1049709 1050031 1050391 1050393 1051301 1051962 1051963 1051984 1051986 1056614 1056615 1056616 1056618 1057083 1057475 1057835 1059019 1061943 1062184 1062820 1063374 1063384 1063407 1063408 1063447 1064563 1066661 1067664 1068821 1068823 1068826 1068827 1069082 1069392 1069558 1069559 1069795 1072021 1072592 1074593 1074609 1074610 1075244 1075864 1075872 1076206 1076235 1076237 1076238 1076276 1076631 1076634 1076640 1076641 1076642 1076643 1077951 1078158 1078163 1080790 1080791 1080792 1080793 1080794 1080795 1080796 1080797 1080805 1080808 1080811 1080831 1081480 1081481 1081561 1081684 1081685 1081686 1081687 1081694 1081695 1081945 1081974 1082191 1082394 1082465 1082498 1082499 1082818 1083035 1083136 1083137 1083500 1084337 1084864 1084865 1085354 1086344 1086812 1086866 1086944 1087864 1087865 1088333 1088540 1089415 1089439 1090210 1090574 1090864 1091294 1091665 1091834 1092015 1092970 1092973 1092978 1093121 1093122 1093154 1093157 1093208 1093209 1093297 1093300 1093696 1094105 1094347 1094705 1094855 1095779 1187165 1187300 1187602 1187615 1187852 1187853 1187950 1188676 1188677 1190388 1190391 1192084 1192085 1192086 1192215 1192789 1193610 1193801 1193952 1193953 1193954 1194036 1194083 1194089 1194210 1194522 1194771 1194778 1194784 1194790 1195002 1195166 1195167 1195343 1197541 1197895 1197913 1197918 1197919 1197920 1197921 1199306 1199535 1199539 1199542 1199545 1199550 1199859 1199860 1199864 1199869 1199936 1199967 1200003 1200004 1200005 1200015 1200079 1200300 1200414 1202756 1202757 1204041 1204557 1205072 1206702 1206706 1207466 1207467 1208838 1208846 1208855 1208863 1208928 1209931 1209939 1211011 1211396 1211834 1211971 1212606 1212609 1212610 1212622 1212795 1213845 1213846 1213926 1214157 1215794 1215802 1215804 1215805 1216380 1217013 1217377 1217689 1217852 1217881 1218419 1218420 1218423 1220013 1220802 1221340 1221569 1222294 1222343 1222585 1222718 1223459 1223464 1223465 1224412 1224785 1225860 1225994 1228488 1229337 1229500 1230103 1232486 1232880 1257934 1458365 1458446 1462013 1462519 1462523 1462526 1462652 1462666 1462669 1462674 1462679 1462681 1462688 1462693 1462706 1462754 1463030 1464059 1464113 1464283 1464284 1464894 1465418 1465420 1465421 1469314 1469315 1469319 1470084 1470490 1475992 1477165 1477674 1481724 1481725 1481779 1482304 1482314 1482315 1482316 1482317 1482878 1483099 1483216 1483218 1483373 1483838 1483968 1485470 1485610 1485637 1485639 1485678 1485682 1485685 1485686 1485692 1485915 1485917 1485919 1485934 1485981 1489704 1489705 1489706 1489708 1489709 1491359 1491778 1492549 1492871 1493603 1494354 1494357 1496205 1496232 1496530 1497310 1497632 1497634 1497879 1498962 1500406 1500408 1500518 1500519 1500521 1500537 1500546 1500557 1500564 1500588 1500958 1502819 1503010)\n(6 2518 37081 282534 282535 282536 525021 598667 599216 600499 682969 872168 920679 949662 1510701 1510939 1511010 1511011 1511012 1511013 1511015 1511026 1511029 1511077 1511331 1511358 1511359 1511474 1511603 1511644 1511655 1511662 1511738 1511990 1512046 1512113 1512142 1512313 1512475 1512495 1512665 1513163 1513806 1513812 1513868 1514490 1514524 1514535 1514562 1514648 1515032 1515099 1515175 1515557 1515859 1515860 1516143 1516692 1517104 1517371 1517645 1517692 1517773 1518145 1518456 1518791 1518792 1518793 1518794 1518803 1518827 1518833 1518834 1519063 1519124 1519134 1519141 1519149 1519254 1519623 1519724 1519727 1519739 1519878 1520108 1520109 1520153 1520222 1563691)\n(7 2429 2430 2431 2668 2673 3459 6354 6355 6356 6357 6358 27548 27549 28440 31964 32235 33614 34651 34652 34653 34654 34655 34662 36060 36062 36063 39311 40324 41124 42058 43342 43343 86705 86949 260223 260305 260307 260308 260309 260310 326968 326970 326974 326975 326976 326977 326978 326980 326981 326982 326985 326986 326987 326988 326992 326993 326994 326995 326996 326998 327000 327001 327002 327004 327008 327011 327014 327016 327017 327018 327019 327020 327022 327023 327024 327025 327029 327031 327034 327035 327036 327037 327038 327041 327042 327048 327049 327050 327052 327055 327057 327058 327060 327061 327062 327063 327064 327065 327066 327067 327068 327070 327072 327074 327075 327077 327078 327079 327080 327083 327084 327085 327086 327087 327089 327091 376341 392731 597830 597890 995135 998985 998988 998989 998991 998992 998993 998994 998995 998997 998998 998999 999000 999001 999002 999003 999004 999006 999007 999008 999009 999010 999011 999012 999013 999014 999015 999016 999017 999018 999019 999020 999021 999022 999025 999026 999027 999029 999030 999031 999032 999033 999034 999035 999037 999038 999039 999040 999041 999042 999043 999047 999050 999051 999052 999053 999054 999057 999058 999059 999060 999061 999062 1001583 1003176 1003177 1003178 1003179 1003180 1003181 1003183 1003184 1003188 1003189 1003190 1003192 1003193 1003194 1003195 1003197 1003198 1003199 1003200 1003203 1003204 1003205 1003206 1003207 1003208 1003210 1003838 1004206 1005406 1006194 1006195 1008299 1008300 1008301 1008306 1008309 1008314 1008315 1008316 1009646 1010496 1010497 1010498 1010500 1010532 1010774 1010781 1010809 1010810 1010814 1010815 1010827 1010828 1010835 1010846 1010847 1010852 1011372 1011375 1012101 1013355 1013357 1013362 1013365 1013369 1013371 1013381 1013382 1013383 1013384 1013385 1013386 1015635 1015859 1015925 1015926 1016128 1016326 1016433 1016437 1019891 1020230 1020231 1020236 1020250 1020893 1020898 1022661 1022797 1022934 1026946 1026947 1026949 1026950 1026951 1026955 1026960 1027491 1027492 1027690 1027804 1028174 1028773 1031572 1031573 1031574 1031575 1031631 1031633 1033482 1033483 1033484 1033934 1036399 1036400 1036401 1036403 1037168 1037504 1037814 1038016 1038887 1038888 1039174 1039175 1041721 1041724 1041725 1041729 1041732 1042179 1042180 1042611 1043033 1043239 1043240 1043241 1043243 1043244 1043249 1044730 1047200 1047689 1047733 1047735 1047737 1048091 1048093 1048094 1048637 1048916 1048951 1048952 1048953 1048954 1050073 1050453 1050479 1051230 1051232 1051233 1051726 1051727 1051730 1051776 1051777 1051780 1051789 1051790 1051791 1051792 1051793 1051800 1052321 1052327 1052328 1052346 1052367 1052376 1052504 1052581 1052582 1053617 1053836 1053837 1053840 1056539 1056555 1057480 1057481 1057951 1057952 1057953 1057960 1058355 1058358 1058361 1058362 1058363 1058743 1058821 1061229 1061237 1061238 1061270 1061574 1061579 1062227 1062234 1062242 1062243 1062343 1062359 1062675 1062676 1065029 1065030 1065608 1065610 1068440 1069667 1069947 1070867 1071155 1071166 1072082 1072458 1072912 1072913 1073796 1073806 1074875 1074876 1074877 1074878 1074879 1074887 1075196 1075737 1075738 1076568 1076569 1076570 1076571 1076979 1078464 1079147 1079516 1081146 1081149 1081152 1081634 1081635 1081636 1081637 1081638 1082287 1082290 1082291 1082589 1082633 1082640 1082642 1082646 1082647 1083007 1083450 1083994 1083996 1083997 1084045 1084047 1084080 1084949 1084952 1086402 1088143 1088555 1088749 1089049 1089050 1089197 1089683 1090091 1090156 1090253 1090641 1091121 1091289 1091783 1092262 1092263 1092339 1093028 1093367 1093369 1093552 1093704 1094472 1094666 1094719 1095356 1095780 1187069 1187108 1188029 1188251 1188279 1188324 1188426 1189197 1190850 1190851 1190856 1190860 1190870 1190871 1190872 1190874 1190885 1190918 1190926 1190927 1190951 1190956 1190959 1190961 1191004 1191009 1191010 1191011 1193400 1193401 1193403 1193425 1193462 1194625 1194626 1194628 1194631 1194634 1195332 1195551 1195552 1202751 1204765 1213008 1213009 1213288 1213290 1213291 1213292 1213988 1214030 1214221 1214222 1214225 1214226 1214227 1214781 1215248 1215250 1215252 1215259 1215265 1216139 1216293 1216299 1216306 1216386 1216387 1216388 1225602 1225603 1227460 1227462 1227463 1228208 1228211 1304607 1306843 1444149 1458211 1458212 1458595 1458734 1458737 1458751 1458752 1458753 1458759 1460536 1460537 1460542 1460543 1460544 1460713 1461928 1462839 1463279 1463385 1464401 1464564 1466122 1466125 1468494 1468961 1469692 1469693 1469696 1470110 1470115 1470119 1470127 1470155 1470158 1470203 1470211 1472424 1472607 1472610 1473116 1475145 1475162 1476624 1476625 1476630 1476631 1477061 1477337 1477454 1477910 1479742 1479743 1479744 1479745 1479766 1479767 1481759 1482210 1482211 1482214 1482256 1483141 1485822 1489418 1490953 1490962 1492469 1492471 1492473 1492480 1492486 1492489 1492492 1497788 1498073 1498154 1498159 1499582 1501371 1502135 1502139 1502146 1502940 1502941 1503233)\n(8 2940 2959 3486 3534 3843 3855 5136 5690 5745 6262 7479 9376 9451 10051 10709 11361 11998 12811 12817 14067 14511 14670 14854 14856 15207 16169 16202 16506 17128 18536 18564 18789 18946 19270 19284 19287 19288 19291 19294 19295 19296 19311 19316 19319 19326 20449 20496 21833 21846 21934 21935 22680 22821 22906 23075 23221 24003 24215 24421 24636 25514 25585 26686 27430 29293 29436 29531 30290 30795 31925 32584 33377 33998 34089 34884 34895 36094 36420 36439 37157 37932 38355 38358 38449 39137 39147 39273 40456 40588 40963 41974 42253 42282 42454 42582 79238 79943 80107 80304 85686 86543 86783 86809 149614 149659 149662 149773 149952 151261 151536 151790 151919 152102 152454 154724 154933 155116 155136 155247 155251 155369 155509 155512 155675 155676 155730 155738 155740 155796 155940 155944 155947 156088 156183 156246 156272 158053 158100 158288 158364 158505 162019 162868 205792 205929 221224 221373 221375 221766 221782 235761 235942 237065 238093 238126 238127 238129 238130 238133 238134 238397 238424 238441 238492 238521 239005 239337 240140 240295 240309 240310 240547 240880 241593 242150 259770 262375 262391 262549 262621 262627 263532 263886 263905 264000 264585 264998 265004 265008 265019 265048 265098 265101 265913 265982 266030 266061 266751 266752 266757 266758 266762 266763 266764 266785 266786 266839 266840 266915 267079 267080 267081 267091 267180 267353 267358 267359 267360 267361 267465 267482 267483 267484 267485 267486 267561 267571 267581 267588 267635 267665 267672 267725 267732 267733 267747 267748 267789 267790 267791 267898 267899 267928 268709 268842 268843 268844 268845 268846 268889 268892 269121 269133 269136 269141 269143 269144 269145 269147 269185 269199 269207 269251 269269 269852 270675 270720 271004 271128 271131 271134 271135 271165 271409 275873 278440 281771 281790 281830 281842 281857 281892 281914 281970 302142 302146 302501 302850 332447 332472 332482 332561 332599 332886 333010 333044 333047 333056 333062 333068 333091 333093 333094 333095 333097 333099 333100 333101 333105 333108 333109 333111 333113 333115 333157 333187 333188 333190 333311 333336 333338 333339 333342 333372 334067 334088 339182 339429 339462 340214 340235 340278 340570 340572 340573 340574 340613 340616 340617 340618 340621 340622 340625 340630 340635 340636 340637 340638 340639 340643 340647 340775 340776 340791 340985 341029 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442888 443227 445180 456274 457193 460148 472842 473244 474356 477611 494956 500526 500527 500585 521605 521618 521619 521620 544015 544754 544755 546297 546303 546466 546487 546964 549189 549198 549397 549423 549618 553718 555248 558374 559255 561921 567335 574027 574041 574042 574046 575157 576093 576339 576416 578510 578575 582253 585012 585173 585263 585984 595997 596384 597984 600039 679403 684903 685105 700253 700510 700638 701805 729847 730201 730202 730203 730204 730206 740280 740375 741092 741333 741880 742352 742922 743007 743857 743968 744321 744400 745357 746766 748858 748924 749104 749867 750033 750101 751105 751315 751457 752155 752156 752158 752159 795693 838019 838245 850304 851256 852390 853954 854141 854282 854288 854371 854494 854719 854720 854723 856749 856771 856861 856862 857548 858213 859257 859994 860144 860260 860498 860573 866038 866718 871080 877104 877306 919617 919717 919880 920052 920299 940885 941132 948017 948370 1096086 1096096 1096098 1096099 1096100 1096212 1096611 1112206 1112371 1112380 1112561 1112599 1136179 1138421 1142216 1142533 1142543 1168154 1168292 1260954 1262208 1262242 1262266 1265572 1265574 1265575 1265601 1265602 1265603 1265604 1265605 1265606 1265679 1265730 1265735 1265736 1265751 1265752 1265753 1265754 1265764 1265777 1265780 1265781 1265782 1265786 1265787 1265788 1265789 1265790 1265817 1265818 1265859 1269784 1275286 1275287 1275289 1275957 1285497 1285498 1288350 1290398 1290520 1291129 1299541 1301149 1302359 1302869 1305122 1306065 1306529 1306710 1318539 1318999 1328363 1328512 1373220 1384594 1390868 1396413 1397399 1401568 1404246 1408443 1409431 1409519 1409763 1442998 1446299 1446783 1504507 1510412 1510420 1510475 1510497 1525420 1527161 1531581 1533013 1536875 1541919 1556534 1557678 1557689 1557971 1557989 1557995 1558001 1558040 1559461 1559502 1559508 1560348 1562176 1563275 1563282 1608420 1608953 1608977 1610055 1610089 1611719)\n(9 3043 3062 3063 3064 3065 3066 3067 3069 3070 3071 12656 31268 162318 562690 562691 562693 562694 596888 597685 598744 599779 682496 682501 682502 683949 684068 869004 870553 870830 887965 887966 920312 920362 950152 969757 1171352 1171353 1511501 1514783 1516786)\n(10 6629 6933 85088 222052 332862 443322 444584 444911 546245 588441 700276 1268086 1285097 1305737 1508506 1511493 1513264 1517053)\n(11 488 699 1086 1259 1268 1714 1897 2151 2435 2436 2475 2499 2501 2645 2679 2680 3082 3167 3232 3233 3234 3235 3236 3237 3238 3240 3387 3388 4480 4499 4521 4599 4717 5736 5738 5739 5740 6200 6319 6487 6834 6835 6926 6968 6976 7241 7537 7538 7541 7545 7546 7549 7550 7551 7552 7553 7554 7555 7556 7557 7558 7559 7560 7561 7562 7714 7716 7721 7727 7732 7735 7736 7737 7738 7741 8168 8293 8861 8877 8947 9077 9315 9316 9317 9318 10523 10572 10590 10861 10934 11276 12024 12025 12093 12317 12750 13089 13090 13508 13603 14405 14806 14809 14810 14813 16095 16187 16267 16610 16611 16673 16875 16898 17436 17449 18157 18160 18164 18165 18242 18547 20759 20933 22419 22487 22723 22914 23410 23726 24072 25373 25603 25643 25893 26186 26187 26202 26234 26408 26458 26651 26933 27324 27444 27515 27519 27521 27603 27607 27780 27781 27783 28076 28458 28741 28743 28902 28923 28951 28967 29983 30092 30178 30576 30811 30820 30821 30827 30829 30830 30840 30842 31559 31955 32032 32535 32538 32539 32697 34145 34146 34208 34217 35554 35608 35609 35654 35750 35835 35891 35947 35972 36291 36548 37209 37490 37496 37509 37531 37536 37540 37759 37796 37962 37963 38155 38425 38426 38427 38429 38430 38432 38665 38666 38702 39184 39266 39644 39651 39854 39861 39947 40193 40341 40563 41058 41157 41165 41385 41441 41442 41499 42287 42313 42697 42754 43480 44370 49519 50133 50383 50561 50642 50646 50663 50713 50991 51587 51653 51897 51936 51991 52078 52145 52523 52585 52614 52615 52669 52709 52713 52717 52767 52772 52796 52865 52913 52918 53065 53154 53155 53326 53327 53557 53834 53841 53842 53847 53853 53882 53951 53961 54036 54066 54256 54362 54539 54548 54583 54615 54638 54667 54700 54879 54995 54996 54999 55000 55001 55003 55004 55005 55006 55007 55008 55011 55013 55014 55015 55017 55074 55075 55081 55208 55274 55283 55465 55856 55860 55871 55880 55881 55915 55921 56081 56209 56224 57085 57144 57193 57197 57387 57507 57572 57993 58170 58445 58815 58837 58868 58964 59041 59362 59374 59424 59433 59508 59561 59562 59564 59566 59567 60112 60400 60405 60591 60680 60739 60839 60856 60859 60879 61264 61335 61935 62073 62076 62114 62561 62587 62986 63217 63512 63850 64108 64116 64165 64250 64267 64376 65295 65485 65514 65718 65841 66005 66012 66082 66506 66511 66531 66546 66588 66707 66822 66998 67010 67012 67693 68391 68474 68506 68536 68555 68758 68828 68901 68918 69386 69403 69448 69584 69684 69733 70056 70233 70238 70557 71128 71289 71979 72176 72513 72520 72849 72863 72952 72972 72980 73012 73215 73371 73372 73380 73491 73574 73575 73616 73688 73712 73987 74024 74135 74143 74144 74153 74156 74491 74494 74506 74558 75280 75299 75300 75321 75342 75416 75504 75512 75544 75620 75629 75637 75719 75748 75786 75858 75859 75870 76079 76131 76394 76433 76673 76681 76686 76821 77063 77235 77236 78047 78285 78490 78763 80320 81959 82037 85259 85795 85855 85884 85905 85937 85939 86513 86725 90409 92502 93841 97728 100301 100690 101744 101883 102284 103148 103149 104311 104449 104693 104732 105301 106603 106732 106734 106750 107203 108936 108938 108941 108946 108947 108950 109003 109035 109054 109114 109739 110038 110462 110802 111018 111374 111402 111914 112748 113171 115636 117117 117253 117793 117794 118631 118632 122398 122813 123418 124008 124134 124206 124231 124500 124551 124734 124967 125179 125457 125577 126571 127260 127399 128443 128444 128496 128562 128678 128686 129210 130887 132129 134502 135607 135717 135719 135981 135982 137725 137902 137997 139817 140149 140575 140755 141017 141689 142106 142817 144299 145106 145918 146210 147814 148185 149070 149232 149233 162312 162724 163029 163557 165380 166136 166138 169614 170089 171230 171273 174195 205881 205992 205994 205996 205997 206788 208578 209475 213540 213609 220589 220892 243392 243641 245477 245519 245581 246584 250480 250482 254093 255738 258560 262960 262964 262967 279516 280049 281209 282052 282105 282125 282155 282215 282219 282242 282252 282265 282269 282355 282361 282390 282391 282531 282713 284657 284728 284915 285868 286095 286424 286425 286511 287722 296895 300156 301322 304311 304315 304317 304319 304320 304323 304324 304325 304326 304674 308277 308335 308454 308626 308875 309567 310362 338196 350711 350794 354772 355824 355853 355946 356164 358859 358860 358877 360319 360320 360332 360334 360339 360342 360343 360351 360357 360358 360365 360366 360367 360372 360373 361823 369246 377011 377076 377919 378363 384266 385222 391524 449845 520529 521886 521887 521891 521892 521894 521898 521899 521900 521901 521918 524652 524961 525570 526512 526513 531848 533545 539935 540564 540565 543454 546866 546879 546880 591076 591081 591132 591239 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1528937 1529601 1529767 1529803 1529965 1561590 1562785 1563655 1563657 1563974 1563980 1563996 1564187 1564344 1564557 1565220 1565388 1565404 1565772 1566394 1567123 1567133 1567134 1567490 1568233 1568300 1568573 1568574 1568612 1571718 1579335 1579336 1586728 1586734 1601917 1608618 1610936 1612792 1614132 1614523 1614700 1615061 1615658 1619965 1846989)\n(12 3732 18539 18540 25621 39820 85445 85456 85457 85458 85459 85521 85522 85523 85524 85526 85527 85528 85529 85530 86382 524777 524778 524779 524780 524820 524821 524822 524826 524827 524829 524830 524831 524833 524834 524835 524836 524839 524840 524841 524842 524843 524845 524846 524847 524848 524849 524853 524854 524855 524856 524857 524915 524916 524917 524918 524919 597901 597902 597903 598547 598862 599690 599691 600435 872166 872384 995869 995870 995871 995872 995873 995875 995877 995878 995879 995882 995883 995884 995885 995886 995887 995888 995889 995890 995892 995893 995894 995895 995896 995897 995899 995900 995901 995903 995904 995905 995906 995907 995908 995909 995910 995911 995912 995913 995914 995915 995916 995917 995918 995919 995920 995921 995922 995923 995924 995925 995926 995927 995938 995939 995940 995942 995944 995945 995946 995947 1000472 1000891 1000892 1002016 1002576 1002577 1002578 1002580 1002582 1002583 1002674 1005703 1005789 1005790 1005791 1005792 1005793 1005794 1005795 1006406 1007223 1008013 1008203 1008353 1009651 1009653 1009869 1010519 1010942 1011005 1011441 1011659 1011821 1012319 1012691 1012692 1012751 1012850 1013208 1014967 1014968 1015266 1015835 1016081 1017376 1017745 1017746 1017813 1017814 1017915 1017917 1017918 1017919 1017921 1017923 1017924 1017926 1017927 1018992 1019598 1019599 1019637 1019970 1022439 1022440 1023084 1023383 1023384 1023847 1024358 1024361 1024833 1026196 1026197 1026614 1027183 1027200 1027204 1027205 1027592 1028207 1028475 1028476 1029072 1029073 1029453 1029594 1030652 1030923 1030924 1032211 1033927 1034759 1035200 1035807 1036067 1036101 1036294 1036323 1036407 1036409 1036410 1036411 1036527 1040208 1040391 1040392 1040661 1041117 1043002 1044580 1045373 1046689 1049214 1049215 1049481 1051823 1051824 1052883 1054275 1054279 1054385 1056431 1058744 1058745 1062629 1062801 1064697 1065059 1069414 1069941 1069942 1069943 1069944 1070697 1070731 1074493 1078503 1080744 1080745 1081564 1082586 1082699 1083664 1093188 1188193 1188357 1188586 1192305 1194220 1195389 1198243 1198848 1204869 1206440 1208424 1208436 1208462 1208463 1211448 1211449 1213796 1215394 1215815 1217481 1217500 1217783 1222277 1224500 1227238 1234791 1235489 1257748 1458332 1458347 1459104 1463981 1464876 1475435 1480578 1481878 1486326 1486818 1498319)\n(13 84 137 257 376 392 407 412 427 464 481 545 578 588 656 657 702 829 843 996 1003 1026 1055 1056 1097 1157 1158 1237 1239 1245 1271 1291 1347 1369 1374 1407 1412 1413 1443 1455 1459 1460 1461 1465 1468 1480 1652 1657 1694 1734 1814 1898 1924 2052 2083 2129 2139 2151 2189 2190 2191 2193 2198 2205 2210 2211 2215 2240 2241 2248 2255 2256 2257 2258 2261 2269 2270 2274 2278 2287 2309 2310 2311 2318 2340 2358 2520 2521 2525 2527 2531 2553 2563 2607 2612 2670 2677 2716 2721 2722 2727 2728 2791 2843 2854 2976 3009 3012 3017 3018 3134 3136 3284 3320 3410 3438 3440 3521 3574 3590 3591 3592 3593 3594 3595 3601 3641 3679 3682 3731 3765 3899 3987 3995 4011 4015 4029 4130 4221 4338 4409 4434 4525 4625 4627 4630 4638 4641 4891 4920 4954 5151 5153 5157 5179 5186 5187 5198 5203 5204 5221 5239 5248 5249 5250 5254 5280 5281 5286 5290 5294 5390 5402 5404 5433 5437 5444 5445 5446 5515 5522 5554 5562 5789 5832 6052 6054 6062 6070 6136 6232 6353 6360 6558 6618 6631 6639 6643 6675 6678 6685 6730 6746 6772 6774 6785 6786 6787 6788 6825 6960 7012 7061 7267 7269 7271 7289 7292 7332 7364 7420 7578 7630 7640 7648 7745 7746 7810 7831 7839 7910 7937 8013 8024 8134 8141 8240 8260 8262 8368 8377 8387 8404 8405 8454 8466 8468 8518 8574 8600 8601 8731 8738 8746 8776 8831 8861 8864 8905 8988 9140 9147 9148 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199664 199668 199678 199729 199747 199751 199763 199769 199850 199873 199900 199915 199972 199994 199995 200000 200005 200007 200008 200009 200044 200045 200046 200048 200068 200069 200086 200087 200101 200113 200116 200118 200119 200123 200125 200134 200140 200150 200152 200154 200156 200159 200161 200182 200189 200193 200199 200200 200204 200205 200208 200211 200292 200297 200798 200801 202529 202542 202603 202606 202610 202613 202616 202657 202659 202660 202662 202681 202691 202702 202703 202732 202744 202745 202750 202752 202757 202765 202766 202767 202784 202808 202811 202812 202820 202823 202833 202845 202847 202850 202855 202859 202868 202890 202896 202897 202909 202910 202921 202926 202930 202931 202936 202951 202952 202956 202957 202961 202962 202974 202977 202983 202984 202985 202986 202990 202991 202994 203026 203027 203031 203032 203033 203039 203042 203043 203047 203049 203051 203054 203057 203064 203065 203071 203075 203079 203081 203082 203083 203084 203085 203086 203101 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1500447 1500520 1500522 1500709 1500806 1500807 1501241 1501244 1501265 1501266 1501346 1501383 1501409 1501424 1501434 1501435 1501492 1501506 1501509 1501511 1501517 1501559 1501807 1501902 1501931 1501937 1501945 1502060 1502063 1502158 1502165 1502237 1502255 1502355 1502394 1502404 1502410 1502411 1502627 1502917 1502925 1502930 1502931 1502934 1502942 1502944 1502954 1502955 1502957 1503139 1503210 1503211 1503225 1503241 1503320 1503328 1503378 1503420 1503421 1503422 1503562 1503578 1503652 1503658 1503670 1503672 1503679 1503685 1503695 1503705 1503732 1503810 1503836 1503838 1504080 1504640 1504651 1504664 1510492 1517584 1532045 1532046 1532047 1533160 1562369 1562578 1562715 1562882)\n(76 103 176 232 248 287 481 665 983 1004 1017 1185 1187 1204 1595 1730 1771 1933 2374 2406 2485 2496 2503 2560 2578 2593 2613 2620 2676 2677 2696 2710 3072 3162 3817 4334 4338 4754 5070 5104 5429 5430 5432 5436 5449 5667 6215 6216 6239 6247 6251 6312 6353 6528 6556 6617 6692 6703 6714 6926 6991 7043 7250 7445 7974 8232 8238 8247 8248 8577 8583 8584 8599 8762 8996 9185 9742 9924 9979 10360 10454 10460 10467 10511 10564 10573 10574 10974 11051 11145 11148 11182 11953 12004 12005 12007 12018 12124 12256 12384 12398 12402 12426 12456 12460 12463 12531 12533 12584 12695 12783 12784 12786 12788 12790 12893 12894 12895 13254 13343 13618 13714 14129 14444 14448 14639 14824 14839 14991 15018 15051 15082 15101 15205 15893 16071 16184 16312 16314 16320 16321 16342 16349 16575 16576 16849 16945 16979 16984 17440 17542 17776 17814 18302 18964 19215 19832 19941 20259 20281 20282 20368 20411 20738 20929 21075 21212 21219 21225 21234 21717 21936 21961 21971 21972 21973 21983 21990 22003 22004 22005 22014 22026 22028 22029 22032 22033 22034 22038 22041 22049 22086 22115 22124 22216 22399 23341 23850 24075 24076 24100 24574 24577 24728 25416 25701 25729 25746 25809 25869 25870 25876 26234 26323 26381 26485 26800 27506 27941 28098 28132 28147 28187 28193 28375 28604 28752 28952 28967 30120 30123 30966 30981 31068 31243 31430 31478 31492 31505 31566 31567 31730 31855 31858 31951 32434 32486 32830 32837 32838 32881 32884 33259 33468 33470 33501 33505 33509 34131 34251 34303 34316 34330 34338 34404 34423 34440 34548 34551 34759 34760 35483 35486 35683 35857 35975 36008 36137 36584 36775 37191 37375 37498 37499 37521 37523 37524 37525 37533 37534 37545 37558 37626 37638 37914 38071 38128 38135 38142 38164 38738 38753 38770 39329 39415 39416 39418 39419 39672 39681 39690 39694 39696 39704 39883 39958 40099 40242 40270 40380 40494 40854 40976 40982 41018 41066 41081 41175 41213 41289 41411 41483 41738 42068 42093 42694 43141 43164 43166 43367 43368 43697 43780 43858 43863 44018 44046 44052 44054 44078 44122 44131 44178 44235 44291 44292 44478 44493 44499 44517 44565 44587 44613 44614 44951 44972 45089 45127 45129 45246 45259 45279 45293 45384 45391 45511 45673 45715 45758 45834 45916 45917 45919 45920 45921 45967 46056 46064 46088 46096 46204 46252 46269 46272 46302 46352 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54126 54130 54135 54147 54302 54391 54418 54476 54486 54495 54634 54642 54673 54677 54692 54696 54697 54801 54924 55019 55040 55113 55114 55136 55138 55270 55280 55307 55313 55361 55406 55552 55555 55560 55612 55613 55614 55622 55630 55633 55644 55645 55882 55978 56208 56215 56270 56300 56341 56403 56484 56528 56588 56592 56593 56594 56598 56604 56655 56692 56813 56895 57107 57109 57110 57122 57124 57128 57134 57253 57269 57290 57582 57593 57664 57700 57785 57821 57885 57942 57948 58123 58136 58163 58219 58243 58251 58288 58375 58387 58391 58437 58438 58441 58470 58494 58635 58640 58714 58834 58862 58869 58943 59466 59515 59526 59617 59696 59720 59722 59748 59749 59754 59759 59792 59799 59821 59883 60083 60120 60158 60205 60234 60255 60259 60264 60468 60520 60524 60527 60528 60533 60538 60549 60552 60559 60562 60600 60621 60752 60930 60933 60934 61011 61013 61198 61228 61587 61641 61700 61756 61856 61890 61926 62071 62168 62183 62204 62546 62552 62571 62597 62607 62612 62620 62640 62687 62714 62740 63118 63196 63263 63369 63397 63476 63753 63757 63765 63766 63773 63775 63788 63793 63805 63810 63813 63816 63817 63828 63864 63908 63910 63914 63930 64037 64061 64136 64137 64598 64606 64698 64711 64720 64724 64964 64970 65020 65037 65086 65220 65234 65274 65555 65603 65605 65636 65723 65729 65749 65758 65881 65884 65885 65912 65985 66018 66052 66069 66070 66072 66116 66220 66222 66274 66279 66287 66314 66315 66367 66375 66402 66696 66724 66732 66736 66912 67005 67297 67314 67319 67332 67453 67525 67560 67562 67578 67768 67860 67864 67878 67879 68005 68023 68087 68103 68264 68294 68424 68460 68467 68511 68660 68661 68686 68703 68752 68765 68792 68806 68818 68824 68828 68858 68935 69130 69316 69324 69360 69388 69464 69591 69592 69596 69597 69670 69715 69748 69881 69925 69954 70115 70139 70198 70281 70300 70386 70427 70429 70431 70619 70626 70665 70672 70673 70674 70711 70732 70824 70889 70912 70953 70969 71037 71044 71047 71072 71109 71175 71519 71525 71574 71632 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27944 27945 28627 29142 29205 29392 30291 30495 30605 30625 30944 31067 31509 31752 31753 32004 32102 32181 32184 32366 32428 32520 32847 32853 32935 33085 33629 33676 33707 33779 34109 34532 34554 34580 34584 34586 34589 34596 34603 35269 35376 35864 35965 36406 36743 36759 36776 36782 36786 36787 36788 36792 36799 36806 36807 36812 36813 36816 36820 36828 36833 36836 36837 36871 37024 37300 37612 37711 37802 37803 37804 37805 37806 37807 37808 37810 37812 37813 37815 37842 38026 38568 38577 39129 39479 39773 39807 39813 40130 40228 40284 40839 40901 41372 41394 41609 42014 42038 42044 42879 43159 43301 78964 79126 79168 79240 79365 79366 79367 79603 79604 79607 79608 79609 79611 79639 79718 79721 79837 80003 80004 85108 85115 85117 85184 85185 85186 85188 85192 85194 85197 85254 85531 85672 86013 86231 86621 86984 87085 87124 87129 149634 150890 162401 162461 162462 162621 162622 162676 162731 162788 162789 162801 162802 162803 177881 178563 178748 189587 199524 200345 200354 200363 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920103 920175 920178 920269 920393 920394 920474 920563 920569 920645 920710 920711 920747 920779 947637 947878 947897 947898 948016 948031 948108 948163 948191 948233 948273 948309 948493 948591 948642 948645 948646 948652 948686 948713 948725 948782 948809 948846 948887 948915 948973 949015 949085 1096045 1096093 1096198 1096404 1096406 1096438 1096439 1096561 1096619 1096647 1096720 1110554 1112143 1112318 1112343 1112354 1112470 1112480 1112483 1112488 1112625 1112658 1112728 1140716 1140999 1141861 1141921 1141928 1141930 1142004 1142069 1142083 1142113 1142157 1142164 1142172 1142174 1142175 1142189 1142250 1142259 1142264 1142338 1142380 1142389 1142450 1142464 1142471 1142492 1142506 1142511 1142527 1142549 1142551 1154505 1154712 1155265 1155266 1156244 1167661 1167684 1167947 1168151 1168152 1168153 1168158 1168241 1168281 1168521 1260413 1260961 1261287 1261562 1262013 1262019 1262023 1262109 1262114 1262141 1262205 1262246 1262301 1262308 1263727 1263829 1263983 1263985 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1410098 1442418 1442903 1443257 1443897 1444073 1444079 1444174 1444781 1446325 1446357 1452968 1455874 1455875 1455886 1455887 1455907 1456184 1456185 1456250 1456352 1456863 1458137 1504364 1504365 1504421 1504450 1504464 1504476 1504518 1504524 1504558 1504566 1504586 1510411 1510493 1516670 1518304 1518979 1519279 1519659 1519660 1519683 1519697 1520005 1521846 1522056 1522058 1527304 1527348 1531527 1531559 1531582 1531833 1533637 1533651 1533689 1535935 1535987 1536023 1536148 1536163 1536216 1536255 1536256 1536705 1536756 1537049 1537065 1540677 1549006 1549011 1549017 1556247 1558956 1560244 1560305 1560581 1560740 1560751 1560774 1561230 1561256 1561381 1561656 1561662 1562197 1562413 1562540 1562898 1563155 1563255 1563264 1563296 1563937 1566590 1608322 1608422 1608974 1608975 1608981 1609526 1609536 1610046 1610068 1610079 1610624 1611170)\n(105 2217 33159 282671 336529 336535 336666 337115 337141 376432 949783 1136288 1136289 1283254)\n(106 894 912 924 929 930 931 932 2035 11117 12618 12652 13829 13956 14415 14499 14676 15191 15329 15333 15619 15744 16141 16462 16477 23670 23672 23983 24069 24920 28263 28264 30011 33095 33586 33902 34106 34533 34897 35020 86562 86898 175921 175961 178796 178812 221188 234402 241842 241922 242679 242833 242918 259913 260009 261372 282165 301644 311435 314672 337027 337034 337074 337196 337200 337201 337209 376293 376522 376590 414085 418391 441722 441723 444690 444709 449421 449428 450027 452216 456453 458142 489547 522732 563027 563028 563030 563034 563290 563291 563531 563538 563540 563547 563557 563559 563595 596043 596262 596311 596319 596438 596491 596565 596801 596837 596891 596965 597225 597490 597538 597598 597599 598393 598528 598554 598636 598972 599225 599226 599281 599506 599746 677038 680082 681792 814828 867551 868945 869032 870079 870107 870455 870945 871732 871915 871918 871956 872366 1254481 1257789 1258199 1328815 1367973 1510610 1512196 1514233 1521871 1522240 1562835 1579887 1615608)\n(107 5529 5551 5775 5848 9348 13012 14272 15928 16017 18767 20119 20964 25320 26841 29237 29968 31327 31764 31843 31845 35203 39971 40480 42380 42401 149784 162536 162537 162567 178490 178498 178665 205835 205836 206158 206502 220844 221102 231197 232091 232368 232851 232896 232911 232914 232916 233947 233972 234073 234103 234104 234173 234192 234451 234685 234810 237476 237866 241186 242414 242599 242675 242703 242730 242731 242732 242733 242734 242736 243056 243107 243144 277826 278133 282546 301626 301627 301628 301873 301874 301905 301931 301944 302020 312550 312643 334214 334215 334216 349389 391841 391850 423561 442687 442688 442692 442694 442695 442696 442699 442700 442701 442702 442703 442704 442705 442706 442707 442710 443158 443214 444425 444692 444705 449430 456261 489815 520930 522307 524490 524671 524828 542478 544570 548934 596137 596194 596246 596987 597144 597170 597666 597675 598282 598362 598656 599130 599241 599242 599255 599256 599422 599423 599535 599949 678304 678662 678663 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1512206 1512207 1512229 1512231 1512232 1512280 1512467 1512468 1512675 1512827 1512835 1512853 1512854 1513396 1514154 1514155 1514195 1514501 1514503 1514541 1514610 1514892 1515424 1515425 1515681 1516004 1516005 1516007 1516008 1516011 1516019 1516026 1516314 1516491 1516703 1516704 1516744 1516746 1516891 1516894 1517825 1517826 1518161 1518287 1519259 1519260 1519684 1519686 1521964 1522792 1522860 1522909 1522910 1523018 1523742 1524081 1533574)\n(108 39 96 107 151 167 172 173 190 254 263 266 268 275 289 294 364 378 379 392 399 402 424 473 477 481 490 503 506 523 545 546 578 589 598 608 610 618 661 665 666 782 855 946 948 949 956 959 960 970 973 974 975 979 981 983 992 1002 1040 1041 1046 1047 1050 1060 1061 1066 1097 1120 1134 1143 1157 1159 1187 1210 1237 1275 1367 1413 1443 1448 1480 1506 1521 1551 1590 1617 1636 1637 1640 1641 1644 1645 1647 1648 1655 1716 1771 1822 1888 1911 1927 1937 1947 1962 1975 1981 2006 2007 2025 2026 2027 2039 2040 2073 2083 2119 2132 2144 2157 2158 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1481889 1484480 1487088 1495786)\n(121 791 6361 6540 6912 9807 9809 9811 10328 13200 13201 13277 18717 18719 18735 18898 19565 21430 21954 23150 23252 23255 23256 23257 23258 23259 23261 23262 23636 23914 25071 26335 27413 29032 30650 36547 38877 39368 40487 78977 79817 79818 80147 220813 220842 220868 220872 220905 237416 237704 242364 243115 243117 243118 243119 243120 243121 282191 282291 360835 376631 376633 524771 600417 600418 600580 600593 680513 680515 680516 680517 680518 680519 680520 680521 680522 680537 680538 680542 680545 680553 680574 680575 680582 680584 680595 680596 680606 680609 680613 680633 680635 680797 681122 681627 683603 683676 683686 683691 683692 683907 683908 683909 687755 687756 687758 728724 752072 752075 752076 814675 814682 814685 814692 814695 814697 814701 814703 814705 814715 815228 851832 870116 870180 870424 870841 870875 871600 920448 1547181)\n(122 1861 1863 4714 5332 8038 9255 11468 12152 13330 13878 14018 16613 16710 17109 18613 21264 22611 24765 25938 30634 30739 32167 36499 37390 37592 37633 40338 43045 43217 43220 85785 86805 150765 183753 225386 282222 301612 302908 302909 303745 304060 304063 304069 304638 304639 304640 304643 304644 304645 304646 333034 333035 333037 337081 370003 370214 370215 370229 376611 439861 439962 440019 440265 440266 440409 444185 444220 444315 444318 449942 456205 458047 458048 458100 475332 520449 520510 524581 556613 567416 596442 598248 599638 610171 636044 678428 678463 678465 678468 682895 683094 724557 729372 729407 729443 729650 729651 743798 776006 868922 868994 870129 870255 872367 940886 1095832 1154182 1179809 1254373 1258025 1258026 1289919 1289920 1289928 1289929 1292461 1299533 1322478 1441399 1442235 1442323 1442324 1445674 1519355 1533157 1550142 1550151 1550648 1576386)\n(123 1796 1972 7962 9482 25005 30733 31527 34907 36606 37440 42114 86993 175938 184591 681136 681138 681139 681141 681142 681145 681146 681147 681148 683805 740818 814780 814783 814784 870320 870593 870692 870936 871195 871385 871462 1456532 1520062)\n(124 943 1593 1817 2357 3046 3824 5639 6875 8062 9236 9452 9465 9793 9829 9964 9990 10226 10383 12742 13011 13772 13989 15582 15608 15609 16684 17253 17426 17510 18261 18265 18896 19421 19872 19900 20936 21297 21417 21797 23133 23181 23676 24818 24841 24909 24919 26590 26763 27536 27776 28651 28658 30209 30542 30653 31829 31830 32492 32505 32942 32968 33595 34502 34668 35009 35015 35050 35644 35820 37020 37046 37051 37363 37395 37397 37400 37408 37409 37410 37412 37413 37415 37421 37431 37438 39564 39565 42693 78984 79341 79631 79634 80141 85091 85092 85849 86025 86597 86660 86792 150499 150526 150820 162388 162664 162665 162790 175800 178556 178573 178647 178775 195076 206072 221179 221483 233448 233512 233517 233925 233926 233983 234057 237101 237445 237488 237531 237548 237553 237576 237731 237868 237949 242270 242448 242449 277648 278074 282623 282657 344340 376298 392337 392359 392367 403893 418946 424324 424333 425152 457801 556482 556628 557963 558125 558182 562366 562558 562561 596467 597109 597535 597728 599432 678640 678975 679133 679151 679152 679154 679155 679157 679426 679498 679748 679932 679959 679969 679970 679972 679982 679997 680009 680011 680012 680051 680056 680064 680074 680075 680076 680147 680207 680211 680215 680220 680226 680230 680238 680240 680242 680243 680281 680282 680372 680382 680405 680406 680408 680411 680412 680420 680431 680432 680446 680472 680473 680495 680501 680502 680512 680727 680967 680969 683256 683607 683624 683653 683666 687123 699797 699798 740872 814554 814566 814571 814574 814580 814583 814584 814586 814588 814620 814623 815198 815225 851537 857118 868443 869014 870084 870340 870379 870380 870494 870532 870609 870624 870745 870759 870917 870926 870937 870985 871012 871062 871164 871226 871262 871270 871355 871381 871442 871523 871661 871703 871831 871858 871985 871991 949640 1154350 1154352 1261512 1510520 1510632 1510636 1510647)\n(125 727 729 737 765 790 1416 1726 1800 2020 2962 3078 3107 3123 3126 3129 3564 3862 4059 4093 4134 4158 4604 4941 5687 5858 5874 5904 6370 6625 7398 7758 7859 7939 7942 7943 8031 8033 8035 8039 8489 8631 9024 9090 9193 9269 9806 9812 10200 10201 10263 10520 11991 11992 12766 12833 12872 13132 13144 13196 13362 13390 13404 13421 13428 13456 13609 13911 14034 14394 14724 14745 14811 15411 15468 15644 15672 15676 15970 16199 16204 16242 16382 16512 16579 17672 18520 18681 18772 18808 18834 18933 18934 18991 19079 19086 19209 19214 19559 19825 20040 20175 20440 20450 20453 20530 20639 20672 21177 21479 21712 23218 23222 24031 24902 25287 25587 26210 26635 26821 26825 26826 26827 26837 26838 26858 27066 27424 27427 27497 27498 27796 28081 28643 28818 28838 28961 29089 29166 30193 30196 30200 30201 30214 30218 30232 30552 30554 30794 32230 32617 32781 33774 33776 33777 33778 34642 34880 34886 34933 35508 36356 36396 36572 36660 37011 37088 37090 37195 37219 37285 37383 37384 37763 37771 38002 38186 38187 38450 38506 38605 38758 39070 39591 40264 40460 40485 40822 41834 42256 42571 42755 42818 42963 42964 43066 43144 85383 85593 85594 85598 85602 85619 85620 85622 85624 85625 85631 85632 85635 85636 85641 85688 85923 86132 86189 86395 86437 86439 87169 149651 149671 149696 149707 149714 149736 149738 149741 149746 149751 149758 149793 149840 150019 150041 150044 150045 151205 151206 151310 151315 151442 151443 151564 151596 151602 151767 151818 151825 151826 151827 151828 151830 151838 151908 152030 152031 152032 152116 152149 152165 152169 152172 152219 152225 152228 152447 152457 154693 154694 154729 155001 155002 155003 155227 155533 155534 155536 155542 156308 156405 156677 158290 158369 159028 159034 159040 159047 159066 159075 162275 162292 162298 175848 178419 178422 178424 178782 184567 206160 220870 221098 221100 221150 221151 221154 221166 221169 221170 221200 221201 221226 221232 221261 221470 221490 221512 221586 221588 221727 221730 221755 221758 221776 231217 231218 231230 231239 231243 231246 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234615 234616 234663 234664 234665 234750 234757 234760 234764 234804 234835 234838 234840 234848 234851 234853 234861 234868 234966 234979 234981 234992 235002 235004 235014 235018 235031 235044 235055 235068 235078 235081 235082 235083 235088 235108 235135 235150 235153 235162 235169 235198 235218 235234 235240 235242 235250 235263 235267 235287 235290 235295 235299 235309 235318 235338 235477 235496 235524 235632 235633 235634 235641 235678 235698 235706 235707 235708 235710 235717 235728 235744 235777 235792 235886 235956 235980 236000 236056 236075 236078 236080 236082 236083 236084 236858 237322 237326 238532 238551 238552 238566 238571 238576 238637 238656 238659 238740 238741 238742 238745 238774 238807 238861 238865 238883 238977 238997 239008 239091 239134 239169 239175 239180 239181 239182 239191 239214 239223 239230 239233 239278 239284 239313 239314 239325 239333 239340 239341 239375 239376 239377 239385 239386 239430 239431 239454 239511 239512 239517 239518 239532 239548 239575 239591 239596 239610 239618 239667 239668 239682 239725 239730 239739 239762 239772 239779 239783 239814 239819 239833 239886 239888 239889 240007 240031 240061 240094 240101 240122 240129 240135 240141 240155 240194 240204 240211 240273 240299 240311 240315 240327 240330 240352 240382 240419 240444 240515 240521 240557 240608 240646 240715 240717 240723 240735 240805 240812 240813 240877 240899 240920 240940 240941 240952 240958 240959 240962 240991 241032 241037 241039 241040 241042 241044 241050 241068 241114 241136 241144 241164 241165 241219 241235 241237 241288 241289 241310 241333 241340 241353 241372 241374 241375 241387 241388 241426 241477 241494 241498 241538 241539 241540 241601 241633 241700 241705 241718 241727 241745 241762 241768 241850 241885 241898 241902 241981 242002 242155 242429 242453 242706 242843 259813 262384 262397 262445 262471 262491 262504 262527 262578 262977 263355 263358 263531 263534 263540 263571 263634 264272 264273 264588 264598 264679 266836 266996 267028 267169 267373 267633 270229 270327 270541 270697 270795 270844 270996 271052 271185 271190 271276 271379 271380 271411 271412 277787 277788 277792 277794 277799 277820 277821 277834 277837 277845 277849 277852 277855 277856 277863 277873 277925 277928 277930 277959 277961 277962 277967 277977 277978 277981 277984 277986 277999 278005 278007 278008 278009 278010 278012 278014 278018 278021 278034 278053 278107 278115 278119 278125 278126 278134 278138 278139 278140 278141 278143 278144 278145 278146 278147 278148 278155 278161 278180 278184 278216 278217 278230 278234 281841 281856 282005 282666 302540 302851 311392 312414 312416 312422 314719 332544 332565 332566 332573 332579 332600 332601 332605 332606 332615 333228 333240 333243 333244 333245 333246 333247 333248 333249 333252 333255 333271 333274 333300 333370 333410 333422 333648 338642 339667 339693 340979 341742 341773 343211 343239 343494 344231 344240 344241 344242 344246 344304 344306 344307 344329 344370 344374 344375 349231 349506 349681 375546 375552 375553 375571 391860 392071 392162 392171 392176 392194 392389 392513 392674 392678 392680 392681 392699 392701 393588 393610 393738 393751 393756 393758 393759 393773 393916 393917 395923 399459 399590 401020 401148 401149 401152 401155 401157 404555 405472 405473 405584 406146 406216 406218 406403 406407 406670 406672 406833 406845 406846 409326 410918 410919 422825 422826 422833 422854 422879 422885 422943 423006 423042 423128 423156 423178 423320 423386 423479 423520 423571 423572 423575 423610 423617 423618 423619 423621 423622 423623 423625 423626 423628 423630 423634 423636 423637 423640 423641 423642 423643 423644 423645 423647 423660 423665 423667 423669 423670 423673 423684 423686 423690 423693 423700 423701 423703 423707 423708 423709 423716 423717 423718 423719 423729 423732 423735 423736 423773 423798 423812 423823 423869 423875 424068 424072 424083 424276 424284 424359 424512 424535 424653 424790 424805 424818 424853 425258 425449 425481 425485 425512 425722 426070 426317 426359 426390 426471 426481 426484 426487 426498 426576 426577 426579 426590 426601 426632 426633 426640 426649 426768 426769 426785 426885 426980 427008 427055 427086 427154 427190 427201 427202 427285 429219 429563 438432 438434 438716 439035 439053 439814 443306 451633 451941 452143 454539 454545 454596 454597 454598 454644 455270 455880 455968 456122 456669 456800 457558 457950 458085 458102 458104 458105 458109 458111 458118 458171 458172 458224 458225 458226 458228 458229 458232 458234 458235 458239 458240 458242 458259 458959 458960 473137 473234 473235 473236 473240 473249 473546 473563 474366 474368 474424 474500 474520 475858 476217 476223 476236 476237 476261 476262 476270 476273 476278 476280 476281 476287 476288 476289 476292 476293 476303 476305 476306 476307 476311 476312 476481 477491 494475 497134 497135 497173 497219 497364 497365 497366 497406 497456 497481 497546 497548 518179 520587 520588 520821 520825 520897 520899 520901 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576690 576705 576707 577100 577115 577213 577256 577294 577593 577655 577659 577660 577697 577698 577725 577978 577979 577982 578026 578046 578050 578057 578058 578089 578451 578454 578475 578675 578685 578687 578735 578738 578739 581291 581293 581294 581299 581311 581323 581325 581330 581358 581362 581394 581860 581867 581868 581869 581870 581880 581881 581882 581909 582474 585011 585134 585540 585542 586392 586407 586738 587048 587050 587051 587058 587246 589386 589525 595961 596240 596601 598047 598689 599766 600097 600142 677481 677500 677600 678687 679309 679314 684219 686768 687681 687713 694542 694544 694563 700075 700078 700184 700200 700590 701824 702164 729341 740275 740389 740396 740397 740398 740408 740418 740425 740426 740428 740432 740433 740518 740524 740577 740594 740651 740880 740903 740961 741392 741403 741426 741451 741548 741585 741709 741933 742281 742337 742339 743546 743667 743724 744002 744025 744034 744176 744247 744318 744648 745185 745329 745411 745417 745551 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1000374 1000378 1000379 1000380 1000381 1000382 1000385 1000388 1000393 1000400 1000401 1000402 1000407 1000408 1000413 1000416 1000417 1000418 1000419 1000421 1000423 1000424 1000425 1000426 1000428 1000431 1000432 1000434 1000435 1000437 1000441 1000442 1000445 1000448 1000449 1000450 1000451 1000453 1000456 1000457 1000458 1000459 1000460 1000461 1000462 1000463 1000464 1000466 1000467 1000469 1001954 1001958 1001959 1001960 1001961 1001967 1001970 1001971 1001972 1001976 1001977 1001978 1001979 1001981 1001982 1001983 1001984 1001985 1001987 1001989 1001990 1001992 1002305 1002310 1002562 1002563 1002564 1002565 1002566 1002568 1002570 1002571 1002572 1002573 1003688 1003689 1003690 1003691 1003693 1003695 1003696 1003697 1003698 1003700 1003701 1003702 1003711 1003714 1003721 1003726 1003728 1003730 1003731 1003732 1003733 1003734 1003735 1003736 1003737 1003738 1003739 1003740 1003741 1003743 1003744 1003745 1003840 1004252 1004253 1004258 1004261 1004262 1004263 1004264 1004664 1004665 1004667 1004676 1004678 1004679 1004680 1004683 1004684 1004686 1005545 1005547 1005551 1005555 1005556 1005558 1005560 1005561 1005563 1005565 1005566 1005567 1005568 1005569 1005571 1005572 1005575 1005577 1005579 1005582 1005587 1005589 1005591 1005592 1005593 1005594 1005595 1005700 1006212 1006216 1006218 1006219 1006226 1006228 1006231 1006232 1006240 1006246 1006640 1006642 1006643 1006646 1006647 1006648 1006650 1006651 1006653 1006777 1006937 1007003 1007051 1007055 1007182 1007188 1007189 1007219 1007229 1007248 1007333 1007406 1007942 1007974 1007975 1007998 1008191 1008204 1008205 1008206 1008216 1008336 1008337 1008369 1008397 1008398 1008399 1008401 1008405 1008406 1008409 1008424 1008444 1008537 1008556 1008579 1008756 1008759 1008761 1008805 1008900 1008902 1008912 1008913 1008981 1008987 1009001 1009185 1009477 1009511 1009512 1009656 1009681 1009718 1009719 1009788 1009886 1009888 1009953 1009986 1010316 1010347 1010348 1010411 1010432 1010452 1010454 1010542 1010550 1010625 1010938 1010940 1010996 1010998 1010999 1011410 1011501 1011502 1011503 1011632 1011751 1011752 1011834 1011846 1011911 1011958 1011975 1011981 1011982 1011998 1012096 1012334 1012339 1012482 1012549 1012619 1012629 1012744 1012933 1012934 1013029 1013152 1013158 1013207 1013266 1013268 1013269 1013454 1013462 1013497 1013578 1013622 1013624 1013625 1013626 1013640 1013812 1013813 1013827 1014136 1014254 1014332 1014408 1014536 1014960 1015018 1015227 1015229 1015653 1015717 1015718 1015719 1015912 1015924 1015929 1015951 1016103 1016147 1016148 1016150 1016463 1016555 1016654 1016663 1017042 1017049 1017052 1017063 1017067 1017074 1017210 1017212 1017214 1017343 1017398 1017747 1017759 1017941 1018465 1018466 1018789 1018790 1018815 1018951 1019050 1019103 1019124 1019501 1019547 1019600 1019731 1019826 1019931 1020027 1020057 1020179 1020183 1020184 1020254 1021420 1021576 1021578 1021718 1021729 1021770 1021771 1021886 1022235 1022970 1023206 1023220 1023221 1024304 1024350 1024540 1024643 1024661 1024662 1024666 1024670 1024879 1025310 1025340 1025370 1025549 1025782 1025791 1026103 1026188 1026286 1026524 1026536 1026609 1026615 1026616 1026923 1026924 1026933 1027034 1027079 1027160 1027555 1027556 1027758 1027767 1027789 1027857 1027866 1027956 1028110 1028175 1028239 1028240 1028391 1028498 1028688 1028759 1029130 1029173 1029397 1029509 1029559 1029806 1029808 1030006 1030019 1030065 1030067 1030441 1030570 1030599 1030633 1030691 1030740 1031088 1031344 1031420 1031421 1031519 1031623 1031775 1031998 1032245 1032310 1032540 1032695 1032743 1032744 1032748 1032854 1032996 1033034 1033186 1033869 1034054 1034125 1034127 1034153 1034865 1035097 1035349 1035687 1036006 1036087 1036290 1036304 1036324 1036325 1036898 1037539 1037540 1037541 1037611 1037612 1038214 1038747 1038775 1038959 1039433 1039753 1039758 1039857 1040101 1040385 1040645 1040647 1040694 1040886 1041133 1041205 1041206 1041448 1041671 1041844 1042132 1042265 1042424 1042690 1043004 1043544 1043558 1043621 1043770 1043785 1043948 1044154 1044545 1044631 1045020 1045494 1045655 1045724 1045875 1046093 1046096 1046402 1046421 1046487 1046492 1046528 1046951 1046965 1047031 1047447 1047448 1047618 1047846 1047901 1047902 1047903 1047945 1047962 1048001 1048311 1048316 1048452 1049676 1050017 1050028 1050117 1050528 1051145 1051302 1051737 1051830 1051957 1052575 1052809 1052894 1053087 1053088 1053089 1053252 1053359 1053828 1053968 1054493 1054605 1054636 1054638 1055212 1055298 1055299 1055346 1056100 1056473 1056474 1057134 1057135 1057151 1057153 1057158 1057287 1057473 1057592 1057710 1057759 1057955 1057959 1058504 1058843 1059537 1059647 1060690 1061010 1061070 1061217 1061477 1061520 1062140 1062207 1062216 1062217 1062312 1062314 1062474 1062576 1062577 1062582 1062658 1062659 1062668 1062727 1062953 1062954 1063060 1063197 1063458 1064058 1064684 1064883 1064974 1064994 1065162 1065189 1065501 1065555 1065772 1065809 1066251 1066451 1066657 1066980 1067141 1067449 1067900 1067901 1068031 1068686 1068687 1068703 1068818 1069175 1069669 1069685 1069851 1070251 1070328 1070335 1070399 1070522 1070523 1070856 1071062 1071338 1071409 1071594 1071595 1071678 1071727 1071840 1072774 1072791 1072852 1072984 1073250 1073616 1073617 1073656 1073657 1073960 1074177 1074525 1074600 1074601 1074747 1074840 1074956 1075093 1075213 1075300 1075727 1075736 1077093 1077173 1078152 1078403 1078593 1078787 1079186 1079214 1079231 1079232 1079471 1079475 1079534 1079894 1079895 1080459 1081208 1081209 1081210 1081211 1081215 1081216 1081217 1081243 1081244 1081245 1081246 1081250 1081251 1081252 1081253 1081254 1081255 1081256 1081258 1081259 1081260 1081263 1081264 1081267 1081703 1081704 1081787 1081847 1081950 1082081 1082082 1082087 1082115 1082295 1082297 1082335 1082587 1082715 1082767 1082807 1082819 1082947 1083034 1083038 1083329 1083376 1084083 1084201 1084351 1084434 1084810 1084909 1084948 1085287 1085473 1085622 1085628 1086020 1086068 1086210 1086288 1086321 1086460 1086611 1086789 1086911 1087049 1087185 1087195 1087535 1087806 1088016 1088386 1088399 1088411 1088475 1088652 1089136 1089174 1089324 1089827 1090094 1090137 1090355 1090421 1090509 1090698 1090731 1090735 1090841 1091162 1092085 1092150 1092336 1092439 1092678 1093045 1093046 1093047 1093048 1093055 1093056 1093214 1093215 1093267 1093316 1093665 1093723 1093811 1093929 1093940 1093999 1094063 1094092 1094157 1094577 1094635 1113681 1136253 1145669 1148555 1175743 1176457 1187073 1187074 1187076 1187078 1187081 1187103 1187227 1187240 1187264 1187446 1187503 1187536 1187854 1188351 1189820 1190048 1190213 1190392 1191554 1192200 1192287 1193041 1193744 1193793 1194388 1194523 1194617 1195077 1195292 1195297 1195563 1196538 1196546 1196678 1196707 1197533 1197537 1197673 1198019 1198189 1198823 1198829 1198832 1198878 1198946 1198993 1199005 1199006 1199014 1199053 1199056 1199304 1199468 1200122 1200354 1200526 1200847 1201813 1202460 1203440 1203443 1203888 1205033 1205078 1205079 1205378 1205628 1205681 1205682 1205893 1206070 1206071 1206072 1206102 1206180 1206584 1208150 1208505 1208985 1208986 1209201 1209719 1209720 1209766 1209814 1209815 1209816 1209817 1209818 1209819 1209821 1209839 1209844 1209845 1209937 1209938 1210106 1210126 1210255 1210351 1210455 1210456 1210532 1210533 1210534 1210617 1211502 1211812 1211829 1212070 1212223 1212635 1212917 1212918 1212928 1212930 1213122 1213123 1213124 1213429 1213446 1213692 1214005 1214067 1214195 1214218 1214219 1214220 1214229 1214783 1215015 1215121 1215307 1215466 1215467 1216313 1216330 1216531 1216700 1216701 1216704 1216705 1217668 1217694 1217707 1217709 1217710 1218146 1218729 1218734 1218959 1219002 1219098 1219255 1219668 1219710 1219891 1219985 1219986 1220376 1220459 1221189 1221384 1221820 1221821 1221822 1222018 1222019 1222379 1222848 1222862 1223236 1223248 1223285 1223741 1223751 1223753 1223755 1223849 1224110 1224227 1224353 1224408 1224415 1224433 1224714 1224716 1224804 1224868 1225182 1225340 1225544 1225771 1226635 1226688 1226799 1226800 1226900 1227418 1227493 1229119 1229250 1229561 1229614 1230230 1230253 1230266 1230417 1230436 1230443 1230630 1230667 1230696 1231069 1231070 1231246 1231262 1231438 1231785 1231826 1231827 1231830 1231979 1232177 1232178 1232179 1232181 1232184 1232186 1232187 1232188 1232192 1232196 1232198 1232199 1232201 1232203 1232206 1232207 1232510 1232660 1232700 1232727 1233139 1233191 1233611 1234164 1234165 1234255 1234581 1234715 1234716 1234717 1235054 1235143 1235144 1235145 1235731 1258014 1258015 1260939 1261191 1265372 1265373 1265375 1265377 1265378 1265379 1265380 1265381 1265382 1265385 1265386 1265388 1300302 1300303 1304600 1304619 1317473 1317483 1318703 1318704 1318709 1318712 1319857 1319861 1319870 1319881 1319931 1319932 1319933 1319937 1319939 1319951 1319952 1320146 1320227 1321775 1328925 1328963 1328965 1331054 1440173 1440175 1440201 1440502 1440503 1440504 1440505 1440506 1440507 1440508 1440509 1440511 1440513 1440514 1440515 1440516 1440517 1440537 1440564 1440571 1440575 1440576 1440577 1440578 1440579 1440582 1440591 1440599 1440600 1440601 1440665 1440692 1440694 1440695 1440696 1440733 1440769 1440784 1440786 1440790 1440791 1440794 1440798 1440800 1440802 1440814 1440816 1441038 1441039 1441047 1441099 1441100 1441101 1441139 1444092 1449642 1449643 1449645 1449648 1449649 1449650 1456463 1457865 1458265 1458293 1458323 1458666 1459291 1460078 1460572 1460712 1461646 1461649 1462017 1462407 1462586 1462641 1463474 1463537 1463707 1463708 1463898 1464313 1465255 1465621 1465622 1465757 1466126 1466211 1467098 1467326 1467468 1467469 1467471 1468472 1468801 1469325 1470031 1470394 1470395 1470456 1470636 1470637 1472138 1472139 1472606 1473345 1474171 1474518 1474796 1474850 1476058 1476322 1476325 1476405 1476407 1476593 1476650 1477008 1477010 1477012 1477064 1477233 1477235 1477896 1477944 1478004 1478437 1478509 1478824 1479226 1479290 1479463 1479694 1481067 1481132 1481993 1482339 1483391 1483794 1483953 1484870 1485102 1485740 1485943 1485976 1486096 1486429 1488335 1489080 1489254 1489766 1490977 1491083 1491112 1491364 1491365 1491783 1491885 1493203 1493983 1494281 1494640 1494644 1494820 1494845 1494973 1495732 1495832 1496164 1496166 1497315 1497559 1497792 1497793 1497794 1497920 1497991 1498008 1498052 1498081 1498586 1498682 1498827 1498828 1498831 1499075 1499137 1499165 1499166 1499393 1500791 1501363 1503051 1503249 1503271 1503441 1503442 1503451 1503927 1510466 1510658 1510995 1512048 1512261 1512716 1513408 1514432 1514636 1517745 1518095 1518831 1519356 1521966 1527239 1532266 1533723 1562144 1562330 1562345 1562668 1562676 1563125 1563246 1564874 1609672 1612293 1612845 1613396 1613950 1614502 1615053 1615607 1620282)\n(132 343 473 1040 3968 5575 6657 6674 6709 7258 8318 9156 9213 12299 12328 14705 16410 16598 17054 20316 20337 21547 23413 23791 25270 27996 28027 28049 30242 30314 30342 31862 33997 34263 34266 34268 34272 34392 35331 35527 39669 39840 39845 39848 39853 40642 42839 42845 42849 42866 42874 42878 42890 44410 46682 53396 56559 57090 57370 57610 65844 65932 65933 65936 67138 72819 73109 73115 77410 78373 78375 78379 78381 78382 84980 86024 86308 86605 86709 87096 87161 87162 87163 101739 115296 122874 127516 148373 167620 178487 178638 178731 178793 206828 249582 259753 259754 280123 281666 290026 301532 301542 304915 305578 309049 309311 312532 443766 520456 522273 535968 591729 597667 598186 616267 625741 628462 682742 699376 699465 700484 700496 701064 718133 718674 718778 719053 719058 719214 719575 720360 721591 722389 722728 722767 723685 723905 731033 770309 770962 772413 805413 815051 887557 896117 911722 912026 912567 949647 965472 966846 969677 1122205 1137765 1173774 1323100 1453926 1520059 1571357 1608780 1615526)\n(133 33271 42567 206334 324044 324045 600529 1328859 1480907 1480908)\n" }, { "path": "attic/code/semmed-index-predicate.rkt", "content": "#lang racket/base\n(require\n \"edge.rkt\"\n racket/file\n )\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(SEMMED_DIR))\n\n(define semmed-dir (vector-ref argv 0))\n(define ebs-detail-file (build-path semmed-dir \"edge-by-subject/detail.bin\"))\n(define ebp-dir (build-path semmed-dir \"edge-by-predicate\"))\n(define index-file (expand-user-path (build-path ebp-dir \"index.scm\")))\n(define detail-file (expand-user-path (build-path ebp-dir \"detail.bin\")))\n\n(make-directory* (expand-user-path ebp-dir))\n\n(define (ebp-keyedge e-bytes))\n (define key (vector (edge-predicate e)\n (edge-src-type e)\n (edge-dst-type e)))\n (hash-set edges key\n (cons e-bytes (hash-ref edges key '())))))\n (printf \"Processing ~s edge buckets\\n\" (hash-count ebp))\n (for/fold ((offset 0))\n ((key (in-list (sort (hash-keys ebp) ebp-keyconcept* concept* '(\"fish\" \"oil\") #t))\n(define raynaud* (fuzzy-name->concept* concept* \"raynaud\" #t))\n\n(define epoprostenol* (fuzzy-name->concept* concept* \"epoprostenol\" #t))\n(define prostaglandin* (fuzzy-name->concept* concept* \"prostaglandin\" #t))\n\n;; This seems to be the one we're looking for.\n(define prostaglandins (fuzzy-name->concept* concept* \"prostaglandins\" #t))\n\n(define platelet* (fuzzy-name*->concept* concept* '(\"platelet\" \"aggregation\") #t))\n\n;; Why are these two edge groups so different from what we expect to see?\n;; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031661/figure/F1/\n(define dfo-epoprostenol-edge* (direct-edge* dfo* epoprostenol*))\n(define dfo-prostaglandin-edge* (direct-edge* dfo* prostaglandin*))\n\n;; These groups have edges we're expecting.\n(define epoprostenol-raynaud-edge* (direct-edge* epoprostenol* raynaud*))\n(define prostaglandin-raynaud-edge* (direct-edge* prostaglandin* raynaud*))\n(define prostaglandin-epoprostenol-edge* (direct-edge* prostaglandin* epoprostenol*))\n(define prostaglandin-platelet-edge* (direct-edge* prostaglandin* platelet*))\n\n;; Expected edges are missing here.\n(define platelet-raynaud-edge* (direct-edge* platelet* raynaud*))\n\n;; No direct edges here.\n(define dfo-raynaud-edge* (direct-edge* dfo* raynaud*))\n" }, { "path": "attic/code/study-imatinib.rkt", "content": "#lang racket\n(require\n \"mk-db.rkt\"\n )\n\n(displayln\n \"Finished loading mk-db.rkt.\")\n\n;; we want a direct link bewteen imatinib and GIST\n;; like TREATS predicate\n;; or something like that\n;; and no direct link bwteen imatinib and Asthma\n;; which is what we are \"discovering\"\n;; I think that is the basic idea\n;; we already \"know\" that imatinib treats CML and GIST\n;; through direct links\n;; and are trying to discover other diseases it might treat\n;; but want to go through genes that are already known to be safe\n;; that imatinib is already known to target\n\n;; the example is interesting because the query isn't just linear\n;; we want to find a tree, not a path\n\n;; Julian's SPARQL query:\n;;\n;; select ?activation ?disease where {\n;; :imatinib :inhibits ?gene .\n;; ?gene :associatedWith ?activation .\n;; ?activation :associatedWith ?disease\n;; FILTER EXISTS {\n;; ?gene :associatedWith ?activation2 .\n;; ?activation2 :associatedWith ?disease2 .\n;; :imatinib :treats ?disease2\n;; }\n;; FILTER NOT EXISTS {\n;; :imatinib :treats ?disease\n;; }\n;; }\n\n\n\"ASSOCIATED_WITH\"\n\"AFFECTS\"\n\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n(define set-subtraction\n (lambda (l1 l2)\n (cond\n [(null? l1) '()]\n [(member (car l1) l2) (set-subtraction (cdr l1) l2)]\n [else (cons (car l1) (set-subtraction (cdr l1) l2))])))\n\n(define union\n (lambda (l1 l2)\n (cond\n [(null? l1) l2]\n [(member (car l1) l2) (union (cdr l1) l2)]\n [else (cons (car l1) (union (cdr l1) l2))])))\n\n(define union*\n (lambda args\n (union*-aux args)))\n\n(define union*-aux\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(null? (cdr ls)) (car ls)]\n [else (union (car ls) (union*-aux (cdr ls)))])))\n\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n(define not-membero\n (lambda (x ls)\n (conde\n [(== '() ls)]\n [(fresh (y rest)\n (== `(,y . ,rest) ls)\n (=/= x y)\n (not-membero x rest))])))\n\n(define path-to-diseaseo\n (lambda (x path)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) x)\n (conde\n [(membero \"dsyn\" concept-type*)\n (== `(,x) path)]\n [(not-membero \"dsyn\" concept-type*)\n (fresh (y p e e-rest path^)\n (== `(,e . ,path^) path)\n (== `(,x ,y ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (path-to-diseaseo y path^))]))))\n\n\n\n\n\n\n\n\n\n;; Greg says:\n\n;; the structure of an edge is:\n;; (subject object predicate subject-type object-type pred-info)\n\n;; So instead of looking for \"gngm\" in the type list of a concept, you can instead use subject-type or object-type to constrain the edge itself.\n;; so:\n;; (== `(,s-imatinib/gene ,m-imatinib/gene ,p-imatinib/gene . ,e-rest-imatinib/gene) e-imatinib/gene)\n\n;; becomes (with fresh st-imatinib/gene):\n;; (== `(,s-imatinib/gene ,m-imatinib/gene ,p-imatinib/gene st-imatinib/gene \"gngm\". ,e-rest-imatinib/gene) e-imatinib/gene)\n\n;; then you no longer have to use membero\n\n\n\n;; Will says:\n\n;; What Greg says above, but stronger! Using member can allow too many entry types--think of it as a \"fuzzy\" version of a query! You asked for a gene? Well, here are genes, and proteins, and ...\n\n\n\n;;; one step at a time!\n\n;; TODO all direct edges from all types of imatinib\n\n;; TODO count the number of times each gene appears inhibited, across all versions of imatinib\n\n;; TODO find all the subgraphs of the form 'some variant of imatinib INHIBITS some specific gene which CAUSES some specific disease or neoplasm which is directly TREATED by that version of imatinib'. Ideally, fully explore most specific entities before broadening to categories.\n\n\n;; Ah! Now Will is enlightened! I *need* to use \"gngm\" as the object type in the query, rather than calling membero on the list of associated types.\n;; This will keep me from accidentally picking up aapp|T116|Amino Acid, Peptide, or Protein, for example, when I want genes.\n\n\n\n\n\n;; TODO try strategy of most-specific to least-specific, based on branching factor for the next \"hop\" during a query\n\n\n\n\n;; TODO intersection of relatively specific \"dsyn\", \"neop\", and \"patf\" directly treated by the relatively specific imatinib synonyms with the relatively specific \"dsyn\", \"neop\", and \"patf\" directly caused by the relatively specific genes (or gene groups) inhibited by the relatively specific imatinib synonyms\n\n\n\n;; TODO relatively specific \"dsyn\", \"neop\", and \"patf\" that are directly caused by relatively specific genes inhibited by relatively specific imatinib synonyms\n\n\n;; TODO intersection of \"dsyn\", \"neop\", and \"patf\" directly treated by the imatinib synonyms with the \"dsyn\", \"neop\", and \"patf\" directly caused by the genes (or gene groups) inhibited by the imatinib synonyms\n\n\n;; TODO \"dsyn\", \"neop\", and \"patf\" that are directly caused by the genes (or gene groups) inhibited by the imatinib synonyms\n\n;; TODO: How many of the cell functions below for KIT/C-KIT are unique? And how many of those are specific enough to be meaningful/useful?\n;; try taking the union* of all the non-silly entries\n\n\n;; Can I use this to help weed out bogus answers?\n;;\n;; (1290829 \"Non-human disorder\" (\"dsyn\"))\n;;\n;; #(3047 \"Animal Diseases\" (#(41 1)))\n;; #(5591 \"Bird Diseases\" (#(41 1)))\n;; #(7350 \"Cat Diseases\" (#(41 1)))\n;; #(7453 \"Cattle Diseases\" (#(41 1)))\n;; #(12979 \"Dog Diseases\" (#(41 1)))\n;; #(16154 \"Fish Diseases\" (#(41 1)))\n;; #(18018 \"Goat Diseases\" (#(41 1)))\n;; #(19940 \"Horse Diseases\" (#(41 1)))\n;; #(26431 \"Monkey Diseases\" (#(41 1)))\n;; #(32851 \"Poultry Diseases\" (#(41 1)))\n;; #(35801 \"Rodent Diseases\" (#(41 1)))\n;; #(36946 \"Sheep Diseases\" (#(41 1)))\n;; #(39006 \"Swine Diseases\" (#(41 1)))\n;;\n;; Maybe allow this one?\n;;\n;; #(242634 \"Primate Diseases\" (#(41 1)))\n;;\n;; Hmmm. None of these seem useful.\n;;\n;; the results don't seem useful, with (1290829 \"Non-human disorder\"\n;; (\"dsyn\")) as either the subject or object\n(run* (q)\n (fresh (e subj obj pred st ot rest)\n (== e q)\n (== '(1290829 \"Non-human disorder\" (\"dsyn\")) obj)\n (== `(,subj ,obj ,pred ,st ,ot . ,rest) e)\n (edgeo e)))\n\n\n\n\n;; For the diseases affected by the celfs of interest, how many are MANIFESTATION_OF that celf?\n;;\n;; (Might also want to explore which are MANIFESTATION_OF any of the celfs of interest.)\n> (sort\n (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 disorder celf-type disorder-type rest1 rest2)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,celf ,disorder \"AFFECTS\" ,celf-type ,disorder-type . ,rest1) e1)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type ,celf-type . ,rest2) e2)\n (edgeo e2)\n (edgeo e1)))))\n (list (length disorders) celf)))\n '((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\"))))\n (lambda (l1 l2) (< (car l1) (car l2))))\n=>\n'((0 (312862 \"Lymphocyte chemotaxis\" (\"celf\")))\n (0 (1159455 \"syncytium formation\" (\"celf\")))\n (0 (1372294 \"Increased Endocytosis\" (\"celf\")))\n (0 (598948 \"axonal guidance\" (\"celf\")))\n (0 (1326501 \"eosinophil chemotaxis\" (\"celf\")))\n (0 (1155303 \"ER-overload response\" (\"celf\")))\n (0 (1156259 \"cell ion homeostasis\" (\"celf\")))\n (0 (1276855 \"Monocyte chemotaxis\" (\"celf\")))\n (0 (1326474 \"vesicle fusion\" (\"celf\")))\n (0 (1516338 \"Cell Death Induction\" (\"celf\")))\n (0 (598949 \"axonal sprouting\" (\"celf\")))\n (0 (1156042 \"endosome transport\" (\"celf\")))\n (0 (1159824 \"nuclear fragmentation\" (\"celf\")))\n (0 (1326121 \"astrocyte activation\" (\"celf\")))\n (0 (1155874 \"Cell Cycle Checkpoint\" (\"celf\")))\n (0 (1155876 \"DNA replication checkpoint\" (\"celf\")))\n (0 (1156132 \"vacuolar acidification\" (\"celf\")))\n (0 (1326080 \"muscle cell differentiation\" (\"celf\")))\n (0 (1155013 \"T-cell differentiation\" (\"celf\")))\n (0 (598838 \"membrane assembly\" (\"celf\")))\n (0 (7580 \"Cell Aggregation\" (\"celf\")))\n (0 (392710 \"Megakaryocytic maturation\" (\"celf\")))\n (0 (1156032 \"Microtubule Polymerization\" (\"celf\")))\n (0 (1159339 \"Protein Secretion\" (\"celf\")))\n (0 (1159938 \"eosinophil differentiation\" (\"celf\")))\n (0 (1159966 \"myoblast differentiation\" (\"celf\")))\n (0 (1326236 \"filopodium formation\" (\"celf\")))\n (0 (1326504 \"neuronal migration\" (\"celf\")))\n (0 (1513082 \"Megakaryocyte Proliferation\" (\"celf\")))\n (0 (312861 \"Neutrophil chemotaxis\" (\"celf\")))\n (0 (1155792 \"Meiotic Recombination\" (\"celf\")))\n (0 (1372847 \"Increased Cellular Migration\" (\"celf\")))\n (0 (312860 \"Neutrophil migration, function\" (\"celf\")))\n (0 (37841 \"Sperm Capacitation\" (\"celf\")))\n (0 (1159958 \"neutrophil differentiation\" (\"celf\")))\n (0 (31945 \"Pinocytosis\" (\"celf\")))\n (0 (600430 \"Calcium Waves\" (\"celf\")))\n (0 (1155752 \"positive regulation of mitosis\" (\"celf\")))\n (0 (1155949 \"lamellipodium biogenesis\" (\"celf\")))\n (0 (1156031 \"Microtubule Depolymerization\" (\"celf\")))\n (0 (1325887 \"focal adhesion formation\" (\"celf\")))\n (0 (1326356 \"amino acid import\" (\"celf\")))\n (0 (1155046 \"T-Cell Proliferation\" (\"celf\")))\n (0 (1325893 \"histamine secretion\" (\"celf\")))\n (0 (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\")))\n (0 (1159909 \"keratinocyte differentiation\" (\"celf\")))\n (0 (79396 \"G2 Phase\" (\"celf\")))\n (0\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\")))\n (0 (1326346 \"urothelial cell proliferation\" (\"celf\")))\n (0 (1155004 \"B-cell differentiation\" (\"celf\")))\n (0 (1155008 \"B Cell Proliferation\" (\"celf\")))\n (0 (1155229 \"humoral immune response\" (\"celf\")))\n (0 (1155980 \"actin filament depolymerization\" (\"celf\")))\n (0 (1327616 \"Cell secretion\" (\"celf\")))\n (0 (7591 \"Cell division phases\" (\"celf\")))\n (0 (85416 \"Respiratory Burst\" (\"celf\")))\n (0 (302167 \"Cap formation\" (\"celf\")))\n (0 (599893 \"Protein translocation\" (\"celf\")))\n (0 (600485 \"Acrosome Reaction\" (\"celf\")))\n (0 (887839 \"Nuclear Import\" (\"celf\")))\n (0 (949629 \"Bystander Effect\" (\"celf\")))\n (0 (1155607 \"autophagic vacuole formation\" (\"celf\")))\n (0 (1155631 \"Chromosome Condensation\" (\"celf\")))\n (0 (1155734 \"lamin depolymerization\" (\"celf\")))\n (0 (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\")))\n (0 (1155871 \"nuclear migration\" (\"celf\")))\n (0 (1155893 \"unidimensional cell growth\" (\"celf\")))\n (0 (1158774 \"negative regulation of transcription by glucose\" (\"celf\")))\n (0 (1159442 \"sporulation\" (\"celf\")))\n (0 (1159512 \"maltose transport\" (\"celf\")))\n (0 (1159521 \"hexose transport\" (\"celf\")))\n (0 (1160602 \"cholesterol absorption\" (\"celf\")))\n (0 (1326207 \"Programmed Cell Death, Type II\" (\"celf\")))\n (0 (1326220 \"synergid cell death\" (\"celf\")))\n (0 (1326347 \"fibroblast proliferation\" (\"celf\")))\n (0 (1511632 \"Cytoskeletal Modeling\" (\"celf\")))\n (0 (1515126 \"T-Cell Development\" (\"celf\")))\n (0 (1516340 \"Cell Death Process\" (\"celf\")))\n (0 (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\")))\n (0 (1517348 \"G2 Phase Arrest\" (\"celf\")))\n (0 (1519167 \"S Phase Arrest\" (\"celf\")))\n (0 (1523105 \"nuclear envelope disassembly\" (\"celf\")))\n (0 (1523795 \"stress fiber formation\" (\"celf\")))\n (0 (25564 \"Metaphase\" (\"celf\")))\n (0 (1450355 \"Prometaphase\" (\"celf\")))\n (0 (1156237 \"Stimulation of Cell Proliferation\" (\"celf\")))\n (0 (1155766 \"centrosome cycle\" (\"celf\")))\n (0 (1326205 \"Induction of Apoptosis\" (\"celf\")))\n (0 (1326225 \"cell homeostasis\" (\"celf\")))\n (0 (544888 \"Mitotic arrest\" (\"celf\")))\n (0 (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\")))\n (0 (598087 \"cell dedifferentiation\" (\"celf\")))\n (0 (872097 \"Anoikis\" (\"celf\")))\n (0 (887840 \"Nuclear Export\" (\"celf\")))\n (0 (1154382 \"Cell-Cell Adhesion\" (\"celf\")))\n (0 (1158951 \"maintenance of protein localization\" (\"celf\")))\n (0 (1159946 \"macrophage differentiation\" (\"celf\")))\n (0 (1257985 \"Cross-Priming\" (\"celf\")))\n (0 (1372180 \"Increased Cellular Death\" (\"celf\")))\n (0 (1515136 \"T-Cell Transformation\" (\"celf\")))\n (0 (1515432 \"Thymocyte Development\" (\"celf\")))\n (0 (1518147 \"M Phase Arrest\" (\"celf\")))\n (0 (1155781 \"spindle assembly\" (\"celf\")))\n (1 (1159821 \"apoptotic program\" (\"celf\")))\n (1 (1318468 \"cell-mediated immune response\" (\"celf\")))\n (1 (25186 \"Meiosis\" (\"celf\")))\n (1 (1159689 \"potassium ion transport\" (\"celf\")))\n (1 (301896 \"Cell-Mediated Cytolysis\" (\"celf\")))\n (1 (596991 \"myelination\" (\"celf\")))\n (1 (1160520 \"oocyte maturation\" (\"celf\")))\n (1 (599702 \"reuptake\" (\"celf\")))\n (1 (19595 \"Histamine Release\" (\"celf\")))\n (1 (7588 \"Cell Degranulation\" (\"celf\")))\n (1 (1514761 \"Receptor Inhibition\" (\"celf\")))\n (1 (1511002 \"B-Cell Development\" (\"celf\")))\n (1 (1326502 \"macrophage chemotaxis\" (\"celf\")))\n (1 (1155711 \"stem cell division\" (\"celf\")))\n (1 (1159974 \"osteoblast differentiation\" (\"celf\")))\n (1 (1326057 \"epithelial cell differentiation\" (\"celf\")))\n (1 (1515979 \"Anchorage-Independent Growth\" (\"celf\")))\n (1 (1540661 \"cell fate\" (\"celf\")))\n (1 (40682 \"cell transformation\" (\"celf\")))\n (1 (221117 \"Anergy\" (\"celf\")))\n (2 (32174 \"Platelet adhesion\" (\"celf\")))\n (2 (282636 \"Cell Respiration\" (\"celf\")))\n (2 (1159978 \"osteoclast differentiation\" (\"celf\")))\n (2 (1516349 \"Cell Maturation\" (\"celf\")))\n (2 (525010 \"Autocrine Communication\" (\"celf\")))\n (2 (1326341 \"Epithelial Cell Proliferation\" (\"celf\")))\n (2 (24262 \"Lymphocyte Activation\" (\"celf\")))\n (2 (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\")))\n (2 (10813 \"Cytokinesis\" (\"celf\")))\n (2 (596286 \"Cell Growth Regulation\" (\"celf\")))\n (2 (1154401 \"cell invasion\" (\"celf\")))\n (2 (1154413 \"Intercellular Communication\" (\"celf\")))\n (2 (1523169 \"smooth muscle cell differentiation\" (\"celf\")))\n (3 (1159709 \"cholesterol transport\" (\"celf\")))\n (3 (1522821 \"acidification\" (\"celf\")))\n (3 (3261 \"Antibody Formation\" (\"celf\")))\n (3 (1155003 \"B-Cell Activation\" (\"celf\")))\n (3 (26255 \"Mitosis\" (\"celf\")))\n (3 (37848 \"Sperm Motility\" (\"celf\")))\n (3 (600431 \"Calcium Signaling\" (\"celf\")))\n (3 (1516334 \"Cell Cycle Progression\" (\"celf\")))\n (3 (1155074 \"mast cell activation\" (\"celf\")))\n (4 (1159884 \"adipocyte differentiation\" (\"celf\")))\n (4 (230871 \"Mitochondrion in division\" (\"celf\")))\n (4 (206431 \"Antigen Presentation\" (\"celf\")))\n (4 (4462 \"Axonal Transport\" (\"celf\")))\n (4 (8018 \"Chemotaxis\" (\"celf\")))\n (4 (25251 \"Membrane Potentials\" (\"celf\")))\n (4 (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\")))\n (4 (1523298 \"epithelial to mesenchymal transition\" (\"celf\")))\n (4 (1155873 \"Cell Cycle Arrest\" (\"celf\")))\n (5 (14139 \"Endocytosis\" (\"celf\")))\n (5 (31308 \"Phagocytosis\" (\"celf\")))\n (5 (32176 \"Platelet aggregation\" (\"celf\")))\n (5 (178666 \"glucose transport\" (\"celf\")))\n (5 (678903 \"Neuronal Transmission\" (\"celf\")))\n (5 (7595 \"Cell Growth\" (\"celf\")))\n (6 (1155872 \"Cell Cycle Regulation\" (\"celf\")))\n (6 (24426 \"Macrophage Activation\" (\"celf\")))\n (7 (7590 \"Cell division\" (\"celf\")))\n (7 (1326120 \"cell activation\" (\"celf\")))\n (8 (1260960 \"Cytolysis\" (\"celf\")))\n (8 (1155065 \"T-Cell Activation\" (\"celf\")))\n (8 (7613 \"Cell physiology\" (\"celf\")))\n (8 (7581 \"Cell Aging\" (\"celf\")))\n (8 (1514758 \"Receptor Activation\" (\"celf\")))\n (9 (7582 \"Cell Communication\" (\"celf\")))\n (9 (7608 \"cell motility\" (\"celf\")))\n (9 (1158770 \"Transcriptional Regulation\" (\"celf\")))\n (10 (7577 \"Cell Adhesion\" (\"celf\")))\n (11 (1256369 \"insulin secretion\" (\"celf\")))\n (11 (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\")))\n (11 (7620 \"Cell Survival\" (\"celf\")))\n (13 (7586 \"Cell Cycle\" (\"celf\")))\n (15 (1159816 \"anti-apoptosis\" (\"celf\")))\n (16 (598501 \"Chromosome Pairing\" (\"celf\")))\n (16 (37080 \"Signal Pathways\" (\"celf\" \"moft\")))\n (17 (599894 \"targeting\" (\"celf\")))\n (18 (13081 \"Down-Regulation\" (\"celf\")))\n (19 (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\")))\n (24 (15283 \"Exocytosis\" (\"celf\")))\n (29 (596290 \"Cell Proliferation\" (\"celf\")))\n (32 (4391 \"Autophagy\" (\"celf\")))\n (77 (7587 \"Cell Death\" (\"celf\")))\n (88 (37083 \"Signal Transduction\" (\"celf\")))\n (168 (162638 \"Apoptosis\" (\"celf\"))))\n\n;; just test out for the celf (1155074 \"mast cell activation\" (\"celf\")):\n;;\n;; which disorders are affected by the celf, and are manifestations of the celf?\n> (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 disorder celf-type disorder-type rest1 rest2)\n (== (list e1 e2) q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,celf ,disorder \"AFFECTS\" ,celf-type ,disorder-type . ,rest1) e1)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type ,celf-type . ,rest2) e2)\n (edgeo e2)\n (edgeo e1)))))\n disorders))\n '((1155074 \"mast cell activation\" (\"celf\"))))\n'(((((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24486828\n 23394523\n 22300345\n 19909359\n 19508371\n 19290788\n 18485675\n 17336609\n 15589479\n 12574324\n 12217398\n 10213671\n 8376778\n 7964480\n 7964480))\n ((12634 \"Disease\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (12217411)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (242184 \"Hypoxia\" (\"patf\"))\n \"AFFECTS\"\n \"celf\"\n \"patf\"\n (22188111))\n ((242184 \"Hypoxia\" (\"patf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"patf\"\n \"celf\"\n (16572929)))))\n\n;; interesting! A direct causal link between KIT/C-KIT and asthma\n;; seems unknown. So we are not just trying to connect a drug and\n;; disease, but also KIT and the disease.\n(map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 celf disorder pred disorder-type rest0)\n (== e0 q)\n (fuzzy-concepto \"asthma\" disorder)\n (== `(,gene ,disorder ,pred \"gngm\" ,disorder-type . ,rest0) e0)\n (edgeo e0)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))))\n=>\n'(()\n (((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n \"ASSOCIATED_WITH\"\n \"gngm\"\n \"dsyn\"\n (25337192 22505052)))\n ())\n\n;; Look at the indirect connections between the 47 genes of interest and asthma.\n;;\n;; Query takes 2 minutes.\n;;\n;; The only *specfic* gene that uses mast cell activation as its celf is KIT (not C-KIT).\n;; There are various other genes that use signal transduction.\n;; And 'Antibodies' and 'Proteins' both use mast cell activation.\n;; While the genes aren't specific, the celf used is.\n(map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 e3 celf disorder disorder-type rest1 rest2 rest3)\n (== (list e1 e2 e3) q)\n (fuzzy-concepto \"asthma\" disorder)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e1)\n (edgeo e3)\n (edgeo e2)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))))\n=>\n;; cpu time: 127629 real time: 128505 gc time: 1446\n'(()\n ((((919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (24564241 1281217))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (26467500))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (24188406\n 24188406\n 22841885\n 22841885\n 21978835\n 21978835\n 20597478\n 20597478\n 18256384\n 12176746\n 12176746))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23340802 23340802))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ()\n ()\n ((((915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (16789903 11409908 7835966))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (26758977 25633229))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22262845\n 19170657\n 19048108\n 17503113\n 15163542\n 14620151\n 14580993\n 12949238\n 12482196\n 12482196\n 12324469\n 9450748))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (25539676 16461989))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ((((33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22357971 19290922 18492778 16790031 16790031 16415076))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (17426060 12035499 7882988))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23222563))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (26023679\n 24850739\n 23682925\n 23660250\n 22498774\n 22319212\n 21601104\n 20036637\n 17203870\n 15180972\n 15180972\n 15053611\n 12670482\n 12477288\n 12194978\n 12112690\n 11175815\n 11073315\n 9676989\n 8616803\n 7902881))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (12393403))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ((((246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22095643 16883913 16557224 8619925))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (15650217 15590688 9916027))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23222563 14505491 12960248))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ()\n ()\n ()\n ()\n ()\n ()\n ()\n ()\n ((((1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (9517496))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (27224507))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (23103565 19711112 19458196 17956356 7802667 2783138))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (24743893\n 20806817\n 17118962\n 16727886\n 15176971\n 13678963\n 11916364\n 11912280\n 11802165\n 9627110\n 9047384\n 7784069\n 7537742))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ()\n ((((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22885698 15887041 15494014 15494014 11406357 11406357))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (27904762\n 27479325\n 27194789\n 26748340\n 26283964\n 26198787\n 26001588\n 25954136\n 25522385\n 25457352\n 25250214\n 24987288\n 24847082\n 24404331\n 24098092\n 23380704\n 22310710\n 22132325\n 22014238\n 21824992\n 21291419\n 21050922\n 20505987\n 20003820\n 19888967\n 19465516\n 19348466\n 19203114\n 19001047\n 18952824\n 18380671\n 18367502\n 17920519\n 17632123\n 17485341\n 17466390\n 17373355\n 17355284\n 17303405\n 17254012\n 16956790\n 16956790\n 16371473\n 15827888\n 15795223\n 15583862\n 15356058\n 14731813\n 14731813\n 12919066\n 12110144\n 11544033\n 10917832\n 10859220\n 10762594\n 10629036\n 10533704\n 10374695\n 9842573\n 9380811\n 9136757\n 8875430\n 7669492\n 7532590\n 7512770\n 1326354\n 1323348))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (27994757\n 26852687\n 25367076\n 24931696\n 23979726\n 23862981\n 22002603\n 21848862\n 21629734\n 20159963\n 19636563\n 17408432\n 12881713\n 11896598\n 11491654\n 11280802\n 11049052\n 1840317\n 1838150))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (20956018))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ()\n ()\n ()\n ((((79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (17230190 15735964))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ((((105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (25534229 20926645 19717519 10347231))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910))))\n ()\n ((((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (18538998))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (12373338))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114)))))\n\n;; KIT gene *indirectly* is connected with asthma through two celfs:\n;; mast cell activation and Signal Transduction. Signal Transduction is also\n;; the indirect connection bewteen BCR gene and asthma.\n> (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 e3 celf disorder disorder-type rest1 rest2 rest3)\n (== (list e1 e2 e3) q)\n (fuzzy-concepto \"asthma\" disorder)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e1)\n (edgeo e3)\n (edgeo e2)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))))\n=>\n'(((((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (18538998))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))\n (((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (12373338))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))))\n ()\n ())\n\n> (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 e3 celf disorder disorder-type rest1 rest2 rest3)\n (== (list e1 e2 e3) q)\n (fuzzy-concepto \"asthma\" disorder)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e1)\n (edgeo e3)\n (edgeo e2)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))))\n=>\n'(((((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (22885698 15887041 15494014 15494014 11406357 11406357))\n ((37083 \"Signal Transduction\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24447081 22447942 19530997 19075672 18699801))\n ((4096 \"Asthma\" (\"dsyn\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (11197605 10087910)))))\n\n;; look at the reasoning chain for BCR gene and asthma (which seems dubious to me)\n(map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 e1 e2 e3 celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== (list e0 e1 e2 e3) q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e2)\n (edgeo e1)))))\n (let ((disorders (rem-dups disorders)))\n disorders)))\n '((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))))\n\n;; which of the 47 genes of interest are known to cause asthma, and\n;; also to cause a celf that affects asthma, and for which asthma is a\n;; manifestation of that celf?\n;;\n;;\n;; (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n;;\n;; Hmmm\n;;\n;; (((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n;; (4096 \"Asthma\" (\"dsyn\"))\n;; \"CAUSES\"\n;; \"gngm\"\n;; \"dsyn\"\n;; (20528593 20528593))\n;; ((812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n;; (37083 \"Signal Transduction\" (\"celf\"))\n;; \"CAUSES\"\n;; \"gngm\"\n;; \"celf\"\n;; (22885698 15887041 15494014 15494014 11406357 11406357))\n;; ((37083 \"Signal Transduction\" (\"celf\"))\n;; (4096 \"Asthma\" (\"dsyn\"))\n;; \"AFFECTS\"\n;; \"celf\"\n;; \"dsyn\"\n;; (24447081 22447942 19530997 19075672 18699801))\n;; ((4096 \"Asthma\" (\"dsyn\"))\n;; (37083 \"Signal Transduction\" (\"celf\"))\n;; \"MANIFESTATION_OF\"\n;; \"dsyn\"\n;; \"celf\"\n;; (11197605 10087910)))\n;;\n;; From the abstract of this paper, I can't tell that BCR gene CAUSES asthma\n;; is a reasonable claim:\n;;\n;; https://www.ncbi.nlm.nih.gov/pubmed/20528593\n(map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 e1 e2 e3 celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e2)\n (edgeo e1)))))\n (let ((disorders (rem-dups disorders)))\n (list (and (member '(4096 \"Asthma\" (\"dsyn\")) disorders) #t) disorders gene))))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))))\n\n;; Check that the gene (such as KIT) that causes a celf that affects a\n;; disorder is also know to directly cause that disorder? Seems like\n;; this is a basic check we should do, to both increase confidence and\n;; perhaps reduce answers.\n;;\n;; Restrict the disease to \"dsyn\" or \"patf\", but not \"neop\" (since in\n;; the case of imatinib/Gleevec, we already know it treats cancer).\n;;\n;; Try across all 47 genes of interest.\n;;\n;; cpu time: 18586 real time: 18595 gc time: 286\n;;\n;; 93 answers\n;;\n;; includes (4096 \"Asthma\" (\"dsyn\")) and (11847 \"Diabetes\" (\"dsyn\"))\n(apply\n union*\n (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 e1 e2 e3 celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n ; [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e1)\n (edgeo e2)))))\n (rem-dups disorders)))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))))\n=>\n'((7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (15376 \"Extravasation\" (\"patf\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (28778 \"Obstruction\" (\"patf\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\")))\n;; Now, remove all the diseases that imatinib variants are known to treat.\n;;\n;; 52 left, including asthma\n(set-subtraction\n '((7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (15376 \"Extravasation\" (\"patf\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (28778 \"Obstruction\" (\"patf\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\")))\n '((2871 \"Anemia\" (\"dsyn\"))\n (2874 \"Aplastic Anemia\" (\"dsyn\"))\n (2895 \"Sickle Cell Anemia\" (\"dsyn\"))\n (3047 \"Animal Diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (5940 \"Bone Diseases\" (\"dsyn\"))\n (18944 \"Hematoma\" (\"patf\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7682 \"CNS disorder\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6118 \"Brain Neoplasms\" (\"neop\"))\n (21368 \"Inflammation\" (\"patf\"))\n (8728 \"Churg-Strauss Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (10403 \"Cryoglobulinemia\" (\"dsyn\"))\n (11644 \"Scleroderma\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (29435 \"Osteolysis\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36429 \"Sclerosis\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (86565 \"Liver Dysfunction\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (151654 \"Myocardial fibrosis\" (\"patf\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (15624 \"Fanconi Syndrome\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (7114 \"Malignant neoplasm of skin\" (\"neop\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (231178 \"Chronic failure\" (\"patf\"))\n (19196 \"Hepatitis C\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (21141 \"Inappropriate ADH Syndrome\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (23890 \"Liver Cirrhosis\" (\"dsyn\"))\n (9404 \"Colorectal Neoplasms\" (\"neop\"))\n (24115 \"Lung diseases\" (\"dsyn\"))\n (333606 \"Dystrophy\" (\"patf\"))\n (24440 \"Macular Edema, Cystoid\" (\"dsyn\"))\n (443146 \"Autoimmune\" (\"patf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27697 \"Nephritis\" (\"dsyn\"))\n (549593 \"kidney functional\" (\"patf\"))\n (27947 \"Neutropenia\" (\"dsyn\"))\n (16048 \"Fibromatosis\" (\"neop\"))\n (33838 \"Kimura Disease\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (34063 \"Pulmonary Edema\" (\"dsyn\"))\n (744813 \"Hepatic embolisation\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (35920 \"Rubella\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (18923 \"Hemangiosarcoma\" (\"neop\"))\n (36992 \"Short Bowel Syndrome\" (\"dsyn\"))\n (1265815 \"Multiple ulcers\" (\"patf\"))\n (38013 \"Ankylosing spondylitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (1608322 \"Leak NOS\" (\"patf\"))\n (39103 \"Synovitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (85786 \"Hamman-Rich syndrome\" (\"dsyn\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (86438 \"Hypogammaglobulinemia\" (\"dsyn\"))\n (151859 \"Polyserositis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (158168 \"Villonodular synovitis\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206062 \"Lung Diseases, Interstitial\" (\"dsyn\"))\n (206143 \"Loeffler's Endocarditis\" (\"dsyn\"))\n (236178 \"Intraabdominal hemorrhage\" (\"dsyn\"))\n (238644 \"anemia; profound\" (\"dsyn\"))\n (238790 \"destruction; bone\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (263664 \"Generalized morphea\" (\"dsyn\"))\n (264939 \"Systemic vasculitis\" (\"dsyn\"))\n (23475 \"Leukemia, Myeloid, Philadelphia-Negative\" (\"neop\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n (276653 \"Invasive pulmonary aspergillosis\" (\"dsyn\"))\n (277554 \"Primary disease\" (\"dsyn\"))\n (277556 \"Recurrent disease\" (\"dsyn\"))\n (334102 \"Lymphangiomatosis\" (\"dsyn\"))\n (23484 \"Leukemia, Plasmacytic\" (\"neop\"))\n (340548 \"Pulmonary capillary hemangiomatosis\" (\"dsyn\"))\n (23601 \"Leydig Cell Tumor\" (\"neop\"))\n (341213 \"External gastric fistula\" (\"dsyn\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (341439 \"Chronic liver disease NOS\" (\"dsyn\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (442867 \"Malignant disease\" (\"dsyn\"))\n (549567 \"Pigmentation Disorders\" (\"dsyn\"))\n (678236 \"Rare Diseases\" (\"dsyn\"))\n (743496 \"END ORGAN DAMAGE\" (\"dsyn\"))\n (25286 \"meningioma\" (\"neop\"))\n (25500 \"Mesothelioma\" (\"neop\"))\n (854467 \"Myelosuppression\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (855227 \"Purging\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (920627 \"Orphan Diseases\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (948908 \"Nephrotoxic serum nephritis\" (\"dsyn\"))\n (1273070 \"Left ventricular diastolic dysfunction\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (27832 \"Neurofibromatosis 2\" (\"neop\"))\n (1299884 \"Eosinophilic myositis\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1332309 \"Anti-Basement Membrane Glomerulonephritis\" (\"dsyn\"))\n (1533022 \"Histiocytic proliferation\" (\"dsyn\"))\n (1565489 \"Renal Insufficiency\" (\"dsyn\"))\n (36221 \"Mast-Cell Sarcoma\" (\"neop\"))\n (41341 \"Tuberous Sclerosis\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (79772 \"T-Cell Lymphoma\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (162678 \"Neurofibromatoses\" (\"neop\"))\n (205853 \"Neoplasms, Epithelial\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206657 \"Sarcoma, Alveolar Soft Part\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (220650 \"Metastatic malignant neoplasm to brain\" (\"neop\"))\n (238463 \"Papillary thyroid carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (278517 \"Non-small cell lung cancer recurrent\" (\"neop\"))\n (278695 \"recurrent neuroblastoma\" (\"neop\"))\n (278704 \"Malignant Childhood Neoplasm\" (\"neop\"))\n (278727 \"Small cell lung cancer recurrent\" (\"neop\"))\n (279068 \"childhood solid tumor\" (\"neop\"))\n (279087 \"recurrent Kaposi's sarcoma\" (\"neop\"))\n (281361 \"Adenocarcinoma pancreas\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (334410 \"Leydig cell tumor, malignant\" (\"neop\"))\n (334695 \"Endometrial Stromal Tumors\" (\"neop\"))\n (349636 \"Pre B-cell acute lymphoblastic leukemia\" (\"neop\"))\n (553580 \"Ewings sarcoma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (685938 \"Malignant neoplasm of gastrointestinal tract\" (\"neop\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (854850 \"Mycosis fungoides refractory\" (\"neop\"))\n (855054 \"Fibrosarcoma metastatic\" (\"neop\"))\n (855211 \"Seminoma of testis\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (1266042 \"Chromophobe Renal Cell Carcinoma\" (\"neop\"))\n (1266101 \"Thymic epithelial neoplasm\" (\"neop\"))\n (1266119 \"Solitary fibrous tumor\" (\"neop\"))\n (1266120 \"Solitary fibrous tumor, malignant\" (\"neop\"))\n (1300127 \"Perivascular epithelial cell tumor\" (\"neop\"))\n (1306837 \"Papillary Renal Cell Carcinoma\" (\"neop\"))\n (1318543 \"Tenosynovial giant cell tumor\" (\"neop\"))\n (1319185 \"Chiasmal glioma\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1332884 \"Central Nervous System Leukemia\" (\"neop\"))\n (1333614 \"Fibrosarcomatous Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (1334432 \"Low Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1335996 \"Small Intestinal Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1378050 \"Oncocytic Neoplasm\" (\"neop\"))\n (1411997 \"Acute biphenotypic leukemia\" (\"neop\"))\n (1512409 \"Hepatocarcinogenesis\" (\"neop\"))\n (1524028 \"Intraepithelial Neoplasia of the Mouse Mammary Gland\" (\"neop\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (6272 \"Bronchiolitis Obliterans\" (\"dsyn\"))\n (9782 \"Connective Tissue Diseases\" (\"dsyn\"))\n (10828 \"Cytopenia\" (\"patf\"))\n (11603 \"Dermatitis\" (\"dsyn\"))\n (11633 \"Dermatomyositis\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (7102 \"Malignant tumor of colon\" (\"neop\"))\n (19618 \"Histiocytosis\" (\"dsyn\"))\n (243083 \"associated disease\" (\"patf\"))\n (19621 \"Histiocytosis, Langerhans-Cell\" (\"dsyn\"))\n (7115 \"Malignant neoplasm of thyroid\" (\"neop\"))\n (19624 \"Histiocytosis, Non-Langerhans-Cell\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (19625 \"Sinus histiocytosis\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (399498 \"Oral lichenoid reaction\" (\"patf\"))\n (24901 \"Mastocytosis, Diffuse Cutaneous\" (\"dsyn\"))\n (26272 \"Mixed Connective Tissue Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (31154 \"Peritonitis\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (7140 \"Carcinosarcoma\" (\"neop\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (33687 \"Proteinuria\" (\"dsyn\"))\n (7847 \"Malignant neoplasm of cervix uteri\" (\"neop\"))\n (34069 \"Pulmonary Fibrosis\" (\"dsyn\"))\n (34155 \"Purpura, Thrombotic Thrombocytopenic\" (\"dsyn\"))\n (8479 \"Chondrosarcoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (39106 \"Pigmented villonodular synovitis\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (42384 \"Vasculitis\" (\"dsyn\"))\n (18206 \"granulosa cell tumor\" (\"neop\"))\n (152171 \"Primary pulmonary hypertension\" (\"dsyn\"))\n (162835 \"Hypopigmentation\" (\"dsyn\"))\n (206061 \"Pneumonitis, Interstitial\" (\"dsyn\"))\n (23435 \"Leukemia, B-Cell, Acute\" (\"neop\"))\n (267437 \"Allergic diarrhea\" (\"dsyn\"))\n (282548 \"Leukostasis\" (\"dsyn\"))\n (339143 \"Thyroid associated opthalmopathies\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (341697 \"Renal impairment\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (745283 \"INFECTIOUS PROCESS\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (748159 \"PULMONARY INVOLVEMENT\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (836924 \"thrombocytosis\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (949690 \"Spondylarthritis\" (\"dsyn\"))\n (1112486 \"Aggressive Systemic Mastocytosis\" (\"dsyn\"))\n (1136033 \"Cutaneous Mastocytosis\" (\"dsyn\"))\n (1142420 \"Hepatitis B reactivation\" (\"dsyn\"))\n (1261469 \"End stage renal failure\" (\"dsyn\"))\n (23479 \"Leukemia, Myelomonocytic, Acute\" (\"neop\"))\n (1279945 \"Acute interstitial pneumonia\" (\"dsyn\"))\n (1368107 \"Aplastic bone marrow\" (\"dsyn\"))\n (1619734 \"Pulmonary arterial hypertension\" (\"dsyn\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23494 \"Leukemia, T-Cell, Chronic\" (\"neop\"))\n (23827 \"liposarcoma\" (\"neop\"))\n (26987 \"Myelofibrosis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (35412 \"Rhabdomyosarcoma\" (\"neop\"))\n (36220 \"Kaposi Sarcoma\" (\"neop\"))\n (36631 \"Seminoma\" (\"neop\"))\n (39101 \"synovial sarcoma\" (\"neop\"))\n (40100 \"Thymoma\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (151779 \"[X]Malignant melanoma of skin, unspecified\" (\"neop\"))\n (205851 \"Germ cell tumor\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (206630 \"Endometrial Stromal Sarcoma\" (\"neop\"))\n (206693 \"Medullary carcinoma\" (\"neop\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (276535 \"AIDS with Kaposi's sarcoma\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278678 \"Metastatic renal cell carcinoma\" (\"neop\"))\n (278694 \"Disseminated neuroblastoma\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (279549\n \"Philadelphia chromosome negative chronic myelogenous leukemia\"\n (\"neop\"))\n (280449 \"secondary acute myeloid leukemia\" (\"neop\"))\n (334664 \"Mast Cell Neoplasm\" (\"neop\"))\n (338113 \"Uterine Corpus Sarcoma\" (\"neop\"))\n (341823 \"Epithelial tumor of ovary\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (346421 \"Chronic eosinophilic leukemia\" (\"neop\"))\n (346976 \"Secondary malignant neoplasm of pancreas\" (\"neop\"))\n (349640 \"[M]Subacute myeloid leukemia\" (\"neop\"))\n (431109 \"Choroid Plexus Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (521158 \"Recurrent tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (549379 \"Recurrent Carcinoma\" (\"neop\"))\n (598798 \"Lymphoid neoplasm\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (677936 \"Refractory Carcinoma\" (\"neop\"))\n (699889 \"Female reproductive neoplasm malignant NOS\" (\"neop\"))\n (740267 \"Ocular melanomas\" (\"neop\"))\n (740277 \"Bile duct carcinoma\" (\"neop\"))\n (743535 \"EOSINOPHILIC GRANULOMATOSIS\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (812413 \"Malignant Pleural Mesothelioma\" (\"neop\"))\n (855013 \"Chondrosarcoma recurrent\" (\"neop\"))\n (936223 \"Prostate cancer metastatic\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1327920 \"childhood chronic myelogenous leukemia\" (\"neop\"))\n (1333768 \"Gastric Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334699 \"Mesenchymal Cell Neoplasm\" (\"neop\"))\n (1335711 \"Recurrent Mature T- and NK-Cell Non-Hodgkin's Lymphoma\" (\"neop\"))\n (1335713 \"Recurrent Meningioma\" (\"neop\"))\n (1335729 \"Refractory Neoplasm\" (\"neop\"))\n (1336746 \"Thymus Carcinoid Tumor\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (235063 \"Respiratory Depression\" (\"patf\"))\n (679222 \"functional insufficiency\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (1815 \"Primary Myelofibrosis\" (\"neop\"))\n (12634 \"Disease\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (24228 \"Lymphatic Diseases\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (37354 \"Smallpox\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (221013 \"Mastocytosis, Systemic\" (\"dsyn\"))\n (1318485 \"Liver regeneration disorder\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (456070 \"Growth delay\" (\"patf\"))\n (17638 \"Glioma\" (\"neop\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23453 \"Leukemia, Lymphocytic, Acute, L2\" (\"neop\"))\n (23476 \"Leukemia, Myeloid, Philadelphia-Positive\" (\"neop\"))\n (23480 \"Leukemia, Myelomonocytic, Chronic\" (\"neop\"))\n (23481 \"Leukemia, Neutrophilic, Chronic\" (\"neop\"))\n (27022 \"Myeloproliferative disease\" (\"neop\"))\n (27819 \"Neuroblastoma\" (\"neop\"))\n (29463 \"osteosarcoma\" (\"neop\"))\n (85136 \"Central Nervous System Neoplasms\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (152018 \"Esophageal carcinoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (206093 \"Neuroectodermal Tumors\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (238461 \"Anaplastic thyroid carcinoma\" (\"neop\"))\n (238462 \"Medullary carcinoma of thyroid\" (\"neop\"))\n (278726 \"Small cell lung cancer extensive stage\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (555198 \"Malignant Glioma\" (\"neop\"))\n (677930 \"Primary Neoplasm\" (\"neop\"))\n (699791 \"Stomach Carcinoma\" (\"neop\"))\n (750952 \"Biliary Tract Cancer\" (\"neop\"))\n (751606 \"Adult Acute Lymphocytic Leukemia\" (\"neop\"))\n (860582 \"Peritoneal metastases\" (\"neop\"))\n (877373 \"Advanced cancer\" (\"neop\"))\n (879615 \"Stromal Neoplasm\" (\"neop\"))\n (887833 \"Carcinoma, Pancreatic Ductal\" (\"neop\"))\n (920028 \"Leukaemia recurrent\" (\"neop\"))\n (1266137 \"Gastrointestinal stromal sarcoma\" (\"neop\"))\n (1279296 \"Chronic leukemia (category)\" (\"neop\"))\n (1370868 \"refractory CML\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n=>\n'((19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\")))\n\n;; Check that the gene (such as KIT) that causes a celf that affects a\n;; disorder is also know to directly cause that disorder? Seems like\n;; this is a basic check we should do, to both increase confidence and\n;; perhaps reduce answers.\n;;\n;; Try across all 47 genes of interest.\n;;\n;; cpu time: 34833 real time: 34942 gc time: 405\n;;\n;; 143 answers\n;;\n;; includes (4096 \"Asthma\" (\"dsyn\")) and (11847 \"Diabetes\" (\"dsyn\"))\n(apply\n union*\n (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 e1 e2 e3 celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e1)\n (edgeo e2)))))\n (rem-dups disorders)))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))))\n=>\n'((7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (333641 \"Atrophic\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (37286 \"Skin Neoplasms\" (\"neop\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (1458155 \"Mammary Neoplasms\" (\"neop\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (13604 \"Edema\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (23903 \"Liver neoplasms\" (\"neop\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (9566 \"Complication\" (\"patf\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (7117 \"Basal cell carcinoma\" (\"neop\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (17638 \"Glioma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (23458 \"Leukemia, Lymphocytic, Chronic\" (\"neop\"))\n (24121 \"Lung Neoplasms\" (\"neop\"))\n (24299 \"Lymphoma\" (\"neop\"))\n (24305 \"Lymphoma, Non-Hodgkin's\" (\"neop\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32580 \"Adenomatous Polyposis Coli\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (279626 \"Squamous cell carcinoma of esophagus\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (596263 \"Carcinogenesis\" (\"neop\"))\n (598935 \"Tumor Initiation\" (\"neop\"))\n (678222 \"Breast Carcinoma\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (28778 \"Obstruction\" (\"patf\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n;; Now, remove all the diseases that imatinib variants are known to treat.\n;;\n;; 66 left, including asthma\n(set-subtraction\n '((7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (333641 \"Atrophic\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (37286 \"Skin Neoplasms\" (\"neop\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (1458155 \"Mammary Neoplasms\" (\"neop\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (13604 \"Edema\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (23903 \"Liver neoplasms\" (\"neop\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (9566 \"Complication\" (\"patf\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (7117 \"Basal cell carcinoma\" (\"neop\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (17638 \"Glioma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (23458 \"Leukemia, Lymphocytic, Chronic\" (\"neop\"))\n (24121 \"Lung Neoplasms\" (\"neop\"))\n (24299 \"Lymphoma\" (\"neop\"))\n (24305 \"Lymphoma, Non-Hodgkin's\" (\"neop\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32580 \"Adenomatous Polyposis Coli\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (279626 \"Squamous cell carcinoma of esophagus\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (596263 \"Carcinogenesis\" (\"neop\"))\n (598935 \"Tumor Initiation\" (\"neop\"))\n (678222 \"Breast Carcinoma\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (28778 \"Obstruction\" (\"patf\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n '((2871 \"Anemia\" (\"dsyn\"))\n (2874 \"Aplastic Anemia\" (\"dsyn\"))\n (2895 \"Sickle Cell Anemia\" (\"dsyn\"))\n (3047 \"Animal Diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (5940 \"Bone Diseases\" (\"dsyn\"))\n (18944 \"Hematoma\" (\"patf\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7682 \"CNS disorder\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6118 \"Brain Neoplasms\" (\"neop\"))\n (21368 \"Inflammation\" (\"patf\"))\n (8728 \"Churg-Strauss Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (10403 \"Cryoglobulinemia\" (\"dsyn\"))\n (11644 \"Scleroderma\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (29435 \"Osteolysis\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36429 \"Sclerosis\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (86565 \"Liver Dysfunction\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (151654 \"Myocardial fibrosis\" (\"patf\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (15624 \"Fanconi Syndrome\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (7114 \"Malignant neoplasm of skin\" (\"neop\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (231178 \"Chronic failure\" (\"patf\"))\n (19196 \"Hepatitis C\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (21141 \"Inappropriate ADH Syndrome\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (23890 \"Liver Cirrhosis\" (\"dsyn\"))\n (9404 \"Colorectal Neoplasms\" (\"neop\"))\n (24115 \"Lung diseases\" (\"dsyn\"))\n (333606 \"Dystrophy\" (\"patf\"))\n (24440 \"Macular Edema, Cystoid\" (\"dsyn\"))\n (443146 \"Autoimmune\" (\"patf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27697 \"Nephritis\" (\"dsyn\"))\n (549593 \"kidney functional\" (\"patf\"))\n (27947 \"Neutropenia\" (\"dsyn\"))\n (16048 \"Fibromatosis\" (\"neop\"))\n (33838 \"Kimura Disease\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (34063 \"Pulmonary Edema\" (\"dsyn\"))\n (744813 \"Hepatic embolisation\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (35920 \"Rubella\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (18923 \"Hemangiosarcoma\" (\"neop\"))\n (36992 \"Short Bowel Syndrome\" (\"dsyn\"))\n (1265815 \"Multiple ulcers\" (\"patf\"))\n (38013 \"Ankylosing spondylitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (1608322 \"Leak NOS\" (\"patf\"))\n (39103 \"Synovitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (85786 \"Hamman-Rich syndrome\" (\"dsyn\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (86438 \"Hypogammaglobulinemia\" (\"dsyn\"))\n (151859 \"Polyserositis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (158168 \"Villonodular synovitis\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206062 \"Lung Diseases, Interstitial\" (\"dsyn\"))\n (206143 \"Loeffler's Endocarditis\" (\"dsyn\"))\n (236178 \"Intraabdominal hemorrhage\" (\"dsyn\"))\n (238644 \"anemia; profound\" (\"dsyn\"))\n (238790 \"destruction; bone\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (263664 \"Generalized morphea\" (\"dsyn\"))\n (264939 \"Systemic vasculitis\" (\"dsyn\"))\n (23475 \"Leukemia, Myeloid, Philadelphia-Negative\" (\"neop\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n (276653 \"Invasive pulmonary aspergillosis\" (\"dsyn\"))\n (277554 \"Primary disease\" (\"dsyn\"))\n (277556 \"Recurrent disease\" (\"dsyn\"))\n (334102 \"Lymphangiomatosis\" (\"dsyn\"))\n (23484 \"Leukemia, Plasmacytic\" (\"neop\"))\n (340548 \"Pulmonary capillary hemangiomatosis\" (\"dsyn\"))\n (23601 \"Leydig Cell Tumor\" (\"neop\"))\n (341213 \"External gastric fistula\" (\"dsyn\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (341439 \"Chronic liver disease NOS\" (\"dsyn\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (442867 \"Malignant disease\" (\"dsyn\"))\n (549567 \"Pigmentation Disorders\" (\"dsyn\"))\n (678236 \"Rare Diseases\" (\"dsyn\"))\n (743496 \"END ORGAN DAMAGE\" (\"dsyn\"))\n (25286 \"meningioma\" (\"neop\"))\n (25500 \"Mesothelioma\" (\"neop\"))\n (854467 \"Myelosuppression\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (855227 \"Purging\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (920627 \"Orphan Diseases\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (948908 \"Nephrotoxic serum nephritis\" (\"dsyn\"))\n (1273070 \"Left ventricular diastolic dysfunction\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (27832 \"Neurofibromatosis 2\" (\"neop\"))\n (1299884 \"Eosinophilic myositis\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1332309 \"Anti-Basement Membrane Glomerulonephritis\" (\"dsyn\"))\n (1533022 \"Histiocytic proliferation\" (\"dsyn\"))\n (1565489 \"Renal Insufficiency\" (\"dsyn\"))\n (36221 \"Mast-Cell Sarcoma\" (\"neop\"))\n (41341 \"Tuberous Sclerosis\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (79772 \"T-Cell Lymphoma\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (162678 \"Neurofibromatoses\" (\"neop\"))\n (205853 \"Neoplasms, Epithelial\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206657 \"Sarcoma, Alveolar Soft Part\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (220650 \"Metastatic malignant neoplasm to brain\" (\"neop\"))\n (238463 \"Papillary thyroid carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (278517 \"Non-small cell lung cancer recurrent\" (\"neop\"))\n (278695 \"recurrent neuroblastoma\" (\"neop\"))\n (278704 \"Malignant Childhood Neoplasm\" (\"neop\"))\n (278727 \"Small cell lung cancer recurrent\" (\"neop\"))\n (279068 \"childhood solid tumor\" (\"neop\"))\n (279087 \"recurrent Kaposi's sarcoma\" (\"neop\"))\n (281361 \"Adenocarcinoma pancreas\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (334410 \"Leydig cell tumor, malignant\" (\"neop\"))\n (334695 \"Endometrial Stromal Tumors\" (\"neop\"))\n (349636 \"Pre B-cell acute lymphoblastic leukemia\" (\"neop\"))\n (553580 \"Ewings sarcoma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (685938 \"Malignant neoplasm of gastrointestinal tract\" (\"neop\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (854850 \"Mycosis fungoides refractory\" (\"neop\"))\n (855054 \"Fibrosarcoma metastatic\" (\"neop\"))\n (855211 \"Seminoma of testis\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (1266042 \"Chromophobe Renal Cell Carcinoma\" (\"neop\"))\n (1266101 \"Thymic epithelial neoplasm\" (\"neop\"))\n (1266119 \"Solitary fibrous tumor\" (\"neop\"))\n (1266120 \"Solitary fibrous tumor, malignant\" (\"neop\"))\n (1300127 \"Perivascular epithelial cell tumor\" (\"neop\"))\n (1306837 \"Papillary Renal Cell Carcinoma\" (\"neop\"))\n (1318543 \"Tenosynovial giant cell tumor\" (\"neop\"))\n (1319185 \"Chiasmal glioma\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1332884 \"Central Nervous System Leukemia\" (\"neop\"))\n (1333614 \"Fibrosarcomatous Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (1334432 \"Low Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1335996 \"Small Intestinal Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1378050 \"Oncocytic Neoplasm\" (\"neop\"))\n (1411997 \"Acute biphenotypic leukemia\" (\"neop\"))\n (1512409 \"Hepatocarcinogenesis\" (\"neop\"))\n (1524028 \"Intraepithelial Neoplasia of the Mouse Mammary Gland\" (\"neop\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (6272 \"Bronchiolitis Obliterans\" (\"dsyn\"))\n (9782 \"Connective Tissue Diseases\" (\"dsyn\"))\n (10828 \"Cytopenia\" (\"patf\"))\n (11603 \"Dermatitis\" (\"dsyn\"))\n (11633 \"Dermatomyositis\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (7102 \"Malignant tumor of colon\" (\"neop\"))\n (19618 \"Histiocytosis\" (\"dsyn\"))\n (243083 \"associated disease\" (\"patf\"))\n (19621 \"Histiocytosis, Langerhans-Cell\" (\"dsyn\"))\n (7115 \"Malignant neoplasm of thyroid\" (\"neop\"))\n (19624 \"Histiocytosis, Non-Langerhans-Cell\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (19625 \"Sinus histiocytosis\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (399498 \"Oral lichenoid reaction\" (\"patf\"))\n (24901 \"Mastocytosis, Diffuse Cutaneous\" (\"dsyn\"))\n (26272 \"Mixed Connective Tissue Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (31154 \"Peritonitis\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (7140 \"Carcinosarcoma\" (\"neop\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (33687 \"Proteinuria\" (\"dsyn\"))\n (7847 \"Malignant neoplasm of cervix uteri\" (\"neop\"))\n (34069 \"Pulmonary Fibrosis\" (\"dsyn\"))\n (34155 \"Purpura, Thrombotic Thrombocytopenic\" (\"dsyn\"))\n (8479 \"Chondrosarcoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (39106 \"Pigmented villonodular synovitis\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (42384 \"Vasculitis\" (\"dsyn\"))\n (18206 \"granulosa cell tumor\" (\"neop\"))\n (152171 \"Primary pulmonary hypertension\" (\"dsyn\"))\n (162835 \"Hypopigmentation\" (\"dsyn\"))\n (206061 \"Pneumonitis, Interstitial\" (\"dsyn\"))\n (23435 \"Leukemia, B-Cell, Acute\" (\"neop\"))\n (267437 \"Allergic diarrhea\" (\"dsyn\"))\n (282548 \"Leukostasis\" (\"dsyn\"))\n (339143 \"Thyroid associated opthalmopathies\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (341697 \"Renal impairment\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (745283 \"INFECTIOUS PROCESS\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (748159 \"PULMONARY INVOLVEMENT\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (836924 \"thrombocytosis\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (949690 \"Spondylarthritis\" (\"dsyn\"))\n (1112486 \"Aggressive Systemic Mastocytosis\" (\"dsyn\"))\n (1136033 \"Cutaneous Mastocytosis\" (\"dsyn\"))\n (1142420 \"Hepatitis B reactivation\" (\"dsyn\"))\n (1261469 \"End stage renal failure\" (\"dsyn\"))\n (23479 \"Leukemia, Myelomonocytic, Acute\" (\"neop\"))\n (1279945 \"Acute interstitial pneumonia\" (\"dsyn\"))\n (1368107 \"Aplastic bone marrow\" (\"dsyn\"))\n (1619734 \"Pulmonary arterial hypertension\" (\"dsyn\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23494 \"Leukemia, T-Cell, Chronic\" (\"neop\"))\n (23827 \"liposarcoma\" (\"neop\"))\n (26987 \"Myelofibrosis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (35412 \"Rhabdomyosarcoma\" (\"neop\"))\n (36220 \"Kaposi Sarcoma\" (\"neop\"))\n (36631 \"Seminoma\" (\"neop\"))\n (39101 \"synovial sarcoma\" (\"neop\"))\n (40100 \"Thymoma\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (151779 \"[X]Malignant melanoma of skin, unspecified\" (\"neop\"))\n (205851 \"Germ cell tumor\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (206630 \"Endometrial Stromal Sarcoma\" (\"neop\"))\n (206693 \"Medullary carcinoma\" (\"neop\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (276535 \"AIDS with Kaposi's sarcoma\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278678 \"Metastatic renal cell carcinoma\" (\"neop\"))\n (278694 \"Disseminated neuroblastoma\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (279549\n \"Philadelphia chromosome negative chronic myelogenous leukemia\"\n (\"neop\"))\n (280449 \"secondary acute myeloid leukemia\" (\"neop\"))\n (334664 \"Mast Cell Neoplasm\" (\"neop\"))\n (338113 \"Uterine Corpus Sarcoma\" (\"neop\"))\n (341823 \"Epithelial tumor of ovary\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (346421 \"Chronic eosinophilic leukemia\" (\"neop\"))\n (346976 \"Secondary malignant neoplasm of pancreas\" (\"neop\"))\n (349640 \"[M]Subacute myeloid leukemia\" (\"neop\"))\n (431109 \"Choroid Plexus Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (521158 \"Recurrent tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (549379 \"Recurrent Carcinoma\" (\"neop\"))\n (598798 \"Lymphoid neoplasm\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (677936 \"Refractory Carcinoma\" (\"neop\"))\n (699889 \"Female reproductive neoplasm malignant NOS\" (\"neop\"))\n (740267 \"Ocular melanomas\" (\"neop\"))\n (740277 \"Bile duct carcinoma\" (\"neop\"))\n (743535 \"EOSINOPHILIC GRANULOMATOSIS\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (812413 \"Malignant Pleural Mesothelioma\" (\"neop\"))\n (855013 \"Chondrosarcoma recurrent\" (\"neop\"))\n (936223 \"Prostate cancer metastatic\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1327920 \"childhood chronic myelogenous leukemia\" (\"neop\"))\n (1333768 \"Gastric Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334699 \"Mesenchymal Cell Neoplasm\" (\"neop\"))\n (1335711 \"Recurrent Mature T- and NK-Cell Non-Hodgkin's Lymphoma\" (\"neop\"))\n (1335713 \"Recurrent Meningioma\" (\"neop\"))\n (1335729 \"Refractory Neoplasm\" (\"neop\"))\n (1336746 \"Thymus Carcinoid Tumor\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (235063 \"Respiratory Depression\" (\"patf\"))\n (679222 \"functional insufficiency\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (1815 \"Primary Myelofibrosis\" (\"neop\"))\n (12634 \"Disease\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (24228 \"Lymphatic Diseases\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (37354 \"Smallpox\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (221013 \"Mastocytosis, Systemic\" (\"dsyn\"))\n (1318485 \"Liver regeneration disorder\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (456070 \"Growth delay\" (\"patf\"))\n (17638 \"Glioma\" (\"neop\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23453 \"Leukemia, Lymphocytic, Acute, L2\" (\"neop\"))\n (23476 \"Leukemia, Myeloid, Philadelphia-Positive\" (\"neop\"))\n (23480 \"Leukemia, Myelomonocytic, Chronic\" (\"neop\"))\n (23481 \"Leukemia, Neutrophilic, Chronic\" (\"neop\"))\n (27022 \"Myeloproliferative disease\" (\"neop\"))\n (27819 \"Neuroblastoma\" (\"neop\"))\n (29463 \"osteosarcoma\" (\"neop\"))\n (85136 \"Central Nervous System Neoplasms\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (152018 \"Esophageal carcinoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (206093 \"Neuroectodermal Tumors\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (238461 \"Anaplastic thyroid carcinoma\" (\"neop\"))\n (238462 \"Medullary carcinoma of thyroid\" (\"neop\"))\n (278726 \"Small cell lung cancer extensive stage\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (555198 \"Malignant Glioma\" (\"neop\"))\n (677930 \"Primary Neoplasm\" (\"neop\"))\n (699791 \"Stomach Carcinoma\" (\"neop\"))\n (750952 \"Biliary Tract Cancer\" (\"neop\"))\n (751606 \"Adult Acute Lymphocytic Leukemia\" (\"neop\"))\n (860582 \"Peritoneal metastases\" (\"neop\"))\n (877373 \"Advanced cancer\" (\"neop\"))\n (879615 \"Stromal Neoplasm\" (\"neop\"))\n (887833 \"Carcinoma, Pancreatic Ductal\" (\"neop\"))\n (920028 \"Leukaemia recurrent\" (\"neop\"))\n (1266137 \"Gastrointestinal stromal sarcoma\" (\"neop\"))\n (1279296 \"Chronic leukemia (category)\" (\"neop\"))\n (1370868 \"refractory CML\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n=>\n'((19158 \"Hepatitis\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (333641 \"Atrophic\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (2878 \"Anemia, Hemolytic\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (37286 \"Skin Neoplasms\" (\"neop\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (1458155 \"Mammary Neoplasms\" (\"neop\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (13604 \"Edema\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (23903 \"Liver neoplasms\" (\"neop\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (7117 \"Basal cell carcinoma\" (\"neop\"))\n (23458 \"Leukemia, Lymphocytic, Chronic\" (\"neop\"))\n (24121 \"Lung Neoplasms\" (\"neop\"))\n (24299 \"Lymphoma\" (\"neop\"))\n (24305 \"Lymphoma, Non-Hodgkin's\" (\"neop\"))\n (32580 \"Adenomatous Polyposis Coli\" (\"neop\"))\n (279626 \"Squamous cell carcinoma of esophagus\" (\"neop\"))\n (596263 \"Carcinogenesis\" (\"neop\"))\n (598935 \"Tumor Initiation\" (\"neop\"))\n (678222 \"Breast Carcinoma\" (\"neop\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\")))\n\n\n;; Check that the gene (such as KIT) that causes a celf that affects a\n;; disorder is also know to directly cause that disorder? Seems like\n;; this is a basic check we should do, to both increase confidence and\n;; perhaps reduce answers.\n;;\n;; test abstracted version using KIT and C-KIT\n(apply\n union*\n (map\n (lambda (gene)\n (let ((disorders\n (run* (q)\n (fresh (e0 e1 e2 e3 celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e1)\n (edgeo e2)))))\n (rem-dups disorders)))\n '((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\")))))\n=>\n'((2871 \"Anemia\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (12634 \"Disease\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (25202 \"melanoma\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n\n;; For our main query, shouldn't we also be checking that the gene\n;; (such as KIT) that causes a celf that affects a disorder is also\n;; know to directly cause that disorder? Seems like this is a basic\n;; check we should do, to both increase confidence and perhaps reduce\n;; answers. We are interested in finding new drug/disease\n;; connections, not new gene/disease connections, so this seems like\n;; an obvious move. Try it out using KIT/C-KIT!\n(rem-dups\n (run* (q)\n (fresh (e0 e1 e2 e3 gene celf disorder disorder-type rest0 rest1 rest2 rest3)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)]) \n (conde\n [(== '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) gene)]\n [(== '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) gene)]\n [(== '(72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\")) gene)])\n (== `(,gene ,disorder \"CAUSES\" \"gngm\" ,disorder-type . ,rest0) e0)\n (== `(,gene ,celf \"CAUSES\" \"gngm\" \"celf\" . ,rest1) e1)\n (== `(,celf ,disorder \"AFFECTS\" \"celf\" ,disorder-type . ,rest2) e2)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type \"celf\" . ,rest3) e3)\n (edgeo e0)\n (edgeo e3)\n (edgeo e1)\n (edgeo e2))))\n=>\n'((2871 \"Anemia\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n;; Now, remove all the diseases that imatinib variants are known to treat.\n;; There are only 4 left for the KIT variants:\n;;\n;; '((27051 \"Myocardial Infarction\" (\"dsyn\"))\n;; (1140999 \"Contraction\" (\"patf\"))\n;; (1608408 \"Malignant transformation\" (\"neop\"))\n;; (1510411 \"metaplastic cell transformation\" (\"patf\")))\n(set-subtraction\n '((2871 \"Anemia\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n '((2871 \"Anemia\" (\"dsyn\"))\n (2874 \"Aplastic Anemia\" (\"dsyn\"))\n (2895 \"Sickle Cell Anemia\" (\"dsyn\"))\n (3047 \"Animal Diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (5940 \"Bone Diseases\" (\"dsyn\"))\n (18944 \"Hematoma\" (\"patf\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7682 \"CNS disorder\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6118 \"Brain Neoplasms\" (\"neop\"))\n (21368 \"Inflammation\" (\"patf\"))\n (8728 \"Churg-Strauss Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (10403 \"Cryoglobulinemia\" (\"dsyn\"))\n (11644 \"Scleroderma\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (29435 \"Osteolysis\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36429 \"Sclerosis\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (86565 \"Liver Dysfunction\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (151654 \"Myocardial fibrosis\" (\"patf\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (15624 \"Fanconi Syndrome\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (7114 \"Malignant neoplasm of skin\" (\"neop\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (231178 \"Chronic failure\" (\"patf\"))\n (19196 \"Hepatitis C\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (21141 \"Inappropriate ADH Syndrome\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (23890 \"Liver Cirrhosis\" (\"dsyn\"))\n (9404 \"Colorectal Neoplasms\" (\"neop\"))\n (24115 \"Lung diseases\" (\"dsyn\"))\n (333606 \"Dystrophy\" (\"patf\"))\n (24440 \"Macular Edema, Cystoid\" (\"dsyn\"))\n (443146 \"Autoimmune\" (\"patf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27697 \"Nephritis\" (\"dsyn\"))\n (549593 \"kidney functional\" (\"patf\"))\n (27947 \"Neutropenia\" (\"dsyn\"))\n (16048 \"Fibromatosis\" (\"neop\"))\n (33838 \"Kimura Disease\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (34063 \"Pulmonary Edema\" (\"dsyn\"))\n (744813 \"Hepatic embolisation\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (35920 \"Rubella\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (18923 \"Hemangiosarcoma\" (\"neop\"))\n (36992 \"Short Bowel Syndrome\" (\"dsyn\"))\n (1265815 \"Multiple ulcers\" (\"patf\"))\n (38013 \"Ankylosing spondylitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (1608322 \"Leak NOS\" (\"patf\"))\n (39103 \"Synovitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (85786 \"Hamman-Rich syndrome\" (\"dsyn\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (86438 \"Hypogammaglobulinemia\" (\"dsyn\"))\n (151859 \"Polyserositis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (158168 \"Villonodular synovitis\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206062 \"Lung Diseases, Interstitial\" (\"dsyn\"))\n (206143 \"Loeffler's Endocarditis\" (\"dsyn\"))\n (236178 \"Intraabdominal hemorrhage\" (\"dsyn\"))\n (238644 \"anemia; profound\" (\"dsyn\"))\n (238790 \"destruction; bone\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (263664 \"Generalized morphea\" (\"dsyn\"))\n (264939 \"Systemic vasculitis\" (\"dsyn\"))\n (23475 \"Leukemia, Myeloid, Philadelphia-Negative\" (\"neop\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n (276653 \"Invasive pulmonary aspergillosis\" (\"dsyn\"))\n (277554 \"Primary disease\" (\"dsyn\"))\n (277556 \"Recurrent disease\" (\"dsyn\"))\n (334102 \"Lymphangiomatosis\" (\"dsyn\"))\n (23484 \"Leukemia, Plasmacytic\" (\"neop\"))\n (340548 \"Pulmonary capillary hemangiomatosis\" (\"dsyn\"))\n (23601 \"Leydig Cell Tumor\" (\"neop\"))\n (341213 \"External gastric fistula\" (\"dsyn\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (341439 \"Chronic liver disease NOS\" (\"dsyn\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (442867 \"Malignant disease\" (\"dsyn\"))\n (549567 \"Pigmentation Disorders\" (\"dsyn\"))\n (678236 \"Rare Diseases\" (\"dsyn\"))\n (743496 \"END ORGAN DAMAGE\" (\"dsyn\"))\n (25286 \"meningioma\" (\"neop\"))\n (25500 \"Mesothelioma\" (\"neop\"))\n (854467 \"Myelosuppression\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (855227 \"Purging\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (920627 \"Orphan Diseases\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (948908 \"Nephrotoxic serum nephritis\" (\"dsyn\"))\n (1273070 \"Left ventricular diastolic dysfunction\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (27832 \"Neurofibromatosis 2\" (\"neop\"))\n (1299884 \"Eosinophilic myositis\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1332309 \"Anti-Basement Membrane Glomerulonephritis\" (\"dsyn\"))\n (1533022 \"Histiocytic proliferation\" (\"dsyn\"))\n (1565489 \"Renal Insufficiency\" (\"dsyn\"))\n (36221 \"Mast-Cell Sarcoma\" (\"neop\"))\n (41341 \"Tuberous Sclerosis\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (79772 \"T-Cell Lymphoma\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (162678 \"Neurofibromatoses\" (\"neop\"))\n (205853 \"Neoplasms, Epithelial\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206657 \"Sarcoma, Alveolar Soft Part\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (220650 \"Metastatic malignant neoplasm to brain\" (\"neop\"))\n (238463 \"Papillary thyroid carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (278517 \"Non-small cell lung cancer recurrent\" (\"neop\"))\n (278695 \"recurrent neuroblastoma\" (\"neop\"))\n (278704 \"Malignant Childhood Neoplasm\" (\"neop\"))\n (278727 \"Small cell lung cancer recurrent\" (\"neop\"))\n (279068 \"childhood solid tumor\" (\"neop\"))\n (279087 \"recurrent Kaposi's sarcoma\" (\"neop\"))\n (281361 \"Adenocarcinoma pancreas\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (334410 \"Leydig cell tumor, malignant\" (\"neop\"))\n (334695 \"Endometrial Stromal Tumors\" (\"neop\"))\n (349636 \"Pre B-cell acute lymphoblastic leukemia\" (\"neop\"))\n (553580 \"Ewings sarcoma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (685938 \"Malignant neoplasm of gastrointestinal tract\" (\"neop\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (854850 \"Mycosis fungoides refractory\" (\"neop\"))\n (855054 \"Fibrosarcoma metastatic\" (\"neop\"))\n (855211 \"Seminoma of testis\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (1266042 \"Chromophobe Renal Cell Carcinoma\" (\"neop\"))\n (1266101 \"Thymic epithelial neoplasm\" (\"neop\"))\n (1266119 \"Solitary fibrous tumor\" (\"neop\"))\n (1266120 \"Solitary fibrous tumor, malignant\" (\"neop\"))\n (1300127 \"Perivascular epithelial cell tumor\" (\"neop\"))\n (1306837 \"Papillary Renal Cell Carcinoma\" (\"neop\"))\n (1318543 \"Tenosynovial giant cell tumor\" (\"neop\"))\n (1319185 \"Chiasmal glioma\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1332884 \"Central Nervous System Leukemia\" (\"neop\"))\n (1333614 \"Fibrosarcomatous Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (1334432 \"Low Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1335996 \"Small Intestinal Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1378050 \"Oncocytic Neoplasm\" (\"neop\"))\n (1411997 \"Acute biphenotypic leukemia\" (\"neop\"))\n (1512409 \"Hepatocarcinogenesis\" (\"neop\"))\n (1524028 \"Intraepithelial Neoplasia of the Mouse Mammary Gland\" (\"neop\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (6272 \"Bronchiolitis Obliterans\" (\"dsyn\"))\n (9782 \"Connective Tissue Diseases\" (\"dsyn\"))\n (10828 \"Cytopenia\" (\"patf\"))\n (11603 \"Dermatitis\" (\"dsyn\"))\n (11633 \"Dermatomyositis\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (7102 \"Malignant tumor of colon\" (\"neop\"))\n (19618 \"Histiocytosis\" (\"dsyn\"))\n (243083 \"associated disease\" (\"patf\"))\n (19621 \"Histiocytosis, Langerhans-Cell\" (\"dsyn\"))\n (7115 \"Malignant neoplasm of thyroid\" (\"neop\"))\n (19624 \"Histiocytosis, Non-Langerhans-Cell\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (19625 \"Sinus histiocytosis\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (399498 \"Oral lichenoid reaction\" (\"patf\"))\n (24901 \"Mastocytosis, Diffuse Cutaneous\" (\"dsyn\"))\n (26272 \"Mixed Connective Tissue Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (31154 \"Peritonitis\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (7140 \"Carcinosarcoma\" (\"neop\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (33687 \"Proteinuria\" (\"dsyn\"))\n (7847 \"Malignant neoplasm of cervix uteri\" (\"neop\"))\n (34069 \"Pulmonary Fibrosis\" (\"dsyn\"))\n (34155 \"Purpura, Thrombotic Thrombocytopenic\" (\"dsyn\"))\n (8479 \"Chondrosarcoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (39106 \"Pigmented villonodular synovitis\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (42384 \"Vasculitis\" (\"dsyn\"))\n (18206 \"granulosa cell tumor\" (\"neop\"))\n (152171 \"Primary pulmonary hypertension\" (\"dsyn\"))\n (162835 \"Hypopigmentation\" (\"dsyn\"))\n (206061 \"Pneumonitis, Interstitial\" (\"dsyn\"))\n (23435 \"Leukemia, B-Cell, Acute\" (\"neop\"))\n (267437 \"Allergic diarrhea\" (\"dsyn\"))\n (282548 \"Leukostasis\" (\"dsyn\"))\n (339143 \"Thyroid associated opthalmopathies\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (341697 \"Renal impairment\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (745283 \"INFECTIOUS PROCESS\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (748159 \"PULMONARY INVOLVEMENT\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (836924 \"thrombocytosis\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (949690 \"Spondylarthritis\" (\"dsyn\"))\n (1112486 \"Aggressive Systemic Mastocytosis\" (\"dsyn\"))\n (1136033 \"Cutaneous Mastocytosis\" (\"dsyn\"))\n (1142420 \"Hepatitis B reactivation\" (\"dsyn\"))\n (1261469 \"End stage renal failure\" (\"dsyn\"))\n (23479 \"Leukemia, Myelomonocytic, Acute\" (\"neop\"))\n (1279945 \"Acute interstitial pneumonia\" (\"dsyn\"))\n (1368107 \"Aplastic bone marrow\" (\"dsyn\"))\n (1619734 \"Pulmonary arterial hypertension\" (\"dsyn\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23494 \"Leukemia, T-Cell, Chronic\" (\"neop\"))\n (23827 \"liposarcoma\" (\"neop\"))\n (26987 \"Myelofibrosis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (35412 \"Rhabdomyosarcoma\" (\"neop\"))\n (36220 \"Kaposi Sarcoma\" (\"neop\"))\n (36631 \"Seminoma\" (\"neop\"))\n (39101 \"synovial sarcoma\" (\"neop\"))\n (40100 \"Thymoma\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (151779 \"[X]Malignant melanoma of skin, unspecified\" (\"neop\"))\n (205851 \"Germ cell tumor\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (206630 \"Endometrial Stromal Sarcoma\" (\"neop\"))\n (206693 \"Medullary carcinoma\" (\"neop\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (276535 \"AIDS with Kaposi's sarcoma\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278678 \"Metastatic renal cell carcinoma\" (\"neop\"))\n (278694 \"Disseminated neuroblastoma\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (279549\n \"Philadelphia chromosome negative chronic myelogenous leukemia\"\n (\"neop\"))\n (280449 \"secondary acute myeloid leukemia\" (\"neop\"))\n (334664 \"Mast Cell Neoplasm\" (\"neop\"))\n (338113 \"Uterine Corpus Sarcoma\" (\"neop\"))\n (341823 \"Epithelial tumor of ovary\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (346421 \"Chronic eosinophilic leukemia\" (\"neop\"))\n (346976 \"Secondary malignant neoplasm of pancreas\" (\"neop\"))\n (349640 \"[M]Subacute myeloid leukemia\" (\"neop\"))\n (431109 \"Choroid Plexus Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (521158 \"Recurrent tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (549379 \"Recurrent Carcinoma\" (\"neop\"))\n (598798 \"Lymphoid neoplasm\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (677936 \"Refractory Carcinoma\" (\"neop\"))\n (699889 \"Female reproductive neoplasm malignant NOS\" (\"neop\"))\n (740267 \"Ocular melanomas\" (\"neop\"))\n (740277 \"Bile duct carcinoma\" (\"neop\"))\n (743535 \"EOSINOPHILIC GRANULOMATOSIS\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (812413 \"Malignant Pleural Mesothelioma\" (\"neop\"))\n (855013 \"Chondrosarcoma recurrent\" (\"neop\"))\n (936223 \"Prostate cancer metastatic\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1327920 \"childhood chronic myelogenous leukemia\" (\"neop\"))\n (1333768 \"Gastric Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334699 \"Mesenchymal Cell Neoplasm\" (\"neop\"))\n (1335711 \"Recurrent Mature T- and NK-Cell Non-Hodgkin's Lymphoma\" (\"neop\"))\n (1335713 \"Recurrent Meningioma\" (\"neop\"))\n (1335729 \"Refractory Neoplasm\" (\"neop\"))\n (1336746 \"Thymus Carcinoid Tumor\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (235063 \"Respiratory Depression\" (\"patf\"))\n (679222 \"functional insufficiency\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (1815 \"Primary Myelofibrosis\" (\"neop\"))\n (12634 \"Disease\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (24228 \"Lymphatic Diseases\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (37354 \"Smallpox\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (221013 \"Mastocytosis, Systemic\" (\"dsyn\"))\n (1318485 \"Liver regeneration disorder\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (456070 \"Growth delay\" (\"patf\"))\n (17638 \"Glioma\" (\"neop\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23453 \"Leukemia, Lymphocytic, Acute, L2\" (\"neop\"))\n (23476 \"Leukemia, Myeloid, Philadelphia-Positive\" (\"neop\"))\n (23480 \"Leukemia, Myelomonocytic, Chronic\" (\"neop\"))\n (23481 \"Leukemia, Neutrophilic, Chronic\" (\"neop\"))\n (27022 \"Myeloproliferative disease\" (\"neop\"))\n (27819 \"Neuroblastoma\" (\"neop\"))\n (29463 \"osteosarcoma\" (\"neop\"))\n (85136 \"Central Nervous System Neoplasms\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (152018 \"Esophageal carcinoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (206093 \"Neuroectodermal Tumors\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (238461 \"Anaplastic thyroid carcinoma\" (\"neop\"))\n (238462 \"Medullary carcinoma of thyroid\" (\"neop\"))\n (278726 \"Small cell lung cancer extensive stage\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (555198 \"Malignant Glioma\" (\"neop\"))\n (677930 \"Primary Neoplasm\" (\"neop\"))\n (699791 \"Stomach Carcinoma\" (\"neop\"))\n (750952 \"Biliary Tract Cancer\" (\"neop\"))\n (751606 \"Adult Acute Lymphocytic Leukemia\" (\"neop\"))\n (860582 \"Peritoneal metastases\" (\"neop\"))\n (877373 \"Advanced cancer\" (\"neop\"))\n (879615 \"Stromal Neoplasm\" (\"neop\"))\n (887833 \"Carcinoma, Pancreatic Ductal\" (\"neop\"))\n (920028 \"Leukaemia recurrent\" (\"neop\"))\n (1266137 \"Gastrointestinal stromal sarcoma\" (\"neop\"))\n (1279296 \"Chronic leukemia (category)\" (\"neop\"))\n (1370868 \"refractory CML\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n=>\n'((27051 \"Myocardial Infarction\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\")))\n\n\n\n;; through which edges do we have the connection that Gleevec inhibits some gene G\n;; which causes a cell function that affects Diabetes Mellitus?\n;;\n;; (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n\n\n;; subtract from the 154 disorders (no neoplasms or pathologic functions)\n;; of interest those 456 disorders, neoplasms, or pathologic functions\n;; directly treated by *any* form of imatinib (not just Gleevec)\n;;\n;; results in 111 disorders\n;;\n;; Should be able to pare down more using ontologies to see which\n;; entries are forms of diabetes, for example. And use ontologies to\n;; group remaning entries.\n(set-subtraction\n '((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n '((2871 \"Anemia\" (\"dsyn\"))\n (2874 \"Aplastic Anemia\" (\"dsyn\"))\n (2895 \"Sickle Cell Anemia\" (\"dsyn\"))\n (3047 \"Animal Diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (5684 \"Malignant neoplasm of urinary bladder\" (\"neop\"))\n (5940 \"Bone Diseases\" (\"dsyn\"))\n (18944 \"Hematoma\" (\"patf\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7682 \"CNS disorder\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (6118 \"Brain Neoplasms\" (\"neop\"))\n (21368 \"Inflammation\" (\"patf\"))\n (8728 \"Churg-Strauss Syndrome\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (10403 \"Cryoglobulinemia\" (\"dsyn\"))\n (11644 \"Scleroderma\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (29435 \"Osteolysis\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36429 \"Sclerosis\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (86565 \"Liver Dysfunction\" (\"patf\"))\n (7095 \"Carcinoid Tumor\" (\"neop\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (151654 \"Myocardial fibrosis\" (\"patf\"))\n (15230 \"Exanthema\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (15624 \"Fanconi Syndrome\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (151746 \"Abnormal renal function\" (\"patf\"))\n (7114 \"Malignant neoplasm of skin\" (\"neop\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (231178 \"Chronic failure\" (\"patf\"))\n (19196 \"Hepatitis C\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (21141 \"Inappropriate ADH Syndrome\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (23890 \"Liver Cirrhosis\" (\"dsyn\"))\n (9404 \"Colorectal Neoplasms\" (\"neop\"))\n (24115 \"Lung diseases\" (\"dsyn\"))\n (333606 \"Dystrophy\" (\"patf\"))\n (24440 \"Macular Edema, Cystoid\" (\"dsyn\"))\n (443146 \"Autoimmune\" (\"patf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27697 \"Nephritis\" (\"dsyn\"))\n (549593 \"kidney functional\" (\"patf\"))\n (27947 \"Neutropenia\" (\"dsyn\"))\n (16048 \"Fibromatosis\" (\"neop\"))\n (33838 \"Kimura Disease\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (34063 \"Pulmonary Edema\" (\"dsyn\"))\n (744813 \"Hepatic embolisation\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (35920 \"Rubella\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (18923 \"Hemangiosarcoma\" (\"neop\"))\n (36992 \"Short Bowel Syndrome\" (\"dsyn\"))\n (1265815 \"Multiple ulcers\" (\"patf\"))\n (38013 \"Ankylosing spondylitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (1608322 \"Leak NOS\" (\"patf\"))\n (39103 \"Synovitis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (85786 \"Hamman-Rich syndrome\" (\"dsyn\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (86438 \"Hypogammaglobulinemia\" (\"dsyn\"))\n (151859 \"Polyserositis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (158168 \"Villonodular synovitis\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206062 \"Lung Diseases, Interstitial\" (\"dsyn\"))\n (206143 \"Loeffler's Endocarditis\" (\"dsyn\"))\n (236178 \"Intraabdominal hemorrhage\" (\"dsyn\"))\n (238644 \"anemia; profound\" (\"dsyn\"))\n (238790 \"destruction; bone\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (263664 \"Generalized morphea\" (\"dsyn\"))\n (264939 \"Systemic vasculitis\" (\"dsyn\"))\n (23475 \"Leukemia, Myeloid, Philadelphia-Negative\" (\"neop\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n (276653 \"Invasive pulmonary aspergillosis\" (\"dsyn\"))\n (277554 \"Primary disease\" (\"dsyn\"))\n (277556 \"Recurrent disease\" (\"dsyn\"))\n (334102 \"Lymphangiomatosis\" (\"dsyn\"))\n (23484 \"Leukemia, Plasmacytic\" (\"neop\"))\n (340548 \"Pulmonary capillary hemangiomatosis\" (\"dsyn\"))\n (23601 \"Leydig Cell Tumor\" (\"neop\"))\n (341213 \"External gastric fistula\" (\"dsyn\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (341439 \"Chronic liver disease NOS\" (\"dsyn\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (442867 \"Malignant disease\" (\"dsyn\"))\n (549567 \"Pigmentation Disorders\" (\"dsyn\"))\n (678236 \"Rare Diseases\" (\"dsyn\"))\n (743496 \"END ORGAN DAMAGE\" (\"dsyn\"))\n (25286 \"meningioma\" (\"neop\"))\n (25500 \"Mesothelioma\" (\"neop\"))\n (854467 \"Myelosuppression\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (855227 \"Purging\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (920627 \"Orphan Diseases\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (948908 \"Nephrotoxic serum nephritis\" (\"dsyn\"))\n (1273070 \"Left ventricular diastolic dysfunction\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (27832 \"Neurofibromatosis 2\" (\"neop\"))\n (1299884 \"Eosinophilic myositis\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1306759 \"Eosinophilic disorder\" (\"dsyn\"))\n (1332309 \"Anti-Basement Membrane Glomerulonephritis\" (\"dsyn\"))\n (1533022 \"Histiocytic proliferation\" (\"dsyn\"))\n (1565489 \"Renal Insufficiency\" (\"dsyn\"))\n (36221 \"Mast-Cell Sarcoma\" (\"neop\"))\n (41341 \"Tuberous Sclerosis\" (\"neop\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (79772 \"T-Cell Lymphoma\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (153633 \"Malignant neoplasm of brain\" (\"neop\"))\n (162678 \"Neurofibromatoses\" (\"neop\"))\n (205853 \"Neoplasms, Epithelial\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206647 \"Dermatofibrosarcoma\" (\"neop\"))\n (206657 \"Sarcoma, Alveolar Soft Part\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (206754 \"Neuroendocrine Tumors\" (\"neop\"))\n (220650 \"Metastatic malignant neoplasm to brain\" (\"neop\"))\n (238463 \"Papillary thyroid carcinoma\" (\"neop\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (278517 \"Non-small cell lung cancer recurrent\" (\"neop\"))\n (278695 \"recurrent neuroblastoma\" (\"neop\"))\n (278704 \"Malignant Childhood Neoplasm\" (\"neop\"))\n (278727 \"Small cell lung cancer recurrent\" (\"neop\"))\n (279068 \"childhood solid tumor\" (\"neop\"))\n (279087 \"recurrent Kaposi's sarcoma\" (\"neop\"))\n (281361 \"Adenocarcinoma pancreas\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (302592 \"Cervix carcinoma\" (\"neop\"))\n (334410 \"Leydig cell tumor, malignant\" (\"neop\"))\n (334695 \"Endometrial Stromal Tumors\" (\"neop\"))\n (349636 \"Pre B-cell acute lymphoblastic leukemia\" (\"neop\"))\n (553580 \"Ewings sarcoma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (677865 \"Brain stem glioma\" (\"neop\"))\n (685938 \"Malignant neoplasm of gastrointestinal tract\" (\"neop\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (854850 \"Mycosis fungoides refractory\" (\"neop\"))\n (855054 \"Fibrosarcoma metastatic\" (\"neop\"))\n (855211 \"Seminoma of testis\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (948380 \"Colorectal cancer metastatic\" (\"neop\"))\n (1266042 \"Chromophobe Renal Cell Carcinoma\" (\"neop\"))\n (1266101 \"Thymic epithelial neoplasm\" (\"neop\"))\n (1266119 \"Solitary fibrous tumor\" (\"neop\"))\n (1266120 \"Solitary fibrous tumor, malignant\" (\"neop\"))\n (1300127 \"Perivascular epithelial cell tumor\" (\"neop\"))\n (1306837 \"Papillary Renal Cell Carcinoma\" (\"neop\"))\n (1318543 \"Tenosynovial giant cell tumor\" (\"neop\"))\n (1319185 \"Chiasmal glioma\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1328504 \"Hormone-refractory prostate cancer\" (\"neop\"))\n (1332884 \"Central Nervous System Leukemia\" (\"neop\"))\n (1333614 \"Fibrosarcomatous Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (1334432 \"Low Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1335996 \"Small Intestinal Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1378050 \"Oncocytic Neoplasm\" (\"neop\"))\n (1411997 \"Acute biphenotypic leukemia\" (\"neop\"))\n (1512409 \"Hepatocarcinogenesis\" (\"neop\"))\n (1524028 \"Intraepithelial Neoplasia of the Mouse Mammary Gland\" (\"neop\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (6272 \"Bronchiolitis Obliterans\" (\"dsyn\"))\n (9782 \"Connective Tissue Diseases\" (\"dsyn\"))\n (10828 \"Cytopenia\" (\"patf\"))\n (11603 \"Dermatitis\" (\"dsyn\"))\n (11633 \"Dermatomyositis\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (14457 \"Eosinophilia\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (7102 \"Malignant tumor of colon\" (\"neop\"))\n (19618 \"Histiocytosis\" (\"dsyn\"))\n (243083 \"associated disease\" (\"patf\"))\n (19621 \"Histiocytosis, Langerhans-Cell\" (\"dsyn\"))\n (7115 \"Malignant neoplasm of thyroid\" (\"neop\"))\n (19624 \"Histiocytosis, Non-Langerhans-Cell\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (19625 \"Sinus histiocytosis\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (399498 \"Oral lichenoid reaction\" (\"patf\"))\n (24901 \"Mastocytosis, Diffuse Cutaneous\" (\"dsyn\"))\n (26272 \"Mixed Connective Tissue Disease\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (31154 \"Peritonitis\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (7140 \"Carcinosarcoma\" (\"neop\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (867389 \"Chronic graft-versus-host disease\" (\"patf\"))\n (33687 \"Proteinuria\" (\"dsyn\"))\n (7847 \"Malignant neoplasm of cervix uteri\" (\"neop\"))\n (34069 \"Pulmonary Fibrosis\" (\"dsyn\"))\n (34155 \"Purpura, Thrombotic Thrombocytopenic\" (\"dsyn\"))\n (8479 \"Chondrosarcoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (8487 \"Chordoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (10606 \"Adenoid Cystic Carcinoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (39106 \"Pigmented villonodular synovitis\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (42384 \"Vasculitis\" (\"dsyn\"))\n (18206 \"granulosa cell tumor\" (\"neop\"))\n (152171 \"Primary pulmonary hypertension\" (\"dsyn\"))\n (162835 \"Hypopigmentation\" (\"dsyn\"))\n (206061 \"Pneumonitis, Interstitial\" (\"dsyn\"))\n (23435 \"Leukemia, B-Cell, Acute\" (\"neop\"))\n (267437 \"Allergic diarrhea\" (\"dsyn\"))\n (282548 \"Leukostasis\" (\"dsyn\"))\n (339143 \"Thyroid associated opthalmopathies\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (341697 \"Renal impairment\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (745091 \"Hypereosinophilia\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (745283 \"INFECTIOUS PROCESS\" (\"dsyn\"))\n (23470 \"Myeloid Leukemia\" (\"neop\"))\n (748159 \"PULMONARY INVOLVEMENT\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (836924 \"thrombocytosis\" (\"dsyn\"))\n (23472 \"Leukemia, Myeloid, Aggressive-Phase\" (\"neop\"))\n (949690 \"Spondylarthritis\" (\"dsyn\"))\n (1112486 \"Aggressive Systemic Mastocytosis\" (\"dsyn\"))\n (1136033 \"Cutaneous Mastocytosis\" (\"dsyn\"))\n (1142420 \"Hepatitis B reactivation\" (\"dsyn\"))\n (1261469 \"End stage renal failure\" (\"dsyn\"))\n (23479 \"Leukemia, Myelomonocytic, Acute\" (\"neop\"))\n (1279945 \"Acute interstitial pneumonia\" (\"dsyn\"))\n (1368107 \"Aplastic bone marrow\" (\"dsyn\"))\n (1619734 \"Pulmonary arterial hypertension\" (\"dsyn\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23487 \"Acute Promyelocytic Leukemia\" (\"neop\"))\n (23494 \"Leukemia, T-Cell, Chronic\" (\"neop\"))\n (23827 \"liposarcoma\" (\"neop\"))\n (26987 \"Myelofibrosis\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (32463 \"Polycythemia Vera\" (\"neop\"))\n (35412 \"Rhabdomyosarcoma\" (\"neop\"))\n (36220 \"Kaposi Sarcoma\" (\"neop\"))\n (36631 \"Seminoma\" (\"neop\"))\n (39101 \"synovial sarcoma\" (\"neop\"))\n (40100 \"Thymoma\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (151779 \"[X]Malignant melanoma of skin, unspecified\" (\"neop\"))\n (205851 \"Germ cell tumor\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (205969 \"Thymic Carcinoma\" (\"neop\"))\n (206630 \"Endometrial Stromal Sarcoma\" (\"neop\"))\n (206693 \"Medullary carcinoma\" (\"neop\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (276535 \"AIDS with Kaposi's sarcoma\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (278678 \"Metastatic renal cell carcinoma\" (\"neop\"))\n (278694 \"Disseminated neuroblastoma\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278787 \"relapsing chronic myelogenous leukemia\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (278883 \"Metastatic melanoma\" (\"neop\"))\n (279549\n \"Philadelphia chromosome negative chronic myelogenous leukemia\"\n (\"neop\"))\n (280449 \"secondary acute myeloid leukemia\" (\"neop\"))\n (334664 \"Mast Cell Neoplasm\" (\"neop\"))\n (338113 \"Uterine Corpus Sarcoma\" (\"neop\"))\n (341823 \"Epithelial tumor of ovary\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (345967 \"Malignant mesothelioma\" (\"neop\"))\n (346421 \"Chronic eosinophilic leukemia\" (\"neop\"))\n (346976 \"Secondary malignant neoplasm of pancreas\" (\"neop\"))\n (349640 \"[M]Subacute myeloid leukemia\" (\"neop\"))\n (431109 \"Choroid Plexus Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (521158 \"Recurrent tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (543478 \"Residual Tumor\" (\"neop\"))\n (549379 \"Recurrent Carcinoma\" (\"neop\"))\n (598798 \"Lymphoid neoplasm\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (677936 \"Refractory Carcinoma\" (\"neop\"))\n (699889 \"Female reproductive neoplasm malignant NOS\" (\"neop\"))\n (740267 \"Ocular melanomas\" (\"neop\"))\n (740277 \"Bile duct carcinoma\" (\"neop\"))\n (743535 \"EOSINOPHILIC GRANULOMATOSIS\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (751690 \"Malignant Peripheral Nerve Sheath Tumor\" (\"neop\"))\n (812413 \"Malignant Pleural Mesothelioma\" (\"neop\"))\n (855013 \"Chondrosarcoma recurrent\" (\"neop\"))\n (936223 \"Prostate cancer metastatic\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1292778 \"Chronic myeloproliferative disorder (morphology)\" (\"neop\"))\n (1327920 \"childhood chronic myelogenous leukemia\" (\"neop\"))\n (1333768 \"Gastric Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334026 \"High Risk Gastrointestinal Stromal Tumor\" (\"neop\"))\n (1334699 \"Mesenchymal Cell Neoplasm\" (\"neop\"))\n (1335711 \"Recurrent Mature T- and NK-Cell Non-Hodgkin's Lymphoma\" (\"neop\"))\n (1335713 \"Recurrent Meningioma\" (\"neop\"))\n (1335729 \"Refractory Neoplasm\" (\"neop\"))\n (1336746 \"Thymus Carcinoid Tumor\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (1540912 \"Hypereosinophilic syndrome\" (\"neop\"))\n (235063 \"Respiratory Depression\" (\"patf\"))\n (679222 \"functional insufficiency\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (1815 \"Primary Myelofibrosis\" (\"neop\"))\n (12634 \"Disease\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (24228 \"Lymphatic Diseases\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (37354 \"Smallpox\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (221013 \"Mastocytosis, Systemic\" (\"dsyn\"))\n (1318485 \"Liver regeneration disorder\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (456070 \"Growth delay\" (\"patf\"))\n (17638 \"Glioma\" (\"neop\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23269 \"leiomyosarcoma\" (\"neop\"))\n (23453 \"Leukemia, Lymphocytic, Acute, L2\" (\"neop\"))\n (23476 \"Leukemia, Myeloid, Philadelphia-Positive\" (\"neop\"))\n (23480 \"Leukemia, Myelomonocytic, Chronic\" (\"neop\"))\n (23481 \"Leukemia, Neutrophilic, Chronic\" (\"neop\"))\n (27022 \"Myeloproliferative disease\" (\"neop\"))\n (27819 \"Neuroblastoma\" (\"neop\"))\n (29463 \"osteosarcoma\" (\"neop\"))\n (85136 \"Central Nervous System Neoplasms\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (152018 \"Esophageal carcinoma\" (\"neop\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (206093 \"Neuroectodermal Tumors\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (238461 \"Anaplastic thyroid carcinoma\" (\"neop\"))\n (238462 \"Medullary carcinoma of thyroid\" (\"neop\"))\n (278726 \"Small cell lung cancer extensive stage\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (555198 \"Malignant Glioma\" (\"neop\"))\n (677930 \"Primary Neoplasm\" (\"neop\"))\n (699791 \"Stomach Carcinoma\" (\"neop\"))\n (750952 \"Biliary Tract Cancer\" (\"neop\"))\n (751606 \"Adult Acute Lymphocytic Leukemia\" (\"neop\"))\n (860582 \"Peritoneal metastases\" (\"neop\"))\n (877373 \"Advanced cancer\" (\"neop\"))\n (879615 \"Stromal Neoplasm\" (\"neop\"))\n (887833 \"Carcinoma, Pancreatic Ductal\" (\"neop\"))\n (920028 \"Leukaemia recurrent\" (\"neop\"))\n (1266137 \"Gastrointestinal stromal sarcoma\" (\"neop\"))\n (1279296 \"Chronic leukemia (category)\" (\"neop\"))\n (1370868 \"refractory CML\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n=>\n'((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\")))\n\n\n\n\n;; remove from the 154 disorders (no neoplasms or pathologic functions)\n;; of interest those 53 disorders, neoplasms, or pathologic functions\n;; directly treated by Gleevec\n;;\n;; result is 151 diseases, including the useless \"Disease\" and \"Syndrome\" and \"Degenerative disorder\",\n;; and including:\n;; * at least 4 entries for epilepsy\n;; * approximately 7 entries related to kidney/renal disease\n;; * approximately 9 entries related to diabetes\n;; etc.\n;;\n;; Seems like there are a number of groups of diseases within the 151\n;; diseases. For example, diabetes is probably worth a look.\n;;\n;; And, of course, there is the 1 entry for asthma\n;;\n;; Wow!\n;;\n;; https://www.nbcnews.com/health/health-news/cancer-drug-gleevec-might-slow-type-1-diabetes-n771241\n;;\n;; https://www.medscape.com/viewarticle/882089\n;;\n;; http://www.ajmc.com/newsroom/scientists-find-accidental-cure-for-type-2-diabetes-imatinib\n;;\n;; March 29, 2016\n;;\n;; \"The cancer drug imatinib—marketed as Gleevec and known as a game-changer for conditions like chronic myeloid leukemia—may prove the same in type 2 diabetes (T2D), according to a study published recently in Diabetes.\"\n;;\n;;\n;; The article:\n;;\n;; http://diabetes.diabetesjournals.org/content/65/4/829\n;;\n;; Oh, SemMedDB does contain this information! The list of diseases Gleevec treats includes:\n;;\n;; (11847 \"Diabetes\" (\"dsyn\"))\n;; (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n;;\n;; The problem, of course, is that without doing more reasoning using\n;; an ontology or external information, or maybe getting lucky with\n;; the ISA predicate, the query has no way of knowing that those 9\n;; diabetes-related entries are actually related to the entry\n;; (11847 \"Diabetes\" (\"dsyn\")).\n;;\n;; Still, I was pleased that *I* learned something from the query, and\n;; that the signal was quite strong after all of that filtering.\n;;\n;; So, with more resoning, perhaps using an ontology, we should be\n;; able to reduce the ~150 answers by removing (or at least ranking\n;; lower) answers related to the diseases we know Gleevec treats.\n;;\n;; Seems that the full story is a bit complicated. There are papers\n;; indicating that imatinib/Gleevec treats diabetes in mouse models.\n;; At least one clinical trial on humans didn't seem to show\n;; improvement.\n(set-subtraction\n '((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n '((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n=>\n'((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n\n;; remove from the 223 disorders or pathologic functions (no neoplasms)\n;; of interest those 53 disorders, neoplasms, or pathologic functions\n;; directly treated by Gleevec\n;;\n;; result is 216 diseases\n(set-subtraction\n '((20522 \"Delayed Hypersensitivity\" (\"patf\"))\n (10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (2994 \"Angioneurotic Edema\" (\"patf\"))\n (4372 \"Autolysis\" (\"patf\"))\n (2792 \"Anaphylaxis\" (\"patf\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (3811 \"cardiac arrhythmia\" (\"patf\"))\n (12359 \"Pathological Dilatation\" (\"patf\"))\n (40053 \"Thrombosis\" (\"patf\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (20963 \"Immune Tolerance\" (\"patf\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (1563937 \"Atherogenesis\" (\"patf\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (1349 \"Acute-Phase Reaction\" (\"patf\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (13604 \"Edema\" (\"patf\"))\n (15376 \"Extravasation\" (\"patf\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (232910 \"Teratogenesis\" (\"patf\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (751015 \"Brain Injury, Ischemic\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (4238 \"Atrial Fibrillation\" (\"patf\"))\n (4366 \"Autoimmune Response\" (\"patf\"))\n (9566 \"Complication\" (\"patf\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1155265 \"innate immune response\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1122 \"Acidosis\" (\"patf\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (11304 \"Demyelination\" (\"patf\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (21376 \"Chronic inflammation\" (\"patf\"))\n (27540 \"Necrosis\" (\"patf\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (29445 \"Bone necrosis\" (\"patf\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (36679 \"Diastasis\" (\"patf\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36983 \"Septic Shock\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (85605 \"Liver Failure\" (\"patf\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (151763 \"Liver damage\" (\"patf\"))\n (231170 \"Disability NOS\" (\"patf\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (332448 \"Infiltration\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (334096 \"Intimal proliferation\" (\"patf\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (340515 \"Myocardial dysfunction\" (\"patf\"))\n (342649 \"Vascular calcification\" (\"patf\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (599877 \"loss; bone\" (\"patf\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (728867 \"Drug effect disorder\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (877042 \"Graft loss\" (\"patf\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (1395184 \"depolarization\" (\"patf\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (1516670 \"Clonal Expansion\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (21368 \"Inflammation\" (\"patf\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n '((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n=>\n'((20522 \"Delayed Hypersensitivity\" (\"patf\"))\n (10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (2994 \"Angioneurotic Edema\" (\"patf\"))\n (4372 \"Autolysis\" (\"patf\"))\n (2792 \"Anaphylaxis\" (\"patf\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (3811 \"cardiac arrhythmia\" (\"patf\"))\n (12359 \"Pathological Dilatation\" (\"patf\"))\n (40053 \"Thrombosis\" (\"patf\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (20963 \"Immune Tolerance\" (\"patf\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (18188 \"Granuloma\" (\"patf\"))\n (1563937 \"Atherogenesis\" (\"patf\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (1349 \"Acute-Phase Reaction\" (\"patf\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (13604 \"Edema\" (\"patf\"))\n (15376 \"Extravasation\" (\"patf\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (232910 \"Teratogenesis\" (\"patf\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (751015 \"Brain Injury, Ischemic\" (\"patf\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (4238 \"Atrial Fibrillation\" (\"patf\"))\n (4366 \"Autoimmune Response\" (\"patf\"))\n (9566 \"Complication\" (\"patf\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (1155265 \"innate immune response\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1122 \"Acidosis\" (\"patf\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (11304 \"Demyelination\" (\"patf\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (21308 \"Infarction\" (\"patf\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (21376 \"Chronic inflammation\" (\"patf\"))\n (27540 \"Necrosis\" (\"patf\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (29445 \"Bone necrosis\" (\"patf\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (36679 \"Diastasis\" (\"patf\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (36983 \"Septic Shock\" (\"patf\"))\n (85605 \"Liver Failure\" (\"patf\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (151763 \"Liver damage\" (\"patf\"))\n (231170 \"Disability NOS\" (\"patf\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (333641 \"Atrophic\" (\"patf\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (334096 \"Intimal proliferation\" (\"patf\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (340515 \"Myocardial dysfunction\" (\"patf\"))\n (342649 \"Vascular calcification\" (\"patf\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (599877 \"loss; bone\" (\"patf\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (728867 \"Drug effect disorder\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (877042 \"Graft loss\" (\"patf\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (1395184 \"depolarization\" (\"patf\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (1516670 \"Clonal Expansion\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (21368 \"Inflammation\" (\"patf\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n\n;; remove from the 295 disorders, neoplasms, or pathologic functions\n;; of interest those 53 disorders, neoplasms, or pathologic functions\n;; directly treated by Gleevec\n;;\n;; result is 275 diseases\n(set-subtraction\n '((20522 \"Delayed Hypersensitivity\" (\"patf\"))\n (10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (2994 \"Angioneurotic Edema\" (\"patf\"))\n (4372 \"Autolysis\" (\"patf\"))\n (2792 \"Anaphylaxis\" (\"patf\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (3811 \"cardiac arrhythmia\" (\"patf\"))\n (12359 \"Pathological Dilatation\" (\"patf\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (40053 \"Thrombosis\" (\"patf\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (20963 \"Immune Tolerance\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (598935 \"Tumor Initiation\" (\"neop\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (153381 \"Malignant neoplasm of mouth\" (\"neop\"))\n (279702 \"Conventional (Clear Cell) Renal Cell Carcinoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (334634\n \"Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse\"\n (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (278688 \"Ovarian cancer metastatic\" (\"neop\"))\n (18188 \"Granuloma\" (\"patf\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (1563937 \"Atherogenesis\" (\"patf\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (1349 \"Acute-Phase Reaction\" (\"patf\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (28880 \"Odontogenic Tumors\" (\"neop\"))\n (334044 \"Dysplasia\" (\"neop\"))\n (1519670 \"Tumor Angiogenesis\" (\"neop\"))\n (1519689 \"Tumor Promotion\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (13604 \"Edema\" (\"patf\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (232910 \"Teratogenesis\" (\"patf\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (751015 \"Brain Injury, Ischemic\" (\"patf\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (23458 \"Leukemia, Lymphocytic, Chronic\" (\"neop\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4238 \"Atrial Fibrillation\" (\"patf\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (4366 \"Autoimmune Response\" (\"patf\"))\n (9566 \"Complication\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (1391732 \"Cancer cachexia\" (\"neop\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (1155265 \"innate immune response\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (279626 \"Squamous cell carcinoma of esophagus\" (\"neop\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (5001 \"Benign prostatic hypertrophy\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (1122 \"Acidosis\" (\"patf\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (7117 \"Basal cell carcinoma\" (\"neop\"))\n (11304 \"Demyelination\" (\"patf\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (21308 \"Infarction\" (\"patf\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (17638 \"Glioma\" (\"neop\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (18916 \"Hemangioma\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (21376 \"Chronic inflammation\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (27540 \"Necrosis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (23418 \"leukemia\" (\"neop\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (29445 \"Bone necrosis\" (\"patf\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (23436 \"Chronic B-Cell Leukemias\" (\"neop\"))\n (36679 \"Diastasis\" (\"patf\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (36983 \"Septic Shock\" (\"patf\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (23903 \"Liver neoplasms\" (\"neop\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (85605 \"Liver Failure\" (\"patf\"))\n (24121 \"Lung Neoplasms\" (\"neop\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (24299 \"Lymphoma\" (\"neop\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (151763 \"Liver damage\" (\"patf\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (231170 \"Disability NOS\" (\"patf\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (24305 \"Lymphoma, Non-Hodgkin's\" (\"neop\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (25202 \"melanoma\" (\"neop\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (333641 \"Atrophic\" (\"patf\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (32580 \"Adenomatous Polyposis Coli\" (\"neop\"))\n (334096 \"Intimal proliferation\" (\"patf\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (33578 \"Prostatic Neoplasms\" (\"neop\"))\n (340515 \"Myocardial dysfunction\" (\"patf\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (342649 \"Vascular calcification\" (\"patf\"))\n (37286 \"Skin Neoplasms\" (\"neop\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (599877 \"loss; bone\" (\"patf\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (728867 \"Drug effect disorder\" (\"patf\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (877042 \"Graft loss\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (279000 \"Liver and Intrahepatic Biliary Tract Carcinoma\" (\"neop\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (596263 \"Carcinogenesis\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (678222 \"Breast Carcinoma\" (\"neop\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (1458155 \"Mammary Neoplasms\" (\"neop\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1519346 \"Skin Carcinogenesis\" (\"neop\"))\n (1519665 \"Tumor-Associated Process\" (\"neop\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (1516670 \"Clonal Expansion\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (21368 \"Inflammation\" (\"patf\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n '((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (206141 \"Idiopathic Hypereosinophilic Syndrome\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (878773 \"Overactive Bladder\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1167698 \"Leukaemic retinopathy\" (\"dsyn\"))\n (7129 \"Merkel cell carcinoma\" (\"neop\"))\n (1258104 \"Diffuse Scleroderma\" (\"dsyn\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17185 \"Gastrointestinal Neoplasms\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (24221 \"Lymphangioma\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (26948 \"Mycosis Fungoides\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (152276 \"Granulocytic Sarcoma\" (\"neop\"))\n (153658 \"Malignant neoplasm of endocrine gland\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (220633 \"Intraocular melanoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (242596 \"Neoplasm, Residual\" (\"neop\"))\n (279543\n \"Philadelphia chromosome positive chronic myelogenous leukemia\"\n (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (334486 \"Sarcoma, Endometrial Stromal, Low-Grade\" (\"neop\"))\n (334569 \"Odontogenic myxoma\" (\"neop\"))\n (346429 \"Multiple malignancy\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (1336869 \"Unresectable Malignant Neoplasm\" (\"neop\"))\n (1370723 \"Stromal sarcoma\" (\"neop\"))))\n\n;; union up all the disorders (\"dysn\"s) affected by celfs of interest which are also manifestations of that celf\n;;\n;; here we are only interested in \"dysn\"s, not neoplasms or pathologic functions\n;;\n;; 154 disorders\n;;\n;; This represents 0.6% of all diseases in the KB,\n;; down from 7.0% if we don't require the backwards MANIFESTATION_OF edge.\n(apply\n union*\n (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 disorder celf-type disorder-type rest1 rest2)\n (== disorder q)\n (== \"dsyn\" disorder-type)\n (== `(,celf ,disorder \"AFFECTS\" ,celf-type ,disorder-type . ,rest1) e1)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type ,celf-type . ,rest2) e2)\n (edgeo e2)\n (edgeo e1)))))\n disorders))\n '((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\")))))\n=>\n'((10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (23882 \"Little's Disease\" (\"dsyn\")))\n\n;; union up all the diseases affected by celfs of interest which are also manifestations of that celf\n;;\n;; 295 diseases (223 if neoplasms aren't included, or 154 if neplasms and pathologic functions aren't included)\n;;\n;; This represents 1.2% (or 1.1% or 0.6%) of all diseases in the KB,\n;; down from 7.7% (7.8% or 7.0%) if we don't require the backwards MANIFESTATION_OF edge.\n(apply\n union*\n (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 disorder celf-type disorder-type rest1 rest2)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,celf ,disorder \"AFFECTS\" ,celf-type ,disorder-type . ,rest1) e1)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type ,celf-type . ,rest2) e2)\n (edgeo e2)\n (edgeo e1)))))\n disorders))\n '((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\")))))\n=>\n'((20522 \"Delayed Hypersensitivity\" (\"patf\"))\n (10054 \"Coronary Arteriosclerosis\" (\"dsyn\"))\n (41107 \"Trisomy\" (\"dsyn\"))\n (25517 \"Metabolic Diseases\" (\"dsyn\"))\n (2994 \"Angioneurotic Edema\" (\"patf\"))\n (4372 \"Autolysis\" (\"patf\"))\n (2792 \"Anaphylaxis\" (\"patf\"))\n (15695 \"Fatty Liver\" (\"dsyn\"))\n (752304 \"Hypoxic-Ischemic Encephalopathy\" (\"dsyn\"))\n (17732 \"Glucose Intolerance\" (\"dsyn\"))\n (158981 \"Neonatal diabetes mellitus\" (\"dsyn\"))\n (6267 \"Bronchiectasis\" (\"dsyn\"))\n (11616 \"Contact Dermatitis\" (\"dsyn\"))\n (32285 \"Pneumonia\" (\"dsyn\"))\n (1519680 \"Tumor Immunity\" (\"dsyn\"))\n (242231 \"Coronary Stenosis\" (\"dsyn\"))\n (729353 \"Subfertility\" (\"dsyn\"))\n (9447 \"Common Variable Immunodeficiency\" (\"dsyn\"))\n (33860 \"Psoriasis\" (\"dsyn\"))\n (3811 \"cardiac arrhythmia\" (\"patf\"))\n (12359 \"Pathological Dilatation\" (\"patf\"))\n (30920 \"Peptic Ulcer\" (\"dsyn\"))\n (87086 \"Thrombus\" (\"dsyn\"))\n (40053 \"Thrombosis\" (\"patf\"))\n (339510 \"Vitelliform dystrophy\" (\"dsyn\"))\n (1857 \"AIDS related complex\" (\"dsyn\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (20963 \"Immune Tolerance\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (35334 \"Retinitis Pigmentosa\" (\"dsyn\"))\n (598935 \"Tumor Initiation\" (\"neop\"))\n (19163 \"Hepatitis B\" (\"dsyn\"))\n (27055 \"Myocardial Reperfusion Injury\" (\"patf\"))\n (153381 \"Malignant neoplasm of mouth\" (\"neop\"))\n (279702 \"Conventional (Clear Cell) Renal Cell Carcinoma\" (\"neop\"))\n (35435 \"Rheumatism\" (\"dsyn\"))\n (38525 \"Subarachnoid Hemorrhage\" (\"dsyn\"))\n (221757 \"alpha 1-Antitrypsin Deficiency\" (\"dsyn\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (231341 \"Premature aging syndrome\" (\"dsyn\"))\n (334634\n \"Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse\"\n (\"neop\"))\n (476089 \"Endometrial Carcinoma\" (\"neop\"))\n (278688 \"Ovarian cancer metastatic\" (\"neop\"))\n (18188 \"Granuloma\" (\"patf\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (24623 \"Malignant neoplasm of stomach\" (\"neop\"))\n (1563937 \"Atherogenesis\" (\"patf\"))\n (14553 \"Absence Epilepsy\" (\"dsyn\"))\n (19151 \"Hepatic Encephalopathy\" (\"dsyn\"))\n (1349 \"Acute-Phase Reaction\" (\"patf\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (1519697 \"Tumorigenicity\" (\"patf\"))\n (20437 \"Hypercalcemia\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (23448 \"Lymphoblastic Leukemia\" (\"neop\"))\n (178664 \"Glomerulosclerosis\" (\"dsyn\"))\n (28880 \"Odontogenic Tumors\" (\"neop\"))\n (334044 \"Dysplasia\" (\"neop\"))\n (1519670 \"Tumor Angiogenesis\" (\"neop\"))\n (1519689 \"Tumor Promotion\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (4153 \"Atherosclerosis\" (\"dsyn\"))\n (4623 \"Bacterial Infections\" (\"dsyn\"))\n (13604 \"Edema\" (\"patf\"))\n (15397 \"Eye diseases\" (\"dsyn\"))\n (15376 \"Extravasation\" (\"patf\"))\n (21051 \"Immunologic Deficiency Syndromes\" (\"dsyn\"))\n (376545 \"Hematologic Neoplasms\" (\"neop\"))\n (26848 \"Myopathy\" (\"dsyn\"))\n (232910 \"Teratogenesis\" (\"patf\"))\n (35304 \"Retinal Degeneration\" (\"dsyn\"))\n (242656 \"Disease Progression\" (\"patf\"))\n (35309 \"Retinal Diseases\" (\"dsyn\"))\n (333467 \"Cytopathic effect\" (\"patf\"))\n (38220 \"Status Epilepticus\" (\"dsyn\"))\n (751015 \"Brain Injury, Ischemic\" (\"patf\"))\n (85084 \"Motor Neuron Disease\" (\"dsyn\"))\n (339573 \"Primary open angle glaucoma\" (\"dsyn\"))\n (1285162 \"Degenerative disorder\" (\"dsyn\"))\n (1290884 \"Inflammatory disorder\" (\"dsyn\"))\n (1536085 \"Geographic atrophy\" (\"dsyn\"))\n (23458 \"Leukemia, Lymphocytic, Chronic\" (\"neop\"))\n (18133 \"Graft-vs-Host Disease\" (\"dsyn\"))\n (20459 \"Hyperinsulinism\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (4238 \"Atrial Fibrillation\" (\"patf\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (4366 \"Autoimmune Response\" (\"patf\"))\n (9566 \"Complication\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (1391732 \"Cancer cachexia\" (\"neop\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (1140999 \"Contraction\" (\"patf\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (1155265 \"innate immune response\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (24301 \"Lymphoma, Follicular\" (\"neop\"))\n (235974 \"Pancreatic carcinoma\" (\"neop\"))\n (279626 \"Squamous cell carcinoma of esophagus\" (\"neop\"))\n (1175 \"Acquired Immunodeficiency Syndrome\" (\"dsyn\"))\n (1824 \"Agranulocytosis\" (\"dsyn\"))\n (5001 \"Benign prostatic hypertrophy\" (\"neop\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (1122 \"Acidosis\" (\"patf\"))\n (2736 \"Amyotrophic Lateral Sclerosis\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (2871 \"Anemia\" (\"dsyn\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (4364 \"Autoimmune Diseases\" (\"dsyn\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (7193 \"Cardiomyopathy, Dilated\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (7785 \"Cerebral Infarction\" (\"dsyn\"))\n (7117 \"Basal cell carcinoma\" (\"neop\"))\n (11304 \"Demyelination\" (\"patf\"))\n (8312 \"Primary biliary cirrhosis\" (\"dsyn\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (8370 \"Cholestasis\" (\"dsyn\"))\n (11615 \"Dermatitis, Atopic\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (11849 \"Diabetes Mellitus\" (\"dsyn\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (17639 \"Gliosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (21308 \"Infarction\" (\"patf\"))\n (11884 \"Diabetic Retinopathy\" (\"dsyn\"))\n (17638 \"Glioma\" (\"neop\"))\n (13595 \"Eczema\" (\"dsyn\"))\n (18916 \"Hemangioma\" (\"neop\"))\n (14175 \"Endometriosis, site unspecified\" (\"dsyn\"))\n (21376 \"Chronic inflammation\" (\"patf\"))\n (17152 \"Gastritis\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (27540 \"Necrosis\" (\"patf\"))\n (17658 \"Glomerulonephritis\" (\"dsyn\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (23418 \"leukemia\" (\"neop\"))\n (19693 \"HIV Infections\" (\"dsyn\"))\n (29445 \"Bone necrosis\" (\"patf\"))\n (23434 \"Chronic Lymphocytic Leukemia\" (\"neop\"))\n (20179 \"Huntington Disease\" (\"dsyn\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (23436 \"Chronic B-Cell Leukemias\" (\"neop\"))\n (36679 \"Diastasis\" (\"patf\"))\n (20542 \"Hypertension, Pulmonary\" (\"dsyn\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (21311 \"Infection\" (\"dsyn\"))\n (21359 \"Infertility\" (\"dsyn\"))\n (36983 \"Septic Shock\" (\"patf\"))\n (21364 \"Infertility, Male\" (\"dsyn\"))\n (23903 \"Liver neoplasms\" (\"neop\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (85605 \"Liver Failure\" (\"patf\"))\n (24121 \"Lung Neoplasms\" (\"neop\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (22658 \"Kidney Diseases\" (\"dsyn\"))\n (24299 \"Lymphoma\" (\"neop\"))\n (22660 \"Kidney Failure, Acute\" (\"dsyn\"))\n (151763 \"Liver damage\" (\"patf\"))\n (23530 \"Leukopenia\" (\"dsyn\"))\n (231170 \"Disability NOS\" (\"patf\"))\n (23895 \"Liver diseases\" (\"dsyn\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (24312 \"Lymphopenia\" (\"dsyn\"))\n (24305 \"Lymphoma, Non-Hodgkin's\" (\"neop\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (25202 \"melanoma\" (\"neop\"))\n (27765 \"nervous system disorder\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (26764 \"Multiple Myeloma\" (\"neop\"))\n (29408 \"Degenerative polyarthritis\" (\"dsyn\"))\n (332448 \"Infiltration\" (\"patf\"))\n (29456 \"Osteoporosis\" (\"dsyn\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (30567 \"Parkinson Disease\" (\"dsyn\"))\n (31763 \"Photosensitization\" (\"dsyn\"))\n (32914 \"Pre-Eclampsia\" (\"dsyn\"))\n (29925 \"Ovarian Carcinoma\" (\"neop\"))\n (333641 \"Atrophic\" (\"patf\"))\n (35305 \"Retinal Detachment\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (32580 \"Adenomatous Polyposis Coli\" (\"neop\"))\n (334096 \"Intimal proliferation\" (\"patf\"))\n (36690 \"Septicemia\" (\"dsyn\"))\n (33578 \"Prostatic Neoplasms\" (\"neop\"))\n (340515 \"Myocardial dysfunction\" (\"patf\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (39082 \"Syndrome\" (\"dsyn\"))\n (342649 \"Vascular calcification\" (\"patf\"))\n (37286 \"Skin Neoplasms\" (\"neop\"))\n (40034 \"Thrombocytopenia\" (\"dsyn\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (79731 \"B-Cell Lymphomas\" (\"neop\"))\n (42024 \"Urinary Incontinence\" (\"dsyn\"))\n (599877 \"loss; bone\" (\"patf\"))\n (42341 \"Varicocele\" (\"dsyn\"))\n (42721 \"Viral hepatitis\" (\"dsyn\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (86543 \"Cataract\" (\"anab\" \"dsyn\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (151650 \"Renal fibrosis\" (\"dsyn\"))\n (728867 \"Drug effect disorder\" (\"patf\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (158266 \"Degenerative disc disease NOS\" (\"dsyn\"))\n (162557 \"Liver Failure, Acute\" (\"dsyn\"))\n (206698 \"Cholangiocarcinoma\" (\"neop\"))\n (877042 \"Graft loss\" (\"patf\"))\n (162871 \"Aortic Aneurysm, Abdominal\" (\"dsyn\"))\n (206139 \"Lichen Planus, Oral\" (\"dsyn\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (238806 \"BONE MASS\" (\"dsyn\"))\n (242379 \"Malignant neoplasm of lung\" (\"neop\"))\n (242350 \"Erectile dysfunction\" (\"dsyn\"))\n (279000 \"Liver and Intrahepatic Biliary Tract Carcinoma\" (\"neop\"))\n (242383 \"Age related macular degeneration\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (242422 \"Parkinsonian Disorders\" (\"dsyn\"))\n (268731 \"Renal glomerular disease\" (\"dsyn\"))\n (1395184 \"depolarization\" (\"patf\"))\n (270994 \"Steroid-induced myopathy\" (\"dsyn\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (339527 \"Leber's amaurosis\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (340970 \"Congenital neutropenia\" (\"dsyn\"))\n (343641 \"Human papilloma virus infection\" (\"dsyn\"))\n (494165 \"Secondary malignant neoplasm of liver\" (\"neop\"))\n (456909 \"Blind Vision\" (\"dsyn\"))\n (596263 \"Carcinogenesis\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (678222 \"Breast Carcinoma\" (\"neop\"))\n (677607 \"Hashimoto Disease\" (\"dsyn\"))\n (686619 \"Secondary malignant neoplasm of lymph node\" (\"neop\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (857357 \"Hepatic pathology\" (\"dsyn\"))\n (1458155 \"Mammary Neoplasms\" (\"neop\"))\n (917798 \"Cerebral Ischemia\" (\"dsyn\"))\n (1519346 \"Skin Carcinogenesis\" (\"neop\"))\n (1519665 \"Tumor-Associated Process\" (\"neop\"))\n (1281300 \"Vascular degeneration\" (\"dsyn\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (1456670 \"Nerve Diseases\" (\"dsyn\"))\n (1516670 \"Clonal Expansion\" (\"patf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (22661 \"Kidney Failure, Chronic\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (21368 \"Inflammation\" (\"patf\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\")))\n\n;; only the celfs Signal Transduction and mast cell activation affect asthma, and\n;; for which asthma is a manifestation of that celf (of the 189 celfs of interest)\n> (filter\n (lambda (l) (cadr l))\n (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e1 e2 disorder celf-type disorder-type rest1 rest2)\n (== disorder q)\n (conde\n [(== \"dsyn\" disorder-type)]\n [(== \"neop\" disorder-type)]\n [(== \"patf\" disorder-type)])\n (== `(,celf ,disorder \"AFFECTS\" ,celf-type ,disorder-type . ,rest1) e1)\n (== `(,disorder ,celf \"MANIFESTATION_OF\" ,disorder-type ,celf-type . ,rest2) e2)\n (edgeo e2)\n (edgeo e1)))))\n (list celf (and (member '(4096 \"Asthma\" (\"dsyn\")) disorders)#t) disorders)))\n '((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\")))))\n'(((37083 \"Signal Transduction\" (\"celf\"))\n #t\n ((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (1418 \"Adenocarcinoma\" (\"neop\"))\n (3873 \"Rheumatoid Arthritis\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (6142 \"Malignant neoplasm of breast\" (\"neop\"))\n (4135 \"Ataxia Telangiectasia\" (\"dsyn\"))\n (7222 \"Cardiovascular Diseases\" (\"dsyn\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (4238 \"Atrial Fibrillation\" (\"patf\"))\n (7097 \"Carcinoma\" (\"neop\"))\n (9319 \"Colitis\" (\"dsyn\"))\n (4366 \"Autoimmune Response\" (\"patf\"))\n (7103 \"Malignant neoplasm of endometrium\" (\"neop\"))\n (4368 \"Autoimmunity\" (\"patf\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (9566 \"Complication\" (\"patf\"))\n (11881 \"Diabetic Nephropathy\" (\"dsyn\"))\n (19204 \"Primary carcinoma of the liver cells\" (\"neop\"))\n (11164 \"Degenerative abnormality\" (\"patf\"))\n (12634 \"Disease\" (\"dsyn\"))\n (19829 \"Hodgkin Disease\" (\"neop\"))\n (11304 \"Demyelination\" (\"patf\"))\n (14544 \"Epilepsy\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (17601 \"Glaucoma\" (\"dsyn\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (18799 \"Heart Diseases\" (\"dsyn\"))\n (20564 \"Hypertrophy\" (\"patf\"))\n (18801 \"Heart failure\" (\"dsyn\"))\n (19158 \"Hepatitis\" (\"dsyn\"))\n (20456 \"Hyperglycemia\" (\"dsyn\"))\n (20538 \"Hypertensive disease\" (\"dsyn\"))\n (21368 \"Inflammation\" (\"patf\"))\n (20550 \"Hyperthyroidism\" (\"dsyn\"))\n (20615 \"hypoglycemia\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (21053 \"Immune System Diseases\" (\"dsyn\"))\n (21311 \"Infection\" (\"dsyn\"))\n (27540 \"Necrosis\" (\"patf\"))\n (21390 \"Inflammatory Bowel Diseases\" (\"dsyn\"))\n (178874 \"Neoplasm progression\" (\"neop\"))\n (22116 \"Ischemia\" (\"dsyn\"))\n (27686 \"Pathologic Neovascularization\" (\"patf\"))\n (23882 \"Little's Disease\" (\"dsyn\"))\n (28778 \"Obstruction\" (\"patf\"))\n (24117 \"Chronic Obstructive Airway Disease\" (\"dsyn\"))\n (278488 \"Breast cancer metastatic\" (\"neop\"))\n (24141 \"Lupus Erythematosus, Systemic\" (\"dsyn\"))\n (29396 \"Ossification, Heterotopic\" (\"patf\"))\n (30660 \"Pathologic Processes\" (\"patf\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (28754 \"Obesity\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (30305 \"Pancreatitis\" (\"dsyn\"))\n (376358 \"Malignant neoplasm of prostate\" (\"neop\"))\n (33626 \"Protein Deficiency\" (\"dsyn\"))\n (596263 \"Carcinogenesis\" (\"neop\"))\n (598934 \"tumor growth\" (\"neop\"))\n (36421 \"Systemic Scleroderma\" (\"dsyn\"))\n (38454 \"Cerebrovascular accident\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (42769 \"Virus Diseases\" (\"dsyn\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (1391732 \"Cancer cachexia\" (\"neop\"))\n (332448 \"Infiltration\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (151744 \"Myocardial Ischemia\" (\"dsyn\"))\n (333951 \"Growth arrest\" (\"patf\"))\n (151747 \"Renal tubular disorder\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1140999 \"Contraction\" (\"patf\"))\n (239946 \"Fibrosis, Liver\" (\"dsyn\"))\n (1155265 \"innate immune response\" (\"patf\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (1383860 \"Cardiac Hypertrophy\" (\"patf\"))\n (270814 \"Spastic syndrome\" (\"dsyn\"))\n (400966 \"Non-alcoholic fatty liver\" (\"dsyn\"))\n (1521846 \"Permissiveness, Biological Function\" (\"patf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\"))\n (856169 \"Endothelial dysfunction\" (\"dsyn\"))\n (878544 \"Cardiomyopathies\" (\"dsyn\"))\n (948008 \"Ischemic stroke\" (\"dsyn\"))))\n ((1155074 \"mast cell activation\" (\"celf\"))\n #t\n ((4096 \"Asthma\" (\"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\")))))\n\n;; which disorders, neoplasms, or pathologic functions are directly\n;; affected by the 189 celfs directly caused by the 44 genes of\n;; interest?\n;;\n;; 1937 disorders are unique (1556 if we don't include 'neop')\n;;\n;; answer includes howlers such as:\n;;\n;; (1314 \"Acute Disease\" (\"dsyn\"))\n;; (7453 \"Cattle Diseases\" (\"dsyn\"))\n;; (32080 \"Plant Diseases\" (\"dsyn\"))\n;; (678236 \"Rare Diseases\" (\"dsyn\"))\n;; (8679 \"Chronic Disease\" (\"dsyn\"))\n;; (12634 \"Disease\" (\"dsyn\"))\n;; (242656 \"Disease Progression\" (\"patf\"))\n(length\n (apply\n union*\n (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e subj obj pred st ot rest)\n (== obj q)\n (conde\n [(== \"dsyn\" ot)]\n [(== \"neop\" ot)]\n [(== \"patf\" ot)])\n (== `(,celf ,obj \"AFFECTS\" ,st ,ot . ,rest) e)\n (edgeo e)))))\n disorders))\n '((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\"))))))\n\n\n;; how many disorders, neoplasms, or pathologic functions are in the KB?\n> (length (filter (lambda (c) (member (vector (hash-ref semtype=>id \"dsyn\") 1) (concept-type c))) concept*))\n17720\n> (length (filter (lambda (c) (member (vector (hash-ref semtype=>id \"neop\") 1) (concept-type c))) concept*))\n5280\n> (length (filter (lambda (c) (member (vector (hash-ref semtype=>id \"patf\") 1) (concept-type c))) concept*))\n2316\n\n;; total number of disorders, neoplasms, or pathologic functions in the KB:\n(+ 17720 5280 2316)\n=>\n25316\n\n;; total number of disorders or pathologic functions in the KB (no neoplasms):\n(+ 17720 2316)\n=>\n20036\n\n\n;; Andrew pointed me to this disease ontology:\n;;\n;; http://disease-ontology.org/\n;;\n;; which also includes SNOMED IDs.\n\n\n;; which disorders, neoplasms, or pathologic functions are directly\n;; affected by the 189 celfs directly caused by the 44 genes of\n;; interest?\n;;\n;; 8025, with possible duplicates across the celfs\n;;\n;; 1937 are actually unique, out of 25,316 disorders, neoplasms, or pathologic functions in the KB (7.7%)\n;;\n;; 1556 unique if we don't include 'neop' (seems reasonable, since we know that Gleevec is primarily a cancer\n;; drug, and we are looking for *unknown* disorders that it treats).\n;; 1556 / 20,036 = 7.8%\n;;\n;;\n;; 1232 unique if we insist on only 'dsyn'. This may be reasonable,\n;; since 'dysn' seem more likely to be diseases rather than symptoms.\n;; Depends on what exactly we are looking for.\n;; 1232 / 17,720 = 7.0%\n;;\n;; \n;;\n;; 26 of the 189 celfs directly affect (4096 \"Asthma\" (\"dsyn\"))\n;; and 29 of the celfs affect some variant of asthma\n;;\n;; Perhaps entries like\n;;\n;; (1 #t ((4096 \"Asthma\" (\"dsyn\"))) (1326501 \"eosinophil chemotaxis\" (\"celf\")))\n;;\n;; are actually resonable. See 'Eosinophils in asthma.' Busse WW, Sedgwick JB.\n;; https://www.ncbi.nlm.nih.gov/pubmed/1546825\n(sort\n (map\n (lambda (celf)\n (let ((disorders\n (run* (q)\n (fresh (e subj obj pred st ot rest)\n (== obj q)\n (conde\n [(== \"dsyn\" ot)]\n [(== \"neop\" ot)]\n [(== \"patf\" ot)])\n (== `(,celf ,obj \"AFFECTS\" ,st ,ot . ,rest) e)\n (edgeo e)))))\n (let ((disorders (rem-dups disorders)))\n (list (length disorders)\n (and (member '(4096 \"Asthma\" (\"dsyn\")) disorders) #t)\n (filter\n (lambda (d)\n (member d\n '((4096 \"Asthma\" (\"dsyn\"))\n (4099 \"Asthma, Exercise-Induced\" (\"dsyn\"))\n (14434 \"Detergent asthma\" (\"dsyn\"))\n (38218 \"Status Asthmaticus\" (\"dsyn\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n (155880 \"Intrinsic asthma NOS\" (\"dsyn\"))\n (238266 \"Meat-wrappers' asthma\" (\"dsyn\"))\n (238375 \"Platinum asthma\" (\"dsyn\"))\n (259745 \"Asthma, infective\" (\"dsyn\"))\n (259808 \"Asthma, endogenous\" (\"dsyn\"))\n (264348 \"Chronic asthmatic bronchitis\" (\"dsyn\"))\n (264408 \"Childhood asthma\" (\"dsyn\"))\n (264411 \"Hay fever with asthma\" (\"dsyn\"))\n (264413 \"Late onset asthma\" (\"dsyn\"))\n (264423 \"Occupational asthma\" (\"dsyn\"))\n (264480 \"Bakers' asthma\" (\"dsyn\"))\n (282556 \"Anti-Asthmatic Agents\" (\"phsu\"))\n (340067 \"Drug-induced asthma\" (\"dsyn\"))\n (340069 \"Colophony asthma\" (\"dsyn\"))\n (340070 \"Millers' asthma\" (\"dsyn\"))\n (340073 \"Factitious asthma\" (\"dsyn\"))\n (340076 \"Asthmatic pulmonary eosinophilia\" (\"dsyn\"))\n (340094 \"Wood asthma\" (\"dsyn\"))\n (347950 \"Asthma attack NOS\" (\"dsyn\"))\n (348819 \"Mixed asthma\" (\"dsyn\"))\n (349790 \"Exacerbation of asthma\" (\"fndg\"))\n (350348 \"Asthma prophylaxis\" (\"phsu\"))\n (392681 \"Asthmatic breathing\" (\"sosy\"))\n (420048 \"Asthma screening\" (\"hlca\"))\n (420293 \"Emergency admission, asthma\" (\"hlca\"))\n (543699 \"ASA intolerant asthma\" (\"dsyn\"))\n (554832 \"Asthma monitoring\" (\"hlca\"))\n (581122 \"Asthma severity\" (\"hlca\"))\n (581124 \"Mild asthma\" (\"fndg\"))\n (581125 \"Moderate asthma\" (\"fndg\"))\n (581126 \"Severe asthma\" (\"fndg\"))\n (582415 \"Acute asthma\" (\"dsyn\"))\n (606809 \"Asthma 23D\" (\"phsu\"))\n (684913 \"Chemical-induced asthma\" (\"dsyn\"))\n (729337 \"Brittle asthma\" (\"dsyn\"))\n (741266 \"ASTHMA STABLE\" (\"fndg\"))\n (856716 \"Asthma aspirin-sensitive\" (\"dsyn\"))\n (859987 \"Asthmatoid bronchitis\" (\"dsyn\"))\n (876293 \"Asthma Monitoring System\" (\"medd\"))\n (877264 \"Infantile asthma\" (\"dsyn\"))\n (877430 \"Asthma chronic\" (\"dsyn\"))\n (1135801 \"Tylophora asthmatica\" (\"plnt\"))\n (1261327 \"Family history of asthma\" (\"fndg\"))\n (1271086 \"Suspected asthma\" (\"fndg\"))\n (1272273 \"Asthma finding\" (\"fndg\"))\n (1303029 \"Asthma trigger\" (\"clna\"))\n (1318955 \"Asthma management\" (\"hlca\"))\n (1319018 \"Asthmatic bronchitis\" (\"dsyn\"))\n (1319853 \"Aspirin-induced asthma\" (\"fndg\"))\n (1328364 \"Analgesic asthma syndrome\" (\"inpo\")))))\n disorders)\n celf))))\n '((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\"))))\n (lambda (l1 l2) (< (car l1) (car l2))))\n=>\n'((0 #f () (312862 \"Lymphocyte chemotaxis\" (\"celf\")))\n (0 #f () (1326474 \"vesicle fusion\" (\"celf\")))\n (0 #f () (1156132 \"vacuolar acidification\" (\"celf\")))\n (0 #f () (1326080 \"muscle cell differentiation\" (\"celf\")))\n (0 #f () (392710 \"Megakaryocytic maturation\" (\"celf\")))\n (0 #f () (1326236 \"filopodium formation\" (\"celf\")))\n (0 #f () (37841 \"Sperm Capacitation\" (\"celf\")))\n (0 #f () (1159958 \"neutrophil differentiation\" (\"celf\")))\n (0 #f () (1155949 \"lamellipodium biogenesis\" (\"celf\")))\n (0 #f () (1326346 \"urothelial cell proliferation\" (\"celf\")))\n (0 #f () (1155734 \"lamin depolymerization\" (\"celf\")))\n (0 #f () (1159512 \"maltose transport\" (\"celf\")))\n (0 #f () (1159521 \"hexose transport\" (\"celf\")))\n (0 #f () (1326220 \"synergid cell death\" (\"celf\")))\n (0 #f () (1523105 \"nuclear envelope disassembly\" (\"celf\")))\n (0 #f () (1257985 \"Cross-Priming\" (\"celf\")))\n (1 #f () (1372294 \"Increased Endocytosis\" (\"celf\")))\n (1 #f () (598948 \"axonal guidance\" (\"celf\")))\n (1 #t ((4096 \"Asthma\" (\"dsyn\"))) (1326501 \"eosinophil chemotaxis\" (\"celf\")))\n (1 #f () (1155303 \"ER-overload response\" (\"celf\")))\n (1 #f () (1516338 \"Cell Death Induction\" (\"celf\")))\n (1 #f () (1155876 \"DNA replication checkpoint\" (\"celf\")))\n (1 #f () (598838 \"membrane assembly\" (\"celf\")))\n (1 #f () (1156032 \"Microtubule Polymerization\" (\"celf\")))\n (1 #f () (1159938 \"eosinophil differentiation\" (\"celf\")))\n (1 #f () (1159966 \"myoblast differentiation\" (\"celf\")))\n (1 #f () (1513082 \"Megakaryocyte Proliferation\" (\"celf\")))\n (1 #f () (600430 \"Calcium Waves\" (\"celf\")))\n (1 #f () (1325893 \"histamine secretion\" (\"celf\")))\n (1 #f () (1155871 \"nuclear migration\" (\"celf\")))\n (1 #f () (1155893 \"unidimensional cell growth\" (\"celf\")))\n (1 #f () (1326502 \"macrophage chemotaxis\" (\"celf\")))\n (1 #f () (1517348 \"G2 Phase Arrest\" (\"celf\")))\n (1 #f () (1515136 \"T-Cell Transformation\" (\"celf\")))\n (2 #f () (1156259 \"cell ion homeostasis\" (\"celf\")))\n (2 #f () (1156042 \"endosome transport\" (\"celf\")))\n (2 #f () (1372847 \"Increased Cellular Migration\" (\"celf\")))\n (2 #f () (31945 \"Pinocytosis\" (\"celf\")))\n (2 #f () (1325887 \"focal adhesion formation\" (\"celf\")))\n (2 #f () (1155980 \"actin filament depolymerization\" (\"celf\")))\n (2 #f () (1155631 \"Chromosome Condensation\" (\"celf\")))\n (2 #f () (1523795 \"stress fiber formation\" (\"celf\")))\n (2 #f () (1450355 \"Prometaphase\" (\"celf\")))\n (2 #f () (1155766 \"centrosome cycle\" (\"celf\")))\n (2 #f () (1158951 \"maintenance of protein localization\" (\"celf\")))\n (3 #f () (1159455 \"syncytium formation\" (\"celf\")))\n (3 #f () (1276855 \"Monocyte chemotaxis\" (\"celf\")))\n (3 #f () (1159824 \"nuclear fragmentation\" (\"celf\")))\n (3 #f () (79396 \"G2 Phase\" (\"celf\")))\n (3 #f () (1519167 \"S Phase Arrest\" (\"celf\")))\n (3 #f () (1518147 \"M Phase Arrest\" (\"celf\")))\n (3 #f () (1155781 \"spindle assembly\" (\"celf\")))\n (4 #f () (1160520 \"oocyte maturation\" (\"celf\")))\n (4 #f () (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\")))\n (4 #f () (600485 \"Acrosome Reaction\" (\"celf\")))\n (4 #f () (1155607 \"autophagic vacuole formation\" (\"celf\")))\n (4 #f () (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\")))\n (4 #f () (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\")))\n (5 #f () (1159821 \"apoptotic program\" (\"celf\")))\n (5 #f () (1155792 \"Meiotic Recombination\" (\"celf\")))\n (5 #f () (1156031 \"Microtubule Depolymerization\" (\"celf\")))\n (5\n #f\n ()\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\")))\n (5 #f () (25564 \"Metaphase\" (\"celf\")))\n (5 #f () (1515432 \"Thymocyte Development\" (\"celf\")))\n (6 #f () (598949 \"axonal sprouting\" (\"celf\")))\n (6 #f () (599702 \"reuptake\" (\"celf\")))\n (6\n #f\n ((155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (1159442 \"sporulation\" (\"celf\")))\n (6 #f () (544888 \"Mitotic arrest\" (\"celf\")))\n (6 #f () (887840 \"Nuclear Export\" (\"celf\")))\n (7 #f () (1326121 \"astrocyte activation\" (\"celf\")))\n (7 #f () (7580 \"Cell Aggregation\" (\"celf\")))\n (7 #f () (1155008 \"B Cell Proliferation\" (\"celf\")))\n (7 #f () (7591 \"Cell division phases\" (\"celf\")))\n (7 #f () (1160602 \"cholesterol absorption\" (\"celf\")))\n (7 #f () (1515126 \"T-Cell Development\" (\"celf\")))\n (7 #f () (1516340 \"Cell Death Process\" (\"celf\")))\n (7 #f () (1523169 \"smooth muscle cell differentiation\" (\"celf\")))\n (8 #f () (1326504 \"neuronal migration\" (\"celf\")))\n (8 #f () (312860 \"Neutrophil migration, function\" (\"celf\")))\n (8 #f () (1326356 \"amino acid import\" (\"celf\")))\n (8 #f () (599893 \"Protein translocation\" (\"celf\")))\n (8 #f () (887839 \"Nuclear Import\" (\"celf\")))\n (8 #f () (1155711 \"stem cell division\" (\"celf\")))\n (8 #f () (598087 \"cell dedifferentiation\" (\"celf\")))\n (8 #f () (1326057 \"epithelial cell differentiation\" (\"celf\")))\n (9 #f () (1155874 \"Cell Cycle Checkpoint\" (\"celf\")))\n (9 #f () (1155752 \"positive regulation of mitosis\" (\"celf\")))\n (9\n #f\n ()\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\")))\n (9 #f () (1372180 \"Increased Cellular Death\" (\"celf\")))\n (10 #f () (1159689 \"potassium ion transport\" (\"celf\")))\n (10 #f () (1159339 \"Protein Secretion\" (\"celf\")))\n (10 #f () (1326207 \"Programmed Cell Death, Type II\" (\"celf\")))\n (10 #f () (1511632 \"Cytoskeletal Modeling\" (\"celf\")))\n (10 #f () (1515979 \"Anchorage-Independent Growth\" (\"celf\")))\n (11 #f () (302167 \"Cap formation\" (\"celf\")))\n (11 #f () (1156237 \"Stimulation of Cell Proliferation\" (\"celf\")))\n (12 #f () (1327616 \"Cell secretion\" (\"celf\")))\n (12 #f () (10813 \"Cytokinesis\" (\"celf\")))\n (12 #f () (1159946 \"macrophage differentiation\" (\"celf\")))\n (13 #f () (1155004 \"B-cell differentiation\" (\"celf\")))\n (13\n #f\n ()\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\")))\n (14 #f () (525010 \"Autocrine Communication\" (\"celf\")))\n (14 #f () (1511002 \"B-Cell Development\" (\"celf\")))\n (15 #f () (1159909 \"keratinocyte differentiation\" (\"celf\")))\n (15 #f () (1326205 \"Induction of Apoptosis\" (\"celf\")))\n (16 #f () (596286 \"Cell Growth Regulation\" (\"celf\")))\n (17 #f () (230871 \"Mitochondrion in division\" (\"celf\")))\n (17 #f () (872097 \"Anoikis\" (\"celf\")))\n (18 #f () (1159709 \"cholesterol transport\" (\"celf\")))\n (18 #f () (25186 \"Meiosis\" (\"celf\")))\n (18 #f () (1540661 \"cell fate\" (\"celf\")))\n (19 #f () (1159884 \"adipocyte differentiation\" (\"celf\")))\n (19 #f () (1514761 \"Receptor Inhibition\" (\"celf\")))\n (20 #f () (1159978 \"osteoclast differentiation\" (\"celf\")))\n (20 #t ((4096 \"Asthma\" (\"dsyn\"))) (312861 \"Neutrophil chemotaxis\" (\"celf\")))\n (21 #f () (37848 \"Sperm Motility\" (\"celf\")))\n (21 #f () (949629 \"Bystander Effect\" (\"celf\")))\n (22 #f () (1155013 \"T-cell differentiation\" (\"celf\")))\n (22 #f () (85416 \"Respiratory Burst\" (\"celf\")))\n (23 #f () (4462 \"Axonal Transport\" (\"celf\")))\n (23 #f () (1159974 \"osteoblast differentiation\" (\"celf\")))\n (24 #f () (1326347 \"fibroblast proliferation\" (\"celf\")))\n (25 #f () (32174 \"Platelet adhesion\" (\"celf\")))\n (27 #f () (1326341 \"Epithelial Cell Proliferation\" (\"celf\")))\n (27 #f () (221117 \"Anergy\" (\"celf\")))\n (28 #t ((4096 \"Asthma\" (\"dsyn\"))) (1154382 \"Cell-Cell Adhesion\" (\"celf\")))\n (29 #f () (178666 \"glucose transport\" (\"celf\")))\n (29 #f () (1326225 \"cell homeostasis\" (\"celf\")))\n (30 #f () (1154401 \"cell invasion\" (\"celf\")))\n (31 #f () (282636 \"Cell Respiration\" (\"celf\")))\n (31 #f () (1516349 \"Cell Maturation\" (\"celf\")))\n (32 #f () (40682 \"cell transformation\" (\"celf\")))\n (33 #f () (600431 \"Calcium Signaling\" (\"celf\")))\n (35 #f () (596991 \"myelination\" (\"celf\")))\n (35\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (7588 \"Cell Degranulation\" (\"celf\")))\n (35 #f () (1155003 \"B-Cell Activation\" (\"celf\")))\n (35\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (1155074 \"mast cell activation\" (\"celf\")))\n (38\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (264423 \"Occupational asthma\" (\"dsyn\")))\n (19595 \"Histamine Release\" (\"celf\")))\n (39 #f () (25251 \"Membrane Potentials\" (\"celf\")))\n (39 #f () (1516334 \"Cell Cycle Progression\" (\"celf\")))\n (40 #f () (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\")))\n (41 #f () (301896 \"Cell-Mediated Cytolysis\" (\"celf\")))\n (41 #f () (1155046 \"T-Cell Proliferation\" (\"celf\")))\n (41 #f () (1154413 \"Intercellular Communication\" (\"celf\")))\n (44 #t ((4096 \"Asthma\" (\"dsyn\"))) (206431 \"Antigen Presentation\" (\"celf\")))\n (44 #t ((4096 \"Asthma\" (\"dsyn\"))) (1155872 \"Cell Cycle Regulation\" (\"celf\")))\n (47 #f () (1155873 \"Cell Cycle Arrest\" (\"celf\")))\n (50 #f () (14139 \"Endocytosis\" (\"celf\")))\n (50 #f () (7590 \"Cell division\" (\"celf\")))\n (53 #f () (1155229 \"humoral immune response\" (\"celf\")))\n (56 #t ((4096 \"Asthma\" (\"dsyn\"))) (1522821 \"acidification\" (\"celf\")))\n (56 #t ((4096 \"Asthma\" (\"dsyn\"))) (26255 \"Mitosis\" (\"celf\")))\n (60 #f () (1523298 \"epithelial to mesenchymal transition\" (\"celf\")))\n (61 #f () (1158770 \"Transcriptional Regulation\" (\"celf\")))\n (63 #t ((4096 \"Asthma\" (\"dsyn\"))) (24426 \"Macrophage Activation\" (\"celf\")))\n (63 #f () (1326120 \"cell activation\" (\"celf\")))\n (64 #f () (1256369 \"insulin secretion\" (\"celf\")))\n (65\n #t\n ((4096 \"Asthma\" (\"dsyn\"))\n (4099 \"Asthma, Exercise-Induced\" (\"dsyn\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (24262 \"Lymphocyte Activation\" (\"celf\")))\n (68 #f () (1318468 \"cell-mediated immune response\" (\"celf\")))\n (72 #f () (7581 \"Cell Aging\" (\"celf\")))\n (74 #f () (1159816 \"anti-apoptosis\" (\"celf\")))\n (76 #f () (598501 \"Chromosome Pairing\" (\"celf\")))\n (76 #f () (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\")))\n (80 #f () (7577 \"Cell Adhesion\" (\"celf\")))\n (86 #t ((4096 \"Asthma\" (\"dsyn\"))) (8018 \"Chemotaxis\" (\"celf\")))\n (87 #f () (1260960 \"Cytolysis\" (\"celf\")))\n (89 #f () (678903 \"Neuronal Transmission\" (\"celf\")))\n (91 #f () (31308 \"Phagocytosis\" (\"celf\")))\n (95 #f () (32176 \"Platelet aggregation\" (\"celf\")))\n (103 #f () (7620 \"Cell Survival\" (\"celf\")))\n (104 #f () (7595 \"Cell Growth\" (\"celf\")))\n (106 #f () (7586 \"Cell Cycle\" (\"celf\")))\n (106 #t ((4096 \"Asthma\" (\"dsyn\"))) (7608 \"cell motility\" (\"celf\")))\n (113\n #f\n ((264423 \"Occupational asthma\" (\"dsyn\")))\n (3261 \"Antibody Formation\" (\"celf\")))\n (114\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (264408 \"Childhood asthma\" (\"dsyn\")))\n (1155065 \"T-Cell Activation\" (\"celf\")))\n (141 #t ((4096 \"Asthma\" (\"dsyn\"))) (7582 \"Cell Communication\" (\"celf\")))\n (150 #t ((4096 \"Asthma\" (\"dsyn\"))) (1514758 \"Receptor Activation\" (\"celf\")))\n (164 #t ((4096 \"Asthma\" (\"dsyn\"))) (599894 \"targeting\" (\"celf\")))\n (165\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (15283 \"Exocytosis\" (\"celf\")))\n (218 #t ((4096 \"Asthma\" (\"dsyn\"))) (7613 \"Cell physiology\" (\"celf\")))\n (231\n #f\n ((155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\")))\n (241 #f () (596290 \"Cell Proliferation\" (\"celf\")))\n (268 #f () (7587 \"Cell Death\" (\"celf\")))\n (292 #t ((4096 \"Asthma\" (\"dsyn\"))) (4391 \"Autophagy\" (\"celf\")))\n (332\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\")))\n (335\n #t\n ((4096 \"Asthma\" (\"dsyn\")))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\")))\n (358\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (13081 \"Down-Regulation\" (\"celf\")))\n (423\n #t\n ((4096 \"Asthma\" (\"dsyn\")) (155877 \"Extrinsic asthma NOS\" (\"dsyn\")))\n (37083 \"Signal Transduction\" (\"celf\")))\n (819 #t ((4096 \"Asthma\" (\"dsyn\"))) (162638 \"Apoptosis\" (\"celf\"))))\n\n\n\n;; How many \"celf\"s are caused by the genes of interest, across all 47\n;; genes (the \"naive\" list of genes) that are directly inhibited by\n;; Gleevec *and* directly cause diseases that Gleevec directly treats?\n;;\n;; Throw out the 'howler' genes:\n;;\n;; (100 (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\")))\n;; (104 (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\")))\n;; (174 (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))))\n;;\n;; Throwing out the top three super-broad classes of genes reduces\n;; the number of results from 298 to 189.\n(apply\n union*\n (map\n (lambda (gene)\n (let ((cell-functions\n (run* (q)\n (fresh (cell-function e-gene/cell-function st-gene/cell-function ot-gene/cell-function e-gene/cell-function-rest)\n (== cell-function q)\n (== \"celf\" ot-gene/cell-function) \n (== `(,gene ,cell-function \"CAUSES\" ,st-gene/cell-function ,ot-gene/cell-function . ,e-gene/cell-function-rest) e-gene/cell-function)\n (edgeo e-gene/cell-function)))))\n cell-functions))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n ;; ignore howler!\n ;; (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n ;; ignore howler!\n ;; (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n ;; ignore howler\n ;; (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))))\n=>\n'((312862 \"Lymphocyte chemotaxis\" (\"celf\"))\n (1159455 \"syncytium formation\" (\"celf\"))\n (1372294 \"Increased Endocytosis\" (\"celf\"))\n (598948 \"axonal guidance\" (\"celf\"))\n (1159821 \"apoptotic program\" (\"celf\"))\n (1318468 \"cell-mediated immune response\" (\"celf\"))\n (1326501 \"eosinophil chemotaxis\" (\"celf\"))\n (1155303 \"ER-overload response\" (\"celf\"))\n (1156259 \"cell ion homeostasis\" (\"celf\"))\n (1159709 \"cholesterol transport\" (\"celf\"))\n (1276855 \"Monocyte chemotaxis\" (\"celf\"))\n (1326474 \"vesicle fusion\" (\"celf\"))\n (1516338 \"Cell Death Induction\" (\"celf\"))\n (598949 \"axonal sprouting\" (\"celf\"))\n (1156042 \"endosome transport\" (\"celf\"))\n (1159824 \"nuclear fragmentation\" (\"celf\"))\n (1326121 \"astrocyte activation\" (\"celf\"))\n (25186 \"Meiosis\" (\"celf\"))\n (1155874 \"Cell Cycle Checkpoint\" (\"celf\"))\n (1155876 \"DNA replication checkpoint\" (\"celf\"))\n (1156132 \"vacuolar acidification\" (\"celf\"))\n (1159689 \"potassium ion transport\" (\"celf\"))\n (1326080 \"muscle cell differentiation\" (\"celf\"))\n (1155013 \"T-cell differentiation\" (\"celf\"))\n (598838 \"membrane assembly\" (\"celf\"))\n (7580 \"Cell Aggregation\" (\"celf\"))\n (32174 \"Platelet adhesion\" (\"celf\"))\n (282636 \"Cell Respiration\" (\"celf\"))\n (301896 \"Cell-Mediated Cytolysis\" (\"celf\"))\n (392710 \"Megakaryocytic maturation\" (\"celf\"))\n (596991 \"myelination\" (\"celf\"))\n (1156032 \"Microtubule Polymerization\" (\"celf\"))\n (1159339 \"Protein Secretion\" (\"celf\"))\n (1159884 \"adipocyte differentiation\" (\"celf\"))\n (1159938 \"eosinophil differentiation\" (\"celf\"))\n (1159966 \"myoblast differentiation\" (\"celf\"))\n (1159978 \"osteoclast differentiation\" (\"celf\"))\n (1160520 \"oocyte maturation\" (\"celf\"))\n (1326236 \"filopodium formation\" (\"celf\"))\n (1326504 \"neuronal migration\" (\"celf\"))\n (1513082 \"Megakaryocyte Proliferation\" (\"celf\"))\n (599702 \"reuptake\" (\"celf\"))\n (312861 \"Neutrophil chemotaxis\" (\"celf\"))\n (1155792 \"Meiotic Recombination\" (\"celf\"))\n (1516349 \"Cell Maturation\" (\"celf\"))\n (1372847 \"Increased Cellular Migration\" (\"celf\"))\n (312860 \"Neutrophil migration, function\" (\"celf\"))\n (37841 \"Sperm Capacitation\" (\"celf\"))\n (1159958 \"neutrophil differentiation\" (\"celf\"))\n (19595 \"Histamine Release\" (\"celf\"))\n (31945 \"Pinocytosis\" (\"celf\"))\n (230871 \"Mitochondrion in division\" (\"celf\"))\n (525010 \"Autocrine Communication\" (\"celf\"))\n (600430 \"Calcium Waves\" (\"celf\"))\n (1155752 \"positive regulation of mitosis\" (\"celf\"))\n (1155949 \"lamellipodium biogenesis\" (\"celf\"))\n (1156031 \"Microtubule Depolymerization\" (\"celf\"))\n (1260960 \"Cytolysis\" (\"celf\"))\n (1325887 \"focal adhesion formation\" (\"celf\"))\n (1326341 \"Epithelial Cell Proliferation\" (\"celf\"))\n (1326356 \"amino acid import\" (\"celf\"))\n (1522821 \"acidification\" (\"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\"))\n (7588 \"Cell Degranulation\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1159816 \"anti-apoptosis\" (\"celf\"))\n (1159909 \"keratinocyte differentiation\" (\"celf\"))\n (1514761 \"Receptor Inhibition\" (\"celf\"))\n (79396 \"G2 Phase\" (\"celf\"))\n (1155846\n \"negative regulation of cyclin dependent protein kinase activity\"\n (\"celf\"))\n (1256369 \"insulin secretion\" (\"celf\"))\n (1326346 \"urothelial cell proliferation\" (\"celf\"))\n (3261 \"Antibody Formation\" (\"celf\"))\n (24262 \"Lymphocyte Activation\" (\"celf\"))\n (206431 \"Antigen Presentation\" (\"celf\"))\n (1155003 \"B-Cell Activation\" (\"celf\"))\n (1155004 \"B-cell differentiation\" (\"celf\"))\n (1155008 \"B Cell Proliferation\" (\"celf\"))\n (1155229 \"humoral immune response\" (\"celf\"))\n (1155980 \"actin filament depolymerization\" (\"celf\"))\n (1327616 \"Cell secretion\" (\"celf\"))\n (1511002 \"B-Cell Development\" (\"celf\"))\n (3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (7591 \"Cell division phases\" (\"celf\"))\n (10813 \"Cytokinesis\" (\"celf\"))\n (14139 \"Endocytosis\" (\"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (31308 \"Phagocytosis\" (\"celf\"))\n (32176 \"Platelet aggregation\" (\"celf\"))\n (37848 \"Sperm Motility\" (\"celf\"))\n (85416 \"Respiratory Burst\" (\"celf\"))\n (178666 \"glucose transport\" (\"celf\"))\n (302167 \"Cap formation\" (\"celf\"))\n (599893 \"Protein translocation\" (\"celf\"))\n (600485 \"Acrosome Reaction\" (\"celf\"))\n (887839 \"Nuclear Import\" (\"celf\"))\n (949629 \"Bystander Effect\" (\"celf\"))\n (1155065 \"T-Cell Activation\" (\"celf\"))\n (1155607 \"autophagic vacuole formation\" (\"celf\"))\n (1155631 \"Chromosome Condensation\" (\"celf\"))\n (1155734 \"lamin depolymerization\" (\"celf\"))\n (1155750 \"Mitotic/Spindle Checkpoint\" (\"celf\"))\n (1155871 \"nuclear migration\" (\"celf\"))\n (1155872 \"Cell Cycle Regulation\" (\"celf\"))\n (1155893 \"unidimensional cell growth\" (\"celf\"))\n (1158774 \"negative regulation of transcription by glucose\" (\"celf\"))\n (1159442 \"sporulation\" (\"celf\"))\n (1159512 \"maltose transport\" (\"celf\"))\n (1159521 \"hexose transport\" (\"celf\"))\n (1160602 \"cholesterol absorption\" (\"celf\"))\n (1326207 \"Programmed Cell Death, Type II\" (\"celf\"))\n (1326220 \"synergid cell death\" (\"celf\"))\n (1326347 \"fibroblast proliferation\" (\"celf\"))\n (1326502 \"macrophage chemotaxis\" (\"celf\"))\n (1511632 \"Cytoskeletal Modeling\" (\"celf\"))\n (1515126 \"T-Cell Development\" (\"celf\"))\n (1516340 \"Cell Death Process\" (\"celf\"))\n (1516743 \"Complement-Dependent Cytotoxicity\" (\"celf\"))\n (1517348 \"G2 Phase Arrest\" (\"celf\"))\n (1519167 \"S Phase Arrest\" (\"celf\"))\n (1523105 \"nuclear envelope disassembly\" (\"celf\"))\n (1523795 \"stress fiber formation\" (\"celf\"))\n (4462 \"Axonal Transport\" (\"celf\"))\n (15283 \"Exocytosis\" (\"celf\"))\n (25564 \"Metaphase\" (\"celf\"))\n (1450355 \"Prometaphase\" (\"celf\"))\n (8018 \"Chemotaxis\" (\"celf\"))\n (1156237 \"Stimulation of Cell Proliferation\" (\"celf\"))\n (25251 \"Membrane Potentials\" (\"celf\"))\n (7590 \"Cell division\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (596286 \"Cell Growth Regulation\" (\"celf\"))\n (598501 \"Chromosome Pairing\" (\"celf\"))\n (599894 \"targeting\" (\"celf\"))\n (1155711 \"stem cell division\" (\"celf\"))\n (1155766 \"centrosome cycle\" (\"celf\"))\n (1326205 \"Induction of Apoptosis\" (\"celf\"))\n (1326225 \"cell homeostasis\" (\"celf\"))\n (4391 \"Autophagy\" (\"celf\"))\n (7577 \"Cell Adhesion\" (\"celf\"))\n (7581 \"Cell Aging\" (\"celf\"))\n (7582 \"Cell Communication\" (\"celf\"))\n (7586 \"Cell Cycle\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (24426 \"Macrophage Activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (41904 \"Up-Regulation (Physiology)\" (\"moft\" \"celf\"))\n (544888 \"Mitotic arrest\" (\"celf\"))\n (596233 \"release of sequestered calcium ion into cytoplasm\" (\"celf\"))\n (598087 \"cell dedifferentiation\" (\"celf\"))\n (600431 \"Calcium Signaling\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (872097 \"Anoikis\" (\"celf\"))\n (887840 \"Nuclear Export\" (\"celf\"))\n (1154382 \"Cell-Cell Adhesion\" (\"celf\"))\n (1154401 \"cell invasion\" (\"celf\"))\n (1154413 \"Intercellular Communication\" (\"celf\"))\n (1158770 \"Transcriptional Regulation\" (\"celf\"))\n (1158951 \"maintenance of protein localization\" (\"celf\"))\n (1159946 \"macrophage differentiation\" (\"celf\"))\n (1159974 \"osteoblast differentiation\" (\"celf\"))\n (1257985 \"Cross-Priming\" (\"celf\"))\n (1326057 \"epithelial cell differentiation\" (\"celf\"))\n (1326120 \"cell activation\" (\"celf\"))\n (1330957 \"Cytokinesis of the fertilized ovum\" (\"celf\"))\n (1372180 \"Increased Cellular Death\" (\"celf\"))\n (1515136 \"T-Cell Transformation\" (\"celf\"))\n (1515432 \"Thymocyte Development\" (\"celf\"))\n (1515979 \"Anchorage-Independent Growth\" (\"celf\"))\n (1516334 \"Cell Cycle Progression\" (\"celf\"))\n (1518147 \"M Phase Arrest\" (\"celf\"))\n (1523169 \"smooth muscle cell differentiation\" (\"celf\"))\n (1523298 \"epithelial to mesenchymal transition\" (\"celf\"))\n (1540661 \"cell fate\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\")))\n\n;; How many \"celf\"s are caused by the genes of interest, across all 47\n;; genes (the \"naive\" list of genes) that are directly inhibited by\n;; Gleevec *and* directly cause diseases that Gleevec directly treats?\n;;\n;; 298 \"celfs\"\n;;\n(length\n (apply\n union*\n (map\n (lambda (gene)\n (let ((cell-functions\n (run* (q)\n (fresh (cell-function e-gene/cell-function st-gene/cell-function ot-gene/cell-function e-gene/cell-function-rest)\n (== cell-function q)\n (== \"celf\" ot-gene/cell-function) \n (== `(,gene ,cell-function \"CAUSES\" ,st-gene/cell-function ,ot-gene/cell-function . ,e-gene/cell-function-rest) e-gene/cell-function)\n (edgeo e-gene/cell-function)))))\n cell-functions))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))))))\n=>\n298\n\n;; There are 47 genes are directly inhibited by Gleevec *and* directly cause diseases that Gleevec directly treats\n;; (vs. 50 genes that are inhibited directly by Gleevec). (See query below that produces these answers.)\n;;\n;; For each gene, how many cell functions (celf|T043|Cell Function) are directly caused by that gene?\n(sort\n (map\n (lambda (gene)\n (let ((cell-functions\n (run* (q)\n (fresh (cell-function e-gene/cell-function st-gene/cell-function ot-gene/cell-function e-gene/cell-function-rest)\n (== cell-function q)\n (== \"celf\" ot-gene/cell-function) \n (== `(,gene ,cell-function \"CAUSES\" ,st-gene/cell-function ,ot-gene/cell-function . ,e-gene/cell-function-rest) e-gene/cell-function)\n (edgeo e-gene/cell-function)))))\n (list (length (rem-dups cell-functions)) gene)))\n '((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))))\n (lambda (l1 l2) (< (car l1) (car l2))))\n=>\n'((1 (79413 \"Genes, abl\" (\"gngm\" \"aapp\")))\n (2\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\")))\n (3 (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\")))\n (3 (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\")))\n (4 (1428985 \"PDGFD gene\" (\"aapp\" \"gngm\")))\n (4 (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\")))\n (4 (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\")))\n (4 (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\")))\n (5 (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\")))\n (7 (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\")))\n (7 (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\")))\n (7 (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")))\n (8 (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\")))\n (8 (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\")))\n (8 (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\")))\n (8 (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\")))\n (8\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\")))\n (9 (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\")))\n (10 (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))\n (11 (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\")))\n (11\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\")))\n (11 (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\")))\n (11 (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\")))\n (12 (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\")))\n (12 (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\")))\n (14 (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\")))\n (15 (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\")))\n (17 (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\")))\n (18 (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\")))\n (19 (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\")))\n (24 (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\")))\n (26 (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\")))\n (28 (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\")))\n (30\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\")))\n (33 (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\")))\n (33 (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\")))\n (34 (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\")))\n (39 (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\")))\n (43 (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\")))\n (45 (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\")))\n (52 (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\")))\n (57 (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\")))\n (71 (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\")))\n ;; marginal at best\n (80 (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\")))\n ;; below here are silly answers\n (100 (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\")))\n (104 (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\")))\n (174 (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))))\n\n\n\n;; only 14 dsyn, neop, or patf directly caused by a celf,\n;; and many of these are so general as to be almost meaningless\n(rem-dups (run* (q)\n (fresh (e subj obj pred st ot rest)\n (== (list subj obj) q)\n (== \"celf\" st)\n (conde\n [(== \"dsyn\" ot)]\n [(== \"neop\" ot)]\n [(== \"patf\" ot)])\n (== \"CAUSES\" pred)\n (== `(,subj ,obj ,pred ,st ,ot . ,rest) e)\n (edgeo e))))\n'(((3272 \"Antibody -dependent cell cytotoxicity\" (\"celf\"))\n (11854 \"Diabetes Mellitus, Insulin-Dependent\" (\"dsyn\")))\n ((7613 \"Cell physiology\" (\"celf\"))\n (4153 \"Atherosclerosis\" (\"dsyn\")))\n ((7577 \"Cell Adhesion\" (\"celf\"))\n (242184 \"Hypoxia\" (\"patf\")))\n ((7577 \"Cell Adhesion\" (\"celf\"))\n (852964 \"Shunt occlusion\" (\"patf\")))\n ((24262 \"Lymphocyte Activation\" (\"celf\"))\n (20517 \"Hypersensitivity\" (\"patf\")))\n ((920567 \"leukocyte activation\" (\"celf\"))\n (332448 \"Infiltration\" (\"patf\")))\n ((1159339 \"Protein Secretion\" (\"celf\"))\n (277785 \"Functional disorder\" (\"patf\")))\n ((7613 \"Cell physiology\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\")))\n ((7613 \"Cell physiology\" (\"celf\"))\n (42769 \"Virus Diseases\" (\"dsyn\")))\n ((7613 \"Cell physiology\" (\"celf\"))\n (524851 \"Neurodegenerative Disorders\" (\"dsyn\")))\n ((7613 \"Cell physiology\" (\"celf\"))\n (751651 \"Mitochondrial Diseases\" (\"dsyn\")))\n ((1154987 \"anti-inflammatory response\" (\"celf\"))\n (21290 \"Infant, Newborn, Diseases\" (\"dsyn\")))\n ((1158770 \"Transcriptional Regulation\" (\"celf\"))\n (42373 \"Vascular Diseases\" (\"dsyn\")))\n ((1524026 \"Metabolic Process, Cellular\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))))\n\n;; 9 results\n(run* (q)\n (fresh (e subj obj pred st ot rest)\n (== e q)\n (fuzzy-concepto \"mast cell activation\" obj)\n (conde\n [(== \"dsyn\" st)]\n [(== \"neop\" st)]\n [(== \"patf\" st)])\n (== \"MANIFESTATION_OF\" pred)\n (== `(,subj ,obj ,pred ,st ,ot . ,rest) e)\n (edgeo e)))\n=>\n'(((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))\n ((12634 \"Disease\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (12217411))\n ((36221 \"Mast-Cell Sarcoma\" (\"neop\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"neop\"\n \"celf\"\n (26659448))\n ((343378 \"Helicobacter-associated gastritis\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (21932987))\n ((13604 \"Edema\" (\"patf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"patf\"\n \"celf\"\n (21130119))\n ((745283 \"INFECTIOUS PROCESS\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (20706702))\n ((598934 \"tumor growth\" (\"neop\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"neop\"\n \"celf\"\n (24931643))\n ((242184 \"Hypoxia\" (\"patf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"patf\"\n \"celf\"\n (16572929))\n ((332448 \"Infiltration\" (\"patf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"patf\"\n \"celf\"\n (21130119)))\n\n\n;; mast cell activation directly AFFECTS which disorders, neoplasms,\n;; or pathologic functions?\n;;\n;; 35 results, 2 of which are super overly broad (Disease, Chronic Disease)\n(run* (q)\n (fresh (e subj obj pred st ot rest)\n (== obj q) \n (fuzzy-concepto \"mast cell activation\" subj)\n (== \"AFFECTS\" pred)\n (conde\n [(== \"dsyn\" ot)]\n [(== \"neop\" ot)]\n [(== \"patf\" ot)])\n (== `(,subj ,obj ,pred ,st ,ot . ,rest) e)\n (edgeo e)))\n=>\n'((3864 \"Arthritis\" (\"dsyn\"))\n (4096 \"Asthma\" (\"dsyn\"))\n (2792 \"Anaphylaxis\" (\"patf\"))\n ;; junky\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (2994 \"Angioneurotic Edema\" (\"patf\"))\n (9766 \"Allergic Conjunctivitis\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n ;; junk\n (12634 \"Disease\" (\"dsyn\"))\n (20452 \"Hyperemia\" (\"patf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n (20523 \"Immediate hypersensitivity\" (\"patf\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n (21368 \"Inflammation\" (\"patf\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n (21375 \"Inflammation, allergic\" (\"patf\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n (36974 \"Shock\" (\"patf\"))\n (263338 \"Chronic urticaria\" (\"dsyn\"))\n (242184 \"Hypoxia\" (\"patf\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (282488 \"Interstitial Cystitis\" (\"dsyn\"))\n (333390 \"Chronic eosinophilic inflammation\" (\"patf\"))\n (340865 \"Anaphylactoid reaction\" (\"dsyn\"))\n (392707 \"Atopy\" (\"patf\"))\n (853897 \"Diabetic cardiomyopathy\" (\"dsyn\"))\n (553697 \"Granulomatous inflammation\" (\"patf\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1290886 \"Chronic inflammatory disorder\" (\"dsyn\"))\n (1155266 \"Inflammatory Response\" (\"patf\"))\n (1449852 \"Erythematotelangiectatic Rosacea\" (\"dsyn\"))\n (1527304 \"Allergic Reaction\" (\"patf\")))\n\n;; 41 results, none of which are CAUSES. Most are AFFECTS.\n;;\n;; Results related to asthma include:\n;;\n;; ((1155074 \"mast cell activation\" (\"celf\"))\n;; (4096 \"Asthma\" (\"dsyn\"))\n;; \"AFFECTS\"\n;; \"celf\"\n;; \"dsyn\"\n;; (18209484 10352758))\n;;\n;; ((1155074 \"mast cell activation\" (\"celf\"))\n;; (4096 \"Asthma\" (\"dsyn\"))\n;; \"ASSOCIATED_WITH\"\n;; \"celf\"\n;; \"dsyn\"\n;; (2645347))\n;;\n;; ((1155074 \"mast cell activation\" (\"celf\"))\n;; (4099 \"Asthma, Exercise-Induced\" (\"dsyn\"))\n;; \"NEG_AFFECTS\"\n;; \"celf\"\n;; \"dsyn\"\n;; (1730841))\n;;\n;; ((1155074 \"mast cell activation\" (\"celf\"))\n;; (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n;; \"AFFECTS\"\n;; \"celf\"\n;; \"dsyn\"\n;; (24509414))\n;;\n(run* (q)\n (fresh (e subj obj pred st ot rest)\n (== e q)\n (fuzzy-concepto \"mast cell activation\" subj)\n (conde\n [(== \"dsyn\" ot)]\n [(== \"neop\" ot)]\n [(== \"patf\" ot)])\n (== `(,subj ,obj ,pred ,st ,ot . ,rest) e)\n (edgeo e)))\n\n;; find all direct edges between mast cell activation and asthma\n;;\n;; interesting!\n;;\n;; 'Asthma MANIFESTATION_OF mast cell activation' seems like the strongest claim,\n;; followed by 'mast cell activation AFFECTS Asthma'\n(run* (q)\n (fresh (e subj obj pred st ot rest)\n (== e q)\n (conde\n [(fuzzy-concepto \"mast cell activation\" subj)\n (fuzzy-concepto \"asthma\" obj)]\n [(fuzzy-concepto \"asthma\" subj)\n (fuzzy-concepto \"mast cell activation\" obj)])\n (== `(,subj ,obj ,pred ,st ,ot . ,rest) e)\n (edgeo e)))\n=>\n'(((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (18209484 10352758))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"ASSOCIATED_WITH\"\n \"celf\"\n \"dsyn\"\n (2645347))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"AFFECTS\"\n \"dsyn\"\n \"celf\"\n (17498066 17192558))\n ((4096 \"Asthma\" (\"dsyn\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"MANIFESTATION_OF\"\n \"dsyn\"\n \"celf\"\n (2741114))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4099 \"Asthma, Exercise-Induced\" (\"dsyn\"))\n \"NEG_AFFECTS\"\n \"celf\"\n \"dsyn\"\n (1730841))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (24509414)))\n\n\n\n;; KIT or C-KIT directly causing some cell function (celf|T043|Cell Function)\n;;\n;; 22 results\n(let ((diseases (run* (q)\n (fresh (disease gene e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== disease q)\n (== \"celf\" ot-gene/disease)\n (conde\n [(== '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) gene)]\n [(== '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) gene)]\n [(== '(72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\")) gene)])\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-gene/disease)))))\n (rem-dups diseases))\n=>\n'((7587 \"Cell Death\" (\"celf\"))\n (7620 \"Cell Survival\" (\"celf\"))\n (7595 \"Cell Growth\" (\"celf\"))\n (7608 \"cell motility\" (\"celf\"))\n (37083 \"Signal Transduction\" (\"celf\"))\n (13081 \"Down-Regulation\" (\"celf\"))\n (40682 \"cell transformation\" (\"celf\"))\n (7613 \"Cell physiology\" (\"celf\"))\n (86982 \"Signal Transduction Pathways\" (\"moft\" \"celf\"))\n (26255 \"Mitosis\" (\"celf\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n (37080 \"Signal Pathways\" (\"celf\" \"moft\"))\n (1155781 \"spindle assembly\" (\"celf\"))\n (162638 \"Apoptosis\" (\"celf\"))\n (1155873 \"Cell Cycle Arrest\" (\"celf\"))\n (221117 \"Anergy\" (\"celf\"))\n (1514758 \"Receptor Activation\" (\"celf\"))\n (596290 \"Cell Proliferation\" (\"celf\"))\n (678903 \"Neuronal Transmission\" (\"celf\"))\n (949469 \"Receptor Down-Regulation\" (\"moft\" \"celf\"))\n (1155046 \"T-Cell Proliferation\" (\"celf\"))\n (1325893 \"histamine secretion\" (\"celf\")))\n\n(let ((diseases (run* (q)\n (fresh (disease gene e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== disease q)\n (conde\n [(== '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) gene)]\n [(== '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) gene)]\n [(== '(72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\")) gene)])\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-gene/disease)))))\n (length (rem-dups diseases)))\n=>\n104\n\n;; which diseases, neoplasms, pathologic functions are directly caused by KIT or C-KIT?\n;;\n;; 62 results, including\n;;\n;; (12634 \"Disease\" (\"dsyn\"))\n;; (678236 \"Rare Diseases\" (\"dsyn\"))\n;; (879626 \"Adverse effects\" (\"patf\"))\n;;\n;; notice asthma isn't one of them!\n(let ((diseases (run* (q)\n (fresh (disease gene e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== disease q)\n (conde\n [(== \"dsyn\" ot-gene/disease)]\n [(== \"neop\" ot-gene/disease)]\n [(== \"patf\" ot-gene/disease)])\n (conde\n [(== '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) gene)]\n [(== '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) gene)]\n [(== '(72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\")) gene)])\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-gene/disease)))))\n (rem-dups diseases))\n=>\n'((2871 \"Anemia\" (\"dsyn\"))\n (11603 \"Dermatitis\" (\"dsyn\"))\n (1511 \"Adhesions\" (\"acab\" \"dsyn\"))\n (12634 \"Disease\" (\"dsyn\"))\n (16663 \"Pathological fracture\" (\"dsyn\"))\n (2874 \"Aplastic Anemia\" (\"dsyn\"))\n (17178 \"Gastrointestinal Diseases\" (\"dsyn\"))\n (4509 \"Azoospermia\" (\"dsyn\"))\n (37277 \"Skin Diseases, Genetic\" (\"dsyn\"))\n (41408 \"Turner's Syndrome\" (\"cgab\" \"dsyn\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (15625 \"Fanconi's Anemia\" (\"dsyn\"))\n (85215 \"Ovarian Failure, Premature\" (\"dsyn\"))\n (24899 \"mastocytosis\" (\"dsyn\"))\n (23435 \"Leukemia, B-Cell, Acute\" (\"neop\"))\n (25218 \"Chloasma\" (\"dsyn\"))\n (339789 \"Congenital deafness\" (\"cgab\" \"dsyn\"))\n (27051 \"Myocardial Infarction\" (\"dsyn\"))\n (29453 \"Osteopenia\" (\"dsyn\"))\n (43154 \"Dental White Spot\" (\"dsyn\"))\n (1136033 \"Cutaneous Mastocytosis\" (\"dsyn\"))\n (25286 \"meningioma\" (\"neop\"))\n (80024 \"Piebaldism\" (\"dsyn\"))\n (221013 \"Mastocytosis, Systemic\" (\"dsyn\"))\n (27022 \"Myeloproliferative disease\" (\"neop\"))\n (242354 \"Congenital Disorders\" (\"dsyn\"))\n (595978 \"Idiopathic megacolon\" (\"dsyn\"))\n (678236 \"Rare Diseases\" (\"dsyn\"))\n (948710 \"Ureteropelvic junction obstruction\" (\"dsyn\"))\n (7137 \"Squamous cell carcinoma\" (\"neop\"))\n (152254 \"Fatty degeneration\" (\"patf\"))\n (9402 \"Carcinoma of the Large Intestine\" (\"neop\"))\n (346421 \"Chronic eosinophilic leukemia\" (\"neop\"))\n (20507 \"Hyperplasia\" (\"patf\"))\n (1334699 \"Mesenchymal Cell Neoplasm\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (1140999 \"Contraction\" (\"patf\"))\n (20517 \"Hypersensitivity\" (\"patf\"))\n (27708 \"Nephroblastoma\" (\"neop\"))\n (27819 \"Neuroblastoma\" (\"neop\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (25874 \"Metrorrhagia\" (\"patf\"))\n (37579 \"Soft Tissue Neoplasms\" (\"neop\"))\n (79218 \"Fibromatosis, Aggressive\" (\"neop\"))\n (151686 \"Growth retardation\" (\"patf\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (149925 \"Small cell carcinoma of lung\" (\"neop\"))\n (277785 \"Functional disorder\" (\"patf\"))\n (206728 \"Plexiform Neurofibroma\" (\"neop\"))\n (26986 \"Dysmyelopoietic Syndromes\" (\"neop\"))\n (679316 \"MOTILITY DISORDER NOS\" (\"patf\"))\n (334664 \"Mast Cell Neoplasm\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (345905 \"Intrahepatic Cholangiocarcinoma\" (\"neop\"))\n (699748 \"Pathogenesis\" (\"patf\"))\n (1261473 \"sarcoma\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (1326912 \"Tumorigenesis\" (\"neop\"))\n (879626 \"Adverse effects\" (\"patf\"))\n (1608408 \"Malignant transformation\" (\"neop\"))\n (1510411 \"metaplastic cell transformation\" (\"patf\")))\n\n\n;; Combine two of the queries below: which of the Diseases or\n;; Syndromes or Neoplastic Processes or Pathologic Functions directly\n;; treated by imatinib synonyms are *directly* caused by the genes\n;; directly inhibited by the imatinib synonyms?\n(map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest\n gene e-drug/gene p-st-drug/gene e-drug/gene-rest\n e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== disease q)\n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)]\n [(== \"patf\" p-ob-drug/disease)])\n (== `(,drug ,disease \"TREATS\" ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== `(,drug ,gene \"INHIBITS\" ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-drug/disease)\n (edgeo e-drug/gene)\n (edgeo e-gene/disease)))))\n (list (length (rem-dups diseases)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n(time (map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest\n gene e-drug/gene p-st-drug/gene e-drug/gene-rest\n e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== disease q)\n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)]\n [(== \"patf\" p-ob-drug/disease)])\n (== `(,drug ,disease \"TREATS\" ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== `(,drug ,gene \"INHIBITS\" ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-drug/disease)\n (edgeo e-drug/gene)\n (edgeo e-gene/disease)))))\n (list (length (rem-dups diseases)) drug)))\n '(\n ;;(935989 \"imatinib\" (\"phsu\" \"orch\"))\n ;;(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n ;;(385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n ;;(906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))\n )))\ncpu time: 7663 real time: 7680 gc time: 48\n'((35 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n> (time (map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest\n gene e-drug/gene p-st-drug/gene e-drug/gene-rest\n e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== disease q)\n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)]\n [(== \"patf\" p-ob-drug/disease)])\n (== `(,drug ,disease \"TREATS\" ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== `(,drug ,gene \"INHIBITS\" ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-drug/disease)\n (edgeo e-drug/gene)\n (edgeo e-gene/disease)))))\n (rem-dups diseases)))\n '(\n ;;(935989 \"imatinib\" (\"phsu\" \"orch\"))\n ;;(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n ;;(385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n ;;(906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))\n )))\ncpu time: 7748 real time: 7763 gc time: 56\n'(((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n (5699 \"Blast Phase\" (\"neop\"))\n (11847 \"Diabetes\" (\"dsyn\"))\n (16059 \"Fibrosis\" (\"patf\"))\n (11860 \"Diabetes Mellitus, Non-Insulin-Dependent\" (\"dsyn\"))\n (37274 \"skin disorder\" (\"dsyn\"))\n (21655 \"Insulin Resistance\" (\"patf\"))\n (6826 \"Malignant Neoplasms\" (\"neop\"))\n (332448 \"Infiltration\" (\"patf\"))\n (920563 \"insulin sensitivity\" (\"patf\"))\n (7131 \"Carcinoma, Non-Small-Cell Lung\" (\"neop\"))\n (7134 \"Renal Cell Carcinoma\" (\"neop\"))\n (17636 \"Glioblastoma\" (\"neop\"))\n (23418 \"leukemia\" (\"neop\"))\n (23449 \"Leukemia, Lymphocytic, Acute\" (\"neop\"))\n (23467 \"Leukemia, Myelocytic, Acute\" (\"neop\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n (25149 \"medulloblastoma\" (\"neop\"))\n (25202 \"melanoma\" (\"neop\"))\n (27627 \"Neoplasm Metastasis\" (\"neop\"))\n (27831 \"Neurofibromatosis 1\" (\"neop\"))\n (27651 \"Neoplasm\" (\"neop\"))\n (27859 \"Acoustic Neuroma\" (\"neop\"))\n (35335 \"Retinoblastoma\" (\"neop\"))\n (85669 \"Acute leukemia\" (\"neop\"))\n (153690 \"Secondary malignant neoplasm of bone\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (279671 \"Cervical Squamous Cell Carcinoma\" (\"neop\"))\n (280100 \"Solid tumor\" (\"neop\"))\n (392784 \"Dermatofibrosarcoma Protuberans\" (\"neop\"))\n (677886 \"Epithelial ovarian cancer\" (\"neop\"))\n (856536 \"Philadelphia chromosome positive\" (\"neop\"))\n (1261473 \"sarcoma\" (\"neop\"))))\n\n\n;; instead of diseases from the above query, lets look at the genes\n;;\n;; 47 genes are directly inhibited by Gleevec *and* directly cause diseases that Gleevec directly treats\n;; (vs. 50 genes that are inhibited directly by Gleevec)\n;;\n;; still some slop:\n;;\n;; (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n;; (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n;; (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n;;\n;; At most 43 of these results are specific or semi-specific (and arguably fewer than 43).\n;; 3 of these are KIT or C-KIT.\n> (time (map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (disease e-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest\n gene e-drug/gene p-st-drug/gene e-drug/gene-rest\n e-gene/disease st-gene/disease ot-gene/disease e-gene/disease-rest)\n (== gene q)\n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)]\n [(== \"patf\" p-ob-drug/disease)])\n (== `(,drug ,disease \"TREATS\" ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== `(,drug ,gene \"INHIBITS\" ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== `(,gene ,disease \"CAUSES\" ,st-gene/disease ,ot-gene/disease . ,e-gene/disease-rest) e-gene/disease)\n (edgeo e-drug/disease)\n (edgeo e-drug/gene)\n (edgeo e-gene/disease)))))\n (rem-dups genes)))\n '(\n ;;(935989 \"imatinib\" (\"phsu\" \"orch\"))\n ;;(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n ;;(385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n ;;(906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))\n )))\ncpu time: 7566 real time: 7580 gc time: 43\n'(((1428985 \"PDGFD gene\" (\"aapp\" \"gngm\"))\n (919477 \"LCK gene\" (\"aapp\" \"enzy\" \"gngm\"))\n (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n (1366876 \"MAPK14 gene\" (\"gngm\" \"aapp\" \"enzy\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1333568 \"FLT3 gene\" (\"gngm\" \"phsu\" \"bacs\" \"aapp\"))\n (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n (812253 \"CRKL gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (33681 \"Protein Tyrosine Kinase\" (\"enzy\" \"gngm\" \"aapp\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n (246681 \"platelet-derived growth factor BB\" (\"gngm\" \"phsu\" \"aapp\"))\n (290068\n \"Platelet-Derived Growth Factor beta Receptor\"\n (\"aapp\" \"gngm\" \"rcpt\" \"enzy\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (812375 \"ELK3 gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (1335239 \"PPBP gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (1419240 \"RAD51 gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1421416 \"UVRAG gene\" (\"gngm\" \"phsu\" \"aapp\"))\n (1422009 \"TP63 gene\" (\"rcpt\" \"phsu\" \"imft\" \"aapp\" \"gngm\"))\n (1424677 \"CKAP4 gene\" (\"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (1425835 \"KCNH8 gene\" (\"gngm\" \"aapp\" \"bacs\"))\n (1439347 \"BTG1 gene\" (\"gngm\" \"aapp\"))\n (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (80092\n \"Macrophage Colony-Stimulating Factor Receptor\"\n (\"enzy\" \"aapp\" \"imft\" \"gngm\"))\n (879468 \"CSF1R gene\" (\"aapp\" \"imft\" \"rcpt\" \"gngm\" \"enzy\"))\n (32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (174680 \"Cyclin D1\" (\"gngm\" \"bacs\" \"aapp\"))\n (812385 \"BCR gene\" (\"gngm\" \"bacs\" \"enzy\" \"aapp\"))\n (1335202 \"PDGFRB gene\" (\"bacs\" \"gngm\" \"rcpt\" \"enzy\" \"aapp\"))\n (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412097 \"ABL1 gene\" (\"imft\" \"enzy\" \"gngm\" \"aapp\" \"bacs\" \"phsu\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (1826328 \"MTTP gene\" (\"aapp\" \"lipd\" \"gngm\" \"imft\" \"phsu\" \"bacs\"))\n (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n (105770 \"beta catenin\" (\"aapp\" \"gngm\" \"bacs\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))))\n\n;; Disease or Syndromes/Neoplastic Processes or Pathologic Functions directly treated by imatinib synonyms.\n;; (seems like \"dsyn\", \"neop\", and \"patf\" cover the actual disorders)\n(map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest)\n (== disease q)\n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)]\n [(== \"patf\" p-ob-drug/disease)])\n (== `(,drug ,disease ,p-drug/disease ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== \"TREATS\" p-drug/disease)\n (edgeo e-drug/disease)))))\n (list (length (rem-dups diseases)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((303 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (195 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (5 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (65 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (53 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n\n;; *anything* directly treated by imatinib synonyms (not restricted to Disease or Syndromes/Neoplastic Processes)\n(map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest)\n (== disease q) \n (== `(,drug ,disease ,p-drug/disease ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== \"TREATS\" p-drug/disease)\n (edgeo e-drug/disease)))))\n (list (length (rem-dups diseases)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((430 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (247 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (5 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (84 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (65 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; Disease or Syndromes/Neoplastic Processes directly treated by imatinib synonyms.\n(map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest)\n (== disease q) \n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)])\n (== `(,drug ,disease ,p-drug/disease ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== \"TREATS\" p-drug/disease)\n (edgeo e-drug/disease)))))\n (list (length (rem-dups diseases)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((277 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (184 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (3 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (60 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (49 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n\n;; if we remove \"dsyn\" and \"neop\", we see CGP 57148 also directly\n;; treats patf-related disorders (patf|T046|Pathologic Function)\n;;\n;; CML and Respiratory Depression are the only two specific disorders, though.\n(map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest)\n (== e-drug/disease q) \n (== `(,drug ,disease ,p-drug/disease ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== \"TREATS\" p-drug/disease)\n (edgeo e-drug/disease)))))\n diseases))\n '(\n ;;(935989 \"imatinib\" (\"phsu\" \"orch\"))\n ;;(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n ;;(906802 \"STI571\" (\"phsu\" \"orch\"))\n ;;(935987 \"Gleevec\" (\"orch\" \"phsu\"))\n ))\n=>\n'((((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (8548747))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n \"TREATS\"\n \"orch\"\n \"neop\"\n (10501919))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n \"TREATS\"\n \"orch\"\n \"neop\"\n (10501919))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (235063 \"Respiratory Depression\" (\"patf\"))\n \"TREATS\"\n \"orch\"\n \"patf\"\n (11477209))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (679222 \"functional insufficiency\" (\"patf\"))\n \"TREATS\"\n \"orch\"\n \"patf\"\n (12578692))))\n\n;; there really is only one specific disease directly treated by CGP 57148\n(map\n (lambda (drug)\n (let ((diseases (run* (q)\n (fresh (disease e-drug/disease p-drug/disease p-st-drug/disease p-ob-drug/disease e-drug/disease-rest)\n\n ;; (== disease q)\n (== e-drug/disease q)\n \n (conde\n [(== \"dsyn\" p-ob-drug/disease)]\n [(== \"neop\" p-ob-drug/disease)])\n (== `(,drug ,disease ,p-drug/disease ,p-st-drug/disease ,p-ob-drug/disease . ,e-drug/disease-rest) e-drug/disease)\n (== \"TREATS\" p-drug/disease)\n (edgeo e-drug/disease)))))\n diseases))\n '(\n ;(935989 \"imatinib\" (\"phsu\" \"orch\"))\n ;(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n ;(906802 \"STI571\" (\"phsu\" \"orch\"))\n ;(935987 \"Gleevec\" (\"orch\" \"phsu\"))\n ))\n'((((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (8548747))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (23473 \"Myeloid Leukemia, Chronic\" (\"neop\"))\n \"TREATS\"\n \"orch\"\n \"neop\"\n (10501919))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (23474 \"Leukemia, Myeloid, Chronic-Phase\" (\"neop\"))\n \"TREATS\"\n \"orch\"\n \"neop\"\n (10501919))))\n\n\n\n;; So, insisting on \"gngm\" as the subject type cuts down on stray proteins when we want genes. What about \"orch\" (orch|T109|Organic Chemical) vs. \"phsu\" (phsu|T121|Pharmacologic Substance) for the subject type? For \"CGP 57148\", the INHIBITS edges always have \"orch\" as the subject type. What about for \"imatinib\", \"Imatinib mesylate\", \"STI571\", and \"Gleevec\"? There are a handful of uses of \"phsu\" as the edge type for the other aliases, but these seem more noise than a specific pattern. Doesn't look like anything we can exploit.\n\n\n\n;; the right way to do it\n;; every drug other than \"CGP 57148\" INHIBITS both KIT and C-KIT\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene p-st-drug/gene e-drug/gene-rest)\n (== gene q)\n (== `(,drug ,gene ,p-drug/gene ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)))))\n (let ((genes (rem-dups genes)))\n (list (length genes)\n (and (member '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) genes) #t)\n (and (member '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) genes) #t)\n drug))))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((206 #t #t (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (86 #t #t (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n ;; Of the 5 results for CGP 57148, 3 of them are for specific genes. 0 of those 3 are for KIT or C-KIT.\n (5 #f #f (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (61 #t #t (906802 \"STI571\" (\"phsu\" \"orch\")))\n ;; Of the 50 results for Gleevec, perhaps 38 of them are specific genes, rather than groupings of genes.\n ;; 3 of those 38 are for KIT or C-KIT.\n (50 #t #t (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; the wrong way to do it\n;; every drug other than \"CGP 57148\" INHIBITS both KIT and C-KIT\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (let ((genes (rem-dups genes)))\n (list (length genes)\n (and (member '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) genes) #t)\n (and (member '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) genes) #t)\n drug))))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((206 #t #t (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (86 #t #t (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (8 #f #f (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (61 #t #t (906802 \"STI571\" (\"phsu\" \"orch\")))\n (52 #t #t (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; the right way to do it!\n;; a few of the genes for some of the drugs are dups for \"imatinib\", \"Imatinib mesylate\", and \"STI571\"\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene p-st-drug/gene e-drug/gene-rest) \n (== gene q)\n (== `(,drug ,gene ,p-drug/gene ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)))))\n (list (length (rem-dups genes)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((206 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (86 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (5 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (61 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (50 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; the wrong way to do it!\n;; a few of the genes for some of the drugs are dups\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (list (length (rem-dups genes)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((206 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (86 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (8 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (61 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (52 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n\n;; The right way! Notice there are fewer answers\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene p-st-drug/gene e-drug/gene-rest)\n (== gene q)\n (== `(,drug ,gene ,p-drug/gene ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)))))\n (list (length genes) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((213 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (88 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (5 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (62 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (50 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; The wrong way\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (list (length genes) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((219 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (90 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (8 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (63 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (55 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; The right way to do it\n;; Notice only 3 of the 5 answers are specific genes.\n(map\n (lambda (drug)\n (let ((e-drug/genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene p-st-drug/gene e-drug/gene-rest)\n (== e-drug/gene q)\n (== `(,drug ,gene ,p-drug/gene ,p-st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)))))\n e-drug/genes))\n '((385728 \"CGP 57148\" (\"phsu\" \"orch\"))))\n'((((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (11680792 10979973 10815921 9389713 9345054))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (9446752))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (10815921))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (1417708 \"NFKB1 gene\" (\"bacs\" \"aapp\" \"imft\" \"gngm\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (10979973))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (10200527 9389713))))\n\n;; The wrong way to do it! Notice that some of the edges include 'aapp' as their object type.\n(map\n (lambda (drug)\n (let ((e-drug/genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== e-drug/gene q)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n e-drug/genes))\n '((385728 \"CGP 57148\" (\"phsu\" \"orch\"))))\n'((((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (11680792 10979973 10815921 9389713 9345054))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (9446752))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n \"INHIBITS\"\n \"orch\"\n \"aapp\"\n (9389713))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n \"INHIBITS\"\n \"orch\"\n \"aapp\"\n (10979973))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (10815921))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n \"INHIBITS\"\n \"orch\"\n \"aapp\"\n (10979973))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (10200527 9389713))\n ((385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (1417708 \"NFKB1 gene\" (\"bacs\" \"aapp\" \"imft\" \"gngm\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (10979973))))\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n;; these entries seem very similar (based on alias and synonym information)\n;; If the user asks for 'imatinib' in a query, may want to look for all of these,\n;; and perhaps in most-specific to least-specific order.\n(935989 \"imatinib\" (\"phsu\" \"orch\"))\n(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n(385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n(906802 \"STI571\" (\"phsu\" \"orch\"))\n(935987 \"Gleevec\" (\"orch\" \"phsu\"))\n\n;; how many genes do each of the imatinib synonyms INHIBIT?\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (list (length genes) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((219 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (90 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (8 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (63 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (55 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n;; a few of the genes for some of the drugs are dups\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (list (length (rem-dups genes)) drug)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((206 (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (86 (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (8 (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (61 (906802 \"STI571\" (\"phsu\" \"orch\")))\n (52 (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n\n;; every drug other than \"CGP 57148\" INHIBITS both KIT and C-KIT\n(map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (let ((genes (rem-dups genes)))\n (list (length genes)\n (and (member '(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")) genes) #t)\n (and (member '(920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")) genes) #t)\n drug))))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n=>\n'((206 #t #t (935989 \"imatinib\" (\"phsu\" \"orch\")))\n (86 #t #t (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")))\n (8 #f #f (385728 \"CGP 57148\" (\"phsu\" \"orch\")))\n (61 #t #t (906802 \"STI571\" (\"phsu\" \"orch\")))\n (52 #t #t (935987 \"Gleevec\" (\"orch\" \"phsu\"))))\n\n\n;; 286 genes combined across all synonyms\n(let ((all-genes\n (map\n (lambda (drug)\n (let ((genes (run* (q)\n (fresh (gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n (rem-dups genes)))\n '((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))))))\n (length (apply union* all-genes)))\n=>\n286\n\n;; Genes inhibited by Gleevec\n;;\n;; Of the 52 results, at least a few appear to be classes of genes\n;; rather than specific genes:\n;;\n;; (3241 \"Antibodies\" (\"gngm\" \"aapp\" \"imft\"))\n;; (4891 \"Fusion Proteins, bcr-abl\" (\"aapp\" \"gngm\" \"bacs\"))\n;; (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n;; (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n;; (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n;; (79050 \"c-abl Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n;; (79413 \"Genes, abl\" (\"gngm\" \"aapp\"))\n;; (79427 \"Tumor Suppressor Genes\" (\"gngm\" \"aapp\"))\n;; (80298 \"v-src Oncogenes\" (\"gngm\" \"aapp\" \"enzy\" \"aapp\" \"gngm\" \"bacs\"))\n;; (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n;; (1136340 \"Semaphorins\" (\"bacs\" \"gngm\" \"aapp\"))\n;;\n;; Of course, is something like (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))\n;; even considered a gene class?\n;;\n;; Oh wow--I had missed the first one of the c-kit names before!\n;; So there are actually three synonyms, not two.\n;;\n;; (72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n;; (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n;; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;;\n;; So, of the 52 results, ~10 are actually categories rather\n;; than specific genes. Of the remaining ~40 specific genes, 3 of\n;; them are synonyms/aliases for KIT.\n(time (rem-dups\n (run* (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== '(935987 \"Gleevec\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))))))\n\n;; I think these two are *classes* of genes, not specific genes\n;;\n;; (31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n;; (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n;;\n;; notice there is no KIT or C-KIT\n(time (run* (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== gene q) \n (== '(385728 \"CGP 57148\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*)))))\n=>\n'((31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (33640 \"PROTEIN KINASE\" (\"gngm\" \"enzy\" \"aapp\"))\n (71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (164786 \"Proto-Oncogene Proteins c-akt\" (\"gngm\" \"aapp\" \"enzy\"))\n (915156 \"Ephrin Receptor EphA8\" (\"gngm\" \"enzy\" \"aapp\"))\n (812228 \"AKT1 gene\" (\"aapp\" \"phsu\" \"enzy\" \"gngm\" \"bacs\"))\n (1439337 \"tyrosine kinase ABL1\" (\"aapp\" \"gngm\" \"enzy\"))\n (1417708 \"NFKB1 gene\" (\"bacs\" \"aapp\" \"imft\" \"gngm\")))\n\n\n\n(time (run 1 (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest) \n (== e-drug/gene q) \n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*)))))\n\n\n\n;; https://pubchem.ncbi.nlm.nih.gov/compound/Imatinib_mesylate#section=Synonyms\n\n;; MeSH Entry Terms\n;;\n;; alpha-(4-methyl-1-piperazinyl)-3'-((4-(3-pyridyl)-2-pyrimidinyl)amino)-p-tolu-p-toluidide\n;; CGP 57148\n;; CGP-57148\n;; CGP57148\n;; CGP57148B\n;; Gleevec\n;; Glivec\n;; imatinib\n;; imatinib mesylate\n;; imatinib methanesulfonate\n;; Mesylate, Imatinib\n;; Methanesulfonate, Imatinib\n;; ST 1571\n;; ST1571\n;; STI 571\n;; STI-571\n;; STI571\n\n;; https://pubchem.ncbi.nlm.nih.gov/compound/5291#section=MeSH-Entry-Terms\n\n;; Depositor-Supplied Synonyms\n;;\n;; Imatinib\n;; 152459-95-5\n;; sti-571\n;; STI571\n;; Cgp 57148\n;; STI 571\n;; Imatinib [INN:BAN]\n;; N-(4-Methyl-3-((4-(pyridin-3-yl)pyrimidin-2-yl)amino)phenyl)-4-((4-methylpiperazin-1-yl)methyl)benzamide\n;; Imatinib free base\n;; UNII-BKJ8M8G5HI\n;; CCRIS 9076\n;; Imatinib (STI571)\n;; CHEMBL941\n;; 1iep\n;; 1xbb\n;; CGP-57148\n;; Imatinib (INN)\n;; Glamox (TN)\n;; CHEBI:45783\n;; CGP 57148B\n;; Imatinib Methansulfonate\n;; Kinome_3724\n;; Imatinib base(IMA-3)\n;; NSC743414\n;; STK617705\n;; BKJ8M8G5HI\n;; AC1L1K0Z\n;; BIDD:GT0047\n;; 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE\n\n;; https://pubchem.ncbi.nlm.nih.gov/compound/Imatinib_mesylate#section=Related-Records\n;;\n;; related compounds\n;;\n;; Same Connectivity \t3 records\n;; Same Parent, Connectivity \t115 records\n;; Same Parent, Exact \t89 records\n;; Mixtures, Components, and Neutralized Forms \t2 records\n;; Similar Compounds \t416 records\n\n> (time (pretty-print (run* (s) (fuzzy-concepto \"imatinib\" s))))\n'((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (1127612 \"imatinib 100 MG\" (\"clnd\"))\n (1329083 \"imatinib 100 MG Oral Tablet\" (\"clnd\"))\n (1331284 \"imatinib 400 MG\" (\"clnd\")))\ncpu time: 93 real time: 94 gc time: 1\n\n> (time (pretty-print (run* (s) (fuzzy-concepto \"Gleevec\" s))))\n'((935987 \"Gleevec\" (\"orch\" \"phsu\")))\ncpu time: 94 real time: 96 gc time: 0\n\n> (time (pretty-print (run* (s) (fuzzy-concepto \"CGP 57148\" s))))\n'((385728 \"CGP 57148\" (\"phsu\" \"orch\")))\ncpu time: 93 real time: 95 gc time: 0\n\n> (time (pretty-print (run* (s) (fuzzy-concepto \"57148\" s))))\n'((385728 \"CGP 57148\" (\"phsu\" \"orch\")))\ncpu time: 105 real time: 106 gc time: 1\n\n> (time (pretty-print (run* (s) (fuzzy-concepto \"1571\" s))))\n'((760931 \"LY 315712\" (\"phsu\"))\n (964110 \"UK 157147\" (\"orch\"))\n (1097576 \"ST 1571\" (\"orch\" \"phsu\"))\n (1175579 \"GPI 15715\" (\"orch\")))\ncpu time: 109 real time: 112 gc time: 1\n\n\n\n\n;; playing with ISA\n;; ??? ISA Protein-tyrosine kinase inhibitor\n;;\n;; cpu time: 4 real time: 10 gc time: 0\n'((13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (13982 \"Emodin\" (\"orch\" \"bacs\" \"phsu\"))\n (53622 \"biochanin A\" (\"phsu\" \"orch\"))\n (57090 \"daidzein\" (\"orch\" \"vita\"))\n (61202 \"Genistein\" (\"phsu\" \"orch\" \"bacs\"))\n (61202 \"Genistein\" (\"phsu\" \"orch\" \"bacs\"))\n (61202 \"Genistein\" (\"phsu\" \"orch\" \"bacs\"))\n (64695 \"lavendustin A\" (\"phsu\" \"orch\"))\n (83406 \"methyl 2,5-dihydroxycinnamate\" (\"orch\" \"phsu\"))\n (207800 \"monorden\" (\"phsu\" \"orch\"))\n (212399 \"damnacanthal\" (\"phsu\" \"orch\"))\n (213654 \"tyrphostin 25\" (\"orch\" \"phsu\"))\n (213997 \"lavendustin C6\" (\"orch\" \"phsu\"))\n (253468 \"tyrphostin A46\" (\"orch\" \"phsu\"))\n (258114 \"PD 153035\" (\"phsu\" \"orch\"))\n (295108 \"lavendustin B\" (\"phsu\" \"orch\"))\n (381676 \"tyrphostin B46\" (\"orch\" \"phsu\"))\n (384553 \"tyrphostin A47\" (\"phsu\" \"orch\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (528985 \"tyrphostin AG 1478\" (\"orch\" \"phsu\"))\n (538431 \"SU 5402\" (\"phsu\" \"orch\"))\n (539578 \"tyrphostin AG 1296\" (\"orch\" \"phsu\"))\n (638102 \"tyrphostin A23\" (\"orch\" \"phsu\"))\n (663164 \"tyrphostin B42\" (\"phsu\"))\n (758539 \"tyrphostin A51\" (\"orch\" \"phsu\"))\n (879396 \"ZD1839\" (\"orch\" \"phsu\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (912413 \"PTK 787\" (\"phsu\" \"orch\"))\n (913199 \"tyrphostin A9\" (\"orch\" \"phsu\"))\n (919281 \"Iressa\" (\"orch\" \"phsu\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))\n (935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (1122962 \"gefitinib\" (\"phsu\" \"orch\"))\n (1135135 \"erlotinib\" (\"phsu\" \"orch\"))\n (1135136 \"Tarceva\" (\"orch\" \"phsu\"))\n (1135137 \"OSI-774\" (\"orch\" \"phsu\"))\n (1176007 \"3,3',4,5'-tetrahydroxystilbene\" (\"orch\" \"phsu\"))\n (1176021 \"SU 11248\" (\"orch\" \"phsu\"))\n (1412731 \"BAG3 gene\" (\"gngm\" \"enzy\" \"aapp\"))\n (1511179 \"Bis-Tyrphostin\" (\"aapp\"))\n (1519728\n \"2-amino-4-(4'-hydroxyphenyl)-1,1,3-tricyanobuta-1,3-diene\"\n (\"aapp\"))\n (1533491 \"Erlotinib Hydrochloride\" (\"phsu\" \"orch\"))\n (1570599 \"AG 112\" (\"orch\")))\n(time\n (run* (q)\n (fresh (drug what-is-it e-drug/what st-drug/what ot-drug/what e-drug/what-rest) \n (== drug q)\n (== '(1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\")) what-is-it)\n (== `(,drug ,what-is-it \"ISA\" ,st-drug/what ,ot-drug/what . ,e-drug/what-rest) e-drug/what)\n (edgeo e-drug/what))))\n\n;; playing with ISA\n;; Gleevec ISA ???\n;;\n;; These answers seem mostly reasonable.\n;; Of course there is more structure/a richer relationship between these answers than may be apparent. Different levels of hierarchy.\n'((3392 \"Antineoplastic Agents\" (\"phsu\"))\n (13216 \"Pharmacotherapy\" (\"topp\"))\n (13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (87111 \"Therapeutic procedure\" (\"topp\"))\n (243076 \"antagonists\" (\"chvf\"))\n (920425 \"Cancer Treatment\" (\"topp\"))\n (935989 \"imatinib\" (\"phsu\" \"orch\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (1254351 \"Pharmacologic Substance\" (\"phsu\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\"))\n (1449702 \"Protein Kinase Inhibitors\" (\"phsu\"))\n (1611640 \"Therapeutic agent (substance)\" (\"phsu\")))\n(time\n (run* (q)\n (fresh (drug what-is-it e-drug/what st-drug/what ot-drug/what e-drug/what-rest) \n (== what-is-it q)\n (== '(935987 \"Gleevec\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,what-is-it \"ISA\" ,st-drug/what ,ot-drug/what . ,e-drug/what-rest) e-drug/what)\n (edgeo e-drug/what))))\n\n;; playing with ISA\n;; ??? ISA Gleevec\n;;\n;; once again, this seems backwards.\n;; 'Protein-tyrosine kinase inhibitor ISA Gleevec' seems backwards.\n'((13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\")))\n(time\n (run* (q)\n (fresh (what-is-it drug e-what/drug st-what/drug ot-what/drug e-what/drug-rest) \n (== what-is-it q)\n (== '(935987 \"Gleevec\" (\"orch\" \"phsu\")) drug)\n (== `(,what-is-it ,drug \"ISA\" ,st-what/drug ,ot-what/drug . ,e-what/drug-rest) e-what/drug)\n (edgeo e-what/drug))))\n\n;; playing with ISA\n;; ??? ISA Imatinib mesylate\n;;\n;; Gleevec, CGP 57148, and STI571 are okay.\n;; imatinib is marginal, at best.\n;; The others are either backwards (Protein-tyrosine kinase inhibitor) or\n;; non-sensical (Operative Surgical Procedures).\n'((13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (87111 \"Therapeutic procedure\" (\"topp\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (543467 \"Operative Surgical Procedures\" (\"topp\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))\n (935989 \"imatinib\" (\"phsu\" \"orch\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\")))\n(time\n (run* (q)\n (fresh (what-is-it drug e-what/drug st-what/drug ot-what/drug e-what/drug-rest) \n (== what-is-it q)\n (== '(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")) drug)\n (== `(,what-is-it ,drug \"ISA\" ,st-what/drug ,ot-what/drug . ,e-what/drug-rest) e-what/drug)\n (edgeo e-what/drug))))\n\n;; playing with ISA\n;; ??? ISA imatinib\n;;\n;; Gleevec makes sense (brand name), and probably Imatinib mesylate.\n;; STI571 is okay, probably. http://chemocare.com/chemotherapy/drug-info/STI-571.aspx\n;; And CGP 57148. https://www.biovision.com/imatinib-mesylate-cgp-57148b-sti-571.html\n;;\n;; The others seem...less good. 'Therapeutic procedure ISA imatinib' seems non-sensical.\n;; 'Protein-tyrosine kinase inhibitor ISA imatinib' seems backwards.\n'((3392 \"Antineoplastic Agents\" (\"phsu\"))\n (13216 \"Pharmacotherapy\" (\"topp\"))\n (13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (87111 \"Therapeutic procedure\" (\"topp\"))\n (385728 \"CGP 57148\" (\"phsu\" \"orch\"))\n (543467 \"Operative Surgical Procedures\" (\"topp\"))\n (906802 \"STI571\" (\"phsu\" \"orch\"))\n (935987 \"Gleevec\" (\"orch\" \"phsu\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\")))\n(time\n (run* (q)\n (fresh (what-is-it drug e-what/drug st-what/drug ot-what/drug e-what/drug-rest) \n (== what-is-it q)\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,what-is-it ,drug \"ISA\" ,st-what/drug ,ot-what/drug . ,e-what/drug-rest) e-what/drug)\n (edgeo e-what/drug))))\n\n;; playing with ISA\n;; imatinib ISA ???\n'((3392 \"Antineoplastic Agents\" (\"phsu\"))\n (13216 \"Pharmacotherapy\" (\"topp\"))\n (13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (13227 \"Pharmaceutical Preparations\" (\"phsu\"))\n (39796 \"The science and art of healing\" (\"topp\"))\n (87111 \"Therapeutic procedure\" (\"topp\"))\n (87111 \"Therapeutic procedure\" (\"topp\"))\n (243076 \"antagonists\" (\"chvf\"))\n (418981 \"Medical therapy\" (\"topp\"))\n (543467 \"Operative Surgical Procedures\" (\"topp\"))\n (679607 \"treatment method\" (\"topp\"))\n (920425 \"Cancer Treatment\" (\"topp\"))\n (935451 \"neoplasm/cancer chemotherapy\" (\"topp\"))\n (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (1254351 \"Pharmacologic Substance\" (\"phsu\"))\n (1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\"))\n (1372955 \"Active Ingredients\" (\"phsu\"))\n (1449702 \"Protein Kinase Inhibitors\" (\"phsu\"))\n (1519313 \"Signal Transduction Inhibitor\" (\"phsu\"))\n (1533685 \"Injection procedure\" (\"topp\"))\n (1579409 \"Molecular Target Inhibitors\" (\"phsu\"))\n (1611640 \"Therapeutic agent (substance)\" (\"phsu\")))\n(time\n (run* (q)\n (fresh (drug what-is-it e-drug/what st-drug/what ot-drug/what e-drug/what-rest) \n (== what-is-it q)\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,what-is-it \"ISA\" ,st-drug/what ,ot-drug/what . ,e-drug/what-rest) e-drug/what)\n (edgeo e-drug/what))))\n\n\n\n\n;; let's test the individual parts of the query\n\n;; compare\n;;\n;; (32 (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\")))\n;;\n;; and\n;;\n;; (35 (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\")))\n;;\n;; which cause 32 and 35 diseases, respectively, with these monstrosities:\n;;\n;; (291 (597357 \"receptor\" (\"aapp\" \"gngm\" \"rcpt\")))\n;; (296 (1823619 \"VEGFA gene\" (\"bacs\" \"phsu\" \"rcpt\" \"gngm\" \"imft\" \"enzy\" \"aapp\")))\n;; (418 (1456820 \"Tumor Necrosis Factor-alpha\" (\"imft\" \"gngm\" \"aapp\")))\n;; (506 (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\")))\n;; (579 (79189 \"cytokine\" (\"aapp\" \"imft\" \"gngm\")))\n;; (1171 (17337 \"Genes\" (\"aapp\" \"gngm\"))))\n;;\n;; Could either just drop entries like (1171 (17337 \"Genes\" (\"aapp\" \"gngm\")))\n;; and (506 (33684 \"Proteins\" (\"bacs\" \"gngm\" \"aapp\"))), or prioritize search\n;; to start with smallest number of diseases (or both).\n;;\n;; Also, should make sure to remove duplicate diseases in the results!\n;; And remove ridiculous entries like (12634 \"Disease\" (\"dsyn\"))\n;;\n;; Also, should take the union of diseases caused by C-KIT and KIT,\n;; rather than trying them both separately (and getting duplicate\n;; answers).\n;;\n;; Should also consider taking the union of all diseases produced by\n;; all genes, to avoid duplicate work, or do caching/memoization/tabling.\n;;\n(let ((genes-inhibited-by-imatinib\n (run* (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== gene q)\n\n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (edgeo e-drug/gene)\n\n ))))\n (let ((genes-inhibited-by-imatinib (rem-dups genes-inhibited-by-imatinib)))\n (sort\n (map (lambda (gene)\n (let ((num-diseases-caused-by-gene\n (length\n (run* (q)\n (fresh (drug known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== e-gene/known-disease q)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease \"CAUSES\" ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease))))))\n (list num-diseases-caused-by-gene gene)))\n genes-inhibited-by-imatinib)\n (lambda (l1 l2) (< (car l1) (car l2))))))\n\n;; how many genes are inhibited by imatinib?\n;;\n;; cpu time: 10 real time: 10 gc time: 0\n;; 213 genes inhibited by imatinib\n;;\n;; some of these genes are dups! why?\n;; 206 unique genes\n;;\n;; one of these answers is (17337 \"Genes\" (\"aapp\" \"gngm\")), as opposed to a specific gene--does this result in a degenerate blowup? This seems fishy!!\n(time\n (length\n (run* (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== gene q)\n\n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (edgeo e-drug/gene)\n\n ))))\n\n;; how many diseases is imatinib known to treat (directly)?\n;;\n;; cpu time: 11 real time: 11 gc time: 0\n;; 349 diseases that imatinib is known to treat\n;;\n;; hmmm--list contains dups! why is that?\n;;\n;; only 277 of the diseases are unique--the rest are dups\n;;\n;; also, once again we see general categories of diseases--do they result in degenerate blowup?\n;;\n;; (3047 \"Animal Diseases\" (\"dsyn\"))\n;; (8679 \"Chronic Disease\" (\"dsyn\"))\n;; (12634 \"Disease\" (\"dsyn\"))\n;; (12634 \"Disease\" (\"dsyn\"))\n;; (920627 \"Orphan Diseases\" (\"dsyn\"))\n;;\n;; many of these diseases seen overlapping, or members of another class of disease\n;;\n;; (598934 \"tumor growth\" (\"neop\"))\n;; (877373 \"Advanced cancer\" (\"neop\"))\n;;\n;; (1266119 \"Solitary fibrous tumor\" (\"neop\"))\n;; (1266120 \"Solitary fibrous tumor, malignant\" (\"neop\"))\n;;\n;; (6118 \"Brain Neoplasms\" (\"neop\"))\n;; (17636 \"Glioblastoma\" (\"neop\"))\n;;\n;; (17638 \"Glioma\" (\"neop\"))\n;; (555198 \"Malignant Glioma\" (\"neop\"))\n;; (677865 \"Brain stem glioma\" (\"neop\"))\n;; (1319185 \"Chiasmal glioma\" (\"neop\"))\n;;\n;;\n;; wut!?\n;; (1524028 \"Intraepithelial Neoplasia of the Mouse Mammary Gland\" (\"neop\"))\n;;\n;; I'm pretty sure we don't want animal diseases, unless humans are considered animals!\n(time\n (length\n (run* (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease st-drug/known-disease ot-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== known-disease q)\n \n ;; imatinib\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n \n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease \"TREATS\" ,st-drug/known-disease ,ot-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n\n (conde\n [(== \"dsyn\" ot-drug/known-disease)]\n [(== \"neop\" ot-drug/known-disease)])\n \n (edgeo e-drug/known-disease) \n\n ))))\n\n;; let's look at the duplicate entries for (12634 \"Disease\" (\"dsyn\")), treated by imatinib\n;;\n;; That seems a bit unfortunate! imatinib is considered 'orch'\n;; (Organic Chemical) in one entry, and 'phsu' (Pharmacologic\n;; Substance) in the other.\n;;\n;; (((935989 \"imatinib\" (\"phsu\" \"orch\"))\n;; (12634 \"Disease\" (\"dsyn\"))\n;; \"TREATS\"\n;; \"orch\"\n;; \"dsyn\"\n;; (86095345 67097950 63793027))\n;;\n;; ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n;; (12634 \"Disease\" (\"dsyn\"))\n;; \"TREATS\"\n;; \"phsu\"\n;; \"dsyn\"\n;; (89407082 ... 41787008)))\n;;\n(run* (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease st-drug/known-disease ot-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== e-drug/known-disease q)\n \n ;; imatinib\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n \n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease \"TREATS\" ,st-drug/known-disease ,ot-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n\n (== '(12634 \"Disease\" (\"dsyn\")) known-disease)\n \n (conde\n [(== \"dsyn\" ot-drug/known-disease)]\n [(== \"neop\" ot-drug/known-disease)])\n \n (edgeo e-drug/known-disease) \n\n ))\n\n;; more minor cleanup/inlining\n;;\n;; same speed, as expected\n;; cpu time: 17898 real time: 17893 gc time: 462\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease \"CAUSES\" ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease \"TREATS\" . ,e-drug/known-disease-rest) e-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease ,st-something/unknown-disease ,ot-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n (conde\n [(== \"dsyn\" ot-something/unknown-disease)]\n [(== \"neop\" ot-something/unknown-disease)])\n \n (edgeo e-something/unknown-disease)\n \n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; replace\n;;\n;; (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n;; (== \"INHIBITS\" p-drug/gene)\n;;\n;; with\n;;\n;; (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n;;\n;; same time, as expected\n;; cpu time: 17960 real time: 17956 gc time: 431\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene \"INHIBITS\" ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease ,st-something/unknown-disease ,ot-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n (conde\n [(== \"dsyn\" ot-something/unknown-disease)]\n [(== \"neop\" ot-something/unknown-disease)])\n \n (edgeo e-something/unknown-disease)\n \n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; replace (fuzzy-concepto \"imatinib\" drug) with (935989 \"imatinib\" (\"phsu\" \"orch\"))\n;;\n;; a bit faster\n;; cpu time: 17844 real time: 17840 gc time: 297\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease ,st-something/unknown-disease ,ot-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n (conde\n [(== \"dsyn\" ot-something/unknown-disease)]\n [(== \"neop\" ot-something/unknown-disease)])\n \n (edgeo e-something/unknown-disease)\n \n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; replaced\n;;\n;; (fresh (cui name concept-type*)\n;; (== `(,cui ,name ,concept-type*) unknown-disease)\n;; (conde\n;; [(membero \"dsyn\" concept-type*)]\n;; [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n;;\n;; with\n;;\n;; (conde\n;; [(== \"dsyn\" ot-something/unknown-disease)]\n;; [(== \"neop\" ot-something/unknown-disease)])\n;;\n;; faster!\n;; cpu time: 19553 real time: 19547 gc time: 507\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease ,st-something/unknown-disease ,ot-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n (conde\n [(== \"dsyn\" ot-something/unknown-disease)]\n [(== \"neop\" ot-something/unknown-disease)])\n \n (edgeo e-something/unknown-disease)\n \n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; pushed down conde slightly\n;;\n;; same time\n;; cpu time: 23358 real time: 23358 gc time: 1408\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n \n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; moved disequality constraints before conde\n;;\n;; same speed\n;; cpu time: 23023 real time: 23015 gc time: 1251\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n \n (edgeo e-gene/something)\n \n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; removed\n;;\n;; (fresh (cui name concept-type*)\n;; (== `(,cui ,name ,concept-type*) something)\n;; (not-membero \"dsyn\" concept-type*)\n;; (not-membero \"neop\" concept-type*))\n;;\n;; no slower, but no faster\n;; cpu time: 23124 real time: 23118 gc time: 1233\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n \n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; added\n;;\n;; (=/= \"dsyn\" ot-gene/something)\n;; (=/= \"neop\" ot-gene/something)\n;;\n;; same time\n;; cpu time: 23524 real time: 23522 gc time: 1462\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n (=/= \"dsyn\" ot-gene/something)\n (=/= \"neop\" ot-gene/something)\n \n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; baby step!\n;;\n;; added st-gene/something ot-gene/something\n;;\n;; time is the same\n;; cpu time: 23438 real time: 23430 gc time: 1282\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n\n;; replaced\n;;\n;; (fresh (cui name concept-type*)\n;; (== `(,cui ,name ,concept-type*) known-disease)\n;; (conde\n;; [(membero \"dsyn\" concept-type*)]\n;; [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n;;\n;; with\n;;\n;; (conde\n;; [(== \"dsyn\" ot-gene/known-disease)]\n;; [(== \"neop\" ot-gene/known-disease)])\n;;\n;; slight speedup\n;; cpu time: 23177 real time: 23178 gc time: 1245\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n\n;; replaced\n;;\n;; (fresh (cui name concept-type*)\n;; (== `(,cui ,name ,concept-type*) gene)\n;; (membero \"gngm\" concept-type*))\n;;\n;; (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n;;\n;; no faster!\n;;\n;; cpu time: 26518 real time: 26509 gc time: 1552\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; original\n;; cpu time: 26492 real time: 26486 gc time: 1671\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n\n\n\n\n\n\n\n\n\n\n\n;;; messed up somehow...\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene st-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease st-gene/known-disease ot-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something st-gene/something ot-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease st-something/unknown-disease ot-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene ,st-drug/gene \"gngm\" . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease ,st-gene/known-disease ,ot-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (conde\n [(== \"dsyn\" ot-gene/known-disease)]\n [(== \"neop\" ot-gene/known-disease)])\n (edgeo e-gene/known-disease)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something ,st-gene/something ,ot-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease ,st-something/unknown-disease ,ot-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n\n ;; (=/= \"dsyn\" ot-gene/something)\n ;; (=/= \"neop\" ot-gene/something)\n\n ;; (=/= \"dsyn\" st-something/unknown-disease)\n ;; (=/= \"neop\" st-something/unknown-disease)\n\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n \n (edgeo e-gene/something)\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n\n ;; ** cheat **\n (fuzzy-concepto \"KIT gene\" gene)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; generate and test!!\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n )))\n\n;; =>\n;;\n;; cpu time: 26928 real time: 27177 gc time: 1541\n;; '((((935989 \"imatinib\" (\"phsu\" \"orch\"))\n;; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; \"INHIBITS\"\n;; \"orch\"\n;; \"gngm\"\n;; (88094027\n;; 82038640\n;; 78690628\n;; 78513788\n;; 70397515\n;; 60608992\n;; 57775955\n;; 56779144\n;; 55866397\n;; 55866394\n;; 54750176\n;; 54602555\n;; 54524739\n;; 53954674\n;; 53827456\n;; 53794226\n;; 53155624\n;; 51843305\n;; 51685933\n;; 50494576\n;; 50287491\n;; 50287227\n;; 49443008\n;; 48324562\n;; 47259531\n;; 45719202\n;; 44323647\n;; 44187569\n;; 43969275\n;; 40811261\n;; 40130263\n;; 35363677\n;; 35363677))\n;; ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;; \"CAUSES\"\n;; \"aapp\"\n;; \"neop\"\n;; (59625558 59480455 43196727 40249098))\n;; ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n;; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;; \"TREATS\"\n;; \"orch\"\n;; \"neop\"\n;; (89468570\n;; 89468569\n;; 89468568\n;; 89258086\n;; 89258085\n;; 89205362\n;; 88927657\n;; 88924013\n;; 88642836\n;; 88557822\n;; 88416696\n;; 88236035\n;; 87703148\n;; 87639342\n;; 87563133\n;; 87355756\n;; 87277832\n;; 87259474\n;; 87190645\n;; 87155663\n;; 86726495\n;; 86726307\n;; 86567237\n;; 86229065\n;; 86172855\n;; 86172792\n;; 86131660\n;; 86095366\n;; 86035145\n;; 86029120\n;; 85975403\n;; 85946745\n;; 85712439\n;; 85533589\n;; 85460959\n;; 85258429\n;; 85258243\n;; 85102393\n;; 84799502\n;; 84760780\n;; 84600823\n;; 84489940\n;; 84455598\n;; 84282070\n;; 84199399\n;; 84031770\n;; 83839275\n;; 83526901\n;; 83164056\n;; 82850336\n;; 82797211\n;; 82613490\n;; 82405375\n;; 82317721\n;; 82174866\n;; 81986594\n;; 81966494\n;; 81868093\n;; 81836303\n;; 81836299\n;; 81821592\n;; 81821568\n;; 81779900\n;; 81749438\n;; 81749298\n;; 81693422\n;; 81660653\n;; 81532546\n;; 81446896\n;; 81292173\n;; 81292146\n;; 81187916\n;; 81096155\n;; 81085475\n;; 80369749\n;; 80098508\n;; 80091451\n;; 80030026\n;; 80007514\n;; 80007503\n;; 80007484\n;; 79704637\n;; 78892177\n;; 78600687\n;; 78533753\n;; 78245623\n;; 78014091\n;; 77943557\n;; 77943438\n;; 77510203\n;; 76776701\n;; 76743653\n;; 76743620\n;; 76462669\n;; 76289046\n;; 76148449\n;; 76070843\n;; 76070756\n;; 75933563\n;; 75933518\n;; 75933507\n;; 75779308\n;; 75779235\n;; 75722646\n;; 75678381\n;; 75574053\n;; 75393814\n;; 75385321\n;; 75385290\n;; 75335029\n;; 74891979\n;; 74719196\n;; 74658329\n;; 74658173\n;; 74617628\n;; 74612683\n;; 74510446\n;; 74436697\n;; 74324960\n;; 74324751\n;; 73941360\n;; 73846632\n;; 73821917\n;; 73790920\n;; 73636829\n;; 73619092\n;; 73604638\n;; 73358651\n;; 73358394\n;; 73338468\n;; 73192059\n;; 72992017\n;; 72991953\n;; 72925441\n;; 72925432\n;; 72387590\n;; 72235834\n;; 72163957\n;; 72163916\n;; 72152875\n;; 72006640\n;; 71966871\n;; 71819909\n;; 71747166\n;; 71634856\n;; 71548303\n;; 71548302\n;; 71458205\n;; 71302542\n;; 71290202\n;; 71193021\n;; 71178655\n;; 71047643\n;; 70800725\n;; 70795678\n;; 70677512\n;; 70592280\n;; 70531661\n;; 70516256\n;; 70480367\n;; 70407945\n;; 70392775\n;; 70218140\n;; 70065532\n;; 70064632\n;; 70064228\n;; 69980656\n;; 69922277\n;; 69798593\n;; 69628693\n;; 69574355\n;; 69574200\n;; 69326210\n;; 69173266\n;; 69143520\n;; 69073207\n;; 68990202\n;; 68961183\n;; 68805644\n;; 68756725\n;; 68695975\n;; 68641330\n;; 68543097\n;; 68490316\n;; 68490176\n;; 68451659\n;; 68428455\n;; 68428435\n;; 68128844\n;; 67447723\n;; 67447408\n;; 67447259\n;; 67420026\n;; 67420012\n;; 67395342\n;; 67377234\n;; 67353857\n;; 67224404\n;; 67097947\n;; 67020602\n;; 67020578\n;; 66947994\n;; 66947973\n;; 66919135\n;; 66907557\n;; 66794112\n;; 66717719\n;; 66717457\n;; 66700212\n;; 66658747\n;; 66548225\n;; 66498273\n;; 66492422\n;; 66464075\n;; 66437854\n;; 66316788\n;; 66259767\n;; 66030713\n;; 66030305\n;; 66030298\n;; 65997826\n;; 65895363\n;; 65895259\n;; 65895230\n;; 65847488\n;; 65628134\n;; 65617569\n;; 65512937\n;; 65498233\n;; 65154906\n;; 64925006\n;; 64924970\n;; 64812649\n;; 64812611\n;; 64812607\n;; 64752721\n;; 64721564\n;; 64711818\n;; 64711731\n;; 64656080\n;; 64624730\n;; 64622704\n;; 64156886\n;; 63841948\n;; 63817256\n;; 63816481\n;; 63816454\n;; 63683436\n;; 63571342\n;; 63405183\n;; 63405085\n;; 63381482\n;; 63331732\n;; 63324444\n;; 63319121\n;; 63318913\n;; 63316021\n;; 63315694\n;; 63185401\n;; 63070375\n;; 63054852\n;; 62989453\n;; 62973318\n;; 62841282\n;; 62830344\n;; 62785280\n;; 62784978\n;; 62784892\n;; 62784888\n;; 62784843\n;; 62784801\n;; 62462377\n;; 62428126\n;; 62426332\n;; 62378768\n;; 62378584\n;; 62330072\n;; 62324461\n;; 61797261\n;; 61735158\n;; 61548783\n;; 61207268\n;; 61202221\n;; 60969371\n;; 60969364\n;; 60866909\n;; 60850115\n;; 60662946\n;; 60621352\n;; 60621253\n;; 60551995\n;; 60440052\n;; 60428943\n;; 60428934\n;; 60428660\n;; 60393093\n;; 60392934\n;; 60211135\n;; 60205838\n;; 60062650\n;; 59973854\n;; 59954856\n;; 59807933\n;; 59797232\n;; 59683223\n;; 59554449\n;; 59554240\n;; 59553994\n;; 59553949\n;; 59234656\n;; 59060757\n;; 58957292\n;; 58911796\n;; 58800894\n;; 58782655\n;; 58759216\n;; 58758787\n;; 58758746\n;; 58650526\n;; 58547505\n;; 58547365\n;; 58489364\n;; 58489286\n;; 58489283\n;; 58489063\n;; 58488102\n;; 58370475\n;; 58082575\n;; 58036800\n;; 57952675\n;; 57925861\n;; 57528381\n;; 57461748\n;; 57396831\n;; 57173003\n;; 56779264\n;; 56779187\n;; 56736216\n;; 56675689\n;; 56644042\n;; 56635283\n;; 56581542\n;; 56521000\n;; 56516740\n;; 56305864\n;; 56246713\n;; 55788664\n;; 55669371\n;; 55504860\n;; 55461710\n;; 55144263\n;; 54972005\n;; 54899752\n;; 54750165\n;; 54655723\n;; 54637785\n;; 54185481\n;; 54167702\n;; 54131652\n;; 54065003\n;; 54064819\n;; 54063323\n;; 54033257\n;; 53990272\n;; 53844942\n;; 53790979\n;; 53789312\n;; 53781555\n;; 53770969\n;; 53756949\n;; 53514462\n;; 53485394\n;; 53408441\n;; 53348483\n;; 53324991\n;; 53090376\n;; 53035552\n;; 52986131\n;; 52774289\n;; 52626484\n;; 52626456\n;; 52401003\n;; 52400997\n;; 52384984\n;; 52383401\n;; 52145581\n;; 52080520\n;; 52080500\n;; 51966571\n;; 51966533\n;; 51940444\n;; 51843289\n;; 51785870\n;; 51517762\n;; 51429637\n;; 51233058\n;; 50980581\n;; 50980537\n;; 50965433\n;; 50781404\n;; 50721080\n;; 50508999\n;; 50503416\n;; 50494443\n;; 50443602\n;; 50428979\n;; 50221877\n;; 50221071\n;; 50146289\n;; 49793801\n;; 49662175\n;; 49459434\n;; 49235490\n;; 49234707\n;; 49217344\n;; 49217224\n;; 49188407\n;; 48984520\n;; 48956187\n;; 48740985\n;; 48710539\n;; 48710399\n;; 48658118\n;; 48629524\n;; 48629262\n;; 48629096\n;; 48456328\n;; 48420003\n;; 48222031\n;; 48189351\n;; 48111387\n;; 48019056\n;; 47581439\n;; 47261164\n;; 47241719\n;; 47241687\n;; 47038924\n;; 46851427\n;; 46841532\n;; 46821633\n;; 46603672\n;; 46590734\n;; 46440408\n;; 46423016\n;; 46090733\n;; 46075210\n;; 45928498\n;; 45928268\n;; 45878480\n;; 45605920\n;; 45412106\n;; 45295271\n;; 45253578\n;; 45182073\n;; 45147147\n;; 45071160\n;; 44966652\n;; 44860680\n;; 44776669\n;; 44760794\n;; 44677169\n;; 44310963\n;; 44045613\n;; 44045160\n;; 44013797\n;; 44013731\n;; 44013557\n;; 44005189\n;; 43500401\n;; 43500051\n;; 43499908\n;; 43467372\n;; 43412654\n;; 43255365\n;; 43254694\n;; 43254568\n;; 43065434\n;; 43064602\n;; 42945181\n;; 42944957\n;; 42932034\n;; 42866660\n;; 42860840\n;; 42860208\n;; 42859293\n;; 42797774\n;; 42621694\n;; 42598154\n;; 42593639\n;; 42592914\n;; 42483339\n;; 42475709\n;; 42473986\n;; 41934602\n;; 41934289\n;; 41934141\n;; 41824732\n;; 41823994\n;; 41823990\n;; 41823884\n;; 41823658\n;; 41770028\n;; 41719972\n;; 41636739\n;; 41636678\n;; 41474558\n;; 41474110\n;; 41417515\n;; 41357545\n;; 41047174\n;; 41047053\n;; 40913879\n;; 40913586\n;; 40882088\n;; 40879546\n;; 40810835\n;; 40670230\n;; 40628283\n;; 40618412\n;; 40508813\n;; 40264027\n;; 40263635\n;; 40263369\n;; 40248842\n;; 40213767\n;; 40159841\n;; 39984065\n;; 39953257\n;; 39841942\n;; 39833972\n;; 39787674\n;; 39649770\n;; 38920751\n;; 38459993\n;; 37901924\n;; 36961724\n;; 36754535\n;; 36753213\n;; 36012874\n;; 35363283\n;; 35363160\n;; 35129115\n;; 34362294\n;; 33891695\n;; 33891545\n;; 33891150\n;; 31900490\n;; 29766172\n;; 26570601\n;; 26548765))\n;; ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; (1155074 \"mast cell activation\" (\"celf\"))\n;; \"CAUSES\"\n;; \"gngm\"\n;; \"celf\"\n;; (36804978))\n;; ((1155074 \"mast cell activation\" (\"celf\"))\n;; (4096 \"Asthma\" (\"dsyn\"))\n;; \"AFFECTS\"\n;; \"celf\"\n;; \"dsyn\"\n;; (54247735 38643255))))\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n(run* (possible-treatment)\n (fresh (drug gene disease1 disease2)\n (fuzzy-match \"imatinib\" drug)\n (inhibits-gene drug gene)\n (causes-disease gene disease1 mechanism1)\n (treats-disease drug disease1)\n (causes-disease gene disease2 mechanism2)\n (unknown-if-treats-disease drug disease2)\n (== (list drug gene mechanism2 disease2) possible-treatment)))\n\n\n\n\n(run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n ))\n\n\n\n\n\n\n\n\n\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n \n ;; imatinib \n (== '(935989 \"imatinib\" (\"phsu\" \"orch\")) drug)\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n\n ;; imatinib inhibits some gene\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n\n (== \"AFFECTS\" p-something/unknown-disease)\n \n ;(conde\n ; [(== \"AFFECTS\" p-something/unknown-disease)]\n ; [(== \"CAUSES\" p-something/unknown-disease)])\n \n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n\n ;; generate and test!!\n (fuzzy-concepto \"KIT gene\" gene)\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n \n )))\n\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n\n ;; generate and test!!, cheating (move down for realz)\n (fuzzy-concepto \"KIT gene\" gene)\n ;; (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n ;; (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n \n )))\n\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n\n ;; generate and test!!, cheating (move down for realz)\n (fuzzy-concepto \"KIT gene\" gene)\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n \n )))\n\n(time (run 1 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n\n ;; generate and test!!, cheating (move down for realz)\n (fuzzy-concepto \"KIT gene\" gene)\n (fuzzy-concepto \"Gastrointestinal Stromal Tumors\" known-disease)\n (fuzzy-concepto \"mast cell activation\" something)\n (fuzzy-concepto \"asthma\" unknown-disease)\n\n \n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n \n )))\n\n(time (length (run 100 (q)\n (fresh (drug gene known-disease something unknown-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest\n e-gene/something p-gene/something e-gene/something-rest\n e-something/unknown-disease p-something/unknown-disease e-something/unknown-disease-rest)\n\n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease ,e-gene/something ,e-something/unknown-disease) q)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene indirectly causes & indirectly affects some other disease\n (== `(,gene ,something ,p-gene/something . ,e-gene/something-rest) e-gene/something)\n (== `(,something ,unknown-disease ,p-something/unknown-disease . ,e-something/unknown-disease-rest) e-something/unknown-disease)\n (== \"CAUSES\" p-gene/something)\n (conde\n [(== \"AFFECTS\" p-something/unknown-disease)]\n [(== \"CAUSES\" p-something/unknown-disease)])\n (edgeo e-gene/something)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) something)\n (not-membero \"dsyn\" concept-type*)\n (not-membero \"neop\" concept-type*))\n\n (edgeo e-something/unknown-disease)\n \n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) unknown-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(not-membero \"dsyn\" concept-type*) (membero \"neop\" concept-type*)]))\n \n ))))\n\n; cpu time: 31325 real time: 31336 gc time: 490\n; 6518\n(time (length (run* (q)\n (fresh (drug gene known-disease\n e-drug/gene p-drug/gene e-drug/gene-rest\n e-gene/known-disease p-gene/known-disease e-gene/known-disease-rest\n e-drug/known-disease p-drug/known-disease e-drug/known-disease-rest)\n\n (== `(,e-drug/gene ,e-gene/known-disease ,e-drug/known-disease) q)\n \n ;; imatinib inhibits some gene\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene)\n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n\n ;; that gene directly causes some disease...\n (== `(,gene ,known-disease ,p-gene/known-disease . ,e-gene/known-disease-rest) e-gene/known-disease)\n (== \"CAUSES\" p-gene/known-disease)\n (edgeo e-gene/known-disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) known-disease)\n (conde\n [(membero \"dsyn\" concept-type*)]\n [(membero \"neop\" concept-type*)]))\n\n ;; ...which imatinib is known to treat\n (== `(,drug ,known-disease ,p-drug/known-disease . ,e-drug/known-disease-rest) e-drug/known-disease)\n (== \"TREATS\" p-drug/known-disease)\n (edgeo e-drug/known-disease) \n \n ;; and that gene directly or indirectly causes&affects some other disease\n \n \n ))))\n\n(time (length (run* (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest)\n (== '(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene) \n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (conde\n [(fresh (e d p e-rest)\n (== `(,e-drug/gene ,e) q)\n (== `(,gene ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*)))]\n [(fresh (e e2 y z p e-rest p2 e2-rest)\n (== `(,e-drug/gene ,e ,e2) q)\n (== `(,gene ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (conde\n [(== \"AFFECTS\" p2)]\n [(== \"CAUSES\" p2)]) \n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) y)\n (not-membero \"dsyn\" concept-type*))\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*)))])))))\n\n\n> (time (length (run 1000000 (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest)\n (== '(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene) \n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (fresh (e e2 y z p e-rest p2 e2-rest)\n (== `(,e-drug/gene ,e ,e2) q)\n (== `(,gene ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (== \"CAUSES\" p2) \n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) y)\n (not-membero \"dsyn\" concept-type*))\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*)))))))\ncpu time: 68505 real time: 69284 gc time: 7253\n773840\n\n> (time (length (run 100000 (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest)\n (== '(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene) \n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (conde\n [(fresh (e d p e-rest)\n (== `(,e-drug/gene ,e) q)\n (== `(,gene ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*)))])))))\ncpu time: 1173 real time: 1190 gc time: 71\n8237\n\n> (time (length (run 100000 (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest)\n (== '(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene) \n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (fresh (e d p e-rest)\n (== `(,e-drug/gene ,e) q)\n (== `(,gene ,d ,p . ,e-rest) e)\n (== \"CAUSES\" p)\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*)))))))\ncpu time: 466 real time: 468 gc time: 23\n5028\n\n(time (length (run* (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest)\n (== '(939537 \"Imatinib mesylate\" (\"orch\" \"phsu\")) drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene) \n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (conde\n [(fresh (e d p e-rest)\n (== `(,e-drug/gene ,e) q)\n (== `(,gene ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*)))]\n [(fresh (e e2 y z p e-rest p2 e2-rest)\n (== `(,e-drug/gene ,e ,e2) q)\n (== `(,gene ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (conde\n [(== \"AFFECTS\" p2)]\n [(== \"CAUSES\" p2)]) \n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) y)\n (not-membero \"dsyn\" concept-type*))\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*)))])))))\n\n;; diseases that are directly affected or caused by gene G,\n;; or diseases that are directly affected or caused by Y, where Y is any *non-disease* caused by gene G [one level deep],\n;; where gene G is directly inhibited by \n(time (length (run* (q)\n (fresh (drug gene e-drug/gene p-drug/gene e-drug/gene-rest)\n (fuzzy-concepto \"imatinib\" drug)\n (== `(,drug ,gene ,p-drug/gene . ,e-drug/gene-rest) e-drug/gene)\n (== \"INHIBITS\" p-drug/gene) \n (edgeo e-drug/gene)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) gene)\n (membero \"gngm\" concept-type*))\n (conde\n [(fresh (e d p e-rest)\n (== `(,e-drug/gene ,e) q)\n (== `(,gene ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*)))]\n [(fresh (e e2 y z p e-rest p2 e2-rest)\n (== `(,e-drug/gene ,e ,e2) q)\n (== `(,gene ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (conde\n [(== \"AFFECTS\" p2)]\n [(== \"CAUSES\" p2)]) \n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) y)\n (not-membero \"dsyn\" concept-type*))\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*)))])))))\n\n;; diseases that are directly affected or caused by KIT gene,\n;; or diseases that are directly affected or caused by Y, where Y is any *non-disease* caused by KIT gene [one level deep]\n;;\n;; cpu time: 1750 real time: 1753 gc time: 294\n;; 16574 total = 40 + 16534, as expected from the queries below\n(time (length (run* (q)\n (fresh (x)\n (fuzzy-concepto \"KIT gene\" x)\n (conde\n [(fresh (e d p e-rest)\n (== `(,e) q)\n (== `(,x ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*)))]\n [(fresh (e e2 y z p e-rest p2 e2-rest)\n (== `(,e ,e2) q)\n (== `(,x ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (conde\n [(== \"AFFECTS\" p2)]\n [(== \"CAUSES\" p2)]) \n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) y)\n (not-membero \"dsyn\" concept-type*))\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*)))])))))\n\n;; diseases that are directly affected or caused by Y, where Y is any *non-disease* caused by KIT gene (16534) [one level deep]\n;; cpu time: 1589 real time: 1592 gc time: 81\n(time (length (run* (e e2)\n (fresh (x y z p e-rest p2 e2-rest)\n (fuzzy-concepto \"KIT gene\" x)\n (== `(,x ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (conde\n [(== \"AFFECTS\" p2)]\n [(== \"CAUSES\" p2)]) \n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) y)\n (not-membero \"dsyn\" concept-type*))\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*))\n ))))\n\n;; diseases that are directly affected or caused by Y, where Y is anything caused by KIT gene (22012) [one level deep]\n;;\n;; cpu time: 2251 real time: 2273 gc time: 315\n#|\n(time (length (run* (e e2)\n (fresh (x y z p e-rest p2 e2-rest)\n (fuzzy-concepto \"KIT gene\" x)\n (== `(,x ,y ,p . ,e-rest) e)\n (== `(,y ,z ,p2 . ,e2-rest) e2)\n (== \"CAUSES\" p)\n (conde\n [(== \"AFFECTS\" p2)]\n [(== \"CAUSES\" p2)]) \n (edgeo e)\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) z)\n (membero \"dsyn\" concept-type*))\n ))))\n|#\n\n;; find diseases *directly* caused or affected by KIT gene (40)\n;; cpu time: 104 real time: 106 gc time: 2\n#|\n(time (run* (e)\n (fresh (x d p e-rest)\n (fuzzy-concepto \"KIT gene\" x)\n (== `(,x ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*))\n )))\n|#\n\n;; diseases directly caused by or affected by mast cell activation,\n;; and which are *not* directly treated by imatinib\n;;\n;; uh oh! wanted to try negation as failure, but faster-mk doesn't include\n;; conda or condu, and probably isn't sound to use them anyway in the presence of\n;; constraints and violation of the g-rule.\n;;\n;; rethink!\n#|\n(time (run* (e-mast/disease e-imatinib/disease)\n (fresh (x d p e-rest)\n (fuzzy-concepto \"mast cell activation\" x)\n (== `(,x ,d ,p . ,e-rest) e-mast/disease)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e-mast/disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*))\n\n (fresh (s-imatinib/disease m-imatinib/disease p-imatinib/disease e-rest-imatinib/disease)\n (== `(,s-imatinib/disease ,m-imatinib/disease ,p-imatinib/disease . ,e-rest-imatinib/disease) e-imatinib/disease)\n (fuzzy-concepto \"imatinib\" s-imatinib/disease)\n (== m-imatinib/disease d)\n (== \"TREATS\" p-imatinib/disease)\n (conda\n [(edgeo e-imatinib/disease)\n (== #f #t) ; negation as failure -- yuck!\n ]\n [(== #f #f) ; succeed!\n ]))\n )))\n|#\n\n;; diseases directly caused by or affected by mast cell activation,\n;; and which are directly treated by imatinib (12)\n;; cpu time: 1495 real time: 1496 gc time: 7\n'((((1155074 \"mast cell activation\" (\"celf\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (76040540))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (80123007 63539282)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (76040540))\n ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (62390822 47235373)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (22892042 22892027))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n \"TREATS\"\n \"orch\"\n \"dsyn\"\n (83824572)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (22892042 22892027))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (80065397 70145883)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85156399\n 66251757\n 65830637\n 61542167\n 55781135\n 55026706\n 52273769\n 48853539\n 41997247\n 34204920\n 30957315\n 30619348\n 22892051\n 22892032\n 22074757))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"orch\"\n \"dsyn\"\n (86095345 67097950 63793027)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85156399\n 66251757\n 65830637\n 61542167\n 55781135\n 55026706\n 52273769\n 48853539\n 41997247\n 34204920\n 30957315\n 30619348\n 22892051\n 22892032\n 22074757))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (89407082\n 87982863\n 84505267\n 83839341\n 82894881\n 79751398\n 77831693\n 74132108\n 73588617\n 71258609\n 68415786\n 67458023\n 64623720\n 63394606\n 63276539\n 62770748\n 61655728\n 61327847\n 59631443\n 58825872\n 57593433\n 56055322\n 55987577\n 55898005\n 55505236\n 54274523\n 54274472\n 54245112\n 53414031\n 53353967\n 51836186\n 50884827\n 50551010\n 47162081\n 44666378\n 44579312\n 43522756\n 41787008)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85156399\n 66251757\n 65830637\n 61542167\n 55781135\n 55026706\n 52273769\n 48853539\n 41997247\n 34204920\n 30957315\n 30619348\n 22892051\n 22892032\n 22074757))\n ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"orch\"\n \"dsyn\"\n (54632685)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85156399\n 66251757\n 65830637\n 61542167\n 55781135\n 55026706\n 52273769\n 48853539\n 41997247\n 34204920\n 30957315\n 30619348\n 22892051\n 22892032\n 22074757))\n ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (79915447 62155051 53028960 51345693 35868680 35397483)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85156399\n 66251757\n 65830637\n 61542167\n 55781135\n 55026706\n 52273769\n 48853539\n 41997247\n 34204920\n 30957315\n 30619348\n 22892051\n 22892032\n 22074757))\n ((1331284 \"imatinib 400 MG\" (\"clnd\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"TREATS\"\n \"clnd\"\n \"dsyn\"\n (82894882)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (17260890))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (84787125 64871514)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (62139776))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (55204927)))\n (((1155074 \"mast cell activation\" (\"celf\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (75547483))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (86365747 86365718))))\n;;\n(time (run* (e-mast/disease e-imatinib/disease)\n (fresh (x d p e-rest)\n (fuzzy-concepto \"mast cell activation\" x)\n (== `(,x ,d ,p . ,e-rest) e-mast/disease)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e-mast/disease)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*))\n\n (fresh (s-imatinib/disease m-imatinib/disease p-imatinib/disease e-rest-imatinib/disease)\n (== `(,s-imatinib/disease ,m-imatinib/disease ,p-imatinib/disease . ,e-rest-imatinib/disease) e-imatinib/disease)\n (fuzzy-concepto \"imatinib\" s-imatinib/disease)\n (== m-imatinib/disease d)\n (== \"TREATS\" p-imatinib/disease)\n (edgeo e-imatinib/disease)) \n )))\n\n;; diseases directly caused by or affected by mast cell activation (18 of them)\n'(((1155074 \"mast cell activation\" (\"celf\"))\n (3864 \"Arthritis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (76040540))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (54247735 38643255))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (8679 \"Chronic Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (22892042 22892027))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (9766 \"Allergic Conjunctivitis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (59114948))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (12634 \"Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85156399\n 66251757\n 65830637\n 61542167\n 55781135\n 55026706\n 52273769\n 48853539\n 41997247\n 34204920\n 30957315\n 30619348\n 22892051\n 22892032\n 22074757))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (14038 \"Encephalitis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (65637409))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (26769 \"Multiple Sclerosis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (17260890))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (38644 \"Sudden infant death syndrome\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (26368942))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (41296 \"Tuberculosis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (62139776))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (83500602))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (263338 \"Chronic urticaria\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (62388241))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (272203 \"Indolent Systemic Mastocytosis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (75547483))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (282488 \"Interstitial Cystitis\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (23789469))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (340865 \"Anaphylactoid reaction\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (43841329))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (853897 \"Diabetic cardiomyopathy\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (72760736))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (948089 \"Acute coronary syndrome\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (85902244\n 70809425\n 63933449\n 62132544\n 61479825\n 58213540\n 58052580\n 56749622\n 48540985\n 43841336))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (1290886 \"Chronic inflammatory disorder\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (58131314))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (1449852 \"Erythematotelangiectatic Rosacea\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (71577548)))\n;;\n#|\n(time (run* (e)\n (fresh (x d p e-rest)\n (fuzzy-concepto \"mast cell activation\" x)\n (== `(,x ,d ,p . ,e-rest) e)\n (conde\n [(== \"AFFECTS\" p)]\n [(== \"CAUSES\" p)])\n (edgeo e)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) d)\n (membero \"dsyn\" concept-type*))\n )))\n|#\n\n;; cpu time: 132126 real time: 132712 gc time: 6589\n;; 20000 paths\n#|\n(time (length (run 20000 (path)\n (fresh (x)\n (fuzzy-concepto \"mast cell activation\" x)\n (path-to-diseaseo x path)))))\n|#\n\n;; time to generate all genes that are inhibited by imatinib that in turn cause some disease, and where imatinib is known to directly treat that disease\n;; cpu time: 88571 real time: 89553 gc time: 1150\n;; 9681\n\n(time (pretty-print (run* (tree)\n (fresh (e-imatinib/known-disease s-imatinib/known-disease m-imatinib/known-disease p-imatinib/known-disease e-rest-imatinib/known-disease\n e-imatinib/gene s-imatinib/gene m-imatinib/gene p-imatinib/gene e-rest-imatinib/gene\n e-gene/known-disease s-gene/known-disease m-gene/known-disease p-gene/known-disease e-rest-gene/known-disease\n )\n\n (== `(,s-imatinib/known-disease ,m-imatinib/known-disease ,p-imatinib/known-disease . ,e-rest-imatinib/known-disease) e-imatinib/known-disease)\n (== `(,s-imatinib/gene ,m-imatinib/gene ,p-imatinib/gene . ,e-rest-imatinib/gene) e-imatinib/gene)\n (== `(,s-gene/known-disease ,m-gene/known-disease ,p-gene/known-disease . ,e-rest-gene/known-disease) e-gene/known-disease)\n\n ;; need to add types! https://mmtx.nlm.nih.gov/MMTx/semanticTypes.shtml\n ;; (map (lambda (cui) (hash-ref cui=>concept cui)) (hash-ref semtype-id=>cui* (hash-ref semtype=>id \"gngm\")))\n ;; * gene: gngm\tT028\tGene or Genome (hash-ref semtype=>id \"gngm\") => 59 (hash-ref semtype-id=>cui* (hash-ref semtype=>id \"gngm\"))\n ;; * known disease\n ;; * unknown disease\n \n (fuzzy-concepto \"imatinib\" s-imatinib/known-disease)\n\n ;; same imatinib\n (== s-imatinib/known-disease s-imatinib/gene)\n\n ;; same gene\n (== s-gene/known-disease m-imatinib/gene)\n\n ;; same known disease\n (== m-imatinib/known-disease m-gene/known-disease)\n \n (== \"TREATS\" p-imatinib/known-disease)\n\n (== \"CAUSES\" p-gene/known-disease)\n \n (== \"INHIBITS\" p-imatinib/gene)\n \n (edgeo e-imatinib/gene)\n\n ;; filter to make sure 'gene' is actually a gene!\n ;; what is a cleaner way to do this?\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) m-imatinib/gene)\n (membero \"gngm\" concept-type*))\n \n (edgeo e-gene/known-disease)\n (edgeo e-imatinib/known-disease)\n\n (== `(,e-imatinib/gene ,e-gene/known-disease ,e-imatinib/known-disease) tree)))))\n\n\n;; no results! good! what we would hope for\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (fuzzy-concepto \"imatinib\" s)\n (fuzzy-concepto \"asthma\" m)\n (edgeo e)))))\n|#\n\n;; no results! good! what we would hope for\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (fuzzy-concepto \"imatinib\" s)\n (fuzzy-concepto \"mast cell activation\" m)\n (edgeo e)))))\n|#\n\n'(((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"AFFECTS\"\n \"gngm\"\n \"celf\"\n (45683353))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (1155074 \"mast cell activation\" (\"celf\"))\n \"CAUSES\"\n \"gngm\"\n \"celf\"\n (36804978)))\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (fuzzy-concepto \"KIT gene\" s)\n (fuzzy-concepto \"mast cell activation\" m)\n (edgeo e)))))\n|#\n\n'((4096 \"Asthma\" (\"dsyn\"))\n (4099 \"Asthma, Exercise-Induced\" (\"dsyn\"))\n (14434 \"Detergent asthma\" (\"dsyn\"))\n (38218 \"Status Asthmaticus\" (\"dsyn\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n (155880 \"Intrinsic asthma NOS\" (\"dsyn\"))\n (238266 \"Meat-wrappers' asthma\" (\"dsyn\"))\n (238375 \"Platinum asthma\" (\"dsyn\"))\n (259745 \"Asthma, infective\" (\"dsyn\"))\n (259808 \"Asthma, endogenous\" (\"dsyn\"))\n (264348 \"Chronic asthmatic bronchitis\" (\"dsyn\"))\n (264408 \"Childhood asthma\" (\"dsyn\"))\n (264411 \"Hay fever with asthma\" (\"dsyn\"))\n (264413 \"Late onset asthma\" (\"dsyn\"))\n (264423 \"Occupational asthma\" (\"dsyn\"))\n (264480 \"Bakers' asthma\" (\"dsyn\"))\n (282556 \"Anti-Asthmatic Agents\" (\"phsu\"))\n (340067 \"Drug-induced asthma\" (\"dsyn\"))\n (340069 \"Colophony asthma\" (\"dsyn\"))\n (340070 \"Millers' asthma\" (\"dsyn\"))\n (340073 \"Factitious asthma\" (\"dsyn\"))\n (340076 \"Asthmatic pulmonary eosinophilia\" (\"dsyn\"))\n (340094 \"Wood asthma\" (\"dsyn\"))\n (347950 \"Asthma attack NOS\" (\"dsyn\"))\n (348819 \"Mixed asthma\" (\"dsyn\"))\n (349790 \"Exacerbation of asthma\" (\"fndg\"))\n (350348 \"Asthma prophylaxis\" (\"phsu\"))\n (392681 \"Asthmatic breathing\" (\"sosy\"))\n (420048 \"Asthma screening\" (\"hlca\"))\n (420293 \"Emergency admission, asthma\" (\"hlca\"))\n (543699 \"ASA intolerant asthma\" (\"dsyn\"))\n (554832 \"Asthma monitoring\" (\"hlca\"))\n (581122 \"Asthma severity\" (\"hlca\"))\n (581124 \"Mild asthma\" (\"fndg\"))\n (581125 \"Moderate asthma\" (\"fndg\"))\n (581126 \"Severe asthma\" (\"fndg\"))\n (582415 \"Acute asthma\" (\"dsyn\"))\n (606809 \"Asthma 23D\" (\"phsu\"))\n (684913 \"Chemical-induced asthma\" (\"dsyn\"))\n (729337 \"Brittle asthma\" (\"dsyn\"))\n (741266 \"ASTHMA STABLE\" (\"fndg\"))\n (856716 \"Asthma aspirin-sensitive\" (\"dsyn\"))\n (859987 \"Asthmatoid bronchitis\" (\"dsyn\"))\n (876293 \"Asthma Monitoring System\" (\"medd\"))\n (877264 \"Infantile asthma\" (\"dsyn\"))\n (877430 \"Asthma chronic\" (\"dsyn\"))\n (1135801 \"Tylophora asthmatica\" (\"plnt\"))\n (1261327 \"Family history of asthma\" (\"fndg\"))\n (1271086 \"Suspected asthma\" (\"fndg\"))\n (1272273 \"Asthma finding\" (\"fndg\"))\n (1303029 \"Asthma trigger\" (\"clna\"))\n (1318955 \"Asthma management\" (\"hlca\"))\n (1319018 \"Asthmatic bronchitis\" (\"dsyn\"))\n (1319853 \"Aspirin-induced asthma\" (\"fndg\"))\n (1328364 \"Analgesic asthma syndrome\" (\"inpo\")))\n#|\n(run* (m) (fuzzy-concepto \"asthma\" m))\n|#\n\n'(((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (54247735 38643255))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4096 \"Asthma\" (\"dsyn\"))\n \"ASSOCIATED_WITH\"\n \"celf\"\n \"dsyn\"\n (13130971))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (4099 \"Asthma, Exercise-Induced\" (\"dsyn\"))\n \"NEG_AFFECTS\"\n \"celf\"\n \"dsyn\"\n (17055287))\n ((1155074 \"mast cell activation\" (\"celf\"))\n (155877 \"Extrinsic asthma NOS\" (\"dsyn\"))\n \"AFFECTS\"\n \"celf\"\n \"dsyn\"\n (83500602)))\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (fuzzy-concepto \"mast cell activation\" s)\n (fuzzy-concepto \"asthma\" m)\n (edgeo e)))))\n|#\n\n'(\"AFFECTS\" \"ASSOCIATED_WITH\" \"NEG_AFFECTS\" \"AFFECTS\")\n#|\n(time (pretty-print (run* (p)\n (fresh (e s m e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (fuzzy-concepto \"mast cell activation\" s)\n (fuzzy-concepto \"asthma\" m)\n (edgeo e)))))\n|#\n\n\n'(\"AFFECTS\" \"ASSOCIATED_WITH\")\n#|\n(time (pretty-print (run* (p)\n (fresh (e s m e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (cuio s 1155074) ; (1155074 \"mast cell activation\" (\"celf\"))\n (cuio m 4096) ; (4096 \"Asthma\" (\"dsyn\"))\n (edgeo e)))))\n|#\n\n\n'(\"AFFECTS\"\n \"AFFECTS\"\n \"ASSOCIATED_WITH\"\n \"ASSOCIATED_WITH\"\n \"ASSOCIATED_WITH\"\n \"ASSOCIATED_WITH\"\n \"AUGMENTS\"\n \"CAUSES\"\n \"AUGMENTS\"\n \"NEG_ASSOCIATED_WITH\"\n \"CAUSES\"\n \"PART_OF\"\n \"CAUSES\"\n \"PREDISPOSES\"\n \"DISRUPTS\"\n \"TREATS\"\n \"NEG_ASSOCIATED_WITH\"\n \"NEG_PART_OF\"\n \"NEG_TREATS\"\n \"PART_OF\"\n \"PREDISPOSES\"\n \"PREDISPOSES\"\n \"PREVENTS\"\n \"TREATS\"\n \"compared_with\"\n \"higher_than\")\n#|\n(time (pretty-print (run* (p)\n (fresh (e s m e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (conde\n [(cuio s 1416655)] ; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n [(cuio s 920288)]) ; (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (cuio m 238198) ; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (edgeo e)))))\n|#\n\n\n\n\n'(((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (88094027\n 82038640\n 78690628\n 78513788\n 70397515\n 60608992\n 57775955\n 56779144\n 55866397\n 55866394\n 54750176\n 54602555\n 54524739\n 53954674\n 53827456\n 53794226\n 53155624\n 51843305\n 51685933\n 50494576\n 50287491\n 50287227\n 49443008\n 48324562\n 47259531\n 45719202\n 44323647\n 44187569\n 43969275\n 40811261\n 40130263\n 35363677\n 35363677))\n ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (78245416\n 60923184\n 52405281\n 50198713\n 48733408\n 48658568\n 46535660\n 45216976\n 44323573\n 42932218\n 41594062\n 41594059\n 41109626\n 41017098\n 40494392\n 37687910))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (88061703\n 85297819\n 84466544\n 80622734\n 80622529\n 80622496\n 80602335\n 80602240\n 74425222\n 73925398\n 72612280\n 70407634\n 68644392\n 68644322\n 61811120\n 57954791\n 57560853\n 57461754\n 56194601\n 56139137\n 55779007\n 54837106\n 53185505\n 53155624\n 52291848\n 51896005\n 49170588\n 46720307\n 45481706\n 42521897\n 41357396\n 40935122))\n ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n \"INHIBITS\"\n \"orch\"\n \"gngm\"\n (82419991\n 73925304\n 61340408\n 56865479\n 55254090\n 54481089\n 50302706\n 47020133\n 43901262\n 42424750\n 41410459\n 41146783\n 39633613)))\n#|\n(time (pretty-print (run* (e)\n (fresh (s m p e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (conde\n [(cuio s 935989)] ; (935989 \"imatinib\" (\"phsu\" \"orch\"))\n [(cuio s 939537)]) ; (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (conde\n [(cuio m 1416655)] ; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n [(cuio m 920288)]) ; (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (== \"INHIBITS\" p)\n (edgeo e)))))\n|#\n\n'(\"COEXISTS_WITH\"\n \"INHIBITS\"\n \"COEXISTS_WITH\"\n \"INTERACTS_WITH\"\n \"INTERACTS_WITH\"\n \"INHIBITS\"\n \"NEG_INTERACTS_WITH\"\n \"STIMULATES\"\n \"COEXISTS_WITH\"\n \"INTERACTS_WITH\"\n \"compared_with\"\n \"COEXISTS_WITH\"\n \"lower_than\"\n \"NEG_INHIBITS\"\n \"INHIBITS\"\n \"STIMULATES\"\n \"INHIBITS\"\n \"USES\"\n \"INTERACTS_WITH\"\n \"INTERACTS_WITH\"\n \"INTERACTS_WITH\"\n \"INTERACTS_WITH\"\n \"NEG_INTERACTS_WITH\")\n#|\n(time (pretty-print (run* (p)\n (fresh (e s m e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (conde\n [(cuio s 935989)] ; (935989 \"imatinib\" (\"phsu\" \"orch\"))\n [(cuio s 939537)]) ; (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (conde\n [(cuio m 1416655)] ; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n [(cuio m 920288)]) ; (920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (edgeo e)))))\n|#\n\n\n;; no answers! good! This means we will need to find the connection ourselves, assuming it exists in SemMedDB\n#|\n(time (pretty-print (run* (p)\n (fresh (e s m e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (conde\n [(cuio s 935989)] ; (935989 \"imatinib\" (\"phsu\" \"orch\"))\n [(cuio s 939537)]) ; (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (fuzzy-concepto \"asthma\" m)\n (edgeo e)))))\n|#\n\n\n;; imatinib\n;; \"AFFECTS\"\n;; \"AUGMENTS\"\n;; \"CAUSES\"\n;; \"NEG_AFFECTS\"\n;; \"NEG_TREATS\"\n;; \"PREDISPOSES\"\n;; \"PREVENTS\"\n;; \"TREATS\"\n;; Gastrointestinal Stromal Tumors\n#|\n(time (pretty-print (run* (p)\n (fresh (e s m e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (conde\n [(cuio s 935989)] ; (935989 \"imatinib\" (\"phsu\" \"orch\"))\n [(cuio s 939537)]) ; (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (cuio m 238198) ; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n (edgeo e)))))\n|#\n\n;; What else, other than \"KIT gene\", causes \"Gastrointestinal Stromal Tumors\"?\n;;\n;; 46 entries in the list\n;;\n;; hmmm...\n;;\n;; ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n;; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;; \"CAUSES\"\n;; \"orch\"\n;; \"neop\"\n;; (76776830 56175577 55046179))\n;; ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n;; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;; \"CAUSES\"\n;; \"orch\"\n;; \"neop\"\n;; (81096076 44044998))\n;;\n;;\n;; Genes\n;; Proto-Oncogenes\n;;\n;; CCND3\n;; FRAP1\n;; KIT\n;; PDGFRA\n;; SARDH\n;; SDHB\n;; SDS\n;; VEGFA\n;;\n;; Oncogene Proteins\n;;\n;; Proto-Oncogene Protein c-kit\n;; FRAP1 protein, human\n;; PDGFA protein, human\n;;\n;; Receptor Protein-Tyrosine Kinases\n;; Mitogen-Activated Protein Kinases\n;;\n;; Protein-tyrosine kinase inhibitor\n;;\n'(((6674 \"Calcitriol\" (\"horm\" \"strd\" \"phsu\" \"vita\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"horm\"\n \"neop\"\n (77145307))\n ((7090 \"Carcinogens\" (\"hops\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"hops\"\n \"neop\"\n (65449228 50883408))\n ((7621 \"Cell Transformation, Neoplastic\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"neop\"\n \"neop\"\n (63043249))\n ((13299 \"Duodenogastric Reflux\" (\"dsyn\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"dsyn\"\n \"neop\"\n (42175197))\n ((17337 \"Genes\" (\"aapp\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (58489737))\n ((24002 \"Lorazepam\" (\"phsu\" \"orch\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"orch\"\n \"neop\"\n (48186889))\n ((26336 \"Study models\" (\"inpr\" \"resd\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"resd\"\n \"neop\"\n (45629888))\n ((27627 \"Neoplasm Metastasis\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"neop\"\n \"neop\"\n (63071652))\n ((29005 \"Oncogene Proteins\" (\"gngm\" \"bacs\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (46756812))\n ((31727 \"Phosphotransferases\" (\"aapp\" \"gngm\" \"enzy\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (65449233))\n ((32200 \"Platelet-Derived Growth Factor\" (\"gngm\" \"aapp\" \"bacs\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (85323763 85323762))\n ((33713 \"Proto-Oncogenes\" (\"aapp\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (62178248 59318007 39441233))\n ((36442 \"Scopolamine\" (\"orch\" \"phsu\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"orch\"\n \"neop\"\n (48186893))\n ((37659 \"Somatostatin\" (\"phsu\" \"aapp\" \"gngm\" \"horm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (61820493))\n ((38615 \"Succinate Dehydrogenase\" (\"aapp\" \"enzy\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (85537008 55521924 42919388))\n ((40646 \"Transcriptase\" (\"gngm\" \"aapp\" \"enzy\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (76380814))\n ((55817 \"citrate carrier\" (\"bacs\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (57723826))\n ((71253 \"Platelet-Derived Growth Factor Receptor\" (\"aapp\" \"gngm\" \"enzy\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (53789101 53789073 50274414))\n ((72470 \"Proto-Oncogene Protein c-kit\" (\"aapp\" \"gngm\" \"rcpt\" \"imft\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59480455 47920692))\n ((206364 \"Receptor Protein-Tyrosine Kinases\" (\"enzy\" \"rcpt\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (86726299 50789329 29550497))\n ((206530 \"Germ-Line Mutation\" (\"genf\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"genf\"\n \"neop\"\n (73582365))\n ((243077 \"inhibitors\" (\"chvf\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"chvf\"\n \"neop\"\n (70292056))\n ((244104 \"Pyruvate\" (\"orch\" \"bacs\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"bacs\"\n \"neop\"\n (75527580))\n ((290067\n \"Platelet-Derived Growth Factor alpha Receptor\"\n (\"rcpt\" \"aapp\" \"gngm\" \"enzy\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (43196739 40249105))\n ((450442 \"Agent\" (\"chvf\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"chvf\"\n \"neop\"\n (68259613))\n ((534628 \"Endostatins\" (\"aapp\" \"phsu\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (50654712))\n ((725066 \"Advance\" (\"medd\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"medd\"\n \"neop\"\n (59465228))\n ((752312 \"Mitogen-Activated Protein Kinases\" (\"enzy\" \"aapp\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (54020272))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87384637 51889889 37195338 33819150 33819075))\n ((935989 \"imatinib\" (\"phsu\" \"orch\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"orch\"\n \"neop\"\n (76776830 56175577 55046179))\n ((939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"orch\"\n \"neop\"\n (81096076 44044998))\n ((1268567 \"Protein-tyrosine kinase inhibitor\" (\"phsu\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"phsu\"\n \"neop\"\n (63024462))\n ((1307407 \"FRAP1 protein, human\" (\"aapp\" \"enzy\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (54020280))\n ((1333132 \"Common Neoplasm\" (\"neop\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"neop\"\n \"neop\"\n (43813786))\n ((1335200 \"PDGFA gene\" (\"gngm\" \"horm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59625566))\n ((1335201 \"PDGFRA gene\" (\"rcpt\" \"enzy\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (43196739 40249105))\n ((1335201 \"PDGFRA gene\" (\"rcpt\" \"enzy\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87264286\n 87264286\n 86468474\n 86468474\n 83221033\n 83221033\n 77629821\n 77629821\n 61335412\n 61335412\n 60497536\n 60497536\n 48640418\n 48640418\n 42671657\n 42671657\n 41043821\n 41043821\n 41043806\n 41043806))\n ((1335430 \"PDGFA protein, human\" (\"horm\" \"aapp\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59625566))\n ((1413175 \"CCND3 gene\" (\"aapp\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (41147975 41147975))\n ((1414805 \"FRAP1 gene\" (\"aapp\" \"gngm\" \"enzy\" \"bacs\" \"aapp\" \"gngm\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (54020280))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59625558 59480455 43196727 40249098))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87384637\n 85323758\n 85323753\n 83221026\n 61335391\n 58431044\n 57775929\n 55436679\n 54253302\n 53789085\n 53789078\n 52927884\n 50274407\n 50049773\n 49635451\n 46841526\n 46757085\n 46299485\n 44187839\n 42671642\n 41287669\n 37195338\n 34247527\n 33819150\n 33819075\n 33114772\n 32425400\n 31543639\n 31187106\n 27728484\n 27728480))\n ((1419817 \"SARDH gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (66904284))\n ((1419907 \"SDHB gene\" (\"aapp\" \"gngm\" \"enzy\" \"bacs\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (66904284))\n ((1419917 \"SDS gene\" (\"gngm\" \"enzy\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (66904284))\n ((1823619 \"VEGFA gene\" (\"bacs\" \"phsu\" \"rcpt\" \"gngm\" \"imft\" \"enzy\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (50654702)))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m p e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (cuio m 238198)\n (== \"CAUSES\" p)\n (edgeo e)))))\n|#\n\n;; \"KIT gene\" CUI 1416655\n;; \"Gastrointestinal Stromal Tumors\" CUI 238198\n;; \"CAUSES\"\n;;\n'(((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59625558 59480455 43196727 40249098))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87384637\n 85323758\n 85323753\n 83221026\n 61335391\n 58431044\n 57775929\n 55436679\n 54253302\n 53789085\n 53789078\n 52927884\n 50274407\n 50049773\n 49635451\n 46841526\n 46757085\n 46299485\n 44187839\n 42671642\n 41287669\n 37195338\n 34247527\n 33819150\n 33819075\n 33114772\n 32425400\n 31543639\n 31187106\n 27728484\n 27728480)))\n;;\n;; Sometimes we just want to target a specific cui or set of cuis.\n;;\n;; #(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; #(238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m p e-rest)\n (== `(,s ,m ,p . ,e-rest) e)\n (cuio s 1416655)\n (cuio m 238198)\n (== \"CAUSES\" p)\n (edgeo e)))))\n|#\n\n\n;; \"KIT gene\"\n;; \"Gastrointestinal Stromal Tumors\"\n;; (any predicate, using CUIs for S and M)\n'(((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AFFECTS\"\n \"gngm\"\n \"neop\"\n (76251827 71712139 66437646 51229875 45105359 44957091))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"ASSOCIATED_WITH\"\n \"aapp\"\n \"neop\"\n (88816704\n 84460940\n 82018014\n 80113913\n 78220375\n 68676785\n 64194050\n 62488657\n 62488417\n 60516197\n 59023488\n 57460066\n 55504934\n 51048056\n 50221433\n 49515351\n 42281387\n 39806474\n 39806458\n 38471241\n 36205524\n 32077844\n 27305882))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"ASSOCIATED_WITH\"\n \"gngm\"\n \"neop\"\n (88816957\n 88816951\n 88816950\n 88786674\n 88707141\n 87354026\n 87354024\n 86927567\n 85526693\n 85323889\n 85258402\n 85131831\n 84724778\n 84460748\n 84460694\n 84031830\n 84026339\n 83653907\n 83346329\n 83173556\n 83173380\n 82814810\n 82814708\n 82174828\n 80961594\n 80611295\n 78681164\n 77814508\n 77327848\n 76776638\n 76419851\n 76251730\n 75963048\n 75962942\n 75527334\n 75208407\n 74994400\n 74617283\n 74420763\n 74324760\n 73846506\n 73776862\n 73338226\n 73151949\n 72728471\n 72728225\n 71621316\n 71588638\n 71193030\n 71047813\n 70628389\n 70628117\n 70576282\n 70576118\n 70575948\n 69690124\n 69539621\n 69450585\n 69450375\n 69393867\n 69063607\n 68636078\n 68635898\n 67326540\n 66443153\n 66443088\n 66245060\n 66000227\n 65490262\n 65393355\n 65260310\n 64512628\n 64194332\n 64038744\n 63974605\n 63909178\n 63900746\n 63874949\n 63557002\n 63556951\n 63247245\n 63247245\n 62577550\n 62470425\n 62318601\n 62318554\n 62076711\n 62065944\n 61963535\n 61807548\n 61800883\n 61785532\n 61273686\n 61273686\n 60839259\n 60522504\n 60449191\n 59983733\n 59983622\n 59867401\n 59853109\n 59625513\n 59092968\n 59092805\n 59092335\n 59023393\n 58702914\n 58430466\n 58195432\n 58194874\n 58155550\n 58155464\n 58155283\n 58155041\n 58038459\n 56779325\n 56779149\n 56778962\n 56736280\n 56175619\n 55308106\n 55122597\n 54971952\n 54602893\n 54602798\n 54602493\n 54348559\n 54348197\n 54348120\n 54086008\n 54019767\n 53993460\n 53993388\n 53838851\n 53617803\n 53455495\n 53161441\n 53155629\n 53124815\n 52370481\n 52188869\n 51979898\n 51938438\n 51764519\n 51764101\n 51764046\n 51650446\n 51650436\n 50862437\n 50658113\n 50427094\n 50221579\n 50122432\n 49416815\n 49178731\n 49156492\n 48740872\n 48230769\n 48230016\n 48229895\n 48229849\n 48061753\n 47300231\n 47273474\n 47179155\n 47085455\n 46756696\n 46673762\n 46054806\n 45858226\n 45698328\n 45698328\n 45431595\n 45253719\n 45216614\n 45106015\n 45105926\n 45105310\n 44823438\n 44574166\n 44574034\n 44464738\n 44395150\n 44383506\n 44382955\n 44382901\n 44153320\n 43711388\n 43604490\n 43229970\n 42932350\n 42860155\n 42860155\n 42224429\n 42190272\n 42190171\n 41720202\n 41253388\n 41053204\n 41016754\n 41016696\n 40493615\n 40429006\n 40428933\n 40249147\n 40248995\n 40247013\n 39580372\n 39482360\n 39185794\n 37687613\n 37195326\n 37195320\n 36962598\n 36788987\n 36751918\n 36434304\n 36204927\n 35865596\n 35667659\n 35667587\n 35363207\n 35363207\n 34290017\n 34246396\n 34246279\n 33114693\n 33114682\n 32970840\n 32815113\n 32656219\n 32655995\n 32424902\n 31894299\n 31275672\n 29441440\n 29440617\n 28577961\n 28372002\n 28371887\n 28181385\n 28115930\n 27578892\n 27427757\n 26885688\n 26862862\n 26407311))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AUGMENTS\"\n \"aapp\"\n \"neop\"\n (48230271))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AUGMENTS\"\n \"gngm\"\n \"neop\"\n (50049662))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59625558 59480455 43196727 40249098))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87384637\n 85323758\n 85323753\n 83221026\n 61335391\n 58431044\n 57775929\n 55436679\n 54253302\n 53789085\n 53789078\n 52927884\n 50274407\n 50049773\n 49635451\n 46841526\n 46757085\n 46299485\n 44187839\n 42671642\n 41287669\n 37195338\n 34247527\n 33819150\n 33819075\n 33114772\n 32425400\n 31543639\n 31187106\n 27728484\n 27728480))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"DISRUPTS\"\n \"gngm\"\n \"neop\"\n (44804518))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_ASSOCIATED_WITH\"\n \"gngm\"\n \"neop\"\n (58372927 42789720))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_PART_OF\"\n \"gngm\"\n \"neop\"\n (42672081))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_TREATS\"\n \"aapp\"\n \"neop\"\n (53583614))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PART_OF\"\n \"gngm\"\n \"neop\"\n (88816701\n 88504351\n 87664119\n 86527022\n 86527021\n 85431031\n 84724497\n 82274147\n 81758346\n 81503677\n 81503592\n 80572441\n 80301506\n 80113871\n 79973963\n 79689424\n 78726567\n 77821336\n 77196050\n 77196050\n 76776826\n 76776713\n 76548783\n 76252420\n 75385720\n 75385282\n 75385190\n 74686997\n 74324816\n 73776735\n 73151923\n 72884934\n 71444438\n 70575975\n 70335620\n 70335615\n 69854253\n 69854002\n 68641343\n 67432607\n 67356874\n 67246601\n 67092734\n 67092730\n 66938421\n 66938290\n 64461732\n 64424903\n 63702674\n 63702626\n 63702530\n 63556857\n 63556721\n 63556717\n 63491002\n 61959886\n 61806767\n 61806198\n 60522410\n 60096404\n 60096404\n 58546477\n 58546256\n 58155422\n 58155406\n 57723933\n 56641477\n 56216003\n 55455524\n 55122648\n 55122468\n 54602884\n 54602791\n 54281565\n 53839416\n 52398498\n 52189617\n 52064489\n 52064364\n 51366471\n 51366401\n 51232846\n 50359952\n 50359900\n 49606405\n 49527188\n 49527185\n 49527095\n 48065218\n 48065150\n 48061838\n 47942137\n 46383271\n 46115797\n 45811639\n 45811639\n 45256545\n 45105920\n 45105498\n 45105492\n 45097136\n 44823923\n 44357089\n 44356901\n 43533383\n 43229922\n 43066454\n 42789714\n 42628108\n 42119394\n 41205270\n 40864010\n 40674289\n 40347845\n 40036044\n 38954984\n 38954930\n 38398428\n 36262989\n 36202499\n 35397427\n 35363368\n 34259788\n 31893874\n 28372275\n 28372177\n 28372114\n 28372013\n 28372007\n 28371822))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREDISPOSES\"\n \"aapp\"\n \"neop\"\n (83625667 76441483 64529929 28452099))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREDISPOSES\"\n \"gngm\"\n \"neop\"\n (82889672 76270951 70297541 68769591 67716993 53756432 51412256 27939940))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREVENTS\"\n \"aapp\"\n \"neop\"\n (54419758))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"TREATS\"\n \"aapp\"\n \"neop\"\n (89381133\n 87264300\n 84046111\n 83347331\n 83212313\n 83212026\n 78726651\n 76441724\n 73846868\n 73616831\n 72119603\n 71290296\n 63973922\n 63557099\n 62693228\n 61564880\n 58650608\n 58510784\n 58431141\n 58431135\n 57460563\n 56215499\n 54580204\n 53770840\n 51513499\n 51414870\n 50287763\n 48710463\n 48636064\n 45867849\n 45629899\n 42593053\n 40213719\n 40162438\n 38953465\n 38953454\n 36434207\n 34247121\n 32462103\n 32462099\n 31121291\n 27939123))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"compared_with\"\n \"gngm\"\n \"neop\"\n (42860729))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"higher_than\"\n \"gngm\"\n \"neop\"\n (42860733)))\n;;\n;; Sometimes we just want to target a specific cui or set of cuis.\n;;\n;; #(1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; #(238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (cuio s 1416655)\n (cuio m 238198)\n (edgeo e)))))\n|#\n\n\n; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;\n; directly connected to\n;\n; (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;\n; results:\n;\n;; predicates between KIT and GIST\n;\n;; AFFECTS\n;; ASSOCIATED_WITH\n;; AUGMENTS\n;; CAUSES\n;; compared_with\n;; DISRUPTS\n;; higher_than\n;; NEG_ASSOCIATED_WITH\n;; NEG_PART_OF\n;; NEG_TREATS\n;; PREDISPOSES\n;; PREVENTS\n;; TREATS\n;\n; also, C-KIT and KIT seem redundanct\n;\n'(((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AFFECTS\"\n \"gngm\"\n \"neop\"\n (46760540))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AFFECTS\"\n \"gngm\"\n \"neop\"\n (76251827 71712139 66437646 51229875 45105359 44957091))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"ASSOCIATED_WITH\"\n \"aapp\"\n \"neop\"\n (49526961))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"ASSOCIATED_WITH\"\n \"aapp\"\n \"neop\"\n (88816704\n 84460940\n 82018014\n 80113913\n 78220375\n 68676785\n 64194050\n 62488657\n 62488417\n 60516197\n 59023488\n 57460066\n 55504934\n 51048056\n 50221433\n 49515351\n 42281387\n 39806474\n 39806458\n 38471241\n 36205524\n 32077844\n 27305882))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"ASSOCIATED_WITH\"\n \"gngm\"\n \"neop\"\n (85460993\n 84198758\n 83346329\n 82814810\n 82814708\n 76419851\n 76368784\n 75672079\n 74687151\n 74617283\n 74510694\n 74420763\n 73304122\n 70922298\n 70922287\n 70480510\n 70480448\n 68259646\n 63841800\n 63557002\n 63556951\n 62624485\n 62378661\n 60839259\n 60370637\n 59983733\n 59092805\n 59092335\n 58702780\n 58430466\n 57840570\n 56779149\n 56778962\n 56627960\n 56175619\n 56140915\n 55608208\n 54980002\n 54971952\n 53617803\n 53603127\n 53595646\n 53496246\n 53496201\n 53155629\n 51764519\n 51764101\n 51764046\n 51690076\n 50869476\n 50427094\n 50128173\n 50128133\n 49526823\n 49471986\n 49416815\n 49388946\n 48018585\n 46774667\n 46760302\n 46645481\n 46459742\n 46318460\n 46188441\n 46188438\n 46036844\n 45813589\n 45811969\n 45408733\n 43977736\n 43762035\n 43384567\n 43257978\n 43257961\n 42977994\n 42235291\n 42190272\n 42190171\n 41774698\n 41435074\n 41345067\n 41204705\n 40493615\n 40429006\n 40428933\n 39750509\n 39580372\n 38960183\n 38011762\n 38011758\n 37544890\n 37544516\n 37195326\n 37195320\n 37116085\n 36434304\n 35667587\n 35247619\n 34156014\n 33679770\n 32970840\n 32815393\n 32656219\n 31172044\n 30747520\n 30062221\n 29441443\n 29440617\n 28877968\n 28877765\n 28877668\n 28455552\n 27839749\n 27720966\n 27427757\n 26918073\n 26738840))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"ASSOCIATED_WITH\"\n \"gngm\"\n \"neop\"\n (88816957\n 88816951\n 88816950\n 88786674\n 88707141\n 87354026\n 87354024\n 86927567\n 85526693\n 85323889\n 85258402\n 85131831\n 84724778\n 84460748\n 84460694\n 84031830\n 84026339\n 83653907\n 83346329\n 83173556\n 83173380\n 82814810\n 82814708\n 82174828\n 80961594\n 80611295\n 78681164\n 77814508\n 77327848\n 76776638\n 76419851\n 76251730\n 75963048\n 75962942\n 75527334\n 75208407\n 74994400\n 74617283\n 74420763\n 74324760\n 73846506\n 73776862\n 73338226\n 73151949\n 72728471\n 72728225\n 71621316\n 71588638\n 71193030\n 71047813\n 70628389\n 70628117\n 70576282\n 70576118\n 70575948\n 69690124\n 69539621\n 69450585\n 69450375\n 69393867\n 69063607\n 68636078\n 68635898\n 67326540\n 66443153\n 66443088\n 66245060\n 66000227\n 65490262\n 65393355\n 65260310\n 64512628\n 64194332\n 64038744\n 63974605\n 63909178\n 63900746\n 63874949\n 63557002\n 63556951\n 63247245\n 63247245\n 62577550\n 62470425\n 62318601\n 62318554\n 62076711\n 62065944\n 61963535\n 61807548\n 61800883\n 61785532\n 61273686\n 61273686\n 60839259\n 60522504\n 60449191\n 59983733\n 59983622\n 59867401\n 59853109\n 59625513\n 59092968\n 59092805\n 59092335\n 59023393\n 58702914\n 58430466\n 58195432\n 58194874\n 58155550\n 58155464\n 58155283\n 58155041\n 58038459\n 56779325\n 56779149\n 56778962\n 56736280\n 56175619\n 55308106\n 55122597\n 54971952\n 54602893\n 54602798\n 54602493\n 54348559\n 54348197\n 54348120\n 54086008\n 54019767\n 53993460\n 53993388\n 53838851\n 53617803\n 53455495\n 53161441\n 53155629\n 53124815\n 52370481\n 52188869\n 51979898\n 51938438\n 51764519\n 51764101\n 51764046\n 51650446\n 51650436\n 50862437\n 50658113\n 50427094\n 50221579\n 50122432\n 49416815\n 49178731\n 49156492\n 48740872\n 48230769\n 48230016\n 48229895\n 48229849\n 48061753\n 47300231\n 47273474\n 47179155\n 47085455\n 46756696\n 46673762\n 46054806\n 45858226\n 45698328\n 45698328\n 45431595\n 45253719\n 45216614\n 45106015\n 45105926\n 45105310\n 44823438\n 44574166\n 44574034\n 44464738\n 44395150\n 44383506\n 44382955\n 44382901\n 44153320\n 43711388\n 43604490\n 43229970\n 42932350\n 42860155\n 42860155\n 42224429\n 42190272\n 42190171\n 41720202\n 41253388\n 41053204\n 41016754\n 41016696\n 40493615\n 40429006\n 40428933\n 40249147\n 40248995\n 40247013\n 39580372\n 39482360\n 39185794\n 37687613\n 37195326\n 37195320\n 36962598\n 36788987\n 36751918\n 36434304\n 36204927\n 35865596\n 35667659\n 35667587\n 35363207\n 35363207\n 34290017\n 34246396\n 34246279\n 33114693\n 33114682\n 32970840\n 32815113\n 32656219\n 32655995\n 32424902\n 31894299\n 31275672\n 29441440\n 29440617\n 28577961\n 28372002\n 28371887\n 28181385\n 28115930\n 27578892\n 27427757\n 26885688\n 26862862\n 26407311))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87384637 51889889 37195338 33819150 33819075))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AUGMENTS\"\n \"aapp\"\n \"neop\"\n (48230271))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_ASSOCIATED_WITH\"\n \"gngm\"\n \"neop\"\n (39466339))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"AUGMENTS\"\n \"gngm\"\n \"neop\"\n (50049662))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PART_OF\"\n \"gngm\"\n \"neop\"\n (83399926\n 77057096\n 76771910\n 76770354\n 76769868\n 68641343\n 60522410\n 56141218\n 54281565\n 49025814\n 47942137\n 45811599\n 45436399\n 45097136\n 44567254\n 42421331\n 41205270\n 40425019\n 40347845\n 36202499\n 31410208))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"aapp\"\n \"neop\"\n (59625558 59480455 43196727 40249098))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREDISPOSES\"\n \"gngm\"\n \"neop\"\n (76270951 70297541 51412256 27939940))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"CAUSES\"\n \"gngm\"\n \"neop\"\n (87384637\n 85323758\n 85323753\n 83221026\n 61335391\n 58431044\n 57775929\n 55436679\n 54253302\n 53789085\n 53789078\n 52927884\n 50274407\n 50049773\n 49635451\n 46841526\n 46757085\n 46299485\n 44187839\n 42671642\n 41287669\n 37195338\n 34247527\n 33819150\n 33819075\n 33114772\n 32425400\n 31543639\n 31187106\n 27728484\n 27728480))\n ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"TREATS\"\n \"aapp\"\n \"neop\"\n (88061705\n 85835773\n 85241243\n 81607888\n 61093492\n 60354773\n 58510784\n 58431141\n 48276039\n 45629899\n 42053369\n 41029401\n 40351927))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"DISRUPTS\"\n \"gngm\"\n \"neop\"\n (44804518))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_ASSOCIATED_WITH\"\n \"gngm\"\n \"neop\"\n (58372927 42789720))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_PART_OF\"\n \"gngm\"\n \"neop\"\n (42672081))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"NEG_TREATS\"\n \"aapp\"\n \"neop\"\n (53583614))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PART_OF\"\n \"gngm\"\n \"neop\"\n (88816701\n 88504351\n 87664119\n 86527022\n 86527021\n 85431031\n 84724497\n 82274147\n 81758346\n 81503677\n 81503592\n 80572441\n 80301506\n 80113871\n 79973963\n 79689424\n 78726567\n 77821336\n 77196050\n 77196050\n 76776826\n 76776713\n 76548783\n 76252420\n 75385720\n 75385282\n 75385190\n 74686997\n 74324816\n 73776735\n 73151923\n 72884934\n 71444438\n 70575975\n 70335620\n 70335615\n 69854253\n 69854002\n 68641343\n 67432607\n 67356874\n 67246601\n 67092734\n 67092730\n 66938421\n 66938290\n 64461732\n 64424903\n 63702674\n 63702626\n 63702530\n 63556857\n 63556721\n 63556717\n 63491002\n 61959886\n 61806767\n 61806198\n 60522410\n 60096404\n 60096404\n 58546477\n 58546256\n 58155422\n 58155406\n 57723933\n 56641477\n 56216003\n 55455524\n 55122648\n 55122468\n 54602884\n 54602791\n 54281565\n 53839416\n 52398498\n 52189617\n 52064489\n 52064364\n 51366471\n 51366401\n 51232846\n 50359952\n 50359900\n 49606405\n 49527188\n 49527185\n 49527095\n 48065218\n 48065150\n 48061838\n 47942137\n 46383271\n 46115797\n 45811639\n 45811639\n 45256545\n 45105920\n 45105498\n 45105492\n 45097136\n 44823923\n 44357089\n 44356901\n 43533383\n 43229922\n 43066454\n 42789714\n 42628108\n 42119394\n 41205270\n 40864010\n 40674289\n 40347845\n 40036044\n 38954984\n 38954930\n 38398428\n 36262989\n 36202499\n 35397427\n 35363368\n 34259788\n 31893874\n 28372275\n 28372177\n 28372114\n 28372013\n 28372007\n 28371822))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREDISPOSES\"\n \"aapp\"\n \"neop\"\n (83625667 76441483 64529929 28452099))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREDISPOSES\"\n \"gngm\"\n \"neop\"\n (82889672 76270951 70297541 68769591 67716993 53756432 51412256 27939940))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"PREVENTS\"\n \"aapp\"\n \"neop\"\n (54419758))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"TREATS\"\n \"aapp\"\n \"neop\"\n (89381133\n 87264300\n 84046111\n 83347331\n 83212313\n 83212026\n 78726651\n 76441724\n 73846868\n 73616831\n 72119603\n 71290296\n 63973922\n 63557099\n 62693228\n 61564880\n 58650608\n 58510784\n 58431141\n 58431135\n 57460563\n 56215499\n 54580204\n 53770840\n 51513499\n 51414870\n 50287763\n 48710463\n 48636064\n 45867849\n 45629899\n 42593053\n 40213719\n 40162438\n 38953465\n 38953454\n 36434207\n 34247121\n 32462103\n 32462099\n 31121291\n 27939123))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"compared_with\"\n \"gngm\"\n \"neop\"\n (42860729))\n ((1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n (238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n \"higher_than\"\n \"gngm\"\n \"neop\"\n (42860733)))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (fuzzy-concepto \"KIT gene\" s)\n (fuzzy-concepto \"Gastoirntestinal Stromal Tumors\" m)\n (edgeo e)))))\n|#\n\n\n\n\n\n;; A zillion answers, many with a staggering number of pubmed entries\n;;\n;; ((4096 \"Asthma\" (\"dsyn\"))\n;; (11616 \"Contact Dermatitis\" (\"dsyn\"))\n;; \"COEXISTS_WITH\"\n;; \"dsyn\"\n;; \"dsyn\"\n;; (41036104 35093327))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"asthma\" s)]\n [(fuzzy-concepto \"asthma\" m)])\n (edgeo e)))))\n|#\n\n;; A zillion answers!\n;;\n;; ((3147201 \"ERVK-2 gene\" (\"gngm\" \"aapp\"))\n;; (1155074 \"mast cell activation\" (\"celf\"))\n;; \"AUGMENTS\"\n;; \"gngm\"\n;; \"celf\"\n;; (20160432))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"mast cell activation\" s)]\n [(fuzzy-concepto \"mast cell activation\" m)])\n (edgeo e)))))\n|#\n\n;; A zillion answers!\n;;\n;; ((238198 \"Gastrointestinal Stromal Tumors\" (\"neop\"))\n;; (596290 \"Cell Proliferation\" (\"celf\"))\n;; \"AFFECTS\"\n;; \"neop\"\n;; \"celf\"\n;; (76749721 53497234 41583304))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"Gastrointestinal Stromal Tumor\" s)]\n [(fuzzy-concepto \"Gastrointestinal Stromal Tumor\" m)])\n (edgeo e)))))\n|#\n\n;; A zillion results! But none of them are relevant, I think. Wrong name!\n;; Instead, try 'Gastrointestinal Stromal Tumor'\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"GIST\" s)]\n [(fuzzy-concepto \"GIST\" m)])\n (edgeo e)))))\n|#\n\n\n;; 'overactivation' doesn't seem to be a thing in SemMedDB.\n;; I'm just going to look for any connections between the KIT gene and Gastrointestinal Stromal Tumors;\n;; ((17255 \"Gene Activation\" (\"genf\"))\n;; (3242 \"Antibodies, Anti-Idiotypic\" (\"aapp\" \"imft\" \"gngm\"))\n;; \"AFFECTS\"\n;; \"genf\"\n;; \"aapp\"\n;; (27977575))\n\n;; ((14429 \"Enzyme Activation\" (\"moft\"))\n;; (1150005 \"epoxide hydrolase activity\" (\"moft\"))\n;; \"NEG_CAUSES\"\n;; \"moft\"\n;; \"moft\"\n;; (10230110))\n\n;; ((9528 \"Complement Activation\" (\"moft\"))\n;; (1516369 \"Cellular Infiltration\" (\"celf\"))\n;; \"CAUSES\"\n;; \"moft\"\n;; \"celf\"\n;; (38511543))\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"overactivation\" s)]\n [(fuzzy-concepto \"overactivation\" m)])\n (edgeo e)))))\n|#\n\n;; A zillion results. 'KIT gene' and 'C-KIT Gene' show up a ton. For example:\n;;\n;; ((1323046 \"Detection Kits\" (\"medd\"))\n;; (1416655 \"KIT gene\" (\"bacs\" \"imft\" \"gngm\" \"aapp\"))\n;; \"COEXISTS_WITH\"\n;; \"medd\"\n;; \"gngm\"\n;; (55842475))\n;; ((920288 \"C-KIT Gene\" (\"gngm\" \"aapp\"))\n;; (1335214 \"PIK3CG gene\" (\"gngm\" \"aapp\" \"enzy\"))\n;; \"STIMULATES\"\n;; \"gngm\"\n;; \"gngm\"\n;; (85338529))\n;;\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"Kit\" s)]\n [(fuzzy-concepto \"Kit\" m)])\n (edgeo e)))))\n|#\n\n\n;; a zillion answers!\n;;\n;; (935989 \"imatinib\" (\"phsu\" \"orch\"))\n;;\n;; (939537 \"Imatinib mesylate\" (\"orch\" \"phsu\"))\n#|\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"imatinib\" s)]\n [(fuzzy-concepto \"imatinib\" m)])\n (edgeo e)))))\n|#\n" }, { "path": "attic/code/study-sickle-malaria.rkt", "content": "#lang racket\n(require\n \"mk-db.rkt\"\n )\n\n(displayln\n \"Finished loading mk-db.rkt (which probably took longer than the query).\")\n\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (fuzzy-concepto \"sickle\" s)\n (fuzzy-concepto \"malaria\" m)\n (edgeo e)))))\n\n\n;; Sometimes we just want to target a specific cui or set of cuis.\n;#(37054 \"Sickle Cell Trait\" (#(\"dsyn\" 1)))\n;#(19043 \"Sickle Hemoglobin\" (#(\"bacs\" 1) #(\"gngm\" 1) #(\"aapp\" 1))\n;#(24530 \"Malaria\" (#(\"dsyn\" 1)))\n\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (cui*o s '(37054 19043))\n (cuio m 24530)\n (edgeo e)))))\n\n\n\n\n;;; Will's explorations...\n\n;; https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n\n;; Nothing here... HbAS is the technical term for someone who is heterozygous for the sickle cell gene.\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"HbAS\" s)]\n [(fuzzy-concepto \"HbAS\" m)]) \n (edgeo e)))))\n\n;; try this variant\n;;\n;; alas, this version picks up 'THBS1 gene'\n;;\n;; is there a way to tighten up the query slightly, or at least post-filter the results?\n;;\n;; answers include things like:\n;;\n;; ((1415488 \"HBS1L gene\" (1 59))\n;; (20114 \"Human\" (68 62))\n;; \"PART_OF\"\n;; \"gngm\"\n;; \"humn\"\n;; (88838886))\n;; \n;; http://www.genecards.org/cgi-bin/carddisp.pl?gene=HBS1L\n;;\n;; GeneCards Summary for HBS1L Gene\n;;\n;; HBS1L (HBS1 Like Translational GTPase) is a Protein Coding gene. Diseases associated with HBS1L include Sickle Cell Disease and Sickle Cell Anemia. Among its related pathways are Deadenylation-dependent mRNA decay and Gene Expression. GO annotations related to this gene include GTP binding and translation elongation factor activity. An important paralog of this gene is GSPT2.\n;;\n;; also see https://www.ncbi.nlm.nih.gov/gene/10767\n;;\n;; This gene encodes a member of the GTP-binding elongation factor family. It is expressed in multiple tissues with the highest expression in heart and skeletal muscle. The intergenic region of this gene and the MYB gene has been identified to be a quantitative trait locus (QTL) controlling fetal hemoglobin level, and this region influnces erythrocyte, platelet, and monocyte counts as well as erythrocyte volume and hemoglobin content. DNA polymorphisms at this region associate with fetal hemoglobin levels and pain crises in sickle cell disease. A single nucleotide polymorphism in exon 1 of this gene is significantly associated with severity in beta-thalassemia/Hemoglobin E. Multiple alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, May 2009]\n;;\n;; and https://www.omim.org/entry/612450\n;;\n;; and http://www.uniprot.org/uniprot/Q9Y450\n;; \n;; this is the first query I learned something from: I wouldn't have known to look for HBS1L if I hadn't looked at the results from this query. That's something, I suppose.\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"HbS\" s)]\n [(fuzzy-concepto \"HbS\" m)]) \n (edgeo e)))))\n\n;; same as above\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"HBS1L\" s)]\n [(fuzzy-concepto \"HBS1L\" m)]) \n (edgeo e)))))\n\n;; https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n;; \n;; HbAS and protection against malaria\n;;\n;; Despite the obvious deleterious nature of HbSS, it is now widely accepted that the persistence of the sickle mutation in human populations is due to the protection from malaria afforded to heterozygous individuals. Haldane first proposed the concept of a heterozygote advantage against malaria in 1949 [11]. In this seminal paper, Haldane suggested that individuals heterozygous for thalassaemia, another haemoglobinopathy, were protected against malaria.\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"THBS1\" s)]\n [(fuzzy-concepto \"THBS1\" m)])\n (edgeo e)))))\n\n;; a few entries, such as\n;;\n;; ((39730 \"Thalassemia\" (41))\n;; (1328338 \"Haemoglobin E-thalassaemia disease\" (41))\n;; \"COEXISTS_WITH\"\n;; \"dsyn\"\n;; \"dsyn\"\n;; (87633595))\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"thalassaemia\" s)]\n [(fuzzy-concepto \"thalassaemia\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"haemoglobinopathy\" s)]\n [(fuzzy-concepto \"haemoglobinopathy\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"Haemoglobin disease\" s)]\n [(fuzzy-concepto \"Haemoglobin disease\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"parasitaemia\" s)]\n [(fuzzy-concepto \"parasitaemia\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"red blood cell polymorphism\" s)]\n [(fuzzy-concepto \"red blood cell polymorphism\" m)])\n (edgeo e)))))\n\n\n\n;; From https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n;;\n;; Sickle haemoglobin, sickle cell disease and sickle cell trait\n;;\n;; Sickle haemoglobin (HbS) is a structural variant of normal adult haemoglobin. Adult haemoglobin (HbAA) is made up of two alpha and two beta globin chains. HbS is the result of a single point mutation (Glu → Val) on the sixth codon of the beta globin gene [9]. Homozygotes for haemoglobin S (HbSS) with two affected beta chains develop sickle cell disease, in which polymerized haemoglobin causes red blood cells to sickle and occlude blood vessels. Vaso-occlusion affects many organs and tissues, and results in high morbidity and mortality. Heterozygotes for sickle haemoglobin (HbAS) have sickle cell trait and are generally asymptomatic [10].\n;;\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"HbAS\" s)]\n [(fuzzy-concepto \"HbAS\" m)]) \n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"sickle haemoglobin\" s)]\n [(fuzzy-concepto \"sickle haemoglobin\" m)]) \n (edgeo e)))))\n\n\n;; Aliaseses for sickle cell anemia, according to http://www.genecards.org/cgi-bin/carddisp.pl?gene=HBS1L#diseases:\n;;\n;; drepanocytosis\n;; hb sc disease\n;; hb-s/hb-c disease\n;; hb-ss disease without crisis\n;; hemoglobin s disease without crisis\n;; hemoglobin sc disease\n;; sickle-cell/hb-c disease without crisis\n;; hbsc disease\n;; sickle cell - hemoglobin c disease\n;; sickle cell-hemoglobin c disease syndrome\n;; hbs disease\n;; hemoglobin s disease\n;; sickling disorder due to hemoglobin s\n;; hemoglobin sc\n;; sc disease\n;; hemoglobin ss\n;; sickle cell disease\n;; skca\n;; anemia, sickle cell\n;; sickle cell trait\n\n;; 'Antisickling Agents' and 'Sickling test' entries show up, although these don't appear critical for our query.\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"sickling\" s)]\n [(fuzzy-concepto \"sickling\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"drepanocytosis\" s)]\n [(fuzzy-concepto \"drepanocytosis\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"hemoglobinose S\" s)]\n [(fuzzy-concepto \"hemoglobinose S\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"sicklemia\" s)]\n [(fuzzy-concepto \"sicklemia\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"hbsc\" s)]\n [(fuzzy-concepto \"hbsc\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"skca\" s)]\n [(fuzzy-concepto \"skca\" m)])\n (edgeo e)))))\n\n;; lots of results! 'Hemoglobin SS disease with crisis'\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"hemoglobin ss\" s)]\n [(fuzzy-concepto \"hemoglobin ss\" m)])\n (edgeo e)))))\n\n;; nothing\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"hemoglobin s disease\" s)]\n [(fuzzy-concepto \"hemoglobin s disease\" m)])\n (edgeo e)))))\n\n\n;; Ah! There are a ton of entries here!\n;;\n;; There are entries under 'falciparum' that we are missing from looking for 'malaria', such as 'Plasmodium falciparum infection'.\n;;\n;; https://en.wikipedia.org/wiki/Plasmodium_falciparum\n;;\n;; Plasmodium falciparum is a unicelluar protozoan parasite of humans, and the deadliest species of Plasmodium that cause malaria in humans.[2] It is transmitted through the bite of a female Anopheles mosquito. It is responsible for roughly 50% of all malaria cases.[3] It causes the disease's most dangerous form called falciparum malaria.[4][5] It is therefore regarded as the deadliest parasite in humans, causing a conservative estimate of one million deaths every year.[6]\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"falciparum\" s)]\n [(fuzzy-concepto \"falciparum\" m)]) \n (edgeo e)))))\n\n;; https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n;;\n;; Biochemical and mechanical changes in infected HbAS red blood cells have been shown to alter disease progression. Rosette formation, which is the binding of P. falciparum-infected red blood cells to uninfected red blood cells, is thought to lead to microcirculatory obstruction in cerebral malaria [55, 56, 57, 58, 59]. Rosette formation was found to be impaired in P. falciparum-infected HbAS red blood cells under deoxygenated conditions [57]. Impaired rosette formation with HbAS red blood cells may be due to increased sickling of these cells in deoxygenated conditions [47, 48] or to reduced expression of erythrocyte surface adherence proteins [60]. Decreased rosette formation and the resulting decreased circulatory obstruction might contribute to protection against severe malaria in HbAS individuals.\n;;\n;; 'Rosette formation' entries!\n;;\n;; ((35863 \"Rosette formation\" (53))\n;; (24535 \"Malaria, Falciparum\" (41))\n;; \"COEXISTS_WITH\"\n;; \"fndg\"\n;; \"dsyn\"\n;; (14312565))\n;;\n;; ((24530 \"Malaria\" (41))\n;; (35863 \"Rosette formation\" (53))\n;; \"COEXISTS_WITH\"\n;; \"dsyn\"\n;; \"fndg\"\n;; (33906042 32437650))\n;;\n;; ((24534 \"Malaria, Cerebral\" (41))\n;; (35863 \"Rosette formation\" (53))\n;; \"COEXISTS_WITH\"\n;; \"dsyn\"\n;; \"fndg\"\n;; (25261309))\n;;\n;; ((35863 \"Rosette formation\" (53))\n;; (858320 \"Plasmodium ovale infection\" (41))\n;; \"COEXISTS_WITH\"\n;; \"fndg\"\n;; \"dsyn\"\n;; (18527923))\n;;\n;; look at this one\n;;\n;; ((11501 \"Deoxyglucose\" (25 108))\n;; (35863 \"Rosette formation\" (53))\n;; \"INHIBITS\"\n;; \"phsu\"\n;; \"fndg\"\n;; (2653977))\n;;\n;; and\n;;\n;; ((142009 \"erythrocyte receptor\" (116 59 1))\n;; (35863 \"Rosette formation\" (53))\n;; \"AFFECTS\"\n;; \"aapp\"\n;; \"fndg\"\n;; (12083367 6642028))\n;;\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"Rosette\" s)]\n [(fuzzy-concepto \"Rosette\" m)])\n (edgeo e)))))\n\n;; a few answers. perhaps this one?\n;;\n;; ((35864 \"Immunocytoadherence\" (78))\n;; (275518 \"Acute infectious disease\" (41))\n;; \"DIAGNOSES\"\n;; \"lbpr\"\n;; \"dsyn\"\n;; (1752119))\n;;\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"cytoadherence\" s)]\n [(fuzzy-concepto \"cytoadherence\" m)])\n (edgeo e)))))\n\n;; this is a good one!\n;; full of entries like this:\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (1511 \"Adhesions\" (2 41))\n;; \"ASSOCIATED_WITH\"\n;; \"aapp\"\n;; \"dsyn\"\n;; (81338955 73350498 42416200 31920224))\n;;\n;; https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n;;\n;; Reduced cytoadherence has also been implicated as a mechanism of protection in HbAS individuals. Infected red blood cells express one of a family of parasite-encoded P. falciparum erythrocyte membrane protein 1 (PfEMP-1) molecules on the erythrocyte surface, and via this protein adhere to endothelial cells in the microvasculature [61, 62, 63, 64] .This process, termed cytoadherence, enables parasites to sequester in the vasculature and avoid clearance by the spleen [64].\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (1511 \"Adhesions\" (2 41))\n;; \"AUGMENTS\"\n;; \"aapp\"\n;; \"acab\"\n;; (75786625))\n;;\n;; ((14792 \"Erythrocytes\" (28))\n;; (1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; \"LOCATION_OF\"\n;; \"cell\"\n;; \"aapp\"\n;; (45103237 45103232))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (6904 \"Capillary Endothelium\" (128))\n;; \"PART_OF\"\n;; \"aapp\"\n;; \"tisu\"\n;; (27874897))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (14257 \"Endothelium\" (128))\n;; \"PART_OF\"\n;; \"aapp\"\n;; \"tisu\"\n;; (81466965 59207003))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (20964 \"Immunity\" (107))\n;; \"AFFECTS\"\n;; \"aapp\"\n;; \"phsf\"\n;; (42255905))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (21311 \"Infection\" (41))\n;; \"CAUSES\"\n;; \"aapp\"\n;; \"dsyn\"\n;; (67457041))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (24530 \"Malaria\" (41))\n;; \"AFFECTS\"\n;; \"aapp\"\n;; \"dsyn\"\n;; (36678097))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (24530 \"Malaria\" (41))\n;; \"ASSOCIATED_WITH\"\n;; \"aapp\"\n;; \"dsyn\"\n;; (89492035 87380723 87061566 78738418 74230694 54367939))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (24530 \"Malaria\" (41))\n;; \"PREVENTS\"\n;; \"imft\"\n;; \"dsyn\"\n;; (81990442))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (24534 \"Malaria, Cerebral\" (41))\n;; \"ASSOCIATED_WITH\"\n;; \"aapp\"\n;; \"dsyn\"\n;; (82747148))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (24535 \"Malaria, Falciparum\" (41))\n;; \"CAUSES\"\n;; \"aapp\"\n;; \"dsyn\"\n;; (74670901 67457034))\n;;\n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (24535 \"Malaria, Falciparum\" (41))\n;; \"PREVENTS\"\n;; \"imft\"\n;; \"dsyn\"\n;; (48365380 36796545))\n;;\n;; and look at this one!\n;; \n;; ((1429928 \"erythrocyte membrane protein 1, Plasmodium falciparum\" (59 1 70))\n;; (1368474 \"rosetting\" (27))\n;; \"AFFECTS\"\n;; \"aapp\"\n;; \"celf\"\n;; (75067858 58808770 37978092))\n;;\n(time (pretty-print (run* (e)\n (fresh (s m e-rest)\n (== `(,s ,m . ,e-rest) e)\n (conde\n [(fuzzy-concepto \"erythrocyte membrane protein\" s)]\n [(fuzzy-concepto \"erythrocyte membrane protein\" m)])\n (edgeo e)))))\n\n\n\n\n\n;; https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n;;\n;; These discrepancies suggest that the mechanism of protection afforded by HbAS is complex, with impacts on both the development of parasitaemia and the control of parasitaemia once it is established.\n\n\n;; https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-12-317\n;;\n;; Other related diseases to explore:\n;;\n;; These data provide comprehensive evidence for a global geographical association between malaria burden and HbS allele frequency, particularly in sub-Saharan Africa. Furthermore, evidence for the protective effects of other red blood cell polymorphisms against malaria, including haemoglobin C, haemoglobin E, thalassaemias, and ovalocytosis have also been described [17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28].\n" }, { "path": "attic/code/tacrine.rkt", "content": "#lang racket\n;; We are using Racket as our base language.\n\n;; Load the mediKanren logic engine, and the Racket-formatted version\n;; of a lightly curated and lightly normalized version of the SemMedDB\n;; knowledge base.\n(require\n \"db.rkt\"\n \"mk-db.rkt\"\n \"concept.rkt\"\n \"edge.rkt\"\n;; \"helpers.rkt\"\n )\n\n(displayln\n \"Finished loading mk-db.rkt.\")\n\n;; find connections between tacrine and alzheimer's disease\n\n;; What concepts related to tacrine and alzheimer's disease does\n;; SemMedDB know about?\n\n;; tacrine\n;;\n;; (39245 \"Tacrine\" (\"orch\" \"phsu\"))\n;; seems like the winner\n(run* (q) (fuzzy-concepto \"tacrine\" q))\n;; =>\n'((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (99894 \"7-methoxytacrine\" (\"orch\" \"phsu\"))\n (295379 \"4-hydroxytacrine\" (\"orch\" \"phsu\"))\n (295380 \"2-hydroxytacrine\" (\"phsu\" \"orch\"))\n (386973 \"6-chlorotacrine\" (\"orch\"))\n (659809 \"N-methyltacrine\" (\"orch\"))\n (771182 \"Tacrine Hydrochloride\" (\"phsu\" \"orch\"))\n (1435294 \"N-butyramide-tacrine\" (\"orch\")))\n\n;; Same query as above, but restrict to pharmacologic substances\n;; (\"phsu\").\n(run* (q)\n (fuzzy-concepto \"tacrine\" q)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) q)\n (membero \"phsu\" concept-type*)))\n;; =>\n'((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (99894 \"7-methoxytacrine\" (\"orch\" \"phsu\"))\n (295379 \"4-hydroxytacrine\" (\"orch\" \"phsu\"))\n (295380 \"2-hydroxytacrine\" (\"phsu\" \"orch\"))\n (771182 \"Tacrine Hydrochloride\" (\"phsu\" \"orch\")))\n\n\n;; alzheimer\n;;\n;; (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n;; seems like the winner\n(run* (q) (fuzzy-concepto \"alzheimer\" q))\n;; =>\n'((2395 \"Alzheimer's Disease\" (\"dsyn\"))\n (51532 \"Alzheimer's disease antigen\" (\"aapp\"))\n (276496 \"Familial Alzheimer's disease\" (\"dsyn\"))\n (333736 \"Alzheimer type II glial cell\" (\"cell\"))\n (338450 \"Focal Alzheimer's disease\" (\"dsyn\"))\n (494463 \"Alzheimer Disease, Late Onset\" (\"mobd\"))\n (528480 \"PS2 protein (alzheimer-associated)\" (\"aapp\" \"gngm\" \"bacs\"))\n (750901 \"Alzheimer Disease, Early Onset\" (\"dsyn\"))\n (949574 \"Alzheimer Vaccines\" (\"phsu\" \"imft\"))\n (1456623 \"Alzheimer's Caregivers\" (\"humn\" \"popg\")))\n\n\n;; What are the direct connections between Tacrine (a Pharmacologic Substance, or \"phsu\")\n;; and Alzheimer's Disease (a Disease or Syndrome, or \"dsyn\")?\n;;\n;; We are using the semantic types for the edges to improve\n;; performance, and the CUI's from the \"Tacrine\" and \"Alzheimer's\n;; Disease\" concepts we discovered above.\n;;\n;; There are two results, both with TREATS amnd NEG_TREATES predicates.\n;; There are many more PubMed entries for TREATS (278) than for NEG_TREATS (2).\n(run* (e)\n (fresh (s o predicate pubref)\n (== e `(,s ,o ,predicate \"phsu\" \"dsyn\" ,pubref))\n (cuio s 39245) (cuio o 2395) (edgeo e)))\n;;\n;; which is equivalent to the slightly more verbose\n;;\n(run* (e)\n (fresh (s o predicate pubref)\n (== e `(,s ,o ,predicate \"phsu\" \"dsyn\" ,pubref))\n (== '(39245 \"Tacrine\" (\"orch\" \"phsu\")) s)\n (== '(2395 \"Alzheimer's Disease\" (\"dsyn\")) o)\n (edgeo e)))\n;; =>\n'(((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n \"NEG_TREATS\"\n \"phsu\"\n \"dsyn\"\n (20371996 1984813))\n ;;\n ((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n \"TREATS\"\n \"phsu\"\n \"dsyn\"\n (27694908\n 27128182\n 27128182\n 27100474\n 27055393\n 26985691\n 26797191\n 26760993\n 26043757\n 25747977\n 25694076\n 24706520\n 24560791\n 24343873\n 24283645\n 24283645\n 24283645\n 23931443\n 23523257\n 23481643\n 23256654\n 23256654\n 23176115\n 22302942\n 22216416\n 22032870\n 22000936\n 21728972\n 21699076\n 21472092\n 21199749\n 21148081\n 21143111\n 20925094\n 20650219\n 19714494\n 19595868\n 19393253\n 19041670\n 18004213\n 17883890\n 17636619\n 16914883\n 16914883\n 16880719\n 16762377\n 16296676\n 16296676\n 15969312\n 15767760\n 15203897\n 15071608\n 15009666\n 14519085\n 14513664\n 12939598\n 12860473\n 12725862\n 12605726\n 12568834\n 12070846\n 11924005\n 11924005\n 11914957\n 11819153\n 11819153\n 11475012\n 11400868\n 11125238\n 11044776\n 11022244\n 10956426\n 10908463\n 10886308\n 10886308\n 10886308\n 10871308\n 10840182\n 10801254\n 10796507\n 10755847\n 10733605\n 10613616\n 10559571\n 10559571\n 10559571\n 10557569\n 10386551\n 10364647\n 10364647\n 10332935\n 10325444\n 10325444\n 10232064\n 10210906\n 10172459\n 10172130\n 10088136\n 9923574\n 9923574\n 9923574\n 9923574\n 9880090\n 9850772\n 9824956\n 9813462\n 9813462\n 9813462\n 9813282\n 9808364\n 9803773\n 9789247\n 9772028\n 9771828\n 9764962\n 9764962\n 9764962\n 9676739\n 9652334\n 9579280\n 9579280\n 9547467\n 9521254\n 9521254\n 9472847\n 9472847\n 9472847\n 9460755\n 9438743\n 9437436\n 9344406\n 9344406\n 9342788\n 9329726\n 9329702\n 9329702\n 9329702\n 9280671\n 9236571\n 9223063\n 9170813\n 9152571\n 9152571\n 9125881\n 9072868\n 9065747\n 9062655\n 9010644\n 9010644\n 9010644\n 8993489\n 8993489\n 8973053\n 8973053\n 8969979\n 8962456\n 8928167\n 8923803\n 8909368\n 8899701\n 8849507\n 8845704\n 8845704\n 8845704\n 8838779\n 8838779\n 8835781\n 8804554\n 8804553\n 8649552\n 8649552\n 8649552\n 8600428\n 8548601\n 8534422\n 8497088\n 8437606\n 8437605\n 8437604\n 8437603\n 8404544\n 8361451\n 8358504\n 8341950\n 8341950\n 8341134\n 8319751\n 8312036\n 8139083\n 8139061\n 8137602\n 8128836\n 8128835\n 8128835\n 8128831\n 8084981\n 8046778\n 8046778\n 7990234\n 7990233\n 7990232\n 7919566\n 7914636\n 7907454\n 7904023\n 7893376\n 7893376\n 7870908\n 7870908\n 7868848\n 7848488\n 7825478\n 7727536\n 7727536\n 7690228\n 7690228\n 7669991\n 7664190\n 7653420\n 7640148\n 7550603\n 7517383\n 7225483\n 3587295\n 3185960\n 2893967\n 2779475\n 2754707\n 2721578\n 2693104\n 2693104\n 2693104\n 2684292\n 2594683\n 2569126\n 2567933\n 2557101\n 2503129\n 2502236\n 2497817\n 2444444\n 2395447\n 2348794\n 2236461\n 2078308\n 2053502\n 2030370\n 1986300\n 1984813\n 1984813\n 1967197\n 1953964\n 1893185\n 1881606\n 1818685\n 1813659\n 1781972\n 1763782\n 1684233\n 1676097\n 1675337\n 1673209\n 1611059\n 1572123\n 1544011\n 1491741\n 1491741\n 1454836\n 1454836\n 1454835\n 1448787\n 1414271\n 1406817\n 1406817\n 1404825\n 1404819\n 1404819\n 1384265)))\n\n\n;; This variant of the query, using \"orch\" instead of \"phsu\" as the\n;; semantic type, has AFFECTS and TREATS as predicates on direct\n;; edges.\n(run* (e)\n (fresh (s o predicate pubref)\n (== e `(,s ,o ,predicate \"orch\" \"dsyn\" ,pubref))\n (cuio s 39245) (cuio o 2395) (edgeo e)))\n;; =>\n'(((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n \"AFFECTS\"\n \"orch\"\n \"dsyn\"\n (20533758\n 17908041\n 17908041\n 11900820\n 9733331\n 8090107\n 7888087\n 7884402\n 7710524\n 1544011))\n ;;\n ((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n \"TREATS\"\n \"orch\"\n \"dsyn\"\n (24515838\n 22750583\n 22192081\n 19374459\n 17636619\n 16544849\n 15258105\n 11400868\n 10886308\n 10796507\n 9813462\n 9305568\n 9249126\n 8989658\n 8496822\n 8128831\n 7656503\n 2789791\n 1981736\n 1438050)))\n\n;; Indirect connections between Tacrine and Alzheimer's, of the form\n;;\n;; Tacrine -> INHIBITS -> X -> CAUSES -> Alzheimer's\n;;\n(run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (cuio s 39245) ;; Tacrine\n (cuio o 2395) ;; Alzheimer's\n (edgeo e1)\n (edgeo e2)\n ))\n;; => 47 answers, 215 ms\n;;\n;; Not all of these answers involve inhibiting genes.\n;; For example, Acetylcholine (a neurotransmitter) is inhibited by\n;; Tacrine, and causes Alzheimer's (according to SemMedDB)\n;;\n;; We have duplicate answers, in that we have multiple answers for the same X for which\n;;\n;; Tacrine -> INHIBITS -> X -> CAUSES -> Alzheimer's\n;;\n;; This is because the INHIBITS edge Tacrine -> INHIBITS -> X can have multiple\n;; semantic types for the same X, provided X is associated with more than one semantic\n;; type. Similarly for the X -> CAUSES -> Alzheimer's edge.\n;;\n;; For example, consider these two answers:\n;;\n'(((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (1041 \"Acetylcholine\" (\"phsu\" \"nsba\" \"orch\"))\n \"INHIBITS\"\n \"orch\"\n \"nsba\"\n (27876467 9881590 9374189 8842691 8336816))\n ((1041 \"Acetylcholine\" (\"phsu\" \"nsba\" \"orch\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n \"CAUSES\"\n \"nsba\"\n \"dsyn\"\n (12770689)))\n;;\n;; and\n;;\n'(((39245 \"Tacrine\" (\"orch\" \"phsu\"))\n (1041 \"Acetylcholine\" (\"phsu\" \"nsba\" \"orch\"))\n \"INHIBITS\"\n \"orch\"\n \"nsba\"\n (27876467 9881590 9374189 8842691 8336816))\n ((1041 \"Acetylcholine\" (\"phsu\" \"nsba\" \"orch\"))\n (2395 \"Alzheimer's Disease\" (\"dsyn\"))\n \"CAUSES\"\n \"phsu\"\n \"dsyn\"\n (16863459)))\n;;\n;; In both cases X is (1041 \"Acetylcholine\" (\"phsu\" \"nsba\" \"orch\")), but\n;; the semantic types for the X -> CAUSES -> Alzheimer's edges differ:\n;;\n;; nsba|T124|Neuroreactive Substance or Biogenic Amine\n;;\n;; vs.\n;;\n;; phsu|T121|Pharmacologic Substance\n\n;; Here is a variant of the query that just returns the entities X\n;; being inhibited in the X -> CAUSES -> Alzheimer's path:\n;;\n(remove-duplicates\n (run* (m)\n (fresh (e1 e2\n s\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (cuio s 39245) ;; Tacrine\n (cuio o 2395) ;; Alzheimer's\n (edgeo e1)\n (edgeo e2)\n )))\n;; => 30 answers, 205 ms\n'((1041 \"Acetylcholine\" (\"phsu\" \"nsba\" \"orch\"))\n (1044 \"Acetylcholinesterase\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (6675 \"Calcium\" (\"bacs\" \"elii\"))\n (6685 \"Calcium Channel\" (\"bacs\" \"gngm\" \"aapp\"))\n (8377 \"Cholesterol\" (\"strd\" \"bacs\"))\n (8425 \"Cholinesterase Inhibitors\" (\"phsu\" \"orch\"))\n (8429 \"Cholinesterases\" (\"enzy\" \"gngm\" \"aapp\"))\n (17817 \"Glutathione\" (\"bacs\" \"aapp\" \"gngm\"))\n (21753 \"Interleukin-1 beta\" (\"gngm\" \"imft\" \"aapp\"))\n (22023 \"Ions\" (\"elii\"))\n (26455 \"Monoamine Oxidase A\" (\"aapp\" \"gngm\" \"enzy\"))\n (28040 \"Nicotine\" (\"phsu\" \"hops\" \"orch\"))\n (33634 \"Protein Kinase C\" (\"aapp\" \"enzy\" \"gngm\"))\n (34826 \"Muscarinic Acetylcholine Receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (34830 \"Nicotinic Receptors\" (\"rcpt\" \"gngm\" \"aapp\"))\n (36442 \"Scopolamine\" (\"orch\" \"phsu\"))\n (36751 \"Serotonin\" (\"nsba\" \"orch\"))\n (72132 \"prolyl oligopeptidase\" (\"enzy\" \"aapp\" \"gngm\"))\n (79883 \"N-Methylaspartate\" (\"aapp\" \"phsu\" \"gngm\"))\n (220839 \"Glutamate\" (\"gngm\" \"bacs\" \"aapp\"))\n (243192 \"agonists\" (\"phsu\"))\n (728810 \"Butyrylcholinesterase\" (\"enzy\" \"aapp\" \"gngm\"))\n (812281 \"ROS1 gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (965087 \"beta-site APP cleaving enzyme 1\" (\"gngm\" \"enzy\" \"aapp\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1412727 \"BACE1 gene\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412756 \"BCHE gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1413043 \"CA2 gene\" (\"gngm\" \"enzy\" \"bacs\" \"aapp\" \"rcpt\" \"phsu\"))\n (1422569\n \"SPANXC gene\"\n (\"gngm\" \"aapp\" \"enzy\" \"imft\" \"phsu\" \"horm\" \"bacs\" \"antb\")))\n\n\n;; Just return the entities X being inhibited in the\n;; Tacrine -> INHIBITS -> X -> CAUSES -> Alzheimer's path,\n;; where X has the concept type \"gngm\" (gngm|T028|Gene or Genome)\n;; \n(remove-duplicates\n (run* (m)\n (fresh (e1 e2\n s\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (cuio s 39245) ;; Tacrine\n (cuio o 2395) ;; Alzheimer's\n (edgeo e1)\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) m)\n (membero \"gngm\" concept-type*))\n )))\n;; => 21 answers, 200 ms\n'((1044 \"Acetylcholinesterase\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (6685 \"Calcium Channel\" (\"bacs\" \"gngm\" \"aapp\"))\n (8429 \"Cholinesterases\" (\"enzy\" \"gngm\" \"aapp\"))\n (17817 \"Glutathione\" (\"bacs\" \"aapp\" \"gngm\"))\n (21753 \"Interleukin-1 beta\" (\"gngm\" \"imft\" \"aapp\"))\n (26455 \"Monoamine Oxidase A\" (\"aapp\" \"gngm\" \"enzy\"))\n (33634 \"Protein Kinase C\" (\"aapp\" \"enzy\" \"gngm\"))\n (34826 \"Muscarinic Acetylcholine Receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (34830 \"Nicotinic Receptors\" (\"rcpt\" \"gngm\" \"aapp\"))\n (72132 \"prolyl oligopeptidase\" (\"enzy\" \"aapp\" \"gngm\"))\n (79883 \"N-Methylaspartate\" (\"aapp\" \"phsu\" \"gngm\"))\n (220839 \"Glutamate\" (\"gngm\" \"bacs\" \"aapp\"))\n (728810 \"Butyrylcholinesterase\" (\"enzy\" \"aapp\" \"gngm\"))\n (812281 \"ROS1 gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (965087 \"beta-site APP cleaving enzyme 1\" (\"gngm\" \"enzy\" \"aapp\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1412727 \"BACE1 gene\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412756 \"BCHE gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1413043 \"CA2 gene\" (\"gngm\" \"enzy\" \"bacs\" \"aapp\" \"rcpt\" \"phsu\"))\n (1422569\n \"SPANXC gene\"\n (\"gngm\" \"aapp\" \"enzy\" \"imft\" \"phsu\" \"horm\" \"bacs\" \"antb\")))\n\n;; Just return the entities X being inhibited in the\n;; -> INHIBITS -> X -> CAUSES -> \n;; path, where X has the concept type \"gngm\"\n;; (gngm|T028|Gene or Genome)\n;; and where concepts must have the \"phsu\" concept type\n;; associated with them,\n;; and where concepts must have the \"dsyn\" concept type\n;; associated with them.\n;;\n;; Interestingly, the same 21 answers are returned as when we use\n;; the specific CUIs\n;;\n;; (cuio s 39245) ;; Tacrine\n;; (cuio o 2395) ;; Alzheimer's\n;;\n;; Keep in mind that there are only 21 X's, but more than 21 paths from\n;; -> INHIBITS -> X -> CAUSES -> \n;; since sometimes there are multiple direct edges between the same concepts,\n;; with different semantic types (and PubMed Ids).\n;;\n;; Note that requiring a concept has a concept type associated with it is *less*\n;; specific than requiring an edge of the path have that type.\n(remove-duplicates\n (run* (m)\n (fresh (e1 e2\n s\n o p1 p2 ts t1 t2 t3 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 ,t3 ,r2))\n (fuzzy-concepto \"tacrine\" s)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) s)\n (membero \"phsu\" concept-type*))\n (fuzzy-concepto \"alzheimer\" o)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) o)\n (membero \"dsyn\" concept-type*))\n (edgeo e1)\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) m)\n (membero \"gngm\" concept-type*))\n )))\n;; => 21 answers, 935 ms\n'((1044 \"Acetylcholinesterase\" (\"gngm\" \"enzy\" \"aapp\"))\n (2716 \"Amyloid\" (\"bacs\" \"aapp\" \"gngm\"))\n (6685 \"Calcium Channel\" (\"bacs\" \"gngm\" \"aapp\"))\n (8429 \"Cholinesterases\" (\"enzy\" \"gngm\" \"aapp\"))\n (17817 \"Glutathione\" (\"bacs\" \"aapp\" \"gngm\"))\n (21753 \"Interleukin-1 beta\" (\"gngm\" \"imft\" \"aapp\"))\n (26455 \"Monoamine Oxidase A\" (\"aapp\" \"gngm\" \"enzy\"))\n (33634 \"Protein Kinase C\" (\"aapp\" \"enzy\" \"gngm\"))\n (34826 \"Muscarinic Acetylcholine Receptor\" (\"aapp\" \"gngm\" \"rcpt\"))\n (34830 \"Nicotinic Receptors\" (\"rcpt\" \"gngm\" \"aapp\"))\n (72132 \"prolyl oligopeptidase\" (\"enzy\" \"aapp\" \"gngm\"))\n (79883 \"N-Methylaspartate\" (\"aapp\" \"phsu\" \"gngm\"))\n (220839 \"Glutamate\" (\"gngm\" \"bacs\" \"aapp\"))\n (728810 \"Butyrylcholinesterase\" (\"enzy\" \"aapp\" \"gngm\"))\n (812281 \"ROS1 gene\" (\"bacs\" \"aapp\" \"gngm\"))\n (965087 \"beta-site APP cleaving enzyme 1\" (\"gngm\" \"enzy\" \"aapp\"))\n (1364818 \"APP gene\" (\"enzy\" \"gngm\" \"bacs\" \"aapp\" \"imft\"))\n (1412727 \"BACE1 gene\" (\"aapp\" \"gngm\" \"enzy\"))\n (1412756 \"BCHE gene\" (\"enzy\" \"gngm\" \"aapp\"))\n (1413043 \"CA2 gene\" (\"gngm\" \"enzy\" \"bacs\" \"aapp\" \"rcpt\" \"phsu\"))\n (1422569\n \"SPANXC gene\"\n (\"gngm\" \"aapp\" \"enzy\" \"imft\" \"phsu\" \"horm\" \"bacs\" \"antb\")))\n\n;; \"Canned\" query schema.\n;;\n;; Return the entities X being inhibited in the\n;; -> INHIBITS -> X -> CAUSES -> \n;; path, where X has the concept type \"gngm\"\n;; (gngm|T028|Gene or Genome)\n;; and where concepts must have the \"phsu\" concept type\n;; associated with them,\n;; and where concepts must have the \"dsyn\" concept type\n;; associated with them.\n(define (find-inhibited-genes fuzzy-drug-name fuzzy-disease-name)\n (remove-duplicates\n (run* (m)\n (fresh (e1 e2\n s\n o p1 p2 ts t1 t2 t3 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 ,t3 ,r2))\n (fuzzy-concepto fuzzy-drug-name s)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) s)\n (membero \"phsu\" concept-type*))\n (fuzzy-concepto fuzzy-disease-name o)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) o)\n (membero \"dsyn\" concept-type*))\n (edgeo e1)\n (edgeo e2)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) m)\n (membero \"gngm\" concept-type*))\n ))))\n\n(find-inhibited-genes \"tacrine\" \"alzheimer\")\n;; => 21 answers, 900 ms\n\n\n;; variants of the basic query above\n\n\n;; Use full concept entries, rather than CUIs, for Tacrine and Alzheimer's Disease.\n;; This is equivalent to using the CUIs, but is more verbose and easier for humans to read.\n(run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (== '(39245 \"Tacrine\" (\"orch\" \"phsu\")) s)\n (== '(2395 \"Alzheimer's Disease\" (\"dsyn\")) o)\n (edgeo e1)\n (edgeo e2)\n ))\n;; => 47 answers, 215 ms\n\n\n;; Instead of using one specific concept each for tacrine and for\n;; alzheimer's, do fuzzy concept searches.\n;;\n;; This query is a bit sloppy, since we are not removing duplicate\n;; answers, and are also not using concept types to ensure tacrine is\n;; a pharmacologic substance.\n;;\n;; As a result, the query may produce duplicate answers, and answers\n;; in which tacrine is not restricted to pharmacologic substances.\n(run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (fuzzy-concepto \"tacrine\" s)\n (fuzzy-concepto \"alzheimer\" o)\n (edgeo e1)\n (edgeo e2)\n ))\n;; => 57 answers, 2 seconds\n\n\n;; As above, but remove duplicate answers.\n;;\n;; Turns out there aren't duplicates for this query.\n(remove-duplicates\n (run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (fuzzy-concepto \"tacrine\" s)\n (fuzzy-concepto \"alzheimer\" o)\n (edgeo e1)\n (edgeo e2)\n )))\n;; => 57 answers, 2 seconds\n\n\n;; As above, but remove duplicate answers, and also restrict tacrine\n;; to pharmacologic substances.\n(remove-duplicates\n (run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (fuzzy-concepto \"tacrine\" s)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) s)\n (membero \"phsu\" concept-type*))\n (fuzzy-concepto \"alzheimer\" o) \n (edgeo e1)\n (edgeo e2)\n )))\n;; => 55 answers, 2 seconds\n\n;; Same query as above, but with the fuzzy alzheimer's goal moved last\n;; to improve performance.\n(remove-duplicates\n (run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 \"dsyn\" ,r2))\n (fuzzy-concepto \"tacrine\" s)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) s)\n (membero \"phsu\" concept-type*)) \n (edgeo e1) \n (edgeo e2)\n (fuzzy-concepto \"alzheimer\" o)\n )))\n;; => 55 answers, 425 ms\n\n;; Slightly different query: here we allow any fuzzy variant of\n;; alzheimer's that has semantic type \"dsyn\" associated with it (as\n;; opposed to requiring the CAUSES edge have type \"dsyn\").\n(remove-duplicates\n (run* (e1 e2)\n (fresh (s\n m ;; unknown gene or other entity being inhibited\n o p1 p2 ts t1 t2 t3 r1 r2)\n (== e1 `(,s ,m \"INHIBITS\" ,ts ,t1 ,r1))\n (== e2 `(,m ,o \"CAUSES\" ,t2 ,t3 ,r2))\n (fuzzy-concepto \"tacrine\" s)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) s)\n (membero \"phsu\" concept-type*))\n (fuzzy-concepto \"alzheimer\" o)\n (fresh (cui name concept-type*)\n (== `(,cui ,name ,concept-type*) o)\n (membero \"dsyn\" concept-type*))\n (edgeo e1)\n (edgeo e2)\n )))\n;; => 55 answers, 915 ms\n" }, { "path": "attic/medikanren/CACNA1A-full.rkt", "content": "#lang racket\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n\n membero\n rem-dups\n edgeo\n ~name-concepto\n DECREASES\n\n semmed\n monarch\n rtx\n scigraph\n )\n\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"data/semmed\")))\n(displayln \"loading monarch-lite\")\n(define monarch (time (make-db \"data/monarch-lite\")))\n(displayln \"loading rtx\")\n(define rtx (time (make-db \"data/rtx\")))\n(displayln \"loading scigraph\")\n(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; remove duplicates from a list\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))))\n\n\n(define (DECREASES pred)\n (fresh (_)\n (conde\n [(== `(,_ . \"treats\") pred)]\n [(== `(,_ . \"prevents\") pred)]\n [(== `(,_ . \"negatively_regulates\") pred)])))\n\n(displayln \"preds for X ANY-PRED CACNA1A\")\n(time (rem-dups\n (run* (q)\n (fresh (edge eid tacrine-details subject object pred eprops db)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (~name-concepto \"CACNA1A\" `(,db . ,object)) \n (edgeo `(,db . ,edge))\n (== pred q)))))\n;; =>\n'((0 . \"interacts_with\")\n (3 . \"part_of\")\n (5 . \"negatively_regulates\")\n (6 . \"coexists_with\")\n (8 . \"related_to\")\n (9 . \"affects\")\n (10 . \"produces\")\n (13 . \"positively_regulates\")\n (0 . \"directly_interacts_with\")\n (6 . \"part_of\")\n (3 . \"interacts_with\")\n (3 . \"regulates\")\n (10 . \"coexists_with\")\n (16 . \"location_of\")\n (17 . \"produces\")\n (18 . \"positively_regulates\")\n (19 . \"negatively_regulates\"))\n\n\n(displayln \"X ANY-PRED CACNA1A\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (~name-concepto \"CACNA1A\" `(,db . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo `(,db . ,edge)))))))\n\n(newline)\n(displayln \"X DECREASES CACNA1A:\")\n(time (pretty-print\n (run* (edge)\n (fresh (eid tacrine-details subject object pred eprops db)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (~name-concepto \"CACNA1A\" `(,db . ,object))\n (DECREASES pred)\n (edgeo `(,db . ,edge))))))\n" }, { "path": "attic/medikanren/DNM1L-full.rkt", "content": "#lang racket\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n\n membero\n rem-dups\n edgeo\n ~name-concepto\n DECREASES\n\n semmed\n monarch\n rtx\n ;scigraph\n )\n\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"data/semmed\")))\n(displayln \"loading monarch-lite\")\n(define monarch (time (make-db \"data/monarch-lite\")))\n(displayln \"loading rtx\")\n(define rtx (time (make-db \"data/rtx\")))\n;(displayln \"loading scigraph\")\n;(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; remove duplicates from a list\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ;((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))\n ))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ;((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))\n ))\n\n\n(define (DECREASES pred)\n (fresh (_)\n (conde\n [(== `(,_ . \"treats\") pred)]\n [(== `(,_ . \"prevents\") pred)]\n [(== `(,_ . \"negatively_regulates\") pred)])))\n\n(define (INCREASES pred)\n (fresh (_)\n (conde\n [(== `(,_ . \"produces\") pred)]\n [(== `(,_ . \"positively_regulates\") pred)])))\n\n\n(rem-dups\n (run* (q)\n (fresh (edge eid tacrine-details subject object pred eprops db\n scid scui sname sdetails\n ocid ocui oname odetails\n pred-id pred-name)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (conde\n [(~name-concepto \"DNM1L\" `(,db . ,object))]\n [(~name-concepto \"DNM1L\" `(,db . ,subject))]) \n (edgeo `(,db . ,edge))\n (== `(,pred-id . ,pred-name) pred)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== pred-name q))))\n\n(sort\n (rem-dups\n (run* (q)\n (fresh (edge eid tacrine-details subject object pred eprops db\n scid scui sname sdetails\n ocid ocui oname odetails\n pred-id pred-name)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (~name-concepto \"DNM1L\" `(,db . ,object)) \n (edgeo `(,db . ,edge)) \n (== `(,pred-id . ,pred-name) pred)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,db ,sname ,pred-name ,oname) q))))\n (lambda (e1 e2)\n (match `(,e1 ,e2)\n [`((,db1 ,sname1 ,pred-name1 ,oname1)\n (,db2 ,sname2 ,pred-name2 ,oname2))\n (string\n'((semmed \"Post-Translational Protein Processing\" \"affects\" \"DNM1L wt Allele\")\n (semmed \"RNA Interference\" \"affects\" \"DNM1L wt Allele\")\n (semmed \"Signal Transduction Pathways\" \"affects\" \"DNM1L wt Allele\")\n (semmed \"Transcription, Genetic\" \"affects\" \"DNM1L wt Allele\")\n (semmed \"Glycolysis\" \"affects\" \"DNM1L wt Allele\")\n (semmed \"Phosphorylation\" \"affects\" \"DNM1L wt Allele\")\n (semmed \"Point Mutation\" \"affects\" \"DNM1L wt Allele\")\n (semmed\n \"GTP-Binding Protein alpha Subunit, Gq\"\n \"coexists_with\"\n \"DNM1L wt Allele\")\n (semmed \"CDC2 Protein Kinase\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"GNAQ wt Allele\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"AFG3L2 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"Genes\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"FIS1 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"E2F5 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"MFF gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"ANXA6 wt Allele\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"SPG7 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"MFN1 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"Genes, cdc\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"PPARGC1A wt Allele\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"OPA1 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"SAMM50 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"OPA3 gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"CCNC wt Allele\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"Homologous Gene\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"MFN2 wt Allele\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"Lysergic Acid Diethylamide\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"Methysergide\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"Calcium\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed \"honokiol\" \"coexists_with\" \"DNM1L wt Allele\")\n (semmed\n \"2-bromolysergic acid diethylamide\"\n \"coexists_with\"\n \"DNM1L wt Allele\")\n (rtx \"GTP\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"H2O\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"Orthophosphate\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"GDP\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"APEH\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"COPS5\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"CYHR1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"ATIC\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"CDCA5\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"ATP6V1C1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"PROP1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"NUFIP1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"UBE2H\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MIEF2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"FZR1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"ARFIP1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"CPNE2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SSB\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"BCL2L1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"LLGL2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"JMJD6\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"VIM\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"VPS26A\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"TES\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"HAX1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SAMM50\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SOX2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SIRT3\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"NTRK1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MIEF1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"TBC1D15\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"PPIA\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"PSMG3\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"RRM2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SCG3\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"DUSP23\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MFF\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MARCH5\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"PGAM5\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"ESR1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"WDR5\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SCRIB\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SH3GL1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"CDC5L\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"HSPD1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"LRRK2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"ZBTB24\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"A0A0G2JQ02\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"CA14\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"EGFR\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"FIS1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"PINK1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"TMEM11\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"PEX14\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"DGUOK\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"DNAAF2\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"GSK3B\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"DIABLO\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MAGEA1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MAGEA3\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MUL1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SNW1\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"MAP3K10\" \"directly_interacts_with\" \"DNM1L\")\n (rtx \"SEC24A\" \"directly_interacts_with\" \"DNM1L\")\n (semmed \"Cyclin-Dependent Kinase 5\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed\n \"calmodulin-dependent protein kinase II\"\n \"interacts_with\"\n \"DNM1L wt Allele\")\n (semmed\n \"mitogen-activated protein kinase p38\"\n \"interacts_with\"\n \"DNM1L wt Allele\")\n (monarch \"MFF\" \"interacts_with\" \"DNM1L\")\n (semmed\n \"Cyclic AMP-Dependent Protein Kinases\"\n \"interacts_with\"\n \"DNM1L wt Allele\")\n (semmed \"CDC2 Protein Kinase\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"DGUOK\" \"interacts_with\" \"DNM1L\")\n (semmed \"Ligase\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"Actins\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"CASP8\" \"interacts_with\" \"DNM1L\")\n (semmed \"TRANSCRIPTION FACTOR\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"Mitochondrial Proteins\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"DNM1L\" \"interacts_with\" \"DNM1L\")\n (semmed \"Calmodulin\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"Insulin\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"PINK1\" \"interacts_with\" \"DNM1L\")\n (semmed \"Specific antibody\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"PKA inhibitor\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"EGFR\" \"interacts_with\" \"DNM1L\")\n (semmed \"Soluble ErbB-1\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"SOD1\" \"interacts_with\" \"DNM1L\")\n (semmed \"TGFB1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"SQSTM1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"SOX2\" \"interacts_with\" \"DNM1L\")\n (semmed \"FUNDC1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"GSKIP gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"CSNK2A1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"PEX11B\" \"interacts_with\" \"DNM1L\")\n (semmed \"APP gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"MUL1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"PEX14\" \"interacts_with\" \"DNM1L\")\n (semmed \"GRAP2 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"PARK7 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"MFN2\" \"interacts_with\" \"DNM1L\")\n (semmed \"MIEF2 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"FIS1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"HAX1\" \"interacts_with\" \"DNM1L\")\n (semmed \"EGFR gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"CAMK2G gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"DNAAF2\" \"interacts_with\" \"DNM1L\")\n (semmed \"POLDIP2 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"NUP62 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"PRKN\" \"interacts_with\" \"DNM1L\")\n (semmed \"MIEF1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"CA2 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"NTRK1\" \"interacts_with\" \"DNM1L\")\n (semmed \"MAPK1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"LRRK2\" \"interacts_with\" \"DNM1L\")\n (semmed \"MAPT gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"APP wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"SNW1\" \"interacts_with\" \"DNM1L\")\n (semmed \"AIMP2 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"MAPK14 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"FIS1\" \"interacts_with\" \"DNM1L\")\n (semmed \"KHDRBS1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"OPA1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"CHCHD3\" \"interacts_with\" \"DNM1L\")\n (semmed \"RAB32 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"CAMP gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"GABRR1\" \"interacts_with\" \"DNM1L\")\n (semmed \"RAD50 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"PHEX gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"FZR1\" \"interacts_with\" \"DNM1L\")\n (semmed \"SAMM50 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"AHSA1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"SAMM50\" \"interacts_with\" \"DNM1L\")\n (semmed \"CDK1 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"mfn2\" \"interacts_with\" \"dnm1l\")\n (semmed \"CANX wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"MFN1\" \"interacts_with\" \"DNM1L\")\n (semmed \"MYH14 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"DCTN4 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"Itsn2\" \"interacts_with\" \"Dnm1l\")\n (monarch \"MIEF1\" \"interacts_with\" \"DNM1L\")\n (semmed \"GTF2H1 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"EHD1 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"TBC1D15\" \"interacts_with\" \"DNM1L\")\n (semmed \"CRK gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"MFN2 wt Allele\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"MUL1\" \"interacts_with\" \"DNM1L\")\n (semmed \"SEPT2 gene\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"LLGL2\" \"interacts_with\" \"DNM1L\")\n (semmed \"Plasmids\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"arenobufagin\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"CDC5L\" \"interacts_with\" \"DNM1L\")\n (semmed \"Calcium\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"sodium bisulfide\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"Syngap1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"CA14\" \"interacts_with\" \"DNM1L\")\n (semmed \"Staurosporine\" \"interacts_with\" \"DNM1L wt Allele\")\n (semmed \"15-deoxyprostaglandin J2\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"MTFP1\" \"interacts_with\" \"DNM1L\")\n (semmed \"Reactive Oxygen Species\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"synj1\" \"interacts_with\" \"dnm1l\")\n (semmed \"Cyclic AMP\" \"interacts_with\" \"DNM1L wt Allele\")\n (monarch \"ATP6V1C1\" \"interacts_with\" \"DNM1L\")\n (monarch \"Mysm1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"MARCH5\" \"interacts_with\" \"DNM1L\")\n (monarch \"Eed\" \"interacts_with\" \"Dnm1l\")\n (monarch \"PPIA\" \"interacts_with\" \"DNM1L\")\n (monarch \"PEX11A\" \"interacts_with\" \"DNM1L\")\n (monarch \"NUFIP1\" \"interacts_with\" \"DNM1L\")\n (monarch \"AVL9\" \"interacts_with\" \"DNM1L\")\n (monarch \"Lrrk2\" \"interacts_with\" \"Dnm1l\")\n (monarch \"FGL1\" \"interacts_with\" \"DNM1L\")\n (monarch \"CDCA5\" \"interacts_with\" \"DNM1L\")\n (monarch \"gak\" \"interacts_with\" \"dnm1l\")\n (monarch \"PGAM5\" \"interacts_with\" \"DNM1L\")\n (monarch \"Pgam5\" \"interacts_with\" \"Dnm1l\")\n (monarch \"ARFIP1\" \"interacts_with\" \"DNM1L\")\n (monarch \"DUSP23\" \"interacts_with\" \"DNM1L\")\n (monarch \"COPS5\" \"interacts_with\" \"DNM1L\")\n (monarch \"CPNE2\" \"interacts_with\" \"DNM1L\")\n (monarch \"MYSM1\" \"interacts_with\" \"DNM1L\")\n (monarch \"Cyfip1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"BCL2L1\" \"interacts_with\" \"DNM1L\")\n (monarch \"PEX11G\" \"interacts_with\" \"DNM1L\")\n (monarch \"synrg\" \"interacts_with\" \"dnm1l\")\n (monarch \"UNK\" \"interacts_with\" \"DNM1L\")\n (monarch \"Synj1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"Nek2\" \"interacts_with\" \"DNM1L\")\n (monarch \"Akap1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"['Kif19a', 'Kif19']\" \"interacts_with\" \"DNM1L\")\n (monarch \"Wdr5\" \"interacts_with\" \"DNM1L\")\n (monarch \"Foxp3\" \"interacts_with\" \"Dnm1l\")\n (monarch \"Unk\" \"interacts_with\" \"Dnm1l\")\n (monarch \"eps15\" \"interacts_with\" \"dnm1l\")\n (monarch \"Ppp3r1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"casp8\" \"interacts_with\" \"dnm1l\")\n (monarch \"LOC100911485\" \"interacts_with\" \"Dnm1l\")\n (monarch \"grapa\" \"interacts_with\" \"dnm1l\")\n (monarch \"Grb2\" \"interacts_with\" \"Dnm1l\")\n (monarch \"mfn1b\" \"interacts_with\" \"dnm1l\")\n (monarch \"Exoc5\" \"interacts_with\" \"Dnm1l\")\n (monarch \"itsn2a\" \"interacts_with\" \"dnm1l\")\n (monarch \"Casp8\" \"interacts_with\" \"Dnm1l\")\n (monarch \"grb2b\" \"interacts_with\" \"dnm1l\")\n (monarch \"Sept7\" \"interacts_with\" \"Dnm1l\")\n (monarch \"grb2a\" \"interacts_with\" \"dnm1l\")\n (monarch \"Mfn1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"eps15l1a\" \"interacts_with\" \"dnm1l\")\n (monarch \"Eps15l1\" \"interacts_with\" \"Dnm1l\")\n (monarch \"grapb\" \"interacts_with\" \"dnm1l\")\n (monarch \"Eps15\" \"interacts_with\" \"Dnm1l\")\n (monarch \"itsn2b\" \"interacts_with\" \"dnm1l\")\n (monarch \"Mfn2\" \"interacts_with\" \"Dnm1l\")\n (monarch \"itsn1\" \"interacts_with\" \"dnm1l\")\n (monarch \"Trip12\" \"interacts_with\" \"Dnm1l\")\n (monarch \"Fis1\" \"interacts_with\" \"Dnm1l\")\n (monarch #f \"interacts_with\" \"dnm1l\")\n (semmed \"Entire hippocampus\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Retina\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Tissue membrane\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Muscle\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Heart\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Neostriatum\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Brain\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Ovary\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Body tissue\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Cerebral cortex\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Common carotid artery\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Kidney\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"HeLa Cells\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Hepatocyte\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Differentiated muscle cell\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Mammalian Cell\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Neurons\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Lymphocyte\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Primary spermatocyte\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Cells\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Peripheral Blood Lymphocyte\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Chinese Hamster Ovary Cell\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Cultured Cells\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Oocytes\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Fibroblasts\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Neuroglia\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Adipocytes\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Clone Cells\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Purkinje Cells\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"trans-Golgi Network\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Golgi Apparatus\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Mitochondria\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Mitochondrial Membrane, Outer\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Dendritic Spines\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Organelles\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Membrane\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"cell cortex\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Cytoplasm\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Chromosomes, Human, Pair 21\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Cell Fraction\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Endoplasmic Reticulum\" \"location_of\" \"DNM1L wt Allele\")\n (semmed \"Mitochondrial Membranes\" \"location_of\" \"DNM1L wt Allele\")\n (semmed\n \"Mitochondrial electron transport chain\"\n \"location_of\"\n \"DNM1L wt Allele\")\n (semmed\n \"mitogen-activated protein kinase p38\"\n \"negatively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"Citrate (si)-Synthase\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed\n \"Cyclic AMP-Dependent Protein Kinases\"\n \"negatively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"angiogenin\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PRDX3 peroxidase\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Mitochondrial Proteins\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Collagen Type I\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"alpha-Synuclein\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"SIRT4 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"SQSTM1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"GRAP2 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MIEF2 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"HTRA2 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ACSM3 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"GPAM gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MFF gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ANXA6 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PKM2 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"CS gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PRKAB1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"POLDIP2 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"TP53 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"TP53 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MIEF1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MAPK1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"S100A7 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"AIMP2 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MAPK14 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ERVK-15 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"CUX1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ANG gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PRDX3 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PRKAA2 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"SART3 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PRKAA1 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"AHSA1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PINK1 gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"CRK gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"SIX1 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Homologous Gene\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MFN2 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ROS1 wt Allele\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed\n \"Carbonyl Cyanide m-Chlorophenyl Hydrazone\"\n \"negatively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"Bicuculline\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Niclosamide\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MicroRNAs\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"15-deoxyprostaglandin J2\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Reactive Oxygen Species\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ginkgolide K\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed\n \"9-deoxy-delta-9-prostaglandin D2\"\n \"negatively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"Small Molecule\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"cryptolepine\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Ru 360\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"RNA, Small Interfering\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Lithium Chloride\" \"negatively_regulates\" \"DNM1L wt Allele\")\n (semmed \"E-Cadherin\" \"part_of\" \"DNM1L wt Allele\")\n (semmed \"ezrin\" \"part_of\" \"DNM1L wt Allele\")\n (semmed \"Cytoplasmic Protein\" \"part_of\" \"DNM1L wt Allele\")\n (semmed \"alpha-Synuclein\" \"part_of\" \"DNM1L wt Allele\")\n (semmed \"Regulatory Sequences, Nucleic Acid\" \"part_of\" \"DNM1L wt Allele\")\n (semmed \"RNA, Small Interfering\" \"part_of\" \"DNM1L wt Allele\")\n (semmed \"Cyclin-Dependent Kinase 5\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed\n \"Proto-Oncogene Proteins c-akt\"\n \"positively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"Calcineurin\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Mitochondrial Proteins\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed\n \"Receptor Protein-Tyrosine Kinases\"\n \"positively_regulates\"\n \"DNM1L wt Allele\")\n (semmed\n \"mitochondrial calcium uniporter\"\n \"positively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"SQSTM1 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"BAX wt Allele\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"E2F5 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ATG5 wt Allele\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"AKT1 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"FAS gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"BAK1 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"OPA1 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"PRKAA2 wt Allele\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MAP1LC3A gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"BECN1 wt Allele\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"BAX gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ROCK1 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"MFN2 wt Allele\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"ROS1 wt Allele\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed\n \"Lysergic Acid Diethylamide Tartrate\"\n \"positively_regulates\"\n \"DNM1L wt Allele\")\n (semmed \"Reactive Oxygen Species\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Cadmium\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Ceramides\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Hydrogen Peroxide\" \"positively_regulates\" \"DNM1L wt Allele\")\n (semmed \"Cells\" \"produces\" \"DNM1L protein, human\")\n (semmed \"Phosphotransferases\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"CATALASE\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Mitochondrial Proteins\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"SOD2 gene\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"MFN1 gene\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"CAT gene\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"OPA1 gene\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"PINK1 gene\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"MFN2 wt Allele\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Neurons\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Cells\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Oocytes\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Podocytes\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Myocytes, Cardiac\" \"produces\" \"DNM1L wt Allele\")\n (semmed \"Mitochondria\" \"produces\" \"DNM1L wt Allele\")\n (rtx \"TFAP2A\" \"regulates\" \"DNM1L\")\n (rtx \"TBP\" \"regulates\" \"DNM1L\")\n (rtx \"RCOR1\" \"regulates\" \"DNM1L\")\n (rtx \"CHD7\" \"regulates\" \"DNM1L\")\n (rtx \"ELK1\" \"regulates\" \"DNM1L\")\n (rtx \"EOMES\" \"regulates\" \"DNM1L\")\n (rtx \"IRF3\" \"regulates\" \"DNM1L\")\n (rtx \"JUND\" \"regulates\" \"DNM1L\")\n (rtx \"MAPK3\" \"regulates\" \"DNM1L\")\n (rtx \"MAZ\" \"regulates\" \"DNM1L\")\n (rtx \"ZNF143\" \"regulates\" \"DNM1L\")\n (rtx \"HNF4A\" \"regulates\" \"DNM1L\")\n (rtx \"ZC3H11A\" \"regulates\" \"DNM1L\")\n (rtx \"CTCF\" \"regulates\" \"DNM1L\")\n (rtx \"E2F4\" \"regulates\" \"DNM1L\")\n (rtx \"E2F1\" \"regulates\" \"DNM1L\")\n (rtx \"JUN\" \"regulates\" \"DNM1L\")\n (rtx \"KDM4A\" \"regulates\" \"DNM1L\")\n (rtx \"KDM5B\" \"regulates\" \"DNM1L\")\n (rtx \"GTF2F1\" \"regulates\" \"DNM1L\")\n (rtx \"CDX2\" \"regulates\" \"DNM1L\")\n (rtx \"STAT1\" \"regulates\" \"DNM1L\")\n (rtx \"KLF4\" \"regulates\" \"DNM1L\")\n (rtx \"CEBPB\" \"regulates\" \"DNM1L\")\n (rtx \"HMGN3\" \"regulates\" \"DNM1L\")\n (rtx \"POU5F1\" \"regulates\" \"DNM1L\")\n (rtx \"ZNF384\" \"regulates\" \"DNM1L\")\n (rtx \"NFYA\" \"regulates\" \"DNM1L\")\n (rtx \"SMARCB1\" \"regulates\" \"DNM1L\")\n (rtx \"ZMIZ1\" \"regulates\" \"DNM1L\")\n (rtx \"IRF1\" \"regulates\" \"DNM1L\")\n (rtx \"SMC3\" \"regulates\" \"DNM1L\")\n (rtx \"MAPK1\" \"regulates\" \"DNM1L\")\n (rtx \"SMARCC1\" \"regulates\" \"DNM1L\")\n (rtx \"TBL1XR1\" \"regulates\" \"DNM1L\")\n (rtx \"SPI1\" \"regulates\" \"DNM1L\")\n (rtx \"BRD7\" \"regulates\" \"DNM1L\")\n (rtx \"TAL1\" \"regulates\" \"DNM1L\")\n (rtx \"SP1\" \"regulates\" \"DNM1L\")\n (rtx \"HDAC1\" \"regulates\" \"DNM1L\")\n (rtx \"CHD1\" \"regulates\" \"DNM1L\")\n (rtx \"SMARCC2\" \"regulates\" \"DNM1L\")\n (rtx \"GATA3\" \"regulates\" \"DNM1L\")\n (rtx \"HDAC2\" \"regulates\" \"DNM1L\")\n (rtx \"EP300\" \"regulates\" \"DNM1L\")\n (rtx \"SETDB1\" \"regulates\" \"DNM1L\")\n (rtx \"MGEA5\" \"regulates\" \"DNM1L\")\n (rtx \"PPARG\" \"regulates\" \"DNM1L\")\n (rtx \"MXI1\" \"regulates\" \"DNM1L\")\n (rtx \"NRF1\" \"regulates\" \"DNM1L\")\n (rtx \"PRKCD\" \"regulates\" \"DNM1L\")\n (rtx \"ZNF274\" \"regulates\" \"DNM1L\")\n (rtx \"NFATC1\" \"regulates\" \"DNM1L\")\n (rtx \"MAFK\" \"regulates\" \"DNM1L\")\n (rtx \"USF2\" \"regulates\" \"DNM1L\")\n (rtx \"RBBP5\" \"regulates\" \"DNM1L\")\n (rtx \"RFX5\" \"regulates\" \"DNM1L\")\n (rtx \"TRIM28\" \"regulates\" \"DNM1L\")\n (rtx \"BRCA1\" \"regulates\" \"DNM1L\")\n (rtx \"SIRT6\" \"regulates\" \"DNM1L\")\n (rtx \"SMARCA4\" \"regulates\" \"DNM1L\")\n (rtx \"SAP30\" \"regulates\" \"DNM1L\")\n (rtx \"RAD21\" \"regulates\" \"DNM1L\")\n (rtx \"ZNF263\" \"regulates\" \"DNM1L\")\n (rtx \"MAX\" \"regulates\" \"DNM1L\")\n (rtx \"ETV1\" \"regulates\" \"DNM1L\")\n (rtx \"EZH2\" \"regulates\" \"DNM1L\")\n (rtx \"KDM5A\" \"regulates\" \"DNM1L\")\n (rtx \"CDK1\" \"regulates\" \"DNM1L\")\n (rtx \"UBTF\" \"regulates\" \"DNM1L\")\n (rtx \"CUX1\" \"regulates\" \"DNM1L\")\n (rtx \"PINK1\" \"regulates\" \"DNM1L\")\n (rtx \"GATA2\" \"regulates\" \"DNM1L\")\n (rtx \"BACH1\" \"regulates\" \"DNM1L\")\n (rtx \"PHF8\" \"regulates\" \"DNM1L\")\n (rtx \"CDK5\" \"regulates\" \"DNM1L\")\n (rtx \"PRKACA\" \"regulates\" \"DNM1L\")\n (rtx \"CHD2\" \"regulates\" \"DNM1L\")\n (rtx \"MYC\" \"regulates\" \"DNM1L\")\n (rtx \"SREBF1\" \"regulates\" \"DNM1L\")\n (rtx \"STAT3\" \"regulates\" \"DNM1L\")\n (rtx \"SUZ12\" \"regulates\" \"DNM1L\")\n (rtx \"INS\" \"regulates\" \"DNM1L\")\n (rtx \"E2F6\" \"regulates\" \"DNM1L\")\n (rtx \"FOXA1\" \"regulates\" \"DNM1L\")\n (rtx \"GSK3B\" \"regulates\" \"DNM1L\")\n (rtx \"WRNIP1\" \"regulates\" \"DNM1L\")\n (rtx \"BCL6\" \"regulates\" \"DNM1L\")\n (rtx \"BHLHE40\" \"regulates\" \"DNM1L\")\n (rtx \"ESRRA\" \"regulates\" \"DNM1L\")\n (rtx \"ETS1\" \"regulates\" \"DNM1L\")\n (rtx \"GATA1\" \"regulates\" \"DNM1L\")\n (rtx \"HCFC1\" \"regulates\" \"DNM1L\")\n (rtx \"CCNT2\" \"regulates\" \"DNM1L\")\n (rtx \"CDK2\" \"regulates\" \"DNM1L\")\n (rtx \"MIR3183\" \"regulates\" \"DNM1L\")\n (rtx \"MIR371B\" \"regulates\" \"DNM1L\")\n (rtx \"MIR3132\" \"regulates\" \"DNM1L\")\n (rtx \"MIR516A1\" \"regulates\" \"DNM1L\")\n (rtx \"MIR711\" \"regulates\" \"DNM1L\")\n (rtx \"MIR365A\" \"regulates\" \"DNM1L\")\n (rtx \"MIR4723\" \"regulates\" \"DNM1L\")\n (rtx \"MIR4687\" \"regulates\" \"DNM1L\")\n (rtx \"MIR197\" \"regulates\" \"DNM1L\")\n (rtx \"MIR4782\" \"regulates\" \"DNM1L\")\n (rtx \"MIR513C\" \"regulates\" \"DNM1L\")\n (rtx \"MIR5001\" \"regulates\" \"DNM1L\")\n (rtx \"MIR4633\" \"regulates\" \"DNM1L\")\n (rtx \"MIR5706\" \"regulates\" \"DNM1L\")\n (rtx \"MIR502\" \"regulates\" \"DNM1L\")\n (rtx \"MIR516A2\" \"regulates\" \"DNM1L\"))\n\n'((scigraph\n \"GTP-Binding Protein alpha Subunit, Gq\"\n \"coexists_with\"\n \"DNM1L gene\")\n (scigraph \"CDC2 Protein Kinase\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"XRCC1 protein, human\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"porin\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"arenobufagin\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Lysergic Acid Diethylamide\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Cardiolipins\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Staurosporine\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Glucose\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Calcium\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"MFN1 gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"FIS1 gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"SAMM50 gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"CCNC gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Genes, cdc\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Genes\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"Homologous Gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"MFN2 gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"cyclin C\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"GNAQ gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"ANXA6 gene\" \"coexists_with\" \"DNM1L gene\")\n (scigraph \"MFF\" \"interacts_with\" \"DNM1L\")\n (scigraph \"DGUOK\" \"interacts_with\" \"DNM1L\")\n (scigraph \"CASP8\" \"interacts_with\" \"DNM1L\")\n (scigraph \"CSNK2A1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"DNM1L\" \"interacts_with\" \"DNM1L\")\n (scigraph \"PINK1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"EGFR\" \"interacts_with\" \"DNM1L\")\n (scigraph \"SOD1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"SOX2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"mfn2\" \"interacts_with\" \"dnm1l\")\n (scigraph \"PEX11B\" \"interacts_with\" \"DNM1L\")\n (scigraph \"PEX14\" \"interacts_with\" \"DNM1L\")\n (scigraph \"MFN2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"HAX1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"synj1\" \"interacts_with\" \"dnm1l\")\n (scigraph \"DNAAF2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Syngap1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"PRKN\" \"interacts_with\" \"DNM1L\")\n (scigraph \"NTRK1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Eed\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"LRRK2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"gak\" \"interacts_with\" \"dnm1l\")\n (scigraph \"SNW1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Lrrk2\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"Itsn2\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"FIS1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"CHCHD3\" \"interacts_with\" \"DNM1L\")\n (scigraph \"MUL1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"GABRR1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"synrg\" \"interacts_with\" \"dnm1l\")\n (scigraph \"FZR1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Cyfip1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"SAMM50\" \"interacts_with\" \"DNM1L\")\n (scigraph \"MFN1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Akap1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MIEF1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"eps15\" \"interacts_with\" \"dnm1l\")\n (scigraph \"TBC1D15\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Foxp3\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"Mysm1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"Unk\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MUL1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"MIEF2 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"LLGL2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"casp8\" \"interacts_with\" \"dnm1l\")\n (scigraph \"CDC5L\" \"interacts_with\" \"DNM1L\")\n (scigraph \"CA14\" \"interacts_with\" \"DNM1L\")\n (scigraph \"grapa\" \"interacts_with\" \"dnm1l\")\n (scigraph \"Pgam5\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MTFP1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"FIS1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"ATP6V1C1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"mfn1b\" \"interacts_with\" \"dnm1l\")\n (scigraph \"MARCH5\" \"interacts_with\" \"DNM1L\")\n (scigraph \"PPIA\" \"interacts_with\" \"DNM1L\")\n (scigraph \"itsn2a\" \"interacts_with\" \"dnm1l\")\n (scigraph \"Synj1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"PEX11A\" \"interacts_with\" \"DNM1L\")\n (scigraph \"MYH14 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"NUFIP1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"grb2b\" \"interacts_with\" \"dnm1l\")\n (scigraph \"AVL9\" \"interacts_with\" \"DNM1L\")\n (scigraph \"FGL1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"grb2a\" \"interacts_with\" \"dnm1l\")\n (scigraph \"Ppp3r1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"CDCA5\" \"interacts_with\" \"DNM1L\")\n (scigraph \"SAMM50 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"PGAM5\" \"interacts_with\" \"DNM1L\")\n (scigraph \"eps15l1a\" \"interacts_with\" \"dnm1l\")\n (scigraph \"ARFIP1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"DUSP23\" \"interacts_with\" \"DNM1L\")\n (scigraph \"grapb\" \"interacts_with\" \"dnm1l\")\n (scigraph \"LOC100911485\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"COPS5\" \"interacts_with\" \"DNM1L\")\n (scigraph \"FUNDC1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"CPNE2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"itsn2b\" \"interacts_with\" \"dnm1l\")\n (scigraph \"MYSM1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"BCL2L1\" \"interacts_with\" \"DNM1L\")\n (scigraph \"itsn1\" \"interacts_with\" \"dnm1l\")\n (scigraph \"Grb2\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"PEX11G\" \"interacts_with\" \"DNM1L\")\n (scigraph \"OPA1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"UNK\" \"interacts_with\" \"DNM1L\")\n (scigraph #f \"interacts_with\" \"dnm1l\")\n (scigraph \"Nek2\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Exoc5\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"['Kif19a', 'Kif19']\" \"interacts_with\" \"DNM1L\")\n (scigraph \"MAPT gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Wdr5\" \"interacts_with\" \"DNM1L\")\n (scigraph \"Casp8\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MIEF1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Sept7\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"PARK7 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Mfn1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MFN2 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Eps15l1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MAPK1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Eps15\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"NIN gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Mfn2\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"CDK1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Trip12\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"MFF gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Fis1\" \"interacts_with\" \"Dnm1l\")\n (scigraph \"CAMP gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"RAD50 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"CANX gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"TGFB1 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"RAB32 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"CAMK2G gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"CA2 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"PHEX gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"SEPT2 gene\" \"interacts_with\" \"DNM1L gene\")\n (scigraph \"Purkinje Cells\" \"location_of\" \"DNM1L gene\")\n (scigraph \"trans-Golgi Network\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Dendritic Spines\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Peripheral Blood Lymphocyte\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Chinese Hamster Ovary Cell\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Mitochondrial Membrane, Outer\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Differentiated muscle cell\" \"location_of\" \"DNM1L gene\")\n (scigraph \"perinuclear region\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Primary spermatocyte\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Cytosol\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Golgi Apparatus\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Cytoplasm\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Mitochondrial Membranes\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Mammalian Cell\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Tissue membrane\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Clone Cells\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Neostriatum\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Endoplasmic Reticulum\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Entire substantia nigra\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Lymphocyte\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Cultured Cells\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Common carotid artery\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Hela Cells\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Cell Fraction\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Neuroglia\" \"location_of\" \"DNM1L gene\")\n (scigraph \"cell cortex\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Fibroblasts\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Mitochondria\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Muscle\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Retina\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Heart\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Cells\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Organelles\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Brain\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Kidney\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Oocytes\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Adipocytes\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Entire hippocampus\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Chromosomes, Human, Pair 12\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Membrane\" \"location_of\" \"DNM1L gene\")\n (scigraph \"Neurons\" \"location_of\" \"DNM1L gene\")\n (scigraph \"alpha-Synuclein\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"Chaperonin 10\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"PRDX3 peroxidase\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph\n \"Cyclic AMP-Dependent Protein Kinases\"\n \"negatively_regulates\"\n \"DNM1L gene\")\n (scigraph \"Citrate (si)-Synthase\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"Mitochondrial Proteins\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph\n \"Guanosine Triphosphate Phosphohydrolases\"\n \"negatively_regulates\"\n \"DNM1L gene\")\n (scigraph \"angiogenin\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph\n \"9-deoxy-delta-9-prostaglandin D2\"\n \"negatively_regulates\"\n \"DNM1L gene\")\n (scigraph \"Ru 360\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"15-deoxyprostaglandin J2\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"Bicuculline\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph\n \"Carbonyl Cyanide m-Chlorophenyl Hydrazone\"\n \"negatively_regulates\"\n \"DNM1L gene\")\n (scigraph \"Niclosamide\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"Reactive Oxygen Species\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"Lithium Chloride\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"small molecule\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"RNA, Small Interfering\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"MIEF2 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"GPAM gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"SIRT4 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"PKM gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"MIEF1 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"CUX1 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"S100A7 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"ANG gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"Homologous Gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"MFN2 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"MFF gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"PRDX3 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"ROS1 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"PINK1 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"SART3 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"HTRA2 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"ERVK-15 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"CS gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"ANXA6 gene\" \"negatively_regulates\" \"DNM1L gene\")\n (scigraph \"E-Cadherin\" \"part_of\" \"DNM1L gene\")\n (scigraph \"ezrin\" \"part_of\" \"DNM1L gene\")\n (scigraph \"Ubiquitin\" \"part_of\" \"DNM1L gene\")\n (scigraph \"RNA, Small Interfering\" \"part_of\" \"DNM1L gene\")\n (scigraph \"Guanosine Triphosphate\" \"part_of\" \"DNM1L gene\")\n (scigraph \"Regulatory Sequences, Nucleic Acid\" \"part_of\" \"DNM1L gene\")\n (scigraph \"BECN1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"ROCK1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"MAP1LC3A gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"OPA1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"AKT1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph\n \"tumor necrosis factor alpha receptor\"\n \"positively_regulates\"\n \"DNM1L gene\")\n (scigraph \"SQSTM1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"FAS gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"ROS1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"BAK1 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"BAX gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"ATG5 gene\" \"positively_regulates\" \"DNM1L gene\")\n (scigraph \"Myocytes, Cardiac\" \"produces\" \"DNM1L gene\")\n (scigraph \"Mitochondria\" \"produces\" \"DNM1L gene\")\n (scigraph \"Cells\" \"produces\" \"DNM1L gene\")\n (scigraph \"Oocytes\" \"produces\" \"DNM1L gene\")\n (scigraph \"Neurons\" \"produces\" \"DNM1L gene\")\n (scigraph \"Phosphotransferases\" \"produces\" \"DNM1L gene\")\n (scigraph \"CATALASE\" \"produces\" \"DNM1L gene\")\n (scigraph \"CAT gene\" \"produces\" \"DNM1L gene\")\n (scigraph \"PINK1 gene\" \"produces\" \"DNM1L gene\")\n (scigraph \"SOD2 gene\" \"produces\" \"DNM1L gene\"))\n\n\n#|\n(semmed \"SQSTM1 gene\" \"positively_regulates\" \"DNM1L wt Allele\")\n\n(run* (q)\n (fresh (edge eid tacrine-details subject object pred eprops db\n scid scui sname sdetails\n ocid ocui oname odetails\n pred-id pred-name)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (~name-concepto \"DNM1L\" `(,db . ,object)) \n (edgeo `(,db . ,edge)) \n (== `(,pred-id . ,pred-name) pred)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== \"SQSTM1 gene\" sname)\n (== \"positively_regulates\" pred-name)\n (== `(,db . ,edge) q)))\n\n(sort\n (rem-dups\n (run* (q)\n (fresh (edge eid tacrine-details subject object pred eprops db\n scid scui sname sdetails\n ocid ocui oname odetails\n pred-id pred-name)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (~name-concepto \"DNM1L\" `(,db . ,object)) \n (edgeo `(,db . ,edge)) \n (== `(,pred-id . ,pred-name) pred)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,db ,sname ,pred-name ,oname) q))))\n (lambda (e1 e2)\n (match `(,e1 ,e2)\n [`((,db1 ,sname1 ,pred-name1 ,oname1)\n (,db2 ,sname2 ,pred-name2 ,oname2))\n (string\n'((0 . \"interacts_with\")\n (3 . \"part_of\")\n (5 . \"negatively_regulates\")\n (6 . \"coexists_with\")\n (9 . \"affects\")\n (10 . \"produces\")\n (0 . \"directly_interacts_with\")\n (13 . \"positively_regulates\")\n (3 . \"interacts_with\")\n (6 . \"part_of\")\n (3 . \"regulates\")\n (10 . \"coexists_with\")\n (16 . \"location_of\")\n (17 . \"produces\")\n (18 . \"positively_regulates\")\n (19 . \"negatively_regulates\"))\n\n#|\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (~name-concepto \"NF1\" `(,db . ,object))\n (== `(,db . ,object) q))))))\n\n(displayln \"X ANY-PRED NF1\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (~name-concepto \"NF1\" `(,db . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo `(,db . ,edge)))))))\n\n(displayln \"X ANY-PRED HFNF1A\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,db . ,object)\n `(monarch\n 728\n \"HGNC:11621\"\n \"HNF1A\"\n (1 . \"['gene', 'sequence feature']\")\n (\"iri\" . \"http://identifiers.org/hgnc/HGNC:11621\")\n (\"clique\"\n .\n \"['HGNC:11621', 'NCBIGene:6927', 'Orphanet:158583', 'OMIM:142410', 'ENSEMBL:ENSG00000135100', 'ENSEMBL:ENSP00000443964', 'ENSEMBL:ENSP00000439721', 'ENSEMBL:ENSP00000443112', 'ENSEMBL:ENSP00000445445', 'ENSEMBL:ENSP00000481967', 'ENSEMBL:ENSP00000257555', 'UniProtKB:P20823', 'ENSEMBL:ENSP00000440361', 'ENSEMBL:ENSP00000483994', 'ENSEMBL:ENSP00000438565', 'ENSEMBL:ENSP00000438804', 'ENSEMBL:ENSP00000453965', 'ENSEMBL:ENSP00000476181']\")\n (\"http://purl.org/dc/elements/1.1/description\" . \"HNF1 homeobox A\")\n (\"http://www.w3.org/2000/01/rdf-schema#label\" . \"HNF1A\")\n (\"id\" . \"HGNC:11621\")\n (\"label\" . \"HNF1A\")\n (\"https://monarchinitiative.org/MONARCH_cliqueLeader\" . \"True\")\n (\"labels\"\n .\n \"['gene', 'sequence_feature', 'Class', 'cliqueLeader', 'Node']\")))\n (== `(,sname ,pred ,oname) q)\n (edgeo `(,db . ,edge)))))))\n\n(displayln \"X ANY-PRED RNF183\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,db . ,object)\n `(rtx\n 18446\n \"UniProtKB:Q96D59\"\n \"RNF183\"\n (1 . \"protein\")\n (\"symbol\" . \"RNF183\")\n (\"expanded\" . \"True\")\n (\"rtx_name\" . \"Q96D59\")\n (\"description\" . \"None\")\n (\"id\" . \"UniProtKB:Q96D59\")\n (\"accession\" . \"Q96D59\")\n (\"UUID\" . \"de83c902-5907-11e8-95d6-060473434358\")\n (\"uri\" . \"http://identifiers.org/uniprot/Q96D59\")\n (\"seed_node_uuid\" . \"dbf1734c-5907-11e8-95d6-060473434358\")\n (\"labels\" . \"['protein', 'Base']\")))\n (== `(,sname ,pred ,oname) q)\n (edgeo `(,db . ,edge)))))))\n\n(displayln \"X ANY-PRED HNF1A\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,db . ,object)\n `(scigraph\n 728\n \"HGNC:11621\"\n \"HNF1A\"\n (1 . \"['gene', 'sequence feature']\")\n (\"iri\" . \"http://identifiers.org/hgnc/HGNC:11621\")\n (\"clique\"\n .\n \"['HGNC:11621', 'NCBIGene:6927', 'Orphanet:158583', 'OMIM:142410', 'ENSEMBL:ENSG00000135100', 'ENSEMBL:ENSP00000443964', 'ENSEMBL:ENSP00000439721', 'ENSEMBL:ENSP00000443112', 'ENSEMBL:ENSP00000445445', 'ENSEMBL:ENSP00000481967', 'ENSEMBL:ENSP00000257555', 'UniProtKB:P20823', 'ENSEMBL:ENSP00000440361', 'ENSEMBL:ENSP00000483994', 'ENSEMBL:ENSP00000438565', 'ENSEMBL:ENSP00000438804', 'ENSEMBL:ENSP00000453965', 'ENSEMBL:ENSP00000476181']\")\n (\"http://purl.org/dc/elements/1.1/description\" . \"HNF1 homeobox A\")\n (\"http://www.w3.org/2000/01/rdf-schema#label\" . \"HNF1A\")\n (\"id\" . \"HGNC:11621\")\n (\"label\" . \"HNF1A\")\n (\"https://monarchinitiative.org/MONARCH_cliqueLeader\" . \"True\")\n (\"labels\" . \"['gene', 'Node']\")))\n (== `(,sname ,pred ,oname) q)\n (edgeo `(,db . ,edge)))))))\n\n|#\n\n(newline)\n(displayln \"X INCREASES NF1:\")\n(time (pretty-print\n (run* (edge)\n (fresh (eid tacrine-details subject object pred eprops db)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n (~name-concepto \"NF1\" `(,db . ,object))\n (INCREASES pred)\n (edgeo `(,db . ,edge))))))\n\n(time (pretty-print\n (run* (q)\n (fresh (edge eid tacrine-details subject object pred eprops db)\n (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n ;(~name-concepto \"congenital cataract\" `(,db . ,object))\n (== `(81155\n \"HP:0000519\"\n \"Congenital cataract\"\n (5 . \"phenotypic_feature\")\n (\"expanded\" . \"True\")\n (\"rtx_name\" . \"HP:0000519\")\n (\"description\" . \"A congenital cataract.\")\n (\"id\" . \"HP:0000519\")\n (\"accession\" . \"0000519\")\n (\"UUID\" . \"ec2d2c9c-5907-11e8-95d6-060473434358\")\n (\"uri\" . \"http://purl.obolibrary.org/obo/HP_0000519\")\n (\"seed_node_uuid\" . \"dbf1734c-5907-11e8-95d6-060473434358\")\n (\"labels\" . \"['Base', 'phenotypic_feature']\"))\n object)\n (edgeo `(,db . ,edge))\n (== `(,db . ,edge) q)\n ))))\n" }, { "path": "attic/medikanren/brca1-full.rkt", "content": "#lang racket\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n\n membero\n edgeo\n ~name-concepto)\n\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"data/semmed\")))\n(displayln \"loading monarch-lite\")\n(define monarch (time (make-db \"data/monarch-lite\")))\n(displayln \"loading rtx\")\n(define rtx (time (make-db \"data/rtx\")))\n(displayln \"loading scigraph\")\n(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))))\n\n(time (pretty-print\n (run* (concept)\n (~name-concepto \"BRCA1\" concept))))\n\n(displayln \"X ANY-PRED ANY-BRCA1-SYNONYM:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (membero name '(\"BRCA1\"\n \"RING Finger Protein 53\"\n \"RNF53\"))\n (~name-concepto name `(,obd . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo edge))))))\n\n" }, { "path": "attic/medikanren/brca1.rkt", "content": "#lang racket\n(require\n \"mk-db.rkt\"\n )\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n(define x-anypred-anybrca1-synonym\n (lambda (db-name)\n (printf \"loading db: ~s\\n\" db-name)\n (define db (time (make-db db-name)))\n (newline)\n (displayln \"X ANY-PRED ANY-BRCA1-SYNONYM:\")\n (time (pretty-print\n (run* (q)\n (fresh (edge name)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (membero name '(\"BRCA1\"\n \"RING Finger Protein 53\"\n \"RNF53\"))\n (db:~name-concepto db name object)\n (== `(,sname ,pred ,oname) q)\n (db:edgeo db edge))))))))\n\n\n;(define db-name \"data/monarch-lite\")\n(define db-name \"data/rtx\") ;; regulates\n;(define db-name \"data/scigraph\")\n;(define db-name \"data/semmed\")\n\n(x-anypred-anybrca1-synonym db-name)\n" }, { "path": "attic/medikanren/create-all-hashtables.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\"\n \"create-doid-cui-to-cid-hashtable.rkt\"\n \"create-ensembl-cui-to-cid-hashtable.rkt\"\n \"create-hgnc-cui-to-cid-hashtable.rkt\"\n \"create-hpo-cui-to-cid-hashtable.rkt\"\n \"create-mondo-cui-to-cid-hashtable.rkt\"\n \"create-omim-cui-to-cid-hashtable.rkt\"\n \"create-umls-cui-to-cid-hashtable.rkt\"\n \"create-uniprotkb-cui-to-cid-hashtable.rkt\")\n\n(provide\n (all-defined-out))\n\n(define doid-ht #f)\n(define ensembl-ht #f)\n(define hgnc-ht #f)\n(define hpo-ht #f)\n(define omim-ht #f)\n(define mondo-ht #f)\n(define umls-ht #f)\n(define uniprotkb-ht #f)\n\n(define (load-or-create/save-all-hashtables!)\n\n (set! doid-ht (load-or-create/save-doid-ht!))\n (set! ensembl-ht (load-or-create/save-ensembl-ht!))\n (set! hgnc-ht (load-or-create/save-hgnc-ht!))\n (set! hpo-ht (load-or-create/save-hpo-ht!))\n (set! mondo-ht (load-or-create/save-mondo-ht!))\n (set! omim-ht (load-or-create/save-omim-ht!))\n (set! umls-ht (load-or-create/save-umls-ht!)) \n (set! uniprotkb-ht (load-or-create/save-uniprotkb-ht!))\n\n )\n" }, { "path": "attic/medikanren/create-doid-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n\n(define doid-ht (make-hash))\n(define doid-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"doid-hash.rkt\"))\n\n(define (fill-doid-ht!)\n\n (set! doid-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! doid-ht))\n\n (add-to-ht! SEMMED #rx\"DOID:([0-9]+)\")\n (add-to-ht! RTX #rx\"DOID:([0-9]+)\")\n (add-to-ht! ROBOKOP #rx\"DOID:([0-9]+)\")\n (add-to-ht! ORANGE #rx\"DOID:([0-9]+)\")\n\n )\n\n(define (save-doid-ht!)\n (save-hashtable! doid-ht doid-ht-file-path))\n\n(define (load-doid-ht)\n (load-hashtable doid-ht-file-path))\n\n(define (load-or-create/save-doid-ht!)\n (load-or-create/save-hashtable!\n 'doid\n load-doid-ht\n fill-doid-ht!\n save-doid-ht!))\n" }, { "path": "attic/medikanren/create-ensembl-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n(define ensembl-ht (make-hash))\n(define ensembl-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"ensembl-hash.rkt\"))\n\n(define (fill-ensembl-ht!)\n\n (set! ensembl-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! ensembl-ht))\n\n ;; apparently semmed doesn't have ENSEMBL synonyms\n ;; apparently rtx doesn't have ENSEMBL synonyms \n (add-to-ht! ROBOKOP #rx\"ENSEMBL:([A-Z0-9]+)\")\n (add-to-ht! ORANGE #rx\"ENSEMBL:([A-Z0-9]+)\")\n\n )\n\n(define (save-ensembl-ht!)\n (save-hashtable! ensembl-ht ensembl-ht-file-path))\n\n(define (load-ensembl-ht)\n (load-hashtable ensembl-ht-file-path))\n\n(define (load-or-create/save-ensembl-ht!)\n (load-or-create/save-hashtable!\n 'ensembl\n load-ensembl-ht\n fill-ensembl-ht!\n save-ensembl-ht!))\n\n\n\n#|\n\napparently semmed doesn't have ENSEMBL synonyms (but semmed does have\nOMIM and HGNC, which could be useful for cross-referencing):\n\n(semmed 160183 \"UMLS:C1413407\" \"CHRNB1 gene\" (4 . \"gene\") ((\"umls_type_label\" . \"['Gene or Genome']\") (\"xrefs\" . \"['MTH:NOCODE', 'OMIM:100710', 'HGNC:HGNC:1961']\") (\"id\" . \"UMLS:C1413407\") (\"umls_type\" . \"['T028']\") (\"labels\" . \"['gene']\")))\n\n\n\napparently rtx doesn't have ENSEMBL synonyms\n\n\n\nThese two are supposedly the same:\n\n(robokop 19861 \"HGNC:1961\" \"CHRNB1\" (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\") ((\"locus_group\" . \"protein-coding gene\") (\"chromosome\" . \"17\") (\"taxon\" . \"9606\") (\"gene_family\" . \"(\\\"Cholinergic receptors nicotinic subunits\\\")\") (\"location\" . \"17p13.1\") (\"id\" . \"HGNC:1961\") (\"gene_family_id\" . \"(173)\") (\"equivalent_identifiers\" . \"(\\\"UniProtKB:I3L4N5\\\" \\\"UniProtKB:I3L535\\\" \\\"ENSEMBL:ENSG00000170175\\\" \\\"UniProtKB:P11230\\\" \\\"UniProtKB:I3L1T7\\\" \\\"UniProtKB:I3L3Q9\\\" \\\"NCBIGENE:1140\\\" \\\"HGNC:1961\\\")\")))\n\n(orange 13750 \"NCBIGene:1140\" \"CHRNB1\" (6 . \"(\\\"gene\\\")\") ((\"iri\" . \"http://www.ncbi.nlm.nih.gov/gene/1140\") (\"synonym\" . \"(\\\"acetylcholine receptor, nicotinic, beta 1 (muscle)\\\" \\\"Acetylcholine Receptor, Muscle, Beta Subunit\\\" \\\"CHOLINERGIC RECEPTOR, NICOTINIC, BETA POLYPEPTIDE 1; CHRNB1\\\" \\\"CHRNB1\\\" \\\"Chrnb\\\")\") (\"in_taxon\" . \"NCBITaxon:9606\") (\"same_as\" . \"(\\\"ENSEMBL:ENSG00000170175\\\" \\\"HGNC:1961\\\" \\\"OMIM:100710\\\" \\\"Orphanet:119419\\\")\") (\"provided_by\" . \"(\\\"orphanet.ttl\\\" \\\"omim.ttl\\\")\") (\"description\" . \"cholinergic receptor nicotinic beta 1 subunit\") (\"id\" . \"NCBIGene:1140\")))\n\n\n\nAnother random Robokop entry:\n\n(robokop 20027 \"HGNC:11016\" \"SLC31A1\" (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\") ((\"locus_group\" . \"protein-coding gene\") (\"chromosome\" . \"9\") (\"taxon\" . \"9606\") (\"gene_family\" . \"(\\\"Solute carriers\\\")\") (\"location\" . \"9q32\") (\"id\" . \"HGNC:11016\") (\"gene_family_id\" . \"(752)\") (\"equivalent_identifiers\" . \"(\\\"HGNC:11016\\\" \\\"UniProtKB:A0A024R824\\\" \\\"NCBIGENE:1317\\\" \\\"UniProtKB:O15431\\\" \\\"ENSEMBL:ENSG00000136868\\\")\")))\n|#\n" }, { "path": "attic/medikanren/create-hashtable-common.rkt", "content": "#lang racket\n\n(require\n )\n\n(provide\n SEMMED\n RTX\n ROBOKOP\n ORANGE\n HASHTABLE_SAVE_DIRECTORY\n filled-hashtable?\n add-concept-key/cid-associations-to-hashtable!\n save-hashtable!\n load-hashtable \n load-or-create/save-hashtable!\n )\n\n(define SEMMED 'semmed)\n(define RTX 'rtx)\n(define ROBOKOP 'robokop)\n(define ORANGE 'orange)\n\n(define HASHTABLE_SAVE_DIRECTORY \"tmp\")\n\n(define DB/concept-file-alist\n '((semmed . \"data/semmed/concepts.scm\")\n (rtx . \"data/rtx/concepts.scm\")\n (robokop . \"data/robokop/concepts.scm\")\n (orange . \"data/orange/concepts.scm\")))\n\n(define DB/props-key-alist\n '((semmed . \"xrefs\")\n (rtx . \"id\")\n (robokop . \"equivalent_identifiers\")\n (orange . \"same_as\")))\n\n\n(define filled-hashtable?\n (lambda (ht)\n (and ht (hash? ht) (> (hash-count ht) 0))))\n\n(define (add-concept-key/cid-associations-to-hashtable! ht)\n (lambda (db-name key-regex)\n (let ((concepts-file-name (cdr (assoc db-name DB/concept-file-alist)))\n (props-key (cdr (assoc db-name DB/props-key-alist))))\n (let ((concept-vector->keys (make-prop-lookup props-key key-regex)))\n (let ((ip (open-input-file concepts-file-name)))\n (let loop ([cid 0]\n [data (read ip)])\n (cond\n [(eof-object? data)\n (close-input-port ip)\n (void)]\n [else\n (when (= (modulo cid 10000) 0)\n (printf \"~s cid: ~s\\n\" db-name cid))\n (let ((keys (concept-vector->keys data)))\n (when keys\n (for-each\n (lambda (key)\n (let ((entry (hash-ref ht key '())))\n (hash-set! ht key (cons (cons db-name cid) entry))))\n keys)))\n (loop (add1 cid) (read ip))])))))))\n\n(define (make-prop-lookup props-key key-regex)\n (lambda (data)\n (let ((props (vector-ref data 3)))\n ;; all the KG's have an 'id' entry with the CUI for the concept, which we should also include\n (define (find-cids-by-prop-list-key prop-list-key)\n (cond\n ((assoc prop-list-key props)\n =>\n (lambda (pr)\n (let ((str (cdr pr)))\n (let ((keys (regexp-match* key-regex str #:match-select cadr)))\n keys))))\n (else '())))\n (define id-keys (find-cids-by-prop-list-key \"id\"))\n (define equivalent-keys (find-cids-by-prop-list-key props-key))\n (set->list\n (set-union\n (list->set id-keys)\n (list->set equivalent-keys))))))\n\n(define (save-hashtable! ht ht-file-name)\n (define op (open-output-file ht-file-name #:exists 'replace))\n (write ht op)\n (close-output-port op))\n\n(define (load-hashtable ht-file-name)\n (if (file-exists? ht-file-name)\n (let ()\n (define ip (open-input-file ht-file-name))\n (let ((ht (read ip)))\n (close-input-port ip)\n ht))\n #f))\n\n(define (load-or-create/save-hashtable! ht-name load-ht fill-ht! save-ht!)\n (printf \"attempting to load hashtable for ~s\\n\" ht-name)\n (let ((ht (load-ht)))\n (if (filled-hashtable? ht)\n (begin\n (printf \"loaded non-empty hashtable for ~s, with ~s entries\\n\" ht-name (hash-count ht))\n ht)\n (begin\n (printf \"unable to load a non-empty hashtable for ~s\\n\" ht-name)\n (printf \"trying to create a hashtable for ~s...\\n\" ht-name)\n (fill-ht!)\n (printf \"filled a hashtable for ~s. Trying to save hashtable...\\n\" ht-name)\n (save-ht!)\n (printf \"saved the hashtable for ~s. Trying to load saved hashtable...\\n\" ht-name)\n (let ((ht (load-ht)))\n (printf \"load the saved hashtable for ~s. Checking if non-empty valid hashtable...\\n\" ht-name)\n (if (filled-hashtable? ht)\n (begin\n (printf \"loaded hashtable for ~s is non-empty, with ~s entries\\n\" ht-name (hash-count ht))\n ht)\n (error \"Unable to load or create hashtable ~s\" ht-name)))))))\n" }, { "path": "attic/medikanren/create-hgnc-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n\n(define hgnc-ht (make-hash))\n(define hgnc-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"hgnc-hash.rkt\"))\n\n(define (fill-hgnc-ht!)\n\n (set! hgnc-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! hgnc-ht))\n\n (add-to-ht! SEMMED #rx\"HGNC:([0-9]+)\")\n ;; apparently rtx doesn't have HGNC synonyms \n (add-to-ht! ROBOKOP #rx\"HGNC:([0-9]+)\")\n (add-to-ht! ORANGE #rx\"HGNC:([0-9]+)\")\n\n )\n\n(define (save-hgnc-ht!)\n (save-hashtable! hgnc-ht hgnc-ht-file-path))\n\n(define (load-hgnc-ht)\n (load-hashtable hgnc-ht-file-path))\n\n(define (load-or-create/save-hgnc-ht!)\n (load-or-create/save-hashtable!\n 'hgnc\n load-hgnc-ht\n fill-hgnc-ht!\n save-hgnc-ht!))\n" }, { "path": "attic/medikanren/create-hpo-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n\n(define hpo-ht (make-hash))\n(define hpo-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"hpo-hash.rkt\"))\n\n(define (fill-hpo-ht!)\n\n (set! hpo-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! hpo-ht))\n\n (add-to-ht! SEMMED #rx\"HPO:HP:([0-9]+)\")\n (add-to-ht! RTX #rx\"HP:([0-9]+)\")\n (add-to-ht! ROBOKOP #rx\"HP:([0-9]+)\")\n (add-to-ht! ORANGE #rx\"HP:([0-9]+)\")\n\n )\n\n(define (save-hpo-ht!)\n (save-hashtable! hpo-ht hpo-ht-file-path))\n\n(define (load-hpo-ht)\n (load-hashtable hpo-ht-file-path))\n\n(define (load-or-create/save-hpo-ht!)\n (load-or-create/save-hashtable!\n 'hpo\n load-hpo-ht\n fill-hpo-ht!\n save-hpo-ht!))\n" }, { "path": "attic/medikanren/create-mondo-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n(define mondo-ht (make-hash))\n(define mondo-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"mondo-hash.rkt\"))\n\n(define (fill-mondo-ht!)\n\n (set! mondo-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! mondo-ht))\n\n ;; Apparently Semmed doesn't have MONDO mappings\n (add-to-ht! RTX #rx\"MONDO:([A-Z0-9]+)\")\n (add-to-ht! ROBOKOP #rx\"MONDO:([A-Z0-9]+)\")\n (add-to-ht! ORANGE #rx\"MONDO:([A-Z0-9]+)\")\n\n )\n\n(define (save-mondo-ht!)\n (save-hashtable! mondo-ht mondo-ht-file-path))\n\n(define (load-mondo-ht)\n (load-hashtable mondo-ht-file-path))\n\n(define (load-or-create/save-mondo-ht!)\n (load-or-create/save-hashtable!\n 'mondo\n load-mondo-ht\n fill-mondo-ht!\n save-mondo-ht!))\n" }, { "path": "attic/medikanren/create-omim-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n(define omim-ht (make-hash))\n(define omim-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"omim-hash.rkt\"))\n\n(define (fill-omim-ht!)\n\n (set! omim-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! omim-ht))\n\n (add-to-ht! SEMMED #rx\"OMIM:([A-Z0-9]+)\") \n ;; apparently rtx doesn't have OMIM synonyms\n (add-to-ht! ROBOKOP #rx\"OMIM:([A-Z0-9]+)\")\n (add-to-ht! ORANGE #rx\"OMIM:([A-Z0-9]+)\")\n\n )\n\n(define (save-omim-ht!)\n (save-hashtable! omim-ht omim-ht-file-path))\n\n(define (load-omim-ht)\n (load-hashtable omim-ht-file-path))\n\n(define (load-or-create/save-omim-ht!)\n (load-or-create/save-hashtable!\n 'omim\n load-omim-ht\n fill-omim-ht!\n save-omim-ht!))\n\n\n\n#|\n\nNeed to recognize occurrences of the CUI in the \"id\" field as well as the \"same_as\"/\"xrefs\" type fields:\n\n(orange 13749 \"OMIM:PS601462\" \"Myasthenic syndrome, congenital\" (2 . \"(\\\"named thing\\\")\") ((\"iri\" . \"http://purl.obolibrary.org/obo/OMIM_PS601462\") (\"provided_by\" . \"(\\\"omim.ttl\\\")\") (\"id\" . \"OMIM:PS601462\")))\n\n(robokop 172408 \"OMIM:607514\" \"BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 10\" (3 . \"(\\\"named_thing\\\" \\\"disease\\\")\") ((\"id\" . \"OMIM:607514\") (\"equivalent_identifiers\" . \"(\\\"UMLS:C2675659\\\" \\\"OMIM:607514\\\")\")))\n\n|#\n" }, { "path": "attic/medikanren/create-umls-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n\n(define umls-ht (make-hash))\n(define umls-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"umls-hash.rkt\"))\n\n(define (fill-umls-ht!)\n\n (set! umls-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! umls-ht))\n\n (add-to-ht! SEMMED #rx\"UMLS:([A-Z0-9]+)\")\n ;; Apparently RTX doesn't have UMLS mappings\n (add-to-ht! ROBOKOP #rx\"UMLS:([A-Z0-9]+)\")\n ;; Apparently Orange doesn't have UMLS mappings\n\n )\n\n(define (save-umls-ht!)\n (save-hashtable! umls-ht umls-ht-file-path))\n\n(define (load-umls-ht)\n (load-hashtable umls-ht-file-path))\n\n(define (load-or-create/save-umls-ht!)\n (load-or-create/save-hashtable!\n 'umls\n load-umls-ht\n fill-umls-ht!\n save-umls-ht!))\n" }, { "path": "attic/medikanren/create-uniprotkb-cui-to-cid-hashtable.rkt", "content": "#lang racket\n\n(require\n \"create-hashtable-common.rkt\")\n\n(provide\n (all-defined-out))\n\n\n(define uniprotkb-ht (make-hash))\n(define uniprotkb-ht-file-path (build-path HASHTABLE_SAVE_DIRECTORY \"uniprotkb-hash.rkt\"))\n\n(define (fill-uniprotkb-ht!)\n\n (set! uniprotkb-ht (make-hash))\n\n (define add-to-ht! (add-concept-key/cid-associations-to-hashtable! uniprotkb-ht))\n\n (add-to-ht! SEMMED #rx\"UNIPROT:([A-Z0-9]+)\")\n (add-to-ht! RTX #rx\"UniProtKB:([A-Z0-9]+)\")\n (add-to-ht! ROBOKOP #rx\"UniProtKB:([A-Z0-9]+)\")\n ;; apparently orange doesn't have UniProtKB synonyms \n\n )\n\n(define (save-uniprotkb-ht!)\n (save-hashtable! uniprotkb-ht uniprotkb-ht-file-path))\n\n(define (load-uniprotkb-ht)\n (load-hashtable uniprotkb-ht-file-path))\n\n(define (load-or-create/save-uniprotkb-ht!)\n (load-or-create/save-hashtable!\n 'uniprotkb\n load-uniprotkb-ht\n fill-uniprotkb-ht!\n save-uniprotkb-ht!))\n\n\n\n#|\nThree supposedly equivalent concepts:\n\n(semmed 244 \"UMLS:C0962796\" \"SLC31A1 protein, human\" (2 . \"biological_entity\") ((\"umls_type_label\" . \"['Biologically Active Substance', 'Amino Acid, Peptide, or Protein']\") (\"xrefs\" . \"['MESH:C490079', 'NCI:C127860', 'UNIPROT:O15431', 'MTH:NOCODE']\") (\"id\" . \"UMLS:C0962796\") (\"umls_type\" . \"['T116', 'T123']\") (\"labels\" . \"['biological_entity']\")))\n\n(rtx 5771 \"UniProtKB:O15431\" \"solute carrier family 31 member 1\" (1 . \"protein\") ((\"symbol\" . \"SLC31A1\") (\"expanded\" . \"True\") (\"rtx_name\" . \"O15431\") (\"description\" . \"The protein encoded by this gene is a high-affinity copper transporter found in the cell membrane. The encoded protein functions as a homotrimer to effect the uptake of dietary copper. [provided by RefSeq, Aug 2011].\") (\"id\" . \"UniProtKB:O15431\") (\"accession\" . \"O15431\") (\"UUID\" . \"4be807f8-390c-11e9-8caf-0242ac110004\") (\"uri\" . \"http://identifiers.org/uniprot/O15431\") (\"seed_node_uuid\" . \"39368ad0-390c-11e9-8caf-0242ac110004\")))\n\n(robokop 20027 \"HGNC:11016\" \"SLC31A1\" (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\") ((\"locus_group\" . \"protein-coding gene\") (\"chromosome\" . \"9\") (\"taxon\" . \"9606\") (\"gene_family\" . \"(\\\"Solute carriers\\\")\") (\"location\" . \"9q32\") (\"id\" . \"HGNC:11016\") (\"gene_family_id\" . \"(752)\") (\"equivalent_identifiers\" . \"(\\\"HGNC:11016\\\" \\\"UniProtKB:A0A024R824\\\" \\\"NCBIGENE:1317\\\" \\\"UniProtKB:O15431\\\" \\\"ENSEMBL:ENSG00000136868\\\")\")))\n\n\nAnother concept:\n\n(rtx 4 \"UniProtKB:P36404\" \"ADP ribosylation factor like GTPase 2\" (1 . \"protein\") ((\"symbol\" . \"ARL2\") (\"expanded\" . \"True\") (\"rtx_name\" . \"P36404\") (\"description\" . \"This gene encodes a small GTP-binding protein of the RAS superfamily which functions as an ADP-ribosylation factor (ARF). The encoded protein is one of a functionally distinct group of ARF-like genes. [provided by RefSeq, Jul 2008].\") (\"id\" . \"UniProtKB:P36404\") (\"accession\" . \"P36404\") (\"UUID\" . \"4da5df48-390c-11e9-8caf-0242ac110004\") (\"uri\" . \"http://identifiers.org/uniprot/P36404\") (\"seed_node_uuid\" . \"39368ad0-390c-11e9-8caf-0242ac110004\")))\n\n\norange doesn't seem to contain UniProtKB synonyms\n|#\n\n\n\n#|\n> (hash-count uniprotkb-ht)\n89196\n> (hash-ref uniprotkb-ht \"P36404\" #f)\n'((robokop . 166967) (rtx . 4))\n> (hash-ref uniprotkb-ht \"11016\" #f)\n#f\n> (hash-ref uniprotkb-ht \"A0A024R824\" #f)\n'((robokop . 20027))\n> (hash-ref uniprotkb-ht \"O15431\" #f)\n'((robokop . 20027) (rtx . 5771) (semmed . 244))\n|#\n" }, { "path": "attic/medikanren/dhx30-full.rkt", "content": "#lang racket\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n\n membero\n edgeo\n ~name-concepto\n\n semmed\n monarch\n rtx\n scigraph\n )\n\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"data/semmed\")))\n(displayln \"loading monarch-lite\")\n(define monarch (time (make-db \"data/monarch-lite\")))\n(displayln \"loading rtx\")\n(define rtx (time (make-db \"data/rtx\")))\n(displayln \"loading scigraph\")\n(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))))\n\n(displayln \"X ANY-PRED ANY-DHX30-SYNONYM:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name db)\n (fresh (subject scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (membero name '(\"DHX30\"\n \"DExH-Box Helicase 30\"\n \"DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 30\"\n \"DEAH-Box Helicase 30\"\n \"DEAH Box Protein 30\"\n \"DDX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Polypeptide 30\"\n \"Putative ATP-Dependent RNA Helicase DHX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Helicase 30\"\n \"Retina Co-Repressor\"\n \"EC 3.6.4.13\"\n \"KIAA0890\"\n \"NEDMIAL\"\n \"RETCOR\"\n ))\n (~name-concepto name `(,db . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo `(,db . ,edge)))))))\n" }, { "path": "attic/medikanren/dhx30.rkt", "content": "#lang racket\n(require\n \"mk-db.rkt\"\n )\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n(define x-anypred-anydhx30-synonym\n (lambda (db-name)\n (printf \"loading db: ~s\\n\" db-name)\n (define db (time (make-db db-name)))\n (newline)\n (displayln \"X ANY-PRED ANY-DHX30-SYNONYM:\")\n (time (pretty-print (run* (q)\n (fresh (edge name)\n (fresh (scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n (,pid . ,pred) ,eprops) edge)\n (membero name '(\"DHX30\"\n \"DExH-Box Helicase 30\"\n \"DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 30\"\n \"DEAH-Box Helicase 30\"\n \"DEAH Box Protein 30\"\n \"DDX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Polypeptide 30\"\n \"Putative ATP-Dependent RNA Helicase DHX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Helicase 30\"\n \"Retina Co-Repressor\"\n \"EC 3.6.4.13\"\n \"KIAA0890\"\n \"NEDMIAL\"\n \"RETCOR\"\n ))\n (project (name)\n (db:~name-concepto db name `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))))\n (== `(,sname ,pred ,oname) q)\n (db:edgeo db edge))))))))\n\n\n;(define db-name \"data/monarch-lite\")\n(define db-name \"data/rtx\") ;; regulates\n;(define db-name \"data/scigraph\")\n;(define db-name \"data/semmed\")\n\n(x-anypred-anydhx30-synonym db-name)\n" }, { "path": "attic/medikanren/examine-concepts.rkt", "content": "#lang racket\n\n(provide\n\n concept-info\n concept-count-alist-sorted-by-tag-name\n concept-count-alist-sorted-by-tag-count\n alist-of-concept-lists\n alist-of-concept-sets\n concept-tag-intersections\n concept-tag-set-symmetric-difference\n )\n\n(define get-concepts-in-db\n (lambda (db)\n (printf \"reading ~s concept tags...\\n\" db)\n (let ((p (open-input-file (string-append \"data/\" db \"/concepts.scm\"))))\n (let loop ((concept (read p))\n (concept-sources '())\n (concept-count-ht (hash)))\n (cond\n [(eof-object? concept)\n (close-input-port p)\n (printf \"read ~s ~s concept tags\\n\" (length concept-sources) db)\n (list (sort concept-sources stringlist (caddr (assoc \"monarch-lite\" concept-info))))\n (scigraph-concept-counts (hash->list (caddr (assoc \"scigraph\" concept-info)))))\n (let ((scigraph-concept-counts-minus-semmed (remove (assoc \"UMLS\" scigraph-concept-counts) scigraph-concept-counts)))\n (let ((same (equal? monarch-lite-concept-counts\n scigraph-concept-counts-minus-semmed)))\n (printf \"** is scigraph just monarch-lite + semmeddb? ~s\\n\" same)\n same)))\n\n;; how many concepts are there in the scigraph version of semmeddb, versus the cleaned up semmeddb?\n;;\n;; the semmeddb in scigraph is much larger than the cleaned up semmeddb\n(let ((scigraph-semmed-UMLS-concept-coount (hash-ref (caddr (assoc \"scigraph\" concept-info)) \"UMLS\"))\n (cleand-up-esemmed-UMLS-concept-coount (hash-ref (caddr (assoc \"semmed\" concept-info)) \"UMLS\")))\n (printf \"** semmed UMLS concepts in scigraph: ~s\\n\" scigraph-semmed-UMLS-concept-coount)\n (printf \"** semmed UMLS concepts in cleaned up semmeddb: ~s\\n\" cleand-up-esemmed-UMLS-concept-coount)\n (list scigraph-semmed-UMLS-concept-coount\n cleand-up-esemmed-UMLS-concept-coount))\n\n(define concept-count-alist-sorted-by-tag-name\n (map (lambda (c)\n (list (car c)\n (sort (hash->list (caddr c))\n (lambda (e1 e2)\n (stringlist (caddr c))\n (lambda (e1 e2)\n (> (cdr e1) (cdr e2))))))\n concept-info))\n\n(define alist-of-concept-lists\n (map (lambda (info)\n (cons (car info) (cadr info)))\n concept-info))\n\n(define alist-of-concept-sets\n (map (lambda (e)\n (cons (car e) (apply set (cdr e))))\n alist-of-concept-lists))\n\n;; calculate intersections (overlaps) between data sources\n(define concept-tag-intersections\n (let loop ((alist-of-concept-sets alist-of-concept-sets)\n (intersections '()))\n (match alist-of-concept-sets\n ['() intersections]\n [`((,db1 . ,concept-set1) . ,rest)\n (loop (cdr alist-of-concept-sets)\n (append (map (lambda (e)\n (match e\n [`(,db2 . ,concept-set2)\n (list (list db1 db2)\n (sort (set->list (set-intersect concept-set1 concept-set2)) string\n'((4728\n \"HGNC:16716\"\n \"DHX30\"\n (1 . \"['gene', 'sequence feature']\")\n ((\"iri\" . \"http://identifiers.org/hgnc/HGNC:16716\")\n (\"clique\"\n .\n \"['HGNC:16716', 'NCBIGene:22907', 'OMIM:616423', 'ENSEMBL:ENSG00000132153', 'ENSEMBL:ENSP00000343442', 'ENSEMBL:ENSP00000392601', 'ENSEMBL:ENSP00000394682', 'ENSEMBL:ENSP00000379094', 'ENSEMBL:ENSP00000405620', 'UniProtKB:Q7L2E3', 'ENSEMBL:ENSP00000483160', 'ENSEMBL:ENSP00000395166', 'ENSEMBL:ENSP00000410571']\")\n (\"http://purl.org/dc/elements/1.1/description\" . \"DExH-box helicase 30\")\n (\"http://www.w3.org/2000/01/rdf-schema#label\" . \"DHX30\")\n (\"id\" . \"HGNC:16716\")\n (\"label\" . \"DHX30\")\n (\"https://monarchinitiative.org/MONARCH_cliqueLeader\" . \"True\")\n (\"labels\"\n .\n \"['gene', 'sequence_feature', 'Class', 'cliqueLeader', 'Node']\")))\n (28624\n \"MGI:1920081\"\n \"Dhx30\"\n (1 . \"['gene', 'sequence feature']\")\n ((\"iri\" . \"http://www.informatics.jax.org/accession/MGI:1920081\")\n (\"clique\"\n .\n \"['MGI:1920081', 'NCBIGene:72831', 'ENSEMBL:ENSMUSG00000032480', 'ENSEMBL:ENSMUSP00000143371', 'ENSEMBL:ENSMUSP00000062622', 'ENSEMBL:ENSMUSP00000143529', 'ENSEMBL:ENSMUSP00000142659', 'UniProtKB:Q99PU8', 'ENSEMBL:ENSMUSP00000143616', 'ENSEMBL:ENSMUSP00000143607', 'ENSEMBL:ENSMUSP00000143700', 'ENSEMBL:ENSMUSP00000143751', 'ENSEMBL:ENSMUSP00000142549', 'ENSEMBL:ENSMUSP00000142489', 'ENSEMBL:ENSMUSP00000129174', 'ENSEMBL:ENSMUSP00000142952', 'ENSEMBL:ENSMUSP00000142636', 'ENSEMBL:ENSMUSP00000143272', 'ENSEMBL:ENSMUSP00000107622', 'ENSEMBL:ENSMUSP00000142836', 'ENSEMBL:ENSMUSP00000142846']\")\n (\"synonym\"\n .\n \"['PTN000433446', 'helG', 'Ddx30', 'C130058C04Rik', 'UniProtKB:Q99PU8', '2810477H02Rik', 'DEAH (Asp-Glu-Ala-His) box polypeptide 30']\")\n (\"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym\"\n .\n \"['PTN000433446', 'helG', 'Ddx30', 'C130058C04Rik', 'UniProtKB:Q99PU8', '2810477H02Rik', 'DEAH (Asp-Glu-Ala-His) box polypeptide 30']\")\n (\"http://purl.org/dc/elements/1.1/description\"\n .\n \"['Putative ATP-dependent RNA helicase DHX30', 'DEAH (Asp-Glu-Ala-His) box polypeptide 30']\")\n (\"http://www.w3.org/2000/01/rdf-schema#label\" . \"Dhx30\")\n (\"id\" . \"MGI:1920081\")\n (\"label\" . \"Dhx30\")\n (\"https://monarchinitiative.org/MONARCH_cliqueLeader\" . \"True\")\n (\"labels\"\n .\n \"['gene', 'sequence_feature', 'Class', 'cliqueLeader', 'Node']\")))\n (75120\n \"ZFIN:ZDB-GENE-130530-833\"\n \"dhx30\"\n (1 . \"['gene', 'sequence feature']\")\n ((\"iri\" . \"http://zfin.org/ZDB-GENE-130530-833\")\n (\"synonym\" . \"zmp:0000000830\")\n (\"clique\"\n .\n \"['ZFIN:ZDB-GENE-130530-833', 'ENSEMBL:ENSDARG00000077839', 'NCBIGene:570735', 'ENSEMBL:ENSDARP00000101025']\")\n (\"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym\"\n .\n \"zmp:0000000830\")\n (\"http://purl.org/dc/elements/1.1/description\"\n .\n \"DEAH (Asp-Glu-Ala-His) box helicase 30\")\n (\"http://www.w3.org/2000/01/rdf-schema#label\" . \"dhx30\")\n (\"id\" . \"ZFIN:ZDB-GENE-130530-833\")\n (\"label\" . \"dhx30\")\n (\"https://monarchinitiative.org/MONARCH_cliqueLeader\" . \"True\")\n (\"labels\"\n .\n \"['gene', 'sequence_feature', 'Class', 'cliqueLeader', 'Node']\")))\n (268417\n \"RGD:1308888\"\n \"Dhx30\"\n (1 . \"['gene', 'sequence feature']\")\n ((\"iri\" . \"http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=1308888\")\n (\"clique\" . \"['RGD:1308888', 'NCBIGene:367172']\")\n (\"synonym\" . \"['UniProtKB:Q5BJS0', 'PTN000433447']\")\n (\"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym\"\n .\n \"['UniProtKB:Q5BJS0', 'PTN000433447']\")\n (\"http://purl.org/dc/elements/1.1/description\"\n .\n \"['Putative ATP-dependent RNA helicase DHX30', 'DExH-box helicase 30']\")\n (\"http://www.w3.org/2000/01/rdf-schema#label\" . \"Dhx30\")\n (\"id\" . \"RGD:1308888\")\n (\"label\" . \"Dhx30\")\n (\"https://monarchinitiative.org/MONARCH_cliqueLeader\" . \"True\")\n (\"labels\"\n .\n \"['gene', 'sequence_feature', 'Class', 'cliqueLeader', 'Node']\"))))\n\n(newline)\n(displayln \"X ANY-PRED DHX30:\")\n(time (pretty-print (run* (edge)\n (fresh (scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n (,pid . ,pred) ,eprops) edge)\n (db:~name-concepto monarch-lite \"DHX30\" `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops)))\n (db:edgeo monarch-lite edge)))))\n\n(newline)\n(displayln \"DHX30 ANY-PRED X\")\n(time (pretty-print (run* (edge)\n (fresh (scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n (,pid . ,pred) ,eprops) edge)\n (db:~name-concepto monarch-lite \"DHX30\" `(,scid . (,scui ,sname (,scatid . ,scat) . ,sprops)))\n (db:edgeo monarch-lite edge)))))\n" }, { "path": "attic/medikanren/example-dhx30-scigraph.rkt", "content": "#lang racket\n(require\n \"mk-db.rkt\"\n )\n\n(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n\n#|\n(displayln \"categories:\")\n(pretty-print (run* (c) (db:categoryo scigraph c)))\n\n(newline)\n(displayln \"predicates:\")\n(pretty-print (run* (p) (db:predicateo scigraph p)))\n\n(newline)\n(displayln \"some concepts:\")\n(pretty-print (run 10 (c) (db:concepto scigraph c)))\n\n(newline)\n(displayln \"some edges:\")\n(pretty-print (run 10 (e) (db:edgeo scigraph e)))\n\n(newline)\n(displayln \"fuzzy search:\")\n(time (pretty-print (run* (c) (db:~name-concepto scigraph \"imatin\" c))))\n|#\n\n#|\n(newline)\n(displayln \"fuzzy search DHX30:\")\n(time (pretty-print (run* (c) (db:~name-concepto scigraph \"DHX30\" c))))\n|#\n\n#|\n(newline)\n(displayln \"fuzzy search for DHX30 synonyms:\")\n(time (pretty-print (run* (c)\n (fresh (name)\n ;; Gene Card synonyms\n ;; https://www.genecards.org/cgi-bin/carddisp.pl?gene=DHX30&keywords=DHX30\n (membero name '(\"DHX30\"\n \"DExH-Box Helicase 30\"\n \"DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 30\"\n \"DEAH-Box Helicase 30\"\n \"DEAH Box Protein 30\"\n \"DDX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Polypeptide 30\"\n \"Putative ATP-Dependent RNA Helicase DHX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Helicase 30\"\n \"Retina Co-Repressor\"\n \"EC 3.6.4.13\"\n \"KIAA0890\"\n \"NEDMIAL\"\n \"RETCOR\"\n ))\n (project (name)\n (db:~name-concepto scigraph name c))))))\n|#\n\n\n\n(newline)\n(displayln \"X ANY-PRED ANY-DHX30-SYNONYM:\")\n(time (pretty-print (run* (q)\n (fresh (edge name)\n (fresh (scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n (,pid . ,pred) ,eprops) edge)\n (membero name '(\"DHX30\"\n \"DExH-Box Helicase 30\"\n \"DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 30\"\n \"DEAH-Box Helicase 30\"\n \"DEAH Box Protein 30\"\n \"DDX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Polypeptide 30\"\n \"Putative ATP-Dependent RNA Helicase DHX30\"\n \"DEAH (Asp-Glu-Ala-His) Box Helicase 30\"\n \"Retina Co-Repressor\"\n \"EC 3.6.4.13\"\n \"KIAA0890\"\n \"NEDMIAL\"\n \"RETCOR\"\n ))\n (project (name)\n (db:~name-concepto scigraph name `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))))\n (== `(,sname ,pred ,oname) q)\n (db:edgeo scigraph edge))))))\n\n\n#|\n(newline)\n(displayln \"X ANY-PRED DHX30:\")\n(time (pretty-print (run* (edge)\n (fresh (scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n (,pid . ,pred) ,eprops) edge)\n (db:~name-concepto scigraph \"DHX30\" `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops)))\n (db:edgeo scigraph edge)))))\n\n(newline)\n(displayln \"DHX30 ANY-PRED X\")\n(time (pretty-print (run* (edge)\n (fresh (scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n (,pid . ,pred) ,eprops) edge)\n (db:~name-concepto scigraph \"DHX30\" `(,scid . (,scui ,sname (,scatid . ,scat) . ,sprops)))\n (db:edgeo scigraph edge)))))\n|#\n" }, { "path": "attic/medikanren/find-edges-by-pubmed-id.rkt", "content": "#lang racket\n\n(provide\n (all-from-out \"../../medikanren/mk.rkt\")\n (all-from-out \"../../medikanren/db.rkt\")\n (all-from-out \"../../medikanren/mk-db.rkt\")\n \n (all-defined-out))\n\n(require\n \"../../medikanren/mk.rkt\"\n \"../../medikanren/db.rkt\"\n \"../../medikanren/mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"../../medikanren/data/semmed\")))\n;; (displayln \"loading monarch-lite\")\n;; (define monarch (time (make-db \"data/monarch-lite\")))\n;; (displayln \"loading rtx\")\n;; (define rtx (time (make-db \"data/rtx\")))\n;; (displayln \"loading scigraph\")\n;; (define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; remove duplicates from a list\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ;((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ;((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ;((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))\n ))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ;((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ;((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ;((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))\n ))\n\n;; Greg's examples from example-semmed.rkt\n(displayln \"associating pubmed ids with edge ids:\")\n(time (pretty-print (run 10 (pmid eid) (db:pmid-eido semmed pmid eid))))\n(time (pretty-print (run* (eid) (db:pmid-eido semmed \"1000085\" eid))))\n(time (pretty-print (run* (eid) (db:pmid-eido semmed \"10000\" eid))))\n(time (pretty-print (run* (eid) (db:pmid-eido semmed \"999999\" eid))))\n\n\n(run 1 (e)\n (fresh (dbname eid rest)\n (db:pmid-eido semmed \"1000085\" eid)\n (== `(,dbname ,eid . ,rest) e)\n (edgeo e)))\n\n(run* (e)\n (fresh (dbname eid rest)\n (db:pmid-eido semmed \"1000085\" eid)\n (== `(,dbname ,eid . ,rest) e)\n (edgeo e)))\n\n(run* (q)\n (fresh (dbname eid e\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n pid pred eprops)\n (db:pmid-eido semmed \"1000085\" eid)\n (== `(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) . ,eprops)\n e)\n (== (list sname pred oname) q)\n (edgeo e)))\n\n(define find-edges-by-pubmed-id\n (lambda (pubmed-id)\n (let ((pubmed-id-str (if (string? pubmed-id)\n pubmed-id\n (~a pubmed-id))))\n (printf \"finding edges for PubMed entry ~s\\n\" pubmed-id-str)\n (run* (q)\n (fresh (dbname eid e\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n pid pred eprops)\n (db:pmid-eido semmed pubmed-id-str eid)\n (== `(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) . ,eprops)\n e)\n (== (list sname pred oname eid) q)\n (edgeo e))))))\n\n(define find-pubmed-ids-by-eid\n (lambda (eid)\n (printf \"finding PubMed Ids that support edge ~s\\n\" eid)\n (let ((ans (run* (q)\n (fresh (dbname e\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n pid pred eprops)\n (== 'semmed dbname)\n (== `(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) . ,eprops)\n e)\n (edgeo e)\n (project (eprops)\n (let ((pmid-pr (assoc \"pmids\" (car eprops))))\n (cond\n [pmid-pr\n (let ((pmid-str* (string-split (cdr pmid-pr) \";\")))\n (== pmid-str* q))]\n [else\n (printf \"bad edge: ~s\\n\" e)\n (printf \"bad properties: ~s\\n\" eprops)\n (printf \"bad pmid-pr: ~s\\n\" pmid-pr)\n (error 'loop \"missing pmids entry\")])))))))\n (if (null? ans)\n '()\n (sort (rem-dups (map string->number (car ans))) <)))))\n\n; (find-pubmed-ids-by-eid 4759781)\n; (find-edges-by-pubmed-id 28230014)\n\n(map find-edges-by-pubmed-id (find-pubmed-ids-by-eid 4759781))\n\n(define find-edges-related-to-given-edge\n (lambda (eid)\n (printf \"finding edges supported by publications that support edge ~s\\n\" eid)\n (sort\n (rem-dups (foldr (lambda (pmid l)\n (append (find-edges-by-pubmed-id pmid) l))\n '()\n (find-pubmed-ids-by-eid eid)))\n (lambda (l1 l2)\n (let ((o1 (string-downcase (car l1)))\n (o2 (string-downcase (car l2)))\n (p1 (string-downcase (cadr l1)))\n (p2 (string-downcase (cadr l2)))\n (s1 (string-downcase (caddr l1)))\n (s2 (string-downcase (caddr l2))))\n (or (stringedge semmed 5337181)\n\n(let ((v (db:eid->edge semmed 5337181)))\n (let ((eprops (vector-ref v 3)))\n (let ((pmid-pr (assoc \"pmids\" eprops)))\n (cond\n [pmid-pr\n (let ((pmid-str* (rem-dups (string-split (cdr pmid-pr) \";\"))))\n (map (lambda (p) (string-append \"https://www.ncbi.nlm.nih.gov/pubmed/\" p)) pmid-str*))]\n [else\n (printf \"bad edge: ~s\\n\" v)\n (printf \"bad properties: ~s\\n\" eprops)\n (printf \"bad pmid-pr: ~s\\n\" pmid-pr)\n (error 'loop \"missing pmids entry\")]))))\n" }, { "path": "attic/medikanren/gui-simple-v3.rkt", "content": "#lang racket\n\n#|\nGUI bug:\n\nstart GUI\n\nCURIE search for HGNC 15840 in Concept 1\nclick on some predicate\n\nthen do CURIE search for HGNC 15840 in Concept 1\nclick on some predicate\n\nno concept X\n\nthen delete CURIE string in Concept 1\n\nno concept X still\n\nif switch from CURIE to string search for concept 1,\nthen click on pred in concept 2, X is populated\n\n\nTODO:\n\n* bring in related concepts\n\n* support additional CURIE types\n\n* refactor CURIE-related code, including string-trim nightmare\n|#\n\n(require\n \"common.rkt\"\n racket/sandbox\n racket/gui/base\n framework\n racket/engine\n racket/date\n racket/string\n net/sendurl\n \"db.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==)\n (only-in srfi/1 iota))\n\n(provide\n launch-gui)\n\n(define MEDIKANREN_VERSION_STRING \"mediKanren Explorer 0.2.29\")\n\n(define argv (current-command-line-arguments))\n(define argv-optional '#(CONFIG_FILE))\n\n(when (not (<= (vector-length argv) (vector-length argv-optional)))\n (error \"optional arguments ~s; given ~s\" argv-optional argv))\n\n(displayln \"Starting mediKanren Explorer...\")\n(newline)\n(displayln \"************************************************\")\n(displayln \"*** mediKanren is for research purposes only ***\")\n(displayln \"************************************************\")\n(newline)\n(displayln MEDIKANREN_VERSION_STRING)\n;; Loading will occur at first use if not explicitly forced like this.\n(load-config #t (and (<= 1 (vector-length argv)) (vector-ref argv 0)))\n(load-databases #t)\n\n;;; Query save file settings\n(define WRITE_QUERY_RESULTS_TO_FILE (config-ref 'query-results.write-to-file?))\n(define QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name))\n(define HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name-human))\n(define SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name-spreadsheet))\n(define QUERY_RESULTS_FILE_MODE (config-ref 'query-results.file-mode))\n\n;;; Initial window size\n(define HORIZ-SIZE (config-ref 'initial-window-size.horizontal))\n(define VERT-SIZE (config-ref 'initial-window-size.vertical))\n\n;;; Decreases/increases predicate names\n(define DECREASES_PREDICATE_NAMES (config-ref 'decreases-predicate-names))\n(define INCREASES_PREDICATE_NAMES (config-ref 'increases-predicate-names))\n\n\n#|\nconcept format (subject or object), without dbname at front:\n\n`(,cid ,cui ,name (,catid . ,cat) ,props)\n\nconcept format (subject or object), with dbname at front:\n\n`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)\n\n\nedge format, without dbname at front:\n\n`(,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n (,pid . ,pred) ,eprops)\n\nedge format, with dbname at front (as used in edgeo):\n\n`(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n (,pid . ,pred) ,eprops)\n|#\n\n(define (split-name-string name)\n (string-split name #px\"\\\\s+\"))\n\n(define (empty-string? str)\n (not (not (regexp-match #px\"^[\\\\s]*$\" str))))\n\n(define *verbose* #t)\n\n(define input-response-latency 50)\n\n(define MAX-CHAR-WIDTH 150)\n\n(define smart-column-width-list-box%\n (class list-box%\n (super-new)\n (define (on-size width height)\n (super on-size width height)\n (set-default-column-widths this))\n (override on-size)))\n\n(define (set-default-column-widths list-box)\n (define label* (send list-box get-column-labels))\n (define num-cols (length label*))\n (define window-width (send list-box get-width))\n (define min-width 5)\n (define max-width 1000)\n (define fudge-factor 4) ;; column divider width\n (define width (min (max (- (floor (/ window-width num-cols)) fudge-factor)\n min-width)\n max-width))\n (let loop ((col-num (sub1 num-cols)))\n (cond\n [(zero? col-num) (void)]\n [else\n (send list-box\n set-column-width\n col-num\n width\n min-width\t \n max-width)\n (loop (sub1 col-num))])))\n\n(define construct-predicate-label-string\n (lambda (pred-string pred-name-list)\n (~a\n (string-append pred-string\n \" (\"\n (foldr (lambda (str1 str2)\n (if (equal? \"\" str2)\n (string-append str1 \"\" str2)\n (string-append str1 \", \" str2)))\n \"\"\n pred-name-list)\n \")\")\n #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")))\n\n(define DECREASES_PREDICATE_PREFIX_STRING \"decreases [synthetic]\")\n(define DECREASES_PREDICATE_STRING\n (construct-predicate-label-string DECREASES_PREDICATE_PREFIX_STRING DECREASES_PREDICATE_NAMES))\n(define INCREASES_PREDICATE_PREFIX_STRING \"increases [synthetic]\")\n(define INCREASES_PREDICATE_STRING\n (construct-predicate-label-string INCREASES_PREDICATE_PREFIX_STRING INCREASES_PREDICATE_NAMES))\n\n(define SYNTHETIC_PREDICATE_PREFIXES (list DECREASES_PREDICATE_PREFIX_STRING\n INCREASES_PREDICATE_PREFIX_STRING\n ))\n\n\n(define SORT_COLUMN_INCREASING 'sort-column-increasing)\n(define SORT_COLUMN_DECREASING 'sort-column-decreasing)\n\n(define *concept-1-column-sort-order*\n (vector SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING))\n(define *last-concept-1-column-clicked-for-sorting* (box -1))\n\n(define *concept-2-column-sort-order*\n (vector SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING))\n(define *last-concept-2-column-clicked-for-sorting* (box -1))\n\n(define *concept-X-column-sort-order*\n (vector SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_INCREASING\n SORT_COLUMN_DECREASING\n SORT_COLUMN_DECREASING\n SORT_COLUMN_DECREASING\n SORT_COLUMN_DECREASING\n SORT_COLUMN_DECREASING))\n(define *last-concept-X-column-clicked-for-sorting* (box -1))\n\n\n(define *concept-1-name-string* (box \"\"))\n(define *concept-1-isa-flag* (box #f))\n(define *curie-1-string* (box \"\"))\n(define *concept-1-choices* (box '()))\n(define *predicate-1-choices* (box '()))\n\n(define *concept-2-name-string* (box \"\"))\n(define *concept-2-isa-flag* (box #f))\n(define *curie-2-string* (box \"\"))\n(define *concept-2-choices* (box '()))\n(define *predicate-2-choices* (box '()))\n\n(define *concept-X-choices* (box '()))\n(define *full-path-choices* (box '()))\n(define *pubmed-choices* (box '()))\n\n;; saved choices used to generate\n;; paths when clicking on a concept in the X list box.\n(define *solution-concept-1-name-string* (box \"\"))\n(define *solution-concept-2-name-string* (box \"\"))\n;;\n(define *solution-curie-1-string* (box \"\"))\n(define *solution-curie-2-string* (box \"\"))\n;;\n(define *solution-concept-1-isa-flag* (box #f))\n(define *solution-concept-2-isa-flag* (box #f))\n(define *solution-concept-1-choices* (box '()))\n(define *solution-concept-2-choices* (box '()))\n(define *solution-predicate-1-choices* (box '()))\n(define *solution-predicate-2-choices* (box '()))\n\n(define handle-search-in-Xs\n (lambda (search-in-Xs-field\n concept-X-list-box\n search-in-Xs-previous-button\n search-in-Xs-next-button\n . rest)\n (define direction (if (and (list? rest) (= (length rest) 1)) (car rest) #f))\n (define search-str (send search-in-Xs-field get-value))\n\n (define current-selection (send concept-X-list-box get-selection))\n\n (cond\n [direction\n\n (define count (send concept-X-list-box get-number))\n\n (define add1/sub1 (case direction\n [(previous) sub1]\n [(next) add1]\n [else (error 'add1/sub1 \"unknown direction in inc/dec\")]))\n \n (define found-selection\n (and (> count 0)\n (let loop ((i (add1/sub1 current-selection)))\n (cond\n [(>= i count) (loop 0)]\n [(< i 0) (loop (- count 1))]\n [else\n (define data (send concept-X-list-box get-data i))\n (define name-str (list-ref data 3))\n (define matches?\n (smart-string-matches? #f\n chars:ignore-typical\n \"\"\n (string-split search-str \" \")\n name-str))\n (cond\n [matches? i]\n [(= i current-selection)\n ;; wrapped around without a match\n #f]\n [else (loop (add1/sub1 i))])]))))\n\n (if found-selection\n (when (not (equal? found-selection current-selection))\n (when current-selection\n (send concept-X-list-box select current-selection #f))\n (send concept-X-list-box select found-selection #t)\n (send concept-X-list-box set-first-visible-item found-selection))\n (begin\n (when current-selection\n (send concept-X-list-box select current-selection #f))))]\n [(empty-string? search-str)\n (when current-selection\n (send concept-X-list-box select current-selection #f)) \n (send search-in-Xs-previous-button enable #f)\n (send search-in-Xs-next-button enable #f)]\n [else\n (define count (send concept-X-list-box get-number))\n (define found-selection\n (and (> count 0)\n (let loop ((i 0))\n (cond\n [(>= i count) #f]\n [else\n (define data (send concept-X-list-box get-data i))\n (define name-str (list-ref data 3))\n (define matches?\n (smart-string-matches? #f\n chars:ignore-typical\n \"\"\n (string-split search-str \" \")\n name-str))\n (if matches?\n i\n (loop (add1 i)))]))))\n\n (if found-selection\n (begin\n (send search-in-Xs-previous-button enable #t)\n (send search-in-Xs-next-button enable #t))\n (begin\n (send search-in-Xs-previous-button enable #f)\n (send search-in-Xs-next-button enable #f)))\n \n (if found-selection\n (when (not (equal? found-selection current-selection))\n (when current-selection\n (send concept-X-list-box select current-selection #f))\n (send concept-X-list-box select found-selection #t)\n (send concept-X-list-box set-first-visible-item found-selection))\n (begin\n (when current-selection\n (send concept-X-list-box select current-selection #f))))])))\n\n(define (convert-concept-1/2-to-list-box-format concept)\n (match concept\n [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)\n (list (format \"~a\" dbname)\n (format \"~a\" cid)\n (format \"~a\" cui)\n (format \"~a\" `(,catid . ,cat))\n (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\"))]))\n\n(define (convert-X-concept-to-list-box-format concept)\n (match concept\n [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-length ,confidence)\n (list (format \"~a\" dbname)\n (format \"~a\" cid)\n (format \"~a\" cui)\n (format \"~a\" `(,catid . ,cat))\n (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n (format \"~a\" max-pubmed-count)\n (format \"~a\" min-pubmed-count)\n (string-join pred-names \", \")\n (format \"~a\" path-length)\n (format \"~a\" confidence))]))\n\n(define (convert-concept-1/2-to-column-sorting-format concept)\n (match concept\n [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props) \n (list (format \"~a\" dbname)\n cid\n (format \"~a\" cui)\n catid\n (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\"))]))\n\n(define (convert-X-concept-to-column-sorting-format concept)\n (match concept\n [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-length ,confidence)\n (list (format \"~a\" dbname)\n cid\n (format \"~a\" cui)\n catid\n (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n max-pubmed-count\n min-pubmed-count\n (string-join pred-names \", \")\n path-length\n confidence)]))\n\n(define (make-send-concepts-to-concept-1/2-list-box concept-1/2-list-box-thunk)\n (lambda (concepts)\n (define concept-1/2-list-box (concept-1/2-list-box-thunk))\n (define formatted-concepts (map convert-concept-1/2-to-list-box-format concepts))\n (send concept-1/2-list-box\n set\n (map (lambda (e) (list-ref e 0)) formatted-concepts)\n (map (lambda (e) (list-ref e 1)) formatted-concepts)\n (map (lambda (e) (list-ref e 2)) formatted-concepts)\n (map (lambda (e) (list-ref e 3)) formatted-concepts)\n (map (lambda (e) (list-ref e 4)) formatted-concepts))))\n\n(define (make-send-concepts-to-concept-X-list-box concept-X-list-box)\n (lambda (concepts)\n (define formatted-concepts (map convert-X-concept-to-list-box-format concepts))\n (send concept-X-list-box\n set\n (map (lambda (e) (list-ref e 0)) formatted-concepts)\n (map (lambda (e) (list-ref e 1)) formatted-concepts)\n (map (lambda (e) (list-ref e 2)) formatted-concepts)\n (map (lambda (e) (list-ref e 3)) formatted-concepts)\n (map (lambda (e) (list-ref e 4)) formatted-concepts)\n (map (lambda (e) (list-ref e 5)) formatted-concepts)\n (map (lambda (e) (list-ref e 6)) formatted-concepts)\n (map (lambda (e) (list-ref e 7)) formatted-concepts)\n (map (lambda (e) (list-ref e 8)) formatted-concepts)\n (map (lambda (e) (list-ref e 9)) formatted-concepts))))\n\n(define (handle-sort-by-column-header-click event\n list-box\n last-column-clicked-for-sorting-box\n column-sort-order-vector\n choices-box\n convert-values-to-column-sorting-format\n send-values-to-list-box)\n\n (printf \"handle-sort-by-column-header-click called\\n\")\n \n ;; get previously selected choice's data, if any\n (define current-selection (send list-box get-selection))\n (printf \"current-selection: ~s\\n\" current-selection)\n (define current-selection-data (and current-selection\n (send list-box get-data current-selection)))\n (printf \"current-selection-data: ~s\\n\" current-selection-data)\n\n (when current-selection\n (send list-box select current-selection #f))\n \n ;; sort by column\n (define column-clicked (send event get-column))\n (define last-column-clicked (unbox last-column-clicked-for-sorting-box))\n\n (define sort-order (vector-ref column-sort-order-vector column-clicked))\n\n ;; swap sort order if user clicks on same column twice in a row\n (when (= column-clicked last-column-clicked)\n (set! sort-order\n (if (eqv? sort-order SORT_COLUMN_INCREASING)\n SORT_COLUMN_DECREASING\n SORT_COLUMN_INCREASING))\n (vector-set! column-sort-order-vector\n column-clicked\n sort-order))\n\n (printf \"sorting by column ~s in ~s order\\n\" column-clicked sort-order)\n\n (define choices (unbox choices-box))\n\n (define sorted-choices (sort choices\n (lambda (c1 c2) \n (let ((fc1 (convert-values-to-column-sorting-format c1))\n (fc2 (convert-values-to-column-sorting-format c2)))\n (let ((v1 (list-ref fc1 column-clicked))\n (v2 (list-ref fc2 column-clicked)))\n (let ((num-compare\n (if (eqv? sort-order SORT_COLUMN_INCREASING)\n <\n >))\n (string-compare\n (if (eqv? sort-order SORT_COLUMN_INCREASING)\n string?)))\n (if (and (number? v1) (number? v2))\n (num-compare v1 v2)\n (string-compare (string-downcase v1)\n (string-downcase v2)))))))))\n\n (set-box! last-column-clicked-for-sorting-box column-clicked)\n\n (set-box! choices-box sorted-choices)\n\n (send-values-to-list-box sorted-choices)\n\n ;; add choice data to each list-box entry\n (define len (length sorted-choices))\n (let loop ((i 0)\n (c* sorted-choices))\n (cond\n [(= len i) (void)]\n [else\n (send list-box set-data i (car c*))\n (loop (add1 i)\n (cdr c*))]))\n \n ;; select previously selected choice in its new location, if any\n (when (and current-selection current-selection-data)\n (define count (send list-box get-number))\n (printf \"count: ~s\\n\" count)\n (define new-selection\n (let loop ((i 0))\n (cond\n [(>= i count) #f]\n [else\n (let ((d (send list-box get-data i)))\n (printf \"--------\\n\")\n (printf \"d: ~s\\n\" d)\n (printf \"(equal? d current-selection-data): ~s\\n\" (equal? d current-selection-data))\n (if (equal? d current-selection-data)\n i\n (loop (add1 i))))])))\n (printf \"new-selection: ~s\\n\" new-selection)\n (when new-selection\n (send list-box select new-selection #t)\n (send list-box set-first-visible-item new-selection)))\n \n (void))\n\n(define (concept-list parent\n parent-search/isa-panel\n parent-list-boxes-panel\n label\n name-string\n isa-flag\n curie-string\n choices\n predicate-list-box-thunk\n predicate-choices\n edge-type\n last-column-clicked-for-sorting-box\n column-sort-order-vector\n choices-box\n convert-values-to-column-sorting-format\n send-values-to-list-box)\n (define concept-message (new message%\n (parent parent-search/isa-panel)\n (label label)))\n (define search-type-choice (new choice%\n (label \"\")\n (parent parent-search/isa-panel)\n ;; TODO make constants for these strings\n (choices (list \"String search\" \"CURIE search\"))\n (stretchable-width #f)\n (callback (lambda (self event)\n (printf \"event called for search-type-choice: ~s\\n\" event)\n (define event-type (send event get-event-type))\n (when (eqv? 'choice event-type)\n (printf \"event-type is 'choice\\n\")\n ;; TODO check event type\n ;; event type 'choice\n ;;\n (let ((str (send self get-string-selection)))\n (printf \"str: ~s\\n\" str)\n (case str\n [(\"String search\")\n (send string-search-panel show #t)\n (send curie-search-panel show #f)\n \n (send parent-search/isa-panel reflow-container)\n ;; TODO refactor repeated reset code\n ;; reset everythinggggggggg\n (send curie-field set-value \"\")\n (send name-field set-value \"\")\n (set-box! curie-string \"\")\n (set-box! name-string \"\")\n ;;\n (set-box! predicate-choices '())\n (send (predicate-list-box-thunk) set '())\n ;;\n (handle)]\n [(\"CURIE search\")\n (send string-search-panel show #f)\n (send curie-search-panel show #t)\n \n (send parent-search/isa-panel reflow-container)\n ;; TODO refactor repeated reset code\n ;; reset everythinggggggggg\n (send curie-field set-value \"\")\n (send name-field set-value \"\")\n (set-box! curie-string \"\")\n (set-box! name-string \"\")\n ;;\n (set-box! predicate-choices '())\n (send (predicate-list-box-thunk) set '())\n ;; \n (handle)]\n [else (error 'search-type-choice\n (format \"unknown search type ~s\\n\" str))])\n \n )\n )\n (void)\n ))))\n\n (define string/curie-search-parent-panel (new panel%\n (parent parent-search/isa-panel)\n (alignment '(center center))))\n\n (define string-search-panel (new horizontal-panel%\n (parent string/curie-search-parent-panel)\n (alignment '(left center))\n (stretchable-height #f)))\n\n (define curie-search-panel (new horizontal-panel%\n (parent string/curie-search-parent-panel)\n (alignment '(left center))\n (stretchable-height #f)))\n \n\n (define name-field (new text-field%\n (label \"\")\n (parent string-search-panel)\n (init-value \"\")\n (callback (lambda (self event)\n (define name (send self get-value))\n (send curie-field set-value \"\")\n (set-box! curie-string \"\")\n (set-box! name-string name)\n (set-box! predicate-choices '())\n (send (predicate-list-box-thunk) set '())\n (handle)))))\n (define isa-field (new check-box%\n (parent string-search-panel)\n (label \"Include ISA-related concepts\")\n (value #f)\n (callback (lambda (self event) (handle)))))\n\n\n \n (define curie-type-choice (new choice%\n (label \"\")\n (parent curie-search-panel)\n (choices (list \"HGNC\" \"OMIM\"))\n (stretchable-width #f)\n (callback (lambda (self event)\n ;; TODO refactor repeated reset code\n ;; reset everythinggggggggg\n (send curie-field set-value \"\")\n (send name-field set-value \"\")\n (set-box! curie-string \"\")\n (set-box! name-string \"\")\n (set-box! predicate-choices '())\n (send (predicate-list-box-thunk) set '())\n ;;\n (handle)))))\n (define curie-field (new text-field%\n (label \":\")\n (parent curie-search-panel)\n (init-value \"\")\n (callback (lambda (self event)\n ;; TODO refactor\n (define curie-prefix (send curie-type-choice get-string-selection))\n (define curie-suffix (string-trim (send self get-value)))\n (define full-curie (string-append curie-prefix \":\" curie-suffix))\n (printf \"full curie: ~s\\n\" full-curie)\n (send name-field set-value \"\")\n (set-box! name-string \"\")\n (set-box! curie-string full-curie)\n (set-box! predicate-choices '())\n (send (predicate-list-box-thunk) set '())\n (handle)))))\n \n \n (define concept-listbox (new smart-column-width-list-box%\n (label label)\n (choices '())\n (columns '(\"KG\" \"CID\" \"CURIE\" \"Category\" \"Name\"))\n (parent parent-list-boxes-panel)\n (style '(column-headers clickable-headers reorderable-headers extended))\n (callback (lambda (self event)\n (define event-type (send event get-event-type))\n (cond\n [(eqv? event-type 'list-box-column) \n (handle-sort-by-column-header-click\n event\n concept-listbox\n last-column-clicked-for-sorting-box\n column-sort-order-vector\n choices-box\n convert-values-to-column-sorting-format\n send-values-to-list-box)]\n [else\n (define selections (send self get-selections))\n (define selected-concepts (foldr (lambda (i l) (cons (list-ref (unbox choices) i) l)) '() selections))\n (when *verbose*\n (printf \"selected concepts:\\n~s\\n\" selected-concepts))\n (define preds-by-concept\n (time (case edge-type\n [(in-edge) (map caddr (find-predicates/concepts #f #t selected-concepts))]\n [(out-edge) (map cadr (find-predicates/concepts #t #f selected-concepts))]\n [else (error 'concept-listbox/predicates)])))\n (define predicates\n (sort (remove-duplicates (map cddr (append* preds-by-concept))) string Predicate 1 -> [X] -> Predicate 2 -> Concept 2\")))\n\n (define concept-2-overall-pane (new vertical-pane%\n (parent upper-pane)\n (alignment '(left center))))\n \n (define concept-2-search/isa-panel (new horizontal-panel%\n (parent concept-2-overall-pane)\n (alignment '(left center))\n (stretchable-height #f)))\n (define concept-2-list-boxes-panel (new panel:horizontal-dragable%\n (parent concept-2-overall-pane)\n (alignment '(left center))))\n (define predicate-2-list-box (new list-box%\n (label \"Predicate 2\")\n (choices (unbox *predicate-2-choices*))\n (columns '(\"Name\"))\n (parent concept-2-list-boxes-panel)\n (style '(extended))\n (callback go-callback)))\n (define concept-2-list-box (concept-list concept-2-overall-pane\n concept-2-search/isa-panel\n concept-2-list-boxes-panel\n \"Concept 2\"\n *concept-2-name-string*\n *concept-2-isa-flag*\n *curie-2-string*\n *concept-2-choices*\n (lambda () predicate-2-list-box)\n *predicate-2-choices*\n 'in-edge\n *last-concept-2-column-clicked-for-sorting*\n *concept-2-column-sort-order*\n *concept-2-choices*\n convert-concept-1/2-to-column-sorting-format\n (make-send-concepts-to-concept-1/2-list-box (lambda () concept-2-list-box))))\n\n (define running-status-description/search-in-Xs-panel\n (new\n horizontal-panel%\n (parent concept-2-overall-pane)\n (alignment '(left center))\n (stretchable-height #f)))\n \n (define running-status-description (new message%\n (parent running-status-description/search-in-Xs-panel)\n (label \" \")))\n \n (define search-in-Xs-field (new text-field%\n (label \"Find in X's\")\n (parent running-status-description/search-in-Xs-panel)\n (init-value \"\")\n (callback (lambda (self event)\n (handle-search-in-Xs self\n concept-X-list-box\n search-in-Xs-previous-button\n search-in-Xs-next-button\n )))))\n \n (define search-in-Xs-previous-button (new button%\n (parent running-status-description/search-in-Xs-panel)\n (label \"Previous\")\n (callback (lambda (self event)\n (handle-search-in-Xs search-in-Xs-field\n concept-X-list-box\n search-in-Xs-previous-button\n search-in-Xs-next-button\n 'previous)))))\n\n (define search-in-Xs-next-button (new button%\n (parent running-status-description/search-in-Xs-panel)\n (label \"Next\")\n (callback (lambda (self event)\n (handle-search-in-Xs search-in-Xs-field\n concept-X-list-box\n search-in-Xs-previous-button\n search-in-Xs-next-button\n 'next)))))\n \n (define concept-X-list-box (new smart-column-width-list-box%\n (label \"X\")\n (choices (unbox *concept-X-choices*))\n (columns '(\"KG\" \"CID\" \"CURIE\" \"Category\" \"Name\" \"Max PubMed #\" \"Min PubMed #\" \"Predicates\" \"Path Length\" \"Path Confidence\"))\n (parent lower-pane)\n (style '(column-headers clickable-headers reorderable-headers single))\n (callback (lambda (self event)\n (define event-type (send event get-event-type))\n (cond\n [(eqv? event-type 'list-box-column)\n (handle-sort-by-column-header-click\n event\n concept-X-list-box\n *last-concept-X-column-clicked-for-sorting*\n *concept-X-column-sort-order*\n *concept-X-choices*\n convert-X-concept-to-column-sorting-format\n (make-send-concepts-to-concept-X-list-box self))]\n [(eqv? event-type 'list-box-dclick)\n (printf \"double-click!! copy name of the concept to the clipboard\\n\")\n (define time-stamp (send event get-time-stamp))\n (printf \"time stamp: ~s\\n\" time-stamp)\n (define concept-name\n (let ((sel* (send concept-X-list-box get-selections)))\n (if (= (length sel*) 1)\n (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n (match selected-X\n [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-count ,confidence)\n name]\n [else \"\"]))\n \"\")))\n (printf \"concept name: ~s\\n\" concept-name)\n (send the-clipboard set-clipboard-string concept-name time-stamp)]\n [else\n\n ;; empty the entries in the full-path-list-box\n (send full-path-list-box set '() '() '() '() '() '() '() '())\n \n ;; empty the entries in the properties list-boxes\n (send subject-properties-list-box set '() '())\n (send edge-properties-list-box set '() '())\n (send object-properties-list-box set '() '())\n\n ;; empty the entries in the pubmed-list-box\n (send pubmed-list-box set '())\n\n (let ((sel* (send concept-X-list-box get-selections)))\n (when (= (length sel*) 1)\n (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n (let ((selected-X\n (match selected-X\n [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-count ,confidence)\n `(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)])))\n (printf \"selected ~s\\n\" selected-X)\n (define concept-1* (unbox *solution-concept-1-choices*))\n (define concept-2* (unbox *solution-concept-2-choices*))\n (printf \"concept-1* ~s\\n\" concept-1*)\n (printf \"concept-2* ~s\\n\" concept-2*)\n (define predicate-1* (unbox *solution-predicate-1-choices*))\n (define predicate-2* (unbox *solution-predicate-2-choices*))\n (printf \"predicate-1* ~s\\n\" predicate-1*)\n (printf \"predicate-2* ~s\\n\" predicate-2*)\n\n (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates (unbox *predicate-1-choices*) predicate-1*))\n (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates (unbox *predicate-2-choices*) predicate-2*))\n\n (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n\n (define paths '())\n\n\n (cond\n [;; TODO refactor all of these tests/logic (duplicate code)\n (and\n ;; CURIE search\n (string=? \"\" (string-trim (unbox *solution-curie-1-string*)))\n (string=? \"\" (string-trim (unbox *solution-curie-2-string*)))\n ;; String search\n (and\n (null?\n (split-name-string\n (unbox *solution-concept-1-name-string*)))\n (null?\n (split-name-string\n (unbox *solution-concept-2-name-string*)))))\n\n (set! paths '())]\n [(and\n ;; CURIE search\n (string=? \"\" (string-trim (unbox *solution-curie-1-string*)))\n ;; String search\n (null? (split-name-string (unbox *solution-concept-1-name-string*))))\n\n (set! paths '())\n ;; run synthetic queries here\n (set! paths\n (remove-duplicates\n (append paths\n (run* (q)\n (fresh (e dbname eid x o pid pred eprops)\n (== (list `(,dbname ,eid ,x ,o (,pid . ,pred) ,eprops)) q)\n (== `(,dbname . ,x) selected-X)\n (== `(,dbname ,eid ,x ,o (,pid . ,pred) ,eprops) e)\n (membero `(,dbname . ,o) concept-2*)\n (membero pred atomic-predicate-2*)\n (edgeo e))))))]\n [(and\n ;; CURIE search\n (string=? \"\" (string-trim (unbox *solution-curie-2-string*)))\n ;; String search\n (null? (split-name-string (unbox *solution-concept-2-name-string*))))\n\n (set! paths '())\n ;; run synthetic queries here\n (set! paths\n (remove-duplicates\n (append paths\n (run* (q)\n (fresh (e dbname eid s x pid pred eprops)\n (== (list `(,dbname ,eid ,s ,x (,pid . ,pred) ,eprops)) q)\n (== `(,dbname . ,x) selected-X)\n (== `(,dbname ,eid ,s ,x (,pid . ,pred) ,eprops) e)\n (membero `(,dbname . ,s) concept-1*)\n (membero pred atomic-predicate-1*)\n (edgeo e))))))]\n [else\n (set! paths '())\n ;; run synthetic queries here\n (set! paths\n (remove-duplicates\n (append paths\n (run* (q)\n (fresh (e1 e2 dbname eid1 eid2 s x o pid1 pid2 p1 p2 eprops1 eprops2)\n (== `(,dbname . ,x) selected-X)\n (== (list\n `(,dbname ,eid1 ,s ,x (,pid1 . ,p1) ,eprops1)\n `(,dbname ,eid2 ,x ,o (,pid2 . ,p2) ,eprops2))\n q)\n (== `(,dbname ,eid1 ,s ,x (,pid1 . ,p1) ,eprops1) e1)\n (== `(,dbname ,eid2 ,x ,o (,pid2 . ,p2) ,eprops2) e2)\n (membero `(,dbname . ,s) concept-1*)\n (membero `(,dbname . ,o) concept-2*)\n (membero p1 atomic-predicate-1*)\n (membero p2 atomic-predicate-2*)\n (edgeo e1)\n (edgeo e2))))))])\n\n (printf \"paths: ~s\\n\" paths)\n (newline)\n\n ;; This sorting affects the order of the \"Path\" list\n ;; for the selected concept.\n (set! paths (sort-paths paths))\n \n (define flattened-paths\n (let ((ls (foldr\n (lambda (p l)\n (cons\n 'path-separator\n (append (reverse p) l)))\n '()\n paths)))\n (if (null? ls)\n ;; ls should never be null!\n '()\n (reverse (cdr ls)))))\n\n\n\n (define full-path-dbname-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n (~a dbname)]))\n flattened-paths))\n\n (define full-path-eid-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n (~a eid)]))\n flattened-paths))\n\n (define full-path-subj-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n (~a subj #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-pred-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n (~a `(,pid . ,pred) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-obj-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n (~a obj #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-subj-cat-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid (,cid ,cui ,name (,catid . ,cat) ,props) ,obj (,pid . ,pred) ,eprops)\n (~a `(,catid . ,cat) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-obj-cat-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj (,cid ,cui ,name (,catid . ,cat) ,props) (,pid . ,pred) ,eprops)\n (~a `(,catid . ,cat) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n flattened-paths))\n\n (define full-path-PubMed-count-list\n (map (lambda (x)\n (match x\n ['path-separator \"----\"]\n [`(,dbname ,eid ,subj (,cid ,cui ,name (,catid . ,cat) ,props) (,pid . ,pred) ,eprops)\n (~a (length (pubmed-URLs-from-edge x)))]))\n flattened-paths))\n\n (send full-path-list-box\n set\n full-path-dbname-list\n full-path-eid-list\n full-path-subj-list\n full-path-pred-list\n full-path-obj-list\n full-path-subj-cat-list\n full-path-obj-cat-list\n full-path-PubMed-count-list\n )\n\n (set-box! *full-path-choices* flattened-paths)\n\n ;; unselect all items\n (for ([i (length flattened-paths)])\n (send full-path-list-box select i #f))\n\n ;; select first item\n (send full-path-list-box select 0 #t)\n )))\n (void))])))))\n\n (define full-path-list-box (new smart-column-width-list-box%\n (label \"Paths\")\n (choices (unbox *full-path-choices*))\n (columns '(\"KG\" \"EID\" \"Subject\" \"Predicate\" \"Object\" \"Subj Cat\" \"Obj Cat\" \"PubMed #\"))\n (parent lower-pane)\n (style '(column-headers reorderable-headers extended))\n (callback (lambda (self event)\n (when *verbose*\n (printf \"(unbox *full-path-choices*):\\n~s\\n\" (unbox *full-path-choices*)))\n (define selections (send self get-selections))\n (when *verbose*\n (printf \"selection for full path:\\n~s\\n\" selections))\n (define selected-full-paths\n (foldr (lambda (i l) (cons (list-ref (unbox *full-path-choices*) i) l))\n '()\n selections))\n (for-each\n (lambda (x)\n (match x\n ['path-separator\n (send subject-properties-list-box set '() '())\n (send edge-properties-list-box set '() '())\n (send object-properties-list-box set '() '())]\n [`(,dbname ,eid\n (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n ,p\n ,eprops)\n (define (set-properties-list-box prop-list-box props)\n (send prop-list-box\n set\n (map\n (lambda (p)\n (~a (car p)\n #:max-width\n MAX-CHAR-WIDTH\n #:limit-marker\n \"...\"))\n props)\n (map\n (lambda (p)\n (~a (cdr p)\n #:max-width\n MAX-CHAR-WIDTH\n #:limit-marker\n \"...\"))\n props)))\n (set-properties-list-box subject-properties-list-box sprops)\n (set-properties-list-box edge-properties-list-box eprops)\n (set-properties-list-box object-properties-list-box oprops)]))\n selected-full-paths)\n (for-each\n (lambda (edge)\n (let ((URLs (pubmed-URLs-from-edge edge)))\n (set-box! *pubmed-choices* URLs)\n (send pubmed-list-box set URLs)))\n selected-full-paths)\n (when *verbose*\n (printf \"selected full path:\\n\")\n (for-each\n (lambda (x)\n (match x\n ['path-separator\n (printf \"-----------------------\\n\")]\n [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n (pretty-print `(,dbname ,eid ,subj ,obj ,p ,eprops))]))\n selected-full-paths))\n ))))\n\n (define properties/pubmed-panel (new panel:horizontal-dragable%\n (parent lower-pane)\n (alignment '(left center))\n (stretchable-height #t)))\n\n (define subject-properties-list-box (new smart-column-width-list-box%\n (label \"Subject\")\n (choices '())\n (columns '(\"Property\" \"Value\"))\n (parent properties/pubmed-panel)\n (style '(column-headers reorderable-headers extended))\n (callback (lambda (self event)\n (void)))))\n \n (define edge-properties-list-box (new smart-column-width-list-box%\n (label \"Edge\")\n (choices '())\n (columns '(\"Property\" \"Value\"))\n (parent properties/pubmed-panel)\n (style '(column-headers reorderable-headers extended))\n (callback (lambda (self event)\n (void)))))\n\n (define object-properties-list-box (new smart-column-width-list-box%\n (label \"Object\")\n (choices '())\n (columns '(\"Property\" \"Value\"))\n (parent properties/pubmed-panel)\n (style '(column-headers reorderable-headers extended))\n (callback (lambda (self event)\n (void)))))\n \n (define pubmed-list-box (new list-box%\n (label \"Pubmed\")\n (choices (unbox *pubmed-choices*))\n (columns '(\"URL\"))\n (parent properties/pubmed-panel)\n (style '(column-headers reorderable-headers single))\n (callback (lambda (self event) \n (define event-type (send event get-event-type))\n (define selections (send self get-selections))\n (define selected-pubmeds\n (foldr (lambda (i l) (cons (list-ref (unbox *pubmed-choices*) i) l))\n '()\n selections))\n (for-each\n (lambda (url)\n (printf \"url: ~s\\n\" url)\n (when (eqv? event-type 'list-box-dclick)\n ;; if the user double-clicked on the URL, open it in a web browser\n (send-url url)))\n selected-pubmeds)))))\n \n ;; trigger reflowing of object sizes\n (send frame reflow-container)\n\n ;; disable previous and next buttons by default\n (send search-in-Xs-previous-button enable #f)\n (send search-in-Xs-next-button enable #f)\n \n (set-default-column-widths concept-1-list-box)\n (set-default-column-widths concept-2-list-box)\n (set-default-column-widths concept-X-list-box)\n (set-default-column-widths full-path-list-box)\n (set-default-column-widths edge-properties-list-box)\n (set-default-column-widths edge-properties-list-box)\n (set-default-column-widths object-properties-list-box)\n \n (send frame show #t)))\n\n(define (launch-gene-window)\n (let ((frame (new frame%\n (label \"Gene Explorer\")\n (width HORIZ-SIZE)\n (height VERT-SIZE))))\n\n (define gene-name-field (new text-field%\n (label \"Gene Name\")\n (parent frame)\n (init-value \"\")\n (callback (lambda (self event)\n (void)))))\n\n (define gene-listbox (new smart-column-width-list-box%\n (label \"Gene\")\n (choices '())\n (columns '(\"KG\" \"CID\" \"CURIE\" \"Category\" \"Name\"))\n (parent frame)\n (style '(column-headers reorderable-headers extended))\n (callback (lambda (self event)\n (void)))))\n\n\n (define current-gene-name \"\")\n\n (send frame show #t)\n ))\n\n\n(define (split-atomic/synthetic-predicates choices predicate*)\n (define (synthetic? pred)\n (memf (lambda (syn-prefix) (string-prefix? pred syn-prefix))\n SYNTHETIC_PREDICATE_PREFIXES))\n\n (define atomic-predicate* (filter-not synthetic? predicate*))\n (define synthetic-predicate* (filter synthetic? predicate*))\n\n (when (memf (lambda (pred) (string-prefix? pred DECREASES_PREDICATE_PREFIX_STRING))\n synthetic-predicate*)\n (set! atomic-predicate* (append DECREASES_PREDICATE_NAMES atomic-predicate*)))\n\n (when (memf (lambda (pred) (string-prefix? pred INCREASES_PREDICATE_PREFIX_STRING))\n synthetic-predicate*)\n (set! atomic-predicate* (append INCREASES_PREDICATE_NAMES atomic-predicate*)))\n\n (set! atomic-predicate* (set-intersect choices (remove-duplicates atomic-predicate*)))\n\n (printf \"atomic-predicate*: ~s\\n\" atomic-predicate*)\n (printf \"synthetic-predicate*: ~s\\n\" synthetic-predicate*)\n\n (list atomic-predicate* synthetic-predicate*))\n\n\n(define (find-X-concepts concept-1* concept-2* predicate-1* predicate-2* predicate-1-choices predicate-2-choices concept-X-list-box running-status-description full-path-list-box subject-properties-list-box edge-properties-list-box object-properties-list-box pubmed-list-box search-in-Xs-field search-in-Xs-previous-button search-in-Xs-next-button)\n\n (printf \"&&&&&&&&&&&&&&& called find-X-concepts &&&&&&&&&&&&&&&&&&\\n\")\n \n (printf \"concept-1*: ~s\\n\" concept-1*)\n (printf \"concept-2*: ~s\\n\" concept-2*)\n\n (printf \"predicate-1*: ~s\\n\" predicate-1*)\n (printf \"predicate-2*: ~s\\n\" predicate-2*) \n \n\n (define start-time (current-milliseconds))\n\n (printf \"\\nfinding concepts X for which\\n[C1] -> P1 -> [X] -> P2 -> [C2]\\n\")\n (printf \"=============================\\n\")\n\n (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates predicate-1-choices predicate-1*))\n (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates predicate-2-choices predicate-2*))\n\n (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n (define all-X-concepts-with-edges '())\n\n (printf \"atomic/synthetic-predicate-1*: ~s\\n\" atomic/synthetic-predicate-1*)\n (printf \"atomic/synthetic-predicate-2*: ~s\\n\" atomic/synthetic-predicate-2*)\n (newline)\n (printf \"atomic-predicate-1*: ~s\\n\" atomic-predicate-1*)\n (printf \"atomic-predicate-2*: ~s\\n\" atomic-predicate-2*)\n (newline)\n (printf \"synthetic-predicate-1*: ~s\\n\" synthetic-predicate-1*)\n (printf \"synthetic-predicate-2*: ~s\\n\" synthetic-predicate-2*)\n (newline)\n\n (cond\n [;; TODO refactor all of these tests/logic (duplicate code)\n (and\n ;; CURIE search\n (string=? \"\" (string-trim (unbox *curie-1-string*)))\n (string=? \"\" (string-trim (unbox *curie-2-string*)))\n ;; String search\n (and\n (null?\n (split-name-string\n (unbox *concept-1-name-string*)))\n (null?\n (split-name-string\n (unbox *concept-2-name-string*)))))\n\n (printf \"find-X-concepts cond case 1\\n\")\n\n (set! all-X-concepts-with-edges '())]\n [(and\n ;; CURIE search\n (string=? \"\" (string-trim (unbox *curie-1-string*)))\n ;; String search\n (null? (split-name-string (unbox *concept-1-name-string*))))\n\n (printf \"find-X-concepts cond case 2\\n\")\n \n (set! all-X-concepts-with-edges '())\n (set! all-X-concepts-with-edges\n (remove-duplicates\n (append all-X-concepts-with-edges\n (run* (q)\n (fresh (dbname eid s o pid pred eprops e)\n (== (list dbname s (list eprops) (list e)) q)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) ,eprops) e)\n (membero `(,dbname . ,o) concept-2*)\n (membero pred atomic-predicate-2*)\n (edgeo e))))))]\n [(and\n ;; CURIE search\n (string=? \"\" (string-trim (unbox *curie-2-string*)))\n ;; String search\n (null? (split-name-string (unbox *concept-2-name-string*))))\n\n (printf \"find-X-concepts cond case 3\\n\")\n \n (set! all-X-concepts-with-edges '())\n ;; run synthetic queries here\n (set! all-X-concepts-with-edges\n (remove-duplicates\n (append all-X-concepts-with-edges\n (run* (q)\n (fresh (dbname eid s o pid pred eprops e)\n (== (list dbname o (list eprops) (list e)) q)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) ,eprops) e)\n (membero `(,dbname . ,s) concept-1*)\n (membero pred atomic-predicate-1*)\n (edgeo e))))))]\n [else\n\n (printf \"find-X-concepts cond case 4\\n\")\n \n (set! all-X-concepts-with-edges '())\n ;; run synthetic queries here\n (set! all-X-concepts-with-edges\n (remove-duplicates\n (append all-X-concepts-with-edges\n (run* (q)\n (fresh (dbname eid1 eid2 s m o pid1 pid2 p1 p2 eprops1 eprops2 e1 e2)\n (== (list dbname m (list eprops1 eprops2) (list e1 e2)) q)\n (== `(,dbname ,eid1 ,s ,m (,pid1 . ,p1) ,eprops1) e1)\n (== `(,dbname ,eid2 ,m ,o (,pid2 . ,p2) ,eprops2) e2)\n (membero `(,dbname . ,s) concept-1*)\n (membero `(,dbname . ,o) concept-2*)\n (membero p1 atomic-predicate-1*)\n (membero p2 atomic-predicate-2*)\n (edgeo e1)\n (edgeo e2))))))])\n\n (define end-time (current-milliseconds))\n\n (define elapsed-time (- end-time start-time))\n\n (printf \"elapsed query time: ~s seconds\\n\" (/ elapsed-time 1000.0))\n (printf \"=============================\\n\")\n\n ;; This sorting affects order of appearance in the \"X\" concept list\n (set! all-X-concepts-with-edges\n (sort\n all-X-concepts-with-edges\n (lambda (c1 c2)\n (match (list c1 c2)\n [`((,_ ,_ ,_ ,e1*) (,_ ,_ ,_ ,e2*))\n (not (path-confidencestring (seconds->date (current-seconds)) #t))\n (newline)\n\n\n (define number-Xs-found (length all-X-concepts))\n (define query-seconds (/ elapsed-time 1000.0))\n (define query-time-format-string \"Found ~s X's after ~s seconds\")\n (send running-status-description set-label (format query-time-format-string number-Xs-found query-seconds))\n (printf query-time-format-string number-Xs-found query-seconds)\n (newline)\n (newline)\n\n\n (set-box! *concept-X-choices* all-X-concepts)\n\n (set-box! *solution-concept-1-name-string* (unbox *concept-1-name-string*))\n (set-box! *solution-concept-2-name-string* (unbox *concept-2-name-string*))\n\n (set-box! *solution-concept-1-isa-flag* (unbox *concept-1-isa-flag*))\n (set-box! *solution-concept-2-isa-flag* (unbox *concept-2-isa-flag*))\n ;;\n (set-box! *solution-curie-1-string* (unbox *curie-1-string*))\n (set-box! *solution-curie-2-string* (unbox *curie-2-string*))\n ;;\n (set-box! *solution-concept-1-choices* concept-1*)\n (set-box! *solution-concept-2-choices* concept-2*)\n (set-box! *solution-predicate-1-choices* predicate-1*)\n (set-box! *solution-predicate-2-choices* predicate-2*)\n\n (printf \"*solution-concept-1-name-string*:\\n~s\\n\" (unbox *solution-concept-1-name-string*))\n (printf \"*solution-concept-1-isa-flag*:\\n~s\\n\" (unbox *solution-concept-1-isa-flag*))\n ;;\n (printf \"*solution-curie-1-string*:\\n~s\\n\" (unbox *solution-curie-1-string*))\n ;;\n (printf \"*solution-concept-1-choices*:\\n\")\n (pretty-print (unbox *solution-concept-1-choices*))\n (printf \"*solution-predicate-1-choices*:\\n\")\n (pretty-print (unbox *solution-predicate-1-choices*))\n (newline)\n\n (printf \"*solution-concept-2-name-string*:\\n~s\\n\" (unbox *solution-concept-2-name-string*))\n (printf \"*solution-concept-2-isa-flag*:\\n~s\\n\" (unbox *solution-concept-2-isa-flag*))\n ;;\n (printf \"*solution-curie-2-string*:\\n~s\\n\" (unbox *solution-curie-2-string*))\n ;;\n (printf \"*solution-concept-2-choices*:\\n\")\n (pretty-print (unbox *solution-concept-2-choices*))\n (printf \"*solution-predicate-2-choices*:\\n\")\n (pretty-print (unbox *solution-predicate-2-choices*))\n (newline)\n\n (define pretty-print-X-concepts-with-edges\n (lambda (file-name pretty-printer print-basic-header print-low-level-query-information X-concepts-with-edges)\n (with-output-to-file\n file-name\n (lambda ()\n (when print-basic-header\n (printf \";; mediKanren query output\\n\")\n (printf \";; ~a\\n\" MEDIKANREN_VERSION_STRING)\n (printf \";; \\n\")\n (let ((local-date (seconds->date (current-seconds))))\n (printf \";; Query run at date/time: ~s ~s ~s ~s:~s:~s (Year Month Day Hour:Minute:Second)\\n\"\n (date-year local-date)\n (date-month local-date)\n (date-day local-date)\n (date-hour local-date)\n (date-minute local-date)\n (date-second local-date)))\n (printf \";; \\n\"))\n (when print-low-level-query-information\n (printf \";; ===================================================\\n\")\n (printf \";; Low-level query information from the mediKanren GUI\\n\")\n (printf \";; ===================================================\\n\")\n (printf \";; \\n\")\n (printf \";; *concept-1-name-string*: ~s\\n\" (unbox *concept-1-name-string*))\n (printf \";; *solution-concept-1-name-string*: ~s\\n\" (unbox *solution-concept-1-name-string*))\n (printf \";; *solution-concept-1-isa-flag*: ~s\\n\" (unbox *solution-concept-1-isa-flag*))\n ;;\n (printf \";; *curie-1-string*: ~s\\n\" (unbox *curie-1-string*))\n (printf \";; *solution-curie-1-string* ~s\\n\" (unbox *solution-curie-1-string*))\n ;;\n (printf \";; *solution-concept-1-choices*:\\n\")\n (printf \"#|\\n\")\n (pretty-print (unbox *solution-concept-1-choices*))\n (printf \"|#\\n\")\n (printf \";; atomic/synthetic-predicate-1*: ~s\\n\" atomic/synthetic-predicate-1*)\n (printf \";; atomic-predicate-1*: ~s\\n\" atomic-predicate-1*)\n (printf \";; synthetic-predicate-1*: ~s\\n\" synthetic-predicate-1*)\n (printf \";; *solution-predicate-1-choices*:\\n\")\n (printf \"#|\\n\")\n (pretty-print (unbox *solution-predicate-1-choices*))\n (printf \"|#\\n\")\n (printf \";; \\n\")\n (printf \";; \\n\")\n (printf \";; \\n\")\n (printf \";; atomic/synthetic-predicate-2*: ~s\\n\" atomic/synthetic-predicate-2*)\n (printf \";; atomic-predicate-2*: ~s\\n\" atomic-predicate-2*)\n (printf \";; synthetic-predicate-2*: ~s\\n\" synthetic-predicate-2*)\n (printf \";; *solution-predicate-2-choices*:\\n\")\n (printf \"#|\\n\")\n (pretty-print (unbox *solution-predicate-2-choices*))\n (printf \"|#\\n\")\n (printf \";; *concept-2-name-string*: ~s\\n\" (unbox *concept-2-name-string*))\n (printf \";; *solution-concept-2-name-string*: ~s\\n\" (unbox *solution-concept-2-name-string*))\n (printf \";; *solution-concept-2-isa-flag*: ~s\\n\" (unbox *solution-concept-2-isa-flag*))\n ;;\n (printf \";; *curie-2-string*: ~s\\n\" (unbox *curie-2-string*))\n (printf \";; *solution-curie-2-string* ~s\\n\" (unbox *solution-curie-2-string*)) \n ;;\n (printf \";; *solution-concept-2-choices*:\\n\")\n (printf \"#|\\n\")\n (pretty-print (unbox *solution-concept-2-choices*))\n (printf \"|#\\n\")\n (printf \"\\n\"))\n (when print-basic-header\n (printf \";; ======================================\\n\")\n (printf \";; Query results (list of complete edges)\\n\")\n (printf \";; ======================================\\n\"))\n (pretty-printer X-concepts-with-edges))\n #:mode 'text\n #:exists QUERY_RESULTS_FILE_MODE)))\n\n (define human-friendly-pretty-print-X-concepts-with-edges\n (lambda (X-concepts-with-edges)\n (for-each\n (lambda (entry index)\n (match entry\n [`(,dbname\n ,s\n ,eprops*\n ,edges)\n (printf \"*** Edge group:\")\n (for-each\n (lambda (edge)\n (match edge\n [`(,dbname\n ,eid\n (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) ,eprops)\n (let ((pubmed* (pubmed-URLs-from-edge edge)))\n (printf \"\\n~s\\t~s\\t~s\\t~s\\t~s\\t~s\\t~s\\t~s PubMed Entries\\n~s\\n\" index dbname sname scat pred oname ocat (length pubmed*) pubmed*))]))\n edges)\n (printf \"***\\n\\n\") ]))\n X-concepts-with-edges\n (iota (length X-concepts-with-edges) 1))))\n\n (define spreadsheet-friendly-pretty-print-X-concepts-with-edges\n (lambda (X-concepts-with-edges)\n (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n \"Subject Category\"\n \"Subject Name\"\n \n \"Predicate\"\n \n \"Object Category\"\n \"Object Name\"\n \n \"PubMed URL\"\n \n \"KG Name\")\n (for-each\n (lambda (entry index)\n (match entry\n [`(,dbname\n ,s\n ,eprops*\n ,edges)\n (for-each\n (lambda (edge)\n (match edge\n [`(,dbname\n ,eid\n (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) ,eprops)\n (let ((pubmed* (pubmed-URLs-from-edge edge)))\n (for-each\n (lambda (pubmed)\n (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n scat\n sname\n\n pred\n\n ocat\n oname \n\n pubmed\n \n dbname))\n pubmed*))]))\n edges)]))\n X-concepts-with-edges\n (iota (length X-concepts-with-edges) 1))))\n\n (when WRITE_QUERY_RESULTS_TO_FILE\n\n (printf \"saving all-X-concepts-with-edges to '~a' file...\\n\"\n QUERY_RESULTS_FILE_NAME)\n (pretty-print-X-concepts-with-edges\n QUERY_RESULTS_FILE_NAME\n pretty-print\n #t ;; print-basic-header flag\n #t ;; print-low-level-query-information flag\n all-X-concepts-with-edges)\n (printf \"saved all-X-concepts-with-edges to '~a' file\\n\"\n QUERY_RESULTS_FILE_NAME)\n\n (printf \"saving human-friendly version of all-X-concepts-with-edges to '~a' file...\\n\"\n HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n (pretty-print-X-concepts-with-edges\n HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME\n human-friendly-pretty-print-X-concepts-with-edges\n #t ;; print-basic-header flag\n #f ;; print-low-level-query-information flag\n all-X-concepts-with-edges)\n (printf \"saved human-friendly version of all-X-concepts-with-edges to '~a' file\\n\"\n HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n\n (printf \"saving spreadsheet-friendly version of all-X-concepts-with-edges to '~a' file...\\n\"\n SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n (pretty-print-X-concepts-with-edges\n SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME\n spreadsheet-friendly-pretty-print-X-concepts-with-edges\n #f ;; print-basic-header flag\n #f ;; print-low-level-query-information flag\n all-X-concepts-with-edges)\n (printf \"saved spreadsheet-friendly version of all-X-concepts-with-edges to '~a' file\\n\"\n SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n\n )\n\n (printf \"========== end query results =============\\n\")\n\n ((make-send-concepts-to-concept-X-list-box concept-X-list-box) all-X-concepts)\n\n ;; unselect all items\n (for ([i (length all-X-concepts)])\n (send concept-X-list-box select i #f))\n\n ;; add X concept data for each list-box entry\n (let loop ((i 0)\n (c* all-X-concepts))\n (cond\n [(null? c*) (void)]\n [else\n (send concept-X-list-box set-data i (car c*))\n (loop (add1 i)\n (cdr c*))]))\n\n ;; empty the search in X's field, and disable the previous/next buttons\n (send search-in-Xs-field set-value \"\")\n (send search-in-Xs-previous-button enable #f)\n (send search-in-Xs-next-button enable #f)\n \n ;; empty the entries in the full-path-list-box\n (send full-path-list-box set '() '() '() '() '() '() '() '())\n\n ;; empty the entries in the properties list-boxes\n (send subject-properties-list-box set '() '())\n (send edge-properties-list-box set '() '())\n (send object-properties-list-box set '() '())\n\n ;; empty the entries in the pubmed-list-box\n (send pubmed-list-box set '())\n\n )\n\n(displayln\n \"Launching GUI\")\n\n(launch-gui)\n" }, { "path": "attic/medikanren/sialic-full-will.rkt", "content": "#lang racket\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n\n membero\n edgeo\n ~name-concepto\n\n semmed\n monarch\n rtx\n scigraph)\n\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"data/semmed\")))\n(displayln \"loading monarch-lite\")\n(define monarch (time (make-db \"data/monarch-lite\")))\n(displayln \"loading rtx\")\n(define rtx (time (make-db \"data/rtx\")))\n(displayln \"loading scigraph\")\n(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; remove duplicates from a list\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))))\n\n#|\n(time (pretty-print\n (run* (concept)\n (~name-concepto \"sialic acid\" concept))))\n|#\n\n(time (rem-dups\n (run* (q)\n (fresh (edge name db)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== \"negatively_regulates\" pred)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)\n (db:edgeo semmed edge)\n (== 'semmed db)]\n [(db:~name-concepto monarch \"sialic acid\" object)\n (db:edgeo monarch edge)\n (== 'monarch db)]\n [(db:~name-concepto rtx \"sialic acid\" object)\n (db:edgeo rtx edge)\n (== 'rtx db)]\n [(db:~name-concepto scigraph \"sialic acid\" object)\n (db:edgeo scigraph edge)\n (== 'scigraph db)]) \n (== (list db edge) q))))))\n\n(time (rem-dups\n (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)\n (db:edgeo semmed edge)]\n [(db:~name-concepto monarch \"sialic acid\" object)\n (db:edgeo monarch edge)]\n [(db:~name-concepto rtx \"sialic acid\" object)\n (db:edgeo rtx edge)]\n [(db:~name-concepto scigraph \"sialic acid\" object)\n (db:edgeo scigraph edge)]) \n (== (list pid pred) q))))))\n\n#|\n;;; Error 1\n(time (rem-dups\n (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n [(db:~name-concepto monarch \"sialic acid\" object)]\n [(db:~name-concepto rtx \"sialic acid\" object)]\n [(db:~name-concepto scigraph \"sialic acid\" object)]) \n (== (list pid pred) q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n [(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]\n ))))))\n; integer-bytes->integer: contract violation\n; expected: bytes?\n; given: #\n; argument position: 1st\n; [,bt for context]\n\n\n;;; Error 2\n(displayln \"X ANY-PRED sialic acid:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name dbid)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,dbid ,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (~name-concepto \"sialic acid\" `(,odb . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo edge))))))\n; *: contract violation\n; expected: number?\n; given: '(#((unbound) (scope) 6270) #((unbound) (scope) 6271) #((unbound)\n; (scope) 6272) . #((unbound) (scope) 6273))\n; argument position: 1st\n; [,bt for context]\n|#\n\n#|\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n [(db:~name-concepto monarch \"sialic acid\" object)]\n [(db:~name-concepto rtx \"sialic acid\" object)]\n [(db:~name-concepto scigraph \"sialic acid\" object)]) \n (== (list pid pred) q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n [(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]))))\n\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n [(db:~name-concepto monarch \"sialic acid\" object)]\n [(db:~name-concepto rtx \"sialic acid\" object)]\n [(db:~name-concepto scigraph \"sialic acid\" object)]) \n (== edge q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n [(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]))))\n\n\n(time (rem-dups (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n ;[(db:~name-concepto monarch \"sialic acid\" object)]\n ;[(db:~name-concepto rtx \"sialic acid\" object)]\n ;[(db:~name-concepto scigraph \"sialic acid\" object)]\n ) \n (== (list pid pred) q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n ;[(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]\n ))))))\n|#\n\n#|\n(displayln \"X ANY-PRED sialic acid:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (~name-concepto \"sialic acid\" `(,odb . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo edge))))))\n|#\n\n#|\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,sname ,pred ,oname) q)\n (db:edgeo scigraph edge))))\n|#\n\n#|\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,sname ,pred ,oname) q)\n (edgeo edge))))\n|#\n" }, { "path": "attic/medikanren/sialic-full.rkt", "content": "#lang racket\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n\n membero\n edgeo\n ~name-concepto\n\n remdups\n\n semmed\n monarch\n rtx\n scigraph)\n\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n(displayln \"loading semmed\")\n(define semmed (time (make-db \"data/semmed\")))\n(displayln \"loading monarch-lite\")\n(define monarch (time (make-db \"data/monarch-lite\")))\n(displayln \"loading rtx\")\n(define rtx (time (make-db \"data/rtx\")))\n(displayln \"loading scigraph\")\n(define scigraph (time (make-db \"data/scigraph\")))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; remove duplicates from a list\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ((fresh (ee) (== `(scigraph . ,ee) e) (db:edgeo scigraph ee)))))\n\n(define (~name-concepto n c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed n cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch n cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx n cc)))\n ((fresh (cc) (== `(scigraph . ,cc) c) (db:~name-concepto scigraph n cc)))))\n\n(time (pretty-print\n (run* (concept)\n (~name-concepto \"sialic acid\" concept))))\n\n(time (rem-dups\n (run* (q)\n (fresh (edge name dbid)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,dbid ,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== (list pid pred) q)\n (~name-concepto \"sialic acid\" `(,dbid . ,object))\n (edgeo edge))))))\n\n(displayln \"X ANY-PRED sialic acid:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name dbid)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,dbid ,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,sname ,pred ,oname) q)\n (~name-concepto \"sialic acid\" `(,dbid . ,object))\n (edgeo edge))))))\n\n(displayln \"X produces sialic acid:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name dbid)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,dbid ,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== (list dbid edge) q)\n (== \"produces\" pred)\n (~name-concepto \"sialic acid\" `(,dbid . ,object))\n (edgeo edge))))))\n\n(displayln \"X produces sialic acid (defined by):\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name dbid)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `() eprops)\n (== `(,dbid ,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== (list dbid edge) q)\n (== \"produces\" pred)\n (~name-concepto \"sialic acid\" `(,dbid . ,object))\n (edgeo edge))))))\n\n\n(displayln \"sialic acid ANY-PRED X:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name dbid)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,dbid ,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,sname ,pred ,oname) q)\n (~name-concepto \"sialic acid\" `(,dbid . ,subject))\n (edgeo edge))))))\n\n#|\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n [(db:~name-concepto monarch \"sialic acid\" object)]\n [(db:~name-concepto rtx \"sialic acid\" object)]\n [(db:~name-concepto scigraph \"sialic acid\" object)]) \n (== (list pid pred) q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n [(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]))))\n\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n [(db:~name-concepto monarch \"sialic acid\" object)]\n [(db:~name-concepto rtx \"sialic acid\" object)]\n [(db:~name-concepto scigraph \"sialic acid\" object)]) \n (== edge q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n [(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]))))\n\n\n(time (rem-dups (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (conde\n [(db:~name-concepto semmed \"sialic acid\" object)]\n ;[(db:~name-concepto monarch \"sialic acid\" object)]\n ;[(db:~name-concepto rtx \"sialic acid\" object)]\n ;[(db:~name-concepto scigraph \"sialic acid\" object)]\n ) \n (== (list pid pred) q)\n (conde\n [(db:edgeo semmed edge)]\n [(db:edgeo monarch edge)]\n ;[(db:edgeo rtx edge)]\n [(db:edgeo scigraph edge)]\n ))))))\n|#\n\n#|\n(displayln \"X ANY-PRED sialic acid:\")\n(time (pretty-print\n (run* (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (~name-concepto \"sialic acid\" `(,odb . ,object))\n (== `(,sname ,pred ,oname) q)\n (edgeo edge))))))\n|#\n\n#|\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,sname ,pred ,oname) q)\n (db:edgeo scigraph edge))))\n|#\n\n#|\n(run 1 (q)\n (fresh (edge name)\n (fresh (subject sdb scid scui sname sdetails\n object odb ocid ocui oname odetails\n eid pid pred eprops)\n (== `(,scid ,scui ,sname . ,sdetails) subject)\n (== `(,ocid ,ocui ,oname . ,odetails) object)\n (== `(,eid ,subject ,object (,pid . ,pred) . ,eprops) edge)\n (== `(,sname ,pred ,oname) q)\n (edgeo edge))))\n|#\n" }, { "path": "attic/medikanren/test-POST.rkt", "content": "#lang racket\n(require net/http-client\n json)\n\n(define (named-cuis->json named-cuis)\n (define (node cui name)\n (hash 'description \"something profound goes here\"\n 'id cui\n 'name name\n 'node_attributes 'null\n 'symbol 'null\n 'type \"chemical_substance\"\n 'uri 'null))\n (define (result cui name)\n (hash 'confidence 0.00000000000000001\n 'description 'null\n 'essence name\n 'id 'null\n 'reasoner_id 'null\n 'result_graph (hash 'edge_list '()\n 'node_list (list (node cui name)))\n 'result_group 'null\n 'result_group_similarity_score 'null\n 'result_type 'null\n 'row_data '()\n 'score 'null\n 'score_direction 'null\n 'score_name 'null\n 'text 'null))\n (hash 'context 'null\n 'datetime 'null\n 'id 'null\n 'known_query_type_id 'null\n 'message 'null\n 'n_results 'null\n 'original_question_text 'null\n 'query_type_id 'null\n 'reasoner_id \"mediKanren-0.00000000000000zerozero...\"\n 'response_code \"OK\"\n 'restated_question_text 'null\n 'result_code 'null\n 'result_list (map result (map car named-cuis) (map cdr named-cuis))\n 'schema_version \"0.5\"\n 'table_column_names '()\n 'terms 'null\n 'tool_version \"Nope\"\n 'type \"medical_translator_query_result\"))\n\n(define data (jsexpr->bytes\n (named-cuis->json\n '((\"OMIM:600001\" . \"HEART DEFECTS, CONGENITAL, AND OTHER CONGENITAL ANOMALIES; HDCA\")))))\n\n;(define data\n;\"\n;{\n ;\\\"context\\\": null,\n ;\\\"datetime\\\": null,\n ;\\\"id\\\": null,\n ;\\\"known_query_type_id\\\": null,\n ;\\\"message\\\": \\\"25 results found\\\",\n ;\\\"n_results\\\": null,\n ;\\\"original_question_text\\\": null,\n ;\\\"query_type_id\\\": null,\n ;\\\"reasoner_id\\\": null,\n ;\\\"response_code\\\": \\\"OK\\\",\n ;\\\"restated_question_text\\\": null,\n ;\\\"result_code\\\": null,\n ;\\\"result_list\\\": [\n ;{\n ;\\\"confidence\\\": 0.9993358516965531,\n ;\\\"description\\\": null,\n ;\\\"essence\\\": \\\"HEART DEFECTS, CONGENITAL, AND OTHER CONGENITAL ANOMALIES; HDCA\\\",\n ;\\\"id\\\": null,\n ;\\\"reasoner_id\\\": null,\n ;\\\"result_graph\\\": {\n ;\\\"edge_list\\\": [\n ;{\n ;\\\"attribute_list\\\": null,\n ;\\\"confidence\\\": null,\n ;\\\"evidence_type\\\": null,\n ;\\\"is_defined_by\\\": \\\"RTX\\\",\n ;\\\"negated\\\": null,\n ;\\\"provided_by\\\": \\\"BioLink\\\",\n ;\\\"publications\\\": null,\n ;\\\"qualifiers\\\": null,\n ;\\\"relation\\\": null,\n ;\\\"source_id\\\": \\\"DOID:9352\\\",\n ;\\\"target_id\\\": \\\"HP:0011466\\\",\n ;\\\"type\\\": \\\"has_phenotype\\\"\n ;},\n ;{\n ;\\\"attribute_list\\\": null,\n ;\\\"confidence\\\": null,\n ;\\\"evidence_type\\\": null,\n ;\\\"is_defined_by\\\": \\\"RTX\\\",\n ;\\\"negated\\\": null,\n ;\\\"provided_by\\\": \\\"BioLink\\\",\n ;\\\"publications\\\": null,\n ;\\\"qualifiers\\\": null,\n ;\\\"relation\\\": null,\n ;\\\"source_id\\\": \\\"OMIM:600001\\\",\n ;\\\"target_id\\\": \\\"HP:0011466\\\",\n ;\\\"type\\\": \\\"has_phenotype\\\"\n ;}\n ;],\n ;\\\"node_list\\\": [\n ;{\n ;\\\"description\\\": \\\"Absence or underdevelopment of the gallbladder.\\\",\n ;\\\"id\\\": \\\"HP:0011466\\\",\n ;\\\"name\\\": \\\"Aplasia/Hypoplasia of the gallbladder\\\",\n ;\\\"node_attributes\\\": null,\n ;\\\"symbol\\\": null,\n ;\\\"type\\\": \\\"phenotypic_feature\\\",\n ;\\\"uri\\\": \\\"http://purl.obolibrary.org/obo/HP_0011466\\\"\n ;},\n ;{\n ;\\\"description\\\": \\\"A diabetes mellitus that involves high blood glucose resulting from cells fail to use insulin properly.\\\",\n ;\\\"id\\\": \\\"DOID:9352\\\",\n ;\\\"name\\\": \\\"type 2 diabetes mellitus\\\",\n ;\\\"node_attributes\\\": null,\n ;\\\"symbol\\\": null,\n ;\\\"type\\\": \\\"disease\\\",\n ;\\\"uri\\\": \\\"http://purl.obolibrary.org/obo/DOID_9352\\\"\n ;},\n ;{\n ;\\\"description\\\": \\\"None\\\",\n ;\\\"id\\\": \\\"OMIM:600001\\\",\n ;\\\"name\\\": \\\"HEART DEFECTS, CONGENITAL, AND OTHER CONGENITAL ANOMALIES; HDCA\\\",\n ;\\\"node_attributes\\\": null,\n ;\\\"symbol\\\": null,\n ;\\\"type\\\": \\\"disease\\\",\n ;\\\"uri\\\": \\\"http://purl.obolibrary.org/obo/OMIM_600001\\\"\n ;}\n ;]\n ;},\n ;\\\"result_group\\\": null,\n ;\\\"result_group_similarity_score\\\": null,\n ;\\\"result_type\\\": null,\n ;\\\"row_data\\\": [\n ;\\\"type 2 diabetes mellitus\\\",\n ;\\\"DOID:9352\\\",\n ;\\\"HEART DEFECTS, CONGENITAL, AND OTHER CONGENITAL ANOMALIES; HDCA\\\",\n ;\\\"OMIM:600001\\\",\n ;\\\"0.000664\\\"\n ;],\n ;\\\"score\\\": null,\n ;\\\"score_direction\\\": null,\n ;\\\"score_name\\\": null,\n ;\\\"text\\\": \\\"The drug HEART DEFECTS, CONGENITAL, AND OTHER CONGENITAL ANOMALIES; HDCA is predicted to treat type 2 diabetes mellitus.\\\"\n ;},\n ;],\n ;\\\"schema_version\\\": \\\"0.5\\\",\n ;\\\"table_column_names\\\": [\n ;\\\"input disease name\\\",\n ;\\\"input disease ID\\\",\n ;\\\"output disease name\\\",\n ;\\\"output disease ID\\\",\n ;\\\"path weight\\\"\n ;],\n ;\\\"terms\\\": null,\n ;\\\"tool_version\\\": \\\"RTX 0.5.4\\\",\n ;\\\"type\\\": \\\"medical_translator_query_result\\\"\n;}\n;\"\n ;)\n\n(displayln `(sending: ,data))\n\n(define-values (status headers in)\n (http-sendrecv \"localhost\"\n \"/query\"\n #:port 8000\n #:ssl? #f\n #:version \"1.1\"\n #:method \"POST\"\n #:data data))\n\n(displayln status)\n(displayln headers)\n(displayln (port->string in))\n(close-input-port in)\n" }, { "path": "attic/medikanren/w1m2-direct-POST.rkt", "content": "#lang racket\n(require net/http-client\n json)\n\n(define data (jsexpr->bytes\n '(\n ;(\"UMLS:C0282687\" \"Ebola hemorrhagic fever\")\n ;(\"OMIM:600807\" \"Asthma\")\n (\"DOID:3302\" \"Chordoma\")\n ;(\"OMIM:215400\" \"Chordoma\")\n ;(\"OMIM:125853\" \"Type 2 Diabetes Mellitus\")\n )))\n\n(displayln `(sending: ,data))\n\n(define-values (status headers in)\n (http-sendrecv \"localhost\"\n \"/direct-query\"\n #:port 8000\n #:ssl? #f\n #:version \"1.1\"\n #:method \"POST\"\n #:data data))\n\n(displayln status)\n(displayln headers)\n(displayln (port->string in))\n(close-input-port in)\n" }, { "path": "attic/medikanren/web-server.rkt", "content": "#lang racket/base\n(require\n \"common.rkt\"\n racket/match\n racket/port\n racket/pretty\n racket/string\n web-server/servlet\n web-server/servlet-env\n web-server/managers/none\n net/url\n xml)\n\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n\n(define argv (current-command-line-arguments))\n(define argv-optional '#(CONFIG_FILE))\n\n(when (not (<= (vector-length argv) (vector-length argv-optional)))\n (error \"optional arguments ~s; given ~s\" argv-optional argv))\n\n;; Loading will occur at first use if not explicitly forced like this.\n(load-config #t (and (<= 1 (vector-length argv)) (vector-ref argv 0)))\n(load-databases #t)\n\n;; TODO:\n;;; Query save file settings\n(define WRITE_QUERY_RESULTS_TO_FILE (config-ref 'query-results.write-to-file?))\n(define QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name))\n(define HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name-human))\n(define SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name-spreadsheet))\n(define QUERY_RESULTS_FILE_MODE (config-ref 'query-results.file-mode))\n;;; Decreases/increases predicate names\n(define DECREASES_PREDICATE_NAMES (config-ref 'decreases-predicate-names))\n(define INCREASES_PREDICATE_NAMES (config-ref 'increases-predicate-names))\n\n(define (xexpr->html-string xe)\n (string-append \"\" (xexpr->string xe)))\n(define mime:text/plain (string->bytes/utf-8 \"text/plain;charset=utf-8\"))\n(define mime:text/s-expr (string->bytes/utf-8 \"text/plain;charset=utf-8\"))\n(define mime:text/html (string->bytes/utf-8 \"text/html;charset=utf-8\"))\n(define mime:text/css (string->bytes/utf-8 \"text/css;charset=utf-8\"))\n(define mime:text/js (string->bytes/utf-8 \"text/javascript;charset=utf-8\"))\n(define mime:json (string->bytes/utf-8 \"application/json;charset=utf-8\"))\n(define mime:binary (string->bytes/utf-8 \"application/octet-stream\"))\n(define (respond code message headers mime-type body)\n (response/full code (string->bytes/utf-8 message)\n (current-seconds) mime-type headers\n (list (string->bytes/utf-8 body))))\n\n(define (css->string cexprs)\n (string-append*\n (map (lambda (cexpr)\n (define selector (car cexpr))\n (define attrs\n (map (lambda (a) (format \"~a: ~a;\\n\" (car a) (cadr a)))\n (cdr cexpr)))\n (format \"~a {\\n~a}\\n\" selector (string-append* attrs)))\n cexprs)))\n(define (js->string jsexpr) (string-join jsexpr \"\\n\"))\n\n(define (read*/string s)\n (define (read*)\n (define datum (read))\n (if (eof-object? datum) '() (cons datum (read*))))\n (with-handlers (((lambda _ #t)\n (lambda _ (printf \"unreadable input string: ~s\\n\" s)\n #f)))\n (with-input-from-string s read*)))\n\n(define (/query req)\n (define post-data (request-post-data/raw req))\n (define (e400/body body)\n (respond 400 \"Bad Request\" '() mime:text/plain body))\n (define (e400 reason)\n (e400/body (with-output-to-string\n (lambda () (printf \"~a:\\n~s\\n\" reason\n (bytes->string/utf-8 post-data))))))\n (define (e400/failure failure)\n (e400/body (with-output-to-string\n (lambda ()\n (printf \"Query failed:\\n~s\\n\"\n (bytes->string/utf-8 post-data))\n (pretty-print failure)))))\n (define (ok200 data)\n (respond 200 \"OK\" '() mime:text/s-expr\n (with-output-to-string (lambda () (pretty-print data)))))\n (cond ((not post-data) (e400/body \"Invalid POST data.\"))\n ((read*/string (bytes->string/utf-8 post-data))\n => (lambda (data)\n (match data\n ('() (e400 \"Empty POST\"))\n ((list* x y z) (e400 \"Too many POST s-expressions\"))\n ((list datum)\n (match datum\n (`(concept ,subject? ,object? ,isa-count ,via-cui? ,strings)\n (with-handlers\n (((lambda _ #t) e400/failure))\n (ok200 (find-predicates/concepts\n subject? object?\n (find-concepts/options\n subject? object? isa-count\n via-cui? strings)))))\n (`(X ,subject ,object)\n (with-handlers\n (((lambda _ #t) e400/failure))\n (ok200 (find-Xs subject object))))\n (_ (e400 \"Invalid query\")))))))\n (else (e400 \"Bad POST s-expression format\"))))\n\n(define (xe200 xexpr)\n (respond 200 \"OK\" '() mime:text/html (xexpr->html-string xexpr)))\n\n;; TODO: define simple read/write for s-expressions.\n(define ui.js\n '(\"window.addEventListener('load', function(){\"\n \"function query(show, data) {\"\n \" var xhr = new XMLHttpRequest();\"\n \" xhr.addEventListener('load', function(event){\"\n \" show(xhr.responseText);\"\n \" });\"\n \" xhr.addEventListener('error', function(event){\"\n \" alert('Server communication failure: ' + xhr.status + ' ' + xhr.statusText);\"\n \" });\"\n \" xhr.open('POST', '/query');\"\n \" xhr.setRequestHeader('Content-Type', 'text/plain;charset=utf-8');\"\n \" xhr.send(data);\"\n \"}\"\n\n \"function displayClear(display) {\"\n \" while (display.lastChild) {\"\n \" display.removeChild(display.lastChild);\"\n \" }\"\n \"}\"\n \"function displayShow(display, data) {\"\n \" displayClear(display);\"\n \" var option = document.createElement('option');\"\n \" var text = document.createTextNode(data);\"\n \" option.appendChild(text);\"\n \" option.setAttribute('value', data);\"\n \" display.appendChild(option);\"\n \"}\"\n\n \"var subjectSearch = document.getElementById('subject:text-search');\"\n \"var subjectC = document.getElementById('subject:concepts');\"\n \"var subjectP = document.getElementById('subject:predicates');\"\n \"var objectSearch = document.getElementById('object:text-search');\"\n \"var objectC = document.getElementById('object:concepts');\"\n \"var objectP = document.getElementById('object:predicates');\"\n\n \"subjectSearch.addEventListener('change', function(event){\"\n \" var strings = subjectSearch.value.split(/(\\\\s+)/);\"\n \" var joined = '\\\"' + strings.join('\\\" \\\"') + '\\\"';\"\n \" var qdatum = '(concept #t #f 0 #f (' + joined + '))'\"\n \" query(function(data){displayShow(subjectC,data);}, qdatum);\"\n \"}, false);\"\n \"objectSearch.addEventListener('change', function(event){\"\n \" var strings = objectSearch.value.split(/(\\\\s+)/);\"\n \" var joined = '\\\"' + strings.join('\\\" \\\"') + '\\\"';\"\n \" var qdatum = '(concept #f #t 0 #f (' + joined + '))'\"\n \" query(function(data){displayShow(objectC,data);}, qdatum);\"\n \"}, false);\"\n \"});\"))\n(define ui.css\n '((\"body\"\n (font-family \"'Lucida Grande', Verdana, Helvetica, sans-serif\")\n (font-size \"80%\")\n (line-height \"120%\"))\n (\".concept-box label\"\n (vertical-align \"top\"))\n (\".result-box label\"\n (vertical-align \"top\"))\n ))\n(define ui.html\n `(html (head (title \"mediKanren User Interface\"))\n (body (script ,(js->string ui.js))\n (style ,(css->string ui.css))\n ;; TODO: label these.\n (div (input ((id \"subject:text-search\") (type \"text\") (autocomplete \"off\")))\n (input ((id \"subject:isa\") (type \"checkbox\")))\n (label \"Include ISA-related concepts\"))\n (div ((class \"concept-box\"))\n (label \"Concept 1\")\n (select ((id \"subject:concepts\") (multiple \"\") (size \"15\"))\n (option ((value \"c1\")) \"concept 1\"))\n (label \"Predicate 1\")\n (select ((id \"subject:predicates\") (multiple \"\") (size \"15\"))\n (option ((value \"p1\")) \"predicate 1\")))\n (div (label \"Concept 1 -> Predicate 1 -> [X] -> Predicate 2 -> Concept 2\"))\n (div (input ((id \"object:text-search\") (type \"text\") (autocomplete \"off\")))\n (input ((id \"object:isa\") (type \"checkbox\")))\n (label \"Include ISA-related concepts\"))\n (div ((class \"concept-box\"))\n (label \"Predicate 2\")\n (select ((id \"object:predicates\") (multiple \"\") (size \"15\"))\n (option ((value \"p2\")) \"predicate 2\"))\n (label \"Concept 2\")\n (select ((id \"object:concepts\") (multiple \"\") (size \"15\"))\n (option ((value \"c2\")) \"concept 2\")))\n (div (label \"Found Xs\"))\n (div ((class \"result-box\"))\n (label \"X\")\n (select ((id \"X:concepts\") (multiple \"\"))\n (option ((value \"X1\")) \"Subject - X1 - Object\"))))))\n\n(define (/ui req) (xe200 ui.html))\n\n(define index.js\n '(\"window.addEventListener('load', function(){\"\n \"var display = document.getElementById('display');\"\n \"var formC = document.getElementById('form:concept');\"\n \"var formX = document.getElementById('form:X');\"\n \"var textC = document.getElementById('text:concept');\"\n \"var textX = document.getElementById('text:X');\"\n \"var submitC = document.getElementById('submit:concept');\"\n \"var submitX = document.getElementById('submit:X');\"\n \"var buttonClear = document.getElementById('button:clear');\"\n\n \"function show(data) {\"\n ;\" display.innerText = data;\"\n \" var p = document.createElement('pre');\"\n \" var text = document.createTextNode(data);\"\n \" p.appendChild(text);\"\n \" display.appendChild(p);\"\n \"}\"\n \"function clearDisplay() {\"\n \" while (display.lastChild) {\"\n \" display.removeChild(display.lastChild);\"\n \" }\"\n \"}\"\n\n \"function query(data) {\"\n \" var xhr = new XMLHttpRequest();\"\n \" xhr.addEventListener('load', function(event){\"\n \" show(xhr.responseText);\"\n \" });\"\n \" xhr.addEventListener('error', function(event){\"\n \" show('POST error');\"\n \" });\"\n \" xhr.open('POST', '/query');\"\n \" xhr.setRequestHeader('Content-Type', 'text/plain;charset=utf-8');\"\n \" xhr.send(data);\"\n \"}\"\n\n \"formC.addEventListener('submit', function(event){\"\n \" event.preventDefault();\"\n \" query(textC.value);\"\n \"}, false);\"\n \"formX.addEventListener('submit', function(event){\"\n \" event.preventDefault();\"\n \" query(textX.value);\"\n \"}, false);\"\n \"buttonClear.addEventListener('click', function(){\"\n \" clearDisplay();\"\n \"}, false);\"\n \"});\"\n ))\n(define index.html\n `(html (head (title \"mediKanren\"))\n (body (script ,(js->string index.js))\n (div (p \"Databases loaded:\") .\n ,(map (lambda (dbname) `(p (pre ,(symbol->string dbname))))\n (config-ref 'databases)))\n (p \"Use the \" (a ((href \"/ui\")) \"Interface\"))\n (p \"Or POST to /query using a form:\")\n (form ((method \"post\") (action \"/query\") (id \"form:concept\"))\n (div (textarea ((id \"text:concept\"))\n \"(concept ...)\"))\n (div (button ((type \"submit\") (id \"submit:concept\"))\n \"Find concepts\")))\n (form ((method \"post\") (action \"/query\") (id \"form:X\"))\n (div (textarea ((id \"text:X\"))\n \"(X ...)\"))\n (div (button ((type \"submit\") (id \"submit:X\"))\n \"Find Xs\")))\n (button ((id \"button:clear\")) \"Clear\")\n (div ((id \"display\"))))))\n(define (index req) (xe200 index.html))\n\n(define (method-not-allowed req)\n (respond 405 \"Method Not Allowed\" '() mime:text/html\n (xexpr->html-string\n `(html (head (title \"Method Not Allowed\"))\n (body (h1 \"Method Not Allowed\")\n (pre ,(url->string (request-uri req)))\n (p \"does not support\")\n (pre ,(bytes->string/utf-8 (request-method req))))))))\n\n(define (not-found req)\n (respond 404 \"Not Found\" '() mime:text/html\n (xexpr->html-string\n `(html (head (title \"Not Found\"))\n (body (h1 \"What are you looking for?\")\n (p \"There was nothing found at\")\n (pre ,(url->string (request-uri req))))))))\n\n(define-values (dispatcher _)\n (dispatch-rules\n ((\"\") #:method \"get\" index)\n ((\"query\") #:method \"post\" /query)\n ((\"ui\") #:method \"get\" /ui)\n ((\"\") #:method (regexp \".*\") method-not-allowed)\n ((\"query\") #:method (regexp \".*\") method-not-allowed)\n ((\"ui\") #:method (regexp \".*\") method-not-allowed)\n (else not-found)))\n\n(serve/servlet dispatcher\n ;; The none-manager offers better performance when not using\n ;; web continuations.\n #:manager (create-none-manager #f)\n #:servlet-regexp #rx\"\"\n #:launch-browser? #f)\n" }, { "path": "attic/medikanren/workflow-web-server.rkt", "content": "#lang racket\n(require \"workflow1.rkt\"\n web-server/servlet\n web-server/servlet-env\n web-server/managers/none\n net/uri-codec\n xml\n json)\n\n(define index.html\n `(html (head (title \"mediKanren for workflows\"))\n (body (p \"POST your queries in JSON format to /query\")\n (p (a ((href \"https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI\"))\n \"Standard\"))\n (p (a ((href \"https://www.dropbox.com/s/auqt6gedhnz5bbt/WF1MOD1_results_DOID9352.json?dl=0\"))\n \"Example input\"))\n (p (a ((href \"https://www.dropbox.com/s/u6zik652qojkmgb/WF1MOD1-MOD2_results_DOID9352.json?dl=0\"))\n \"Example output\")))))\n\n(define (not-found.html uri)\n `(html (head (title \"Sad Face\"))\n (body (h1 \"What are you looking for?\")\n (p \"There was nothing found at\")\n (pre ,uri))))\n\n(define (omim? cui) (string-prefix? cui \"OMIM:\"))\n\n(define (json->cuis jsdata)\n (map (lambda (r)\n (define essence (hash-ref r 'essence))\n (define (essence? n) (equal? (hash-ref n 'name) essence))\n (define nodes (hash-ref (hash-ref r 'result_graph) 'node_list))\n (car (filter omim? (map (lambda (n) (hash-ref n 'id))\n (filter essence? nodes)))))\n (hash-ref jsdata 'result_list)))\n\n(define (json->all-cuis jsdata)\n (map (lambda (named-cui)\n ;(define name (cadr jsdata))\n (car named-cui))\n jsdata))\n\n(define reasoner-id \"mediKanren-0.00000000000000zerozero...\")\n\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n(define (edge->json edge)\n (define db (car edge))\n (define type (cdr (cadddr (cdr edge))))\n (define src (cadr (caddr edge)))\n (define tgt (cadr (cadddr edge)))\n (define eprops (cddddr (cdr edge)))\n (define kpmids (assoc \"pmids\" eprops))\n (define kpubs (assoc \"publications\" eprops))\n (define pmids (rem-dups (if kpmids (cdr kpmids) '())))\n (define pubs (rem-dups (if kpubs (cdr kpubs) '())))\n (define publications\n (append (map (lambda (id)\n (string-append \"https://www.ncbi.nlm.nih.gov/pubmed/\" id))\n pmids) pubs))\n (hash 'type type\n 'source_id src\n 'target_id tgt\n 'provided_by db\n 'confidence 0.00000000000000001\n 'publications publications\n 'attribute_list '()))\n\n(define (concept->json concept)\n (define cui (list-ref concept 2))\n (define name (list-ref concept 3))\n ;; TODO: more general type.\n (define type \"chemical_substance\")\n (define props (list-tail concept 4))\n (define description (cdr (or (assoc \"description\" props) '(#f . \"\"))))\n (define uri (cdr (or (assoc \"uri\" props) '(#f . \"\"))))\n (hash 'description description\n 'id cui\n 'name name\n 'type type\n 'uri uri\n 'node_attributes '()))\n\n(define (result->json result)\n ;; TODO:\n (define essence \"\")\n (define confidence 0.00000000000000001)\n (define concepts (cdr (assoc 'concepts result)))\n (define edges (cdr (assoc 'edges result)))\n (hash 'confidence confidence\n 'description \"\"\n 'essence essence\n 'id \"\"\n 'reasoner_id reasoner-id\n 'result_graph (hash 'edge_list (map edge->json edges)\n 'node_list (map concept->json concepts))\n 'result_type \"answer\"\n 'row_data '()\n 'text \"\"))\n\n(define (response->json results)\n (define (pad n) (~a n #:width 2 #:align 'right #:pad-string \"0\"))\n (define datetime\n (let ((dt (seconds->date (current-seconds) #f)))\n (format\n \"~a-~a-~a ~a:~a:~a\"\n (date-year dt) (pad (date-month dt)) (pad (date-day dt))\n (pad (date-hour dt)) (pad (date-minute dt)) (pad (date-second dt)))))\n (hash 'context \"https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld\"\n 'datetime datetime\n 'id \"\"\n 'message \"\"\n 'n_results (length results)\n 'original_question_text \"\"\n 'query_type_id \"\"\n 'reasoner_id reasoner-id\n 'response_code \"OK\"\n 'restated_question_text \"\"\n 'result_list (map result->json results)\n 'schema_version \"0.8.0\"\n 'table_column_names '()\n 'terms (hash 'disease \"\")\n 'tool_version \"Nope\"\n 'type \"medical_translator_query_result\"))\n\n(define (query.json jsdata)\n (define cuis (json->cuis jsdata))\n (displayln `(cuis-received: ,cuis))\n (define concepts (append* (map workflow1module2 cuis)))\n (response->json (list (list (cons 'concepts concepts) (cons 'edges '())))))\n\n(define (direct-query.json jsdata)\n (define cuis (json->all-cuis jsdata))\n (displayln `(cuis-received: ,cuis))\n (define concepts (append* (map workflow1module2 cuis)))\n (response->json (list (list (cons 'concepts concepts) (cons 'edges '())))) )\n\n(define mime:html (string->bytes/utf-8 \"text/html; charset=utf-8\"))\n(define mime:json (string->bytes/utf-8 \"application/json; charset=utf-8\"))\n\n\n(define (respond code message headers mime-type body)\n (response/full code (string->bytes/utf-8 message)\n (current-seconds) mime-type headers\n (list (string->bytes/utf-8 body))))\n\n(define (index req)\n (respond 200 \"ok\" '() mime:html (xexpr->html-string index.html)))\n\n(define (query req)\n (respond 200 \"OK\" '() mime:json\n (jsexpr->string\n (query.json\n (bytes->jsexpr (request-post-data/raw req))))))\n\n(define (direct-query req)\n (respond 200 \"OK\" '() mime:json\n (jsexpr->string\n (direct-query.json\n (bytes->jsexpr (request-post-data/raw req))))))\n\n(define (not-found req)\n (respond 404 \"Not Found\" '() mime:html\n (xexpr->html-string (not-found.html\n (url->string (request-uri req))))))\n\n;(define (repr d) (with-output-to-string (lambda () (write d))))\n(define (xexpr->html-string xe)\n (string-append \"\" (xexpr->string xe)))\n\n\n(define-values (dispatcher _)\n (dispatch-rules\n ((\"\") #:method \"get\" index)\n ((\"query\") #:method (regexp \".*\") query)\n ((\"direct-query\") #:method (regexp \".*\") direct-query)\n (else not-found)))\n\n;; after loading this file, launch the server by evaluating\n(serve/servlet dispatcher\n #:manager (create-none-manager #f) ;; better performance if you're not using web continuations\n #:servlet-regexp #rx\"\"\n #:launch-browser? #f)\n" }, { "path": "attic/medikanren/workflow1.rkt", "content": ";;; Workflow 1\n\n#|\nconcept format (subject or object), without dbname at front:\n\n`(,cid ,cui ,name (,catid . ,cat) . ,props)\n\nconcept format (subject or object), with dbname at front (as used in fuzzy-concepto):\n\n`(,dbname ,cid ,cui ,name (,catid . ,cat) . ,props)\n\n\nedge format, without dbname at front:\n\n`(,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) . ,eprops)\n\nedge format, with dbname at front (as used in edgeo):\n\n`(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n (,pid . ,pred) . ,eprops)\n|#\n\n\n#|\nNOTES\n\nTH2LCRR in concept 1\nhas_phenotype aggressive behavior\n(\"publications\"\n .\n \"['http://www.ncbi.nlm.nih.gov/pubmed/27611488', 'http://www.ncbi.nlm.nih.gov/pubmed/10220955', 'http://www.ncbi.nlm.nih.gov/pubmed/10557854', 'http://www.ncbi.nlm.nih.gov/pubmed/15611893', 'http://www.ncbi.nlm.nih.gov/pubmed/550177', 'http://www.ncbi.nlm.nih.gov/pubmed/14572559']\")\n\n\n*** talk with Greg and Chris about doing a clique merge to avoid\nhaving duplicate concepts that are equivalent but with dfferent\nsources\n\n\n*** Ask Greg to take a look:\nmonarch-lite has many type of 'diabetes', but apparently none has 'has_phenotype' predicate\n\nhow to find monogenetic diabetes in these data sources? I suppose, look for genes that cause diabetes? how do we know it is truly monogenic?\n\none such gene is KCNJ11\n\nrtx:\nKCNJ11 has_phenotype HP:00005978 Type II diabetes mellitus (source: biolink)\n\nrtx:\nKCNJ11 causes_or_contributes_to OMIM:606176 DIABETES MELITUS, PERMANENT NEONATAL; PNDM (source: OMIM)\n\nrtx:\nKCNJ11 participates_in 'Defective ABCD1 causes ALD' what?? does that make sense? (reactome pathway)\n\nrtx and monarch:\n'HP:00005978 Type II diabetes mellitus' subclass_of 'HP:0000819 Diabetes mellitus'\n\n'HP:0000819 Diabetes mellitus' subclass_of 'HP:0011014 Abnormal glucose homeostasis'\n\n*** unable to reproduce in mediKanren GUI--run queries in Racket to see if any fields that should be strings are actually #f\nmonarch:\ndiabetes mellitus in concept 1 gives:\nOMIA:000284-9825 with 'Name' #f what gives?\n\nalso returns 'type 1 diabetes mellitus 7', 'type 1 diabetes mellitus 8', etc, as MONDO terms--what does this mean???\n\n\nmonarch:\nX has_phenotype HPO:0000819 Diabetes mellitus\n\n2729 results\nappear to all be genes\nbut, dfferent categories:\nHGNC (2 . [molec entity, gene, sequence feat])\nHGNC (1 . [gene, sequence feature])\nNCBIGene (1 . [gene, sequence feature])\n\ninteresting--have both for HGNC--what is the difference? are the gene names duplicated?\n\nbetween OMIM, semmed, HGNC, etc, tricky to try to find the equivalent gene name/protein across sources (UMLS term for semmed, UniProt for OMIM in rtx, HGNC in monarch)\n\n\nMonarch \n\n|#\n\n\n\n#|\n\t\tWhat are some potential treatments for [common condition], based on knowledge of related rare conditions?\t\nInstance\t\t\"Monogenic diabetes and sporadic (common) diabetes\"\n\nComponent\tStandard Query Type Id\tLogical Operation\tBid\n\tQ61\tPath/Module 1 (condition similarity)\t\n*** MOD1.1\tQ5\tWhat are the defining symptoms / phenotypes of [condition x]?\t0/2/3 (what does \"defining\" mean?)\n*** MOD1.2\tQ60\tWhat conditions present [symptoms]?\t3\nMOD1.3\tFilter\tFilter [conditions] to only keep ones with defined genetic causes.\t0/2\nMOD1.4\tFilter\tWhat subset of conditions are most representative of [conditions]? (find archetypes)\t0\n\t\t\t\n\tQ62\tPath/Module 2 (gene centric)\t\n*** MOD2.1\tQ7\tWhat genes are implicated in [condition]?\t3\nMOD2.2\tFilter\tWhat subset of genes are most representative of [conditions]? (find archetypes)\t0\n*** MOD2.3\t\tWhat pathways/processes are [genes] involved in?\t2/3\n*** MOD2.4\tQ4\tWhat genes are involved in [pathway/process]?\t2/3\n*** MOD2.5\tQ9\tWhat drugs/compounds target gene products of [gene]?\t3\nMOD2.6\t?\tWhat [non human genes] are similar to [human gene]? (Can be phenotypic, functional, or structural similarity)\t\n\t\t\t\n\t\tPath/Module 3 (agent-centric)\t\nMOD3.1\t\tWhat toxicants (chemical agent / toxic protein) does [condition] have specific sensitivity to?\t\n*** MOD3.2\t\tWhat proteins produce agent [x]?\t3\n*** MOD3.3\t\tWhat drugs/compounds decrease (inhibit / down-regulate) these?\t3\nMOD3.2a\t\tWhat proteins consume/sequester agent [x]?\t2\n*** MOD3.3a\t\tWhat drugs increase (activate / promote ) these?\t3\nMOD3.2b\t\tWhat phenotypes / conditions are associated with high exposure to [x]?\t1\nMOD3.3b\t\tWhat drugs rarely produce these adverse events? (possibly protective effect)\t0/2\n\t\t(the end of the agent-centric path continues to the annotations path (component 6)\t\n\t\t\t\n\t\tAnnotations Path\t\nPathA.1\t\tWhat are the common side effects of [drug]?\t2\nPathA.2\t\tWhat is the approval status of [drug]?\t2\nPathA.3\t\tWhat are the approved indications for [drug]?\t2\nPathA.4\t\tWhat is the established pharm class for [drug]?\t2\n\t\t\t\n\t\tScoring Path\t\nPathS.1\t\tDoes the drug (or a metabolite) get to the target tissues / cell-types?\t0/1/2\nPathS.2\t\tIs the drug approved / in clinical trials?\t2\nPathS.3\t\tIs the drug relatively non-toxic?\t2\nPathS.4\t\tIs the drug already being investigated for the same/similar condition?\t2\nPathS.5\t\tDoes the drug have favorable intellectual property (IP) status?\t2\nPathS.6\t\tDoes the drug have available analogs?\t2\nPathS.7\t\tDo any analogs of the drug satisfy 10-15 above?\t2\n\t\t\t\n\t\tDrug Set Expansion Path\t\nPathD.1\t\tidentify defining features\t0\nPathD.2\t\tfind groups\t0\n|#\n#lang racket\n\n(provide\n (all-from-out \"mk.rkt\")\n (all-from-out \"mk-db.rkt\")\n (all-defined-out))\n\n(require\n \"mk.rkt\"\n \"mk-db.rkt\"\n (except-in racket/match ==))\n\n;(displayln \"loading semmed\")\n(define semmed (make-db \"data/semmed\"))\n;(displayln \"loading monarch-lite\")\n(define monarch (make-db \"data/monarch-lite\"))\n;(displayln \"loading rtx\")\n(define rtx (make-db \"data/rtx\"))\n\n;; list membership\n(define membero\n (lambda (x ls)\n (fresh (y rest)\n (== `(,y . ,rest) ls)\n (conde\n [(== x y)]\n [(=/= x y) (membero x rest)]))))\n\n;; remove duplicates from a list\n(define rem-dups\n (lambda (ls)\n (cond\n [(null? ls) '()]\n [(member (car ls) (cdr ls)) (rem-dups (cdr ls))]\n [else (cons (car ls) (rem-dups (cdr ls)))])))\n\n\n(define (edgeo e)\n (conde\n ((fresh (ee) (== `(semmed . ,ee) e) (db:edgeo semmed ee)))\n ((fresh (ee) (== `(monarch . ,ee) e) (db:edgeo monarch ee)))\n ((fresh (ee) (== `(rtx . ,ee) e) (db:edgeo rtx ee)))\n ))\n\n(define (~cui-concepto cui c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~cui-concepto semmed cui cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~cui-concepto monarch cui cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~cui-concepto rtx cui cc)))\n ))\n\n(define (~name-concepto name c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:~name-concepto semmed name cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:~name-concepto monarch name cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:~name-concepto rtx name cc)))\n ))\n\n(define (concepto c)\n (conde\n ((fresh (cc) (== `(semmed . ,cc) c) (db:concepto semmed cc)))\n ((fresh (cc) (== `(monarch . ,cc) c) (db:concepto monarch cc)))\n ((fresh (cc) (== `(rtx . ,cc) c) (db:concepto rtx cc)))\n ))\n\n(define get-concepts-from-cui\n (lambda (cui)\n (run* (concept)\n (~cui-concepto cui concept))))\n\n\n(define (DECREASES pred)\n (fresh (_)\n (conde\n [(== `(,_ . \"negatively_regulates\") pred)]\n [(== `(,_ . \"prevents\") pred)]\n [(== `(,_ . \"treats\") pred)])))\n\n(define (INCREASES pred)\n (fresh (_)\n (conde\n [(== `(,_ . \"positively_regulates\") pred)]\n [(== `(,_ . \"causes\") pred)]\n [(== `(,_ . \"produces\") pred)])))\n\n;; \tQ62\tPath/Module 2 (gene centric)\t\n;; *** MOD2.1\tQ7\tWhat genes are implicated in [condition]?\t3\n;; MOD2.2\tFilter\tWhat subset of genes are most representative of [conditions]? (find archetypes)\t0\n;; *** MOD2.3\t\tWhat pathways/processes are [genes] involved in?\t2/3\n;; *** MOD2.4\tQ4\tWhat genes are involved in [pathway/process]?\t2/3\n;; *** MOD2.5\tQ9\tWhat drugs/compounds target gene products of [gene]?\t3\n;; forget it MOD2.6\t?\tWhat [non human genes] are similar to [human gene]? (Can be phenotypic, functional, or structural similarity)\t\n\n\n;; *** MOD2.1\tQ7\tWhat genes are implicated in [condition]?\t3\n\n;; get a list of conditions from the JSON blob:\n;;\n;; \"result_list\": [\n;; \"result_graph\": {\n;; \"node_list\": [\n;;\n;; for this particular example, for each result_list, we just pick the\n;; node in the node_list that has \"type\": \"disease\" and which has the OMIM ID (as\n;; opposed to the DOID ID): \"id\": \"OMIM:600001\"\n\n\n;; example condition: \n;; \"source_id\": \"OMIM:600001\",\n\n\n\n\n\n;; *** MOD2.1\tQ7\tWhat genes are implicated in [condition]?\t3\n\n#|\n(define condition-concepts (rem-dups (get-concepts-from-cui \"OMIM:606176\")))\n|#\n\n;; causes_or_contributes_to\n\n;; protein\n\n#|\n;;; get list of proteins from edges 'protein X causes_or_contributes_to disease Y'\n(define proteins-causing-condition\n (run 50 (proteins)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n cond-con)\n (== `(,dbname . ,s) proteins)\n (membero cond-con condition-concepts)\n (== `(,dbname . ,o) cond-con)\n (== \"causes_or_contributes_to\" pred)\n (== \"protein\" scat)\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e))))\n|#\n\n;; MOD2.2\tFilter\tWhat subset of genes are most representative of [conditions]? (find archetypes)\t0\n\n;; ignore for now--null/identity filter!\n\n\n;; *** MOD2.3\t\tWhat pathways/processes are [genes] involved in?\t2/3\n\n;; rtx\n;; protein 36056 \"UniProtKB:Q14654\" \"KCNJ11\" (1 . \"protein\")\n;; participates_in (2 . \"participates_in\")\n;; pathway (115579 \"REACT:R-HSA-199992\" \"trans-Golgi Network Vesicle Budding\" (8 . \"pathway\")\n\n#|\n(define pathways-involved-in-genes-causing-condition\n (rem-dups\n (run 50 (pathway)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n protein)\n (membero protein proteins-causing-condition)\n (== `(,dbname . ,o) pathway)\n (== `(,dbname . ,s) protein)\n (== \"protein\" scat)\n (== \"participates_in\" pred)\n (== \"pathway\" ocat)\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e)))))\n|#\n\n;; *** MOD2.4\tQ4\tWhat genes are involved in [pathway/process]?\t2/3\n\n#|\n(define proteins-involved-in-pathways-of-interest\n (rem-dups\n (run 50 (protein)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n pathway)\n (membero pathway pathways-involved-in-genes-causing-condition)\n (== `(,dbname . ,o) pathway)\n (== `(,dbname . ,s) protein)\n (== \"protein\" scat)\n (== \"participates_in\" pred)\n (== \"pathway\" ocat)\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e)))))\n|#\n\n;; *** MOD2.5\tQ9\tWhat drugs/compounds target gene products of [gene]?\t3\n\n;; mygene.info to convert Uniprot protein to UMLS gene (perhaps through HGNC:HGNC:795)\n\n;; then, change the UMLS term for the drug to the Chembl id\n\n;; punt! use fuzzy lookup in semmed, based on protein name from rtx, looking for gene in semmed\n\n#|\n(define semmed-genes\n (rem-dups\n (run 50 (gene)\n (fresh (procid procui proname procatid procat proprops\n scid scui sname scatid sprops\n protein)\n (membero protein proteins-involved-in-pathways-of-interest)\n (== `(rtx ,procid ,procui ,proname (,procatid . ,procat) . ,proprops) protein)\n (== `(semmed ,scid ,scui ,sname (,scatid . \"gene\") . ,sprops) gene)\n (~name-concepto proname gene)))))\n|#\n\n#|\n(define semmed-drugs\n (rem-dups\n (run 50 (drug)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n gene)\n (membero gene semmed-genes)\n (== `(semmed . ,s) drug)\n (== `(semmed . ,o) gene)\n (== \"chemical_substance\" scat)\n (conde\n [(== \"positively_regulates\" pred)]\n [(== \"negatively_regulates\" pred)])\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(semmed ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e)))))\n|#\n\n#|\n(define rtx-drugs\n (rem-dups\n (run 20 (rtx-drug)\n (fresh (semmed scid scui sname scatid scat sprops\n rcid rcui rname rcatid rprops\n semmed-drug)\n (membero semmed-drug semmed-drugs)\n (== `(semmed ,scid ,scui ,sname (,scatid . ,scat) . ,sprops) semmed-drug)\n (== `(rtx ,rcid ,rcui ,rname (,rcatid . \"chemical_substance\") . ,rprops) rtx-drug)\n (~name-concepto sname rtx-drug)))))\n|#\n\n;; positively_regulates\n;; negatively_regulates\n;; semmed (5 . chemical_substance)\n\n;; fuzzy search back to rtx\n;; (10 . chemical_substance)\n\n\n\n(define workflow1module2\n (lambda (my-cui)\n (define condition-concepts (rem-dups (get-concepts-from-cui my-cui)))\n ;; *** MOD2.1\tQ7\tWhat genes are implicated in [condition]?\t3\n ;;(printf \"condition-concepts\\n\")\n (define proteins-causing-condition\n (run 50 (proteins)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n cond-con)\n (== `(,dbname . ,s) proteins)\n (membero cond-con condition-concepts)\n (== `(,dbname . ,o) cond-con)\n (== \"causes_or_contributes_to\" pred)\n (== \"protein\" scat)\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e))))\n ;; MOD2.2\tFilter\tWhat subset of genes are most representative of [conditions]? (find archetypes)\t0\n ;; ignore for now--null/identity filter!\n\n ;;(printf \"pathways-involved-in-genes-causing-condition\\n\")\n \n ;; *** MOD2.3\t\tWhat pathways/processes are [genes] involved in?\t2/3 \n (define pathways-involved-in-genes-causing-condition\n (rem-dups\n (run 50 (pathway)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n protein)\n (membero protein proteins-causing-condition)\n (== `(,dbname . ,o) pathway)\n (== `(,dbname . ,s) protein)\n (== \"protein\" scat)\n (== \"participates_in\" pred)\n (== \"pathway\" ocat)\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e)))))\n\n ;(printf \"proteins-involved-in-pathways-of-interest\")\n \n ;; *** MOD2.4\tQ4\tWhat genes are involved in [pathway/process]?\t2/3\n (define proteins-involved-in-pathways-of-interest\n (rem-dups\n (run 50 (protein)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n pathway)\n (membero pathway pathways-involved-in-genes-causing-condition)\n (== `(,dbname . ,o) pathway)\n (== `(,dbname . ,s) protein)\n (== \"protein\" scat)\n (== \"participates_in\" pred)\n (== \"pathway\" ocat)\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(,dbname ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e)))))\n ;; *** MOD2.5\tQ9\tWhat drugs/compounds target gene products of [gene]?\t3\n (define semmed-genes\n (rem-dups\n (run 50 (gene)\n (fresh (procid procui proname procatid procat proprops\n scid scui sname scatid sprops\n protein)\n (membero protein proteins-involved-in-pathways-of-interest)\n (== `(rtx ,procid ,procui ,proname (,procatid . ,procat) . ,proprops) protein)\n (== `(semmed ,scid ,scui ,sname (,scatid . \"gene\") . ,sprops) gene)\n (~name-concepto proname gene)))))\n (define semmed-drugs\n (rem-dups\n (run 50 (drug)\n (fresh (dbname eid s o pid pred eprops\n scid scui sname scatid scat sprops\n ocid ocui oname ocatid ocat oprops\n e\n gene)\n (membero gene semmed-genes)\n (== `(semmed . ,s) drug)\n (== `(semmed . ,o) gene)\n (== \"chemical_substance\" scat)\n (conde\n [(== \"positively_regulates\" pred)]\n [(== \"negatively_regulates\" pred)])\n (== `(,scid ,scui ,sname (,scatid . ,scat) . ,sprops) s)\n (== `(,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops) o)\n (== `(semmed ,eid ,s ,o (,pid . ,pred) . ,eprops) e)\n (edgeo e))))) \n (define rtx-drugs\n (rem-dups\n (run 20 (rtx-drug)\n (fresh (semmed scid scui sname scatid scat sprops\n rcid rcui rname rcatid rprops\n semmed-drug)\n (membero semmed-drug semmed-drugs)\n (== `(semmed ,scid ,scui ,sname (,scatid . ,scat) . ,sprops) semmed-drug)\n (== `(rtx ,rcid ,rcui ,rname (,rcatid . \"chemical_substance\") . ,rprops) rtx-drug)\n (~name-concepto sname rtx-drug)))))\n rtx-drugs))\n\n;; (pretty-print (workflow1module2 \"OMIM:606176\"))\n" }, { "path": "attic/pharos/.gitignore", "content": "/data\n/schema.sql\n/schema-tokens.scm\n/schema.scm\n" }, { "path": "attic/pharos/README.md", "content": "# mediKanren Pharos Interface\n\nThis is a mediKanren interface into the data provided by Pharos: https://pharos.nih.gov/idg/about\n\nCurrently, we only provide tools for converting the Pharos DB to SQLite3 for interactive use.\n\n\n## Setup\n\n### Download and install SQLite\n\nYou can find this at: https://www.sqlite.org/download.html\n\nYour OS's package manager may provide a more appropriate version.\n\n\n### Obtain a MySQL dump of the Pharos DB\n\nDownload it from: http://juniper.health.unm.edu/tcrd/download/\n\nThe file to download will have a name with either the form `tcrd_vX.Y.Z.sql.gz` or `latest.sql.gz`, depending on what version of the data you want.\n\nNOTE: though the filename ends with `.gz`, it's probably not gzipped.\n\n\n### Convert MySQL dump to a SQLite DB\n\nGiven `data.sql.gz`\n\nRun: `./pharos-mysql-to-sqlite3-to-db data.sql.gz`\n\nThis may take a while to finish, as there are two transformation steps being performed on a large file.\n\n\n## Use\n\n### Interact with SQLite DB\n\nRun: `./interact-sqlite3`\n\nInteract using SQL and dot-commands.\n\nBy default, output is in CSV format with headers and command echoing.\n\nTo write output to a file instead of stdout, issue the dot-command: `.output your-file-name.csv`\n\n\n## Process SQLite DB\n\nConvert SQLite DB to an internal form usable by mediKanren queries.\n\n### Output schema.sql\n\nRun: `./interact-sqlite3`\n\nThen use the following commands to output the `schema.sql` file.\n\n```\n.output schema.sql\n.schema\n.exit\n```\n\n### Tokenize schema.sql -> schema-tokens.scm\n\n`racket sql-tokenize.rkt < schema.sql > schema-tokens.scm `\n\n### Parse schema-tokens.scm -> schema.scm\n\n`racket sql-schema-parse.rkt < schema-tokens.scm > schema.scm`\n\n### Translate SQLite DB to internal format\n\nFrom the `pharos` directory, run: `racket sqlite-to-db.rkt schema.scm data`\n\n\n## Interact using miniKanren\n\n`mk-db.rkt` provides the `pharos-metao` and `pharoso` relations.\n\n```\n(require \"mk-db.rkt\")\n\n(run 10 (table-name metadata)\n (pharos-metao table-name metadata))\n\n(run 20 (tuple)\n (fresh (p q) (== `(,p 19295 . ,q) tuple))\n (pharoso \"gene_attribute\" tuple))\n```\n" }, { "path": "attic/pharos/csv.rkt", "content": "#lang racket/base\n(provide\n csv-records\n set-field-separator!\n )\n\n;; Informal CSV Grammar\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record ::= field | field FIELD-SEPARATOR record\n;field ::= \\\" inner-content* \\\" | CONTENT*\n;inner-content ::= CONTENT | \\\"\\\" | FIELD-SEPARATOR | WHITESPACE\n;; CONTENT includes anything other than double-quote, field separator, whitespace\n\n(define *field-separator* #\\,)\n(define (set-field-separator! ch) (set! *field-separator* ch))\n\n(define (end-of-record?! in)\n (define ch (peek-char in))\n (or (and (char=? #\\return ch)\n (or (and (char=? #\\newline (peek-char in 1)) (read-string 2 in) #t)\n (and (read-char in) #t)))\n (and (char=? #\\newline ch) (read-char in) #t)\n (eof-object? ch)))\n\n(define (end-of-field?! in)\n (define ch (peek-char in))\n (or (char=? *field-separator* ch)\n (char=? #\\return ch) (char=? #\\newline ch) (eof-object? ch)))\n\n(define (field-quoted-begin?! in)\n (define ch (peek-char in))\n (and (char=? #\\\" ch) (read-char in) #t))\n\n(define (field-quoted-end?! in)\n (define ch (peek-char in))\n (and (char=? #\\\" ch) (read-char in) (not (char=? #\\\" (peek-char in)))))\n\n(define (csv-records yield-record!)\n (lambda (in)\n (let record-stream ()\n (when (not (eof-object? (peek-char in)))\n (yield-record!\n (let record ()\n (cons (list->string\n (let field ()\n (cond ((end-of-field?! in) '())\n ((field-quoted-begin?! in)\n (let field-quoted ()\n (if (field-quoted-end?! in) (field)\n (cons (read-char in) (field-quoted)))))\n (else (cons (read-char in) (field))))))\n (if (end-of-record?! in) '()\n (begin (read-char in) (record))))))\n (record-stream)))))\n\n;; Test using:\n;; (call-with-input-file PATH\n;; (csv-records (lambda (record) (printf \"~s\\n\" `(record: ,record)))))\n" }, { "path": "attic/pharos/db.rkt", "content": "#lang racket\n(provide\n db-info\n table-info->metadata\n table-info->detail-stream\n )\n\n(require\n \"read.rkt\"\n \"repr.rkt\"\n )\n\n(define (db-info dir)\n (define tables-dir (build-path dir \"tables\"))\n (define table-names\n (map path->string (directory-list tables-dir #:build? #f)))\n (define table-dirs (directory-list tables-dir #:build? #t))\n (make-immutable-hash\n (map (lambda (name dir) (cons name (table-info dir)))\n table-names table-dirs)))\n\n(define (read-one-from-file path)\n (define data (read-all-from-file path))\n (if (= 1 (length data))\n (car data)\n (error \"found more data than expected:\" path (length data))))\n\n(define (table-info->metadata tinfo) (vector-ref tinfo 0))\n(define (table-info->detail-stream tinfo) (vector-ref tinfo 1))\n(define (table-info dir)\n ;; columns: [(name, type)]\n ;; indexed keys: [col-names]\n ;; foreign keys: [(local-col-names, table-name, foreign-col-names)]\n (define cols (read-one-from-file (build-path dir \"columns.scm\")))\n (define ixs (read-one-from-file (build-path dir \"indexes.scm\")))\n (define fks (read-one-from-file (build-path dir \"foreign-keys.scm\")))\n (define not-indexed? (equal? ixs '(#f)))\n (define masks (map (lambda (ix) (index->mask cols (or ix '()))) ixs))\n (define t->ks (map (lambda (m) (mask->tuple->key m)) masks))\n (define c2s (map (lambda (m) (mask->compare2 cols m)) masks))\n\n (define (detail-stream tmask tuple)\n (define i (choose-index masks tmask 0))\n (define key (and i ((list-ref t->ks i) tuple)))\n (define compare (if i ((list-ref c2s i) key) (lambda (_) 0)))\n (define ipath (build-path dir (number->string (or i 0))))\n (define detail-path (build-path ipath \"detail.scm\"))\n (define offset-path (build-path ipath \"offset.bin\"))\n (define (stream-from pos)\n (call-with-input-file\n detail-path\n (lambda (detail-in)\n (file-position detail-in pos)\n (define detail (read detail-in))\n (define next-pos (file-position detail-in))\n (if (or (eof-object? detail)\n (not (or not-indexed? (= 0 (compare detail)))))\n '() (stream-cons detail (stream-from next-pos))))))\n\n (call-with-input-file\n detail-path\n (lambda (detail-in)\n (call-with-input-file\n offset-path\n (lambda (offset-in)\n (define detail (if (or not-indexed? (not i))\n (read detail-in)\n (detail-find detail-in offset-in compare)))\n (define pos (file-position detail-in))\n (if (not (eof-object? detail))\n (stream-cons detail (stream-from pos))\n '()))))))\n\n `#(((columns . ,cols) (indexes . ,ixs) (foreign-keys ,fks))\n ,detail-stream\n ;; TODO: resolve foreign keys.\n ;; detail-stream->elaborated-detail-stream\n ))\n\n(define (compare2-number key candidate)\n (cond ((not candidate) -1)\n ((< candidate key) -1)\n ((> candidate key) 1)\n (else 0)))\n(define (compare2-text key candidate)\n (cond ((not candidate) -1)\n ((string? candidate key) 1)\n (else 0)))\n\n(define (index->mask cols icols)\n (define ncols (map (lambda (n col) (cons (car col) n))\n (range (length cols)) cols))\n (sort (map (lambda (icol) (cdr (assoc icol ncols))) icols) <))\n\n(define (mask->tuple->key ns)\n (lambda (tuple) (list->vector (map (lambda (n) (vector-ref tuple n)) ns))))\n\n(define (mask->compare2 cols ns)\n (define compare2s\n (map (lambda (n) (case (cadr (list-ref cols n))\n ((\"integer\" \"decimal\") compare2-number)\n (else compare2-text))) ns))\n (lambda (key)\n (lambda (candidate)\n (let loop ((cs compare2s) (ns ns) (ki 0) (k1 key) (k2 candidate))\n (cond\n ((null? cs) 0)\n (else (define n (car ns))\n (define cmp ((car cs) (vector-ref k1 ki) (vector-ref k2 n)))\n (if (= 0 cmp) (loop (cdr cs) (cdr ns) (+ 1 ki) k1 k2)\n cmp)))))))\n\n(define (masked? mask tmask)\n (cond ((null? mask) #t)\n ((null? tmask) #f)\n (else (define m0 (car mask))\n (define mrest (cdr mask))\n (define t0 (car tmask))\n (define trest (cdr tmask))\n (cond ((< m0 t0) #f)\n ((> m0 t0) (masked? mask trest))\n (else (masked? mrest trest))))))\n\n(define (choose-index masks tmask i)\n (cond ((null? masks) #f)\n ((masked? (car masks) tmask) i)\n (else (choose-index (cdr masks) tmask (+ i 1)))))\n" }, { "path": "attic/pharos/interact-sqlite3", "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\nsqlite_db=\"file:$here/data/pharos-sqlite3.db?mode=ro\"\n\nsqlite3 -bail -header -csv -echo \"$sqlite_db\"\n" }, { "path": "attic/pharos/mk-db.rkt", "content": "#lang racket\n(provide\n pharos-metao\n pharoso\n )\n\n(require\n \"db.rkt\"\n \"mk.rkt\"\n )\n\n(define db (db-info \"data/db\"))\n\n(define (pharos-metao table-name metadata)\n (project (table-name)\n (if (var? table-name)\n (let loop ((kv (hash->list db)))\n (if (null? kv) (== #f #t)\n (conde\n ((== (caar kv) table-name) (pharos-metao (caar kv) metadata))\n ((loop (cdr kv))))))\n (== (table-info->metadata (hash-ref db table-name)) metadata))))\n\n(define (pharoso table-name tuple)\n (project (table-name tuple)\n (cond ((var? table-name)\n (let loop ((kv (hash->list db)))\n (if (null? kv) (== #f #t)\n (conde\n ((== (caar kv) table-name) (pharoso (caar kv) tuple))\n ((loop (cdr kv)))))))\n (else (define ti (hash-ref db table-name))\n (define tt (list-truncate tuple))\n (define ds ((table-info->detail-stream ti)\n (tuple->mask tt 0) (list->vector tt)))\n (let loop ((ds ds))\n (cond ((stream-empty? ds) (== #f #t))\n (else (conde\n ((== (vector->list (stream-first ds)) tuple))\n ((loop (stream-rest ds)))))))))))\n\n(define (list-truncate xs)\n (cond ((var? xs) '())\n (else (cons (car xs) (list-truncate (cdr xs))))))\n\n(define (tuple->mask tuple i)\n (cond ((or (var? tuple) (null? tuple)) '())\n ((var? (car tuple)) (tuple->mask (cdr tuple) (+ i 1)))\n (else (cons i (tuple->mask (cdr tuple) (+ i 1))))))\n" }, { "path": "attic/pharos/mk-parse.rkt", "content": "#lang racket/base\n(provide\n fresh/p\n\n fail/p\n unit/p\n end\n\n single\n single-not\n one-of\n none-of\n\n many*\n many+\n many*-while\n many+-while\n many*-until\n many+-until\n\n skip*\n skip+\n skip*-while\n skip+-while\n skip*-until\n skip+-until\n\n seq\n\n and/p\n or/p\n\n peek\n remember1\n remember*\n ignore\n ignored\n )\n\n(require\n \"mk.rkt\"\n )\n\n(define (k/last&initial xs k)\n (define rxs (reverse xs))\n (k (car rxs) (reverse (cdr rxs))))\n\n(define (appendo l s ls)\n (conde\n ((== '() l) (== s ls))\n ((fresh (a d ms)\n (== `(,a . ,d) l)\n (== `(,a . ,ms) ls)\n (appendo d s ms)))))\n\n;; Common parser combinators\n(define-syntax fresh/p\n (syntax-rules ()\n ((_ (vname ...) g ... p)\n (lambda (in out)\n (fresh (vname ...)\n g ...\n (p in out))))))\n\n(define (fail/p in out) (== #t #f))\n(define (unit/p in out) (== in out))\n(define (end in out) (fresh () (== '() in) (== in out)))\n\n(define (single d) (lambda (in out) (== `(,d . ,out) in)))\n(define (single-lift d) (if (procedure? d) d (single d)))\n(define (single-not d)\n (lambda (in out) (fresh (item) (== `(,item . ,out) in) (=/= item d))))\n\n(define (seq2 pa pb) (lambda (in out) (fresh (mid) (pa in mid) (pb mid out))))\n(define (seq . ds) (foldr seq2 unit/p (map single-lift ds)))\n\n;; NOTE: and/p only commits with the last parser given.\n(define (and2/p pa pb) (lambda (in out) (fresh (_) (pa in _) (pb in out))))\n(define (and/p . ps)\n (if (null? ps) unit/p\n (k/last&initial ps (lambda (last initial) (foldr and2/p last initial)))))\n(define (or2/p pa pb) (lambda (in out) (conde ((pa in out)) ((pb in out)))))\n(define (or/p . ps) (foldr or2/p fail/p ps))\n\n(define (one-of ds) (apply or/p (map single ds)))\n(define (none-of ds) (apply and/p (map single-not ds)))\n\n(define (peek p) (and/p p unit/p))\n(define (remember1 p) (lambda (result) (and/p p (single result))))\n(define (remember* p)\n (lambda (result)\n (lambda (in out)\n (fresh () (p in out) (appendo result out in)))))\n(define (ignore p) (fresh/p (_) (p _)))\n(define (ignored p) (lambda (result) p))\n\n(define (many* pattern)\n (lambda (result)\n (or/p (fresh/p () (== '() result) unit/p)\n ((many+ pattern) result))))\n(define (many+ pattern)\n (lambda (result)\n (fresh/p (first rest)\n (== `(,first . ,rest) result)\n (seq2 (pattern first) ((many* pattern) rest)))))\n(define (many*-while ds)\n (lambda (result)\n (seq ((many* (remember1 (one-of ds))) result)\n (or/p end (peek (none-of ds))))))\n(define (many+-while ds)\n (lambda (result) (seq (peek (one-of ds)) ((many*-while ds) result))))\n(define (many*-until ds)\n (lambda (result)\n (seq ((many* (remember1 (none-of ds))) result)\n (or/p end (peek (one-of ds))))))\n(define (many+-until ds)\n (lambda (result) (seq (peek (none-of ds)) ((many*-until ds) result))))\n\n(define (skip* pattern) (ignore (many* (ignored pattern))))\n(define (skip+ pattern) (ignore (many+ (ignored pattern))))\n(define (skip*-while ds)\n (seq (skip* (one-of ds)) (or/p end (peek (none-of ds)))))\n(define (skip+-while ds) (seq (peek (one-of ds)) (skip* (one-of ds))))\n(define (skip*-until ds)\n (seq (skip* (none-of ds)) (or/p end (peek (one-of ds)))))\n(define (skip+-until ds) (seq (peek (none-of ds)) (skip*-until ds)))\n" }, { "path": "attic/pharos/mk.rkt", "content": "#lang racket/base\n\n(require racket/list\n racket/include\n racket/stream\n )\n\n(provide\n run run* run-stream\n == =/=\n fresh\n conde\n symbolo numbero\n absento\n project\n var?\n fail\n succeed\n choice\n inc\n unify\n walk\n walk*\n mplus\n mplus*\n bind\n bind*\n take take-stream\n reify\n )\n\n;; extra stuff for racket\n;; due mostly to samth\n(define (list-sort f l) (sort l f))\n\n(define (remp f l) (filter-not f l))\n\n(define (call-with-string-output-port f)\n (define p (open-output-string))\n (f p)\n (get-output-string p))\n\n(define (exists f l) (ormap f l))\n\n(define for-all andmap)\n\n(define (find f l)\n (cond [(memf f l) => car] [else #f]))\n\n(define memp memf)\n\n(define (var*? v) (var? (car v)))\n\n\n; Substitution representation\n\n(define empty-subst-map (hasheq))\n\n(define subst-map-length hash-count)\n\n; Returns #f if not found, or a pair of u and the result of the lookup.\n; This distinguishes between #f indicating absence and being the result.\n(define subst-map-lookup\n (lambda (u S)\n (hash-ref S u unbound)))\n\n(define (subst-map-add S var val)\n (hash-set S var val))\n\n(define subst-map-eq? eq?)\n\n\n; Constraint store representation\n\n(define empty-C (hasheq))\n\n(define set-c\n (lambda (v c st)\n (state (state-S st) (hash-set (state-C st) v c))))\n\n(define lookup-c\n (lambda (v st)\n (hash-ref (state-C st) v empty-c)))\n\n(define remove-c\n (lambda (v st)\n (state (state-S st) (hash-remove (state-C st) v))))\n\n\n; Scope object.\n; Used to determine whether a branch has occured between variable creation\n; and unification to allow the set-var-val! optimization in subst-add. Both variables\n; and substitutions will contain a scope. When a substitution flows through a\n; conde it is assigned a new scope.\n\n; Creates a new scope that is not scope-eq? to any other scope\n(define new-scope\n (lambda ()\n (list 'scope)))\n\n; Scope used when variable bindings should always be made in the substitution,\n; as in disequality solving and reification. We don't want to set-var-val! a\n; variable when checking if a disequality constraint holds!\n(define nonlocal-scope\n (list 'non-local-scope))\n\n(define scope-eq? eq?)\n\n\n; Logic variable object.\n; Contains:\n; val - value for variable assigned by unification using set-var-val! optimization.\n; unbound if not yet set or stored in substitution.\n; scope - scope that the variable was created in.\n; idx - unique numeric index for the variable. Used by the trie substitution representation.\n; Variable objects are compared by object identity.\n\n; The unique val for variables that have not yet been bound to a value\n; or are bound in the substitution\n(define unbound (list 'unbound))\n\n(define var\n (let ((counter -1))\n (lambda (scope)\n (set! counter (+ 1 counter))\n (vector unbound scope counter))))\n\n; Vectors are not allowed as terms, so terms that are vectors are variables.\n(define var?\n (lambda (x)\n (vector? x)))\n\n(define var-eq? eq?)\n\n(define var-val\n (lambda (x)\n (vector-ref x 0)))\n\n(define set-var-val!\n (lambda (x v)\n (vector-set! x 0 v)))\n\n(define var-scope\n (lambda (x)\n (vector-ref x 1)))\n\n(define var-idx\n (lambda (x)\n (vector-ref x 2)))\n\n\n; Substitution object.\n; Contains:\n; map - mapping of variables to values\n; scope - scope at current program point, for set-var-val! optimization. Updated at conde.\n; Included in the substitution because it is required to fully define the substitution\n; and how it is to be extended.\n;\n; Implementation of the substitution map depends on the Scheme used, as we need a map. See mk.rkt\n; and mk-vicare.scm.\n\n(define subst\n (lambda (mapping scope)\n (cons mapping scope)))\n\n(define subst-map car)\n\n(define subst-scope cdr)\n\n(define subst-length\n (lambda (S)\n (subst-map-length (subst-map S))))\n\n(define subst-with-scope\n (lambda (S new-scope)\n (subst (subst-map S) new-scope)))\n\n(define empty-subst (subst empty-subst-map (new-scope)))\n\n(define subst-add\n (lambda (S x v)\n ; set-var-val! optimization: set the value directly on the variable\n ; object if we haven't branched since its creation\n ; (the scope of the variable and the substitution are the same).\n ; Otherwise extend the substitution mapping.\n (if (scope-eq? (var-scope x) (subst-scope S))\n (begin\n (set-var-val! x v)\n S)\n (subst (subst-map-add (subst-map S) x v) (subst-scope S)))))\n\n(define subst-lookup\n (lambda (u S)\n ; set-var-val! optimization.\n ; Tried checking the scope here to avoid a subst-map-lookup\n ; if it was definitely unbound, but that was slower.\n (if (not (eq? (var-val u) unbound))\n (var-val u)\n (subst-map-lookup u (subst-map S)))))\n\n; Association object.\n; Describes an association mapping the lhs to the rhs. Returned by unification\n; to describe the associations that were added to the substitution (whose representation\n; is opaque) and used to represent disequality constraints.\n\n(define lhs car)\n\n(define rhs cdr)\n\n; Constraint record object.\n;\n; Describes the constraints attached to a single variable.\n;\n; Contains:\n; T - type constraint. 'symbolo 'numbero or #f to indicate no constraint\n; D - list of disequality constraints. Each disequality is a list of associations.\n; The constraint is violated if all associated variables are equal in the\n; substitution simultaneously. D could contain duplicate constraints (created\n; by distinct =/= calls). A given disequality constraint is only attached to\n; one of the variables involved, as all components of the constraint must be\n; violated to cause failure.\n; A - list of absento constraints. Each constraint is a ground atom. The list contains\n; no duplicates.\n\n(define empty-c `(#f () ()))\n\n(define c-T\n (lambda (c)\n (car c)))\n\n(define c-D\n (lambda (c)\n (cadr c)))\n\n(define c-A\n (lambda (c)\n (caddr c)))\n\n(define c-with-T\n (lambda (c T)\n (list T (c-D c) (c-A c))))\n\n(define c-with-D\n (lambda (c D)\n (list (c-T c) D (c-A c))))\n\n(define c-with-A\n (lambda (c A)\n (list (c-T c) (c-D c) A)))\n\n; Constraint store object.\n; Mapping of representative variable to constraint record. Constraints are\n; always on the representative element and must be moved / merged when that\n; element changes.\n\n; Implementation depends on the Scheme used, as we need a map. See mk.rkt\n; and mk-vicare.scm.\n\n; State object.\n; The state is the value that is monadically passed through the search.\n; Contains:\n; S - the substitution\n; C - the constraint store\n\n(define state\n (lambda (S C)\n (cons S C)))\n\n(define state-S (lambda (st) (car st)))\n(define state-C (lambda (st) (cdr st)))\n\n(define empty-state (state empty-subst empty-C))\n\n(define state-with-scope\n (lambda (st new-scope)\n (state (subst-with-scope (state-S st) new-scope) (state-C st))))\n\n; Unification\n\n(define walk\n (lambda (u S)\n (if (var? u)\n (let ((val (subst-lookup u S)))\n (if (eq? val unbound)\n u\n (walk val S)))\n u)))\n\n(define occurs-check\n (lambda (x v S)\n (let ((v (walk v S)))\n (cond\n ((var? v) (var-eq? v x))\n ((pair? v)\n (or\n (occurs-check x (car v) S)\n (occurs-check x (cdr v) S)))\n (else #f)))))\n\n(define ext-s-check\n (lambda (x v S)\n (cond\n ((occurs-check x v S) (values #f #f))\n (else (values (subst-add S x v) `((,x . ,v)))))))\n\n; Returns as values the extended substitution and a list of associations added\n; during the unification, or (values #f #f) if the unification failed.\n;\n; Right now appends the list of added values from sub-unifications. Alternatively\n; could be threaded monadically, which could be faster or slower.\n(define unify\n (lambda (u v s)\n (let ((u (walk u s))\n (v (walk v s)))\n (cond\n ((eq? u v) (values s '()))\n ((var? u) (ext-s-check u v s))\n ((var? v) (ext-s-check v u s))\n ((and (pair? u) (pair? v))\n (let-values (((s added-car) (unify (car u) (car v) s)))\n (if s\n (let-values (((s added-cdr) (unify (cdr u) (cdr v) s)))\n (values s (append added-car added-cdr)))\n (values #f #f))))\n ((equal? u v) (values s '()))\n (else (values #f #f))))))\n\n(define unify*\n (lambda (S+ S)\n (unify (map lhs S+) (map rhs S+) S)))\n\n\n; Search\n\n; SearchStream: #f | Procedure | State | (Pair State (-> SearchStream))\n\n; SearchStream constructor types. Names inspired by the plus monad?\n\n; -> SearchStream\n(define mzero (lambda () #f))\n\n; c: State\n; -> SearchStream\n(define unit (lambda (c) c))\n\n; c: State\n; f: (-> SearchStream)\n; -> SearchStream\n;\n; f is a thunk to avoid unnecessary computation in the case that c is the\n; last answer needed to satisfy the query.\n(define choice (lambda (c f) (cons c f)))\n\n; e: SearchStream\n; -> (-> SearchStream)\n(define-syntax inc\n (syntax-rules ()\n ((_ e) (lambda () e))))\n\n; Goal: (State -> SearchStream)\n\n; e: SearchStream\n; -> Goal\n(define-syntax lambdag@\n (syntax-rules ()\n ((_ (st) e) (lambda (st) e))))\n\n; Match on search streams. The state type must not be a pair with a procedure\n; in its cdr.\n;\n; (() e0) failure\n; ((f) e1) inc for interleaving. separate from success or failure to ensure\n; it goes all the way to the top of the tree.\n; ((c) e2) single result. Used rather than (choice c (inc (mzero))) to avoid\n; returning to search a part of the tree that will inevitably fail.\n; ((c f) e3) multiple results.\n(define-syntax case-inf\n (syntax-rules ()\n ((_ e (() e0) ((f^) e1) ((c^) e2) ((c f) e3))\n (let ((c-inf e))\n (cond\n ((not c-inf) e0)\n ((procedure? c-inf) (let ((f^ c-inf)) e1))\n ((not (and (pair? c-inf)\n (procedure? (cdr c-inf))))\n (let ((c^ c-inf)) e2))\n (else (let ((c (car c-inf)) (f (cdr c-inf)))\n e3)))))))\n\n; c-inf: SearchStream\n; f: (-> SearchStream)\n; -> SearchStream\n;\n; f is a thunk to avoid unnecesarry computation in the case that the first\n; answer produced by c-inf is enough to satisfy the query.\n(define mplus\n (lambda (c-inf f)\n (case-inf c-inf\n (() (f))\n ((f^) (inc (mplus (f) f^)))\n ((c) (choice c f))\n ((c f^) (choice c (inc (mplus (f) f^)))))))\n\n; c-inf: SearchStream\n; g: Goal\n; -> SearchStream\n(define bind\n (lambda (c-inf g)\n (case-inf c-inf\n (() (mzero))\n ((f) (inc (bind (f) g)))\n ((c) (g c))\n ((c f) (mplus (g c) (inc (bind (f) g)))))))\n\n; Int, SearchStream -> (ListOf SearchResult)\n(define take\n (lambda (n f)\n (cond\n ((and n (zero? n)) '())\n (else\n (case-inf (f)\n (() '())\n ((f) (take n f))\n ((c) (cons c '()))\n ((c f) (cons c\n (take (and n (- n 1)) f))))))))\n\n(define take-stream\n (lambda (f)\n (case-inf (f)\n (() '())\n ((f) (take-stream f))\n ((c) (stream-cons c '()))\n ((c f) (stream-cons c (take-stream f))))))\n\n; -> SearchStream\n(define-syntax bind*\n (syntax-rules ()\n ((_ e) e)\n ((_ e g0 g ...) (bind* (bind e g0) g ...))))\n\n; -> SearchStream\n(define-syntax mplus*\n (syntax-rules ()\n ((_ e) e)\n ((_ e0 e ...) (mplus e0\n (inc (mplus* e ...))))))\n\n; -> Goal\n(define-syntax fresh\n (syntax-rules ()\n ((_ (x ...) g0 g ...)\n (lambdag@ (st)\n ; this inc triggers interleaving\n (inc\n (let ((scope (subst-scope (state-S st))))\n (let ((x (var scope)) ...)\n (bind* (g0 st) g ...))))))))\n\n\n; -> Goal\n(define-syntax conde\n (syntax-rules ()\n ((_ (g0 g ...) (g1 g^ ...) ...)\n (lambdag@ (st)\n ; this inc triggers interleaving\n (inc\n (let ((st (state-with-scope st (new-scope))))\n (mplus*\n (bind* (g0 st) g ...)\n (bind* (g1 st) g^ ...) ...)))))))\n\n(define-syntax run\n (syntax-rules ()\n ((_ n (q) g0 g ...)\n (take n\n (inc\n ((fresh (q) g0 g ...\n (lambdag@ (st)\n (let ((st (state-with-scope st nonlocal-scope)))\n (let ((z ((reify q) st)))\n (choice z (lambda () (lambda () #f)))))))\n empty-state))))\n ((_ n (q0 q1 q ...) g0 g ...)\n (run n (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n(define-syntax run*\n (syntax-rules ()\n ((_ (q0 q ...) g0 g ...) (run #f (q0 q ...) g0 g ...))))\n\n(define-syntax run-stream\n (syntax-rules ()\n ((_ (q) g0 g ...)\n (take-stream\n (inc\n ((fresh (q) g0 g ...\n (lambdag@ (st)\n (let ((st (state-with-scope st nonlocal-scope)))\n (let ((z ((reify q) st)))\n (choice z (lambda () (lambda () #f)))))))\n empty-state))))\n ((_ (q0 q1 q ...) g0 g ...)\n (run-stream (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n; Constraints\n; C refers to the constraint store map\n; c refers to an individual constraint record\n\n; Constraint: State -> #f | State\n;\n; (note that a Constraint is a Goal but a Goal is not a Constraint.\n; Constraint implementations currently use this more restrained type. See `and-foldl`\n; and `update-constraints`.)\n\n; Requirements for type constraints:\n; 1. Must be positive, not negative. not-pairo wouldn't work.\n; 2. Each type must have infinitely many possible values to avoid\n; incorrectness in combination with disequality constraints, like:\n; (fresh (x) (booleano x) (=/= x #t) (=/= x #f))\n(define type-constraint\n (lambda (type-pred type-id)\n (lambda (u)\n (lambdag@ (st)\n (let ((term (walk u (state-S st))))\n (cond\n ((type-pred term) st)\n ((var? term)\n (let* ((c (lookup-c term st))\n (T (c-T c)))\n (cond\n ((eq? T type-id) st)\n ((not T) (set-c term (c-with-T c type-id) st))\n (else #f))))\n (else #f)))))))\n\n(define symbolo (type-constraint symbol? 'symbolo))\n(define numbero (type-constraint number? 'numbero))\n\n(define (add-to-D st v d)\n (let* ((c (lookup-c v st))\n (c^ (c-with-D c (cons d (c-D c)))))\n (set-c v c^ st)))\n\n(define =/=*\n (lambda (S+)\n (lambdag@ (st)\n (let-values (((S added) (unify* S+ (subst-with-scope (state-S st) nonlocal-scope))))\n (cond\n ((not S) st)\n ((null? added) #f)\n (else\n ; Choose one of the disequality elements (el) to attach the constraint to. Only\n ; need to choose one because all must fail to cause the constraint to fail.\n (let ((el (car added)))\n (let ((st (add-to-D st (car el) added)))\n (if (var? (cdr el))\n (add-to-D st (cdr el) added)\n st)))))))))\n\n(define =/=\n (lambda (u v)\n (=/=* `((,u . ,v)))))\n\n(define absento\n (lambda (ground-atom term)\n (lambdag@ (st)\n (let ((term (walk term (state-S st))))\n (cond\n ((pair? term)\n (let ((st^ ((absento ground-atom (car term)) st)))\n (and st^ ((absento ground-atom (cdr term)) st^))))\n ((eqv? term ground-atom) #f)\n ((var? term)\n (let* ((c (lookup-c term st))\n (A (c-A c)))\n (if (memv ground-atom A)\n st\n (let ((c^ (c-with-A c (cons ground-atom A))))\n (set-c term c^ st)))))\n (else st))))))\n\n; Fold lst with proc and initial value init. If proc ever returns #f,\n; return with #f immediately. Used for applying a series of constraints\n; to a state, failing if any operation fails.\n(define (and-foldl proc init lst)\n (if (null? lst)\n init\n (let ([res (proc (car lst) init)])\n (and res (and-foldl proc res (cdr lst))))))\n\n(define ==\n (lambda (u v)\n (lambdag@ (st)\n (let-values (((S added) (unify u v (state-S st))))\n (if S\n (and-foldl update-constraints (state S (state-C st)) added)\n #f)))))\n\n\n; Not fully optimized. Could do absento update with fewer hash-refs / hash-sets.\n(define update-constraints\n (lambda (a st)\n (let ([old-c (lookup-c (lhs a) st)])\n (if (eq? old-c empty-c)\n st\n (let ((st (remove-c (lhs a) st)))\n (and-foldl (lambda (op st) (op st)) st\n (append\n (if (eq? (c-T old-c) 'symbolo)\n (list (symbolo (rhs a)))\n '())\n (if (eq? (c-T old-c) 'numbero)\n (list (numbero (rhs a)))\n '())\n (map (lambda (atom) (absento atom (rhs a))) (c-A old-c))\n (map (lambda (d) (=/=* d)) (c-D old-c)))))))))\n\n\n; Reification\n\n(define walk*\n (lambda (v S)\n (let ((v (walk v S)))\n (cond\n ((var? v) v)\n ((pair? v)\n (cons (walk* (car v) S) (walk* (cdr v) S)))\n (else v)))))\n\n(define vars\n (lambda (term acc)\n (cond\n ((var? term) (cons term acc))\n ((pair? term)\n (vars (cdr term) (vars (car term) acc)))\n (else acc))))\n\n(define-syntax project\n (syntax-rules ()\n ((_ (x ...) g g* ...)\n (lambdag@ (st)\n (let ((x (walk* x (state-S st))) ...)\n ((fresh () g g* ...) st))))))\n\n\n; Create a constraint store of the old representation from a state object,\n; so that we can use the old reifier. Only accumulates constraints related\n; to the variable being reified which makes things a bit faster.\n(define c-from-st\n (lambda (st x)\n (let ((vs (vars (walk* x (state-S st)) '())))\n (foldl\n (lambda (v c-store)\n (let ((c (lookup-c v st)))\n (let ((S (state-S st))\n (D (c->D c-store))\n (Y (c->Y c-store))\n (N (c->N c-store))\n (T (c->T c-store))\n (T^ (c-T c))\n (D^ (c-D c))\n (A^ (c-A c)))\n `(,S\n ,(append D^ D)\n ,(if (eq? T^ 'symbolo)\n (cons v Y)\n Y)\n ,(if (eq? T^ 'numbero)\n (cons v N)\n N)\n ,(append\n (map (lambda (atom) (cons atom v)) A^)\n T)))))\n `(,(state-S st) () () () ())\n (remove-duplicates vs)))))\n\n(define reify\n (lambda (x)\n (lambda (st)\n (let ((c (c-from-st st x)))\n (let ((c (cycle c)))\n (let* ((S (c->S c))\n (D (walk* (c->D c) S))\n (Y (walk* (c->Y c) S))\n (N (walk* (c->N c) S))\n (T (walk* (c->T c) S)))\n (let ((v (walk* x S)))\n (let ((R (reify-S v (subst empty-subst-map nonlocal-scope))))\n (reify+ v R\n (let ((D (remp\n (lambda (d)\n (let ((dw (walk* d S)))\n (anyvar? dw R)))\n (rem-xx-from-d c))))\n (rem-subsumed D))\n (remp\n (lambda (y) (var? (walk y R)))\n Y)\n (remp\n (lambda (n) (var? (walk n R)))\n N)\n (remp (lambda (t)\n (anyvar? t R)) T))))))))))\n\n\n; Bits from the old constraint implementation, still used for reification.\n\n; In this part of the code, c refers to the\n; old constraint store with components:\n; S - substitution\n; D - disequality constraints\n; Y - symbolo\n; N - numbero\n; T - absento\n\n(define c->S (lambda (c) (car c)))\n(define c->D (lambda (c) (cadr c)))\n(define c->Y (lambda (c) (caddr c)))\n(define c->N (lambda (c) (cadddr c)))\n(define c->T (lambda (c) (cadddr (cdr c))))\n\n; Syntax for reification goal objects using the old constraint store\n(define-syntax lambdar@\n (syntax-rules (:)\n ((_ (c) e) (lambda (c) e))\n ((_ (c : S D Y N T) e)\n (lambda (c)\n (let ((S (c->S c)) (D (c->D c)) (Y (c->Y c)) (N (c->N c)) (T (c->T c)))\n e)))))\n\n(define tagged?\n (lambda (S Y y^)\n (exists (lambda (y) (eqv? (walk y S) y^)) Y)))\n\n(define untyped-var?\n (lambda (S Y N t^)\n (let ((in-type? (lambda (y) (var-eq? (walk y S) t^))))\n (and (var? t^)\n (not (exists in-type? Y))\n (not (exists in-type? N))))))\n\n(define reify-S\n (lambda (v S)\n (let ((v (walk v S)))\n (cond\n ((var? v)\n (let ((n (subst-length S)))\n (let ((name (reify-name n)))\n (subst-add S v name))))\n ((pair? v)\n (let ((S (reify-S (car v) S)))\n (reify-S (cdr v) S)))\n (else S)))))\n\n(define reify-name\n (lambda (n)\n (string->symbol\n (string-append \"_\" \".\" (number->string n)))))\n\n(define drop-dot\n (lambda (X)\n (map (lambda (t)\n (let ((a (lhs t))\n (d (rhs t)))\n `(,a ,d)))\n X)))\n\n(define sorter\n (lambda (ls)\n (list-sort lex<=? ls)))\n\n(define lex<=?\n (lambda (x y)\n (string<=? (datum->string x) (datum->string y))))\n\n(define datum->string\n (lambda (x)\n (call-with-string-output-port\n (lambda (p) (display x p)))))\n\n(define anyvar?\n (lambda (u r)\n (cond\n ((pair? u)\n (or (anyvar? (car u) r)\n (anyvar? (cdr u) r)))\n (else (var? (walk u r))))))\n\n(define member*\n (lambda (u v)\n (cond\n ((equal? u v) #t)\n ((pair? v)\n (or (member* u (car v)) (member* u (cdr v))))\n (else #f))))\n\n(define drop-N-b/c-const\n (lambdar@ (c : S D Y N T)\n (let ((const? (lambda (n)\n (not (var? (walk n S))))))\n (cond\n ((find const? N) =>\n (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n (else c)))))\n\n(define drop-Y-b/c-const\n (lambdar@ (c : S D Y N T)\n (let ((const? (lambda (y)\n (not (var? (walk y S))))))\n (cond\n ((find const? Y) =>\n (lambda (y) `(,S ,D ,(remq1 y Y) ,N ,T)))\n (else c)))))\n\n(define remq1\n (lambda (elem ls)\n (cond\n ((null? ls) '())\n ((eq? (car ls) elem) (cdr ls))\n (else (cons (car ls) (remq1 elem (cdr ls)))))))\n\n(define same-var?\n (lambda (v)\n (lambda (v^)\n (and (var? v) (var? v^) (var-eq? v v^)))))\n\n(define find-dup\n (lambda (f S)\n (lambda (set)\n (let loop ((set^ set))\n (cond\n ((null? set^) #f)\n (else\n (let ((elem (car set^)))\n (let ((elem^ (walk elem S)))\n (cond\n ((find (lambda (elem^^)\n ((f elem^) (walk elem^^ S)))\n (cdr set^))\n elem)\n (else (loop (cdr set^))))))))))))\n\n(define drop-N-b/c-dup-var\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-dup same-var? S) N) =>\n (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n (else c))))\n\n(define drop-Y-b/c-dup-var\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-dup same-var? S) Y) =>\n (lambda (y)\n `(,S ,D ,(remq1 y Y) ,N ,T)))\n (else c))))\n\n(define var-type-mismatch?\n (lambda (S Y N t1^ t2^)\n (cond\n ((num? S N t1^) (not (num? S N t2^)))\n ((sym? S Y t1^) (not (sym? S Y t2^)))\n (else #f))))\n\n(define term-ununifiable?\n (lambda (S Y N t1 t2)\n (let ((t1^ (walk t1 S))\n (t2^ (walk t2 S)))\n (cond\n ((or (untyped-var? S Y N t1^) (untyped-var? S Y N t2^)) #f)\n ((var? t1^) (var-type-mismatch? S Y N t1^ t2^))\n ((var? t2^) (var-type-mismatch? S Y N t2^ t1^))\n ((and (pair? t1^) (pair? t2^))\n (or (term-ununifiable? S Y N (car t1^) (car t2^))\n (term-ununifiable? S Y N (cdr t1^) (cdr t2^))))\n (else (not (eqv? t1^ t2^)))))))\n\n(define T-term-ununifiable?\n (lambda (S Y N)\n (lambda (t1)\n (let ((t1^ (walk t1 S)))\n (letrec\n ((t2-check\n (lambda (t2)\n (let ((t2^ (walk t2 S)))\n (if (pair? t2^)\n (and\n (term-ununifiable? S Y N t1^ t2^)\n (t2-check (car t2^))\n (t2-check (cdr t2^)))\n (term-ununifiable? S Y N t1^ t2^))))))\n t2-check)))))\n\n(define num?\n (lambda (S N n)\n (let ((n (walk n S)))\n (cond\n ((var? n) (tagged? S N n))\n (else (number? n))))))\n\n(define sym?\n (lambda (S Y y)\n (let ((y (walk y S)))\n (cond\n ((var? y) (tagged? S Y y))\n (else (symbol? y))))))\n\n(define drop-T-b/c-Y-and-N\n (lambdar@ (c : S D Y N T)\n (let ((drop-t? (T-term-ununifiable? S Y N)))\n (cond\n ((find (lambda (t) ((drop-t? (lhs t)) (rhs t))) T) =>\n (lambda (t) `(,S ,D ,Y ,N ,(remq1 t T))))\n (else c)))))\n\n(define move-T-to-D-b/c-t2-atom\n (lambdar@ (c : S D Y N T)\n (cond\n ((exists (lambda (t)\n (let ((t2^ (walk (rhs t) S)))\n (cond\n ((and (not (untyped-var? S Y N t2^))\n (not (pair? t2^)))\n (let ((T (remq1 t T)))\n `(,S ((,t) . ,D) ,Y ,N ,T)))\n (else #f))))\n T))\n (else c))))\n\n(define terms-pairwise=?\n (lambda (pr-a^ pr-d^ t-a^ t-d^ S)\n (or\n (and (term=? pr-a^ t-a^ S)\n (term=? pr-d^ t-a^ S))\n (and (term=? pr-a^ t-d^ S)\n (term=? pr-d^ t-a^ S)))))\n\n(define T-superfluous-pr?\n (lambda (S Y N T)\n (lambda (pr)\n (let ((pr-a^ (walk (lhs pr) S))\n (pr-d^ (walk (rhs pr) S)))\n (cond\n ((exists\n (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S)))\n T)\n (for-all\n (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (or\n (not (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S))\n (untyped-var? S Y N t-d^)\n (pair? t-d^))))\n T))\n (else #f))))))\n\n(define drop-from-D-b/c-T\n (lambdar@ (c : S D Y N T)\n (cond\n ((find\n (lambda (d)\n (exists\n (T-superfluous-pr? S Y N T)\n d))\n D) =>\n (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n (else c))))\n\n(define drop-t-b/c-t2-occurs-t1\n (lambdar@ (c : S D Y N T)\n (cond\n ((find (lambda (t)\n (let ((t-a^ (walk (lhs t) S))\n (t-d^ (walk (rhs t) S)))\n (mem-check t-d^ t-a^ S)))\n T) =>\n (lambda (t)\n `(,S ,D ,Y ,N ,(remq1 t T))))\n (else c))))\n\n(define split-t-move-to-d-b/c-pair\n (lambdar@ (c : S D Y N T)\n (cond\n ((exists\n (lambda (t)\n (let ((t2^ (walk (rhs t) S)))\n (cond\n ((pair? t2^) (let ((ta `(,(lhs t) . ,(car t2^)))\n (td `(,(lhs t) . ,(cdr t2^))))\n (let ((T `(,ta ,td . ,(remq1 t T))))\n `(,S ((,t) . ,D) ,Y ,N ,T))))\n (else #f))))\n T))\n (else c))))\n\n(define find-d-conflict\n (lambda (S Y N)\n (lambda (D)\n (find\n (lambda (d)\n (exists (lambda (pr)\n (term-ununifiable? S Y N (lhs pr) (rhs pr)))\n d))\n D))))\n\n(define drop-D-b/c-Y-or-N\n (lambdar@ (c : S D Y N T)\n (cond\n (((find-d-conflict S Y N) D) =>\n (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n (else c))))\n\n(define cycle\n (lambdar@ (c)\n (let loop ((c^ c)\n (fns^ (LOF))\n (n (length (LOF))))\n (cond\n ((zero? n) c^)\n ((null? fns^) (loop c^ (LOF) n))\n (else\n (let ((c^^ ((car fns^) c^)))\n (cond\n ((not (eq? c^^ c^))\n (loop c^^ (cdr fns^) (length (LOF))))\n (else (loop c^ (cdr fns^) (sub1 n))))))))))\n\n(define mem-check\n (lambda (u t S)\n (let ((t (walk t S)))\n (cond\n ((pair? t)\n (or (term=? u t S)\n (mem-check u (car t) S)\n (mem-check u (cdr t) S)))\n (else (term=? u t S))))))\n\n(define term=?\n (lambda (u t S)\n (let-values (((S added) (unify u t (subst-with-scope S nonlocal-scope))))\n (and S (null? added)))))\n\n(define ground-non-?\n (lambda (pred)\n (lambda (u S)\n (let ((u (walk u S)))\n (cond\n ((var? u) #f)\n (else (not (pred u))))))))\n\n(define ground-non-symbol?\n (ground-non-? symbol?))\n\n(define ground-non-number?\n (ground-non-? number?))\n\n(define succeed (== #f #f))\n\n(define fail (== #f #t))\n\n(define ==fail-check\n (lambda (S0 D Y N T)\n (let ([S0 (subst-with-scope S0 nonlocal-scope)])\n (cond\n ((atomic-fail-check S0 Y ground-non-symbol?) #t)\n ((atomic-fail-check S0 N ground-non-number?) #t)\n ((symbolo-numbero-fail-check S0 Y N) #t)\n ((=/=-fail-check S0 D) #t)\n ((absento-fail-check S0 T) #t)\n (else #f)))))\n\n(define atomic-fail-check\n (lambda (S A pred)\n (exists (lambda (a) (pred (walk a S) S)) A)))\n\n(define symbolo-numbero-fail-check\n (lambda (S A N)\n (let ((N (map (lambda (n) (walk n S)) N)))\n (exists (lambda (a) (exists (same-var? (walk a S)) N))\n A))))\n\n(define absento-fail-check\n (lambda (S T)\n (exists (lambda (t) (mem-check (lhs t) (rhs t) S)) T)))\n\n(define =/=-fail-check\n (lambda (S D)\n (exists (d-fail-check S) D)))\n\n(define d-fail-check\n (lambda (S)\n (lambda (d)\n (let-values (((S added) (unify* d S)))\n (and S (null? added))))))\n\n(define reify+\n (lambda (v R D Y N T)\n (form (walk* v R)\n (walk* D R)\n (walk* Y R)\n (walk* N R)\n (rem-subsumed-T (walk* T R)))))\n\n(define form\n (lambda (v D Y N T)\n (let ((fd (sort-D D))\n (fy (sorter Y))\n (fn (sorter N))\n (ft (sorter T)))\n (let ((fd (if (null? fd) fd\n (let ((fd (drop-dot-D fd)))\n `((=/= . ,fd)))))\n (fy (if (null? fy) fy `((sym . ,fy))))\n (fn (if (null? fn) fn `((num . ,fn))))\n (ft (if (null? ft) ft\n (let ((ft (drop-dot ft)))\n `((absento . ,ft))))))\n (cond\n ((and (null? fd) (null? fy)\n (null? fn) (null? ft))\n v)\n (else (append `(,v) fd fn fy ft)))))))\n\n(define sort-D\n (lambda (D)\n (sorter\n (map sort-d D))))\n\n(define sort-d\n (lambda (d)\n (list-sort\n (lambda (x y)\n (lex<=? (car x) (car y)))\n (map sort-pr d))))\n\n(define drop-dot-D\n (lambda (D)\n (map drop-dot D)))\n\n(define lex<-reified-name?\n (lambda (r)\n (charstring r) 0)\n #\\_)))\n\n(define sort-pr\n (lambda (pr)\n (let ((l (lhs pr))\n (r (rhs pr)))\n (cond\n ((lex<-reified-name? r) pr)\n ((lex<=? r l) `(,r . ,l))\n (else pr)))))\n\n(define rem-subsumed\n (lambda (D)\n (let rem-subsumed ((D D) (d^* '()))\n (cond\n ((null? D) d^*)\n ((or (subsumed? (car D) (cdr D))\n (subsumed? (car D) d^*))\n (rem-subsumed (cdr D) d^*))\n (else (rem-subsumed (cdr D)\n (cons (car D) d^*)))))))\n\n(define subsumed?\n (lambda (d d*)\n (cond\n ((null? d*) #f)\n (else\n (let-values (((S ignore) (unify* d (subst empty-subst-map nonlocal-scope))))\n (let-values (((S+ added) (unify* (car d*) S)))\n (or\n (and S+ (null? added))\n (subsumed? d (cdr d*)))))))))\n\n\n\n(define rem-xx-from-d\n (lambdar@ (c : S D Y N T)\n (let ((D (walk* D S)))\n (remp not\n (map (lambda (d)\n (let-values (((S0 ignore) (unify* d S)))\n (cond\n ((not S0) #f)\n ((==fail-check S0 '() Y N T) #f)\n (else\n (let-values (((S added) (unify* d (subst empty-subst-map nonlocal-scope))))\n added)))))\n D)))))\n\n(define rem-subsumed-T\n (lambda (T)\n (let rem-subsumed ((T T) (T^ '()))\n (cond\n ((null? T) T^)\n (else\n (let ((lit (lhs (car T)))\n (big (rhs (car T))))\n (cond\n ((or (subsumed-T? lit big (cdr T))\n (subsumed-T? lit big T^))\n (rem-subsumed (cdr T) T^))\n (else (rem-subsumed (cdr T)\n (cons (car T) T^))))))))))\n\n(define subsumed-T?\n (lambda (lit big T)\n (cond\n ((null? T) #f)\n (else\n (let ((lit^ (lhs (car T)))\n (big^ (rhs (car T))))\n (or\n (and (eq? big big^) (member* lit^ lit))\n (subsumed-T? lit big (cdr T))))))))\n\n(define LOF\n (lambda ()\n `(,drop-N-b/c-const ,drop-Y-b/c-const ,drop-Y-b/c-dup-var\n ,drop-N-b/c-dup-var ,drop-D-b/c-Y-or-N ,drop-T-b/c-Y-and-N\n ,move-T-to-D-b/c-t2-atom ,split-t-move-to-d-b/c-pair\n ,drop-from-D-b/c-T ,drop-t-b/c-t2-occurs-t1)))\n\n" }, { "path": "attic/pharos/mysql2sqlite/LICENSE", "content": "The MIT License (MIT)\n\nCopyright (c) 2015 esperlu, 2016 dumblob\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n\n" }, { "path": "attic/pharos/mysql2sqlite/mysql2sqlite", "content": "#!/usr/bin/awk -f\n\n# Authors: @esperlu, @artemyk, @gkuenning, @dumblob\n\n# FIXME detect empty input file and issue a warning\n\nfunction printerr( s ){ print s | \"cat >&2\" }\n\nBEGIN {\n if( ARGC != 2 ){\n printerr( \\\n \"USAGE: mysql2sqlite dump_mysql.sql > dump_sqlite3.sql\\n\" \\\n \" file name - (dash) is not supported, because - means stdin\")\n no_END = 1\n exit 1\n }\n\n # Find INT_MAX supported by both this AWK (usually an ISO C signed int)\n # and SQlite.\n # On non-8bit-based architectures, the additional bits are safely ignored.\n\n # 8bit (lower precision should not exist)\n s=\"127\"\n # \"63\" + 0 avoids potential parser misbehavior\n if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"63\" + 0 }\n # 16bit\n s=\"32767\"\n if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"16383\" + 0 }\n # 32bit\n s=\"2147483647\"\n if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"1073741823\" + 0 }\n # 64bit (as INTEGER in SQlite3)\n s=\"9223372036854775807\"\n if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"4611686018427387904\" + 0 }\n# # 128bit\n# s=\"170141183460469231731687303715884105728\"\n# if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"85070591730234615865843651857942052864\" + 0 }\n# # 256bit\n# s=\"57896044618658097711785492504343953926634992332820282019728792003956564819968\"\n# if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"28948022309329048855892746252171976963317496166410141009864396001978282409984\" + 0 }\n# # 512bit\n# s=\"6703903964971298549787012499102923063739682910296196688861780721860882015036773488400937149083451713845015929093243025426876941405973284973216824503042048\"\n# if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"3351951982485649274893506249551461531869841455148098344430890360930441007518386744200468574541725856922507964546621512713438470702986642486608412251521024\" + 0 }\n# # 1024bit\n# s=\"89884656743115795386465259539451236680898848947115328636715040578866337902750481566354238661203768010560056939935696678829394884407208311246423715319737062188883946712432742638151109800623047059726541476042502884419075341171231440736956555270413618581675255342293149119973622969239858152417678164812112068608\"\n# if( (s + 0) \"\" == s ){ INT_MAX_HALF = \"44942328371557897693232629769725618340449424473557664318357520289433168951375240783177119330601884005280028469967848339414697442203604155623211857659868531094441973356216371319075554900311523529863270738021251442209537670585615720368478277635206809290837627671146574559986811484619929076208839082406056034304\" + 0 }\n# # higher precision probably not needed\n\n FS=\",$\"\n print \"PRAGMA synchronous = OFF;\"\n print \"PRAGMA journal_mode = MEMORY;\"\n print \"BEGIN TRANSACTION;\"\n}\n\n# historically 3 spaces separate non-argument local variables\nfunction bit_to_int( str_bit, powtwo, i, res, bit, overflow ){\n powtwo = 1\n overflow = 0\n # 011101 = 1*2^0 + 0*2^1 + 1*2^2 ...\n for( i = length( str_bit ); i > 0; --i ){\n bit = substr( str_bit, i, 1 )\n if( overflow || ( bit == 1 && res > INT_MAX_HALF ) ){\n printerr( \\\n NR \": WARN Bit field overflow, number truncated (LSBs saved, MSBs ignored).\" )\n break\n }\n res = res + bit * powtwo\n # no warning here as it might be the last iteration\n if( powtwo > INT_MAX_HALF ){ overflow = 1; continue }\n powtwo = powtwo * 2\n }\n return res\n}\n\n# CREATE TRIGGER statements have funny commenting. Remember we are in trigger.\n/^\\/\\*.*(CREATE.*TRIGGER|create.*trigger)/ {\n gsub( /^.*(TRIGGER|trigger)/, \"CREATE TRIGGER\" )\n print\n inTrigger = 1\n next\n}\n# The end of CREATE TRIGGER has a stray comment terminator\n/(END|end) \\*\\/;;/ { gsub( /\\*\\//, \"\" ); print; inTrigger = 0; next }\n# The rest of triggers just get passed through\ninTrigger != 0 { print; next }\n\n# CREATE VIEW looks like a TABLE in comments\n/^\\/\\*.*(CREATE.*TABLE|create.*table)/ {\n inView = 1\n next\n}\n# end of CREATE VIEW\n/^(\\).*(ENGINE|engine).*\\*\\/;)/ {\n inView = 0\n next\n}\n# content of CREATE VIEW\ninView != 0 { next }\n\n# skip comments\n/^\\/\\*/ { next }\n\n# print all INSERT lines\n( /^ *\\(/ && /\\) *[,;] *$/ ) || /^(INSERT|insert)/ {\n prev = \"\"\n\n # first replace \\\\ by \\_ that mysqldump never generates to deal with\n # sequnces like \\\\n that should be translated into \\n, not \\.\n # After we convert all escapes we replace \\_ by backslashes.\n gsub( /\\\\\\\\/, \"\\\\_\" )\n\n # single quotes are escaped by another single quote\n gsub( /\\\\'/, \"''\" )\n gsub( /\\\\n/, \"\\n\" )\n gsub( /\\\\r/, \"\\r\" )\n gsub( /\\\\\"/, \"\\\"\" )\n gsub( /\\\\\\032/, \"\\032\" ) # substitute char\n\n gsub( /\\\\_/, \"\\\\\" )\n\n # sqlite3 is limited to 16 significant digits of precision\n while( match( $0, /0x[0-9a-fA-F]{17}/ ) ){\n hexIssue = 1\n sub( /0x[0-9a-fA-F]+/, substr( $0, RSTART, RLENGTH-1 ), $0 )\n }\n if( hexIssue ){\n printerr( \\\n NR \": WARN Hex number trimmed (length longer than 16 chars).\" )\n hexIssue = 0\n }\n print\n next\n}\n\n# CREATE DATABASE is not supported\n/^(CREATE.*DATABASE|create.*database)/ { next }\n\n# print the CREATE line as is and capture the table name\n/^(CREATE|create)/ {\n if( $0 ~ /IF NOT EXISTS|if not exists/ || $0 ~ /TEMPORARY|temporary/ ){\n caseIssue = 1\n printerr( \\\n NR \": WARN Potential case sensitivity issues with table/column naming\\n\" \\\n \" (see INFO at the end).\" )\n }\n if( match( $0, /`[^`]+/ ) ){\n tableName = substr( $0, RSTART+1, RLENGTH-1 )\n }\n aInc = 0\n prev = \"\"\n firstInTable = 1\n print\n next\n}\n\n# Replace `FULLTEXT KEY` (probably other `XXXXX KEY`)\n/^ (FULLTEXT KEY|fulltext key)/ { gsub( /.+(KEY|key)/, \" KEY\" ) }\n\n# Get rid of field lengths in KEY lines\n/ (PRIMARY |primary )?(KEY|key)/ { gsub( /\\([0-9]+\\)/, \"\" ) }\n\naInc == 1 && /PRIMARY KEY|primary key/ { next }\n\n# Replace COLLATE xxx_xxxx_xx statements with COLLATE BINARY\n/ (COLLATE|collate) [a-z0-9_]*/ { gsub( /(COLLATE|collate) [a-z0-9_]*/, \"COLLATE BINARY\" ) }\n\n# Print all fields definition lines except the `KEY` lines.\n/^ / && !/^( (KEY|key)|\\);)/ {\n if( match( $0, /[^\"`]AUTO_INCREMENT|auto_increment[^\"`]/) ){\n aInc = 1\n gsub( /AUTO_INCREMENT|auto_increment/, \"PRIMARY KEY AUTOINCREMENT\" )\n }\n gsub( /(UNIQUE KEY|unique key) (`.*`|\".*\") /, \"UNIQUE \" )\n gsub( /(CHARACTER SET|character set) [^ ]+[ ,]/, \"\" )\n # FIXME\n # CREATE TRIGGER [UpdateLastTime]\n # AFTER UPDATE\n # ON Package\n # FOR EACH ROW\n # BEGIN\n # UPDATE Package SET LastUpdate = CURRENT_TIMESTAMP WHERE ActionId = old.ActionId;\n # END\n gsub( /ON UPDATE CURRENT_TIMESTAMP|on update current_timestamp/, \"\" )\n gsub( /(COLLATE|collate) [^ ]+ /, \"\" )\n gsub( /(ENUM|enum)[^)]+\\)/, \"text \" )\n gsub( /(SET|set)\\([^)]+\\)/, \"text \" )\n gsub( /UNSIGNED|unsigned/, \"\" )\n gsub( /` [^ ]*(INT|int|BIT|bit)[^ ]*/, \"` integer\" )\n gsub( /\" [^ ]*(INT|int|BIT|bit)[^ ]*/, \"\\\" integer\" )\n ere_bit_field = \"[bB]'[10]+'\"\n if( match($0, ere_bit_field) ){\n sub( ere_bit_field, bit_to_int( substr( $0, RSTART +2, RLENGTH -2 -1 ) ) )\n }\n # field comments are not supported\n gsub( / (COMMENT|comment).+$/, \"\" )\n # Get commas off end of line\n gsub( /,.?$/, \"\" )\n if( prev ){\n if( firstInTable ){\n print prev\n firstInTable = 0\n }\n else {\n print \",\" prev\n }\n }\n else {\n # FIXME check if this is correct in all cases\n if( match( $1,\n /(CONSTRAINT|constraint) \\\".*\\\" (FOREIGN KEY|foreign key)/ ) ){\n print \",\"\n }\n }\n prev = $1\n}\n\n/ ENGINE| engine/ {\n if( prev ){\n if( firstInTable ){\n print prev\n firstInTable = 0\n }\n else {\n print \",\" prev\n }\n }\n prev=\"\"\n print \");\"\n next\n}\n# `KEY` lines are extracted from the `CREATE` block and stored in array for later print\n# in a separate `CREATE KEY` command. The index name is prefixed by the table name to\n# avoid a sqlite error for duplicate index name.\n/^( (KEY|key)|\\);)/ {\n if( prev ){\n if( firstInTable ){\n print prev\n firstInTable = 0\n }\n else {\n print \",\" prev\n }\n }\n prev = \"\"\n if( $0 == \");\" ){\n print\n }\n else {\n if( match( $0, /`[^`]+/ ) ){\n indexName = substr( $0, RSTART+1, RLENGTH-1 )\n }\n if( match( $0, /\\([^()]+/ ) ){\n indexKey = substr( $0, RSTART+1, RLENGTH-1 )\n }\n # idx_ prefix to avoid name clashes (they really happen!)\n key[tableName] = key[tableName] \"CREATE INDEX \\\"idx_\" \\\n tableName \"_\" indexName \"\\\" ON \\\"\" tableName \"\\\" (\" indexKey \");\\n\"\n }\n}\n\nEND {\n if( no_END ){ exit 1}\n # print all KEY creation lines.\n for( table in key ){ printf key[table] }\n\n print \"END TRANSACTION;\"\n\n if( caseIssue ){\n printerr( \\\n \"INFO Pure sqlite identifiers are case insensitive (even if quoted\\n\" \\\n \" or if ASCII) and doesnt cross-check TABLE and TEMPORARY TABLE\\n\" \\\n \" identifiers. Thus expect errors like \\\"table T has no column named F\\\".\")\n }\n}\n" }, { "path": "attic/pharos/mysql2sqlite/mysql2sqlite.README", "content": "# mysql2sqlite\n\nConverts MySQL dump to SQLite3 compatible dump (including MySQL `KEY xxxxx` statements from the `CREATE` block).\n\n## Usage\n\n1. Dump MySQL DB\n\n ~~~~\n mysqldump --skip-extended-insert --compact [options]... DB_name > dump_mysql.sql\n # or\n #mysqldump --no-data -u root -pmyPassword [options]... DB_name > dump_mysql.sql\n ~~~~\n\n1. Convert the dump to SQLite3 DB\n\n ~~~~\n ./mysql2sqlite dump_mysql.sql | sqlite3 mysqlite3.db\n ~~~~\n\n## Development\n\nThe script is written in *awk* (tested with gawk, but should work with original awk, and the lightning fast mawk) and shall be fully POSIX compliant.\n\nIt's originally based on the newest fork (https://gist.github.com/bign8/9055981/05e65fd90c469c5eaa730823910c0c5f9de40ab4) of the original `mysql2sqlite.sh` (https://gist.github.com/esperlu/943776/be469f0a0ab8962350f3c5ebe8459218b915f817) with the following patches:\n\n* fix the non-standard `COMMENT` field statement removal\n* ignore `CREATE DATABASE` statements (`USE` statements were already ignored)\n* add support for multiple-record `INSERT INTO VALUES`\n* revise support for lower-case SQL statements\n* fix `AUTO_INCREMENT` handling\n* trim hexadecimal values longer than 16 characters and issue a warning about it\n* add identifier case sensitivity warning in case `IF NOT EXISTS` or `TEMPORARY` has been detected (on unix sqlite3 treats temporary table name `FILES` the same as `files`; in other words, sqlite3 doesn't issue any warning about cross-collisions between `TABLE` and `TEMPORARY TABLE` identifiers)\n* replace `COLLATE xxx_xxxx_xx` statements with `COLLATE BINARY` (https://gist.github.com/4levels/0d5da65bf9d70479fbe3/d0ac3d295dc5e2f72411ad06c07a22931368a1b7)\n* handle `CONSTRAINT FOREIGN KEY` (https://gist.github.com/BastienDurel/7f413d13d7b858aef31c/922be110d011b9da340ae545372214b597ad7b84)\n\nFeel free to **contribute** (preferably by issuing a pull request)!\n\n## License\n\nMIT\n\n## History\n\n* @esperlu created initial version in 2011 as gist on GitHub\n* many different contributors forked the gist and made wildly varying changes, because @esperlu stopped working on it and didn't respond\n* @dumblob took over in Aug 2015 and applied the most important patches from all the forks as well as many his own patches tested on Drupal DB\n* @dumblob added the MIT license under assumption, that the original gist was released into public domain, because despite significant changes, it wasn't clean room engineering.\n* 2016-05-11 17:32 UTC+2 [@esperlu declared](https://github.com/dumblob/mysql2sqlite/issues/2 ) MIT as a fitting license (also retrospectively) and the [original gist](https://gist.github.com/esperlu/943776 ) as deprecated.\n" }, { "path": "attic/pharos/mysql2sqlite/unit_tests.sh", "content": "#/bin/sh\n\nM2S=./mysql2sqlite\nS=sqlite3\n\ntype \"$S\" >/dev/null 2>&1 || {\n printf 'ERR command \"%s\" not available\\n' \"$S\" >&2\n exit 1\n}\n\n[ -r \"$M2S\" ] || {\n printf 'ERR file \"%s\" not found\\n' \"$M2S\" >&2\n exit 1\n}\n\n# FIXME\nprintf 'ERR Unit testing not yet fully implemented\\n' >&2\nexit 1\n\n# Hex numbers with 15, 16, and 17 characters\n\ncat <<\\SQL\nINSERT INTO `cache` (`cid`, `data`, `expire`, `created`, `headers`, `serialized`) VALUES\n('ctools_plugin_files:ctools:style_bases', 0x613a313a7b733a3, 0, 1440573529, '', 1),\n('ctools_plugin_files:ctools:content_types', 0xa343a226e6f64652, 0, 1440573529, '', 1);\nINSERT INTO `cache` (`cid`, `data`, `expire`, `created`, `headers`, `serialized`) VALUES\n('theme_registry:my_theme', 0x613a3234353a7b733, 0, 1440572933, '', 1);\nSQL\n\n# WARN Potential case sensitivity issues... for each line\n\n# Bit Fields\n\ncat <<\\SQL\nCREATE TABLE \"bit_type\" (\n \"a\" int(10) unsigned NOT NULL AUTO_INCREMENT,\n \"b\" bit(1) NOT NULL DEFAULT b'1',\n \"c\" bit(8) NOT NULL DEFAULT B'11111111',\n \"d\" BIT(4) NOT NULL DEFAULT b'1010',\n \"e\" BIT(4) NOT NULL DEFAULT B'00111111110000111',\n \"f\" int(10) unsigned NOT NULL AUTO_INCREMENT,\n);\nSQL\n\n# big bit field num\n# big bit field num with overflow\n# big bit field num with potential overflow, but zeros\n\ncat <<\\SQL\nCREATE TABLE \"map\" (\n \"ID\" int(10) NOT NULL,\n \"f\" int(11) NOT NULL,\n \"direct\" bit(1) NOT NULL DEFAULT 1,\n \"t\" int(11) NOT NULL\n);\ninsert into \"map\" (\"ID\", \"f\", \"t\") values (5, 6, 7);\ninsert into \"map\" (\"ID\", \"f\", \"direct\", \"t\") values (55, 66, 99, 77);\nSQL\n\ncat <<\\SQL\nCREATE TABLE \"map\" (\n \"ID\" int(10) NOT NULL,\n \"f\" int(11) NOT NULL,\n \"direct\" bit(1) NOT NULL DEFAULT 199,\n \"t\" int(11) NOT NULL\n);\ninsert into \"map\" (\"ID\", \"f\", \"t\") values (5, 6, 7);\ninsert into \"map\" (\"ID\", \"f\", \"direct\", \"t\") values (55, 66, 99, 77);\nSQL\n\ncat <<\\SQL\nDROP TABLE IF EXISTS `AAAA`;\n/*!40101 SET @saved_cs_client = @@character_set_client */;\n/*!40101 SET character_set_client = utf8 */;\nCREATE TABLE `AAAA` (\n `id` bigint(10) NOT NULL AUTO_INCREMENT COMMENT 'PK.',\n `llll` varchar(10) NOT NULL COMMENT 'Some Comment',\n `rrrr` timestamp NULL DEFAULT CURRENT_TIMESTAMP COMMENT 'Created date',\n `ssss` timestamp NULL DEFAULT NULL ON UPDATE CURRENT_TIMESTAMP COMMENT 'Modified Date. Some Comment',\n `tttt` varchar(1) DEFAULT 'A' COMMENT 'Some Comment',\n PRIMARY KEY (`id`),\n UNIQUE KEY `aaaa_pk` (`id`) COMMENT 'PK Index',\n KEY `bbbb_fk` (`bbbb`) COMMENT 'Index for FK, Reference Category',\n CONSTRAINT `bbbb_fk` FOREIGN KEY (`bbbb`) REFERENCES `category` (`id`)\n) ENGINE=InnoDB DEFAULT CHARSET=utf8;\n/*!40101 SET character_set_client = @saved_cs_client */;\n\n--\n-- Dumping data for table `AAAA`\n--\n\nLOCK TABLES `AAAA` WRITE;\n/*!40000 ALTER TABLE `AAAA` DISABLE KEYS */;\n/*!40000 ALTER TABLE `AAAA` ENABLE KEYS */;\nUNLOCK TABLES;\nSQL\n\ncat <<\\SQL\nSQL\n" }, { "path": "attic/pharos/pharos-mysql-to-sqlite3-to-db", "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\nmysql_dump=\"$1\"\n\nmkdir -p \"$here/data\"\nsqlite_dump=\"$here/data/pharos-sqlite3.sql\"\nsqlite_db=\"$here/data/pharos-sqlite3.db\"\n\n\"$here/mysql2sqlite/mysql2sqlite\" \"$mysql_dump\" > \"$sqlite_dump\"\n\nsqlite3 \"$sqlite_db\" < \"$sqlite_dump\"\n\nrm \"$sqlite_dump\"\n" }, { "path": "attic/pharos/read.rkt", "content": "#lang racket/base\n(provide\n read-all\n read-all/stream\n read-all-from-file\n )\n\n(require\n racket/stream\n )\n\n(define (read-all in)\n (define datum (read in))\n (if (eof-object? datum) '() (cons datum (read-all in))))\n\n(define (read-all/stream in)\n (define datum (read in))\n (if (eof-object? datum) '() (stream-cons datum (read-all/stream in))))\n\n(define (read-all-from-file path)\n (call-with-input-file (expand-user-path path) read-all))\n" }, { "path": "attic/pharos/repr.rkt", "content": "#lang racket\n(provide\n integer->repr\n repr->integer\n decimal->repr\n repr->decimal\n string->repr\n repr->string\n data->repr\n repr->data\n write-repr\n\n detail-find\n detail-next\n detail-write\n )\n\n(define (integer->repr i) i)\n(define (repr->integer i) i)\n(define (decimal->repr d) d)\n(define (repr->decimal d) d)\n(define (string->repr str) str)\n(define (repr->string str) str)\n(define (data->repr d) (list->vector d))\n(define (repr->data v) (vector->list v))\n(define (write-repr repr out) (fprintf out \"~s\\n\" repr))\n\n;(define (integer->enc i) (integer->integer-bytes (or i 0) 4 #t #f))\n;(define (enc->integer bs) (integer-bytes->integer bs #t #f 0 4))\n;(define (decimal->enc d) (real->floating-point-bytes (or d 0.0) 4 #f))\n;(define (enc->decimal bs) (floating-point-bytes->real bs #f 0 4))\n;(define (string->enc str)\n ;(define bs (string->bytes/utf-8 str))\n ;(bytes-append (integer->integer-bytes (bytes-length bs) 2 #f #f) bs))\n;(define (enc->string bs)\n ;(define len (integer-bytes->integer bs #f #f 0 2))\n ;(bytes->string/utf-8 bs #f 2 (+ 2 len)))\n;(define (data->enc d) (bytes-append* d))\n;(define (enc->data bs) bs)\n;(define (write-repr repr out) (write-bytes repr out))\n\n(define offset-size 8)\n(define (offset->repr o) (integer->integer-bytes o offset-size #f #f))\n(define (offset-write out offset) (write-bytes (offset->repr offset) out))\n(define (offset-count in)\n (file-position in eof)\n (/ (file-position in) offset-size))\n(define (offset-ref in n)\n (file-position in (* n offset-size))\n (integer-bytes->integer (read-bytes offset-size in) #f #f 0 offset-size))\n\n(define (detail-write detail-out offset-out detail)\n (offset-write offset-out (file-position detail-out))\n (write-repr detail detail-out))\n(define (detail-ref detail-in offset-in n)\n (file-position detail-in (offset-ref offset-in n))\n (read detail-in))\n(define (detail-next detail-in) (read detail-in))\n\n(define (detail-find detail-in offset-in compare)\n (let loop ((start 0) (end (offset-count offset-in)) (best #f))\n (cond ((< start end)\n (define n (+ start (quotient (- end start) 2)))\n (define detail (detail-ref detail-in offset-in n))\n (case (compare detail)\n ((-1) (loop (+ 1 n) end best))\n ((0) (loop start n n))\n ((1) (loop start n best))))\n (best (detail-ref detail-in offset-in best))\n (else eof))))\n" }, { "path": "attic/pharos/sql-schema-parse.rkt", "content": "#lang racket/base\n(require\n \"mk.rkt\"\n \"mk-parse.rkt\"\n )\n\n;; Parse SQL schema\n(define delimiters '(\",\" \")\") )\n(define delimiter (one-of delimiters))\n\n(define (sq name) (seq \"\\'\" (single name) \"\\'\"))\n(define (dq name) (seq \"\\\"\" (single name) \"\\\"\"))\n(define (bq name) (seq \"`\" (single name) \"`\"))\n\n(define (paren p items)\n (define (comma-prefixed item) (seq \",\" (p item)))\n (fresh/p (first rest)\n (== `(,first . ,rest) items)\n (seq \"(\" (p first) ((many* comma-prefixed) rest) \")\")))\n\n(define (field-type type)\n (or/p ((remember1 (one-of '(\"integer\" \"text\" \"timestamp\" \"date\"))) type)\n (fresh/p (m n)\n (== \"decimal\" type)\n (seq \"decimal\" \"(\" (single m) \",\" (single n) \")\"))\n (fresh/p (_)\n (== \"text\" type)\n (seq \"varchar\" \"(\" (single _) \")\"))\n (fresh/p (_)\n (== \"text\" type)\n (seq \"char\" \"(\" (single _) \")\"))))\n\n(define (field/primary-key name type)\n (seq (bq name) (field-type type)\n (skip*-until (append '(\"PRIMARY\") delimiters))\n \"PRIMARY\" \"KEY\" (skip*-until delimiters)))\n\n(define (field/non-primary-key name type)\n (seq (bq name) (field-type type)\n (skip* (none-of (append '(\"PRIMARY\" \"KEY\") delimiters)))\n (peek delimiter)))\n\n(define (primary-key names)\n (seq \"PRIMARY\" \"KEY\" (paren bq names) (peek delimiter)))\n\n(define (unique names) (seq \"UNIQUE\" (paren bq names) (peek delimiter)))\n\n(define (foreign-key fk-name local-names table foreign-names)\n (seq \"CONSTRAINT\" (bq fk-name) \"FOREIGN\" \"KEY\" (paren bq local-names)\n \"REFERENCES\" (bq table) (paren bq foreign-names)\n (skip*-until delimiters)))\n\n(define (create-table table-name body*)\n (define (field-or-cx datum)\n (or/p (fresh/p (name type)\n (== `(field primary-key ,name ,type) datum)\n (field/primary-key name type))\n (fresh/p (name type)\n (== `(field #f ,name ,type) datum)\n (field/non-primary-key name type))\n (fresh/p (names)\n (== `(primary-key ,names) datum)\n (primary-key names))\n (fresh/p (names)\n (== `(unique ,names) datum)\n (unique names))\n (fresh/p (fk-name locals table foreigns)\n (== `(foreign-key ,fk-name ,locals ,table ,foreigns) datum)\n (foreign-key fk-name locals table foreigns))))\n (seq \"CREATE\" \"TABLE\" (bq table-name) (paren field-or-cx body*) \";\"))\n\n(define (create-index index-name table-name field-names)\n (seq \"CREATE\" \"INDEX\" (dq index-name) \"ON\"\n (dq table-name) (paren bq field-names) \";\"))\n\n(define (schema body*)\n (define (table-or-index datum)\n (or/p (fresh/p (name tbody)\n (== `(table ,name ,tbody) datum)\n (create-table name tbody))\n (fresh/p (name tname fnames)\n (== `(index ,name ,tname ,fnames) datum)\n (create-index name tname fnames))))\n (seq ((many* table-or-index) body*) end))\n\n(define (entries->schema entry*)\n (define (entry->table entry)\n (define name (cadr entry))\n (let loop ((field* '()) (unique* '()) (foreign* '()) (attr* (caddr entry)))\n (if (null? attr*)\n `(,name (field . ,(reverse field*))\n (unique . ,(reverse unique*))\n (foreign . ,(reverse foreign*)))\n (let* ((attr (car attr*)) (tag (car attr)) (attr* (cdr attr*)))\n (cond ((eqv? 'field tag)\n (define primary? (cadr attr))\n (define name (caddr attr))\n (define type (cadddr attr))\n (define field `(,name ,type))\n (loop (cons field field*)\n (if primary? (cons (list name) unique*) unique*)\n foreign* attr*))\n ((or (eqv? 'unique tag) (eqv? 'primary-key tag))\n (define names (cadr attr))\n (loop field* (cons names unique*) foreign* attr*))\n ((eqv? 'foreign-key tag)\n (define name (cadr attr))\n (define local (caddr attr))\n (define table (cadddr attr))\n (define remote (cadddr (cdr attr)))\n (define foreign `(,name ,local ,table ,remote))\n (loop field* unique* (cons foreign foreign*) attr*))\n (else (error \"invalid attribute:\" attr)))))))\n (define (entry->index entry)\n (define name (cadr entry))\n (define table (caddr entry))\n (define fields (cadddr entry))\n `(,name ,table ,fields))\n (let loop ((table* '()) (index* '()) (entry* entry*))\n (if (null? entry*) `((tables . ,(reverse table*))\n (indexes . ,(reverse index*)))\n (let ((entry (car entry*)) (entry* (cdr entry*)))\n (cond ((eqv? 'table (car entry))\n (loop (cons (entry->table entry) table*) index* entry*))\n ((eqv? 'index (car entry))\n (loop table* (cons (entry->index entry) index*) entry*))\n (else (error \"invalid schema entry:\" entry)))))))\n\n(define (tokens->entries tokens)\n (define results (run* (body*) ((schema body*) tokens '())))\n (when (= 0 (length results)) (error \"failed to parse\"))\n (when (< 1 (length results))\n (error \"ambiguous parse: count=\" (length results)))\n (car results))\n\n(write (entries->schema (tokens->entries (read))))\n" }, { "path": "attic/pharos/sql-tokenize.rkt", "content": "#lang racket/base\n(require\n \"mk.rkt\"\n \"mk-parse.rkt\"\n racket/port\n )\n\n;; Tokenization\n(define chars-ws '(#\\space #\\tab #\\newline #\\return #\\vtab #\\page))\n(define chars-hws '(#\\space #\\tab))\n\n(define chars-quote '(#\\' #\\\" #\\`))\n(define chars-bracket '(#\\( #\\) #\\[ #\\] #\\{ #\\}))\n(define chars-separator '(#\\, #\\; #\\: #\\.))\n(define chars-symbolic (append chars-quote chars-bracket chars-separator))\n\n(define skip-ws (skip*-while chars-ws))\n(define skip-hws (skip*-while chars-hws))\n\n(define (token* ts)\n (define chars-ws&symbolic (append chars-symbolic chars-ws))\n (define (token t)\n (seq skip-ws\n (or/p (fresh/p (c)\n (== (list c) t)\n ((remember1 (one-of chars-symbolic)) c))\n ((many+-until chars-ws&symbolic) t))))\n (seq ((many* token) ts) skip-ws end))\n\n(define (tokenize str)\n (define results (run* (ts) ((token* ts) (string->list str) '())))\n (when (= 0 (length results)) (error \"failed to tokenize\"))\n (when (< 1 (length results))\n (error \"ambiguous tokenization: count=\" (length results)))\n (map list->string (car results)))\n\n(write (tokenize (port->string)))\n\n;; First attempt at token*, factoring out split-ws*. It's a lot more involved.\n;(define (split-ws* blocks)\n ;(define (non-ws* block)\n ;(seq skip-ws\n ;((many+ (remember1 (none-of chars-ws))) block)\n ;(or/p end (peek (one-of chars-ws)))))\n ;(seq ((many* non-ws*) blocks) skip-ws end))\n\n;(define (split-symbolic* bs)\n ;(define (block s)\n ;(or/p (lambda (in out)\n ;(fresh (c)\n ;(== (list c) s)\n ;(((remember1 (one-of chars-symbolic)) c) in out)))\n ;((many+-until chars-symbolic) s)))\n ;(seq ((many* block) bs) end))\n\n;(define (appendo l s ls)\n ;(conde\n ;((== '() l) (== s ls))\n ;((fresh (a d ms)\n ;(== `(,a . ,d) l)\n ;(== `(,a . ,ms) ls)\n ;(appendo d s ms)))))\n\n;(define (flatteno xss flattened)\n ;(conde\n ;((== '() xss) (== '() flattened))\n ;((fresh (xs yss yflattened)\n ;(== `(,xs . ,yss) xss)\n ;(flatteno yss yflattened)\n ;(appendo xs yflattened flattened)))))\n\n;(define (mapo R xs zs)\n ;(conde\n ;((== '() xs) (== '() zs))\n ;((fresh (a d y ys)\n ;(== `(,a . ,d) xs)\n ;(== `(,y . ,ys) zs)\n ;(R a y)\n ;(mapo R d ys)))))\n\n;(define (token* ts)\n ;(define (parse in bs) ((split-symbolic* bs) in '()))\n ;(lambda (in out)\n ;(fresh (bs tss)\n ;((split-ws* bs) in out)\n ;(mapo parse bs tss)\n ;(flatteno tss ts))))\n" }, { "path": "attic/pharos/sqlite-to-db.rkt", "content": "#lang racket/base\n(require\n \"csv.rkt\"\n \"repr.rkt\"\n racket/file\n racket/list\n racket/set\n racket/string\n racket/system\n )\n\n(define set-empty (set))\n(define hash-empty (hash))\n\n(define (subsumed? rs s) (ormap (lambda (r) (subset? r s)) rs))\n(define (unique-add/subsume unique uniques)\n (define us (set->list uniques))\n (if (subsumed? us unique) uniques\n (set-add (list->set (filter (lambda (u) (not (subset? unique u))) us))\n unique)))\n\n(define (schema-table->table t)\n (define name (car t))\n (define fields (cdr (assoc 'field (cdr t))))\n (define foreigns (map cdr (cdr (assoc 'foreign (cdr t)))))\n (define raw-uniques (map list->set (cdr (assoc 'unique (cdr t)))))\n (define uniques (list->set (foldl unique-add/subsume '() raw-uniques)))\n (table-new name fields foreigns uniques set-empty))\n\n(define (table-new name fields foreigns uniques sortings)\n `(,name ,fields ,foreigns ,uniques ,sortings))\n(define (table-name t) (car t))\n(define (table-fields t) (cadr t))\n(define (table-foreigns t) (caddr t))\n(define (table-uniques t) (cadddr t))\n(define (table-sortings t) (cadddr (cdr t)))\n(define (table-uniques-add t unique)\n (if (set-member? (table-uniques t) unique) t\n (table-new (table-name t) (table-fields t) (table-foreigns t)\n (unique-add/subsume unique (table-uniques t))\n (set-remove (table-sortings t) unique))))\n(define (table-sortings-add t sorting)\n (if (or (set-member? (table-sortings t) sorting)\n (set-member? (table-uniques t) (list->set sorting))) t\n (table-new (table-name t) (table-fields t) (table-foreigns t)\n (table-uniques t) (set-add (table-sortings t) sorting))))\n\n(define (schema->tables schema)\n (define tables (cdr (assoc 'tables schema)))\n (define indexes (cdr (assoc 'indexes schema)))\n (define name=>table\n (foldl (lambda (s name=>table)\n (define t (schema-table->table s))\n (hash-set name=>table (table-name t) t))\n hash-empty tables))\n (foldl (lambda (index name=>table)\n (define tname (cadr index))\n (define tfields (caddr index))\n (define table (hash-ref name=>table tname))\n (hash-set name=>table tname (table-sortings-add table tfields)))\n name=>table indexes))\n\n(define (table->dump* t)\n (define field-names (map car (table-fields t)))\n (define (select ordering)\n (string-join (list \"SELECT\" (string-join field-names \",\")\n \"FROM\" (table-name t)\n ordering) \" \"))\n (define (sorting->ordering sorting)\n (string-append\n \"ORDER BY \"\n (string-join (map (lambda (col) (string-join (list col \"ASC\") \" \"))\n sorting)\n \", \")))\n (define sortings (append (map set->list (set->list (table-uniques t)))\n (set->list (table-sortings t))))\n (define orderings (map sorting->ordering sortings))\n (map list\n (if (null? sortings) (list #f) sortings)\n (map select (if (null? orderings) (list \"\") orderings))))\n\n(define (string->datum type str)\n (cond ((string=? \"integer\" type) (integer->repr (string->number str)))\n ((string=? \"decimal\" type) (decimal->repr (string->number str)))\n ;; \"text\" \"timestamp\" \"date\"\n (else (string->repr str))))\n\n(define (csv->scm table-name field-types detail-out offset-out)\n (lambda (in)\n (define (record->datum record)\n (when (not (= (length field-types) (length record)))\n (printf \"~s\\n\" `(record->datum\n ,table-name ,(length field-types) ,(length record)\n ,field-types ,record)))\n (data->repr (map string->datum field-types record)))\n (define (yield-record! record)\n (detail-write detail-out offset-out (record->datum record)))\n ((csv-records yield-record!) in)\n (flush-output detail-out)\n (flush-output offset-out)))\n\n(define (run-sql consume sql)\n (define proc\n (process\n (string-append\n \"sqlite3 -bail -csv \" (path->string sqlite-db-path) \" '\" sql \"'\")))\n (define pout (car proc))\n (define pin (cadr proc))\n (define perr (cadddr proc))\n (close-output-port pin)\n (consume pout)\n (close-input-port pout)\n (close-input-port perr))\n\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(SCHEMA_FILE DATA_DIR))\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n (error (format \"cmd-line-args expected ~s; given ~s\" argv-expected argv)))\n\n(define schema-path (expand-user-path (vector-ref argv 0)))\n(define data-dir (expand-user-path (vector-ref argv 1)))\n(define sqlite-db-path (build-path data-dir \"pharos-sqlite3.db\"))\n(define db-dir (build-path data-dir \"db\"))\n(define tables-dir (build-path db-dir \"tables\"))\n\n(define name=>table-info\n (make-immutable-hash\n (map (lambda (t) (cons (table-name t) (list t (table->dump* t))))\n (hash-values\n (schema->tables (call-with-input-file schema-path read))))))\n\n(for (((name tinfo) (in-hash name=>table-info)))\n (define t (car tinfo))\n (define field-types (map cadr (table-fields t)))\n (define indexes (cadr tinfo))\n (define tpath (build-path tables-dir name))\n (define cpath (build-path tpath \"columns.scm\"))\n (define ipath (build-path tpath \"indexes.scm\"))\n (define fkpath (build-path tpath \"foreign-keys.scm\"))\n (make-directory* (expand-user-path tpath))\n (call-with-output-file cpath (lambda (out) (write (table-fields t) out)))\n (call-with-output-file\n ipath (lambda (out) (write (map car indexes) out)))\n (call-with-output-file\n fkpath (lambda (out) (write (table-foreigns t) out)))\n (for ((ix indexes) (i (range (length indexes))))\n (define sorting-dir (build-path tpath (number->string i)))\n (define detail-path (build-path sorting-dir \"detail.scm\"))\n (define offset-path (build-path sorting-dir \"offset.bin\"))\n (make-directory* (expand-user-path sorting-dir))\n (call-with-output-file\n detail-path\n (lambda (detail-out)\n (call-with-output-file\n offset-path\n (lambda (offset-out)\n (run-sql (csv->scm name field-types detail-out offset-out)\n (cadr ix))))))))\n" }, { "path": "attic/yaml/biolink-model.scm", "content": "(define biolink-model\n'(\n (\n \"id\"\n . \"https://w3id.org/biolink/biolink-model\"\n )\n (\n \"name\"\n . \"biolink_model\"\n )\n (\n \"description\"\n . \"Entity and association taxonomy and datamodel for life-sciences data\"\n )\n (\n \"license\"\n . \"https://creativecommons.org/publicdomain/zero/1.0/\"\n )\n (\n \"prefixes\"\n (\n \"biolink\"\n . \"https://w3id.org/biolink/vocab/\"\n )\n (\n \"biolinkml\"\n . \"https://w3id.org/biolink/biolinkml/\"\n )\n (\n \"OBAN\"\n . \"http://purl.org/oban/\"\n )\n (\n \"SIO\"\n . \"http://semanticscience.org/resource/SIO_\"\n )\n (\n \"wgs\"\n . \"http://www.w3.org/2003/01/geo/wgs84_pos\"\n )\n (\n \"UMLSSG\"\n . \"https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/GROUP/\"\n )\n (\n \"UMLSST\"\n . \"https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/STY/\"\n )\n (\n \"UMLSSC\"\n . \"https://uts-ws.nlm.nih.gov/rest/semantic-network/semantic-network/current/TUI/\"\n )\n )\n (\n \"default_prefix\"\n . \"biolink\"\n )\n (\n \"default_range\"\n . \"string\"\n )\n (\n \"default_curi_maps\"\n \"obo_context\"\n \"monarch_context\"\n \"idot_context\"\n \"semweb_context\"\n )\n (\n \"emit_prefixes\"\n \"rdf\"\n \"rdfs\"\n \"xsd\"\n \"skos\"\n \"OIO\"\n \"BIOGRID\"\n )\n (\n \"subsets\"\n (\n \"translator_minimal\"\n (\n \"description\"\n . \"Minimum subset of translator work\"\n )\n )\n (\n \"testing\"\n (\n \"description\"\n . \"(tbd)\"\n )\n )\n )\n (\n \"imports\"\n \"biolinkml:types\"\n )\n (\n \"types\"\n (\n \"chemical formula value\"\n (\n \"uri\"\n . \"xsd:string\"\n )\n (\n \"base\"\n . \"str\"\n )\n (\n \"description\"\n . \"A chemical formula\"\n )\n (\n \"notes\"\n \"Should be implemented as a stronger type\"\n )\n )\n (\n \"identifier type\"\n (\n \"base\"\n . \"ElementIdentifier\"\n )\n (\n \"uri\"\n . \"xsd:anyURI\"\n )\n (\n \"description\"\n . \"A string that is intended to uniquely identify a thing May be URI in full or compact (CURIE) form\"\n )\n )\n (\n \"iri type\"\n (\n \"typeof\"\n . \"uriorcurie\"\n )\n (\n \"description\"\n . \"An IRI\"\n )\n )\n (\n \"label type\"\n (\n \"typeof\"\n . \"string\"\n )\n (\n \"description\"\n . \"A string that provides a human-readable name for a thing\"\n )\n )\n (\n \"narrative text\"\n (\n \"typeof\"\n . \"string\"\n )\n (\n \"description\"\n . \"A string that provides a human-readable description of something\"\n )\n )\n (\n \"symbol type\"\n (\n \"typeof\"\n . \"string\"\n )\n )\n (\n \"frequency\"\n (\n \"typeof\"\n . \"string\"\n )\n (\n \"uri\"\n . \"UO:0000105\"\n )\n )\n (\n \"perecentage frequency value\"\n (\n \"typeof\"\n . \"double\"\n )\n (\n \"uri\"\n . \"UO:0000187\"\n )\n )\n (\n \"quotient\"\n (\n \"aliases\"\n \"ratio\"\n )\n (\n \"typeof\"\n . \"double\"\n )\n (\n \"uri\"\n . \"UO:0010006\"\n )\n )\n (\n \"unit\"\n (\n \"typeof\"\n . \"string\"\n )\n (\n \"uri\"\n . \"UO:0000000\"\n )\n (\n \"id_prefixes\"\n \"UO\"\n )\n )\n (\n \"time type\"\n (\n \"typeof\"\n . \"time\"\n )\n )\n (\n \"biological sequence\"\n (\n \"typeof\"\n . \"string\"\n )\n )\n )\n (\n \"slots\"\n (\n \"related to\"\n (\n \"description\"\n . \"A relationship that is asserted between two named things\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"named thing\"\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"slot_uri\"\n . \"owl:ObjectProperty\"\n )\n (\n \"inherited\"\n . #t\n )\n (\n \"mappings\"\n \"SEMMEDDB:ASSOCIATED_WITH\"\n )\n )\n (\n \"interacts with\"\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"holds between any two entities that directly or indirectly interact with each other\"\n )\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002434\"\n )\n )\n (\n \"physically interacts with\"\n (\n \"is_a\"\n . \"interacts with\"\n )\n (\n \"description\"\n . \"holds between two entities that make physical contact as part of some interaction\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"symmetric\"\n . #t\n )\n (\n \"slot_uri\"\n . \"WD:P129\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:INTERACTS_WITH\"\n )\n )\n (\n \"molecularly interacts with\"\n (\n \"is_a\"\n . \"physically interacts with\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002436\"\n )\n )\n (\n \"genetically interacts with\"\n (\n \"is_a\"\n . \"interacts with\"\n )\n (\n \"description\"\n . \"holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.\"\n )\n (\n \"domain\"\n . \"gene\"\n )\n (\n \"range\"\n . \"gene\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002435\"\n )\n )\n (\n \"affects\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"describes an entity that has a direct affect on the state or quality of another existing entity. Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"SEMMEDDB:AFFECTS\"\n )\n )\n (\n \"affects abundance of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one changes the amount of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases abundance of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the amount of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects abundance of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases abundance of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects abundance of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects activity of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases activity of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects activity of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases activity of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects activity of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects expression of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"increases expression of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects expression of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"decreases expression of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects expression of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"affects folding of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases folding of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other\"\n )\n (\n \"is_a\"\n . \"affects folding of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases folding of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other\"\n )\n (\n \"is_a\"\n . \"affects folding of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects localization of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases localization of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects localization of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases localization of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects localization of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects metabolic processing of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases metabolic processing of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects metabolic processing of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases metabolic processing of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects metabolic processing of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects molecular modification of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases molecular modification of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\"\n )\n (\n \"is_a\"\n . \"affects molecular modification of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases molecular modification of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\"\n )\n (\n \"is_a\"\n . \"affects molecular modification of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects synthesis of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases synthesis of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other\"\n )\n (\n \"is_a\"\n . \"affects synthesis of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases synthesis of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other\"\n )\n (\n \"is_a\"\n . \"affects synthesis of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects degradation of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases degradation of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects degradation of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases degradation of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects degradation of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects mutation rate of\"\n (\n \"description\"\n . \"holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"increases mutation rate of\"\n (\n \"description\"\n . \"holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects mutation rate of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"decreases mutation rate of\"\n (\n \"description\"\n . \"holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects mutation rate of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"affects response to\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases response to\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other\"\n )\n (\n \"is_a\"\n . \"affects response to\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases response to\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other\"\n )\n (\n \"is_a\"\n . \"affects response to\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects splicing of\"\n (\n \"description\"\n . \"holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"transcript\"\n )\n )\n (\n \"increases splicing of\"\n (\n \"description\"\n . \"holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA\"\n )\n (\n \"is_a\"\n . \"affects splicing of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"transcript\"\n )\n )\n (\n \"decreases splicing of\"\n (\n \"description\"\n . \"holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA\"\n )\n (\n \"is_a\"\n . \"affects splicing of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"transcript\"\n )\n )\n (\n \"affects stability of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases stability of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects stability of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases stability of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest\"\n )\n (\n \"is_a\"\n . \"affects stability of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects transport of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases transport of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest\"\n )\n (\n \"is_a\"\n . \"affects transport of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases transport of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest\"\n )\n (\n \"is_a\"\n . \"affects transport of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects secretion of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases secretion of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ\"\n )\n (\n \"is_a\"\n . \"affects secretion of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases secretion of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ\"\n )\n (\n \"is_a\"\n . \"affects secretion of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"affects uptake of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"increases uptake of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ\"\n )\n (\n \"is_a\"\n . \"affects uptake of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"decreases uptake of\"\n (\n \"description\"\n . \"holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ\"\n )\n (\n \"is_a\"\n . \"affects uptake of\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"regulates\"\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"comments\"\n \"This is a grouping for process-process and entity-entity relations\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"slot_uri\"\n . \"WD:P128\"\n )\n )\n (\n \"positively regulates\"\n (\n \"comments\"\n \"This is a grouping for process-process and entity-entity relations\"\n )\n (\n \"is_a\"\n . \"regulates\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"abstract\"\n . #t\n )\n )\n (\n \"negatively regulates\"\n (\n \"comments\"\n \"This is a grouping for process-process and entity-entity relations\"\n )\n (\n \"is_a\"\n . \"regulates\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"abstract\"\n . #t\n )\n )\n (\n \"regulates, process to process\"\n (\n \"is_a\"\n . \"regulates\"\n )\n (\n \"domain\"\n . \"occurrent\"\n )\n (\n \"range\"\n . \"occurrent\"\n )\n (\n \"slot_uri\"\n . \"RO:0002211\"\n )\n )\n (\n \"positively regulates, process to process\"\n (\n \"is_a\"\n . \"regulates, process to process\"\n )\n (\n \"mixins\"\n \"positively regulates\"\n )\n (\n \"slot_uri\"\n . \"RO:0002213\"\n )\n )\n (\n \"negatively regulates, process to process\"\n (\n \"is_a\"\n . \"regulates, process to process\"\n )\n (\n \"mixins\"\n \"negatively regulates\"\n )\n (\n \"slot_uri\"\n . \"RO:0002212\"\n )\n )\n (\n \"regulates, entity to entity\"\n (\n \"aliases\"\n \"activity directly regulates activity of\"\n )\n (\n \"is_a\"\n . \"regulates\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n (\n \"local_names\"\n (\n \"translator\"\n . \"regulates\"\n )\n (\n \"ro\"\n . \"activity directly regulates activity of\"\n )\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002448\"\n )\n )\n (\n \"positively regulates, entity to entity\"\n (\n \"aliases\"\n \"activity directly positively regulates activity of\"\n )\n (\n \"is_a\"\n . \"regulates, entity to entity\"\n )\n (\n \"mixins\"\n \"positively regulates\"\n )\n (\n \"local_names\"\n (\n \"translator\"\n . \"positively regulates\"\n )\n (\n \"ro\"\n . \"activity directly positively regulates activity of\"\n )\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002450\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:STIMULATES\"\n )\n )\n (\n \"negatively regulates, entity to entity\"\n (\n \"aliases\"\n \"activity directly negatively regulates activity of\"\n )\n (\n \"is_a\"\n . \"regulates, entity to entity\"\n )\n (\n \"mixins\"\n \"negatively regulates\"\n )\n (\n \"local_names\"\n (\n \"translator\"\n . \"negatively regulates\"\n )\n (\n \"ro\"\n . \"activity directly negatively regulates activity of\"\n )\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002449\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:INHIBITS\"\n )\n )\n (\n \"disrupts\"\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"description\"\n . \"describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"SEMMEDDB:DISRUPTS\"\n )\n )\n (\n \"has gene product\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a gene and a transcribed and/or translated product generated from it\"\n )\n (\n \"domain\"\n . \"gene\"\n )\n (\n \"range\"\n . \"gene product\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002205\"\n )\n (\n \"mappings\"\n \"WD:P688\"\n )\n )\n (\n \"homologous to\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"aliases\"\n \"in homology relationship with\"\n )\n (\n \"description\"\n . \"holds between two biological entities that have common evolutionary origin\"\n )\n (\n \"comments\"\n \"typically used to describe homology relationships between genes or gene products\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:HOM0000001\"\n )\n (\n \"mappings\"\n \"SIO:010302\"\n )\n )\n (\n \"paralogous to\"\n (\n \"is_a\"\n . \"homologous to\"\n )\n (\n \"description\"\n . \"a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:HOM0000011\"\n )\n )\n (\n \"orthologous to\"\n (\n \"is_a\"\n . \"homologous to\"\n )\n (\n \"description\"\n . \"a homology relationship between entities (typically genes) that diverged after a speciation event.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:HOM0000017\"\n )\n (\n \"mappings\"\n \"WD:P684\"\n )\n )\n (\n \"xenologous to\"\n (\n \"is_a\"\n . \"homologous to\"\n )\n (\n \"description\"\n . \"a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:HOM0000018\"\n )\n )\n (\n \"coexists with\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"SEMMEDDB:COEXISTS_WITH\"\n )\n )\n (\n \"in pathway with\"\n (\n \"description\"\n . \"holds between two genes or gene products that are part of in the same biological pathway\"\n )\n (\n \"is_a\"\n . \"coexists with\"\n )\n (\n \"domain\"\n . \"gene or gene product\"\n )\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n )\n (\n \"in complex with\"\n (\n \"description\"\n . \"holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex\"\n )\n (\n \"is_a\"\n . \"coexists with\"\n )\n (\n \"domain\"\n . \"gene or gene product\"\n )\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n )\n (\n \"in cell population with\"\n (\n \"description\"\n . \"holds between two genes or gene products that are expressed in the same cell type or population\"\n )\n (\n \"is_a\"\n . \"coexists with\"\n )\n (\n \"domain\"\n . \"gene or gene product\"\n )\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n )\n (\n \"colocalizes with\"\n (\n \"description\"\n . \"holds between two entities that are observed to be located in the same place.\"\n )\n (\n \"is_a\"\n . \"coexists with\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:00002325\"\n )\n )\n (\n \"gene associated with condition\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with\"\n )\n (\n \"domain\"\n . \"gene\"\n )\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"WD:P2293\"\n )\n )\n (\n \"affects risk for\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two entities where exposure to one entity alters the chance of developing the other\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n )\n (\n \"predisposes\"\n (\n \"is_a\"\n . \"affects risk for\"\n )\n (\n \"description\"\n . \"holds between two entities where exposure to one entity increases the chance of developing the other\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"SEMMEDDB:PREDISPOSES\"\n )\n )\n (\n \"contributes to\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two entities where the occurrence, existence, or activity of one causes or contributes to the occurrence or generation of the other\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002326\"\n )\n )\n (\n \"causes\"\n (\n \"description\"\n . \"holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other\"\n )\n (\n \"is_a\"\n . \"contributes to\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002410\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:CAUSES\"\n \"WD:P1542\"\n )\n )\n (\n \"treats\"\n (\n \"aliases\"\n \"is substance that treats\"\n )\n (\n \"is_a\"\n . \"affects\"\n )\n (\n \"description\"\n . \"holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat\"\n )\n (\n \"domain\"\n . \"treatment\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"treated by\"\n )\n (\n \"slot_uri\"\n . \"RO:0002606\"\n )\n (\n \"mappings\"\n \"RO:0003307\"\n \"SEMMEDDB:TREATS\"\n \"WD:P2175\"\n )\n )\n (\n \"prevents\"\n (\n \"is_a\"\n . \"affects risk for\"\n )\n (\n \"description\"\n . \"holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical substance, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002599\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:PREVENTS\"\n )\n )\n (\n \"correlated with\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.\"\n )\n (\n \"domain\"\n . \"disease or phenotypic feature\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002610\"\n )\n )\n (\n \"has biomarker\"\n (\n \"is_a\"\n . \"correlated with\"\n )\n (\n \"description\"\n . \"holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.\"\n )\n (\n \"domain\"\n . \"disease or phenotypic feature\"\n )\n (\n \"range\"\n . \"molecular entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"biomarker for\"\n )\n )\n (\n \"biomarker for\"\n (\n \"is_a\"\n . \"correlated with\"\n )\n (\n \"description\"\n . \"holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.\"\n )\n (\n \"domain\"\n . \"molecular entity\"\n )\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"has biomarker\"\n )\n (\n \"slot_uri\"\n . \"RO:0002607\"\n )\n )\n (\n \"treated by\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a disease or phenotypic feature and a therapeutic process or chemical substance that is used to treat the condition\"\n )\n (\n \"domain\"\n . \"disease or phenotypic feature\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"treats\"\n )\n (\n \"slot_uri\"\n . \"RO:0002302\"\n )\n (\n \"mappings\"\n \"WD:P2176\"\n )\n )\n (\n \"expressed in\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a gene or gene product and an anatomical entity in which it is expressed\"\n )\n (\n \"domain\"\n . \"gene or gene product\"\n )\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"expresses\"\n )\n (\n \"slot_uri\"\n . \"RO:0002206\"\n )\n )\n (\n \"expresses\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between an anatomical entity and gene or gene product that is expressed there\"\n )\n (\n \"domain\"\n . \"anatomical entity\"\n )\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"expressed in\"\n )\n (\n \"slot_uri\"\n . \"RO:0002292\"\n )\n )\n (\n \"has phenotype\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature).\"\n )\n (\n \"domain\"\n . \"biological entity\"\n )\n (\n \"range\"\n . \"phenotypic feature\"\n )\n (\n \"notes\"\n \"check the range\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002200\"\n )\n )\n (\n \"occurs in\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a process and a material entity or site within which the process occurs\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"BFO:0000066\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:OCCURS_IN\"\n \"SEMMEDDB:PROCESS_OF\"\n )\n )\n (\n \"located in\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a material entity and a material entity or site within which it is located (but of which it is not considered a part)\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"location of\"\n )\n (\n \"slot_uri\"\n . \"RO:0001025\"\n )\n )\n (\n \"location of\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between material entity or site and a material entity that is located within it (but not considered a part of it)\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"located in\"\n )\n (\n \"slot_uri\"\n . \"RO:0001015\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:LOCATION_OF\"\n \"WD:276\"\n )\n )\n (\n \"model of\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between an entity and some other entity it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0003301\"\n )\n )\n (\n \"overlaps\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between entties that overlap in their extents (materials or processes)\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002131\"\n )\n )\n (\n \"has part\"\n (\n \"is_a\"\n . \"overlaps\"\n )\n (\n \"description\"\n . \"holds between wholes and their parts (material entities or processes)\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"part of\"\n )\n (\n \"slot_uri\"\n . \"BFO:0000051\"\n )\n (\n \"mappings\"\n \"WD:P527\"\n )\n )\n (\n \"part of\"\n (\n \"is_a\"\n . \"overlaps\"\n )\n (\n \"description\"\n . \"holds between parts and wholes (material entities or processes)\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"has part\"\n )\n (\n \"slot_uri\"\n . \"BFO:0000050\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:PART_OF\"\n \"WD:P361\"\n )\n )\n (\n \"has participant\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a process and a continuant, where the continuant is somehow involved in the process\"\n )\n (\n \"domain\"\n . \"occurrent\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"participates in\"\n )\n (\n \"slot_uri\"\n . \"RO:0000057\"\n )\n (\n \"mappings\"\n \"WD:P2283\"\n )\n )\n (\n \"has input\"\n (\n \"is_a\"\n . \"has participant\"\n )\n (\n \"description\"\n . \"holds between a process and a continuant, where the continuant is an input into the process\"\n )\n (\n \"domain\"\n . \"occurrent\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002233\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:USES\"\n )\n )\n (\n \"participates in\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a continuant and a process, where the continuant is somehow involved in the process\"\n )\n (\n \"range\"\n . \"occurrent\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"has participant\"\n )\n (\n \"slot_uri\"\n . \"RO:0000056\"\n )\n )\n (\n \"actively involved in\"\n (\n \"is_a\"\n . \"participates in\"\n )\n (\n \"description\"\n . \"holds between a continuant and a process or function, where the continuant actively contributes to part or all of the process or function it realizes\"\n )\n (\n \"range\"\n . \"occurrent\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002331\"\n )\n )\n (\n \"capable of\"\n (\n \"is_a\"\n . \"actively involved in\"\n )\n (\n \"description\"\n . \"holds between a continuant and process or function, where the continuant alone has the ability to carry out the process or function.\"\n )\n (\n \"range\"\n . \"occurrent\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002215\"\n )\n )\n (\n \"derives into\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"derives from\"\n )\n (\n \"slot_uri\"\n . \"RO:0001001\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:CONVERTS_TO\"\n )\n )\n (\n \"derives from\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"inverse\"\n . \"derives into\"\n )\n (\n \"slot_uri\"\n . \"RO:0001000\"\n )\n )\n (\n \"manifestation of\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome\"\n )\n (\n \"range\"\n . \"disease\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"SEMMEDDB:MANIFESTATION_OF\"\n )\n (\n \"mappings\"\n \"WD:P1557\"\n )\n )\n (\n \"produces\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0003000\"\n )\n (\n \"mappings\"\n \"WD:P1056\"\n \"SEMMEDDB:PRODUCES\"\n )\n )\n (\n \"precedes\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two processes, where one completes before the other begins\"\n )\n (\n \"domain\"\n . \"occurrent\"\n )\n (\n \"range\"\n . \"occurrent\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"BFO:0000063\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:PRECEDES\"\n \"WD:P156\"\n )\n )\n (\n \"same as\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two entities that are considered equivalent to each other\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"owl:equivalentClass\"\n )\n (\n \"mappings\"\n \"owl:sameAs\"\n \"skos:exactMatch\"\n \"WD:P2888\"\n )\n )\n (\n \"subclass of\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"holds between two classes where the domain class is a specialization of the range class\"\n )\n (\n \"domain\"\n . \"ontology class\"\n )\n (\n \"range\"\n . \"iri type\"\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"rdfs:subClassOf\"\n )\n (\n \"mappings\"\n \"SEMMEDDB:IS_A\"\n \"WD:P279\"\n )\n )\n (\n \"node property\"\n (\n \"description\"\n . \"A grouping for any property that holds between a node and a value\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n )\n (\n \"title\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"data set version\"\n )\n (\n \"slot_uri\"\n . \"dct:title\"\n )\n )\n (\n \"source data file\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"data set version\"\n )\n (\n \"range\"\n . \"data file\"\n )\n (\n \"slot_uri\"\n . \"dcterms:source\"\n )\n )\n (\n \"source web page\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"data set summary\"\n )\n (\n \"slot_uri\"\n . \"dcterms:source\"\n )\n )\n (\n \"retrievedOn\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"source file\"\n )\n (\n \"range\"\n . \"date\"\n )\n (\n \"slot_uri\"\n . \"pav:retrievedOn\"\n )\n )\n (\n \"versionOf\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"data set version\"\n )\n (\n \"range\"\n . \"data set\"\n )\n (\n \"slot_uri\"\n . \"dct:isVersionOf\"\n )\n )\n (\n \"source version\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"source file\"\n )\n (\n \"slot_uri\"\n . \"pav:version\"\n )\n )\n (\n \"downloadURL\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"distribution level\"\n )\n (\n \"slot_uri\"\n . \"dct:downloadURL\"\n )\n )\n (\n \"distribution\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"data set version\"\n )\n (\n \"range\"\n . \"distribution level\"\n )\n (\n \"slot_uri\"\n . \"void:Dataset\"\n )\n )\n (\n \"type\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"slot_uri\"\n . \"rdf:type\"\n )\n )\n (\n \"id\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"identifier\"\n . #t\n )\n (\n \"description\"\n . \"A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"identifier type\"\n )\n (\n \"required\"\n . #t\n )\n )\n (\n \"association_id\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"identifier\"\n . #t\n )\n (\n \"description\"\n . \"A unique identifier for an association\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"association\"\n )\n (\n \"range\"\n . \"identifier type\"\n )\n (\n \"ifabsent\"\n . \"bnode\"\n )\n (\n \"alias\"\n . \"id\"\n )\n )\n (\n \"iri\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"description\"\n . \"An IRI for the node. This is determined by the id using expansion rules.\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"iri type\"\n )\n )\n (\n \"name\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"aliases\"\n \"label\"\n \"display name\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"label type\"\n )\n (\n \"description\"\n . \"A human-readable name for a thing\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"slot_uri\"\n . \"rdfs:label\"\n )\n )\n (\n \"synonym\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"aliases\"\n \"alias\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"label type\"\n )\n (\n \"description\"\n . \"Alternate human-readable names for a thing\"\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n )\n (\n \"category\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"iri type\"\n )\n (\n \"description\"\n . \"Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag\"\n )\n (\n \"is_class_field\"\n . #t\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"slot_uri\"\n . \"rdfs:subClassOf\"\n )\n )\n (\n \"full name\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"label type\"\n )\n (\n \"description\"\n . \"a long-form human readable name for a thing\"\n )\n )\n (\n \"description\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"narrative text\"\n )\n (\n \"description\"\n . \"a human-readable description of a thing\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"dcterms:description\"\n )\n )\n (\n \"systematic synonym\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"domain\"\n . \"named thing\"\n )\n (\n \"range\"\n . \"label type\"\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"description\"\n . \"more commonly used for gene symbols in yeast\"\n )\n )\n (\n \"association slot\"\n (\n \"abstract\"\n . #t\n )\n (\n \"domain\"\n . \"association\"\n )\n (\n \"aliases\"\n \"edge property\"\n \"statement property\"\n )\n (\n \"description\"\n . \"any slot that relates an association to another entity\"\n )\n )\n (\n \"subject\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"local_names\"\n (\n \"ga4gh\"\n . \"annotation subject\"\n )\n (\n \"neo4j\"\n . \"node with outgoing relationship\"\n )\n )\n (\n \"description\"\n . \"connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"range\"\n . \"named thing\"\n )\n (\n \"slot_uri\"\n . \"rdf:subject\"\n )\n (\n \"mappings\"\n \"owl:annotatedSource\"\n \"oban:association_has_subject\"\n )\n )\n (\n \"object\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"description\"\n . \"connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"range\"\n . \"named thing\"\n )\n (\n \"local_names\"\n (\n \"ga4gh\"\n . \"descriptor\"\n )\n (\n \"neo4j\"\n . \"node with incoming relationship\"\n )\n )\n (\n \"slot_uri\"\n . \"rdf:object\"\n )\n (\n \"mappings\"\n \"owl:annotatedTarget\"\n \"oban:association_has_object\"\n )\n )\n (\n \"edge label\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"description\"\n . \"A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.\"\n )\n (\n \"domain\"\n . \"association\"\n )\n (\n \"notes\"\n \"in neo4j this corresponds to the relationship type and the convention is for a snake_case label\"\n )\n (\n \"range\"\n . \"label type\"\n )\n (\n \"required\"\n . #t\n )\n )\n (\n \"relation\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"description\"\n . \"the relationship type by which a subject is connected to an object in an association\"\n )\n (\n \"domain\"\n . \"association\"\n )\n (\n \"range\"\n . \"uriorcurie\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"local_names\"\n (\n \"ga4gh\"\n . \"annotation predicate\"\n )\n (\n \"translator\"\n . \"predicate\"\n )\n )\n (\n \"slot_uri\"\n . \"rdf:predicate\"\n )\n (\n \"mappings\"\n \"owl:annotatedProperty\"\n \"oban:association_has_predicate\"\n )\n )\n (\n \"negated\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"boolean\"\n )\n (\n \"description\"\n . \"if set to true, then the association is negated i.e. is not true\"\n )\n )\n (\n \"has confidence level\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"confidence level\"\n )\n (\n \"description\"\n . \"connects an association to a qualitative term denoting the level of confidence\"\n )\n )\n (\n \"has evidence\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"evidence type\"\n )\n (\n \"description\"\n . \"connects an association to an instance of supporting evidence\"\n )\n (\n \"slot_uri\"\n . \"RO:0002558\"\n )\n )\n (\n \"provided by\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"provider\"\n )\n (\n \"description\"\n . \"connects an association to the agent (person, organization or group) that provided it\"\n )\n (\n \"slot_uri\"\n . \"pav:providedBy\"\n )\n )\n (\n \"association type\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"ontology class\"\n )\n (\n \"description\"\n . \"connects an association to the type of association (e.g. gene to phenotype)\"\n )\n (\n \"slot_uri\"\n . \"rdf:type\"\n )\n )\n (\n \"creation date\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"date\"\n )\n (\n \"description\"\n . \"date on which thing was created. This can be applied to nodes or edges\"\n )\n (\n \"slot_uri\"\n . \"dcterms:created\"\n )\n )\n (\n \"update date\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"date\"\n )\n (\n \"description\"\n . \"date on which thing was updated. This can be applied to nodes or edges\"\n )\n )\n (\n \"in taxon\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"domain\"\n . \"thing with taxon\"\n )\n (\n \"range\"\n . \"organism taxon\"\n )\n (\n \"description\"\n . \"connects a thing to a class representing a taxon\"\n )\n (\n \"in_subset\"\n \"translator_minimal\"\n )\n (\n \"slot_uri\"\n . \"RO:0002162\"\n )\n (\n \"mappings\"\n \"WD:P703\"\n )\n )\n (\n \"latitude\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"float\"\n )\n (\n \"description\"\n . \"latitude\"\n )\n (\n \"slot_uri\"\n . \"wgs:lat\"\n )\n )\n (\n \"longitude\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"float\"\n )\n (\n \"description\"\n . \"longitude\"\n )\n (\n \"slot_uri\"\n . \"wgs:long\"\n )\n )\n (\n \"has chemical formula\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"chemical formula value\"\n )\n (\n \"description\"\n . \"description of chemical compound based on element symbols\"\n )\n (\n \"slot_uri\"\n . \"WD:P274\"\n )\n )\n (\n \"aggregate statistic\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"abstract\"\n . #t\n )\n )\n (\n \"has count\"\n (\n \"description\"\n . \"number of things with a particular property\"\n )\n (\n \"is_a\"\n . \"aggregate statistic\"\n )\n (\n \"range\"\n . \"integer\"\n )\n )\n (\n \"has total\"\n (\n \"description\"\n . \"total number of things in a particular reference set\"\n )\n (\n \"is_a\"\n . \"aggregate statistic\"\n )\n (\n \"range\"\n . \"integer\"\n )\n )\n (\n \"has quotient\"\n (\n \"is_a\"\n . \"aggregate statistic\"\n )\n (\n \"range\"\n . \"double\"\n )\n )\n (\n \"has percentage\"\n (\n \"description\"\n . \"equivalent to has quotient multiplied by 100\"\n )\n (\n \"is_a\"\n . \"aggregate statistic\"\n )\n (\n \"range\"\n . \"double\"\n )\n )\n (\n \"timepoint\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"time type\"\n )\n (\n \"description\"\n . \"a point in time\"\n )\n )\n (\n \"stage qualifier\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"life stage\"\n )\n (\n \"description\"\n . \"stage at which expression takes place\"\n )\n )\n (\n \"quantifier qualifier\"\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"ontology class\"\n )\n (\n \"description\"\n . \"A measurable quantity for the object of the association\"\n )\n )\n (\n \"qualifiers\"\n (\n \"singular_name\"\n . \"qualifier\"\n )\n (\n \"description\"\n . \"connects an association to qualifiers that modify or qualify the meaning of that association\"\n )\n (\n \"local_names\"\n (\n \"ga4gh\"\n . \"annotation qualifier\"\n )\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"range\"\n . \"ontology class\"\n )\n )\n (\n \"frequency qualifier\"\n (\n \"description\"\n . \"a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"frequency value\"\n )\n )\n (\n \"severity qualifier\"\n (\n \"description\"\n . \"a qualifier used in a phenotypic association to state how severe the phenotype is in the subject\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"severity value\"\n )\n )\n (\n \"sex qualifier\"\n (\n \"description\"\n . \"a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"biological sex\"\n )\n )\n (\n \"onset qualifier\"\n (\n \"description\"\n . \"a qualifier used in a phenotypic association to state when the phenotype appears is in the subject\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"onset\"\n )\n )\n (\n \"clinical modifier qualifier\"\n (\n \"description\"\n . \"Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"clinical modifier\"\n )\n )\n (\n \"sequence variant qualifier\"\n (\n \"description\"\n . \"a qualifier used in an association where the variant\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"range\"\n . \"sequence variant\"\n )\n )\n (\n \"publications\"\n (\n \"singular_name\"\n . \"publication\"\n )\n (\n \"description\"\n . \"connects an association to publications supporting the association\"\n )\n (\n \"is_a\"\n . \"association slot\"\n )\n (\n \"multivalued\"\n . #t\n )\n (\n \"range\"\n . \"publication\"\n )\n )\n (\n \"has biological sequence\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"description\"\n . \"connects a genomic feature to its sequence\"\n )\n (\n \"range\"\n . \"biological sequence\"\n )\n )\n (\n \"has molecular consequence\"\n (\n \"is_a\"\n . \"related to\"\n )\n (\n \"description\"\n . \"connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583\"\n )\n (\n \"range\"\n . \"ontology class\"\n )\n )\n (\n \"has gene\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"description\"\n . \"connects and entity to a single gene\"\n )\n (\n \"range\"\n . \"gene\"\n )\n )\n (\n \"has zygosity\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"zygosity\"\n )\n )\n (\n \"filler\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"range\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"The value in a property-value tuple\"\n )\n )\n (\n \"phase\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"description\"\n . \"TODO\"\n )\n )\n (\n \"genome build\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"description\"\n . \"TODO\"\n )\n )\n (\n \"interbase coordinate\"\n (\n \"is_a\"\n . \"node property\"\n )\n (\n \"description\"\n . \"TODO\"\n )\n )\n (\n \"start interbase coordinate\"\n (\n \"is_a\"\n . \"interbase coordinate\"\n )\n )\n (\n \"end interbase coordinate\"\n (\n \"is_a\"\n . \"interbase coordinate\"\n )\n )\n )\n (\n \"classes\"\n (\n \"attribute\"\n (\n \"subclass_of\"\n . \"PATO:0000001\"\n )\n (\n \"mixins\"\n \"ontology class\"\n )\n (\n \"description\"\n . \"A property or characteristic of an entity\"\n )\n )\n (\n \"biological sex\"\n (\n \"subclass_of\"\n . \"PATO:0000047\"\n )\n (\n \"is_a\"\n . \"attribute\"\n )\n )\n (\n \"phenotypic sex\"\n (\n \"description\"\n . \"An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.\"\n )\n (\n \"subclass_of\"\n . \"PATO:0001894\"\n )\n (\n \"is_a\"\n . \"biological sex\"\n )\n )\n (\n \"genotypic sex\"\n (\n \"description\"\n . \"An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.\"\n )\n (\n \"subclass_of\"\n . \"PATO:0020000\"\n )\n (\n \"is_a\"\n . \"biological sex\"\n )\n )\n (\n \"severity value\"\n (\n \"description\"\n . \"describes the severity of a phenotypic feature or disease\"\n )\n (\n \"is_a\"\n . \"attribute\"\n )\n )\n (\n \"frequency value\"\n (\n \"description\"\n . \"describes the frequency of occurrence of an event or condition\"\n )\n (\n \"is_a\"\n . \"attribute\"\n )\n )\n (\n \"clinical modifier\"\n (\n \"description\"\n . \"Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects\"\n )\n (\n \"subclass_of\"\n . \"HP:0012823\"\n )\n (\n \"is_a\"\n . \"attribute\"\n )\n )\n (\n \"onset\"\n (\n \"description\"\n . \"The age group in which manifestations appear\"\n )\n (\n \"class_uri\"\n . \"HP:0003674\"\n )\n (\n \"is_a\"\n . \"attribute\"\n )\n )\n (\n \"relationship quantifier\"\n (\n \"abstract\"\n . #t\n )\n (\n \"mixin\"\n . #t\n )\n )\n (\n \"sensitivity quantifier\"\n (\n \"is_a\"\n . \"relationship quantifier\"\n )\n (\n \"mixin\"\n . #t\n )\n )\n (\n \"specificity quantifier\"\n (\n \"is_a\"\n . \"relationship quantifier\"\n )\n (\n \"mixin\"\n . #t\n )\n )\n (\n \"pathognomonicity quantifier\"\n (\n \"is_a\"\n . \"specificity quantifier\"\n )\n (\n \"description\"\n . \"A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease\"\n )\n (\n \"mixin\"\n . #t\n )\n )\n (\n \"frequency quantifier\"\n (\n \"is_a\"\n . \"relationship quantifier\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"slots\"\n \"has count\"\n \"has total\"\n \"has quotient\"\n \"has percentage\"\n )\n )\n (\n \"named thing\"\n (\n \"description\"\n . \"a databased entity or concept/class\"\n )\n (\n \"slots\"\n \"id\"\n \"name\"\n \"category\"\n )\n (\n \"subclass_of\"\n . \"BFO:0000001\"\n )\n (\n \"class_uri\"\n . \"WD:Q35120\"\n )\n (\n \"mappings\"\n \"UMLSSG:OBJC\"\n \"UMLSSC:T071\"\n \"UMLSST:enty\"\n \"UMLSSC:T072\"\n \"UMLSST:phob\"\n \"UMLSSC:T073\"\n \"UMLSST:mnob\"\n \"UMLSSC:T168\"\n \"UMLSST:food\"\n )\n )\n (\n \"data file\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"class_uri\"\n . \"EFO:0004095\"\n )\n )\n (\n \"source file\"\n (\n \"is_a\"\n . \"data file\"\n )\n (\n \"slots\"\n \"source version\"\n \"retrievedOn\"\n )\n )\n (\n \"data set\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"class_uri\"\n . \"IAO:0000100\"\n )\n )\n (\n \"data set version\"\n (\n \"is_a\"\n . \"data set\"\n )\n (\n \"slots\"\n \"title\"\n \"source data file\"\n \"versionOf\"\n \"type\"\n \"distribution\"\n )\n )\n (\n \"distribution level\"\n (\n \"is_a\"\n . \"data set version\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"slots\"\n \"downloadURL\"\n )\n )\n (\n \"data set summary\"\n (\n \"is_a\"\n . \"data set version\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"slots\"\n \"source web page\"\n )\n )\n (\n \"biological entity\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"class_uri\"\n . \"WD:Q28845870\"\n )\n (\n \"mappings\"\n \"UMLSSC:T050\"\n \"UMLSST:emod\"\n )\n )\n (\n \"ontology class\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"a concept or class in an ontology, vocabulary or thesaurus\"\n )\n )\n (\n \"relationship type\"\n (\n \"is_a\"\n . \"ontology class\"\n )\n (\n \"description\"\n . \"An OWL property used as an edge label\"\n )\n )\n (\n \"gene ontology class\"\n (\n \"description\"\n . \"an ontology class that describes a functional aspect of a gene, gene prodoct or complex\"\n )\n (\n \"is_a\"\n . \"ontology class\"\n )\n (\n \"in_subset\"\n \"testing\"\n )\n )\n (\n \"thing with taxon\"\n (\n \"abstract\"\n . #t\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"description\"\n . \"A mixin that can be used on any entity with a taxon\"\n )\n (\n \"slots\"\n \"in taxon\"\n )\n )\n (\n \"organism taxon\"\n (\n \"is_a\"\n . \"ontology class\"\n )\n (\n \"values_from\"\n \"NCBITaxon\"\n )\n (\n \"class_uri\"\n . \"WD:Q16521\"\n )\n )\n (\n \"organismal entity\"\n (\n \"description\"\n . \"A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"is_a\"\n . \"biological entity\"\n )\n (\n \"class_uri\"\n . \"WD:Q7239\"\n )\n )\n (\n \"individual organism\"\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"is_a\"\n . \"organismal entity\"\n )\n (\n \"subclass_of\"\n . \"NCBITaxon:1\"\n )\n (\n \"class_uri\"\n . \"SIO:010000\"\n )\n (\n \"mappings\"\n \"WD:Q795052\"\n \"UMLSSG:LIVB\"\n \"UMLSSC:T001\"\n \"UMLSST:orgm\"\n \"UMLSSC:T002\"\n \"UMLSST:plnt\"\n \"UMLSSC:T004\"\n \"UMLSST:fngs\"\n \"UMLSSC:T005\"\n \"UMLSST:virs\"\n \"UMLSSC:T007\"\n \"UMLSST:bact\"\n \"UMLSSC:T008\"\n \"UMLSST:anim\"\n \"UMLSSC:T010\"\n \"UMLSST:vtbt\"\n \"UMLSSC:T011\"\n \"UMLSST:amph\"\n \"UMLSSC:T012\"\n \"UMLSST:bird\"\n \"UMLSSC:T013\"\n \"UMLSST:fish\"\n \"UMLSSC:T014\"\n \"UMLSST:rept\"\n \"UMLSSC:T015\"\n \"UMLSST:mamm\"\n \"UMLSSC:T016\"\n \"UMLSST:humn\"\n \"UMLSSC:T096\"\n \"UMLSST:grup\"\n \"UMLSSC:T097\"\n \"UMLSST:prog\"\n \"UMLSSC:T099\"\n \"UMLSST:famg\"\n \"UMLSSC:T100\"\n \"UMLSST:aggp\"\n \"UMLSSC:T101\"\n \"UMLSST:podg\"\n \"UMLSSC:T194\"\n \"UMLSST:arch\"\n \"UMLSSC:T204\"\n \"UMLSST:euka\"\n )\n )\n (\n \"case\"\n (\n \"aliases\"\n \"patient\"\n \"proband\"\n )\n (\n \"is_a\"\n . \"individual organism\"\n )\n (\n \"description\"\n . \"An individual organism that has a patient role in some clinical context.\"\n )\n )\n (\n \"population of individual organisms\"\n (\n \"description\"\n . \"A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes [Alliance for Genome Resources]\"\n )\n (\n \"local_names\"\n (\n \"ga4gh\"\n . \"population\"\n )\n (\n \"agr\"\n . \"population\"\n )\n )\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"is_a\"\n . \"organismal entity\"\n )\n (\n \"subclass_of\"\n . \"PCO:0000001\"\n )\n (\n \"class_uri\"\n . \"SIO:001061\"\n )\n (\n \"mappings\"\n \"UMLSSC:T098\"\n \"UMLSST:popg\"\n )\n (\n \"id_prefixes\"\n \"HANCESTRO\"\n )\n )\n (\n \"biosample\"\n (\n \"aliases\"\n \"biospecimen\"\n \"sample\"\n )\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"is_a\"\n . \"organismal entity\"\n )\n (\n \"class_uri\"\n . \"SIO:001050\"\n )\n )\n (\n \"disease or phenotypic feature\"\n (\n \"aliases\"\n \"phenome\"\n )\n (\n \"is_a\"\n . \"biological entity\"\n )\n (\n \"description\"\n . \"Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.\"\n )\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"union_of\"\n \"disease\"\n \"phenotypic feature\"\n )\n (\n \"mappings\"\n \"UMLSSC:T033\"\n \"UMLSST:fndg\"\n )\n )\n (\n \"disease\"\n (\n \"aliases\"\n \"condition\"\n \"disorder\"\n \"medical condition\"\n )\n (\n \"is_a\"\n . \"disease or phenotypic feature\"\n )\n (\n \"class_uri\"\n . \"MONDO:0000001\"\n )\n (\n \"mappings\"\n \"WD:Q12136\"\n \"SIO:010299\"\n \"UMLSSG:DISO\"\n \"UMLSSC:T019\"\n \"UMLSST:cgab\"\n \"UMLSSC:T020\"\n \"UMLSST:acab\"\n \"UMLSSC:T037\"\n \"UMLSST:inpo\"\n \"UMLSSC:T046\"\n \"UMLSST:patf\"\n \"UMLSSC:T047\"\n \"UMLSST:dsyn\"\n \"UMLSSC:T048\"\n \"UMLSST:mobd\"\n \"UMLSSC:T049\"\n \"UMLSST:comd\"\n \"UMLSSC:T184\"\n \"UMLSST:sosy\"\n \"UMLSSC:T190\"\n \"UMLSST:anab\"\n \"UMLSSC:T191\"\n \"UMLSST:neop\"\n )\n )\n (\n \"phenotypic feature\"\n (\n \"aliases\"\n \"sign\"\n \"symptom\"\n \"phenotype\"\n \"trait\"\n \"endophenotype\"\n )\n (\n \"is_a\"\n . \"disease or phenotypic feature\"\n )\n (\n \"subclass_of\"\n . \"UPHENO:0001001\"\n )\n (\n \"class_uri\"\n . \"UPHENO:0001001\"\n )\n (\n \"mappings\"\n \"SIO:010056\"\n \"WD:Q169872\"\n )\n )\n (\n \"environment\"\n (\n \"aliases\"\n \"environment\"\n \"exposure\"\n \"experimental condition\"\n )\n (\n \"is_a\"\n . \"biological entity\"\n )\n (\n \"description\"\n . \"A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes\"\n )\n (\n \"class_uri\"\n . \"SIO:000955\"\n )\n )\n (\n \"information content entity\"\n (\n \"aliases\"\n \"information\"\n \"information artefact\"\n \"information entity\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"a piece of information that typically describes some piece of biology or is used as support.\"\n )\n (\n \"class_uri\"\n . \"IAO:0000030\"\n )\n (\n \"mappings\"\n \"UMLSSG:CONC\"\n \"UMLSSC:T077\"\n \"UMLSST:cnce\"\n \"UMLSSC:T078\"\n \"UMLSST:idcn\"\n \"UMLSSC:T079\"\n \"UMLSST:tmco\"\n \"UMLSSC:T080\"\n \"UMLSST:qlco\"\n \"UMLSSC:T081\"\n \"UMLSST:qnco\"\n \"UMLSSC:T082\"\n \"UMLSST:spco\"\n \"UMLSSC:T089\"\n \"UMLSST:rnlw\"\n \"UMLSSC:T102\"\n \"UMLSST:grpa\"\n \"UMLSSC:T169\"\n \"UMLSST:ftcn\"\n \"UMLSSC:T171\"\n \"UMLSST:lang\"\n \"UMLSSC:T185\"\n \"UMLSST:clas\"\n )\n )\n (\n \"confidence level\"\n (\n \"is_a\"\n . \"information content entity\"\n )\n (\n \"description\"\n . \"Level of confidence in a statement\"\n )\n (\n \"values_from\"\n \"cio\"\n )\n (\n \"class_uri\"\n . \"CIO:0000028\"\n )\n )\n (\n \"evidence type\"\n (\n \"is_a\"\n . \"information content entity\"\n )\n (\n \"aliases\"\n \"evidence code\"\n )\n (\n \"description\"\n . \"Class of evidence that supports an association\"\n )\n (\n \"values_from\"\n \"eco\"\n )\n (\n \"class_uri\"\n . \"ECO:0000000\"\n )\n )\n (\n \"publication\"\n (\n \"is_a\"\n . \"information content entity\"\n )\n (\n \"aliases\"\n \"reference\"\n )\n (\n \"description\"\n . \"Any published piece of information. Can refer to a whole publication, or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web as well as journals.\"\n )\n (\n \"class_uri\"\n . \"IAO:0000311\"\n )\n (\n \"mappings\"\n \"UMLSSC:T170\"\n \"UMLSST:inpr\"\n )\n (\n \"id_prefixes\"\n \"PMID\"\n )\n )\n (\n \"administrative entity\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"abstract\"\n . #t\n )\n )\n (\n \"provider\"\n (\n \"is_a\"\n . \"administrative entity\"\n )\n (\n \"aliases\"\n \"agent\"\n \"group\"\n )\n (\n \"description\"\n . \"person, group, organization or project that provides a piece of information\"\n )\n (\n \"mappings\"\n \"UMLSSG:ORGA\"\n \"UMLSSC:T092\"\n \"UMLSST:orgt\"\n \"UMLSSC:T093\"\n \"UMLSST:hcro\"\n \"UMLSSC:T094\"\n \"UMLSST:pros\"\n \"UMLSSC:T095\"\n \"UMLSST:shro\"\n )\n )\n (\n \"molecular entity\"\n (\n \"is_a\"\n . \"biological entity\"\n )\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"aliases\"\n \"bioentity\"\n )\n (\n \"description\"\n . \"A gene, gene product, small molecule or macromolecule (including protein complex)\"\n )\n (\n \"class_uri\"\n . \"SIO:010341\"\n )\n (\n \"mappings\"\n \"WD:Q43460564\"\n \"UMLSSG:GENE\"\n \"UMLSSC:T085\"\n \"UMLSST:mosq\"\n )\n )\n (\n \"chemical substance\"\n (\n \"is_a\"\n . \"molecular entity\"\n )\n (\n \"description\"\n . \"May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part\"\n )\n (\n \"subclass_of\"\n . \"CHEBI:24431\"\n )\n (\n \"class_uri\"\n . \"SIO:010004\"\n )\n (\n \"mappings\"\n \"WD:Q79529\"\n \"UMLSSC:T167\"\n \"UMLSST:sbst\"\n \"UMLSSG:CHEM\"\n \"UMLSSC:T103\"\n \"UMLSST:chem\"\n \"UMLSSC:T104\"\n \"UMLSST:chvs\"\n \"UMLSSC:T109\"\n \"UMLSST:orch\"\n \"UMLSSC:T114\"\n \"UMLSST:nnon\"\n \"UMLSSC:T120\"\n \"UMLSST:chvf\"\n \"UMLSSC:T121\"\n \"UMLSST:phsu\"\n \"UMLSSC:T122\"\n \"UMLSST:bodm\"\n \"UMLSSC:T123\"\n \"UMLSST:bacs\"\n \"UMLSSC:T125\"\n \"UMLSST:horm\"\n \"UMLSSC:T126\"\n \"UMLSST:enzy\"\n \"UMLSSC:T127\"\n \"UMLSST:vita\"\n \"UMLSSC:T129\"\n \"UMLSST:imft\"\n \"UMLSSC:T130\"\n \"UMLSST:irda\"\n \"UMLSSC:T131\"\n \"UMLSST:hops\"\n \"UMLSSC:T192\"\n \"UMLSST:rcpt\"\n \"UMLSSC:T195\"\n \"UMLSST:antb\"\n \"UMLSSC:T196\"\n \"UMLSST:elii\"\n \"UMLSSC:T197\"\n \"UMLSST:inch\"\n )\n (\n \"id_prefixes\"\n \"CHEBI\"\n \"CHEMBL.COMPOUND\"\n )\n )\n (\n \"carbohydrate\"\n (\n \"is_a\"\n . \"chemical substance\"\n )\n (\n \"mappings\"\n \"UMLSSC:T088\"\n \"UMLSST:crbs\"\n )\n )\n (\n \"drug\"\n (\n \"is_a\"\n . \"chemical substance\"\n )\n (\n \"description\"\n . \"A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease\"\n )\n (\n \"comments\"\n \"The CHEBI ID represents a role rather than a substance\"\n )\n (\n \"class_uri\"\n . \"WD:Q12140\"\n )\n (\n \"mappings\"\n \"CHEBI:23888\"\n \"UMLSSC:T200\"\n \"UMLSST:clnd\"\n )\n )\n (\n \"metabolite\"\n (\n \"is_a\"\n . \"chemical substance\"\n )\n (\n \"description\"\n . \"Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.\"\n )\n (\n \"comments\"\n \"The CHEBI ID represents a role rather than a substance\"\n )\n (\n \"class_uri\"\n . \"CHEBI:25212\"\n )\n )\n (\n \"anatomical entity\"\n (\n \"is_a\"\n . \"organismal entity\"\n )\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"subclass_of\"\n . \"UBERON:0001062\"\n )\n (\n \"description\"\n . \"A subcellular location, cell type or gross anatomical part\"\n )\n (\n \"class_uri\"\n . \"SIO:010046\"\n )\n (\n \"mappings\"\n \"WD:Q4936952\"\n \"UMLSSG:ANAT\"\n \"UMLSSC:T022\"\n \"UMLSST:bdsy\"\n \"UMLSSC:T029\"\n \"UMLSST:blor\"\n \"UMLSSC:T030\"\n \"UMLSST:bsoj\"\n \"UMLSSC:T031\"\n \"UMLSST:bdsu\"\n )\n )\n (\n \"life stage\"\n (\n \"is_a\"\n . \"organismal entity\"\n )\n (\n \"mixins\"\n \"thing with taxon\"\n )\n (\n \"subclass_of\"\n . \"UBERON:0000105\"\n )\n (\n \"description\"\n . \"A stage of development or growth of an organism, including post-natal adult stages\"\n )\n )\n (\n \"planetary entity\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"Any entity or process that exists at the level of the whole planet\"\n )\n )\n (\n \"environmental process\"\n (\n \"is_a\"\n . \"planetary entity\"\n )\n (\n \"mixins\"\n \"occurrent\"\n )\n (\n \"subclass_of\"\n . \"ENVO:02500000\"\n )\n )\n (\n \"environmental feature\"\n (\n \"is_a\"\n . \"planetary entity\"\n )\n (\n \"subclass_of\"\n . \"ENVO:00002297\"\n )\n )\n (\n \"clinical entity\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities\"\n )\n )\n (\n \"clinical trial\"\n (\n \"is_a\"\n . \"clinical entity\"\n )\n )\n (\n \"clinical intervention\"\n (\n \"is_a\"\n . \"clinical entity\"\n )\n )\n (\n \"device\"\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"description\"\n . \"A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment\"\n )\n (\n \"mappings\"\n \"UMLSSG:DEVI\"\n \"UMLSSC:T074\"\n \"UMLSST:medd\"\n \"UMLSSC:T075\"\n \"UMLSST:resd\"\n \"UMLSSC:T203\"\n \"UMLSST:drdd\"\n )\n )\n (\n \"genomic entity\"\n (\n \"is_a\"\n . \"molecular entity\"\n )\n (\n \"aliases\"\n \"sequence feature\"\n )\n (\n \"description\"\n . \"an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)\"\n )\n (\n \"slots\"\n \"has biological sequence\"\n )\n (\n \"class_uri\"\n . \"SO:0000110\"\n )\n (\n \"mappings\"\n \"UMLSSC:T028\"\n \"UMLSST:gngm\"\n \"UMLSSC:T086\"\n \"UMLSST:nusq\"\n )\n )\n (\n \"genome\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"description\"\n . \"A genome is the sum of genetic material within a cell or virion.\"\n )\n (\n \"class_uri\"\n . \"SO:0001026\"\n )\n (\n \"mappings\"\n \"SIO:000984\"\n \"WD:Q7020\"\n )\n )\n (\n \"transcript\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"description\"\n . \"An RNA synthesized on a DNA or RNA template by an RNA polymerase\"\n )\n (\n \"class_uri\"\n . \"SO:0000673\"\n )\n (\n \"mappings\"\n \"SIO:010450\"\n )\n )\n (\n \"exon\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"description\"\n . \"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing\"\n )\n (\n \"class_uri\"\n . \"SO:0000147\"\n )\n (\n \"mappings\"\n \"SIO:010445\"\n \"WD:Q373027\"\n )\n )\n (\n \"coding sequence\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"class_uri\"\n . \"SO:0000316\"\n )\n (\n \"mappings\"\n \"SIO:001390\"\n )\n )\n (\n \"macromolecular machine\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"union_of\"\n \"gene\"\n \"gene product\"\n \"macromolecular complex\"\n )\n (\n \"description\"\n . \"A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.\"\n )\n (\n \"slot_usage\"\n (\n \"name\"\n (\n \"range\"\n . \"symbol type\"\n )\n (\n \"description\"\n . \"genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name\"\n )\n )\n )\n )\n (\n \"gene or gene product\"\n (\n \"is_a\"\n . \"macromolecular machine\"\n )\n (\n \"union_of\"\n \"gene\"\n \"gene product\"\n )\n (\n \"description\"\n . \"a union of genes or gene products. Frequently an identifier for one will be used as proxy for another\"\n )\n (\n \"id_prefixes\"\n \"CHEMBL.TARGET\"\n )\n )\n (\n \"gene\"\n (\n \"is_a\"\n . \"gene or gene product\"\n )\n (\n \"aliases\"\n \"locus\"\n )\n (\n \"class_uri\"\n . \"SO:0000704\"\n )\n (\n \"mappings\"\n \"SIO:010035\"\n \"WD:Q7187\"\n )\n (\n \"id_prefixes\"\n \"NCBIGene\"\n \"ENSEMBL\"\n \"HGNC\"\n \"MGI\"\n \"ZFIN\"\n \"dictyBase\"\n \"WB\"\n \"SGD\"\n \"PomBase\"\n )\n )\n (\n \"gene product\"\n (\n \"is_a\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules\"\n )\n (\n \"union_of\"\n \"protein\"\n \"RNA product\"\n )\n (\n \"class_uri\"\n . \"WD:Q424689\"\n )\n )\n (\n \"protein\"\n (\n \"is_a\"\n . \"gene product\"\n )\n (\n \"aliases\"\n \"polypeptide\"\n )\n (\n \"description\"\n . \"A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA\"\n )\n (\n \"class_uri\"\n . \"PR:000000001\"\n )\n (\n \"mappings\"\n \"SIO:010043\"\n \"WD:Q8054\"\n \"UMLSSC:T087\"\n \"UMLSST:amas\"\n \"UMLSSC:T116\"\n \"UMLSST:aapp\"\n )\n (\n \"id_prefixes\"\n \"UniProtKB\"\n \"PR\"\n \"ENSEMBL\"\n )\n )\n (\n \"gene product isoform\"\n (\n \"is_a\"\n . \"gene product\"\n )\n (\n \"description\"\n . \"This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.\"\n )\n (\n \"abstract\"\n . #t\n )\n )\n (\n \"protein isoform\"\n (\n \"aliases\"\n \"proteoform\"\n )\n (\n \"is_a\"\n . \"protein\"\n )\n (\n \"description\"\n . \"Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\"\n )\n (\n \"mixins\"\n \"gene product isoform\"\n )\n (\n \"id_prefixes\"\n \"UniProtKB\"\n \"PR\"\n \"ENSEMBL\"\n )\n )\n (\n \"RNA product\"\n (\n \"is_a\"\n . \"gene product\"\n )\n (\n \"class_uri\"\n . \"CHEBI:33697\"\n )\n (\n \"mappings\"\n \"SIO:010450\"\n \"WD:Q11053\"\n )\n (\n \"id_prefixes\"\n \"RNAcentral\"\n )\n )\n (\n \"RNA product isoform\"\n (\n \"is_a\"\n . \"RNA product\"\n )\n (\n \"description\"\n . \"Represents a protein that is a specific isoform of the canonical or reference RNA\"\n )\n (\n \"mixins\"\n \"gene product isoform\"\n )\n (\n \"id_prefixes\"\n \"RNAcentral\"\n )\n )\n (\n \"noncoding RNA product\"\n (\n \"is_a\"\n . \"RNA product\"\n )\n (\n \"id_prefixes\"\n \"RNAcentral\"\n \"NCBIGene\"\n \"ENSEMBL\"\n )\n (\n \"subclass_of\"\n . \"SO:0000655\"\n )\n (\n \"class_uri\"\n . \"SIO:001235\"\n )\n )\n (\n \"microRNA\"\n (\n \"is_a\"\n . \"noncoding RNA product\"\n )\n (\n \"subclass_of\"\n . \"SO:0000276\"\n )\n (\n \"class_uri\"\n . \"SIO:001397\"\n )\n (\n \"mappings\"\n \"WD:Q310899\"\n )\n (\n \"id_prefixes\"\n \"MIR\"\n )\n )\n (\n \"macromolecular complex\"\n (\n \"is_a\"\n . \"macromolecular machine\"\n )\n (\n \"subclass_of\"\n . \"GO:0032991\"\n )\n (\n \"class_uri\"\n . \"SIO:010046\"\n )\n (\n \"mappings\"\n \"WD:Q22325163\"\n )\n (\n \"id_prefixes\"\n \"IntAct\"\n \"GO\"\n \"PR\"\n \"Reactome\"\n )\n )\n (\n \"gene grouping\"\n (\n \"abstract\"\n . #t\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"description\"\n . \"any grouping of multiple genes or gene products\"\n )\n )\n (\n \"gene family\"\n (\n \"is_a\"\n . \"molecular entity\"\n )\n (\n \"class_uri\"\n . \"SIO:001380\"\n )\n (\n \"mappings\"\n \"NCIT:C20130\"\n \"WD:Q417841\"\n )\n (\n \"mixins\"\n \"gene grouping\"\n )\n (\n \"description\"\n . \"any grouping of multiple genes or gene products related by common descent\"\n )\n (\n \"id_prefixes\"\n \"PANTHER\"\n )\n )\n (\n \"zygosity\"\n (\n \"is_a\"\n . \"attribute\"\n )\n (\n \"class_uri\"\n . \"GENO:0000133\"\n )\n )\n (\n \"genotype\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"description\"\n . \"An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background\"\n )\n (\n \"comments\"\n \"Consider renaming as genotypic entity\"\n )\n (\n \"slots\"\n \"has zygosity\"\n )\n (\n \"class_uri\"\n . \"GENO:0000536\"\n )\n (\n \"mappings\"\n \"SIO:001079\"\n )\n )\n (\n \"haplotype\"\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"description\"\n . \"A set of zero or more Alleles on a single instance of a Sequence[VMC]\"\n )\n (\n \"class_uri\"\n . \"GENO:0000871\"\n )\n (\n \"mappings\"\n \"VMC:Haplotype\"\n )\n )\n (\n \"sequence variant\"\n (\n \"aliases\"\n \"allele\"\n )\n (\n \"local_names\"\n (\n \"agr\"\n . \"allele\"\n )\n )\n (\n \"is_a\"\n . \"genomic entity\"\n )\n (\n \"description\"\n . \"An allele that varies in its sequence from what is considered the reference allele at that locus.\"\n )\n (\n \"comments\"\n \"This class is for modeling the specific state at a locus. A single dbSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\"\n )\n (\n \"class_uri\"\n . \"GENO:0000002\"\n )\n (\n \"mappings\"\n \"WD:Q15304597\"\n \"SIO:010277\"\n \"VMC:Allele\"\n )\n (\n \"id_prefixes\"\n \"ClinVar\"\n \"WD\"\n \"CIViC\"\n )\n (\n \"alt_descriptions\"\n (\n \"AGR\"\n . \"An enitity that describes a single affected, endogenous allele. These can be of any type that matches that definition\"\n )\n (\n \"VMC\"\n . \"A contiguous change at a Location\"\n )\n )\n (\n \"slots\"\n \"has gene\"\n )\n (\n \"slot_usage\"\n (\n \"has gene\"\n (\n \"multivalued\"\n . #t\n )\n (\n \"description\"\n . \"Each allele can be associated with any number of genes\"\n )\n )\n (\n \"has biological sequence\"\n (\n \"description\"\n . \"The state of the sequence w.r.t a reference sequence\"\n )\n )\n (\n \"id\"\n (\n \"examples\"\n (\n (\n \"value\"\n . \"ZFIN:ZDB-ALT-980203-1091\"\n )\n (\n \"description\"\n . \"ti282a allele from ZFIN\"\n )\n )\n (\n (\n \"value\"\n . \"ClinVarVariant:17681\"\n )\n (\n \"description\"\n . \"NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\"\n )\n )\n )\n )\n )\n )\n (\n \"drug exposure\"\n (\n \"aliases\"\n \"drug intake\"\n \"drug dose\"\n )\n (\n \"is_a\"\n . \"environment\"\n )\n (\n \"description\"\n . \"A drug exposure is an intake of a particular chemical substance\"\n )\n (\n \"slot_usage\"\n (\n \"drug\"\n (\n \"range\"\n . \"chemical substance\"\n )\n (\n \"required\"\n . #t\n )\n (\n \"multivalued\"\n . #t\n )\n )\n )\n (\n \"class_uri\"\n . \"ECTO:0000509\"\n )\n (\n \"mappings\"\n \"SIO:001005\"\n )\n )\n (\n \"treatment\"\n (\n \"aliases\"\n \"medical action\"\n )\n (\n \"is_a\"\n . \"environment\"\n )\n (\n \"description\"\n . \"A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures'\"\n )\n (\n \"slot_usage\"\n (\n \"has exposure parts\"\n (\n \"multivalued\"\n . #t\n )\n (\n \"range\"\n . \"drug exposure\"\n )\n (\n \"required\"\n . #t\n )\n )\n )\n (\n \"class_uri\"\n . \"OGMS:0000090\"\n )\n (\n \"mappings\"\n \"SIO:001398\"\n )\n )\n (\n \"geographic location\"\n (\n \"is_a\"\n . \"planetary entity\"\n )\n (\n \"description\"\n . \"a location that can be described in lat/long coordinates\"\n )\n (\n \"slots\"\n \"latitude\"\n \"longitude\"\n )\n (\n \"mappings\"\n \"UMLSSG:GEOG\"\n \"UMLSST:geoa\"\n \"UMLSSC:T083\"\n )\n )\n (\n \"geographic location at time\"\n (\n \"is_a\"\n . \"geographic location\"\n )\n (\n \"description\"\n . \"a location that can be described in lat/long coordinates, for a particular time\"\n )\n (\n \"slots\"\n \"timepoint\"\n )\n )\n (\n \"association\"\n (\n \"description\"\n . \"A typed association between two entities, supported by evidence\"\n )\n (\n \"comments\"\n \"This is roughly the model used by biolink and ontobio at the moment\"\n )\n (\n \"slots\"\n \"subject\"\n \"relation\"\n \"object\"\n \"association_id\"\n \"negated\"\n \"association type\"\n \"qualifiers\"\n \"publications\"\n \"provided by\"\n )\n (\n \"class_uri\"\n . \"OBAN:association\"\n )\n (\n \"mappings\"\n \"rdf:Statement\"\n \"owl:Axiom\"\n )\n )\n (\n \"genotype to genotype part association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"Any association between one genotype and a genotypic entity that is a sub-component of it\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"has variant part\"\n )\n )\n (\n \"subject\"\n (\n \"range\"\n . \"genotype\"\n )\n (\n \"description\"\n . \"parent genotype\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"genotype\"\n )\n (\n \"description\"\n . \"child genotype\"\n )\n )\n )\n )\n (\n \"genotype to gene association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"description\"\n . \"the relationship type used to connect genotype to gene\"\n )\n )\n (\n \"subject\"\n (\n \"range\"\n . \"genotype\"\n )\n (\n \"description\"\n . \"parent genotype\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene\"\n )\n (\n \"description\"\n . \"gene implicated in genotype\"\n )\n )\n )\n )\n (\n \"genotype to variant association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"Any association between a genotype and a sequence variant.\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"description\"\n . \"the relationship type used to connect genotype to gene\"\n )\n )\n (\n \"subject\"\n (\n \"range\"\n . \"genotype\"\n )\n (\n \"description\"\n . \"parent genotype\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"sequence variant\"\n )\n (\n \"description\"\n . \"gene implicated in genotype\"\n )\n )\n )\n )\n (\n \"gene to gene association\"\n (\n \"aliases\"\n \"molecular or genetic interaction\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as proxy for the gene or vice versa\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as proxy for the gene or vice versa\"\n )\n )\n )\n )\n (\n \"gene to gene homology association\"\n (\n \"is_a\"\n . \"gene to gene association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n \"relation\"\n )\n (\n \"description\"\n . \"A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"homologous to\"\n )\n (\n \"symmetric\"\n . #t\n )\n (\n \"description\"\n . \"homology relationship type\"\n )\n )\n )\n )\n (\n \"pairwise interaction association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"description\"\n . \"An interaction at the molecular level between two physical entities\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n \"relation\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"id\"\n (\n \"description\"\n . \"identifier for the interaction. This may come from an interaction database such as IMEX.\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"WB:WBInteraction000538741\"\n )\n )\n )\n (\n \"values_from\"\n \"IMEX\"\n \"BioGRID\"\n )\n )\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"molecularly interacts with\"\n )\n (\n \"values_from\"\n \"ro\"\n \"mi\"\n )\n (\n \"description\"\n . \"interaction relationship type\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"RO:0002447\"\n )\n (\n \"description\"\n . \"the subject molecular phosphorylates the object molecule\"\n )\n )\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"molecular entity\"\n )\n )\n (\n \"interacting molecules category\"\n (\n \"range\"\n . \"ontology class\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"MI:1048\"\n )\n (\n \"description\"\n . \"smallmolecule-protein\"\n )\n )\n )\n )\n )\n )\n (\n \"pairwise gene to gene interaction\"\n (\n \"is_a\"\n . \"gene to gene association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n \"relation\"\n )\n (\n \"mixins\"\n \"pairwise interaction association\"\n )\n (\n \"description\"\n . \"An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"molecularly interacts with\"\n )\n (\n \"symmetric\"\n . #t\n )\n (\n \"values_from\"\n \"ro\"\n \"mi\"\n )\n (\n \"description\"\n . \"interaction relationship type\"\n )\n )\n )\n )\n (\n \"cell line to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"description\"\n . \"An relationship between a cell line and another entity\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"cell line\"\n )\n )\n )\n )\n (\n \"cell line to disease or phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"mixins\"\n \"cell line to thing association\"\n \"thing to disease or phenotypic feature association\"\n )\n (\n \"description\"\n . \"An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n )\n )\n )\n (\n \"chemical to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"description\"\n . \"An interaction between a chemical entity and another entity\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"chemical substance\"\n )\n (\n \"description\"\n . \"the chemical substance or entity that is an interactor\"\n )\n )\n )\n )\n (\n \"case to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"description\"\n . \"An abstract association for use where the case is the subject\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"case\"\n )\n (\n \"description\"\n . \"the case (e.g. patient) that has the property\"\n )\n )\n )\n )\n (\n \"chemical to disease or phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"class_uri\"\n . \"SIO:000993\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"chemical to thing association\"\n \"thing to disease or phenotypic feature association\"\n )\n (\n \"description\"\n . \"An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n (\n \"description\"\n . \"the disease or phenotype that is affected by the chemical\"\n )\n )\n )\n )\n (\n \"chemical to pathway association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"class_uri\"\n . \"SIO:001250\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"chemical to thing association\"\n )\n (\n \"description\"\n . \"An interaction between a chemical entity and a biological process or pathway\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"pathway\"\n )\n (\n \"description\"\n . \"the pathway that is affected by the chemical\"\n )\n )\n )\n )\n (\n \"chemical to gene association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"class_uri\"\n . \"SIO:001257\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"chemical to thing association\"\n )\n (\n \"description\"\n . \"An interaction between a chemical entity and a gene or gene product\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"the gene or gene product that is affected by the chemical\"\n )\n )\n )\n )\n (\n \"biosample to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"description\"\n . \"An association between a biosample and something\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"biosample\"\n )\n (\n \"description\"\n . \"the biosample being described\"\n )\n )\n )\n )\n (\n \"biosample to disease or phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"biosample to thing association\"\n \"thing to disease or phenotypic feature association\"\n )\n (\n \"description\"\n . \"An association between a biosample and a disease or phenotype\"\n )\n )\n (\n \"frequency qualifier mixin\"\n (\n \"mixin\"\n . #t\n )\n (\n \"description\"\n . \"Qualifier for freqency type associations\"\n )\n (\n \"slots\"\n \"frequency qualifier\"\n )\n )\n (\n \"entity to feature or disease qualifiers\"\n (\n \"abstract\"\n . #t\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"is_a\"\n . \"frequency qualifier mixin\"\n )\n (\n \"description\"\n . \"Qualifiers for entity to disease or phenotype associations\"\n )\n (\n \"slots\"\n \"severity qualifier\"\n \"onset qualifier\"\n )\n )\n (\n \"entity to phenotypic feature association\"\n (\n \"abstract\"\n . #t\n )\n (\n \"defining_slots\"\n \"object\"\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"mixins\"\n \"entity to feature or disease qualifiers\"\n )\n (\n \"slot_usage\"\n (\n \"description\"\n (\n \"description\"\n . \"A description of specific aspects of this phenotype, not otherwise covered by the phenotype ontology class\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"phenotypic feature\"\n )\n (\n \"description\"\n . \"phenotypic class\"\n )\n (\n \"values_from\"\n \"upheno\"\n \"hp\"\n \"mp\"\n \"wbphenotypic feature\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"HP:0002487\"\n )\n (\n \"description\"\n . \"Hyperkinesis\"\n )\n )\n (\n (\n \"value\"\n . \"WBPhenotype:0000180\"\n )\n (\n \"description\"\n . \"axon morphology variant\"\n )\n )\n (\n (\n \"value\"\n . \"MP:0001569\"\n )\n (\n \"description\"\n . \"abnormal circulating bilirubin level\"\n )\n )\n )\n )\n )\n (\n \"slots\"\n \"sex qualifier\"\n )\n )\n (\n \"entity to disease association\"\n (\n \"description\"\n . \"mixin class for any association whose object (target node) is a disease\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"is_a\"\n . \"entity to feature or disease qualifiers\"\n )\n (\n \"defining_slots\"\n \"object\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"disease\"\n )\n (\n \"description\"\n . \"disease\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"MONDO:0020066\"\n )\n (\n \"description\"\n . \"Ehlers-Danlos syndrome\"\n )\n )\n )\n )\n )\n )\n (\n \"disease or phenotypic feature association to thing association\"\n (\n \"abstract\"\n . #t\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n (\n \"description\"\n . \"disease or phenotype\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"MONDO:0017314\"\n )\n (\n \"description\"\n . \"Ehlers-Danlos syndrome, vascular type\"\n )\n )\n (\n (\n \"value\"\n . \"MP:0013229\"\n )\n (\n \"description\"\n . \"abnormal brain ventricle size\"\n )\n )\n )\n )\n )\n )\n (\n \"disease or phenotypic feature association to location association\"\n (\n \"is_a\"\n . \"disease or phenotypic feature association to thing association\"\n )\n (\n \"description\"\n . \"An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.\"\n )\n (\n \"class_uri\"\n . \"NCIT:R100\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"anatomical entity in which the disease or feature is found\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"UBERON:0002048\"\n )\n (\n \"description\"\n . \"lung\"\n )\n )\n )\n )\n )\n )\n (\n \"thing to disease or phenotypic feature association\"\n (\n \"abstract\"\n . #t\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"object\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"disease or phenotypic feature\"\n )\n (\n \"description\"\n . \"disease or phenotype\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"MONDO:0017314\"\n )\n (\n \"description\"\n . \"Ehlers-Danlos syndrome, vascular type\"\n )\n )\n (\n (\n \"value\"\n . \"MP:0013229\"\n )\n (\n \"description\"\n . \"abnormal brain ventricle size\"\n )\n )\n )\n )\n )\n )\n (\n \"disease to thing association\"\n (\n \"abstract\"\n . #t\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"disease\"\n )\n (\n \"description\"\n . \"disease class\"\n )\n (\n \"values_from\"\n \"mondo\"\n \"omim\"\n \"orphanet\"\n \"ncit\"\n \"doid\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"MONDO:0017314\"\n )\n (\n \"description\"\n . \"Ehlers-Danlos syndrome, vascular type\"\n )\n )\n )\n )\n )\n )\n (\n \"genotype to phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment\"\n )\n (\n \"mixins\"\n \"entity to phenotypic feature association\"\n \"genotype to thing association\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"has phenotype\"\n )\n )\n (\n \"subject\"\n (\n \"range\"\n . \"genotype\"\n )\n (\n \"description\"\n . \"genotype that is associated with the phenotypic feature\"\n )\n )\n )\n )\n (\n \"environment to phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype\"\n )\n (\n \"mixins\"\n \"entity to phenotypic feature association\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"environment\"\n )\n )\n )\n )\n (\n \"disease to phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way\"\n )\n (\n \"mixins\"\n \"entity to phenotypic feature association\"\n \"disease to thing association\"\n )\n )\n (\n \"case to phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype\"\n )\n (\n \"mixins\"\n \"entity to phenotypic feature association\"\n \"case to thing association\"\n )\n )\n (\n \"gene to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"gene that is the subject of the association\"\n )\n )\n )\n )\n (\n \"variant to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"local_names\"\n (\n \"ga4gh\"\n . \"variant annotation\"\n )\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"mixin\"\n . #t\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"sequence variant\"\n )\n (\n \"description\"\n . \"a sequence variant in which the allele state is associated with some other entity\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"ClinVar:38077\"\n )\n (\n \"description\"\n . \"ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n )\n )\n (\n (\n \"value\"\n . \"ClinGen:CA024716\"\n )\n (\n \"description\"\n . \"chr13:g.32921033G>C (hg19) in ClinGen\"\n )\n )\n )\n )\n )\n )\n (\n \"gene to phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"class_uri\"\n . \"http://bio2rdf.org/wormbase_vocabulary:Gene-Phenotype-Association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"entity to phenotypic feature association\"\n \"gene to thing association\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"gene in which variation is correlated with the phenotypic feature\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"HGNC:2197\"\n )\n (\n \"description\"\n . \"COL1A1 (Human)\"\n )\n )\n )\n )\n )\n )\n (\n \"gene to disease association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"comments\"\n \"NCIT:R176 refers to the inverse relationship\"\n )\n (\n \"class_uri\"\n . \"SIO:000983\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"entity to disease association\"\n \"gene to thing association\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"gene in which variation is correlated with the disease - may be protective or causative or associative, or as a model\"\n )\n )\n )\n )\n (\n \"variant to population association\"\n (\n \"description\"\n . \"An association between a variant and a population, where the variant has particular frequency in the population\"\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"variant to thing association\"\n \"frequency quantifier\"\n \"frequency qualifier mixin\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"sequence variant\"\n )\n (\n \"description\"\n . \"an allele that has a certain frequency in a given population\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"NC_000017.11:g.43051071A>T\"\n )\n (\n \"description\"\n . \"17:41203088 A/C in gnomad\"\n )\n )\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"population of individual organisms\"\n )\n (\n \"description\"\n . \"the population that is observed to have the frequency\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"HANCESTRO:0010\"\n )\n (\n \"description\"\n . \"African\"\n )\n )\n )\n )\n (\n \"has quotient\"\n (\n \"description\"\n . \"frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"0.0001666\"\n )\n )\n )\n )\n (\n \"has count\"\n (\n \"description\"\n . \"number in object population that carry a particular allele, aka allele count\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"4\"\n )\n (\n \"description\"\n . \"4 individuals in gnomad set\"\n )\n )\n )\n )\n (\n \"has total\"\n (\n \"description\"\n . \"number all populations that carry a particular allele, aka allele number\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"24014\"\n )\n (\n \"description\"\n . \"24014 individuals in gnomad set\"\n )\n )\n )\n )\n )\n )\n (\n \"population to population association\"\n (\n \"description\"\n . \"An association between a two populations\"\n )\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"population of individual organisms\"\n )\n (\n \"description\"\n . \"the population that form the subject of the association\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"population of individual organisms\"\n )\n (\n \"description\"\n . \"the population that form the object of the association\"\n )\n )\n (\n \"relation\"\n (\n \"description\"\n . \"A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used\"\n )\n )\n )\n )\n (\n \"variant to phenotypic feature association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"variant to thing association\"\n \"entity to phenotypic feature association\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"sequence variant\"\n )\n (\n \"description\"\n . \"a sequence variant in which the allele state is associated in some way with the phenotype state\"\n )\n )\n )\n )\n (\n \"variant to disease association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"comments\"\n \"TODO decide no how to model pathogenicity\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"mixins\"\n \"variant to thing association\"\n \"entity to disease association\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"description\"\n . \"a sequence variant in which the allele state is associated in some way with the disease state\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"ClinVar:52241\"\n )\n (\n \"description\"\n . \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n )\n )\n )\n )\n (\n \"relation\"\n (\n \"description\"\n . \"E.g. is pathogenic for\"\n )\n (\n \"subproperty_of\"\n . \"related condition\"\n )\n )\n (\n \"object\"\n (\n \"description\"\n . \"a disease that is associated with that variant\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"MONDO:0016419\"\n )\n (\n \"description\"\n . \"hereditary breast cancer\"\n )\n )\n )\n )\n )\n )\n (\n \"model to disease mixin\"\n (\n \"mixin\"\n . #t\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"description\"\n . \"This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"description\"\n . \"The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease\"\n )\n )\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"model of\"\n )\n (\n \"description\"\n . \"The relationship to the disease\"\n )\n )\n )\n )\n (\n \"gene as a model of disease association\"\n (\n \"is_a\"\n . \"gene to disease association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n \"relation\"\n )\n (\n \"mixins\"\n \"model to disease mixin\"\n \"entity to disease association\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.\"\n )\n )\n )\n )\n (\n \"gene has variant that contributes to disease association\"\n (\n \"is_a\"\n . \"gene to disease association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n \"relation\"\n )\n (\n \"slots\"\n \"sequence variant qualifier\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.\"\n )\n )\n )\n )\n (\n \"genotype to thing association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"genotype\"\n )\n (\n \"description\"\n . \"genotype that is the subject of the association\"\n )\n )\n )\n )\n (\n \"gene to expression site association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n \"relation\"\n )\n (\n \"description\"\n . \"An association between a gene and an expression site, possibly qualified by stage/timing info.\"\n )\n (\n \"notes\"\n \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n )\n (\n \"see_also\"\n . \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n )\n (\n \"slots\"\n \"stage qualifier\"\n \"quantifier qualifier\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"description\"\n . \"gene in which variation is correlated with the phenotypic feature\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"location in which the gene is expressed\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"UBERON:0002037\"\n )\n (\n \"description\"\n . \"cerebellum\"\n )\n )\n )\n )\n (\n \"relation\"\n (\n \"description\"\n . \"expression relationship\"\n )\n (\n \"subproperty_of\"\n . \"expressed in\"\n )\n )\n (\n \"stage qualifier\"\n (\n \"range\"\n . \"life stage\"\n )\n (\n \"description\"\n . \"stage at which the gene is expressed in the site\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"UBERON:0000069\"\n )\n (\n \"description\"\n . \"larval stage\"\n )\n )\n )\n )\n (\n \"quantifier qualifier\"\n (\n \"description\"\n . \"can be used to indicate magnitude, or also ranking\"\n )\n )\n )\n )\n (\n \"sequence variant modulates treatment association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"description\"\n . \"An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used.\"\n )\n (\n \"comments\"\n \"An alternate way to model the same information could be via a qualifier\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"abstract\"\n . #t\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"sequence variant\"\n )\n (\n \"description\"\n . \"variant that modulates the treatment of some disease\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"treatment\"\n )\n (\n \"description\"\n . \"treatment whose efficacy is modulated by the subject variant\"\n )\n )\n )\n )\n (\n \"functional association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"description\"\n . \"An association between a macromolecular machine (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"macromolecular machine\"\n )\n (\n \"description\"\n . \"gene, product or macromolecular complex that has the function associated with the GO term\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"ZFIN:ZDB-GENE-050417-357\"\n )\n (\n \"description\"\n . \"twist1b\"\n )\n )\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene ontology class\"\n )\n (\n \"description\"\n . \"class describing the activity, process or localization of the gene product\"\n )\n (\n \"values_from\"\n \"go\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"GO:0016301\"\n )\n (\n \"description\"\n . \"kinase activity\"\n )\n )\n (\n (\n \"value\"\n . \"GO:0045211\"\n )\n (\n \"description\"\n . \"postsynaptic membrane\"\n )\n )\n )\n )\n )\n )\n (\n \"macromolecular machine to molecular activity association\"\n (\n \"is_a\"\n . \"functional association\"\n )\n (\n \"description\"\n . \"A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"molecular activity\"\n )\n )\n )\n )\n (\n \"macromolecular machine to biological process association\"\n (\n \"is_a\"\n . \"functional association\"\n )\n (\n \"description\"\n . \"A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"biological process\"\n )\n )\n )\n )\n (\n \"macromolecular machine to cellular component association\"\n (\n \"is_a\"\n . \"functional association\"\n )\n (\n \"description\"\n . \"A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component\"\n )\n (\n \"slot_usage\"\n (\n \"object\"\n (\n \"range\"\n . \"cellular component\"\n )\n )\n )\n )\n (\n \"gene to go term association\"\n (\n \"aliases\"\n \"functional association\"\n )\n (\n \"is_a\"\n . \"functional association\"\n )\n (\n \"class_uri\"\n . \"http://bio2rdf.org/wormbase_vocabulary:Gene-GO-Association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"molecular entity\"\n )\n (\n \"description\"\n . \"gene, product or macromolecular complex that has the function associated with the GO term\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"ZFIN:ZDB-GENE-050417-357\"\n )\n (\n \"description\"\n . \"twist1b\"\n )\n )\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene ontology class\"\n )\n (\n \"description\"\n . \"class describing the activity, process or localization of the gene product\"\n )\n (\n \"values_from\"\n \"go\"\n )\n (\n \"examples\"\n (\n (\n \"value\"\n . \"GO:0016301\"\n )\n (\n \"description\"\n . \"kinase activity\"\n )\n )\n )\n )\n )\n )\n (\n \"genomic sequence localization\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"description\"\n . \"A relationship between a sequence feature and an entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"aliases\"\n \"sequence feature\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"object\"\n (\n \"aliases\"\n \"reference\"\n )\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n )\n (\n \"slots\"\n \"start interbase coordinate\"\n \"end interbase coordinate\"\n \"genome build\"\n \"phase\"\n )\n (\n \"class_uri\"\n . \"faldo:location\"\n )\n )\n (\n \"sequence feature relationship\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"For example, a particular exon is part of a particular transcript or gene\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"genomic entity\"\n )\n )\n )\n )\n (\n \"transcript to gene relationship\"\n (\n \"is_a\"\n . \"sequence feature relationship\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"A gene is a collection of transcripts\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"transcript\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene\"\n )\n )\n )\n )\n (\n \"gene to gene product relationship\"\n (\n \"is_a\"\n . \"sequence feature relationship\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"A gene is transcribed and potentially translated to a gene product\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"gene\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene product\"\n )\n )\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"has gene product\"\n )\n )\n )\n )\n (\n \"exon to transcript relationship\"\n (\n \"is_a\"\n . \"sequence feature relationship\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"description\"\n . \"A transcript is formed from multiple exons\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"exon\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"transcript\"\n )\n )\n )\n )\n (\n \"gene regulatory relationship\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"description\"\n . \"A regulatory relationship between two genes\"\n )\n (\n \"slot_usage\"\n (\n \"relation\"\n (\n \"description\"\n . \"the direction is always from regulator to regulated\"\n )\n )\n (\n \"subject\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"role\"\n . \"regulatory gene\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"gene or gene product\"\n )\n (\n \"role\"\n . \"regulated gene\"\n )\n )\n )\n )\n (\n \"anatomical entity to anatomical entity association\"\n (\n \"is_a\"\n . \"association\"\n )\n (\n \"defining_slots\"\n \"subject\"\n \"object\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n )\n )\n )\n (\n \"anatomical entity to anatomical entity part of association\"\n (\n \"is_a\"\n . \"anatomical entity to anatomical entity association\"\n )\n (\n \"description\"\n . \"A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms\"\n )\n (\n \"defining_slots\"\n \"relation\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"the part\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"the whole\"\n )\n )\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"part of\"\n )\n )\n )\n )\n (\n \"anatomical entity to anatomical entity ontogenic association\"\n (\n \"is_a\"\n . \"anatomical entity to anatomical entity association\"\n )\n (\n \"description\"\n . \"A relationship between two anatomical entities where the relationship is ontogenic, i.e the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship\"\n )\n (\n \"defining_slots\"\n \"relation\"\n )\n (\n \"slot_usage\"\n (\n \"subject\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"the structure at a later time\"\n )\n )\n (\n \"object\"\n (\n \"range\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"the structure at an earlier time\"\n )\n )\n (\n \"relation\"\n (\n \"subproperty_of\"\n . \"develops from\"\n )\n )\n )\n )\n (\n \"occurrent\"\n (\n \"description\"\n . \"A processual entity\"\n )\n (\n \"is_a\"\n . \"named thing\"\n )\n (\n \"class_uri\"\n . \"BFO:0000003\"\n )\n )\n (\n \"biological process or activity\"\n (\n \"is_a\"\n . \"biological entity\"\n )\n (\n \"description\"\n . \"Either an individual molecular activity, or a collection of causally connected molecular activities\"\n )\n (\n \"id_prefixes\"\n \"GO\"\n \"Reactome\"\n )\n )\n (\n \"molecular activity\"\n (\n \"is_a\"\n . \"biological process or activity\"\n )\n (\n \"aliases\"\n \"molecular function\"\n \"molecular event\"\n \"reaction\"\n )\n (\n \"mixins\"\n \"occurrent\"\n )\n (\n \"description\"\n . \"An execution of a molecular function carried out by a gene product or macromolecular complex.\"\n )\n (\n \"class_uri\"\n . \"GO:0003674\"\n )\n (\n \"mappings\"\n \"UMLSSC:T044\"\n \"UMLSST:moft\"\n )\n (\n \"id_prefixes\"\n \"GO\"\n \"Reactome\"\n )\n )\n (\n \"activity and behavior\"\n (\n \"is_a\"\n . \"occurrent\"\n )\n (\n \"description\"\n . \"Activity or behavior of any independent integral living, organization or mechanical actor in the world\"\n )\n (\n \"mappings\"\n \"UMLSSG:ACTI\"\n \"UMLSSC:T051\"\n \"UMLSST:evnt\"\n \"UMLSSC:T052\"\n \"UMLSST:acty\"\n \"UMLSSC:T053\"\n \"UMLSST:bhvr\"\n \"UMLSSC:T054\"\n \"UMLSST:socb\"\n \"UMLSSC:T055\"\n \"UMLSST:inbe\"\n \"UMLSSC:T056\"\n \"UMLSST:dora\"\n \"UMLSSC:T057\"\n \"UMLSST:ocac\"\n \"UMLSSC:T064\"\n \"UMLSST:gora\"\n \"UMLSSC:T066\"\n \"UMLSST:mcha\"\n )\n )\n (\n \"procedure\"\n (\n \"is_a\"\n . \"occurrent\"\n )\n (\n \"description\"\n . \"A series of actions conducted in a certain order or manner\"\n )\n (\n \"mappings\"\n \"UMLSSG:PROC\"\n \"UMLSSC:T058\"\n \"UMLSST:hlca\"\n \"UMLSSC:T059\"\n \"UMLSST:lbpr\"\n \"UMLSSC:T060\"\n \"UMLSST:diap\"\n \"UMLSSC:T061\"\n \"UMLSST:topp\"\n \"UMLSSC:T062\"\n \"UMLSST:resa\"\n \"UMLSSC:T063\"\n \"UMLSST:mbrt\"\n \"UMLSSC:T065\"\n \"UMLSST:edac\"\n )\n )\n (\n \"phenomenon\"\n (\n \"is_a\"\n . \"occurrent\"\n )\n (\n \"description\"\n . \"a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question\"\n )\n (\n \"mappings\"\n \"UMLSSG:PHEN\"\n \"UMLSSC:T034\"\n \"UMLSST:lbtr\"\n \"UMLSSC:T038\"\n \"UMLSST:biof\"\n \"UMLSSC:T067\"\n \"UMLSST:phpr\"\n \"UMLSSC:T068\"\n \"UMLSST:hcpp\"\n \"UMLSSC:T069\"\n \"UMLSST:eehu\"\n \"UMLSSC:T070\"\n \"UMLSST:npop\"\n )\n )\n (\n \"biological process\"\n (\n \"is_a\"\n . \"biological process or activity\"\n )\n (\n \"mixins\"\n \"occurrent\"\n )\n (\n \"description\"\n . \"One or more causally connected executions of molecular functions\"\n )\n (\n \"class_uri\"\n . \"GO:0008150\"\n )\n (\n \"mappings\"\n \"SIO:000006\"\n \"WD:Q2996394\"\n )\n (\n \"id_prefixes\"\n \"GO\"\n \"Reactome\"\n )\n )\n (\n \"pathway\"\n (\n \"is_a\"\n . \"biological process\"\n )\n (\n \"class_uri\"\n . \"GO:0007165\"\n )\n (\n \"mappings\"\n \"SIO:010526\"\n \"PW:0000001\"\n \"WD:Q4915012\"\n )\n (\n \"id_prefixes\"\n \"GO\"\n \"Reactome\"\n )\n )\n (\n \"physiological process\"\n (\n \"aliases\"\n \"physiology\"\n )\n (\n \"is_a\"\n . \"biological process\"\n )\n (\n \"mappings\"\n \"UMLSSG:PHYS\"\n \"UMLSSC:T032\"\n \"UMLSST:orga\"\n \"UMLSSC:T039\"\n \"UMLSST:phsf\"\n \"UMLSSC:T040\"\n \"UMLSST:orgf\"\n \"UMLSSC:T041\"\n \"UMLSST:menp\"\n \"UMLSSC:T042\"\n \"UMLSST:ortf\"\n \"UMLSSC:T043\"\n \"UMLSST:celf\"\n \"UMLSSC:T045\"\n \"UMLSST:genf\"\n \"UMLSSC:T201\"\n \"UMLSST:clna\"\n )\n )\n (\n \"cellular component\"\n (\n \"is_a\"\n . \"anatomical entity\"\n )\n (\n \"description\"\n . \"A location in or around a cell\"\n )\n (\n \"class_uri\"\n . \"GO:0005575\"\n )\n (\n \"mappings\"\n \"SIO:001400\"\n \"WD:Q5058355\"\n \"UMLSSC:T026\"\n \"UMLSST:celc\"\n )\n (\n \"id_prefixes\"\n \"GO\"\n )\n )\n (\n \"cell\"\n (\n \"is_a\"\n . \"anatomical entity\"\n )\n (\n \"class_uri\"\n . \"GO:0005623\"\n )\n (\n \"mappings\"\n \"CL:0000000\"\n \"SIO:010001\"\n \"WD:Q7868\"\n \"UMLSSC:T025\"\n \"UMLSST:cell\"\n )\n (\n \"id_prefixes\"\n \"CL\"\n \"PO\"\n )\n )\n (\n \"cell line\"\n (\n \"is_a\"\n . \"biosample\"\n )\n (\n \"class_uri\"\n . \"CLO:0000031\"\n )\n (\n \"id_prefixes\"\n \"CLO\"\n )\n )\n (\n \"gross anatomical structure\"\n (\n \"aliases\"\n \"tissue\"\n \"organ\"\n )\n (\n \"is_a\"\n . \"anatomical entity\"\n )\n (\n \"class_uri\"\n . \"UBERON:0010000\"\n )\n (\n \"mappings\"\n \"SIO:010046\"\n \"WD:Q4936952\"\n \"UMLSSC:T017\"\n \"UMLSST:anst\"\n \"UMLSSC:T021\"\n \"UMLSST:ffas\"\n \"UMLSSC:T023\"\n \"UMLSST:bpoc\"\n \"UMLSSC:T024\"\n \"UMLSST:tisu\"\n \"UMLSSC:T018\"\n \"UMLSST:emst\"\n )\n (\n \"id_prefixes\"\n \"UBERON\"\n \"PO\"\n \"FAO\"\n )\n )\n )\n)\n)\n" }, { "path": "attic/yaml/example1.scm", "content": "(define example1\n'(\n (\n \"id\"\n . \"http://example.org/sample/example1\"\n )\n (\n \"name\"\n . \"synopsis2\"\n )\n (\n \"prefixes\"\n (\n \"foaf\"\n . \"http://xmlns.com/foaf/0.1/\"\n )\n (\n \"samp\"\n . \"http://example.org/model/\"\n )\n (\n \"xsd\"\n . \"http://www.w3.org/2001/XMLSchema#\"\n )\n )\n (\n \"default_prefix\"\n . \"samp\"\n )\n (\n \"default_curi_maps\"\n \"semweb_context\"\n )\n (\n \"default_range\"\n . \"string\"\n )\n (\n \"types\"\n (\n \"string\"\n (\n \"base\"\n . \"str\"\n )\n (\n \"uri\"\n . \"xsd:string\"\n )\n )\n (\n \"int\"\n (\n \"base\"\n . \"int\"\n )\n (\n \"uri\"\n . \"xsd:integer\"\n )\n )\n (\n \"boolean\"\n (\n \"base\"\n . \"Bool\"\n )\n (\n \"uri\"\n . \"xsd:boolean\"\n )\n )\n )\n (\n \"classes\"\n (\n \"person\"\n (\n \"description\"\n . \"A person, living or dead\"\n )\n (\n \"slots\"\n \"id\"\n \"first name\"\n \"last name\"\n \"age\"\n \"living\"\n \"knows\"\n )\n )\n (\n \"friendly_person\"\n (\n \"description\"\n . \"Any person that knows someone\"\n )\n (\n \"is_a\"\n . \"person\"\n )\n (\n \"slot_usage\"\n (\n \"knows\"\n (\n \"required\"\n . #t\n )\n )\n )\n )\n )\n (\n \"slots\"\n (\n \"id\"\n (\n \"description\"\n . \"Unique identifier of a person\"\n )\n (\n \"identifier\"\n . #t\n )\n )\n (\n \"first name\"\n (\n \"description\"\n . \"The first name of a person\"\n )\n (\n \"slot_uri\"\n . \"foaf:firstName\"\n )\n (\n \"multivalued\"\n . #t\n )\n )\n (\n \"last name\"\n (\n \"description\"\n . \"The last name of a person\"\n )\n (\n \"slot_uri\"\n . \"foaf:lastName\"\n )\n (\n \"required\"\n . #t\n )\n )\n (\n \"living\"\n (\n \"description\"\n . \"Whether the person is alive\"\n )\n (\n \"range\"\n . \"boolean\"\n )\n (\n \"comments\"\n \"unspecified means unknown\"\n )\n )\n (\n \"age\"\n (\n \"description\"\n . \"The age of a person if living or age of death if not\"\n )\n (\n \"range\"\n . \"int\"\n )\n (\n \"slot_uri\"\n . \"foaf:age\"\n )\n )\n (\n \"knows\"\n (\n \"description\"\n . \"A person known by this person (indicating some level of reciprocated interaction between the parties).\"\n )\n (\n \"range\"\n . \"person\"\n )\n (\n \"slot_uri\"\n . \"foaf:knows\"\n )\n (\n \"multivalued\"\n . #t\n )\n )\n )\n)\n)\n" }, { "path": "attic/yaml/example1.yaml", "content": "id: http://example.org/sample/example1\nname: synopsis2\nprefixes:\n foaf: http://xmlns.com/foaf/0.1/\n samp: http://example.org/model/\n xsd: http://www.w3.org/2001/XMLSchema#\n \ndefault_prefix: samp\n\ndefault_curi_maps:\n - semweb_context\n \ndefault_range: string\n\ntypes:\n string:\n base: str\n uri: xsd:string\n int:\n base: int\n uri: xsd:integer\n boolean:\n base: Bool\n uri: xsd:boolean\n \n\nclasses:\n person:\n description: A person, living or dead\n slots:\n - id\n - first name\n - last name\n - age\n - living\n - knows\n \n friendly_person:\n description: Any person that knows someone\n is_a: person\n slot_usage:\n knows:\n required: True\n\nslots:\n id:\n description: Unique identifier of a person\n identifier: true\n\n first name:\n description: The first name of a person\n slot_uri: foaf:firstName\n multivalued: true\n \n last name:\n description: The last name of a person\n slot_uri: foaf:lastName\n required: true\n \n living:\n description: Whether the person is alive\n range: boolean\n comments:\n - unspecified means unknown\n \n age:\n description: The age of a person if living or age of death if not\n range: int\n slot_uri: foaf:age\n \n knows:\n description: A person known by this person (indicating some level of reciprocated interaction between the parties).\n range: person\n slot_uri: foaf:knows\n multivalued: true" }, { "path": "attic/yaml/yaml.scm", "content": "#|\n\nTODOs\n\n* handle 'abstract' or 'mixin' associations -- mixin and abstract classes can never be instantiated!\n\n|#\n\n\n(load \"biolink-model.scm\")\n(define model biolink-model)\n\n(define (cat l1)\n (map (lambda (c) (car c)) (cdr (assoc l1 model))))\n\n(define (rel l1 l2)\n (map (lambda (c) (cons (car c)\n (let ((p (assoc l2 (cdr c))))\n (if p (cdr p) #f))))\n (cdr (assoc l1 model))))\n\n(define (chain k r)\n (cons k\n (let ((p (assoc k r)))\n (if (cdr p)\n (chain (cdr p) r)\n '()))))\n(define (refl-trans-closure r)\n (map (lambda (p) (chain (car p) r)) r))\n(define (complement w r)\n (if (null? r) w (complement (remove (car r) w) (cdr r))))\n(define (r-complement w r)\n (map (lambda (p) (cons (car p) (complement w (cdr p)))) r))\n\n(define categories (cat \"classes\"))\n(define categories-is-a (rel \"classes\" \"is_a\"))\n(define categories-mixin (rel \"classes\" \"mixin\"))\n(define categories-abstract (rel \"classes\" \"abstract\"))\n(define categories-subs (refl-trans-closure categories-is-a))\n;;(define complement-categories-subs (r-complement categories categories-subs))\n\n(define categories-slots (filter (lambda (x) (cdr x)) (rel \"classes\" \"slots\")))\n(define categories-slot_usage (filter (lambda (x) (cdr x)) (rel \"classes\" \"slot_usage\")))\n\n(define predicates (cat \"slots\"))\n(define predicates-is-a (rel \"slots\" \"is_a\"))\n(define predicates-mixin (rel \"slots\" \"mixin\"))\n(define predicates-abstract (rel \"slots\" \"abstract\"))\n(define predicates-subs (refl-trans-closure predicates-is-a))\n;;(define complement-predicates-subs (r-complement predicates predicates-subs))\n\n(define predicates-domain (rel \"slots\" \"domain\"))\n\n(define predicates-range (rel \"slots\" \"range\"))\n\n(define (mk-sub name subs)\n `(define (,name s u)\n (conde\n ,@(map (lambda (cs) `((== s ,(car cs))\n ,`(conde\n ,@(map (lambda (c) `((== u ,c))) cs))))\n subs))))\n\n(define (mk-=/=-sub name subs)\n `(define (,name s u)\n (conde\n ,@(map (lambda (cs) (cons `(== s ,(car cs))\n (map (lambda (c) `(=/= u ,c)) cs)))\n subs))))\n\n(define (mk-pred name r)\n `(define (,name s u)\n (conde\n ,@(map (lambda (cs) `((== s ,(car cs))\n (== u ,(cdr cs))))\n r))))\n\n(load \"../code/mk/mk.scm\")\n(load \"../code/mk/test-check.scm\")\n(eval (mk-sub 'categories-subo categories-subs))\n(eval (mk-sub 'predicates-subo predicates-subs))\n;;(eval (mk-sub 'complement-categories-subo complement-categories-subs))\n;;(eval (mk-sub 'complement-predicates-subo complement-predicates-subs))\n(eval (mk-=/=-sub 'not-categories-subo categories-subs))\n(eval (mk-=/=-sub 'not-predicates-subo predicates-subs))\n(eval (mk-pred 'categories-mixino categories-mixin))\n(eval (mk-pred 'categories-abstracto categories-abstract))\n(eval (mk-pred 'predicates-mixino predicates-mixin))\n(eval (mk-pred 'predicates-abstracto predicates-abstract))\n\n(test \"sub-1\"\n (run* (q) (categories-subo q \"pathway\"))\n '((\"pathway\")))\n;; (test \"complement-sub-1\"\n;; (length (run* (q) (complement-categories-subo q \"pathway\")))\n;; 153)\n;; (test \"complement-sub-1b\"\n;; (length (run* (q) (complement-categories-subo \"pathway\" q)))\n;; 149)\n(test \"not-sub-1\"\n (length (run* (q) (not-categories-subo q \"pathway\")))\n 151)\n(test \"not-sub-1b\"\n (run* (q) (not-categories-subo \"pathway\" q))\n '((_.0 (=/= ((_.0 \"biological entity\"))\n ((_.0 \"biological process or activity\"))\n ((_.0 \"biological process\")) ((_.0 \"named thing\"))\n ((_.0 \"pathway\"))))))\n(test \"sub-2\"\n (run* (q) (categories-subo q \"gene or gene product\"))\n '((\"gene or gene product\")\n (\"gene\") (\"gene product\") (\"protein\") (\"gene product isoform\")\n (\"protein isoform\") (\"RNA product\") (\"RNA product isoform\")\n (\"noncoding RNA product\") (\"microRNA\")))\n(test \"super-1\"\n (run* (q) (categories-subo \"protein\" q))\n '((\"protein\")\n (\"gene product\") (\"gene or gene product\") (\"macromolecular machine\")\n (\"genomic entity\") (\"molecular entity\")\n (\"biological entity\") (\"named thing\")))\n(test \"super-2\"\n (run* (q) (predicates-subo \"regulates\" q))\n '((\"regulates\") (\"affects\") (\"related to\")))\n(test \"super-3\"\n (run* (q) (predicates-subo q \"homologous to\"))\n '((\"homologous to\")\n (\"paralogous to\")\n (\"orthologous to\")\n (\"xenologous to\")))\n\n(define (find-spec domain p)\n (if p\n (if (cdr p)\n (cdr p)\n (let ((parent (assoc (car p) predicates-is-a)))\n (if parent\n (find-spec domain (assoc (cdr parent) domain))\n (error 'find-spec \"no parent\" (car p)))))\n #f))\n\n(define (mk-valid-type name name_csubo name_psubo)\n `(define (,name subject verb object)\n (conde\n ,@(map (lambda (pd pr)\n (assert (equal? (car pd) (car pr)))\n `((== verb ,(car pd))\n (== subject ,(find-spec predicates-domain pd))\n (== object ,(find-spec predicates-range pr))))\n predicates-domain predicates-range))))\n\n(eval (mk-valid-type 'valid-typeo 'categories-subo 'predicates-subo))\n\n(test \"valid-1\"\n (run* (q)\n (fresh (a b)\n (valid-typeo a \"regulates\" b)\n (categories-subo \"pathway\" a)\n (categories-subo \"disease\" b)))\n '((_.0)))\n\n(test \"valid-2\"\n (run* (q p) (valid-typeo q \"homologous to\" p))\n '(((\"named thing\" \"named thing\"))))\n\n(test \"valid-sub-1\"\n (run* (s v o)\n (predicates-subo v \"homologous to\")\n (valid-typeo s v o))\n '(((\"named thing\" \"homologous to\" \"named thing\"))\n ((\"named thing\" \"paralogous to\" \"named thing\"))\n ((\"named thing\" \"orthologous to\" \"named thing\"))\n ((\"named thing\" \"xenologous to\" \"named thing\"))))\n\n(test \"valid-sub-2\"\n (run* (s v o)\n (predicates-subo \"homologous to\" v)\n (valid-typeo s v o))\n '(((\"named thing\" \"homologous to\" \"named thing\"))\n ((\"named thing\" \"related to\" \"named thing\"))))\n\n(test \"valid-sub-3\"\n (run* (s s1 v o o1)\n (predicates-subo v \"genetically interacts with\")\n (valid-typeo s v o)\n (categories-subo s1 s)\n (categories-subo o1 o))\n '(((\"gene\" \"gene\" \"genetically interacts with\" \"gene\" \"gene\"))))\n\n(test \"valid-4\"\n (run* (s v o)\n (== \"molecularly interacts with\" v)\n (valid-typeo s v o))\n '(((\"molecular entity\"\n \"molecularly interacts with\"\n \"molecular entity\"))))\n\n(test \"valid-sub-4\"\n (length (run* (s v o o1)\n (== \"molecularly interacts with\" v)\n (valid-typeo s v o)\n (categories-subo o1 o)))\n 26)\n\n(test \"valid-sub-5\"\n (run* (s v o o1)\n (== \"molecularly interacts with\" v)\n (== o1 \"sequence variant\")\n (valid-typeo s v o)\n (categories-subo o1 o))\n '(((\"molecular entity\"\n \"molecularly interacts with\"\n \"molecular entity\"\n \"sequence variant\"))))\n\n(test \"mol-sub-1\"\n (length (run* (q)\n (fresh (x)\n (== \"molecular entity\" x)\n (=/= x q)\n (categories-subo q x))))\n 25)\n\n(test \"gtga-1\"\n (run* (q)\n (fresh (x)\n (== \"gene to gene association\" x)\n (categories-subo x q)))\n '((\"gene to gene association\")\n (\"association\")))\n\n(assoc \"range\" (cdr (assoc \"subject\" (cdr (assoc \"gene to gene association\" categories-slot_usage)))))\n\n(define (mk-slot-table name slot)\n `(define (,name category slot)\n (conde\n ,@(filter (lambda (x) x)\n (map\n (lambda (c)\n (let ((s (assoc slot (cdr c))))\n (if s\n (let ((r (assoc \"range\" (cdr s))))\n (if r\n `((== category ,(car c))\n (== slot ,(cdr r)))\n #f))\n #f)))\n categories-slot_usage)))))\n\n(eval (mk-slot-table 'categories-subjecto \"subject\"))\n(eval (mk-slot-table 'categories-objecto \"object\"))\n\n(test \"slot-challenge-0a\"\n (run* (b)\n (categories-subo \"protein\" b))\n '((\"protein\")\n (\"gene product\")\n (\"gene or gene product\")\n (\"macromolecular machine\")\n (\"genomic entity\")\n (\"molecular entity\")\n (\"biological entity\")\n (\"named thing\")))\n\n(test \"slot-challenge-0b\"\n (run* (a)\n (categories-subo a \"association\"))\n '((\"association\")\n (\"genotype to genotype part association\")\n (\"genotype to gene association\")\n (\"genotype to variant association\")\n (\"gene to gene association\")\n (\"gene to gene homology association\")\n (\"pairwise interaction association\")\n (\"pairwise gene to gene interaction\")\n (\"cell line to thing association\")\n (\"cell line to disease or phenotypic feature association\")\n (\"chemical to thing association\")\n (\"case to thing association\")\n (\"chemical to disease or phenotypic feature association\")\n (\"chemical to pathway association\")\n (\"chemical to gene association\")\n (\"biosample to thing association\")\n (\"biosample to disease or phenotypic feature association\")\n (\"entity to phenotypic feature association\")\n (\"disease or phenotypic feature association to thing association\")\n (\"disease or phenotypic feature association to location association\")\n (\"thing to disease or phenotypic feature association\")\n (\"disease to thing association\")\n (\"genotype to phenotypic feature association\")\n (\"environment to phenotypic feature association\")\n (\"disease to phenotypic feature association\")\n (\"case to phenotypic feature association\")\n (\"gene to thing association\")\n (\"variant to thing association\")\n (\"gene to phenotypic feature association\")\n (\"gene to disease association\")\n (\"variant to population association\")\n (\"population to population association\")\n (\"variant to phenotypic feature association\")\n (\"variant to disease association\")\n (\"gene as a model of disease association\")\n (\"gene has variant that contributes to disease association\")\n (\"genotype to thing association\")\n (\"gene to expression site association\")\n (\"sequence variant modulates treatment association\")\n (\"functional association\")\n (\"macromolecular machine to molecular activity association\")\n (\"macromolecular machine to biological process association\")\n (\"macromolecular machine to cellular component association\")\n (\"gene to go term association\")\n (\"genomic sequence localization\")\n (\"sequence feature relationship\")\n (\"transcript to gene relationship\")\n (\"gene to gene product relationship\")\n (\"exon to transcript relationship\")\n (\"gene regulatory relationship\")\n (\"anatomical entity to anatomical entity association\")\n (\"anatomical entity to anatomical entity part of association\")\n (\"anatomical entity to anatomical entity ontogenic association\")))\n\n(test \"slot-challenge-0c\"\n (run* (b)\n (categories-subjecto \"gene to gene association\" b))\n '((\"gene or gene product\")))\n\n(test \"slot-challenge-0d\"\n (run* (a)\n (categories-subjecto a \"gene or gene product\"))\n '((\"gene to gene association\")\n (\"gene to thing association\")\n (\"gene to phenotypic feature association\")\n (\"gene to disease association\")\n (\"gene as a model of disease association\")\n (\"gene has variant that contributes to disease association\")\n (\"gene to expression site association\")\n (\"gene regulatory relationship\")))\n\n(test \"slot-challenge-0e\"\n (run* (a)\n (categories-objecto a \"gene or gene product\"))\n '((\"gene to gene association\")\n (\"chemical to gene association\")\n (\"gene regulatory relationship\")))\n\n(test \"slot-challenge-0f\"\n (run* (q)\n (fresh (a)\n (conde\n ((categories-subjecto \"chemical to gene association\" a)\n (== `(categories-subjecto ,a) q))\n ((categories-objecto \"chemical to gene association\" a)\n (== `(categories-objecto ,a) q)))))\n '(((categories-objecto \"gene or gene product\"))))\n\n(test \"slot-challenge-1\"\n (run 1 (a b)\n (categories-subo a \"association\")\n (categories-subo \"protein\" b)\n (categories-subjecto a b))\n '(((\"gene to gene association\" \"gene or gene product\"))))\n\n(test \"slot-challenge-2\"\n (run 1 (a b)\n (categories-subo a \"association\")\n (categories-subo \"protein\" b)\n (categories-objecto a b))\n '(((\"gene to gene association\" \"gene or gene product\"))))\n\n(define (specific-predo s1 v1 o1 s2 v2 o2)\n (fresh ()\n (categories-subo v2 v1)\n (categories-subjecto v2 s2)\n (categories-objecto v2 o2)\n (categories-subo s1 s2)\n (categories-subo o1 o2)))\n\n(test \"slot-challenge-3\"\n (run 1 (a b c)\n (specific-predo \"protein\" \"association\" \"protein\" a b c))\n '(((\"gene or gene product\"\n \"gene to gene association\"\n \"gene or gene product\"))))\n\n(test \"slot-challenge-4\"\n (run* (b)\n (fresh (a c)\n (specific-predo \"protein\" \"association\" \"protein\" a b c)))\n '((\"gene to gene association\")\n (\"pairwise interaction association\")\n (\"genomic sequence localization\")\n (\"sequence feature relationship\")\n (\"gene regulatory relationship\")))\n\n(test \"slot-challenge-5\"\n (run* (a b c)\n (specific-predo \"protein\" \"association\" \"protein\" a b c))\n '(((\"gene or gene product\" \"gene to gene association\" \"gene or gene product\"))\n ((\"molecular entity\" \"pairwise interaction association\" \"molecular entity\")) ;; abstract! shouldn't exist\n ((\"genomic entity\" \"genomic sequence localization\" \"genomic entity\"))\n ((\"genomic entity\" \"sequence feature relationship\" \"genomic entity\"))\n ((\"gene or gene product\" \"gene regulatory relationship\" \"gene or gene product\")) ;; does this association apply for a protein?\n ))\n\n(test \"slot-challenge-6\"\n (run* (a b c)\n (specific-predo \"protein\" \"association\" \"protein\" a b c)\n (categories-mixino a #f)\n (categories-mixino b #f)\n (categories-mixino c #f))\n '(((\"gene or gene product\" \"gene to gene association\" \"gene or gene product\"))\n ((\"genomic entity\" \"genomic sequence localization\" \"genomic entity\"))\n ((\"genomic entity\" \"sequence feature relationship\" \"genomic entity\"))\n ((\"gene or gene product\" \"gene regulatory relationship\" \"gene or gene product\"))))\n\n\n;;; \"homologous to\" should inherit the range and domain\n;;;\n;;; \"homologous to\" \"is_a\" \"related to\"\n;;;\n;;; related to\n;;;\n;;; (\n;;; \"domain\"\n;;; . \"named thing\"\n;;; )\n;;; (\n;;; \"range\"\n;;; . \"named thing\"\n;;; )\n;;; (\n;;; \"multivalued\"\n;;; . #t\n;;; )\n\n\n(test \"inherit-1\"\n (run* (q p)\n (valid-typeo q \"homologous to\" p))\n '(((\"named thing\" \"named thing\"))))\n\n(test \"inherit-2\"\n (run* (q)\n (fresh (pred)\n (== \"homologous to\" pred)\n (=/= pred q)\n (predicates-subo pred q)))\n '((\"related to\")))\n\n(test \"inherit-3\"\n (run* (x y)\n (valid-typeo x \"related to\" y))\n '(((\"named thing\" \"named thing\"))))\n\n(test \"inherit-4\"\n (run* (q) (categories-subo \"named thing\" q))\n '((\"named thing\")))\n\n(test \"inherit-5\"\n (run* (q p r)\n (predicates-subo \"homologous to\" r)\n (valid-typeo q r p))\n '(((\"named thing\" \"named thing\" \"homologous to\"))\n ((\"named thing\" \"named thing\" \"related to\"))))\n\n#!eof\n\n;;; Tricky case from Chris Mungall:\ngene_to_gene_association\n is_a association\n defining_slots [ subject : gene\n object : gene ]\n slot_usage [ subject.range = gene\n object.range = gene ]\n\n\n\nx = association\nx.subject = protein_coding_gene\nx.object = protein_coding_gene\n\nprotein_coding_gene is_a gene\n\n=> (implies)\n\ngene_to_gene_association(x)\n\n\n\n(test \"Chris-1\"\n (run* (pred)\n (most-specific-predo \"protein coding gene\" \"association\" \"protein coding gene\" pred))\n '(((\"gene to gene association\"))))\n" }, { "path": "attic/yaml/yaml2sexp.py", "content": "def sexp(r, indent=0, dot=''):\n i = indent*' '\n j = (indent+2)*' '\n if type(r) == dict:\n if dot=='':\n print(i+'(')\n for k,v in r.items():\n print(j+'(')\n sexp(k, indent+4, '')\n sexp(v, indent+4, '. ')\n print(j+')')\n if dot=='':\n print(i+')')\n elif type(r) == list:\n if dot=='':\n print(i+'(')\n for x in r:\n sexp(x,indent+2,'')\n if dot=='':\n print(i+')')\n elif type(r) == bool:\n if r:\n print(i+dot+'#t')\n else:\n print(i+dot+'#f')\n else:\n print(i+dot+'\"'+r+'\"')\n\nif __name__ == '__main__':\n from ruamel.yaml import YAML\n yaml=YAML(typ='safe') # default, if not specfied, is 'rt' (round-trip)\n import sys\n m = 'example1' if len(sys.argv)<2 else sys.argv[1]\n r = yaml.load(open(m+'.yaml'))\n import ntpath\n k = ntpath.basename(m)\n print('(define '+k)\n print(\"'\", end='')\n sexp(r)\n print(')')\n\n" }, { "path": "contrib/README.md", "content": "# Synopsis\n\nContributed use cases, queries and applications are now located in this directory, separate from medikanren itself.\n\n# Directory organization\n\nContributions are broken down by medikanren version:\n\n- [contrib/medikanren](medikanren) Contributions for medikanren version 1\n- [contrib/medikanren2](medikanren2) Contributions for medikanren version 2\n\n\n\n" }, { "path": "contrib/medikanren/2020_NCATS_relay/INTEGRATED-QUERY/textmining->rtx2.rkt", "content": "#lang racket\n(provide (all-defined-out))\n(require \"../../../../medikanren/pieces-parts/query.rkt\" \n racket/engine)\n\n(define crosskg-mondo-disease-curies\n '(\"MONDO:0016192\"\n \"DOID:0050890\"\n \"MONDO:0016153\"\n \"MONDO:0016147\"\n \"MONDO:0016191\"\n \"MONDO:0016196\"\n \"MONDO:0016187\"))\n\n(define CHEBI--negatively-regulates-->PR-->MONDO\n (curies/query\n (time (query/graph\n ((Drug #f)\n (PR #f)\n ;(Disease \"MONDO:0000510\")\n (Disease \"MONDO:0016147\")\n )\n ((Drug->PR (list \"biolink:negatively_regulates_entity_to_entity\") (edge/db? 'textminingprovider)) \n (PR->Disease\n (list\n \"gene_mapped_to_disease\"\n \"gene_involved_in_pathogenesis_of_disease\"\n \"gene_associated_with_disease\"\n \"associated_with_disease\"\n \"INVERTED:disease_has_basis_in_dysfunction_of\") (edge/db? 'rtx2_2020_09_16)))\n (Drug Drug->PR PR) \n (PR PR->Disease Disease)))\n 'Drug))\n\n(define CHEBI--postively-regulates-->PR-->MONDO\n (curies/query\n (time (query/graph\n ((Drug #f)\n (PR #f)\n (Disease \"MONDO:0000510\"))\n ((Drug->PR (list \"biolink:positively_regulates_entity_to_entity\") (edge/db? 'textminingprovider)) \n (PR->Disease\n (list\n \"gene_mapped_to_disease\"\n \"gene_involved_in_pathogenesis_of_disease\"\n \"gene_associated_with_disease\"\n \"associated_with_disease\"\n \"INVERTED:disease_has_basis_in_dysfunction_of\") (edge/db? 'rtx2_2020_09_16)))\n (Drug Drug->PR PR) \n (PR PR->Disease Disease)))\n 'Drug))\n\n" }, { "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/rtx2_2020_09_16-map.html", "content": "\n\n RTX2 KG Map\n \n\n\n
\n\n\n" }, { "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/rtx2_2020_09_16-stats.txt", "content": "predicates: 848\ncategories: 54\nconcepts: 10,527,134\nedges: 53,589,306\n" }, { "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/rtx2_2020_09_16-subject_predicate_object_count.tsv", "content": "subject CURIE prefix\tobject CURIE prefix\tpredicate\tedge count\nRXNORM\tRXNORM\trxcui:precise_ingredient_of\t6138\nEFO\tUMLS\txref\t2202\nUMLS\tNCBIGene\tuses\t27329\nGO\tGO\timmediately_causally_upstream_of\t2\nPR\tCHEBI\tsubclass_of\t206\nPR\tPR\tderives_from\t57\nARO\tBFO\tsubclass_of\t1\nEFO\tIAO\tsubclass_of\t38\nNCIT\tNCIT\tINVERTED:pathway_has_gene_element\t7181\nUBERON\tFBbt\tpart_of\t1\nUBERON\tCL\tsynapsed_by\t1\nOBI\tGENEPIO\tderives_from\t1\nCHEBI\tCHEBI\tis_tautomer_of\t1748\nEFO\tNCBITaxon\tsubclass_of\t305\nFMA\tFMA\tsurrounded_by\t139\nORPHANET\tOMIM\txref\t12142\nGO\tOBA\tregulates\t80\nGO\tOBA\tpositively_regulates\t11\nCHEBI\tEFO\tINVERTED:has_participant\t1\nOBO\tPR\tINVERTED:has_gene_template\t1013\nEPO\tTRANS\tsubclass_of\t1\nLOINC\tLOINC\thas_answer\t85940\nGO\tCL\tis_about\t1\nORPHANET\tORPHANET\torphanet:465410\t44\nSNOMED\tSNOMED\thas_process_output\t158\nMONDO\tGO\tdisease_triggers\t2\nNCIT\tNCIT\tdisease_is_stage\t6155\nGO\tGO\thas_primary_input\t2\nCL\tUBERON\tsubclass_of\t5\nEO\tIAO\tsubclass_of\t1\nUBERON\tUBERON\thas_potential_to_develop_into\t132\nNCIT\tNCIT\tINVERTED:gene_product_sequence_variation_encoded_by_gene_mutant\t556\nEO\tNCBITaxon\tsubclass_of\t2\nCL\tGO\tcapable_of\t308\nSO\tOBO\tsubclass_of\t4\nGAZ\tNCIT\ttype\t189\nUMLS\tUMLS\toccurs_in\t17801\nICD9\tUMLS\txref\t22406\nEFO\tMONDO\txref\t2604\nENVO\tMONDO\tINVERTED:realized_in_response_to\t1\nFMA\tFMA\tprojects_to\t117\nENVO\tENVO\toverlaps\t9\nSNOMED\tSNOMED\thas_dose_form_release_characteristic\t295\nDOID\tAQTLTrait\thas_phenotype\t1\nDOID\tEFO\tsubclass_of\t3\nSNOMED\tSNOMED\thas_disposition\t8941\nOBO\tSIO\tsubclass_of\t1\nGO\tCL\tresults_in_specification_of\t26\nFMA\tFMA\thas_full_grown_phenotype\t3\nIAO\tIAO\tINVERTED:type\t3\nGENEPIO\tARO\tequivalent_to\t1\nARO\tIAO\tsubclass_of\t3\nExO\tEPO\tsubclass_of\t1\nGO\tGO\tregulates\t5322\nGO\tGO\tpositively_regulates\t4656\nOBO\tOGG\thas_input\t1\nGENEPIO\tExO\tsubclass_of\t9\nUBERON\tUBERON\thas_potential_to_developmentally_contribute_to\t12\nCL\tBFO\tsubclass_of\t1\nENVO\tRO\tsubclass_of\t1\nORPHANET\tICD9\txref\t920\nUMLS\tNCBIGene\tcoexists_with\t92085\nMA\tUBERON\tpart_of\t1\nBTO\tEFO\tbearer_of\t5\nHMDB\tEHDAA2\tat_tissue\t1\nUBERON\tUBERON\taboral_to\t1\nENVO\tCHEBI\thas_increased_levels_of\t4\nEFO\tEFO\tinverse_of\t3\nCHEMBL.COMPOUND\tNCBIGene\tpositive_allosteric_modulator\t601\nUBERON\tUBERON\tattaches_to\t159\nOBO\tOBO\tsubclass_of\t286\nGO\tOBO\thas_primary_output\t16\nSNOMED\tSNOMED\thas_indirect_device\t77\nDRUGBANK\tUMLS\tclinically_tested_withdrawn_phase_1_or_phase_2\t30\nGTPI\tNCBIGene\tactivator\t87\nGO\tSO\texports\t4\nFMA\tFMA\tanterosuperior_to\t16\nMI\tOBO\tsubclass_of\t4\nUBERON\tUBERON\tlumen_of\t2\nEFO\tHANCESTRO\tpart_of\t12\nCHEBI\tGENEPIO\tsubclass_of\t72\nDRUGBANK\tPathWhiz.ProteinComplex\tINVERTED:has_protein_in_complex\t15\nFMA\tFMA\tnerve_supply_of\t2129\nHP\tEFO\txref\t1\nUniProtKB\tOMIM\tgene_mutations_contribute_to\t5765\nCL\tGO\thas_low_plasma_membrane_amount\t6\nUBERON\tUBERON\tINVERTED:produced_by\t46\nMONDO\tEFO\tpredisposes_towards\t14\nEFO\tPO\tlocated_in\t1\nLOINC\tLOINC\tproperty_of\t86472\nXCO\tGENEPIO\tsubclass_of\t2\nEFO\tEFO\tdisease_causes_feature\t1\nEFO\tPATO\tbearer_of\t19\nUBERON\tNCBITaxon\tonly_in_taxon\t749\nFMA\tFMA\tfuses_with\t26\nUBERON\tUBERON\timmediately_superficial_to\t13\nPO\tPO\txref\t1\nGO\tCL\thas_end_location\t3\nHMDB\tUMLS\tat_tissue\t137\nSNOMED\tMONDO\tequivalent_to\t9000\nSIO\tENVO\tsubclass_of\t1\nNCBIGene\tNCBIGene\tinhibits\t18289\nFMA\tFMA\thomonym_of\t73\nGO\tGO\tresults_in_fusion_of\t33\nIAO\tBFO\tsubclass_of\t1\nNCIT\tNCIT\tsubclass_of\t160929\nGO\tGO\tINVERTED:preceded_by\t1\nGO\tGO\thas_end_location\t5\nPathWhiz.Reaction\tPathWhiz.NucleicAcid\thas_right_element\t210\nUMLS\tNCBIGene\tcompared_with\t23729\nNCIT\tNCIT\tregimen_has_accepted_use_for_disease\t395\nMONDO\tOBO\tequivalent_to\t154\nCL\tCL\tpart_of\t1\nGO\tCL\thas_start_location\t3\nBTO\tUBERON\tpart_of\t5\nFMA\tFMA\tcontinuation_branch_of\t43\nPathWhiz.Reaction\tPathWhiz.Compound\thas_right_element\t336013\nGO\tGO\tends_during\t1\nPO\tPO\tINVERTED:develops_from\t60\nOBI\tOBI\tinheres_in\t3\nPathWhiz\tNCBITaxon\tin_species\t1905194\nSNOMED\tSNOMED\thas_finding_informer\t2207\nOMP\tGENEPIO\tsubclass_of\t1\nGO\tGO\thas_start_location\t8\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tbinding_agent\t136\nPATO\tPATO\tINVERTED:towards\t6\nENVO\tENVO\tINVERTED:composed_primarily_of\t34\nFMA\tUBERON\tpart_of\t2\nCLO\tCL\tsubclass_of\t428\nFMA\tFMA\tinverse_of_derives\t264\nPATO\tNBO\tINVERTED:has_participant\t1\nGTPI\tNCBIGene\tantagonist\t729\nRO\towl\tsub_property_of\t12\nGENEPIO\tGENEPIO\tINVERTED:after\t18\nENSEMBL\tNCBITaxon\tonly_in_taxon\t110\nCHEBI\tFOODON\tmember_of\t1\nIAO\tIAO\tsubclass_of\t30\nOBI\tGENEPIO\taligned_with\t1\nMPATH\tMPATH\tsubclass_of\t83\nGO\tMONDO\tINVERTED:realized_in_response_to_stimulus\t1\nNCIT\tNCIT\tdisease_is_grade\t1303\nUMLS\tUMLS\tpart_of\t893692\nUMLS\tUMLS\towning_section_of\t9\nDOID\tNCBITaxon\ttransmitted_by\t74\nPathWhiz.Reaction\tPathWhiz.NucleicAcid\thas_left_element\t349\nRXNORM\tRXNORM\trxcui:has_form\t2941\nHANCESTRO\tOBI\tsubclass_of\t2\nMP\tHP\tsubclass_of\t2\nHP\tUBERON\tinheres_in_part_of\t2\nHANCESTRO\tHANCESTRO\tinverse_of\t1\nUBERON\tUBERON\tbounding_layer_of\t37\nGENEPIO\tOBI\tis_about\t7\nEFO\tORPHANET\tsubclass_of\t328\nNCBIGene\tUMLS\ttreats\t1364\nSO\tCHEBI\tequivalent_to\t3\nPathWhiz.Reaction\tPathWhiz.Compound\thas_left_element\t317671\nGO\tBFO\tsubclass_of\t7\nNCIT\tNCIT\thas_pharmaceutical_basic_dose_form\t597\nCPT\tCPT\tsubclass_of\t14292\nENVO\tFOODON\tsubclass_of\t2\nFMA\tFMA\trelated_part\t3094\nICD10PCS\tUMLS\txref\t189499\nSNOMED\tSNOMED\thas_recipient_category\t117\nUMLS\tNCBIGene\tstimulates\t104111\nHP\tUBERON\tinheres_in\t1\nCHEBI\tCL\txref\t1\nEFO\tOBI\tis_about\t22\nZFA\tUBERON\tpart_of\t4\nPCO\tENVO\thas_habitat\t1\nPATO\tPATO\thas_relative_magnitude\t7\nMESH\tUMLS\txref\t402615\nMONDO\tUBERON\tdisease_has_basis_in_development_of\t2\nNBO\tGO\txref\t15\nCL\tUBERON\tINVERTED:composed_primarily_of\t83\nNCIT\tNCIT\teo_disease_has_associated_cell_type\t13\nMONDO\tOGMS\txref\t1\nPathWhiz.ElementCollection\tKEGG\tsame_as\t61\nOBI\tSTATO\tsubclass_of\t1\nNCBIGene\tUMLS\tinteracts_with\t183359\nGO\tCHEBI\thas_input\t967\nMONDO\tNCIT\tequivalent_to\t6777\nMESH\tMESH\tsubclass_of\t40243\nCL\tUBERON\tINVERTED:produced_by\t4\nCHEMBL.TARGET\tUniProtKB\tpart_of\t5700\nEHDAA2\tAEO\tsubclass_of\t1703\nOBI\tBTO\txref\t1\nEFO\tOBI\tinheres_in\t9\nFMA\tFMA\tsub_property_of\t3\nMONDO\tNCIT\tdisease_has_feature\t18\nNCIT\tNCIT\tINVERTED:organism_has_gene\t1635\nEFO\tOGMS\tsubclass_of\t3\nGO\tCHEBI\ttransports_or_maintains_localization_of\t969\nHP\tUMLS\txref\t16527\nUO\tUO\tsubclass_of\t228\nBTO\tEFO\tequivalent_to\t1\nCL\tFBbt\txref\t1\nEFO\tEFO\tINVERTED:has_participant\t69\nHGNC\tUniProtKB\thas_gene_product\t20312\nDOID\tMONDO\tsubclass_of\t5\nOMIM\tDOID\tcontributes_to_condition\t181\nSNOMED\tSNOMED\thas_dose_form_intended_site\t333\nUMLS\tNCBIGene\tassociated_with\t8728\nNCIT\tNCIT\tgene_product_malfunction_associated_with_disease\t509\nOBO\tMONDO\tequivalent_to\t154\nGENEPIO\tIDO\tis_about\t6\nSNOMED\tSNOMED\tcomponent_of\t4259\nSNOMED\tSNOMED\tuses_substance\t3187\nNCIT\tNCIT\tgene_product_has_structural_domain_or_motif\t4960\nFMA\tFMA\tcorresponds_to\t46\nOBI\tBFO\tsubclass_of\t18\nUBERON\tNBO\tcapable_of_part_of\t9\nNCBIGene\tUMLS\taffects\t154949\nUBERON\tUBERON\toverlaps\t70\nNCIT\tNCIT\tgene_product_has_chemical_classification\t1688\nSO\tGO\tINVERTED:has_participant\t4\nFOODON\tGENEPIO\tsubclass_of\t15\nUBERON\tGO\tcapable_of_part_of\t135\nDOID\tCL\tderives_from\t355\nSNOMED\tSNOMED\tinherent_location_of\t1\nPATO\tPATO\thas_cross_section\t5\nNCBITaxon\tENVO\tINVERTED:composed_primarily_of\t1\nGO\tCL\tINVERTED:has_plasma_membrane_part\t1\nKEGG\tPathWhiz.Bound\tINVERTED:has_element_in_bound\t162\nNCIT\tNCIT\tanatomic_structure_is_physical_part_of\t9339\nPathWhiz.NucleicAcid\tPathWhiz\tINVERTED:has_nucleic_acid\t1763\nNPO\tNPO\tsubclass_of\t3\nUniProtKB\tGO\tpart_of\t80696\nMONDO\tHGNC\thas_material_basis_in_gain_of_function_germline_mutation_in\t6\nCL\tUBERON\tparticipates_in\t4\nGO\tOMIM\tINVERTED:disease_caused_by_disruption_of\t4\nORPHANET\tUBERON\thas_disease_location\t65\nCARO\tCARO\tsubclass_of\t49\nGO\tMONDO\tINVERTED:realized_in_response_to\t4\nSNOMED\tSNOMED\thas_time_aspect\t23\nOGMS\tUBERON\tsubclass_of\t1\nBSPO\tCARO\tpasses_through\t1\nNCBIGene\tNCBIGene\tproduces\t3596\nMONDO\tMESH\txref\t7875\nOBO\tGENEPIO\tis_about\t1\nFOODON\tFOODON\tmember_of\t5921\nSNOMED\tSNOMED\thas_laterality\t12116\nMONDO\tMONDO\tpredisposes_towards\t143\nCHEMBL.COMPOUND\tNCBIGene\tgating_inhibitor\t24\nTO\tTO\tsubclass_of\t1\nGO\tCHEBI\timports\t179\nGENEPIO\tENVO\tis_about\t1\nOBO\tUBERON\txref\t6\nPO\tNCBITaxon\tonly_in_taxon\t2\nOBI\tIAO\tsubclass_of\t35\nEFO\tMONDO\tdisease_causes_feature\t1\nEFO\tCL\tpart_of\t2\nOGMS\tBFO\tsubclass_of\t4\nRGD\tPR\tINVERTED:has_gene_template\t8114\nCPT\tUMLS\txref\t46941\nAEO\tCARO\tsurrounds\t1\nEFO\tDOID\txref\t2350\nPCO\tENVO\tINVERTED:determined_by\t3\nUBERON\tUBERON\tsurrounds\t78\nSO\tDOID\tINVERTED:disease_has_basis_in\t251\nUBERON\tNCIT\txref\t2580\nUBERON\tMONDO\tINVERTED:realized_in_response_to_stimulus\t1\nNBO\tNBO\tINVERTED:by_means\t2\nGO\tUBERON\tresults_in_maturation_of\t53\nwb\tSO\tsubclass_of\t4479\nGO\tOMIM\txref\t4\nBTO\tUBERON\txref\t1\nBSPO\tCARO\tsubclass_of\t7\nSO\tSO\tINVERTED:has_member\t1\nGTPI\tNCBIGene\tantibody\t25\nFBbt\tCL\txref\t1\nNCIT\tNCIT\tgene_plays_role_in_process\t13660\nFOODON\towl\tsub_property_of\t1\nNCIT\tNCIT\tINVERTED:may_be_normal_cell_origin_of_disease\t183\nUMLS\tUMLS\tinverse_of_rq\t1560\nDRUGBANK\tUniProtKB\texternal_identifier\t69\nCHEMBL.COMPOUND\tDRUGBANK\tsame_as\t6926\nEFO\tMP\tsubclass_of\t7\nPATO\tPATO\tsubclass_of\t2113\nPR\tMONDO\tINVERTED:realized_in_response_to_stimulus\t1\nNCBIGene\tUMLS\tINVERTED:location_of\t332757\nSNOMED\tSNOMED\thas_access\t1520\nSNOMED\tOBI\tsubclass_of\t1\nUMLS\tUMLS\tmapped_to\t456\nFMA\tFMA\tleft_medial_to\t3\nCPT\tCPT\thas_add_on_code\t6931\nDOID\tEFO\txref\t130\nEFO\tEFO\tdisease_has_basis_in_feature\t18\nOBI\tRO\tsub_property_of\t7\nBTO\tUBERON\tsubclass_of\t9\nNCIT\tNCIT\thas_target\t727\nBSPO\tBSPO\torthogonal_to\t3\nGENEPIO\tGENEPIO\taligned_with\t1\nENVO\tENVO\tINVERTED:process_has_causal_agent\t3\nCL\tBTO\txref\t4\nPathWhiz.Reaction\tPathWhiz.ProteinComplex\thas_right_element\t906\nNCIT\tNCIT\tgene_product_is_physical_part_of\t616\nExO\tGENEPIO\tsubclass_of\t1\nUBERON\tGO\tINVERTED:process_has_causal_agent\t1\nttd.target\tNCBIGene\tantibody\t22\nGO\tCL\toccurs_in\t129\nPO\tFOODON\tsubclass_of\t2\nENVO\tENVO\tINVERTED:has_participant\t10\nMONDO\tMEDDRA\tequivalent_to\t1\nUBERON\tUBERON\tcontinuous_with\t120\nBTO\tBFO\tsubclass_of\t3\nFOODON\tFOODON\tsurrounded_by\t1\nSNOMED\tSNOMED\thas_direct_site\t27\nGO\tGO\toccurs_in\t270\nMESH\tMESH\tINVERTED:inverse_of_isa\t5029\nFMA\tFMA\trelated_developmental_entity_of\t13\nFMA\tFMA\thas_segmental_supply\t613\nEFO\tCL\tinheres_in_part_of\t1\nNCBIGene\tUMLS\tconverts_to\t2870\nEFO\tBTO\txref\t3\nENVO\tOBI\tsubclass_of\t2\nLOINC\tLOINC\thas_imaging_focus\t5463\nGENEPIO\tOBI\tmember_of\t1\nDOID\tGO\tdisease_has_basis_in_dysfunction_of\t8\nUMLS\tUMLS\tpredisposes\t256197\nFBdv\tEFO\tsubclass_of\t1\nPathWhiz.ProteinComplex\tPathWhiz.Reaction\tINVERTED:has_enzyme\t165371\nUBERON\tUBERON\tdeep_to\t12\nHP\tHP\tsubclass_of\t22195\nORPHANET\tGO\tparticipates_in\t3\nMONDO\tUBERON\thas_modifier\t1\nGO\tFAO\tpart_of\t3\nLOINC\tLOINC\thas_method\t66244\nHP\tEFO\tsubclass_of\t46\nIDO\tCHEBI\tsubclass_of\t1\nUMLS\tNCBIGene\tinteracts_with\t141256\nOBI\tOBI\tinverse_of\t2\nFMA\tFMA\tdevelops_into\t3\nAEO\tAEO\tpart_of\t22\nCHEMBL.TARGET\tCHEMBL.TARGET\tINVERTED:superset_of\t1116\nPathWhiz.Reaction\tPathWhiz.ProteinComplex\thas_left_element\t734\nUBERON\tUBERON\tINVERTED:location_of\t9\nBTO\tEFO\tparticipates_in\t2\nFMA\tFMA\tgerm_origin_of\t1\nNCIT\tNCIT\tallele_has_abnormality\t180\nLOINC\tLOINC\thas_timing_of\t2693\nMONDO\tSO\thas_modifier\t22\nDRUGBANK\tUMLS\tclinically_tested_withdrawn_phase_0\t7\nEFO\tUO\tequivalent_to\t1\nGO\tPR\texports\t1\nEFO\tMA\thas_disease_location\t1\nEnsemblGenomes\tNCBITaxon\tonly_in_taxon\t278\nEFO\tHP\tdisease_has_feature\t1\nUniProtKB\tREACT\tparticipates_in\t779447\nSNOMED\tSNOMED\thas_indirect_morphology\t544\nNCIT\tVCARD\tsubclass_of\t1\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tpositive_modulator\t18\nSNOMED\tSNOMED\thas_dependent\t6\nUMLS\tNCBIGene\taffects\t12913\nFOODON\tGAZ\tsubclass_of\t13\nUMLS\tUMLS\tcomponent_of\t13\nEFO\tEFO\tdisease_has_feature\t34\nHMDB\tFMA\tat_cellular_location\t1\nFMA\tFMA\tconstitutional_part_of\t21424\nPathWhiz.Reaction\tPathWhiz.Bound\thas_right_element\t167\nUBERON\tBSPO\tsub_property_of\t6\nNCIT\tNCIT\tgene_is_biomarker_of\t18\nOBO\tOBO\thas_interaction_type\t1\nUMLS\tUMLS\tsame_as\t15124\nBFO\tRO\tsub_property_of\t4\nNCIT\tNCIT\tdisease_has_associated_anatomic_site\t30160\nRO\tUBERON\tsub_property_of\t1\nHMDB\tEHDAA2\tin_biospecimen\t1\nMOD\tPR\tsubclass_of\t41\nFMA\tFMA\thas_adherent\t7\nCL\tCARO\tsubclass_of\t2\nGENEPIO\tOBI\tinheres_in\t1\nGO\tCL\tresults_in_acquisition_of_features_of\t300\nNDDF\tNDDF\tINVERTED:has_ingredient\t24\nSNOMED\tSNOMED\thas_concentration_strength_denominator_unit\t2065\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tnegative_modulator\t4\nCHEMBL.COMPOUND\tCHEMBL.TARGET\topener\t38\nSNOMED\tSNOMED\thas_finding_method\t4099\nRXNORM\tRXNORM\tINVERTED:rxcui:inverse_isa\t44612\nMONDO\tGARD\txref\t5818\nNBO\tUBERON\tINVERTED:input_of\t1\nRO\tBFO\tsub_property_of\t26\nGO\tPR\tdirectly_positively_regulates\t2\nSNOMED\tSNOMED\toccurs_before\t2413\nCHEMBL.COMPOUND\tNCBIGene\tinducer\t4\nDRUGBANK\tCHEMBL.COMPOUND\texternal_identifier\t7632\nUBERON\tUBERON\timmediately_preceded_by\t7\nSTATO\tGENEPIO\tsubclass_of\t6\nMPATH\tBFO\tsubclass_of\t1\nVANDF\tVANDF\tINVERTED:has_ingredient\t14304\nPDQ\tPDQ\tINVERTED:has_component\t4862\nGENEPIO\tPATO\tsubclass_of\t2\nGENEPIO\tEDAM\tsubclass_of\t1\nLOINC\tLOINC\thas_evaluation\t10553\nFMA\tFMA\tfull_grown_phenotype_of\t3\nNCIT\tNCIT\tgene_product_has_organism_source\t825\nOPL\tOPL\tsubclass_of\t27\nSNOMED\tSNOMED\tprecise_active_ingredient_of\t7240\nHP\tCL\taffects\t110\nPathWhiz.Reaction\tPathWhiz.Bound\thas_left_element\t157\nUBERON\tUBERON\textends_fibers_into\t127\nDRUGBANK\tHMDB\tsame_as\t1565\nBSPO\tRO\tsub_property_of\t4\nHMDB\tUMLS\tin_biospecimen\t11184\nDRUGBANK\tUMLS\tclinically_tested_terminated_phase_2_or_phase_3\t39\nUMLS\tUMLS\tadministered_to\t203874\nPathWhiz.Reaction\tPathWhiz\tINVERTED:has_reaction\t747189\nCHEBI\tCHEBI\thas_functional_parent\t17221\nPathWhiz.Reaction\tKEGG\thas_right_element\t263206\nUBERON\tUBERON\tventral_to\t8\nNCBIGene\tUniProtKB\tregulates_expression_of\t332256\nFMA\tFMA\tinverse_of_bounds\t1076\nEFO\tHP\thas_modifier\t30\nDRUGBANK\tMESH\tcategory\t57884\nORPHANET\tNCIT\txref\t1012\nDOID\tUMLS\txref\t6\nNCIT\tNCIT\tprocedure_may_have_completely_excised_anatomy\t6\nENVO\tENVO\tsubclass_of\t590\nORPHANET\tORPHANET\torphanet:317344\t176\nOMOP\tMONDO\tequivalent_to\t1590\nDOID\tDOID\tsubclass_of\t14358\nSNOMED\tSNOMED\tfocus_of\t4294\nFMA\tFMA\thas_tributary\t1007\nGARD\tMONDO\tequivalent_to\t5814\nMONDO\tICD10\tequivalent_to\t1113\nGENEPIO\tOMP\tsubclass_of\t1\nCL\tUBERON\tINVERTED:has_part\t224\nEFO\tEFO\thas_about_it\t2\nCL\tMONDO\tINVERTED:disease_has_basis_in_dysfunction_of\t8\nHMDB\tCHEMBL.TARGET\tat_tissue\t174\nEFO\tHP\tis_about\t19\nUMLS\tUMLS\thas_supported_concept_property\t239\nOBI\tOGMS\tsubclass_of\t2\nUBERON\tUBERON\tINVERTED:develops_from\t1373\nICD10PCS\tICD10PCS\tsubclass_of\t189482\nEFO\tEFO\tis_about\t556\nDRUGBANK\tUMLS\tclinically_tested_suspended_phase_0\t1\nDDANAT\tDDANAT\tpart_of\t134\nSNOMED\tSNOMED\thas_procedure_morphology\t177\nCHEMBL.COMPOUND\tCHEMBL.TARGET\toxidative_enzyme\t2\nAEO\tAEO\tsubclass_of\t89\nUBERON\tUBERON\tin_posterior_side_of\t15\nCL\tUBERON\taxon_synapses_in\t13\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tchelating_agent\t19\nPO\tPO\tpart_of\t132\nNCBIGene\tGO\tinvolved_in\t1417\nHP\tDOID\txref\t34\nGENEPIO\tOMIT\tis_about\t4\nDOID\tMONDO\txref\t6\nEFO\tMONDO\tdisease_has_basis_in_feature\t3\nPathWhiz.Reaction\tKEGG\thas_left_element\t232427\nDOID\tGENEPIO\tsubclass_of\t2\nGO\tCHEBI\tregulates_levels_of\t62\nFMA\tFMA\texternal_to\t1\nNCBITaxon\tPATO\thas_quality\t1\nMA\tUBERON\tsubclass_of\t2\nEFO\tEFO\tinheres_in\t1\nEFO\tGO\tparticipates_in\t25\nEHDAA2\tEHDAA2\tsubclass_of\t155\nUBERON\tUBERON\tderived_from_ancestral_fusion_of\t63\nttd.target\tNCBIGene\tmodulator\t9\nSNOMED\tSNOMED\thas_finding_context\t2531\nUBERON\tUBERON\tdistalmost_part_of\t5\nVT\tEFO\tsubclass_of\t1\nFMA\tFMA\tanteroinferior_to\t27\nCARO\tRO\tsubclass_of\t1\nCHEBI\tGO\tINVERTED:has_intermediate\t83\nUniProtKB\tGO\tcontributes_to\t975\nNCBITaxon\tBFO\tsubclass_of\t1\nGENEPIO\tOBI\tdenotes\t1\nNCIT\tNCIT\thas_pharmaceutical_transformation\t520\nGO\tGO\tresults_in_transport_across\t45\nCL\tEFO\tlocated_in\t1\nNBO\tNBO\tINVERTED:in_response_to\t5\nRXNORM\tRXNORM\tINVERTED:rxcui:contains\t990\nENVO\tOIO\tsubclass_of\t1\nGENEPIO\tUO\tINVERTED:is_unit_of\t1\nSNOMED\tSNOMED\thas_presentation_strength_numerator_value\t4836\nMONDO\tPATO\txref\t1\nNCBIGene\tUniProtKB\thas_gene_product\t19230\nOMIT\tOBI\tsubclass_of\t2\nNCIT\tUBERON\tsubclass_of\t2\nttd.target\tNCBIGene\tantagonist\t121\nUBERON\tUBERON\texistence_starts_during\t13\nGENEPIO\tRO\tinverse_of\t1\nNCIT\tNCIT\tchemical_or_drug_has_physiologic_effect\t2053\nGO\tCARO\tsubclass_of\t21\nEFO\tMA\txref\t1\nCGNC\tNCBITaxon\tonly_in_taxon\t552\nEFO\tPATO\tsubclass_of\t2\nNCBIGene\tNCBITaxon\tonly_in_taxon\t5380\nGO\tGO\tresults_in_distribution_of\t7\nFMA\tFMA\tcontinuous_distally_with\t1879\nHP\tMONDO\tsubclass_of\t1\nMONDO\tWD\tequivalent_to\t2\nOBI\tPR\tsubclass_of\t1\nMONDO\tUBERON\tdisease_has_location\t793\nEFO\tOMIM\txref\t875\nNCIT\tBFO\tsubclass_of\t7\nPathWhiz.Compound\tDRUGBANK\tsame_as\t1539\nHP\tCHEBI\tsubclass_of\t1\nOGG\tBFO\tsubclass_of\t1\nFIX\tGENEPIO\tsubclass_of\t1\nNCBITaxon\tNCBITaxon\tsubclass_of\t1783396\nEFO\tRO\tsub_property_of\t2\nLOINC\tLOINC\tINVERTED:has_subject\t34\nFBbt\tUBERON\tsubclass_of\t22\nGO\tGO\tresults_in_structural_organization_of\t1\nNCBITaxon\tMONDO\tINVERTED:realized_in_response_to_stimulus\t482\nOBO\tSTATO\tsubclass_of\t8\nFMA\tFMA\tinferolateral_to\t8\nOMIM\tHP\thas_phenotype\t94807\nSO\tSO\tsubclass_of\t2326\nNCRO\tGENEPIO\tsubclass_of\t1\nEFO\tMONDO\tdisease_has_feature\t34\nSO\tBFO\tsubclass_of\t4\nSNOMED\tSNOMED\tsubclass_of\t554879\nsgd\tNCBITaxon\tonly_in_taxon\t5938\nHMDB\tGO\tat_cellular_location\t16784\nENVO\tENVO\tinheres_in\t7\nFMA\tFMA\torigin_of\t275\nSNOMED\tSNOMED\thas_modification\t2130\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tnegative_allosteric_modulator\t13\nSNOMED\tSNOMED\thas_specimen_substance\t926\nORPHANET\tPR\thas_disease_location\t1\nHP\tSYMP\thas_symptom\t2\nOPL\tCL\tsubclass_of\t1\nFMA\tFMA\tmember_of\t2295\nEFO\tICD9\txref\t2049\nCHEBI\tKEGG\tsame_as\t1689\nNCIT\tIAO\tsubclass_of\t7\nFOODON\tFOODON\tis_about\t3\nCHEMBL.COMPOUND\tNCBIGene\tbinder\t139\nNCIT\tNCIT\tis_location_of_anatomic_structure\t356\nNCIT\tNCBITaxon\tsubclass_of\t1\nUniProtKB\tGO\tcapable_of\t62677\nFMA\tFMA\tinverse_of_forms\t15\nOBO\tSO\tsubclass_of\t1013\nGO\tSO\thas_primary_output\t2\nFMA\tFMA\tINVERTED:has_part\t12\nPATO\tPATO\tsub_property_of\t4\nOBO\tBFO\tsubclass_of\t11\nNCBIGene\tNCBIGene\tregulates_expression_of\t3812\nFMA\tFMA\tafferent_to\t812\nGO\tUBERON\tINVERTED:output_of\t17\nSNOMED\tSNOMED\thas_associated_morphology\t63873\nOBI\tMONDO\tequivalent_to\t1\nFMA\tFMA\tcontinuous_proximally_with\t1825\nMONDO\tUBERON\tdisease_has_inflammation_site\t163\nSO\tIAO\tsubclass_of\t1\nRO\tRO\txref\t1\nUBERON\tUBERON\tinverse_of\t4\nGO\tCL\tresults_in_formation_of\t15\nEFO\tUBERON\tlocated_in\t6\nEHDAA2\tEHDAA2\tINVERTED:develops_from\t2125\nNCIT\tNCIT\tgene_involved_in_molecular_abnormality\t2464\nUBERON\tENVO\tconfers_advantage_in\t8\nGENEPIO\tFOODON\tsubclass_of\t3\nGO\tGO\tresults_in_formation_of\t2\nLOINC\tLOINC\thas_challenge\t19562\nGO\tPO\txref\t44\nNCIT\tNCI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\tsubclass_of\t30\nEFO\tEFO\tpart_of\t48\nHP\tICD9\txref\t18\nSNOMED\tSNOMED\tactive_ingredient_of\t18593\nPR\tPR\tpart_of\t1\nCHEMBL.TARGET\tCHEMBL.TARGET\tsubset_of\t1389\nOBI\tEDAM\tsubclass_of\t1\nNCIT\tNCIT\tgene_is_biomarker_type\t39\nFOODON\tPO\tsubclass_of\t11\nGO\tGO\thas_occurrence\t258\nFMA\tFMA\thas_nerve_supply\t2127\nNCIT\tNCIT\thas_pharmaceutical_state_of_matter\t620\nUBERON\tUBERON\timmediately_deep_to\t40\nIAO\tIAO\ttype\t22\nOBO\tFMA\txref\t1\nGENEPIO\tNCIT\tINVERTED:after\t2\nFMA\tFMA\tsegmental_composition_of\t2\nUMLS\tUMLS\thas_form\t1\nORPHANET\tORPHANET\tsubclass_of\t25409\nBFO\tBFO\tsubclass_of\t37\nORPHANET\tORPHANET\torphanet:317348\t227\nNCIT\tNCIT\tprocedure_may_have_partially_excised_anatomy\t9\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tdisrupting_agent\t5\nUBERON\tMONDO\tINVERTED:disease_arises_from_structure\t55\nEFO\tEFO\tINVERTED:realized_in_response_to_stimulus\t1\nGO\tGO\tdirectly_positively_regulates\t15\nBTO\tCL\tderives_from\t1\nNCIT\tNCIT\tINVERTED:process_involves_gene\t25114\nUMLS\tUMLS\tmeasures\t183140\nOPL\tOBI\tsubclass_of\t1\nUMLS\tNCBIGene\tproduces\t41274\nLOINC\tLOINC\tmapped_to\t2900\nFMA\tFMA\tINVERTED:has_member\t2243\nUBERON\tUBERON\tserially_homologous_to\t3\nNCIT\tNCIT\tenzyme_metabolizes_chemical_or_drug\t636\nUMLS\tUMLS\thas_mapping_qualifier\t22\nWD\tMONDO\tequivalent_to\t2\nFMA\tFMA\tdirect_right_of\t229\nMONDO\tORPHANET\tequivalent_to\t9149\nFMA\tFMA\tdirect_cell_shape_of\t2\nFAO\tFAO\tINVERTED:develops_from\t2\nGO\tGO\tresults_in_remodeling_of\t10\nFMA\tFMA\tcontinuous_with\t2512\nPathWhiz.ProteinComplex\tPathWhiz.Bound\tINVERTED:has_element_in_bound\t809\nNCIT\tNCIT\tINVERTED:ctcae_5_parent_of\t1721\nFOODON\tGAZ\thas_country_of_origin\t9\nMONDO\tORPHANET\tdisease_has_feature\t1\nGO\tPO\tresults_in_commitment_to\t2\nGEO\tGENEPIO\taligned_with\t1\nNCIT\tNCIT\tdisease_may_have_associated_disease\t1935\nFMA\tFMA\tinsertion_of\t213\nNCIT\tNCIT\thas_pharmaceutical_release_characteristics\t502\nMONDO\tKEGG\txref\t37\nUMLS\tUMLS\tprocess_of\t810370\nNCIT\tNCIT\tINVERTED:is_cytogenetic_abnormality_of_disease\t326\nGO\tCL\tsubclass_of\t1\nGO\tCL\tresults_in_determination_of\t25\nCL\tCARO\tINVERTED:has_part\t3\nCL\tCL\tdevelops_into\t5\nMOD\tPR\tINVERTED:has_part\t5383\nOMIT\tOMIT\tsubclass_of\t7\nUBERON\tCL\tbounding_layer_of\t1\nGO\tGO\tsubclass_of\t80401\nOBI\tGENEPIO\tINVERTED:produced_by\t1\nPO\tPO\tINVERTED:has_part\t9\nDRUGBANK\tUMLS\txref\t9151\nFOODON\tFOODON\tINVERTED:output_of\t15\nCL\tPO\txref\t1\nFOODON\tNCBITaxon\tin_taxon\t1733\nNBO\tMONDO\tINVERTED:disease_has_basis_in_disruption_of\t1\nFBgn\tNCBITaxon\tonly_in_taxon\t3954\nMONDO\tOMIMPS\txref\t477\nUBERON\tUBERON\tdistally_connected_to\t30\nEFO\tBFO\thas_output\t1\nMONDO\tOBI\txref\t1\nSO\tPR\tsubclass_of\t3\nNCIT\tNCIT\tgene_in_chromosomal_location\t3906\nPR\tMONDO\tINVERTED:disease_has_basis_in_dysfunction_of\t18\nDRUGBANK\tUMLS\tclinically_tested_suspended_phase_3\t56\nVANDF\tUMLS\txref\t28951\nORPHANET\tEFO\tdisease_has_feature\t24\nDRUGBANK\tSMPDB\tpathway\t3762\nGO\tCL\tacts_on_population_of\t84\nEFO\tPO\txref\t31\nMONDO\tOGMS\tequivalent_to\t1\nCPT\tCPT\tpanel_element_of\t129\nOBO\tOBO\tINVERTED:has_part\t1\nEFO\tDOID\tis_about\t1\nSO\tGO\tINVERTED:has_primary_input_or_output\t9\nDRUGBANK\tPathWhiz\tINVERTED:has_compound\t492409\nFMA\tFMA\tINVERTED:derives\t274\nSNOMED\tSNOMED\tis_interpreted_by\t37621\nEFO\tOBI\tsubclass_of\t105\nSNOMED\tSNOMED\thas_measurement_method\t17\nSYMP\tARO\tsubclass_of\t1\nGENEPIO\tENVO\tsubclass_of\t3\nGENEPIO\tGENEPIO\tis_about\t8\nUBERON\tUBERON\tprecedes\t2\nFOODON\tNCIT\tsubclass_of\t2\nFMA\tFMA\treceives_projection\t117\nMONDO\tNCBITaxon\ttransmitted_by\t74\nOBO\tGO\tINVERTED:has_primary_input_or_output\t20\nSNOMED\tSNOMED\thas_dose_form\t12616\nGO\tPR\thas_primary_output\t10\nGO\tGO\tresults_in_maintenance_of\t16\nFMA\tFMA\thas_observed_anatomical_entity\t3\nCHEMBL.COMPOUND\tHP\tindicated_for\t2095\nNCIT\tNCIT\tgene_product_has_biochemical_function\t4865\nNCIT\tUMLS\txref\t165880\nGENEPIO\tUO\tsubclass_of\t7\nMOD\tMOD\tsubclass_of\t151\nNCBIGene\tUMLS\tcomplicates\t585\nORPHANET\tORPHANET\torphanet:c016\t6366\nFOODON\tFOODON\thas_output\t1\nMONDO\tBFO\tsubclass_of\t3\nSNOMED\tSNOMED\thas_subject_relationship_context\t5084\nNCIT\tNCIT\tINVERTED:is_organism_source_of_gene_product\t532\nDRUGBANK\tKEGG\tsame_as\t494\nFBbt\tUBERON\tpart_of\t2\nFMA\tFMA\thas_connection_type\t4\nOBI\tGO\tsubclass_of\t1\nCHMO\tCHMO\tsubclass_of\t7\nGENEPIO\tGENEPIO\tINVERTED:has_member\t1\nSNOMED\tSNOMED\thas_priority\t211\nUniProtKB\tGO\tacts_upstream_of_or_within\t293\nGO\tPR\tINVERTED:output_of\t808\nARO\tOBI\tsubclass_of\t2\nUBERON\tUBERON\tdorsal_to\t10\nFOODON\tENVO\tderives_from\t8\nSNOMED\tSNOMED\thas_realization\t1450\nUBERON\tUBERON\tsub_property_of\t3\nEFO\tEFO\tdisease_shares_features_of\t2\nMF\tMONDO\tINVERTED:realized_in_response_to\t3\nGENEPIO\tGENEPIO\ttype\t43\nFOODON\tFOODON\tINVERTED:has_part\t9\nCHEMBL.TARGET\tENSEMBL\tpart_of\t4\nORPHANET\tORPHANET\tdisease_shares_features_of\t11\nMONDO\tMESH\tequivalent_to\t7860\nNCIT\tNCIT\trole_has_range\t97\nGTPI\tNCBIGene\tchannel_blocker\t158\nPATO\tPATO\tINVERTED:has_part\t9\nCHEMBL.COMPOUND\tNCBIGene\tantisense\t3\nMONDO\tPATO\thas_modifier\t78\nNCBITaxon\tDOID\tINVERTED:has_material_basis_in\t300\nPathWhiz.Reaction\tCHEBI\thas_right_element\t169923\nNCBIGene\tUMLS\tprevents\t7331\nORPHANET\tCL\thas_disease_location\t2\nUBERON\tUBERON\tluminal_space_of\t77\nLOINC\tLOINC\tanalyzes\t72330\nORPHANET\tORPHANET\torphanet:410295\t1091\nGENEPIO\tGENEPIO\tpart_of\t1\nGO\tPO\tresults_in_morphogenesis_of\t30\nUBERON\tUBERON\tchannels_from\t25\nNCIT\tNCIT\tINVERTED:disease_is_marked_by_gene\t8\nUBERON\tBFO\tsub_property_of\t3\nEFO\tBTO\tis_about\t3\nCL\tGO\tparticipates_in\t18\nOBO\tCARO\tsubclass_of\t1\nORPHANET\tGO\thas_disease_location\t10\nSNOMED\tSNOMED\thas_finding_site\t91236\nNCBIGene\tNCBITaxon\tin_taxon\t61530\nSNOMED\tSNOMED\tINVERTED:has_occurrence\t5492\nCL\tGO\thas_plasma_membrane_part\t1\nOGMS\tGO\tsubclass_of\t1\nGENEPIO\tOIO\tsubclass_of\t2\nCHEBI\tUBERON\tpart_of\t1\nCL\tNCIT\txref\t2\nUBERON\tUBERON\tposteriorly_connected_to\t1\nRXNORM\tRXNORM\trxcui:has_dose_form\t42707\nEFO\tMP\thas_phenotype\t1\nENVO\tENVO\tbounding_layer_of\t1\nKEGG\tMONDO\tequivalent_to\t37\nCHEMBL.TARGET\tCHEMBL.TARGET\toverlaps_with\t2630\nUBERON\tCL\tsurrounds\t7\nSNOMED\tSNOMED\thas_procedure_site\t3506\nFMA\tFMA\tposteromedial_to\t9\nEFO\tNCIT\txref\t2012\nCHEMBL.COMPOUND\tNCBIGene\tantibody\t180\nEFO\tMONDO\tINVERTED:realized_in_response_to_stimulus\t1\nGO\tCL\tresults_in_maturation_of\t16\nZFIN\tSO\tsubclass_of\t3318\nUBERON\tGO\tsurrounds\t3\nPathWhiz.Reaction\tCHEBI\thas_left_element\t188562\nOMIM\tOMIM\tINVERTED:has_manifestation\t121769\nUniProtKB\tGO\tacts_upstream_of_or_within_positive_effect\t13\nFMA\tFMA\ttransforms_into\t28\nBSPO\tBSPO\tfinishes_axis\t7\nUMLS\tUMLS\thas_physiologic_effect\t1\nOMIT\tCHEBI\tsubclass_of\t3\nGO\tGO\tresults_in_maturation_of\t2\nDOID\tOMIM\txref\t4868\nCHEMBL.COMPOUND\tNCBIGene\tnegative_modulator\t5\nUBERON\tUBERON\tsuperficial_to\t14\nHP\tHP\thas_modifier\t1\nUBERON\tUBERON\tdevelopmentally_replaces\t8\nNCIT\tICO\tis_about\t1\nRXNORM\tUMLS\txref\t108886\nUBERON\tNBO\tINVERTED:has_participant\t2\nSNOMED\tSNOMED\thas_clinical_course\t4570\nUBERON\tGO\tINVERTED:has_participant\t2\nttd.target\tNCBIGene\tagonist\t105\nLOINC\tLOINC\thas_scale\t87167\nNCIT\tMONDO\tINVERTED:realized_in_response_to\t1\nEFO\tUO\tsubclass_of\t38\nFMA\tFMA\tregional_part_of\t27615\nCHEMBL.TARGET\tCHEMBL.TARGET\tequivalent_to\t36\nOBI\tSTATO\tis_about\t1\nUMLS\tUMLS\tINVERTED:has_component\t3\nEFO\tEFO\tparticipates_in\t8\nPR\tNCBITaxon\tonly_in_taxon\t177969\nMGI\tSO\tsubclass_of\t16846\nENSEMBL\tPR\tINVERTED:has_gene_template\t110\nGTPI\tNCBIGene\tgating_inhibitor\t32\nBTO\tCL\tsubclass_of\t6\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tpartial_agonist\t47\nGO\tCL\tpart_of\t150\nUBERON\tMESH\txref\t644\nHGNC\tPR\tINVERTED:has_gene_template\t19823\nCPT\tCPT\tpanel_element_of_possibly_included\t1\nIAO\tEFO\tinverse_of\t1\nCHEBI\tMONDO\tINVERTED:disease_has_basis_in_dysfunction_of\t1\nENVO\tENVO\tadjacent_to\t8\nKEGG\tPathWhiz\tINVERTED:has_compound\t1701455\nEO\tEO\tsubclass_of\t47\nGO\tGO\tpart_of\t5240\nEFO\tBTO\tequivalent_to\t1\nDOID\tICD9\txref\t11\nOBI\tEFO\tINVERTED:has_participant\t1\nVCARD\tGENEPIO\tsubclass_of\t1\nZEA\tEFO\tsubclass_of\t1\nLOINC\tLOINC\tinverse_of_measures\t79662\nEFO\tEFO\tINVERTED:has_input\t4\nUniProtKB\tGO\tacts_upstream_of_positive_effect\t14\nSO\tDOID\tINVERTED:has_material_basis_in\t3\nGO\tOBO\thas_input\t48\nGO\tGO\tbounding_layer_of\t29\nUBERON\tUBERON\tin_innermost_side_of\t2\nRO\tRO\tsub_property_of\t621\nOBO\tOBOREL\tinverse_of\t1\nENVO\tENVO\tlocated_in\t3\nRO\tRO\tinverse_of\t122\nORPHANET\tMONDO\tdisease_has_feature\t25\nNCIT\tNCIT\tbiological_process_has_result_anatomy\t63\nGO\tGO\tresults_in_disassembly_of\t75\nSNOMED\tSNOMED\thas_intent\t5207\nCHEBI\tPR\tINVERTED:has_part\t2\nEFO\tEFO\tpart_of_progression_of_disease\t2\nEnsemblGenomes\tSO\tsubclass_of\t278\nGO\tOBO\ttransports_or_maintains_localization_of\t20\nSNOMED\tSNOMED\thas_unit_of_presentation\t2918\nFAO\tFAO\tsubclass_of\t32\nCL\tRO\tsub_property_of\t2\nUBERON\tCARO\tsubclass_of\t1408\nHMDB\tNCIT\tat_tissue\t217\nGO\tUBERON\tresults_in_developmental_progression_of\t1\nMONDO\tCHEBI\tdisease_has_basis_in_accumulation_of\t1\nGENEPIO\tEFO\tsubclass_of\t1\nCVDO\tGENEPIO\tsubclass_of\t1\nGO\tUBERON\thas_target_end_location\t2\nHP\tARO\tsubclass_of\t1\nFMA\tFMA\tright_medial_to\t4\nGO\tOBI\tsubclass_of\t1\nFOODON\tFOODON\tdevelops_from_part_of\t13\nPR\tCHEBI\tderives_from\t1\nUBERON\tCARO\txref\t42\nENVO\tGENEPIO\tsubclass_of\t17\nGENEPIO\tGENEPIO\tmember_of\t9\nUMLS\tNCBIGene\tpart_of\t41790\nFMA\tFMA\tsegmental_supply_of\t683\nSNOMED\tSNOMED\tcause_of\t7207\nOMIABIS\tOGMS\tsubclass_of\t1\nMF\tMF\tINVERTED:has_occurrent_part\t1\nZFA\tEFO\tsubclass_of\t33\nSYMP\tSYMP\thas_symptom\t1\nGENEPIO\tGENEPIO\tINVERTED:produced_by\t1\ndbpedia\tHANCESTRO\tsubclass_of\t9\nNCBIGene\tUMLS\tsame_as\t617\nMONDO\tORPHANET\tsubclass_of\t669\nPECO\tBFO\tsubclass_of\t1\nSNOMED\tSNOMED\tduring\t118\nGO\tOBO\timports\t3\nCHEMBL.COMPOUND\tCHEMBL.TARGET\treleasing_agent\t26\nEFO\tMONDO\tdisease_shares_features_of\t1\nMONDO\tGARD\tequivalent_to\t5814\nNCIT\tPATO\tsubclass_of\t3\nEFO\tMEDDRA\txref\t2\nEHDAA2\tAEO\tattaches_to\t1\nMF\tBFO\tsubclass_of\t4\nFMA\tFMA\tleft_lateral_to\t5\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tdegrader\t1\nOBO\tOBO\tregulates\t2\nCL\tGO\tINVERTED:results_in_movement_of\t87\nNCIT\tNCIT\tallele_plays_altered_role_in_process\t128\nSNOMED\tSNOMED\thas_procedure_device\t279\nEFO\tEFO\tsub_property_of\t5\nCHEMBL.COMPOUND\tNCBIGene\taffects\t10769\nCHEBI\tMONDO\tINVERTED:disease_responds_to\t13\nEFO\tHANCESTRO\tderives_from\t31\nBTO\tUBERON\tlocated_in\t1\nFMA\tFMA\tsurrounds\t133\nUBERON\tUBERON\tsubdivision_of\t12\nNCIT\tNCIT\tINVERTED:process_includes_biological_process\t642\nFOODON\tECOCORE\tINVERTED:has_participant\t1\nUMLS\tUMLS\tdiagnoses\t259899\nGO\tUBERON\txref\t44\nNCBIGene\tNCBIGene\tinteracts_with\t33756\nUBERON\tUBERON\tsexually_homologous_to\t12\nEFO\tMA\tis_about\t1\nGAZ\tFOODON\tsubclass_of\t162\nUBERON\tCL\textends_fibers_into\t1\nCHEMBL.COMPOUND\tNCBIGene\tantisense_oligonucleotide\t5\nOBI\tOBI\tsubclass_of\t105\nHCPCS\tHCPCS\tmapped_to\t15\nOMIM\tOMIM\tINVERTED:phenotype_of\t13865\nMONDO\tHP\tdisease_has_major_feature\t100\nMONDO\tHP\txref\t565\nCHEBI\tUBERON\tsubclass_of\t1\nNCIT\tNCIT\tchemical_or_drug_has_mechanism_of_action\t2274\nEFO\tHGNC\txref\t8\nPO\tEFO\tequivalent_to\t1\nMONDO\tNCIT\trealized_in\t2\nGENEPIO\tGENEPIO\tinheres_in\t1\nUBERON\tUBERON\tin_deep_part_of\t6\nCL\tMONDO\tINVERTED:realized_in_response_to_stimulus\t4\nGO\tSO\txref\t15\nGENEPIO\tARO\tis_about\t3\nMONDO\tEFO\tdisease_has_major_feature\t6\nMONDO\tEFO\txref\t2857\nOncoTree\tMONDO\tequivalent_to\t556\nENVO\tENVO\tINVERTED:determined_by\t11\nCHEMBL.MECHANISM\tCHEMBL.MECHANISM\tsubclass_of\t27\nUBERON\tUBERON\tproximalmost_part_of\t4\nFOODON\tFOODON\thas_quality\t9\nFMA\tFMA\thas_primary_segmental_supply\t17\nUMLS\tUMLS\tconverts_to\t36699\nPR\tCL\tpart_of\t4\nBSPO\tBSPO\tdorsal_to\t1\nDOID\tUBERON\tlocated_in\t618\nHGNC\tMONDO\tINVERTED:disease_has_basis_in_dysfunction_of\t4393\nCHEMBL.COMPOUND\tCHEMBL.TARGET\treducing_agent\t2\nEFO\tHP\tsubclass_of\t128\nMEDDRA\tMEDDRA\tmember_of\t52438\nUBERON\tUBERON\tdevelopmentally_induced_by\t20\nUniProtKB\tCHEMBL.COMPOUND\ttargets\t39678\nGENEPIO\tGENEPIO\tINVERTED:preceded_by\t1\nCHEBI\tSO\tsubclass_of\t23\nERO\tOBI\tsubclass_of\t4\nGO\tNBO\tINVERTED:by_means\t1\nCHEBI\tBFO\tsubclass_of\t33\nLOINC\tLOINC\thas_fragments_for_synonyms\t96184\nPR\tGO\tpart_of\t4\nIDO\tOBO\tINVERTED:has_participant\t1\nUBERON\tUBERON\tpart_of\t9688\nEFO\tEFO\tsubclass_of\t11372\nDRUGBANK\tUMLS\tclinically_tested_withdrawn_phase_2\t208\nSNOMED\tSNOMED\tcharacterized_by\t346\nGO\tGO\tINVERTED:has_primary_input_or_output\t1\nGENEPIO\tGENEPIO\tbefore\t11\nPathWhiz.Compound\tKEGG\tsame_as\t48957\nSNOMED\tSNOMED\thas_inherent_location\t1\nGO\tGO\tINVERTED:regulated_by\t1913\nGENO\tGENO\tsubclass_of\t24\nCL\tMA\tlocated_in\t1\nOGMS\tOBI\tsubclass_of\t1\nGO\tNCBITaxon\tonly_in_taxon\t683\nbiolink\tbiolink\tsubclass_of\t248\nNCIT\tNCIT\tallele_has_activity\t74\nORPHANET\tMESH\txref\t2518\nDOID\tUBERON\tadjacent_to\t2\nFMA\tFMA\tdrains_into\t212\nHP\tNCIT\txref\t276\nMGI\tPR\tINVERTED:has_gene_template\t16846\nCGNC\tSO\tsubclass_of\t552\nECO\tECO\tsubclass_of\t12\nUMLS\tUMLS\tinverse_of_exhibits\t1082\nOBO\tOBOREL\tsub_property_of\t1\nEO\tEFO\tsubclass_of\t1\nENVO\tENVO\tcausal_agent_in_process\t1\nUniProtKB\tMONDO\tassociated_with_disease\t188\nUBERON\tUBERON\tindirectly_supplies\t4\nOGMS\tOGMS\tINVERTED:has_participant_at_all_times\t1\nUBERON\tUBERON\timmediately_anterior_to\t1\nGENEPIO\tGENEPIO\tINVERTED:specifies_value_of\t12\nHMDB\tMEDDRA\tat_tissue\t2\nCHEMBL.COMPOUND\tNCBIGene\tvaccine\t6\nFOODON\tRO\tsub_property_of\t1\nNCIT\tNCIT\tgene_product_expressed_in_tissue\t1594\nGENEPIO\tGENEPIO\tprecedes\t2\nFMA\tFMA\thas_venous_drainage\t132\nZFIN\tPR\tINVERTED:has_gene_template\t3318\nFMA\tFMA\ttributary_of\t1068\nCL\tUBERON\tINVERTED:develops_from\t2\nAraPort\tNCBITaxon\tonly_in_taxon\t15919\nUMLS\tUMLS\tlarger_than\t1\nHMDB\tUMLS\tat_cellular_location\t1\nNDDF\tNDDF\tingredient_of\t12\nNCBIGene\tUMLS\tadministered_to\t9523\nNCIT\tNCIT\tchemical_or_drug_affects_gene_product\t378\nsgd\tSO\tsubclass_of\t5938\nGENEPIO\tGEO\tsubclass_of\t1\nGO\tSO\tcoincident_with\t6\nUniProtKB\tUniProtKB\tregulates_activity_of\t165005\nKEGG\tDRUGBANK\tsame_as\t978\nPR\tCHEBI\tnon_covalently_bound_to\t7\nNPO\tBFO\tsubclass_of\t1\nCHEMBL.COMPOUND\tCHEMBL.MECHANISM\trelated_to\t4739\nSNOMED\tSNOMED\thas_specimen_source_identity\t126\nMP\tDOID\txref\t1\nUBERON\tUBERON\tsurrounded_by\t35\nNCIT\tGO\tsubclass_of\t1\nCHEBI\tPathWhiz.Bound\tINVERTED:has_element_in_bound\t214\nUBERON\tFMA\txref\t5851\nEFO\tICD10\txref\t2576\nNCIT\tNCIT\tgene_product_has_abnormality\t24\nNCBIGene\tSO\tsubclass_of\t5380\nMONDO\tNCBITaxon\tin_taxon\t1\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tagonist\t720\nGO\tUBERON\tresults_in_transport_along\t1\nUBERON\tNCBITaxon\tpart_of\t4\nFMA\tFMA\tINVERTED:contains\t333\nLOINC\tUMLS\txref\t260568\nNBO\tBFO\tsubclass_of\t1\nEFO\tUBERON\thas_disease_location\t278\nPO\tGENEPIO\tsubclass_of\t1\nSNOMED\tSNOMED\thas_property\t521\nCARO\tCARO\tpart_of\t3\nMONDO\tCL\tdisease_has_location\t49\nORPHANET\tORPHANET\tdisease_has_major_feature\t3\nCHEMBL.COMPOUND\tNCBIGene\tantagonist\t2951\nFMA\tFMA\tsubclass_of\t107543\nOMIM\tOMIM\thas_phenotype\t15337\nMONDO\tNBO\tdisease_causes_disruption_of\t4\nCHEBI\tUBERON\tINVERTED:composed_primarily_of\t11\nSNOMED\tSNOMED\thas_direct_morphology\t7589\nMONDO\tGO\tdisease_causes_disruption_of\t93\nBTO\tOBI\tsubclass_of\t1\nFMA\tFMA\tfusion_of\t2\nMONDO\tGO\tdisease_has_location\t5\nGO\tGO\tresults_in_assembly_of\t316\nCL\tEFO\tsubclass_of\t41\nSNOMED\tSNOMED\tuses_access_device\t1594\nUBERON\tUBERON\tproximal_to\t4\nGENEPIO\tCHEBI\tsubclass_of\t2\nMONDO\tLOINC\txref\t1\nOMIT\tGENEPIO\tsubclass_of\t6\nExO\tGENEPIO\tmember_of\t2\nSNOMED\tSNOMED\thas_associated_finding\t2554\nCL\tCL\tsynapsed_to\t3\nCL\tMONDO\tINVERTED:disease_arises_from_structure\t58\nFMA\tFMA\tsuperomedial_to\t5\nUBERON\tGO\tcomposed_primarily_of\t3\nHGNC\tNCBITaxon\tonly_in_taxon\t19823\nUBERON\tENVO\tINVERTED:determined_by_part_of\t1\nDRUGBANK\tUMLS\tclinically_tested_suspended_phase_1\t9\nCL\tPATO\tbearer_of\t38\nOBO\tGO\tsubclass_of\t5\nGO\tGO\thas_primary_output\t1\nRXNORM\tRXNORM\trxcui:reformulated_to\t9\nUniProtKB\tGO\tis_active_in\t32\nNCBITaxon\tEFO\tpart_of\t1\nNCBIGene\tNCBIGene\tconverts_to\t290\nNCIT\tFOODON\tsubclass_of\t4\nFOODON\tCHEBI\tderives_from\t2\nSIO\tSIO\tsubclass_of\t4\nSNOMED\tSNOMED\tINVERTED:has_basic_dose_form\t274\nSNOMED\tSNOMED\thas_procedure_context\t2641\nNCIT\tNCIT\tconceptual_part_of\t3585\nUMLS\tUMLS\tINVERTED:location_of\t2270476\nMONDO\tUMLS\txref\t14056\nMONDO\tCL\tdisease_has_inflammation_site\t1\nttd.target\tNCBIGene\tactivator\t13\nMONDO\tOBA\tdisease_has_feature\t1\nNCIT\tNCIT\tqualifier_applies_to\t1\nICD10\tMONDO\tequivalent_to\t1113\nNCIT\tGENEPIO\tINVERTED:contains_process\t1\nIAO\tEFO\tsubclass_of\t1\nFOODON\tFOODON\tINVERTED:produced_by\t2\nSO\tSO\thas_quality\t1\nUBERON\tUBERON\tposterior_to\t9\nCGNC\tPR\tINVERTED:has_gene_template\t552\nFMA\tFMA\tdevelopmental_stage_of\t193\nGO\tGO\thappens_during\t12\nFOODON\tUBERON\tsubclass_of\t2\nGO\tGO\tINVERTED:ends_with\t25\nNCIT\tNCIT\tchromosome_mapped_to_disease\t189\nHP\tMEDDRA\txref\t93\nCHEMBL.COMPOUND\tDOID\tindicated_for\t2375\nUBERON\tCL\tchannel_for\t4\nGO\tEFO\tINVERTED:has_input\t1\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tstabiliser\t9\nFOODON\tFOODON\tsub_property_of\t1\nEFO\tCL\tderives_from\t6\nFOODON\tFOODON\thas_input\t3\nENSEMBL\tNCBITaxon\tin_taxon\t67667\nRXNORM\tRXNORM\trxcui:contained_in\t789\nOBO\tFOODON\tsubclass_of\t2\nPDQ\tPDQ\tassociated_disease\t243\nBTO\tEFO\tderives_from\t3\nMONDO\tMONDO\tdisease_has_major_feature\t14\nMONDO\tMONDO\txref\t12\nPO\tPO\tINVERTED:has_participant\t3\nGO\tPO\tresults_in_development_of\t65\nDRUGBANK\tUMLS\tclinically_tested_terminated_phase_3\t437\nFOODON\tBFO\tsubclass_of\t11\nGO\tOBO\tregulates_levels_of\t2\nNCIT\tNCIT\tprocess_initiates_biological_process\t132\nUBERON\tUBERON\tdevelops_in\t9\nGO\tGO\tINVERTED:has_participant\t39\nARO\tIDO\tis_about\t1\nORPHANET\tMONDO\thas_modifier\t257\nUMLS\tNCBIGene\tsame_as\t692\nNCIT\tNCIT\tgene_mapped_to_disease\t5189\nMONDO\tMONDO\tintersection_of\t1\nEFO\tMONDO\tsubclass_of\t2167\nNCIT\tNCIT\tINVERTED:disease_has_molecular_abnormality\t294\nMF\tOGMS\tsubclass_of\t1\nFMA\tFMA\thas_location\t1\nOMIM\tOMIM\tsubclass_of\t59497\nRO\tBFO\tsubclass_of\t2\nEFO\tCHEBI\tsubclass_of\t71\nORPHANET\tGARD\txref\t2968\nUBERON\tUBERON\tin_lateral_side_of\t131\nFAO\tNCBITaxon\tonly_in_taxon\t1\nSNOMED\tSNOMED\toccurs_in\t7221\nNCBITaxon\tMONDO\tINVERTED:realized_in_response_to\t1\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tsequestering_agent\t23\nGO\tCL\toverlaps\t15\nHCPCS\tUMLS\txref\t6948\nNBO\tPATO\tis_about\t5\nGO\tEFO\tsubclass_of\t10\nTRANS\tGO\tsubclass_of\t1\nLOINC\tLOINC\thas_view_type\t1668\nGO\tGO\tresults_in_organization_of\t191\nFOODON\tIAO\tsubclass_of\t7\nMONDO\tHP\tdisease_causes_feature\t5\nPR\tSO\tsubclass_of\t45\nGO\tGO\toverlaps\t26\nPR\tBFO\tsubclass_of\t2\nNCIT\tNCIT\tgene_product_is_biomarker_type\t337\nCP\tPATO\tbearer_of\t4\nENVO\tENVO\thas_role\t1\nUBERON\tCL\tsubclass_of\t2\nMONDO\tEFO\tdisease_causes_feature\t2\nUBERON\tUBERON\thas_boundary\t1\ndictybase.gene\tSO\tsubclass_of\t4540\nFMA\tFMA\tattaches_to\t476\nNCIT\tNCIT\tINVERTED:disease_has_finding\t36775\nKEGG\tHMDB\tsame_as\t3308\nNCBIGene\tUMLS\tstimulates\t110058\nBTO\tEFO\tINVERTED:develops_from\t1\nPATO\tGENEPIO\tsubclass_of\t1\nUBERON\tGO\tsubclass_of\t2\nSIO\tNCIT\tsubclass_of\t1\nEFO\tUBERON\txref\t2\nEFO\tEFO\thas_role\t17\nUBERON\tCL\txref\t1\nCHEMBL.COMPOUND\tHP\tcontraindicated_for\t12221\nEFO\tOBI\tis_executed_in\t2\nGO\tECOCORE\tINVERTED:has_part\t5\nCP\tCL\tINVERTED:has_part\t26\nttd.target\tNCBIGene\tinhibitor\t203\nEHDAA2\tEHDAA2\tattaches_to\t1\nLOINC\tLOINC\thas_approach_guidance\t347\nMEDDRA\tMONDO\tequivalent_to\t1\nUBERON\tGO\txref\t4\nDRUGBANK\tCHEBI\tsame_as\t102\nFAO\tCARO\tsubclass_of\t4\nUBERON\tUBERON\tproduces\t14\nNCBIGene\tUMLS\tcauses\t56542\nCL\tFAO\txref\t8\nUBERON\tUBERON\tin_outermost_side_of\t2\nEFO\tHANCESTRO\thas_quality\t3\nNCIT\tNCIT\tINVERTED:subset_includes_concept\t230272\nMMO\tOBI\tsubclass_of\t1\nNCBITaxon\tOBI\tsubclass_of\t16\nCHEBI\tCL\tINVERTED:has_part\t1\nEHDAA2\tOBO\tsubclass_of\t1\nCHEBI\tCHEBI\tis_enantiomer_of\t2594\nFBgn\tSO\tsubclass_of\t3954\nEDAM\tGENEPIO\tsubclass_of\t1\nDOID\tNCIT\txref\t3\nUMLS\tMONDO\tequivalent_to\t14023\nECTO\tExO\tsubclass_of\t4\nENVO\tBFO\thas_increased_levels_of\t1\nZFIN\tNCBITaxon\tonly_in_taxon\t3318\nOBI\tEFO\tsubclass_of\t39\nCHEBI\tGO\tINVERTED:has_part\t16\nUniProtKB\tDOID\tassociated_with_disease\t3803\nCHEMBL.COMPOUND\tCHEBI\tsame_as\t30201\nFMA\tFMA\tsuperolateral_to\t9\nLOINC\tLOINC\tINVERTED:has_class\t54220\nLOINC\tLOINC\tis_given_pharmaceutical_substance_for\t2418\nPATO\tPATO\tcorrelates_with\t1\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tactivator\t42\nHP\tICD10\txref\t83\nPathWhiz.ElementCollection\tUniProtKB\tsame_as\t7\nNCBIGene\tUBERON\texpressed_in\t1414\nSNOMED\tSNOMED\thas_count_of_base_of_active_ingredient\t13255\nUBERON\tFOODON\tsubclass_of\t34\nFMA\tFMA\tposterosuperior_to\t34\nGO\tCHEBI\texports\t74\nENVO\tENVO\tderives_from\t9\nCL\tGO\tequivalent_to\t1\nNCIT\tNCIT\tdisease_may_have_finding\t16831\nUniProtKB\tKEGG\tphysically_interacts_with\t22304\nNCIT\tOBI\tsubclass_of\t13\nBSPO\tBSPO\tdeep_to\t1\nEnsemblGenomes\tPR\tINVERTED:has_gene_template\t278\nGO\tGO\tresults_in\t9\nCL\tUBERON\tinnervates\t1\nGO\tUBERON\tresults_in_morphogenesis_of\t342\nPR\tUBERON\tINVERTED:composed_primarily_of\t1\nCL\tEFO\tparticipates_in\t1\nGO\tPR\txref\t89\nORPHANET\tEFO\thas_disease_location\t2\nSNOMED\tSNOMED\thas_revision_status\t1031\nFMA\tFMA\thas_developmental_stage\t193\nOBI\tGENEPIO\tINVERTED:specifies_value_of\t7\nMONDO\tPATO\tsubclass_of\t1\nCHEMBL.COMPOUND\tNCBIGene\tcofactor\t2\nFMA\tFMA\trelated_object\t252\nCHEBI\tPR\tsubclass_of\t5\nUMLS\tUMLS\trelated_to\t2823\nGO\tOBO\thas_output\t1\necogene\tNCBITaxon\tonly_in_taxon\t4018\nUBERON\tUBERON\tINVERTED:has_part\t277\nNCIT\tNCIT\tallele_plays_role_in_metabolism_of_chemical_or_drug\t3\nORPHANET\tORPHANET\torphanet:317346\t38\nGENEPIO\tDOID\tsubclass_of\t1\nUMLS\tUMLS\tisa\t313010\nCLO\tPATO\thas_quality\t405\nCL\tAEO\tINVERTED:has_part\t78\nRXNORM\tRXNORM\trxcui:has_quantified_form\t15\nTO\tBFO\tsubclass_of\t1\nNBO\tNBO\tis_about\t7\nHMDB\tUBERON\tat_tissue\t66\nNBO\tGO\tis_about\t8\nMESH\tMESH\tmapped_to\t376217\nGENEPIO\tOBI\thas_quality\t1\nGENEPIO\tPCO\tsubclass_of\t2\nGAZ\tENVO\ttype\t190\nBSPO\tBSPO\toverlaps\t77\nMONDO\tUBERON\tdisease_causes_dysfunction_of\t2\nEFO\tPATO\thas_quality\t522\nGTPI\tNCBIGene\tallosteric_modulator\t139\nPDQ\tPDQ\tcomponent_of\t5952\nSTATO\tSTATO\tsubclass_of\t30\nDRUGBANK\tUniProtKB\ttarget\t16808\nOBO\tOBI\tsubclass_of\t4\nUBERON\tUBERON\texistence_starts_and_ends_during\t15\nFMA\tFMA\thas_continuation_branch\t28\nEHDAA2\tEHDAA2\tlocated_in\t166\nGTPI\tNCBIGene\tinhibitor\t1337\nOBI\tOBI\ttype\t6\nEFO\tGENEPIO\tINVERTED:specifies_value_of\t1\nUniProtKB\tGO\tcolocalizes_with\t1327\nEHDAA2\tOBO\texistence_starts_during\t2268\nOMIM\tOMIM\tmanifestation_of\t121769\nHP\tMONDO\tequivalent_to\t5\nICD10\tICD10\tsubclass_of\t98417\nGENEPIO\tGENEPIO\tsubclass_of\t665\nOBI\tNCIT\tinheres_in\t1\nCHMO\tBFO\tsubclass_of\t1\nMONDO\tKEGG\tequivalent_to\t37\nUBERON\tUBERON\timmediate_transformation_of\t71\nCHEBI\tGO\tINVERTED:has_primary_input_or_output\t1276\nSTATO\tBFO\tsubclass_of\t1\nNCBITaxon\tEFO\tINVERTED:has_member\t1\nNCIT\tNCIT\tchemical_or_drug_initiates_biological_process\t113\nMP\tICD9\txref\t1\nBTO\tEFO\tsubclass_of\t47\nRO\tRO\tINVERTED:has_subsequence\t1\nNCBITaxon\tEO\tsubclass_of\t3\nMONDO\tOMIMPS\tequivalent_to\t472\nGO\tUBERON\thas_input\t8\nUBERON\tUBERON\tanastomoses_with\t4\nENSEMBL\tSO\tsubclass_of\t110\nMONDO\tOBI\tequivalent_to\t1\nMESH\tGENEPIO\tsubclass_of\t5\nUMLS\tUMLS\tcomplicates\t42952\nDOID\tMEDDRA\txref\t33\nGENEPIO\tNCIT\tis_about\t10\nMONDO\tMONDO\tdisease_causes_feature\t7\nEFO\tPO\tequivalent_to\t1\nGO\tUBERON\ttransports_or_maintains_localization_of\t2\nUBERON\tFOODON\tINVERTED:has_defining_ingredient\t2\nUBERON\tGO\tparticipates_in\t8\nNCIT\tENVO\tsubclass_of\t6\nCL\tPR\thas_high_plasma_membrane_amount\t65\nGO\tSO\thas_input\t7\nMONDO\tDOID\txref\t9027\nPathWhiz.ElementCollection\tPathWhiz\tINVERTED:has_element_collection\t9096\nGO\tOBO\thas_primary_input\t20\nPathWhiz.NucleicAcid\tPathWhiz.Bound\tINVERTED:has_element_in_bound\t81\nMONDO\tHP\thas_modifier\t140\nOBO\tIDO\tsubclass_of\t1\nUBERON\tRO\tsub_property_of\t8\nSTATO\tIAO\tsubclass_of\t2\nNBO\tNBO\tregulates\t16\nNCIT\tUO\tsubclass_of\t2\nLOINC\tLOINC\thas_adjustment\t343\nEFO\tCHEBI\thas_role\t3\nOPL\tBTO\tsubclass_of\t1\nGO\tSO\ttransports_or_maintains_localization_of\t4\nGO\tPO\tresults_in_specification_of\t7\nEFO\tDOID\tsubclass_of\t6\nENSEMBL\tHGNC\tsame_as\t42691\nMONDO\tMFOEM\tdisease_causes_disruption_of\t1\nCHEMBL.COMPOUND\tNCBIGene\tpartial_agonist\t62\nFMA\tFMA\thas_development_type\t13\nPW\tOBO\tsubclass_of\t5\nNCIT\tNCIT\tgene_involved_in_pathogenesis_of_disease\t1115\nDOID\tBFO\tsubclass_of\t1\nOBO\tOGMS\tis_about\t1\nCHEBI\tGO\tINVERTED:process_has_causal_agent\t8\nPDQ\tUMLS\txref\t18972\nFBgn\tPR\tINVERTED:has_gene_template\t3954\nRXNORM\tRXNORM\tINVERTED:rxcui:consists_of\t26132\nUBERON\tUBERON\tin_proximal_side_of\t2\nHP\tUBERON\txref\t1\nGO\tNCBITaxon\thas_input\t10\nCL\tDOID\tINVERTED:has_material_basis_in\t41\nOBI\tCHEBI\tsubclass_of\t2\nFMA\tFMA\tlateral_to\t111\nPATO\tPATO\tdecreased_in_magnitude_relative_to\t2\nNDDF\tNDDF\thas_dose_form\t17997\nNCIT\tNCIT\tINVERTED:cdrh_parent_of\t666\nEFO\tGENEPIO\tsubclass_of\t1\nRXNORM\tRXNORM\trxcui:ingredient_of\t36788\nSNOMED\tSNOMED\thas_temporal_context\t5183\nRO\tEFO\tsub_property_of\t1\nGO\tSO\timports\t1\nNCBIGene\tNCBIGene\tpart_of\t128\nENVO\tPATO\thas_quality\t32\nFMA\tFMA\tarterial_supply_of\t622\nsgd\tPR\tINVERTED:has_gene_template\t5940\nSNOMED\tSNOMED\tuses_device\t4753\nFMA\tFMA\tinherent_3d_shape_of\t4\nNCBIGene\tOMIM\tsame_as\t17550\nCL\tNCBITaxon\tonly_in_taxon\t5\nENVO\tSIO\tsubclass_of\t1\nVANDF\tVANDF\tINVERTED:inverse_of_isa\t7426\nCL\tUBERON\tproduces\t6\nLOINC\tLOINC\tmember_of\t22330\nEO\tGENEPIO\tsubclass_of\t1\nUBERON\tUBERON\tconnected_to\t80\nHP\tUPHENO\tsubclass_of\t1\nUniProtKB\tGO\tacts_upstream_of_negative_effect\t5\nGO\tGO\tresults_in_fission_of\t8\nFMA\tFMA\tarticulates_with\t692\nEFO\tBTO\tsubclass_of\t217\nLOINC\tLOINC\thas_parent_group\t6515\nEFO\tOGMS\txref\t1\nGENEPIO\tMI\tsubclass_of\t15\nFMA\tFMA\tinverse_of_contains\t555\nPO\tPO\tparticipates_in\t7\nARO\tGENEPIO\tsubclass_of\t1\nENVO\tENVO\tpartially_surrounded_by\t1\nUniProtKB\tGO\tinvolved_in\t277260\nUniProtKB\tGO\tacts_upstream_of\t169\nUBERON\tUBERON\tINVERTED:inverse_of\t1\nUBERON\tUBERON\tINVERTED:has_skeleton\t38\nFMA\tFMA\tmerges_with\t6\nNCBIGene\tUMLS\tcompared_with\t26838\nOMIM\tOMIM\tallelic_variant_of\t29202\nOBO\tOBO\tnegatively_regulates\t1\nNCBIGene\tPR\tINVERTED:has_gene_template\t5701\nBAO\tCHEBI\tsubclass_of\t2\nGO\tFMA\txref\t10\nOBO\tOIO\tsubclass_of\t5\nPathWhiz.Compound\tCHEBI\tsame_as\t32541\nUBERON\tUBERON\tlocated_in\t152\nPDQ\tPDQ\tsubclass_of\t4291\nDOID\tICD10\txref\t8\nMESH\tMESH\tINVERTED:inverse_of_ro\t13058\nFMA\tFMA\tadheres_to\t7\nEFO\tEFO\tis_executed_in\t2\nPR\tPR\tsubclass_of\t300998\nMONDO\tMF\tdisease_causes_disruption_of\t3\nFOODON\tMONDO\tINVERTED:realized_in_response_to_stimulus\t17\nDOID\tGO\trealized_in_response_to_stimulus\t1\nDRUGBANK\tUMLS\tclinically_tested_withdrawn_phase_2_or_phase_3\t16\nGENEPIO\tUO\thas_measurement_unit_label\t3\nOBO\tOBO\tINVERTED:has_participant\t1\nPathWhiz.Reaction\tUniProtKB\thas_right_element\t12\nUBERON\tUBERON\tin_dorsal_side_of\t6\nUniProtKB\tOMIM\tassociated_with_disease\t2132\nNCBITaxon\tEFO\tsubclass_of\t4\nPR\tGO\tINVERTED:has_primary_input_or_output\t3\nEFO\tSYMP\txref\t2\nFMA\tFMA\tconnected_to\t140\nCHEBI\tFOODON\tINVERTED:has_ingredient\t3\nCHEBI\tPathWhiz\tINVERTED:has_element_collection\t1418\nLOINC\tLOINC\tassociated_with\t1016\nEFO\tMESH\txref\t1631\nNBO\tNBO\tpart_of\t1\nUMLS\tNCBIGene\txref\t34858\nMONDO\tEFO\tdisease_shares_features_of\t1\nNBO\tGO\tpart_of\t2\nGO\tPATO\txref\t1\nSNOMED\tSNOMED\thas_direct_procedure_site\t33347\nUBERON\tAEO\txref\t109\nSYMP\tBFO\tsubclass_of\t1\nGO\tUBERON\tINVERTED:has_part\t43\nFOODON\tPO\tmember_of\t1\nFMA\tFMA\tINVERTED:location_of\t1\nIDO\tBFO\tsubclass_of\t9\nUBERON\tUBERON\thas_muscle_origin\t210\nUBERON\tENVO\txref\t2\nPathWhiz.Reaction\tUniProtKB\thas_left_element\t13\nORPHANET\tORPHANET\torphanet:317343\t4581\nUBERON\tUBERON\tin_ventral_side_of\t5\nSNOMED\tSNOMED\thas_presentation_strength_denominator_unit\t1294\nUBERON\tPR\tproduces\t5\nNCIT\tEFO\tsubclass_of\t3\nENVO\tCHEBI\thas_role\t3\nUMLS\tNCBIGene\tmeasures\t13930\nGO\tUBERON\thas_target_start_location\t2\nUBERON\tUBERON\tskeleton_of\t35\nMONDO\tMONDO\thas_modifier\t867\nFOODON\tDOID\tINVERTED:has_allergic_trigger\t25\nFMA\tFMA\tprimary_segmental_supply_of\t24\nUBERON\tUBERON\tin_central_side_of\t1\nPATO\tPATO\treciprocal_of\t8\nFMA\tFMA\tinferior_to\t401\nUMLS\tUMLS\tprecedes\t149791\nNCIT\tNCIT\tbiological_process_has_result_chemical_or_drug\t32\nCL\tCARO\txref\t2\nSNOMED\tSNOMED\tplays_role\t4304\nCHEBI\tENVO\tINVERTED:has_part\t3\nSO\tPR\tINVERTED:has_part\t6\nGO\tDDANAT\txref\t1\nMONDO\tHP\tdisease_has_basis_in_feature\t42\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tphysically_interacts_with\t4538\nFMA\tFMA\tsends_output_to\t800\nNCBITaxon\tENVO\tINVERTED:determined_by\t3\nGO\tCL\thas_target_end_location\t2\nFBbt\tEFO\tsubclass_of\t77\nMONDO\tEFO\tdisease_has_basis_in_feature\t23\nORPHANET\tKEGG\txref\t4\nUMLS\tUMLS\taugments\t451409\nSNOMED\tSNOMED\ttemporally_related_to\t60\nDOID\tORPHANET\tsubclass_of\t1\nUMLS\tNCBIGene\tprocess_of\t27799\nRXNORM\tRXNORM\trxcui:ingredients_of\t4352\nGO\tGO\thas_target_end_location\t268\nDRUGBANK\tUMLS\tclinically_tested_suspended_phase_1_or_phase_2\t30\nNCBIGene\tUMLS\tcoexists_with\t77418\nGO\tNBO\tINVERTED:in_response_to\t12\nGENEPIO\tARO\tsubclass_of\t4\nICD9\tICD9\tsubclass_of\t22402\nHMDB\tUniProtKB\thas_protein_association\t332823\nNCIT\tOMIT\tsubclass_of\t1\nDRUGBANK\tUMLS\tclinically_tested_withdrawn_phase_3\t81\nOBO\tEFO\tsubclass_of\t7\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tinverse_agonist\t11\nPomBase\tNCBITaxon\tonly_in_taxon\t5124\nENVO\tENVO\tINVERTED:contains_process\t1\nSNOMED\tSNOMED\tuses_energy\t314\nORPHANET\tOMIMPS\txref\t300\nFOODON\tFOODON\tINVERTED:has_defining_ingredient\t190\nPO\tPO\tsubclass_of\t531\nEFO\tPO\tpart_of\t1\nNBO\tPATO\tsubclass_of\t1\nNCBIGene\tUMLS\tdisrupts\t64071\nMONDO\tSNOMED\tequivalent_to\t9000\nDRUGBANK\tKEGG\texternal_identifier\t1670\nBFO\tBFO\tINVERTED:inverse_of\t3\nCHEMBL.COMPOUND\tNCBIGene\tagonist\t2960\nHMDB\tMESH\tat_tissue\t2301\nBTO\tBTO\tderives_from\t2\nUniProtKB\tUniProtKB\tregulates_expression_of\t237781\nOBI\tEFO\tINVERTED:has_input\t2\nEFO\tOBO\tpart_of\t5\nCHEBI\tCHEBI\tis_substituent_group_from\t1267\nORPHANET\tEFO\tsubclass_of\t850\nCHEMBL.COMPOUND\tDOID\tcontraindicated_for\t9264\nUBERON\tNBO\tINVERTED:by_means\t6\nENVO\tCHEBI\tderives_from\t1\nttd.target\tNCBIGene\tantisense\t22\nSNOMED\tSNOMED\thas_interpretation\t12748\nUMLS\tUMLS\tuses\t386689\nUBERON\tUBERON\tINVERTED:has_component\t8\nMONDO\tORPHANET\tpredisposes_towards\t4\nARO\tGENEPIO\tINVERTED:specifies_value_of\t2\nFMA\tFMA\tsuperior_to\t399\nFMA\tFMA\thas_related_developmental_entity\t15\nEFO\tHP\thas_phenotype\t3\nGO\tUBERON\tINVERTED:contains_process\t28\nMONDO\tHP\tequivalent_to\t5\nSNOMED\tSNOMED\thas_severity\t38\nUBERON\tUBERON\tinnervates\t105\nGO\tCL\txref\t258\nMONDO\tOMIM\txref\t8869\nGO\tGO\tcausally_upstream_of\t3\nFOODON\tFOODON\thas_food_substance_analog\t14\nSNOMED\tSNOMED\tspecimen_procedure_of\t944\nMONDO\tHP\tdisease_has_feature\t709\nMONDO\tEFO\tequivalent_to\t2850\nEFO\tUBERON\toccurs_in\t1\nGENEPIO\tNCIT\tbefore\t1\nIAO\tOIO\ttype\t1\nSYMP\tDOID\tINVERTED:disease_has_basis_in\t2\nGO\tGO\txref\t4\nRGD\tNCBITaxon\tonly_in_taxon\t8114\nNCBIGene\tOMIM\tgene_mutations_contribute_to\t4\nUBERON\tUBERON\ttransformation_of\t47\nUBERON\tGO\tsimultaneous_with\t11\nMONDO\tEFO\tdisease_has_feature\t15\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tinhibitor\t2414\nGO\tUBERON\tresults_in_development_of\t588\nEFO\tEFO\tderives_from\t15\nDRUGBANK\tUMLS\tclinically_tested_terminated_phase_0\t29\nMONDO\tMFOMD\trealized_in\t6\nUMLS\tUMLS\tdisrupts\t433181\nSNOMED\tSNOMED\thas_scale_type\t527\nLOINC\tLOINC\thas_imaged_location\t6361\nDOID\tCL\tlocated_in\t10\nttd.target\tNCBIGene\tbinder\t28\nGO\tPO\toccurs_in\t10\nHGNC\tSO\tsubclass_of\t19874\nMGI\tNCBITaxon\tonly_in_taxon\t16846\nFMA\tFMA\tdirect_left_of\t275\nBSPO\tBSPO\topposite_to\t3\nUMLS\tUMLS\tcoexists_with\t1402013\nNCIT\tNCIT\tgene_mutant_encodes_gene_product_sequence_variation\t809\nSIO\tIAO\tsubclass_of\t4\nUBERON\tCL\tpart_of\t6\nMONDO\tICD9\txref\t5741\nBTO\tBTO\tINVERTED:develops_from\t1\nECTO\tRO\tsubclass_of\t4\nPR\tPR\tINVERTED:has_gene_template\t61\nGO\tPR\thas_input\t292\nENVO\tENVO\thas_output\t10\nOBI\tGENEPIO\tsubclass_of\t22\nOAE\tGENEPIO\tsubclass_of\t1\nUBERON\tGO\tpart_of\t11\nPR\tSO\tlacks_part\t3240\nNCIT\tNCIT\tbiological_process_has_associated_location\t545\nUniProtKB\tDOID\tgene_associated_with_condition\t33361\nFMA\tFMA\tdistal_to\t159\nEFO\tGARD\txref\t555\nUBERON\tUBERON\tends\t1\nENVO\tENVO\tINVERTED:has_part\t17\nOBO\tPATO\tbearer_of\t1\nBFO\tOIO\tsubclass_of\t1\nDOID\tGO\tdisease_has_location\t3\nOBO\tOBO\timmediately_preceded_by\t5\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tblocker\t149\nGO\tFAO\tresults_in_development_of\t10\nNCBIGene\tHP\thas_phenotype\t60\nGO\tPR\ttransports_or_maintains_localization_of\t9\nFMA\tFMA\thas_direct_cell_shape\t2\nCL\tUBERON\thas_soma_location\t5\nUMLS\tUMLS\tclass_code_classified_by\t61\nMONDO\tMONDO\tdisease_shares_features_of\t49\nECTO\tMONDO\tINVERTED:realized_in_response_to_stimulus\t6\nFOODON\tPATO\tsubclass_of\t6\nCHEMBL.COMPOUND\tMESH\ttreats\t27892\nCL\tUBERON\thas_synaptic_terminal_in\t2\nERO\tGENEPIO\tsubclass_of\t1\nUBERON\tEFO\tsubclass_of\t311\nAraPort\tSO\tsubclass_of\t15919\nOBI\tBTO\tsubclass_of\t1\nPR\tPR\tINVERTED:has_component\t390\nCL\tCL\tINVERTED:develops_from\t380\nSNOMED\tSNOMED\tassociated_with\t3952\nCHEBI\tFOODON\tsubclass_of\t200\nMF\tMONDO\tINVERTED:disease_has_basis_in_disruption_of\t1\nCL\tFMA\txref\t701\nPR\tUBERON\tINVERTED:has_part\t6\nHP\tBFO\tsubclass_of\t3\nNCBIGene\tUMLS\tdiagnoses\t6\nNCBIGene\tUMLS\tinhibits\t68254\nNCIT\tNCIT\tgenetic_biomarker_related_to\t2607\nPECO\tPECO\tsubclass_of\t8\nUBERON\tEFO\txref\t613\nOGMS\tGENEPIO\tsubclass_of\t1\nLOINC\tLOINC\thas_lateral_location_presence\t3480\nOBI\tEFO\tpart_of\t2\nUMLS\tUMLS\tcompared_with\t348640\nOMIT\tNCIT\tsubclass_of\t2\nARO\tARO\tsubclass_of\t40\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tproteolytic_enzyme\t6\nNBO\tNBO\tsubclass_of\t985\nHP\tMESH\txref\t3\nLOINC\tLOINC\tclass_of\t45064\nNBO\tGO\tsubclass_of\t14\nNCIT\tCHEBI\tsubclass_of\t7\nSNOMED\tSNOMED\thas_specimen_source_morphology\t154\nCHEBI\tEFO\thas_role\t83\nCHEBI\tCHEBI\tis_conjugate_acid_of\t8028\nEFO\tFMA\txref\t57\nLOINC\tLOINC\thas_modality_type\t6030\nFMA\tEFO\tsubclass_of\t1\nPATO\tGENEPIO\tINVERTED:specifies_value_of\t1\nOBI\tUBERON\tINVERTED:produced_by\t1\nUO\tBFO\tsubclass_of\t1\nEFO\tCL\thas_disease_location\t59\nENVO\tENVO\tresults_in_formation_of\t2\nBAO\tGENEPIO\tsubclass_of\t1\nGO\tPR\timports\t1\nNCIT\tNCIT\tgene_is_element_in_pathway\t6246\nCL\tGO\thas_high_plasma_membrane_amount\t15\nGO\tGO\tresults_in_transport_along\t6\nSO\tCHEBI\tsubclass_of\t7\nSNOMED\tSNOMED\trelative_to_part_of\t2\nGENEPIO\tGENEPIO\tlocated_in\t2\nFMA\tFMA\thas_branch\t6906\nFMA\tFMA\tanteromedial_to\t22\nGO\tMI\tsubclass_of\t2\nGO\tPO\tresults_in_acquisition_of_features_of\t31\nUBERON\tPATO\thas_quality\t75\nMONDO\tMONDO\tdisease_has_basis_in_feature\t68\nOBI\tOBI\tis_about\t1\nUniProtKB\tCHEBI\tphysically_interacts_with\t29920\nTypOn\tGENEPIO\tsubclass_of\t1\nFMA\tFMA\tposterolateral_to\t12\nHP\tMP\txref\t1\nDOID\tDOID\thas_symptom\t9\nPathWhiz.Compound\tPathWhiz.Bound\tINVERTED:has_element_in_bound\t142\nGENEPIO\tSTATO\tis_about\t1\nUBERON\tUBERON\tpostaxialmost_part_of\t5\nSNOMED\tSNOMED\thas_specimen\t3075\nHMDB\tOMIM\tdisease\t4222\nIDO\tOGMS\tsubclass_of\t1\nOBO\tCHEBI\tsubclass_of\t5\nLOINC\tLOINC\thas_lateral_anatomic_location\t3498\nGO\tCHEBI\thas_primary_output\t1168\ndictybase.gene\tPR\tINVERTED:has_gene_template\t4540\nRO\tRO\tsubclass_of\t2\nUO\tIAO\tsubclass_of\t2\nDOID\tUBERON\thas_disease_location\t1\nMONDO\tmedgen\tequivalent_to\t2582\nLOINC\tLOINC\tmultipart_of\t21095\nMONDO\tUMLS\tequivalent_to\t14023\nEFO\tPATO\txref\t8\nORPHANET\tORPHANET\torphanet:327767\t309\nOIO\tIAO\tsubclass_of\t1\nFMA\tFMA\tadjacent_to\t22\nCPT\tCPT\tmapped_to\t191\nNCBIGene\tDOID\tassociated_with_disease\t110\nBTO\tGENEPIO\tsubclass_of\t1\nGO\tUBERON\thas_output\t1\nCPT\tCPT\thas_possibly_included_panel_element\t1\nCL\tUBERON\tadjacent_to\t6\nFMA\tFMA\tanterolateral_to\t18\nUniProtKB\tUBERON\texpressed_in\t323101\nDOID\tGO\trealized_in_response_to\t6\nSNOMED\tSNOMED\tINVERTED:has_component\t4159\nLOINC\tLOINC\thas_exam\t454\nHANCESTRO\tBFO\tsubclass_of\t1\nORPHANET\tMONDO\tsubclass_of\t3400\nGENEPIO\tSO\tis_about\t7\nSNOMED\tSNOMED\tINVERTED:has_definitional_manifestation\t13\nNCIT\tNCIT\tgene_found_in_organism\t1840\nGO\tUBERON\tresults_in_growth_of\t20\nUMLS\tUMLS\tstimulates\t663742\nENVO\tENVO\tINVERTED:output_of\t3\nEFO\tUBERON\tis_about\t341\nSNOMED\tSNOMED\thas_technique\t155\nBFO\tEFO\tsubclass_of\t4\nGO\tSO\thas_output\t6\nUBERON\tUBERON\tdirectly_develops_from\t1\nHMDB\tSMPDB\tin_pathway\t482060\nCHEBI\tFOODON\tINVERTED:composed_primarily_of\t3\nMONDO\tRO\tsub_property_of\t1\nEFO\tCHEBI\tlocated_in\t1\nNCIT\tNCIT\tINVERTED:is_normal_cell_origin_of_disease\t18809\nUBERON\tUBERON\ttributary_of\t35\nCHEMBL.COMPOUND\tNCBIGene\tactivator\t316\nGO\tUBERON\tINVERTED:site_of\t16\nGO\tUBERON\tresults_in_transport_to_from_or_in\t2\nBTO\tBTO\tsubclass_of\t7\nFMA\tFMA\tbranch_of\t7586\nPO\tPO\tadjacent_to\t1\nUBERON\tEHDAA2\txref\t1386\nMEDDRA\tMEDDRA\tsubclass_of\t36911\nGENEPIO\tCHMO\tsubclass_of\t5\nSYMP\tSYMP\tsubclass_of\t847\nECTO\tMONDO\tINVERTED:realized_in_response_to\t33\nMONDO\tMONDO\tdisease_has_feature\t298\nLOINC\tLOINC\thas_modality_subtype\t1083\nBSPO\tBSPO\tsub_property_of\t15\nEFO\tUBERON\tinheres_in\t7\nHMDB\tFMA\tat_tissue\t4175\nFMA\tUMLS\txref\t104400\nUBERON\tUBERON\tdrains\t79\nHANCESTRO\tIAO\tsubclass_of\t1\nCL\tGO\thas_not_completed\t12\nOBI\tERO\tsubclass_of\t3\nICO\tGENEPIO\tsubclass_of\t1\nGO\tFAO\tresults_in_growth_of\t1\nPATO\tPATO\tincreased_in_magnitude_relative_to\t4\nNCBIGene\tNCBIGene\tsame_as\t142\nNCIT\tNCIT\tallele_absent_from_wild_type_chromosomal_location\t1\nUMLS\tUMLS\tassociated_with\t699263\nGENEPIO\tNCBITaxon\tis_about\t4\nFMA\tFMA\thas_segmental_composition\t2\nwb\tPR\tINVERTED:has_gene_template\t4479\nIAO\tOBO\tinverse_of\t1\nCL\tUBERON\tlocated_in\t83\nNCIT\tNCIT\tgene_product_plays_role_in_biological_process\t21782\nGAZ\tGENEPIO\tsubclass_of\t16\nEFO\tORPHANET\tdisease_has_basis_in_feature\t1\nGENEPIO\tGENEPIO\tINVERTED:has_component\t38\nGO\tCL\tresults_in_commitment_to\t57\nBSPO\tBSPO\thas_axis\t6\nERO\tERO\tsubclass_of\t2\nUBERON\tUMLS\txref\t2836\nNCIT\tNCIT\tallele_in_chromosomal_location\t104\nUBERON\tUBERON\tdevelops_from_part_of\t5\nNCIT\tNCIT\tdisease_has_primary_anatomic_site\t11480\nUBERON\tNBO\tcapable_of\t2\nPR\tGO\tsubclass_of\t360\nUBERON\tGO\tcapable_of\t122\nNCBIGene\tUMLS\tproduces\t25911\nGO\tMONDO\tINVERTED:disease_has_basis_in_dysfunction_of\t30\nLOINC\tLOINC\thas_suffix\t33614\nMESH\tMONDO\tequivalent_to\t7860\nUBERON\tGO\tfunctionally_related_to\t4\nHCPCS\tHCPCS\tsubclass_of\t6944\nFOODON\tFOODON\tsubclass_of\t23328\nGO\tPO\tresults_in_structural_organization_of\t8\nGO\tGO\tcapable_of_part_of\t298\nGENEPIO\tSIO\tsubclass_of\t8\nFMA\tFMA\tsecondary_segmental_supply_of\t2\nORPHANET\tHP\txref\t87\nNCIT\tNCIT\tINVERTED:complex_has_physical_part\t616\nGEO\tGEO\tsubclass_of\t1\nOBO\tCL\tINVERTED:has_part\t3\nCHEBI\tOBI\tsubclass_of\t1\nCL\tGO\txref\t1\nPO\tPO\tlocated_in\t3\nGO\tGO\tisa\t6463\nEFO\tNCBITaxon\tinheres_in\t9\ndictybase.gene\tNCBITaxon\tonly_in_taxon\t4540\nENVO\tENVO\thas_quality\t4\nEFO\tEFO\tINVERTED:develops_from\t1\nUBERON\tUBERON\tchannels_into\t18\nORPHANET\tEFO\txref\t61\nNCIT\tNCIT\thuman_disease_maps_to_eo_disease\t1829\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tmodulator\t85\nVT\tIAO\tsubclass_of\t1\nGO\tSO\thas_primary_input\t17\nFMA\tFMA\thas_secondary_segmental_supply\t79\nEFO\tCL\txref\t12\nHP\tGARD\txref\t1\nUMLS\tUMLS\tINVERTED:inverse_of_rn\t115122\nUMLS\tNCBIGene\tconverts_to\t1690\nGO\tUBERON\tresults_in_specification_of\t4\nGENEPIO\tOBO\tsubclass_of\t1\nGENEPIO\tGAZ\tlocated_in\t1\nHP\tORPHANET\tsubclass_of\t2\nUBERON\tUBERON\tconnects\t524\nEFO\tGO\txref\t6\nMONDO\tHP\tsubclass_of\t1\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tcross_linking_agent\t33\nSNOMED\tSNOMED\thas_method\t60209\nSNOMED\tSNOMED\thas_presentation_strength_numerator_unit\t4305\nCHEBI\tPathWhiz\tINVERTED:has_compound\t1567712\nCHEBI\tCHEBI\thas_role\t39604\nUBERON\tUBERON\tbranching_part_of\t47\nMONDO\tEFO\tsubclass_of\t1906\nNCBITaxon\tEFO\tINVERTED:has_participant\t16\nEHDAA2\tOBO\texistence_ends_during\t2367\nFOODON\tFOODON\thas_consumer\t6\nUBERON\tZFA\txref\t33\nFOODON\tPO\tderives_from\t5\nSNOMED\tSNOMED\thas_inherent_attribute\t156\nGTPI\tNCBIGene\taffects\t97\nORPHANET\tMONDO\tdisease_shares_features_of\t1\nGAZ\tGENEPIO\ttype\t56\nCHEBI\tCHEBI\tINVERTED:has_part\t3773\nBSPO\tBSPO\tsubclass_of\t179\nUPHENO\tPATO\tsubclass_of\t1\nDRUGBANK\tUMLS\tclinically_tested_suspended_phase_2_or_phase_3\t29\nGO\tGO\timmediately_preceded_by\t7\nPO\tFOODON\tINVERTED:has_part\t1\nUBERON\tUBERON\tattaches_to_part_of\t2\nEFO\tEFO\thas_quality\t10\nUBERON\tUBERON\tanterior_to\t11\nNCIT\tNCIT\tdisease_has_metastatic_anatomic_site\t140\nBSPO\tBSPO\tsurface_of\t12\nGO\tPO\tresults_in_formation_of\t17\nMONDO\tOMOP\tequivalent_to\t1590\nNCBIGene\tCL\texpressed_in\t20\nFBbt\tFBbt\tsubclass_of\t12\nCL\tPR\tlacks_plasma_membrane_part\t454\nDOID\tGO\tdisease_causes_disruption_of\t27\nGO\tUBERON\thas_end_location\t1\nFMA\tFMA\treceives_drainage_from\t195\nNCBITaxon\tUMLS\txref\t1776528\nNCIT\tDOID\tsubclass_of\t1\nHMDB\tMESH\tin_biospecimen\t19\nUMLS\tUMLS\towning_subsection_of\t42\nDOID\tMESH\txref\t3539\nGO\tCL\tresults_in_morphogenesis_of\t10\nNCIT\tPCO\tsubclass_of\t2\nMONDO\tOncoTree\tequivalent_to\t556\nCL\tUBERON\tpart_of\t690\nVCARD\tIAO\tsubclass_of\t1\nGO\tUBERON\thas_start_location\t1\nOBOREL\tRO\tsub_property_of\t1\nBTO\tPATO\tbearer_of\t1\nENVO\tENVO\thas_input\t9\nSIO\tGENEPIO\tINVERTED:specifies_value_of\t2\nUBERON\tBTO\tINVERTED:develops_from\t4\nNCIT\tNCIT\tdisease_has_normal_tissue_origin\t19638\nGO\tGO\tresults_in_morphogenesis_of\t12\nCHEBI\tPathWhiz\tINVERTED:has_nucleic_acid\t816\nCHEMBL.COMPOUND\tUniProtKB\ttargets\t39678\nFMA\tFMA\tmatures_into\t76\nGO\tGO\tINVERTED:negatively_regulated_by\t1632\nUMLS\tUMLS\tinteracts_with\t1297335\nSO\tOBI\tis_about\t2\nFMA\tFMA\tproximal_to\t106\nBSPO\tFMA\txref\t7\nBSPO\tBSPO\tleft_of\t1\nPR\tMOD\tsubclass_of\t2\nSNOMED\tSNOMED\thas_precondition\t14\nMEDDRA\tMEDDRA\tclassified_as\t47649\nEFO\tPO\tsubclass_of\t19\nENVO\tBFO\tsubclass_of\t16\nPR\tGO\tINVERTED:process_has_causal_agent\t5\nUBERON\tUBERON\tinnervated_by\t143\nGENEPIO\tNCIT\tsubclass_of\t33\nttd.target\tNCBIGene\taffects\t6\nHMDB\tCL\tat_tissue\t7\nGO\tOBA\tnegatively_regulates\t11\nMP\tICD10\txref\t2\nPATO\tCARO\txref\t2\nPR\tGO\tINVERTED:has_participant\t3\nFOODON\tFOODON\thas_substance_added\t1\nNCIT\tGENEPIO\tsubclass_of\t38\nUBERON\tUBERON\tin_right_side_of\t49\nPR\tPR\tlacks_part\t3181\nMONDO\tCL\tdisease_causes_dysfunction_of\t4\nOMIM\tMONDO\tequivalent_to\t8717\nUMLS\tUMLS\taffects\t1521984\nNCIT\tNCIT\tgene_has_physical_location\t989\nHGNC\tUMLS\txref\t41638\nUBERON\tUBERON\tINVERTED:composed_primarily_of\t136\nGAZ\tGAZ\tsubclass_of\t273\nUBERON\tUBERON\tpreaxialmost_part_of\t11\nBSPO\tBSPO\tinverse_of\t18\nOBO\tPCO\tsubclass_of\t1\nEFO\tORPHANET\tis_about\t12\nICD9\tMONDO\tequivalent_to\t1883\nSO\tGENEPIO\tsubclass_of\t4\nNCIT\tNCIT\tgene_associated_with_disease\t2175\nCHEBI\tCHEBI\tinheres_in\t41\nttd.target\tNCBIGene\tblocker\t21\nUBERON\tUBERON\tstarts\t3\nORPHANET\tMONDO\tequivalent_to\t9149\nUMLS\tUMLS\thas_structural_class\t2\nGO\tGO\tnegatively_regulates\t4659\nFMA\tFMA\tconnection_type_of\t4\nDOID\tGENEPIO\tINVERTED:specifies_value_of\t1\nPO\tEFO\tpart_of\t10\nNCIT\tMONDO\tequivalent_to\t6777\nFAO\tFAO\tpart_of\t4\nFMA\tFMA\tefferent_to\t820\nPO\tMONDO\tINVERTED:realized_in_response_to_stimulus\t1\nORPHANET\tUMLS\txref\t6226\nCHEBI\tFOODON\tINVERTED:has_defining_ingredient\t2\nUMLS\tNCBIGene\tINVERTED:location_of\t26952\nFMA\tFMA\tposterior_to\t403\nLOINC\tLOINC\tcomponent_of\t126098\nDRUGBANK\tUMLS\tclinically_tested_terminated_phase_2\t1043\nLOINC\tLOINC\tINVERTED:has_member\t22838\nLOINC\tLOINC\tsubclass_of\t250116\nGO\tCARO\tresults_in_development_of\t1\nFLU\tGENEPIO\tsubclass_of\t1\nMF\tMF\tsubclass_of\t8\nOBO\tGENEPIO\tsubclass_of\t3\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tpositive_allosteric_modulator\t67\nNCBIGene\tHGNC\tsame_as\t40970\nPR\tPR\tINVERTED:has_part\t154\nCHEBI\tEFO\tINVERTED:has_input\t14\nHP\tMP\tsubclass_of\t5\nHMDB\tCHEBI\tsame_as\t4846\nGO\tCL\thas_input\t64\nOMP\tNCIT\tis_about\t1\nFMA\tFMA\thas_arterial_supply\t599\nMONDO\tDOID\tequivalent_to\t9000\nCL\tOBO\tINVERTED:has_participant\t3\nEFO\tCHEBI\thas_output\t1\nMONDO\tUMLS\tsubclass_of\t1\nNCIT\tNCIT\teo_disease_has_property_or_attribute\t277\nNCBIGene\tOMIM\tassociated_with_disease\t25\nCHEBI\tOIO\tsubclass_of\t1\nCL\tPR\texpresses\t6\nCHEBI\tNBO\tINVERTED:has_participant\t10\nFOODON\tFOODON\tpart_of\t1\nGO\tGO\thas_input\t116\nFMA\tFMA\tmedial_to\t130\nBSPO\tBSPO\tfollows_axis\t4\nCHEBI\tGO\tINVERTED:has_participant\t23\nFMA\tFMA\tbounds\t1465\nORPHANET\tEFO\tdisease_has_major_feature\t1\nGO\tCL\ttransports_or_maintains_localization_of\t4\nCHEBI\tSO\tequivalent_to\t3\necogene\tPR\tINVERTED:has_gene_template\t4019\nPomBase\tPR\tINVERTED:has_gene_template\t5172\nCHEBI\tBFO\tequivalent_to\t1\nPathWhiz.Bound\tPathWhiz\tINVERTED:has_bound\t946\nORPHANET\tMONDO\txref\t5779\nPathWhiz\tGO\thas_location\t3066986\nMONDO\tNCIT\txref\t6793\nMONDO\tMONDO\tINVERTED:realized_in_response_to_stimulus\t2\nGO\tGO\ttransports_or_maintains_localization_of\t61\nPCO\tENVO\tINVERTED:has_part\t1\nOBO\tOBI\tis_about\t1\nLOINC\tLOINC\thas_system\t129358\nPCO\tPCO\tsubclass_of\t10\nATC\tATC\tsubclass_of\t6317\nMONDO\tNBO\trealized_in\t1\nwb\tNCBITaxon\tonly_in_taxon\t4479\nMONDO\tGO\trealized_in\t9\nSMPDB\tPathWhiz\tsame_as\t110216\nNCIT\tNCIT\tis_abnormal_cell_of_disease\t49398\nRO\tOBOREL\tsub_property_of\t2\nDOID\tUBERON\tderives_from\t18\nMONDO\tMONDO\tsubclass_of\t38341\nRGD\tSO\tsubclass_of\t8114\nRO\tOBOREL\tinverse_of\t1\nUBERON\tFBbt\txref\t4\nCHEBI\tENVO\tINVERTED:composed_primarily_of\t10\nUBERON\tUBERON\thas_developmental_contribution_from\t103\nSNOMED\tSNOMED\thas_pathological_process\t16823\nEHDAA2\tAEO\tpart_of\t36\nGO\tOBO\texports\t4\nHANCESTRO\tdbpedia\tis_demonym_of\t9\nGO\tUBERON\tINVERTED:composed_primarily_of\t25\nORPHANET\tORPHANET\torphanet:410296\t196\nDRUGBANK\tCHEBI\texternal_identifier\t5052\nCHEBI\tCHEBI\thas_parent_hydride\t1623\nPCO\tGENEPIO\tsubclass_of\t1\nRXNORM\tRXNORM\tINVERTED:rxcui:has_part\t3759\nPR\tPR\tequivalent_to\t8\nFMA\tFMA\tINVERTED:transforms_from\t22\nHP\tCL\txref\t4\nEFO\tKEGG\txref\t26\nHANCESTRO\tHANCESTRO\thas_ancestry_status\t2\nLOINC\tLOINC\thas_count\t148\nFOODON\tFOODON\tINVERTED:has_member\t11\nRXNORM\tRXNORM\trxcui:has_doseformgroup\t17677\nCL\tPR\tlacks_part\t10\nNCIT\tNCIT\tcytogenetic_abnormality_involves_chromosome\t684\nEHDAA2\tCARO\tsubclass_of\t927\nHP\tGO\txref\t3\nBSPO\tBSPO\tstarts_axis\t7\nGO\tGO\timports\t2\nUBERON\tMONDO\tINVERTED:disease_has_basis_in_dysfunction_of\t22\nUMLS\tUMLS\tmay_be_qualified_by\t20\nEFO\tUBERON\tpart_of\t22\nARO\tNCIT\tsubclass_of\t3\nSO\tGO\tINVERTED:process_has_causal_agent\t5\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tantisense_inhibitor\t2\nEFO\tOMIMPS\txref\t47\nUBERON\tUBERON\tdistal_to\t2\nNCBIGene\tNCBIGene\tstimulates\t20660\nEFO\tOBI\txref\t1\nARO\tGENEPIO\tequivalent_to\t1\nSNOMED\tSNOMED\tcausative_agent_of\t18961\nDOID\tGARD\txref\t1\nEFO\tPR\tis_about\t3\nUBERON\tUBERON\tproximally_connected_to\t55\nPR\tGO\tinvolved_in\t3\nCLO\tEFO\tbearer_of\t8\nLOINC\tLOINC\thas_divisor\t5470\nNCIT\tNCIT\tchemical_or_drug_affects_abnormal_cell\t28\nFMA\tFMA\thas_lymphatic_drainage\t759\nUBERON\tUBERON\tin_distal_side_of\t2\nPO\tBFO\tsubclass_of\t46\nENVO\tNCIT\tlocated_in\t1\nFMA\tFMA\tlymphatic_drainage_of\t764\nICD10\tUMLS\txref\t109975\nNCIT\tNCIT\tneoplasm_has_special_category\t105\nUBERON\tUBERON\tintersects_midsagittal_plane_of\t27\nCL\tGO\tproduces\t14\nRO\tRO\tINVERTED:inverse_of\t6\nFOODON\tENVO\tsubclass_of\t9\nPomBase\tSO\tsubclass_of\t5124\nUBERON\tGENEPIO\tsubclass_of\t5\nKEGG\tCHEBI\tsame_as\t2516\nMEDDRA\tMEDDRA\tINVERTED:has_member\t17338\nGO\tGO\timmediately_precedes\t4\nNBO\tUBERON\tINVERTED:output_of\t1\nFMA\tFMA\treceives_input_from\t676\nOMIT\tBFO\tsubclass_of\t1\nCHEMBL.COMPOUND\tNCBIGene\tinverse_agonist\t23\nRXNORM\tRXNORM\tINVERTED:rxcui:has_ingredient\t38040\nCHEBI\tCHEBI\tis_conjugate_base_of\t8028\nFMA\tFMA\thas_fusion\t4\nPathWhiz.Reaction\tPathWhiz.ElementCollection\thas_right_element\t1584\nNCBIGene\tUMLS\tpredisposes\t23510\nCHEBI\tEFO\tsubclass_of\t223\nOBO\tMI\tsubclass_of\t15\nHMDB\tFMA\tin_biospecimen\t49\nNCIT\tNCIT\tis_qualified_by\t1\nMI\tMI\tsubclass_of\t101\nCHEMBL.COMPOUND\tCHEMBL.TARGET\tallosteric_antagonist\t1\nGO\tUBERON\toccurs_in\t69\nBSPO\tBSPO\tanterior_to\t1\nIAO\tBFO\tsub_property_of\t2\nEFO\tNCBITaxon\tpart_of\t6\nUBERON\tGO\tlocated_in\t1\nEFO\tORPHANET\tINVERTED:has_part\t1\nPR\tGO\tcapable_of\t25\nGEO\tGENEPIO\tsubclass_of\t2\nECOCORE\tECOCORE\tsubclass_of\t8\nDRUGBANK\tUMLS\tclinically_tested_terminated_phase_1\t499\nGO\tOBO\tsubclass_of\t2\nORPHANET\tEFO\tpredisposes_towards\t4\nUBERON\tEFO\tpart_of\t3\nEFO\tUBERON\tinheres_in_part_of\t13\nCL\tCL\tsynapsed_by\t4\nDRUGBANK\tPathWhiz.Bound\tINVERTED:has_element_in_bound\t6\nOMIT\tIAO\tsubclass_of\t1\nMONDO\tMEDDRA\txref\t3\nUBERON\tBTO\txref\t7\nGO\tPATO\tbearer_of\t5\nFMA\tFMA\tright_lateral_to\t4\nGO\tPR\thas_primary_input\t2\nCL\tAEO\txref\t1\nGO\tGO\tinverse_ends_during\t1\nSNOMED\tSNOMED\thas_dose_form_transformation\t274\nPathWhiz.Reaction\tPathWhiz.ElementCollection\thas_left_element\t1625\nNCIT\tNCIT\tgene_product_has_associated_anatomy\t5253\nUMLS\tUMLS\thas_context_binding\t68\nGENEPIO\tGENEPIO\tINVERTED:has_part\t4\nFOODON\tOIO\tsubclass_of\t11\nIAO\tIAO\tsub_property_of\t1\nUniProtKB\tPathWhiz.ProteinComplex\tINVERTED:has_protein_in_complex\t1903\nCHEMBL.COMPOUND\tNCBIGene\tinhibitor\t5750\nFMA\tFMA\tdevelopment_type_of\t13\nNCIT\tNCIT\thas_nichd_parent\t4081\nGO\tCL\tINVERTED:has_part\t98\nbiolink\tbiolink\tsub_property_of\t141\nDDANAT\tCARO\txref\t4\nORPHANET\tMONDO\tdisease_has_major_feature\t1\nUBERON\tUBERON\timmediately_posterior_to\t1\nOBI\tSIO\tsubclass_of\t1\nGO\tGO\tINVERTED:has_part\t4860\nCHMO\tOBI\tsubclass_of\t1\nBSPO\tBSPO\tposterior_to\t1\nPathWhiz.NucleicAcid\tCHEBI\tsame_as\t35\nMONDO\tHGNC\txref\t56\nUBERON\tUBERON\tsupplies\t132\nNCIT\tNCIT\tis_molecular_abnormality_of_disease\t1195\nNCIT\tNCIT\tis_component_of_chemotherapy_regimen\t11836\nUniProtKB\tHP\thas_phenotype\t11603\nEFO\tEFO\tdisease_has_major_feature\t1\nOBI\tBFO\tsub_property_of\t2\nOPL\tGO\tINVERTED:ends_with\t1\nGO\tCL\thas_target_start_location\t4\nCL\tPR\thas_low_plasma_membrane_amount\t71\nFMA\tFMA\treceives_attachment_from\t458\nNCIT\tARO\tsubclass_of\t2\nSNOMED\tSNOMED\thas_associated_procedure\t2467\nGO\tGO\thas_target_start_location\t96\nEFO\tEFO\thas_disease_location\t14\nFMA\tFMA\thas_projection\t110\nCHEMBL.COMPOUND\tNCBIGene\tblocker\t943\nIDO\tOPL\tINVERTED:realizes\t2\nEFO\tORPHANET\tbearer_of\t3\nHANCESTRO\tHANCESTRO\tsubclass_of\t330\nNCBIGene\tUMLS\taugments\t69744\nNCIT\tNCBITaxon\tin_taxon\t2\nDOID\tHP\thas_phenotype\t649940\nGO\tDDANAT\tresults_in_development_of\t1\nENVO\tENVO\tsurrounded_by\t4\nOBI\tIAO\tsub_property_of\t1\nCL\tGO\tcapable_of_part_of\t1\nLOINC\tLOINC\tINVERTED:has_component\t119855\nENVO\tENVO\ttype\t41\nDRUGBANK\tUMLS\tclinically_tested_terminated_phase_1_or_phase_2\t214\nGOREL\tRO\tsub_property_of\t5\nNCIT\tNCIT\tprocedure_has_excised_anatomy\t401\nDDANAT\tDDANAT\tINVERTED:develops_from\t87\nFOODON\tFOODON\tINVERTED:has_ingredient\t77\nOBO\tIDO\thas_role\t1\nSNOMED\tSNOMED\thas_concentration_strength_numerator_unit\t2123\nHP\tUBERON\taffects\t2853\nPATO\tBFO\tsubclass_of\t13\nGO\tUMLS\txref\t69387\nENVO\tENVO\tpart_of\t72\nORPHANET\tDOID\txref\t1579\nENVO\tMONDO\tINVERTED:realized_in_response_to_stimulus\t13\nLOINC\tLOINC\thas_aggregation_view\t3311\nFBbt\tFBbt\tpart_of\t16\nFBbt\tUBERON\tINVERTED:develops_from\t1\nCL\tCL\tderives_from\t1\nDOID\tOBI\tsubclass_of\t1\nOMIM\tUMLS\txref\t123280\nCL\tCL\tlacks_plasma_membrane_part\t3\nLOINC\tLOINC\tis_presence_guidance_for\t1021\nPATO\tGO\txref\t1\nBFO\tBFO\tinverse_of\t4\nFMA\tFMA\tposteroinferior_to\t22\nMF\tMF\tINVERTED:has_participant_at_all_times\t2\nGO\tPO\tresults_in_maturation_of\t5\nSNOMED\tSNOMED\thas_units\t7\nMONDO\tOMIM\tequivalent_to\t8717\nENVO\tENVO\toccurs_in\t2\nUMLS\tUMLS\tinhibits\t614020\nUMLS\tUMLS\thas_supported_concept_relationship\t342\nNCBITaxon\tDOID\tINVERTED:has_participant\t2\nMONDO\tDOID\tsubclass_of\t1\nCL\tGO\tlacks_plasma_membrane_part\t28\nNCIT\tNCIT\tdisease_may_have_molecular_abnormality\t9292\nMONDO\tICD10\txref\t11520\nUMLS\tUMLS\tmanifestation_of\t41231\nKEGG\tPathWhiz\tINVERTED:has_element_collection\t389\nGO\tCL\tequivalent_to\t1\nSNOMED\tSNOMED\tINVERTED:has_direct_device\t4121\nSNOMED\tSNOMED\thas_route_of_administration\t176\nPathWhiz.Compound\tPathWhiz\tINVERTED:has_compound\t2003771\nORPHANET\tORPHANET\tpart_of\t14694\nEFO\tUBERON\tparticipates_in\t1\nGO\tCHEBI\txref\t919\nOBI\tNCIT\tsubclass_of\t3\nSNOMED\tSNOMED\thas_dose_form_administration_method\t295\nEHDAA2\tEHDAA2\tdevelops_in\t33\nGO\tGO\tcapable_of\t498\nGO\tGO\tINVERTED:starts_with\t58\nOBO\tOBO\texistence_starts_during\t1\nFMA\tFMA\tanterior_to\t355\nOPL\tOPL\toccurs_in\t14\nGO\tCL\tresults_in_development_of\t98\nSNOMED\tSNOMED\thas_process_duration\t136\nGO\tPO\tpart_of\t9\nSNOMED\tSNOMED\tbasis_of_strength_substance_of\t1016\nCHEBI\tCHEBI\tsubclass_of\t193181\nNCBIGene\tUMLS\tassociated_with\t132056\nGO\tZFA\txref\t5\nMONDO\tICD9\tequivalent_to\t1883\nDRUGBANK\tUMLS\tclinically_tested_suspended_phase_2\t311\nCL\tGO\thas_completed\t19\nGENEPIO\tPATO\tis_about\t2\nGO\tUBERON\tresults_in_transport_across\t7\nPO\tGO\tINVERTED:has_participant\t4\nGO\tGO\tresults_in_development_of\t4\nNCIT\tNCIT\tgene_product_is_element_in_pathway\t13536\nFMA\tFMA\tinferomedial_to\t5\nOGMS\tMONDO\tequivalent_to\t1\nCHEMBL.COMPOUND\tNCBIGene\tchannel_blocker\t331\nPathWhiz.Reaction\tDRUGBANK\thas_right_element\t14853\nSNOMED\tSNOMED\tinheres_in\t156\nEDAM\tIAO\tsubclass_of\t1\nDRUGBANK\tDRUGBANK\tdrug_interaction\t2669663\nGO\tGO\tINVERTED:results_in_movement_of\t1\nCARO\tENVO\tINVERTED:determined_by\t1\nUBERON\tUBERON\texistence_ends_during\t32\nORPHANET\tMONDO\tpredisposes_towards\t1\nCHEMBL.COMPOUND\tNCBIGene\tstimulator\t15\nCHEBI\tPR\tequivalent_to\t1\nNCIT\tNCIT\tprocedure_has_imaged_anatomy\t1\nBSPO\tBFO\tsub_property_of\t12\nUBERON\tMA\tsubclass_of\t2\nRXNORM\tRXNORM\trxcui:isa\t47221\nOBA\tPATO\tsubclass_of\t1\nEFO\tSNOMED\txref\t1\nSO\tUO\tINVERTED:is_unit_of\t1\nEHDAA2\tEHDAA2\tpart_of\t2925\nAEO\tCARO\tsubclass_of\t59\nOBO\tOBO\tpart_of\t14\nCHEBI\tDOID\tINVERTED:has_allergic_trigger\t84\nUBERON\tMA\txref\t2\nCHEBI\tENVO\tINVERTED:has_participant\t1\nGO\tGO\tadjacent_to\t22\nGENEPIO\tSTATO\tsubclass_of\t12\nNCIT\tNCIT\tgene_encodes_gene_product\t18713\nGO\tUBERON\tresults_in_structural_organization_of\t28\nGO\tGO\tINVERTED:positively_regulated_by\t1616\nCL\tEFO\txref\t1\nDOID\tMONDO\tequivalent_to\t9000\nRXNORM\tRXNORM\trxcui:part_of\t6788\nNDDF\tUMLS\txref\t33096\nHP\tGO\tsubclass_of\t1\nENVO\tFOODON\tINVERTED:composed_primarily_of\t1\nECTO\tECTO\tsubclass_of\t81\nNCIT\tNCIT\tgene_product_variant_of_gene_product\t457\nNCBIGene\tNCBIGene\tcompared_with\t7200\nEFO\tHP\txref\t237\nPathWhiz.Reaction\tDRUGBANK\thas_left_element\t21859\nPATO\tNBO\tINVERTED:in_response_to\t3\nPR\tCL\tINVERTED:has_part\t675\nNCIT\tNCIT\tchemical_or_drug_affects_cell_type_or_tissue\t572\nORPHANET\tORPHANET\tdisease_has_feature\t25\nEFO\tEFO\tis_input_of\t95\nEFO\tEFO\txref\t27\nSNOMED\tSNOMED\tdirect_substance_of\t5117\nUBERON\tARO\tsubclass_of\t3\nFMA\tFMA\thas_regional_part\t26404\nPR\tGO\tINVERTED:has_part\t2\nZFA\tUBERON\tsubclass_of\t1\nNCBIGene\tENSEMBL\tsame_as\t35031\nUniProtKB\tNCBITaxon\tin_taxon\t24986\nGAZ\tOBO\tsubclass_of\t197\nGENEPIO\tBFO\tsubclass_of\t13\nUBERON\tUBERON\tINVERTED:preceded_by\t13\nUniProtKB\tPathWhiz\tINVERTED:has_protein\t304018\nUMLS\tUMLS\tproduces\t305322\nOPL\tUBERON\tsubclass_of\t8\nRXNORM\tRXNORM\trxcui:has_tradename\t48926\nNCBITaxon\tENVO\tINVERTED:process_has_causal_agent\t3\nNCIT\tNCIT\tprocedure_has_target_anatomy\t916\nUBERON\tUBERON\tINVERTED:ends_with\t1\nUniProtKB\tGO\tacts_upstream_of_or_within_negative_effect\t5\nOMRSE\tGENEPIO\tsubclass_of\t1\nCARO\tBFO\tsubclass_of\t4\nFOODON\tUBERON\tderives_from\t6\nUBERON\tUBERON\tINVERTED:has_member\t15\nSNOMED\tSNOMED\tpart_anatomy_structure_of\t323\nNCIT\tNCIT\teo_disease_has_associated_eo_anatomy\t3128\nIDO\tOBI\tsubclass_of\t3\nENVO\tPO\tderives_from\t1\nNCIT\tNCIT\thas_pharmaceutical_intended_site\t529\nNCIT\tNCIT\tINVERTED:biological_process_involves_chemical_or_drug\t18\nOPL\tBFO\tsubclass_of\t3\nFMA\tFMA\thas_inherent_3d_shape\t4\nUBERON\tUBERON\texistence_starts_during_or_after\t4\nUniProtKB\tGO\tenables\t67759\nNCIT\tNCIT\thas_data_element\t10\nGO\tUBERON\tresults_in_formation_of\t174\nGO\tMONDO\tINVERTED:disease_has_basis_in_disruption_of\t275\nGENEPIO\tIAO\tsubclass_of\t73\nOBI\tGENEPIO\tmember_of\t2\nLOINC\tLOINC\tmth_has_expanded_form\t1\nNCIT\tNCIT\thas_pharmaceutical_administration_method\t542\nCHEMBL.COMPOUND\tNCBIGene\tmodulator\t242\nUBERON\tUBERON\thas_muscle_insertion\t217\nUBERON\tUBERON\tin_anterior_side_of\t13\nPO\tFOODON\tINVERTED:has_defining_ingredient\t1\nOMIT\tPR\tsubclass_of\t1\nUBERON\tUBERON\tfiltered_through\t4\nOBA\tOBA\tsubclass_of\t173\nSNOMED\tSNOMED\tentire_anatomy_structure_of\t7090\nCEPH\tUBERON\tsubclass_of\t1\nmedgen\tMONDO\tequivalent_to\t2582\nFMA\tFMA\thas_origin\t275\nEFO\tOBI\tINVERTED:has_participant\t2\nNCIT\tGENEPIO\tINVERTED:specifies_value_of\t4\nGENEPIO\tGENEPIO\thas_output\t1\nDDANAT\tDDANAT\tsubclass_of\t129\nCL\tGO\tlacks_part\t11\nGO\tGO\tINVERTED:process_has_causal_agent\t20\nUniProtKB\tCL\texpressed_in\t15576\nPR\tMOD\tlacks_part\t48\nMONDO\tMONDO\tpart_of_progression_of_disease\t2\nMONDO\tNCIT\thas_modifier\t2\nTRANS\tTRANS\tsubclass_of\t32\nGO\tCL\tresults_in_growth_of\t5\nLOINC\tLOINC\thas_time_aspect\t90380\nGO\tGO\thas_output\t14\nCL\tEHDAA2\txref\t6\nLOINC\tLOINC\thas_time_modifier\t197\nUniProtKB\tGO\texpressed_in\t74377\nGO\tFAO\tresults_in_formation_of\t6\nCHEBI\tMONDO\tINVERTED:realized_in_response_to_stimulus\t31\nCHEBI\tDRUGBANK\tsame_as\t636\nEFO\tCL\tis_about\t40\nGO\tGO\tresults_in_growth_of\t2\nEFO\tUBERON\tsubclass_of\t82\nMESH\tMESH\thas_mapping_qualifier\t33615\nORPHANET\tORPHANET\tdisease_has_basis_in_feature\t2\nUniProtKB\tUniProtKB\tphysically_interacts_with\t615498\nPO\tCARO\tsubclass_of\t2\nNCIT\tGENEPIO\tbefore\t1\nUBERON\tUBERON\tadjacent_to\t329\nCL\tOBO\tINVERTED:has_part\t1\nCHEBI\tGENEPIO\tINVERTED:specifies_value_of\t3\nttd.target\tNCBIGene\tcofactor\t4\nLOINC\tLOINC\thas_object_guidance\t474\nORPHANET\tORPHANET\torphanet:317345\t496\nEFO\tGO\tis_about\t68\nHMDB\tEFO\tat_tissue\t9\nGAZ\tNCIT\tsubclass_of\t186\nBSPO\tBSPO\tdistal_to\t1\nIDO\tIDO\tsubclass_of\t20\nSNOMED\tSNOMED\thas_indirect_procedure_site\t8311\nFOODON\tCHEBI\tsubclass_of\t14\nORPHANET\tORPHANET\torphanet:317349\t229\nCHEBI\tCHEBI\tinverse_of\t2\nNCBIGene\tNCBIGene\tcoexists_with\t20358\nGO\tGO\tresults_in_transport_to_from_or_in\t17\nEFO\tBFO\tsubclass_of\t66\nGO\tDOID\tINVERTED:disease_caused_by_disruption_of\t53\nRO\tSO\txref\t9\nBFO\tCHEBI\tequivalent_to\t1\nNCBITaxon\tICD9\txref\t7\nNCBITaxon\tOBO\tsubclass_of\t27\nUMLS\tUMLS\thas_owning_affiliate\t4\nDRUGBANK\tPathWhiz\tINVERTED:has_protein\t15\nSNOMED\tSNOMED\thas_state_of_matter\t58\nUniProtKB\tPathWhiz\tINVERTED:has_element_collection\t59\nORPHANET\tORPHANET\torphanet:c017\t9706\nFMA\tFMA\tforms\t15\nMF\tMF\tINVERTED:realizes\t2\nPR\tGO\tlocated_in\t2\nECOCORE\tBFO\tsubclass_of\t1\nOMIM\tOMIM\thas_inheritance_type\t6005\nCHEMBL.COMPOUND\tNCBIGene\tallosteric_modulator\t317\nENVO\tPATO\tsubclass_of\t13\nOBO\tNCBITaxon\tonly_in_taxon\t1013\nNCIT\tNCIT\tprocedure_has_completely_excised_anatomy\t95\nNCIT\tSIO\tsubclass_of\t4\nDOID\tKEGG\txref\t39\n" }, { "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/rtx2_2020_09_16.dot", "content": "digraph{graph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, fontsize=12 ]; node [ fontname=Arial, fontcolor=blue, fontsize=11]; edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ]; splines=\"FALSE\"; rankdir=\"LR\";\t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:precise_ingredient_of (6138)\"]; \t\"EFO\" -> \"UMLS\" [label=\"xref (2202)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"uses (27329)\"]; \t\"GO\" -> \"GO\" [label=\"immediately_causally_upstream_of (2)\"]; \t\"PR\" -> \"CHEBI\" [label=\"subclass_of (206)\"]; \t\"PR\" -> \"PR\" [label=\"derives_from (57)\"]; \t\"ARO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"IAO\" [label=\"subclass_of (38)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:pathway_has_gene_element (7181)\"]; \t\"UBERON\" -> \"FBbt\" [label=\"part_of (1)\"]; \t\"UBERON\" -> \"CL\" [label=\"synapsed_by (1)\"]; \t\"OBI\" -> \"GENEPIO\" [label=\"derives_from (1)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"is_tautomer_of (1748)\"]; \t\"EFO\" -> \"NCBITaxon\" [label=\"subclass_of (305)\"]; \t\"FMA\" -> \"FMA\" [label=\"surrounded_by (139)\"]; \t\"ORPHANET\" -> \"OMIM\" [label=\"xref (12142)\"]; \t\"GO\" -> \"OBA\" [label=\"regulates (80)\"]; \t\"GO\" -> \"OBA\" [label=\"positively_regulates (11)\"]; \t\"CHEBI\" -> \"EFO\" [label=\"INVERTED:has_participant (1)\"]; \t\"OBO\" -> \"PR\" [label=\"INVERTED:has_gene_template (1013)\"]; \t\"EPO\" -> \"TRANS\" [label=\"subclass_of (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_answer (85940)\"]; \t\"GO\" -> \"CL\" [label=\"is_about (1)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:465410 (44)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_process_output (158)\"]; \t\"MONDO\" -> \"GO\" [label=\"disease_triggers (2)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_is_stage (6155)\"]; \t\"GO\" -> \"GO\" [label=\"has_primary_input (2)\"]; \t\"CL\" -> \"UBERON\" [label=\"subclass_of (5)\"]; \t\"EO\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_potential_to_develop_into (132)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:gene_product_sequence_variation_encoded_by_gene_mutant (556)\"]; \t\"EO\" -> \"NCBITaxon\" [label=\"subclass_of (2)\"]; \t\"CL\" -> \"GO\" [label=\"capable_of (308)\"]; \t\"SO\" -> \"OBO\" [label=\"subclass_of (4)\"]; \t\"GAZ\" -> \"NCIT\" [label=\"type (189)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"occurs_in (17801)\"]; \t\"ICD9\" -> \"UMLS\" [label=\"xref (22406)\"]; \t\"EFO\" -> \"MONDO\" [label=\"xref (2604)\"]; \t\"ENVO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"projects_to (117)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"overlaps (9)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_release_characteristic (295)\"]; \t\"DOID\" -> \"AQTLTrait\" [label=\"has_phenotype (1)\"]; \t\"DOID\" -> \"EFO\" [label=\"subclass_of (3)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_disposition (8941)\"]; \t\"OBO\" -> \"SIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_specification_of (26)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_full_grown_phenotype (3)\"]; \t\"IAO\" -> \"IAO\" [label=\"INVERTED:type (3)\"]; \t\"GENEPIO\" -> \"ARO\" [label=\"equivalent_to (1)\"]; \t\"ARO\" -> \"IAO\" [label=\"subclass_of (3)\"]; \t\"ExO\" -> \"EPO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"GO\" [label=\"regulates (5322)\"]; \t\"GO\" -> \"GO\" [label=\"positively_regulates (4656)\"]; \t\"OBO\" -> \"OGG\" [label=\"has_input (1)\"]; \t\"GENEPIO\" -> \"ExO\" [label=\"subclass_of (9)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_potential_to_developmentally_contribute_to (12)\"]; \t\"CL\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"ENVO\" -> \"RO\" [label=\"subclass_of (1)\"]; \t\"ORPHANET\" -> \"ICD9\" [label=\"xref (920)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"coexists_with (92085)\"]; \t\"MA\" -> \"UBERON\" [label=\"part_of (1)\"]; \t\"BTO\" -> \"EFO\" [label=\"bearer_of (5)\"]; \t\"HMDB\" -> \"EHDAA2\" [label=\"at_tissue (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"aboral_to (1)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"has_increased_levels_of (4)\"]; \t\"EFO\" -> \"EFO\" [label=\"inverse_of (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"positive_allosteric_modulator (601)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"attaches_to (159)\"]; \t\"OBO\" -> \"OBO\" [label=\"subclass_of (286)\"]; \t\"GO\" -> \"OBO\" [label=\"has_primary_output (16)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_indirect_device (77)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_1_or_phase_2 (30)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"activator (87)\"]; \t\"GO\" -> \"SO\" [label=\"exports (4)\"]; \t\"FMA\" -> \"FMA\" [label=\"anterosuperior_to (16)\"]; \t\"MI\" -> \"OBO\" [label=\"subclass_of (4)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"lumen_of (2)\"]; \t\"EFO\" -> \"HANCESTRO\" [label=\"part_of (12)\"]; \t\"CHEBI\" -> \"GENEPIO\" [label=\"subclass_of (72)\"]; \t\"DRUGBANK\" -> \"PathWhiz.ProteinComplex\" [label=\"INVERTED:has_protein_in_complex (15)\"]; \t\"FMA\" -> \"FMA\" [label=\"nerve_supply_of (2129)\"]; \t\"HP\" -> \"EFO\" [label=\"xref (1)\"]; \t\"UniProtKB\" -> \"OMIM\" [label=\"gene_mutations_contribute_to (5765)\"]; \t\"CL\" -> \"GO\" [label=\"has_low_plasma_membrane_amount (6)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:produced_by (46)\"]; \t\"MONDO\" -> \"EFO\" [label=\"predisposes_towards (14)\"]; \t\"EFO\" -> \"PO\" [label=\"located_in (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"property_of (86472)\"]; \t\"XCO\" -> \"GENEPIO\" [label=\"subclass_of (2)\"]; \t\"EFO\" -> \"EFO\" [label=\"disease_causes_feature (1)\"]; \t\"EFO\" -> \"PATO\" [label=\"bearer_of (19)\"]; \t\"UBERON\" -> \"NCBITaxon\" [label=\"only_in_taxon (749)\"]; \t\"FMA\" -> \"FMA\" [label=\"fuses_with (26)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"immediately_superficial_to (13)\"]; \t\"PO\" -> \"PO\" [label=\"xref (1)\"]; \t\"GO\" -> \"CL\" [label=\"has_end_location (3)\"]; \t\"HMDB\" -> \"UMLS\" [label=\"at_tissue (137)\"]; \t\"SNOMED\" -> \"MONDO\" [label=\"equivalent_to (9000)\"]; \t\"SIO\" -> \"ENVO\" [label=\"subclass_of (1)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"inhibits (18289)\"]; \t\"FMA\" -> \"FMA\" [label=\"homonym_of (73)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_fusion_of (33)\"]; \t\"IAO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"subclass_of (160929)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:preceded_by (1)\"]; \t\"GO\" -> \"GO\" [label=\"has_end_location (5)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.NucleicAcid\" [label=\"has_right_element (210)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"compared_with (23729)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"regimen_has_accepted_use_for_disease (395)\"]; \t\"MONDO\" -> \"OBO\" [label=\"equivalent_to (154)\"]; \t\"CL\" -> \"CL\" [label=\"part_of (1)\"]; \t\"GO\" -> \"CL\" [label=\"has_start_location (3)\"]; \t\"BTO\" -> \"UBERON\" [label=\"part_of (5)\"]; \t\"FMA\" -> \"FMA\" [label=\"continuation_branch_of (43)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.Compound\" [label=\"has_right_element (336013)\"]; \t\"GO\" -> \"GO\" [label=\"ends_during (1)\"]; \t\"PO\" -> \"PO\" [label=\"INVERTED:develops_from (60)\"]; \t\"OBI\" -> \"OBI\" [label=\"inheres_in (3)\"]; \t\"PathWhiz\" -> \"NCBITaxon\" [label=\"in_species (1905194)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_informer (2207)\"]; \t\"OMP\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"GO\" [label=\"has_start_location (8)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"binding_agent (136)\"]; \t\"PATO\" -> \"PATO\" [label=\"INVERTED:towards (6)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:composed_primarily_of (34)\"]; \t\"FMA\" -> \"UBERON\" [label=\"part_of (2)\"]; \t\"CLO\" -> \"CL\" [label=\"subclass_of (428)\"]; \t\"FMA\" -> \"FMA\" [label=\"inverse_of_derives (264)\"]; \t\"PATO\" -> \"NBO\" [label=\"INVERTED:has_participant (1)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"antagonist (729)\"]; \t\"RO\" -> \"owl\" [label=\"sub_property_of (12)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:after (18)\"]; \t\"ENSEMBL\" -> \"NCBITaxon\" [label=\"only_in_taxon (110)\"]; \t\"CHEBI\" -> \"FOODON\" [label=\"member_of (1)\"]; \t\"IAO\" -> \"IAO\" [label=\"subclass_of (30)\"]; \t\"OBI\" -> \"GENEPIO\" [label=\"aligned_with (1)\"]; \t\"MPATH\" -> \"MPATH\" [label=\"subclass_of (83)\"]; \t\"GO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_is_grade (1303)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"part_of (893692)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"owning_section_of (9)\"]; \t\"DOID\" -> \"NCBITaxon\" [label=\"transmitted_by (74)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.NucleicAcid\" [label=\"has_left_element (349)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_form (2941)\"]; \t\"HANCESTRO\" -> \"OBI\" [label=\"subclass_of (2)\"]; \t\"MP\" -> \"HP\" [label=\"subclass_of (2)\"]; \t\"HP\" -> \"UBERON\" [label=\"inheres_in_part_of (2)\"]; \t\"HANCESTRO\" -> \"HANCESTRO\" [label=\"inverse_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"bounding_layer_of (37)\"]; \t\"GENEPIO\" -> \"OBI\" [label=\"is_about (7)\"]; \t\"EFO\" -> \"ORPHANET\" [label=\"subclass_of (328)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"treats (1364)\"]; \t\"SO\" -> \"CHEBI\" [label=\"equivalent_to (3)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.Compound\" [label=\"has_left_element (317671)\"]; \t\"GO\" -> \"BFO\" [label=\"subclass_of (7)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_basic_dose_form (597)\"]; \t\"CPT\" -> \"CPT\" [label=\"subclass_of (14292)\"]; \t\"ENVO\" -> \"FOODON\" [label=\"subclass_of (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"related_part (3094)\"]; \t\"ICD10PCS\" -> \"UMLS\" [label=\"xref (189499)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_recipient_category (117)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"stimulates (104111)\"]; \t\"HP\" -> \"UBERON\" [label=\"inheres_in (1)\"]; \t\"CHEBI\" -> \"CL\" [label=\"xref (1)\"]; \t\"EFO\" -> \"OBI\" [label=\"is_about (22)\"]; \t\"ZFA\" -> \"UBERON\" [label=\"part_of (4)\"]; \t\"PCO\" -> \"ENVO\" [label=\"has_habitat (1)\"]; \t\"PATO\" -> \"PATO\" [label=\"has_relative_magnitude (7)\"]; \t\"MESH\" -> \"UMLS\" [label=\"xref (402615)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"disease_has_basis_in_development_of (2)\"]; \t\"NBO\" -> \"GO\" [label=\"xref (15)\"]; \t\"CL\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (83)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"eo_disease_has_associated_cell_type (13)\"]; \t\"MONDO\" -> \"OGMS\" [label=\"xref (1)\"]; \t\"PathWhiz.ElementCollection\" -> \"KEGG\" [label=\"same_as (61)\"]; \t\"OBI\" -> \"STATO\" [label=\"subclass_of (1)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"interacts_with (183359)\"]; \t\"GO\" -> \"CHEBI\" [label=\"has_input (967)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"equivalent_to (6777)\"]; \t\"MESH\" -> \"MESH\" [label=\"subclass_of (40243)\"]; \t\"CL\" -> \"UBERON\" [label=\"INVERTED:produced_by (4)\"]; \t\"CHEMBL.TARGET\" -> \"UniProtKB\" [label=\"part_of (5700)\"]; \t\"EHDAA2\" -> \"AEO\" [label=\"subclass_of (1703)\"]; \t\"OBI\" -> \"BTO\" [label=\"xref (1)\"]; \t\"EFO\" -> \"OBI\" [label=\"inheres_in (9)\"]; \t\"FMA\" -> \"FMA\" [label=\"sub_property_of (3)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"disease_has_feature (18)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:organism_has_gene (1635)\"]; \t\"EFO\" -> \"OGMS\" [label=\"subclass_of (3)\"]; \t\"GO\" -> \"CHEBI\" [label=\"transports_or_maintains_localization_of (969)\"]; \t\"HP\" -> \"UMLS\" [label=\"xref (16527)\"]; \t\"UO\" -> \"UO\" [label=\"subclass_of (228)\"]; \t\"BTO\" -> \"EFO\" [label=\"equivalent_to (1)\"]; \t\"CL\" -> \"FBbt\" [label=\"xref (1)\"]; \t\"EFO\" -> \"EFO\" [label=\"INVERTED:has_participant (69)\"]; \t\"HGNC\" -> \"UniProtKB\" [label=\"has_gene_product (20312)\"]; \t\"DOID\" -> \"MONDO\" [label=\"subclass_of (5)\"]; \t\"OMIM\" -> \"DOID\" [label=\"contributes_to_condition (181)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_intended_site (333)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"associated_with (8728)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_malfunction_associated_with_disease (509)\"]; \t\"OBO\" -> \"MONDO\" [label=\"equivalent_to (154)\"]; \t\"GENEPIO\" -> \"IDO\" [label=\"is_about (6)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"component_of (4259)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"uses_substance (3187)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_structural_domain_or_motif (4960)\"]; \t\"FMA\" -> \"FMA\" [label=\"corresponds_to (46)\"]; \t\"OBI\" -> \"BFO\" [label=\"subclass_of (18)\"]; \t\"UBERON\" -> \"NBO\" [label=\"capable_of_part_of (9)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"affects (154949)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"overlaps (70)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_chemical_classification (1688)\"]; \t\"SO\" -> \"GO\" [label=\"INVERTED:has_participant (4)\"]; \t\"FOODON\" -> \"GENEPIO\" [label=\"subclass_of (15)\"]; \t\"UBERON\" -> \"GO\" [label=\"capable_of_part_of (135)\"]; \t\"DOID\" -> \"CL\" [label=\"derives_from (355)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"inherent_location_of (1)\"]; \t\"PATO\" -> \"PATO\" [label=\"has_cross_section (5)\"]; \t\"NCBITaxon\" -> \"ENVO\" [label=\"INVERTED:composed_primarily_of (1)\"]; \t\"GO\" -> \"CL\" [label=\"INVERTED:has_plasma_membrane_part (1)\"]; \t\"KEGG\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (162)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"anatomic_structure_is_physical_part_of (9339)\"]; \t\"PathWhiz.NucleicAcid\" -> \"PathWhiz\" [label=\"INVERTED:has_nucleic_acid (1763)\"]; \t\"NPO\" -> \"NPO\" [label=\"subclass_of (3)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"part_of (80696)\"]; \t\"MONDO\" -> \"HGNC\" [label=\"has_material_basis_in_gain_of_function_germline_mutation_in (6)\"]; \t\"CL\" -> \"UBERON\" [label=\"participates_in (4)\"]; \t\"GO\" -> \"OMIM\" [label=\"INVERTED:disease_caused_by_disruption_of (4)\"]; \t\"ORPHANET\" -> \"UBERON\" [label=\"has_disease_location (65)\"]; \t\"CARO\" -> \"CARO\" [label=\"subclass_of (49)\"]; \t\"GO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (4)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_time_aspect (23)\"]; \t\"OGMS\" -> \"UBERON\" [label=\"subclass_of (1)\"]; \t\"BSPO\" -> \"CARO\" [label=\"passes_through (1)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"produces (3596)\"]; \t\"MONDO\" -> \"MESH\" [label=\"xref (7875)\"]; \t\"OBO\" -> \"GENEPIO\" [label=\"is_about (1)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"member_of (5921)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_laterality (12116)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"predisposes_towards (143)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"gating_inhibitor (24)\"]; \t\"TO\" -> \"TO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"CHEBI\" [label=\"imports (179)\"]; \t\"GENEPIO\" -> \"ENVO\" [label=\"is_about (1)\"]; \t\"OBO\" -> \"UBERON\" [label=\"xref (6)\"]; \t\"PO\" -> \"NCBITaxon\" [label=\"only_in_taxon (2)\"]; \t\"OBI\" -> \"IAO\" [label=\"subclass_of (35)\"]; \t\"EFO\" -> \"MONDO\" [label=\"disease_causes_feature (1)\"]; \t\"EFO\" -> \"CL\" [label=\"part_of (2)\"]; \t\"OGMS\" -> \"BFO\" [label=\"subclass_of (4)\"]; \t\"RGD\" -> \"PR\" [label=\"INVERTED:has_gene_template (8114)\"]; \t\"CPT\" -> \"UMLS\" [label=\"xref (46941)\"]; \t\"AEO\" -> \"CARO\" [label=\"surrounds (1)\"]; \t\"EFO\" -> \"DOID\" [label=\"xref (2350)\"]; \t\"PCO\" -> \"ENVO\" [label=\"INVERTED:determined_by (3)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"surrounds (78)\"]; \t\"SO\" -> \"DOID\" [label=\"INVERTED:disease_has_basis_in (251)\"]; \t\"UBERON\" -> \"NCIT\" [label=\"xref (2580)\"]; \t\"UBERON\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"]; \t\"NBO\" -> \"NBO\" [label=\"INVERTED:by_means (2)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_maturation_of (53)\"]; \t\"wb\" -> \"SO\" [label=\"subclass_of (4479)\"]; \t\"GO\" -> \"OMIM\" [label=\"xref (4)\"]; \t\"BTO\" -> \"UBERON\" [label=\"xref (1)\"]; \t\"BSPO\" -> \"CARO\" [label=\"subclass_of (7)\"]; \t\"SO\" -> \"SO\" [label=\"INVERTED:has_member (1)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"antibody (25)\"]; \t\"FBbt\" -> \"CL\" [label=\"xref (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_plays_role_in_process (13660)\"]; \t\"FOODON\" -> \"owl\" [label=\"sub_property_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:may_be_normal_cell_origin_of_disease (183)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"inverse_of_rq (1560)\"]; \t\"DRUGBANK\" -> \"UniProtKB\" [label=\"external_identifier (69)\"]; \t\"CHEMBL.COMPOUND\" -> \"DRUGBANK\" [label=\"same_as (6926)\"]; \t\"EFO\" -> \"MP\" [label=\"subclass_of (7)\"]; \t\"PATO\" -> \"PATO\" [label=\"subclass_of (2113)\"]; \t\"PR\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"INVERTED:location_of (332757)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_access (1520)\"]; \t\"SNOMED\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"mapped_to (456)\"]; \t\"FMA\" -> \"FMA\" [label=\"left_medial_to (3)\"]; \t\"CPT\" -> \"CPT\" [label=\"has_add_on_code (6931)\"]; \t\"DOID\" -> \"EFO\" [label=\"xref (130)\"]; \t\"EFO\" -> \"EFO\" [label=\"disease_has_basis_in_feature (18)\"]; \t\"OBI\" -> \"RO\" [label=\"sub_property_of (7)\"]; \t\"BTO\" -> \"UBERON\" [label=\"subclass_of (9)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_target (727)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"orthogonal_to (3)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"aligned_with (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:process_has_causal_agent (3)\"]; \t\"CL\" -> \"BTO\" [label=\"xref (4)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.ProteinComplex\" [label=\"has_right_element (906)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_physical_part_of (616)\"]; \t\"ExO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (1)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"antibody (22)\"]; \t\"GO\" -> \"CL\" [label=\"occurs_in (129)\"]; \t\"PO\" -> \"FOODON\" [label=\"subclass_of (2)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:has_participant (10)\"]; \t\"MONDO\" -> \"MEDDRA\" [label=\"equivalent_to (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"continuous_with (120)\"]; \t\"BTO\" -> \"BFO\" [label=\"subclass_of (3)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"surrounded_by (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_direct_site (27)\"]; \t\"GO\" -> \"GO\" [label=\"occurs_in (270)\"]; \t\"MESH\" -> \"MESH\" [label=\"INVERTED:inverse_of_isa (5029)\"]; \t\"FMA\" -> \"FMA\" [label=\"related_developmental_entity_of (13)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_segmental_supply (613)\"]; \t\"EFO\" -> \"CL\" [label=\"inheres_in_part_of (1)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"converts_to (2870)\"]; \t\"EFO\" -> \"BTO\" [label=\"xref (3)\"]; \t\"ENVO\" -> \"OBI\" [label=\"subclass_of (2)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_imaging_focus (5463)\"]; \t\"GENEPIO\" -> \"OBI\" [label=\"member_of (1)\"]; \t\"DOID\" -> \"GO\" [label=\"disease_has_basis_in_dysfunction_of (8)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"predisposes (256197)\"]; \t\"FBdv\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"PathWhiz.ProteinComplex\" -> \"PathWhiz.Reaction\" [label=\"INVERTED:has_enzyme (165371)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"deep_to (12)\"]; \t\"HP\" -> \"HP\" [label=\"subclass_of (22195)\"]; \t\"ORPHANET\" -> \"GO\" [label=\"participates_in (3)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"has_modifier (1)\"]; \t\"GO\" -> \"FAO\" [label=\"part_of (3)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_method (66244)\"]; \t\"HP\" -> \"EFO\" [label=\"subclass_of (46)\"]; \t\"IDO\" -> \"CHEBI\" [label=\"subclass_of (1)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"interacts_with (141256)\"]; \t\"OBI\" -> \"OBI\" [label=\"inverse_of (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"develops_into (3)\"]; \t\"AEO\" -> \"AEO\" [label=\"part_of (22)\"]; \t\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"INVERTED:superset_of (1116)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.ProteinComplex\" [label=\"has_left_element (734)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:location_of (9)\"]; \t\"BTO\" -> \"EFO\" [label=\"participates_in (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"germ_origin_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"allele_has_abnormality (180)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_timing_of (2693)\"]; \t\"MONDO\" -> \"SO\" [label=\"has_modifier (22)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_0 (7)\"]; \t\"EFO\" -> \"UO\" [label=\"equivalent_to (1)\"]; \t\"GO\" -> \"PR\" [label=\"exports (1)\"]; \t\"EFO\" -> \"MA\" [label=\"has_disease_location (1)\"]; \t\"EnsemblGenomes\" -> \"NCBITaxon\" [label=\"only_in_taxon (278)\"]; \t\"EFO\" -> \"HP\" [label=\"disease_has_feature (1)\"]; \t\"UniProtKB\" -> \"REACT\" [label=\"participates_in (779447)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_indirect_morphology (544)\"]; \t\"NCIT\" -> \"VCARD\" [label=\"subclass_of (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"positive_modulator (18)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_dependent (6)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"affects (12913)\"]; \t\"FOODON\" -> \"GAZ\" [label=\"subclass_of (13)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"component_of (13)\"]; \t\"EFO\" -> \"EFO\" [label=\"disease_has_feature (34)\"]; \t\"HMDB\" -> \"FMA\" [label=\"at_cellular_location (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"constitutional_part_of (21424)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.Bound\" [label=\"has_right_element (167)\"]; \t\"UBERON\" -> \"BSPO\" [label=\"sub_property_of (6)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_is_biomarker_of (18)\"]; \t\"OBO\" -> \"OBO\" [label=\"has_interaction_type (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"same_as (15124)\"]; \t\"BFO\" -> \"RO\" [label=\"sub_property_of (4)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_has_associated_anatomic_site (30160)\"]; \t\"RO\" -> \"UBERON\" [label=\"sub_property_of (1)\"]; \t\"HMDB\" -> \"EHDAA2\" [label=\"in_biospecimen (1)\"]; \t\"MOD\" -> \"PR\" [label=\"subclass_of (41)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_adherent (7)\"]; \t\"CL\" -> \"CARO\" [label=\"subclass_of (2)\"]; \t\"GENEPIO\" -> \"OBI\" [label=\"inheres_in (1)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_acquisition_of_features_of (300)\"]; \t\"NDDF\" -> \"NDDF\" [label=\"INVERTED:has_ingredient (24)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_concentration_strength_denominator_unit (2065)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"negative_modulator (4)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"opener (38)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_method (4099)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:inverse_isa (44612)\"]; \t\"MONDO\" -> \"GARD\" [label=\"xref (5818)\"]; \t\"NBO\" -> \"UBERON\" [label=\"INVERTED:input_of (1)\"]; \t\"RO\" -> \"BFO\" [label=\"sub_property_of (26)\"]; \t\"GO\" -> \"PR\" [label=\"directly_positively_regulates (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"occurs_before (2413)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"inducer (4)\"]; \t\"DRUGBANK\" -> \"CHEMBL.COMPOUND\" [label=\"external_identifier (7632)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"immediately_preceded_by (7)\"]; \t\"STATO\" -> \"GENEPIO\" [label=\"subclass_of (6)\"]; \t\"MPATH\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"VANDF\" -> \"VANDF\" [label=\"INVERTED:has_ingredient (14304)\"]; \t\"PDQ\" -> \"PDQ\" [label=\"INVERTED:has_component (4862)\"]; \t\"GENEPIO\" -> \"PATO\" [label=\"subclass_of (2)\"]; \t\"GENEPIO\" -> \"EDAM\" [label=\"subclass_of (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_evaluation (10553)\"]; \t\"FMA\" -> \"FMA\" [label=\"full_grown_phenotype_of (3)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_organism_source (825)\"]; \t\"OPL\" -> \"OPL\" [label=\"subclass_of (27)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"precise_active_ingredient_of (7240)\"]; \t\"HP\" -> \"CL\" [label=\"affects (110)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.Bound\" [label=\"has_left_element (157)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"extends_fibers_into (127)\"]; \t\"DRUGBANK\" -> \"HMDB\" [label=\"same_as (1565)\"]; \t\"BSPO\" -> \"RO\" [label=\"sub_property_of (4)\"]; \t\"HMDB\" -> \"UMLS\" [label=\"in_biospecimen (11184)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_2_or_phase_3 (39)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"administered_to (203874)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz\" [label=\"INVERTED:has_reaction (747189)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"has_functional_parent (17221)\"]; \t\"PathWhiz.Reaction\" -> \"KEGG\" [label=\"has_right_element (263206)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"ventral_to (8)\"]; \t\"NCBIGene\" -> \"UniProtKB\" [label=\"regulates_expression_of (332256)\"]; \t\"FMA\" -> \"FMA\" [label=\"inverse_of_bounds (1076)\"]; \t\"EFO\" -> \"HP\" [label=\"has_modifier (30)\"]; \t\"DRUGBANK\" -> \"MESH\" [label=\"category (57884)\"]; \t\"ORPHANET\" -> \"NCIT\" [label=\"xref (1012)\"]; \t\"DOID\" -> \"UMLS\" [label=\"xref (6)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_may_have_completely_excised_anatomy (6)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"subclass_of (590)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317344 (176)\"]; \t\"OMOP\" -> \"MONDO\" [label=\"equivalent_to (1590)\"]; \t\"DOID\" -> \"DOID\" [label=\"subclass_of (14358)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"focus_of (4294)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_tributary (1007)\"]; \t\"GARD\" -> \"MONDO\" [label=\"equivalent_to (5814)\"]; \t\"MONDO\" -> \"ICD10\" [label=\"equivalent_to (1113)\"]; \t\"GENEPIO\" -> \"OMP\" [label=\"subclass_of (1)\"]; \t\"CL\" -> \"UBERON\" [label=\"INVERTED:has_part (224)\"]; \t\"EFO\" -> \"EFO\" [label=\"has_about_it (2)\"]; \t\"CL\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (8)\"]; \t\"HMDB\" -> \"CHEMBL.TARGET\" [label=\"at_tissue (174)\"]; \t\"EFO\" -> \"HP\" [label=\"is_about (19)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_supported_concept_property (239)\"]; \t\"OBI\" -> \"OGMS\" [label=\"subclass_of (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:develops_from (1373)\"]; \t\"ICD10PCS\" -> \"ICD10PCS\" [label=\"subclass_of (189482)\"]; \t\"EFO\" -> \"EFO\" [label=\"is_about (556)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_0 (1)\"]; \t\"DDANAT\" -> \"DDANAT\" [label=\"part_of (134)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_morphology (177)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"oxidative_enzyme (2)\"]; \t\"AEO\" -> \"AEO\" [label=\"subclass_of (89)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_posterior_side_of (15)\"]; \t\"CL\" -> \"UBERON\" [label=\"axon_synapses_in (13)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"chelating_agent (19)\"]; \t\"PO\" -> \"PO\" [label=\"part_of (132)\"]; \t\"NCBIGene\" -> \"GO\" [label=\"involved_in (1417)\"]; \t\"HP\" -> \"DOID\" [label=\"xref (34)\"]; \t\"GENEPIO\" -> \"OMIT\" [label=\"is_about (4)\"]; \t\"DOID\" -> \"MONDO\" [label=\"xref (6)\"]; \t\"EFO\" -> \"MONDO\" [label=\"disease_has_basis_in_feature (3)\"]; \t\"PathWhiz.Reaction\" -> \"KEGG\" [label=\"has_left_element (232427)\"]; \t\"DOID\" -> \"GENEPIO\" [label=\"subclass_of (2)\"]; \t\"GO\" -> \"CHEBI\" [label=\"regulates_levels_of (62)\"]; \t\"FMA\" -> \"FMA\" [label=\"external_to (1)\"]; \t\"NCBITaxon\" -> \"PATO\" [label=\"has_quality (1)\"]; \t\"MA\" -> \"UBERON\" [label=\"subclass_of (2)\"]; \t\"EFO\" -> \"EFO\" [label=\"inheres_in (1)\"]; \t\"EFO\" -> \"GO\" [label=\"participates_in (25)\"]; \t\"EHDAA2\" -> \"EHDAA2\" [label=\"subclass_of (155)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"derived_from_ancestral_fusion_of (63)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"modulator (9)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_context (2531)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"distalmost_part_of (5)\"]; \t\"VT\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"anteroinferior_to (27)\"]; \t\"CARO\" -> \"RO\" [label=\"subclass_of (1)\"]; \t\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_intermediate (83)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"contributes_to (975)\"]; \t\"NCBITaxon\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"GENEPIO\" -> \"OBI\" [label=\"denotes (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_transformation (520)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_transport_across (45)\"]; \t\"CL\" -> \"EFO\" [label=\"located_in (1)\"]; \t\"NBO\" -> \"NBO\" [label=\"INVERTED:in_response_to (5)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:contains (990)\"]; \t\"ENVO\" -> \"OIO\" [label=\"subclass_of (1)\"]; \t\"GENEPIO\" -> \"UO\" [label=\"INVERTED:is_unit_of (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_numerator_value (4836)\"]; \t\"MONDO\" -> \"PATO\" [label=\"xref (1)\"]; \t\"NCBIGene\" -> \"UniProtKB\" [label=\"has_gene_product (19230)\"]; \t\"OMIT\" -> \"OBI\" [label=\"subclass_of (2)\"]; \t\"NCIT\" -> \"UBERON\" [label=\"subclass_of (2)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"antagonist (121)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"existence_starts_during (13)\"]; \t\"GENEPIO\" -> \"RO\" [label=\"inverse_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_has_physiologic_effect (2053)\"]; \t\"GO\" -> \"CARO\" [label=\"subclass_of (21)\"]; \t\"EFO\" -> \"MA\" [label=\"xref (1)\"]; \t\"CGNC\" -> \"NCBITaxon\" [label=\"only_in_taxon (552)\"]; \t\"EFO\" -> \"PATO\" [label=\"subclass_of (2)\"]; \t\"NCBIGene\" -> \"NCBITaxon\" [label=\"only_in_taxon (5380)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_distribution_of (7)\"]; \t\"FMA\" -> \"FMA\" [label=\"continuous_distally_with (1879)\"]; \t\"HP\" -> \"MONDO\" [label=\"subclass_of (1)\"]; \t\"MONDO\" -> \"WD\" [label=\"equivalent_to (2)\"]; \t\"OBI\" -> \"PR\" [label=\"subclass_of (1)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"disease_has_location (793)\"]; \t\"EFO\" -> \"OMIM\" [label=\"xref (875)\"]; \t\"NCIT\" -> \"BFO\" [label=\"subclass_of (7)\"]; \t\"PathWhiz.Compound\" -> \"DRUGBANK\" [label=\"same_as (1539)\"]; \t\"HP\" -> \"CHEBI\" [label=\"subclass_of (1)\"]; \t\"OGG\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"FIX\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"NCBITaxon\" -> \"NCBITaxon\" [label=\"subclass_of (1783396)\"]; \t\"EFO\" -> \"RO\" [label=\"sub_property_of (2)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_subject (34)\"]; \t\"FBbt\" -> \"UBERON\" [label=\"subclass_of (22)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_structural_organization_of (1)\"]; \t\"NCBITaxon\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (482)\"]; \t\"OBO\" -> \"STATO\" [label=\"subclass_of (8)\"]; \t\"FMA\" -> \"FMA\" [label=\"inferolateral_to (8)\"]; \t\"OMIM\" -> \"HP\" [label=\"has_phenotype (94807)\"]; \t\"SO\" -> \"SO\" [label=\"subclass_of (2326)\"]; \t\"NCRO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"MONDO\" [label=\"disease_has_feature (34)\"]; \t\"SO\" -> \"BFO\" [label=\"subclass_of (4)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"subclass_of (554879)\"]; \t\"sgd\" -> \"NCBITaxon\" [label=\"only_in_taxon (5938)\"]; \t\"HMDB\" -> \"GO\" [label=\"at_cellular_location (16784)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"inheres_in (7)\"]; \t\"FMA\" -> \"FMA\" [label=\"origin_of (275)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_modification (2130)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"negative_allosteric_modulator (13)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_substance (926)\"]; \t\"ORPHANET\" -> \"PR\" [label=\"has_disease_location (1)\"]; \t\"HP\" -> \"SYMP\" [label=\"has_symptom (2)\"]; \t\"OPL\" -> \"CL\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"member_of (2295)\"]; \t\"EFO\" -> \"ICD9\" [label=\"xref (2049)\"]; \t\"CHEBI\" -> \"KEGG\" [label=\"same_as (1689)\"]; \t\"NCIT\" -> \"IAO\" [label=\"subclass_of (7)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"is_about (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"binder (139)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_location_of_anatomic_structure (356)\"]; \t\"NCIT\" -> \"NCBITaxon\" [label=\"subclass_of (1)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"capable_of (62677)\"]; \t\"FMA\" -> \"FMA\" [label=\"inverse_of_forms (15)\"]; \t\"OBO\" -> \"SO\" [label=\"subclass_of (1013)\"]; \t\"GO\" -> \"SO\" [label=\"has_primary_output (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:has_part (12)\"]; \t\"PATO\" -> \"PATO\" [label=\"sub_property_of (4)\"]; \t\"OBO\" -> \"BFO\" [label=\"subclass_of (11)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"regulates_expression_of (3812)\"]; \t\"FMA\" -> \"FMA\" [label=\"afferent_to (812)\"]; \t\"GO\" -> \"UBERON\" [label=\"INVERTED:output_of (17)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_associated_morphology (63873)\"]; \t\"OBI\" -> \"MONDO\" [label=\"equivalent_to (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"continuous_proximally_with (1825)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"disease_has_inflammation_site (163)\"]; \t\"SO\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"RO\" -> \"RO\" [label=\"xref (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"inverse_of (4)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_formation_of (15)\"]; \t\"EFO\" -> \"UBERON\" [label=\"located_in (6)\"]; \t\"EHDAA2\" -> \"EHDAA2\" [label=\"INVERTED:develops_from (2125)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_involved_in_molecular_abnormality (2464)\"]; \t\"UBERON\" -> \"ENVO\" [label=\"confers_advantage_in (8)\"]; \t\"GENEPIO\" -> \"FOODON\" [label=\"subclass_of (3)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_formation_of (2)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_challenge (19562)\"]; \t\"GO\" -> \"PO\" [label=\"xref (44)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_may_have_excised_anatomy (8)\"]; \t\"GENO\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (2007)\"]; \t\"NCBITaxon\" -> \"DOID\" [label=\"INVERTED:has_allergic_trigger (15)\"]; \t\"GAZ\" -> \"GAZ\" [label=\"located_in (720)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"channel_for (32)\"]; \t\"ORPHANET\" -> \"HGNC\" [label=\"xref (3982)\"]; \t\"PR\" -> \"CHEBI\" [label=\"equivalent_to (1)\"]; \t\"OBO\" -> \"GO\" [label=\"causally_upstream_of (1)\"]; \t\"GENEPIO\" -> \"CHEBI\" [label=\"is_about (1)\"]; \t\"OBO\" -> \"IAO\" [label=\"subclass_of (9)\"]; \t\"EFO\" -> \"UBERON\" [label=\"derives_from (6)\"]; \t\"AraPort\" -> \"PR\" [label=\"INVERTED:has_gene_template (15921)\"]; \t\"MI\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:inverse_of_isa (5250)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"hydrolytic_enzyme (38)\"]; \t\"EFO\" -> \"MONDO\" [label=\"has_modifier (125)\"]; \t\"HMDB\" -> \"OMIM\" [label=\"at_tissue (2)\"]; \t\"VANDF\" -> \"VANDF\" [label=\"isa (12198)\"]; \t\"CL\" -> \"EFO\" [label=\"part_of (2)\"]; \t\"GO\" -> \"CHEBI\" [label=\"has_output (93)\"]; \t\"DOID\" -> \"SYMP\" [label=\"has_symptom (839)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"prevents (197498)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:contains (10)\"]; \t\"SIO\" -> \"SIO\" [label=\"aligned_with (1)\"]; \t\"CHEBI\" -> \"OBO\" [label=\"subclass_of (2)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"derives_from (2874)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_source_topography (1401)\"]; \t\"BTO\" -> \"PATO\" [label=\"has_quality (1)\"]; \t\"EFO\" -> \"CL\" [label=\"subclass_of (539)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"protects (9)\"]; \t\"PCO\" -> \"BFO\" [label=\"subclass_of (3)\"]; \t\"CLO\" -> \"EFO\" [label=\"subclass_of (857)\"]; \t\"DOID\" -> \"UBERON\" [label=\"has_origin (3)\"]; \t\"UBERON\" -> \"CL\" [label=\"adjacent_to (1)\"]; \t\"EFO\" -> \"CHEBI\" [label=\"is_about (262)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_left_side_of (52)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:constitutes (23344)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_insertion (210)\"]; \t\"EFO\" -> \"GO\" [label=\"subclass_of (180)\"]; \t\"EFO\" -> \"UO\" [label=\"INVERTED:is_unit_of (4)\"]; \t\"UBERON\" -> \"GO\" [label=\"adjacent_to (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"part_of (4801)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_result_biological_process (91)\"]; \t\"GO\" -> \"CARO\" [label=\"results_in_maturation_of (1)\"]; \t\"UO\" -> \"EFO\" [label=\"equivalent_to (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"inverse_of_sy (450)\"]; \t\"EFO\" -> \"NCBITaxon\" [label=\"located_in (4)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"antagonist (789)\"]; \t\"BFO\" -> \"EFO\" [label=\"INVERTED:has_input (2)\"]; \t\"CP\" -> \"GO\" [label=\"subclass_of (9)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_surgical_approach (688)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"immediately_preceded_by (6)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"treats (1218218)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_action_guidance (1149)\"]; \t\"EFO\" -> \"CHEBI\" [label=\"inheres_in (3)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_germ_origin (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_denominator_value (4074)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"subclass_of (21304)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_constitutional_part (21120)\"]; \t\"PATO\" -> \"DOID\" [label=\"xref (1)\"]; \t\"MEDDRA\" -> \"UMLS\" [label=\"xref (73929)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_archetype (1265)\"]; \t\"PathWhiz.ElementCollection\" -> \"CHEBI\" [label=\"same_as (50)\"]; \t\"EFO\" -> \"NCBITaxon\" [label=\"derives_from (16)\"]; \t\"OBO\" -> \"OBO\" [label=\"positively_regulates (1)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"part_of (119404)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_inc_parent (116)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_pharmaceutical_route (1930)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"agonist (1350)\"]; \t\"FMA\" -> \"FMA\" [label=\"matures_from (76)\"]; \t\"FMA\" -> \"FMA\" [label=\"venous_drainage_of (132)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_has_partially_excised_anatomy (194)\"]; \t\"SNOMED\" -> \"UMLS\" [label=\"xref (361557)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:formed_as_result_of (4)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"inhibits (89138)\"]; \t\"OMIMPS\" -> \"MONDO\" [label=\"equivalent_to (472)\"]; \t\"OBO\" -> \"OBO\" [label=\"realized_in (1)\"]; \t\"MONDO\" -> \"ORPHANET\" [label=\"disease_shares_features_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"existence_starts_with (6)\"]; \t\"UBERON\" -> \"BFO\" [label=\"subclass_of (295)\"]; \t\"ORPHANET\" -> \"ICD10\" [label=\"xref (5735)\"]; \t\"GO\" -> \"GO\" [label=\"precedes (1)\"]; \t\"FMA\" -> \"UBERON\" [label=\"subclass_of (8)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:has_salt_form (1829)\"]; \t\"CL\" -> \"GO\" [label=\"INVERTED:has_participant (28)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"anteriorly_connected_to (22)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"conduit_for (57)\"]; \t\"FMA\" -> \"FMA\" [label=\"projects_from (110)\"]; \t\"ecogene\" -> \"SO\" [label=\"subclass_of (4018)\"]; \t\"GO\" -> \"GO\" [label=\"directly_regulates (12)\"]; \t\"NCIT\" -> \"ExO\" [label=\"subclass_of (2)\"]; \t\"CL\" -> \"NCBITaxon\" [label=\"in_taxon (1)\"]; \t\"PathWhiz.ElementCollection\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (163)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_approved_unknown_phase (6536)\"]; \t\"EFO\" -> \"EFO\" [label=\"related_to (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"contributes_to_morphology_of (633)\"]; \t\"CHEBI\" -> \"UBERON\" [label=\"INVERTED:has_part (20)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"subclass_of (9884)\"]; \t\"EFO\" -> \"MONDO\" [label=\"equivalent_to (2850)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_superficial_part_of (7)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"related_to (1)\"]; \t\"GO\" -> \"CHEBI\" [label=\"has_primary_input (1000)\"]; \t\"GO\" -> \"CHEBI\" [label=\"is_about (4)\"]; \t\"CL\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (24)\"]; \t\"CL\" -> \"CL\" [label=\"subclass_of (3462)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_biomarker_of (32)\"]; \t\"EFO\" -> \"EFO\" [label=\"bearer_of (970)\"]; \t\"MA\" -> \"FMA\" [label=\"xref (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"internal_to (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_supersystem (19700)\"]; \t\"SIO\" -> \"GENEPIO\" [label=\"subclass_of (9)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_related_to_endogenous_product (23)\"]; \t\"GEO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"CL\" -> \"GO\" [label=\"subclass_of (11)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"INVERTED:inverse_of_ro (356197)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_muscle_antagonist (47)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"existence_ends_during_or_before (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_associated_disease_of (1027)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_1 (132)\"]; \t\"UBERON\" -> \"CL\" [label=\"has_potential_to_developmentally_contribute_to (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"ends (1)\"]; \t\"HP\" -> \"OMIM\" [label=\"xref (24)\"]; \t\"GO\" -> \"GO\" [label=\"directly_negatively_regulates (11)\"]; \t\"MESH\" -> \"MESH\" [label=\"isa (9514)\"]; \t\"DOID\" -> \"ARO\" [label=\"subclass_of (4)\"]; \t\"GO\" -> \"GO\" [label=\"exports (4)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"role_has_parent (11)\"]; \t\"EFO\" -> \"NCBITaxon\" [label=\"only_in_taxon (3)\"]; \t\"KEGG\" -> \"UniProtKB\" [label=\"physically_interacts_with (22304)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_abnormal_cell (1194)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"role_has_domain (83)\"]; \t\"ATC\" -> \"UMLS\" [label=\"xref (6331)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"causes (813924)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"approximately_perpendicular_to (1)\"]; \t\"CHEBI\" -> \"PR\" [label=\"INVERTED:has_component (47)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"substrate (6)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_concentration_strength_numerator_value (2313)\"]; \t\"VANDF\" -> \"VANDF\" [label=\"ingredient_of (18404)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:develops_from (18)\"]; \t\"GENEPIO\" -> \"OBI\" [label=\"subclass_of (96)\"]; \t\"PO\" -> \"EFO\" [label=\"subclass_of (30)\"]; \t\"EFO\" -> \"EFO\" [label=\"part_of (48)\"]; \t\"HP\" -> \"ICD9\" [label=\"xref (18)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"active_ingredient_of (18593)\"]; \t\"PR\" -> \"PR\" [label=\"part_of (1)\"]; \t\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"subset_of (1389)\"]; \t\"OBI\" -> \"EDAM\" [label=\"subclass_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_is_biomarker_type (39)\"]; \t\"FOODON\" -> \"PO\" [label=\"subclass_of (11)\"]; \t\"GO\" -> \"GO\" [label=\"has_occurrence (258)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_nerve_supply (2127)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_state_of_matter (620)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"immediately_deep_to (40)\"]; \t\"IAO\" -> \"IAO\" [label=\"type (22)\"]; \t\"OBO\" -> \"FMA\" [label=\"xref (1)\"]; \t\"GENEPIO\" -> \"NCIT\" [label=\"INVERTED:after (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"segmental_composition_of (2)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_form (1)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"subclass_of (25409)\"]; \t\"BFO\" -> \"BFO\" [label=\"subclass_of (37)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317348 (227)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_may_have_partially_excised_anatomy (9)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"disrupting_agent (5)\"]; \t\"UBERON\" -> \"MONDO\" [label=\"INVERTED:disease_arises_from_structure (55)\"]; \t\"EFO\" -> \"EFO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"]; \t\"GO\" -> \"GO\" [label=\"directly_positively_regulates (15)\"]; \t\"BTO\" -> \"CL\" [label=\"derives_from (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:process_involves_gene (25114)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"measures (183140)\"]; \t\"OPL\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"produces (41274)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"mapped_to (2900)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:has_member (2243)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"serially_homologous_to (3)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"enzyme_metabolizes_chemical_or_drug (636)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_mapping_qualifier (22)\"]; \t\"WD\" -> \"MONDO\" [label=\"equivalent_to (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"direct_right_of (229)\"]; \t\"MONDO\" -> \"ORPHANET\" [label=\"equivalent_to (9149)\"]; \t\"FMA\" -> \"FMA\" [label=\"direct_cell_shape_of (2)\"]; \t\"FAO\" -> \"FAO\" [label=\"INVERTED:develops_from (2)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_remodeling_of (10)\"]; \t\"FMA\" -> \"FMA\" [label=\"continuous_with (2512)\"]; \t\"PathWhiz.ProteinComplex\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (809)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:ctcae_5_parent_of (1721)\"]; \t\"FOODON\" -> \"GAZ\" [label=\"has_country_of_origin (9)\"]; \t\"MONDO\" -> \"ORPHANET\" [label=\"disease_has_feature (1)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_commitment_to (2)\"]; \t\"GEO\" -> \"GENEPIO\" [label=\"aligned_with (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_associated_disease (1935)\"]; \t\"FMA\" -> \"FMA\" [label=\"insertion_of (213)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_release_characteristics (502)\"]; \t\"MONDO\" -> \"KEGG\" [label=\"xref (37)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"process_of (810370)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:is_cytogenetic_abnormality_of_disease (326)\"]; \t\"GO\" -> \"CL\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_determination_of (25)\"]; \t\"CL\" -> \"CARO\" [label=\"INVERTED:has_part (3)\"]; \t\"CL\" -> \"CL\" [label=\"develops_into (5)\"]; \t\"MOD\" -> \"PR\" [label=\"INVERTED:has_part (5383)\"]; \t\"OMIT\" -> \"OMIT\" [label=\"subclass_of (7)\"]; \t\"UBERON\" -> \"CL\" [label=\"bounding_layer_of (1)\"]; \t\"GO\" -> \"GO\" [label=\"subclass_of (80401)\"]; \t\"OBI\" -> \"GENEPIO\" [label=\"INVERTED:produced_by (1)\"]; \t\"PO\" -> \"PO\" [label=\"INVERTED:has_part (9)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"xref (9151)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"INVERTED:output_of (15)\"]; \t\"CL\" -> \"PO\" [label=\"xref (1)\"]; \t\"FOODON\" -> \"NCBITaxon\" [label=\"in_taxon (1733)\"]; \t\"NBO\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_disruption_of (1)\"]; \t\"FBgn\" -> \"NCBITaxon\" [label=\"only_in_taxon (3954)\"]; \t\"MONDO\" -> \"OMIMPS\" [label=\"xref (477)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"distally_connected_to (30)\"]; \t\"EFO\" -> \"BFO\" [label=\"has_output (1)\"]; \t\"MONDO\" -> \"OBI\" [label=\"xref (1)\"]; \t\"SO\" -> \"PR\" [label=\"subclass_of (3)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_in_chromosomal_location (3906)\"]; \t\"PR\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (18)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_3 (56)\"]; \t\"VANDF\" -> \"UMLS\" [label=\"xref (28951)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"disease_has_feature (24)\"]; \t\"DRUGBANK\" -> \"SMPDB\" [label=\"pathway (3762)\"]; \t\"GO\" -> \"CL\" [label=\"acts_on_population_of (84)\"]; \t\"EFO\" -> \"PO\" [label=\"xref (31)\"]; \t\"MONDO\" -> \"OGMS\" [label=\"equivalent_to (1)\"]; \t\"CPT\" -> \"CPT\" [label=\"panel_element_of (129)\"]; \t\"OBO\" -> \"OBO\" [label=\"INVERTED:has_part (1)\"]; \t\"EFO\" -> \"DOID\" [label=\"is_about (1)\"]; \t\"SO\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (9)\"]; \t\"DRUGBANK\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (492409)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:derives (274)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"is_interpreted_by (37621)\"]; \t\"EFO\" -> \"OBI\" [label=\"subclass_of (105)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_measurement_method (17)\"]; \t\"SYMP\" -> \"ARO\" [label=\"subclass_of (1)\"]; \t\"GENEPIO\" -> \"ENVO\" [label=\"subclass_of (3)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"is_about (8)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"precedes (2)\"]; \t\"FOODON\" -> \"NCIT\" [label=\"subclass_of (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"receives_projection (117)\"]; \t\"MONDO\" -> \"NCBITaxon\" [label=\"transmitted_by (74)\"]; \t\"OBO\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (20)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form (12616)\"]; \t\"GO\" -> \"PR\" [label=\"has_primary_output (10)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_maintenance_of (16)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_observed_anatomical_entity (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"HP\" [label=\"indicated_for (2095)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_biochemical_function (4865)\"]; \t\"NCIT\" -> \"UMLS\" [label=\"xref (165880)\"]; \t\"GENEPIO\" -> \"UO\" [label=\"subclass_of (7)\"]; \t\"MOD\" -> \"MOD\" [label=\"subclass_of (151)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"complicates (585)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:c016 (6366)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"has_output (1)\"]; \t\"MONDO\" -> \"BFO\" [label=\"subclass_of (3)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_subject_relationship_context (5084)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:is_organism_source_of_gene_product (532)\"]; \t\"DRUGBANK\" -> \"KEGG\" [label=\"same_as (494)\"]; \t\"FBbt\" -> \"UBERON\" [label=\"part_of (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_connection_type (4)\"]; \t\"OBI\" -> \"GO\" [label=\"subclass_of (1)\"]; \t\"CHMO\" -> \"CHMO\" [label=\"subclass_of (7)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:has_member (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_priority (211)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_or_within (293)\"]; \t\"GO\" -> \"PR\" [label=\"INVERTED:output_of (808)\"]; \t\"ARO\" -> \"OBI\" [label=\"subclass_of (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"dorsal_to (10)\"]; \t\"FOODON\" -> \"ENVO\" [label=\"derives_from (8)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_realization (1450)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"sub_property_of (3)\"]; \t\"EFO\" -> \"EFO\" [label=\"disease_shares_features_of (2)\"]; \t\"MF\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (3)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"type (43)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_part (9)\"]; \t\"CHEMBL.TARGET\" -> \"ENSEMBL\" [label=\"part_of (4)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_shares_features_of (11)\"]; \t\"MONDO\" -> \"MESH\" [label=\"equivalent_to (7860)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"role_has_range (97)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"channel_blocker (158)\"]; \t\"PATO\" -> \"PATO\" [label=\"INVERTED:has_part (9)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antisense (3)\"]; \t\"MONDO\" -> \"PATO\" [label=\"has_modifier (78)\"]; \t\"NCBITaxon\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (300)\"]; \t\"PathWhiz.Reaction\" -> \"CHEBI\" [label=\"has_right_element (169923)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"prevents (7331)\"]; \t\"ORPHANET\" -> \"CL\" [label=\"has_disease_location (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"luminal_space_of (77)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"analyzes (72330)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:410295 (1091)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"part_of (1)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_morphogenesis_of (30)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"channels_from (25)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:disease_is_marked_by_gene (8)\"]; \t\"UBERON\" -> \"BFO\" [label=\"sub_property_of (3)\"]; \t\"EFO\" -> \"BTO\" [label=\"is_about (3)\"]; \t\"CL\" -> \"GO\" [label=\"participates_in (18)\"]; \t\"OBO\" -> \"CARO\" [label=\"subclass_of (1)\"]; \t\"ORPHANET\" -> \"GO\" [label=\"has_disease_location (10)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_site (91236)\"]; \t\"NCBIGene\" -> \"NCBITaxon\" [label=\"in_taxon (61530)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_occurrence (5492)\"]; \t\"CL\" -> \"GO\" [label=\"has_plasma_membrane_part (1)\"]; \t\"OGMS\" -> \"GO\" [label=\"subclass_of (1)\"]; \t\"GENEPIO\" -> \"OIO\" [label=\"subclass_of (2)\"]; \t\"CHEBI\" -> \"UBERON\" [label=\"part_of (1)\"]; \t\"CL\" -> \"NCIT\" [label=\"xref (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"posteriorly_connected_to (1)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_dose_form (42707)\"]; \t\"EFO\" -> \"MP\" [label=\"has_phenotype (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"bounding_layer_of (1)\"]; \t\"KEGG\" -> \"MONDO\" [label=\"equivalent_to (37)\"]; \t\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"overlaps_with (2630)\"]; \t\"UBERON\" -> \"CL\" [label=\"surrounds (7)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_site (3506)\"]; \t\"FMA\" -> \"FMA\" [label=\"posteromedial_to (9)\"]; \t\"EFO\" -> \"NCIT\" [label=\"xref (2012)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antibody (180)\"]; \t\"EFO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_maturation_of (16)\"]; \t\"ZFIN\" -> \"SO\" [label=\"subclass_of (3318)\"]; \t\"UBERON\" -> \"GO\" [label=\"surrounds (3)\"]; \t\"PathWhiz.Reaction\" -> \"CHEBI\" [label=\"has_left_element (188562)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"INVERTED:has_manifestation (121769)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_or_within_positive_effect (13)\"]; \t\"FMA\" -> \"FMA\" [label=\"transforms_into (28)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"finishes_axis (7)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_physiologic_effect (1)\"]; \t\"OMIT\" -> \"CHEBI\" [label=\"subclass_of (3)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_maturation_of (2)\"]; \t\"DOID\" -> \"OMIM\" [label=\"xref (4868)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"negative_modulator (5)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"superficial_to (14)\"]; \t\"HP\" -> \"HP\" [label=\"has_modifier (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"developmentally_replaces (8)\"]; \t\"NCIT\" -> \"ICO\" [label=\"is_about (1)\"]; \t\"RXNORM\" -> \"UMLS\" [label=\"xref (108886)\"]; \t\"UBERON\" -> \"NBO\" [label=\"INVERTED:has_participant (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_clinical_course (4570)\"]; \t\"UBERON\" -> \"GO\" [label=\"INVERTED:has_participant (2)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"agonist (105)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_scale (87167)\"]; \t\"NCIT\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (1)\"]; \t\"EFO\" -> \"UO\" [label=\"subclass_of (38)\"]; \t\"FMA\" -> \"FMA\" [label=\"regional_part_of (27615)\"]; \t\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"equivalent_to (36)\"]; \t\"OBI\" -> \"STATO\" [label=\"is_about (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"INVERTED:has_component (3)\"]; \t\"EFO\" -> \"EFO\" [label=\"participates_in (8)\"]; \t\"PR\" -> \"NCBITaxon\" [label=\"only_in_taxon (177969)\"]; \t\"MGI\" -> \"SO\" [label=\"subclass_of (16846)\"]; \t\"ENSEMBL\" -> \"PR\" [label=\"INVERTED:has_gene_template (110)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"gating_inhibitor (32)\"]; \t\"BTO\" -> \"CL\" [label=\"subclass_of (6)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"partial_agonist (47)\"]; \t\"GO\" -> \"CL\" [label=\"part_of (150)\"]; \t\"UBERON\" -> \"MESH\" [label=\"xref (644)\"]; \t\"HGNC\" -> \"PR\" [label=\"INVERTED:has_gene_template (19823)\"]; \t\"CPT\" -> \"CPT\" [label=\"panel_element_of_possibly_included (1)\"]; \t\"IAO\" -> \"EFO\" [label=\"inverse_of (1)\"]; \t\"CHEBI\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"adjacent_to (8)\"]; \t\"KEGG\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (1701455)\"]; \t\"EO\" -> \"EO\" [label=\"subclass_of (47)\"]; \t\"GO\" -> \"GO\" [label=\"part_of (5240)\"]; \t\"EFO\" -> \"BTO\" [label=\"equivalent_to (1)\"]; \t\"DOID\" -> \"ICD9\" [label=\"xref (11)\"]; \t\"OBI\" -> \"EFO\" [label=\"INVERTED:has_participant (1)\"]; \t\"VCARD\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"ZEA\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"inverse_of_measures (79662)\"]; \t\"EFO\" -> \"EFO\" [label=\"INVERTED:has_input (4)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_positive_effect (14)\"]; \t\"SO\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (3)\"]; \t\"GO\" -> \"OBO\" [label=\"has_input (48)\"]; \t\"GO\" -> \"GO\" [label=\"bounding_layer_of (29)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_innermost_side_of (2)\"]; \t\"RO\" -> \"RO\" [label=\"sub_property_of (621)\"]; \t\"OBO\" -> \"OBOREL\" [label=\"inverse_of (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"located_in (3)\"]; \t\"RO\" -> \"RO\" [label=\"inverse_of (122)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"disease_has_feature (25)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_result_anatomy (63)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_disassembly_of (75)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_intent (5207)\"]; \t\"CHEBI\" -> \"PR\" [label=\"INVERTED:has_part (2)\"]; \t\"EFO\" -> \"EFO\" [label=\"part_of_progression_of_disease (2)\"]; \t\"EnsemblGenomes\" -> \"SO\" [label=\"subclass_of (278)\"]; \t\"GO\" -> \"OBO\" [label=\"transports_or_maintains_localization_of (20)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_unit_of_presentation (2918)\"]; \t\"FAO\" -> \"FAO\" [label=\"subclass_of (32)\"]; \t\"CL\" -> \"RO\" [label=\"sub_property_of (2)\"]; \t\"UBERON\" -> \"CARO\" [label=\"subclass_of (1408)\"]; \t\"HMDB\" -> \"NCIT\" [label=\"at_tissue (217)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_developmental_progression_of (1)\"]; \t\"MONDO\" -> \"CHEBI\" [label=\"disease_has_basis_in_accumulation_of (1)\"]; \t\"GENEPIO\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"CVDO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"has_target_end_location (2)\"]; \t\"HP\" -> \"ARO\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"right_medial_to (4)\"]; \t\"GO\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"develops_from_part_of (13)\"]; \t\"PR\" -> \"CHEBI\" [label=\"derives_from (1)\"]; \t\"UBERON\" -> \"CARO\" [label=\"xref (42)\"]; \t\"ENVO\" -> \"GENEPIO\" [label=\"subclass_of (17)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"member_of (9)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"part_of (41790)\"]; \t\"FMA\" -> \"FMA\" [label=\"segmental_supply_of (683)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"cause_of (7207)\"]; \t\"OMIABIS\" -> \"OGMS\" [label=\"subclass_of (1)\"]; \t\"MF\" -> \"MF\" [label=\"INVERTED:has_occurrent_part (1)\"]; \t\"ZFA\" -> \"EFO\" [label=\"subclass_of (33)\"]; \t\"SYMP\" -> \"SYMP\" [label=\"has_symptom (1)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:produced_by (1)\"]; \t\"dbpedia\" -> \"HANCESTRO\" [label=\"subclass_of (9)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"same_as (617)\"]; \t\"MONDO\" -> \"ORPHANET\" [label=\"subclass_of (669)\"]; \t\"PECO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"during (118)\"]; \t\"GO\" -> \"OBO\" [label=\"imports (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"releasing_agent (26)\"]; \t\"EFO\" -> \"MONDO\" [label=\"disease_shares_features_of (1)\"]; \t\"MONDO\" -> \"GARD\" [label=\"equivalent_to (5814)\"]; \t\"NCIT\" -> \"PATO\" [label=\"subclass_of (3)\"]; \t\"EFO\" -> \"MEDDRA\" [label=\"xref (2)\"]; \t\"EHDAA2\" -> \"AEO\" [label=\"attaches_to (1)\"]; \t\"MF\" -> \"BFO\" [label=\"subclass_of (4)\"]; \t\"FMA\" -> \"FMA\" [label=\"left_lateral_to (5)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"degrader (1)\"]; \t\"OBO\" -> \"OBO\" [label=\"regulates (2)\"]; \t\"CL\" -> \"GO\" [label=\"INVERTED:results_in_movement_of (87)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"allele_plays_altered_role_in_process (128)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_device (279)\"]; \t\"EFO\" -> \"EFO\" [label=\"sub_property_of (5)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"affects (10769)\"]; \t\"CHEBI\" -> \"MONDO\" [label=\"INVERTED:disease_responds_to (13)\"]; \t\"EFO\" -> \"HANCESTRO\" [label=\"derives_from (31)\"]; \t\"BTO\" -> \"UBERON\" [label=\"located_in (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"surrounds (133)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"subdivision_of (12)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:process_includes_biological_process (642)\"]; \t\"FOODON\" -> \"ECOCORE\" [label=\"INVERTED:has_participant (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"diagnoses (259899)\"]; \t\"GO\" -> \"UBERON\" [label=\"xref (44)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"interacts_with (33756)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"sexually_homologous_to (12)\"]; \t\"EFO\" -> \"MA\" [label=\"is_about (1)\"]; \t\"GAZ\" -> \"FOODON\" [label=\"subclass_of (162)\"]; \t\"UBERON\" -> \"CL\" [label=\"extends_fibers_into (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antisense_oligonucleotide (5)\"]; \t\"OBI\" -> \"OBI\" [label=\"subclass_of (105)\"]; \t\"HCPCS\" -> \"HCPCS\" [label=\"mapped_to (15)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"INVERTED:phenotype_of (13865)\"]; \t\"MONDO\" -> \"HP\" [label=\"disease_has_major_feature (100)\"]; \t\"MONDO\" -> \"HP\" [label=\"xref (565)\"]; \t\"CHEBI\" -> \"UBERON\" [label=\"subclass_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_has_mechanism_of_action (2274)\"]; \t\"EFO\" -> \"HGNC\" [label=\"xref (8)\"]; \t\"PO\" -> \"EFO\" [label=\"equivalent_to (1)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"realized_in (2)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"inheres_in (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_deep_part_of (6)\"]; \t\"CL\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (4)\"]; \t\"GO\" -> \"SO\" [label=\"xref (15)\"]; \t\"GENEPIO\" -> \"ARO\" [label=\"is_about (3)\"]; \t\"MONDO\" -> \"EFO\" [label=\"disease_has_major_feature (6)\"]; \t\"MONDO\" -> \"EFO\" [label=\"xref (2857)\"]; \t\"OncoTree\" -> \"MONDO\" [label=\"equivalent_to (556)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:determined_by (11)\"]; \t\"CHEMBL.MECHANISM\" -> \"CHEMBL.MECHANISM\" [label=\"subclass_of (27)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"proximalmost_part_of (4)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"has_quality (9)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_primary_segmental_supply (17)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"converts_to (36699)\"]; \t\"PR\" -> \"CL\" [label=\"part_of (4)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"dorsal_to (1)\"]; \t\"DOID\" -> \"UBERON\" [label=\"located_in (618)\"]; \t\"HGNC\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (4393)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"reducing_agent (2)\"]; \t\"EFO\" -> \"HP\" [label=\"subclass_of (128)\"]; \t\"MEDDRA\" -> \"MEDDRA\" [label=\"member_of (52438)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"developmentally_induced_by (20)\"]; \t\"UniProtKB\" -> \"CHEMBL.COMPOUND\" [label=\"targets (39678)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:preceded_by (1)\"]; \t\"CHEBI\" -> \"SO\" [label=\"subclass_of (23)\"]; \t\"ERO\" -> \"OBI\" [label=\"subclass_of (4)\"]; \t\"GO\" -> \"NBO\" [label=\"INVERTED:by_means (1)\"]; \t\"CHEBI\" -> \"BFO\" [label=\"subclass_of (33)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_fragments_for_synonyms (96184)\"]; \t\"PR\" -> \"GO\" [label=\"part_of (4)\"]; \t\"IDO\" -> \"OBO\" [label=\"INVERTED:has_participant (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"part_of (9688)\"]; \t\"EFO\" -> \"EFO\" [label=\"subclass_of (11372)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_2 (208)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"characterized_by (346)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (1)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"before (11)\"]; \t\"PathWhiz.Compound\" -> \"KEGG\" [label=\"same_as (48957)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_inherent_location (1)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:regulated_by (1913)\"]; \t\"GENO\" -> \"GENO\" [label=\"subclass_of (24)\"]; \t\"CL\" -> \"MA\" [label=\"located_in (1)\"]; \t\"OGMS\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"NCBITaxon\" [label=\"only_in_taxon (683)\"]; \t\"biolink\" -> \"biolink\" [label=\"subclass_of (248)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"allele_has_activity (74)\"]; \t\"ORPHANET\" -> \"MESH\" [label=\"xref (2518)\"]; \t\"DOID\" -> \"UBERON\" [label=\"adjacent_to (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"drains_into (212)\"]; \t\"HP\" -> \"NCIT\" [label=\"xref (276)\"]; \t\"MGI\" -> \"PR\" [label=\"INVERTED:has_gene_template (16846)\"]; \t\"CGNC\" -> \"SO\" [label=\"subclass_of (552)\"]; \t\"ECO\" -> \"ECO\" [label=\"subclass_of (12)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"inverse_of_exhibits (1082)\"]; \t\"OBO\" -> \"OBOREL\" [label=\"sub_property_of (1)\"]; \t\"EO\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"causal_agent_in_process (1)\"]; \t\"UniProtKB\" -> \"MONDO\" [label=\"associated_with_disease (188)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"indirectly_supplies (4)\"]; \t\"OGMS\" -> \"OGMS\" [label=\"INVERTED:has_participant_at_all_times (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"immediately_anterior_to (1)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (12)\"]; \t\"HMDB\" -> \"MEDDRA\" [label=\"at_tissue (2)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"vaccine (6)\"]; \t\"FOODON\" -> \"RO\" [label=\"sub_property_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_expressed_in_tissue (1594)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"precedes (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_venous_drainage (132)\"]; \t\"ZFIN\" -> \"PR\" [label=\"INVERTED:has_gene_template (3318)\"]; \t\"FMA\" -> \"FMA\" [label=\"tributary_of (1068)\"]; \t\"CL\" -> \"UBERON\" [label=\"INVERTED:develops_from (2)\"]; \t\"AraPort\" -> \"NCBITaxon\" [label=\"only_in_taxon (15919)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"larger_than (1)\"]; \t\"HMDB\" -> \"UMLS\" [label=\"at_cellular_location (1)\"]; \t\"NDDF\" -> \"NDDF\" [label=\"ingredient_of (12)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"administered_to (9523)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_affects_gene_product (378)\"]; \t\"sgd\" -> \"SO\" [label=\"subclass_of (5938)\"]; \t\"GENEPIO\" -> \"GEO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"SO\" [label=\"coincident_with (6)\"]; \t\"UniProtKB\" -> \"UniProtKB\" [label=\"regulates_activity_of (165005)\"]; \t\"KEGG\" -> \"DRUGBANK\" [label=\"same_as (978)\"]; \t\"PR\" -> \"CHEBI\" [label=\"non_covalently_bound_to (7)\"]; \t\"NPO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.MECHANISM\" [label=\"related_to (4739)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_source_identity (126)\"]; \t\"MP\" -> \"DOID\" [label=\"xref (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"surrounded_by (35)\"]; \t\"NCIT\" -> \"GO\" [label=\"subclass_of (1)\"]; \t\"CHEBI\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (214)\"]; \t\"UBERON\" -> \"FMA\" [label=\"xref (5851)\"]; \t\"EFO\" -> \"ICD10\" [label=\"xref (2576)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_abnormality (24)\"]; \t\"NCBIGene\" -> \"SO\" [label=\"subclass_of (5380)\"]; \t\"MONDO\" -> \"NCBITaxon\" [label=\"in_taxon (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"agonist (720)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_transport_along (1)\"]; \t\"UBERON\" -> \"NCBITaxon\" [label=\"part_of (4)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:contains (333)\"]; \t\"LOINC\" -> \"UMLS\" [label=\"xref (260568)\"]; \t\"NBO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"UBERON\" [label=\"has_disease_location (278)\"]; \t\"PO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_property (521)\"]; \t\"CARO\" -> \"CARO\" [label=\"part_of (3)\"]; \t\"MONDO\" -> \"CL\" [label=\"disease_has_location (49)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_has_major_feature (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antagonist (2951)\"]; \t\"FMA\" -> \"FMA\" [label=\"subclass_of (107543)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"has_phenotype (15337)\"]; \t\"MONDO\" -> \"NBO\" [label=\"disease_causes_disruption_of (4)\"]; \t\"CHEBI\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (11)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_direct_morphology (7589)\"]; \t\"MONDO\" -> \"GO\" [label=\"disease_causes_disruption_of (93)\"]; \t\"BTO\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"fusion_of (2)\"]; \t\"MONDO\" -> \"GO\" [label=\"disease_has_location (5)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_assembly_of (316)\"]; \t\"CL\" -> \"EFO\" [label=\"subclass_of (41)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"uses_access_device (1594)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"proximal_to (4)\"]; \t\"GENEPIO\" -> \"CHEBI\" [label=\"subclass_of (2)\"]; \t\"MONDO\" -> \"LOINC\" [label=\"xref (1)\"]; \t\"OMIT\" -> \"GENEPIO\" [label=\"subclass_of (6)\"]; \t\"ExO\" -> \"GENEPIO\" [label=\"member_of (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_associated_finding (2554)\"]; \t\"CL\" -> \"CL\" [label=\"synapsed_to (3)\"]; \t\"CL\" -> \"MONDO\" [label=\"INVERTED:disease_arises_from_structure (58)\"]; \t\"FMA\" -> \"FMA\" [label=\"superomedial_to (5)\"]; \t\"UBERON\" -> \"GO\" [label=\"composed_primarily_of (3)\"]; \t\"HGNC\" -> \"NCBITaxon\" [label=\"only_in_taxon (19823)\"]; \t\"UBERON\" -> \"ENVO\" [label=\"INVERTED:determined_by_part_of (1)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_1 (9)\"]; \t\"CL\" -> \"PATO\" [label=\"bearer_of (38)\"]; \t\"OBO\" -> \"GO\" [label=\"subclass_of (5)\"]; \t\"GO\" -> \"GO\" [label=\"has_primary_output (1)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:reformulated_to (9)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"is_active_in (32)\"]; \t\"NCBITaxon\" -> \"EFO\" [label=\"part_of (1)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"converts_to (290)\"]; \t\"NCIT\" -> \"FOODON\" [label=\"subclass_of (4)\"]; \t\"FOODON\" -> \"CHEBI\" [label=\"derives_from (2)\"]; \t\"SIO\" -> \"SIO\" [label=\"subclass_of (4)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_basic_dose_form (274)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_context (2641)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"conceptual_part_of (3585)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"INVERTED:location_of (2270476)\"]; \t\"MONDO\" -> \"UMLS\" [label=\"xref (14056)\"]; \t\"MONDO\" -> \"CL\" [label=\"disease_has_inflammation_site (1)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"activator (13)\"]; \t\"MONDO\" -> \"OBA\" [label=\"disease_has_feature (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"qualifier_applies_to (1)\"]; \t\"ICD10\" -> \"MONDO\" [label=\"equivalent_to (1113)\"]; \t\"NCIT\" -> \"GENEPIO\" [label=\"INVERTED:contains_process (1)\"]; \t\"IAO\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"INVERTED:produced_by (2)\"]; \t\"SO\" -> \"SO\" [label=\"has_quality (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"posterior_to (9)\"]; \t\"CGNC\" -> \"PR\" [label=\"INVERTED:has_gene_template (552)\"]; \t\"FMA\" -> \"FMA\" [label=\"developmental_stage_of (193)\"]; \t\"GO\" -> \"GO\" [label=\"happens_during (12)\"]; \t\"FOODON\" -> \"UBERON\" [label=\"subclass_of (2)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:ends_with (25)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chromosome_mapped_to_disease (189)\"]; \t\"HP\" -> \"MEDDRA\" [label=\"xref (93)\"]; \t\"CHEMBL.COMPOUND\" -> \"DOID\" [label=\"indicated_for (2375)\"]; \t\"UBERON\" -> \"CL\" [label=\"channel_for (4)\"]; \t\"GO\" -> \"EFO\" [label=\"INVERTED:has_input (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"stabiliser (9)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"sub_property_of (1)\"]; \t\"EFO\" -> \"CL\" [label=\"derives_from (6)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"has_input (3)\"]; \t\"ENSEMBL\" -> \"NCBITaxon\" [label=\"in_taxon (67667)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:contained_in (789)\"]; \t\"OBO\" -> \"FOODON\" [label=\"subclass_of (2)\"]; \t\"PDQ\" -> \"PDQ\" [label=\"associated_disease (243)\"]; \t\"BTO\" -> \"EFO\" [label=\"derives_from (3)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"disease_has_major_feature (14)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"xref (12)\"]; \t\"PO\" -> \"PO\" [label=\"INVERTED:has_participant (3)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_development_of (65)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_3 (437)\"]; \t\"FOODON\" -> \"BFO\" [label=\"subclass_of (11)\"]; \t\"GO\" -> \"OBO\" [label=\"regulates_levels_of (2)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"process_initiates_biological_process (132)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"develops_in (9)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:has_participant (39)\"]; \t\"ARO\" -> \"IDO\" [label=\"is_about (1)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"has_modifier (257)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"same_as (692)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_mapped_to_disease (5189)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"intersection_of (1)\"]; \t\"EFO\" -> \"MONDO\" [label=\"subclass_of (2167)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:disease_has_molecular_abnormality (294)\"]; \t\"MF\" -> \"OGMS\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_location (1)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"subclass_of (59497)\"]; \t\"RO\" -> \"BFO\" [label=\"subclass_of (2)\"]; \t\"EFO\" -> \"CHEBI\" [label=\"subclass_of (71)\"]; \t\"ORPHANET\" -> \"GARD\" [label=\"xref (2968)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_lateral_side_of (131)\"]; \t\"FAO\" -> \"NCBITaxon\" [label=\"only_in_taxon (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"occurs_in (7221)\"]; \t\"NCBITaxon\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"sequestering_agent (23)\"]; \t\"GO\" -> \"CL\" [label=\"overlaps (15)\"]; \t\"HCPCS\" -> \"UMLS\" [label=\"xref (6948)\"]; \t\"NBO\" -> \"PATO\" [label=\"is_about (5)\"]; \t\"GO\" -> \"EFO\" [label=\"subclass_of (10)\"]; \t\"TRANS\" -> \"GO\" [label=\"subclass_of (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_view_type (1668)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_organization_of (191)\"]; \t\"FOODON\" -> \"IAO\" [label=\"subclass_of (7)\"]; \t\"MONDO\" -> \"HP\" [label=\"disease_causes_feature (5)\"]; \t\"PR\" -> \"SO\" [label=\"subclass_of (45)\"]; \t\"GO\" -> \"GO\" [label=\"overlaps (26)\"]; \t\"PR\" -> \"BFO\" [label=\"subclass_of (2)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_biomarker_type (337)\"]; \t\"CP\" -> \"PATO\" [label=\"bearer_of (4)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"has_role (1)\"]; \t\"UBERON\" -> \"CL\" [label=\"subclass_of (2)\"]; \t\"MONDO\" -> \"EFO\" [label=\"disease_causes_feature (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_boundary (1)\"]; \t\"dictybase.gene\" -> \"SO\" [label=\"subclass_of (4540)\"]; \t\"FMA\" -> \"FMA\" [label=\"attaches_to (476)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:disease_has_finding (36775)\"]; \t\"KEGG\" -> \"HMDB\" [label=\"same_as (3308)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"stimulates (110058)\"]; \t\"BTO\" -> \"EFO\" [label=\"INVERTED:develops_from (1)\"]; \t\"PATO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"GO\" [label=\"subclass_of (2)\"]; \t\"SIO\" -> \"NCIT\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"UBERON\" [label=\"xref (2)\"]; \t\"EFO\" -> \"EFO\" [label=\"has_role (17)\"]; \t\"UBERON\" -> \"CL\" [label=\"xref (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"HP\" [label=\"contraindicated_for (12221)\"]; \t\"EFO\" -> \"OBI\" [label=\"is_executed_in (2)\"]; \t\"GO\" -> \"ECOCORE\" [label=\"INVERTED:has_part (5)\"]; \t\"CP\" -> \"CL\" [label=\"INVERTED:has_part (26)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"inhibitor (203)\"]; \t\"EHDAA2\" -> \"EHDAA2\" [label=\"attaches_to (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_approach_guidance (347)\"]; \t\"MEDDRA\" -> \"MONDO\" [label=\"equivalent_to (1)\"]; \t\"UBERON\" -> \"GO\" [label=\"xref (4)\"]; \t\"DRUGBANK\" -> \"CHEBI\" [label=\"same_as (102)\"]; \t\"FAO\" -> \"CARO\" [label=\"subclass_of (4)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"produces (14)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"causes (56542)\"]; \t\"CL\" -> \"FAO\" [label=\"xref (8)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_outermost_side_of (2)\"]; \t\"EFO\" -> \"HANCESTRO\" [label=\"has_quality (3)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:subset_includes_concept (230272)\"]; \t\"MMO\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"NCBITaxon\" -> \"OBI\" [label=\"subclass_of (16)\"]; \t\"CHEBI\" -> \"CL\" [label=\"INVERTED:has_part (1)\"]; \t\"EHDAA2\" -> \"OBO\" [label=\"subclass_of (1)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"is_enantiomer_of (2594)\"]; \t\"FBgn\" -> \"SO\" [label=\"subclass_of (3954)\"]; \t\"EDAM\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"DOID\" -> \"NCIT\" [label=\"xref (3)\"]; \t\"UMLS\" -> \"MONDO\" [label=\"equivalent_to (14023)\"]; \t\"ECTO\" -> \"ExO\" [label=\"subclass_of (4)\"]; \t\"ENVO\" -> \"BFO\" [label=\"has_increased_levels_of (1)\"]; \t\"ZFIN\" -> \"NCBITaxon\" [label=\"only_in_taxon (3318)\"]; \t\"OBI\" -> \"EFO\" [label=\"subclass_of (39)\"]; \t\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_part (16)\"]; \t\"UniProtKB\" -> \"DOID\" [label=\"associated_with_disease (3803)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEBI\" [label=\"same_as (30201)\"]; \t\"FMA\" -> \"FMA\" [label=\"superolateral_to (9)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_class (54220)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"is_given_pharmaceutical_substance_for (2418)\"]; \t\"PATO\" -> \"PATO\" [label=\"correlates_with (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"activator (42)\"]; \t\"HP\" -> \"ICD10\" [label=\"xref (83)\"]; \t\"PathWhiz.ElementCollection\" -> \"UniProtKB\" [label=\"same_as (7)\"]; \t\"NCBIGene\" -> \"UBERON\" [label=\"expressed_in (1414)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_count_of_base_of_active_ingredient (13255)\"]; \t\"UBERON\" -> \"FOODON\" [label=\"subclass_of (34)\"]; \t\"FMA\" -> \"FMA\" [label=\"posterosuperior_to (34)\"]; \t\"GO\" -> \"CHEBI\" [label=\"exports (74)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"derives_from (9)\"]; \t\"CL\" -> \"GO\" [label=\"equivalent_to (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_finding (16831)\"]; \t\"UniProtKB\" -> \"KEGG\" [label=\"physically_interacts_with (22304)\"]; \t\"NCIT\" -> \"OBI\" [label=\"subclass_of (13)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"deep_to (1)\"]; \t\"EnsemblGenomes\" -> \"PR\" [label=\"INVERTED:has_gene_template (278)\"]; \t\"GO\" -> \"GO\" [label=\"results_in (9)\"]; \t\"CL\" -> \"UBERON\" [label=\"innervates (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_morphogenesis_of (342)\"]; \t\"PR\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (1)\"]; \t\"CL\" -> \"EFO\" [label=\"participates_in (1)\"]; \t\"GO\" -> \"PR\" [label=\"xref (89)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"has_disease_location (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_revision_status (1031)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_developmental_stage (193)\"]; \t\"OBI\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (7)\"]; \t\"MONDO\" -> \"PATO\" [label=\"subclass_of (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"cofactor (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"related_object (252)\"]; \t\"CHEBI\" -> \"PR\" [label=\"subclass_of (5)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"related_to (2823)\"]; \t\"GO\" -> \"OBO\" [label=\"has_output (1)\"]; \t\"ecogene\" -> \"NCBITaxon\" [label=\"only_in_taxon (4018)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_part (277)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"allele_plays_role_in_metabolism_of_chemical_or_drug (3)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317346 (38)\"]; \t\"GENEPIO\" -> \"DOID\" [label=\"subclass_of (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"isa (313010)\"]; \t\"CLO\" -> \"PATO\" [label=\"has_quality (405)\"]; \t\"CL\" -> \"AEO\" [label=\"INVERTED:has_part (78)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_quantified_form (15)\"]; \t\"TO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"NBO\" -> \"NBO\" [label=\"is_about (7)\"]; \t\"HMDB\" -> \"UBERON\" [label=\"at_tissue (66)\"]; \t\"NBO\" -> \"GO\" [label=\"is_about (8)\"]; \t\"MESH\" -> \"MESH\" [label=\"mapped_to (376217)\"]; \t\"GENEPIO\" -> \"OBI\" [label=\"has_quality (1)\"]; \t\"GENEPIO\" -> \"PCO\" [label=\"subclass_of (2)\"]; \t\"GAZ\" -> \"ENVO\" [label=\"type (190)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"overlaps (77)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"disease_causes_dysfunction_of (2)\"]; \t\"EFO\" -> \"PATO\" [label=\"has_quality (522)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"allosteric_modulator (139)\"]; \t\"PDQ\" -> \"PDQ\" [label=\"component_of (5952)\"]; \t\"STATO\" -> \"STATO\" [label=\"subclass_of (30)\"]; \t\"DRUGBANK\" -> \"UniProtKB\" [label=\"target (16808)\"]; \t\"OBO\" -> \"OBI\" [label=\"subclass_of (4)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"existence_starts_and_ends_during (15)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_continuation_branch (28)\"]; \t\"EHDAA2\" -> \"EHDAA2\" [label=\"located_in (166)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"inhibitor (1337)\"]; \t\"OBI\" -> \"OBI\" [label=\"type (6)\"]; \t\"EFO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (1)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"colocalizes_with (1327)\"]; \t\"EHDAA2\" -> \"OBO\" [label=\"existence_starts_during (2268)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"manifestation_of (121769)\"]; \t\"HP\" -> \"MONDO\" [label=\"equivalent_to (5)\"]; \t\"ICD10\" -> \"ICD10\" [label=\"subclass_of (98417)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"subclass_of (665)\"]; \t\"OBI\" -> \"NCIT\" [label=\"inheres_in (1)\"]; \t\"CHMO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"MONDO\" -> \"KEGG\" [label=\"equivalent_to (37)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"immediate_transformation_of (71)\"]; \t\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (1276)\"]; \t\"STATO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"NCBITaxon\" -> \"EFO\" [label=\"INVERTED:has_member (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_initiates_biological_process (113)\"]; \t\"MP\" -> \"ICD9\" [label=\"xref (1)\"]; \t\"BTO\" -> \"EFO\" [label=\"subclass_of (47)\"]; \t\"RO\" -> \"RO\" [label=\"INVERTED:has_subsequence (1)\"]; \t\"NCBITaxon\" -> \"EO\" [label=\"subclass_of (3)\"]; \t\"MONDO\" -> \"OMIMPS\" [label=\"equivalent_to (472)\"]; \t\"GO\" -> \"UBERON\" [label=\"has_input (8)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"anastomoses_with (4)\"]; \t\"ENSEMBL\" -> \"SO\" [label=\"subclass_of (110)\"]; \t\"MONDO\" -> \"OBI\" [label=\"equivalent_to (1)\"]; \t\"MESH\" -> \"GENEPIO\" [label=\"subclass_of (5)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"complicates (42952)\"]; \t\"DOID\" -> \"MEDDRA\" [label=\"xref (33)\"]; \t\"GENEPIO\" -> \"NCIT\" [label=\"is_about (10)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"disease_causes_feature (7)\"]; \t\"EFO\" -> \"PO\" [label=\"equivalent_to (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"transports_or_maintains_localization_of (2)\"]; \t\"UBERON\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (2)\"]; \t\"UBERON\" -> \"GO\" [label=\"participates_in (8)\"]; \t\"NCIT\" -> \"ENVO\" [label=\"subclass_of (6)\"]; \t\"CL\" -> \"PR\" [label=\"has_high_plasma_membrane_amount (65)\"]; \t\"GO\" -> \"SO\" [label=\"has_input (7)\"]; \t\"MONDO\" -> \"DOID\" [label=\"xref (9027)\"]; \t\"PathWhiz.ElementCollection\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (9096)\"]; \t\"GO\" -> \"OBO\" [label=\"has_primary_input (20)\"]; \t\"PathWhiz.NucleicAcid\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (81)\"]; \t\"MONDO\" -> \"HP\" [label=\"has_modifier (140)\"]; \t\"OBO\" -> \"IDO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"RO\" [label=\"sub_property_of (8)\"]; \t\"STATO\" -> \"IAO\" [label=\"subclass_of (2)\"]; \t\"NBO\" -> \"NBO\" [label=\"regulates (16)\"]; \t\"NCIT\" -> \"UO\" [label=\"subclass_of (2)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_adjustment (343)\"]; \t\"EFO\" -> \"CHEBI\" [label=\"has_role (3)\"]; \t\"OPL\" -> \"BTO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"SO\" [label=\"transports_or_maintains_localization_of (4)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_specification_of (7)\"]; \t\"EFO\" -> \"DOID\" [label=\"subclass_of (6)\"]; \t\"ENSEMBL\" -> \"HGNC\" [label=\"same_as (42691)\"]; \t\"MONDO\" -> \"MFOEM\" [label=\"disease_causes_disruption_of (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"partial_agonist (62)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_development_type (13)\"]; \t\"PW\" -> \"OBO\" [label=\"subclass_of (5)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_involved_in_pathogenesis_of_disease (1115)\"]; \t\"DOID\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"OBO\" -> \"OGMS\" [label=\"is_about (1)\"]; \t\"CHEBI\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (8)\"]; \t\"PDQ\" -> \"UMLS\" [label=\"xref (18972)\"]; \t\"FBgn\" -> \"PR\" [label=\"INVERTED:has_gene_template (3954)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:consists_of (26132)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_proximal_side_of (2)\"]; \t\"HP\" -> \"UBERON\" [label=\"xref (1)\"]; \t\"GO\" -> \"NCBITaxon\" [label=\"has_input (10)\"]; \t\"CL\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (41)\"]; \t\"OBI\" -> \"CHEBI\" [label=\"subclass_of (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"lateral_to (111)\"]; \t\"PATO\" -> \"PATO\" [label=\"decreased_in_magnitude_relative_to (2)\"]; \t\"NDDF\" -> \"NDDF\" [label=\"has_dose_form (17997)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:cdrh_parent_of (666)\"]; \t\"EFO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:ingredient_of (36788)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_temporal_context (5183)\"]; \t\"RO\" -> \"EFO\" [label=\"sub_property_of (1)\"]; \t\"GO\" -> \"SO\" [label=\"imports (1)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"part_of (128)\"]; \t\"ENVO\" -> \"PATO\" [label=\"has_quality (32)\"]; \t\"FMA\" -> \"FMA\" [label=\"arterial_supply_of (622)\"]; \t\"sgd\" -> \"PR\" [label=\"INVERTED:has_gene_template (5940)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"uses_device (4753)\"]; \t\"FMA\" -> \"FMA\" [label=\"inherent_3d_shape_of (4)\"]; \t\"NCBIGene\" -> \"OMIM\" [label=\"same_as (17550)\"]; \t\"CL\" -> \"NCBITaxon\" [label=\"only_in_taxon (5)\"]; \t\"ENVO\" -> \"SIO\" [label=\"subclass_of (1)\"]; \t\"VANDF\" -> \"VANDF\" [label=\"INVERTED:inverse_of_isa (7426)\"]; \t\"CL\" -> \"UBERON\" [label=\"produces (6)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"member_of (22330)\"]; \t\"EO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"connected_to (80)\"]; \t\"HP\" -> \"UPHENO\" [label=\"subclass_of (1)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_negative_effect (5)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_fission_of (8)\"]; \t\"FMA\" -> \"FMA\" [label=\"articulates_with (692)\"]; \t\"EFO\" -> \"BTO\" [label=\"subclass_of (217)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_parent_group (6515)\"]; \t\"EFO\" -> \"OGMS\" [label=\"xref (1)\"]; \t\"GENEPIO\" -> \"MI\" [label=\"subclass_of (15)\"]; \t\"FMA\" -> \"FMA\" [label=\"inverse_of_contains (555)\"]; \t\"PO\" -> \"PO\" [label=\"participates_in (7)\"]; \t\"ARO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"partially_surrounded_by (1)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"involved_in (277260)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of (169)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:inverse_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_skeleton (38)\"]; \t\"FMA\" -> \"FMA\" [label=\"merges_with (6)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"compared_with (26838)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"allelic_variant_of (29202)\"]; \t\"OBO\" -> \"OBO\" [label=\"negatively_regulates (1)\"]; \t\"NCBIGene\" -> \"PR\" [label=\"INVERTED:has_gene_template (5701)\"]; \t\"BAO\" -> \"CHEBI\" [label=\"subclass_of (2)\"]; \t\"GO\" -> \"FMA\" [label=\"xref (10)\"]; \t\"OBO\" -> \"OIO\" [label=\"subclass_of (5)\"]; \t\"PathWhiz.Compound\" -> \"CHEBI\" [label=\"same_as (32541)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"located_in (152)\"]; \t\"PDQ\" -> \"PDQ\" [label=\"subclass_of (4291)\"]; \t\"DOID\" -> \"ICD10\" [label=\"xref (8)\"]; \t\"MESH\" -> \"MESH\" [label=\"INVERTED:inverse_of_ro (13058)\"]; \t\"FMA\" -> \"FMA\" [label=\"adheres_to (7)\"]; \t\"EFO\" -> \"EFO\" [label=\"is_executed_in (2)\"]; \t\"PR\" -> \"PR\" [label=\"subclass_of (300998)\"]; \t\"MONDO\" -> \"MF\" [label=\"disease_causes_disruption_of (3)\"]; \t\"FOODON\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (17)\"]; \t\"DOID\" -> \"GO\" [label=\"realized_in_response_to_stimulus (1)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_2_or_phase_3 (16)\"]; \t\"GENEPIO\" -> \"UO\" [label=\"has_measurement_unit_label (3)\"]; \t\"OBO\" -> \"OBO\" [label=\"INVERTED:has_participant (1)\"]; \t\"PathWhiz.Reaction\" -> \"UniProtKB\" [label=\"has_right_element (12)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_dorsal_side_of (6)\"]; \t\"UniProtKB\" -> \"OMIM\" [label=\"associated_with_disease (2132)\"]; \t\"NCBITaxon\" -> \"EFO\" [label=\"subclass_of (4)\"]; \t\"PR\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (3)\"]; \t\"EFO\" -> \"SYMP\" [label=\"xref (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"connected_to (140)\"]; \t\"CHEBI\" -> \"FOODON\" [label=\"INVERTED:has_ingredient (3)\"]; \t\"CHEBI\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (1418)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"associated_with (1016)\"]; \t\"EFO\" -> \"MESH\" [label=\"xref (1631)\"]; \t\"NBO\" -> \"NBO\" [label=\"part_of (1)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"xref (34858)\"]; \t\"MONDO\" -> \"EFO\" [label=\"disease_shares_features_of (1)\"]; \t\"NBO\" -> \"GO\" [label=\"part_of (2)\"]; \t\"GO\" -> \"PATO\" [label=\"xref (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_direct_procedure_site (33347)\"]; \t\"UBERON\" -> \"AEO\" [label=\"xref (109)\"]; \t\"SYMP\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"INVERTED:has_part (43)\"]; \t\"FOODON\" -> \"PO\" [label=\"member_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:location_of (1)\"]; \t\"IDO\" -> \"BFO\" [label=\"subclass_of (9)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_muscle_origin (210)\"]; \t\"UBERON\" -> \"ENVO\" [label=\"xref (2)\"]; \t\"PathWhiz.Reaction\" -> \"UniProtKB\" [label=\"has_left_element (13)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317343 (4581)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_ventral_side_of (5)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_denominator_unit (1294)\"]; \t\"UBERON\" -> \"PR\" [label=\"produces (5)\"]; \t\"NCIT\" -> \"EFO\" [label=\"subclass_of (3)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"has_role (3)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"measures (13930)\"]; \t\"GO\" -> \"UBERON\" [label=\"has_target_start_location (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"skeleton_of (35)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"has_modifier (867)\"]; \t\"FOODON\" -> \"DOID\" [label=\"INVERTED:has_allergic_trigger (25)\"]; \t\"FMA\" -> \"FMA\" [label=\"primary_segmental_supply_of (24)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_central_side_of (1)\"]; \t\"PATO\" -> \"PATO\" [label=\"reciprocal_of (8)\"]; \t\"FMA\" -> \"FMA\" [label=\"inferior_to (401)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"precedes (149791)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_result_chemical_or_drug (32)\"]; \t\"CL\" -> \"CARO\" [label=\"xref (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"plays_role (4304)\"]; \t\"CHEBI\" -> \"ENVO\" [label=\"INVERTED:has_part (3)\"]; \t\"SO\" -> \"PR\" [label=\"INVERTED:has_part (6)\"]; \t\"GO\" -> \"DDANAT\" [label=\"xref (1)\"]; \t\"MONDO\" -> \"HP\" [label=\"disease_has_basis_in_feature (42)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"physically_interacts_with (4538)\"]; \t\"FMA\" -> \"FMA\" [label=\"sends_output_to (800)\"]; \t\"NCBITaxon\" -> \"ENVO\" [label=\"INVERTED:determined_by (3)\"]; \t\"GO\" -> \"CL\" [label=\"has_target_end_location (2)\"]; \t\"FBbt\" -> \"EFO\" [label=\"subclass_of (77)\"]; \t\"MONDO\" -> \"EFO\" [label=\"disease_has_basis_in_feature (23)\"]; \t\"ORPHANET\" -> \"KEGG\" [label=\"xref (4)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"augments (451409)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"temporally_related_to (60)\"]; \t\"DOID\" -> \"ORPHANET\" [label=\"subclass_of (1)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"process_of (27799)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:ingredients_of (4352)\"]; \t\"GO\" -> \"GO\" [label=\"has_target_end_location (268)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_1_or_phase_2 (30)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"coexists_with (77418)\"]; \t\"GO\" -> \"NBO\" [label=\"INVERTED:in_response_to (12)\"]; \t\"GENEPIO\" -> \"ARO\" [label=\"subclass_of (4)\"]; \t\"ICD9\" -> \"ICD9\" [label=\"subclass_of (22402)\"]; \t\"HMDB\" -> \"UniProtKB\" [label=\"has_protein_association (332823)\"]; \t\"NCIT\" -> \"OMIT\" [label=\"subclass_of (1)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_3 (81)\"]; \t\"OBO\" -> \"EFO\" [label=\"subclass_of (7)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"inverse_agonist (11)\"]; \t\"PomBase\" -> \"NCBITaxon\" [label=\"only_in_taxon (5124)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:contains_process (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"uses_energy (314)\"]; \t\"ORPHANET\" -> \"OMIMPS\" [label=\"xref (300)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (190)\"]; \t\"PO\" -> \"PO\" [label=\"subclass_of (531)\"]; \t\"EFO\" -> \"PO\" [label=\"part_of (1)\"]; \t\"NBO\" -> \"PATO\" [label=\"subclass_of (1)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"disrupts (64071)\"]; \t\"MONDO\" -> \"SNOMED\" [label=\"equivalent_to (9000)\"]; \t\"DRUGBANK\" -> \"KEGG\" [label=\"external_identifier (1670)\"]; \t\"BFO\" -> \"BFO\" [label=\"INVERTED:inverse_of (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"agonist (2960)\"]; \t\"HMDB\" -> \"MESH\" [label=\"at_tissue (2301)\"]; \t\"BTO\" -> \"BTO\" [label=\"derives_from (2)\"]; \t\"UniProtKB\" -> \"UniProtKB\" [label=\"regulates_expression_of (237781)\"]; \t\"OBI\" -> \"EFO\" [label=\"INVERTED:has_input (2)\"]; \t\"EFO\" -> \"OBO\" [label=\"part_of (5)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"is_substituent_group_from (1267)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"subclass_of (850)\"]; \t\"CHEMBL.COMPOUND\" -> \"DOID\" [label=\"contraindicated_for (9264)\"]; \t\"UBERON\" -> \"NBO\" [label=\"INVERTED:by_means (6)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"derives_from (1)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"antisense (22)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_interpretation (12748)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"uses (386689)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_component (8)\"]; \t\"MONDO\" -> \"ORPHANET\" [label=\"predisposes_towards (4)\"]; \t\"ARO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"superior_to (399)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_related_developmental_entity (15)\"]; \t\"EFO\" -> \"HP\" [label=\"has_phenotype (3)\"]; \t\"GO\" -> \"UBERON\" [label=\"INVERTED:contains_process (28)\"]; \t\"MONDO\" -> \"HP\" [label=\"equivalent_to (5)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_severity (38)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"innervates (105)\"]; \t\"GO\" -> \"CL\" [label=\"xref (258)\"]; \t\"MONDO\" -> \"OMIM\" [label=\"xref (8869)\"]; \t\"GO\" -> \"GO\" [label=\"causally_upstream_of (3)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"has_food_substance_analog (14)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"specimen_procedure_of (944)\"]; \t\"MONDO\" -> \"HP\" [label=\"disease_has_feature (709)\"]; \t\"MONDO\" -> \"EFO\" [label=\"equivalent_to (2850)\"]; \t\"EFO\" -> \"UBERON\" [label=\"occurs_in (1)\"]; \t\"GENEPIO\" -> \"NCIT\" [label=\"before (1)\"]; \t\"IAO\" -> \"OIO\" [label=\"type (1)\"]; \t\"SYMP\" -> \"DOID\" [label=\"INVERTED:disease_has_basis_in (2)\"]; \t\"GO\" -> \"GO\" [label=\"xref (4)\"]; \t\"RGD\" -> \"NCBITaxon\" [label=\"only_in_taxon (8114)\"]; \t\"NCBIGene\" -> \"OMIM\" [label=\"gene_mutations_contribute_to (4)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"transformation_of (47)\"]; \t\"UBERON\" -> \"GO\" [label=\"simultaneous_with (11)\"]; \t\"MONDO\" -> \"EFO\" [label=\"disease_has_feature (15)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"inhibitor (2414)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_development_of (588)\"]; \t\"EFO\" -> \"EFO\" [label=\"derives_from (15)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_0 (29)\"]; \t\"MONDO\" -> \"MFOMD\" [label=\"realized_in (6)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"disrupts (433181)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_scale_type (527)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_imaged_location (6361)\"]; \t\"DOID\" -> \"CL\" [label=\"located_in (10)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"binder (28)\"]; \t\"GO\" -> \"PO\" [label=\"occurs_in (10)\"]; \t\"HGNC\" -> \"SO\" [label=\"subclass_of (19874)\"]; \t\"MGI\" -> \"NCBITaxon\" [label=\"only_in_taxon (16846)\"]; \t\"FMA\" -> \"FMA\" [label=\"direct_left_of (275)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"opposite_to (3)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"coexists_with (1402013)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_mutant_encodes_gene_product_sequence_variation (809)\"]; \t\"SIO\" -> \"IAO\" [label=\"subclass_of (4)\"]; \t\"UBERON\" -> \"CL\" [label=\"part_of (6)\"]; \t\"MONDO\" -> \"ICD9\" [label=\"xref (5741)\"]; \t\"BTO\" -> \"BTO\" [label=\"INVERTED:develops_from (1)\"]; \t\"ECTO\" -> \"RO\" [label=\"subclass_of (4)\"]; \t\"PR\" -> \"PR\" [label=\"INVERTED:has_gene_template (61)\"]; \t\"GO\" -> \"PR\" [label=\"has_input (292)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"has_output (10)\"]; \t\"OBI\" -> \"GENEPIO\" [label=\"subclass_of (22)\"]; \t\"OAE\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"GO\" [label=\"part_of (11)\"]; \t\"PR\" -> \"SO\" [label=\"lacks_part (3240)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_associated_location (545)\"]; \t\"UniProtKB\" -> \"DOID\" [label=\"gene_associated_with_condition (33361)\"]; \t\"FMA\" -> \"FMA\" [label=\"distal_to (159)\"]; \t\"EFO\" -> \"GARD\" [label=\"xref (555)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"ends (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:has_part (17)\"]; \t\"OBO\" -> \"PATO\" [label=\"bearer_of (1)\"]; \t\"BFO\" -> \"OIO\" [label=\"subclass_of (1)\"]; \t\"DOID\" -> \"GO\" [label=\"disease_has_location (3)\"]; \t\"OBO\" -> \"OBO\" [label=\"immediately_preceded_by (5)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"blocker (149)\"]; \t\"GO\" -> \"FAO\" [label=\"results_in_development_of (10)\"]; \t\"NCBIGene\" -> \"HP\" [label=\"has_phenotype (60)\"]; \t\"GO\" -> \"PR\" [label=\"transports_or_maintains_localization_of (9)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_direct_cell_shape (2)\"]; \t\"CL\" -> \"UBERON\" [label=\"has_soma_location (5)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"class_code_classified_by (61)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"disease_shares_features_of (49)\"]; \t\"ECTO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (6)\"]; \t\"FOODON\" -> \"PATO\" [label=\"subclass_of (6)\"]; \t\"CHEMBL.COMPOUND\" -> \"MESH\" [label=\"treats (27892)\"]; \t\"CL\" -> \"UBERON\" [label=\"has_synaptic_terminal_in (2)\"]; \t\"ERO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"EFO\" [label=\"subclass_of (311)\"]; \t\"AraPort\" -> \"SO\" [label=\"subclass_of (15919)\"]; \t\"OBI\" -> \"BTO\" [label=\"subclass_of (1)\"]; \t\"PR\" -> \"PR\" [label=\"INVERTED:has_component (390)\"]; \t\"CL\" -> \"CL\" [label=\"INVERTED:develops_from (380)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"associated_with (3952)\"]; \t\"CHEBI\" -> \"FOODON\" [label=\"subclass_of (200)\"]; \t\"MF\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_disruption_of (1)\"]; \t\"CL\" -> \"FMA\" [label=\"xref (701)\"]; \t\"PR\" -> \"UBERON\" [label=\"INVERTED:has_part (6)\"]; \t\"HP\" -> \"BFO\" [label=\"subclass_of (3)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"diagnoses (6)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"inhibits (68254)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"genetic_biomarker_related_to (2607)\"]; \t\"PECO\" -> \"PECO\" [label=\"subclass_of (8)\"]; \t\"UBERON\" -> \"EFO\" [label=\"xref (613)\"]; \t\"OGMS\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_lateral_location_presence (3480)\"]; \t\"OBI\" -> \"EFO\" [label=\"part_of (2)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"compared_with (348640)\"]; \t\"OMIT\" -> \"NCIT\" [label=\"subclass_of (2)\"]; \t\"ARO\" -> \"ARO\" [label=\"subclass_of (40)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"proteolytic_enzyme (6)\"]; \t\"NBO\" -> \"NBO\" [label=\"subclass_of (985)\"]; \t\"HP\" -> \"MESH\" [label=\"xref (3)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"class_of (45064)\"]; \t\"NBO\" -> \"GO\" [label=\"subclass_of (14)\"]; \t\"NCIT\" -> \"CHEBI\" [label=\"subclass_of (7)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_source_morphology (154)\"]; \t\"CHEBI\" -> \"EFO\" [label=\"has_role (83)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"is_conjugate_acid_of (8028)\"]; \t\"EFO\" -> \"FMA\" [label=\"xref (57)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_modality_type (6030)\"]; \t\"FMA\" -> \"EFO\" [label=\"subclass_of (1)\"]; \t\"PATO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (1)\"]; \t\"OBI\" -> \"UBERON\" [label=\"INVERTED:produced_by (1)\"]; \t\"UO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"CL\" [label=\"has_disease_location (59)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"results_in_formation_of (2)\"]; \t\"BAO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"PR\" [label=\"imports (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_is_element_in_pathway (6246)\"]; \t\"CL\" -> \"GO\" [label=\"has_high_plasma_membrane_amount (15)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_transport_along (6)\"]; \t\"SO\" -> \"CHEBI\" [label=\"subclass_of (7)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"relative_to_part_of (2)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"located_in (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_branch (6906)\"]; \t\"FMA\" -> \"FMA\" [label=\"anteromedial_to (22)\"]; \t\"GO\" -> \"MI\" [label=\"subclass_of (2)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_acquisition_of_features_of (31)\"]; \t\"UBERON\" -> \"PATO\" [label=\"has_quality (75)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"disease_has_basis_in_feature (68)\"]; \t\"OBI\" -> \"OBI\" [label=\"is_about (1)\"]; \t\"UniProtKB\" -> \"CHEBI\" [label=\"physically_interacts_with (29920)\"]; \t\"TypOn\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"posterolateral_to (12)\"]; \t\"HP\" -> \"MP\" [label=\"xref (1)\"]; \t\"DOID\" -> \"DOID\" [label=\"has_symptom (9)\"]; \t\"PathWhiz.Compound\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (142)\"]; \t\"GENEPIO\" -> \"STATO\" [label=\"is_about (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"postaxialmost_part_of (5)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen (3075)\"]; \t\"HMDB\" -> \"OMIM\" [label=\"disease (4222)\"]; \t\"IDO\" -> \"OGMS\" [label=\"subclass_of (1)\"]; \t\"OBO\" -> \"CHEBI\" [label=\"subclass_of (5)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_lateral_anatomic_location (3498)\"]; \t\"GO\" -> \"CHEBI\" [label=\"has_primary_output (1168)\"]; \t\"dictybase.gene\" -> \"PR\" [label=\"INVERTED:has_gene_template (4540)\"]; \t\"RO\" -> \"RO\" [label=\"subclass_of (2)\"]; \t\"UO\" -> \"IAO\" [label=\"subclass_of (2)\"]; \t\"DOID\" -> \"UBERON\" [label=\"has_disease_location (1)\"]; \t\"MONDO\" -> \"medgen\" [label=\"equivalent_to (2582)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"multipart_of (21095)\"]; \t\"MONDO\" -> \"UMLS\" [label=\"equivalent_to (14023)\"]; \t\"EFO\" -> \"PATO\" [label=\"xref (8)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:327767 (309)\"]; \t\"OIO\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"adjacent_to (22)\"]; \t\"CPT\" -> \"CPT\" [label=\"mapped_to (191)\"]; \t\"NCBIGene\" -> \"DOID\" [label=\"associated_with_disease (110)\"]; \t\"BTO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"has_output (1)\"]; \t\"CPT\" -> \"CPT\" [label=\"has_possibly_included_panel_element (1)\"]; \t\"CL\" -> \"UBERON\" [label=\"adjacent_to (6)\"]; \t\"FMA\" -> \"FMA\" [label=\"anterolateral_to (18)\"]; \t\"UniProtKB\" -> \"UBERON\" [label=\"expressed_in (323101)\"]; \t\"DOID\" -> \"GO\" [label=\"realized_in_response_to (6)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_component (4159)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_exam (454)\"]; \t\"HANCESTRO\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"subclass_of (3400)\"]; \t\"GENEPIO\" -> \"SO\" [label=\"is_about (7)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_definitional_manifestation (13)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_found_in_organism (1840)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_growth_of (20)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"stimulates (663742)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"INVERTED:output_of (3)\"]; \t\"EFO\" -> \"UBERON\" [label=\"is_about (341)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_technique (155)\"]; \t\"BFO\" -> \"EFO\" [label=\"subclass_of (4)\"]; \t\"GO\" -> \"SO\" [label=\"has_output (6)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"directly_develops_from (1)\"]; \t\"HMDB\" -> \"SMPDB\" [label=\"in_pathway (482060)\"]; \t\"CHEBI\" -> \"FOODON\" [label=\"INVERTED:composed_primarily_of (3)\"]; \t\"MONDO\" -> \"RO\" [label=\"sub_property_of (1)\"]; \t\"EFO\" -> \"CHEBI\" [label=\"located_in (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:is_normal_cell_origin_of_disease (18809)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"tributary_of (35)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"activator (316)\"]; \t\"GO\" -> \"UBERON\" [label=\"INVERTED:site_of (16)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_transport_to_from_or_in (2)\"]; \t\"BTO\" -> \"BTO\" [label=\"subclass_of (7)\"]; \t\"FMA\" -> \"FMA\" [label=\"branch_of (7586)\"]; \t\"PO\" -> \"PO\" [label=\"adjacent_to (1)\"]; \t\"UBERON\" -> \"EHDAA2\" [label=\"xref (1386)\"]; \t\"MEDDRA\" -> \"MEDDRA\" [label=\"subclass_of (36911)\"]; \t\"GENEPIO\" -> \"CHMO\" [label=\"subclass_of (5)\"]; \t\"SYMP\" -> \"SYMP\" [label=\"subclass_of (847)\"]; \t\"ECTO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (33)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"disease_has_feature (298)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_modality_subtype (1083)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"sub_property_of (15)\"]; \t\"EFO\" -> \"UBERON\" [label=\"inheres_in (7)\"]; \t\"HMDB\" -> \"FMA\" [label=\"at_tissue (4175)\"]; \t\"FMA\" -> \"UMLS\" [label=\"xref (104400)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"drains (79)\"]; \t\"HANCESTRO\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"CL\" -> \"GO\" [label=\"has_not_completed (12)\"]; \t\"OBI\" -> \"ERO\" [label=\"subclass_of (3)\"]; \t\"ICO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"FAO\" [label=\"results_in_growth_of (1)\"]; \t\"PATO\" -> \"PATO\" [label=\"increased_in_magnitude_relative_to (4)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"same_as (142)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"allele_absent_from_wild_type_chromosomal_location (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"associated_with (699263)\"]; \t\"GENEPIO\" -> \"NCBITaxon\" [label=\"is_about (4)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_segmental_composition (2)\"]; \t\"wb\" -> \"PR\" [label=\"INVERTED:has_gene_template (4479)\"]; \t\"IAO\" -> \"OBO\" [label=\"inverse_of (1)\"]; \t\"CL\" -> \"UBERON\" [label=\"located_in (83)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_plays_role_in_biological_process (21782)\"]; \t\"GAZ\" -> \"GENEPIO\" [label=\"subclass_of (16)\"]; \t\"EFO\" -> \"ORPHANET\" [label=\"disease_has_basis_in_feature (1)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:has_component (38)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_commitment_to (57)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"has_axis (6)\"]; \t\"ERO\" -> \"ERO\" [label=\"subclass_of (2)\"]; \t\"UBERON\" -> \"UMLS\" [label=\"xref (2836)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"allele_in_chromosomal_location (104)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"develops_from_part_of (5)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_has_primary_anatomic_site (11480)\"]; \t\"UBERON\" -> \"NBO\" [label=\"capable_of (2)\"]; \t\"PR\" -> \"GO\" [label=\"subclass_of (360)\"]; \t\"UBERON\" -> \"GO\" [label=\"capable_of (122)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"produces (25911)\"]; \t\"GO\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (30)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_suffix (33614)\"]; \t\"MESH\" -> \"MONDO\" [label=\"equivalent_to (7860)\"]; \t\"UBERON\" -> \"GO\" [label=\"functionally_related_to (4)\"]; \t\"HCPCS\" -> \"HCPCS\" [label=\"subclass_of (6944)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"subclass_of (23328)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_structural_organization_of (8)\"]; \t\"GO\" -> \"GO\" [label=\"capable_of_part_of (298)\"]; \t\"GENEPIO\" -> \"SIO\" [label=\"subclass_of (8)\"]; \t\"FMA\" -> \"FMA\" [label=\"secondary_segmental_supply_of (2)\"]; \t\"ORPHANET\" -> \"HP\" [label=\"xref (87)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:complex_has_physical_part (616)\"]; \t\"GEO\" -> \"GEO\" [label=\"subclass_of (1)\"]; \t\"OBO\" -> \"CL\" [label=\"INVERTED:has_part (3)\"]; \t\"CHEBI\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"CL\" -> \"GO\" [label=\"xref (1)\"]; \t\"PO\" -> \"PO\" [label=\"located_in (3)\"]; \t\"GO\" -> \"GO\" [label=\"isa (6463)\"]; \t\"EFO\" -> \"NCBITaxon\" [label=\"inheres_in (9)\"]; \t\"dictybase.gene\" -> \"NCBITaxon\" [label=\"only_in_taxon (4540)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"has_quality (4)\"]; \t\"EFO\" -> \"EFO\" [label=\"INVERTED:develops_from (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"channels_into (18)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"xref (61)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"human_disease_maps_to_eo_disease (1829)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"modulator (85)\"]; \t\"VT\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"SO\" [label=\"has_primary_input (17)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_secondary_segmental_supply (79)\"]; \t\"EFO\" -> \"CL\" [label=\"xref (12)\"]; \t\"HP\" -> \"GARD\" [label=\"xref (1)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"INVERTED:inverse_of_rn (115122)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"converts_to (1690)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_specification_of (4)\"]; \t\"GENEPIO\" -> \"OBO\" [label=\"subclass_of (1)\"]; \t\"GENEPIO\" -> \"GAZ\" [label=\"located_in (1)\"]; \t\"HP\" -> \"ORPHANET\" [label=\"subclass_of (2)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"connects (524)\"]; \t\"EFO\" -> \"GO\" [label=\"xref (6)\"]; \t\"MONDO\" -> \"HP\" [label=\"subclass_of (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"cross_linking_agent (33)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_method (60209)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_numerator_unit (4305)\"]; \t\"CHEBI\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (1567712)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"has_role (39604)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"branching_part_of (47)\"]; \t\"MONDO\" -> \"EFO\" [label=\"subclass_of (1906)\"]; \t\"NCBITaxon\" -> \"EFO\" [label=\"INVERTED:has_participant (16)\"]; \t\"EHDAA2\" -> \"OBO\" [label=\"existence_ends_during (2367)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"has_consumer (6)\"]; \t\"UBERON\" -> \"ZFA\" [label=\"xref (33)\"]; \t\"FOODON\" -> \"PO\" [label=\"derives_from (5)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_inherent_attribute (156)\"]; \t\"GTPI\" -> \"NCBIGene\" [label=\"affects (97)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"disease_shares_features_of (1)\"]; \t\"GAZ\" -> \"GENEPIO\" [label=\"type (56)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"INVERTED:has_part (3773)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"subclass_of (179)\"]; \t\"UPHENO\" -> \"PATO\" [label=\"subclass_of (1)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_2_or_phase_3 (29)\"]; \t\"GO\" -> \"GO\" [label=\"immediately_preceded_by (7)\"]; \t\"PO\" -> \"FOODON\" [label=\"INVERTED:has_part (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"attaches_to_part_of (2)\"]; \t\"EFO\" -> \"EFO\" [label=\"has_quality (10)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"anterior_to (11)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_has_metastatic_anatomic_site (140)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"surface_of (12)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_formation_of (17)\"]; \t\"MONDO\" -> \"OMOP\" [label=\"equivalent_to (1590)\"]; \t\"NCBIGene\" -> \"CL\" [label=\"expressed_in (20)\"]; \t\"FBbt\" -> \"FBbt\" [label=\"subclass_of (12)\"]; \t\"CL\" -> \"PR\" [label=\"lacks_plasma_membrane_part (454)\"]; \t\"DOID\" -> \"GO\" [label=\"disease_causes_disruption_of (27)\"]; \t\"GO\" -> \"UBERON\" [label=\"has_end_location (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"receives_drainage_from (195)\"]; \t\"NCBITaxon\" -> \"UMLS\" [label=\"xref (1776528)\"]; \t\"NCIT\" -> \"DOID\" [label=\"subclass_of (1)\"]; \t\"HMDB\" -> \"MESH\" [label=\"in_biospecimen (19)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"owning_subsection_of (42)\"]; \t\"DOID\" -> \"MESH\" [label=\"xref (3539)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_morphogenesis_of (10)\"]; \t\"NCIT\" -> \"PCO\" [label=\"subclass_of (2)\"]; \t\"MONDO\" -> \"OncoTree\" [label=\"equivalent_to (556)\"]; \t\"CL\" -> \"UBERON\" [label=\"part_of (690)\"]; \t\"VCARD\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"has_start_location (1)\"]; \t\"OBOREL\" -> \"RO\" [label=\"sub_property_of (1)\"]; \t\"BTO\" -> \"PATO\" [label=\"bearer_of (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"has_input (9)\"]; \t\"SIO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (2)\"]; \t\"UBERON\" -> \"BTO\" [label=\"INVERTED:develops_from (4)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_has_normal_tissue_origin (19638)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_morphogenesis_of (12)\"]; \t\"CHEBI\" -> \"PathWhiz\" [label=\"INVERTED:has_nucleic_acid (816)\"]; \t\"CHEMBL.COMPOUND\" -> \"UniProtKB\" [label=\"targets (39678)\"]; \t\"FMA\" -> \"FMA\" [label=\"matures_into (76)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:negatively_regulated_by (1632)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"interacts_with (1297335)\"]; \t\"SO\" -> \"OBI\" [label=\"is_about (2)\"]; \t\"FMA\" -> \"FMA\" [label=\"proximal_to (106)\"]; \t\"BSPO\" -> \"FMA\" [label=\"xref (7)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"left_of (1)\"]; \t\"PR\" -> \"MOD\" [label=\"subclass_of (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_precondition (14)\"]; \t\"MEDDRA\" -> \"MEDDRA\" [label=\"classified_as (47649)\"]; \t\"EFO\" -> \"PO\" [label=\"subclass_of (19)\"]; \t\"ENVO\" -> \"BFO\" [label=\"subclass_of (16)\"]; \t\"PR\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (5)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"innervated_by (143)\"]; \t\"GENEPIO\" -> \"NCIT\" [label=\"subclass_of (33)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"affects (6)\"]; \t\"HMDB\" -> \"CL\" [label=\"at_tissue (7)\"]; \t\"GO\" -> \"OBA\" [label=\"negatively_regulates (11)\"]; \t\"MP\" -> \"ICD10\" [label=\"xref (2)\"]; \t\"PATO\" -> \"CARO\" [label=\"xref (2)\"]; \t\"PR\" -> \"GO\" [label=\"INVERTED:has_participant (3)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"has_substance_added (1)\"]; \t\"NCIT\" -> \"GENEPIO\" [label=\"subclass_of (38)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_right_side_of (49)\"]; \t\"PR\" -> \"PR\" [label=\"lacks_part (3181)\"]; \t\"MONDO\" -> \"CL\" [label=\"disease_causes_dysfunction_of (4)\"]; \t\"OMIM\" -> \"MONDO\" [label=\"equivalent_to (8717)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"affects (1521984)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_has_physical_location (989)\"]; \t\"HGNC\" -> \"UMLS\" [label=\"xref (41638)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (136)\"]; \t\"GAZ\" -> \"GAZ\" [label=\"subclass_of (273)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"preaxialmost_part_of (11)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"inverse_of (18)\"]; \t\"OBO\" -> \"PCO\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"ORPHANET\" [label=\"is_about (12)\"]; \t\"ICD9\" -> \"MONDO\" [label=\"equivalent_to (1883)\"]; \t\"SO\" -> \"GENEPIO\" [label=\"subclass_of (4)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_associated_with_disease (2175)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"inheres_in (41)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"blocker (21)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"starts (3)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"equivalent_to (9149)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_structural_class (2)\"]; \t\"GO\" -> \"GO\" [label=\"negatively_regulates (4659)\"]; \t\"FMA\" -> \"FMA\" [label=\"connection_type_of (4)\"]; \t\"DOID\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (1)\"]; \t\"PO\" -> \"EFO\" [label=\"part_of (10)\"]; \t\"NCIT\" -> \"MONDO\" [label=\"equivalent_to (6777)\"]; \t\"FAO\" -> \"FAO\" [label=\"part_of (4)\"]; \t\"FMA\" -> \"FMA\" [label=\"efferent_to (820)\"]; \t\"PO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"]; \t\"ORPHANET\" -> \"UMLS\" [label=\"xref (6226)\"]; \t\"CHEBI\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (2)\"]; \t\"UMLS\" -> \"NCBIGene\" [label=\"INVERTED:location_of (26952)\"]; \t\"FMA\" -> \"FMA\" [label=\"posterior_to (403)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"component_of (126098)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_2 (1043)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_member (22838)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"subclass_of (250116)\"]; \t\"GO\" -> \"CARO\" [label=\"results_in_development_of (1)\"]; \t\"FLU\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"MF\" -> \"MF\" [label=\"subclass_of (8)\"]; \t\"OBO\" -> \"GENEPIO\" [label=\"subclass_of (3)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"positive_allosteric_modulator (67)\"]; \t\"NCBIGene\" -> \"HGNC\" [label=\"same_as (40970)\"]; \t\"PR\" -> \"PR\" [label=\"INVERTED:has_part (154)\"]; \t\"CHEBI\" -> \"EFO\" [label=\"INVERTED:has_input (14)\"]; \t\"HP\" -> \"MP\" [label=\"subclass_of (5)\"]; \t\"HMDB\" -> \"CHEBI\" [label=\"same_as (4846)\"]; \t\"GO\" -> \"CL\" [label=\"has_input (64)\"]; \t\"OMP\" -> \"NCIT\" [label=\"is_about (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_arterial_supply (599)\"]; \t\"MONDO\" -> \"DOID\" [label=\"equivalent_to (9000)\"]; \t\"CL\" -> \"OBO\" [label=\"INVERTED:has_participant (3)\"]; \t\"EFO\" -> \"CHEBI\" [label=\"has_output (1)\"]; \t\"MONDO\" -> \"UMLS\" [label=\"subclass_of (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"eo_disease_has_property_or_attribute (277)\"]; \t\"NCBIGene\" -> \"OMIM\" [label=\"associated_with_disease (25)\"]; \t\"CHEBI\" -> \"OIO\" [label=\"subclass_of (1)\"]; \t\"CL\" -> \"PR\" [label=\"expresses (6)\"]; \t\"CHEBI\" -> \"NBO\" [label=\"INVERTED:has_participant (10)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"part_of (1)\"]; \t\"GO\" -> \"GO\" [label=\"has_input (116)\"]; \t\"FMA\" -> \"FMA\" [label=\"medial_to (130)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"follows_axis (4)\"]; \t\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_participant (23)\"]; \t\"FMA\" -> \"FMA\" [label=\"bounds (1465)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"disease_has_major_feature (1)\"]; \t\"GO\" -> \"CL\" [label=\"transports_or_maintains_localization_of (4)\"]; \t\"CHEBI\" -> \"SO\" [label=\"equivalent_to (3)\"]; \t\"ecogene\" -> \"PR\" [label=\"INVERTED:has_gene_template (4019)\"]; \t\"PomBase\" -> \"PR\" [label=\"INVERTED:has_gene_template (5172)\"]; \t\"CHEBI\" -> \"BFO\" [label=\"equivalent_to (1)\"]; \t\"PathWhiz.Bound\" -> \"PathWhiz\" [label=\"INVERTED:has_bound (946)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"xref (5779)\"]; \t\"PathWhiz\" -> \"GO\" [label=\"has_location (3066986)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"xref (6793)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (2)\"]; \t\"GO\" -> \"GO\" [label=\"transports_or_maintains_localization_of (61)\"]; \t\"PCO\" -> \"ENVO\" [label=\"INVERTED:has_part (1)\"]; \t\"OBO\" -> \"OBI\" [label=\"is_about (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_system (129358)\"]; \t\"PCO\" -> \"PCO\" [label=\"subclass_of (10)\"]; \t\"ATC\" -> \"ATC\" [label=\"subclass_of (6317)\"]; \t\"MONDO\" -> \"NBO\" [label=\"realized_in (1)\"]; \t\"wb\" -> \"NCBITaxon\" [label=\"only_in_taxon (4479)\"]; \t\"MONDO\" -> \"GO\" [label=\"realized_in (9)\"]; \t\"SMPDB\" -> \"PathWhiz\" [label=\"same_as (110216)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_abnormal_cell_of_disease (49398)\"]; \t\"RO\" -> \"OBOREL\" [label=\"sub_property_of (2)\"]; \t\"DOID\" -> \"UBERON\" [label=\"derives_from (18)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"subclass_of (38341)\"]; \t\"RGD\" -> \"SO\" [label=\"subclass_of (8114)\"]; \t\"RO\" -> \"OBOREL\" [label=\"inverse_of (1)\"]; \t\"UBERON\" -> \"FBbt\" [label=\"xref (4)\"]; \t\"CHEBI\" -> \"ENVO\" [label=\"INVERTED:composed_primarily_of (10)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_developmental_contribution_from (103)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_pathological_process (16823)\"]; \t\"EHDAA2\" -> \"AEO\" [label=\"part_of (36)\"]; \t\"GO\" -> \"OBO\" [label=\"exports (4)\"]; \t\"HANCESTRO\" -> \"dbpedia\" [label=\"is_demonym_of (9)\"]; \t\"GO\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (25)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:410296 (196)\"]; \t\"DRUGBANK\" -> \"CHEBI\" [label=\"external_identifier (5052)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"has_parent_hydride (1623)\"]; \t\"PCO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:has_part (3759)\"]; \t\"PR\" -> \"PR\" [label=\"equivalent_to (8)\"]; \t\"FMA\" -> \"FMA\" [label=\"INVERTED:transforms_from (22)\"]; \t\"HP\" -> \"CL\" [label=\"xref (4)\"]; \t\"EFO\" -> \"KEGG\" [label=\"xref (26)\"]; \t\"HANCESTRO\" -> \"HANCESTRO\" [label=\"has_ancestry_status (2)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_count (148)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_member (11)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_doseformgroup (17677)\"]; \t\"CL\" -> \"PR\" [label=\"lacks_part (10)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"cytogenetic_abnormality_involves_chromosome (684)\"]; \t\"EHDAA2\" -> \"CARO\" [label=\"subclass_of (927)\"]; \t\"HP\" -> \"GO\" [label=\"xref (3)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"starts_axis (7)\"]; \t\"GO\" -> \"GO\" [label=\"imports (2)\"]; \t\"UBERON\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (22)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"may_be_qualified_by (20)\"]; \t\"EFO\" -> \"UBERON\" [label=\"part_of (22)\"]; \t\"ARO\" -> \"NCIT\" [label=\"subclass_of (3)\"]; \t\"SO\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (5)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"antisense_inhibitor (2)\"]; \t\"EFO\" -> \"OMIMPS\" [label=\"xref (47)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"distal_to (2)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"stimulates (20660)\"]; \t\"EFO\" -> \"OBI\" [label=\"xref (1)\"]; \t\"ARO\" -> \"GENEPIO\" [label=\"equivalent_to (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"causative_agent_of (18961)\"]; \t\"DOID\" -> \"GARD\" [label=\"xref (1)\"]; \t\"EFO\" -> \"PR\" [label=\"is_about (3)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"proximally_connected_to (55)\"]; \t\"PR\" -> \"GO\" [label=\"involved_in (3)\"]; \t\"CLO\" -> \"EFO\" [label=\"bearer_of (8)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_divisor (5470)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_affects_abnormal_cell (28)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_lymphatic_drainage (759)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_distal_side_of (2)\"]; \t\"PO\" -> \"BFO\" [label=\"subclass_of (46)\"]; \t\"ENVO\" -> \"NCIT\" [label=\"located_in (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"lymphatic_drainage_of (764)\"]; \t\"ICD10\" -> \"UMLS\" [label=\"xref (109975)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"neoplasm_has_special_category (105)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"intersects_midsagittal_plane_of (27)\"]; \t\"CL\" -> \"GO\" [label=\"produces (14)\"]; \t\"RO\" -> \"RO\" [label=\"INVERTED:inverse_of (6)\"]; \t\"FOODON\" -> \"ENVO\" [label=\"subclass_of (9)\"]; \t\"PomBase\" -> \"SO\" [label=\"subclass_of (5124)\"]; \t\"UBERON\" -> \"GENEPIO\" [label=\"subclass_of (5)\"]; \t\"KEGG\" -> \"CHEBI\" [label=\"same_as (2516)\"]; \t\"MEDDRA\" -> \"MEDDRA\" [label=\"INVERTED:has_member (17338)\"]; \t\"GO\" -> \"GO\" [label=\"immediately_precedes (4)\"]; \t\"NBO\" -> \"UBERON\" [label=\"INVERTED:output_of (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"receives_input_from (676)\"]; \t\"OMIT\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"inverse_agonist (23)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:has_ingredient (38040)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"is_conjugate_base_of (8028)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_fusion (4)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.ElementCollection\" [label=\"has_right_element (1584)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"predisposes (23510)\"]; \t\"CHEBI\" -> \"EFO\" [label=\"subclass_of (223)\"]; \t\"OBO\" -> \"MI\" [label=\"subclass_of (15)\"]; \t\"HMDB\" -> \"FMA\" [label=\"in_biospecimen (49)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_qualified_by (1)\"]; \t\"MI\" -> \"MI\" [label=\"subclass_of (101)\"]; \t\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"allosteric_antagonist (1)\"]; \t\"GO\" -> \"UBERON\" [label=\"occurs_in (69)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"anterior_to (1)\"]; \t\"IAO\" -> \"BFO\" [label=\"sub_property_of (2)\"]; \t\"EFO\" -> \"NCBITaxon\" [label=\"part_of (6)\"]; \t\"UBERON\" -> \"GO\" [label=\"located_in (1)\"]; \t\"EFO\" -> \"ORPHANET\" [label=\"INVERTED:has_part (1)\"]; \t\"PR\" -> \"GO\" [label=\"capable_of (25)\"]; \t\"GEO\" -> \"GENEPIO\" [label=\"subclass_of (2)\"]; \t\"ECOCORE\" -> \"ECOCORE\" [label=\"subclass_of (8)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_1 (499)\"]; \t\"GO\" -> \"OBO\" [label=\"subclass_of (2)\"]; \t\"ORPHANET\" -> \"EFO\" [label=\"predisposes_towards (4)\"]; \t\"UBERON\" -> \"EFO\" [label=\"part_of (3)\"]; \t\"EFO\" -> \"UBERON\" [label=\"inheres_in_part_of (13)\"]; \t\"CL\" -> \"CL\" [label=\"synapsed_by (4)\"]; \t\"DRUGBANK\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (6)\"]; \t\"OMIT\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"MONDO\" -> \"MEDDRA\" [label=\"xref (3)\"]; \t\"UBERON\" -> \"BTO\" [label=\"xref (7)\"]; \t\"GO\" -> \"PATO\" [label=\"bearer_of (5)\"]; \t\"FMA\" -> \"FMA\" [label=\"right_lateral_to (4)\"]; \t\"GO\" -> \"PR\" [label=\"has_primary_input (2)\"]; \t\"CL\" -> \"AEO\" [label=\"xref (1)\"]; \t\"GO\" -> \"GO\" [label=\"inverse_ends_during (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_transformation (274)\"]; \t\"PathWhiz.Reaction\" -> \"PathWhiz.ElementCollection\" [label=\"has_left_element (1625)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_associated_anatomy (5253)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_context_binding (68)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:has_part (4)\"]; \t\"FOODON\" -> \"OIO\" [label=\"subclass_of (11)\"]; \t\"IAO\" -> \"IAO\" [label=\"sub_property_of (1)\"]; \t\"UniProtKB\" -> \"PathWhiz.ProteinComplex\" [label=\"INVERTED:has_protein_in_complex (1903)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"inhibitor (5750)\"]; \t\"FMA\" -> \"FMA\" [label=\"development_type_of (13)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_nichd_parent (4081)\"]; \t\"GO\" -> \"CL\" [label=\"INVERTED:has_part (98)\"]; \t\"biolink\" -> \"biolink\" [label=\"sub_property_of (141)\"]; \t\"DDANAT\" -> \"CARO\" [label=\"xref (4)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"disease_has_major_feature (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"immediately_posterior_to (1)\"]; \t\"OBI\" -> \"SIO\" [label=\"subclass_of (1)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:has_part (4860)\"]; \t\"CHMO\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"posterior_to (1)\"]; \t\"PathWhiz.NucleicAcid\" -> \"CHEBI\" [label=\"same_as (35)\"]; \t\"MONDO\" -> \"HGNC\" [label=\"xref (56)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"supplies (132)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_molecular_abnormality_of_disease (1195)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"is_component_of_chemotherapy_regimen (11836)\"]; \t\"UniProtKB\" -> \"HP\" [label=\"has_phenotype (11603)\"]; \t\"EFO\" -> \"EFO\" [label=\"disease_has_major_feature (1)\"]; \t\"OBI\" -> \"BFO\" [label=\"sub_property_of (2)\"]; \t\"OPL\" -> \"GO\" [label=\"INVERTED:ends_with (1)\"]; \t\"GO\" -> \"CL\" [label=\"has_target_start_location (4)\"]; \t\"CL\" -> \"PR\" [label=\"has_low_plasma_membrane_amount (71)\"]; \t\"FMA\" -> \"FMA\" [label=\"receives_attachment_from (458)\"]; \t\"NCIT\" -> \"ARO\" [label=\"subclass_of (2)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_associated_procedure (2467)\"]; \t\"GO\" -> \"GO\" [label=\"has_target_start_location (96)\"]; \t\"EFO\" -> \"EFO\" [label=\"has_disease_location (14)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_projection (110)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"blocker (943)\"]; \t\"IDO\" -> \"OPL\" [label=\"INVERTED:realizes (2)\"]; \t\"EFO\" -> \"ORPHANET\" [label=\"bearer_of (3)\"]; \t\"HANCESTRO\" -> \"HANCESTRO\" [label=\"subclass_of (330)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"augments (69744)\"]; \t\"NCIT\" -> \"NCBITaxon\" [label=\"in_taxon (2)\"]; \t\"DOID\" -> \"HP\" [label=\"has_phenotype (649940)\"]; \t\"GO\" -> \"DDANAT\" [label=\"results_in_development_of (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"surrounded_by (4)\"]; \t\"OBI\" -> \"IAO\" [label=\"sub_property_of (1)\"]; \t\"CL\" -> \"GO\" [label=\"capable_of_part_of (1)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_component (119855)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"type (41)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_1_or_phase_2 (214)\"]; \t\"GOREL\" -> \"RO\" [label=\"sub_property_of (5)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_has_excised_anatomy (401)\"]; \t\"DDANAT\" -> \"DDANAT\" [label=\"INVERTED:develops_from (87)\"]; \t\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_ingredient (77)\"]; \t\"OBO\" -> \"IDO\" [label=\"has_role (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_concentration_strength_numerator_unit (2123)\"]; \t\"HP\" -> \"UBERON\" [label=\"affects (2853)\"]; \t\"PATO\" -> \"BFO\" [label=\"subclass_of (13)\"]; \t\"GO\" -> \"UMLS\" [label=\"xref (69387)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"part_of (72)\"]; \t\"ORPHANET\" -> \"DOID\" [label=\"xref (1579)\"]; \t\"ENVO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (13)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_aggregation_view (3311)\"]; \t\"FBbt\" -> \"FBbt\" [label=\"part_of (16)\"]; \t\"FBbt\" -> \"UBERON\" [label=\"INVERTED:develops_from (1)\"]; \t\"CL\" -> \"CL\" [label=\"derives_from (1)\"]; \t\"DOID\" -> \"OBI\" [label=\"subclass_of (1)\"]; \t\"OMIM\" -> \"UMLS\" [label=\"xref (123280)\"]; \t\"CL\" -> \"CL\" [label=\"lacks_plasma_membrane_part (3)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"is_presence_guidance_for (1021)\"]; \t\"PATO\" -> \"GO\" [label=\"xref (1)\"]; \t\"BFO\" -> \"BFO\" [label=\"inverse_of (4)\"]; \t\"FMA\" -> \"FMA\" [label=\"posteroinferior_to (22)\"]; \t\"MF\" -> \"MF\" [label=\"INVERTED:has_participant_at_all_times (2)\"]; \t\"GO\" -> \"PO\" [label=\"results_in_maturation_of (5)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_units (7)\"]; \t\"MONDO\" -> \"OMIM\" [label=\"equivalent_to (8717)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"occurs_in (2)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"inhibits (614020)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_supported_concept_relationship (342)\"]; \t\"NCBITaxon\" -> \"DOID\" [label=\"INVERTED:has_participant (2)\"]; \t\"MONDO\" -> \"DOID\" [label=\"subclass_of (1)\"]; \t\"CL\" -> \"GO\" [label=\"lacks_plasma_membrane_part (28)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_molecular_abnormality (9292)\"]; \t\"MONDO\" -> \"ICD10\" [label=\"xref (11520)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"manifestation_of (41231)\"]; \t\"KEGG\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (389)\"]; \t\"GO\" -> \"CL\" [label=\"equivalent_to (1)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_direct_device (4121)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_route_of_administration (176)\"]; \t\"PathWhiz.Compound\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (2003771)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"part_of (14694)\"]; \t\"EFO\" -> \"UBERON\" [label=\"participates_in (1)\"]; \t\"GO\" -> \"CHEBI\" [label=\"xref (919)\"]; \t\"OBI\" -> \"NCIT\" [label=\"subclass_of (3)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_administration_method (295)\"]; \t\"EHDAA2\" -> \"EHDAA2\" [label=\"develops_in (33)\"]; \t\"GO\" -> \"GO\" [label=\"capable_of (498)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:starts_with (58)\"]; \t\"OBO\" -> \"OBO\" [label=\"existence_starts_during (1)\"]; \t\"FMA\" -> \"FMA\" [label=\"anterior_to (355)\"]; \t\"OPL\" -> \"OPL\" [label=\"occurs_in (14)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_development_of (98)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_process_duration (136)\"]; \t\"GO\" -> \"PO\" [label=\"part_of (9)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"basis_of_strength_substance_of (1016)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"subclass_of (193181)\"]; \t\"NCBIGene\" -> \"UMLS\" [label=\"associated_with (132056)\"]; \t\"GO\" -> \"ZFA\" [label=\"xref (5)\"]; \t\"MONDO\" -> \"ICD9\" [label=\"equivalent_to (1883)\"]; \t\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_2 (311)\"]; \t\"CL\" -> \"GO\" [label=\"has_completed (19)\"]; \t\"GENEPIO\" -> \"PATO\" [label=\"is_about (2)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_transport_across (7)\"]; \t\"PO\" -> \"GO\" [label=\"INVERTED:has_participant (4)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_development_of (4)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_element_in_pathway (13536)\"]; \t\"FMA\" -> \"FMA\" [label=\"inferomedial_to (5)\"]; \t\"OGMS\" -> \"MONDO\" [label=\"equivalent_to (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"channel_blocker (331)\"]; \t\"PathWhiz.Reaction\" -> \"DRUGBANK\" [label=\"has_right_element (14853)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"inheres_in (156)\"]; \t\"EDAM\" -> \"IAO\" [label=\"subclass_of (1)\"]; \t\"DRUGBANK\" -> \"DRUGBANK\" [label=\"drug_interaction (2669663)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:results_in_movement_of (1)\"]; \t\"CARO\" -> \"ENVO\" [label=\"INVERTED:determined_by (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"existence_ends_during (32)\"]; \t\"ORPHANET\" -> \"MONDO\" [label=\"predisposes_towards (1)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"stimulator (15)\"]; \t\"CHEBI\" -> \"PR\" [label=\"equivalent_to (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_has_imaged_anatomy (1)\"]; \t\"BSPO\" -> \"BFO\" [label=\"sub_property_of (12)\"]; \t\"UBERON\" -> \"MA\" [label=\"subclass_of (2)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:isa (47221)\"]; \t\"OBA\" -> \"PATO\" [label=\"subclass_of (1)\"]; \t\"EFO\" -> \"SNOMED\" [label=\"xref (1)\"]; \t\"SO\" -> \"UO\" [label=\"INVERTED:is_unit_of (1)\"]; \t\"EHDAA2\" -> \"EHDAA2\" [label=\"part_of (2925)\"]; \t\"AEO\" -> \"CARO\" [label=\"subclass_of (59)\"]; \t\"OBO\" -> \"OBO\" [label=\"part_of (14)\"]; \t\"CHEBI\" -> \"DOID\" [label=\"INVERTED:has_allergic_trigger (84)\"]; \t\"UBERON\" -> \"MA\" [label=\"xref (2)\"]; \t\"CHEBI\" -> \"ENVO\" [label=\"INVERTED:has_participant (1)\"]; \t\"GO\" -> \"GO\" [label=\"adjacent_to (22)\"]; \t\"GENEPIO\" -> \"STATO\" [label=\"subclass_of (12)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_encodes_gene_product (18713)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_structural_organization_of (28)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:positively_regulated_by (1616)\"]; \t\"CL\" -> \"EFO\" [label=\"xref (1)\"]; \t\"DOID\" -> \"MONDO\" [label=\"equivalent_to (9000)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:part_of (6788)\"]; \t\"NDDF\" -> \"UMLS\" [label=\"xref (33096)\"]; \t\"HP\" -> \"GO\" [label=\"subclass_of (1)\"]; \t\"ENVO\" -> \"FOODON\" [label=\"INVERTED:composed_primarily_of (1)\"]; \t\"ECTO\" -> \"ECTO\" [label=\"subclass_of (81)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"gene_product_variant_of_gene_product (457)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"compared_with (7200)\"]; \t\"EFO\" -> \"HP\" [label=\"xref (237)\"]; \t\"PathWhiz.Reaction\" -> \"DRUGBANK\" [label=\"has_left_element (21859)\"]; \t\"PATO\" -> \"NBO\" [label=\"INVERTED:in_response_to (3)\"]; \t\"PR\" -> \"CL\" [label=\"INVERTED:has_part (675)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_affects_cell_type_or_tissue (572)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_has_feature (25)\"]; \t\"EFO\" -> \"EFO\" [label=\"is_input_of (95)\"]; \t\"EFO\" -> \"EFO\" [label=\"xref (27)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"direct_substance_of (5117)\"]; \t\"UBERON\" -> \"ARO\" [label=\"subclass_of (3)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_regional_part (26404)\"]; \t\"PR\" -> \"GO\" [label=\"INVERTED:has_part (2)\"]; \t\"ZFA\" -> \"UBERON\" [label=\"subclass_of (1)\"]; \t\"NCBIGene\" -> \"ENSEMBL\" [label=\"same_as (35031)\"]; \t\"UniProtKB\" -> \"NCBITaxon\" [label=\"in_taxon (24986)\"]; \t\"GAZ\" -> \"OBO\" [label=\"subclass_of (197)\"]; \t\"GENEPIO\" -> \"BFO\" [label=\"subclass_of (13)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:preceded_by (13)\"]; \t\"UniProtKB\" -> \"PathWhiz\" [label=\"INVERTED:has_protein (304018)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"produces (305322)\"]; \t\"OPL\" -> \"UBERON\" [label=\"subclass_of (8)\"]; \t\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_tradename (48926)\"]; \t\"NCBITaxon\" -> \"ENVO\" [label=\"INVERTED:process_has_causal_agent (3)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_has_target_anatomy (916)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:ends_with (1)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_or_within_negative_effect (5)\"]; \t\"OMRSE\" -> \"GENEPIO\" [label=\"subclass_of (1)\"]; \t\"CARO\" -> \"BFO\" [label=\"subclass_of (4)\"]; \t\"FOODON\" -> \"UBERON\" [label=\"derives_from (6)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_member (15)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"part_anatomy_structure_of (323)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"eo_disease_has_associated_eo_anatomy (3128)\"]; \t\"IDO\" -> \"OBI\" [label=\"subclass_of (3)\"]; \t\"ENVO\" -> \"PO\" [label=\"derives_from (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_intended_site (529)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"INVERTED:biological_process_involves_chemical_or_drug (18)\"]; \t\"OPL\" -> \"BFO\" [label=\"subclass_of (3)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_inherent_3d_shape (4)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"existence_starts_during_or_after (4)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"enables (67759)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_data_element (10)\"]; \t\"GO\" -> \"UBERON\" [label=\"results_in_formation_of (174)\"]; \t\"GO\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_disruption_of (275)\"]; \t\"GENEPIO\" -> \"IAO\" [label=\"subclass_of (73)\"]; \t\"OBI\" -> \"GENEPIO\" [label=\"member_of (2)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"mth_has_expanded_form (1)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_administration_method (542)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"modulator (242)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"has_muscle_insertion (217)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"in_anterior_side_of (13)\"]; \t\"PO\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (1)\"]; \t\"OMIT\" -> \"PR\" [label=\"subclass_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"filtered_through (4)\"]; \t\"OBA\" -> \"OBA\" [label=\"subclass_of (173)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"entire_anatomy_structure_of (7090)\"]; \t\"CEPH\" -> \"UBERON\" [label=\"subclass_of (1)\"]; \t\"medgen\" -> \"MONDO\" [label=\"equivalent_to (2582)\"]; \t\"FMA\" -> \"FMA\" [label=\"has_origin (275)\"]; \t\"EFO\" -> \"OBI\" [label=\"INVERTED:has_participant (2)\"]; \t\"NCIT\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (4)\"]; \t\"GENEPIO\" -> \"GENEPIO\" [label=\"has_output (1)\"]; \t\"DDANAT\" -> \"DDANAT\" [label=\"subclass_of (129)\"]; \t\"CL\" -> \"GO\" [label=\"lacks_part (11)\"]; \t\"GO\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (20)\"]; \t\"UniProtKB\" -> \"CL\" [label=\"expressed_in (15576)\"]; \t\"PR\" -> \"MOD\" [label=\"lacks_part (48)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"part_of_progression_of_disease (2)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"has_modifier (2)\"]; \t\"TRANS\" -> \"TRANS\" [label=\"subclass_of (32)\"]; \t\"GO\" -> \"CL\" [label=\"results_in_growth_of (5)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_time_aspect (90380)\"]; \t\"GO\" -> \"GO\" [label=\"has_output (14)\"]; \t\"CL\" -> \"EHDAA2\" [label=\"xref (6)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_time_modifier (197)\"]; \t\"UniProtKB\" -> \"GO\" [label=\"expressed_in (74377)\"]; \t\"GO\" -> \"FAO\" [label=\"results_in_formation_of (6)\"]; \t\"CHEBI\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (31)\"]; \t\"CHEBI\" -> \"DRUGBANK\" [label=\"same_as (636)\"]; \t\"EFO\" -> \"CL\" [label=\"is_about (40)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_growth_of (2)\"]; \t\"EFO\" -> \"UBERON\" [label=\"subclass_of (82)\"]; \t\"MESH\" -> \"MESH\" [label=\"has_mapping_qualifier (33615)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_has_basis_in_feature (2)\"]; \t\"UniProtKB\" -> \"UniProtKB\" [label=\"physically_interacts_with (615498)\"]; \t\"PO\" -> \"CARO\" [label=\"subclass_of (2)\"]; \t\"NCIT\" -> \"GENEPIO\" [label=\"before (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"adjacent_to (329)\"]; \t\"CL\" -> \"OBO\" [label=\"INVERTED:has_part (1)\"]; \t\"CHEBI\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (3)\"]; \t\"ttd.target\" -> \"NCBIGene\" [label=\"cofactor (4)\"]; \t\"LOINC\" -> \"LOINC\" [label=\"has_object_guidance (474)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317345 (496)\"]; \t\"EFO\" -> \"GO\" [label=\"is_about (68)\"]; \t\"HMDB\" -> \"EFO\" [label=\"at_tissue (9)\"]; \t\"GAZ\" -> \"NCIT\" [label=\"subclass_of (186)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"distal_to (1)\"]; \t\"IDO\" -> \"IDO\" [label=\"subclass_of (20)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_indirect_procedure_site (8311)\"]; \t\"FOODON\" -> \"CHEBI\" [label=\"subclass_of (14)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317349 (229)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"inverse_of (2)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"coexists_with (20358)\"]; \t\"GO\" -> \"GO\" [label=\"results_in_transport_to_from_or_in (17)\"]; \t\"EFO\" -> \"BFO\" [label=\"subclass_of (66)\"]; \t\"GO\" -> \"DOID\" [label=\"INVERTED:disease_caused_by_disruption_of (53)\"]; \t\"RO\" -> \"SO\" [label=\"xref (9)\"]; \t\"BFO\" -> \"CHEBI\" [label=\"equivalent_to (1)\"]; \t\"NCBITaxon\" -> \"ICD9\" [label=\"xref (7)\"]; \t\"NCBITaxon\" -> \"OBO\" [label=\"subclass_of (27)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"has_owning_affiliate (4)\"]; \t\"DRUGBANK\" -> \"PathWhiz\" [label=\"INVERTED:has_protein (15)\"]; \t\"SNOMED\" -> \"SNOMED\" [label=\"has_state_of_matter (58)\"]; \t\"UniProtKB\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (59)\"]; \t\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:c017 (9706)\"]; \t\"FMA\" -> \"FMA\" [label=\"forms (15)\"]; \t\"MF\" -> \"MF\" [label=\"INVERTED:realizes (2)\"]; \t\"PR\" -> \"GO\" [label=\"located_in (2)\"]; \t\"ECOCORE\" -> \"BFO\" [label=\"subclass_of (1)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"has_inheritance_type (6005)\"]; \t\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"allosteric_modulator (317)\"]; \t\"ENVO\" -> \"PATO\" [label=\"subclass_of (13)\"]; \t\"OBO\" -> \"NCBITaxon\" [label=\"only_in_taxon (1013)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"procedure_has_completely_excised_anatomy (95)\"]; \t\"NCIT\" -> \"SIO\" [label=\"subclass_of (4)\"]; \t\"DOID\" -> \"KEGG\" [label=\"xref (39)\"]; }" }, { "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/rtx2_2020_09_16.txt", "content": "\"AEO\" -> \"AEO\" [label=\"part_of (22)\"];\n\"AEO\" -> \"AEO\" [label=\"subclass_of (89)\"];\n\"AEO\" -> \"CARO\" [label=\"subclass_of (59)\"];\n\"AEO\" -> \"CARO\" [label=\"surrounds (1)\"];\n\"ARO\" -> \"ARO\" [label=\"subclass_of (40)\"];\n\"ARO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"ARO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (2)\"];\n\"ARO\" -> \"GENEPIO\" [label=\"equivalent_to (1)\"];\n\"ARO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"ARO\" -> \"IAO\" [label=\"subclass_of (3)\"];\n\"ARO\" -> \"IDO\" [label=\"is_about (1)\"];\n\"ARO\" -> \"NCIT\" [label=\"subclass_of (3)\"];\n\"ARO\" -> \"OBI\" [label=\"subclass_of (2)\"];\n\"ATC\" -> \"ATC\" [label=\"subclass_of (6317)\"];\n\"ATC\" -> \"UMLS\" [label=\"xref (6331)\"];\n\"AraPort\" -> \"NCBITaxon\" [label=\"only_in_taxon (15919)\"];\n\"AraPort\" -> \"PR\" [label=\"INVERTED:has_gene_template (15921)\"];\n\"AraPort\" -> \"SO\" [label=\"subclass_of (15919)\"];\n\"BAO\" -> \"CHEBI\" [label=\"subclass_of (2)\"];\n\"BAO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"BFO\" -> \"BFO\" [label=\"INVERTED:inverse_of (3)\"];\n\"BFO\" -> \"BFO\" [label=\"inverse_of (4)\"];\n\"BFO\" -> \"BFO\" [label=\"subclass_of (37)\"];\n\"BFO\" -> \"CHEBI\" [label=\"equivalent_to (1)\"];\n\"BFO\" -> \"EFO\" [label=\"INVERTED:has_input (2)\"];\n\"BFO\" -> \"EFO\" [label=\"subclass_of (4)\"];\n\"BFO\" -> \"OIO\" [label=\"subclass_of (1)\"];\n\"BFO\" -> \"RO\" [label=\"sub_property_of (4)\"];\n\"BSPO\" -> \"BFO\" [label=\"sub_property_of (12)\"];\n\"BSPO\" -> \"BSPO\" [label=\"anterior_to (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"approximately_perpendicular_to (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"deep_to (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"distal_to (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"dorsal_to (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"finishes_axis (7)\"];\n\"BSPO\" -> \"BSPO\" [label=\"follows_axis (4)\"];\n\"BSPO\" -> \"BSPO\" [label=\"has_axis (6)\"];\n\"BSPO\" -> \"BSPO\" [label=\"inverse_of (18)\"];\n\"BSPO\" -> \"BSPO\" [label=\"left_of (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"opposite_to (3)\"];\n\"BSPO\" -> \"BSPO\" [label=\"orthogonal_to (3)\"];\n\"BSPO\" -> \"BSPO\" [label=\"overlaps (77)\"];\n\"BSPO\" -> \"BSPO\" [label=\"posterior_to (1)\"];\n\"BSPO\" -> \"BSPO\" [label=\"starts_axis (7)\"];\n\"BSPO\" -> \"BSPO\" [label=\"sub_property_of (15)\"];\n\"BSPO\" -> \"BSPO\" [label=\"subclass_of (179)\"];\n\"BSPO\" -> \"BSPO\" [label=\"surface_of (12)\"];\n\"BSPO\" -> \"CARO\" [label=\"passes_through (1)\"];\n\"BSPO\" -> \"CARO\" [label=\"subclass_of (7)\"];\n\"BSPO\" -> \"FMA\" [label=\"xref (7)\"];\n\"BSPO\" -> \"RO\" [label=\"sub_property_of (4)\"];\n\"BTO\" -> \"BFO\" [label=\"subclass_of (3)\"];\n\"BTO\" -> \"BTO\" [label=\"INVERTED:develops_from (1)\"];\n\"BTO\" -> \"BTO\" [label=\"derives_from (2)\"];\n\"BTO\" -> \"BTO\" [label=\"subclass_of (7)\"];\n\"BTO\" -> \"CL\" [label=\"derives_from (1)\"];\n\"BTO\" -> \"CL\" [label=\"subclass_of (6)\"];\n\"BTO\" -> \"EFO\" [label=\"INVERTED:develops_from (1)\"];\n\"BTO\" -> \"EFO\" [label=\"bearer_of (5)\"];\n\"BTO\" -> \"EFO\" [label=\"derives_from (3)\"];\n\"BTO\" -> \"EFO\" [label=\"equivalent_to (1)\"];\n\"BTO\" -> \"EFO\" [label=\"participates_in (2)\"];\n\"BTO\" -> \"EFO\" [label=\"subclass_of (47)\"];\n\"BTO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"BTO\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"BTO\" -> \"PATO\" [label=\"bearer_of (1)\"];\n\"BTO\" -> \"PATO\" [label=\"has_quality (1)\"];\n\"BTO\" -> \"UBERON\" [label=\"located_in (1)\"];\n\"BTO\" -> \"UBERON\" [label=\"part_of (5)\"];\n\"BTO\" -> \"UBERON\" [label=\"subclass_of (9)\"];\n\"BTO\" -> \"UBERON\" [label=\"xref (1)\"];\n\"CARO\" -> \"BFO\" [label=\"subclass_of (4)\"];\n\"CARO\" -> \"CARO\" [label=\"part_of (3)\"];\n\"CARO\" -> \"CARO\" [label=\"subclass_of (49)\"];\n\"CARO\" -> \"ENVO\" [label=\"INVERTED:determined_by (1)\"];\n\"CARO\" -> \"RO\" [label=\"subclass_of (1)\"];\n\"CEPH\" -> \"UBERON\" [label=\"subclass_of (1)\"];\n\"CGNC\" -> \"NCBITaxon\" [label=\"only_in_taxon (552)\"];\n\"CGNC\" -> \"PR\" [label=\"INVERTED:has_gene_template (552)\"];\n\"CGNC\" -> \"SO\" [label=\"subclass_of (552)\"];\n\"CHEBI\" -> \"BFO\" [label=\"equivalent_to (1)\"];\n\"CHEBI\" -> \"BFO\" [label=\"subclass_of (33)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"INVERTED:has_part (3773)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"has_functional_parent (17221)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"has_parent_hydride (1623)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"has_role (39604)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"inheres_in (41)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"inverse_of (2)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"is_conjugate_acid_of (8028)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"is_conjugate_base_of (8028)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"is_enantiomer_of (2594)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"is_substituent_group_from (1267)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"is_tautomer_of (1748)\"];\n\"CHEBI\" -> \"CHEBI\" [label=\"subclass_of (193181)\"];\n\"CHEBI\" -> \"CL\" [label=\"INVERTED:has_part (1)\"];\n\"CHEBI\" -> \"CL\" [label=\"xref (1)\"];\n\"CHEBI\" -> \"DOID\" [label=\"INVERTED:has_allergic_trigger (84)\"];\n\"CHEBI\" -> \"DRUGBANK\" [label=\"same_as (636)\"];\n\"CHEBI\" -> \"EFO\" [label=\"INVERTED:has_input (14)\"];\n\"CHEBI\" -> \"EFO\" [label=\"INVERTED:has_participant (1)\"];\n\"CHEBI\" -> \"EFO\" [label=\"has_role (83)\"];\n\"CHEBI\" -> \"EFO\" [label=\"subclass_of (223)\"];\n\"CHEBI\" -> \"ENVO\" [label=\"INVERTED:composed_primarily_of (10)\"];\n\"CHEBI\" -> \"ENVO\" [label=\"INVERTED:has_part (3)\"];\n\"CHEBI\" -> \"ENVO\" [label=\"INVERTED:has_participant (1)\"];\n\"CHEBI\" -> \"FOODON\" [label=\"INVERTED:composed_primarily_of (3)\"];\n\"CHEBI\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (2)\"];\n\"CHEBI\" -> \"FOODON\" [label=\"INVERTED:has_ingredient (3)\"];\n\"CHEBI\" -> \"FOODON\" [label=\"member_of (1)\"];\n\"CHEBI\" -> \"FOODON\" [label=\"subclass_of (200)\"];\n\"CHEBI\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (3)\"];\n\"CHEBI\" -> \"GENEPIO\" [label=\"subclass_of (72)\"];\n\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_intermediate (83)\"];\n\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_part (16)\"];\n\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_participant (23)\"];\n\"CHEBI\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (1276)\"];\n\"CHEBI\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (8)\"];\n\"CHEBI\" -> \"KEGG\" [label=\"same_as (1689)\"];\n\"CHEBI\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (1)\"];\n\"CHEBI\" -> \"MONDO\" [label=\"INVERTED:disease_responds_to (13)\"];\n\"CHEBI\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (31)\"];\n\"CHEBI\" -> \"NBO\" [label=\"INVERTED:has_participant (10)\"];\n\"CHEBI\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"CHEBI\" -> \"OBO\" [label=\"subclass_of (2)\"];\n\"CHEBI\" -> \"OIO\" [label=\"subclass_of (1)\"];\n\"CHEBI\" -> \"PR\" [label=\"INVERTED:has_component (47)\"];\n\"CHEBI\" -> \"PR\" [label=\"INVERTED:has_part (2)\"];\n\"CHEBI\" -> \"PR\" [label=\"equivalent_to (1)\"];\n\"CHEBI\" -> \"PR\" [label=\"subclass_of (5)\"];\n\"CHEBI\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (1567712)\"];\n\"CHEBI\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (1418)\"];\n\"CHEBI\" -> \"PathWhiz\" [label=\"INVERTED:has_nucleic_acid (816)\"];\n\"CHEBI\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (214)\"];\n\"CHEBI\" -> \"SO\" [label=\"equivalent_to (3)\"];\n\"CHEBI\" -> \"SO\" [label=\"subclass_of (23)\"];\n\"CHEBI\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (11)\"];\n\"CHEBI\" -> \"UBERON\" [label=\"INVERTED:has_part (20)\"];\n\"CHEBI\" -> \"UBERON\" [label=\"part_of (1)\"];\n\"CHEBI\" -> \"UBERON\" [label=\"subclass_of (1)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEBI\" [label=\"same_as (30201)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.MECHANISM\" [label=\"related_to (4739)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"activator (42)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"agonist (720)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"allosteric_antagonist (1)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"antagonist (789)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"antisense_inhibitor (2)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"binding_agent (136)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"blocker (149)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"chelating_agent (19)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"cross_linking_agent (33)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"degrader (1)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"disrupting_agent (5)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"hydrolytic_enzyme (38)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"inhibitor (2414)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"inverse_agonist (11)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"modulator (85)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"negative_allosteric_modulator (13)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"negative_modulator (4)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"opener (38)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"oxidative_enzyme (2)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"partial_agonist (47)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"physically_interacts_with (4538)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"positive_allosteric_modulator (67)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"positive_modulator (18)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"proteolytic_enzyme (6)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"reducing_agent (2)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"releasing_agent (26)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"sequestering_agent (23)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"stabiliser (9)\"];\n\"CHEMBL.COMPOUND\" -> \"CHEMBL.TARGET\" [label=\"substrate (6)\"];\n\"CHEMBL.COMPOUND\" -> \"DOID\" [label=\"contraindicated_for (9264)\"];\n\"CHEMBL.COMPOUND\" -> \"DOID\" [label=\"indicated_for (2375)\"];\n\"CHEMBL.COMPOUND\" -> \"DRUGBANK\" [label=\"same_as (6926)\"];\n\"CHEMBL.COMPOUND\" -> \"HP\" [label=\"contraindicated_for (12221)\"];\n\"CHEMBL.COMPOUND\" -> \"HP\" [label=\"indicated_for (2095)\"];\n\"CHEMBL.COMPOUND\" -> \"MESH\" [label=\"treats (27892)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"activator (316)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"affects (10769)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"agonist (2960)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"allosteric_modulator (317)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antagonist (2951)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antibody (180)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antisense (3)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"antisense_oligonucleotide (5)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"binder (139)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"blocker (943)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"channel_blocker (331)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"cofactor (2)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"gating_inhibitor (24)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"inducer (4)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"inhibitor (5750)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"inverse_agonist (23)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"modulator (242)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"negative_modulator (5)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"partial_agonist (62)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"positive_allosteric_modulator (601)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"stimulator (15)\"];\n\"CHEMBL.COMPOUND\" -> \"NCBIGene\" [label=\"vaccine (6)\"];\n\"CHEMBL.COMPOUND\" -> \"UniProtKB\" [label=\"targets (39678)\"];\n\"CHEMBL.MECHANISM\" -> \"CHEMBL.MECHANISM\" [label=\"subclass_of (27)\"];\n\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"INVERTED:superset_of (1116)\"];\n\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"equivalent_to (36)\"];\n\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"overlaps_with (2630)\"];\n\"CHEMBL.TARGET\" -> \"CHEMBL.TARGET\" [label=\"subset_of (1389)\"];\n\"CHEMBL.TARGET\" -> \"ENSEMBL\" [label=\"part_of (4)\"];\n\"CHEMBL.TARGET\" -> \"UniProtKB\" [label=\"part_of (5700)\"];\n\"CHMO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"CHMO\" -> \"CHMO\" [label=\"subclass_of (7)\"];\n\"CHMO\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"CL\" -> \"AEO\" [label=\"INVERTED:has_part (78)\"];\n\"CL\" -> \"AEO\" [label=\"xref (1)\"];\n\"CL\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"CL\" -> \"BTO\" [label=\"xref (4)\"];\n\"CL\" -> \"CARO\" [label=\"INVERTED:has_part (3)\"];\n\"CL\" -> \"CARO\" [label=\"subclass_of (2)\"];\n\"CL\" -> \"CARO\" [label=\"xref (2)\"];\n\"CL\" -> \"CL\" [label=\"INVERTED:develops_from (380)\"];\n\"CL\" -> \"CL\" [label=\"derives_from (1)\"];\n\"CL\" -> \"CL\" [label=\"develops_into (5)\"];\n\"CL\" -> \"CL\" [label=\"lacks_plasma_membrane_part (3)\"];\n\"CL\" -> \"CL\" [label=\"part_of (1)\"];\n\"CL\" -> \"CL\" [label=\"subclass_of (3462)\"];\n\"CL\" -> \"CL\" [label=\"synapsed_by (4)\"];\n\"CL\" -> \"CL\" [label=\"synapsed_to (3)\"];\n\"CL\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (41)\"];\n\"CL\" -> \"EFO\" [label=\"located_in (1)\"];\n\"CL\" -> \"EFO\" [label=\"part_of (2)\"];\n\"CL\" -> \"EFO\" [label=\"participates_in (1)\"];\n\"CL\" -> \"EFO\" [label=\"subclass_of (41)\"];\n\"CL\" -> \"EFO\" [label=\"xref (1)\"];\n\"CL\" -> \"EHDAA2\" [label=\"xref (6)\"];\n\"CL\" -> \"FAO\" [label=\"xref (8)\"];\n\"CL\" -> \"FBbt\" [label=\"xref (1)\"];\n\"CL\" -> \"FMA\" [label=\"xref (701)\"];\n\"CL\" -> \"GO\" [label=\"INVERTED:has_participant (28)\"];\n\"CL\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (24)\"];\n\"CL\" -> \"GO\" [label=\"INVERTED:results_in_movement_of (87)\"];\n\"CL\" -> \"GO\" [label=\"capable_of (308)\"];\n\"CL\" -> \"GO\" [label=\"capable_of_part_of (1)\"];\n\"CL\" -> \"GO\" [label=\"equivalent_to (1)\"];\n\"CL\" -> \"GO\" [label=\"has_completed (19)\"];\n\"CL\" -> \"GO\" [label=\"has_high_plasma_membrane_amount (15)\"];\n\"CL\" -> \"GO\" [label=\"has_low_plasma_membrane_amount (6)\"];\n\"CL\" -> \"GO\" [label=\"has_not_completed (12)\"];\n\"CL\" -> \"GO\" [label=\"has_plasma_membrane_part (1)\"];\n\"CL\" -> \"GO\" [label=\"lacks_part (11)\"];\n\"CL\" -> \"GO\" [label=\"lacks_plasma_membrane_part (28)\"];\n\"CL\" -> \"GO\" [label=\"participates_in (18)\"];\n\"CL\" -> \"GO\" [label=\"produces (14)\"];\n\"CL\" -> \"GO\" [label=\"subclass_of (11)\"];\n\"CL\" -> \"GO\" [label=\"xref (1)\"];\n\"CL\" -> \"MA\" [label=\"located_in (1)\"];\n\"CL\" -> \"MONDO\" [label=\"INVERTED:disease_arises_from_structure (58)\"];\n\"CL\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (8)\"];\n\"CL\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (4)\"];\n\"CL\" -> \"NCBITaxon\" [label=\"in_taxon (1)\"];\n\"CL\" -> \"NCBITaxon\" [label=\"only_in_taxon (5)\"];\n\"CL\" -> \"NCIT\" [label=\"xref (2)\"];\n\"CL\" -> \"OBO\" [label=\"INVERTED:has_part (1)\"];\n\"CL\" -> \"OBO\" [label=\"INVERTED:has_participant (3)\"];\n\"CL\" -> \"PATO\" [label=\"bearer_of (38)\"];\n\"CL\" -> \"PO\" [label=\"xref (1)\"];\n\"CL\" -> \"PR\" [label=\"expresses (6)\"];\n\"CL\" -> \"PR\" [label=\"has_high_plasma_membrane_amount (65)\"];\n\"CL\" -> \"PR\" [label=\"has_low_plasma_membrane_amount (71)\"];\n\"CL\" -> \"PR\" [label=\"lacks_part (10)\"];\n\"CL\" -> \"PR\" [label=\"lacks_plasma_membrane_part (454)\"];\n\"CL\" -> \"RO\" [label=\"sub_property_of (2)\"];\n\"CL\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (83)\"];\n\"CL\" -> \"UBERON\" [label=\"INVERTED:develops_from (2)\"];\n\"CL\" -> \"UBERON\" [label=\"INVERTED:has_part (224)\"];\n\"CL\" -> \"UBERON\" [label=\"INVERTED:produced_by (4)\"];\n\"CL\" -> \"UBERON\" [label=\"adjacent_to (6)\"];\n\"CL\" -> \"UBERON\" [label=\"axon_synapses_in (13)\"];\n\"CL\" -> \"UBERON\" [label=\"has_soma_location (5)\"];\n\"CL\" -> \"UBERON\" [label=\"has_synaptic_terminal_in (2)\"];\n\"CL\" -> \"UBERON\" [label=\"innervates (1)\"];\n\"CL\" -> \"UBERON\" [label=\"located_in (83)\"];\n\"CL\" -> \"UBERON\" [label=\"part_of (690)\"];\n\"CL\" -> \"UBERON\" [label=\"participates_in (4)\"];\n\"CL\" -> \"UBERON\" [label=\"produces (6)\"];\n\"CL\" -> \"UBERON\" [label=\"subclass_of (5)\"];\n\"CLO\" -> \"CL\" [label=\"subclass_of (428)\"];\n\"CLO\" -> \"EFO\" [label=\"bearer_of (8)\"];\n\"CLO\" -> \"EFO\" [label=\"subclass_of (857)\"];\n\"CLO\" -> \"PATO\" [label=\"has_quality (405)\"];\n\"CP\" -> \"CL\" [label=\"INVERTED:has_part (26)\"];\n\"CP\" -> \"GO\" [label=\"subclass_of (9)\"];\n\"CP\" -> \"PATO\" [label=\"bearer_of (4)\"];\n\"CPT\" -> \"CPT\" [label=\"has_add_on_code (6931)\"];\n\"CPT\" -> \"CPT\" [label=\"has_possibly_included_panel_element (1)\"];\n\"CPT\" -> \"CPT\" [label=\"mapped_to (191)\"];\n\"CPT\" -> \"CPT\" [label=\"panel_element_of (129)\"];\n\"CPT\" -> \"CPT\" [label=\"panel_element_of_possibly_included (1)\"];\n\"CPT\" -> \"CPT\" [label=\"subclass_of (14292)\"];\n\"CPT\" -> \"UMLS\" [label=\"xref (46941)\"];\n\"CVDO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"DDANAT\" -> \"CARO\" [label=\"xref (4)\"];\n\"DDANAT\" -> \"DDANAT\" [label=\"INVERTED:develops_from (87)\"];\n\"DDANAT\" -> \"DDANAT\" [label=\"part_of (134)\"];\n\"DDANAT\" -> \"DDANAT\" [label=\"subclass_of (129)\"];\n\"DOID\" -> \"AQTLTrait\" [label=\"has_phenotype (1)\"];\n\"DOID\" -> \"ARO\" [label=\"subclass_of (4)\"];\n\"DOID\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"DOID\" -> \"CL\" [label=\"derives_from (355)\"];\n\"DOID\" -> \"CL\" [label=\"located_in (10)\"];\n\"DOID\" -> \"DOID\" [label=\"has_symptom (9)\"];\n\"DOID\" -> \"DOID\" [label=\"subclass_of (14358)\"];\n\"DOID\" -> \"EFO\" [label=\"subclass_of (3)\"];\n\"DOID\" -> \"EFO\" [label=\"xref (130)\"];\n\"DOID\" -> \"GARD\" [label=\"xref (1)\"];\n\"DOID\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (1)\"];\n\"DOID\" -> \"GENEPIO\" [label=\"subclass_of (2)\"];\n\"DOID\" -> \"GO\" [label=\"disease_causes_disruption_of (27)\"];\n\"DOID\" -> \"GO\" [label=\"disease_has_basis_in_dysfunction_of (8)\"];\n\"DOID\" -> \"GO\" [label=\"disease_has_location (3)\"];\n\"DOID\" -> \"GO\" [label=\"realized_in_response_to (6)\"];\n\"DOID\" -> \"GO\" [label=\"realized_in_response_to_stimulus (1)\"];\n\"DOID\" -> \"HP\" [label=\"has_phenotype (649940)\"];\n\"DOID\" -> \"ICD10\" [label=\"xref (8)\"];\n\"DOID\" -> \"ICD9\" [label=\"xref (11)\"];\n\"DOID\" -> \"KEGG\" [label=\"xref (39)\"]; }\n\"DOID\" -> \"MEDDRA\" [label=\"xref (33)\"];\n\"DOID\" -> \"MESH\" [label=\"xref (3539)\"];\n\"DOID\" -> \"MONDO\" [label=\"equivalent_to (9000)\"];\n\"DOID\" -> \"MONDO\" [label=\"subclass_of (5)\"];\n\"DOID\" -> \"MONDO\" [label=\"xref (6)\"];\n\"DOID\" -> \"NCBITaxon\" [label=\"transmitted_by (74)\"];\n\"DOID\" -> \"NCIT\" [label=\"xref (3)\"];\n\"DOID\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"DOID\" -> \"OMIM\" [label=\"xref (4868)\"];\n\"DOID\" -> \"ORPHANET\" [label=\"subclass_of (1)\"];\n\"DOID\" -> \"SYMP\" [label=\"has_symptom (839)\"];\n\"DOID\" -> \"UBERON\" [label=\"adjacent_to (2)\"];\n\"DOID\" -> \"UBERON\" [label=\"derives_from (18)\"];\n\"DOID\" -> \"UBERON\" [label=\"has_disease_location (1)\"];\n\"DOID\" -> \"UBERON\" [label=\"has_origin (3)\"];\n\"DOID\" -> \"UBERON\" [label=\"located_in (618)\"];\n\"DOID\" -> \"UMLS\" [label=\"xref (6)\"];\n\"DRUGBANK\" -> \"CHEBI\" [label=\"external_identifier (5052)\"];\n\"DRUGBANK\" -> \"CHEBI\" [label=\"same_as (102)\"];\n\"DRUGBANK\" -> \"CHEMBL.COMPOUND\" [label=\"external_identifier (7632)\"];\n\"DRUGBANK\" -> \"DRUGBANK\" [label=\"drug_interaction (2669663)\"];\n\"DRUGBANK\" -> \"HMDB\" [label=\"same_as (1565)\"];\n\"DRUGBANK\" -> \"KEGG\" [label=\"external_identifier (1670)\"];\n\"DRUGBANK\" -> \"KEGG\" [label=\"same_as (494)\"];\n\"DRUGBANK\" -> \"MESH\" [label=\"category (57884)\"];\n\"DRUGBANK\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (492409)\"];\n\"DRUGBANK\" -> \"PathWhiz\" [label=\"INVERTED:has_protein (15)\"];\n\"DRUGBANK\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (6)\"];\n\"DRUGBANK\" -> \"PathWhiz.ProteinComplex\" [label=\"INVERTED:has_protein_in_complex (15)\"];\n\"DRUGBANK\" -> \"SMPDB\" [label=\"pathway (3762)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_approved_unknown_phase (6536)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_0 (1)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_1 (9)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_1_or_phase_2 (30)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_2 (311)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_2_or_phase_3 (29)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_suspended_phase_3 (56)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_0 (29)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_1 (499)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_1_or_phase_2 (214)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_2 (1043)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_2_or_phase_3 (39)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_terminated_phase_3 (437)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_0 (7)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_1 (132)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_1_or_phase_2 (30)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_2 (208)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_2_or_phase_3 (16)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"clinically_tested_withdrawn_phase_3 (81)\"];\n\"DRUGBANK\" -> \"UMLS\" [label=\"xref (9151)\"];\n\"DRUGBANK\" -> \"UniProtKB\" [label=\"external_identifier (69)\"];\n\"DRUGBANK\" -> \"UniProtKB\" [label=\"target (16808)\"];\n\"ECO\" -> \"ECO\" [label=\"subclass_of (12)\"];\n\"ECOCORE\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"ECOCORE\" -> \"ECOCORE\" [label=\"subclass_of (8)\"];\n\"ECTO\" -> \"ECTO\" [label=\"subclass_of (81)\"];\n\"ECTO\" -> \"ExO\" [label=\"subclass_of (4)\"];\n\"ECTO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (33)\"];\n\"ECTO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (6)\"];\n\"ECTO\" -> \"RO\" [label=\"subclass_of (4)\"];\n\"EDAM\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"EDAM\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"EFO\" -> \"BFO\" [label=\"has_output (1)\"];\n\"EFO\" -> \"BFO\" [label=\"subclass_of (66)\"];\n\"EFO\" -> \"BTO\" [label=\"equivalent_to (1)\"];\n\"EFO\" -> \"BTO\" [label=\"is_about (3)\"];\n\"EFO\" -> \"BTO\" [label=\"subclass_of (217)\"];\n\"EFO\" -> \"BTO\" [label=\"xref (3)\"];\n\"EFO\" -> \"CHEBI\" [label=\"has_output (1)\"];\n\"EFO\" -> \"CHEBI\" [label=\"has_role (3)\"];\n\"EFO\" -> \"CHEBI\" [label=\"inheres_in (3)\"];\n\"EFO\" -> \"CHEBI\" [label=\"is_about (262)\"];\n\"EFO\" -> \"CHEBI\" [label=\"located_in (1)\"];\n\"EFO\" -> \"CHEBI\" [label=\"subclass_of (71)\"];\n\"EFO\" -> \"CL\" [label=\"derives_from (6)\"];\n\"EFO\" -> \"CL\" [label=\"has_disease_location (59)\"];\n\"EFO\" -> \"CL\" [label=\"inheres_in_part_of (1)\"];\n\"EFO\" -> \"CL\" [label=\"is_about (40)\"];\n\"EFO\" -> \"CL\" [label=\"part_of (2)\"];\n\"EFO\" -> \"CL\" [label=\"subclass_of (539)\"];\n\"EFO\" -> \"CL\" [label=\"xref (12)\"];\n\"EFO\" -> \"DOID\" [label=\"is_about (1)\"];\n\"EFO\" -> \"DOID\" [label=\"subclass_of (6)\"];\n\"EFO\" -> \"DOID\" [label=\"xref (2350)\"];\n\"EFO\" -> \"EFO\" [label=\"INVERTED:develops_from (1)\"];\n\"EFO\" -> \"EFO\" [label=\"INVERTED:has_input (4)\"];\n\"EFO\" -> \"EFO\" [label=\"INVERTED:has_participant (69)\"];\n\"EFO\" -> \"EFO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"];\n\"EFO\" -> \"EFO\" [label=\"bearer_of (970)\"];\n\"EFO\" -> \"EFO\" [label=\"derives_from (15)\"];\n\"EFO\" -> \"EFO\" [label=\"disease_causes_feature (1)\"];\n\"EFO\" -> \"EFO\" [label=\"disease_has_basis_in_feature (18)\"];\n\"EFO\" -> \"EFO\" [label=\"disease_has_feature (34)\"];\n\"EFO\" -> \"EFO\" [label=\"disease_has_major_feature (1)\"];\n\"EFO\" -> \"EFO\" [label=\"disease_shares_features_of (2)\"];\n\"EFO\" -> \"EFO\" [label=\"has_about_it (2)\"];\n\"EFO\" -> \"EFO\" [label=\"has_disease_location (14)\"];\n\"EFO\" -> \"EFO\" [label=\"has_quality (10)\"];\n\"EFO\" -> \"EFO\" [label=\"has_role (17)\"];\n\"EFO\" -> \"EFO\" [label=\"inheres_in (1)\"];\n\"EFO\" -> \"EFO\" [label=\"inverse_of (3)\"];\n\"EFO\" -> \"EFO\" [label=\"is_about (556)\"];\n\"EFO\" -> \"EFO\" [label=\"is_executed_in (2)\"];\n\"EFO\" -> \"EFO\" [label=\"is_input_of (95)\"];\n\"EFO\" -> \"EFO\" [label=\"part_of (48)\"];\n\"EFO\" -> \"EFO\" [label=\"part_of_progression_of_disease (2)\"];\n\"EFO\" -> \"EFO\" [label=\"participates_in (8)\"];\n\"EFO\" -> \"EFO\" [label=\"related_to (1)\"];\n\"EFO\" -> \"EFO\" [label=\"sub_property_of (5)\"];\n\"EFO\" -> \"EFO\" [label=\"subclass_of (11372)\"];\n\"EFO\" -> \"EFO\" [label=\"xref (27)\"];\n\"EFO\" -> \"FMA\" [label=\"xref (57)\"];\n\"EFO\" -> \"GARD\" [label=\"xref (555)\"];\n\"EFO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (1)\"];\n\"EFO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"EFO\" -> \"GO\" [label=\"is_about (68)\"];\n\"EFO\" -> \"GO\" [label=\"participates_in (25)\"];\n\"EFO\" -> \"GO\" [label=\"subclass_of (180)\"];\n\"EFO\" -> \"GO\" [label=\"xref (6)\"];\n\"EFO\" -> \"HANCESTRO\" [label=\"derives_from (31)\"];\n\"EFO\" -> \"HANCESTRO\" [label=\"has_quality (3)\"];\n\"EFO\" -> \"HANCESTRO\" [label=\"part_of (12)\"];\n\"EFO\" -> \"HGNC\" [label=\"xref (8)\"];\n\"EFO\" -> \"HP\" [label=\"disease_has_feature (1)\"];\n\"EFO\" -> \"HP\" [label=\"has_modifier (30)\"];\n\"EFO\" -> \"HP\" [label=\"has_phenotype (3)\"];\n\"EFO\" -> \"HP\" [label=\"is_about (19)\"];\n\"EFO\" -> \"HP\" [label=\"subclass_of (128)\"];\n\"EFO\" -> \"HP\" [label=\"xref (237)\"];\n\"EFO\" -> \"IAO\" [label=\"subclass_of (38)\"];\n\"EFO\" -> \"ICD10\" [label=\"xref (2576)\"];\n\"EFO\" -> \"ICD9\" [label=\"xref (2049)\"];\n\"EFO\" -> \"KEGG\" [label=\"xref (26)\"];\n\"EFO\" -> \"MA\" [label=\"has_disease_location (1)\"];\n\"EFO\" -> \"MA\" [label=\"is_about (1)\"];\n\"EFO\" -> \"MA\" [label=\"xref (1)\"];\n\"EFO\" -> \"MEDDRA\" [label=\"xref (2)\"];\n\"EFO\" -> \"MESH\" [label=\"xref (1631)\"];\n\"EFO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"];\n\"EFO\" -> \"MONDO\" [label=\"disease_causes_feature (1)\"];\n\"EFO\" -> \"MONDO\" [label=\"disease_has_basis_in_feature (3)\"];\n\"EFO\" -> \"MONDO\" [label=\"disease_has_feature (34)\"];\n\"EFO\" -> \"MONDO\" [label=\"disease_shares_features_of (1)\"];\n\"EFO\" -> \"MONDO\" [label=\"equivalent_to (2850)\"];\n\"EFO\" -> \"MONDO\" [label=\"has_modifier (125)\"];\n\"EFO\" -> \"MONDO\" [label=\"subclass_of (2167)\"];\n\"EFO\" -> \"MONDO\" [label=\"xref (2604)\"];\n\"EFO\" -> \"MP\" [label=\"has_phenotype (1)\"];\n\"EFO\" -> \"MP\" [label=\"subclass_of (7)\"];\n\"EFO\" -> \"NCBITaxon\" [label=\"derives_from (16)\"];\n\"EFO\" -> \"NCBITaxon\" [label=\"inheres_in (9)\"];\n\"EFO\" -> \"NCBITaxon\" [label=\"located_in (4)\"];\n\"EFO\" -> \"NCBITaxon\" [label=\"only_in_taxon (3)\"];\n\"EFO\" -> \"NCBITaxon\" [label=\"part_of (6)\"];\n\"EFO\" -> \"NCBITaxon\" [label=\"subclass_of (305)\"];\n\"EFO\" -> \"NCIT\" [label=\"xref (2012)\"];\n\"EFO\" -> \"OBI\" [label=\"INVERTED:has_participant (2)\"];\n\"EFO\" -> \"OBI\" [label=\"inheres_in (9)\"];\n\"EFO\" -> \"OBI\" [label=\"is_about (22)\"];\n\"EFO\" -> \"OBI\" [label=\"is_executed_in (2)\"];\n\"EFO\" -> \"OBI\" [label=\"subclass_of (105)\"];\n\"EFO\" -> \"OBI\" [label=\"xref (1)\"];\n\"EFO\" -> \"OBO\" [label=\"part_of (5)\"];\n\"EFO\" -> \"OGMS\" [label=\"subclass_of (3)\"];\n\"EFO\" -> \"OGMS\" [label=\"xref (1)\"];\n\"EFO\" -> \"OMIM\" [label=\"xref (875)\"];\n\"EFO\" -> \"OMIMPS\" [label=\"xref (47)\"];\n\"EFO\" -> \"ORPHANET\" [label=\"INVERTED:has_part (1)\"];\n\"EFO\" -> \"ORPHANET\" [label=\"bearer_of (3)\"];\n\"EFO\" -> \"ORPHANET\" [label=\"disease_has_basis_in_feature (1)\"];\n\"EFO\" -> \"ORPHANET\" [label=\"is_about (12)\"];\n\"EFO\" -> \"ORPHANET\" [label=\"subclass_of (328)\"];\n\"EFO\" -> \"PATO\" [label=\"bearer_of (19)\"];\n\"EFO\" -> \"PATO\" [label=\"has_quality (522)\"];\n\"EFO\" -> \"PATO\" [label=\"subclass_of (2)\"];\n\"EFO\" -> \"PATO\" [label=\"xref (8)\"];\n\"EFO\" -> \"PO\" [label=\"equivalent_to (1)\"];\n\"EFO\" -> \"PO\" [label=\"located_in (1)\"];\n\"EFO\" -> \"PO\" [label=\"part_of (1)\"];\n\"EFO\" -> \"PO\" [label=\"subclass_of (19)\"];\n\"EFO\" -> \"PO\" [label=\"xref (31)\"];\n\"EFO\" -> \"PR\" [label=\"is_about (3)\"];\n\"EFO\" -> \"RO\" [label=\"sub_property_of (2)\"];\n\"EFO\" -> \"SNOMED\" [label=\"xref (1)\"];\n\"EFO\" -> \"SYMP\" [label=\"xref (2)\"];\n\"EFO\" -> \"UBERON\" [label=\"derives_from (6)\"];\n\"EFO\" -> \"UBERON\" [label=\"has_disease_location (278)\"];\n\"EFO\" -> \"UBERON\" [label=\"inheres_in (7)\"];\n\"EFO\" -> \"UBERON\" [label=\"inheres_in_part_of (13)\"];\n\"EFO\" -> \"UBERON\" [label=\"is_about (341)\"];\n\"EFO\" -> \"UBERON\" [label=\"located_in (6)\"];\n\"EFO\" -> \"UBERON\" [label=\"occurs_in (1)\"];\n\"EFO\" -> \"UBERON\" [label=\"part_of (22)\"];\n\"EFO\" -> \"UBERON\" [label=\"participates_in (1)\"];\n\"EFO\" -> \"UBERON\" [label=\"subclass_of (82)\"];\n\"EFO\" -> \"UBERON\" [label=\"xref (2)\"];\n\"EFO\" -> \"UMLS\" [label=\"xref (2202)\"];\n\"EFO\" -> \"UO\" [label=\"INVERTED:is_unit_of (4)\"];\n\"EFO\" -> \"UO\" [label=\"equivalent_to (1)\"];\n\"EFO\" -> \"UO\" [label=\"subclass_of (38)\"];\n\"EHDAA2\" -> \"AEO\" [label=\"attaches_to (1)\"];\n\"EHDAA2\" -> \"AEO\" [label=\"part_of (36)\"];\n\"EHDAA2\" -> \"AEO\" [label=\"subclass_of (1703)\"];\n\"EHDAA2\" -> \"CARO\" [label=\"subclass_of (927)\"];\n\"EHDAA2\" -> \"EHDAA2\" [label=\"INVERTED:develops_from (2125)\"];\n\"EHDAA2\" -> \"EHDAA2\" [label=\"attaches_to (1)\"];\n\"EHDAA2\" -> \"EHDAA2\" [label=\"develops_in (33)\"];\n\"EHDAA2\" -> \"EHDAA2\" [label=\"located_in (166)\"];\n\"EHDAA2\" -> \"EHDAA2\" [label=\"part_of (2925)\"];\n\"EHDAA2\" -> \"EHDAA2\" [label=\"subclass_of (155)\"];\n\"EHDAA2\" -> \"OBO\" [label=\"existence_ends_during (2367)\"];\n\"EHDAA2\" -> \"OBO\" [label=\"existence_starts_during (2268)\"];\n\"EHDAA2\" -> \"OBO\" [label=\"subclass_of (1)\"];\n\"ENSEMBL\" -> \"HGNC\" [label=\"same_as (42691)\"];\n\"ENSEMBL\" -> \"NCBITaxon\" [label=\"in_taxon (67667)\"];\n\"ENSEMBL\" -> \"NCBITaxon\" [label=\"only_in_taxon (110)\"];\n\"ENSEMBL\" -> \"PR\" [label=\"INVERTED:has_gene_template (110)\"];\n\"ENSEMBL\" -> \"SO\" [label=\"subclass_of (110)\"];\n\"ENVO\" -> \"BFO\" [label=\"has_increased_levels_of (1)\"];\n\"ENVO\" -> \"BFO\" [label=\"subclass_of (16)\"];\n\"ENVO\" -> \"CHEBI\" [label=\"derives_from (1)\"];\n\"ENVO\" -> \"CHEBI\" [label=\"has_increased_levels_of (4)\"];\n\"ENVO\" -> \"CHEBI\" [label=\"has_role (3)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:composed_primarily_of (34)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:contains_process (1)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:determined_by (11)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:formed_as_result_of (4)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:has_part (17)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:has_participant (10)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:output_of (3)\"];\n\"ENVO\" -> \"ENVO\" [label=\"INVERTED:process_has_causal_agent (3)\"];\n\"ENVO\" -> \"ENVO\" [label=\"adjacent_to (8)\"];\n\"ENVO\" -> \"ENVO\" [label=\"bounding_layer_of (1)\"];\n\"ENVO\" -> \"ENVO\" [label=\"causal_agent_in_process (1)\"];\n\"ENVO\" -> \"ENVO\" [label=\"derives_from (9)\"];\n\"ENVO\" -> \"ENVO\" [label=\"ends (1)\"];\n\"ENVO\" -> \"ENVO\" [label=\"has_input (9)\"];\n\"ENVO\" -> \"ENVO\" [label=\"has_output (10)\"];\n\"ENVO\" -> \"ENVO\" [label=\"has_quality (4)\"];\n\"ENVO\" -> \"ENVO\" [label=\"has_role (1)\"];\n\"ENVO\" -> \"ENVO\" [label=\"inheres_in (7)\"];\n\"ENVO\" -> \"ENVO\" [label=\"located_in (3)\"];\n\"ENVO\" -> \"ENVO\" [label=\"occurs_in (2)\"];\n\"ENVO\" -> \"ENVO\" [label=\"overlaps (9)\"];\n\"ENVO\" -> \"ENVO\" [label=\"part_of (72)\"];\n\"ENVO\" -> \"ENVO\" [label=\"partially_surrounded_by (1)\"];\n\"ENVO\" -> \"ENVO\" [label=\"results_in_formation_of (2)\"];\n\"ENVO\" -> \"ENVO\" [label=\"subclass_of (590)\"];\n\"ENVO\" -> \"ENVO\" [label=\"surrounded_by (4)\"];\n\"ENVO\" -> \"ENVO\" [label=\"type (41)\"];\n\"ENVO\" -> \"FOODON\" [label=\"INVERTED:composed_primarily_of (1)\"];\n\"ENVO\" -> \"FOODON\" [label=\"subclass_of (2)\"];\n\"ENVO\" -> \"GENEPIO\" [label=\"subclass_of (17)\"];\n\"ENVO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (1)\"];\n\"ENVO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (13)\"];\n\"ENVO\" -> \"NCIT\" [label=\"located_in (1)\"];\n\"ENVO\" -> \"OBI\" [label=\"subclass_of (2)\"];\n\"ENVO\" -> \"OIO\" [label=\"subclass_of (1)\"];\n\"ENVO\" -> \"PATO\" [label=\"has_quality (32)\"];\n\"ENVO\" -> \"PATO\" [label=\"subclass_of (13)\"];\n\"ENVO\" -> \"PO\" [label=\"derives_from (1)\"];\n\"ENVO\" -> \"RO\" [label=\"subclass_of (1)\"];\n\"ENVO\" -> \"SIO\" [label=\"subclass_of (1)\"];\n\"EO\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"EO\" -> \"EO\" [label=\"subclass_of (47)\"];\n\"EO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"EO\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"EO\" -> \"NCBITaxon\" [label=\"subclass_of (2)\"];\n\"EPO\" -> \"TRANS\" [label=\"subclass_of (1)\"];\n\"ERO\" -> \"ERO\" [label=\"subclass_of (2)\"];\n\"ERO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"ERO\" -> \"OBI\" [label=\"subclass_of (4)\"];\n\"EnsemblGenomes\" -> \"NCBITaxon\" [label=\"only_in_taxon (278)\"];\n\"EnsemblGenomes\" -> \"PR\" [label=\"INVERTED:has_gene_template (278)\"];\n\"EnsemblGenomes\" -> \"SO\" [label=\"subclass_of (278)\"];\n\"ExO\" -> \"EPO\" [label=\"subclass_of (1)\"];\n\"ExO\" -> \"GENEPIO\" [label=\"member_of (2)\"];\n\"ExO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"FAO\" -> \"CARO\" [label=\"subclass_of (4)\"];\n\"FAO\" -> \"FAO\" [label=\"INVERTED:develops_from (2)\"];\n\"FAO\" -> \"FAO\" [label=\"part_of (4)\"];\n\"FAO\" -> \"FAO\" [label=\"subclass_of (32)\"];\n\"FAO\" -> \"NCBITaxon\" [label=\"only_in_taxon (1)\"];\n\"FBbt\" -> \"CL\" [label=\"xref (1)\"];\n\"FBbt\" -> \"EFO\" [label=\"subclass_of (77)\"];\n\"FBbt\" -> \"FBbt\" [label=\"part_of (16)\"];\n\"FBbt\" -> \"FBbt\" [label=\"subclass_of (12)\"];\n\"FBbt\" -> \"UBERON\" [label=\"INVERTED:develops_from (1)\"];\n\"FBbt\" -> \"UBERON\" [label=\"part_of (2)\"];\n\"FBbt\" -> \"UBERON\" [label=\"subclass_of (22)\"];\n\"FBdv\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"FBgn\" -> \"NCBITaxon\" [label=\"only_in_taxon (3954)\"];\n\"FBgn\" -> \"PR\" [label=\"INVERTED:has_gene_template (3954)\"];\n\"FBgn\" -> \"SO\" [label=\"subclass_of (3954)\"];\n\"FIX\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"FLU\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"FMA\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:contains (333)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:derives (274)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:develops_from (18)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:has_member (2243)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:has_part (12)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:location_of (1)\"];\n\"FMA\" -> \"FMA\" [label=\"INVERTED:transforms_from (22)\"];\n\"FMA\" -> \"FMA\" [label=\"adheres_to (7)\"];\n\"FMA\" -> \"FMA\" [label=\"adjacent_to (22)\"];\n\"FMA\" -> \"FMA\" [label=\"afferent_to (812)\"];\n\"FMA\" -> \"FMA\" [label=\"anterior_to (355)\"];\n\"FMA\" -> \"FMA\" [label=\"anteroinferior_to (27)\"];\n\"FMA\" -> \"FMA\" [label=\"anterolateral_to (18)\"];\n\"FMA\" -> \"FMA\" [label=\"anteromedial_to (22)\"];\n\"FMA\" -> \"FMA\" [label=\"anterosuperior_to (16)\"];\n\"FMA\" -> \"FMA\" [label=\"arterial_supply_of (622)\"];\n\"FMA\" -> \"FMA\" [label=\"articulates_with (692)\"];\n\"FMA\" -> \"FMA\" [label=\"attaches_to (476)\"];\n\"FMA\" -> \"FMA\" [label=\"bounds (1465)\"];\n\"FMA\" -> \"FMA\" [label=\"branch_of (7586)\"];\n\"FMA\" -> \"FMA\" [label=\"connected_to (140)\"];\n\"FMA\" -> \"FMA\" [label=\"connection_type_of (4)\"];\n\"FMA\" -> \"FMA\" [label=\"constitutional_part_of (21424)\"];\n\"FMA\" -> \"FMA\" [label=\"continuation_branch_of (43)\"];\n\"FMA\" -> \"FMA\" [label=\"continuous_distally_with (1879)\"];\n\"FMA\" -> \"FMA\" [label=\"continuous_proximally_with (1825)\"];\n\"FMA\" -> \"FMA\" [label=\"continuous_with (2512)\"];\n\"FMA\" -> \"FMA\" [label=\"corresponds_to (46)\"];\n\"FMA\" -> \"FMA\" [label=\"development_type_of (13)\"];\n\"FMA\" -> \"FMA\" [label=\"developmental_stage_of (193)\"];\n\"FMA\" -> \"FMA\" [label=\"develops_into (3)\"];\n\"FMA\" -> \"FMA\" [label=\"direct_cell_shape_of (2)\"];\n\"FMA\" -> \"FMA\" [label=\"direct_left_of (275)\"];\n\"FMA\" -> \"FMA\" [label=\"direct_right_of (229)\"];\n\"FMA\" -> \"FMA\" [label=\"distal_to (159)\"];\n\"FMA\" -> \"FMA\" [label=\"drains_into (212)\"];\n\"FMA\" -> \"FMA\" [label=\"efferent_to (820)\"];\n\"FMA\" -> \"FMA\" [label=\"external_to (1)\"];\n\"FMA\" -> \"FMA\" [label=\"forms (15)\"];\n\"FMA\" -> \"FMA\" [label=\"full_grown_phenotype_of (3)\"];\n\"FMA\" -> \"FMA\" [label=\"fuses_with (26)\"];\n\"FMA\" -> \"FMA\" [label=\"fusion_of (2)\"];\n\"FMA\" -> \"FMA\" [label=\"germ_origin_of (1)\"];\n\"FMA\" -> \"FMA\" [label=\"has_adherent (7)\"];\n\"FMA\" -> \"FMA\" [label=\"has_arterial_supply (599)\"];\n\"FMA\" -> \"FMA\" [label=\"has_branch (6906)\"];\n\"FMA\" -> \"FMA\" [label=\"has_connection_type (4)\"];\n\"FMA\" -> \"FMA\" [label=\"has_constitutional_part (21120)\"];\n\"FMA\" -> \"FMA\" [label=\"has_continuation_branch (28)\"];\n\"FMA\" -> \"FMA\" [label=\"has_development_type (13)\"];\n\"FMA\" -> \"FMA\" [label=\"has_developmental_stage (193)\"];\n\"FMA\" -> \"FMA\" [label=\"has_direct_cell_shape (2)\"];\n\"FMA\" -> \"FMA\" [label=\"has_full_grown_phenotype (3)\"];\n\"FMA\" -> \"FMA\" [label=\"has_fusion (4)\"];\n\"FMA\" -> \"FMA\" [label=\"has_germ_origin (1)\"];\n\"FMA\" -> \"FMA\" [label=\"has_inherent_3d_shape (4)\"];\n\"FMA\" -> \"FMA\" [label=\"has_insertion (210)\"];\n\"FMA\" -> \"FMA\" [label=\"has_location (1)\"];\n\"FMA\" -> \"FMA\" [label=\"has_lymphatic_drainage (759)\"];\n\"FMA\" -> \"FMA\" [label=\"has_nerve_supply (2127)\"];\n\"FMA\" -> \"FMA\" [label=\"has_observed_anatomical_entity (3)\"];\n\"FMA\" -> \"FMA\" [label=\"has_origin (275)\"];\n\"FMA\" -> \"FMA\" [label=\"has_primary_segmental_supply (17)\"];\n\"FMA\" -> \"FMA\" [label=\"has_projection (110)\"];\n\"FMA\" -> \"FMA\" [label=\"has_regional_part (26404)\"];\n\"FMA\" -> \"FMA\" [label=\"has_related_developmental_entity (15)\"];\n\"FMA\" -> \"FMA\" [label=\"has_secondary_segmental_supply (79)\"];\n\"FMA\" -> \"FMA\" [label=\"has_segmental_composition (2)\"];\n\"FMA\" -> \"FMA\" [label=\"has_segmental_supply (613)\"];\n\"FMA\" -> \"FMA\" [label=\"has_tributary (1007)\"];\n\"FMA\" -> \"FMA\" [label=\"has_venous_drainage (132)\"];\n\"FMA\" -> \"FMA\" [label=\"homonym_of (73)\"];\n\"FMA\" -> \"FMA\" [label=\"inferior_to (401)\"];\n\"FMA\" -> \"FMA\" [label=\"inferolateral_to (8)\"];\n\"FMA\" -> \"FMA\" [label=\"inferomedial_to (5)\"];\n\"FMA\" -> \"FMA\" [label=\"inherent_3d_shape_of (4)\"];\n\"FMA\" -> \"FMA\" [label=\"insertion_of (213)\"];\n\"FMA\" -> \"FMA\" [label=\"internal_to (1)\"];\n\"FMA\" -> \"FMA\" [label=\"inverse_of_bounds (1076)\"];\n\"FMA\" -> \"FMA\" [label=\"inverse_of_contains (555)\"];\n\"FMA\" -> \"FMA\" [label=\"inverse_of_derives (264)\"];\n\"FMA\" -> \"FMA\" [label=\"inverse_of_forms (15)\"];\n\"FMA\" -> \"FMA\" [label=\"lateral_to (111)\"];\n\"FMA\" -> \"FMA\" [label=\"left_lateral_to (5)\"];\n\"FMA\" -> \"FMA\" [label=\"left_medial_to (3)\"];\n\"FMA\" -> \"FMA\" [label=\"lymphatic_drainage_of (764)\"];\n\"FMA\" -> \"FMA\" [label=\"matures_from (76)\"];\n\"FMA\" -> \"FMA\" [label=\"matures_into (76)\"];\n\"FMA\" -> \"FMA\" [label=\"medial_to (130)\"];\n\"FMA\" -> \"FMA\" [label=\"member_of (2295)\"];\n\"FMA\" -> \"FMA\" [label=\"merges_with (6)\"];\n\"FMA\" -> \"FMA\" [label=\"nerve_supply_of (2129)\"];\n\"FMA\" -> \"FMA\" [label=\"origin_of (275)\"];\n\"FMA\" -> \"FMA\" [label=\"part_of (4801)\"];\n\"FMA\" -> \"FMA\" [label=\"posterior_to (403)\"];\n\"FMA\" -> \"FMA\" [label=\"posteroinferior_to (22)\"];\n\"FMA\" -> \"FMA\" [label=\"posterolateral_to (12)\"];\n\"FMA\" -> \"FMA\" [label=\"posteromedial_to (9)\"];\n\"FMA\" -> \"FMA\" [label=\"posterosuperior_to (34)\"];\n\"FMA\" -> \"FMA\" [label=\"primary_segmental_supply_of (24)\"];\n\"FMA\" -> \"FMA\" [label=\"projects_from (110)\"];\n\"FMA\" -> \"FMA\" [label=\"projects_to (117)\"];\n\"FMA\" -> \"FMA\" [label=\"proximal_to (106)\"];\n\"FMA\" -> \"FMA\" [label=\"receives_attachment_from (458)\"];\n\"FMA\" -> \"FMA\" [label=\"receives_drainage_from (195)\"];\n\"FMA\" -> \"FMA\" [label=\"receives_input_from (676)\"];\n\"FMA\" -> \"FMA\" [label=\"receives_projection (117)\"];\n\"FMA\" -> \"FMA\" [label=\"regional_part_of (27615)\"];\n\"FMA\" -> \"FMA\" [label=\"related_developmental_entity_of (13)\"];\n\"FMA\" -> \"FMA\" [label=\"related_object (252)\"];\n\"FMA\" -> \"FMA\" [label=\"related_part (3094)\"];\n\"FMA\" -> \"FMA\" [label=\"right_lateral_to (4)\"];\n\"FMA\" -> \"FMA\" [label=\"right_medial_to (4)\"];\n\"FMA\" -> \"FMA\" [label=\"secondary_segmental_supply_of (2)\"];\n\"FMA\" -> \"FMA\" [label=\"segmental_composition_of (2)\"];\n\"FMA\" -> \"FMA\" [label=\"segmental_supply_of (683)\"];\n\"FMA\" -> \"FMA\" [label=\"sends_output_to (800)\"];\n\"FMA\" -> \"FMA\" [label=\"sub_property_of (3)\"];\n\"FMA\" -> \"FMA\" [label=\"subclass_of (107543)\"];\n\"FMA\" -> \"FMA\" [label=\"superior_to (399)\"];\n\"FMA\" -> \"FMA\" [label=\"superolateral_to (9)\"];\n\"FMA\" -> \"FMA\" [label=\"superomedial_to (5)\"];\n\"FMA\" -> \"FMA\" [label=\"surrounded_by (139)\"];\n\"FMA\" -> \"FMA\" [label=\"surrounds (133)\"];\n\"FMA\" -> \"FMA\" [label=\"transforms_into (28)\"];\n\"FMA\" -> \"FMA\" [label=\"tributary_of (1068)\"];\n\"FMA\" -> \"FMA\" [label=\"venous_drainage_of (132)\"];\n\"FMA\" -> \"UBERON\" [label=\"part_of (2)\"];\n\"FMA\" -> \"UBERON\" [label=\"subclass_of (8)\"];\n\"FMA\" -> \"UMLS\" [label=\"xref (104400)\"];\n\"FOODON\" -> \"BFO\" [label=\"subclass_of (11)\"];\n\"FOODON\" -> \"CHEBI\" [label=\"derives_from (2)\"];\n\"FOODON\" -> \"CHEBI\" [label=\"subclass_of (14)\"];\n\"FOODON\" -> \"DOID\" [label=\"INVERTED:has_allergic_trigger (25)\"];\n\"FOODON\" -> \"ECOCORE\" [label=\"INVERTED:has_participant (1)\"];\n\"FOODON\" -> \"ENVO\" [label=\"derives_from (8)\"];\n\"FOODON\" -> \"ENVO\" [label=\"subclass_of (9)\"];\n\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (190)\"];\n\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_ingredient (77)\"];\n\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_member (11)\"];\n\"FOODON\" -> \"FOODON\" [label=\"INVERTED:has_part (9)\"];\n\"FOODON\" -> \"FOODON\" [label=\"INVERTED:output_of (15)\"];\n\"FOODON\" -> \"FOODON\" [label=\"INVERTED:produced_by (2)\"];\n\"FOODON\" -> \"FOODON\" [label=\"derives_from (2874)\"];\n\"FOODON\" -> \"FOODON\" [label=\"develops_from_part_of (13)\"];\n\"FOODON\" -> \"FOODON\" [label=\"has_consumer (6)\"];\n\"FOODON\" -> \"FOODON\" [label=\"has_food_substance_analog (14)\"];\n\"FOODON\" -> \"FOODON\" [label=\"has_input (3)\"];\n\"FOODON\" -> \"FOODON\" [label=\"has_output (1)\"];\n\"FOODON\" -> \"FOODON\" [label=\"has_quality (9)\"];\n\"FOODON\" -> \"FOODON\" [label=\"has_substance_added (1)\"];\n\"FOODON\" -> \"FOODON\" [label=\"is_about (3)\"];\n\"FOODON\" -> \"FOODON\" [label=\"member_of (5921)\"];\n\"FOODON\" -> \"FOODON\" [label=\"part_of (1)\"];\n\"FOODON\" -> \"FOODON\" [label=\"sub_property_of (1)\"];\n\"FOODON\" -> \"FOODON\" [label=\"subclass_of (23328)\"];\n\"FOODON\" -> \"FOODON\" [label=\"surrounded_by (1)\"];\n\"FOODON\" -> \"GAZ\" [label=\"has_country_of_origin (9)\"];\n\"FOODON\" -> \"GAZ\" [label=\"subclass_of (13)\"];\n\"FOODON\" -> \"GENEPIO\" [label=\"subclass_of (15)\"];\n\"FOODON\" -> \"IAO\" [label=\"subclass_of (7)\"];\n\"FOODON\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (17)\"];\n\"FOODON\" -> \"NCBITaxon\" [label=\"in_taxon (1733)\"];\n\"FOODON\" -> \"NCIT\" [label=\"subclass_of (2)\"];\n\"FOODON\" -> \"OIO\" [label=\"subclass_of (11)\"];\n\"FOODON\" -> \"PATO\" [label=\"subclass_of (6)\"];\n\"FOODON\" -> \"PO\" [label=\"derives_from (5)\"];\n\"FOODON\" -> \"PO\" [label=\"member_of (1)\"];\n\"FOODON\" -> \"PO\" [label=\"subclass_of (11)\"];\n\"FOODON\" -> \"RO\" [label=\"sub_property_of (1)\"];\n\"FOODON\" -> \"UBERON\" [label=\"derives_from (6)\"];\n\"FOODON\" -> \"UBERON\" [label=\"subclass_of (2)\"];\n\"FOODON\" -> \"owl\" [label=\"sub_property_of (1)\"];\n\"GARD\" -> \"MONDO\" [label=\"equivalent_to (5814)\"];\n\"GAZ\" -> \"ENVO\" [label=\"type (190)\"];\n\"GAZ\" -> \"FOODON\" [label=\"subclass_of (162)\"];\n\"GAZ\" -> \"GAZ\" [label=\"located_in (720)\"];\n\"GAZ\" -> \"GAZ\" [label=\"subclass_of (273)\"];\n\"GAZ\" -> \"GENEPIO\" [label=\"subclass_of (16)\"];\n\"GAZ\" -> \"GENEPIO\" [label=\"type (56)\"];\n\"GAZ\" -> \"NCIT\" [label=\"subclass_of (186)\"];\n\"GAZ\" -> \"NCIT\" [label=\"type (189)\"];\n\"GAZ\" -> \"OBO\" [label=\"subclass_of (197)\"];\n\"GENEPIO\" -> \"ARO\" [label=\"equivalent_to (1)\"];\n\"GENEPIO\" -> \"ARO\" [label=\"is_about (3)\"];\n\"GENEPIO\" -> \"ARO\" [label=\"subclass_of (4)\"];\n\"GENEPIO\" -> \"BFO\" [label=\"subclass_of (13)\"];\n\"GENEPIO\" -> \"CHEBI\" [label=\"is_about (1)\"];\n\"GENEPIO\" -> \"CHEBI\" [label=\"subclass_of (2)\"];\n\"GENEPIO\" -> \"CHMO\" [label=\"subclass_of (5)\"];\n\"GENEPIO\" -> \"DOID\" [label=\"subclass_of (1)\"];\n\"GENEPIO\" -> \"EDAM\" [label=\"subclass_of (1)\"];\n\"GENEPIO\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"GENEPIO\" -> \"ENVO\" [label=\"is_about (1)\"];\n\"GENEPIO\" -> \"ENVO\" [label=\"subclass_of (3)\"];\n\"GENEPIO\" -> \"ExO\" [label=\"subclass_of (9)\"];\n\"GENEPIO\" -> \"FOODON\" [label=\"subclass_of (3)\"];\n\"GENEPIO\" -> \"GAZ\" [label=\"located_in (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:after (18)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:has_component (38)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:has_member (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:has_part (4)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:preceded_by (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:produced_by (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (12)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"aligned_with (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"before (11)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"has_output (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"immediately_preceded_by (6)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"inheres_in (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"is_about (8)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"located_in (2)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"member_of (9)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"part_of (1)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"precedes (2)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"subclass_of (665)\"];\n\"GENEPIO\" -> \"GENEPIO\" [label=\"type (43)\"];\n\"GENEPIO\" -> \"GEO\" [label=\"subclass_of (1)\"];\n\"GENEPIO\" -> \"IAO\" [label=\"subclass_of (73)\"];\n\"GENEPIO\" -> \"IDO\" [label=\"is_about (6)\"];\n\"GENEPIO\" -> \"MI\" [label=\"subclass_of (15)\"];\n\"GENEPIO\" -> \"NCBITaxon\" [label=\"is_about (4)\"];\n\"GENEPIO\" -> \"NCIT\" [label=\"INVERTED:after (2)\"];\n\"GENEPIO\" -> \"NCIT\" [label=\"before (1)\"];\n\"GENEPIO\" -> \"NCIT\" [label=\"is_about (10)\"];\n\"GENEPIO\" -> \"NCIT\" [label=\"subclass_of (33)\"];\n\"GENEPIO\" -> \"OBI\" [label=\"denotes (1)\"];\n\"GENEPIO\" -> \"OBI\" [label=\"has_quality (1)\"];\n\"GENEPIO\" -> \"OBI\" [label=\"inheres_in (1)\"];\n\"GENEPIO\" -> \"OBI\" [label=\"is_about (7)\"];\n\"GENEPIO\" -> \"OBI\" [label=\"member_of (1)\"];\n\"GENEPIO\" -> \"OBI\" [label=\"subclass_of (96)\"];\n\"GENEPIO\" -> \"OBO\" [label=\"subclass_of (1)\"];\n\"GENEPIO\" -> \"OIO\" [label=\"subclass_of (2)\"];\n\"GENEPIO\" -> \"OMIT\" [label=\"is_about (4)\"];\n\"GENEPIO\" -> \"OMP\" [label=\"subclass_of (1)\"];\n\"GENEPIO\" -> \"PATO\" [label=\"is_about (2)\"];\n\"GENEPIO\" -> \"PATO\" [label=\"subclass_of (2)\"];\n\"GENEPIO\" -> \"PCO\" [label=\"subclass_of (2)\"];\n\"GENEPIO\" -> \"RO\" [label=\"inverse_of (1)\"];\n\"GENEPIO\" -> \"SIO\" [label=\"subclass_of (8)\"];\n\"GENEPIO\" -> \"SO\" [label=\"is_about (7)\"];\n\"GENEPIO\" -> \"STATO\" [label=\"is_about (1)\"];\n\"GENEPIO\" -> \"STATO\" [label=\"subclass_of (12)\"];\n\"GENEPIO\" -> \"UO\" [label=\"INVERTED:is_unit_of (1)\"];\n\"GENEPIO\" -> \"UO\" [label=\"has_measurement_unit_label (3)\"];\n\"GENEPIO\" -> \"UO\" [label=\"subclass_of (7)\"];\n\"GENO\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (2007)\"];\n\"GENO\" -> \"GENO\" [label=\"subclass_of (24)\"];\n\"GEO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"GEO\" -> \"GENEPIO\" [label=\"aligned_with (1)\"];\n\"GEO\" -> \"GENEPIO\" [label=\"subclass_of (2)\"];\n\"GEO\" -> \"GEO\" [label=\"subclass_of (1)\"];\n\"GO\" -> \"BFO\" [label=\"subclass_of (7)\"];\n\"GO\" -> \"CARO\" [label=\"results_in_development_of (1)\"];\n\"GO\" -> \"CARO\" [label=\"results_in_maturation_of (1)\"];\n\"GO\" -> \"CARO\" [label=\"subclass_of (21)\"];\n\"GO\" -> \"CHEBI\" [label=\"exports (74)\"];\n\"GO\" -> \"CHEBI\" [label=\"has_input (967)\"];\n\"GO\" -> \"CHEBI\" [label=\"has_output (93)\"];\n\"GO\" -> \"CHEBI\" [label=\"has_primary_input (1000)\"];\n\"GO\" -> \"CHEBI\" [label=\"has_primary_output (1168)\"];\n\"GO\" -> \"CHEBI\" [label=\"imports (179)\"];\n\"GO\" -> \"CHEBI\" [label=\"is_about (4)\"];\n\"GO\" -> \"CHEBI\" [label=\"regulates_levels_of (62)\"];\n\"GO\" -> \"CHEBI\" [label=\"transports_or_maintains_localization_of (969)\"];\n\"GO\" -> \"CHEBI\" [label=\"xref (919)\"];\n\"GO\" -> \"CL\" [label=\"INVERTED:has_part (98)\"];\n\"GO\" -> \"CL\" [label=\"INVERTED:has_plasma_membrane_part (1)\"];\n\"GO\" -> \"CL\" [label=\"acts_on_population_of (84)\"];\n\"GO\" -> \"CL\" [label=\"equivalent_to (1)\"];\n\"GO\" -> \"CL\" [label=\"has_end_location (3)\"];\n\"GO\" -> \"CL\" [label=\"has_input (64)\"];\n\"GO\" -> \"CL\" [label=\"has_start_location (3)\"];\n\"GO\" -> \"CL\" [label=\"has_target_end_location (2)\"];\n\"GO\" -> \"CL\" [label=\"has_target_start_location (4)\"];\n\"GO\" -> \"CL\" [label=\"is_about (1)\"];\n\"GO\" -> \"CL\" [label=\"occurs_in (129)\"];\n\"GO\" -> \"CL\" [label=\"overlaps (15)\"];\n\"GO\" -> \"CL\" [label=\"part_of (150)\"];\n\"GO\" -> \"CL\" [label=\"results_in_acquisition_of_features_of (300)\"];\n\"GO\" -> \"CL\" [label=\"results_in_commitment_to (57)\"];\n\"GO\" -> \"CL\" [label=\"results_in_determination_of (25)\"];\n\"GO\" -> \"CL\" [label=\"results_in_development_of (98)\"];\n\"GO\" -> \"CL\" [label=\"results_in_formation_of (15)\"];\n\"GO\" -> \"CL\" [label=\"results_in_growth_of (5)\"];\n\"GO\" -> \"CL\" [label=\"results_in_maturation_of (16)\"];\n\"GO\" -> \"CL\" [label=\"results_in_morphogenesis_of (10)\"];\n\"GO\" -> \"CL\" [label=\"results_in_specification_of (26)\"];\n\"GO\" -> \"CL\" [label=\"subclass_of (1)\"];\n\"GO\" -> \"CL\" [label=\"transports_or_maintains_localization_of (4)\"];\n\"GO\" -> \"CL\" [label=\"xref (258)\"];\n\"GO\" -> \"DDANAT\" [label=\"results_in_development_of (1)\"];\n\"GO\" -> \"DDANAT\" [label=\"xref (1)\"];\n\"GO\" -> \"DOID\" [label=\"INVERTED:disease_caused_by_disruption_of (53)\"];\n\"GO\" -> \"ECOCORE\" [label=\"INVERTED:has_part (5)\"];\n\"GO\" -> \"EFO\" [label=\"INVERTED:has_input (1)\"];\n\"GO\" -> \"EFO\" [label=\"subclass_of (10)\"];\n\"GO\" -> \"FAO\" [label=\"part_of (3)\"];\n\"GO\" -> \"FAO\" [label=\"results_in_development_of (10)\"];\n\"GO\" -> \"FAO\" [label=\"results_in_formation_of (6)\"];\n\"GO\" -> \"FAO\" [label=\"results_in_growth_of (1)\"];\n\"GO\" -> \"FMA\" [label=\"xref (10)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:ends_with (25)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:has_part (4860)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:has_participant (39)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (1)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:inverse_of_isa (5250)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:negatively_regulated_by (1632)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:positively_regulated_by (1616)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:preceded_by (1)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (20)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:regulated_by (1913)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:results_in_movement_of (1)\"];\n\"GO\" -> \"GO\" [label=\"INVERTED:starts_with (58)\"];\n\"GO\" -> \"GO\" [label=\"adjacent_to (22)\"];\n\"GO\" -> \"GO\" [label=\"bounding_layer_of (29)\"];\n\"GO\" -> \"GO\" [label=\"capable_of (498)\"];\n\"GO\" -> \"GO\" [label=\"capable_of_part_of (298)\"];\n\"GO\" -> \"GO\" [label=\"causally_upstream_of (3)\"];\n\"GO\" -> \"GO\" [label=\"directly_negatively_regulates (11)\"];\n\"GO\" -> \"GO\" [label=\"directly_positively_regulates (15)\"];\n\"GO\" -> \"GO\" [label=\"directly_regulates (12)\"];\n\"GO\" -> \"GO\" [label=\"ends_during (1)\"];\n\"GO\" -> \"GO\" [label=\"exports (4)\"];\n\"GO\" -> \"GO\" [label=\"happens_during (12)\"];\n\"GO\" -> \"GO\" [label=\"has_end_location (5)\"];\n\"GO\" -> \"GO\" [label=\"has_input (116)\"];\n\"GO\" -> \"GO\" [label=\"has_occurrence (258)\"];\n\"GO\" -> \"GO\" [label=\"has_output (14)\"];\n\"GO\" -> \"GO\" [label=\"has_primary_input (2)\"];\n\"GO\" -> \"GO\" [label=\"has_primary_output (1)\"];\n\"GO\" -> \"GO\" [label=\"has_start_location (8)\"];\n\"GO\" -> \"GO\" [label=\"has_target_end_location (268)\"];\n\"GO\" -> \"GO\" [label=\"has_target_start_location (96)\"];\n\"GO\" -> \"GO\" [label=\"immediately_causally_upstream_of (2)\"];\n\"GO\" -> \"GO\" [label=\"immediately_preceded_by (7)\"];\n\"GO\" -> \"GO\" [label=\"immediately_precedes (4)\"];\n\"GO\" -> \"GO\" [label=\"imports (2)\"];\n\"GO\" -> \"GO\" [label=\"inverse_ends_during (1)\"];\n\"GO\" -> \"GO\" [label=\"isa (6463)\"];\n\"GO\" -> \"GO\" [label=\"negatively_regulates (4659)\"];\n\"GO\" -> \"GO\" [label=\"occurs_in (270)\"];\n\"GO\" -> \"GO\" [label=\"overlaps (26)\"];\n\"GO\" -> \"GO\" [label=\"part_of (5240)\"];\n\"GO\" -> \"GO\" [label=\"positively_regulates (4656)\"];\n\"GO\" -> \"GO\" [label=\"precedes (1)\"];\n\"GO\" -> \"GO\" [label=\"regulates (5322)\"];\n\"GO\" -> \"GO\" [label=\"results_in (9)\"];\n\"GO\" -> \"GO\" [label=\"results_in_assembly_of (316)\"];\n\"GO\" -> \"GO\" [label=\"results_in_development_of (4)\"];\n\"GO\" -> \"GO\" [label=\"results_in_disassembly_of (75)\"];\n\"GO\" -> \"GO\" [label=\"results_in_distribution_of (7)\"];\n\"GO\" -> \"GO\" [label=\"results_in_fission_of (8)\"];\n\"GO\" -> \"GO\" [label=\"results_in_formation_of (2)\"];\n\"GO\" -> \"GO\" [label=\"results_in_fusion_of (33)\"];\n\"GO\" -> \"GO\" [label=\"results_in_growth_of (2)\"];\n\"GO\" -> \"GO\" [label=\"results_in_maintenance_of (16)\"];\n\"GO\" -> \"GO\" [label=\"results_in_maturation_of (2)\"];\n\"GO\" -> \"GO\" [label=\"results_in_morphogenesis_of (12)\"];\n\"GO\" -> \"GO\" [label=\"results_in_organization_of (191)\"];\n\"GO\" -> \"GO\" [label=\"results_in_remodeling_of (10)\"];\n\"GO\" -> \"GO\" [label=\"results_in_structural_organization_of (1)\"];\n\"GO\" -> \"GO\" [label=\"results_in_transport_across (45)\"];\n\"GO\" -> \"GO\" [label=\"results_in_transport_along (6)\"];\n\"GO\" -> \"GO\" [label=\"results_in_transport_to_from_or_in (17)\"];\n\"GO\" -> \"GO\" [label=\"subclass_of (80401)\"];\n\"GO\" -> \"GO\" [label=\"transports_or_maintains_localization_of (61)\"];\n\"GO\" -> \"GO\" [label=\"xref (4)\"];\n\"GO\" -> \"MI\" [label=\"subclass_of (2)\"];\n\"GO\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_disruption_of (275)\"];\n\"GO\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (30)\"];\n\"GO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (4)\"];\n\"GO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"];\n\"GO\" -> \"NBO\" [label=\"INVERTED:by_means (1)\"];\n\"GO\" -> \"NBO\" [label=\"INVERTED:in_response_to (12)\"];\n\"GO\" -> \"NCBITaxon\" [label=\"has_input (10)\"];\n\"GO\" -> \"NCBITaxon\" [label=\"only_in_taxon (683)\"];\n\"GO\" -> \"OBA\" [label=\"negatively_regulates (11)\"];\n\"GO\" -> \"OBA\" [label=\"positively_regulates (11)\"];\n\"GO\" -> \"OBA\" [label=\"regulates (80)\"];\n\"GO\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"GO\" -> \"OBO\" [label=\"exports (4)\"];\n\"GO\" -> \"OBO\" [label=\"has_input (48)\"];\n\"GO\" -> \"OBO\" [label=\"has_output (1)\"];\n\"GO\" -> \"OBO\" [label=\"has_primary_input (20)\"];\n\"GO\" -> \"OBO\" [label=\"has_primary_output (16)\"];\n\"GO\" -> \"OBO\" [label=\"imports (3)\"];\n\"GO\" -> \"OBO\" [label=\"regulates_levels_of (2)\"];\n\"GO\" -> \"OBO\" [label=\"subclass_of (2)\"];\n\"GO\" -> \"OBO\" [label=\"transports_or_maintains_localization_of (20)\"];\n\"GO\" -> \"OMIM\" [label=\"INVERTED:disease_caused_by_disruption_of (4)\"];\n\"GO\" -> \"OMIM\" [label=\"xref (4)\"];\n\"GO\" -> \"PATO\" [label=\"bearer_of (5)\"];\n\"GO\" -> \"PATO\" [label=\"xref (1)\"];\n\"GO\" -> \"PO\" [label=\"occurs_in (10)\"];\n\"GO\" -> \"PO\" [label=\"part_of (9)\"];\n\"GO\" -> \"PO\" [label=\"results_in_acquisition_of_features_of (31)\"];\n\"GO\" -> \"PO\" [label=\"results_in_commitment_to (2)\"];\n\"GO\" -> \"PO\" [label=\"results_in_development_of (65)\"];\n\"GO\" -> \"PO\" [label=\"results_in_formation_of (17)\"];\n\"GO\" -> \"PO\" [label=\"results_in_maturation_of (5)\"];\n\"GO\" -> \"PO\" [label=\"results_in_morphogenesis_of (30)\"];\n\"GO\" -> \"PO\" [label=\"results_in_specification_of (7)\"];\n\"GO\" -> \"PO\" [label=\"results_in_structural_organization_of (8)\"];\n\"GO\" -> \"PO\" [label=\"xref (44)\"];\n\"GO\" -> \"PR\" [label=\"INVERTED:output_of (808)\"];\n\"GO\" -> \"PR\" [label=\"directly_positively_regulates (2)\"];\n\"GO\" -> \"PR\" [label=\"exports (1)\"];\n\"GO\" -> \"PR\" [label=\"has_input (292)\"];\n\"GO\" -> \"PR\" [label=\"has_primary_input (2)\"];\n\"GO\" -> \"PR\" [label=\"has_primary_output (10)\"];\n\"GO\" -> \"PR\" [label=\"imports (1)\"];\n\"GO\" -> \"PR\" [label=\"transports_or_maintains_localization_of (9)\"];\n\"GO\" -> \"PR\" [label=\"xref (89)\"];\n\"GO\" -> \"SO\" [label=\"coincident_with (6)\"];\n\"GO\" -> \"SO\" [label=\"exports (4)\"];\n\"GO\" -> \"SO\" [label=\"has_input (7)\"];\n\"GO\" -> \"SO\" [label=\"has_output (6)\"];\n\"GO\" -> \"SO\" [label=\"has_primary_input (17)\"];\n\"GO\" -> \"SO\" [label=\"has_primary_output (2)\"];\n\"GO\" -> \"SO\" [label=\"imports (1)\"];\n\"GO\" -> \"SO\" [label=\"transports_or_maintains_localization_of (4)\"];\n\"GO\" -> \"SO\" [label=\"xref (15)\"];\n\"GO\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (25)\"];\n\"GO\" -> \"UBERON\" [label=\"INVERTED:contains_process (28)\"];\n\"GO\" -> \"UBERON\" [label=\"INVERTED:has_part (43)\"];\n\"GO\" -> \"UBERON\" [label=\"INVERTED:output_of (17)\"];\n\"GO\" -> \"UBERON\" [label=\"INVERTED:site_of (16)\"];\n\"GO\" -> \"UBERON\" [label=\"has_end_location (1)\"];\n\"GO\" -> \"UBERON\" [label=\"has_input (8)\"];\n\"GO\" -> \"UBERON\" [label=\"has_output (1)\"];\n\"GO\" -> \"UBERON\" [label=\"has_start_location (1)\"];\n\"GO\" -> \"UBERON\" [label=\"has_target_end_location (2)\"];\n\"GO\" -> \"UBERON\" [label=\"has_target_start_location (2)\"];\n\"GO\" -> \"UBERON\" [label=\"occurs_in (69)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_development_of (588)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_developmental_progression_of (1)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_formation_of (174)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_growth_of (20)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_maturation_of (53)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_morphogenesis_of (342)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_specification_of (4)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_structural_organization_of (28)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_transport_across (7)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_transport_along (1)\"];\n\"GO\" -> \"UBERON\" [label=\"results_in_transport_to_from_or_in (2)\"];\n\"GO\" -> \"UBERON\" [label=\"transports_or_maintains_localization_of (2)\"];\n\"GO\" -> \"UBERON\" [label=\"xref (44)\"];\n\"GO\" -> \"UMLS\" [label=\"xref (69387)\"];\n\"GO\" -> \"ZFA\" [label=\"xref (5)\"];\n\"GOREL\" -> \"RO\" [label=\"sub_property_of (5)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"activator (87)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"affects (97)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"agonist (1350)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"allosteric_modulator (139)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"antagonist (729)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"antibody (25)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"channel_blocker (158)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"gating_inhibitor (32)\"];\n\"GTPI\" -> \"NCBIGene\" [label=\"inhibitor (1337)\"];\n\"HANCESTRO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"HANCESTRO\" -> \"HANCESTRO\" [label=\"has_ancestry_status (2)\"];\n\"HANCESTRO\" -> \"HANCESTRO\" [label=\"inverse_of (1)\"];\n\"HANCESTRO\" -> \"HANCESTRO\" [label=\"subclass_of (330)\"];\n\"HANCESTRO\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"HANCESTRO\" -> \"OBI\" [label=\"subclass_of (2)\"];\n\"HANCESTRO\" -> \"dbpedia\" [label=\"is_demonym_of (9)\"];\n\"HCPCS\" -> \"HCPCS\" [label=\"mapped_to (15)\"];\n\"HCPCS\" -> \"HCPCS\" [label=\"subclass_of (6944)\"];\n\"HCPCS\" -> \"UMLS\" [label=\"xref (6948)\"];\n\"HGNC\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (4393)\"];\n\"HGNC\" -> \"NCBITaxon\" [label=\"only_in_taxon (19823)\"];\n\"HGNC\" -> \"PR\" [label=\"INVERTED:has_gene_template (19823)\"];\n\"HGNC\" -> \"SO\" [label=\"subclass_of (19874)\"];\n\"HGNC\" -> \"UMLS\" [label=\"xref (41638)\"];\n\"HGNC\" -> \"UniProtKB\" [label=\"has_gene_product (20312)\"];\n\"HMDB\" -> \"CHEBI\" [label=\"same_as (4846)\"];\n\"HMDB\" -> \"CHEMBL.TARGET\" [label=\"at_tissue (174)\"];\n\"HMDB\" -> \"CL\" [label=\"at_tissue (7)\"];\n\"HMDB\" -> \"EFO\" [label=\"at_tissue (9)\"];\n\"HMDB\" -> \"EHDAA2\" [label=\"at_tissue (1)\"];\n\"HMDB\" -> \"EHDAA2\" [label=\"in_biospecimen (1)\"];\n\"HMDB\" -> \"FMA\" [label=\"at_cellular_location (1)\"];\n\"HMDB\" -> \"FMA\" [label=\"at_tissue (4175)\"];\n\"HMDB\" -> \"FMA\" [label=\"in_biospecimen (49)\"];\n\"HMDB\" -> \"GO\" [label=\"at_cellular_location (16784)\"];\n\"HMDB\" -> \"MEDDRA\" [label=\"at_tissue (2)\"];\n\"HMDB\" -> \"MESH\" [label=\"at_tissue (2301)\"];\n\"HMDB\" -> \"MESH\" [label=\"in_biospecimen (19)\"];\n\"HMDB\" -> \"NCIT\" [label=\"at_tissue (217)\"];\n\"HMDB\" -> \"OMIM\" [label=\"at_tissue (2)\"];\n\"HMDB\" -> \"OMIM\" [label=\"disease (4222)\"];\n\"HMDB\" -> \"SMPDB\" [label=\"in_pathway (482060)\"];\n\"HMDB\" -> \"UBERON\" [label=\"at_tissue (66)\"];\n\"HMDB\" -> \"UMLS\" [label=\"at_cellular_location (1)\"];\n\"HMDB\" -> \"UMLS\" [label=\"at_tissue (137)\"];\n\"HMDB\" -> \"UMLS\" [label=\"in_biospecimen (11184)\"];\n\"HMDB\" -> \"UniProtKB\" [label=\"has_protein_association (332823)\"];\n\"HP\" -> \"ARO\" [label=\"subclass_of (1)\"];\n\"HP\" -> \"BFO\" [label=\"subclass_of (3)\"];\n\"HP\" -> \"CHEBI\" [label=\"subclass_of (1)\"];\n\"HP\" -> \"CL\" [label=\"affects (110)\"];\n\"HP\" -> \"CL\" [label=\"xref (4)\"];\n\"HP\" -> \"DOID\" [label=\"xref (34)\"];\n\"HP\" -> \"EFO\" [label=\"subclass_of (46)\"];\n\"HP\" -> \"EFO\" [label=\"xref (1)\"];\n\"HP\" -> \"GARD\" [label=\"xref (1)\"];\n\"HP\" -> \"GO\" [label=\"subclass_of (1)\"];\n\"HP\" -> \"GO\" [label=\"xref (3)\"];\n\"HP\" -> \"HP\" [label=\"has_modifier (1)\"];\n\"HP\" -> \"HP\" [label=\"subclass_of (22195)\"];\n\"HP\" -> \"ICD10\" [label=\"xref (83)\"];\n\"HP\" -> \"ICD9\" [label=\"xref (18)\"];\n\"HP\" -> \"MEDDRA\" [label=\"xref (93)\"];\n\"HP\" -> \"MESH\" [label=\"xref (3)\"];\n\"HP\" -> \"MONDO\" [label=\"equivalent_to (5)\"];\n\"HP\" -> \"MONDO\" [label=\"subclass_of (1)\"];\n\"HP\" -> \"MP\" [label=\"subclass_of (5)\"];\n\"HP\" -> \"MP\" [label=\"xref (1)\"];\n\"HP\" -> \"NCIT\" [label=\"xref (276)\"];\n\"HP\" -> \"OMIM\" [label=\"xref (24)\"];\n\"HP\" -> \"ORPHANET\" [label=\"subclass_of (2)\"];\n\"HP\" -> \"SYMP\" [label=\"has_symptom (2)\"];\n\"HP\" -> \"UBERON\" [label=\"affects (2853)\"];\n\"HP\" -> \"UBERON\" [label=\"inheres_in (1)\"];\n\"HP\" -> \"UBERON\" [label=\"inheres_in_part_of (2)\"];\n\"HP\" -> \"UBERON\" [label=\"xref (1)\"];\n\"HP\" -> \"UMLS\" [label=\"xref (16527)\"];\n\"HP\" -> \"UPHENO\" [label=\"subclass_of (1)\"];\n\"IAO\" -> \"BFO\" [label=\"sub_property_of (2)\"];\n\"IAO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"IAO\" -> \"EFO\" [label=\"inverse_of (1)\"];\n\"IAO\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"IAO\" -> \"IAO\" [label=\"INVERTED:type (3)\"];\n\"IAO\" -> \"IAO\" [label=\"sub_property_of (1)\"];\n\"IAO\" -> \"IAO\" [label=\"subclass_of (30)\"];\n\"IAO\" -> \"IAO\" [label=\"type (22)\"];\n\"IAO\" -> \"OBO\" [label=\"inverse_of (1)\"];\n\"IAO\" -> \"OIO\" [label=\"type (1)\"];\n\"ICD10\" -> \"ICD10\" [label=\"subclass_of (98417)\"];\n\"ICD10\" -> \"MONDO\" [label=\"equivalent_to (1113)\"];\n\"ICD10\" -> \"UMLS\" [label=\"xref (109975)\"];\n\"ICD10PCS\" -> \"ICD10PCS\" [label=\"subclass_of (189482)\"];\n\"ICD10PCS\" -> \"UMLS\" [label=\"xref (189499)\"];\n\"ICD9\" -> \"ICD9\" [label=\"subclass_of (22402)\"];\n\"ICD9\" -> \"MONDO\" [label=\"equivalent_to (1883)\"];\n\"ICD9\" -> \"UMLS\" [label=\"xref (22406)\"];\n\"ICO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"IDO\" -> \"BFO\" [label=\"subclass_of (9)\"];\n\"IDO\" -> \"CHEBI\" [label=\"subclass_of (1)\"];\n\"IDO\" -> \"IDO\" [label=\"subclass_of (20)\"];\n\"IDO\" -> \"OBI\" [label=\"subclass_of (3)\"];\n\"IDO\" -> \"OBO\" [label=\"INVERTED:has_participant (1)\"];\n\"IDO\" -> \"OGMS\" [label=\"subclass_of (1)\"];\n\"IDO\" -> \"OPL\" [label=\"INVERTED:realizes (2)\"];\n\"KEGG\" -> \"CHEBI\" [label=\"same_as (2516)\"];\n\"KEGG\" -> \"DRUGBANK\" [label=\"same_as (978)\"];\n\"KEGG\" -> \"HMDB\" [label=\"same_as (3308)\"];\n\"KEGG\" -> \"MONDO\" [label=\"equivalent_to (37)\"];\n\"KEGG\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (1701455)\"];\n\"KEGG\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (389)\"];\n\"KEGG\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (162)\"];\n\"KEGG\" -> \"UniProtKB\" [label=\"physically_interacts_with (22304)\"];\n\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_class (54220)\"];\n\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_component (119855)\"];\n\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_member (22838)\"];\n\"LOINC\" -> \"LOINC\" [label=\"INVERTED:has_subject (34)\"];\n\"LOINC\" -> \"LOINC\" [label=\"analyzes (72330)\"];\n\"LOINC\" -> \"LOINC\" [label=\"associated_with (1016)\"];\n\"LOINC\" -> \"LOINC\" [label=\"class_of (45064)\"];\n\"LOINC\" -> \"LOINC\" [label=\"component_of (126098)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_action_guidance (1149)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_adjustment (343)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_aggregation_view (3311)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_answer (85940)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_approach_guidance (347)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_archetype (1265)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_challenge (19562)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_count (148)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_divisor (5470)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_evaluation (10553)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_exam (454)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_fragments_for_synonyms (96184)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_imaged_location (6361)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_imaging_focus (5463)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_lateral_anatomic_location (3498)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_lateral_location_presence (3480)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_method (66244)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_modality_subtype (1083)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_modality_type (6030)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_object_guidance (474)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_parent_group (6515)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_pharmaceutical_route (1930)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_scale (87167)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_suffix (33614)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_supersystem (19700)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_system (129358)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_time_aspect (90380)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_time_modifier (197)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_timing_of (2693)\"];\n\"LOINC\" -> \"LOINC\" [label=\"has_view_type (1668)\"];\n\"LOINC\" -> \"LOINC\" [label=\"inverse_of_measures (79662)\"];\n\"LOINC\" -> \"LOINC\" [label=\"is_given_pharmaceutical_substance_for (2418)\"];\n\"LOINC\" -> \"LOINC\" [label=\"is_presence_guidance_for (1021)\"];\n\"LOINC\" -> \"LOINC\" [label=\"mapped_to (2900)\"];\n\"LOINC\" -> \"LOINC\" [label=\"member_of (22330)\"];\n\"LOINC\" -> \"LOINC\" [label=\"mth_has_expanded_form (1)\"];\n\"LOINC\" -> \"LOINC\" [label=\"multipart_of (21095)\"];\n\"LOINC\" -> \"LOINC\" [label=\"property_of (86472)\"];\n\"LOINC\" -> \"LOINC\" [label=\"subclass_of (250116)\"];\n\"LOINC\" -> \"UMLS\" [label=\"xref (260568)\"];\n\"MA\" -> \"FMA\" [label=\"xref (1)\"];\n\"MA\" -> \"UBERON\" [label=\"part_of (1)\"];\n\"MA\" -> \"UBERON\" [label=\"subclass_of (2)\"];\n\"MEDDRA\" -> \"MEDDRA\" [label=\"INVERTED:has_member (17338)\"];\n\"MEDDRA\" -> \"MEDDRA\" [label=\"classified_as (47649)\"];\n\"MEDDRA\" -> \"MEDDRA\" [label=\"member_of (52438)\"];\n\"MEDDRA\" -> \"MEDDRA\" [label=\"subclass_of (36911)\"];\n\"MEDDRA\" -> \"MONDO\" [label=\"equivalent_to (1)\"];\n\"MEDDRA\" -> \"UMLS\" [label=\"xref (73929)\"];\n\"MESH\" -> \"GENEPIO\" [label=\"subclass_of (5)\"];\n\"MESH\" -> \"MESH\" [label=\"INVERTED:inverse_of_isa (5029)\"];\n\"MESH\" -> \"MESH\" [label=\"INVERTED:inverse_of_ro (13058)\"];\n\"MESH\" -> \"MESH\" [label=\"has_mapping_qualifier (33615)\"];\n\"MESH\" -> \"MESH\" [label=\"isa (9514)\"];\n\"MESH\" -> \"MESH\" [label=\"mapped_to (376217)\"];\n\"MESH\" -> \"MESH\" [label=\"subclass_of (40243)\"];\n\"MESH\" -> \"MONDO\" [label=\"equivalent_to (7860)\"];\n\"MESH\" -> \"UMLS\" [label=\"xref (402615)\"];\n\"MF\" -> \"BFO\" [label=\"subclass_of (4)\"];\n\"MF\" -> \"MF\" [label=\"INVERTED:has_occurrent_part (1)\"];\n\"MF\" -> \"MF\" [label=\"INVERTED:has_participant_at_all_times (2)\"];\n\"MF\" -> \"MF\" [label=\"INVERTED:realizes (2)\"];\n\"MF\" -> \"MF\" [label=\"subclass_of (8)\"];\n\"MF\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_disruption_of (1)\"];\n\"MF\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (3)\"];\n\"MF\" -> \"OGMS\" [label=\"subclass_of (1)\"];\n\"MGI\" -> \"NCBITaxon\" [label=\"only_in_taxon (16846)\"];\n\"MGI\" -> \"PR\" [label=\"INVERTED:has_gene_template (16846)\"];\n\"MGI\" -> \"SO\" [label=\"subclass_of (16846)\"];\n\"MI\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"MI\" -> \"MI\" [label=\"subclass_of (101)\"];\n\"MI\" -> \"OBO\" [label=\"subclass_of (4)\"];\n\"MMO\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"MOD\" -> \"MOD\" [label=\"subclass_of (151)\"];\n\"MOD\" -> \"PR\" [label=\"INVERTED:has_part (5383)\"];\n\"MOD\" -> \"PR\" [label=\"subclass_of (41)\"];\n\"MONDO\" -> \"BFO\" [label=\"subclass_of (3)\"];\n\"MONDO\" -> \"CHEBI\" [label=\"disease_has_basis_in_accumulation_of (1)\"];\n\"MONDO\" -> \"CL\" [label=\"disease_causes_dysfunction_of (4)\"];\n\"MONDO\" -> \"CL\" [label=\"disease_has_inflammation_site (1)\"];\n\"MONDO\" -> \"CL\" [label=\"disease_has_location (49)\"];\n\"MONDO\" -> \"DOID\" [label=\"equivalent_to (9000)\"];\n\"MONDO\" -> \"DOID\" [label=\"subclass_of (1)\"];\n\"MONDO\" -> \"DOID\" [label=\"xref (9027)\"];\n\"MONDO\" -> \"EFO\" [label=\"disease_causes_feature (2)\"];\n\"MONDO\" -> \"EFO\" [label=\"disease_has_basis_in_feature (23)\"];\n\"MONDO\" -> \"EFO\" [label=\"disease_has_feature (15)\"];\n\"MONDO\" -> \"EFO\" [label=\"disease_has_major_feature (6)\"];\n\"MONDO\" -> \"EFO\" [label=\"disease_shares_features_of (1)\"];\n\"MONDO\" -> \"EFO\" [label=\"equivalent_to (2850)\"];\n\"MONDO\" -> \"EFO\" [label=\"predisposes_towards (14)\"];\n\"MONDO\" -> \"EFO\" [label=\"subclass_of (1906)\"];\n\"MONDO\" -> \"EFO\" [label=\"xref (2857)\"];\n\"MONDO\" -> \"GARD\" [label=\"equivalent_to (5814)\"];\n\"MONDO\" -> \"GARD\" [label=\"xref (5818)\"];\n\"MONDO\" -> \"GO\" [label=\"disease_causes_disruption_of (93)\"];\n\"MONDO\" -> \"GO\" [label=\"disease_has_location (5)\"];\n\"MONDO\" -> \"GO\" [label=\"disease_triggers (2)\"];\n\"MONDO\" -> \"GO\" [label=\"realized_in (9)\"];\n\"MONDO\" -> \"HGNC\" [label=\"has_material_basis_in_gain_of_function_germline_mutation_in (6)\"];\n\"MONDO\" -> \"HGNC\" [label=\"xref (56)\"];\n\"MONDO\" -> \"HP\" [label=\"disease_causes_feature (5)\"];\n\"MONDO\" -> \"HP\" [label=\"disease_has_basis_in_feature (42)\"];\n\"MONDO\" -> \"HP\" [label=\"disease_has_feature (709)\"];\n\"MONDO\" -> \"HP\" [label=\"disease_has_major_feature (100)\"];\n\"MONDO\" -> \"HP\" [label=\"equivalent_to (5)\"];\n\"MONDO\" -> \"HP\" [label=\"has_modifier (140)\"];\n\"MONDO\" -> \"HP\" [label=\"subclass_of (1)\"];\n\"MONDO\" -> \"HP\" [label=\"xref (565)\"];\n\"MONDO\" -> \"ICD10\" [label=\"equivalent_to (1113)\"];\n\"MONDO\" -> \"ICD10\" [label=\"xref (11520)\"];\n\"MONDO\" -> \"ICD9\" [label=\"equivalent_to (1883)\"];\n\"MONDO\" -> \"ICD9\" [label=\"xref (5741)\"];\n\"MONDO\" -> \"KEGG\" [label=\"equivalent_to (37)\"];\n\"MONDO\" -> \"KEGG\" [label=\"xref (37)\"];\n\"MONDO\" -> \"LOINC\" [label=\"xref (1)\"];\n\"MONDO\" -> \"MEDDRA\" [label=\"equivalent_to (1)\"];\n\"MONDO\" -> \"MEDDRA\" [label=\"xref (3)\"];\n\"MONDO\" -> \"MESH\" [label=\"equivalent_to (7860)\"];\n\"MONDO\" -> \"MESH\" [label=\"xref (7875)\"];\n\"MONDO\" -> \"MF\" [label=\"disease_causes_disruption_of (3)\"];\n\"MONDO\" -> \"MFOEM\" [label=\"disease_causes_disruption_of (1)\"];\n\"MONDO\" -> \"MFOMD\" [label=\"realized_in (6)\"];\n\"MONDO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (2)\"];\n\"MONDO\" -> \"MONDO\" [label=\"disease_causes_feature (7)\"];\n\"MONDO\" -> \"MONDO\" [label=\"disease_has_basis_in_feature (68)\"];\n\"MONDO\" -> \"MONDO\" [label=\"disease_has_feature (298)\"];\n\"MONDO\" -> \"MONDO\" [label=\"disease_has_major_feature (14)\"];\n\"MONDO\" -> \"MONDO\" [label=\"disease_shares_features_of (49)\"];\n\"MONDO\" -> \"MONDO\" [label=\"has_modifier (867)\"];\n\"MONDO\" -> \"MONDO\" [label=\"intersection_of (1)\"];\n\"MONDO\" -> \"MONDO\" [label=\"part_of_progression_of_disease (2)\"];\n\"MONDO\" -> \"MONDO\" [label=\"predisposes_towards (143)\"];\n\"MONDO\" -> \"MONDO\" [label=\"subclass_of (38341)\"];\n\"MONDO\" -> \"MONDO\" [label=\"xref (12)\"];\n\"MONDO\" -> \"NBO\" [label=\"disease_causes_disruption_of (4)\"];\n\"MONDO\" -> \"NBO\" [label=\"realized_in (1)\"];\n\"MONDO\" -> \"NCBITaxon\" [label=\"in_taxon (1)\"];\n\"MONDO\" -> \"NCBITaxon\" [label=\"transmitted_by (74)\"];\n\"MONDO\" -> \"NCIT\" [label=\"disease_has_feature (18)\"];\n\"MONDO\" -> \"NCIT\" [label=\"equivalent_to (6777)\"];\n\"MONDO\" -> \"NCIT\" [label=\"has_modifier (2)\"];\n\"MONDO\" -> \"NCIT\" [label=\"realized_in (2)\"];\n\"MONDO\" -> \"NCIT\" [label=\"xref (6793)\"];\n\"MONDO\" -> \"OBA\" [label=\"disease_has_feature (1)\"];\n\"MONDO\" -> \"OBI\" [label=\"equivalent_to (1)\"];\n\"MONDO\" -> \"OBI\" [label=\"xref (1)\"];\n\"MONDO\" -> \"OBO\" [label=\"equivalent_to (154)\"];\n\"MONDO\" -> \"OGMS\" [label=\"equivalent_to (1)\"];\n\"MONDO\" -> \"OGMS\" [label=\"xref (1)\"];\n\"MONDO\" -> \"OMIM\" [label=\"equivalent_to (8717)\"];\n\"MONDO\" -> \"OMIM\" [label=\"xref (8869)\"];\n\"MONDO\" -> \"OMIMPS\" [label=\"equivalent_to (472)\"];\n\"MONDO\" -> \"OMIMPS\" [label=\"xref (477)\"];\n\"MONDO\" -> \"OMOP\" [label=\"equivalent_to (1590)\"];\n\"MONDO\" -> \"ORPHANET\" [label=\"disease_has_feature (1)\"];\n\"MONDO\" -> \"ORPHANET\" [label=\"disease_shares_features_of (1)\"];\n\"MONDO\" -> \"ORPHANET\" [label=\"equivalent_to (9149)\"];\n\"MONDO\" -> \"ORPHANET\" [label=\"predisposes_towards (4)\"];\n\"MONDO\" -> \"ORPHANET\" [label=\"subclass_of (669)\"];\n\"MONDO\" -> \"OncoTree\" [label=\"equivalent_to (556)\"];\n\"MONDO\" -> \"PATO\" [label=\"has_modifier (78)\"];\n\"MONDO\" -> \"PATO\" [label=\"subclass_of (1)\"];\n\"MONDO\" -> \"PATO\" [label=\"xref (1)\"];\n\"MONDO\" -> \"RO\" [label=\"sub_property_of (1)\"];\n\"MONDO\" -> \"SNOMED\" [label=\"equivalent_to (9000)\"];\n\"MONDO\" -> \"SO\" [label=\"has_modifier (22)\"];\n\"MONDO\" -> \"UBERON\" [label=\"disease_causes_dysfunction_of (2)\"];\n\"MONDO\" -> \"UBERON\" [label=\"disease_has_basis_in_development_of (2)\"];\n\"MONDO\" -> \"UBERON\" [label=\"disease_has_inflammation_site (163)\"];\n\"MONDO\" -> \"UBERON\" [label=\"disease_has_location (793)\"];\n\"MONDO\" -> \"UBERON\" [label=\"has_modifier (1)\"];\n\"MONDO\" -> \"UMLS\" [label=\"equivalent_to (14023)\"];\n\"MONDO\" -> \"UMLS\" [label=\"subclass_of (1)\"];\n\"MONDO\" -> \"UMLS\" [label=\"xref (14056)\"];\n\"MONDO\" -> \"WD\" [label=\"equivalent_to (2)\"];\n\"MONDO\" -> \"medgen\" [label=\"equivalent_to (2582)\"];\n\"MP\" -> \"DOID\" [label=\"xref (1)\"];\n\"MP\" -> \"HP\" [label=\"subclass_of (2)\"];\n\"MP\" -> \"ICD10\" [label=\"xref (2)\"];\n\"MP\" -> \"ICD9\" [label=\"xref (1)\"];\n\"MPATH\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"MPATH\" -> \"MPATH\" [label=\"subclass_of (83)\"];\n\"NBO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"NBO\" -> \"GO\" [label=\"is_about (8)\"];\n\"NBO\" -> \"GO\" [label=\"part_of (2)\"];\n\"NBO\" -> \"GO\" [label=\"subclass_of (14)\"];\n\"NBO\" -> \"GO\" [label=\"xref (15)\"];\n\"NBO\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_disruption_of (1)\"];\n\"NBO\" -> \"NBO\" [label=\"INVERTED:by_means (2)\"];\n\"NBO\" -> \"NBO\" [label=\"INVERTED:in_response_to (5)\"];\n\"NBO\" -> \"NBO\" [label=\"is_about (7)\"];\n\"NBO\" -> \"NBO\" [label=\"part_of (1)\"];\n\"NBO\" -> \"NBO\" [label=\"regulates (16)\"];\n\"NBO\" -> \"NBO\" [label=\"subclass_of (985)\"];\n\"NBO\" -> \"PATO\" [label=\"is_about (5)\"];\n\"NBO\" -> \"PATO\" [label=\"subclass_of (1)\"];\n\"NBO\" -> \"UBERON\" [label=\"INVERTED:input_of (1)\"];\n\"NBO\" -> \"UBERON\" [label=\"INVERTED:output_of (1)\"];\n\"NCBIGene\" -> \"CL\" [label=\"expressed_in (20)\"];\n\"NCBIGene\" -> \"DOID\" [label=\"associated_with_disease (110)\"];\n\"NCBIGene\" -> \"ENSEMBL\" [label=\"same_as (35031)\"];\n\"NCBIGene\" -> \"GO\" [label=\"involved_in (1417)\"];\n\"NCBIGene\" -> \"HGNC\" [label=\"same_as (40970)\"];\n\"NCBIGene\" -> \"HP\" [label=\"has_phenotype (60)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"coexists_with (20358)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"compared_with (7200)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"converts_to (290)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"inhibits (18289)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"interacts_with (33756)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"part_of (128)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"produces (3596)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"regulates_expression_of (3812)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"same_as (142)\"];\n\"NCBIGene\" -> \"NCBIGene\" [label=\"stimulates (20660)\"];\n\"NCBIGene\" -> \"NCBITaxon\" [label=\"in_taxon (61530)\"];\n\"NCBIGene\" -> \"NCBITaxon\" [label=\"only_in_taxon (5380)\"];\n\"NCBIGene\" -> \"OMIM\" [label=\"associated_with_disease (25)\"];\n\"NCBIGene\" -> \"OMIM\" [label=\"gene_mutations_contribute_to (4)\"];\n\"NCBIGene\" -> \"OMIM\" [label=\"same_as (17550)\"];\n\"NCBIGene\" -> \"PR\" [label=\"INVERTED:has_gene_template (5701)\"];\n\"NCBIGene\" -> \"SO\" [label=\"subclass_of (5380)\"];\n\"NCBIGene\" -> \"UBERON\" [label=\"expressed_in (1414)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"INVERTED:location_of (332757)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"administered_to (9523)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"affects (154949)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"associated_with (132056)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"augments (69744)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"causes (56542)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"coexists_with (77418)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"compared_with (26838)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"complicates (585)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"converts_to (2870)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"diagnoses (6)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"disrupts (64071)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"inhibits (68254)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"interacts_with (183359)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"part_of (119404)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"predisposes (23510)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"prevents (7331)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"produces (25911)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"same_as (617)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"stimulates (110058)\"];\n\"NCBIGene\" -> \"UMLS\" [label=\"treats (1364)\"];\n\"NCBIGene\" -> \"UniProtKB\" [label=\"has_gene_product (19230)\"];\n\"NCBIGene\" -> \"UniProtKB\" [label=\"regulates_expression_of (332256)\"];\n\"NCBITaxon\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"NCBITaxon\" -> \"DOID\" [label=\"INVERTED:has_allergic_trigger (15)\"];\n\"NCBITaxon\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (300)\"];\n\"NCBITaxon\" -> \"DOID\" [label=\"INVERTED:has_participant (2)\"];\n\"NCBITaxon\" -> \"EFO\" [label=\"INVERTED:has_member (1)\"];\n\"NCBITaxon\" -> \"EFO\" [label=\"INVERTED:has_participant (16)\"];\n\"NCBITaxon\" -> \"EFO\" [label=\"part_of (1)\"];\n\"NCBITaxon\" -> \"EFO\" [label=\"subclass_of (4)\"];\n\"NCBITaxon\" -> \"ENVO\" [label=\"INVERTED:composed_primarily_of (1)\"];\n\"NCBITaxon\" -> \"ENVO\" [label=\"INVERTED:determined_by (3)\"];\n\"NCBITaxon\" -> \"ENVO\" [label=\"INVERTED:process_has_causal_agent (3)\"];\n\"NCBITaxon\" -> \"EO\" [label=\"subclass_of (3)\"];\n\"NCBITaxon\" -> \"ICD9\" [label=\"xref (7)\"];\n\"NCBITaxon\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (1)\"];\n\"NCBITaxon\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (482)\"];\n\"NCBITaxon\" -> \"NCBITaxon\" [label=\"subclass_of (1783396)\"];\n\"NCBITaxon\" -> \"OBI\" [label=\"subclass_of (16)\"];\n\"NCBITaxon\" -> \"OBO\" [label=\"subclass_of (27)\"];\n\"NCBITaxon\" -> \"PATO\" [label=\"has_quality (1)\"];\n\"NCBITaxon\" -> \"UMLS\" [label=\"xref (1776528)\"];\n\"NCIT\" -> \"ARO\" [label=\"subclass_of (2)\"];\n\"NCIT\" -> \"BFO\" [label=\"subclass_of (7)\"];\n\"NCIT\" -> \"CHEBI\" [label=\"subclass_of (7)\"];\n\"NCIT\" -> \"DOID\" [label=\"subclass_of (1)\"];\n\"NCIT\" -> \"EFO\" [label=\"subclass_of (3)\"];\n\"NCIT\" -> \"ENVO\" [label=\"subclass_of (6)\"];\n\"NCIT\" -> \"ExO\" [label=\"subclass_of (2)\"];\n\"NCIT\" -> \"FOODON\" [label=\"subclass_of (4)\"];\n\"NCIT\" -> \"GENEPIO\" [label=\"INVERTED:contains_process (1)\"];\n\"NCIT\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (4)\"];\n\"NCIT\" -> \"GENEPIO\" [label=\"before (1)\"];\n\"NCIT\" -> \"GENEPIO\" [label=\"subclass_of (38)\"];\n\"NCIT\" -> \"GO\" [label=\"subclass_of (1)\"];\n\"NCIT\" -> \"IAO\" [label=\"subclass_of (7)\"];\n\"NCIT\" -> \"ICO\" [label=\"is_about (1)\"];\n\"NCIT\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to (1)\"];\n\"NCIT\" -> \"MONDO\" [label=\"equivalent_to (6777)\"];\n\"NCIT\" -> \"NCBITaxon\" [label=\"in_taxon (2)\"];\n\"NCIT\" -> \"NCBITaxon\" [label=\"subclass_of (1)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:biological_process_involves_chemical_or_drug (18)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:cdrh_parent_of (666)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:complex_has_physical_part (616)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:ctcae_5_parent_of (1721)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:disease_has_finding (36775)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:disease_has_molecular_abnormality (294)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:disease_is_marked_by_gene (8)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:gene_product_sequence_variation_encoded_by_gene_mutant (556)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:has_salt_form (1829)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:is_cytogenetic_abnormality_of_disease (326)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:is_normal_cell_origin_of_disease (18809)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:is_organism_source_of_gene_product (532)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:may_be_normal_cell_origin_of_disease (183)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:organism_has_gene (1635)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:pathway_has_gene_element (7181)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:process_includes_biological_process (642)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:process_involves_gene (25114)\"];\n\"NCIT\" -> \"NCIT\" [label=\"INVERTED:subset_includes_concept (230272)\"];\n\"NCIT\" -> \"NCIT\" [label=\"allele_absent_from_wild_type_chromosomal_location (1)\"];\n\"NCIT\" -> \"NCIT\" [label=\"allele_has_abnormality (180)\"];\n\"NCIT\" -> \"NCIT\" [label=\"allele_has_activity (74)\"];\n\"NCIT\" -> \"NCIT\" [label=\"allele_in_chromosomal_location (104)\"];\n\"NCIT\" -> \"NCIT\" [label=\"allele_plays_altered_role_in_process (128)\"];\n\"NCIT\" -> \"NCIT\" [label=\"allele_plays_role_in_metabolism_of_chemical_or_drug (3)\"];\n\"NCIT\" -> \"NCIT\" [label=\"anatomic_structure_is_physical_part_of (9339)\"];\n\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_associated_location (545)\"];\n\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_result_anatomy (63)\"];\n\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_result_biological_process (91)\"];\n\"NCIT\" -> \"NCIT\" [label=\"biological_process_has_result_chemical_or_drug (32)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_affects_abnormal_cell (28)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_affects_cell_type_or_tissue (572)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_affects_gene_product (378)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_has_mechanism_of_action (2274)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_has_physiologic_effect (2053)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chemical_or_drug_initiates_biological_process (113)\"];\n\"NCIT\" -> \"NCIT\" [label=\"chromosome_mapped_to_disease (189)\"];\n\"NCIT\" -> \"NCIT\" [label=\"conceptual_part_of (3585)\"];\n\"NCIT\" -> \"NCIT\" [label=\"cytogenetic_abnormality_involves_chromosome (684)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_has_associated_anatomic_site (30160)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_has_metastatic_anatomic_site (140)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_has_normal_tissue_origin (19638)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_has_primary_anatomic_site (11480)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_is_grade (1303)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_is_stage (6155)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_abnormal_cell (1194)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_associated_disease (1935)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_finding (16831)\"];\n\"NCIT\" -> \"NCIT\" [label=\"disease_may_have_molecular_abnormality (9292)\"];\n\"NCIT\" -> \"NCIT\" [label=\"enzyme_metabolizes_chemical_or_drug (636)\"];\n\"NCIT\" -> \"NCIT\" [label=\"eo_disease_has_associated_cell_type (13)\"];\n\"NCIT\" -> \"NCIT\" [label=\"eo_disease_has_associated_eo_anatomy (3128)\"];\n\"NCIT\" -> \"NCIT\" [label=\"eo_disease_has_property_or_attribute (277)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_associated_with_disease (2175)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_encodes_gene_product (18713)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_found_in_organism (1840)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_has_physical_location (989)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_in_chromosomal_location (3906)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_involved_in_molecular_abnormality (2464)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_involved_in_pathogenesis_of_disease (1115)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_is_biomarker_of (18)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_is_biomarker_type (39)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_is_element_in_pathway (6246)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_mapped_to_disease (5189)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_mutant_encodes_gene_product_sequence_variation (809)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_plays_role_in_process (13660)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_expressed_in_tissue (1594)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_abnormality (24)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_associated_anatomy (5253)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_biochemical_function (4865)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_chemical_classification (1688)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_organism_source (825)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_has_structural_domain_or_motif (4960)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_biomarker_of (32)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_biomarker_type (337)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_element_in_pathway (13536)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_is_physical_part_of (616)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_malfunction_associated_with_disease (509)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_plays_role_in_biological_process (21782)\"];\n\"NCIT\" -> \"NCIT\" [label=\"gene_product_variant_of_gene_product (457)\"];\n\"NCIT\" -> \"NCIT\" [label=\"genetic_biomarker_related_to (2607)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_data_element (10)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_inc_parent (116)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_nichd_parent (4081)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_administration_method (542)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_basic_dose_form (597)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_intended_site (529)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_release_characteristics (502)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_state_of_matter (620)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_pharmaceutical_transformation (520)\"];\n\"NCIT\" -> \"NCIT\" [label=\"has_target (727)\"];\n\"NCIT\" -> \"NCIT\" [label=\"human_disease_maps_to_eo_disease (1829)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_abnormal_cell_of_disease (49398)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_associated_disease_of (1027)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_component_of_chemotherapy_regimen (11836)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_location_of_anatomic_structure (356)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_molecular_abnormality_of_disease (1195)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_qualified_by (1)\"];\n\"NCIT\" -> \"NCIT\" [label=\"is_related_to_endogenous_product (23)\"];\n\"NCIT\" -> \"NCIT\" [label=\"neoplasm_has_special_category (105)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_has_completely_excised_anatomy (95)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_has_excised_anatomy (401)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_has_imaged_anatomy (1)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_has_partially_excised_anatomy (194)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_has_target_anatomy (916)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_may_have_completely_excised_anatomy (6)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_may_have_excised_anatomy (8)\"];\n\"NCIT\" -> \"NCIT\" [label=\"procedure_may_have_partially_excised_anatomy (9)\"];\n\"NCIT\" -> \"NCIT\" [label=\"process_initiates_biological_process (132)\"];\n\"NCIT\" -> \"NCIT\" [label=\"qualifier_applies_to (1)\"];\n\"NCIT\" -> \"NCIT\" [label=\"regimen_has_accepted_use_for_disease (395)\"];\n\"NCIT\" -> \"NCIT\" [label=\"role_has_domain (83)\"];\n\"NCIT\" -> \"NCIT\" [label=\"role_has_parent (11)\"];\n\"NCIT\" -> \"NCIT\" [label=\"role_has_range (97)\"];\n\"NCIT\" -> \"NCIT\" [label=\"subclass_of (160929)\"];\n\"NCIT\" -> \"OBI\" [label=\"subclass_of (13)\"];\n\"NCIT\" -> \"OMIT\" [label=\"subclass_of (1)\"];\n\"NCIT\" -> \"PATO\" [label=\"subclass_of (3)\"];\n\"NCIT\" -> \"PCO\" [label=\"subclass_of (2)\"];\n\"NCIT\" -> \"SIO\" [label=\"subclass_of (4)\"];\n\"NCIT\" -> \"UBERON\" [label=\"subclass_of (2)\"];\n\"NCIT\" -> \"UMLS\" [label=\"xref (165880)\"];\n\"NCIT\" -> \"UO\" [label=\"subclass_of (2)\"];\n\"NCIT\" -> \"VCARD\" [label=\"subclass_of (1)\"];\n\"NCRO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"NDDF\" -> \"NDDF\" [label=\"INVERTED:has_ingredient (24)\"];\n\"NDDF\" -> \"NDDF\" [label=\"has_dose_form (17997)\"];\n\"NDDF\" -> \"NDDF\" [label=\"ingredient_of (12)\"];\n\"NDDF\" -> \"UMLS\" [label=\"xref (33096)\"];\n\"NPO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"NPO\" -> \"NPO\" [label=\"subclass_of (3)\"];\n\"OAE\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"OBA\" -> \"OBA\" [label=\"subclass_of (173)\"];\n\"OBA\" -> \"PATO\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"BFO\" [label=\"sub_property_of (2)\"];\n\"OBI\" -> \"BFO\" [label=\"subclass_of (18)\"];\n\"OBI\" -> \"BTO\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"BTO\" [label=\"xref (1)\"];\n\"OBI\" -> \"CHEBI\" [label=\"subclass_of (2)\"];\n\"OBI\" -> \"EDAM\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"EFO\" [label=\"INVERTED:has_input (2)\"];\n\"OBI\" -> \"EFO\" [label=\"INVERTED:has_participant (1)\"];\n\"OBI\" -> \"EFO\" [label=\"part_of (2)\"];\n\"OBI\" -> \"EFO\" [label=\"subclass_of (39)\"];\n\"OBI\" -> \"ERO\" [label=\"subclass_of (3)\"];\n\"OBI\" -> \"GENEPIO\" [label=\"INVERTED:produced_by (1)\"];\n\"OBI\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (7)\"];\n\"OBI\" -> \"GENEPIO\" [label=\"aligned_with (1)\"];\n\"OBI\" -> \"GENEPIO\" [label=\"derives_from (1)\"];\n\"OBI\" -> \"GENEPIO\" [label=\"member_of (2)\"];\n\"OBI\" -> \"GENEPIO\" [label=\"subclass_of (22)\"];\n\"OBI\" -> \"GO\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"IAO\" [label=\"sub_property_of (1)\"];\n\"OBI\" -> \"IAO\" [label=\"subclass_of (35)\"];\n\"OBI\" -> \"MONDO\" [label=\"equivalent_to (1)\"];\n\"OBI\" -> \"NCIT\" [label=\"inheres_in (1)\"];\n\"OBI\" -> \"NCIT\" [label=\"subclass_of (3)\"];\n\"OBI\" -> \"OBI\" [label=\"inheres_in (3)\"];\n\"OBI\" -> \"OBI\" [label=\"inverse_of (2)\"];\n\"OBI\" -> \"OBI\" [label=\"is_about (1)\"];\n\"OBI\" -> \"OBI\" [label=\"subclass_of (105)\"];\n\"OBI\" -> \"OBI\" [label=\"type (6)\"];\n\"OBI\" -> \"OGMS\" [label=\"subclass_of (2)\"];\n\"OBI\" -> \"PR\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"RO\" [label=\"sub_property_of (7)\"];\n\"OBI\" -> \"SIO\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"STATO\" [label=\"is_about (1)\"];\n\"OBI\" -> \"STATO\" [label=\"subclass_of (1)\"];\n\"OBI\" -> \"UBERON\" [label=\"INVERTED:produced_by (1)\"];\n\"OBO\" -> \"BFO\" [label=\"subclass_of (11)\"];\n\"OBO\" -> \"CARO\" [label=\"subclass_of (1)\"];\n\"OBO\" -> \"CHEBI\" [label=\"subclass_of (5)\"];\n\"OBO\" -> \"CL\" [label=\"INVERTED:has_part (3)\"];\n\"OBO\" -> \"EFO\" [label=\"subclass_of (7)\"];\n\"OBO\" -> \"FMA\" [label=\"xref (1)\"];\n\"OBO\" -> \"FOODON\" [label=\"subclass_of (2)\"];\n\"OBO\" -> \"GENEPIO\" [label=\"is_about (1)\"];\n\"OBO\" -> \"GENEPIO\" [label=\"subclass_of (3)\"];\n\"OBO\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (20)\"];\n\"OBO\" -> \"GO\" [label=\"causally_upstream_of (1)\"];\n\"OBO\" -> \"GO\" [label=\"subclass_of (5)\"];\n\"OBO\" -> \"IAO\" [label=\"subclass_of (9)\"];\n\"OBO\" -> \"IDO\" [label=\"has_role (1)\"];\n\"OBO\" -> \"IDO\" [label=\"subclass_of (1)\"];\n\"OBO\" -> \"MI\" [label=\"subclass_of (15)\"];\n\"OBO\" -> \"MONDO\" [label=\"equivalent_to (154)\"];\n\"OBO\" -> \"NCBITaxon\" [label=\"only_in_taxon (1013)\"];\n\"OBO\" -> \"OBI\" [label=\"is_about (1)\"];\n\"OBO\" -> \"OBI\" [label=\"subclass_of (4)\"];\n\"OBO\" -> \"OBO\" [label=\"INVERTED:has_part (1)\"];\n\"OBO\" -> \"OBO\" [label=\"INVERTED:has_participant (1)\"];\n\"OBO\" -> \"OBO\" [label=\"existence_starts_during (1)\"];\n\"OBO\" -> \"OBO\" [label=\"has_interaction_type (1)\"];\n\"OBO\" -> \"OBO\" [label=\"immediately_preceded_by (5)\"];\n\"OBO\" -> \"OBO\" [label=\"negatively_regulates (1)\"];\n\"OBO\" -> \"OBO\" [label=\"part_of (14)\"];\n\"OBO\" -> \"OBO\" [label=\"positively_regulates (1)\"];\n\"OBO\" -> \"OBO\" [label=\"realized_in (1)\"];\n\"OBO\" -> \"OBO\" [label=\"regulates (2)\"];\n\"OBO\" -> \"OBO\" [label=\"subclass_of (286)\"];\n\"OBO\" -> \"OBOREL\" [label=\"inverse_of (1)\"];\n\"OBO\" -> \"OBOREL\" [label=\"sub_property_of (1)\"];\n\"OBO\" -> \"OGG\" [label=\"has_input (1)\"];\n\"OBO\" -> \"OGMS\" [label=\"is_about (1)\"];\n\"OBO\" -> \"OIO\" [label=\"subclass_of (5)\"];\n\"OBO\" -> \"PATO\" [label=\"bearer_of (1)\"];\n\"OBO\" -> \"PCO\" [label=\"subclass_of (1)\"];\n\"OBO\" -> \"PR\" [label=\"INVERTED:has_gene_template (1013)\"];\n\"OBO\" -> \"SIO\" [label=\"subclass_of (1)\"];\n\"OBO\" -> \"SO\" [label=\"subclass_of (1013)\"];\n\"OBO\" -> \"STATO\" [label=\"subclass_of (8)\"];\n\"OBO\" -> \"UBERON\" [label=\"xref (6)\"];\n\"OBOREL\" -> \"RO\" [label=\"sub_property_of (1)\"];\n\"OGG\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"OGMS\" -> \"BFO\" [label=\"subclass_of (4)\"];\n\"OGMS\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"OGMS\" -> \"GO\" [label=\"subclass_of (1)\"];\n\"OGMS\" -> \"MONDO\" [label=\"equivalent_to (1)\"];\n\"OGMS\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"OGMS\" -> \"OGMS\" [label=\"INVERTED:has_participant_at_all_times (1)\"];\n\"OGMS\" -> \"UBERON\" [label=\"subclass_of (1)\"];\n\"OIO\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"OMIABIS\" -> \"OGMS\" [label=\"subclass_of (1)\"];\n\"OMIM\" -> \"DOID\" [label=\"contributes_to_condition (181)\"];\n\"OMIM\" -> \"HP\" [label=\"has_phenotype (94807)\"];\n\"OMIM\" -> \"MONDO\" [label=\"equivalent_to (8717)\"];\n\"OMIM\" -> \"OMIM\" [label=\"INVERTED:has_manifestation (121769)\"];\n\"OMIM\" -> \"OMIM\" [label=\"INVERTED:phenotype_of (13865)\"];\n\"OMIM\" -> \"OMIM\" [label=\"allelic_variant_of (29202)\"];\n\"OMIM\" -> \"OMIM\" [label=\"has_inheritance_type (6005)\"];\n\"OMIM\" -> \"OMIM\" [label=\"has_phenotype (15337)\"];\n\"OMIM\" -> \"OMIM\" [label=\"manifestation_of (121769)\"];\n\"OMIM\" -> \"OMIM\" [label=\"subclass_of (59497)\"];\n\"OMIM\" -> \"UMLS\" [label=\"xref (123280)\"];\n\"OMIMPS\" -> \"MONDO\" [label=\"equivalent_to (472)\"];\n\"OMIT\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"OMIT\" -> \"CHEBI\" [label=\"subclass_of (3)\"];\n\"OMIT\" -> \"GENEPIO\" [label=\"subclass_of (6)\"];\n\"OMIT\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"OMIT\" -> \"NCIT\" [label=\"subclass_of (2)\"];\n\"OMIT\" -> \"OBI\" [label=\"subclass_of (2)\"];\n\"OMIT\" -> \"OMIT\" [label=\"subclass_of (7)\"];\n\"OMIT\" -> \"PR\" [label=\"subclass_of (1)\"];\n\"OMOP\" -> \"MONDO\" [label=\"equivalent_to (1590)\"];\n\"OMP\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"OMP\" -> \"NCIT\" [label=\"is_about (1)\"];\n\"OMRSE\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"OPL\" -> \"BFO\" [label=\"subclass_of (3)\"];\n\"OPL\" -> \"BTO\" [label=\"subclass_of (1)\"];\n\"OPL\" -> \"CL\" [label=\"subclass_of (1)\"];\n\"OPL\" -> \"GO\" [label=\"INVERTED:ends_with (1)\"];\n\"OPL\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"OPL\" -> \"OPL\" [label=\"occurs_in (14)\"];\n\"OPL\" -> \"OPL\" [label=\"subclass_of (27)\"];\n\"OPL\" -> \"UBERON\" [label=\"subclass_of (8)\"];\n\"ORPHANET\" -> \"CL\" [label=\"has_disease_location (2)\"];\n\"ORPHANET\" -> \"DOID\" [label=\"xref (1579)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"disease_has_feature (24)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"disease_has_major_feature (1)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"has_disease_location (2)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"predisposes_towards (4)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"related_to (1)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"subclass_of (850)\"];\n\"ORPHANET\" -> \"EFO\" [label=\"xref (61)\"];\n\"ORPHANET\" -> \"GARD\" [label=\"xref (2968)\"];\n\"ORPHANET\" -> \"GO\" [label=\"has_disease_location (10)\"];\n\"ORPHANET\" -> \"GO\" [label=\"participates_in (3)\"];\n\"ORPHANET\" -> \"HGNC\" [label=\"xref (3982)\"];\n\"ORPHANET\" -> \"HP\" [label=\"xref (87)\"];\n\"ORPHANET\" -> \"ICD10\" [label=\"xref (5735)\"];\n\"ORPHANET\" -> \"ICD9\" [label=\"xref (920)\"];\n\"ORPHANET\" -> \"KEGG\" [label=\"xref (4)\"];\n\"ORPHANET\" -> \"MESH\" [label=\"xref (2518)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"disease_has_feature (25)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"disease_has_major_feature (1)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"disease_shares_features_of (1)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"equivalent_to (9149)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"has_modifier (257)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"predisposes_towards (1)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"subclass_of (3400)\"];\n\"ORPHANET\" -> \"MONDO\" [label=\"xref (5779)\"];\n\"ORPHANET\" -> \"NCIT\" [label=\"xref (1012)\"];\n\"ORPHANET\" -> \"OMIM\" [label=\"xref (12142)\"];\n\"ORPHANET\" -> \"OMIMPS\" [label=\"xref (300)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_has_basis_in_feature (2)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_has_feature (25)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_has_major_feature (3)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"disease_shares_features_of (11)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317343 (4581)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317344 (176)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317345 (496)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317346 (38)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317348 (227)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:317349 (229)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:327767 (309)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:410295 (1091)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:410296 (196)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:465410 (44)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:c016 (6366)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"orphanet:c017 (9706)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"part_of (14694)\"];\n\"ORPHANET\" -> \"ORPHANET\" [label=\"subclass_of (25409)\"];\n\"ORPHANET\" -> \"PR\" [label=\"has_disease_location (1)\"];\n\"ORPHANET\" -> \"UBERON\" [label=\"has_disease_location (65)\"];\n\"ORPHANET\" -> \"UMLS\" [label=\"xref (6226)\"];\n\"OncoTree\" -> \"MONDO\" [label=\"equivalent_to (556)\"];\n\"PATO\" -> \"BFO\" [label=\"subclass_of (13)\"];\n\"PATO\" -> \"CARO\" [label=\"xref (2)\"];\n\"PATO\" -> \"DOID\" [label=\"xref (1)\"];\n\"PATO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (1)\"];\n\"PATO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"PATO\" -> \"GO\" [label=\"xref (1)\"];\n\"PATO\" -> \"NBO\" [label=\"INVERTED:has_participant (1)\"];\n\"PATO\" -> \"NBO\" [label=\"INVERTED:in_response_to (3)\"];\n\"PATO\" -> \"PATO\" [label=\"INVERTED:has_part (9)\"];\n\"PATO\" -> \"PATO\" [label=\"INVERTED:towards (6)\"];\n\"PATO\" -> \"PATO\" [label=\"correlates_with (1)\"];\n\"PATO\" -> \"PATO\" [label=\"decreased_in_magnitude_relative_to (2)\"];\n\"PATO\" -> \"PATO\" [label=\"has_cross_section (5)\"];\n\"PATO\" -> \"PATO\" [label=\"has_relative_magnitude (7)\"];\n\"PATO\" -> \"PATO\" [label=\"increased_in_magnitude_relative_to (4)\"];\n\"PATO\" -> \"PATO\" [label=\"reciprocal_of (8)\"];\n\"PATO\" -> \"PATO\" [label=\"sub_property_of (4)\"];\n\"PATO\" -> \"PATO\" [label=\"subclass_of (2113)\"];\n\"PCO\" -> \"BFO\" [label=\"subclass_of (3)\"];\n\"PCO\" -> \"ENVO\" [label=\"INVERTED:determined_by (3)\"];\n\"PCO\" -> \"ENVO\" [label=\"INVERTED:has_part (1)\"];\n\"PCO\" -> \"ENVO\" [label=\"has_habitat (1)\"];\n\"PCO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"PCO\" -> \"PCO\" [label=\"subclass_of (10)\"];\n\"PDQ\" -> \"PDQ\" [label=\"INVERTED:has_component (4862)\"];\n\"PDQ\" -> \"PDQ\" [label=\"associated_disease (243)\"];\n\"PDQ\" -> \"PDQ\" [label=\"component_of (5952)\"];\n\"PDQ\" -> \"PDQ\" [label=\"subclass_of (4291)\"];\n\"PDQ\" -> \"UMLS\" [label=\"xref (18972)\"];\n\"PECO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"PECO\" -> \"PECO\" [label=\"subclass_of (8)\"];\n\"PO\" -> \"BFO\" [label=\"subclass_of (46)\"];\n\"PO\" -> \"CARO\" [label=\"subclass_of (2)\"];\n\"PO\" -> \"EFO\" [label=\"equivalent_to (1)\"];\n\"PO\" -> \"EFO\" [label=\"part_of (10)\"];\n\"PO\" -> \"EFO\" [label=\"subclass_of (30)\"];\n\"PO\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (1)\"];\n\"PO\" -> \"FOODON\" [label=\"INVERTED:has_part (1)\"];\n\"PO\" -> \"FOODON\" [label=\"subclass_of (2)\"];\n\"PO\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"PO\" -> \"GO\" [label=\"INVERTED:has_participant (4)\"];\n\"PO\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"];\n\"PO\" -> \"NCBITaxon\" [label=\"only_in_taxon (2)\"];\n\"PO\" -> \"PO\" [label=\"INVERTED:develops_from (60)\"];\n\"PO\" -> \"PO\" [label=\"INVERTED:has_part (9)\"];\n\"PO\" -> \"PO\" [label=\"INVERTED:has_participant (3)\"];\n\"PO\" -> \"PO\" [label=\"adjacent_to (1)\"];\n\"PO\" -> \"PO\" [label=\"located_in (3)\"];\n\"PO\" -> \"PO\" [label=\"part_of (132)\"];\n\"PO\" -> \"PO\" [label=\"participates_in (7)\"];\n\"PO\" -> \"PO\" [label=\"subclass_of (531)\"];\n\"PO\" -> \"PO\" [label=\"xref (1)\"];\n\"PR\" -> \"BFO\" [label=\"subclass_of (2)\"];\n\"PR\" -> \"CHEBI\" [label=\"derives_from (1)\"];\n\"PR\" -> \"CHEBI\" [label=\"equivalent_to (1)\"];\n\"PR\" -> \"CHEBI\" [label=\"non_covalently_bound_to (7)\"];\n\"PR\" -> \"CHEBI\" [label=\"subclass_of (206)\"];\n\"PR\" -> \"CL\" [label=\"INVERTED:has_part (675)\"];\n\"PR\" -> \"CL\" [label=\"part_of (4)\"];\n\"PR\" -> \"GO\" [label=\"INVERTED:has_part (2)\"];\n\"PR\" -> \"GO\" [label=\"INVERTED:has_participant (3)\"];\n\"PR\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (3)\"];\n\"PR\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (5)\"];\n\"PR\" -> \"GO\" [label=\"capable_of (25)\"];\n\"PR\" -> \"GO\" [label=\"involved_in (3)\"];\n\"PR\" -> \"GO\" [label=\"located_in (2)\"];\n\"PR\" -> \"GO\" [label=\"part_of (4)\"];\n\"PR\" -> \"GO\" [label=\"subclass_of (360)\"];\n\"PR\" -> \"MOD\" [label=\"lacks_part (48)\"];\n\"PR\" -> \"MOD\" [label=\"subclass_of (2)\"];\n\"PR\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (18)\"];\n\"PR\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"];\n\"PR\" -> \"NCBITaxon\" [label=\"only_in_taxon (177969)\"];\n\"PR\" -> \"PR\" [label=\"INVERTED:has_component (390)\"];\n\"PR\" -> \"PR\" [label=\"INVERTED:has_gene_template (61)\"];\n\"PR\" -> \"PR\" [label=\"INVERTED:has_part (154)\"];\n\"PR\" -> \"PR\" [label=\"derives_from (57)\"];\n\"PR\" -> \"PR\" [label=\"equivalent_to (8)\"];\n\"PR\" -> \"PR\" [label=\"lacks_part (3181)\"];\n\"PR\" -> \"PR\" [label=\"part_of (1)\"];\n\"PR\" -> \"PR\" [label=\"subclass_of (300998)\"];\n\"PR\" -> \"SO\" [label=\"lacks_part (3240)\"];\n\"PR\" -> \"SO\" [label=\"subclass_of (45)\"];\n\"PR\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (1)\"];\n\"PR\" -> \"UBERON\" [label=\"INVERTED:has_part (6)\"];\n\"PW\" -> \"OBO\" [label=\"subclass_of (5)\"];\n\"PathWhiz\" -> \"GO\" [label=\"has_location (3066986)\"];\n\"PathWhiz\" -> \"NCBITaxon\" [label=\"in_species (1905194)\"];\n\"PathWhiz.Bound\" -> \"PathWhiz\" [label=\"INVERTED:has_bound (946)\"];\n\"PathWhiz.Compound\" -> \"CHEBI\" [label=\"same_as (32541)\"];\n\"PathWhiz.Compound\" -> \"DRUGBANK\" [label=\"same_as (1539)\"];\n\"PathWhiz.Compound\" -> \"KEGG\" [label=\"same_as (48957)\"];\n\"PathWhiz.Compound\" -> \"PathWhiz\" [label=\"INVERTED:has_compound (2003771)\"];\n\"PathWhiz.Compound\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (142)\"];\n\"PathWhiz.ElementCollection\" -> \"CHEBI\" [label=\"same_as (50)\"];\n\"PathWhiz.ElementCollection\" -> \"KEGG\" [label=\"same_as (61)\"];\n\"PathWhiz.ElementCollection\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (9096)\"];\n\"PathWhiz.ElementCollection\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (163)\"];\n\"PathWhiz.ElementCollection\" -> \"UniProtKB\" [label=\"same_as (7)\"];\n\"PathWhiz.NucleicAcid\" -> \"CHEBI\" [label=\"same_as (35)\"];\n\"PathWhiz.NucleicAcid\" -> \"PathWhiz\" [label=\"INVERTED:has_nucleic_acid (1763)\"];\n\"PathWhiz.NucleicAcid\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (81)\"];\n\"PathWhiz.ProteinComplex\" -> \"PathWhiz.Bound\" [label=\"INVERTED:has_element_in_bound (809)\"];\n\"PathWhiz.ProteinComplex\" -> \"PathWhiz.Reaction\" [label=\"INVERTED:has_enzyme (165371)\"];\n\"PathWhiz.Reaction\" -> \"CHEBI\" [label=\"has_left_element (188562)\"];\n\"PathWhiz.Reaction\" -> \"CHEBI\" [label=\"has_right_element (169923)\"];\n\"PathWhiz.Reaction\" -> \"DRUGBANK\" [label=\"has_left_element (21859)\"];\n\"PathWhiz.Reaction\" -> \"DRUGBANK\" [label=\"has_right_element (14853)\"];\n\"PathWhiz.Reaction\" -> \"KEGG\" [label=\"has_left_element (232427)\"];\n\"PathWhiz.Reaction\" -> \"KEGG\" [label=\"has_right_element (263206)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz\" [label=\"INVERTED:has_reaction (747189)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.Bound\" [label=\"has_left_element (157)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.Bound\" [label=\"has_right_element (167)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.Compound\" [label=\"has_left_element (317671)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.Compound\" [label=\"has_right_element (336013)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.ElementCollection\" [label=\"has_left_element (1625)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.ElementCollection\" [label=\"has_right_element (1584)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.NucleicAcid\" [label=\"has_left_element (349)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.NucleicAcid\" [label=\"has_right_element (210)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.ProteinComplex\" [label=\"has_left_element (734)\"];\n\"PathWhiz.Reaction\" -> \"PathWhiz.ProteinComplex\" [label=\"has_right_element (906)\"];\n\"PathWhiz.Reaction\" -> \"UniProtKB\" [label=\"has_left_element (13)\"];\n\"PathWhiz.Reaction\" -> \"UniProtKB\" [label=\"has_right_element (12)\"];\n\"PomBase\" -> \"NCBITaxon\" [label=\"only_in_taxon (5124)\"];\n\"PomBase\" -> \"PR\" [label=\"INVERTED:has_gene_template (5172)\"];\n\"PomBase\" -> \"SO\" [label=\"subclass_of (5124)\"];\n\"RGD\" -> \"NCBITaxon\" [label=\"only_in_taxon (8114)\"];\n\"RGD\" -> \"PR\" [label=\"INVERTED:has_gene_template (8114)\"];\n\"RGD\" -> \"SO\" [label=\"subclass_of (8114)\"];\n\"RO\" -> \"BFO\" [label=\"sub_property_of (26)\"];\n\"RO\" -> \"BFO\" [label=\"subclass_of (2)\"];\n\"RO\" -> \"EFO\" [label=\"sub_property_of (1)\"];\n\"RO\" -> \"OBOREL\" [label=\"inverse_of (1)\"];\n\"RO\" -> \"OBOREL\" [label=\"sub_property_of (2)\"];\n\"RO\" -> \"RO\" [label=\"INVERTED:has_subsequence (1)\"];\n\"RO\" -> \"RO\" [label=\"INVERTED:inverse_of (6)\"];\n\"RO\" -> \"RO\" [label=\"inverse_of (122)\"];\n\"RO\" -> \"RO\" [label=\"sub_property_of (621)\"];\n\"RO\" -> \"RO\" [label=\"subclass_of (2)\"];\n\"RO\" -> \"RO\" [label=\"xref (1)\"];\n\"RO\" -> \"SO\" [label=\"xref (9)\"];\n\"RO\" -> \"UBERON\" [label=\"sub_property_of (1)\"];\n\"RO\" -> \"owl\" [label=\"sub_property_of (12)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:consists_of (26132)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:contains (990)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:has_ingredient (38040)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:has_part (3759)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"INVERTED:rxcui:inverse_isa (44612)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:constitutes (23344)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:contained_in (789)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_dose_form (42707)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_doseformgroup (17677)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_form (2941)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_quantified_form (15)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:has_tradename (48926)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:ingredient_of (36788)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:ingredients_of (4352)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:isa (47221)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:part_of (6788)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:precise_ingredient_of (6138)\"];\n\"RXNORM\" -> \"RXNORM\" [label=\"rxcui:reformulated_to (9)\"];\n\"RXNORM\" -> \"UMLS\" [label=\"xref (108886)\"];\n\"SIO\" -> \"ENVO\" [label=\"subclass_of (1)\"];\n\"SIO\" -> \"GENEPIO\" [label=\"INVERTED:specifies_value_of (2)\"];\n\"SIO\" -> \"GENEPIO\" [label=\"subclass_of (9)\"];\n\"SIO\" -> \"IAO\" [label=\"subclass_of (4)\"];\n\"SIO\" -> \"NCIT\" [label=\"subclass_of (1)\"];\n\"SIO\" -> \"SIO\" [label=\"aligned_with (1)\"];\n\"SIO\" -> \"SIO\" [label=\"subclass_of (4)\"];\n\"SMPDB\" -> \"PathWhiz\" [label=\"same_as (110216)\"];\n\"SNOMED\" -> \"MONDO\" [label=\"equivalent_to (9000)\"];\n\"SNOMED\" -> \"OBI\" [label=\"subclass_of (1)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_basic_dose_form (274)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_component (4159)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_definitional_manifestation (13)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_direct_device (4121)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"INVERTED:has_occurrence (5492)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"active_ingredient_of (18593)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"associated_with (3952)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"basis_of_strength_substance_of (1016)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"causative_agent_of (18961)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"cause_of (7207)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"characterized_by (346)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"component_of (4259)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"direct_substance_of (5117)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"during (118)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"entire_anatomy_structure_of (7090)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"focus_of (4294)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_access (1520)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_associated_finding (2554)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_associated_morphology (63873)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_associated_procedure (2467)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_clinical_course (4570)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_concentration_strength_denominator_unit (2065)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_concentration_strength_numerator_unit (2123)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_concentration_strength_numerator_value (2313)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_count_of_base_of_active_ingredient (13255)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_dependent (6)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_direct_morphology (7589)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_direct_procedure_site (33347)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_direct_site (27)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_disposition (8941)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form (12616)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_administration_method (295)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_intended_site (333)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_release_characteristic (295)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_dose_form_transformation (274)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_context (2531)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_informer (2207)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_method (4099)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_finding_site (91236)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_indirect_device (77)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_indirect_morphology (544)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_indirect_procedure_site (8311)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_inherent_attribute (156)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_inherent_location (1)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_intent (5207)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_interpretation (12748)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_laterality (12116)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_measurement_method (17)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_method (60209)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_modification (2130)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_pathological_process (16823)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_precondition (14)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_denominator_unit (1294)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_denominator_value (4074)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_numerator_unit (4305)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_presentation_strength_numerator_value (4836)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_priority (211)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_context (2641)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_device (279)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_morphology (177)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_procedure_site (3506)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_process_duration (136)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_process_output (158)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_property (521)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_realization (1450)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_recipient_category (117)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_revision_status (1031)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_route_of_administration (176)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_scale_type (527)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_severity (38)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen (3075)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_source_identity (126)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_source_morphology (154)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_source_topography (1401)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_specimen_substance (926)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_state_of_matter (58)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_subject_relationship_context (5084)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_surgical_approach (688)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_technique (155)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_temporal_context (5183)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_time_aspect (23)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_unit_of_presentation (2918)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"has_units (7)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"inherent_location_of (1)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"inheres_in (156)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"is_interpreted_by (37621)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"occurs_before (2413)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"occurs_in (7221)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"part_anatomy_structure_of (323)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"plays_role (4304)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"precise_active_ingredient_of (7240)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"relative_to_part_of (2)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"specimen_procedure_of (944)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"subclass_of (554879)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"temporally_related_to (60)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"uses_access_device (1594)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"uses_device (4753)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"uses_energy (314)\"];\n\"SNOMED\" -> \"SNOMED\" [label=\"uses_substance (3187)\"];\n\"SNOMED\" -> \"UMLS\" [label=\"xref (361557)\"];\n\"SO\" -> \"BFO\" [label=\"subclass_of (4)\"];\n\"SO\" -> \"CHEBI\" [label=\"equivalent_to (3)\"];\n\"SO\" -> \"CHEBI\" [label=\"subclass_of (7)\"];\n\"SO\" -> \"DOID\" [label=\"INVERTED:disease_has_basis_in (251)\"];\n\"SO\" -> \"DOID\" [label=\"INVERTED:has_material_basis_in (3)\"];\n\"SO\" -> \"GENEPIO\" [label=\"subclass_of (4)\"];\n\"SO\" -> \"GO\" [label=\"INVERTED:has_participant (4)\"];\n\"SO\" -> \"GO\" [label=\"INVERTED:has_primary_input_or_output (9)\"];\n\"SO\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (5)\"];\n\"SO\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"SO\" -> \"OBI\" [label=\"is_about (2)\"];\n\"SO\" -> \"OBO\" [label=\"subclass_of (4)\"];\n\"SO\" -> \"PR\" [label=\"INVERTED:has_part (6)\"];\n\"SO\" -> \"PR\" [label=\"subclass_of (3)\"];\n\"SO\" -> \"SO\" [label=\"INVERTED:has_member (1)\"];\n\"SO\" -> \"SO\" [label=\"has_quality (1)\"];\n\"SO\" -> \"SO\" [label=\"subclass_of (2326)\"];\n\"SO\" -> \"UO\" [label=\"INVERTED:is_unit_of (1)\"];\n\"STATO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"STATO\" -> \"GENEPIO\" [label=\"subclass_of (6)\"];\n\"STATO\" -> \"IAO\" [label=\"subclass_of (2)\"];\n\"STATO\" -> \"STATO\" [label=\"subclass_of (30)\"];\n\"SYMP\" -> \"ARO\" [label=\"subclass_of (1)\"];\n\"SYMP\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"SYMP\" -> \"DOID\" [label=\"INVERTED:disease_has_basis_in (2)\"];\n\"SYMP\" -> \"SYMP\" [label=\"has_symptom (1)\"];\n\"SYMP\" -> \"SYMP\" [label=\"subclass_of (847)\"];\n\"TO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"TO\" -> \"TO\" [label=\"subclass_of (1)\"];\n\"TRANS\" -> \"GO\" [label=\"subclass_of (1)\"];\n\"TRANS\" -> \"TRANS\" [label=\"subclass_of (32)\"];\n\"TypOn\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"UBERON\" -> \"AEO\" [label=\"xref (109)\"];\n\"UBERON\" -> \"ARO\" [label=\"subclass_of (3)\"];\n\"UBERON\" -> \"BFO\" [label=\"sub_property_of (3)\"];\n\"UBERON\" -> \"BFO\" [label=\"subclass_of (295)\"];\n\"UBERON\" -> \"BSPO\" [label=\"sub_property_of (6)\"];\n\"UBERON\" -> \"BTO\" [label=\"INVERTED:develops_from (4)\"];\n\"UBERON\" -> \"BTO\" [label=\"xref (7)\"];\n\"UBERON\" -> \"CARO\" [label=\"subclass_of (1408)\"];\n\"UBERON\" -> \"CARO\" [label=\"xref (42)\"];\n\"UBERON\" -> \"CL\" [label=\"adjacent_to (1)\"];\n\"UBERON\" -> \"CL\" [label=\"bounding_layer_of (1)\"];\n\"UBERON\" -> \"CL\" [label=\"channel_for (4)\"];\n\"UBERON\" -> \"CL\" [label=\"extends_fibers_into (1)\"];\n\"UBERON\" -> \"CL\" [label=\"has_potential_to_developmentally_contribute_to (1)\"];\n\"UBERON\" -> \"CL\" [label=\"part_of (6)\"];\n\"UBERON\" -> \"CL\" [label=\"subclass_of (2)\"];\n\"UBERON\" -> \"CL\" [label=\"surrounds (7)\"];\n\"UBERON\" -> \"CL\" [label=\"synapsed_by (1)\"];\n\"UBERON\" -> \"CL\" [label=\"xref (1)\"];\n\"UBERON\" -> \"EFO\" [label=\"part_of (3)\"];\n\"UBERON\" -> \"EFO\" [label=\"subclass_of (311)\"];\n\"UBERON\" -> \"EFO\" [label=\"xref (613)\"];\n\"UBERON\" -> \"EHDAA2\" [label=\"xref (1386)\"];\n\"UBERON\" -> \"ENVO\" [label=\"INVERTED:determined_by_part_of (1)\"];\n\"UBERON\" -> \"ENVO\" [label=\"confers_advantage_in (8)\"];\n\"UBERON\" -> \"ENVO\" [label=\"xref (2)\"];\n\"UBERON\" -> \"FBbt\" [label=\"part_of (1)\"];\n\"UBERON\" -> \"FBbt\" [label=\"xref (4)\"];\n\"UBERON\" -> \"FMA\" [label=\"xref (5851)\"];\n\"UBERON\" -> \"FOODON\" [label=\"INVERTED:has_defining_ingredient (2)\"];\n\"UBERON\" -> \"FOODON\" [label=\"subclass_of (34)\"];\n\"UBERON\" -> \"GENEPIO\" [label=\"subclass_of (5)\"];\n\"UBERON\" -> \"GO\" [label=\"INVERTED:has_participant (2)\"];\n\"UBERON\" -> \"GO\" [label=\"INVERTED:process_has_causal_agent (1)\"];\n\"UBERON\" -> \"GO\" [label=\"adjacent_to (1)\"];\n\"UBERON\" -> \"GO\" [label=\"capable_of (122)\"];\n\"UBERON\" -> \"GO\" [label=\"capable_of_part_of (135)\"];\n\"UBERON\" -> \"GO\" [label=\"composed_primarily_of (3)\"];\n\"UBERON\" -> \"GO\" [label=\"functionally_related_to (4)\"];\n\"UBERON\" -> \"GO\" [label=\"located_in (1)\"];\n\"UBERON\" -> \"GO\" [label=\"part_of (11)\"];\n\"UBERON\" -> \"GO\" [label=\"participates_in (8)\"];\n\"UBERON\" -> \"GO\" [label=\"simultaneous_with (11)\"];\n\"UBERON\" -> \"GO\" [label=\"subclass_of (2)\"];\n\"UBERON\" -> \"GO\" [label=\"surrounds (3)\"];\n\"UBERON\" -> \"GO\" [label=\"xref (4)\"];\n\"UBERON\" -> \"MA\" [label=\"subclass_of (2)\"];\n\"UBERON\" -> \"MA\" [label=\"xref (2)\"];\n\"UBERON\" -> \"MESH\" [label=\"xref (644)\"];\n\"UBERON\" -> \"MONDO\" [label=\"INVERTED:disease_arises_from_structure (55)\"];\n\"UBERON\" -> \"MONDO\" [label=\"INVERTED:disease_has_basis_in_dysfunction_of (22)\"];\n\"UBERON\" -> \"MONDO\" [label=\"INVERTED:realized_in_response_to_stimulus (1)\"];\n\"UBERON\" -> \"NBO\" [label=\"INVERTED:by_means (6)\"];\n\"UBERON\" -> \"NBO\" [label=\"INVERTED:has_participant (2)\"];\n\"UBERON\" -> \"NBO\" [label=\"capable_of (2)\"];\n\"UBERON\" -> \"NBO\" [label=\"capable_of_part_of (9)\"];\n\"UBERON\" -> \"NCBITaxon\" [label=\"only_in_taxon (749)\"];\n\"UBERON\" -> \"NCBITaxon\" [label=\"part_of (4)\"];\n\"UBERON\" -> \"NCIT\" [label=\"xref (2580)\"];\n\"UBERON\" -> \"PATO\" [label=\"has_quality (75)\"];\n\"UBERON\" -> \"PR\" [label=\"produces (5)\"];\n\"UBERON\" -> \"RO\" [label=\"sub_property_of (8)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:composed_primarily_of (136)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:contains (10)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:develops_from (1373)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:ends_with (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_component (8)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_member (15)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_part (277)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:has_skeleton (38)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:inverse_of (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:location_of (9)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:preceded_by (13)\"];\n\"UBERON\" -> \"UBERON\" [label=\"INVERTED:produced_by (46)\"];\n\"UBERON\" -> \"UBERON\" [label=\"aboral_to (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"adjacent_to (329)\"];\n\"UBERON\" -> \"UBERON\" [label=\"anastomoses_with (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"anterior_to (11)\"];\n\"UBERON\" -> \"UBERON\" [label=\"anteriorly_connected_to (22)\"];\n\"UBERON\" -> \"UBERON\" [label=\"attaches_to (159)\"];\n\"UBERON\" -> \"UBERON\" [label=\"attaches_to_part_of (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"bounding_layer_of (37)\"];\n\"UBERON\" -> \"UBERON\" [label=\"branching_part_of (47)\"];\n\"UBERON\" -> \"UBERON\" [label=\"channel_for (32)\"];\n\"UBERON\" -> \"UBERON\" [label=\"channels_from (25)\"];\n\"UBERON\" -> \"UBERON\" [label=\"channels_into (18)\"];\n\"UBERON\" -> \"UBERON\" [label=\"conduit_for (57)\"];\n\"UBERON\" -> \"UBERON\" [label=\"connected_to (80)\"];\n\"UBERON\" -> \"UBERON\" [label=\"connects (524)\"];\n\"UBERON\" -> \"UBERON\" [label=\"continuous_with (120)\"];\n\"UBERON\" -> \"UBERON\" [label=\"contributes_to_morphology_of (633)\"];\n\"UBERON\" -> \"UBERON\" [label=\"deep_to (12)\"];\n\"UBERON\" -> \"UBERON\" [label=\"derived_from_ancestral_fusion_of (63)\"];\n\"UBERON\" -> \"UBERON\" [label=\"developmentally_induced_by (20)\"];\n\"UBERON\" -> \"UBERON\" [label=\"developmentally_replaces (8)\"];\n\"UBERON\" -> \"UBERON\" [label=\"develops_from_part_of (5)\"];\n\"UBERON\" -> \"UBERON\" [label=\"develops_in (9)\"];\n\"UBERON\" -> \"UBERON\" [label=\"directly_develops_from (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"distal_to (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"distally_connected_to (30)\"];\n\"UBERON\" -> \"UBERON\" [label=\"distalmost_part_of (5)\"];\n\"UBERON\" -> \"UBERON\" [label=\"dorsal_to (10)\"];\n\"UBERON\" -> \"UBERON\" [label=\"drains (79)\"];\n\"UBERON\" -> \"UBERON\" [label=\"ends (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"existence_ends_during (32)\"];\n\"UBERON\" -> \"UBERON\" [label=\"existence_ends_during_or_before (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"existence_starts_and_ends_during (15)\"];\n\"UBERON\" -> \"UBERON\" [label=\"existence_starts_during (13)\"];\n\"UBERON\" -> \"UBERON\" [label=\"existence_starts_during_or_after (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"existence_starts_with (6)\"];\n\"UBERON\" -> \"UBERON\" [label=\"extends_fibers_into (127)\"];\n\"UBERON\" -> \"UBERON\" [label=\"filtered_through (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_boundary (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_developmental_contribution_from (103)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_muscle_antagonist (47)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_muscle_insertion (217)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_muscle_origin (210)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_potential_to_develop_into (132)\"];\n\"UBERON\" -> \"UBERON\" [label=\"has_potential_to_developmentally_contribute_to (12)\"];\n\"UBERON\" -> \"UBERON\" [label=\"immediate_transformation_of (71)\"];\n\"UBERON\" -> \"UBERON\" [label=\"immediately_anterior_to (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"immediately_deep_to (40)\"];\n\"UBERON\" -> \"UBERON\" [label=\"immediately_posterior_to (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"immediately_preceded_by (7)\"];\n\"UBERON\" -> \"UBERON\" [label=\"immediately_superficial_to (13)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_anterior_side_of (13)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_central_side_of (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_deep_part_of (6)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_distal_side_of (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_dorsal_side_of (6)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_innermost_side_of (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_lateral_side_of (131)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_left_side_of (52)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_outermost_side_of (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_posterior_side_of (15)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_proximal_side_of (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_right_side_of (49)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_superficial_part_of (7)\"];\n\"UBERON\" -> \"UBERON\" [label=\"in_ventral_side_of (5)\"];\n\"UBERON\" -> \"UBERON\" [label=\"indirectly_supplies (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"innervated_by (143)\"];\n\"UBERON\" -> \"UBERON\" [label=\"innervates (105)\"];\n\"UBERON\" -> \"UBERON\" [label=\"intersects_midsagittal_plane_of (27)\"];\n\"UBERON\" -> \"UBERON\" [label=\"inverse_of (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"located_in (152)\"];\n\"UBERON\" -> \"UBERON\" [label=\"lumen_of (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"luminal_space_of (77)\"];\n\"UBERON\" -> \"UBERON\" [label=\"overlaps (70)\"];\n\"UBERON\" -> \"UBERON\" [label=\"part_of (9688)\"];\n\"UBERON\" -> \"UBERON\" [label=\"postaxialmost_part_of (5)\"];\n\"UBERON\" -> \"UBERON\" [label=\"posterior_to (9)\"];\n\"UBERON\" -> \"UBERON\" [label=\"posteriorly_connected_to (1)\"];\n\"UBERON\" -> \"UBERON\" [label=\"preaxialmost_part_of (11)\"];\n\"UBERON\" -> \"UBERON\" [label=\"precedes (2)\"];\n\"UBERON\" -> \"UBERON\" [label=\"produces (14)\"];\n\"UBERON\" -> \"UBERON\" [label=\"protects (9)\"];\n\"UBERON\" -> \"UBERON\" [label=\"proximal_to (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"proximally_connected_to (55)\"];\n\"UBERON\" -> \"UBERON\" [label=\"proximalmost_part_of (4)\"];\n\"UBERON\" -> \"UBERON\" [label=\"serially_homologous_to (3)\"];\n\"UBERON\" -> \"UBERON\" [label=\"sexually_homologous_to (12)\"];\n\"UBERON\" -> \"UBERON\" [label=\"skeleton_of (35)\"];\n\"UBERON\" -> \"UBERON\" [label=\"starts (3)\"];\n\"UBERON\" -> \"UBERON\" [label=\"sub_property_of (3)\"];\n\"UBERON\" -> \"UBERON\" [label=\"subclass_of (21304)\"];\n\"UBERON\" -> \"UBERON\" [label=\"subdivision_of (12)\"];\n\"UBERON\" -> \"UBERON\" [label=\"superficial_to (14)\"];\n\"UBERON\" -> \"UBERON\" [label=\"supplies (132)\"];\n\"UBERON\" -> \"UBERON\" [label=\"surrounded_by (35)\"];\n\"UBERON\" -> \"UBERON\" [label=\"surrounds (78)\"];\n\"UBERON\" -> \"UBERON\" [label=\"transformation_of (47)\"];\n\"UBERON\" -> \"UBERON\" [label=\"tributary_of (35)\"];\n\"UBERON\" -> \"UBERON\" [label=\"ventral_to (8)\"];\n\"UBERON\" -> \"UMLS\" [label=\"xref (2836)\"];\n\"UBERON\" -> \"ZFA\" [label=\"xref (33)\"];\n\"UMLS\" -> \"MONDO\" [label=\"equivalent_to (14023)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"INVERTED:location_of (26952)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"affects (12913)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"associated_with (8728)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"coexists_with (92085)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"compared_with (23729)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"converts_to (1690)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"inhibits (89138)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"interacts_with (141256)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"measures (13930)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"part_of (41790)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"process_of (27799)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"produces (41274)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"same_as (692)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"stimulates (104111)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"uses (27329)\"];\n\"UMLS\" -> \"NCBIGene\" [label=\"xref (34858)\"];\n\"UMLS\" -> \"UMLS\" [label=\"INVERTED:has_component (3)\"];\n\"UMLS\" -> \"UMLS\" [label=\"INVERTED:inverse_of_rn (115122)\"];\n\"UMLS\" -> \"UMLS\" [label=\"INVERTED:inverse_of_ro (356197)\"];\n\"UMLS\" -> \"UMLS\" [label=\"INVERTED:location_of (2270476)\"];\n\"UMLS\" -> \"UMLS\" [label=\"administered_to (203874)\"];\n\"UMLS\" -> \"UMLS\" [label=\"affects (1521984)\"];\n\"UMLS\" -> \"UMLS\" [label=\"associated_with (699263)\"];\n\"UMLS\" -> \"UMLS\" [label=\"augments (451409)\"];\n\"UMLS\" -> \"UMLS\" [label=\"causes (813924)\"];\n\"UMLS\" -> \"UMLS\" [label=\"class_code_classified_by (61)\"];\n\"UMLS\" -> \"UMLS\" [label=\"coexists_with (1402013)\"];\n\"UMLS\" -> \"UMLS\" [label=\"compared_with (348640)\"];\n\"UMLS\" -> \"UMLS\" [label=\"complicates (42952)\"];\n\"UMLS\" -> \"UMLS\" [label=\"component_of (13)\"];\n\"UMLS\" -> \"UMLS\" [label=\"converts_to (36699)\"];\n\"UMLS\" -> \"UMLS\" [label=\"diagnoses (259899)\"];\n\"UMLS\" -> \"UMLS\" [label=\"disrupts (433181)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_context_binding (68)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_form (1)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_mapping_qualifier (22)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_owning_affiliate (4)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_physiologic_effect (1)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_structural_class (2)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_supported_concept_property (239)\"];\n\"UMLS\" -> \"UMLS\" [label=\"has_supported_concept_relationship (342)\"];\n\"UMLS\" -> \"UMLS\" [label=\"inhibits (614020)\"];\n\"UMLS\" -> \"UMLS\" [label=\"interacts_with (1297335)\"];\n\"UMLS\" -> \"UMLS\" [label=\"inverse_of_exhibits (1082)\"];\n\"UMLS\" -> \"UMLS\" [label=\"inverse_of_rq (1560)\"];\n\"UMLS\" -> \"UMLS\" [label=\"inverse_of_sy (450)\"];\n\"UMLS\" -> \"UMLS\" [label=\"isa (313010)\"];\n\"UMLS\" -> \"UMLS\" [label=\"larger_than (1)\"];\n\"UMLS\" -> \"UMLS\" [label=\"manifestation_of (41231)\"];\n\"UMLS\" -> \"UMLS\" [label=\"mapped_to (456)\"];\n\"UMLS\" -> \"UMLS\" [label=\"may_be_qualified_by (20)\"];\n\"UMLS\" -> \"UMLS\" [label=\"measures (183140)\"];\n\"UMLS\" -> \"UMLS\" [label=\"occurs_in (17801)\"];\n\"UMLS\" -> \"UMLS\" [label=\"owning_section_of (9)\"];\n\"UMLS\" -> \"UMLS\" [label=\"owning_subsection_of (42)\"];\n\"UMLS\" -> \"UMLS\" [label=\"part_of (893692)\"];\n\"UMLS\" -> \"UMLS\" [label=\"precedes (149791)\"];\n\"UMLS\" -> \"UMLS\" [label=\"predisposes (256197)\"];\n\"UMLS\" -> \"UMLS\" [label=\"prevents (197498)\"];\n\"UMLS\" -> \"UMLS\" [label=\"process_of (810370)\"];\n\"UMLS\" -> \"UMLS\" [label=\"produces (305322)\"];\n\"UMLS\" -> \"UMLS\" [label=\"related_to (2823)\"];\n\"UMLS\" -> \"UMLS\" [label=\"same_as (15124)\"];\n\"UMLS\" -> \"UMLS\" [label=\"stimulates (663742)\"];\n\"UMLS\" -> \"UMLS\" [label=\"subclass_of (9884)\"];\n\"UMLS\" -> \"UMLS\" [label=\"treats (1218218)\"];\n\"UMLS\" -> \"UMLS\" [label=\"uses (386689)\"];\n\"UO\" -> \"BFO\" [label=\"subclass_of (1)\"];\n\"UO\" -> \"EFO\" [label=\"equivalent_to (1)\"];\n\"UO\" -> \"IAO\" [label=\"subclass_of (2)\"];\n\"UO\" -> \"UO\" [label=\"subclass_of (228)\"];\n\"UPHENO\" -> \"PATO\" [label=\"subclass_of (1)\"];\n\"UniProtKB\" -> \"CHEBI\" [label=\"physically_interacts_with (29920)\"];\n\"UniProtKB\" -> \"CHEMBL.COMPOUND\" [label=\"targets (39678)\"];\n\"UniProtKB\" -> \"CL\" [label=\"expressed_in (15576)\"];\n\"UniProtKB\" -> \"DOID\" [label=\"associated_with_disease (3803)\"];\n\"UniProtKB\" -> \"DOID\" [label=\"gene_associated_with_condition (33361)\"];\n\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of (169)\"];\n\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_negative_effect (5)\"];\n\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_or_within (293)\"];\n\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_or_within_negative_effect (5)\"];\n\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_or_within_positive_effect (13)\"];\n\"UniProtKB\" -> \"GO\" [label=\"acts_upstream_of_positive_effect (14)\"];\n\"UniProtKB\" -> \"GO\" [label=\"capable_of (62677)\"];\n\"UniProtKB\" -> \"GO\" [label=\"colocalizes_with (1327)\"];\n\"UniProtKB\" -> \"GO\" [label=\"contributes_to (975)\"];\n\"UniProtKB\" -> \"GO\" [label=\"enables (67759)\"];\n\"UniProtKB\" -> \"GO\" [label=\"expressed_in (74377)\"];\n\"UniProtKB\" -> \"GO\" [label=\"involved_in (277260)\"];\n\"UniProtKB\" -> \"GO\" [label=\"is_active_in (32)\"];\n\"UniProtKB\" -> \"GO\" [label=\"part_of (80696)\"];\n\"UniProtKB\" -> \"HP\" [label=\"has_phenotype (11603)\"];\n\"UniProtKB\" -> \"KEGG\" [label=\"physically_interacts_with (22304)\"];\n\"UniProtKB\" -> \"MONDO\" [label=\"associated_with_disease (188)\"];\n\"UniProtKB\" -> \"NCBITaxon\" [label=\"in_taxon (24986)\"];\n\"UniProtKB\" -> \"OMIM\" [label=\"associated_with_disease (2132)\"];\n\"UniProtKB\" -> \"OMIM\" [label=\"gene_mutations_contribute_to (5765)\"];\n\"UniProtKB\" -> \"PathWhiz\" [label=\"INVERTED:has_element_collection (59)\"];\n\"UniProtKB\" -> \"PathWhiz\" [label=\"INVERTED:has_protein (304018)\"];\n\"UniProtKB\" -> \"PathWhiz.ProteinComplex\" [label=\"INVERTED:has_protein_in_complex (1903)\"];\n\"UniProtKB\" -> \"REACT\" [label=\"participates_in (779447)\"];\n\"UniProtKB\" -> \"UBERON\" [label=\"expressed_in (323101)\"];\n\"UniProtKB\" -> \"UniProtKB\" [label=\"physically_interacts_with (615498)\"];\n\"UniProtKB\" -> \"UniProtKB\" [label=\"regulates_activity_of (165005)\"];\n\"UniProtKB\" -> \"UniProtKB\" [label=\"regulates_expression_of (237781)\"];\n\"VANDF\" -> \"UMLS\" [label=\"xref (28951)\"];\n\"VANDF\" -> \"VANDF\" [label=\"INVERTED:has_ingredient (14304)\"];\n\"VANDF\" -> \"VANDF\" [label=\"INVERTED:inverse_of_isa (7426)\"];\n\"VANDF\" -> \"VANDF\" [label=\"ingredient_of (18404)\"];\n\"VANDF\" -> \"VANDF\" [label=\"isa (12198)\"];\n\"VCARD\" -> \"GENEPIO\" [label=\"subclass_of (1)\"];\n\"VCARD\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"VT\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"VT\" -> \"IAO\" [label=\"subclass_of (1)\"];\n\"WD\" -> \"MONDO\" [label=\"equivalent_to (2)\"];\n\"XCO\" -> \"GENEPIO\" [label=\"subclass_of (2)\"];\n\"ZEA\" -> \"EFO\" [label=\"subclass_of (1)\"];\n\"ZFA\" -> \"EFO\" [label=\"subclass_of (33)\"];\n\"ZFA\" -> \"UBERON\" [label=\"part_of (4)\"];\n\"ZFA\" -> \"UBERON\" [label=\"subclass_of (1)\"];\n\"ZFIN\" -> \"NCBITaxon\" [label=\"only_in_taxon (3318)\"];\n\"ZFIN\" -> \"PR\" [label=\"INVERTED:has_gene_template (3318)\"];\n\"ZFIN\" -> \"SO\" [label=\"subclass_of (3318)\"];\n\"biolink\" -> \"biolink\" [label=\"sub_property_of (141)\"];\n\"biolink\" -> \"biolink\" [label=\"subclass_of (248)\"];\n\"dbpedia\" -> \"HANCESTRO\" [label=\"subclass_of (9)\"];\n\"dictybase.gene\" -> \"NCBITaxon\" [label=\"only_in_taxon (4540)\"];\n\"dictybase.gene\" -> \"PR\" [label=\"INVERTED:has_gene_template (4540)\"];\n\"dictybase.gene\" -> \"SO\" [label=\"subclass_of (4540)\"];\n\"ecogene\" -> \"NCBITaxon\" [label=\"only_in_taxon (4018)\"];\n\"ecogene\" -> \"PR\" [label=\"INVERTED:has_gene_template (4019)\"];\n\"ecogene\" -> \"SO\" [label=\"subclass_of (4018)\"];\n\"medgen\" -> \"MONDO\" [label=\"equivalent_to (2582)\"];\n\"sgd\" -> \"NCBITaxon\" [label=\"only_in_taxon (5938)\"];\n\"sgd\" -> \"PR\" [label=\"INVERTED:has_gene_template (5940)\"];\n\"sgd\" -> \"SO\" [label=\"subclass_of (5938)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"activator (13)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"affects (6)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"agonist (105)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"antagonist (121)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"antibody (22)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"antisense (22)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"binder (28)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"blocker (21)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"cofactor (4)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"inhibitor (203)\"];\n\"ttd.target\" -> \"NCBIGene\" [label=\"modulator (9)\"];\n\"wb\" -> \"NCBITaxon\" [label=\"only_in_taxon (4479)\"];\n\"wb\" -> \"PR\" [label=\"INVERTED:has_gene_template (4479)\"];\n\"wb\" -> \"SO\" [label=\"subclass_of (4479)\"];\n" }, { "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/shorest-path-graph-visual-hover.html", "content": "\n\n \n Vis Shortest Path Map\n \n \n\n \n \n \n

\n Hover over an arrow to see the predicate(s)\n connecting the concept CURIE prefixes.\n

\n\n
\n\n

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\n\n    \n    \n\n    \n  \n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/shortest_path.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require csv-reading\n         racket/hash\n         racket/set\n         racket/mpair)\n\n;=================================================== example =================================================\n\n#|\n1. load the data from rtx2_2020_09_16-subject_predicate_object_count.tsv\n   (define rtx2-data (load-data \"rtx2_2020_09_16-subject_predicate_object_count.tsv\"))\n\n2. load all required hash tables for finding the shortest path: node-hash edge-hash pred/prefix-pr-hash\n   with a level of restriction or number toward the count of predicates conneting between databases\n   (define all-hash (load-all-hash rtx2-data 0))\n\n   2.1 You may want to assign names to each loaded hash-table\n       (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n\n3. find the shortest path(s) with or without showing the connecting predicate(s)\n   - without showing predicate: (shortest-path* all-hash start end pred)\n   - with showing predicate: (shortest-path*-with-pred all-hash start end pred)\n   - arguments end or pred can be #f, indicating an unknown endding node or an unspecified predicate\n\n3.1 shorest path from node-1 to node-2:  \n\n    * find the shortest paths from \"CHEBI\" to \"UMLS\"\n      (shortest-path* all-hash \"CHEBI\" \"UMLS\" #f)\n      => ((\"CHEBI\" \"DOID\" \"UMLS\"))\n    * find the shortest paths from \"CHEBI\" to \"UMLS\" with the predicates connecting each pair of nodes(databases)\n      (shortest-path*-with-pred all-hash \"CHEBI\" \"UMLS\" #f)\n      => (((\"CHEBI\" \"DOID\" \"UMLS\"))\n          ((((\"CHEBI\" . \"DOID\") (\"INVERTED:has_allergic_trigger\"))\n            ((\"DOID\" . \"UMLS\") (\"xref\")))))\n\n3.2 shortest paths containing predicate pred from node-1 to node-2:\n\n    * find all the (\"shortest\") paths containing predicate \"clinically_tested_terminated_phase_2\" from \"CHEBI\" to \"UMLS\"\n      (shortest-path* all-hash \"CHEBI\" \"UMLS\" \"clinically_tested_terminated_phase_2\")\n      => ((\"CHEBI\" \"DRUGBANK\" \"UMLS\"))\n\n    * combine the result from the step above and show the predicates connecting each pair of nodes(databases) for the shortest path(s)\n      (shortest-path*-with-pred all-hash \"CHEBI\" \"UMLS\" \"clinically_tested_terminated_phase_2\")\n      => (((\"CHEBI\" \"DRUGBANK\" \"UMLS\"))\n          ((((\"CHEBI\" . \"DRUGBANK\") (\"same_as\"))\n            ((\"DRUGBANK\" . \"CHEBI\") (\"external_identifier\" \"same_as\"))\n            ((\"DRUGBANK\" . \"UMLS\")\n            (\"clinically_tested_suspended_phase_2\"\n             \"clinically_tested_terminated_phase_1_or_phase_2\"\n             \"clinically_tested_terminated_phase_1\"\n             \"clinically_tested_terminated_phase_2\"\n             \"clinically_tested_suspended_phase_2_or_phase_3\"\n             \"clinically_tested_terminated_phase_0\"\n             \"clinically_tested_withdrawn_phase_3\"\n             \"clinically_tested_suspended_phase_1_or_phase_2\"\n             \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n             \"clinically_tested_terminated_phase_3\"\n             \"clinically_tested_suspended_phase_1\"\n             \"clinically_tested_withdrawn_phase_2\"\n             \"clinically_tested_suspended_phase_3\"\n             \"xref\"\n             \"clinically_tested_withdrawn_phase_1\"\n             \"clinically_tested_approved_unknown_phase\"\n             \"clinically_tested_suspended_phase_0\"\n             \"clinically_tested_terminated_phase_2_or_phase_3\"\n             \"clinically_tested_withdrawn_phase_0\"\n             \"clinically_tested_withdrawn_phase_1_or_phase_2\")))))\n\n3.3 shortest paths containing predicate pred from node-1 to unknown node:\n\n    * find all the (\"shortest\") paths containing predicate \"clinically_tested_terminated_phase_2\" from \"CHEBI\"\n      (shortest-path* all-hash \"CHEBI\" #f \"clinically_tested_terminated_phase_2\")\n      => ((\"CHEBI\" \"DRUGBANK\" \"UMLS\") (\"CHEBI\" \"DOID\" \"UMLS\" \"DRUGBANK\"))\n\n    * find the shortest path(s) and show the predicates connecting each pair of nodes(databases)\n      (shortest-path*-with-pred all-hash \"CHEBI\" #f \"clinically_tested_terminated_phase_2\")\n      => (((\"CHEBI\" \"DRUGBANK\" \"UMLS\") (\"CHEBI\" \"DOID\" \"UMLS\" \"DRUGBANK\"))\n          ((((\"CHEBI\" . \"DRUGBANK\") (\"same_as\"))\n            ((\"DRUGBANK\" . \"CHEBI\") (\"external_identifier\" \"same_as\"))\n            ((\"DRUGBANK\" . \"UMLS\")\n             (\"clinically_tested_suspended_phase_2\"\n              \"clinically_tested_terminated_phase_1_or_phase_2\"\n              \"clinically_tested_terminated_phase_1\"\n              \"clinically_tested_terminated_phase_2\"\n              \"clinically_tested_suspended_phase_2_or_phase_3\"\n              \"clinically_tested_terminated_phase_0\"\n              \"clinically_tested_withdrawn_phase_3\"\n              \"clinically_tested_suspended_phase_1_or_phase_2\"\n              \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n              \"clinically_tested_terminated_phase_3\"\n              \"clinically_tested_suspended_phase_1\"\n              \"clinically_tested_withdrawn_phase_2\"\n              \"clinically_tested_suspended_phase_3\"\n              \"xref\"\n              \"clinically_tested_withdrawn_phase_1\"\n              \"clinically_tested_approved_unknown_phase\"\n              \"clinically_tested_suspended_phase_0\"\n              \"clinically_tested_terminated_phase_2_or_phase_3\"\n              \"clinically_tested_withdrawn_phase_0\"\n              \"clinically_tested_withdrawn_phase_1_or_phase_2\")))))\n\n4. Tool: print out the connecting predicate(s) for a given/desired path [e.g. (node-1 node-2 ...)]\n   - (single-path=>path-with-pred all-hash single-path)\n\n   * (single-path=>path-with-pred all-hash '(\"CHEBI\" \"DOID\" \"UMLS\" \"DRUGBANK\"))\n|#\n\n;===================================================loading data==============================================\n\n; a tsv reader\n(define make-tsv-reader\n  (make-csv-reader-maker\n   '((separator-chars            #\\tab)\n     (strip-leading-whitespace?  . #t)\n     (strip-trailing-whitespace? . #t))))\n\n#|\n(define convert-to-int\n  (lambda (ls)\n    (list\n     (car ls)\n     (cadr ls)\n     (caddr ls)\n     (string->number (cadddr ls)))))\n|#\n; conver the third item on the list from string to integer\n(define last-ele=>int\n  (lambda (ls)\n    (cond\n      [(null? (cdr ls)) (list (string->number (car ls)))]\n      [else (cons (car ls) (last-ele=>int (cdr ls)))])))\n\n;; load the data from a tsv file\n;; each row is represented as one list\n;; data type (string string string int)\n(define load-data\n  (lambda (file-name)\n    (cdr (load-data-with-header file-name))))\n\n;; header (\"subject CURIE prefix\" \"object CURIE prefix\" \"predicate\" \"edge count\")\n(define load-data-with-header\n  (lambda (file-name)\n    (csv-map last-ele=>int (make-tsv-reader (open-input-file file-name)))))\n\n\n;========================================building graph and loading necessary hash tables======================================\n#|\nThe graph is composed with two hash tables: node hash table and edge hash table.\n\nnode hash table: (key) curie prefix => (value) curie prefix list (two curies are connected by predicate(s))\n^ is based on how it traverses from one database to another database (the path): either sub=>obj or obj=>sub\n\nedge hash table: (key) subject-object-pair => (value) predicate list\n^ edges information are from the KG\n(hash-ref edge-hash-table (B . A)) returning '() means there is no predicate from B to A.\nIf A =\"same_as\"=> B, but there is no predicate from B to A, A => B and B => A are two both possible paths.\n|#\n\n; node-hash with undirected edges (subject <-> object)\n; biuld node-hash with edge/predicate count no less than 100(\"low\" level), 1000(\"medium\" level),\n; or 10000(\"high\" level); or desired number(e.g. no more than 500(int))\n; for filtering low edge count data\n(define make-undirected-node-hash\n  (lambda (ls level/num)\n    (let ((input-graph (make-immutable-hash)))\n      (if (string? level/num)\n          (make-undirected-node-hash-helper ls input-graph (level=>min-count level/num))\n          (make-undirected-node-hash-helper ls input-graph level/num)))))\n\n(define make-undirected-node-hash-helper\n  (lambda (ls graph min-count)\n    (cond\n      [(null? ls) graph]\n      [else\n       (let ((sub (caar ls))\n             (obj (cadar ls))\n             (count (car (cdddar ls))))\n         (if (and (not (equal? sub obj)) (> count min-count))\n             (let ((one-direct-graph\n                    (hash-update graph sub (lambda (v) (set-add v obj)) '())))\n               (let ((two-direct-graph\n                      (hash-update one-direct-graph obj (lambda (v) (set-add v sub)) '())))\n                 (make-undirected-node-hash-helper (cdr ls) two-direct-graph min-count)))\n             (make-undirected-node-hash-helper (cdr ls) graph min-count)))])))\n\n(define level=>min-count\n  (lambda (str)\n    (cond\n      [(equal? str \"high\") 9999]\n      [(equal? str \"medium\") 999]\n      [(equal? str \"low\") 99])))\n\n#| old version; not consider edge/predicate count\n(define make-undirected-node-hash-helper\n  (lambda (ls graph)\n    (cond\n      [(null? ls) graph]\n      [else\n       (let ((sub (caar ls))\n             (obj (cadar ls)))\n         (if (not (equal? sub obj))\n             (let ((one-direct-graph\n                    (hash-update graph sub (lambda (v) (set-add v obj)) '())))\n               (let ((two-direct-graph\n                    (hash-update one-direct-graph obj (lambda (v) (set-add v sub)) '())))\n                 (make-undirected-node-hash-helper (cdr ls) two-direct-graph)))\n               (make-undirected-node-hash-helper (cdr ls) graph)))])))\n|#\n\n#| \n; node-hash with directed edges (subject -> object)\n(define make-directed-graph\n  (lambda (ls)\n    (let ((input-graph (make-immutable-hash)))\n          (make-graph-directed-helper ls input-graph))))\n\n(define make-graph-directed-helper\n  (lambda (ls graph)\n    (cond\n      [(null? ls) graph]\n      [else\n       (let ((sub (caar ls))\n             (obj (cadar ls)))\n         (if (not (equal? sub obj))\n             (let ((one-direct-graph\n                    (hash-update graph sub (lambda (v) (set-add v obj)) '())))\n                 (make-graph-directed-helper (cdr ls) one-direct-graph))\n               (make-graph-directed-helper (cdr ls) graph)))])))\n\n|#\n\n\n; Edges/predicates are stored in a hash table enabling quick search\n; input: data from .tsv file (list) with edge/predicate count no less than 100(\"low\" level), 1000(\"medium\" level),\n; or 10000(\"high\" level); or a desired number(e.g. greater than 500(int)) \n; format: (((subject . object) . (predicates)) ... ) => hash table\n\n(define make-edge-hash\n  (lambda (ls level/num)\n    (let ((pred*-hash (make-immutable-hash)))\n      (if (string? level/num)\n          (make-edge-hash-helper ls pred*-hash (level=>min-count level/num))\n          (make-edge-hash-helper ls pred*-hash level/num)))))\n\n(define make-edge-hash-helper\n  (lambda (ls pred*-hash min-count)\n    (cond\n      [(null? ls) pred*-hash]\n      [else\n       (let ((sub-obj-pr (cons (caar ls) (cadar ls)))\n             (pred (caddar ls))\n             (count (car (cdddar ls))))\n         (if (> count min-count)\n             (let ((pred-hash\n                    (hash-update pred*-hash sub-obj-pr (lambda (v) (set-add v pred)) '())))\n               (make-edge-hash-helper (cdr ls) pred-hash min-count))\n             (make-edge-hash-helper (cdr ls) pred*-hash min-count)))])))\n\n; return a hash table having pred as key and a list of prefix-pairs(connected by the key predicate) as value\n; edge/predicate count no less than 100(\"low\" level), 1000(\"medium\" level), or 10000(\"high\" level)\n; or a desired number(e.g. greater than 500(int)) \n(define preds=>database-pair\n  (lambda (ls level/num)\n    (let ((database-pair*-hash (make-immutable-hash)))\n      (if (string? level/num)\n          (preds=>database-pair-helper ls database-pair*-hash (level=>min-count level/num))\n          (preds=>database-pair-helper ls database-pair*-hash level/num)))))\n\n(define preds=>database-pair-helper\n  (lambda (ls database-pair*-hash min-count)\n    (cond\n      [(null? ls) database-pair*-hash]\n      [else\n       (let ((sub-obj-pr (cons (caar ls) (cadar ls)))\n             (pred (caddar ls))\n             (count (car (cdddar ls))))\n         (if (> count min-count)\n             (let ((database-pair-hash\n                    (hash-update database-pair*-hash pred (lambda (v) (set-add v sub-obj-pr)) '())))\n               (preds=>database-pair-helper (cdr ls) database-pair-hash min-count))\n             (preds=>database-pair-helper (cdr ls) database-pair*-hash min-count)))])))\n\n;===================================================shorest path==============================================\n\n; TODO shortest path containing predicate \"pred\" from \"start\" curie prefix\n; TODO string search for pred\n\n; shortest path containing predicate \"pred\" from \"start\" curie prefix to an unknown curie prefix\n; thoughts:\n; 1. find which two nodes (n1 and n2) contain pred\n; 2. find the shorest paths from start to n1. Then n2 is the end node.\n; 2. find the shorest paths from start to n2.  Then n1 is the end node.\n; 3. combine all the \"shortest\" paths\n; 4. sort the result from above, return the shortest path(s)\n\n(define shortest-path*-contain-pred-unknown-end\n  (lambda (all-hash start pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (let ((prefix-pr-ls (hash-ref pred/prefix-pr-hash pred '())))\n      (let ((undir-prefix-pr-ls (cdr (pr-ls=>undirected-prs-ls prefix-pr-ls (list (list))))))\n            (cdr (shortest-path*-contain-pred-unknown-end-helper node-hash undir-prefix-pr-ls start (list (list))))))))\n\n(define shortest-path*-contain-pred-unknown-end-helper\n  (lambda (node-hash prefix-ls start path-ls)\n    (cond\n      [(null? prefix-ls) path-ls]\n      [else\n       (let ((n1 (caar prefix-ls))\n             (n2 (cdar prefix-ls)))\n         (cond\n           [(equal? start n1)\n            (let ((new-path (list n1 n2)))\n              (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start (append path-ls (list new-path))))]\n           [(equal? start n2)\n            (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start path-ls)]\n           [else\n             (let ((start=>n1-path (BFS node-hash start n1)))\n              (if start=>n1-path\n                  (let ((new-path (append start=>n1-path (list n2))))\n                    (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start (append path-ls (list new-path))))\n                  (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start path-ls)))]))])))\n  \n\n\n\n\n; shortest path containing predicate \"pred\" from \"start\" curie prefix to \"end\" curie prefix\n; thoughts:\n; 1. find which two nodes (n1 and n2) contain pred\n; 2. find the shorest paths from start to n1 and from n2 to end; combine two paths\n; 2. find the shorest paths from start to n2 and from n1 to end; combine two paths\n; 3. combine all the \"shortest\" paths\n; 4. sort the result from above, return the shortest path(s)\n\n; return all the (\"shortest\") paths containing predicate pred\n(define shortest-path*-contain-pred\n  (lambda (all-hash start end pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (let ((prefix-pr-ls (hash-ref pred/prefix-pr-hash pred '())))\n      (if (or (set-member? prefix-pr-ls (cons start end)) (set-member? prefix-pr-ls (cons end start)))\n          (list (list start end))\n          (let ((undir-prefix-pr-ls (cdr (pr-ls=>undirected-prs-ls prefix-pr-ls (list (list))))))\n            (cdr (shortest-path*-contain-pred-helper node-hash undir-prefix-pr-ls start end (list (list)))))))))\n\n(define shortest-path*-contain-pred-helper\n  (lambda (node-hash prefix-ls start end path-ls)\n    (cond\n      [(null? prefix-ls) path-ls]\n      [else\n       (let ((n1 (caar prefix-ls))\n             (n2 (cdar prefix-ls)))\n         (cond\n           ;[(or (and (equal? start n1) (equal? end n2)) (and (equal? start n2) (equal? end n1)))\n            ;(shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list (list n1 n2))))\n            ;(list (list start end))]\n           [(equal? start n1)\n             (let ((n2=>end-path (BFS node-hash n2 end)))\n               (if n2=>end-path\n                   (let ((new-path (append (list n1) n2=>end-path)))\n                         (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list new-path))))\n                   (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)))]\n           [(equal? end n2)\n             (let ((start=>n1-path (BFS node-hash start n1)))\n               (if start=>n1-path\n                   (let ((new-path (append start=>n1-path (list n2))))\n                     (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list new-path))))\n                   (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)))]\n           [(or (equal? start n2) (equal? end n1))\n            (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)]\n           [else\n             (let ((start=>n1-path (BFS node-hash start n1))\n                  (n2=>end-path (BFS node-hash n2 end)))\n              (if (and start=>n1-path n2=>end-path)\n                  (let ((new-path (append start=>n1-path n2=>end-path)))\n                    (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list new-path))))\n                  (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)))]))])))\n\n; sort the result from shortest-path*-contain-pred, and \n; return the shortest path(s) in a list\n(define find-shortest-path-ls\n  (lambda (path-ls)\n    (let ((ordered-path-ls\n           (sort path-ls\n                 #:key length <)))\n      (let ((shortest-path-ls (list (car ordered-path-ls))))\n        (find-shortest-path-ls-helper ordered-path-ls shortest-path-ls)))))\n\n(define find-shortest-path-ls-helper\n  (lambda (ordered-path-ls shortest-path-ls)\n    (cond\n      [(or (null? ordered-path-ls) (null? (cdr ordered-path-ls))) shortest-path-ls]\n      [else\n       (let ((first (car ordered-path-ls))\n             (second (cadr ordered-path-ls)))\n         (if (and (not (null? (cdr ordered-path-ls)))\n                  (equal? (length first)\n                          (length second)))\n             (find-shortest-path-ls-helper (cdr ordered-path-ls)\n                                    (append shortest-path-ls (list second)))\n             shortest-path-ls))])))\n\n\n; return the shorest path(s) from start to end containg predicate pred\n; with the corresponding predicate(s) connect pairs of databases\n(define shortest-path-with-pred\n  (lambda (path-ls edge-hash)\n    (shortest-path-with-pred-helper path-ls edge-hash (mlist (list)))))\n\n(define shortest-path-with-pred-helper\n  (lambda (path-ls edge-hash acc)\n    (for-each\n     (lambda (path)\n       (set-mcdr! acc (append (mcdr acc) (list (path-with-pred-undirected path edge-hash)))))\n     (find-shortest-path-ls path-ls))\n    (mcdr acc)))\n      \n; convert a list of pair to be undirected\n; example: ((d1 . d2) (d5 . d7) (d6 . d6)) => ((d1 . d2) (d2 . d1) (d5 . d7) (d7 . d5) (d6 . d6))\n(define pr-ls=>undirected-prs-ls\n  (lambda (pr-ls undirected-pr-ls)\n    (cond\n      [(null? pr-ls) undirected-pr-ls]\n      [else\n       (let ((sub (caar pr-ls))\n             (obj (cdar pr-ls)))\n         (if (not (equal? sub obj))\n             (let ((one-dir-prls (append undirected-pr-ls (list (car pr-ls)))))\n               (let ((two-dir-prls (append one-dir-prls (list (cons obj sub)))))\n                 (pr-ls=>undirected-prs-ls (cdr pr-ls) two-dir-prls)))\n             (pr-ls=>undirected-prs-ls (cdr pr-ls) (append undirected-pr-ls (list (car pr-ls))))))])))\n\n\n; unweighted shorest path - Breadth First Search\n; input: node-hash, a strart node/vertex, an end node/vertex\n(define BFS\n  (lambda (node-hash start dest)\n    (if (equal? start dest) (list start dest)\n        (let ((Q (mlist start))\n              (visited (mutable-set start))\n              (predecessor (make-hash)))\n          ; whether exist a path from start to dest: (BFS-helper graph Q dest visited pred) (true or false)\n          (if (BFS-helper node-hash Q dest visited predecessor)\n              (let ((cdr-path (get-path start dest predecessor)))\n                (cons start cdr-path))\n              false)))))\n\n; whether exist a path from start to dest\n; return true/false\n(define BFS-helper\n  (lambda (graph Q end visited pred)\n    (cond\n      [(set-member? visited end) true]\n      [(null? Q) false]\n      [else\n       ; v:parent and w:child\n       (let ((v (mcar Q))\n             (Q* (mcdr Q)))\n         (for-each\n          (lambda (w)\n            (when (not (set-member? visited w))\n              (begin\n                (set-add! visited w)\n                (hash-set! pred w v)\n                (set-mcdr! Q (mappend (mcdr Q) (mlist w))))))\n          (hash-ref graph v '()))\n         ;(display visited)\n         ;(display (mcdr Q))\n         (BFS-helper graph (mcdr Q) end visited pred))])))\n\n(define get-path\n  (lambda (start dest pred)\n    (let ((path (list dest)))\n      (get-path-helper start dest pred path))))\n\n(define get-path-helper\n  (lambda (start dest pred path)\n    (let ((pred-of-dest (hash-ref pred dest '())))\n          (cond\n            [(equal? pred-of-dest start) path]\n            [else\n             (let ((path* (cons pred-of-dest path)))\n               (get-path-helper start pred-of-dest pred path*))]))))\n\n\n;; Next: find the corresponding edges/predicates of each database from the result\n\n\n;retun the corresponding edges/predicates of each database(subject object) pair in one path\n;format: (((subject . object) (pred1 pred2 ... )) ... ) => list of lists\n\n#|\n(define path-with-pred-directed\n  (lambda (ls pred*-hash)\n    (let ((sub-obj-pr-ls (cdr (ls=>pr-ls ls (list (list))))))\n      (let ((pred-ls (result-ls=>preds sub-obj-pr-ls pred*-hash)))\n        (cdr (combine-sub-obj-pr-pred sub-obj-pr-ls pred-ls (list (list))))))))\n|#\n\n(define path-with-pred-undirected\n  (lambda (ls pred*-hash)\n    (let ((sub-obj-pr-ls (cdr (ls=>pr-ls-undirected ls (list (list))))))\n      (let ((pred-ls (sub-obj-pr-ls=>preds sub-obj-pr-ls pred*-hash)))\n        (cdr (combine-sub-obj-pr-pred sub-obj-pr-ls pred-ls (list (list))))))))\n\n;map each subject object pair as the key to find the corresponding predicates\n;return list of predicates list\n;format: ((pred1 pred2 ...) (pred1 pred2 ...) ...)\n(define sub-obj-pr-ls=>preds\n  (lambda (sub-obj-pr-ls pred*-hash)\n    (map\n     (lambda (k) (hash-ref pred*-hash k '()))\n     sub-obj-pr-ls)))\n\n;take a list of database name (d1 d2 d3 ...)\n;return a list of database pairs by order ((d1 . d2) (d2 . d3) ...) -> same as saying from d1 to d2, d2 to d3, ...\n;only works for directed edges/graph\n(define ls=>pr-ls-directed\n  (lambda (ls accu-ls-ls)\n    (cond\n      [(null? (cdr ls)) accu-ls-ls]\n      [else\n       (let ((from (car ls))\n             (to (cadr ls)))\n         (ls=>pr-ls-directed (cdr ls) (append accu-ls-ls (list (cons from to)))))])))\n\n;for undirected graph: ((d1 . d2) (d2 . d1) (d2 . d3) (d3 . d2) ...))\n(define ls=>pr-ls-undirected\n  (lambda (ls accu-ls-ls)\n    (cond\n      [(null? (cdr ls)) accu-ls-ls]\n      [else\n       (let ((from (car ls))\n             (to (cadr ls)))\n         (if (equal? from to)\n             (ls=>pr-ls-undirected (cdr ls) (append accu-ls-ls (list (cons from to))))\n             (ls=>pr-ls-undirected (cdr ls) (append accu-ls-ls (list (cons from to) (cons to from))))))])))\n\n;recursively combine each subject object pair to the corresponding list of predicates\n;format: (((subject . object) (pred1 pred2 ... )) ... ) => list of lists\n(define combine-sub-obj-pr-pred\n  (lambda (pr-ls pred-ls accu)\n    (cond\n      [(null? pr-ls) accu]\n      [else\n       (if (not (null? (car pred-ls)))\n           (combine-sub-obj-pr-pred (cdr pr-ls) (cdr pred-ls) (append accu (list (list (car pr-ls) (car pred-ls)))))\n           (combine-sub-obj-pr-pred (cdr pr-ls) (cdr pred-ls) accu))])))\n\n\n;===============================================useful helper functions==================================================\n\n(define build-undirected-graph\n  (lambda (ls level/num)\n    (list (make-undirected-node-hash ls level/num)\n    (make-edge-hash ls level/num))))\n\n;(match-define (list node-hash edge-hash) (build-undirected-graph rtx2-data 2669662))\n\n; load all required hash tables for finding the shortest path\n; input: data from .tsv file; edge/predicate count level or number \n(define load-all-hash\n  (lambda (ls level/num)\n    (list\n     (make-undirected-node-hash ls level/num)\n     (make-edge-hash ls level/num)\n     (preds=>database-pair ls level/num))))\n\n;(match-define (list node-hash edge-hash pred/prefix-pr-hash) (load-all-hash rtx2-data 2669662))\n\n(define shortest-path*\n  (lambda (all-hash start end pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (cond\n      [(equal? pred #f)\n       (list (BFS node-hash start end))]\n      [(equal? end #f)\n       (shortest-path*-contain-pred-unknown-end all-hash start pred)]\n      [else\n       (shortest-path*-contain-pred all-hash start end pred)])))\n       \n(define shortest-path*-with-pred\n  (lambda (all-hash start end pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (cond\n      [(equal? pred #f)\n       (let ((path (list (BFS node-hash start end))))\n         (list path (shortest-path-with-pred path edge-hash)))]\n      [(equal? end #f)\n       (let ((path (shortest-path*-contain-pred-unknown-end all-hash start pred)))\n         (list path (shortest-path-with-pred path edge-hash)))]\n      [else\n       (let ((path (shortest-path*-contain-pred all-hash start end pred)))\n         (list path (shortest-path-with-pred path edge-hash)))])))\n\n(define single-path=>path-with-pred\n  (lambda (all-hash single-path)\n    (if (list? (car single-path))\n        (error \"The second argument should be one single path. e.g. (node-1 node-2)\")\n        (path-with-pred-undirected single-path (cadr all-hash)))))\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/rtx2_2020_09_16/shortest_path_with_visual.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require csv-reading\n         racket/hash\n         racket/set\n         racket/mpair\n         racket/runtime-path)\n\n;=================================================== example & demo =================================================\n\n#|\n1. load the data from rtx2_2020_09_16-subject_predicate_object_count.tsv\n   (define rtx2-data (load-data \"rtx2_2020_09_16-subject_predicate_object_count.tsv\"))\n\n2. load all required hash tables for finding the shortest path: node-hash edge-hash pred/prefix-pr-hash\n   with a level of restriction or number toward the count of predicates conneting between databases\n   (define all-hash (load-all-hash rtx2-data 0))\n\n   2.1 You may want to assign names to each loaded hash-table\n       (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n\n3. find the shortest path(s) with or without showing the connecting predicate(s)\n   - without showing predicate: (shortest-path* all-hash start end pred)\n   - with showing predicate: (shortest-path*-with-pred all-hash start end pred)\n   - arguments end or pred can be #f, indicating an unknown endding node or an unspecified predicate\n\n3.1 shorest path from node-1 to node-2:  \n\n    * find the shortest paths from \"CHEBI\" to \"UMLS\"\n      (shortest-path* all-hash \"CHEBI\" \"UMLS\" #f)\n      => ((\"CHEBI\" \"DOID\" \"UMLS\"))\n    * find the shortest paths from \"CHEBI\" to \"UMLS\" with the predicates connecting each pair of nodes(databases)\n      (shortest-path*-with-pred all-hash \"CHEBI\" \"UMLS\" #f)\n      => (((\"CHEBI\" \"DOID\" \"UMLS\"))\n          ((((\"CHEBI\" . \"DOID\") (\"INVERTED:has_allergic_trigger\"))\n            ((\"DOID\" . \"UMLS\") (\"xref\")))))\n\n3.2 shortest paths containing predicate pred from node-1 to node-2:\n\n    * find all the (\"shortest\") paths containing predicate \"clinically_tested_terminated_phase_2\" from \"CHEBI\" to \"UMLS\"\n      (shortest-path* all-hash \"CHEBI\" \"UMLS\" \"clinically_tested_terminated_phase_2\")\n      => ((\"CHEBI\" \"DRUGBANK\" \"UMLS\"))\n\n    * combine the result from the step above and show the predicates connecting each pair of nodes(databases) for the shortest path(s)\n      (shortest-path*-with-pred all-hash \"CHEBI\" \"UMLS\" \"clinically_tested_terminated_phase_2\")\n      => (((\"CHEBI\" \"DRUGBANK\" \"UMLS\"))\n          ((((\"CHEBI\" . \"DRUGBANK\") (\"same_as\"))\n            ((\"DRUGBANK\" . \"CHEBI\") (\"external_identifier\" \"same_as\"))\n            ((\"DRUGBANK\" . \"UMLS\")\n            (\"clinically_tested_suspended_phase_2\"\n             \"clinically_tested_terminated_phase_1_or_phase_2\"\n             \"clinically_tested_terminated_phase_1\"\n             \"clinically_tested_terminated_phase_2\"\n             \"clinically_tested_suspended_phase_2_or_phase_3\"\n             \"clinically_tested_terminated_phase_0\"\n             \"clinically_tested_withdrawn_phase_3\"\n             \"clinically_tested_suspended_phase_1_or_phase_2\"\n             \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n             \"clinically_tested_terminated_phase_3\"\n             \"clinically_tested_suspended_phase_1\"\n             \"clinically_tested_withdrawn_phase_2\"\n             \"clinically_tested_suspended_phase_3\"\n             \"xref\"\n             \"clinically_tested_withdrawn_phase_1\"\n             \"clinically_tested_approved_unknown_phase\"\n             \"clinically_tested_suspended_phase_0\"\n             \"clinically_tested_terminated_phase_2_or_phase_3\"\n             \"clinically_tested_withdrawn_phase_0\"\n             \"clinically_tested_withdrawn_phase_1_or_phase_2\")))))\n\n3.3 shortest paths containing predicate pred from node-1 to unknown node:\n\n    * find all the (\"shortest\") paths containing predicate \"clinically_tested_terminated_phase_2\" from \"CHEBI\"\n      (shortest-path* all-hash \"CHEBI\" #f \"clinically_tested_terminated_phase_2\")\n      => ((\"CHEBI\" \"DRUGBANK\" \"UMLS\") (\"CHEBI\" \"DOID\" \"UMLS\" \"DRUGBANK\"))\n\n    * find the shortest path(s) and show the predicates connecting each pair of nodes(databases)\n      (shortest-path*-with-pred all-hash \"CHEBI\" #f \"clinically_tested_terminated_phase_2\")\n      => (((\"CHEBI\" \"DRUGBANK\" \"UMLS\") (\"CHEBI\" \"DOID\" \"UMLS\" \"DRUGBANK\"))\n          ((((\"CHEBI\" . \"DRUGBANK\") (\"same_as\"))\n            ((\"DRUGBANK\" . \"CHEBI\") (\"external_identifier\" \"same_as\"))\n            ((\"DRUGBANK\" . \"UMLS\")\n             (\"clinically_tested_suspended_phase_2\"\n              \"clinically_tested_terminated_phase_1_or_phase_2\"\n              \"clinically_tested_terminated_phase_1\"\n              \"clinically_tested_terminated_phase_2\"\n              \"clinically_tested_suspended_phase_2_or_phase_3\"\n              \"clinically_tested_terminated_phase_0\"\n              \"clinically_tested_withdrawn_phase_3\"\n              \"clinically_tested_suspended_phase_1_or_phase_2\"\n              \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n              \"clinically_tested_terminated_phase_3\"\n              \"clinically_tested_suspended_phase_1\"\n              \"clinically_tested_withdrawn_phase_2\"\n              \"clinically_tested_suspended_phase_3\"\n              \"xref\"\n              \"clinically_tested_withdrawn_phase_1\"\n              \"clinically_tested_approved_unknown_phase\"\n              \"clinically_tested_suspended_phase_0\"\n              \"clinically_tested_terminated_phase_2_or_phase_3\"\n              \"clinically_tested_withdrawn_phase_0\"\n              \"clinically_tested_withdrawn_phase_1_or_phase_2\")))))\n\n4. visualize the shortest path\n   - The input of visualize-with-web must be the result returned from shortest-path*-with-pred (i.e. list contains all path(s)\n     and shortest-path(s) with predicates)\n   (define p (shortest-path*-with-pred all-hash \"CHEBI\" #f \"clinically_tested_terminated_phase_2\"))\n   (visualize-with-web p)\n\n   - Open shorest-path-graph-visual-hover.html under the same folder and the path(s) will be displayed on browser.\n\n5. Tool: print out the connecting predicate(s) for a given/desired path [e.g. (node-1 node-2 ...)]\n   - (single-path=>path-with-pred all-hash single-path)\n\n   * (single-path=>path-with-pred all-hash '(\"CHEBI\" \"DOID\" \"UMLS\" \"DRUGBANK\"))\n\n\n|#\n\n;===================================================loading data==============================================\n\n; a tsv reader\n(define make-tsv-reader\n  (make-csv-reader-maker\n   '((separator-chars            #\\tab)\n     (strip-leading-whitespace?  . #t)\n     (strip-trailing-whitespace? . #t))))\n\n#|\n(define convert-to-int\n  (lambda (ls)\n    (list\n     (car ls)\n     (cadr ls)\n     (caddr ls)\n     (string->number (cadddr ls)))))\n|#\n; conver the third item on the list from string to integer\n(define last-ele=>int\n  (lambda (ls)\n    (cond\n      [(null? (cdr ls)) (list (string->number (car ls)))]\n      [else (cons (car ls) (last-ele=>int (cdr ls)))])))\n\n;; load the data from a tsv file\n;; each row is represented as one list\n;; data type (string string string int)\n(define load-data\n  (lambda (file-name)\n    (cdr (load-data-with-header file-name))))\n\n;; header (\"subject CURIE prefix\" \"object CURIE prefix\" \"predicate\" \"edge count\")\n(define load-data-with-header\n  (lambda (file-name)\n    (csv-map last-ele=>int (make-tsv-reader (open-input-file file-name)))))\n\n\n;========================================building graph and loading necessary hash tables======================================\n#|\nThe graph is composed with two hash tables: node hash table and edge hash table.\n\nnode hash table: (key) curie prefix => (value) curie prefix list (two curies are connected by predicate(s))\n^ is based on how it traverses from one database to another database (the path): either sub=>obj or obj=>sub\n\nedge hash table: (key) subject-object-pair => (value) predicate list\n^ edges information are from the KG\n(hash-ref edge-hash-table (B . A)) returning '() means there is no predicate from B to A.\nIf A =\"same_as\"=> B, but there is no predicate from B to A, A => B and B => A are two both possible paths.\n|#\n\n; node-hash with undirected edges (subject <-> object)\n; biuld node-hash with edge/predicate count no less than 100(\"low\" level), 1000(\"medium\" level),\n; or 10000(\"high\" level); or desired number(e.g. no more than 500(int))\n; for filtering low edge count data\n(define make-undirected-node-hash\n  (lambda (ls level/num)\n    (let ((input-graph (make-immutable-hash)))\n      (if (string? level/num)\n          (make-undirected-node-hash-helper ls input-graph (level=>min-count level/num))\n          (make-undirected-node-hash-helper ls input-graph level/num)))))\n\n(define make-undirected-node-hash-helper\n  (lambda (ls graph min-count)\n    (cond\n      [(null? ls) graph]\n      [else\n       (let ((sub (caar ls))\n             (obj (cadar ls))\n             (count (car (cdddar ls))))\n         (if (and (not (equal? sub obj)) (> count min-count))\n             (let ((one-direct-graph\n                    (hash-update graph sub (lambda (v) (set-add v obj)) '())))\n               (let ((two-direct-graph\n                      (hash-update one-direct-graph obj (lambda (v) (set-add v sub)) '())))\n                 (make-undirected-node-hash-helper (cdr ls) two-direct-graph min-count)))\n             (make-undirected-node-hash-helper (cdr ls) graph min-count)))])))\n\n(define level=>min-count\n  (lambda (str)\n    (cond\n      [(equal? str \"high\") 9999]\n      [(equal? str \"medium\") 999]\n      [(equal? str \"low\") 99])))\n\n\n; Edges/predicates are stored in a hash table enabling quick search\n; input: data from .tsv file (list) with edge/predicate count no less than 100(\"low\" level), 1000(\"medium\" level),\n; or 10000(\"high\" level); or a desired number(e.g. greater than 500(int)) \n; format: (((subject . object) . (predicates)) ... ) => hash table\n\n(define make-edge-hash\n  (lambda (ls level/num)\n    (let ((pred*-hash (make-immutable-hash)))\n      (if (string? level/num)\n          (make-edge-hash-helper ls pred*-hash (level=>min-count level/num))\n          (make-edge-hash-helper ls pred*-hash level/num)))))\n\n(define make-edge-hash-helper\n  (lambda (ls pred*-hash min-count)\n    (cond\n      [(null? ls) pred*-hash]\n      [else\n       (let ((sub-obj-pr (cons (caar ls) (cadar ls)))\n             (pred (caddar ls))\n             (count (car (cdddar ls))))\n         (if (> count min-count)\n             (let ((pred-hash\n                    (hash-update pred*-hash sub-obj-pr (lambda (v) (set-add v pred)) '())))\n               (make-edge-hash-helper (cdr ls) pred-hash min-count))\n             (make-edge-hash-helper (cdr ls) pred*-hash min-count)))])))\n\n; return a hash table having pred as key and a list of prefix-pairs(connected by the key predicate) as value\n; edge/predicate count no less than 100(\"low\" level), 1000(\"medium\" level), or 10000(\"high\" level)\n; or a desired number(e.g. greater than 500(int)) \n(define preds=>database-pair\n  (lambda (ls level/num)\n    (let ((database-pair*-hash (make-immutable-hash)))\n      (if (string? level/num)\n          (preds=>database-pair-helper ls database-pair*-hash (level=>min-count level/num))\n          (preds=>database-pair-helper ls database-pair*-hash level/num)))))\n\n(define preds=>database-pair-helper\n  (lambda (ls database-pair*-hash min-count)\n    (cond\n      [(null? ls) database-pair*-hash]\n      [else\n       (let ((sub-obj-pr (cons (caar ls) (cadar ls)))\n             (pred (caddar ls))\n             (count (car (cdddar ls))))\n         (if (> count min-count)\n             (let ((database-pair-hash\n                    (hash-update database-pair*-hash pred (lambda (v) (set-add v sub-obj-pr)) '())))\n               (preds=>database-pair-helper (cdr ls) database-pair-hash min-count))\n             (preds=>database-pair-helper (cdr ls) database-pair*-hash min-count)))])))\n\n;===================================================shorest path==============================================\n\n; TODO shortest path containing predicate \"pred\" from \"start\" curie prefix\n; TODO string search for pred\n\n; shortest path containing predicate \"pred\" from \"start\" curie prefix to an unknown curie prefix\n; thoughts:\n; 1. find which two nodes (n1 and n2) contain pred\n; 2. find the shorest paths from start to n1. Then n2 is the end node.\n; 2. find the shorest paths from start to n2.  Then n1 is the end node.\n; 3. combine all the \"shortest\" paths\n; 4. sort the result from above, return the shortest path(s)\n\n(define shortest-path*-contain-pred-unknown-end\n  (lambda (all-hash start pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (let ((prefix-pr-ls (hash-ref pred/prefix-pr-hash pred '())))\n      (let ((undir-prefix-pr-ls (cdr (pr-ls=>undirected-prs-ls prefix-pr-ls (list (list))))))\n            (cdr (shortest-path*-contain-pred-unknown-end-helper node-hash undir-prefix-pr-ls start (list (list))))))))\n\n(define shortest-path*-contain-pred-unknown-end-helper\n  (lambda (node-hash prefix-ls start path-ls)\n    (cond\n      [(null? prefix-ls) path-ls]\n      [else\n       (let ((n1 (caar prefix-ls))\n             (n2 (cdar prefix-ls)))\n         (cond\n           [(equal? start n1)\n            (let ((new-path (list n1 n2)))\n              (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start (append path-ls (list new-path))))]\n           [(equal? start n2)\n            (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start path-ls)]\n           [else\n             (let ((start=>n1-path (BFS node-hash start n1)))\n              (if start=>n1-path\n                  (let ((new-path (append start=>n1-path (list n2))))\n                    (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start (append path-ls (list new-path))))\n                  (shortest-path*-contain-pred-unknown-end-helper node-hash (cdr prefix-ls) start path-ls)))]))])))\n  \n\n\n\n\n; shortest path containing predicate \"pred\" from \"start\" curie prefix to \"end\" curie prefix\n; thoughts:\n; 1. find which two nodes (n1 and n2) contain pred\n; 2. find the shorest paths from start to n1 and from n2 to end; combine two paths\n; 2. find the shorest paths from start to n2 and from n1 to end; combine two paths\n; 3. combine all the \"shortest\" paths\n; 4. sort the result from above, return the shortest path(s)\n\n; return all the (\"shortest\") paths containing predicate pred\n(define shortest-path*-contain-pred\n  (lambda (all-hash start end pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (let ((prefix-pr-ls (hash-ref pred/prefix-pr-hash pred '())))\n      (if (or (set-member? prefix-pr-ls (cons start end)) (set-member? prefix-pr-ls (cons end start)))\n          (list (list start end))\n          (let ((undir-prefix-pr-ls (cdr (pr-ls=>undirected-prs-ls prefix-pr-ls (list (list))))))\n            (cdr (shortest-path*-contain-pred-helper node-hash undir-prefix-pr-ls start end (list (list)))))))))\n\n(define shortest-path*-contain-pred-helper\n  (lambda (node-hash prefix-ls start end path-ls)\n    (cond\n      [(null? prefix-ls) path-ls]\n      [else\n       (let ((n1 (caar prefix-ls))\n             (n2 (cdar prefix-ls)))\n         (cond\n           [(equal? start n1)\n             (let ((n2=>end-path (BFS node-hash n2 end)))\n               (if n2=>end-path\n                   (let ((new-path (append (list n1) n2=>end-path)))\n                         (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list new-path))))\n                   (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)))]\n           [(equal? end n2)\n             (let ((start=>n1-path (BFS node-hash start n1)))\n               (if start=>n1-path\n                   (let ((new-path (append start=>n1-path (list n2))))\n                     (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list new-path))))\n                   (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)))]\n           [(or (equal? start n2) (equal? end n1))\n            (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)]\n           [else\n             (let ((start=>n1-path (BFS node-hash start n1))\n                  (n2=>end-path (BFS node-hash n2 end)))\n              (if (and start=>n1-path n2=>end-path)\n                  (let ((new-path (append start=>n1-path n2=>end-path)))\n                    (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end (append path-ls (list new-path))))\n                  (shortest-path*-contain-pred-helper node-hash (cdr prefix-ls) start end path-ls)))]))])))\n\n; sort the result from shortest-path*-contain-pred, and \n; return the shortest path(s) in a list\n(define find-shortest-path-ls\n  (lambda (path-ls)\n    (let ((ordered-path-ls\n           (sort path-ls\n                 #:key length <)))\n      (let ((shortest-path-ls (list (car ordered-path-ls))))\n        (find-shortest-path-ls-helper ordered-path-ls shortest-path-ls)))))\n\n(define find-shortest-path-ls-helper\n  (lambda (ordered-path-ls shortest-path-ls)\n    (cond\n      [(or (null? ordered-path-ls) (null? (cdr ordered-path-ls))) shortest-path-ls]\n      [else\n       (let ((first (car ordered-path-ls))\n             (second (cadr ordered-path-ls)))\n         (if (and (not (null? (cdr ordered-path-ls)))\n                  (equal? (length first)\n                          (length second)))\n             (find-shortest-path-ls-helper (cdr ordered-path-ls)\n                                    (append shortest-path-ls (list second)))\n             shortest-path-ls))])))\n\n\n; return the shorest path(s) from start to end containg predicate pred\n; with the corresponding predicate(s) connect pairs of databases\n(define shortest-path-with-pred\n  (lambda (path-ls edge-hash)\n    (shortest-path-with-pred-helper path-ls edge-hash (mlist (list)))))\n\n(define shortest-path-with-pred-helper\n  (lambda (path-ls edge-hash acc)\n    (for-each\n     (lambda (path)\n       (set-mcdr! acc (append (mcdr acc) (list (path-with-pred-undirected path edge-hash)))))\n     (find-shortest-path-ls path-ls))\n    (mcdr acc)))\n      \n; convert a list of pair to be undirected\n; example: ((d1 . d2) (d5 . d7) (d6 . d6)) => ((d1 . d2) (d2 . d1) (d5 . d7) (d7 . d5) (d6 . d6))\n(define pr-ls=>undirected-prs-ls\n  (lambda (pr-ls undirected-pr-ls)\n    (cond\n      [(null? pr-ls) undirected-pr-ls]\n      [else\n       (let ((sub (caar pr-ls))\n             (obj (cdar pr-ls)))\n         (if (not (equal? sub obj))\n             (let ((one-dir-prls (append undirected-pr-ls (list (car pr-ls)))))\n               (let ((two-dir-prls (append one-dir-prls (list (cons obj sub)))))\n                 (pr-ls=>undirected-prs-ls (cdr pr-ls) two-dir-prls)))\n             (pr-ls=>undirected-prs-ls (cdr pr-ls) (append undirected-pr-ls (list (car pr-ls))))))])))\n\n\n; unweighted shorest path - Breadth First Search\n; input: node-hash, a strart node/vertex, an end node/vertex\n(define BFS\n  (lambda (node-hash start dest)\n    (if (equal? start dest) (list start dest)\n        (let ((Q (mlist start))\n              (visited (mutable-set start))\n              (predecessor (make-hash)))\n          ; whether exist a path from start to dest: (BFS-helper graph Q dest visited pred) (true or false)\n          (if (BFS-helper node-hash Q dest visited predecessor)\n              (let ((cdr-path (get-path start dest predecessor)))\n                (cons start cdr-path))\n              false)))))\n\n; whether exist a path from start to dest\n; return true/false\n(define BFS-helper\n  (lambda (graph Q end visited pred)\n    (cond\n      [(set-member? visited end) true]\n      [(null? Q) false]\n      [else\n       ; v:parent and w:child\n       (let ((v (mcar Q))\n             (Q* (mcdr Q)))\n         (for-each\n          (lambda (w)\n            (when (not (set-member? visited w))\n              (begin\n                (set-add! visited w)\n                (hash-set! pred w v)\n                (set-mcdr! Q (mappend (mcdr Q) (mlist w))))))\n          (hash-ref graph v '()))\n         ;(display visited)\n         ;(display (mcdr Q))\n         (BFS-helper graph (mcdr Q) end visited pred))])))\n\n(define get-path\n  (lambda (start dest pred)\n    (let ((path (list dest)))\n      (get-path-helper start dest pred path))))\n\n(define get-path-helper\n  (lambda (start dest pred path)\n    (let ((pred-of-dest (hash-ref pred dest '())))\n          (cond\n            [(equal? pred-of-dest start) path]\n            [else\n             (let ((path* (cons pred-of-dest path)))\n               (get-path-helper start pred-of-dest pred path*))]))))\n\n\n;; Next: find the corresponding edges/predicates of each database from the result\n\n\n;retun the corresponding edges/predicates of each database(subject object) pair in one path\n;format: (((subject . object) (pred1 pred2 ... )) ... ) => list of lists\n\n(define path-with-pred-undirected\n  (lambda (ls pred*-hash)\n    (let ((sub-obj-pr-ls (cdr (ls=>pr-ls-undirected ls (list (list))))))\n      (let ((pred-ls (sub-obj-pr-ls=>preds sub-obj-pr-ls pred*-hash)))\n        (cdr (combine-sub-obj-pr-pred sub-obj-pr-ls pred-ls (list (list))))))))\n\n;map each subject object pair as the key to find the corresponding predicates\n;return list of predicates list\n;format: ((pred1 pred2 ...) (pred1 pred2 ...) ...)\n(define sub-obj-pr-ls=>preds\n  (lambda (sub-obj-pr-ls pred*-hash)\n    (map\n     (lambda (k) (hash-ref pred*-hash k '()))\n     sub-obj-pr-ls)))\n\n;take a list of database name (d1 d2 d3 ...)\n;return a list of database pairs by order ((d1 . d2) (d2 . d3) ...) -> same as saying from d1 to d2, d2 to d3, ...\n;only works for directed edges/graph\n(define ls=>pr-ls-directed\n  (lambda (ls accu-ls-ls)\n    (cond\n      [(null? (cdr ls)) accu-ls-ls]\n      [else\n       (let ((from (car ls))\n             (to (cadr ls)))\n         (ls=>pr-ls-directed (cdr ls) (append accu-ls-ls (list (cons from to)))))])))\n\n;for undirected graph: ((d1 . d2) (d2 . d1) (d2 . d3) (d3 . d2) ...))\n(define ls=>pr-ls-undirected\n  (lambda (ls accu-ls-ls)\n    (cond\n      [(null? (cdr ls)) accu-ls-ls]\n      [else\n       (let ((from (car ls))\n             (to (cadr ls)))\n         (if (equal? from to)\n             (ls=>pr-ls-undirected (cdr ls) (append accu-ls-ls (list (cons from to))))\n             (ls=>pr-ls-undirected (cdr ls) (append accu-ls-ls (list (cons from to) (cons to from))))))])))\n\n;recursively combine each subject object pair to the corresponding list of predicates\n;format: (((subject . object) (pred1 pred2 ... )) ... ) => list of lists\n(define combine-sub-obj-pr-pred\n  (lambda (pr-ls pred-ls accu)\n    (cond\n      [(null? pr-ls) accu]\n      [else\n       (if (not (null? (car pred-ls)))\n           (combine-sub-obj-pr-pred (cdr pr-ls) (cdr pred-ls) (append accu (list (list (car pr-ls) (car pred-ls)))))\n           (combine-sub-obj-pr-pred (cdr pr-ls) (cdr pred-ls) accu))])))\n\n;=============================================== visualization ==========================================================\n\n\n(define path*-with-pred=>set-ls\n  (lambda (path*-with-pred st)\n    (cond\n      [(null? path*-with-pred) st]\n      [else\n       (path*-with-pred=>set-ls (cdr path*-with-pred) (path*-with-pred=>set-ls-helper (car path*-with-pred) st))])))\n\n(define path*-with-pred=>set-ls-helper\n  (lambda (path*-ls st)\n    (cond\n      [(null? path*-ls) st]\n      [else\n         (let ((subject-curie-prefix (caaar path*-ls))\n               (object-curie-prefix (cdaar path*-ls))\n               (predicate-string (string-join (cadar path*-ls) \"\\n\")))\n           (let ((new-st (set-add st (list subject-curie-prefix object-curie-prefix predicate-string))))\n             (path*-with-pred=>set-ls-helper (cdr path*-ls) new-st)))])))\n\n(define path*-ls=>concept-set\n  (lambda (path*-ls concept-set)\n      (let ((shortest-path-ls (find-shortest-path-ls path*-ls)))\n        (shortest-path-ls=>concept-set shortest-path-ls concept-set))))\n\n\n(define shortest-path-ls=>concept-set\n  (lambda (shortest-path-ls concept-set)\n    (cond\n      [(null? shortest-path-ls) concept-set]\n      [else\n       (for-each\n        (lambda(p)\n          (set-add! concept-set p))\n        (car shortest-path-ls))\n       (shortest-path-ls=>concept-set (cdr shortest-path-ls) concept-set)])))\n\n; write a JASON file containing the nodes and edges information for visualization\n(define visualize-with-web\n  (lambda (shortest-path*-with-pred)\n    (with-output-to-file \"shorest-path-graph-vars.js\"\n      (lambda ()\n        (printf \"var nodes = new vis.DataSet([\\n\")\n        (for-each\n         (lambda(c)\n           (printf \"{ id: ~s, label: ~s},\\n\" c c))\n         (set->list (path*-ls=>concept-set (car shortest-path*-with-pred) (mutable-set))))\n        (printf \"]);\\n\")\n        (printf \"var edges = new vis.DataSet([\\n\")\n        (set-map\n         (path*-with-pred=>set-ls (cadr shortest-path*-with-pred) (set))\n         (lambda (ls)\n           (match ls\n             [`(,subject-curie-prefix ,object-curie-prefix ,predicate-string)\n              (printf \"{ from: ~s, to: ~s, arrows: \\\"to\\\", predicate: ~s},\\n\" subject-curie-prefix object-curie-prefix predicate-string)])))\n        (printf \"]);\\n\"))\n      #:mode 'text\n      #:exists 'replace)))\n\n\n;===============================================useful helper functions==================================================\n\n(define build-undirected-graph\n  (lambda (ls level/num)\n    (list (make-undirected-node-hash ls level/num)\n    (make-edge-hash ls level/num))))\n\n;(match-define (list node-hash edge-hash) (build-undirected-graph rtx2-data 2669662))\n\n; load all required hash tables for finding the shortest path\n; input: data from .tsv file; edge/predicate count level or number \n(define load-all-hash\n  (lambda (ls level/num)\n    (list\n     (make-undirected-node-hash ls level/num)\n     (make-edge-hash ls level/num)\n     (preds=>database-pair ls level/num))))\n\n;(match-define (list node-hash edge-hash pred/prefix-pr-hash) (load-all-hash rtx2-data 2669662))\n\n(define shortest-path*\n  (lambda (all-hash start end pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (cond\n      [(equal? pred #f)\n       (list (BFS node-hash start end))]\n      [(equal? end #f)\n       (shortest-path*-contain-pred-unknown-end all-hash start pred)]\n      [else\n       (shortest-path*-contain-pred all-hash start end pred)])))\n       \n(define shortest-path*-with-pred\n  (lambda (all-hash start end pred)\n    (match-define (list node-hash edge-hash pred/prefix-pr-hash) all-hash)\n    (cond\n      [(equal? pred #f)\n       (let ((path (list (BFS node-hash start end))))\n         (list path (shortest-path-with-pred path edge-hash)))]\n      [(equal? end #f)\n       (let ((path (shortest-path*-contain-pred-unknown-end all-hash start pred)))\n         (list path (shortest-path-with-pred path edge-hash)))]\n      [else\n       (let ((path (shortest-path*-contain-pred all-hash start end pred)))\n         (list path (shortest-path-with-pred path edge-hash)))])))\n\n(define single-path=>path-with-pred\n  (lambda (all-hash single-path)\n    (if (list? (car single-path))\n        (error \"The second argument should be one single path. e.g. (node-1 node-2)\")\n        (path-with-pred-undirected single-path (cadr all-hash)))))\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/sri-reference-kg-0.2.0/sri-reference-kg-0.2.0-map.html",
    "content": "\n\n  SRI Reference 0.2.0 KG Map\n  \n\n\n
\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/sri-reference-kg-0.2.0/sri-reference-kg-0.2.0-subject_predicate_object_count.tsv",
    "content": "subject CURIE prefix\tobject CURIE prefix\tpredicate\tedge 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\t\"RO\" -> \"GENO\" [label=\"biolink:subPropertyOf (6)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:overlaps (27)\"]; \t\"KEGG-path\" -> \"GO\" [label=\"biolink:subclass_of (537)\"]; \t\"VGNC\" -> \"SGD\" [label=\"biolink:related_to (4)\"]; \t\"FAO\" -> \"FAO\" [label=\"biolink:part_of (4)\"]; \t\"MONARCH_BNODE\" -> \"EFO\" [label=\"biolink:related_to (3375)\"]; \t\"http\" -> \"foaf\" [label=\"biolink:subclass_of (7)\"]; \t\"RO\" -> \"RO\" [label=\"biolink:subPropertyOf (626)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:overlaps (26)\"]; \t\"ZP\" -> \"UBERON\" [label=\"biolink:subclass_of (5407)\"]; \t\"RGD\" -> \"MP\" [label=\"biolink:has_phenotype (1009)\"]; \t\"NCBIGene\" -> \"OBO\" [label=\"biolink:related_to (578172)\"]; \t\"DOID\" -> \"HP\" [label=\"biolink:subclass_of (12)\"]; \t\"https\" -> \"https\" [label=\"biolink:biomarker_for (97442)\"]; \t\"ZFIN\" -> \"GENO\" [label=\"biolink:subclass_of (15)\"]; \t\"VGNC\" -> \"WormBase\" [label=\"biolink:related_to (1)\"]; \t\"FlyBase\" -> \"GO\" [label=\"biolink:enables (22788)\"]; \t\"Xenbase\" -> \"FlyBase\" [label=\"biolink:orthologous_to (9546)\"]; \t\"JAX\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (114)\"]; \t\"OBI\" -> \"CL\" [label=\"biolink:related_to (5)\"]; \t\"Orphanet\" -> \"HP\" [label=\"biolink:subclass_of (7)\"]; \t\"NCBITaxon\" -> \"OBO\" [label=\"biolink:subclass_of (31)\"]; \t\"HP\" -> \"CL\" [label=\"biolink:subclass_of (116)\"]; \t\"OBI\" -> \"RO\" [label=\"biolink:subPropertyOf (6)\"]; \t\"ZFIN\" -> \"GO\" [label=\"biolink:actively_involved_in (65188)\"]; \t\"HGNC\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (10886)\"]; \t\"OBI\" -> \"GO\" [label=\"biolink:related_to (3)\"]; \t\"GENO\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (3)\"]; \t\"OBI\" -> \"OBO\" [label=\"biolink:has_part (3)\"]; \t\"MONARCH_NODE\" -> \"WormBase\" [label=\"biolink:related_to (7)\"]; \t\"HP\" -> \"GO\" [label=\"biolink:subclass_of (211)\"]; \t\"PMID\" -> \"KEGG-path\" [label=\"biolink:related_to (6336)\"]; \t\"HGNC\" -> \"ENSEMBL\" [label=\"biolink:same_as (1507)\"]; \t\"CL\" -> \"CL\" [label=\"biolink:derives_from (1)\"]; \t\"MP\" -> \"owl\" [label=\"biolink:subclass_of (441)\"]; \t\"OBO\" -> \"OBI\" [label=\"biolink:subclass_of (29)\"]; \t\"chickenQTL\" -> \"NCBIGene\" [label=\"biolink:biomarker_for (6461)\"]; \t\"CL\" -> \"CL\" [label=\"biolink:related_to (411)\"]; \t\"MONARCH\" -> \"HGNC\" [label=\"biolink:model_of (1)\"]; \t\"NCBIGene\" -> \"pigQTL\" [label=\"biolink:biomarker_for (107)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:related_to (149)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"biolink:related_to (7)\"]; \t\"NCBIGene\" -> \"dictyBase\" [label=\"biolink:orthologous_to (399)\"]; \t\"WormBase\" -> \"WBPhenotype\" [label=\"biolink:has_phenotype (106355)\"]; \t\"FlyBase\" -> \"UBERON\" [label=\"biolink:expressed_in (52120)\"]; \t\"GeneReviews\" -> \"DOID\" [label=\"biolink:subclass_of (737)\"]; \t\"KEGG-ko\" -> \"DATA\" [label=\"biolink:subclass_of (23530)\"]; \t\"NCBIGene\" -> \"SGD\" [label=\"biolink:orthologous_to (142)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"biolink:related_to (64258)\"]; \t\"MP\" -> \"UPHENO\" [label=\"biolink:subclass_of (2)\"]; \t\"wgs\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"OMIA\" -> \"CL\" [label=\"biolink:has_phenotype (3)\"]; \t\"SGD\" -> \"GO\" [label=\"biolink:part_of (23564)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:produces (15)\"]; \t\"CHEBI\" -> \"GO\" [label=\"biolink:has_phenotype (10)\"]; \t\"HGNC\" -> \"HGNC\" [label=\"biolink:has_gene_product (2)\"]; \t\"OBO\" -> \"NCIT\" [label=\"biolink:subclass_of (18537)\"]; \t\"CHEBI\" -> \"SO\" [label=\"biolink:subclass_of (26)\"]; \t\"NCBIGene\" -> \"OMIMPS\" [label=\"biolink:related_to (6)\"]; \t\"HGNC\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (82378)\"]; \t\"CHEBI\" -> \"BFO\" [label=\"biolink:subclass_of (7)\"]; \t\"GENO\" -> \"BFO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:has_output (1)\"]; \t\"WormBase\" -> \"PomBase\" [label=\"biolink:related_to (2261)\"]; \t\"OMIA\" -> \"GO\" [label=\"biolink:has_phenotype (11)\"]; \t\"MGI\" -> \"VGNC\" [label=\"biolink:related_to (8)\"]; \t\"VGNC\" -> \"FlyBase\" [label=\"biolink:related_to (7)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"biolink:subclass_of (192269)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"biolink:biomarker_for (22754)\"]; \t\"NCBIGene\" -> \"WormBase\" [label=\"biolink:orthologous_to (986)\"]; \t\"BSPO\" -> \"OBO\" [label=\"biolink:related_to (1)\"]; \t\"WormBase\" -> \"GO\" [label=\"biolink:actively_involved_in (34343)\"]; \t\"MGI\" -> \"Xenbase\" [label=\"biolink:related_to (10621)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:has_output (14)\"]; \t\"PR\" -> \"FlyBase\" [label=\"biolink:related_to (7)\"]; \t\"CLO\" -> \"CLO\" [label=\"biolink:subclass_of (38837)\"]; \t\"GO\" -> \"PR\" [label=\"biolink:has_part (2)\"]; \t\"NCBITaxon\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"ENSEMBL\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (573072)\"]; \t\"ENVO\" -> \"UBERON\" [label=\"biolink:related_to (1)\"]; \t\"CL\" -> \"OBO\" [label=\"biolink:has_part (29)\"]; \t\"ECO\" -> \"OBO\" [label=\"biolink:related_to (2)\"]; \t\"BIOGRID\" -> \"HGNC\" [label=\"biolink:same_as (26)\"]; \t\"UMLS\" -> \"Orphanet\" [label=\"biolink:subclass_of (15436)\"]; \t\"FBcv\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:part_of (153)\"]; \t\"Coriell\" -> \"CLO\" [label=\"biolink:derives_from (119)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:has_part (54)\"]; \t\"MP\" -> \"ZP\" [label=\"biolink:subclass_of (553)\"]; \t\"MONARCH_BNODE\" -> \"NCIT\" [label=\"biolink:has_part (164)\"]; \t\"SGD\" -> \"MONARCH_NODE\" [label=\"biolink:has_phenotype (60168)\"]; \t\"SO\" -> \"GENO\" [label=\"biolink:has_part (1)\"]; \t\"MONARCH_BNODE\" -> \"https\" [label=\"biolink:related_to (75558)\"]; \t\"OBI\" -> \"CL\" [label=\"biolink:derives_from (1)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:part_of (9112)\"]; \t\"MESH\" -> \"OMIM\" [label=\"biolink:biomarker_for (11)\"]; \t\"WormBase\" -> \"UBERON\" [label=\"biolink:expressed_in (25331)\"]; \t\"MONARCH\" -> \"dbSNP\" [label=\"biolink:related_to (13167)\"]; \t\"HGNC\" -> \"EcoGene\" [label=\"biolink:related_to (287)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:capable_of (361)\"]; \t\"ENVO\" -> \"BFO\" [label=\"biolink:related_to (1)\"]; \t\"RGD\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (606)\"]; \t\"FBcv\" -> \"UPHENO\" [label=\"biolink:subclass_of (1)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"biolink:related_to (17)\"]; \t\"ZFIN\" -> \"ZFIN\" [label=\"biolink:genetically_interacts_with (17)\"]; \t\"FlyBase\" -> \"MGI\" [label=\"biolink:interacts_with (3)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:related_to (1243)\"]; \t\"PR\" -> \"OBO\" [label=\"biolink:has_part (7)\"]; \t\"MONARCH_BNODE\" -> \"OMIM\" [label=\"biolink:contributes_to (51)\"]; \t\"HP\" -> \"http\" [label=\"biolink:related_to (400)\"]; \t\"RGD\" -> \"ZFIN\" [label=\"biolink:orthologous_to (18674)\"]; \t\"PANTHER\" -> \"EcoGene\" [label=\"biolink:related_to (631)\"]; \t\"UBERON\" -> \"OBO\" [label=\"biolink:subclass_of (460)\"]; \t\"OBO\" -> \"OGMS\" [label=\"biolink:related_to (1)\"]; \t\"MONARCH_BNODE\" -> \"PMID\" [label=\"biolink:related_to (302498)\"]; \t\"Xenbase\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (249)\"]; \t\"OBAN\" -> \"IAO\" [label=\"biolink:subclass_of (1)\"]; \t\"ZFIN\" -> \"EcoGene\" [label=\"biolink:orthologous_to (1069)\"]; \t\"Xenbase\" -> \"PomBase\" [label=\"biolink:related_to (2173)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:capable_of (124)\"]; \t\"UMLS\" -> \"OBO\" [label=\"biolink:subclass_of (31149)\"]; \t\"FlyBase\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (2587)\"]; \t\"NCBIGene\" -> \"FlyBase\" [label=\"biolink:orthologous_to (1101)\"]; \t\"Orphanet\" -> \"HP\" [label=\"biolink:related_to (69)\"]; \t\"MONARCH_BNODE\" -> \"dbSNPIndividual\" [label=\"biolink:related_to (2961)\"]; \t\"SEPIO\" -> \"RO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"GO\" -> \"SO\" [label=\"biolink:related_to (66)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"biolink:has_part (3795)\"]; \t\"JAX\" -> \"JAX\" [label=\"biolink:related_to (4)\"]; \t\"OBI\" -> \"STATO\" [label=\"biolink:subclass_of (3)\"]; \t\"ENSEMBL\" -> \"EcoGene\" [label=\"biolink:related_to (264)\"]; \t\"PR\" -> \"owl\" [label=\"biolink:subclass_of (59)\"]; \t\"MP\" -> \"HP\" [label=\"biolink:subclass_of (8108)\"]; \t\"OBO\" -> \"ENVO\" [label=\"biolink:subclass_of (4)\"]; \t\"FAO\" -> \"OBO\" [label=\"biolink:subclass_of (4)\"]; \t\"MonarchData\" -> \"https\" [label=\"owl:versionIRI (1)\"]; \t\"WormBase\" -> \"GO\" [label=\"biolink:enables (28231)\"]; \t\"GO\" -> \"CHEBI\" [label=\"biolink:related_to (5698)\"]; \t\"WormBase\" -> \"NCBIGene\" [label=\"biolink:interacts_with (283)\"]; \t\"MGI\" -> \"EcoGene\" [label=\"biolink:orthologous_to (986)\"]; \t\"ENVO\" -> \"NCBITaxon\" [label=\"biolink:related_to (7)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:precedes (1)\"]; \t\"OMIA\" -> \"MONDO\" [label=\"biolink:subclass_of (1758)\"]; \t\"ECO\" -> \"IAO\" [label=\"biolink:subclass_of (1)\"]; \t\"FBcv\" -> \"ZP\" [label=\"biolink:subclass_of (70)\"]; \t\"Orphanet\" -> \"HP\" [label=\"biolink:has_phenotype (95937)\"]; \t\"ECO\" -> \"OBI\" [label=\"biolink:related_to (124)\"]; \t\"DOID\" -> \"UMLS\" [label=\"biolink:subclass_of (13059)\"]; \t\"MGI\" -> \"GO\" [label=\"biolink:enables (82475)\"]; \t\"HGNC\" -> \"OMIM\" [label=\"biolink:contributes_to (843)\"]; \t\"GO\" -> \"FAO\" [label=\"biolink:related_to (17)\"]; \t\"MONARCH_BNODE\" -> \"https\" [label=\"biolink:part_of (29389)\"]; \t\"http\" -> \"DOID\" [label=\"biolink:subclass_of (18439)\"]; \t\"rdf\" -> \"owl\" [label=\"biolink:subclass_of (2)\"]; \t\"MONARCH\" -> \"OMIA\" [label=\"biolink:has_phenotype (897)\"]; \t\"dbSNP\" -> \"MONDO\" [label=\"biolink:related_to (111)\"]; \t\"VGNC\" -> \"SGD\" [label=\"biolink:orthologous_to (2)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:participates_in (18)\"]; \t\"CLO\" -> \"CLO\" [label=\"biolink:derives_from (1)\"]; \t\"http\" -> \"OGMS\" [label=\"biolink:subclass_of (25)\"]; \t\"MONARCH_BNODE\" -> \"NCBITaxon\" [label=\"owl:someValuesFrom (233)\"]; \t\"Orphanet\" -> \"UMLS\" [label=\"biolink:subclass_of (13030)\"]; \t\"MGI\" -> \"UBERON\" [label=\"biolink:expressed_in (356928)\"]; \t\"OBI\" -> \"SO\" [label=\"biolink:subclass_of (2)\"]; \t\"OBI\" -> \"MONDO\" [label=\"biolink:subclass_of (2)\"]; \t\"DOID\" -> \"UBERON\" [label=\"biolink:subclass_of (1)\"]; \t\"WormBase\" -> \"GO\" [label=\"biolink:has_phenotype (3795)\"]; \t\"OBI\" -> \"BFO\" [label=\"biolink:subclass_of (50)\"]; \t\"ZFIN\" -> \"DOID\" [label=\"biolink:model_of (1195)\"]; \t\"chickenQTL\" -> \"chickenQTL\" [label=\"biolink:biomarker_for (2131)\"]; \t\"MONARCH_BNODE\" -> \"MONDO\" [label=\"biolink:related_to (23)\"]; \t\"OBI\" -> \"CHEBI\" [label=\"biolink:subclass_of (15)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:capable_of (14)\"]; \t\"FlyBase\" -> \"HGNC\" [label=\"biolink:interacts_with (42)\"]; \t\"foaf\" -> \"dcterms\" [label=\"biolink:subclass_of (4)\"]; \t\"GO\" -> \"NCBITaxon\" [label=\"biolink:related_to (683)\"]; \t\"HGNC\" -> \"GO\" [label=\"biolink:actively_involved_in (39884)\"]; \t\"ClinVarVariant\" -> \"Orphanet\" [label=\"biolink:related_to (2193)\"]; \t\"NCIT\" -> \"Orphanet\" [label=\"biolink:subclass_of (4801)\"]; \t\"IAO\" -> \"OIO\" [label=\"biolink:type (1)\"]; \t\"ClinVarVariant\" -> \"UMLS\" [label=\"biolink:gene_associated_with_condition (55137)\"]; \t\"UBERON\" -> \"PR\" [label=\"biolink:produces (5)\"]; \t\"Coriell\" -> \"HGNC\" [label=\"biolink:model_of (741)\"]; \t\"IAO\" -> \"owl\" [label=\"biolink:type (2)\"]; \t\"dbSNP\" -> \"https\" [label=\"biolink:biomarker_for (94336)\"]; \t\"OBI\" -> \"OBO\" [label=\"biolink:related_to (6)\"]; \t\"DOID\" -> \"MONDO\" [label=\"biolink:subclass_of (26067)\"]; \t\"UMLS\" -> \"OBI\" [label=\"biolink:subclass_of (18)\"]; \t\"DOID\" -> \"BFO\" [label=\"biolink:subclass_of (1)\"]; \t\"foaf\" -> \"foaf\" [label=\"biolink:inverseOf (4)\"]; \t\"HP\" -> \"OBO\" [label=\"biolink:subclass_of (185)\"]; \t\"WBPhenotype\" -> \"MP\" [label=\"biolink:subclass_of (192)\"]; \t\"dictyBase\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (332)\"]; \t\"FBcv\" -> \"HP\" [label=\"biolink:subclass_of (25)\"]; \t\"NCBIGene\" -> \"HGNC\" [label=\"biolink:same_as (1881)\"]; \t\"NCBIGene\" -> \"MGI\" [label=\"biolink:related_to (14473)\"]; \t\"chickenQTL\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (16494)\"]; \t\"MONARCH\" -> \"OMIM\" [label=\"biolink:related_to (1)\"]; \t\"Orphanet\" -> \"MONDO\" [label=\"biolink:subclass_of (28520)\"]; \t\"NCBIGene\" -> \"chickenQTL\" [label=\"biolink:biomarker_for (1)\"]; \t\"FlyBase\" -> \"dictyBase\" [label=\"biolink:orthologous_to (5816)\"]; \t\"Orphanet\" -> \"BFO\" [label=\"biolink:subclass_of (1)\"]; \t\"SEPIO\" -> \"SEPIO\" [label=\"biolink:has_output (1)\"]; \t\"http\" -> \"http\" [label=\"biolink:subclass_of (28707)\"]; \t\"OBO\" -> \"OIO\" [label=\"biolink:subclass_of (11)\"]; \t\"FlyBase\" -> \"SGD\" [label=\"biolink:orthologous_to (2518)\"]; \t\"OBI\" -> \"IAO\" [label=\"biolink:subclass_of (23)\"]; \t\"ZFIN\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (63616)\"]; \t\"OBO\" -> \"owl\" [label=\"biolink:subclass_of (1378)\"]; \t\"CLO\" -> \"GENO\" [label=\"biolink:subclass_of (1)\"]; \t\"https\" -> \"OIO\" [label=\"biolink:subclass_of (7)\"]; \t\"https\" -> \"AQTLTrait\" [label=\"biolink:biomarker_for (121393)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:related_to (6521)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:affects_localization_of (6)\"]; \t\"PW\" -> \"PW\" [label=\"biolink:subclass_of (3117)\"]; \t\"PomBase\" -> \"GO\" [label=\"biolink:part_of (16735)\"]; \t\"UMLS\" -> \"NCIT\" [label=\"biolink:subclass_of (14968)\"]; \t\"ZFIN\" -> \"NCBIGene\" [label=\"biolink:interacts_with (575)\"]; \t\"ZFIN\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (18712)\"]; \t\"pigQTL\" -> \"NCBIGene\" [label=\"biolink:related_to (662)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:has_input (69)\"]; \t\"SIO\" -> \"BFO\" [label=\"biolink:subclass_of (1)\"]; \t\"MGI\" -> \"GO\" [label=\"biolink:has_phenotype (23069)\"]; \t\"GENO\" -> \"IAO\" [label=\"biolink:inverseOf (1)\"]; \t\"NCIT\" -> \"OBO\" [label=\"biolink:subclass_of (15152)\"]; \t\"HGNC\" -> \"ENSEMBL\" [label=\"biolink:related_to (160551)\"]; \t\"ClinVarVariant\" -> \"MONDO\" [label=\"biolink:gene_associated_with_condition (19155)\"]; \t\"BIOGRID\" -> \"Orphanet\" [label=\"biolink:biomarker_for (1)\"]; \t\"SGD\" -> \"APO\" [label=\"biolink:has_phenotype (8507)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:subclass_of (1)\"]; \t\"Coriell\" -> \"MONARCH_BNODE\" [label=\"biolink:derives_from (30624)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:has_input (123)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:has_participant (10)\"]; \t\"MGI\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (494740)\"]; \t\"KEGG-path\" -> \"PW\" [label=\"biolink:subclass_of (537)\"]; \t\"RO\" -> \"OBO\" [label=\"biolink:subPropertyOf (1)\"]; \t\"OMIA\" -> \"OBO\" [label=\"biolink:has_phenotype (35)\"]; \t\"RGD\" -> \"dictyBase\" [label=\"biolink:related_to (3223)\"]; \t\"MONDO\" -> \"CL\" [label=\"biolink:related_to (126)\"]; \t\"HGNC\" -> \"http\" [label=\"biolink:orthologous_to (966)\"]; \t\"ENVO\" -> \"RO\" [label=\"biolink:subclass_of (1)\"]; \t\"WormBase\" -> \"EcoGene\" [label=\"biolink:orthologous_to (847)\"]; \t\"RGD\" -> \"SGD\" [label=\"biolink:related_to (2352)\"]; \t\"PANTHER\" -> \"ENSEMBL\" [label=\"biolink:related_to (195305)\"]; \t\"ZFIN\" -> \"MONARCH_BNODE\" [label=\"biolink:has_part (5909)\"]; \t\"WormBase\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (973977)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (26)\"]; \t\"UBERON\" -> \"CHEBI\" [label=\"biolink:related_to (12)\"]; \t\"MONDO\" -> \"GO\" [label=\"biolink:related_to (467)\"]; \t\"SEPIO\" -> \"BFO\" [label=\"biolink:subclass_of (7)\"]; \t\"GO\" -> \"BFO\" [label=\"biolink:subclass_of (3)\"]; \t\"foaf\" -> \"owl\" [label=\"biolink:subclass_of (6)\"]; \t\"SEPIO\" -> \"CHEBI\" [label=\"biolink:subclass_of (3)\"]; \t\"SO\" -> \"owl\" [label=\"biolink:subclass_of (242)\"]; \t\"GO\" -> \"PO\" [label=\"biolink:part_of (9)\"]; \t\"RGD\" -> \"WormBase\" [label=\"biolink:related_to (4685)\"]; \t\"ENSEMBL\" -> \"SO\" [label=\"biolink:subclass_of (5384)\"]; \t\"ZFIN\" -> \"GO\" [label=\"biolink:enables (53364)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:related_to (227)\"]; \t\"SIO\" -> \"IAO\" [label=\"biolink:subclass_of (1)\"]; \t\"http\" -> \"MP\" [label=\"biolink:subclass_of (13)\"]; \t\"ENSEMBL\" -> \"ENSEMBL\" [label=\"biolink:related_to (530874)\"]; \t\"NCBIGene\" -> \"ZFIN\" [label=\"biolink:related_to (8456)\"]; \t\"NCBIGene\" -> \"GO\" [label=\"biolink:actively_involved_in (129041)\"]; \t\"IAO\" -> \"OBO\" [label=\"biolink:related_to (3)\"]; \t\"CoriellCollection\" -> \"CoriellCollection\" [label=\"biolink:related_to (4)\"]; \t\"ENSEMBL\" -> \"http\" [label=\"biolink:orthologous_to (890)\"]; \t\"NCBITaxon\" -> \"owl\" [label=\"biolink:subclass_of (148)\"]; \t\"MONARCH_BNODE\" -> \"AQTLTrait\" [label=\"biolink:has_phenotype (1815)\"]; \t\"BFO\" -> \"OIO\" [label=\"biolink:subclass_of (1)\"]; \t\"BFO\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"biolink:has_part (3)\"]; \t\"NCBIGene\" -> \"HGNC\" [label=\"biolink:related_to (7414)\"]; \t\"MGI\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (133358)\"]; \t\"MMRRC\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (50892)\"]; \t\"RO\" -> \"RO\" [label=\"biolink:subclass_of (2)\"]; \t\"sheepQTL\" -> \"sheepQTL\" [label=\"biolink:biomarker_for (3411)\"]; \t\"HP\" -> \"FBcv\" [label=\"biolink:subclass_of (82)\"]; \t\"MONDO\" -> \"Orphanet\" [label=\"biolink:subclass_of (28521)\"]; \t\"ClinVarVariant\" -> \"NCBIGene\" [label=\"biolink:related_to (79)\"]; \t\"NCBIGene\" -> \"OMIM\" [label=\"biolink:contributes_to (11)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:subclass_of (287)\"]; \t\"http\" -> \"wgs\" [label=\"biolink:subclass_of (2)\"]; \t\"dbSNP\" -> \"ENSEMBL\" [label=\"biolink:related_to (51185)\"]; \t\"UBERON\" -> \"NCBITaxon\" [label=\"biolink:related_to (749)\"]; \t\"CL\" -> \"OBI\" [label=\"biolink:related_to (1)\"]; \t\"ClinVarVariant\" -> \"OMIMPS\" [label=\"biolink:related_to (19963)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:has_participant (28)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:has_part (28)\"]; \t\"SEPIO\" -> \"IAO\" [label=\"biolink:subclass_of (10)\"]; \t\"HP\" -> \"NCIT\" [label=\"biolink:subclass_of (6)\"]; \t\"PO\" -> \"OBO\" [label=\"biolink:subclass_of (2)\"]; \t\"NCBIGene\" -> \"RGD\" [label=\"biolink:related_to (8918)\"]; \t\"NCIT\" -> \"OBI\" [label=\"biolink:subclass_of (6)\"]; \t\"Coriell\" -> \"CL\" [label=\"biolink:derives_from (30505)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:has_participant (65)\"]; \t\"MP\" -> \"UMLS\" [label=\"biolink:subclass_of (3)\"]; \t\"UBERON\" -> \"OBO\" [label=\"biolink:capable_of (2)\"]; \t\"GO\" -> \"NCBITaxon\" [label=\"biolink:subclass_of (2)\"]; \t\"CL\" -> \"UBERON\" [label=\"biolink:located_in (13)\"]; \t\"UBERON\" -> \"ENVO\" [label=\"biolink:subclass_of (1)\"]; \t\"FlyBase\" -> \"GO\" [label=\"biolink:actively_involved_in (42834)\"]; \t\"WormBase\" -> \"MGI\" [label=\"biolink:interacts_with (2)\"]; \t\"CoriellCollection\" -> \"Coriell\" [label=\"biolink:related_to (30624)\"]; \t\"NCBIGene\" -> \"FlyBase\" [label=\"biolink:genetically_interacts_with (16)\"]; \t\"ZFIN\" -> \"GO\" [label=\"biolink:part_of (46379)\"]; \t\"http\" -> \"prov\" [label=\"biolink:subclass_of (2)\"]; \t\"ZFIN\" -> \"dictyBase\" [label=\"biolink:related_to (3209)\"]; \t\"CL\" -> \"CL\" [label=\"biolink:subclass_of (4930)\"]; \t\"MP\" -> \"UBERON\" [label=\"biolink:subclass_of (2017)\"]; \t\"MONDO\" -> \"OBO\" [label=\"biolink:subclass_of (60187)\"]; \t\"ZFIN\" -> \"SGD\" [label=\"biolink:related_to (2379)\"]; \t\"NCIT\" -> \"NCIT\" [label=\"biolink:subclass_of (9372)\"]; \t\"RGD\" -> \"FlyBase\" [label=\"biolink:related_to (5488)\"]; \t\"prov\" -> \"SEPIO\" [label=\"biolink:related_to (1)\"]; \t\"OMIM\" -> \"OBO\" [label=\"biolink:related_to (48)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:subclass_of (44)\"]; \t\"OBO\" -> \"PO\" [label=\"biolink:has_part (1)\"]; \t\"OBO\" -> \"HP\" [label=\"biolink:subclass_of (38)\"]; \t\"MONARCH\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (5)\"]; \t\"HGNC\" -> \"PomBase\" [label=\"biolink:orthologous_to (3419)\"]; \t\"NCBIGene\" -> \"BIOGRID\" [label=\"biolink:related_to (1093)\"]; \t\"IAO\" -> \"OBI\" [label=\"biolink:related_to (7)\"]; \t\"MGI\" -> \"dictyBase\" [label=\"biolink:related_to (3358)\"]; \t\"REACT\" -> \"GO\" [label=\"biolink:subclass_of (15909)\"]; \t\"ZFIN\" -> \"WormBase\" [label=\"biolink:related_to (4682)\"]; \t\"Xenbase\" -> \"ZFIN\" [label=\"biolink:orthologous_to (6756)\"]; \t\"MP\" -> \"MONDO\" [label=\"biolink:subclass_of (3)\"]; \t\"MGI\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (297818)\"]; \t\"MGI\" -> \"JAX\" [label=\"biolink:same_as (12)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:affects (6013)\"]; \t\"MGI\" -> \"SGD\" [label=\"biolink:related_to (2452)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:has_part (12)\"]; \t\"ENSEMBL\" -> \"CL\" [label=\"biolink:expressed_in (2195)\"]; \t\"horseQTL\" -> \"AQTLTrait\" [label=\"biolink:biomarker_for (1562)\"]; \t\"foaf\" -> \"SEPIO\" [label=\"biolink:related_to (2)\"]; \t\"ENVO\" -> \"PO\" [label=\"biolink:derives_from (1)\"]; \t\"PomBase\" -> \"GO\" [label=\"biolink:actively_involved_in (13919)\"]; \t\"faldo\" -> \"GENO\" [label=\"biolink:subclass_of (1)\"]; \t\"PR\" -> \"MGI\" [label=\"biolink:related_to (198)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"biolink:overlaps (75)\"]; \t\"ENSEMBL\" -> \"PomBase\" [label=\"biolink:orthologous_to (18699)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:part_of (9960)\"]; \t\"MGI\" -> \"WormBase\" [label=\"biolink:related_to (4875)\"]; \t\"rainbow_troutQTL\" -> \"HGNC\" [label=\"biolink:related_to (2)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:capable_of (511)\"]; \t\"MGI\" -> \"JAX\" [label=\"biolink:related_to (22008)\"]; \t\"STATO\" -> \"STATO\" [label=\"biolink:subclass_of (21)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"biolink:inverseOf (9)\"]; \t\"ENVO\" -> \"WD_Entity\" [label=\"biolink:related_to (1)\"]; \t\"dbSNPIndividual\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (3045)\"]; \t\"FlyBase\" -> \"EcoGene\" [label=\"biolink:related_to (251)\"]; \t\"CLO\" -> \"CL\" [label=\"biolink:derives_from (1)\"]; \t\"ZP\" -> \"MP\" [label=\"biolink:subclass_of (6191)\"]; \t\"UBERON\" -> \"owl\" [label=\"biolink:subclass_of (1507)\"]; \t\"WormBase\" -> \"HGNC\" [label=\"biolink:interacts_with (8)\"]; \t\"RGD\" -> \"GO\" [label=\"biolink:has_phenotype (2)\"]; \t\"ZFIN\" -> \"MGI\" [label=\"biolink:interacts_with (1)\"]; \t\"OMIM\" -> \"NCBIGene\" [label=\"biolink:related_to (24)\"]; \t\"UMLS\" -> \"owl\" [label=\"biolink:subclass_of (15)\"]; \t\"NCBIGene\" -> \"CL\" [label=\"biolink:expressed_in (256)\"]; \t\"RGD\" -> \"OBO\" [label=\"biolink:related_to (43897)\"]; \t\"MONDO\" -> \"OBI\" [label=\"biolink:subclass_of (32)\"]; \t\"GENO\" -> \"GENO\" [label=\"biolink:subclass_of (183)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"biolink:coexists_with (33)\"]; \t\"CHEBI\" -> \"PR\" [label=\"biolink:subclass_of (6)\"]; \t\"PW\" -> \"owl\" [label=\"biolink:subclass_of (106)\"]; \t\"UCSC\" -> \"MONARCH_NODE\" [label=\"biolink:related_to (329)\"]; \t\"VGNC\" -> \"ZFIN\" [label=\"biolink:related_to (7)\"]; \t\"FAO\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"FBcv\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"ZFIN\" -> \"FlyBase\" [label=\"biolink:related_to (5497)\"]; \t\"AQTLTrait\" -> \"OBO\" [label=\"biolink:subclass_of (228)\"]; \t\"IAO\" -> \"OIO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"OMIA\" -> \"DOID\" [label=\"biolink:subclass_of (8)\"]; \t\"NCBIGene\" -> \"MGI\" [label=\"biolink:orthologous_to (102)\"]; \t\"OBO\" -> \"OMIM\" [label=\"biolink:related_to (48)\"]; \t\"MONARCH\" -> \"GO\" [label=\"biolink:related_to (5)\"]; \t\"ZFIN\" -> \"UBERON\" [label=\"biolink:expressed_in (167509)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:has_input (64)\"]; \t\"OBAN\" -> \"OBAN\" [label=\"biolink:inverseOf (2)\"]; \t\"PR\" -> \"ZFIN\" [label=\"biolink:related_to (15)\"]; \t\"HGNC\" -> \"http\" [label=\"biolink:related_to (156)\"]; \t\"RGD\" -> \"EcoGene\" [label=\"biolink:orthologous_to (965)\"]; \t\"MONDO\" -> \"PO\" [label=\"biolink:related_to (1)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"biolink:subclass_of (25596)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:occurs_in (3)\"]; \t\"FlyBase\" -> \"NCBITaxon\" [label=\"biolink:related_to (7)\"]; \t\"MONARCH_NODE\" -> \"ZFIN\" [label=\"biolink:related_to (9372)\"]; \t\"MGI\" -> \"FlyBase\" [label=\"biolink:related_to (5747)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:has_part (371)\"]; \t\"*non-standard CURIE*\" -> \"OBO\" [label=\"owl:someValuesFrom (2914)\"]; \t\"MONDO\" -> \"OBO\" [label=\"biolink:related_to (351)\"]; \t\"OBI\" -> \"DOID\" [label=\"biolink:subclass_of (1)\"]; \t\"PANTHER\" -> \"http\" [label=\"biolink:related_to (435)\"]; \t\"UBERON\" -> \"NCBITaxon\" [label=\"biolink:part_of (4)\"]; \t\"http\" -> \"CLO\" [label=\"biolink:subclass_of (10)\"]; \t\"OGMS\" -> \"MONDO\" [label=\"biolink:subclass_of (1)\"]; \t\"OBO\" -> \"UBERON\" [label=\"biolink:derives_from (3)\"]; \t\"OGMS\" -> \"BFO\" [label=\"biolink:subclass_of (3)\"]; \t\"*non-standard CURIE*\" -> \"GENO\" [label=\"owl:onProperty (1)\"]; \t\"ZFIN\" -> \"http\" [label=\"biolink:orthologous_to (1192)\"]; \t\"WormBase\" -> \"dictyBase\" [label=\"biolink:related_to (2831)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:related_to (61)\"]; \t\"ZFIN\" -> \"ZFIN\" [label=\"biolink:interacts_with (31398)\"]; \t\"WormBase\" -> \"SGD\" [label=\"biolink:related_to (2181)\"]; \t\"HGNC\" -> \"Xenbase\" [label=\"biolink:orthologous_to (3806)\"]; \t\"*non-standard CURIE*\" -> \"RO\" [label=\"owl:onProperty (2932)\"]; \t\"FlyBase\" -> \"HGNC\" [label=\"biolink:same_as (2)\"]; \t\"ClinVarVariant\" -> \"NCBIGene\" [label=\"biolink:has_part (2)\"]; \t\"RGD\" -> \"NCBIGene\" [label=\"biolink:related_to (399)\"]; \t\"STATO\" -> \"IAO\" [label=\"biolink:subclass_of (2)\"]; \t\"ENSEMBL\" -> \"http\" [label=\"biolink:related_to (149)\"]; \t\"ZFIN\" -> \"HGNC\" [label=\"biolink:interacts_with (2)\"]; \t\"DOID\" -> \"DOID\" [label=\"biolink:subclass_of (10473)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:occurs_in (88)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:part_of (129)\"]; \t\"PR\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"UBERON\" -> \"CHEBI\" [label=\"biolink:has_part (20)\"]; \t\"PMID\" -> \"dbSNP\" [label=\"biolink:related_to (36936)\"]; \t\"ENSEMBL\" -> \"VGNC\" [label=\"biolink:orthologous_to (4)\"]; \t\"HP\" -> \"owl\" [label=\"biolink:subclass_of (275)\"]; \t\"DOID\" -> \"OGMS\" [label=\"biolink:subclass_of (8)\"]; \t\"ClinVarVariant\" -> \"ORPHA\" [label=\"biolink:gene_associated_with_condition (4)\"]; \t\"NCBIGene\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (2466)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:located_in (1)\"]; \t\"WBPhenotype\" -> \"WBPhenotype\" [label=\"biolink:subclass_of (3270)\"]; \t\"WD_Entity\" -> \"WD_Entity\" [label=\"biolink:part_of (1)\"]; \t\"WormBase\" -> \"WormBase\" [label=\"biolink:related_to (67569)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:subclass_of (341)\"]; \t\"MGI\" -> \"http\" [label=\"biolink:orthologous_to (994)\"]; \t\"GO\" -> \"PO\" [label=\"biolink:has_participant (4)\"]; \t\"Orphanet\" -> \"DOID\" [label=\"biolink:subclass_of (6294)\"]; \t\"HGNC\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (74428)\"]; \t\"ENSEMBL\" -> \"Xenbase\" [label=\"biolink:orthologous_to (41611)\"]; \t\"NCBIGene\" -> \"ZFIN\" [label=\"biolink:orthologous_to (417)\"]; \t\"ENSEMBL\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (3618)\"]; \t\"ZFIN\" -> \"OBO\" [label=\"biolink:related_to (13888)\"]; \t\"Orphanet\" -> \"OGMS\" [label=\"biolink:subclass_of (5)\"]; \t\"JAX\" -> \"MGI\" [label=\"biolink:related_to (97)\"]; \t\"GO\" -> \"PR\" [label=\"biolink:related_to (64)\"]; \t\"OMIA\" -> \"MESH\" [label=\"biolink:subclass_of (47)\"]; \t\"NCBIGene\" -> \"HGNC\" [label=\"biolink:orthologous_to (5)\"]; \t\"PomBase\" -> \"GO\" [label=\"biolink:has_phenotype (3)\"]; \t\"pigQTL\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (31509)\"]; \t\"HP\" -> \"UPHENO\" [label=\"biolink:subclass_of (2)\"]; \t\"OBO\" -> \"BFO\" [label=\"biolink:subPropertyOf (3)\"]; \t\"OBI\" -> \"http\" [label=\"biolink:subclass_of (1)\"]; \t\"SO\" -> \"GENO\" [label=\"biolink:part_of (1)\"]; \t\"MONARCH_BNODE\" -> \"http\" [label=\"biolink:related_to (11747)\"]; \t\"SO\" -> \"GENO\" [label=\"biolink:related_to (4)\"]; \t\"NCIT\" -> \"owl\" [label=\"biolink:subclass_of (23)\"]; \t\"MGI\" -> \"EMMA\" [label=\"biolink:related_to (1186)\"]; \t\"MGI\" -> \"OBO\" [label=\"biolink:related_to (37098)\"]; \t\"MONARCH_BNODE\" -> \"MP\" [label=\"biolink:has_phenotype (5801)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:has_part (845)\"]; \t\"ENVO\" -> \"OBO\" [label=\"biolink:subclass_of (16)\"]; \t\"OBO\" -> \"UMLS\" [label=\"biolink:subclass_of (28724)\"]; \t\"KEGG-path\" -> \"http\" [label=\"biolink:related_to (537)\"]; \t\"MONARCH_BNODE\" -> \"https\" [label=\"biolink:has_part (26470)\"]; \t\"MGI\" -> \"FlyBase\" [label=\"biolink:interacts_with (5)\"]; \t\"RO\" -> \"OIO\" [label=\"biolink:subPropertyOf (1)\"]; \t\"OBAN\" -> \"IAO\" [label=\"biolink:subPropertyOf (3)\"]; \t\"OBO\" -> \"STATO\" [label=\"biolink:subclass_of (2)\"]; \t\"UCSC\" -> \"SO\" [label=\"biolink:subclass_of (10)\"]; \t\"RO\" -> \"owl\" [label=\"biolink:subPropertyOf (6)\"]; \t\"UMLS\" -> \"HP\" [label=\"biolink:subclass_of (19)\"]; \t\"BIOGRID\" -> \"ENSEMBL\" [label=\"biolink:same_as (21)\"]; \t\"NCBIGene\" -> \"RGD\" [label=\"biolink:orthologous_to (53)\"]; \t\"CL\" -> \"OBO\" [label=\"biolink:has_attribute (70)\"]; \t\"MONARCH_BNODE\" -> \"KEGG-path\" [label=\"biolink:actively_involved_in (81602)\"]; \t\"NCBIGene\" -> \"https\" [label=\"biolink:biomarker_for (15739)\"]; \t\"Xenbase\" -> \"SGD\" [label=\"biolink:related_to (2088)\"]; \t\"DOID\" -> \"http\" [label=\"biolink:subclass_of (12794)\"]; \t\"HGNC\" -> \"PomBase\" [label=\"biolink:related_to (2546)\"]; \t\"CL\" -> \"OBO\" [label=\"biolink:subclass_of (49)\"]; \t\"OMIM\" -> \"OMIMPS\" [label=\"biolink:subclass_of (3809)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"biolink:related_to (80286)\"]; \t\"OBO\" -> \"UBERON\" [label=\"biolink:subclass_of (13717)\"]; \t\"ClinVarVariant\" -> \"HGNC\" [label=\"biolink:related_to (23093)\"]; \t\"ECO\" -> \"ECO\" [label=\"biolink:related_to (1104)\"]; \t\"OMIA\" -> \"MP\" [label=\"biolink:subclass_of (32)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:overlaps (1473)\"]; \t\"Orphanet\" -> \"http\" [label=\"biolink:subclass_of (8031)\"]; \t\"RO\" -> \"UPHENO\" [label=\"biolink:subPropertyOf (3)\"]; \t\"OIO\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"PANTHER\" -> \"PomBase\" [label=\"biolink:related_to (3209)\"]; \t\"HP\" -> \"ZP\" [label=\"biolink:subclass_of (376)\"]; \t\"GENO\" -> \"GENO\" [label=\"biolink:related_to (43)\"]; \t\"WormBase\" -> \"FlyBase\" [label=\"biolink:related_to (4666)\"]; \t\"Xenbase\" -> \"WormBase\" [label=\"biolink:related_to (4052)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:part_of (2)\"]; \t\"PMID\" -> \"Xenbase\" [label=\"biolink:related_to (18617)\"]; \t\"ZFIN\" -> \"NCBIGene\" [label=\"biolink:related_to (6)\"]; \t\"MONDO\" -> \"NCIT\" [label=\"biolink:related_to (39)\"]; \t\"OGMS\" -> \"OGMS\" [label=\"biolink:related_to (1)\"]; \t\"ZFIN\" -> \"PomBase\" [label=\"biolink:orthologous_to (3853)\"]; \t\"OBO\" -> \"SO\" [label=\"biolink:subclass_of (2395)\"]; \t\"OBO\" -> \"MONDO\" [label=\"biolink:subclass_of (60760)\"]; \t\"OBO\" -> \"BFO\" [label=\"biolink:subclass_of (50)\"]; \t\"ENSEMBL\" -> \"OBO\" [label=\"biolink:expressed_in (6202)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:inverseOf (4)\"]; \t\"OBO\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (233)\"]; \t\"https\" -> \"SO\" [label=\"biolink:subclass_of (3867)\"]; \t\"BSPO\" -> \"BFO\" [label=\"biolink:subPropertyOf (12)\"]; \t\"MONARCH_BNODE\" -> \"STATO\" [label=\"biolink:has_part (26306)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:derives_from (1)\"]; \t\"OBO\" -> \"CHEBI\" [label=\"biolink:subclass_of (5)\"]; \t\"FlyBase\" -> \"SO\" [label=\"biolink:subclass_of (39259)\"]; \t\"RGD\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (86014)\"]; \t\"ENSEMBL\" -> \"PomBase\" [label=\"biolink:related_to (11443)\"]; \t\"CLO\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"MGI\" -> \"NCBIGene\" [label=\"biolink:related_to (533)\"]; \t\"MONARCH\" -> \"Orphanet\" [label=\"biolink:related_to (5)\"]; \t\"SGD\" -> \"GO\" [label=\"biolink:actively_involved_in (26956)\"]; \t\"MONARCH_BNODE\" -> \"http\" [label=\"biolink:part_of (23551)\"]; \t\"pav\" -> \"dcterms\" [label=\"biolink:subPropertyOf (4)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:type (17)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:affects (8924)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:derives_from (9)\"]; \t\"MGI\" -> \"PomBase\" [label=\"biolink:orthologous_to (3470)\"]; \t\"WormBase\" -> \"http\" [label=\"biolink:orthologous_to (635)\"]; \t\"PO\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"DOID\" -> \"MP\" [label=\"biolink:subclass_of (10)\"]; \t\"MONARCH_NODE\" -> \"MONARCH_NODE\" [label=\"biolink:related_to (25825)\"]; \t\"ClinVarVariant\" -> \"ClinVarVariant\" [label=\"biolink:related_to (1060)\"]; \t\"ENVO\" -> \"OBI\" [label=\"biolink:subclass_of (2)\"]; \t\"PMID\" -> \"OMIM\" [label=\"biolink:related_to (4935)\"]; \t\"NCBIGene\" -> \"EcoGene\" [label=\"biolink:related_to (1)\"]; \t\"MGI\" -> \"REACT\" [label=\"biolink:actively_involved_in (12605)\"]; \t\"Orphanet\" -> \"MP\" [label=\"biolink:subclass_of (4)\"]; \t\"rainbow_troutQTL\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (584)\"]; \t\"HP\" -> \"HP\" [label=\"biolink:subclass_of (20506)\"]; \t\"OBO\" -> \"IAO\" [label=\"biolink:subclass_of (8)\"]; \t\"SO\" -> \"SO\" [label=\"biolink:subclass_of (2438)\"]; \t\"WormBase\" -> \"DOID\" [label=\"biolink:model_of (10575)\"]; \t\"foaf\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"KEGG-hsa\" -> \"NCBIGene\" [label=\"biolink:same_as (1)\"]; \t\"NCBIGene\" -> \"OBO\" [label=\"biolink:expressed_in (124)\"]; \t\"ENSEMBL\" -> \"REACT\" [label=\"biolink:actively_involved_in (834505)\"]; \t\"CL\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"SO\" -> \"BFO\" [label=\"biolink:subclass_of (1)\"]; \t\"ECO\" -> \"ECO\" [label=\"biolink:inverseOf (1)\"]; \t\"OBO\" -> \"NCBITaxon\" [label=\"biolink:subclass_of (3)\"]; \t\"WBPhenotype\" -> \"CL\" [label=\"biolink:subclass_of (33)\"]; \t\"MONDO\" -> \"owl\" [label=\"biolink:subclass_of (1937)\"]; \t\"UBERON\" -> \"PR\" [label=\"biolink:related_to (1)\"]; \t\"GENO\" -> \"SO\" [label=\"biolink:part_of (4)\"]; \t\"WormBase\" -> \"WormBase\" [label=\"biolink:genetically_interacts_with (531)\"]; \t\"SO\" -> \"CHEBI\" [label=\"biolink:subclass_of (43)\"]; \t\"https\" -> \"GO\" [label=\"biolink:has_phenotype (2)\"]; \t\"Xenbase\" -> \"FlyBase\" [label=\"biolink:related_to (4722)\"]; \t\"OBI\" -> \"prov\" [label=\"biolink:subclass_of (1)\"]; \t\"WormBase\" -> \"OBO\" [label=\"biolink:related_to (10459)\"]; \t\"faldo\" -> \"faldo\" [label=\"biolink:inverseOf (2)\"]; \t\"WBPhenotype\" -> \"GO\" [label=\"biolink:subclass_of (274)\"]; \t\"BFO\" -> \"BFO\" [label=\"biolink:subclass_of (34)\"]; \t\"dcterms\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"PMID\" -> \"GeneReviews\" [label=\"biolink:related_to (31280)\"]; \t\"REACT\" -> \"PW\" [label=\"biolink:subclass_of (15909)\"]; \t\"BFO\" -> \"CHEBI\" [label=\"biolink:subclass_of (1)\"]; \t\"MP\" -> \"DOID\" [label=\"biolink:subclass_of (2)\"]; \t\"HGNC\" -> \"UBERON\" [label=\"biolink:expressed_in (448167)\"]; \t\"NCIT\" -> \"HP\" [label=\"biolink:subclass_of (13)\"]; \t\"OBI\" -> \"CHEBI\" [label=\"biolink:has_part (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:affects (8338)\"]; \t\"dbSNP\" -> \"dbSNP\" [label=\"biolink:related_to (1470)\"]; \t\"HGNC\" -> \"VGNC\" [label=\"biolink:related_to (8)\"]; \t\"OBAN\" -> \"SEPIO\" [label=\"biolink:subclass_of (1)\"]; \t\"OBO\" -> \"GO\" [label=\"biolink:part_of (1)\"]; \t\"pigQTL\" -> \"AQTLTrait\" [label=\"biolink:biomarker_for (14461)\"]; \t\"OBO\" -> \"GO\" [label=\"biolink:related_to (45)\"]; \t\"http\" -> \"MONARCH_NODE\" [label=\"biolink:related_to (142)\"]; \t\"OMIM\" -> \"HGNC\" [label=\"biolink:related_to (3018)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:part_of (1)\"]; \t\"OMIA\" -> \"HP\" [label=\"biolink:has_phenotype (260)\"]; \t\"KEGG-hsa\" -> \"SO\" [label=\"biolink:subclass_of (1)\"]; \t\"MONDO\" -> \"ENVO\" [label=\"biolink:related_to (14)\"]; \t\"MGI\" -> \"NCBIGene\" [label=\"biolink:interacts_with (9)\"]; \t\"HGNC\" -> \"Xenbase\" [label=\"biolink:related_to (10686)\"]; \t\"MONARCH_BNODE\" -> \"dbSNP\" [label=\"biolink:related_to (7199)\"]; \t\"PANTHER\" -> \"VGNC\" [label=\"biolink:related_to (8)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:increases_degradation_of (8)\"]; \t\"BFO\" -> \"RO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"dictyBase\" -> \"GO\" [label=\"biolink:enables (20904)\"]; \t\"MGI\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (26800)\"]; \t\"prov\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"NCBITaxon\" -> \"NCBITaxon\" [label=\"biolink:subclass_of (14540)\"]; \t\"PANTHER\" -> \"Xenbase\" [label=\"biolink:related_to (11866)\"]; \t\"CLO\" -> \"OBI\" [label=\"biolink:derives_from (1)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"biolink:has_participant (1)\"]; \t\"PR\" -> \"https\" [label=\"biolink:related_to (206)\"]; \t\"ZP\" -> \"WBPhenotype\" [label=\"biolink:subclass_of (2937)\"]; \t\"HGNC\" -> \"SO\" [label=\"biolink:subclass_of (60204)\"]; \t\"ENSEMBL\" -> \"VGNC\" [label=\"biolink:related_to (16)\"]; \t\"ENSEMBL\" -> \"ENSEMBL\" [label=\"biolink:interacts_with (305485)\"]; \t\"MONARCH_NODE\" -> \"https\" [label=\"biolink:related_to (24)\"]; \t\"WormBase\" -> \"NCBIGene\" [label=\"biolink:related_to (40)\"]; \t\"MGI\" -> \"SO\" [label=\"biolink:subclass_of (108997)\"]; \t\"ClinVarVariant\" -> \"NCBIGene\" [label=\"biolink:part_of (28122)\"]; \t\"WormBase\" -> \"PomBase\" [label=\"biolink:orthologous_to (2147)\"]; \t\"ZFIN\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (23456)\"]; \t\"GENO\" -> \"OBO\" [label=\"biolink:subclass_of (1)\"]; \t\"Xenbase\" -> \"OBO\" [label=\"biolink:related_to (15731)\"]; \t\"ENSEMBL\" -> \"Xenbase\" [label=\"biolink:related_to (103605)\"]; \t\"MP\" -> \"http\" [label=\"biolink:subclass_of (3)\"]; \t\"prov\" -> \"BFO\" [label=\"biolink:has_participant (1)\"]; \t\"HGNC\" -> \"OMIM\" [label=\"biolink:related_to (3746)\"]; \t\"foaf\" -> \"foaf\" [label=\"biolink:subclass_of (8)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:subclass_of (23397)\"]; \t\"ECO\" -> \"BFO\" [label=\"biolink:related_to (1)\"]; \t\"AQTLTrait\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"MGI\" -> \"Xenbase\" [label=\"biolink:orthologous_to (5098)\"]; \t\"MGI\" -> \"DOID\" [label=\"biolink:model_of (8320)\"]; \t\"RGD\" -> \"ZFIN\" [label=\"biolink:related_to (11501)\"]; \t\"SEPIO\" -> \"prov\" [label=\"biolink:subclass_of (1)\"]; \t\"CL\" -> \"CHEBI\" [label=\"biolink:has_part (1)\"]; \t\"MONARCH_NODE\" -> \"UPHENO\" [label=\"biolink:subclass_of (627)\"]; \t\"MONARCH_NODE\" -> \"UCSC\" [label=\"biolink:related_to (329)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:subclass_of (37688)\"]; \t\"PomBase\" -> \"GO\" [label=\"biolink:enables (11217)\"]; \t\"ClinVarVariant\" -> \"HGNC\" [label=\"biolink:has_part (21)\"]; \t\"OBO\" -> \"AQTLTrait\" [label=\"biolink:subclass_of (221)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:subclass_of (355)\"]; \t\"MONARCH_BNODE\" -> \"OMIM\" [label=\"biolink:has_phenotype (11482)\"]; \t\"owl\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"MPD-strain\" -> \"JAX\" [label=\"biolink:same_as (274)\"]; \t\"MGI\" -> \"MGI\" [label=\"biolink:same_as (8)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:has_output (14)\"]; \t\"ZP\" -> \"GENO\" [label=\"biolink:subclass_of (5)\"]; \t\"faldo\" -> \"GENO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"FlyBase\" -> \"http\" [label=\"biolink:related_to (139)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:expresses (198)\"]; \t\"NCBIGene\" -> \"ENSEMBL\" [label=\"biolink:related_to (1080)\"]; \t\"chickenQTL\" -> \"AQTLTrait\" [label=\"biolink:biomarker_for (7211)\"]; \t\"MONDO\" -> \"HP\" [label=\"biolink:subclass_of (25)\"]; \t\"MESH\" -> \"MESH\" [label=\"biolink:treats (35982)\"]; \t\"UBERON\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:has_part (1)\"]; \t\"OBI\" -> \"SEPIO\" [label=\"biolink:subclass_of (3)\"]; \t\"UMLS\" -> \"MONDO\" [label=\"biolink:subclass_of (46999)\"]; \t\"sheepQTL\" -> \"NCBIGene\" [label=\"biolink:related_to (486)\"]; \t\"UMLS\" -> \"BFO\" [label=\"biolink:subclass_of (1)\"]; \t\"NCBIGene\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (79181)\"]; \t\"OMIM\" -> \"HP\" [label=\"biolink:related_to (10416)\"]; \t\"MP\" -> \"MP\" [label=\"biolink:subclass_of (17670)\"]; \t\"MGI\" -> \"MGI\" [label=\"biolink:related_to (1293126)\"]; \t\"Xenbase\" -> \"NCBIGene\" [label=\"biolink:related_to (176)\"]; \t\"HGNC\" -> \"dictyBase\" [label=\"biolink:orthologous_to (9357)\"]; \t\"PR\" -> \"SO\" [label=\"biolink:related_to (174)\"]; \t\"dbSNP\" -> \"OMIM\" [label=\"biolink:related_to (25133)\"]; \t\"HGNC\" -> \"SGD\" [label=\"biolink:orthologous_to (4012)\"]; \t\"MONARCH_BNODE\" -> \"OMIM\" [label=\"biolink:biomarker_for (8)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:located_in (3)\"]; \t\"GENO\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"WormBase\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (15907)\"]; \t\"ZFIN\" -> \"REACT\" [label=\"biolink:actively_involved_in (12095)\"]; \t\"IAO\" -> \"BFO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"MONARCH_BNODE\" -> \"OMIM\" [label=\"biolink:related_to (481)\"]; \t\"RGD\" -> \"http\" [label=\"biolink:orthologous_to (906)\"]; \t\"NCBIGene\" -> \"AQTLTrait\" [label=\"biolink:biomarker_for (33621)\"]; \t\"GENO\" -> \"GENO\" [label=\"biolink:subPropertyOf (32)\"]; \t\"CLO\" -> \"OIO\" [label=\"biolink:subclass_of (3)\"]; \t\"HGNC\" -> \"WormBase\" [label=\"biolink:orthologous_to (15124)\"]; \t\"HP\" -> \"UMLS\" [label=\"biolink:subclass_of (8)\"]; \t\"GENO\" -> \"GENO\" [label=\"biolink:has_part (4)\"]; \t\"ENSEMBL\" -> \"dictyBase\" [label=\"biolink:orthologous_to (8870)\"]; \t\"HP\" -> \"OBO\" [label=\"biolink:related_to (10)\"]; \t\"KEGG-path\" -> \"OMIM\" [label=\"biolink:related_to (1322)\"]; \t\"GENO\" -> \"RO\" [label=\"biolink:subPropertyOf (5)\"]; \t\"ENSEMBL\" -> \"SGD\" [label=\"biolink:orthologous_to (21415)\"]; \t\"FAO\" -> \"FAO\" [label=\"biolink:subclass_of (32)\"]; \t\"ZFIN\" -> \"ZFIN\" [label=\"biolink:related_to (95569)\"]; \t\"OMIM\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (49)\"]; \t\"OBO\" -> \"*non-standard CURIE*\" [label=\"biolink:subclass_of (5946)\"]; \t\"FlyBase\" -> \"GO\" [label=\"biolink:part_of (23625)\"]; \t\"HP\" -> \"UBERON\" [label=\"biolink:subclass_of (1385)\"]; \t\"ENVO\" -> \"owl\" [label=\"biolink:subclass_of (3)\"]; \t\"MONARCH_BNODE\" -> \"WBPhenotype\" [label=\"biolink:has_phenotype (88885)\"]; \t\"HGNC\" -> \"HGNC\" [label=\"biolink:genetically_interacts_with (625)\"]; \t\"ZP\" -> \"CL\" [label=\"biolink:subclass_of (2294)\"]; \t\"WormBase\" -> \"SO\" [label=\"biolink:subclass_of (99428)\"]; \t\"ENSEMBL\" -> \"WormBase\" [label=\"biolink:orthologous_to (161822)\"]; \t\"ClinVarVariant\" -> \"UMLS\" [label=\"biolink:related_to (248280)\"]; \t\"PR\" -> \"NCBITaxon\" [label=\"biolink:related_to (533)\"]; \t\"WormBase\" -> \"GO\" [label=\"biolink:part_of (31324)\"]; \t\"dbSNP\" -> \"sheepQTL\" [label=\"biolink:biomarker_for (1759)\"]; \t\"NCIT\" -> \"UMLS\" [label=\"biolink:subclass_of (10791)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:regulates_process_to_process (14)\"]; \t\"MPD-strain\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (1013)\"]; \t\"MGI\" -> \"ZFIN\" [label=\"biolink:related_to (12127)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:subPropertyOf (5)\"]; \t\"FBcv\" -> \"MP\" [label=\"biolink:subclass_of (34)\"]; \t\"ZP\" -> \"GO\" [label=\"biolink:subclass_of (4838)\"]; \t\"WormBase\" -> \"NCBIGene\" [label=\"biolink:genetically_interacts_with (7)\"]; \t\"CL\" -> \"owl\" [label=\"biolink:subclass_of (199)\"]; \t\"NCBIGene\" -> \"EcoGene\" [label=\"biolink:orthologous_to (39)\"]; \t\"Xenbase\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (364)\"]; \t\"CL\" -> \"CL\" [label=\"biolink:affects (943)\"]; \t\"OMIM\" -> \"HP\" [label=\"biolink:has_phenotype (97164)\"]; \t\"CL\" -> \"UBERON\" [label=\"biolink:related_to (8)\"]; \t\"OBI\" -> \"BFO\" [label=\"biolink:related_to (11)\"]; \t\"HP\" -> \"MONDO\" [label=\"biolink:subclass_of (12)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:part_of (75)\"]; \t\"RGD\" -> \"GO\" [label=\"biolink:part_of (77299)\"]; \t\"MGI\" -> \"HGNC\" [label=\"biolink:related_to (719)\"]; \t\"MGI\" -> \"MGI\" [label=\"biolink:interacts_with (41740)\"]; \t\"WormBase\" -> \"REACT\" [label=\"biolink:actively_involved_in (6038)\"]; \t\"FlyBase\" -> \"PomBase\" [label=\"biolink:related_to (2383)\"]; \t\"OBI\" -> \"CHEBI\" [label=\"biolink:related_to (24)\"]; \t\"MONARCH_BNODE\" -> \"HGNC\" [label=\"biolink:contributes_to (2)\"]; \t\"SEPIO\" -> \"SEPIO\" [label=\"biolink:subclass_of (34)\"]; \t\"CL\" -> \"UBERON\" [label=\"biolink:produces (6)\"]; \t\"NCIT\" -> \"UBERON\" [label=\"biolink:subclass_of (1)\"]; \t\"ClinVarVariant\" -> \"OMIM\" [label=\"biolink:gene_associated_with_condition (107041)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:inverseOf (3)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:part_of (8537)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:related_to (11912)\"]; \t\"UBERON\" -> \"PR\" [label=\"biolink:has_part (6)\"]; \t\"RO\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"OBO\" -> \"DOID\" [label=\"biolink:subclass_of (19801)\"]; \t\"OMIA\" -> \"UBERON\" [label=\"biolink:has_phenotype (18)\"]; \t\"UCSC\" -> \"MONARCH_NODE\" [label=\"biolink:has_part (26381)\"]; \t\"http\" -> \"Orphanet\" [label=\"biolink:subclass_of (20720)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:subclass_of (1896)\"]; \t\"OBO\" -> \"OGMS\" [label=\"biolink:subclass_of (21)\"]; \t\"PMID\" -> \"SGD\" [label=\"biolink:related_to (242021)\"]; \t\"HGNC\" -> \"FlyBase\" [label=\"biolink:orthologous_to (16085)\"]; \t\"MGI\" -> \"RGD\" [label=\"biolink:related_to (17190)\"]; \t\"PMID\" -> \"OMIA\" [label=\"biolink:related_to (173)\"]; \t\"ClinVarVariant\" -> \"MONDO\" [label=\"biolink:related_to (33553)\"]; \t\"NCIT\" -> \"MONDO\" [label=\"biolink:subclass_of (20766)\"]; \t\"https\" -> \"NCBIGene\" [label=\"biolink:related_to (10095)\"]; \t\"MONDO\" -> \"HP\" [label=\"biolink:related_to (1354)\"]; \t\"NCIT\" -> \"BFO\" [label=\"biolink:subclass_of (1)\"]; \t\"MONARCH_BNODE\" -> \"SO\" [label=\"biolink:subclass_of (23)\"]; \t\"FlyBase\" -> \"CL\" [label=\"biolink:expressed_in (3279)\"]; \t\"OBI\" -> \"IAO\" [label=\"biolink:related_to (8)\"]; \t\"SEPIO\" -> \"SEPIO\" [label=\"biolink:type (2)\"]; \t\"PMID\" -> \"WormBase\" [label=\"biolink:related_to (26012)\"]; \t\"RO\" -> \"BFO\" [label=\"biolink:subPropertyOf (26)\"]; \t\"OBI\" -> \"GO\" [label=\"biolink:has_participant (1)\"]; \t\"RGD\" -> \"PomBase\" [label=\"biolink:orthologous_to (3235)\"]; \t\"ENSEMBL\" -> \"FlyBase\" [label=\"biolink:orthologous_to (163413)\"]; \t\"OMIA\" -> \"MONARCH_BNODE\" [label=\"biolink:subclass_of (3339)\"]; \t\"ZFIN\" -> \"SO\" [label=\"biolink:subclass_of (56890)\"]; \t\"VGNC\" -> \"ENSEMBL\" [label=\"biolink:related_to (67)\"]; \t\"http\" -> \"OBO\" [label=\"biolink:subclass_of (36397)\"]; \t\"MGI\" -> \"ZFIN\" [label=\"biolink:interacts_with (2)\"]; \t\"chickenQTL\" -> \"NCBIGene\" [label=\"biolink:related_to (453)\"]; \t\"FlyBase\" -> \"DOID\" [label=\"biolink:model_of (1626)\"]; \t\"OBI\" -> \"UBERON\" [label=\"biolink:derives_from (4)\"]; \t\"CL\" -> \"NCBITaxon\" [label=\"biolink:related_to (4)\"]; \t\"OBI\" -> \"BFO\" [label=\"biolink:subPropertyOf (2)\"]; \t\"OBO\" -> \"http\" [label=\"biolink:subclass_of (26213)\"]; \t\"IAO\" -> \"BFO\" [label=\"biolink:related_to (3)\"]; \t\"OBO\" -> \"NCBIGene\" [label=\"biolink:related_to (279)\"]; \t\"OBI\" -> \"GENO\" [label=\"biolink:subclass_of (6)\"]; \t\"MGI\" -> \"HGNC\" [label=\"biolink:interacts_with (1731)\"]; \t\"MONARCH_BNODE\" -> \"GENO\" [label=\"biolink:related_to (186309)\"]; \t\"CLO\" -> \"RO\" [label=\"biolink:subPropertyOf (5)\"]; \t\"WBPhenotype\" -> \"FBcv\" [label=\"biolink:subclass_of (256)\"]; \t\"MONARCH_BNODE\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (4741582)\"]; \t\"MONDO\" -> \"UMLS\" [label=\"biolink:subclass_of (44953)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:participates_in (7)\"]; \t\"GENO\" -> \"GENO\" [label=\"biolink:inverseOf (13)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:inverseOf (2)\"]; \t\"MGI\" -> \"GO\" [label=\"biolink:part_of (94768)\"]; \t\"OBO\" -> \"OBI\" [label=\"biolink:related_to (1)\"]; \t\"FlyBase\" -> \"FlyBase\" [label=\"biolink:genetically_interacts_with (2748)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:has_output (1)\"]; \t\"WormBase\" -> \"CL\" [label=\"biolink:expressed_in (33)\"]; \t\"ZFIN\" -> \"GO\" [label=\"biolink:has_phenotype (5907)\"]; \t\"rdfs\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:derives_from (2)\"]; \t\"OBO\" -> \"PR\" [label=\"biolink:subclass_of (1)\"]; \t\"faldo\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"GO\" -> \"FAO\" [label=\"biolink:part_of (3)\"]; \t\"MONARCH\" -> \"HGNC\" [label=\"biolink:related_to (664)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"biolink:subclass_of (1)\"]; \t\"PO\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"MONARCH\" -> \"OMIM\" [label=\"biolink:model_of (948)\"]; \t\"ClinVarVariant\" -> \"HGNC\" [label=\"biolink:part_of (151427)\"]; \t\"XCO\" -> \"owl\" [label=\"biolink:subclass_of (19)\"]; \t\"https\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (279846)\"]; \t\"PMID\" -> \"FlyBase\" [label=\"biolink:related_to (345961)\"]; \t\"NCBIGene\" -> \"http\" [label=\"biolink:related_to (2)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:related_to (798)\"]; \t\"ZFIN\" -> \"MONARCH_NODE\" [label=\"biolink:related_to (9372)\"]; \t\"OIO\" -> \"IAO\" [label=\"biolink:subclass_of (5)\"]; \t\"MONARCH_BNODE\" -> \"GO\" [label=\"biolink:has_phenotype (9501)\"]; \t\"UBERON\" -> \"OBI\" [label=\"biolink:derives_from (1)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:participates_in (9)\"]; \t\"NCBIGene\" -> \"WormBase\" [label=\"biolink:interacts_with (453)\"]; \t\"HGNC\" -> \"dictyBase\" [label=\"biolink:related_to (3338)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:related_to (16)\"]; \t\"ENSEMBL\" -> \"GO\" [label=\"biolink:part_of (63314)\"]; \t\"HGNC\" -> \"NCBIGene\" [label=\"biolink:same_as (1881)\"]; \t\"foaf\" -> \"http\" [label=\"biolink:subclass_of (6)\"]; \t\"horseQTL\" -> \"horseQTL\" [label=\"biolink:biomarker_for (2451)\"]; \t\"HGNC\" -> \"SGD\" [label=\"biolink:related_to (2445)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:related_to (6038)\"]; \t\"SGD\" -> \"GO\" [label=\"biolink:enables (19930)\"]; \t\"HGNC\" -> \"REACT\" [label=\"biolink:actively_involved_in (27687)\"]; \t\"NCBIGene\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (1383)\"]; \t\"OBO\" -> \"MP\" [label=\"biolink:subclass_of (26)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"biolink:subclass_of (41256)\"]; \t\"MONDO\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"MONARCH_NODE\" -> \"HP\" [label=\"biolink:has_phenotype (1082)\"]; \t\"KEGG-path\" -> \"KEGG-ds\" [label=\"biolink:related_to (2498)\"]; \t\"PANTHER\" -> \"dictyBase\" [label=\"biolink:related_to (5429)\"]; \t\"http\" -> \"OBI\" [label=\"biolink:subclass_of (17)\"]; \t\"BIOGRID\" -> \"OMIM\" [label=\"biolink:related_to (488)\"]; \t\"PANTHER\" -> \"SGD\" [label=\"biolink:related_to (3309)\"]; \t\"ZFIN\" -> \"dictyBase\" [label=\"biolink:orthologous_to (11205)\"]; \t\"HGNC\" -> \"WormBase\" [label=\"biolink:related_to (4877)\"]; \t\"ZFIN\" -> \"SGD\" [label=\"biolink:orthologous_to (4666)\"]; \t\"IAO\" -> \"OBI\" [label=\"biolink:subclass_of (6)\"]; \t\"GENO\" -> \"owl\" [label=\"biolink:subclass_of (43)\"]; \t\"OBI\" -> \"CL\" [label=\"biolink:subclass_of (1)\"]; \t\"MONARCH_BNODE\" -> \"OMIA\" [label=\"biolink:has_phenotype (782)\"]; \t\"dbSNP\" -> \"GO\" [label=\"biolink:related_to (5269)\"]; \t\"SO\" -> \"PR\" [label=\"biolink:subclass_of (2)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:has_input (9)\"]; \t\"HGNC\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (1736)\"]; \t\"OMIA\" -> \"GENO\" [label=\"biolink:related_to (1033)\"]; \t\"ENSEMBL\" -> \"dictyBase\" [label=\"biolink:related_to (2963)\"]; \t\"MESH\" -> \"OMIM\" [label=\"biolink:treats (8)\"]; \t\"PANTHER\" -> \"WormBase\" [label=\"biolink:related_to (9055)\"]; \t\"ENSEMBL\" -> \"SGD\" [label=\"biolink:related_to (10980)\"]; \t\"MONDO\" -> \"https\" [label=\"biolink:related_to (4436)\"]; \t\"FlyBase\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (15464)\"]; \t\"OBI\" -> \"GO\" [label=\"biolink:subclass_of (4)\"]; \t\"*non-standard CURIE*\" -> \"SO\" [label=\"biolink:subclass_of (9)\"]; \t\"Xenbase\" -> \"ZFIN\" [label=\"biolink:related_to (9523)\"]; \t\"GO\" -> \"GENO\" [label=\"biolink:subclass_of (1)\"]; \t\"horseQTL\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (4902)\"]; \t\"ZFIN\" -> \"WormBase\" [label=\"biolink:orthologous_to (19169)\"]; \t\"http\" -> \"NCIT\" [label=\"biolink:subclass_of (15591)\"]; \t\"MONARCH_BNODE\" -> \"GO\" [label=\"biolink:related_to (189)\"]; \t\"RGD\" -> \"Xenbase\" [label=\"biolink:orthologous_to (3725)\"]; \t\"MGI\" -> \"dictyBase\" [label=\"biolink:orthologous_to (10253)\"]; \t\"GENO\" -> \"UPHENO\" [label=\"biolink:subclass_of (1)\"]; \t\"MGI\" -> \"CL\" [label=\"biolink:expressed_in (29583)\"]; \t\"STATO\" -> \"SEPIO\" [label=\"biolink:subclass_of (1)\"]; \t\"ClinVarVariant\" -> \"BIOGRID\" [label=\"biolink:part_of (43)\"]; \t\"FlyBase\" -> \"EcoGene\" [label=\"biolink:orthologous_to (945)\"]; \t\"MGI\" -> \"SGD\" [label=\"biolink:orthologous_to (3984)\"]; \t\"OMIA\" -> \"OMIA\" [label=\"biolink:subclass_of (3339)\"]; \t\"RO\" -> \"RO\" [label=\"biolink:inverseOf (102)\"]; \t\"ENSEMBL\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (17431)\"]; \t\"ENSEMBL\" -> \"WormBase\" [label=\"biolink:related_to (48370)\"]; \t\"ZP\" -> \"OBO\" [label=\"biolink:subclass_of (104)\"]; \t\"NCBIGene\" -> \"FlyBase\" [label=\"biolink:interacts_with (12)\"]; \t\"CHEBI\" -> \"REACT\" [label=\"biolink:actively_involved_in (89911)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"biolink:derives_from (1)\"]; \t\"RGD\" -> \"SO\" [label=\"biolink:subclass_of (44108)\"]; \t\"MGI\" -> \"WormBase\" [label=\"biolink:orthologous_to (17089)\"]; \t\"foaf\" -> \"wgs\" [label=\"biolink:subclass_of (1)\"]; \t\"UMLS\" -> \"DOID\" [label=\"biolink:subclass_of (15911)\"]; \t\"dbSNP\" -> \"horseQTL\" [label=\"biolink:biomarker_for (1797)\"]; \t\"MONARCH\" -> \"HP\" [label=\"biolink:related_to (1)\"]; \t\"OBO\" -> \"IAO\" [label=\"biolink:has_part (1)\"]; \t\"MONARCH_BNODE\" -> \"OMIA\" [label=\"biolink:related_to (48)\"]; \t\"AspGD\" -> \"GO\" [label=\"biolink:part_of (130918)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:has_phenotype (18)\"]; \t\"UMLS\" -> \"OGMS\" [label=\"biolink:subclass_of (16)\"]; \t\"RGD\" -> \"EcoGene\" [label=\"biolink:related_to (283)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:has_input (8)\"]; \t\"MP\" -> \"WBPhenotype\" [label=\"biolink:subclass_of (388)\"]; \t\"GENO\" -> \"ENVO\" [label=\"biolink:related_to (1)\"]; \t\"HGNC\" -> \"FlyBase\" [label=\"biolink:related_to (5744)\"]; \t\"NCBIGene\" -> \"PomBase\" [label=\"biolink:related_to (41)\"]; \t\"rainbow_troutQTL\" -> \"rainbow_troutQTL\" [label=\"biolink:biomarker_for (584)\"]; \t\"MONARCH\" -> \"EFO\" [label=\"biolink:related_to (1951)\"]; \t\"OBO\" -> \"ENVO\" [label=\"biolink:part_of (1)\"]; \t\"GENO\" -> \"OBI\" [label=\"biolink:in_taxon (2)\"]; \t\"HGNC\" -> \"OMIM\" [label=\"biolink:biomarker_for (89)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:has_input (1)\"]; \t\"OBO\" -> \"ENVO\" [label=\"biolink:related_to (3)\"]; \t\"HGNC\" -> \"WormBase\" [label=\"biolink:interacts_with (3)\"]; \t\"NCBIGene\" -> \"REACT\" [label=\"biolink:actively_involved_in (547)\"]; \t\"MONARCH_BNODE\" -> \"WormBase\" [label=\"biolink:related_to (106722)\"]; \t\"FlyBase\" -> \"NCBIGene\" [label=\"biolink:genetically_interacts_with (2)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"biolink:related_to (3048)\"]; \t\"MONARCH_BNODE\" -> \"JAX\" [label=\"biolink:related_to (1005)\"]; \t\"UBERON\" -> \"CL\" [label=\"biolink:related_to (112)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"biolink:contributes_to (23)\"]; \t\"PANTHER\" -> \"FlyBase\" [label=\"biolink:related_to (9654)\"]; \t\"GO\" -> \"SO\" [label=\"biolink:has_input (7)\"]; \t\"foaf\" -> \"prov\" [label=\"biolink:subclass_of (2)\"]; \t\"ZFIN\" -> \"FlyBase\" [label=\"biolink:orthologous_to (17802)\"]; \t\"OBO\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (8)\"]; \t\"OBI\" -> \"OBO\" [label=\"biolink:has_participant (1)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:related_to (224)\"]; \t\"GO\" -> \"CHEBI\" [label=\"biolink:has_input (1297)\"]; \t\"HGNC\" -> \"Orphanet\" [label=\"biolink:related_to (7317)\"]; \t\"dcterms\" -> \"foaf\" [label=\"biolink:subclass_of (1)\"]; \t\"FlyBase\" -> \"OBO\" [label=\"biolink:expressed_in (43532)\"]; \t\"SEPIO\" -> \"IAO\" [label=\"biolink:subPropertyOf (5)\"]; \t\"dictyBase\" -> \"GO\" [label=\"biolink:actively_involved_in (21354)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:subclass_of (73)\"]; \t\"CL\" -> \"PR\" [label=\"biolink:has_part (675)\"]; \t\"PMID\" -> \"NCBIGene\" [label=\"biolink:related_to (399176)\"]; \t\"WormBase\" -> \"MONARCH_NODE\" [label=\"biolink:related_to (7)\"]; \t\"*non-standard CURIE*\" -> \"SO\" [label=\"owl:someValuesFrom (1)\"]; \t\"MONDO\" -> \"SO\" [label=\"biolink:related_to (22)\"]; \t\"ENSEMBL\" -> \"FlyBase\" [label=\"biolink:related_to (56918)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"biolink:related_to (1752)\"]; \t\"UBERON\" -> \"http\" [label=\"biolink:subclass_of (20)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:subclass_of (103475)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"biolink:subclass_of (178)\"]; \t\"UMLS\" -> \"http\" [label=\"biolink:subclass_of (21698)\"]; \t\"VGNC\" -> \"ENSEMBL\" [label=\"biolink:orthologous_to (10)\"]; \t\"SGD\" -> \"GO\" [label=\"biolink:has_phenotype (9)\"]; \t\"MONDO\" -> \"CHEBI\" [label=\"biolink:related_to (46)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:has_participant (3)\"]; \t\"http\" -> \"dcterms\" [label=\"biolink:subclass_of (2)\"]; \t\"FlyBase\" -> \"REACT\" [label=\"biolink:actively_involved_in (6083)\"]; \t\"OMIM\" -> \"SO\" [label=\"biolink:subclass_of (96)\"]; \t\"MGI\" -> \"FlyBase\" [label=\"biolink:orthologous_to (17380)\"]; \t\"MGI\" -> \"MGI\" [label=\"biolink:genetically_interacts_with (42)\"]; \t\"WormBase\" -> \"dictyBase\" [label=\"biolink:orthologous_to (7384)\"]; \t\"ZP\" -> \"FBcv\" [label=\"biolink:subclass_of (1818)\"]; \t\"FBcv\" -> \"WBPhenotype\" [label=\"biolink:subclass_of (71)\"]; \t\"WBPhenotype\" -> \"owl\" [label=\"biolink:subclass_of (62)\"]; \t\"MONARCH_BNODE\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (3059)\"]; \t\"WormBase\" -> \"SGD\" [label=\"biolink:orthologous_to (2640)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:participates_in (2)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:has_part (2)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:has_participant (2)\"]; \t\"HP\" -> \"DOID\" [label=\"biolink:subclass_of (6)\"]; \t\"Coriell\" -> \"OMIM\" [label=\"biolink:model_of (12242)\"]; \t\"ENVO\" -> \"OBO\" [label=\"biolink:related_to (36)\"]; \t\"GO\" -> \"NCBITaxon\" [label=\"biolink:has_input (19)\"]; \t\"MONARCH_NODE\" -> \"http\" [label=\"biolink:related_to (142)\"]; \t\"HGNC\" -> \"OBO\" [label=\"biolink:related_to (45014)\"]; \t\"BSPO\" -> \"OBO\" [label=\"biolink:subclass_of (6)\"]; \t\"HGNC\" -> \"FlyBase\" [label=\"biolink:interacts_with (14)\"]; \t\"MONARCH_BNODE\" -> \"FlyBase\" [label=\"biolink:related_to (3)\"]; \t\"GENO\" -> \"owl\" [label=\"biolink:related_to (1)\"]; \t\"ZFIN\" -> \"EcoGene\" [label=\"biolink:related_to (291)\"]; \t\"Xenbase\" -> \"PomBase\" [label=\"biolink:orthologous_to (2473)\"]; \t\"WBPhenotype\" -> \"UPHENO\" [label=\"biolink:subclass_of (1)\"]; \t\"*non-standard CURIE*\" -> \"NCBITaxon\" [label=\"owl:someValuesFrom (9)\"]; \t\"PW\" -> \"PW\" [label=\"biolink:related_to (136)\"]; \t\"MONDO\" -> \"NCBITaxon\" [label=\"biolink:related_to (664)\"]; \t\"GO\" -> \"SO\" [label=\"biolink:has_participant (5)\"]; \t\"GO\" -> \"PO\" [label=\"biolink:related_to (165)\"]; \t\"dbSNP\" -> \"Orphanet\" [label=\"biolink:related_to (1144)\"]; \t\"WormBase\" -> \"OBO\" [label=\"biolink:expressed_in (8988)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:related_to (3)\"]; \t\"MONARCH_BNODE\" -> \"OBO\" [label=\"biolink:has_phenotype (3042)\"]; \t\"FlyBase\" -> \"GO\" [label=\"biolink:has_phenotype (2)\"]; \t\"CL\" -> \"UBERON\" [label=\"biolink:subclass_of (237)\"]; \t\"https\" -> \"NCBIGene\" [label=\"biolink:biomarker_for (42481)\"]; \t\"NCIT\" -> \"DOID\" [label=\"biolink:subclass_of (8101)\"]; \t\"GO\" -> \"CHEBI\" [label=\"biolink:has_participant (24)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:has_participant (6)\"]; \t\"UMLS\" -> \"MP\" [label=\"biolink:subclass_of (14)\"]; \t\"MGI\" -> \"EcoGene\" [label=\"biolink:related_to (291)\"]; \t\"NCIT\" -> \"OGMS\" [label=\"biolink:subclass_of (10)\"]; \t\"MONARCH_BNODE\" -> \"Orphanet\" [label=\"biolink:related_to (18)\"]; \t\"NCBIGene\" -> \"NCBIGene\" [label=\"biolink:interacts_with (73)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:related_to (118)\"]; \t\"ENVO\" -> \"BFO\" [label=\"biolink:subclass_of (15)\"]; \t\"OBO\" -> \"HGNC\" [label=\"biolink:related_to (44422)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:location_of (10)\"]; \t\"PO\" -> \"NCBITaxon\" [label=\"biolink:related_to (2)\"]; \t\"ENVO\" -> \"CHEBI\" [label=\"biolink:subclass_of (1)\"]; \t\"HGNC\" -> \"MGI\" [label=\"biolink:orthologous_to (7064)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:type (41)\"]; \t\"NCBIGene\" -> \"Xenbase\" [label=\"biolink:related_to (1893)\"]; \t\"NCBIGene\" -> \"http\" [label=\"biolink:orthologous_to (40)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:negatively_regulates_process_to_process (3160)\"]; \t\"MP\" -> \"CL\" [label=\"biolink:subclass_of (475)\"]; \t\"HP\" -> \"http\" [label=\"biolink:subclass_of (7)\"]; \t\"XCO\" -> \"XCO\" [label=\"biolink:regulates_process_to_process (35)\"]; \t\"ENSEMBL\" -> \"UBERON\" [label=\"biolink:expressed_in (719942)\"]; \t\"DOID\" -> \"Orphanet\" [label=\"biolink:subclass_of (7042)\"]; \t\"HGNC\" -> \"NCBIGene\" [label=\"biolink:related_to (469)\"]; \t\"ZFIN\" -> \"NCBITaxon\" [label=\"biolink:related_to (15)\"]; \t\"RGD\" -> \"ENSEMBL\" [label=\"biolink:related_to (117939)\"]; \t\"http\" -> \"owl\" [label=\"biolink:subclass_of (54)\"]; \t\"dbSNP\" -> \"OBO\" [label=\"biolink:related_to (4)\"]; \t\"WBPhenotype\" -> \"ZP\" [label=\"biolink:subclass_of (463)\"]; \t\"NCBIGene\" -> \"OMIM\" [label=\"biolink:has_phenotype (17)\"]; \t\"MP\" -> \"GO\" [label=\"biolink:subclass_of (883)\"]; \t\"IAO\" -> \"OIO\" [label=\"biolink:subclass_of (16)\"]; \t\"CL\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (2)\"]; \t\"MONARCH_BNODE\" -> \"ClinVar\" [label=\"biolink:related_to (737221)\"]; \t\"HGNC\" -> \"OMIMPS\" [label=\"biolink:related_to (2415)\"]; \t\"Orphanet\" -> \"Orphanet\" [label=\"biolink:subclass_of (14250)\"]; \t\"ENSEMBL\" -> \"MGI\" [label=\"biolink:orthologous_to (14489)\"]; \t\"foaf\" -> \"SEPIO\" [label=\"biolink:subclass_of (1)\"]; \t\"OBI\" -> \"OBO\" [label=\"biolink:subclass_of (3)\"]; \t\"BIOGRID\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (2192)\"]; \t\"MONARCH_BNODE\" -> \"OBO\" [label=\"biolink:related_to (742)\"]; \t\"RO\" -> \"BFO\" [label=\"biolink:subclass_of (2)\"]; \t\"PANTHER\" -> \"NCBIGene\" [label=\"biolink:related_to (943)\"]; \t\"VGNC\" -> \"PomBase\" [label=\"biolink:related_to (3)\"]; \t\"OBI\" -> \"PR\" [label=\"biolink:related_to (1)\"]; \t\"WormBase\" -> \"FlyBase\" [label=\"biolink:orthologous_to (12853)\"]; \t\"FBcv\" -> \"CL\" [label=\"biolink:related_to (1)\"]; \t\"ZFIN\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (13)\"]; \t\"PMID\" -> \"MONARCH\" [label=\"biolink:related_to (1919)\"]; \t\"MGI\" -> \"NCBITaxon\" [label=\"biolink:related_to (198)\"]; \t\"NCIT\" -> \"http\" [label=\"biolink:subclass_of (9895)\"]; \t\"ENSEMBL\" -> \"GO\" [label=\"biolink:enables (58420)\"]; \t\"GENO\" -> \"IAO\" [label=\"biolink:type (2)\"]; \t\"NCBIGene\" -> \"OMIM\" [label=\"biolink:related_to (24)\"]; \t\"ClinVarVariant\" -> \"Orphanet\" [label=\"biolink:gene_associated_with_condition (3315)\"]; \t\"MGI\" -> \"OBO\" [label=\"biolink:expressed_in (2757)\"]; \t\"https\" -> \"HP\" [label=\"biolink:related_to (2)\"]; \t\"AQTLTrait\" -> \"AQTLTrait\" [label=\"biolink:subclass_of (95)\"]; \t\"RO\" -> \"http\" [label=\"biolink:subPropertyOf (2)\"]; \t\"NCBIGene\" -> \"GO\" [label=\"biolink:enables (54230)\"]; \t\"DOID\" -> \"OBO\" [label=\"biolink:subclass_of (19795)\"]; \t\"CL\" -> \"UBERON\" [label=\"biolink:part_of (880)\"]; \t\"ENSEMBL\" -> \"NCBIGene\" [label=\"biolink:related_to (3225)\"]; \t\"UBERON\" -> \"CL\" [label=\"biolink:part_of (7)\"]; \t\"NCBIGene\" -> \"UBERON\" [label=\"biolink:expressed_in (33356)\"]; \t\"NCBITaxon\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (509)\"]; \t\"OBO\" -> \"BIOGRID\" [label=\"biolink:related_to (900)\"]; \t\"CL\" -> \"PR\" [label=\"biolink:related_to (982)\"]; \t\"https\" -> \"EFO\" [label=\"biolink:related_to (174)\"]; \t\"HGNC\" -> \"ZFIN\" [label=\"biolink:orthologous_to (19849)\"]; \t\"BFO\" -> \"owl\" [label=\"biolink:subPropertyOf (1)\"]; \t\"HP\" -> \"MP\" [label=\"biolink:subclass_of (8972)\"]; \t\"https\" -> \"HP\" [label=\"biolink:has_phenotype (294)\"]; \t\"MGI\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (2423)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:part_of (11)\"]; \t\"Orphanet\" -> \"OBO\" [label=\"biolink:subclass_of (13338)\"]; \t\"FAO\" -> \"FAO\" [label=\"biolink:related_to (2)\"]; \t\"UPHENO\" -> \"OBO\" [label=\"biolink:subclass_of (1)\"]; \t\"*non-standard CURIE*\" -> \"*non-standard CURIE*\" [label=\"biolink:subclass_of (9)\"]; \t\"OBO\" -> \"GO\" [label=\"biolink:capable_of (429)\"]; \t\"WBPhenotype\" -> \"HP\" [label=\"biolink:subclass_of (113)\"]; \t\"SEPIO\" -> \"SEPIO\" [label=\"biolink:inverseOf (3)\"]; \t\"dbSNP\" -> \"NCBIGene\" [label=\"biolink:related_to (4744)\"]; \t\"MONDO\" -> \"DOID\" [label=\"biolink:subclass_of (29074)\"]; \t\"FlyBase\" -> \"dictyBase\" [label=\"biolink:related_to (2987)\"]; \t\"FBcv\" -> \"GO\" [label=\"biolink:subclass_of (38)\"]; \t\"sheepQTL\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (6510)\"]; \t\"MONDO\" -> \"OGMS\" [label=\"biolink:subclass_of (37)\"]; \t\"PMID\" -> \"MGI\" [label=\"biolink:related_to (428695)\"]; \t\"HGNC\" -> \"NCBIGene\" [label=\"biolink:interacts_with (414)\"]; \t\"https\" -> \"MONARCH_NODE\" [label=\"biolink:related_to (24)\"]; \t\"FlyBase\" -> \"SGD\" [label=\"biolink:related_to (2292)\"]; \t\"ENSEMBL\" -> \"ZFIN\" [label=\"biolink:orthologous_to (199624)\"]; \t\"MONARCH_BNODE\" -> \"NCBIGene\" [label=\"biolink:related_to (6413)\"]; \t\"OBO\" -> \"RO\" [label=\"biolink:subPropertyOf (14)\"]; \t\"WormBase\" -> \"EcoGene\" [label=\"biolink:related_to (249)\"]; \t\"NCBIGene\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (1085)\"]; \t\"FAO\" -> \"NCBITaxon\" [label=\"biolink:related_to (1)\"]; \t\"NCIT\" -> \"MP\" [label=\"biolink:subclass_of (10)\"]; \t\"HGNC\" -> \"RGD\" [label=\"biolink:orthologous_to (3331)\"]; \t\"NCBIGene\" -> \"PomBase\" [label=\"biolink:orthologous_to (143)\"]; \t\"UBERON\" -> \"OBO\" [label=\"biolink:related_to (103)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:subclass_of (379)\"]; \t\"HGNC\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (13115)\"]; \t\"ZFIN\" -> \"CL\" [label=\"biolink:expressed_in (735)\"]; \t\"SEPIO\" -> \"pav\" [label=\"biolink:subPropertyOf (1)\"]; \t\"GOREL\" -> \"RO\" [label=\"biolink:subPropertyOf (5)\"]; \t\"OMIA\" -> \"MP\" [label=\"biolink:has_phenotype (1866)\"]; \t\"_\" -> \"GO\" [label=\"biolink:has_phenotype (250)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:has_attribute (26)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:precedes (3)\"]; \t\"OBI\" -> \"prov\" [label=\"biolink:related_to (1)\"]; \t\"faldo\" -> \"SO\" [label=\"biolink:subclass_of (1)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:subclass_of (32)\"]; \t\"dbSNP\" -> \"NCIT\" [label=\"biolink:related_to (25)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:located_in (527)\"]; \t\"UBERON\" -> \"CL\" [label=\"biolink:has_part (233)\"]; \t\"MONARCH_BNODE\" -> \"CoriellFamily\" [label=\"biolink:related_to (21318)\"]; \t\"MGI\" -> \"ENSEMBL\" [label=\"biolink:related_to (126877)\"]; \t\"ENSEMBL\" -> \"RGD\" [label=\"biolink:orthologous_to (8785)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:has_phenotype (1)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:regulates_process_to_process (3664)\"]; \t\"RGD\" -> \"dictyBase\" [label=\"biolink:orthologous_to (9381)\"]; \t\"DOID\" -> \"OBI\" [label=\"biolink:subclass_of (17)\"]; \t\"MP\" -> \"OBO\" [label=\"biolink:related_to (6)\"]; \t\"ENVO\" -> \"OBO\" [label=\"biolink:has_part (1)\"]; \t\"HGNC\" -> \"GO\" [label=\"biolink:enables (19568)\"]; \t\"OBI\" -> \"NCIT\" [label=\"biolink:subclass_of (1)\"]; \t\"RGD\" -> \"SGD\" [label=\"biolink:orthologous_to (3768)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:has_part (44)\"]; \t\"ZP\" -> \"owl\" [label=\"biolink:subclass_of (3742)\"]; \t\"OBO\" -> \"GENO\" [label=\"biolink:subclass_of (1629)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:has_attribute (3)\"]; \t\"GENO\" -> \"UBERON\" [label=\"biolink:subclass_of (1)\"]; \t\"MONDO\" -> \"http\" [label=\"biolink:subclass_of (48830)\"]; \t\"http\" -> \"HP\" [label=\"biolink:subclass_of (19)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:subclass_of (4)\"]; \t\"https\" -> \"GENO\" [label=\"biolink:subclass_of (209)\"]; \t\"Orphanet\" -> \"OBI\" [label=\"biolink:subclass_of (6)\"]; \t\"OBO\" -> \"RO\" [label=\"biolink:subclass_of (5)\"]; \t\"BSPO\" -> \"RO\" [label=\"biolink:subPropertyOf (4)\"]; \t\"PMID\" -> \"ZFIN\" [label=\"biolink:related_to (101474)\"]; \t\"GO\" -> \"CL\" [label=\"biolink:occurs_in (140)\"]; \t\"RGD\" -> \"WormBase\" [label=\"biolink:orthologous_to (15223)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:occurs_in (14)\"]; \t\"XCO\" -> \"XCO\" [label=\"biolink:subclass_of (769)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:related_to (99)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:overlaps (97)\"]; \t\"HGNC\" -> \"HP\" [label=\"biolink:has_phenotype (26)\"]; \t\"DOID\" -> \"NCIT\" [label=\"biolink:subclass_of (9445)\"]; \t\"SIO\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"OBI\" -> \"OBI\" [label=\"biolink:part_of (2)\"]; \t\"GENO\" -> \"SO\" [label=\"biolink:subclass_of (31)\"]; \t\"ClinVarVariant\" -> \"OMIMPS\" [label=\"biolink:gene_associated_with_condition (14066)\"]; \t\"NCBIGene\" -> \"MGI\" [label=\"biolink:interacts_with (30)\"]; \t\"dbSNP\" -> \"MONARCH_BNODE\" [label=\"biolink:has_sequence_location (125680)\"]; \t\"GENO\" -> \"BFO\" [label=\"biolink:subclass_of (11)\"]; \t\"PMID\" -> \"HGNC\" [label=\"biolink:related_to (445544)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:occurs_in (305)\"]; \t\"dbSNP\" -> \"pigQTL\" [label=\"biolink:biomarker_for (87)\"]; \t\"HP\" -> \"https\" [label=\"biolink:related_to (778)\"]; \t\"SEPIO\" -> \"IAO\" [label=\"biolink:has_output (1)\"]; \t\"GENO\" -> \"CHEBI\" [label=\"biolink:subclass_of (1)\"]; \t\"Orphanet\" -> \"NCIT\" [label=\"biolink:subclass_of (5417)\"]; \t\"SEPIO\" -> \"prov\" [label=\"biolink:related_to (1)\"]; \t\"FlyBase\" -> \"FlyBase\" [label=\"biolink:related_to (190338)\"]; \t\"BIOGRID\" -> \"Orphanet\" [label=\"biolink:related_to (24)\"]; \t\"UBERON\" -> \"OBI\" [label=\"biolink:related_to (1)\"]; \t\"GENO\" -> \"OIO\" [label=\"biolink:subPropertyOf (13)\"]; \t\"CHEBI\" -> \"owl\" [label=\"biolink:subclass_of (11)\"]; \t\"FlyBase\" -> \"http\" [label=\"biolink:orthologous_to (664)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:overlaps (9)\"]; \t\"SO\" -> \"GENO\" [label=\"biolink:subclass_of (17)\"]; \t\"GENO\" -> \"owl\" [label=\"biolink:subPropertyOf (2)\"]; \t\"PMID\" -> \"RGD\" [label=\"biolink:related_to (302153)\"]; \t\"HGNC\" -> \"GO\" [label=\"biolink:part_of (23623)\"]; \t\"HGNC\" -> \"MGI\" [label=\"biolink:related_to (16839)\"]; \t\"GO\" -> \"CHEBI\" [label=\"biolink:has_part (16)\"]; \t\"SEPIO\" -> \"OBI\" [label=\"biolink:subclass_of (3)\"]; \t\"GO\" -> \"OBI\" [label=\"biolink:subclass_of (7)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:negatively_regulates_process_to_process (11)\"]; \t\"MONDO\" -> \"MP\" [label=\"biolink:subclass_of (14)\"]; \t\"EFO\" -> \"UPHENO\" [label=\"biolink:subclass_of (2169)\"]; \t\"dbSNP\" -> \"NCBIGene\" [label=\"biolink:biomarker_for (66968)\"]; \t\"MGI\" -> \"APB\" [label=\"biolink:same_as (331)\"]; \t\"BIOGRID\" -> \"OMIM\" [label=\"biolink:has_phenotype (900)\"]; \t\"PANTHER\" -> \"MGI\" [label=\"biolink:related_to (20718)\"]; \t\"ENSEMBL\" -> \"ENSEMBL\" [label=\"biolink:has_gene_product (7595)\"]; \t\"ZP\" -> \"ZP\" [label=\"biolink:subclass_of (53288)\"]; \t\"GENO\" -> \"IAO\" [label=\"biolink:subclass_of (2)\"]; \t\"OBAN\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"MP\" -> \"OBO\" [label=\"biolink:subclass_of (336)\"]; \t\"OBO\" -> \"CL\" [label=\"biolink:subclass_of (1959)\"]; \t\"NCBIGene\" -> \"GO\" [label=\"biolink:part_of (65726)\"]; \t\"MONARCH_BNODE\" -> \"MONARCH\" [label=\"biolink:related_to (3051)\"]; \t\"RGD\" -> \"http\" [label=\"biolink:related_to (149)\"]; \t\"NCBIGene\" -> \"Xenbase\" [label=\"biolink:orthologous_to (93)\"]; \t\"BIOGRID\" -> \"OBO\" [label=\"biolink:related_to (3931)\"]; \t\"RGD\" -> \"FlyBase\" [label=\"biolink:orthologous_to (15099)\"]; \t\"OBO\" -> \"GO\" [label=\"biolink:subclass_of (37)\"]; \t\"NCBIGene\" -> \"ZFIN\" [label=\"biolink:interacts_with (826)\"]; \t\"MGI\" -> \"APB\" [label=\"biolink:related_to (37)\"]; \t\"ENSEMBL\" -> \"MGI\" [label=\"biolink:related_to (31253)\"]; \t\"MONARCH\" -> \"ENSEMBL\" [label=\"biolink:related_to (2)\"]; \t\"PMID\" -> \"BIOGRID\" [label=\"biolink:related_to (2207)\"]; \t\"XCO\" -> \"XCO\" [label=\"biolink:part_of (14)\"]; \t\"NCBIGene\" -> \"HGNC\" [label=\"biolink:interacts_with (496)\"]; \t\"ECO\" -> \"owl\" [label=\"biolink:subclass_of (42)\"]; \t\"FBcv\" -> \"OBO\" [label=\"biolink:related_to (1)\"]; \t\"FlyBase\" -> \"OBO\" [label=\"biolink:related_to (11462)\"]; \t\"HGNC\" -> \"ZFIN\" [label=\"biolink:related_to (12161)\"]; \t\"HGNC\" -> \"Orphanet\" [label=\"biolink:biomarker_for (414)\"]; \t\"UBERON\" -> \"OBO\" [label=\"biolink:part_of (1)\"]; \t\"FlyBase\" -> \"FBcv\" [label=\"biolink:has_phenotype (149834)\"]; \t\"HGNC\" -> \"MGI\" [label=\"biolink:interacts_with (308)\"]; \t\"SO\" -> \"SO\" [label=\"biolink:part_of (1)\"]; \t\"ZP\" -> \"HP\" [label=\"biolink:subclass_of (4014)\"]; \t\"MGI\" -> \"GENO\" [label=\"biolink:subclass_of (198)\"]; \t\"HGNC\" -> \"HGNC\" [label=\"biolink:related_to (3197)\"]; \t\"SO\" -> \"SO\" [label=\"biolink:related_to (628)\"]; \t\"WBPhenotype\" -> \"UBERON\" [label=\"biolink:subclass_of (106)\"]; \t\"MONARCH_BNODE\" -> \"MGI\" [label=\"biolink:related_to (197626)\"]; \t\"https\" -> \"MONDO\" [label=\"biolink:related_to (7)\"]; \t\"PANTHER\" -> \"ZFIN\" [label=\"biolink:related_to (19245)\"]; \t\"horseQTL\" -> \"NCBIGene\" [label=\"biolink:related_to (153)\"]; \t\"GO\" -> \"PR\" [label=\"biolink:has_input (298)\"]; \t\"APO\" -> \"UPHENO\" [label=\"biolink:subclass_of (8)\"]; \t\"KEGG-ko\" -> \"MONARCH_BNODE\" [label=\"biolink:has_gene_product (12747)\"]; \t\"HGNC\" -> \"NCBIGene\" [label=\"biolink:has_gene_product (1)\"]; \t\"FBcv\" -> \"OBO\" [label=\"biolink:subclass_of (22)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:produces (22)\"]; \t\"PANTHER\" -> \"HGNC\" [label=\"biolink:related_to (19206)\"]; \t\"MGI\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (7104)\"]; \t\"NCBITaxon\" -> \"GO\" [label=\"biolink:subclass_of (46)\"]; \t\"FlyBase\" -> \"FlyBase\" [label=\"biolink:interacts_with (60276)\"]; \t\"BFO\" -> \"BFO\" [label=\"biolink:inverseOf (5)\"]; \t\"FlyBase\" -> \"PomBase\" [label=\"biolink:orthologous_to (1980)\"]; \t\"MGI\" -> \"MP\" [label=\"biolink:has_phenotype (598266)\"]; \t\"OBO\" -> \"UBERON\" [label=\"biolink:related_to (8)\"]; \t\"HGNC\" -> \"RGD\" [label=\"biolink:related_to (15668)\"]; \t\"ZFIN\" -> \"HGNC\" [label=\"biolink:orthologous_to (4748)\"]; \t\"Xenbase\" -> \"SO\" [label=\"biolink:subclass_of (15904)\"]; \t\"MONARCH_BNODE\" -> \"HGNC\" [label=\"biolink:has_phenotype (627)\"]; \t\"dbSNP\" -> \"rainbow_troutQTL\" [label=\"biolink:biomarker_for (440)\"]; \t\"MONDO\" -> \"PR\" [label=\"biolink:related_to (20)\"]; \t\"ENSEMBL\" -> \"ZFIN\" [label=\"biolink:related_to (119500)\"]; \t\"NCBIGene\" -> \"dictyBase\" [label=\"biolink:related_to (42)\"]; \t\"OMIM\" -> \"dbSNP\" [label=\"biolink:related_to (108)\"]; \t\"faldo\" -> \"faldo\" [label=\"biolink:subclass_of (13)\"]; \t\"NCBIGene\" -> \"SGD\" [label=\"biolink:related_to (45)\"]; \t\"SEPIO\" -> \"SEPIO\" [label=\"biolink:related_to (9)\"]; \t\"Xenbase\" -> \"ENSEMBL\" [label=\"biolink:related_to (113)\"]; \t\"BIOGRID\" -> \"SO\" [label=\"biolink:subclass_of (2219)\"]; \t\"ClinVarVariant\" -> \"OMIM\" [label=\"biolink:related_to (135398)\"]; \t\"MONDO\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (1)\"]; \t\"MP\" -> \"FBcv\" [label=\"biolink:subclass_of (263)\"]; \t\"NCBIGene\" -> \"SO\" [label=\"biolink:subclass_of (542874)\"]; \t\"MONARCH_NODE\" -> \"DOID\" [label=\"biolink:has_phenotype (38)\"]; \t\"SGD\" -> \"OBO\" [label=\"biolink:related_to (6439)\"]; \t\"ZFIN\" -> \"http\" [label=\"biolink:related_to (146)\"]; \t\"GENO\" -> \"SO\" [label=\"biolink:related_to (9)\"]; \t\"ZFIN\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (2755)\"]; \t\"MGI\" -> \"ZFIN\" [label=\"biolink:orthologous_to (26613)\"]; \t\"PANTHER\" -> \"RGD\" [label=\"biolink:related_to (18137)\"]; \t\"CLO\" -> \"owl\" [label=\"biolink:subPropertyOf (1)\"]; \t\"UBERON\" -> \"ENVO\" [label=\"biolink:related_to (8)\"]; \t\"BIOGRID\" -> \"NCBIGene\" [label=\"biolink:same_as (55)\"]; \t\"FlyBase\" -> \"NCBIGene\" [label=\"biolink:related_to (11963)\"]; \t\"MGI\" -> \"GO\" [label=\"biolink:actively_involved_in (148562)\"]; \t\"ZFIN\" -> \"OBO\" [label=\"biolink:expressed_in (512)\"]; \t\"HGNC\" -> \"CL\" [label=\"biolink:expressed_in (9853)\"]; \t\"http\" -> \"UMLS\" [label=\"biolink:subclass_of (27412)\"]; \t\"UBERON\" -> \"GENO\" [label=\"biolink:subclass_of (2)\"]; \t\"ZFIN\" -> \"ZP\" [label=\"biolink:has_phenotype (189573)\"]; \t\"RGD\" -> \"PomBase\" [label=\"biolink:related_to (2450)\"]; \t\"MP\" -> \"NCIT\" [label=\"biolink:subclass_of (3)\"]; \t\"NCBIGene\" -> \"WormBase\" [label=\"biolink:related_to (144)\"]; \t\"https\" -> \"NCBITaxon\" [label=\"biolink:related_to (206)\"]; \t\"OBO\" -> \"CHEBI\" [label=\"biolink:related_to (25)\"]; \t\"GO\" -> \"ENVO\" [label=\"biolink:subclass_of (4)\"]; \t\"OBO\" -> \"PO\" [label=\"biolink:derives_from (4)\"]; \t\"GO\" -> \"OBO\" [label=\"biolink:regulates_process_to_process (80)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:has_participant (3)\"]; \t\"ENSEMBL\" -> \"GO\" [label=\"biolink:actively_involved_in (120005)\"]; \t\"MGI\" -> \"http\" [label=\"biolink:related_to (158)\"]; \t\"HGNC\" -> \"ZFIN\" [label=\"biolink:interacts_with (2)\"]; \t\"dbSNP\" -> \"HGNC\" [label=\"biolink:related_to (97824)\"]; \t\"ENSEMBL\" -> \"RGD\" [label=\"biolink:related_to (29189)\"]; \t\"MONARCH_BNODE\" -> \"HGNC\" [label=\"biolink:biomarker_for (1)\"]; \t\"HGNC\" -> \"BIOGRID\" [label=\"biolink:related_to (1)\"]; \t\"MONARCH_BNODE\" -> \"ZFIN\" [label=\"biolink:related_to (51246)\"]; \t\"MESH\" -> \"MESH\" [label=\"biolink:biomarker_for (64340)\"]; \t\"RO\" -> \"RO\" [label=\"biolink:related_to (1)\"]; \t\"ENVO\" -> \"ENVO\" [label=\"biolink:has_part (20)\"]; \t\"OBO\" -> \"BSPO\" [label=\"biolink:subPropertyOf (6)\"]; \t\"DOID\" -> \"owl\" [label=\"biolink:subclass_of (8)\"]; \t\"http\" -> \"UBERON\" [label=\"biolink:subclass_of (14)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:derives_from (18)\"]; \t\"HGNC\" -> \"HGNC\" [label=\"biolink:interacts_with (63079)\"]; \t\"MGI\" -> \"RGD\" [label=\"biolink:orthologous_to (4850)\"]; \t\"MONARCH_BNODE\" -> \"HGNC\" [label=\"biolink:related_to (50)\"]; \t\"GO\" -> \"PO\" [label=\"biolink:occurs_in (10)\"]; \t\"GO\" -> \"PR\" [label=\"biolink:has_participant (3)\"]; \t\"HP\" -> \"biolink\" [label=\"biolink:subclass_of (394)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:has_participant (3)\"]; \t\"HP\" -> \"WBPhenotype\" [label=\"biolink:subclass_of (121)\"]; \t\"Orphanet\" -> \"owl\" [label=\"biolink:subclass_of (13)\"]; \t\"BIOGRID\" -> \"OMIM\" [label=\"biolink:biomarker_for (56)\"]; \t\"AspGD\" -> \"GO\" [label=\"biolink:actively_involved_in (244871)\"]; \t\"UPHENO\" -> \"owl\" [label=\"biolink:subclass_of (7)\"]; \t\"MONARCH_NODE\" -> \"MONARCH_BNODE\" [label=\"biolink:related_to (78988)\"]; \t\"faldo\" -> \"rdf\" [label=\"biolink:subclass_of (2)\"]; \t\"RGD\" -> \"NCBIGene\" [label=\"biolink:orthologous_to (1175)\"]; \t\"GENO\" -> \"NCBITaxon\" [label=\"biolink:related_to (2)\"]; \t\"CLO\" -> \"CLO\" [label=\"biolink:related_to (2)\"]; \t\"dbSNP\" -> \"chickenQTL\" [label=\"biolink:biomarker_for (1992)\"]; \t\"OBO\" -> \"IAO\" [label=\"biolink:related_to (1)\"]; \t\"MGI\" -> \"MMRRC\" [label=\"biolink:same_as (2)\"]; \t\"OBO\" -> \"NCBITaxon\" [label=\"biolink:part_of (12616)\"]; \t\"http\" -> \"MONDO\" [label=\"biolink:subclass_of (57130)\"]; \t\"STATO\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"http\" -> \"BFO\" [label=\"biolink:subclass_of (5)\"]; \t\"OBO\" -> \"NCBITaxon\" [label=\"biolink:related_to (7)\"]; \t\"HGNC\" -> \"HP\" [label=\"biolink:related_to (6)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:subPropertyOf (17)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:has_part (109)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:has_output (1)\"]; \t\"MONARCH_BNODE\" -> \"RGD\" [label=\"biolink:related_to (1)\"]; \t\"ECO\" -> \"GO\" [label=\"biolink:related_to (83)\"]; \t\"FBcv\" -> \"FBcv\" [label=\"biolink:subclass_of (198)\"]; \t\"IAO\" -> \"BFO\" [label=\"biolink:subclass_of (5)\"]; \t\"RGD\" -> \"GO\" [label=\"biolink:actively_involved_in (146383)\"]; \t\"BIOGRID\" -> \"OMIM\" [label=\"biolink:contributes_to (341)\"]; \t\"pigQTL\" -> \"pigQTL\" [label=\"biolink:biomarker_for (60)\"]; \t\"IAO\" -> \"CHEBI\" [label=\"biolink:subclass_of (1)\"]; \t\"OBO\" -> \"Orphanet\" [label=\"biolink:subclass_of (19463)\"]; \t\"Xenbase\" -> \"SGD\" [label=\"biolink:orthologous_to (2900)\"]; \t\"WormBase\" -> \"UniProtKB\" [label=\"biolink:has_gene_product (2671)\"]; \t\"WD_Entity\" -> \"ENVO\" [label=\"biolink:type (4)\"]; \t\"MGI\" -> \"MMRRC\" [label=\"biolink:related_to (459)\"]; \t\"NCBIGene\" -> \"FlyBase\" [label=\"biolink:related_to (133)\"]; \t\"GO\" -> \"SO\" [label=\"biolink:has_output (6)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:has_attribute (10)\"]; \t\"HGNC\" -> \"EcoGene\" [label=\"biolink:orthologous_to (952)\"]; \t\"SEPIO\" -> \"SEPIO\" [label=\"biolink:has_input (1)\"]; \t\"UBERON\" -> \"CL\" [label=\"biolink:subclass_of (5)\"]; \t\"BSPO\" -> \"BSPO\" [label=\"biolink:subPropertyOf (8)\"]; \t\"BIOGRID\" -> \"HGNC\" [label=\"biolink:interacts_with (3)\"]; \t\"SEPIO\" -> \"owl\" [label=\"biolink:subclass_of (1)\"]; \t\"dictyBase\" -> \"GO\" [label=\"biolink:part_of (20328)\"]; \t\"sheepQTL\" -> \"AQTLTrait\" [label=\"biolink:biomarker_for (2922)\"]; \t\"GO\" -> \"CHEBI\" [label=\"biolink:has_output (100)\"]; \t\"Xenbase\" -> \"WormBase\" [label=\"biolink:orthologous_to (9980)\"]; \t\"GO\" -> \"owl\" [label=\"biolink:subclass_of (6154)\"]; \t\"ClinVarVariant\" -> \"HGNC\" [label=\"biolink:gene_associated_with_condition (329)\"]; \t\"foaf\" -> \"foaf\" [label=\"biolink:subPropertyOf (12)\"]; \t\"HGNC\" -> \"BIOGRID\" [label=\"biolink:interacts_with (13)\"]; \t\"ZFIN\" -> \"PomBase\" [label=\"biolink:related_to (2482)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:has_part (9)\"]; \t\"OBO\" -> \"PO\" [label=\"biolink:subclass_of (1)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:coexists_with (59)\"]; \t\"UBERON\" -> \"GO\" [label=\"biolink:subclass_of (10)\"]; \t\"pigQTL\" -> \"NCBIGene\" [label=\"biolink:biomarker_for (16045)\"]; \t\"OMIM\" -> \"OMIM\" [label=\"biolink:related_to (4268)\"]; \t\"PR\" -> \"OBI\" [label=\"biolink:subclass_of (1)\"]; \t\"IAO\" -> \"IAO\" [label=\"biolink:subclass_of (167)\"]; \t\"NCBIGene\" -> \"Orphanet\" [label=\"biolink:related_to (2)\"]; \t\"FlyBase\" -> \"NCBIGene\" [label=\"biolink:interacts_with (23)\"]; \t\"ENSEMBL\" -> \"EcoGene\" [label=\"biolink:orthologous_to (926)\"]; \t\"MONARCH_NODE\" -> \"MP\" [label=\"biolink:has_phenotype (34185)\"]; \t\"OBO\" -> \"OBO\" [label=\"biolink:subclass_of (93638)\"]; \t\"MONARCH_BNODE\" -> \"RO\" [label=\"owl:onProperty (233)\"]; \t\"GENO\" -> \"OBAN\" [label=\"biolink:subclass_of (1)\"]; \t\"dbSNP\" -> \"HP\" [label=\"biolink:related_to (2703)\"]; \t\"ECO\" -> \"ECO\" [label=\"biolink:subclass_of (3014)\"]; \t\"PO\" -> \"PO\" [label=\"biolink:located_in (2)\"]; \t\"RGD\" -> \"VGNC\" [label=\"biolink:related_to (8)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:related_to (89)\"]; \t\"MGI\" -> \"PomBase\" [label=\"biolink:related_to (2554)\"]; \t\"pav\" -> \"SEPIO\" [label=\"biolink:subPropertyOf (3)\"]; }"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/sri_semmeddb/sri_semmeddb-map.html",
    "content": "\n\n  SRI Import of SemmedDB KG Map\n  \n\n\n
\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/sri_semmeddb/sri_semmeddb-stats.txt",
    "content": "predicates: 21\ncategories: 12\nconcepts: 171,431\nedges: 14,180,763\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/sri_semmeddb/sri_semmeddb-subject_predicate_object_count.tsv",
    "content": "subject CURIE prefix\tobject CURIE prefix\tpredicate\tedge count\nUMLS\tUMLS\tbiolink:prevents\t143669\nUMLS\tUMLS\tbiolink:gene_associated_with_condition\t343651\nUMLS\tUMLS\tbiolink:produces\t462408\nUMLS\tUMLS\tbiolink:prep\t3\nUMLS\tUMLS\tbiolink:positively_regulates\t1256571\nUMLS\tUMLS\tbiolink:interacts_with\t2111999\nUMLS\tUMLS\tbiolink:negatively_regulates\t1072555\nUMLS\tUMLS\tbiolink:measures\t1047\nUMLS\tUMLS\tbiolink:manifestation_of\t37727\nUMLS\tUMLS\tbiolink:location_of\t1958392\nUMLS\tUMLS\tbiolink:affects\t1886243\nUMLS\tUMLS\tbiolink:subclass_of\t228568\nUMLS\tUMLS\tbiolink:treats\t477872\nUMLS\tUMLS\tbiolink:precedes\t54661\nUMLS\tUMLS\tbiolink:coexists_with\t1774480\nUMLS\tUMLS\tbiolink:causes\t757162\nUMLS\tUMLS\tbiolink:measurement_of\t44\nUMLS\tUMLS\tbiolink:related_to\t573780\nUMLS\tUMLS\tbiolink:part_of\t726915\nUMLS\tUMLS\tbiolink:derives_into\t48615\nUMLS\tUMLS\tbiolink:predisposes\t264401\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/sri_semmeddb/sri_semmeddb.dot",
    "content": "digraph{graph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, fontsize=12 ]; node [ fontname=Arial, fontcolor=blue, fontsize=11]; edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ]; splines=\"FALSE\"; rankdir=\"LR\";\t\"UMLS\" -> \"UMLS\" [label=\"biolink:prevents (143669)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:gene_associated_with_condition (343651)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:produces (462408)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:prep (3)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:positively_regulates (1256571)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:interacts_with (2111999)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:negatively_regulates (1072555)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:measures (1047)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:manifestation_of (37727)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:location_of (1958392)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:affects (1886243)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:subclass_of (228568)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:treats (477872)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:precedes (54661)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:coexists_with (1774480)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:causes (757162)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:measurement_of (44)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:related_to (573780)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:part_of (726915)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:derives_into (48615)\"]; \t\"UMLS\" -> \"UMLS\" [label=\"biolink:predisposes (264401)\"]; }"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/co-occur/co-occur-map.html",
    "content": "\n\n  TextMining Provider Co-occurrence KG Map\n  \n\n\n
\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/co-occur/co-occur-stats.txt",
    "content": "predicates: 1\ncategories: 12\nconcepts: 88,696\nedges: 96,684,414\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/co-occur/co-occur-subject_predicate_object_count.tsv",
    "content": "subject CURIE prefix\tobject CURIE prefix\tpredicate\tedge count\nMONDO\tSO\tbiolink:related_to\t1138140\nCHEBI\tMOP\tbiolink:related_to\t102304\nMOP\tUBERON\tbiolink:related_to\t24664\nMONDO\tNCBITaxon\tbiolink:related_to\t1313061\nCHEBI\tHP\tbiolink:related_to\t1666319\nHP\tUBERON\tbiolink:related_to\t1195221\nMONDO\tMONDO\tbiolink:related_to\t4358876\nCL\tUBERON\tbiolink:related_to\t465319\nPR\tPR\tbiolink:related_to\t2616847\nCHEBI\tCL\tbiolink:related_to\t1056654\nCL\tNCBITaxon#\tbiolink:related_to\t14\nGO\tUBERON\tbiolink:related_to\t2398348\nNCBITaxon\tUBERON\tbiolink:related_to\t706563\nGO\tNCBITaxon#\tbiolink:related_to\t1\nNCBITaxon#\tNCBITaxon\tbiolink:related_to\t10\nMOP\tMOP\tbiolink:related_to\t769\nHP\tMOP\tbiolink:related_to\t17148\nCL\tMOP\tbiolink:related_to\t10217\nMONDO\tPR\tbiolink:related_to\t5623765\nHP\tHP\tbiolink:related_to\t594487\nCHEBI\tSO\tbiolink:related_to\t1105945\nGO\tMOP\tbiolink:related_to\t81244\nCL\tHP\tbiolink:related_to\t261760\nSO\tUBERON\tbiolink:related_to\t427808\nCHEBI\tNCBITaxon\tbiolink:related_to\t2024568\nCL\tCL\tbiolink:related_to\t95616\nCHEBI\tGO\tbiolink:related_to\t7062269\nCHEBI\tMONDO\tbiolink:related_to\t6055640\nGO\tHP\tbiolink:related_to\t1401647\nUBERON\tUBERON\tbiolink:related_to\t1068014\nPR\tUBERON\tbiolink:related_to\t2584357\nNCBITaxon#\tPR\tbiolink:related_to\t3\nMOP\tSO\tbiolink:related_to\t12108\nCHEBI\tCHEBI\tbiolink:related_to\t5405491\nHP\tSO\tbiolink:related_to\t358148\nMOP\tNCBITaxon\tbiolink:related_to\t18847\nCL\tSO\tbiolink:related_to\t159279\nHP\tNCBITaxon\tbiolink:related_to\t387407\nCHEBI\tPR\tbiolink:related_to\t7199237\nCL\tNCBITaxon\tbiolink:related_to\t237330\nHP\tMONDO\tbiolink:related_to\t2922545\nGO\tSO\tbiolink:related_to\t1237576\nCL\tMONDO\tbiolink:related_to\t942228\nCL\tGO\tbiolink:related_to\t1051790\nMONDO\tUBERON\tbiolink:related_to\t3459772\nGO\tNCBITaxon\tbiolink:related_to\t1786461\nNCBITaxon\tSO\tbiolink:related_to\t410701\nGO\tMONDO\tbiolink:related_to\t5135667\nGO\tGO\tbiolink:related_to\t3631022\nMONDO\tNCBITaxon#\tbiolink:related_to\t5\nNCBITaxon\tNCBITaxon\tbiolink:related_to\t406814\nMOP\tPR\tbiolink:related_to\t117278\nSO\tSO\tbiolink:related_to\t126269\nMONDO\tMOP\tbiolink:related_to\t63154\nHP\tPR\tbiolink:related_to\t1384046\nCL\tPR\tbiolink:related_to\t1274878\nGO\tPR\tbiolink:related_to\t6790146\nPR\tSO\tbiolink:related_to\t1853926\nNCBITaxon\tPR\tbiolink:related_to\t2034974\nCHEBI\tUBERON\tbiolink:related_to\t2819717\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/co-occur/co-occur.dot",
    "content": "digraph{graph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, fontsize=12 ]; node [ fontname=Arial, fontcolor=blue, fontsize=11]; edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ]; splines=\"FALSE\"; rankdir=\"LR\";\t\"MONDO\" -> \"SO\" [label=\"biolink:related_to (1138140)\"]; \t\"CHEBI\" -> \"MOP\" [label=\"biolink:related_to (102304)\"]; \t\"MOP\" -> \"UBERON\" [label=\"biolink:related_to (24664)\"]; \t\"MONDO\" -> \"NCBITaxon\" [label=\"biolink:related_to (1313061)\"]; \t\"CHEBI\" -> \"HP\" [label=\"biolink:related_to (1666319)\"]; \t\"HP\" -> \"UBERON\" [label=\"biolink:related_to (1195221)\"]; \t\"MONDO\" -> \"MONDO\" [label=\"biolink:related_to (4358876)\"]; \t\"CL\" -> \"UBERON\" [label=\"biolink:related_to (465319)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:related_to (2616847)\"]; \t\"CHEBI\" -> \"CL\" [label=\"biolink:related_to (1056654)\"]; \t\"CL\" -> \"NCBITaxon#\" [label=\"biolink:related_to (14)\"]; \t\"GO\" -> \"UBERON\" [label=\"biolink:related_to (2398348)\"]; \t\"NCBITaxon\" -> \"UBERON\" [label=\"biolink:related_to (706563)\"]; \t\"GO\" -> \"NCBITaxon#\" [label=\"biolink:related_to (1)\"]; \t\"NCBITaxon#\" -> \"NCBITaxon\" [label=\"biolink:related_to (10)\"]; \t\"MOP\" -> \"MOP\" [label=\"biolink:related_to (769)\"]; \t\"HP\" -> \"MOP\" [label=\"biolink:related_to (17148)\"]; \t\"CL\" -> \"MOP\" [label=\"biolink:related_to (10217)\"]; \t\"MONDO\" -> \"PR\" [label=\"biolink:related_to (5623765)\"]; \t\"HP\" -> \"HP\" [label=\"biolink:related_to (594487)\"]; \t\"CHEBI\" -> \"SO\" [label=\"biolink:related_to (1105945)\"]; \t\"GO\" -> \"MOP\" [label=\"biolink:related_to (81244)\"]; \t\"CL\" -> \"HP\" [label=\"biolink:related_to (261760)\"]; \t\"SO\" -> \"UBERON\" [label=\"biolink:related_to (427808)\"]; \t\"CHEBI\" -> \"NCBITaxon\" [label=\"biolink:related_to (2024568)\"]; \t\"CL\" -> \"CL\" [label=\"biolink:related_to (95616)\"]; \t\"CHEBI\" -> \"GO\" [label=\"biolink:related_to (7062269)\"]; \t\"CHEBI\" -> \"MONDO\" [label=\"biolink:related_to (6055640)\"]; \t\"GO\" -> \"HP\" [label=\"biolink:related_to (1401647)\"]; \t\"UBERON\" -> \"UBERON\" [label=\"biolink:related_to (1068014)\"]; \t\"PR\" -> \"UBERON\" [label=\"biolink:related_to (2584357)\"]; \t\"NCBITaxon#\" -> \"PR\" [label=\"biolink:related_to (3)\"]; \t\"MOP\" -> \"SO\" [label=\"biolink:related_to (12108)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"biolink:related_to (5405491)\"]; \t\"HP\" -> \"SO\" [label=\"biolink:related_to (358148)\"]; \t\"MOP\" -> \"NCBITaxon\" [label=\"biolink:related_to (18847)\"]; \t\"CL\" -> \"SO\" [label=\"biolink:related_to (159279)\"]; \t\"HP\" -> \"NCBITaxon\" [label=\"biolink:related_to (387407)\"]; \t\"CHEBI\" -> \"PR\" [label=\"biolink:related_to (7199237)\"]; \t\"CL\" -> \"NCBITaxon\" [label=\"biolink:related_to (237330)\"]; \t\"HP\" -> \"MONDO\" [label=\"biolink:related_to (2922545)\"]; \t\"GO\" -> \"SO\" [label=\"biolink:related_to (1237576)\"]; \t\"CL\" -> \"MONDO\" [label=\"biolink:related_to (942228)\"]; \t\"CL\" -> \"GO\" [label=\"biolink:related_to (1051790)\"]; \t\"MONDO\" -> \"UBERON\" [label=\"biolink:related_to (3459772)\"]; \t\"GO\" -> \"NCBITaxon\" [label=\"biolink:related_to (1786461)\"]; \t\"NCBITaxon\" -> \"SO\" [label=\"biolink:related_to (410701)\"]; \t\"GO\" -> \"MONDO\" [label=\"biolink:related_to (5135667)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:related_to (3631022)\"]; \t\"MONDO\" -> \"NCBITaxon#\" [label=\"biolink:related_to (5)\"]; \t\"NCBITaxon\" -> \"NCBITaxon\" [label=\"biolink:related_to (406814)\"]; \t\"MOP\" -> \"PR\" [label=\"biolink:related_to (117278)\"]; \t\"SO\" -> \"SO\" [label=\"biolink:related_to (126269)\"]; \t\"MONDO\" -> \"MOP\" [label=\"biolink:related_to (63154)\"]; \t\"HP\" -> \"PR\" [label=\"biolink:related_to (1384046)\"]; \t\"CL\" -> \"PR\" [label=\"biolink:related_to (1274878)\"]; \t\"GO\" -> \"PR\" [label=\"biolink:related_to (6790146)\"]; \t\"PR\" -> \"SO\" [label=\"biolink:related_to (1853926)\"]; \t\"NCBITaxon\" -> \"PR\" [label=\"biolink:related_to (2034974)\"]; \t\"CHEBI\" -> \"UBERON\" [label=\"biolink:related_to (2819717)\"]; }"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/pr-owl/pr-owl-map.html",
    "content": "\n\n  TextMining Provider PR-OWL KG Map\n  \n\n\n
\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/pr-owl/pr-owl-stats.txt",
    "content": "predicates: 15\ncategories: 11\nconcepts: 486,322\nedges: 1,003,564\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/pr-owl/pr-owl-subject_predicate_object_count.tsv",
    "content": "subject CURIE prefix\tobject CURIE prefix\tpredicate\tedge count\nPR\tGO\tbiolink:located_in\t2\nPR\tCHEBI\tbiolink:non_covalently_bound_to*\t7\nPR\tCGNC\tbiolink:has_gene_template*\t545\nEcoGene\tNCBITaxon\tbiolink:in_taxon\t4046\nPR\tMOD\tbiolink:has_part\t5385\nPR\tMOD\tbiolink:has_component*\t5\nPR\tUniProtKB\tbiolink:same_as\t170034\nPomBase\tSO\tbiolink:subClassOf\t5124\nWormBase\tSO\tbiolink:subClassOf\t4518\nPR\tEnsembleBacteria\tbiolink:has_gene_template*\t984\nPR\tPR\tbiolink:lacks_part*\t3181\nCHEBI\tPR\tbiolink:subClassOf\t21\nPR\tMOD\tbiolink:subClassOf\t3\nPR\tRGD\tbiolink:has_gene_template*\t8136\nSO\tSO\tbiolink:subClassOf\t3\nPR\tMGI\tbiolink:has_gene_template*\t16873\nPR\tCL\tbiolink:part_of\t9\nSO\tBFO\tbiolink:subClassOf\t1\nPR\tFlyBase\tbiolink:has_gene_template*\t3965\nEnsemblGene\tNCBITaxon\tbiolink:in_taxon\t278\nTAIR\tNCBITaxon\tbiolink:in_taxon\t15986\nPR\tNCBITaxon\tbiolink:in_taxon\t178406\nCGNC\tSO\tbiolink:subClassOf\t545\ndictyBase\tSO\tbiolink:subClassOf\t4545\nNCBIGene\tSO\tbiolink:subClassOf\t5379\nBFO\tBFO\tbiolink:subClassOf\t2\nEnsembleBacteria\tSO\tbiolink:subClassOf\t984\nEnsembl\tNCBITaxon\tbiolink:in_taxon\t138\nPR\tPomBase\tbiolink:has_gene_template*\t5172\nPR\tdictyBase\tbiolink:has_gene_template*\t4545\nFlyBase\tNCBITaxon\tbiolink:in_taxon\t3965\nOBI\tBFO\tbiolink:subClassOf\t1\nPR\tGO\tbiolink:part_of\t9\nPR\tGO\tbiolink:capable_of\t25\nHGNC\tSO\tbiolink:subClassOf\t19818\nPR\tSGD\tbiolink:has_gene_template*\t5940\nPR\tPR\tbiolink:has_part\t153\nPR\tPR\tbiolink:has_component*\t1491\nCL\tCL\tbiolink:subClassOf\t1\nPR\tPR\tbiolink:subClassOf\t339987\nMOD\tMOD\tbiolink:subClassOf\t152\nPR\tNCBIGene\tbiolink:has_gene_template*\t5456\nEcoGene\tSO\tbiolink:subClassOf\t4046\nPR\tSO\tbiolink:lacks_part*\t3248\nPR\tGO\tbiolink:participates_in\t3\nSGD\tSO\tbiolink:subClassOf\t5938\nTAIR\tSO\tbiolink:subClassOf\t15986\nPR\tGO\tbiolink:output_of*\t808\nMGI\tNCBITaxon\tbiolink:in_taxon\t16873\nCHEBI\tBFO\tbiolink:subClassOf\t1\nPR\tWormBase\tbiolink:has_gene_template*\t4518\nWormBase\tNCBITaxon\tbiolink:in_taxon\t4518\nPR\tPR\tbiolink:has_gene_template*\t44\nCHEBI\tCHEBI\tbiolink:subClassOf\t36\nEnsemblGene\tSO\tbiolink:subClassOf\t278\nPR\tPR\tbiolink:derives_from\t57\nRGD\tNCBITaxon\tbiolink:in_taxon\t8136\nMOD\tPR\tbiolink:subClassOf\t62\nPomBase\tNCBITaxon\tbiolink:in_taxon\t5124\ndictyBase\tNCBITaxon\tbiolink:in_taxon\t4545\nPR\tSO\tbiolink:has_part\t6\nFlyBase\tSO\tbiolink:subClassOf\t3965\nPR\tSO\tbiolink:subClassOf\t45\nHGNC\tNCBITaxon\tbiolink:in_taxon\t19818\nSO\tPR\tbiolink:subClassOf\t3\nPR\tGO\tbiolink:subClassOf\t382\nPR\tBFO\tbiolink:subClassOf\t1\nPR\tZFIN\tbiolink:has_gene_template*\t3339\nCGNC\tNCBITaxon\tbiolink:in_taxon\t545\nGO\tGO\tbiolink:subClassOf\t131\nGO\tBFO\tbiolink:subClassOf\t2\nPR\tCHEBI\tbiolink:has_part\t2\nPR\tEnsembl\tbiolink:has_gene_template*\t138\nZFIN\tNCBITaxon\tbiolink:in_taxon\t3339\nEnsembleBacteria\tNCBITaxon\tbiolink:in_taxon\t984\nNCBITaxon\tNCBITaxon\tbiolink:subClassOf\t686\nPR\tCHEBI\tbiolink:has_component*\t123\nPR\tMOD\tbiolink:lacks_part*\t48\nPR\tCHEBI\tbiolink:subClassOf\t24\nZFIN\tSO\tbiolink:subClassOf\t3339\nPR\tPR\tbiolink:part_of\t1\nPR\tHGNC\tbiolink:has_gene_template*\t19818\nEnsembl\tSO\tbiolink:subClassOf\t138\nMGI\tSO\tbiolink:subClassOf\t16873\nNCBIGene\tNCBITaxon\tbiolink:in_taxon\t5379\nSGD\tNCBITaxon\tbiolink:in_taxon\t5938\nRGD\tSO\tbiolink:subClassOf\t8136\nPR\tSO\tbiolink:has_gene_template*\t1\nPR\tEcoGene\tbiolink:has_gene_template*\t4047\nNCBITaxon\tOBI\tbiolink:subClassOf\t4\nSO\tSO\tbiolink:has_quality*\t1\nPR\tTAIR\tbiolink:has_gene_template*\t15989\nPR\tEnsemblGene\tbiolink:has_gene_template*\t278\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/pr-owl/pr-owl.dot",
    "content": "digraph{graph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, fontsize=12 ]; node [ fontname=Arial, fontcolor=blue, fontsize=11]; edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ]; splines=\"FALSE\"; rankdir=\"LR\";\t\"PR\" -> \"GO\" [label=\"biolink:located_in (2)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:non_covalently_bound_to* (7)\"]; \t\"PR\" -> \"CGNC\" [label=\"biolink:has_gene_template* (545)\"]; \t\"EcoGene\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (4046)\"]; \t\"PR\" -> \"MOD\" [label=\"biolink:has_part (5385)\"]; \t\"PR\" -> \"MOD\" [label=\"biolink:has_component* (5)\"]; \t\"PR\" -> \"UniProtKB\" [label=\"biolink:same_as (170034)\"]; \t\"PomBase\" -> \"SO\" [label=\"biolink:subClassOf (5124)\"]; \t\"WormBase\" -> \"SO\" [label=\"biolink:subClassOf (4518)\"]; \t\"PR\" -> \"EnsembleBacteria\" [label=\"biolink:has_gene_template* (984)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:lacks_part* (3181)\"]; \t\"CHEBI\" -> \"PR\" [label=\"biolink:subClassOf (21)\"]; \t\"PR\" -> \"MOD\" [label=\"biolink:subClassOf (3)\"]; \t\"PR\" -> \"RGD\" [label=\"biolink:has_gene_template* (8136)\"]; \t\"SO\" -> \"SO\" [label=\"biolink:subClassOf (3)\"]; \t\"PR\" -> \"MGI\" [label=\"biolink:has_gene_template* (16873)\"]; \t\"PR\" -> \"CL\" [label=\"biolink:part_of (9)\"]; \t\"SO\" -> \"BFO\" [label=\"biolink:subClassOf (1)\"]; \t\"PR\" -> \"FlyBase\" [label=\"biolink:has_gene_template* (3965)\"]; \t\"EnsemblGene\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (278)\"]; \t\"TAIR\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (15986)\"]; \t\"PR\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (178406)\"]; \t\"CGNC\" -> \"SO\" [label=\"biolink:subClassOf (545)\"]; \t\"dictyBase\" -> \"SO\" [label=\"biolink:subClassOf (4545)\"]; \t\"NCBIGene\" -> \"SO\" [label=\"biolink:subClassOf (5379)\"]; \t\"BFO\" -> \"BFO\" [label=\"biolink:subClassOf (2)\"]; \t\"EnsembleBacteria\" -> \"SO\" [label=\"biolink:subClassOf (984)\"]; \t\"Ensembl\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (138)\"]; \t\"PR\" -> \"PomBase\" [label=\"biolink:has_gene_template* (5172)\"]; \t\"PR\" -> \"dictyBase\" [label=\"biolink:has_gene_template* (4545)\"]; \t\"FlyBase\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (3965)\"]; \t\"OBI\" -> \"BFO\" [label=\"biolink:subClassOf (1)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:part_of (9)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:capable_of (25)\"]; \t\"HGNC\" -> \"SO\" [label=\"biolink:subClassOf (19818)\"]; \t\"PR\" -> \"SGD\" [label=\"biolink:has_gene_template* (5940)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:has_part (153)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:has_component* (1491)\"]; \t\"CL\" -> \"CL\" [label=\"biolink:subClassOf (1)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:subClassOf (339987)\"]; \t\"MOD\" -> \"MOD\" [label=\"biolink:subClassOf (152)\"]; \t\"PR\" -> \"NCBIGene\" [label=\"biolink:has_gene_template* (5456)\"]; \t\"EcoGene\" -> \"SO\" [label=\"biolink:subClassOf (4046)\"]; \t\"PR\" -> \"SO\" [label=\"biolink:lacks_part* (3248)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:participates_in (3)\"]; \t\"SGD\" -> \"SO\" [label=\"biolink:subClassOf (5938)\"]; \t\"TAIR\" -> \"SO\" [label=\"biolink:subClassOf (15986)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:output_of* (808)\"]; \t\"MGI\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (16873)\"]; \t\"CHEBI\" -> \"BFO\" [label=\"biolink:subClassOf (1)\"]; \t\"PR\" -> \"WormBase\" [label=\"biolink:has_gene_template* (4518)\"]; \t\"WormBase\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (4518)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:has_gene_template* (44)\"]; \t\"CHEBI\" -> \"CHEBI\" [label=\"biolink:subClassOf (36)\"]; \t\"EnsemblGene\" -> \"SO\" [label=\"biolink:subClassOf (278)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:derives_from (57)\"]; \t\"RGD\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (8136)\"]; \t\"MOD\" -> \"PR\" [label=\"biolink:subClassOf (62)\"]; \t\"PomBase\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (5124)\"]; \t\"dictyBase\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (4545)\"]; \t\"PR\" -> \"SO\" [label=\"biolink:has_part (6)\"]; \t\"FlyBase\" -> \"SO\" [label=\"biolink:subClassOf (3965)\"]; \t\"PR\" -> \"SO\" [label=\"biolink:subClassOf (45)\"]; \t\"HGNC\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (19818)\"]; \t\"SO\" -> \"PR\" [label=\"biolink:subClassOf (3)\"]; \t\"PR\" -> \"GO\" [label=\"biolink:subClassOf (382)\"]; \t\"PR\" -> \"BFO\" [label=\"biolink:subClassOf (1)\"]; \t\"PR\" -> \"ZFIN\" [label=\"biolink:has_gene_template* (3339)\"]; \t\"CGNC\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (545)\"]; \t\"GO\" -> \"GO\" [label=\"biolink:subClassOf (131)\"]; \t\"GO\" -> \"BFO\" [label=\"biolink:subClassOf (2)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:has_part (2)\"]; \t\"PR\" -> \"Ensembl\" [label=\"biolink:has_gene_template* (138)\"]; \t\"ZFIN\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (3339)\"]; \t\"EnsembleBacteria\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (984)\"]; \t\"NCBITaxon\" -> \"NCBITaxon\" [label=\"biolink:subClassOf (686)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:has_component* (123)\"]; \t\"PR\" -> \"MOD\" [label=\"biolink:lacks_part* (48)\"]; \t\"PR\" -> \"CHEBI\" [label=\"biolink:subClassOf (24)\"]; \t\"ZFIN\" -> \"SO\" [label=\"biolink:subClassOf (3339)\"]; \t\"PR\" -> \"PR\" [label=\"biolink:part_of (1)\"]; \t\"PR\" -> \"HGNC\" [label=\"biolink:has_gene_template* (19818)\"]; \t\"Ensembl\" -> \"SO\" [label=\"biolink:subClassOf (138)\"]; \t\"MGI\" -> \"SO\" [label=\"biolink:subClassOf (16873)\"]; \t\"NCBIGene\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (5379)\"]; \t\"SGD\" -> \"NCBITaxon\" [label=\"biolink:in_taxon (5938)\"]; \t\"RGD\" -> \"SO\" [label=\"biolink:subClassOf (8136)\"]; \t\"PR\" -> \"SO\" [label=\"biolink:has_gene_template* (1)\"]; \t\"PR\" -> \"EcoGene\" [label=\"biolink:has_gene_template* (4047)\"]; \t\"NCBITaxon\" -> \"OBI\" [label=\"biolink:subClassOf (4)\"]; \t\"SO\" -> \"SO\" [label=\"biolink:has_quality* (1)\"]; \t\"PR\" -> \"TAIR\" [label=\"biolink:has_gene_template* (15989)\"]; \t\"PR\" -> \"EnsemblGene\" [label=\"biolink:has_gene_template* (278)\"]; }"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/textminingprovider/textminingprovider-map.html",
    "content": "\n\n  TextMining Provider PR-OWL KG Map\n  \n\n\n
\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/textminingprovider/textminingprovider-stats.txt",
    "content": "predicates: 2\ncategories: 3\nconcepts: 188,342\nedges: 87,798\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/textminingprovider/textminingprovider-subject_predicate_object_count.tsv",
    "content": "subject CURIE prefix\tobject CURIE prefix\tpredicate\tedge count\nCHEBI\tPR\tbiolink:positively_regulates_entity_to_entity\t41563\nCHEBI\tPR\tbiolink:negatively_regulates_entity_to_entity\t46235\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg-maps/textminingprovider/textminingprovider/textminingprovider.dot",
    "content": "digraph{graph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, fontsize=12 ]; node [ fontname=Arial, fontcolor=blue, fontsize=11]; edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ]; splines=\"FALSE\"; rankdir=\"LR\";\t\"CHEBI\" -> \"PR\" [label=\"biolink:positively_regulates_entity_to_entity (41563)\"]; \t\"CHEBI\" -> \"PR\" [label=\"biolink:negatively_regulates_entity_to_entity (46235)\"]; }"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/kg_statistics_table_generator.R",
    "content": "### LIBRARIES\nlibrary(gt) \nlibrary(gtsummary)\nlibrary(lubridate)\nlibrary(tidyverse)\nlibrary(stringr)\nlibrary(readr)\n\nco_occur_kg <- read_tsv(\n  # tsv file-path-here\n)\n\nco_occur_kg <- co_occur_kg %>%\n  arrange(desc(`edge count`)) %>%\n  mutate(`Subject CURIE Prefix` = `subject CURIE prefix`, \n         `Object CURIE Prefix` = `object CURIE prefix`, \n         `Predicate` = predicate, \n         `Edge Count` = `edge count`) %>% \n  select(`Subject CURIE Prefix`:`Edge Count`)\n  \n\nco_occur_kg %>%\n  gt() %>%\n  tab_header(title = \"Textmining Provider Co-occurrence Knowledge Graph Statistics\") %>%\n  gtsave(\n    # file-path-here, extension .pdf\n  )\n\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/rtx2-KG-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../../../medikanren/pieces-parts/query.rkt\"         \n         racket/engine)\n\n;; \"MONDO:0004989\" = carcinoma of the breast\n;; hand this off to molepro for drug->disease query\n;; all genes from gene->disease query in rtx2 can be handed off to molepro \n(define test-ls\n  '(\"MONDO:0004989\"))\n\n#|\n    \"MONDO:0004989\"\n    \"MONDO:0021100\"\n    \"NCIT:C4872\"\n\n    \"MESH:D001943\"\n|#\n\n(define test-query/gene->disease\n  (time\n   (map (lambda (curie) \n            (query/graph\n             ((S #f)\n              (O curie))\n             ((S->O (list\n                     \"gene_mapped_to_disease\"\n                     \"gene_involved_in_pathogenesis_of_disease\"\n                     \"gene_associated_with_disease\"\n                     \"associated_with_disease\"\n                     \"INVERTED:disease_has_basis_in_dysfunction_of\"\n                     )) (edge/db? #f))\n             (S S->O O)))       \n       test-ls)))\n\n(define test-query/edges:gene->disease\n  (map (lambda (edge) (edges/query edge 'S->O))\n       test-query/gene->disease))\n\n(define gene->PR\n  (map\n   (lambda (edge-ls)\n     (map (lambda (edge)\n            (let ((gene-curie (concept->curie (edge->subject edge))))\n              (printf \"~a\" gene-curie)\n              (query/graph\n               ((S gene-curie)\n                (O #f))\n               ((S->O (list \"INVERTED:has_gene_template\")) (edge/db? #f))\n               (S S->O O))))\n          edge-ls))\n   test-query/edges:gene->disease))\n\n\n(map (lambda (edge) (edges/query edge 'S->O))\n     gene->PR)\n\n;; working query \n(define test-query/drug->disease\n  (time\n   (map (lambda (curie) \n            (query/graph\n             ((S #f)\n              (O curie))\n             ((S->O (list \"treats\")) (edge/db? #f))\n             (S S->O O)))       \n       test-ls)))\n\n(define test-query/test-query/drug->disease\n  (map (lambda (edge) (edges/query edge 'S->O))\n       test-query/drug->disease))\n\n\n"
  },
  {
    "path": "contrib/medikanren/2020_NCATS_relay/textmining-KG-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../../../medikanren/pieces-parts/query.rkt\"         \n         racket/engine)\n\n#|NOTES FOR SYNONYMIZATION CACHE |#\n#|\nSafe Predicates to synonymize with\n-   rtx2_2020_09_16 (487 . \"equivalent_to\")\n-   rtx2_2020_09_16 (228 . \"gene_encodes_gene_product\")\n-   rtx2_2020_09_16 (737 . \"has_gene_product\")\n-   pr-owl (2 . \"biolink:same_as\")\n-   pr-owl (3 . \"biolink:has_gene_template*\")\n|#\n\n#|test queries|#\n;; \"biolink:positively_regulates_entity_to_entity\"\n;; \"biolink:negatively_regulates_entity_to_entity\"\n\n(define predicate:neg-reg/text-mining\n  (list \"biolink:negatively_regulates_entity_to_entity\"))\n\n(define predicate:pos-reg/text-mining\n  (list \"biolink:positively_regulates_entity_to_entity\"))\n\n(define predicate:co-occur/text-mining\n  (list \"biolink:related_to\"))\n\n(define predicate:PR->HGNC\n  '(\"biolink:has_gene_template*\"))\n\n;; breast cancer HP terms\n;; co-occurence KG requires HP terms for Disease->Gene Associations\n(define test-ls\n  '(\"HP:0006625\"\n    \"HP:0100013\"\n    \"HP:0100783\"))\n\n;; - get co-occurs edges HP --> PR\n;; - transform PR: to HGNC with PR: --biolink_has_gene_template*--> HGNC\n\n(define gene/gene-product '(\"biolink:GeneOrGeneProduct\"))\n\n(define drug '(\"biolink:ChemicalSubstance\"))\n\n;; HP --> PR query\n(define test-query/disease->gene\n  (map (lambda (curie)\n            (query/graph\n             ((S curie)\n              (O gene/gene-product))\n             ((S->O #f) (edge/db? #f))\n             (S S->O O)))       \n       test-ls\n       ))\n\n;; HP --> PR edges\n(define test-query/edges:disease->gene\n  (map (lambda (edge) (edges/query edge 'S->O)) test-query/disease->gene))\n\n;; scrape object out of HP->PR edges, and requery PR codes in the PR-OWL KG for HGNCs\n\n(define x\n  (map\n   (lambda (edge-ls)\n     (map (lambda (edge)\n            (let ((PR-curie (concept->curie (edge->object edge))))\n              (printf \"~a\\n\" PR-curie)\n              #;(filter (lambda (object) (string-)))\n              (curies/query\n                (query/graph\n                 ((S PR-curie)\n                  (O #f))\n                 ((S->O '(\"biolink:in_taxon\")) (edge/db? #f))\n                 (S S->O O))\n                'O)))\n          edge-ls))\n   test-query/edges:disease->gene)) \n\n(edges/query\n (query/graph\n  ((S \"PR:P30042\")\n   (O '(\"biolink:OrganismTaxon\")))\n  ((S->O #f) (edge/db? #f))\n  (S S->O O)) 'S->O) \n\n\n\n\n\n\n\n\n\n\n#|\n;; lots of noise/non-specific drug findings in these edges \n(define test-query/drug->disease\n  (map (lambda (curie)\n            (query/graph\n             ((S drug)\n              (O curie))\n             ((S->O #f) (edge/db? #f))\n             (S S->O O)))\n       test-ls\n       ))\n\n;; CHEBI -> PR edges \n(define test-query/edges:drug->disease\n  (map (lambda (edge) (edges/query edge 'S->O)) test-query/drug->disease))\n|#\n\n\n\n\n\n\n\n\n\n#|\n\n|#\n\n;; X co-occurs--> breast-cancer MONDO\n#;(edges/query\n (query/graph\n  ((X gene/protein-concept?)\n   (TC \"MONDO:0004989\"))\n  ((TC->X (list \"biolink:related_to\")))\n  (TC TC->X X))\n 'TC->X)\n\n#|\nco-occurence breast cancer disease concepts\n\n|#\n\n\n\n#|\nminikanren queries for edge types\n(time\n (run 1 (eid subject object)\n  (fresh (eprops)\n    (edgeo\n     `(rtx2_2020_09_16 ,eid ,subject ,object (228 . \"gene_encodes_gene_product\") ,eprops)))))\n\n|#\n\n"
  },
  {
    "path": "contrib/medikanren/README.md",
    "content": "# Synopsis\n\nContributions for medikanren version 1 go in this directory.\n\n"
  },
  {
    "path": "contrib/medikanren/X-Y-C.rkt",
    "content": ";;; X-Y-C queries\n;;; unknown-unknown-known concepts\n;;;\n;;; example:\n;;;\n;;; X - increases - G1 - increases - G2\n;;;\n;;; where G1 and G2 are genes.\n;;;\n;;; Also want to report what other things that G1 increases (as part\n;;; of tox info)\n\n\n;;; Hmm--need to be smarter here!\n;;;\n;;; Suppose we want to increase expression of gene G2, and that genes\n;;; A, B, and C increase expression of G2, and genes D, E, and F\n;;; decrease expression of G2.  It may be that a drug D increases\n;;; expression of A, but decreases expression of B and C, and\n;;; increases expression of D, E, and F!  Since we don't have\n;;; quantitative data, we have to assume this would be\n;;; counter-productive!\n;;;\n;;; So, really, we need to calculate the effects of D on *all* genes\n;;; known to regulate G2, use this information for ranking, and\n;;; display the info as part of the output.  And, of course, we need\n;;; to consider the strength of the evidence for all of these claims.\n\n;;; Also, the approach I'm taking with\n;;; G1-G2-edges-without-duplicate-dbname/scui seems wrong.  Really\n;;; need to separate evidence of G1 increasing G2 from evidence that D\n;;; increases G1.  After all, the evidence that G1 increases G2 can\n;;; already be complex: should be calculating all the ways in which G1\n;;; positively or negatively affects G2, weighing the evidence, etc.,\n;;; and producing a full mini-report just for the 'G1 increases G2'\n;;; claim.  Then the user can pick a G2, and get a full mini-report\n;;; for each D that interacts with G2.  This is probably easier in a\n;;; GUI or custom text interface than in the REPL.\n\n;;; And still need to create the 'tox report' showing what other genes\n;;; G1 affects, what other genes D affects, etc.  Probably also want\n;;; to list what diseases/symptoms both G1 and D are associated with,\n;;; ranked by evidence.\n\n;;; Also, given how noisy semmed is, prolly want to cross-reference\n;;; the genes against the NLM list of genes/pubmed ids to flag/filter\n;;; those associations that are bogus, picked up through bad NLP.\n;;; May be best to incorporate this list as an actual relation we\n;;; can query over, although we might need to index it as well.\n;;; This would be the most consistent and flexible approach, though,\n;;; as opposed to putting the info in a hash table or whatever.\n\n;;; Example problems:\n;;;\n;;; X that downregulates GMPPB resulting in a decrease of GMPPA expression\n;;; X that increases KLF4 in order to compensate for a decrease in SOX5.\n;;; X that increases the expression of the CDKL5 gene to increase CDKL5 protein expression\n\n#lang racket\n\n(provide\n  (all-from-out \"mk.rkt\")\n  (all-from-out \"mk-db.rkt\")\n  (all-from-out \"common.rkt\")\n  (all-defined-out))\n\n(require\n  \"mk.rkt\"\n  \"db.rkt\"\n  \"mk-db.rkt\"\n  \"common.rkt\"\n  (except-in racket/match ==)\n  (only-in srfi/1 iota))\n\n(define X-Y-C_VERSION_STRING \"X-Y-C Tool 0.1.0\")\n\n(define argv (current-command-line-arguments))\n(define argv-optional '#(CONFIG_FILE))\n\n(when (not (<= (vector-length argv) (vector-length argv-optional)))\n  (error \"optional arguments ~s; given ~s\" argv-optional argv))\n\n(displayln \"Starting X-Y-C tool...\")\n(displayln X-Y-C_VERSION_STRING)\n;; Loading will occur at first use if not explicitly forced like this.\n(load-config #t (and (<= 1 (vector-length argv)) (vector-ref argv 0)))\n(load-databases #t)\n\n;;; Decreases/increases predicate names\n(define DECREASES_PREDICATE_NAMES (config-ref 'decreases-predicate-names))\n(define INCREASES_PREDICATE_NAMES (config-ref 'increases-predicate-names))\n\n\n\n(define G-G-increases-predicate-names\n  '(\"positively_regulates\"\n    ;; \"causes\"\n    ;; \"produces\"  ;;; maybe??\n    ;; \"causes_condition\"\n    ;; \"causally_related_to\"\n    ;; \"contributes_to\"\n    ;; \"causes_adverse_event\"\n    ;; \"gene_associated_with_condition\"\n    ;; \"gene_mutations_contribute_to\"\n    ;; \"disease_to_gene_association\"\n    \"increases_activity_of\"\n    \"increases_expression_of\"\n    \"increases_molecular_interaction\"\n    \"increases_response_to\"\n    \"increases_secretion_of\"\n    \"increases_stability_of\"\n    \"increases_synthesis_of\"\n    \"increases_transport_of\"\n    \"increases_uptake_of\"\n    \"decreases_degradation_of\"\n    \"posetively_regulates\" ;;; robokop typo??\n    ;; \"positively_regulates__entity_to_entity\"\n    ;; \"increases_molecular_modification_of\"\n    ;; \"increases_localization_of\"\n    ;; \"increases_splicing_of\"\n    ;; \"decreases_mutation_rate_of\"\n    ;; \"predisposes\"\n    ;; \"decreases_metabolic_processing_of\"\n    ))\n\n(define D-G-increases-predicate-names\n  '(\"positively_regulates\"\n    ;; \"causes\"\n    ;; \"produces\"  ;;; maybe??\n    ;; \"causes_condition\"\n    ;; \"causally_related_to\"\n    ;; \"contributes_to\"\n    ;; \"causes_adverse_event\"\n    ;; \"gene_associated_with_condition\"\n    ;; \"gene_mutations_contribute_to\"\n    ;; \"disease_to_gene_association\"\n    \"increases_activity_of\"\n    \"increases_expression_of\"\n    \"increases_molecular_interaction\"\n    \"increases_response_to\"\n    \"increases_secretion_of\"\n    \"increases_stability_of\"\n    \"increases_synthesis_of\"\n    \"increases_transport_of\"\n    \"increases_uptake_of\"\n    \"decreases_degradation_of\"\n    \"posetively_regulates\" ;;; robokop typo??\n    ;; \"positively_regulates__entity_to_entity\"\n    ;; \"increases_molecular_modification_of\"\n    ;; \"increases_localization_of\"\n    ;; \"increases_splicing_of\"\n    ;; \"decreases_mutation_rate_of\"\n    ;; \"predisposes\"\n    ;; \"decreases_metabolic_processing_of\"\n    ))\n\n;;; X - increases - G1 - increases - G2\n\n\n\n#|\n;;; let's try NGLY1 as an example\n(define G2-concepts\n  '((semmed 141262 \"UMLS:C1425023\" \"NGLY1 gene\" (4 . \"gene\") ((\"umls_type_label\" . \"['Gene or Genome']\") (\"xrefs\" . \"['HGNC:HGNC:17646', 'OMIM:610661', 'MTH:NOCODE']\") (\"id\" . \"UMLS:C1425023\") (\"umls_type\" . \"['T028']\") (\"labels\" . \"['gene']\")))\n (robokop 22660 \"HGNC:17646\" \"NGLY1\" (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\") ((\"locus_group\" . \"protein-coding gene\") (\"chromosome\" . \"3\") (\"location\" . \"3p24.2\") (\"taxon\" . \"9606\") (\"id\" . \"HGNC:17646\") (\"equivalent_identifiers\" . \"(\\\"UniProtKB:H0Y2P2\\\" \\\"ENSEMBL:ENSG00000151092\\\" \\\"UniProtKB:Q96IV0\\\" \\\"UniProtKB:C9JU75\\\" \\\"HGNC:17646\\\" \\\"NCBIGENE:55768\\\" \\\"UniProtKB:A0A0C4DFP4\\\")\")))\n (orange 16958 \"NCBIGene:55768\" \"NGLY1\" (6 . \"(\\\"gene\\\")\") ((\"iri\" . \"http://www.ncbi.nlm.nih.gov/gene/55768\") (\"synonym\" . \"(\\\"FLJ11005\\\" \\\"PNG1\\\" \\\"peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase\\\" \\\"Peptide-N-Glycanase 1, S. Cerevisiae, Homolog of\\\" \\\"N-GLYCANASE 1; NGLY1\\\" \\\"NGLY1\\\")\") (\"in_taxon\" . \"NCBITaxon:9606\") (\"description\" . \"N-glycanase 1\") (\"same_as\" . \"(\\\"ENSEMBL:ENSG00000151092\\\" \\\"HGNC:17646\\\" \\\"OMIM:610661\\\" \\\"Orphanet:406885\\\")\") (\"provided_by\" . \"(\\\"orphanet.ttl\\\" \\\"omim.ttl\\\")\") (\"id\" . \"NCBIGene:55768\")))))\n|#\n\n\n;;; let's try BRCA1 as an example\n(define G2-concepts\n  '((semmed 74686 \"UMLS:C0376571\" \"BRCA1 gene\" (4 . \"gene\") ((\"umls_type_label\" . \"['Gene or Genome']\") (\"xrefs\" . \"['NCI_NCI-HGNC:HGNC:1100', 'CHV:0000031821', 'PDQ:CDR0000043111', 'MESH:D019398', 'CSP:4005-0006', 'MTH:NOCODE', 'LNC:LP36227-4', 'NCI:C17965', 'LNC:LP19666-4', 'OMIM:113705', 'HGNC:HGNC:1100']\") (\"id\" . \"UMLS:C0376571\") (\"umls_type\" . \"['T028']\") (\"labels\" . \"['gene']\")))\n    (robokop 26 \"HGNC:1100\" \"BRCA1\" (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\") ((\"locus_group\" . \"protein-coding gene\") (\"chromosome\" . \"17\") (\"taxon\" . \"9606\") (\"gene_family\" . \"(\\\"Ring finger proteins\\\" \\\"FA complementation groups\\\" \\\"Protein phosphatase 1 regulatory subunits\\\" \\\"BRCA1 A complex\\\" \\\"BRCA1 B complex\\\" \\\"BRCA1 C complex\\\")\") (\"location\" . \"17q21.31\") (\"id\" . \"HGNC:1100\") (\"gene_family_id\" . \"(58 548 694 1328 1335 1336)\") (\"equivalent_identifiers\" . \"(\\\"UniProtKB:C9IZW4\\\" \\\"UniProtKB:E9PC22\\\" \\\"UniProtKB:A0A2R8Y7V5\\\" \\\"UniProtKB:H0Y8D8\\\" \\\"UniProtKB:E9PH68\\\" \\\"UniProtKB:K7EPC7\\\" \\\"UniProtKB:E7EQW4\\\" \\\"UniProtKB:H0Y881\\\" \\\"UniProtKB:E7EWN5\\\" \\\"UniProtKB:H0Y850\\\" \\\"UniProtKB:C6YB45\\\" \\\"UniProtKB:E7EUM2\\\" \\\"UniProtKB:A0A024R1V0\\\" \\\"HGNC:1100\\\" \\\"UniProtKB:A0A0U1RRA9\\\" \\\"UniProtKB:E7ENB7\\\" \\\"UniProtKB:K7EJW3\\\" \\\"UniProtKB:H0Y8B8\\\" \\\"UniProtKB:A0A2R8Y6Y9\\\" \\\"UniProtKB:Q5YLB2\\\" \\\"UniProtKB:P38398\\\" \\\"UniProtKB:B7ZA85\\\" \\\"UniProtKB:A0A0A0MSN1\\\" \\\"ENSEMBL:ENSG00000012048\\\" \\\"UniProtKB:Q3B891\\\" \\\"UniProtKB:G1UI37\\\" \\\"NCBIGENE:672\\\" \\\"UniProtKB:A0A2R8Y587\\\")\")))\n    (orange 32553 \"NCBIGene:672\" \"BRCA1\" (6 . \"(\\\"gene\\\")\") ((\"iri\" . \"http://www.ncbi.nlm.nih.gov/gene/672\") (\"synonym\" . \"(\\\"BRCA1/BRCA2-containing complex, subunit 1\\\" \\\"Fanconi anemia, complementation group S\\\" \\\"protein phosphatase 1, regulatory subunit 53\\\" \\\"BRCC1\\\" \\\"FANCS\\\" \\\"PPP1R53\\\" \\\"RNF53\\\" \\\"BREAST CANCER 1 GENE; BRCA1\\\" \\\"BRCA1\\\")\") (\"in_taxon\" . \"NCBITaxon:9606\") (\"same_as\" . \"(\\\"ENSEMBL:ENSG00000012048\\\" \\\"HGNC:1100\\\" \\\"OMIM:113705\\\" \\\"Orphanet:119068\\\")\") (\"provided_by\" . \"(\\\"orphanet.ttl\\\" \\\"omim.ttl\\\")\") (\"description\" . \"BRCA1, DNA repair associated\") (\"id\" . \"NCBIGene:672\")))))\n\n\n;;; Want to restrict to gene/protein/whatever\n;;;\n;;; This is pretty restrictive, and doesn't include 'rtx' (which seems\n;;; to use 'protein' instead of gene).\n(define (restrict-concept-to-gene dbname c)\n  (fresh (cid cui name catid cat props)\n    (== `(,cid ,cui ,name (,catid . ,cat) ,props) c)\n    (membero `(,dbname (,catid . ,cat))\n             `((semmed (4 . \"gene\"))\n               (robokop (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\"))    \n               (orange (6 . \"(\\\"gene\\\")\"))))))\n\n;;; pretty restrictive!\n;;; what about orange?\n(define (restrict-concept-to-drug dbname c)\n  (fresh (cid cui name catid cat props)\n    (== `(,cid ,cui ,name (,catid . ,cat) ,props) c)\n    (membero `(,dbname (,catid . ,cat))\n             `((semmed (5 . \"chemical_substance\"))\n               (rtx (0 . \"chemical_substance\"))\n               (robokop (1 . \"(\\\"named_thing\\\" \\\"chemical_substance\\\")\"))))))\n\n;;; don't allow gene classes, such as \"Genes\", \"Tumor Suppressor Genes\", etc.\n(define (filter-out-bogus-genes dbname c)\n  (fresh (cid cui name catid cat props)\n    (== `(,cid ,cui ,name (,catid . ,cat) ,props) c)\n    (conde\n      ((== 'semmed dbname)\n       (=/= \"Genes\" name)\n       (=/= \"Homologous Gene\" name)\n       (=/= \"Tumor Suppressor Genes\" name))\n      ((=/= 'semmed dbname)))))\n\n#|\n;; seems like this might be a better/more general way to determine if\n;; a concept is really a class of concepts; alas, semmed's 'subclass_of'\n;; seems horrible:  A subclass_of B subclass_of A\n;;; So, not sure how to use this!\n(define (concept-has-subclass dbname c)\n  (not (null? (run 1 (o)\n                (fresh (dbname eid pid eprops e)\n                  (== 'semmed dbname) ;; how to handle others?\n                  (== `(,dbname ,eid ,c ,o (4 . \"subclass_of\") ,eprops) e)\n                  (edgeo e))))))\n|#\n\n#|\n;;; uh oh!!  sigh\n(time\n (concept-has-subclass\n  'semmed\n  '(74686\n    \"UMLS:C0376571\"\n    \"BRCA1 gene\"\n    (4 . \"gene\")\n    ((\"umls_type_label\" . \"['Gene or Genome']\")\n     (\"xrefs\" . \"['NCI_NCI-HGNC:HGNC:1100', 'CHV:0000031821', 'PDQ:CDR0000043111', 'MESH:D019398', 'CSP:4005-0006', 'MTH:NOCODE', 'LNC:LP36227-4', 'NCI:C17965', 'LNC:LP19666-4', 'OMIM:113705', 'HGNC:HGNC:1100']\")\n     (\"id\" . \"UMLS:C0376571\")\n     (\"umls_type\" . \"['T028']\")\n     (\"labels\" . \"['gene']\")))))\ncpu time: 1 real time: 3 gc time: 0\n#t\n\n(time\n  (concept-has-subclass\n    'semmed\n    '(17324\n      \"UMLS:C0017337\"\n      \"Genes\"\n      (4 . \"gene\")\n      ((\"umls_type_label\" . \"['Gene or Genome']\")\n       (\"xrefs\"\n        .\n        \"['CSP:1256-5501', 'NCI:C16612', 'LNC:LP32747-5', 'NCI_NCI-GLOSS:CDR0000045693', 'LNC:LP199195-1', 'NCI_CDISC:C16612', 'PDQ:CDR0000042941', 'SNMI:F-E0000', 'MESH:D005796', 'LCH_NW:sh91000344', 'NCI:TCGA', 'AOD:0000002944', 'SNOMEDCT_US:67271001', 'UWDA:74402', 'CHV:0000005419', 'HL7V3.0:GENE', 'FMA:74402', 'PSY:20820']\")\n       (\"id\" . \"UMLS:C0017337\")\n       (\"umls_type\" . \"['T028']\")\n       (\"labels\" . \"['gene']\")))))\n;; cpu time: 3 real time: 3 gc time: 0\n;; #t\n\n(time\n (concept-has-subclass\n  'semmed\n  '(141262\n    \"UMLS:C1425023\"\n    \"NGLY1 gene\"\n    (4 . \"gene\")\n    ((\"umls_type_label\" . \"['Gene or Genome']\")\n     (\"xrefs\" . \"['HGNC:HGNC:17646', 'OMIM:610661', 'MTH:NOCODE']\")\n     (\"id\" . \"UMLS:C1425023\")\n     (\"umls_type\" . \"['T028']\")\n     (\"labels\" . \"['gene']\")))))\n;; cpu time: 1 real time: 2 gc time: 0\n;; #f\n\n(time\n (concept-has-subclass\n  'semmed\n  '(33093\n    \"UMLS:C0079427\"\n    \"Tumor Suppressor Genes\"\n    (4 . \"gene\")\n    ((\"umls_type_label\" . \"['Gene or Genome']\")\n     (\"xrefs\" . \"['SNOMEDCT_US:77864004', 'NCI_NCI-GLOSS:CDR0000046657', 'MESH:D016147', 'CHV:0000015171', 'MTH:NOCODE', 'SNMI:F-E00A0', 'NCI_NCI-GLOSS:CDR0000583866', 'SNOMEDCT_US:405842004', 'LCH_NW:sh90002154', 'OMIM:MTHU005882', 'NCI:C17362', 'CSP:1256-6400']\")\n     (\"id\" . \"UMLS:C0079427\")\n     (\"umls_type\" . \"['T028']\")\n     (\"labels\" . \"['gene']\")))))\n;; cpu time: 1 real time: 1 gc time: 0\n;; #t\n|#\n\n;;; Filter out \"Genes\", \"Tumor Suppressor Genes\", and other losers etc.\n;;; Or provide interface for hoomon to do so.\n;;;\n;;; Also, can end up with duplicate concepts/CUIs, due to different KGs and also different predicates;\n;;; be smart about this!!\n(define G1-G2-edges\n  (remove-duplicates\n   (run* (e)\n     (fresh (dbname eid G1 G2 pid pred eprops)\n       (== `(,dbname ,eid ,G1 ,G2 (,pid . ,pred) ,eprops) e)\n       ;; don't want G1 and G2 to be the same gene!\n       (=/= G1 G2)\n       (membero `(,dbname . ,G2) G2-concepts)\n       (edgeo e)\n       (membero pred G-G-increases-predicate-names)\n       (restrict-concept-to-gene dbname G1)\n       ;; should be configurable which concepts are \"bogus\"\n       (filter-out-bogus-genes dbname G1)))))\n\n#|\n(remove-duplicates\n (map\n  (lambda (e)\n    (match e\n      [`(,dbname ,eid\n                 (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n                 (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n                 (,pid . ,pred) ,eprops)\n       (list scui sname pred ocui oname (pubmed-URLs-from-edge e) dbname)]))\n  G1-G2-edges))\n|#\n\n;;; Can end up with duplicate concepts/CUIs, due to different KGs and also different predicates;\n;;; be smart about this!!\n(define G1-G2-edges-without-duplicate-dbname/scui\n  (let loop ([edges G1-G2-edges])\n    (match edges\n      ['() '()]\n      [`(,e . ,rest)\n       (match e\n         [`(,dbname ,eid\n                    (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n                    (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n                    (,pid . ,pred) ,eprops)\n          (let ((e^ (memf\n                     (lambda (e^)\n                       (match e^\n                         [`(,dbname^ ,eid^\n                                     (,scid^ ,scui^ ,sname^ (,scatid^ . ,scat^) ,sprops^)\n                                     (,ocid^ ,ocui^ ,oname^ (,ocatid^ . ,ocat^) ,oprops^)\n                                     (,pid^ . ,pred^) ,eprops^)\n                          (equal? (list dbname scui) (list dbname^ scui^))]))\n                     rest)))\n            (if e^\n                (loop rest)\n                (cons e (loop rest))))])])))\n\n(define D-G1-G2-paths\n  (remove-duplicates\n   (run 150 (q)\n     (fresh (dbname1 eid1 D G1 pid1 pred1 eprops1 e1\n                     dbname2 eid2 G2^ G2 pid2 pred2 eprops2 e2\n                     cid0 cui0 name0 catid0 cat0 props0\n                     cid1 cui1 name1 catid1 cat1 props1\n                     cid2 cui2 name2 catid2 cat2 props2\n                     cid3 cui3 name3 catid3 cat3 props3)\n       (== `(,dbname1 ,eid1 ,D ,G1 (,pid1 . ,pred1) ,eprops1) e1)\n       (== `(,dbname2 ,eid2 ,G2^ ,G2 (,pid2 . ,pred2) ,eprops2) e2)\n\n       (== `(,e1 ,e2) q)\n\n       (== `(,cid0 ,cui0 ,name0 (,catid0 . ,cat0) ,props0) D)\n       (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) G1)\n       (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) G2^)\n       (== `(,cid3 ,cui3 ,name3 (,catid3 . ,cat3) ,props3) G2)\n       \n       (== cui1 cui2)\n       (== dbname1 dbname2)\n       \n       (membero e2 G1-G2-edges-without-duplicate-dbname/scui)\n       (edgeo e1)\n       (restrict-concept-to-drug dbname1 D)\n       (membero pred1 D-G-increases-predicate-names)\n       ))))\n\n(map\n (lambda (p)\n   (match p\n     [`(,e1 ,e2)\n      (match `(,e1 ,e2)\n        [`((,dbname1 ,eid1\n                     (,cid0 ,cui0 ,name0 (,catid0 . ,cat0) ,props0)\n                     (,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1)\n                     (,pid1 . ,pred1)\n                     ,eprops1)\n           (,dbname2 ,eid2\n                     (,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2)\n                     (,cid3 ,cui3 ,name3 (,catid3 . ,cat3) ,props3)\n                     (,pid2 . ,pred2)\n                     ,eprops2))\n         `(,name0 ,pred1 ,(pubmed-URLs-from-edge e1) ,name1 ,dbname1\n                  ,pred2 ,(pubmed-URLs-from-edge e2) ,name3 ,dbname2)])]))\n D-G1-G2-paths)\n\n#|\n(time\n (remove-duplicates\n   (run 1 (q)\n     (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n             dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n             cid0 cui0 name0 catid0 cat0 props0\n             cid1 cui1 name1 catid1 cat1 props1\n             cid2 cui2 name2 catid2 cat2 props2\n             cid3 cui3 name3 catid3 cat3 props3)\n       (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n       (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n\n       (== `(,name0 ,pred1 ,name1 ,pred2 ,name3 ,dbname1) q)\n\n       (== `(,cid0 ,cui0 ,name0 (,catid0 . ,cat0) ,props0) s1)\n       (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n       (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n       (== `(,cid3 ,cui3 ,name3 (,catid3 . ,cat3) ,props3) o2)\n       \n       (== cui1 cui2)\n       (== dbname1 dbname2)\n       \n       (membero e2 G1-G2-edges-without-duplicate-dbname/scui)\n       (edgeo e1)\n       (restrict-concept-to-drug dbname1 s1)\n       (membero pred1 D-G-increases-predicate-names)\n       ))))\n|#\n\n#|\n(time\n (remove-duplicates\n   (run 1 (q)\n     (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n             dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n             cid0 cui0 name0 catid0 cat0 props0\n             cid1 cui1 name1 catid1 cat1 props1\n             cid2 cui2 name2 catid2 cat2 props2\n             cid3 cui3 name3 catid3 cat3 props3)\n       (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n       (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n\n       (== `(,name0 ,pred1 ,name1 ,pred2 ,name3 ,dbname1) q)\n\n       (== `(,cid0 ,cui0 ,name0 (,catid0 . ,cat0) ,props0) s1)\n       (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n       (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n       (== `(,cid3 ,cui3 ,name3 (,catid3 . ,cat3) ,props3) o2)\n       \n       (== cui1 cui2)\n       (== dbname1 dbname2)\n       \n       (membero e2 G1-G2-edges)\n       (edgeo e1)\n       (restrict-concept-to-drug dbname1 s1)\n       (membero pred1 D-G-increases-predicate-names)\n       ))))\n\n(time\n (remove-duplicates\n   (run 1 (q)\n     (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n             dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n             cid0 cui0 name0 catid0 cat0 props0\n             cid1 cui1 name1 catid1 cat1 props1\n             cid2 cui2 name2 catid2 cat2 props2\n             cid3 cui3 name3 catid3 cat3 props3)\n       (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n       (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n\n       (== `(,name0 ,pred1 ,name1 ,pred2 ,name3 ,dbname1) q)\n\n       (== `(,cid0 ,cui0 ,name0 (,catid0 . ,cat0) ,props0) s1)\n       (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n       (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n       (== `(,cid3 ,cui3 ,name3 (,catid3 . ,cat3) ,props3) o2)\n       \n       (== cui1 cui2)\n       (== dbname1 dbname2)\n       \n       (membero e2 G1-G2-edges)\n       (edgeo e1)\n       (restrict-concept-to-drug dbname1 s1)\n       (membero pred1 D-G-increases-predicate-names)\n       ))))\n|#\n\n#|\n;;; slow query 1\n;;; cpu time: 24794 real time: 25191 gc time: 3238\n(time\n (length\n  (remove-duplicates\n   (run 1 (path)\n     (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n                     dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n                     cid1 cui1 name1 catid1 cat1 props1\n                     cid2 cui2 name2 catid2 cat2 props2)\n       (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n       (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n       (== `(,e1 ,e2) path)\n\n       (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n       (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n       (== cui1 cui2)\n       (membero e2 G1-G2-edges)\n       (edgeo e1)\n       (restrict-concept-to-drug dbname1 s1)\n       (membero pred1 D-G-increases-predicate-names)\n       )))))\n\n;;; swap two goals in the query above to make it suuuupeeer slow\n(time\n  (length\n    (remove-duplicates\n      (run 1 (path)\n        (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n                        dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n                        cid1 cui1 name1 catid1 cat1 props1\n                        cid2 cui2 name2 catid2 cat2 props2)\n          (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n          (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n          (== `(,e1 ,e2) path)\n\n          (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n          (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n          (== cui1 cui2)\n          (membero e2 G1-G2-edges)\n          (restrict-concept-to-drug dbname1 s1)\n          (edgeo e1)\n          (membero pred1 D-G-increases-predicate-names)\n          )))))\n|#\n\n\n\n\n\n\n#|\n(time\n  (length\n    (remove-duplicates\n      (run 1 (path)\n        (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n                        dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n                        cid1 cui1 name1 catid1 cat1 props1\n                        cid2 cui2 name2 catid2 cat2 props2)\n          (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n          (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n          (== `(,e1 ,e2) path)\n\n          (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n          (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n          (== cui1 cui2)\n          (membero e2 G1-G2-edges)\n          (restrict-concept-to-drug dbname1 s1)\n          (edgeo e1)\n          (membero pred1 D-G-increases-predicate-names)\n          )))))\n|#\n\n#|\n(define D-G1-G2-paths\n  (remove-duplicates\n   (run* (path)\n     (fresh (dbname1 eid1 s1 o1 pid1 pred1 eprops1 e1\n             dbname2 eid2 s2 o2 pid2 pred2 eprops2 e2\n             cid1 cui1 name1 catid1 cat1 props1\n             cid2 cui2 name2 catid2 cat2 props2)\n       (== `(,dbname1 ,eid1 ,s1 ,o1 (,pid1 . ,pred1) ,eprops1) e1)\n       (== `(,dbname2 ,eid2 ,s2 ,o2 (,pid2 . ,pred2) ,eprops2) e2)\n       (== `(,e1 ,e2) path)\n\n       (== `(,cid1 ,cui1 ,name1 (,catid1 . ,cat1) ,props1) o1)\n       (== `(,cid2 ,cui2 ,name2 (,catid2 . ,cat2) ,props2) s2)\n       (== cui1 cui2) ;; tie the KG's together\n       \n       (membero e2 G1-G2-edges)\n       (edgeo e1)\n       (membero pred1 D-G-increases-predicate-names)\n       (restrict-concept-to-drug dbname1 s1)))))\n|#\n\n\n\n#|\nExclude list?\n\n(160755\n \"UMLS:C1334043\"\n \"Homologous Gene\"\n (4 . \"gene\")\n ((\"umls_type_label\" . \"['Gene or Genome']\")\n  (\"xrefs\" . \"['NCI:C28709', 'MTH:NOCODE']\")\n  (\"id\" . \"UMLS:C1334043\")\n  (\"umls_type\" . \"['T028']\")\n  (\"labels\" . \"['gene']\")))\n\n|#\n\n#|\n(~name*-concepto ~name* concept)\n\n(~cui-concepto ~cui concept)\n\n(~categoryo ~category-name category)\n\n(~predicateo ~predicate-name predicate)\n\n(sort-paths paths)\n\n(pmid-edgeo pmid edge)\n\n(pubmed-URLs-from-edge edge)\n\n(define predicates\n  (sort (remove-duplicates\n         (time (run* (predicate)\n                 (fresh (dbname pid c)\n                   (membero c selected-concepts)\n                   (concept-predicateo c `(,dbname ,pid . ,predicate))))))\n        stringsubclass_of-->HP-input=>concepts\n       A-->subclass_of-->HP-input=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (HP-input HP-symptoms-from-input/concept-ls))\n   ((--subclass_of--> subclass_of))\n   (A --subclass_of--> HP-input))))\n|# \n\n;;orange only\n(match-define\n (list A-->subclass_of-->HP-input=>concepts\n       A-->subclass_of-->HP-input=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (HP-input HP-symptoms-from-input/concept-ls))\n   ((--subclass_of--> '((orange 0 . \"subclass_of\"))))\n   (A --subclass_of--> HP-input))))\n\n(define A-->subclass_of-->HP-input/concepts\n  (hash-ref A-->subclass_of-->HP-input=>concepts 'A))\n\n(define HP-concept-ls\n  (set-union A-->subclass_of-->HP-input/concepts\n             HP-symptoms-from-input/concept-ls))\n\n(newline)\n(displayln (format \"~a CONCEPTS FROM:\\nA --subclass_of--> HP-concept-ls\" (length HP-concept-ls)))\n(newline)\n(pretty-print (extract-name/curie/category-from-concept-ls HP-concept-ls '()))\n(newline)\n\n#|\n(match-define\n (list A--has_phenotype-->HP-ls=>concepts\n       A--has_phenotype-->HP-ls=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (HP-ls HP-concept-ls))\n   ((--has_phenotype--> has_phenotype))\n   (A --has_phenotype--> HP-ls))))\n|#\n\n;;orange only\n(match-define\n (list A--has_phenotype-->HP-ls=>concepts\n       A--has_phenotype-->HP-ls=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (HP-ls HP-concept-ls))\n   ((--has_phenotype--> '((orange 2 . \"has_phenotype\"))))\n   (A --has_phenotype--> HP-ls))))\n\n(define A-->has_phenotype-->HP-input/concepts\n  (hash-ref A--has_phenotype-->HP-ls=>concepts 'A))\n\n(define A-->has_phenotype-->HP-input/edges\n  (hash-ref A--has_phenotype-->HP-ls=>edges '--has_phenotype-->))\n\n(newline)\n(displayln (format \"~a CONCEPTS FROM:\\nA --has_phenotype--> HP-concept-ls\" (length A-->has_phenotype-->HP-input/concepts)))\n(newline)\n(pretty-print (extract-name/curie/category-from-concept-ls A-->has_phenotype-->HP-input/concepts '()))\n(newline)\n\n#|\n(match-define\n (list B--contributes_to-->A--has_phenotype-->HP-ls=>concepts\n       B--contributes_to-->A--has_phenotype-->HP-ls=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (B molecular_entity)\n    (HP-ls HP-concept-ls))\n   ((--has_phenotype--> has_phenotype)\n    (--contributes_to--> contributes_to))\n   (B --contributes_to--> A --has_phenotype--> HP-ls))))\n|#\n\n\n(match-define\n (list B--contributes_to-->A--has_phenotype-->HP-ls=>concepts\n       B--contributes_to-->A--has_phenotype-->HP-ls=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (B #f)\n    (HP-ls HP-concept-ls))\n   ((--has_phenotype--> '((orange 2 . \"has_phenotype\")))\n    (--contributes_to--> '((orange 11 . \"contributes_to\"))))\n   (B --contributes_to--> A --has_phenotype--> HP-ls))))\n\n(define B--contributes_to-->A--has_phenotype-->HP-ls/concepts \n  (hash-ref B--contributes_to-->A--has_phenotype-->HP-ls=>concepts 'B))\n \n(define B--contributes_to-->A--has_phenotype-->HP-ls/edges\n  (hash-ref B--contributes_to-->A--has_phenotype-->HP-ls=>edges '--contributes_to-->)) \n\n(newline)\n(displayln (format \"~a CONCEPTS FROM:\\nB--contributes_to-->A--has_phenotype-->HP-ls/concepts\" (length B--contributes_to-->A--has_phenotype-->HP-ls/concepts)))\n(newline)\n(pretty-print (extract-name/curie/category-from-concept-ls B--contributes_to-->A--has_phenotype-->HP-ls/concepts '()))\n(newline)\n\n(define NCBIGenes-from-symptoms/orange\n  (flatten (extract-curie-from-concept-ls B--contributes_to-->A--has_phenotype-->HP-ls/concepts '())))\n\n(define NCBIGenes-from-symptoms/orange/concept-ls\n  (find-concepts #t NCBIGenes-from-symptoms/orange))\n\n;; NCBIGene from orange --> HGNC gene in robokop/rtx2\n\n(match-define\n (list NCBIGene_input--equivalent_to-->HGNC--encodes-->UniProtKB=>concepts\n       NCBIGene_input--equivalent_to-->HGNC--encodes-->UniProtKB=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (B #f)\n    (NCBIGene_input NCBIGenes-from-symptoms/orange/concept-ls)) \n   ((--equivalent_to--> '((rtx2 57 . \"equivalent_to\")))\n    (--encodes--> '((rtx2 775 . \"encodes\"))))\n   (NCBIGene_input --equivalent_to--> A --encodes--> B))))\n\n(define NCBIGene_input--equivalent_to-->HGNC/concepts\n  (hash-ref NCBIGene_input--equivalent_to-->HGNC--encodes-->UniProtKB=>concepts 'A))\n(define NCBIGene_input--equivalent_to-->HGNC--encodes-->UniProtKB/concepts\n  (hash-ref NCBIGene_input--equivalent_to-->HGNC--encodes-->UniProtKB=>concepts 'B))\n \n(define HGNC-from-symptoms\n  (flatten (extract-curie-from-concept-ls NCBIGene_input--equivalent_to-->HGNC/concepts '())))\n\n(define HGNC-from-symptoms/concept-ls\n  (find-concepts #t HGNC-from-symptoms))\n\n(define UniProtKB-from-symptoms\n  (flatten (extract-curie-from-concept-ls NCBIGene_input--equivalent_to-->HGNC--encodes-->UniProtKB/concepts '())))\n\n(define UniProtKB-from-symptoms/concept-ls\n  (find-concepts #t UniProtKB-from-symptoms))\n\n\n;; rtx2 uniprotkb --> GO\n\n;; GO is 3 separate ontologies: Cellular Component, Biological Process, Molecular Function\n;; isa predicate operates within one ontology and will not cross\n;; part_of , regulates cross between the ontologies\n;; isa --> biological_process GO ontology\n;; biological process is broken into 3 nodes = cellular process, development, physiologic process\n;; regulates repdicate not really useful \n#|\n(match-define\n (list UniProtKB_input--involved_in-->GO--regulates-->GOparent=>concepts\n       UniProtKB_input--involved_in-->GO--regulates-->GOparent=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (B #f)\n    (UniProtKB_input UniProtKB-from-symptoms/concept-ls)) \n   ((--involved_in--> '((rtx2 182 . \"involved_in\"))) \n    (--regulates--> '((rtx2 185 . \"regulates\"))))\n   (UniProtKB_input --involved_in--> A --regulates--> B))))\n\n(define UniProtKB_input--involved_in-->GO/concepts\n  (hash-ref UniProtKB_input--involved_in-->GO--regulates-->GOparent=>concepts 'A))\n(define UniProtKB_input--involved_in-->GO--regulates-->GOparent/concepts\n  (hash-ref UniProtKB_input--involved_in-->GO--regulates-->GOparent=>concepts 'B))\n(define UniProtKB_input--involved_in-->GO/edges\n  (hash-ref UniProtKB_input--involved_in-->GO--regulates-->GOparent=>edges '--involved_in-->))\n(define UniProtKB_input--involved_in-->GO--regulates-->GOparent/edges \n  (hash-ref UniProtKB_input--involved_in-->GO--regulates-->GOparent=>edges '--regulates-->))\n\n;;rtx2 involved_in gives regulation/positive/negative terms back\n(pretty-print (extract-name/curie/category-from-concept-ls UniProtKB_input--involved_in-->GO/concepts '()))\n \n;; isa--> \"biological process\"\n(pretty-print (extract-name/curie/category-from-concept-ls UniProtKB_input--involved_in-->GO--regulates-->GOparent/concepts '()))\n|#\n\n;; use to get \n(rtx2 188 . \"positively_regulates\")\n(rtx2 189 . \"negatively_regulates\")\n\n(match-define\n (list UniProtKB_input--involved_in-->GO--part_of-->GOparent=>concepts\n       UniProtKB_input--involved_in-->GO--part_of-->GOparent=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (B #f)\n    (UniProtKB_input UniProtKB-from-symptoms/concept-ls)) \n   ((--involved_in--> '((rtx2 182 . \"involved_in\")))\n    (--part_of--> '((rtx2 14 . \"part_of\")))\n    (--subclass_of--> '((rtx2 15 . \"subclass_of\")))) \n   (UniProtKB_input --involved_in--> A --subclass_of--> B)))) \n\n(define UniProtKB_input--involved_in-->GO/concepts\n  (hash-ref UniProtKB_input--involved_in-->GO--part_of-->GOparent=>concepts 'A))\n(define UniProtKB_input--involved_in-->GO--part_of-->GOparent/concepts\n  (hash-ref UniProtKB_input--involved_in-->GO--part_of-->GOparent=>concepts 'B)) \n(define UniProtKB_input--involved_in-->GO/edges\n  (hash-ref UniProtKB_input--involved_in-->GO--part_of-->GOparent=>edges '--involved_in-->))\n(define UniProtKB_input--involved_in-->GO--part_of-->GOparent/edges \n  (hash-ref UniProtKB_input--involved_in-->GO--part_of-->GOparent=>edges '--part_of-->)) \n\n;;rtx2 involved_in gives 21\n(pretty-print (extract-name/curie/category-from-concept-ls UniProtKB_input--involved_in-->GO/concepts '()))  \n ;; part_of--> gives 25 \n(pretty-print (extract-name/curie/category-from-concept-ls UniProtKB_input--involved_in-->GO--part_of-->GOparent/concepts '()))\n\n\n(define UniProtKB_input--involved_in-->GO/edges/edges-for-print\n  (edge-matcher UniProtKB_input--involved_in-->GO/edges '()))\n\n(define UniProtKB_input--involved_in-->GO--part_of-->GOparent/edges-for-print\n  (edge-matcher UniProtKB_input--involved_in-->GO--part_of-->GOparent/edges '()))\n\n(define UniProtKB_input--involved_in-->GO/edges\n  (hash-ref UniProtKB_input--involved_in-->GO--involved_in-->GOparent=>edges '--involved_in-->))\n\n;;gives most relevant GO pathways\n(define UniProtKB_input--involved_in-->GO--involved_in-->GOparent/edges\n  (hash-ref UniProtKB_input--involved_in-->GO--involved_in-->GOparent=>edges '--involved_in-->))\n\n(define edge-matcher\n  (lambda (ls els)\n    (cond\n      ((null? ls) (set-union els))\n      (else\n       (match (car ls)\n         [`(,db ,edge-cui\n               (,subject-cui ,subject-id ,subject-name (,_ . ,subject-category) ,subject-props-assoc)\n               (,object-cui ,object-id ,object-name (,_ . ,object-category) ,object-props-assoc)\n               (,_ . ,pred)\n               ,pred-props-assoc)\n          (edge-matcher\n           (cdr ls)\n           (set-union\n            (list `((,subject-name . ,subject-id) ,pred (,object-name . ,object-id)) `(,db))\n            els))])))))\n\n(define UniProtKB_input--involved_in-->GO/edges-for-print\n  (edge-matcher UniProtKB_input--involved_in-->GO/edges '()))\n\n(define UniProtKB_input--involved_in-->GO--involved_in-->GOparent/edges-for-print\n  (edge-matcher UniProtKB_input--involved_in-->GO--involved_in-->GOparent/edges '()))\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n#|\n(define encodes (find-exact-predicates (list \"encodes\")))\n(define gene_associated_with_condition (find-exact-predicates (list \"gene_associated_with_condition\"))) \n\n(match-define\n (list hgnc--encodes-->B--gene_associated_with_condition-->D=>concepts\n       B--contributes_to-->A--has_phenotype-->HP-ls=>edges)\n (time\n  (run/graph\n   ((B #f)\n    (D #f)\n    (hgnc gene-concept-ls))\n   ((--encodes--> encodes)\n    (--gene_associated_with_condition--> '((rtx2 717 . \"gene_associated_with_condition\"))))\n   (hgnc --encodes--> B --gene_associated_with_condition--> D))))\n\n(define hgnc--encodes-->B--gene_associated_with_condition-->D/concepts \n  (hash-ref hgnc--encodes-->B--gene_associated_with_condition-->D=>concepts 'D))\n\n(filter-concept-by-f\n   (find-concepts\n    #t\n    (list\n     \"HP:0001531\"\n     \"HP:0003550\"\n     \"HP:0001004\"\n     \"HP:0008513\"\n     \"HP:0002144\"\n     \"HP:0001790\")) '() 'orange member?)\n\n(match-define\n (list B--contributes_to-->A--has_phenotype-->HP-ls=>concepts\n       B--contributes_to-->A--has_phenotype-->HP-ls=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (B molecular_entity)\n    (HP-ls HP-concept-ls))\n   ((--has_phenotype--> has_phenotype)\n    (--contributes_to--> contributes_to))\n   (B --contributes_to--> A --has_phenotype--> HP-ls))))\n|#\n\n#|\n;; need an exact predicate function \n(define (find-exact-predicates names)\n(append* (map (lambda (name) (run* (x) (~predicateo name x))) names)))\n(define (find-categories names)\n(append* (map (lambda (name) (run* (x) (~categoryo name x))) names)))\n(define (find-exact-categories names)\n(run* (cat) (fresh (db catid name)\n(membero name names)\n(== cat `(,db ,catid . ,name))\n(categoryo cat))))\n(define (find-exact-predicates names)\n(run* (cat) (fresh (db catid name)\n(membero name names)\n(== cat `(,db ,catid . ,name))\n(categoryo cat))))\n|#\n          \n;;TODO, load with only orange db to prevent has-phenotype from using other dbs \n#|\n(match-define\n (list A-->HP-ls=>concepts\n       A-->HP-ls=>edges)\n (time\n  (run/graph\n   ((A #f)\n    (HP-ls HP-concept-ls))\n   ((--has_phenotype--> has_phenotype)\n    (--subclass_of--> subclass_of))\n   (A --subclass_of--> HP-ls)\n   (A --has_phenotype--> HP-ls))))\n\n(define A-->has_phenotype-->HP-input/concepts\n  (hash-ref A-->HP-ls=>concepts 'A))\n\n(define A-->subclass_of-->HP-input/concepts\n  (hash-ref A-->HP-ls=>concepts 'A))\n\n(define A-->has_phenotype-->HP-input/edges\n  (hash-ref A-->HP-ls=>edges '--has_phenotype-->))\n\n(define A-->subclass_of-->HP-input/edges\n  (hash-ref A-->HP-ls=>concepts 'subclass_of))\n\n;; missing a DOID --has_phenotype--> HP in my orange KG\n;; DOID concepts appear to have \"disease\" only names in Orange\n;; that are clearly not disease in RTX2 robokop etc DOID:3457 example\n;; perhaps filter by mondo concepts \n|#\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"
  },
  {
    "path": "contrib/medikanren/example-dhx30-rtx.rkt",
    "content": "#lang racket\n(provide\n  (all-from-out \"../../medikanren/mk.rkt\")\n  (all-from-out \"../../medikanren/mk-db.rkt\")\n\n  membero\n  edgeo\n  ~name-concepto\n\n  rtx)\n\n\n(require\n  \"mk.rkt\"\n  \"mk-db.rkt\"\n  (except-in racket/match ==))\n\n\n(define rtx (time (make-db \"data/rtx\")))\n\n(newline)\n(displayln \"X regulates DHX30:\")\n(time (pretty-print\n        (run* (edge)\n          (fresh (eid subject object pred eprops)\n            (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n            (db:~name-concepto rtx \"DHX30\" object)\n            (== `(3 . \"regulates\") pred)\n            (db:edgeo rtx edge)))))\n\n\n#|\n(displayln \"categories:\")\n(pretty-print (run* (c) (db:categoryo rtx c)))\n\n(newline)\n(displayln \"predicates:\")\n(pretty-print (run* (p) (db:predicateo rtx p)))\n\n(newline)\n(displayln \"some concepts:\")\n(pretty-print (run 10 (c) (db:concepto rtx c)))\n\n(newline)\n(displayln \"some edges:\")\n(pretty-print (run 10 (e) (db:edgeo rtx e)))\n\n(newline)\n(displayln \"fuzzy search:\")\n(time (pretty-print (run* (c) (db:~name-concepto rtx \"imatin\" c))))\n\n(newline)\n(displayln \"fuzzy search DHX30:\")\n(time (pretty-print (run* (c) (db:~name-concepto rtx \"DHX30\" c))))\n|#\n\n#|\n(newline)\n(displayln \"X ANY-PRED DHX30:\")\n(time (pretty-print (run* (edge)\n                      (fresh (scid scui sname scatid scat sprops\n                                   ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n                        (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n                                   (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n                                   (,pid . ,pred) ,eprops) edge)\n                        (db:~name-concepto rtx \"DHX30\" `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops)))\n                        (db:edgeo rtx edge)))))\n\n(newline)\n(displayln \"DHX30 ANY-PRED X\")\n(time (pretty-print (run* (edge)\n                      (fresh (scid scui sname scatid scat sprops\n                                   ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n                        (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n                                   (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n                                   (,pid . ,pred) ,eprops) edge)\n                        (db:~name-concepto rtx \"DHX30\" `(,scid . (,scui ,sname (,scatid . ,scat) . ,sprops)))\n                        (db:edgeo rtx edge)))))\n|#\n"
  },
  {
    "path": "contrib/medikanren/example-dhx30-semmed.rkt",
    "content": "#lang racket\n(require\n  \"../../medikanren/mk-db.rkt\"\n  )\n\n(define semmed (make-db \"data/semmed\"))\n\n\n(displayln \"------- DHX30 examples, using semmed ---------\")\n\n(newline)\n(displayln \"fuzzy search for DHX30:\")\n(time (pretty-print (run* (c) (db:~name-concepto semmed \"DHX30\" c))))\n;; =>\n'((107213\n   \"UMLS:C1424502\"\n   \"DHX30 gene\"\n   (4 . \"gene\")\n   ((\"umls_type_label\" . \"['Gene or Genome']\")\n    (\"xrefs\" . \"['OMIM:616423', 'HGNC:HGNC:16716', 'MTH:NOCODE']\")\n    (\"id\" . \"UMLS:C1424502\")\n    (\"umls_type\" . \"['T028']\")\n    (\"labels\" . \"['gene']\"))))\n\n(newline)\n(displayln \"semmedb predicates:\")\n(pretty-print (run* (p) (db:predicateo semmed p)))\n;; =>\n'((0 . \"interacts_with\")\n  (1 . \"treats\")\n  (2 . \"predisposes\")\n  (3 . \"part_of\")\n  (4 . \"subclass_of\")\n  (5 . \"negatively_regulates\")\n  (6 . \"coexists_with\")\n  (7 . \"causes\")\n  (8 . \"related_to\")\n  (9 . \"affects\")\n  (10 . \"produces\")\n  (11 . \"gene_associated_with_condition\")\n  (12 . \"manifestation_of\")\n  (13 . \"positively_regulates\")\n  (14 . \"prevents\")\n  (15 . \"derives_into\")\n  (16 . \"location_of\")\n  (17 . \"precedes\"))\n\n(newline)\n(displayln \"X DECREASES DHX30:\")\n(time (pretty-print (let ((DECREASES (lambda (pred-info)\n                                       (conde\n                                         [(== `(1 . \"treats\") pred-info)]\n                                         [(== `(14 . \"prevents\") pred-info)]))))\n                      (run* (edge)\n                        (fresh (scid scui sname scatid scat sprops\n                                     ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n                          (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n                                     (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n                                     (,pid . ,pred) ,eprops) edge)\n                          (db:~name-concepto semmed \"DHX30\" `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops)))\n                          (DECREASES `(,pid . ,pred))\n                          (db:edgeo semmed edge))))))\n\n(newline)\n(displayln \"X ANY-PRED DHX30:\")\n(time (pretty-print (run* (edge)\n                      (fresh (scid scui sname scatid scat sprops\n                                   ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n                        (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n                                   (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n                                   (,pid . ,pred) ,eprops) edge)\n                        (db:~name-concepto semmed \"DHX30\" `(,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops)))\n                        (db:edgeo semmed edge)))))\n\n(newline)\n(displayln \"DHX30 ANY-PRED X\")\n(time (pretty-print (run* (edge)\n                      (fresh (scid scui sname scatid scat sprops\n                                   ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n                        (== `(,eid (,scid . (,scui ,sname (,scatid . ,scat) . ,sprops))\n                                   (,ocid . (,ocui ,oname (,ocatid . ,ocat) . ,oprops))\n                                   (,pid . ,pred) ,eprops) edge)\n                        (db:~name-concepto semmed \"DHX30\" `(,scid . (,scui ,sname (,scatid . ,scat) . ,sprops)))\n                        (db:edgeo semmed edge)))))\n"
  },
  {
    "path": "contrib/medikanren/example-tacrine-semmed.rkt",
    "content": "#lang racket\n(require\n  \"../../medikanren/pieces-parts/mk-db.rkt\"\n  )\n\n(define semmed (make-db \"data/semmed\"))\n\n\n(displayln \"------- tacrine examples, using semmed ---------\")\n\n(newline)\n(displayln \"fuzzy search for tacrine:\")\n(time (pretty-print (run* (c) (db:~name-concepto semmed \"tacrine\" c))))\n\n(newline)\n(displayln \"first two responses for fuzzy search for tacrine:\")\n(time (pretty-print (run 2 (c) (db:~name-concepto semmed \"tacrine\" c))))\n;; =>\n'((35887\n   \"UMLS:C0386973\"\n   \"6-chlorotacrine\"\n   (5 . \"chemical_substance\")\n   (\"umls_type_label\" . \"['Organic Chemical']\")\n   (\"xrefs\" . \"['MESH:C098212']\")\n   (\"id\" . \"UMLS:C0386973\")\n   (\"umls_type\" . \"['T109']\")\n   (\"labels\" . \"['chemical_substance']\"))\n  (70919\n   \"UMLS:C0295380\"\n   \"2-hydroxytacrine\"\n   (5 . \"chemical_substance\")\n   (\"umls_type_label\" . \"['Pharmacologic Substance', 'Organic Chemical']\")\n   (\"xrefs\" . \"['MESH:C092548']\")\n   (\"id\" . \"UMLS:C0295380\")\n   (\"umls_type\" . \"['T121', 'T109']\")\n   (\"labels\" . \"['chemical_substance']\")))\n\n\n(newline)\n(displayln \"fuzzy search for tacrine, displayed with something similar to the old format:\")\n(time (pretty-print (map\n                      (lambda (e)\n                        (match e\n                          [`(,id ,cui ,name ,ignore2 . ,props)\n                           (let ((type-p (assoc \"umls_type_label\" props)))\n                             (let ((type (if type-p\n                                             (cdr type-p)\n                                             'no-type-found)))\n                               (list id cui name type)))]))\n                      (run* (c) (db:~name-concepto semmed \"tacrine\" c)))))\n;; =>\n'((35887 \"UMLS:C0386973\" \"6-chlorotacrine\" \"['Organic Chemical']\")\n  (70919 \"UMLS:C0295380\" \"2-hydroxytacrine\" \"['Pharmacologic Substance', 'Organic Chemical']\")\n  (75842 \"UMLS:C0039245\" \"Tacrine\" \"['Pharmacologic Substance', 'Organic Chemical']\")\n  (98097 \"UMLS:C1435294\" \"N-butyramide-tacrine\" \"['Pharmacologic Substance', 'Organic Chemical']\")\n  (98688 \"UMLS:C0771182\" \"Tacrine Hydrochloride\" \"['Pharmacologic Substance', 'Organic Chemical']\")\n  (101040 \"UMLS:C0659809\" \"N-methyltacrine\" \"['Organic Chemical']\")\n  (123792 \"UMLS:C0295379\" \"4-hydroxytacrine\" \"['Pharmacologic Substance', 'Organic Chemical']\")\n  (154109 \"UMLS:C0099894\" \"7-methoxytacrine\" \"['Pharmacologic Substance', 'Organic Chemical']\"))\n\n(newline)\n(displayln \"semmedb predicates:\")\n(pretty-print (run* (p) (db:predicateo semmed p)))\n;; =>\n'((0 . \"interacts_with\")\n  (1 . \"treats\")\n  (2 . \"predisposes\")\n  (3 . \"part_of\")\n  (4 . \"subclass_of\")\n  (5 . \"negatively_regulates\")\n  (6 . \"coexists_with\")\n  (7 . \"causes\")\n  (8 . \"related_to\")\n  (9 . \"affects\")\n  (10 . \"produces\")\n  (11 . \"gene_associated_with_condition\")\n  (12 . \"manifestation_of\")\n  (13 . \"positively_regulates\")\n  (14 . \"prevents\")\n  (15 . \"derives_into\")\n  (16 . \"location_of\")\n  (17 . \"precedes\"))\n\n(newline)\n(displayln \"X interacts with tacrine:\")\n(time (pretty-print\n        (run* (edge)\n          (fresh (eid subject tacrine-details pred eprops)\n            (== `(,eid ,subject (75842 . ,tacrine-details) ,pred . ,eprops) edge)\n            (== `(0 . \"interacts_with\") pred)\n            (db:edgeo semmed edge)))))\n\n(newline)\n(displayln \"tacrine treats X:\")\n(time (pretty-print\n        (run* (edge)\n          (fresh (eid tacrine-details object pred eprops)\n            (== `(,eid (75842 . ,tacrine-details) ,object ,pred . ,eprops) edge)\n            (== `(1 . \"treats\") pred)\n            (db:edgeo semmed edge)))))\n\n(define (DECREASES pred)\n  (conde\n    [(== `(1 . \"treats\") pred)]\n    [(== `(14 . \"prevents\") pred)]))\n\n(newline)\n(displayln \"tacrine DECREASES X:\")\n(time (pretty-print\n        (run* (edge)\n          (fresh (eid tacrine-details object pred eprops)\n            (== `(,eid (75842 . ,tacrine-details) ,object ,pred . ,eprops) edge)\n            (DECREASES pred)\n            (db:edgeo semmed edge)))))\n"
  },
  {
    "path": "contrib/medikanren/genes-perturbed.rkt",
    "content": "#lang racket/base\n(provide (all-defined-out) (all-from-out \"../../medikanren/common.rkt\"))\n(require \"../../medikanren/common.rkt\" \"../../medikanren/repr.rkt\"\n         (except-in racket/match ==) racket/set racket/string)\n\n(define increases\n  (find-predicates '(;; common\n                     \"causes\" \"positively_regulates\"\n                     ;; semmed\n                     \"produces\"\n                     ;; robokop\n                     \"decreases_degradation_of\"\n                     \"increases_secretion_of\"\n                     \"increases_transport_of\"\n                     \"increases_activity_of\"\n                     \"increases_synthesis_of\"\n                     \"increases_expression_of\"\n                     \"positively_regulates__entity_to_entity\"\n                     )))\n\n(define decreases\n  (find-predicates '(;; common\n                     \"prevents\" \"negatively_regulates\"\n                     ;; semmed\n                     ;; robokop\n                     \"decreases_secretion_of\"\n                     \"decreases_transport_of\"\n                     \"decreases_activity_of\"\n                     \"decreases_synthesis_of\"\n                     \"decreases_expression_of\"\n                     \"increases_degradation_of\"\n                     \"negatively_regulates__entity_to_entity\"\n                     \"disrupts\"\n                     )))\n\n(define gene (find-exact-categories '(;; semmed\n                                      \"gene\"\n                                      ;; robokop\n                                      \"(\\\"named_thing\\\" \\\"gene\\\")\")))\n(define drug (find-exact-categories '(;; semmed\n                                      \"chemical_substance\"\n                                      ;; robokop\n                                      \"(\\\"named_thing\\\" \\\"chemical_substance\\\")\")))\n\n(define (file->strings filename)\n  (call-with-input-file\n    filename\n    (lambda (in) (let loop ()\n                   (define line (read-line in))\n                   (if (eof-object? line) '()\n                     (cons (string-trim line) (loop)))))))\n\n(define (xref-curies curies)\n  (time (run* (c) (fresh (xref)\n                    (membero xref curies)\n                    (xref-concepto xref c)))))\n\n(define hgnc-ids (file->strings \"hgnc-ids.txt\"))\n(printf \"HGNC gene total: ~s\\n\" (length hgnc-ids))\n\n;; This will only work with robokop.\n;(define human-genes (time (run* (c) (~cui*-concepto hgnc-ids c))))\n\n;(define drugs\n  ;(time (run* (c) (fresh (db dbcat)\n                    ;(membero dbcat drug)\n                    ;(category-concepto dbcat c)))))\n;(printf \"Total drug count: ~s\\n\" (length drugs))\n\n;; This will work for either semmed or robokop, but isn't as complete.\n(define genes\n  (time (run* (c) (fresh (db dbcat)\n                    (membero dbcat gene)\n                    (category-concepto dbcat c)))))\n(printf \"Total gene count: ~s\\n\" (length genes))\n\n;; TODO: This set-based deduping is due to one duplicate semmed entry.\n;; We need to fix this by re-indexing xrefs.\n(define human-genes (set->list (list->set (xref-curies hgnc-ids))))\n(define human-genes-alt\n  (time (filter (lambda (g)\n                  (ormap (lambda (xref) (string-prefix? xref \"HGNC:\"))\n                         (concept->xrefs (list->vector (cddr g)))))\n                genes)))\n(printf \"HGNC genes found: ~s ~s ~s\\n\" (length human-genes) (length human-genes-alt)\n        (set-count (set-intersect (list->set human-genes) (list->set human-genes-alt))))\n\n(define (%hgnc-total count)\n  (/ count (exact->inexact (length hgnc-ids))))\n(define (%hgnc-found count)\n  (/ count (exact->inexact (length human-genes))))\n\n;; This also works (and is faster) for robokop:\n;(define human-genes\n  ;(time (filter (lambda (g) (string-prefix? (caddr g) \"HGNC:\"))\n                ;genes)))\n\n(define (perturb-1-hop direction)\n  (match-define\n    (list name=>concepts _)\n    (time (run/graph ((D drug)\n                      (G human-genes))\n                     ((D->G direction))\n                     (D D->G G))))\n  (list->set (hash-ref name=>concepts 'G)))\n\n(define (perturb-next-hop X direction)\n  (set-intersect\n    (list->set human-genes)\n    (list->set\n      (time (run* (concept)\n              (fresh (x c cid cui name cat props db eid pred eprops)\n                (membero `(,db . ,cat) gene)\n                (== c `(,cid ,cui ,name ,cat ,props))\n                (membero `(,db . ,x) X)\n                (edgeo `(,db ,eid ,x ,c ,pred ,eprops))\n                (membero `(,db . ,pred) direction)\n                (=/= x c)\n                (== concept `(,db . ,c))))))))\n\n;; 1-hop\n\n(define increased-1-hop (perturb-1-hop increases))\n(printf \"increased 1-hop: ~s\\n\" (set-count increased-1-hop))\n(define decreased-1-hop (perturb-1-hop decreases))\n(printf \"decreased 1-hop: ~s\\n\" (set-count decreased-1-hop))\n(define perturbed-1-hop (set-union increased-1-hop decreased-1-hop))\n(printf \"perturbed 1-hop: ~s ~s ~s\\n\"\n        (set-count perturbed-1-hop)\n        (%hgnc-found (set-count perturbed-1-hop))\n        (%hgnc-total (set-count perturbed-1-hop)))\n\n;; 2-hop\n\n;; increase\n(define inc&inc-2-hop (perturb-next-hop (set->list increased-1-hop) increases))\n(printf \"inc&inc 2-hop: ~s\\n\" (set-count inc&inc-2-hop))\n(define dec&dec-2-hop (perturb-next-hop (set->list decreased-1-hop) decreases))\n(printf \"dec&dec 2-hop: ~s\\n\" (set-count dec&dec-2-hop))\n(define increased-2-hop (set-union inc&inc-2-hop dec&dec-2-hop))\n(define increased<=2-hop (set-union increased-1-hop increased-2-hop))\n(printf \"increased 2-hop: ~s ~s\\n\"\n        (set-count increased-2-hop)\n        (set-count increased<=2-hop))\n\n;; decrease\n(define dec&inc-2-hop (perturb-next-hop (set->list decreased-1-hop) increases))\n(printf \"dec&inc 2-hop: ~s\\n\" (set-count dec&inc-2-hop))\n(define inc&dec-2-hop (perturb-next-hop (set->list increased-1-hop) decreases))\n(printf \"inc&dec 2-hop: ~s\\n\" (set-count inc&dec-2-hop))\n(define decreased-2-hop (set-union dec&inc-2-hop inc&dec-2-hop))\n(define decreased<=2-hop (set-union decreased-1-hop decreased-2-hop))\n(printf \"decreased 2-hop: ~s ~s\\n\"\n        (set-count decreased-2-hop)\n        (set-count decreased<=2-hop))\n\n(define perturbed-2-hop (set-union increased-2-hop decreased-2-hop))\n(define perturbed<=2-hop (set-union increased<=2-hop decreased<=2-hop))\n(printf \"perturbed 2-hop: ~s ~s ~s ~s ~s ~s\\n\"\n        (set-count perturbed-2-hop)\n        (%hgnc-found (set-count perturbed-2-hop))\n        (%hgnc-total (set-count perturbed-2-hop))\n        (set-count perturbed<=2-hop)\n        (%hgnc-found (set-count perturbed<=2-hop))\n        (%hgnc-total (set-count perturbed<=2-hop)))\n\n;; 3-hop\n\n;; increase\n(define inc&inc-3-hop (perturb-next-hop (set->list (set-subtract increased-2-hop increased-1-hop)) increases))\n(printf \"inc&inc 3-hop: ~s\\n\" (set-count inc&inc-3-hop))\n(define dec&dec-3-hop (perturb-next-hop (set->list (set-subtract decreased-2-hop decreased-1-hop)) decreases))\n(printf \"dec&dec 3-hop: ~s\\n\" (set-count dec&dec-3-hop))\n(define increased-3-hop (set-union inc&inc-3-hop dec&dec-3-hop))\n(define increased<=3-hop (set-union increased<=2-hop increased-3-hop))\n(printf \"increased 3-hop: ~s ~s\\n\"\n        (set-count increased-3-hop)\n        (set-count increased<=3-hop))\n\n;; decrease\n(define dec&inc-3-hop (perturb-next-hop (set->list (set-subtract decreased-2-hop decreased-1-hop)) increases))\n(printf \"dec&inc 3-hop: ~s\\n\" (set-count dec&inc-3-hop))\n(define inc&dec-3-hop (perturb-next-hop (set->list (set-subtract increased-2-hop increased-1-hop)) decreases))\n(printf \"inc&dec 3-hop: ~s\\n\" (set-count inc&dec-3-hop))\n(define decreased-3-hop (set-union dec&inc-3-hop inc&dec-3-hop))\n(define decreased<=3-hop (set-union decreased<=2-hop decreased-3-hop))\n(printf \"decreased 3-hop: ~s ~s\\n\"\n        (set-count decreased-3-hop)\n        (set-count decreased<=3-hop))\n\n(define perturbed-3-hop (set-union increased-3-hop decreased-3-hop))\n(define perturbed<=3-hop (set-union increased<=3-hop decreased<=3-hop))\n(printf \"perturbed 3-hop: ~s ~s ~s ~s ~s ~s\\n\"\n        (set-count perturbed-3-hop)\n        (%hgnc-found (set-count perturbed-3-hop))\n        (%hgnc-total (set-count perturbed-3-hop))\n        (set-count perturbed<=3-hop)\n        (%hgnc-found (set-count perturbed<=3-hop))\n        (%hgnc-total (set-count perturbed<=3-hop)))\n\n;; Only do this when generating Robokop data.\n;(call-with-output-file\n  ;\"hgnc-robokop.txt\"\n  ;(lambda (out)\n    ;(for-each\n      ;(lambda (c) (fprintf out \"~a\\n\" (caddr c)))\n      ;(set->list perturbed<=3-hop))))\n\n;; Only do this comparison when we have Robokop data.\n;(define hgnc-robokop-ids (file->strings \"hgnc-robokop.txt\"))\n;(define hgnc-robokop-concepts (list->set (xref-curies hgnc-robokop-ids)))\n;(define hgnc-robokop-missing (- (length hgnc-robokop-ids) (set-count hgnc-robokop-concepts)))\n;(define hgnc-common (set-intersect hgnc-robokop-concepts perturbed<=3-hop))\n;(define hgnc-combined (set-union hgnc-robokop-concepts perturbed<=3-hop))\n;(define hgnc-total-perturbed (+ hgnc-robokop-missing (set-count hgnc-combined)))\n;(define extra         (- (set-count perturbed<=3-hop)\n                         ;(set-count hgnc-common)))\n;(define extra-robokop (- (length hgnc-robokop-ids)\n                         ;(set-count hgnc-common)))\n\n;(printf \"overlap with Robokop: this=~s robokop=~s; common=~s ~s\\n\"\n        ;(set-count perturbed<=3-hop)\n        ;(set-count hgnc-robokop-concepts)\n        ;(set-count hgnc-common)\n        ;(%hgnc-total (set-count hgnc-common)))\n\n;(printf \"missing: ~s\\n\" hgnc-robokop-missing)\n\n;(printf \"extra and combined contributions: extra=~s ~s; extra-robokop=~s ~s; combined=~s ~s\\n\"\n        ;extra                (%hgnc-total extra)\n        ;extra-robokop        (%hgnc-total extra-robokop)\n        ;hgnc-total-perturbed (%hgnc-total hgnc-total-perturbed))\n"
  },
  {
    "path": "contrib/medikanren/get-all-hgncs-from-raw-data.rkt",
    "content": "#lang racket\n(provide (all-defined-out)\n         (all-from-out \"../../medikanren/pieces-parts/synonymize.rkt\"))\n(require \"../../medikanren/pieces-parts/synonymize.rkt\")\n\n\n;; rtx2 contains a bunch of weird entries of the form:\n;;\n;; \"HGNC:24039/HGNC:\"\n;;\n;; \"HGNC:24039/HGNC:877\"\n;; \"HGNC:24039/HGNC:2602\"\n;; \"HGNC:24039/HGNC:470\"\n;;\n;; These are presumably errors.  We filter these out.\n\n(define get-hgncs-for-concept-file-path\n  (lambda (concept-file-path)\n    (let ((ip (open-input-file concept-file-path)))\n      (let loop ([cid 0]\n                 [data (read ip)]\n                 [s (set)])\n        (cond\n          [(eof-object? data)\n           (close-input-port ip)\n           (printf \"read ~s entries\\n\" cid)\n           s]\n          [else\n           (when (= (modulo cid 10000) 0)\n             (printf \"cid: ~s\\n\" cid))\n           (let ((s\n                  (let ((curie (vector-ref data 0)))\n                    (if (regexp-match #px\"^HGNC:[0-9]*$\" curie)\n                        (set-add s curie)\n                        s))))\n             (loop (add1 cid) (read ip) s))])))))\n\n(define (save-hgncs-to-file! s hgnc-file-path)\n  (define op (open-output-file hgnc-file-path #:exists 'replace))\n  (for-each (lambda (str) (write str op) (newline op)) (set->list s))\n  (close-output-port op))\n\n\n(printf \"processing robokop-hgncs\\n\")\n(define robokop-hgncs\n  (get-hgncs-for-concept-file-path \"data/robokop/concepts.scm\"))\n\n(printf \"processing rtx2-hgncs\\n\")\n(define rtx2-hgncs\n  (get-hgncs-for-concept-file-path \"data/rtx2/concepts.scm\"))\n\n(printf \"sorting all hgncs\\n\")\n(define all-hgncs\n  (sort (set->list (set-union robokop-hgncs\n                              rtx2-hgncs))\n        (lambda (str1 str2)\n          (let ((hgnc-curie->n (lambda (str)\n                                 (string->number (cadr (regexp-match #px\"^HGNC:([0-9]*)$\" str))))))\n            (let ((n1 (hgnc-curie->n str1))\n                  (n2 (hgnc-curie->n str2)))\n              (< n1 n2))))))\n\n; (printf \"saving all hgncs\\n\")\n; (save-hgncs-to-file! all-hgncs \"./all-hgnc-curies.scm\")\n\n(printf \"synonymizing hgncs\\n\")\n(define synonymized-hashes\n  (map\n    (lambda (curie)\n      (printf \"*** HGNC curie: ~s\\n\" curie)\n      (HGNC-CURIE->synonymized-concepts curie))\n    all-hgncs))\n\n;; > (begin (HGNC-CURIE->synonymized-concepts '(\"HGNC:8\")) 2)\n;; car: contract violation\n;;   expected: pair?\n;;   given: '()\n;; [,bt for context]\n\n(define ht (make-hash))\n\n(for-each\n  (lambda (h)\n    (let ((all-genes/proteins (set->list (hash-ref h 'all-genes/proteins))))\n      (for-each\n        (lambda (curie)\n          (hash-set! ht curie h))\n        all-genes/proteins)))\n  synonymized-hashes)\n\n;; TODO\n;; save ht to disk!\n"
  },
  {
    "path": "contrib/medikanren/make-kg-edge-covid19.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.edge.scm\n:ID :START :END\n\nex-row: 1 ENSEMBL:ENSG00000004059 ENSEMBL:ENSP00000000233\n\nname-file.edge-props.scm\n:ID propname value\n\nex-row: 1 edge_label biolink:has_gene_product\n  1 provided_by blah\n  1\n|#\n\n(define directory-path\n  \"data/covid19/\")\n(define edges-file\n  \"merged-kg_edges.tsv\")\n(define export-path directory-path)\n(define edges-export-path\n  (format \"~acovid19.edge.tsv\" export-path))\n(define edge-props-export-path\n  (format \"~acovid19.edgeprop.tsv\" export-path))\n\n(define edges-export-file\n  (open-output-file edges-export-path))\n(fprintf edges-export-file \":ID\\t:START\\t:END\\n\")\n(define edge-props-export-file\n  (open-output-file edge-props-export-path))\n(fprintf edge-props-export-file \":ID\\tpropname\\tvalue\\n\")\n(define input-edges\n  (open-input-file (format \"~a~a\" directory-path edges-file)))\n(let* ((header (read-line input-edges))\n       (header (cdr (string-split header \"\\t\" #:trim? #f))))\n  (let loop ((i 0)\n             (line-str (read-line input-edges)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-edges)\n       (close-output-port edges-export-file)\n       (close-output-port edge-props-export-file))\n      (else\n        (let ((line (cdr (string-split line-str \"\\t\" #:trim? #f))))\n          (fprintf edges-export-file \"~a\\t~a\\t~a\\n\" i (car line) (cadr line))\n          (let loop-inner ((props (cddr line))\n                           (headers (cddr header)))\n            (when (not (null? props))\n              (unless (string=? \"\" (car props))\n                (fprintf edge-props-export-file \"~a\\t~a\\t~s\\n\" i (car headers) (car props)))\n              (loop-inner (cdr props) (cdr headers)))))\n        (loop\n          (+ 1 i)\n          (read-line input-edges))))))\n"
  },
  {
    "path": "contrib/medikanren/make-kg-edge-general.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.edge.scm\n:ID :START :END\n\nex-row: 1 ENSEMBL:ENSG00000004059 ENSEMBL:ENSP00000000233\n\nname-file.edge-props.scm\n:ID propname value\n|#\n\n(define directory-path\n  ;; \"data/textminingprovider/\"\n  \"data/sri_semmeddb/\"\n  )\n(define edges-file\n  ;; \"sample-craft-edges.v0.1.kgx.tsv\"\n  \"semmeddb_edges.tsv\"\n  )\n(define export-path directory-path)\n(define edges-export-path\n  (format\n   ;; \"~atextminingprovider.edge.tsv\"\n   \"~asri_semmeddb.edge.tsv\"\n   export-path))\n(define edge-props-export-path\n  (format\n   ;; \"~atextminingprovider.edgeprop.tsv\"\n   \"~asri_semmeddb.edgeprop.tsv\"\n   export-path))\n\n(define edges-export-file\n  (open-output-file edges-export-path))\n(fprintf edges-export-file \":ID\\t:START\\t:END\\n\")\n(define edge-props-export-file\n  (open-output-file edge-props-export-path))\n(fprintf edge-props-export-file \":ID\\tpropname\\tvalue\\n\")\n(define input-edges\n  (open-input-file (format \"~a~a\" directory-path edges-file)))\n(let* ((header (read-line input-edges))\n       (header (string-split header \"\\t\" #:trim? #f)))\n  (let loop ((i 0)\n             (line-str (read-line input-edges)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-edges)\n       (close-output-port edges-export-file)\n       (close-output-port edge-props-export-file))\n      (else\n        (let ((line (string-split line-str \"\\t\" #:trim? #f)))\n          (fprintf edges-export-file \"~a\\t~a\\t~a\\n\" i (car line) (caddr line))\n          (let loop-inner ((props (cons (cadr line) (cddr line)))\n                           (headers (cons (cadr header) (cddr header))))\n            (when (not (null? props))\n              (unless (string=? \"\" (car props))\n                (fprintf edge-props-export-file \"~a\\t~a\\t~s\\n\" i (car headers) (car props)))\n              (loop-inner (cdr props) (cdr headers)))))\n        (loop\n          (+ 1 i)\n          (read-line input-edges))))))\n"
  },
  {
    "path": "contrib/medikanren/make-kg-edge-sri-reference-kg.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.edge.scm\n:ID :START :END\n\nex-row: 1 ENSEMBL:ENSG00000004059 ENSEMBL:ENSP00000000233\n\nname-file.edge-props.scm\n:ID propname value\n\nex-row: 1 edge_label biolink:has_gene_product\n  1 provided_by blah\n  1\n|#\n\n(define directory-path\n    \"data/sri-reference-kg-0.2.0/\")\n(define edges-file\n    \"sri-reference-kg-0.2.0_edges.tsv\")\n(define export-path directory-path)\n(define edges-export-path\n  (format \"~asri-reference-kg-0.2.0.edge.tsv\" export-path))\n(define edge-props-export-path\n  (format \"~asri-reference-kg-0.2.0.edgeprop.tsv\" export-path))\n\n(define edges-export-file\n  (open-output-file edges-export-path))\n(fprintf edges-export-file \":ID\\t:START\\t:END\\n\")\n\n(define edge-props-export-file\n  (open-output-file edge-props-export-path))\n(fprintf edge-props-export-file \":ID\\tpropname\\tvalue\\n\")\n\n(define input-edges\n  (open-input-file (format \"~a~a\" directory-path edges-file)))\n\n(let* ((header (read-line input-edges))\n       (header (string-split header \"\\t\" #:trim? #f)))\n  (let loop ((i 0)\n             (line-str (read-line input-edges)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-edges)\n       (close-output-port edges-export-file)\n       (close-output-port edge-props-export-file))\n      (else\n        (let ((line (string-split (string-trim line-str \"\\n\" #:left? #f) \"\\t\" #:trim? #f)))\n          (match line\n            [`(,id ,subject ,edge_label ,object . ,prop*)\n             (fprintf edges-export-file \"~a\\t~a\\t~a\\n\" i subject object)\n             (let loop-inner ((props (cons edge_label prop*))\n                              (headers (match header\n                                         [`(,id ,subject ,edge_label ,object . ,prop*)\n                                          (cons edge_label prop*)])))\n               (when (not (null? props))\n                 (unless (string=? \"\" (car props))\n                   (fprintf edge-props-export-file \"~a\\t~a\\t~s\\n\" i (car headers) (car props)))\n                 (loop-inner (cdr props) (cdr headers))))]))\n        (loop\n          (+ 1 i)\n          (read-line input-edges))))))\n"
  },
  {
    "path": "contrib/medikanren/make-kg-edge.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.edge.scm\n:ID :START :END\n\nex-row: 1 ENSEMBL:ENSG00000004059 ENSEMBL:ENSP00000000233\n\nname-file.edge-props.scm\n:ID propname value\n\nex-row: 1 edge_label biolink:has_gene_product\n        1 provided_by blah\n        1 \n\nname-file.node.scm\n:ID\n\nname-file.node-props.scm\n:ID propname value \n\n|#\n\n\n(define directory-path\n  \"/Users/michaelpatton/Desktop/data 2/merged/\")\n\n(define edges-file\n  \"merged-kg_edges.tsv\")\n\n\n(define export-path\n  (format \"~a\" (path->string (find-system-path 'desk-dir))))\n\n(define edges-export-path\n  (format \"~acovid19.edge.tsv\" export-path))\n\n(define edges-export-file\n  (open-output-file edges-export-path))\n\n(define edge-props-export-path\n  (format \"~acovid19.edgeprops.tsv\" export-path))\n\n(define edge-props-export-file\n  (open-output-file edge-props-export-path))\n\n(define input-edges\n  (open-input-file (format \"~a/~a\" directory-path edges-file)))\n\n(define input-nodes\n  (open-input-file (format \"~a/~a\" directory-path nodes-file)))\n\n(let* ((header (read-line input-edges))\n       (header (string-split header \"\\t\")))\n  (let loop ((i 0)\n             (line-str (read-line input-edges)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-edges)\n       (close-output-port edges-export-file)\n       (close-output-port edge-props-export-file))\n      (else\n       (let ((line (string-split line-str \"\\t\")))\n         (fprintf edges-export-file \"~a\\t~a\\t~a\\n\" i (car line) (cadr line))\n         (let loop-inner ((props (cddr line))\n                          (headers (cddr header)))\n           (when (not (null? props))\n             (unless (string=? \"\" (car props))\n               (fprintf edge-props-export-file \"~a\\t~a\\t~a\\n\" i (car headers) (car props)))             \n             (loop-inner (cdr props) (cdr headers)))))\n       (loop\n        (+ 1 i)\n        (read-line input-edges))))))\n\n\n\n\n \n"
  },
  {
    "path": "contrib/medikanren/make-kg-node-general.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.node.scm\n:ID\n\nname-file.node-props.scm\n:ID propname value\n|#\n\n\n(define directory-path\n  ;; \"data/covid19/\"\n  ;; \"data/textminingprovider/\"\n  \"data/sri_semmeddb/\"\n  )\n(define nodes-file\n  ;; \"merged-kg_nodes.tsv\"\n  ;; \"sample-craft-nodes.v0.1.kgx.tsv\"\n  \"semmeddb_nodes.tsv\"\n  )\n(define export-path directory-path)\n(define node-export-path\n  (format\n   ;; \"~acovid19.node.tsv\"\n   ;; \"~atextminingprovider.node.tsv\"\n   \"~asri_semmeddb.node.tsv\"\n   export-path))\n(define node-props-export-path\n  (format\n   ;; \"~acovid19.nodeprop.tsv\"\n   ;; \"~atextminingprovider.nodeprop.tsv\"\n   \"~asri_semmeddb.nodeprop.tsv\"\n   export-path))\n\n(define nodes-export-file\n  (open-output-file node-export-path))\n(fprintf nodes-export-file \":ID\\n\")\n(define node-props-export-file\n  (open-output-file node-props-export-path))\n(fprintf node-props-export-file \":ID\\tpropname\\tvalue\\n\")\n(define input-nodes\n  (open-input-file (format \"~a~a\" directory-path nodes-file)))\n(let* ((header (read-line input-nodes))\n       (header (string-split header \"\\t\" #:trim? #f)))\n  (let loop ((seen-nodes (set))\n             (line-str (read-line input-nodes)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-nodes)\n       (close-output-port nodes-export-file)\n       (close-output-port node-props-export-file))\n      (else\n        (let* ((line (string-split line-str \"\\t\" #:trim? #f))\n               (node (car line)))\n          (when (set-member? seen-nodes node)\n            (error 'make-kg-node (format \"already seen node: ~a\" node)))\n          (fprintf nodes-export-file \"~a\\n\" node)\n          (let loop-inner ((props (cdr line))\n                           (headers (cdr header)))\n            (when (not (null? props))\n              (unless (string=? \"\" (car props))\n                (fprintf node-props-export-file \"~a\\t~a\\t~s\\n\" node (car headers) (car props)))\n              (loop-inner (cdr props) (cdr headers))))\n          (loop\n            (set-add seen-nodes node)\n            (read-line input-nodes)))))))\n"
  },
  {
    "path": "contrib/medikanren/make-kg-node-sri-reference-kg.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.node.scm\n:ID\n\nname-file.node-props.scm\n:ID propname value\n|#\n\n\n(define directory-path\n  \"data/sri-reference-kg-0.2.0/\")\n(define nodes-file\n  \"sri-reference-kg-0.2.0_nodes.tsv\")\n(define export-path directory-path)\n(define node-export-path\n  (format \"~asri-reference-kg-0.2.0.node.tsv\" export-path))\n(define node-props-export-path\n  (format \"~asri-reference-kg-0.2.0.nodeprop.tsv\" export-path))\n\n(define nodes-export-file\n  (open-output-file node-export-path))\n(fprintf nodes-export-file \":ID\\n\")\n\n(define node-props-export-file\n  (open-output-file node-props-export-path))\n(fprintf node-props-export-file \":ID\\tpropname\\tvalue\\n\")\n\n(define input-nodes\n  (open-input-file (format \"~a~a\" directory-path nodes-file)))\n\n(let* ((header (read-line input-nodes))\n       (header (string-split header \"\\t\" #:trim? #f)))\n  (let loop ((seen-nodes (set))\n             (line-str (read-line input-nodes)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-nodes)\n       (close-output-port nodes-export-file)\n       (close-output-port node-props-export-file))\n      (else\n        (let* ((line (string-split line-str \"\\t\" #:trim? #f))\n               (node (car line)))\n          (when (set-member? seen-nodes node)\n            (error 'make-kg-node (format \"already seen node: ~a\" node)))\n          (fprintf nodes-export-file \"~a\\n\" node)\n          (let loop-inner ((props (cdr line))\n                           (headers (cdr header)))\n            (when (not (null? props))\n              (unless (string=? \"\" (car props))\n                (fprintf node-props-export-file \"~a\\t~a\\t~s\\n\" node (car headers) (car props)))\n              (loop-inner (cdr props) (cdr headers))))\n          (loop\n            (set-add seen-nodes node)\n            (read-line input-nodes)))))))\n"
  },
  {
    "path": "contrib/medikanren/make-kg-node.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n\n#|\nname-file.edge.scm\n:ID :START :END\n\nex-row: 1 ENSEMBL:ENSG00000004059 ENSEMBL:ENSP00000000233\n\nname-file.edge-props.scm\n:ID propname value\n\nex-row: 1 edge_label biolink:has_gene_product\n        1 provided_by blah\n        1\n\nname-file.node.scm\n:ID\n\nname-file.node-props.scm\n:ID propname value \n\n|#\n\n\n(define directory-path\n  \"/Users/michaelpatton/Desktop/data 2/merged/\")\n\n(define nodes-file\n  \"merged-kg_nodes.tsv\")\n\n(define export-path\n  (format \"~a\" (path->string (find-system-path 'desk-dir))))\n\n(define node-export-path\n  (format \"~acovid19.node.tsv\" export-path))\n\n(define nodes-export-file\n  (open-output-file node-export-path))\n\n(define node-props-export-path\n  (format \"~acovid19.nodeprops.tsv\" export-path))\n\n(define node-props-export-file\n  (open-output-file node-props-export-path))\n\n(define input-nodes\n  (open-input-file (format \"~a/~a\" directory-path nodes-file)))\n\n(let* ((header (read-line input-nodes))\n       (header (string-split header \"\\t\")))\n  (let loop ((seen-nodes (set))\n             (line-str (read-line input-nodes)))\n    (cond\n      ((eof-object? line-str)\n       (close-input-port input-nodes)\n       (close-output-port nodes-export-file)\n       (close-output-port node-props-export-file))\n      (else\n       (let* ((line (string-split line-str \"\\t\"))\n              (node (car line)))\n         (fprintf nodes-export-file \"~a\\n\" node)\n         (let loop-inner ((props (cdr line))\n                          (headers (cdr header)))\n           (when (not (null? props))\n             (unless (string=? \"\" (car props))\n               (fprintf node-props-export-file \"~a\\t~a\\t~a\\n\" node (car headers) (car props)))             \n             (loop-inner (cdr props) (cdr headers))))\n         (loop        \n          (set-add seen-nodes node)\n          (read-line input-nodes)))))))\n\n\n\n\n \n"
  },
  {
    "path": "contrib/medikanren/marissa/migraine-case.rkt",
    "content": "#lang racket\n(require \"../../medikanren/pieces-parts/query.rkt\")\n\n#|\nThis file focuses on migraine conditions as an example case, but these functions can be applied\nto many different conditions.\n\nThe functions in this file can be used to find pathways involved in diseases/conditions that are\nnot yet targeted by drug treatments. This information can be useful for drug discovery or finding\ndrug repurposing candidates.\n\nIt can also be used for patient cases. It can help determine what pathways were targeted by\ntreatments that were or weren't effective for a patient. Then, if a treatment was effective but\ncaused many side effects, the user can look for another drug that targets the same pathway in\nthe same way, and may be as effective whithout as many side effects. Or if no treatments have\nbeen effective, the user can look for pathways that the patient has not yet tried to target\nand can see if there are any available treatments that target those pathways.\n\nKGs loaded*:\nuab-pmi\nsemmed\numlsmeta\norange\nrobokop\nrtx2\ncovid19\ntextminingprovider\npr-owl\nsri_semmeddb\nsri-reference-kg\n\n*Although loading all of these is more comprehensive, rtx2 is necessary and sufficient for\ngetting some useful results.\n|#\n\n#|\nHelpful functions for reporting and viewing results\n|#\n(define (unwrap lst)\n  (cond [(or (null? lst) (not (list? lst))) lst]\n        [(list? (car lst)) (append (car lst) (unwrap (cdr lst)))]\n        [else (cons (car lst) (unwrap (cdr lst)))]))\n\n(define (curie->curie/name curie)\n  (assoc curie (curie-synonyms/names curie)))\n\n(define (concept->curie/name concept)\n  (cons (concept->curie concept) (concept->name concept)))\n\n(define (edges->preds edges)\n  (remove-duplicates (map edge->pred edges)))\n\n(define (summarize-curie curie)\n  (let ([concepts (find-concepts #t (list curie))])\n    (map (lambda (c) (list (concept->dbname c) (concept->curie c) (concept->name c) (concept->category c))) concepts)))\n\n#|\nRedefining category filters. The ones in query.rkt don't include \"biolink\" categories\n|#\n(define gene-or-protein '(;; rtx2\n                          \"biolink:Protein\"\n                          \"biolink:GeneProduct\"\n                          \"biolink:Gene\"\n                          \"biolink:GeneFamily\"\n                          \"biolink:GenomicEntity\"\n                          ;; semmed\n                          \"gene\"\n                          ;; robokop\n                          \"(\\\"named_thing\\\" \\\"gene\\\")\"\n                          ;; orange\n                          \"(\\\"gene\\\")\"\n                          \"(\\\"genomic entity\\\" \\\"gene\\\")\"\n                          \"(\\\"gene\\\" \\\"genomic entity\\\")\"\n                          ;; semmed\n                          \"biological_entity\" ;; with \\\"Amino Acid, Peptide, or Protein\\\" in \"umls_type_label\"\n                          ;; robokop\n                          ;; orange\n                          \"(\\\"gene\\\" \\\"genomic entity\\\")\"))\n\n(define drug '(;; rtx2\n               \"biolink:Drug\"\n               \"biolink:ChemicalSubstance\"\n               ;; semmed\n               \"chemical_substance\"\n               ;; robokop\n               \"(\\\"named_thing\\\" \\\"chemical_substance\\\")\"))\n\n\n;;------------------------------------------Migraine case-------------------------------------------------\n\n#|\nDefining all parent migraine curies found using find-concepts, filtering by categories, and manual\nfiltering and checking of heirarchy\n|#\n;; UMLS\n(define migraine-disorders-umls \"UMLS:C0149931\") ;; has same supers as migraine-disorders-cui\n(define migraine-variant-umls \"UMLS:C0042331\") ;; suclass_of -> CUI-supers\n(define common-migraine-umls \"UMLS:C0338480\")\n(define migraine-with-aura-umls \"UMLS:C0154723\")\n\n;; HP\n(define migraine-hp \"HP:0002076\")\n\n;; DOID\n(define migraine-disorder-doid \"DOID:6364\")\n\n;; MONDO\n(define migraine-disorder-mondo \"MONDO:0005277\")\n\n;; OMIM\n(define migraine-omim \"OMIM:157300\")\n\n#|\nCompiles all curies into one list\n|#\n(define migraine-parent-curies (list migraine-disorders-umls\n                                    migraine-variant-umls\n                                    common-migraine-umls\n                                    migraine-with-aura-umls\n                                    migraine-hp\n                                    migraine-disorder-doid\n                                    migraine-disorder-mondo\n                                    migraine-omim))\n\n#|\nGets the concepts associated with all the parent curies\n|#\n(define migraine-parent-concepts (find-concepts #t migraine-parent-curies))\n\n#|\nGiven a list of disease concepts, this uses run/graph to find the drugs that are indicated for\nor used to treat/prevent the disease concepts. It is meant to be run for one disease at a time,\nbut it allows for the input of a list of disease concepts because you often need multiple concepts\nto comprehensively represent a disease for the query.\n\nReturns a list of the drug to disease edges from the query. The drug concepts can be extracted\nusing calls to (edge->subject), and the curies can be extracted using (edge->subject) and\n(concept->curie).\n|#\n(define (drugs-indicated-for-r/g disease-concepts)\n  (define treats (find-exact-predicates '(\"biolink:treats\"\n                                          \"treats\"\n                                          \"biolink:prevents\"\n                                          \"prevents\"\n                                          )))\n  (match-define\n    (list concepts edges)\n    (run/graph\n     ((Dr #f)\n      (Dis disease-concepts))\n     ((Dr->Dis treats))\n     (Dr Dr->Dis Dis)))\n  \n  (hash-ref edges 'Dr->Dis))\n\n#|\nDoes the same thing as (drugs-indicated-for-r/g) except it takes a list of curies rather than\nconcepts and uses query/graph rather than run/graph.\n\nReturns the same thing as (drugs-indicated-for-r/g), a list of drug to disease edges.\n|#\n(define (drugs-indicated-for-q/g disease-curies)\n  (define drug-lst '())\n  (define treats '(\"biolink:treats\"\n                   \"treats\"))\n  (for-each\n   (lambda (d)\n     (define q (query/graph\n                ((Dr drug)\n                 (Dis d))\n                ((Dr->Dis treats))\n                (Dr Dr->Dis Dis)))\n     (set! drug-lst (set-union drug-lst (edges/query q 'Dr->Dis))))\n   disease-curies)\n  drug-lst\n  )\n\n#|\nTakes in a list of drug concepts and uses run/graph to find the biological pathways those drugs\ntarget.\n\nReturns a list of the drug to pathway edges. Pathway concepts can be extracted using (edge->object),\nand the pathway curies can be extracted using (edge->object) and (concept->curie).\n|#\n(define (find-drug-target-pathways-r/g drug-concepts)\n  (define participates-in (find-predicates '(\"biolink:participates_in\")))\n  (match-define\n    (list concepts edges)\n    (run/graph\n     ((D drug-concepts)\n      (P #f))\n     ((D->P participates-in))\n     (D D->P P)))\n  (hash-ref edges 'D->P))\n\n#|\nDoes the same thing as (find-drug-target-pathways-r/g) except it takes a list of drug curies instead\nof concepts and uses query/graph instead of run/graph.\n\nReturns the same thing as (find-drug-target-pathways-r/g), a list of drug to pathway edges.\n|#\n(define (find-drug-target-pathways-q/g drug-curies)\n  (define pathway-lst '())\n  (for-each\n   (lambda (d)\n     (define q (query/graph\n                ((D d)\n                 (P #f))\n                ((D->P '(\"biolink:participates_in\")))\n                (D D->P P)))\n     (set! pathway-lst (set-union pathway-lst (edges/query q 'D->P))))\n   drug-curies)\n  pathway-lst)\n\n#|\nTakes a list of pathway concepts and uses run/graph to find the proteins that participate in that\npathway.\n\nReturns a list of protein to pathway edges.\n|#\n(define (find-prots-in-pathways pathway-concepts)\n  (define participates-in (find-predicates '(\"biolink:participates_in\")))\n  (match-define\n    (list concepts edges)\n    (run/graph\n     ((U #f)\n      (P pathway-concepts))\n     ((U->P participates-in))\n     (U U->P P)))\n  \n  (filter (lambda (e)\n            (string-prefix? (concept->curie (edge->subject e))\n                            \"UniProtKB\"))\n          (hash-ref edges 'U->P)))\n\n#|\nTakes a list of protein concepts and uses run/graph to find all the pathways the proteins participate in.\n\nReturns a list of protein to pathway edges.\n|#\n(define (find-pathways-invovled-in prot-concepts)\n  (define participates-in (find-predicates '(\"biolink:participates_in\")))\n  (match-define\n    (list concepts edges)\n    (run/graph\n     ((U prot-concepts)\n      (P #f))\n     ((U->P participates-in))\n     (U U->P P)))\n  \n  (filter (lambda (e)\n            (string-prefix? (concept->curie (edge->object e))\n                            \"PathWhiz\"))\n          (hash-ref edges 'U->P)))\n  \n#|\nGiven a list of disease curies, uses query/graph to find the genes or proteins associated with that\ndisease/condition.\n\nReturns a list of gene/protein to disease edges.\n|#\n(define (genes/prots-assoc-with-disease disease-curies)\n  (define associated-with '(;; UniProt -> DOID, MONDO, OMIM\n                            \"biolink:correlated_with\"\n                            ;; UniProt -> DOID\n                            \"biolink:gene_associated_with_condition\"\n                            ;; UniProt -> HP\n                            \"biolink:has_phenotype\"\n                            ;; \" -> OMIM, MONDO\n                            \"biolink:causes\"\n                            \"biolink:participates_in\"\n                            ;;\n                            \"predisposes\"\n                            \"has_phenotype\"\n                            \"contributes_to\"\n                            \"causes\"\n                            \"gene_associated_with_condition\"\n                            \"biomarker_for\"))\n  (define gene/prot-lst '())\n  (for-each\n   (lambda (d)\n     (define q (query/graph\n                ((G/P gene-or-protein)\n                 (Dis d))\n                ((G/P->Dis associated-with))\n                (G/P G/P->Dis Dis)))\n     (set! gene/prot-lst (set-union gene/prot-lst (edges/query q 'G/P->Dis)))\n     )\n   disease-curies)\n  gene/prot-lst\n  )\n\n#|\nTakes a list of biological pathway curies and uses query/graph to find the drugs that target them.\n\nReturns a list of drug to pathway edges.\n|#\n(define (find-drugs-for-pathways pathway-curies)\n  (define pathway-lst '())\n  (for-each\n   (lambda (p)\n     (define q (query/graph\n                ((D drug)\n                 (P p))\n                ((D->P '(\"biolink:participates_in\")))\n                (D D->P P)))\n     (set! pathway-lst (set-union pathway-lst (edges/query q 'D->P))))\n   pathway-curies)\n  pathway-lst)\n\n#|Example\n;;Drugs that treat migraines\n(define drug->migraine (drugs-indicated-for-q/g migraine-parent-curies))\n(define migraine-drug-concepts (map edge->subject drug->migraine))\n(define migraine-drug-curies (map concept->curie (map edge->subject drug->migraine)))\n\n;;Pathways targeted by drugs\n(define drug->target-pathways (find-drug-target-pathways-q/g migraine-drug-curies))\n(define drug-pathway-concepts (map edge->object drug->target-pathways))\n(define drug-pathway-curies (map concept->curie (map edge->object drug->target-pathways)))\n\n;;Proteins involved in pathways targeted by drugs\n(define prots->drug-pathways (find-prots-in-pathways drug-pathway-concepts))\n(define prots-in-drug-pathways-concepts (map edge->subject prots->drug-pathways))\n(define prots-in-drug-pathways-curies (remove-duplicates (map concept->curie (map edge->subject prots->drug-pathways))))\n\n;;Genes/prots associated with migraines\n(define g/p->disease (genes/prots-assoc-with-disease migraine-parent-curies))\n(define g/p-concepts (map edge->subject g/p->disease))\n(define g/p-curies (map concept->curie (map edge->subject g/p->disease)))\n\n;;Pathways involved in migraine conditions\n(define g/p->disease-pathways (find-pathways-invovled-in g/p-concepts))\n(define disease-pathway-concepts (map edge->object g/p->disease-pathways))\n(define disease-pathway-curies (map concept->curie (map edge->object g/p->disease-pathways)))\n\n;;Cross-referencing disease and drug pathways\n(define targeted-pathways (set-intersect drug-pathway-curies disease-pathway-curies))\n(define non-targeted-pathways (set-subtract disease-pathway-curies drug-pathway-curies))\n\n(map curie->curie/name targeted-pathways)\n(map curie->curie/name non-targeted-pathways)\n\n;;Find drugs for pathways not yet targeted by migraine drugs\n(define repurposing-candidates->pathways (find-drugs-for-pathways non-targeted-pathways))\n(define drug-repurposing-candidate-concepts (map edge->subject repurposing-candidates->pathways))\n(define drug-repurposing-candidate-curies (map concept->curie (map edge->subject repurposing-candidates->pathways)))\n|#"
  },
  {
    "path": "contrib/medikanren/marissa/patient-case-workflow.rkt",
    "content": "#lang racket\n(require \"../../medikanren/pieces-parts/query.rkt\")\n\n(define (unwrap lst)\n  (cond [(or (null? lst) (not (list? lst))) lst]\n        [(list? (car lst)) (append (car lst) (unwrap (cdr lst)))]\n        [else (cons (car lst) (unwrap (cdr lst)))]))\n\n(define (PR-prefix? curie)\n  (string-prefix? curie \"PR:\"))\n\n(define (curie->curie/name curie)\n  (assoc curie (curie-synonyms/names curie)))\n\n(define (concept->curie/name concept)\n  (cons (concept->curie concept) (concept->name concept)))\n\n(define (edges->preds edges)\n  (remove-duplicates (map edge->pred edges)))\n  \n\n(define (summarize-curie curie)\n  (let ([concepts (find-concepts #t (list curie))])\n    (map (lambda (c) (list (concept->dbname c) (concept->curie c) (concept->name c) (concept->category c))) concepts)))\n\n(define cell-categories '(;;rtx2\n                          \"biolink:CellularComponent\"\n                          \"biolink:Cell\"\n                          \"biolink:OntologyClass|biolink:CellularComponent\"\n                          \"biolink:OntologyClass|biolink:Cell\"\n                          ;;robokop\n                          \"\\\"cellular_component\\\"\"\n                          \"\\\"cell\\\"\"\n                          ;;semmed\n                          \"cell\"\n                          \"cell_component\"))\n\n(define subclass-of '(\"biolink:subClassOf\"\n                      \"subclass_of\"))\n\n(define subclass-of-r/g (find-predicates subclass-of))\n\n(define pos/neg-regulates-entity-to-entity '(\"biolink:negatively_regulates_entity_to_entity\"\n                                             \"biolink:positively_regulates_entity_to_entity\"))\n\n;;----------------------------------------Traversing PR----------------------------------------------\n#|HGNC -> PR -> general PR code\n  Drug or gene/protein -> general PR code|#\n\n(define hum-P450 \"PR:P10635\")\n(define hum-TP53 \"PR:P04637\")\n\n#|\nGiven a PR curie, uses query/graph to traverse the textminingprovider kg to find the parent curie or\nsuper curie.\n\nReturns a list of the super curie, name pairs.\n|#\n(define (find-supers-q/g curie)\n  (let ([q (query/graph\n            ((Sub curie)\n             (Sup #f))\n            ((Sub->Sup subclass-of))\n            (Sub Sub->Sup Sup))])\n    (map curie->curie/name (curies/query q 'Sup))))\n\n#|\nDoes the same thing as (find-supers-q/g) except using run/graph.\n|#\n(define (find-supers-r/g curie)\n  (define concept (find-concepts #t (list curie)))\n  (match-define\n    (list concepts edges)\n    (run/graph\n     ((Sub concept)\n      (Sup #f))\n     ((Sub->Sup subclass-of-r/g))\n     (Sub Sub->Sup Sup)))\n  \n  (map concept->curie/name (hash-ref concepts 'Sup)))\n\n#|\nTakes a PR curie and uses query/graph to find its subclasses.\n\nReturns a list of subclass curie, name pairs.\n|#\n(define (find-subclasses curie)\n  (let ([q (query/graph\n            ((Sub #f)\n             (Sup curie))\n            ((Sub->Sup subclass-of))\n            (Sub Sub->Sup Sup))])\n    (map curie->curie/name (curies/query q 'Sub))))\n\n#|\nTakes a list of human genes and uses query/graph to find their orthologs.\n\nReturns a list of ortholog curie, name pairs.\n|#\n(define (find-orthologs superclass-curie)\n  (let ([q (query/graph\n            ((O #f)\n             (Sup superclass-curie))\n            ((O->Sup subclass-of))\n            (O O->Sup Sup))])\n    (map curie->curie/name (curies/query q 'O))))\n\n#|\nTakes a PR curie and uses query/graph to find any drugs that positively or negatively regulate\nthat gene or ortholog.\n|#\n(define (find-drugs/chems curie)\n  (let ([q (query/graph\n            ((D/G #f)\n             (P/G curie))\n            ((D/G->P/G pos/neg-regulates-entity-to-entity))\n            (D/G D/G->P/G P/G))])\n    (map curie->curie/name (curies/query q 'D/G))))\n\n#|Examples-----------------------------------------------------------------------------\n(find-supers-q/g hum-TP53)\n;; User selects correct curie from dropdown, something along those lines\n(define super-TP53 \"PR:000003035\")\n(find-orthologs super-TP53)\n;; User selects all orthologs they're interested in\n(map (lambda (x) (find-drugs/chems (car x))) (find-orthologs super-TP53))\n(find-drugs/chems super-TP53)\n\n(find-supers-q/g hum-P450)\n;; User selects correct curie from dropdown, something along those lines\n(define super-P450 \"PR:000006121\")\n(find-orthologs super-P450)\n|#"
  },
  {
    "path": "contrib/medikanren/marvin.rkt",
    "content": "#lang racket\n\n;;; Find drugs that budge a given gene/set of genes up or down\n\n;;; Prototype for more sophisticated automated/semi-automated\n;;; workflows and workflow interfaces\n\n(provide\n  (all-from-out \"mk.rkt\")\n  (all-from-out \"db.rkt\")\n  (all-from-out \"mk-db.rkt\")\n  (all-from-out \"common.rkt\")  \n  (all-from-out racket/date)\n  (all-defined-out))\n\n(require\n  \"../../medikanren/mk.rkt\"\n  \"../../medikanren/db.rkt\"\n  \"../../medikanren/mk-db.rkt\"\n  \"../../medikanren/pieces-parts/common.rkt\"\n  \"../../medikanren/pieces-parts/create-all-hashtables.rkt\"\n  racket/date\n  (except-in racket/match ==))\n\n;;; Dont' print a quote at the beginning of values.\n(print-as-expression #f)\n\n;;; directions\n(define DECREASE 'DECREASE)\n(define INCREASE 'INCREASE)\n(define DECREASE/INCREASE 'DECREASE/INCREASE)\n\n(define D-G-increases-predicate-names\n  '(\"positively_regulates\"\n    ;; \"causes\"\n    ;; \"produces\"  ;;; maybe??\n    ;; \"causes_condition\"\n    ;; \"causally_related_to\"\n    ;; \"contributes_to\"\n    ;; \"causes_adverse_event\"\n    ;; \"gene_associated_with_condition\"\n    ;; \"gene_mutations_contribute_to\"\n    ;; \"disease_to_gene_association\"\n    \"increases_activity_of\"\n    \"increases_expression_of\"\n    \"increases_molecular_interaction\"\n    \"increases_response_to\"\n    \"increases_secretion_of\"\n    \"increases_stability_of\"\n    \"increases_synthesis_of\"\n    \"increases_transport_of\"\n    \"increases_uptake_of\"\n    \"decreases_degradation_of\"\n    \"posetively_regulates\" ;;; robokop typo??\n    ;; \"positively_regulates__entity_to_entity\"\n    ;; \"increases_molecular_modification_of\"\n    ;; \"increases_localization_of\"\n    ;; \"increases_splicing_of\"\n    ;; \"decreases_mutation_rate_of\"\n    ;; \"predisposes\"\n    ;; \"decreases_metabolic_processing_of\"\n    ))\n\n(define D-G-decreases-predicate-names\n  '(\"negatively_regulates\"\n    \"prevents\"\n    \"treats\"\n    \"indicated_for\"\n    \"decreases_activity_of\"\n    \"decreases_expression_of\"\n    \"decreases_molecular_interaction\"\n    \"decreases_secretion_of\"\n    \"decreases_synthesis_of\"\n    \"decreases_transport_of\"\n    \"decreases_uptake_of\"\n    \"disrupts\"\n    \"increases_degradation_of\"\n    ;; \"negatively_regulates__entity_to_entity\"\n    ;; \"increases_metabolic_processing_of\"\n    ;; \"decreases_response_to\"\n    ;; \"decreases_localization_of\"\n    ;; \"decreases_molecular_modification_of\"\n    ))\n\n\n(define ROBOKOP_GENE_CATEGORY '(0 . \"(\\\"named_thing\\\" \\\"gene\\\")\"))\n(define ROBOKOP_EQUIVALENT_IDENTIFIERS_KEY \"equivalent_identifiers\")\n\n\n(define VERSION_STRING \"mediKanren Marvin Prototype 0.1.0 (Simple Drug-for-Gene Workflow Module)\")\n(displayln VERSION_STRING)\n\n\n(printf \"loading or creating hashtables, as necessary...\\n\")\n(load-or-create/save-all-hashtables!)\n\n\n(displayln \"loading semmed knowledge graph\")\n(define semmed (make-db \"data/semmed\"))\n(displayln \"loading rtx knowledge graph\")\n(define rtx (make-db \"data/rtx\"))\n(displayln \"loading robokop knowledge graph\")\n(define robokop (make-db \"data/robokop\"))\n(displayln \"loading orange knowledge graph\")\n(define orange (make-db \"data/orange\"))\n\n\n(printf \"Marvin online.\\n\")\n\n\n(define (simple-drug-for-gene-workflow gene-symbol-string direction)\n  (printf \"Running simple-drug-for-target-gene-workflow for gene ~s in direction ~s\\n\" gene-symbol-string direction)\n  (printf \"Trying to find a drug or biological entity that will budge target gene ~s in direction ~s\\n\" gene-symbol-string direction)\n  (printf \"Starting workflow for ~s/~s at date/time: ~a\\n\" gene-symbol-string direction (date->string (seconds->date (current-seconds)) #t))\n\n  ;;; Do a concept lookup in Robokop for the gene-symbol-string as the CUI (exact match, case sensitive).\n  ;;; Error is none is found, or if more than one is found.\n  ;;; Error if the type of the concept isn't \n  ;;; [Eventually need to be able to recover from error.]\n  (printf \"Looking up a concept in the Robokop Knowledge graph containing the concept name ~s...\\n\" gene-symbol-string)\n\n  (define robokop-concepts-containing-gene-symbol-name\n    (run* (concept)\n      (db:~name*-concepto/options\n       #t ;;case-sensitive?\n       \"\" ;; chars:ignore\n       \"\" ;; chars:split\n       robokop\n       (list gene-symbol-string)\n       concept)))\n\n  (printf \"Found ~s concept(s) in Robokop that contain the concept name ~s:\\n\\n\"\n          (length robokop-concepts-containing-gene-symbol-name)\n          gene-symbol-string)\n\n  (for-each\n    (lambda (c) (pretty-print c) (newline))\n    robokop-concepts-containing-gene-symbol-name)\n  \n  (printf \"Filtering out all found concepts whose name doesn't exactly match the string ~s\\n\" gene-symbol-string)\n\n  (define robokop-concepts-with-exact-gene-name\n    (filter\n     (lambda (c)\n       (match c\n         [`(,cid ,cui ,name (,catid . ,cat) ,props)\n          (string=? gene-symbol-string name)]))\n     robokop-concepts-containing-gene-symbol-name))\n\n  ;; make sure we no longer use the old concept list\n  (set! robokop-concepts-containing-gene-symbol-name #f)\n \n  (printf \"Keeping ~s Robokop concept(s) whose name exactly matches ~s:\\n\\n\"\n          (length robokop-concepts-with-exact-gene-name)\n          gene-symbol-string)\n\n  (for-each\n    (lambda (c) (pretty-print c) (newline))\n    robokop-concepts-with-exact-gene-name)\n\n  ;;; In the case of \"KRAS\", should produce the concept:\n  ;;;\n  ;; (23561\n  ;;  \"HGNC:6407\"\n  ;;  \"KRAS\"\n  ;;  (0 . \"(\\\"named_thing\\\" \\\"gene\\\")\")\n  ;;  ((\"locus_group\" . \"protein-coding gene\")\n  ;;   (\"chromosome\" . \"12\")\n  ;;   (\"taxon\" . \"9606\")\n  ;;   (\"location\" . \"12p12.1\")\n  ;;   (\"gene_family\" . \"(\\\"RAS type GTPase family\\\")\")\n  ;;   (\"id\" . \"HGNC:6407\")\n  ;;   (\"gene_family_id\" . \"(389)\")\n  ;;   (\"equivalent_identifiers\"\n  ;;    .\n  ;;    \"(\\\"ENSEMBL:ENSG00000133703\\\" \\\"UniProtKB:P01116\\\" \\\"NCBIGENE:3845\\\" \\\"UniProtKB:I1SRC5\\\" \\\"UniProtKB:L7RSL8\\\" \\\"HGNC:6407\\\" \\\"UniProtKB:G3V5T7\\\" \\\"UniProtKB:G3V4K2\\\" \\\"UniProtKB:A0A024RAV5\\\")\")))\n\n  \n  (if (= (length robokop-concepts-with-exact-gene-name) 1)\n      (printf \"Exactly 1 Robokop concept has a name that exactly matches ~s, as expected.  Continuing...\\n\\n\" gene-symbol-string)\n      (error (format \"ERROR  Expected exactly 1 Robokop concept whose name exactly matches ~s.  Found ~s instead.\"\n                     gene-symbol-string\n                     (length robokop-concepts-with-exact-gene-name))))\n  \n  (define robokop-target-gene-concept (car robokop-concepts-with-exact-gene-name))\n  ;; make sure we no longer use the old concept list\n  (set! robokop-concepts-with-exact-gene-name #f)\n    \n  (match robokop-target-gene-concept\n    [`(,cid ,cui ,name ,category ,props)\n\n     (if (equal? category ROBOKOP_GENE_CATEGORY)\n         (printf \"The remaining Robokop concept has the expected category, ~s.  Continuing...\\n\\n\" ROBOKOP_GENE_CATEGORY)\n         (error (format \"ERROR  The remaining Robokop concept has the category ~s rather than the expected category ~s\"\n                        category\n                        ROBOKOP_GENE_CATEGORY))) \n     \n     ])\n\n  ;;; Next step: extract the HGNC code from the CUI, and extract the ENSEMBL and UniProtKB names (hmm--should we lookup all the UniProtKB equivalents, if there is more than one?  Is that okay?) (What about the NCBIGENE name?  Is that useful at all?)\n  (define robokop-target-gene-concept-CUI/props\n    (match robokop-target-gene-concept\n      [`(,cid ,cui ,name (,catid . ,cat) ,props)\n       (list cui props)]))\n\n  (printf \"Extracted CUI and properties from Robokop target gene concept:\\n\\n~s\\n\\n\" robokop-target-gene-concept-CUI/props)\n  \n  (define robokop-target-gene-concept-CUI (car robokop-target-gene-concept-CUI/props))\n\n  (printf \"Robokop target gene concept CUI: ~s\\n\" robokop-target-gene-concept-CUI)\n\n  (printf \"Checking that Robokop target gene concept CUI is a valid HGNC identifier of the form \\\"HGNC:\\\"\\n\")\n  (if (regexp-match #rx\"^HGNC:[0-9]+$\" robokop-target-gene-concept-CUI)\n      (printf \"Robokop target gene concept CUI ~s is a valid HGNC identifier of the form \\\"HGNC:\\\", as expected.  Continuing...\\n\\n\" robokop-target-gene-concept-CUI)\n      (error (format \"ERROR  Robokop target gene concept CUI ~s is not a valid HGNC identifier of the form \\\"HGNC:\\\"\"\n                     robokop-target-gene-concept-CUI)))\n\n  (define robokop-target-gene-concept-HGNC-ID robokop-target-gene-concept-CUI)\n\n  (define robokop-target-gene-concept-property-list (cadr robokop-target-gene-concept-CUI/props))\n   \n  (printf \"Looking up ~s list in Robokop target gene property list:\\n\\n~s\\n\\n\" ROBOKOP_EQUIVALENT_IDENTIFIERS_KEY robokop-target-gene-concept-property-list)\n\n  (define robokop-target-gene-concept-equivalent-identifiers\n    (let ((v (assoc ROBOKOP_EQUIVALENT_IDENTIFIERS_KEY robokop-target-gene-concept-property-list)))\n      (and v (cdr v))))\n\n  (if robokop-target-gene-concept-equivalent-identifiers\n      (printf \"Found equivalent identifiers list for Robokop target gene, as expected:\\n~s\\nContinuing...\\n\\n\"\n              robokop-target-gene-concept-equivalent-identifiers)\n      (error (format \"ERROR  Unable to find key ~s in property list ~s\"\n                     ROBOKOP_EQUIVALENT_IDENTIFIERS_KEY\n                     robokop-target-gene-concept-property-list)))\n\n  (printf \"Extracting ENSMBL equivalent identifiers...\\n\") \n  (define robokop-target-gene-concept-ENSEMBL-CUIs\n    (regexp-match* #rx\"ENSEMBL:[A-Z0-9]+\" robokop-target-gene-concept-equivalent-identifiers))\n  (printf \"Extracted ENSMBL equivalent identifiers:\\n~s\\n\\n\" robokop-target-gene-concept-ENSEMBL-CUIs)\n\n  (printf \"Extracting HGNC equivalent identifiers...\\n\") \n  (define robokop-target-gene-concept-HGNC-CUIs\n    (regexp-match* #rx\"HGNC:[0-9]+\" robokop-target-gene-concept-equivalent-identifiers))\n  (printf \"Extracted HGNC equivalent identifiers:\\n~s\\n\\n\" robokop-target-gene-concept-HGNC-CUIs)\n\n  (printf \"Extracting OMIM equivalent identifiers...\\n\") \n  (define robokop-target-gene-concept-OMIM-CUIs\n    (regexp-match* #rx\"OMIM:[A-Z0-9]+\" robokop-target-gene-concept-equivalent-identifiers))\n  (printf \"Extracted OMIM equivalent identifiers:\\n~s\\n\\n\" robokop-target-gene-concept-OMIM-CUIs)\n  \n  (printf \"Extracting UniProtKB equivalent identifiers...\\n\")\n  (define robokop-target-gene-concept-UniProtKB-CUIs\n    (regexp-match* #rx\"UniProtKB:[A-Z0-9]+\" robokop-target-gene-concept-equivalent-identifiers))\n  (printf \"Extracted UniProtKB equivalent identifiers:\\n~s\\n\\n\" robokop-target-gene-concept-UniProtKB-CUIs)\n\n\n  (define (find-CIDs-for-CUI CUI hashtable CUI-ID-regex)\n    (define ID* (regexp-match* CUI-ID-regex CUI #:match-select cadr))\n    (define ID #f)\n    (if (and (list? ID*) (= (length ID*) 1))\n        (set! ID (car ID*))\n        (error (format \"ERROR  find-CIDs-for-CUI expected ID* to be a singleton list, instead got ~s\" ID*)))\n    (printf \"Looking up ID ~s from CUI ~s in hashtable...\\n\"\n            ID\n            CUI)\n    (define concept-DB/IDs-for-CUI (hash-ref hashtable ID '()))\n    (printf \"Found these concept DB/CIDs for ID ~s from CUI ~s in hashtable:\\n\\n~s\\n\\n\"\n            ID\n            CUI\n            concept-DB/IDs-for-CUI)\n    concept-DB/IDs-for-CUI)\n\n  (define (find-CIDs-for-multiple-CUIs CUI* hashtable CUI-ID-regex)\n    (let loop ([CUI* CUI*]\n               [CID* (set)])\n      (cond\n        ((null? CUI*)\n         (let ((CID* (set->list CID*)))\n           (printf \"in aggregate, found these CIDs for all CUIs:\\n~s\\n\\n\" CID*)\n           CID*))\n        (else (let ((CUI (car CUI*))\n                    (rest (cdr CUI*)))\n                (printf \"looking up CIDs for CUI ~s...\\n\" CUI)\n                (let ((res (find-CIDs-for-CUI CUI hashtable CUI-ID-regex)))\n                  (printf \"found these CIDs for CUI ~s:\\n~s\\n\" CUI res)\n                  (loop rest\n                        (set-union (list->set res) CID*))))))))\n\n  (define (find-concepts-for-CIDs CID*)\n    (printf \"finding concepts for concept IDs ~s...\\n\" CID*)\n    (define concepts\n      (apply append\n             (map\n              (lambda (db-key/cid)\n                (let ((db-key (car db-key/cid))\n                      (cid (cdr db-key/cid)))\n                  (let ((db (case db-key\n                              ((semmed) semmed)\n                              ((rtx) rtx)\n                              ((robokop) robokop)\n                              ((orange) orange))))\n                    (map (lambda (c) (cons db-key c))\n                         (run* (concept)\n                           (fresh (rest)\n                             (== `(,cid . ,rest) concept)\n                             (db:concepto db concept)))))))\n              CID*)))\n    (printf \"found these concepts for concept IDs ~s:\\n\" CID*)\n    (for-each (lambda (c) (printf \"~s\\n\" c)) concepts)\n    (newline)\n    concepts)\n  \n  ;; special case: single HGNCI CUI as the Robokop main CUI\n  (printf \"finding concept IDs for canonical Robolop HGNC CUI...\\n\")\n  (define CIDs-for-single-HGNCI-CUI\n    (find-CIDs-for-CUI robokop-target-gene-concept-CUI hgnc-ht #rx\"^HGNC:([0-9]+)$\"))\n\n  (define concepts-for-single-HGNCI-CUI\n    (find-concepts-for-CIDs CIDs-for-single-HGNCI-CUI))\n\n  \n  \n  (printf \"finding concept IDs for ENSEMBL equivalents...\\n\")\n  (define CIDs-for-ENSEMBL-CUIs\n    (find-CIDs-for-multiple-CUIs\n      robokop-target-gene-concept-ENSEMBL-CUIs\n      ensembl-ht\n      #rx\"^ENSEMBL:([A-Z0-9]+)$\"))\n  \n  (define concepts-for-ENSEMBL-CUIs\n    (find-concepts-for-CIDs CIDs-for-ENSEMBL-CUIs))\n\n  \n  (printf \"finding concept IDs for HGNC equivalents...\\n\")\n  (define CIDs-for-HGNC-CUIs\n    (find-CIDs-for-multiple-CUIs\n      robokop-target-gene-concept-HGNC-CUIs\n      hgnc-ht\n      #rx\"^HGNC:([0-9]+)$\"))\n\n  (define concepts-for-HGNC-CUIs\n    (find-concepts-for-CIDs CIDs-for-HGNC-CUIs))\n\n  \n  (printf \"finding concept IDs for UniProtKB equivalents...\\n\")\n  (define CIDs-for-UniProtKB-CUIs\n    (find-CIDs-for-multiple-CUIs\n      robokop-target-gene-concept-UniProtKB-CUIs\n      uniprotkb-ht\n      #rx\"^UniProtKB:([A-Z0-9]+)$\"))\n\n  (define concepts-for-UniProtKB-CUIs\n    (find-concepts-for-CIDs CIDs-for-UniProtKB-CUIs))\n\n\n  (define all-concepts-from-original-robokop-concept\n    (set->list\n      (set-union\n        (set (cons 'robokop robokop-target-gene-concept))\n        (list->set concepts-for-single-HGNCI-CUI)\n        (list->set concepts-for-ENSEMBL-CUIs)\n        (list->set concepts-for-HGNC-CUIs)\n        (list->set concepts-for-UniProtKB-CUIs))))\n  (printf \"all concepts equivalent to original Robokop concept:\\n\")\n  (for-each (lambda (c) (printf \"~s\\n\" c)) all-concepts-from-original-robokop-concept)\n  (newline)\n\n\n  (printf \"looking for equivalent semmed concepts, by concept name...\\n\")\n\n  (define semmed-protein-name (string-append gene-symbol-string \" Protein\"))\n  (printf \"looking for ' Protein' (~s) concept name in semmed...\\n\" semmed-protein-name)\n  (define semmed-protein-concepts\n    (map\n      (lambda (c) (cons 'semmed c))\n      (filter\n        (lambda (c)\n          (match c\n            [`(,cid ,cui ,name (,catid . ,cat) ,props)\n             (string=? (string-downcase name)\n                       (string-downcase semmed-protein-name))]))\n        (run* (concept)\n          (db:~name*-concepto/options\n           #f ;;case-sensitive?\n           \"\" ;; chars:ignore\n           \"\" ;; chars:split\n           semmed\n           (list semmed-protein-name)\n           concept)))))\n  (printf \"' Protein' (~s) concepts in semmed:\\n\" semmed-protein-name)\n  (for-each (lambda (c) (printf \"~s\\n\" c)) semmed-protein-concepts)\n  (newline)\n\n  (define semmed-wt-allele-name (string-append gene-symbol-string \" wt Allele\"))\n  (printf \"looking for ' wt Allele' (~s) concept name in semmed...\\n\" semmed-wt-allele-name)\n  (define semmed-wt-allele-concepts\n    (map\n      (lambda (c) (cons 'semmed c))\n      (filter\n        (lambda (c)\n          (match c\n            [`(,cid ,cui ,name (,catid . ,cat) ,props)\n             (string=? (string-downcase name)\n                       (string-downcase semmed-wt-allele-name))]))\n        (run* (concept)\n          (db:~name*-concepto/options\n           #f ;;case-sensitive?\n           \"\" ;; chars:ignore\n           \"\" ;; chars:split\n           semmed\n           (list semmed-wt-allele-name)\n           concept)))))\n  (printf \"' wt Allele' (~s) concepts in semmed:\\n\" semmed-wt-allele-name)\n  (for-each (lambda (c) (printf \"~s\\n\" c)) semmed-wt-allele-concepts)\n  (newline)\n\n  (define semmed-gene-mutation-name (string-append gene-symbol-string \" gene mutation\"))\n  (printf \"looking for ' gene mutation' (~s) concept name in semmed...\\n\" semmed-gene-mutation-name)\n  (define semmed-gene-mutation-concepts\n    (map\n      (lambda (c) (cons 'semmed c))\n      (filter\n        (lambda (c)\n          (match c\n            [`(,cid ,cui ,name (,catid . ,cat) ,props)\n             (string=? (string-downcase name)\n                       (string-downcase semmed-gene-mutation-name))]))\n        (run* (concept)\n          (db:~name*-concepto/options\n           #f ;;case-sensitive?\n           \"\" ;; chars:ignore\n           \"\" ;; chars:split\n           semmed\n           (list semmed-gene-mutation-name)\n           concept)))))\n  (printf \"' gene mutation' (~s) concepts in semmed:\\n\" semmed-gene-mutation-name)\n  (for-each (lambda (c) (printf \"~s\\n\" c)) semmed-gene-mutation-concepts)\n  (newline)\n  \n  \n  (define all-concepts-under-consideration-from-original-gene-name\n    (set->list\n      (set-union\n        (list->set all-concepts-from-original-robokop-concept)\n        (list->set semmed-protein-concepts)\n        (list->set semmed-wt-allele-concepts)\n        (list->set semmed-gene-mutation-concepts))))\n  (printf \"all concepts under consideration from original gene symbol name (~s):\\n\" gene-symbol-string)\n  (for-each (lambda (c) (printf \"~s\\n\" c)) all-concepts-under-consideration-from-original-gene-name)\n  (newline)\n  \n  \n  (newline)\n  (printf \"Ending Marvin workflow for ~s/~s at date/time: ~a\\n\" gene-symbol-string direction (date->string (seconds->date (current-seconds)) #t))\n  (displayln \"-----------------------------------------------------\")\n  (newline)\n  (newline)\n  )\n\n\n\n\n\n(simple-drug-for-gene-workflow \"KRAS\" DECREASE)\n\n;; RTX has many BRCA1-related concepts, such as\n;; 'BRCA1/BRCA2-containing complex subunit 3'.  How many of these\n;; would be relevant for increase/decrease queries?\n;;\n;; Make a best effort to select the relevant concepts, and show user\n;; the concepts that include 'BRCA1' in their name but *aren't* being\n;; selected (and give user a chance to intervene and change the\n;; selections).\n(simple-drug-for-gene-workflow \"BRCA1\" DECREASE)\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/CHAMP1_RNA_seq_original.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/pieces-parts/query.rkt\"\n  \"Thi-useful-functions.rkt\")\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*********GENERAL SEARCH********;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; *** Data Sources:\n;; - Processed CHAMP1 RNAseq data from outside of mediKanren\n;; - RNA was obtained from patients or control\n;;  cultured fibroblasts derived from skin biopsies\n;;\n;; *** Objective:\n;; Repurpose drugs for CHAMP1 genetic disorder using RNAseq data from patients-derived skin fibroblasts\n\n;; First, I'm doing exploratory searches for the disease information related to CHAMP1 genes:\n;; Find disease conditions that are related to CHAMP1 genes\n(curie-synonyms/names \"HGNC:20311\")\n(define CHAMP1 \"HGNC:20311\")\n;; Check the diseases and conditions associted with the CHAMP1 gene\n(define q-disease-CHAMP1 (time (query/graph\n                     ((S disease)\n                      (O CHAMP1))\n                     ((S->O #f))\n                     (S S->O O))))\n\n(define disease-CHAMP1-edges (edges/query q-disease-CHAMP1 'S->O))\n\n;; The results show that CHAMP1 gene (chromosome alignment-maintaining phosphoprotein, is a protein-coding gene,\n;; a member of the zinc fingers C2H2-types protein, located on chromosome 13q34)\n;; is associated with certain disease conditions such as\n;; mental retardation (autosomal dominant), rare (non-syndromic) intellectual disability, monogenic genetic\n;; central nervous system disorder, mental disorder, and psychiatric disorder. \n\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******STRATEGY NUMBER 1*******;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; In this strategy, we want to find drugs that target the genes that belong to enriched functional categories\n;; such as cell cycle and cell senescence, retinol metabolism (which are results from gene set enrichemnet analysis (GSEA) performed\n;; outside of medikanren).\n;; GSEA has identified a number of genes that are upregulated in CHAMP1 fibroblasts compared to control fibroblasts.\n\n;; First, find HGNC CURIEs (\"HGNC:\") of each gene from the gene name (either by using\n;; genecards database \"https://www.genecards.org/\" or using mediKanren's find-concepts\n;; ,then check if they are synonymized.\n;; If the CURIE is synonymized, we use it to define the gene/protein in query/graph\n;; eg:\n\n(find-concepts #f (list \"VIM\"))\n(curie-synonyms/names \"HGNC:1583\")\n\n\n;; genes that are altered in the cell cycle pathway:\n(define CCND2 \"HGNC:1583\") ;; cell cycle up-regulated\n(define TUBA1A \"HGNC:20766\") ;; cell cycle down-regulated\n;; cell senescence pathway:\n;(define CCND2 \"HGNC:1583\") ;; up-regulated\n(define RASSF5 \"HGNC:17609\") ;; up-regulated\n;; DNA replication| apoptosis \n(define PSMA5 \"HGNC:9534\");; up-regulated\n;; Oocyte meiosis | progesterone-mediated oocyte maturation| calcium signaling\n(define ADCY4 \"HGNC:235\");; up-regulate\n;; retinol metabolism:\n(define ALDH1A1 \"HGNC:402\");; up-regulated\n;; ABC transporter:\n(define ABCA13 \"HGNC:14638\");; up-regulated\n;; HIV infection| calcium\n(define PTK2B \"HGNC:9612\");; up-regulated\n(define AP1G2 \"HGNC:556\");; up-regulated\n;; amyotropic lateral sclerosis | apoptosis\n(define TNFRSF1B \"HGNC:11917\");; down-regulated\n;; regulation of actin cytoskeleton:\n(define FGF10 \"HGNC:3666\");;  up-regulated\n(define CHRM2 \"HGNC:1951\");; down-regulated\n;; Gonadotropin hormone-releasing\n(define KCNN4 \"HGNC:6293\");; down-regulated\n;; ECM receptor interaction:\n(define CD36 \"HGNC:1663\");;  up-regulated\n;; Neuroactive ligand-receptor interaction | calcium\n(define EDNRB \"HGNC:3180\") ;;  up-regulated\n(define LHB \"HGNC:6584\");; down-regulated\n;; mRNA surveillance:\n(define MSI2 \"HGNC:18585\") ;; down-regulated\n;; calcium\n;(define ADCY4 \"HGNC:235\");; up-regulated\n;(define PTK2B \"HGNC:9612\");; up-regulated\n(define ERBB4 \"HGNC:3432\");; up-regulated\n;(define CHRM2 \"HGNC:1951\");; down-regulated\n;(define EDNRB \"HGNC:3180\") ;;  up-regulated\n;; apoptosis:\n(define VIM \"HGNC:12692\");; down-regulated\n\n\n;; All selected upregulated genes in enriched functional categories are:\n(define functional-cat-up (list CCND2 RASSF5 PSMA5 ADCY4 ALDH1A1 ABCA13 PTK2B\n                                AP1G2 FGF10 CD36 EDNRB EDNRB ERBB4))\n(define functional-cat-down (list TUBA1A TNFRSF1B CHRM2 KCNN4 LHB MSI2 VIM))\n\n\n(define results-CHAMP1-functional-cat-down (find-drugs-for-genes functional-cat-up positively-regulates))\n(define results-CHAMP1-functional-cat-up (find-drugs-for-genes functional-cat-up negatively-regulates))\n;;extract drug=>gene hash-table:\n(define drug=>gene-CHAMP1-functional-cat-down (car results-CHAMP1-functional-cat-down))\n(define drug=>gene-CHAMP1-functional-cat-up (car results-CHAMP1-functional-cat-up))\n;;extract gene=>drug hash-table:\n(define gene=>drug-CHAMP1-functional-cat-down (cadr results-CHAMP1-functional-cat-down))\n(define gene=>drug-CHAMP1-functional-cat-up (car results-CHAMP1-functional-cat-up))\n(define drug=>gene-strategy1 (merge-assoc-lists (list drug=>gene-CHAMP1-functional-cat-down drug=>gene-CHAMP1-functional-cat-up)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******STRATEGY NUMBER 2*******;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n\n;; Based on literature research, we identifed 5 different disease conditions that are associated with CHAMP1 genetic disorder:\n\n(define hypotonia-concepts (find-concepts #f (list \"hypotonia\")))\n(define cerebral-palsy-concepts (find-concepts #f (list \"cerebral palsy\")))\n(define autism-concepts (find-concepts #f (list \"autism\")))\n(define dev-delay-concepts (find-concepts #f (list \"developmental delay\")))\n(define epilepsy-concepts (find-concepts #f (list \"epilepsy\")))\n\n\n;; In this 2nd strategy, we first search for all the genes that are associated with the five CHAMP1\n;; disease associated conditions using run/graph\n\n(match-define\n  (list name=>concepts name=>edges)\n  (run/graph\n   ((S #f)\n    (O (set-union hypotonia-concepts\n                  cerebral-palsy-concepts\n                  autism-concepts\n                  dev-delay-concepts\n                  epilepsy-concepts)))\n   ((S->O gene-to-disease-preds))\n   (S S->O O)))\n\n;; filter the subjects to retain only genes or proteins and get their names:\n(map (lambda (y) (cons (concept->curie y) (concept->name y)))\n     (filter (lambda (x)\n               (gene/protein-concept? (concept->curie x))) (hash-ref name=>concepts 'S)))\n\n;; This filter results in 1397 genes/proteins that are related to CHAMP1 patients' phenotypes.\n;; I then cleaned the data, converted it to .csv and mapped different gene/protein identifers to HGNC symbols\n;; then I removed duplicates and NA.\n;; This resulted in 934 genes.\n;; Using these genes, I plot a volcano plot that show differences in expression levels between\n;; CHAMP1 patients fibroblasts vs control fibroblasts.\n;; This visualisation shows genes that are statistically significantly altered between these\n;; two conditions. These genes become our drug targets.\n\n\n;; Now we want to find drugs that reverse the directions of DEG genes (which are genes found to be associated\n;; with CHAMP1 patients' phenotypes- the results from the run/graph above.\n;; Directionality is provided by gene expression values (determined by experiments on CHAMP1 patients' fibroblasts).\n;; For genes that are significantly upregulated, we want to find drugs that decrease their expression, and vice versa.\n\n\n;; Abstract genes that are upregulated:\n(define CACNB4 \"HGNC:1404\")\n(define PRICKLE1 \"HGNC:17019\")\n(define DMD \"HGNC:2928\")\n(define SHANK2 \"HGNC:14295\")\n(define MAP2 \"HGNC:6839\")\n(define H19 \"HGNC:4713\")\n(define BCHE \"HGNC:983\")\n(define EFNA5 \"HGNC:3225\")\n(define CNTNAP2 \"HGNC:13830\")\n(define ANKH \"HGNC:15492\")\n(define SLC12A6 \"HGNC:10914\")\n(define CHAMP1-phenotype-RNA-up\n  (list CACNB4 PRICKLE1 DMD SHANK2 MAP2 H19 BCHE EFNA5 CNTNAP2 ANKH SLC12A6))\n\n;; Alternatively, for genes that are significantly downregulatated, we want to find drugs that increase their expression: \n(define GABRA5 \"HGNC:4079\")\n;(define TNFRSF1B \"HGNC:11917\")\n(define STX1B \"HGNC:18539\")\n(define RBFA \"HGNC:26120\")\n(define CHAMP1-phenotype-RNA-down\n  (list GABRA5 TNFRSF1B STX1B RBFA))\n\n\n\n;; Now we use the function find-drugs-for-genes in Thi's-useful-functions:\n(define results-CHAMP1-phenotype-RNA-up (find-drugs-for-genes CHAMP1-phenotype-RNA-up negatively-regulates))\n(define drug=>gene-CHAMP1-phenotype-RNA-up (car results-CHAMP1-phenotype-RNA-up))\n(define gene=>drug-CHAMP1-phenotype-RNA-up (cadr results-CHAMP1-phenotype-RNA-up))\n\n(define results-CHAMP1-phenotype-RNA-down (find-drugs-for-genes CHAMP1-phenotype-RNA-down positively-regulates))\n(define drug=>gene-CHAMP1-phenotype-RNA-down (car results-CHAMP1-phenotype-RNA-down))\n(define gene=>drug-CHAMP1-phenotype-RNA-down (cadr results-CHAMP1-phenotype-RNA-down))\n\n;; use the get-num-values function in Thi's-useful-functions:\n(define drug=>gene-CHAMP1-phenotype-RNA-up-with-stats (get-num-values drug=>gene-CHAMP1-phenotype-RNA-up))\n(define gene=>drug-CHAMP1-phenotype-RNA-up-with-stats (get-num-values gene=>drug-CHAMP1-phenotype-RNA-up))\n\n(define drug=>gene-CHAMP1-phenotype-RNA-down-with-stats (get-num-values drug=>gene-CHAMP1-phenotype-RNA-down))\n(define gene=>drug-CHAMP1-phenotype-RNA-down-with-stats (get-num-values gene=>drug-CHAMP1-phenotype-RNA-down))\n\n(define merged_strategy2 (merge-2-assoc-list drug=>gene-CHAMP1-phenotype-RNA-up drug=>gene-CHAMP1-phenotype-RNA-down))\n(define merged_trategy2_count (get-num-values (car merged_strategy2)))\n\n(define merged_strategy2_genes (merge-2-assoc-list gene=>drug-CHAMP1-phenotype-RNA-up gene=>drug-CHAMP1-phenotype-RNA-down))\n(define merged_trategy2_genes_count (get-num-values (car merged_strategy2_genes)))\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******STRATEGY NUMBER 3*******;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; 2-edge queries to find drugs that treat the CHAMP1 disease conditions and reverse the gene expression directions:\n;; These are all significantly altered genes in differential expression analyses performed outside of mediKanren\n\n(define CHAMP1-DE-RNA-up (list \"ENSEMBL:ENSG00000228630\"\n                               \"ENSEMBL:ENSG00000261340\"\n                               \"ENSEMBL:ENSG00000083937\"\n                               \"ENSEMBL:ENSG00000143106\"\n                               \"ENSEMBL:ENSG00000140199\"\n                               \"ENSEMBL:ENSG00000065357\"\n                               \"ENSEMBL:ENSG00000129480\"\n                               \"ENSEMBL:ENSG00000162688\"\n                               \"ENSEMBL:ENSG00000180818\"\n                               \"ENSEMBL:ENSG00000136478\"\n                               \"ENSEMBL:ENSG00000065413\"\n                               \"ENSEMBL:ENSG00000167394\"\n                               \"ENSEMBL:ENSG00000163249\"\n                               \"ENSEMBL:ENSG00000118762\"\n                               \"ENSEMBL:ENSG00000185070\"\n                               \"ENSEMBL:ENSG00000089060\"\n                               \"ENSEMBL:ENSG00000173221\"\n                               \"ENSEMBL:ENSG00000175040\"\n                               \"ENSEMBL:ENSG00000112964\"\n                               \"ENSEMBL:ENSG00000111670\"\n                               \"ENSEMBL:ENSG00000119986\"\n                               \"ENSEMBL:ENSG00000106415\"\n                               \"ENSEMBL:ENSG00000038427\"\n                               \"ENSEMBL:ENSG00000154122\"\n                               \"ENSEMBL:ENSG00000176531\"\n                               \"ENSEMBL:ENSG00000121413\"\n                               \"ENSEMBL:ENSG00000176809\"\n                               \"ENSEMBL:ENSG00000165804\"\n                               \"ENSEMBL:ENSG00000198948\"\n                               \"ENSEMBL:ENSG00000012171\"\n                               \"ENSEMBL:ENSG00000267454\"\n                               \"ENSEMBL:ENSG00000182379\"\n                               \"ENSEMBL:ENSG00000213983\"\n                               \"ENSEMBL:ENSG00000169313\"\n                               \"ENSEMBL:ENSG00000137573\"\n                               \"ENSEMBL:ENSG00000174469\"\n                               \"ENSEMBL:ENSG00000189129\"\n                               \"ENSEMBL:ENSG00000112378\"\n                               \"ENSEMBL:ENSG00000136048\"\n                               \"ENSEMBL:ENSG00000101134\"\n                               \"ENSEMBL:ENSG00000176928\"\n                               \"ENSEMBL:ENSG00000184916\"\n                               \"ENSEMBL:ENSG00000162643\"\n                               \"ENSEMBL:ENSG00000266094\"\n                               \"ENSEMBL:ENSG00000150540\"\n                               \"ENSEMBL:ENSG00000176771\"\n                               \"ENSEMBL:ENSG00000138772\"\n                               \"ENSEMBL:ENSG00000115271\"\n                               \"ENSEMBL:ENSG00000250133\"\n                               \"ENSEMBL:ENSG00000179104\"\n                               \"ENSEMBL:ENSG00000145390\"\n                               \"ENSEMBL:ENSG00000184349\"\n                               \"ENSEMBL:ENSG00000101605\"\n                               \"ENSEMBL:ENSG00000205002\"\n                               \"ENSEMBL:ENSG00000198133\"\n                               \"ENSEMBL:ENSG00000205835\"\n                               \"ENSEMBL:ENSG00000165113\"\n                               \"ENSEMBL:ENSG00000172403\"\n                               \"ENSEMBL:ENSG00000120899\"\n                               \"ENSEMBL:ENSG00000174600\"\n                               \"ENSEMBL:ENSG00000099260\"\n                               \"ENSEMBL:ENSG00000137727\"\n                               \"ENSEMBL:ENSG00000136160\"\n                               \"ENSEMBL:ENSG00000182901\"\n                               \"ENSEMBL:ENSG00000112981\"\n                               \"ENSEMBL:ENSG00000242600\"\n                               \"ENSEMBL:ENSG00000115604\"\n                               \"ENSEMBL:ENSG00000144229\"\n                               \"ENSEMBL:ENSG00000151623\"\n                               \"ENSEMBL:ENSG00000165023\"\n                               \"ENSEMBL:ENSG00000152804\"\n                               \"ENSEMBL:ENSG00000112379\"\n                               \"ENSEMBL:ENSG00000082497\"\n                               \"ENSEMBL:ENSG00000144645\"\n                               \"ENSEMBL:ENSG00000196208\"\n                               \"ENSEMBL:ENSG00000228495\"\n                               \"ENSEMBL:ENSG00000135919\"\n                               \"ENSEMBL:ENSG00000211448\"\n                               \"ENSEMBL:ENSG00000141449\"\n                               \"ENSEMBL:ENSG00000203727\"\n                               \"ENSEMBL:ENSG00000013588\"\n                               \"ENSEMBL:ENSG00000130600\"\n                               \"ENSEMBL:ENSG00000126861\"\n                               \"ENSEMBL:ENSG00000165084\"\n                               \"ENSEMBL:ENSG00000179869\"\n                               \"ENSEMBL:ENSG00000114200\"\n                               \"ENSEMBL:ENSG00000143028\"\n                               \"ENSEMBL:ENSG00000164106\"\n                               \"ENSEMBL:ENSG00000138449\"\n                               \"ENSEMBL:ENSG00000110723\"\n                               \"ENSEMBL:ENSG00000162687\"\n                               \"ENSEMBL:ENSG00000183775\"\n                               \"ENSEMBL:ENSG00000106538\"\n                               \"ENSEMBL:ENSG00000064225\"\n                               \"ENSEMBL:ENSG00000086289\"\n                               \"ENSEMBL:ENSG00000070193\"\n                               \"ENSEMBL:ENSG00000116183\"\n                               \"ENSEMBL:ENSG00000102109\"\n                               \"ENSEMBL:ENSG00000078018\"\n                               \"ENSEMBL:ENSG00000099864\"\n                               \"ENSEMBL:ENSG00000173391\"\n                               \"ENSEMBL:ENSG00000198947\"\n                               \"ENSEMBL:ENSG00000139174\"\n                               \"ENSEMBL:ENSG00000165092\"\n                               \"ENSEMBL:ENSG00000162105\"\n                               \"ENSEMBL:ENSG00000137672\"\n                               \"ENSEMBL:ENSG00000178568\"\n                               \"ENSEMBL:ENSG00000064042\"\n                               \"ENSEMBL:ENSG00000135218\"\n                               \"ENSEMBL:ENSG00000126785\"\n                               \"ENSEMBL:ENSG00000240694\"\n                               \"ENSEMBL:ENSG00000248874\"\n                               \"ENSEMBL:ENSG00000118971\"\n                               \"ENSEMBL:ENSG00000182389\"\n                               \"ENSEMBL:ENSG00000129467\"\n                               \"ENSEMBL:ENSG00000106483\"\n                               \"ENSEMBL:ENSG00000123572\"))\n\n\n(define CHAMP1-DE-RNA-down (list   \"EMSEMBL:ENSG00000204792\"\n                                   \"EMSEMBL:ENSG00000166796\"\n                                   \"EMSEMBL:ENSG00000186297\"\n                                   \"EMSEMBL:ENSG00000005379\"\n                                   \"EMSEMBL:ENSG00000234465\"\n                                   \"EMSEMBL:ENSG00000165887\"\n                                   \"EMSEMBL:ENSG00000115648\"\n                                   \"EMSEMBL:ENSG00000102575\"\n                                   \"EMSEMBL:ENSG00000175084\"\n                                   \"EMSEMBL:ENSG00000145824\"\n                                   \"EMSEMBL:ENSG00000213030\"\n                                   \"EMSEMBL:ENSG00000132639\"\n                                   \"EMSEMBL:ENSG00000006606\"\n                                   \"EMSEMBL:ENSG00000101017\"\n                                   \"EMSEMBL:ENSG00000154451\"\n                                   \"EMSEMBL:ENSG00000169429\"\n                                   \"EMSEMBL:ENSG00000104826\"\n                                   \"EMSEMBL:ENSG00000163618\"\n                                   \"EMSEMBL:ENSG00000147573\"\n                                   \"EMSEMBL:ENSG00000171517\"\n                                   \"EMSEMBL:ENSG00000130720\"\n                                   \"EMSEMBL:ENSG00000157557\"\n                                   \"EMSEMBL:ENSG00000178882\"\n                                   \"EMSEMBL:ENSG00000156453\"\n                                   \"EMSEMBL:ENSG00000148803\"\n                                   \"EMSEMBL:ENSG00000107611\"\n                                   \"EMSEMBL:ENSG00000175294\"\n                                   \"EMSEMBL:ENSG00000181072\"\n                                   \"EMSEMBL:ENSG00000104783\"\n                                   \"EMSEMBL:ENSG00000128285\"\n                                   \"EMSEMBL:ENSG00000080823\"\n                                   \"EMSEMBL:ENSG00000167889\"\n                                   \"EMSEMBL:ENSG00000124191\"\n                                   \"EMSEMBL:ENSG00000163701\"\n                                   \"EMSEMBL:ENSG00000076706\"\n                                   \"EMSEMBL:ENSG00000144354\"\n                                   \"EMSEMBL:ENSG00000103034\"\n                                   \"EMSEMBL:ENSG00000164929\"\n                                   \"EMSEMBL:ENSG00000204103\"\n                                   \"EMSEMBL:ENSG00000242265\"\n                                   \"EMSEMBL:ENSG00000196460\"\n                                   \"EMSEMBL:ENSG00000138395\"\n                                   \"EMSEMBL:ENSG00000225968\"\n                                   \"EMSEMBL:ENSG00000028137\"\n                                   \"EMSEMBL:ENSG00000091622\"\n                                   \"EMSEMBL:ENSG00000125968\"\n                                   \"EMSEMBL:ENSG00000173848\"\n                                   \"EMSEMBL:ENSG00000239332\"\n                                   \"EMSEMBL:ENSG00000139278\"\n                                   \"EMSEMBL:ENSG00000137563\"\n                                   \"EMSEMBL:ENSG00000163814\"\n                                   \"EMSEMBL:ENSG00000121904\"\n                                   \"EMSEMBL:ENSG00000186847\"\n                                   \"EMSEMBL:ENSG00000099365\"\n                                   \"EMSEMBL:ENSG00000136490\"\n                                   \"EMSEMBL:ENSG00000100181\"\n                                   \"EMSEMBL:ENSG00000079462\"\n                                   \"EMSEMBL:ENSG00000026025\"\n                                   \"EMSEMBL:ENSG00000105255\"\n                                   \"EMSEMBL:ENSG00000188064\"\n                                   \"EMSEMBL:ENSG00000103449\"\n                                   \"EMSEMBL:ENSG00000235162\"\n                                   \"EMSEMBL:ENSG00000074410\"\n                                   \"EMSEMBL:ENSG00000170961\"\n                                   \"EMSEMBL:ENSG00000140280\"\n                                   \"EMSEMBL:ENSG00000187583\"\n                                   \"EMSEMBL:ENSG00000205683\"\n                                   \"EMSEMBL:ENSG00000109062\"\n                                   \"EMSEMBL:ENSG00000159231\"\n                                   \"EMSEMBL:ENSG00000183077\"\n                                   \"EMSEMBL:ENSG00000173588\"\n                                   \"EMSEMBL:ENSG00000167552\"\n                                   \"EMSEMBL:ENSG00000243156\"\n                                   \"EMSEMBL:ENSG00000166886\"\n                                   \"EMSEMBL:ENSG00000153944\"\n                                   \"EMSEMBL:ENSG00000196912\"\n                                   \"EMSEMBL:ENSG00000183506\"\n                                   \"EMSEMBL:ENSG00000156535\"\n                                   \"EMSEMBL:ENSG00000087266\"\n                                   \"EMSEMBL:ENSG00000170921\"\n                                   \"EMSEMBL:ENSG00000185052\"\n                                   \"EMSEMBL:ENSG00000089486\"\n                                   \"EMSEMBL:ENSG00000196155\"\n                                   \"EMSEMBL:ENSG00000101546\"\n                                   \"EMSEMBL:ENSG00000038382\"\n                                   \"EMSEMBL:ENSG00000167460\"\n                                   \"EMSEMBL:ENSG00000186281\"\n                                   \"EMSEMBL:ENSG00000130309\"\n                                   \"EMSEMBL:ENSG00000054523\"\n                                   \"EMSEMBL:ENSG00000100097\"\n                                   \"EMSEMBL:ENSG00000142892\"\n                                   \"EMSEMBL:ENSG00000231419\"\n                                   \"EMSEMBL:ENSG00000163687\"))\n\n;; define CHAMP1 disease related conditions:\n(define dev-delay \"HP:0001263\")\n(define hypotonia \"HP:0001252\")\n(define cerebral-palsy \"HP:0100021\")\n(define autism \"MONDO:0005260\")\n(define epilepsy \"MONDO:0005027\")\n\n;; The function find-drug-for-condition takes a disease condition, a gene list (derived from RNA-seq DEG results)\n;; a list of drug-to-gene predicates that we want the drug to modulate.\n;; This function will run a query/graph that does a 2-edge query which find drugs that modify the disease condition\n;; while also modulate the gene in the gene list\n;; this function will return a list which contains 2 hash-tables which are sorted based on the number\n;; of genes or drugs available:\n\n; Use the find-drug-for-condition from Thi-useful-functions.rkt:\n(define dev-delay-drug-results-RNA-up (find-drug-for-condition dev-delay CHAMP1-DE-RNA-up negatively-regulates))\n(define dev-delay-drug-results-RNA-down (find-drug-for-condition dev-delay CHAMP1-DE-RNA-down positively-regulates))\n\n(define hypotonia-drug-results-RNA-up (find-drug-for-condition hypotonia CHAMP1-DE-RNA-up negatively-regulates))\n(define hypotonia-drug-results-RNA-down (find-drug-for-condition hypotonia CHAMP1-DE-RNA-up negatively-regulates))\n\n(define cerebral-palsy-drug-results-RNA-up (find-drug-for-condition cerebral-palsy CHAMP1-DE-RNA-up negatively-regulates))\n(define cerebral-palsy-drug-results-RNA-down (find-drug-for-condition cerebral-palsy CHAMP1-DE-RNA-down positively-regulates))\n\n(define autism-drug-results-RNA-up (find-drug-for-condition autism CHAMP1-DE-RNA-up negatively-regulates))\n(define autism-drug-results-RNA-down (find-drug-for-condition autism CHAMP1-DE-RNA-down positively-regulates))\n\n(define epilepsy-drug-results-RNA-up (find-drug-for-condition epilepsy CHAMP1-DE-RNA-up negatively-regulates))\n(define epilepsy-drug-results-RNA-down (find-drug-for-condition epilepsy CHAMP1-DE-RNA-down positively-regulates))\n\n;; Extract gene=>drug and drug=>gene tables:\n\n(define drug=>gene-dev-delay-drug-results-RNA-up (car dev-delay-drug-results-RNA-up))\n(define gene=>drug-dev-delay-drug-results-RNA-up (cadr dev-delay-drug-results-RNA-up))\n(define drug=>gene-dev-delay-drug-results-RNA-down (car dev-delay-drug-results-RNA-down))\n(define gene=>drug-dev-delay-drug-results-RNA-down (cadr dev-delay-drug-results-RNA-down))\n\n(define drug=>gene-hypotonia-drug-results-RNA-up (car hypotonia-drug-results-RNA-up))\n(define gene=>drug-hypotonia-drug-results-RNA-up (cadr hypotonia-drug-results-RNA-up))\n(define drug=>gene-hypotonia-drug-results-RNA-down (car hypotonia-drug-results-RNA-down))\n(define gene=>drug-hypotonia-drug-results-RNA-down (cadr hypotonia-drug-results-RNA-down))\n\n(define drug=>gene-cerebral-palsy-drug-results-RNA-up (car cerebral-palsy-drug-results-RNA-up))\n(define gene=>drug-cerebral-palsy-drug-results-RNA-up (cadr cerebral-palsy-drug-results-RNA-up))\n(define drug=>gene-cerebral-palsy-drug-results-RNA-down (car cerebral-palsy-drug-results-RNA-down))\n(define gene=>drug-cerebral-palsy-drug-results-RNA-down (cadr cerebral-palsy-drug-results-RNA-down))\n\n(define drug=>gene-autism-drug-results-RNA-up (car autism-drug-results-RNA-up))\n(define gene=>drug-autism-drug-results-RNA-up (cadr autism-drug-results-RNA-up))\n(define drug=>gene-autism-drug-results-RNA-down (car autism-drug-results-RNA-down))\n(define gene=>drug-autism-drug-results-RNA-down (cadr autism-drug-results-RNA-down))\n\n(define drug=>gene-epilepsy-drug-results-RNA-up (car epilepsy-drug-results-RNA-up))\n(define gene=>drug-epilepsy-drug-results-RNA-up (cadr epilepsy-drug-results-RNA-up))\n(define drug=>gene-epilepsy-drug-results-RNA-down (car epilepsy-drug-results-RNA-down))\n(define gene=>drug-epilepsy-drug-results-RNA-down (cadr epilepsy-drug-results-RNA-down))\n\n; combine 10 association lists:\n(define strategy3_results\n  (merge-assoc-lists\n   (list drug=>gene-dev-delay-drug-results-RNA-up\n         drug=>gene-dev-delay-drug-results-RNA-down\n         drug=>gene-hypotonia-drug-results-RNA-up \n         drug=>gene-hypotonia-drug-results-RNA-down\n         drug=>gene-cerebral-palsy-drug-results-RNA-up\n         drug=>gene-cerebral-palsy-drug-results-RNA-down\n         drug=>gene-autism-drug-results-RNA-up\n         drug=>gene-autism-drug-results-RNA-down\n         drug=>gene-epilepsy-drug-results-RNA-up\n         drug=>gene-epilepsy-drug-results-RNA-down)))\n\n\n(define strategy3_genes_results\n  (merge-assoc-lists\n   (list gene=>drug-dev-delay-drug-results-RNA-up\n         gene=>drug-dev-delay-drug-results-RNA-down\n         gene=>drug-hypotonia-drug-results-RNA-up \n         gene=>drug-hypotonia-drug-results-RNA-down\n         gene=>drug-cerebral-palsy-drug-results-RNA-up\n         gene=>drug-cerebral-palsy-drug-results-RNA-down\n         gene=>drug-autism-drug-results-RNA-up\n         gene=>drug-autism-drug-results-RNA-down\n         gene=>drug-epilepsy-drug-results-RNA-up\n         gene=>drug-epilepsy-drug-results-RNA-down)))\n\n; sort them by the values:\n(define strategy3_results-count (get-num-values (car strategy3_results)))\n(define strategy3_results-genes-count (get-num-values (car strategy3_genes_results)))\n\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/README_VISJS.md",
    "content": "# VIS.JS Instructions\nAfter using make-map.rkt to create the DOT graph for whichever knowledge graph you would like to visualize, it is then possible to visualize this DOT graph using Vis.js. \n\nIn order to do so, create a new html file and add the following to the header: \n\n```\n\n  [Your Title Here]\n\n  \n\n```\n\n\nThen, to insert the DOT graph, do the following:\n```\n
\n\n```\nThen, close the body of the html file and display its contents to navigate the graph. For the options variable, there is documentation on possible options at this link: https://visjs.github.io/vis-network/docs/network/#options\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/Thi-useful-functions.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"query.rkt\")\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;USEFUL FUNCTIONS;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; useful-drug-curie filter:\n(define (useful-drug-curie? curie)\n  (or (string-prefix? curie \"CHEMBL:\")\n      (string-prefix? curie \"CHEBI:\")\n      (string-prefix? curie \"TTD:\")\n      (string-prefix? curie \"GTPI:\")))\n\n;; sort-hash function to sort hash tables by the values and return an association list\n(define (sort-hash h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (length (cdr x)))))\n\n\n;; This is a helper function for the find-drugs-for-genes function below:\n(define gene-to-disease-preds (find-predicates '(\"associated_with_disease\"\n                                                 \"contributes_to\"\n                                                 \"biomarker_for\"\n                                                 \"gene_associated_with_condition\"\n                                                 \"affects\"\n                                                 \"causes\"\n                                                 \"prevents\"\n                                                 \"treats\"\n                                                 \"related_to\"\n                                                 \"predisposes\"\n                                                 \"gene_associated_with_condition\"\n                                                 \"associated_with\"\n                                                 \"complicates\"\n                                                 \"predisposes\"\n                                                 \"prevents\"\n                                                 \"treats\"\n                                                 \"disrupts\"\n                                                 \"augments\")))\n\n\n;; The find-drugs-for-genes function takes a gene-list and a list of drug-gene predicates (direction that we\n;; want the drugs to influence on the genes, one gene at a time) and return a list of two hash-tables: a sorted drug=>gene table and\n;; a sorted gene=>drug table, which is sorted by the number of genes that have drugs available to modify them or\n;; the number of drugs that can are available to target multiple genes:\n\n(define (find-drugs-for-genes gene-list drug-gene-preds)\n  (let ((gene=>drug (make-hash))\n        (drug=>gene (make-hash)))\n    (for-each\n     (lambda (g)\n       (define q (time (query/graph\n                        ((D useful-drug-curie?)\n                         (G g))\n                        ((D->G drug-gene-preds))\n                       (D D->G G))))\n       (hash-set! gene=>drug (assoc g (curie-synonyms/names g))\n                  (map (lambda (d) (assoc d (curie-synonyms/names d))) (curies/query q 'D)))\n       (for-each\n        (lambda (d)\n          (hash-update! drug=>gene (assoc d (curie-synonyms/names d))\n                        (lambda(v) (set-add v (assoc g (curie-synonyms/names g)))) '()))\n        (filter (lambda(x) (not (string-prefix? x \"CUI:\"))) (curies/query q 'D))))\n     gene-list)\n  (list (sort-hash drug=>gene) (sort-hash gene=>drug))))\n\n;;; examples of how to extract these two hash-tables result from find-drugs-for-genes functions:\n\n;(define results-CHAMP1-phenotype-RNA-down (find-drugs-for-genes CHAMP1-phenotype-RNA-down positively-regulates))\n;;extract drug=>gene hash-table:\n;(define drug=>gene-CHAMP1-phenotype-RNA-down (car results-CHAMP1-phenotype-RNA-down))\n;;extract gene=>drug hash-table:\n;(define gene=>drug-CHAMP1-phenotype-RNA-down (cadr results-CHAMP1-phenotype-RNA-down))\n\n;;; get-num-values takes a hash-table and count how many values are for each key:\n(define (get-num-values hash-table)\n  (map (lambda (x) (cons (car x) (length (cdr x)))) hash-table))\n\n\n(define drug-treat-disease-preds\n  '(;; common\n     \"prevents\"\n     \"negatively_regulates\"\n    ;; semmed\n    ;; robokop\n     \"negatively_regulates__entity_to_entity\"\n     \"disrupts\"\n     ;; orange\n     ;; rtx2\n     \"inhibits\"\n     \"inhibitor\"\n     \"channel_blocker\"\n     \"treats\"\n     \"disrupts\"\n     \"may_inhibit_effect_of\"\n     \"may_prevent\"\n     \"may_treat\"))\n\n\n;; find-drug-for-condition takes a disease condition, a gene list (which are derived from RNA-seq DEG results),\n;; a list of drug-to-gene predicates that we want the drug to reverse.\n;; This function will generate a query/graph that does a 2-edge query which find drugs that modify a disease condition\n;; while also modulate the gene in the gene list\n;; this function will return a list which contains 2 hash-tables which are sorted based on the number\n;; of genes or drugs available:\n\n(define (find-drug-for-condition disease-condition gene-list drug-gene-preds)\n  (let ((gene=>drug (make-hash))\n        (drug=>gene (make-hash)))\n    (for-each\n     (lambda (g)\n       (define q (time (query/graph\n                        ((D useful-drug-curie?)\n                         (C disease-condition)\n                         (G g))\n                        ((D->C drug-treat-disease-preds)\n                         (D->G drug-gene-preds))\n                        (D D->C C)\n                        (D D->G G))))\n       (hash-set! gene=>drug (assoc g (curie-synonyms/names g))\n                  (map (lambda (d) (assoc d (curie-synonyms/names d))) (curies/query q 'D)))\n       (for-each\n        (lambda (d)\n          (hash-update! drug=>gene (assoc d (curie-synonyms/names d))\n                        (lambda (v) (set-add v (assoc g (curie-synonyms/names g)))) '()))\n        (filter (lambda (x) (not (string-prefix? x \"CUI:\"))) (curies/query q 'D))))\n     gene-list)\n    (list (sort-hash drug=>gene) (sort-hash gene=>drug))))\n\n\n;; combine-keys returns a list of keys from the input as a list of association list \n\n(define combine-keys\n  (lambda (ls-of-alist)\n    (cond\n      [(null? ls-of-alist) '()]\n      [else\n       (let ((keys (map car (car ls-of-alist))))\n         (set-union keys (combine-keys (cdr ls-of-alist))))])))\n\n\n;; merge-2-assoc-list takes 2 association lists and return\n;; a merged and sorted association list with unique keys and values\n(define (merge-2-assoc-list alist1 alist2)\n  (let ((merged (make-hash))\n        (keys (set-union (map car alist1) (map car alist2))))\n    (for-each\n     (lambda (k)\n       (let ((genes-pr-1 (assoc k alist1))\n             (genes-pr-2 (assoc k alist2)))\n         (let ((genes-1\n                (if genes-pr-1\n                    (cdr genes-pr-1)\n                    '()))\n               (genes-2\n                (if genes-pr-2\n                    (cdr genes-pr-2)\n                    '())))\n           (let ((genes (set-union genes-1 genes-2)))\n             (hash-set! merged k genes)))))\n     keys)\n    (list (sort-hash merged))))\n\n;; expanding form the merge-2-assoc-list function above, the merge-assoc-lists function takes a list of association\n;; lists and return a merged and sorted association list with unique keys and values\n(define (merge-assoc-lists ls-of-alist)\n  (cond\n    [(null? ls-of-alist) '()]\n    [(> (length ls-of-alist) 1)\n     (let ((merged (make-hash))\n           (keys (set-union (map car (car ls-of-alist)) (map car (cadr ls-of-alist)))))\n       (for-each\n        (lambda (k)\n          (let ((genes-pr-1 (assoc k (car ls-of-alist)))\n                (genes-pr-2 (assoc k (cadr ls-of-alist))))\n            (let ((genes-1\n                   (if genes-pr-1\n                       (cdr genes-pr-1)\n                       '()))\n                  (genes-2\n                   (if genes-pr-2\n                       (cdr genes-pr-2)\n                       '())))\n              (let ((genes (set-union genes-1 genes-2)))\n                (hash-set! merged k genes)))))\n        keys)\n       (merge-assoc-lists (cons (sort-hash merged) (cddr ls-of-alist))))]\n    [else\n     (car ls-of-alist)]))\n\n\n;;recursively merge values of a ls-of-alist with the given key \n(define merge-values\n  (lambda (ls-of-alist key)\n    (cond\n      [(null? ls-of-alist) '()]\n      [else\n       (let ((first (car ls-of-alist))\n             (rest (cdr ls-of-alist)))\n         (let ((genes-pr-first (assoc key first)))\n           (let ((genes-first\n                  (if genes-pr-first\n                    (list (cdr genes-pr-first))\n                    '())))\n             (let ((genes (set-union genes-first (merge-values rest key))))\n               genes))))])))\n\n#|\nwrite-list-to-tsv takes a (header-list), a list of list and  a path-to-file name and\nconvert the list to tsv format. This has been defined in query.rkt\n\n*example usage, where 'results' is bound to a list of lists:\n\n(write-list-to-tsv\n  (list \"db\" \"subject\" \"predicate\" \"object\")\n  results\n  \"my-tsv.tsv\")\n|#\n#|\n(define write-list-to-tsv\n  (lambda (header-ls lol path)\n    (with-output-to-file path\n      ;; thunk -- procedure that takes no arguments\n      (lambda ()\n        (for-each\n          (lambda (l)\n            (let loop ([l l])\n              (cond\n                ((null? l)\n                 (error 'output-to-tsv \"where's the data!?\"))\n                ((null? (cdr l)) ;; l contains exactly 1 element\n                 (display (car l))\n                 (display #\\newline))\n                (else\n                 (display (car l))\n                 (display #\\tab)\n                 (loop (cdr l))))))\n          (cons header-ls lol)))\n      #:mode 'text\n      #:exists 'replace)))\n|#\n\n;; unwrap function flattens a list one level\n(define (unwrap lst)\n  (if (null? lst) lst\n      (append (car lst) (unwrap (cdr lst)))))\n\n\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/causal-discovery.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/db.rkt\"\n  \"query.rkt\")\n\n;; Note:  we should check if the 'negated' property on an edge is set to 'true'!\n\n;; since synonymization seems to be broken, here is the hand-crafted\n;; list of synonyms from RTX2\n\n;; SNOMED --equivalent_to--> MONDO\n\n;; need the UMLS and MONDO from an ICD10 or SNOMED,\n;; since UMLS and MONDO have the causal info we need\n(define handcrafted-thrombotic-events\n  '(\"MONDO:0005279\"\n    \"MESH:D011655\"\n    \"OMOP:440417\"\n    \"UMLS:C0034065\"\n    \"NCIT:C50713\"\n    \"SNOMED:59282003\"\n    \"EFO:0003827\"\n    \"DOID:9477\"))\n\n(define causal-predicates\n  '(\"biolink:causes\"\n    \"biolink:predisposes\"\n    \"causes\"\n    \"contributes_to\"\n    ))\n\n#|\nUMLS --biolink:causes--> UMLS:C0034065   sri_semmeddb\n\n(reverse direction:)\nUMLS:C0034065 --biolink:causes--> UMLS   sri_semmeddb\n\nUMLS --biolink:predisposes--> UMLS:C0034065   sri_semmeddb\n\n(reverse direction:)\nUMLS:C0034065 --biolink:predisposes--> UMLS   sri_semmeddb\n\n(same preds as above, but without the biolink: prefix)\nUMLS --causes--> UMLS:C0034065           semmeddb\nUMLS --causes--> UMLS:C0034065           rtx2\n\nCHEBI --contributes_to--> MONDO:0005279   robokop\n\n\npossibly useful:\n\n(and the revsersed version)\nUMLS --biolink:coexists_with--> UMLS:C0034065  sri_semmeddb\n\n(and the revsersed version)\nUMLS --biolink:precedes--> UMLS:C0034065   sri_semmeddb\n\nCHEMBL.COMPUND:CHEMBL --indicated_for--> DOID:9477   rtx2\n|#\n\n;(define thrombotic-events (curie-synonyms-raw \"MONDO:0005279\"))\n\n(printf \"running query\\n\")\n\n(define qa (time\n            (map\n             (lambda (te)\n               (query/graph\n                ((X #f)\n                 (thrombotic-event te))\n                ((X->thrombotic-event causal-predicates))\n                (X X->thrombotic-event thrombotic-event)))\n             handcrafted-thrombotic-events\n             )))\n\n#|\n\n(define qb (time (query/graph\n                  ((X #f)\n                   (thrombotic-event \"MONDO:0005279\"))\n                  ((X->thrombotic-event #f))\n                  (X X->thrombotic-event thrombotic-event))))\n\n(printf \"found results\\n\")\n\n; (pretty-print (time (report/query qb)))\n\n(printf \"ranking paths\\n\")\n\n(define r (ranked-paths qb))\n\n(printf \"getting counts\\n\")\n\n(length (curies/query qb 'X))\n(length (curies/query qb 'thrombotic-event))\n(length (edges/query qb 'X->thrombotic-event))\n\n(map\n (lambda (e)\n   (match e\n     [`(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n               (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n               (,pid . ,pred) ,eprops)\n      `(,sname ,pred ,oname)]))\n (edges/query qb 'X->thrombotic-event))\n\n(remove-duplicates\n (map\n  (lambda (e)\n    (match e\n      [`(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n                 (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n                 (,pid . ,pred) ,eprops)\n       pred]))\n  (edges/query qb 'X->thrombotic-event)))\n\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/chemical->drug-filter.rkt",
    "content": "#lang racket\n(require \"../../../medikanren/pieces-parts/query.rkt\")\n\n\n;; chemical->drug-filter functions take a chemical list and\n;; return a list of chemicals that have drug-safe predicates (i.e, drugs)\n;; In this function, I use a 2-hop query to get from CHEBI:  to a DRUGBANK:\n;; so that I can assess if a particular chemical has any drug-safe predicates\n\n(define (chemical->drug-filter chemical-list)\n  (filter \n   (lambda (chemical) \n     (define q\n       (query/graph\n        ((C chemical)\n         (D #f)\n         (Disease #f))\n        ((C->D '(\"same_as\"))\n         (D->Disease drug-safe))\n        (C C->D D)\n        (D D->Disease Disease)))\n     (empty? (curies/query q 'D)))\n   chemical-list))\n\n;; examples:\n(define strategy1_chemicals\n  '(\"CHEBI:28119\"\n  \"CHEBI:16469\"\n  \"CHEBI:37537\"\n  \"CHEBI:41879\"\n  \"CHEBI:17026\"\n  \"CHEBI:6541\"\n  \"CHEBI:4903\"\n  \"CHEBI:33216\"\n  \"CHEBI:9168\"\n  \"CHEBI:41774\"\n  \"CHEBI:65329\"\n  \"CHEBI:17347\"\n  \"CHEMBL:CHEMBL460433\"\n  \"CHEBI:17747\"\n  \"CHEBI:49662\"\n  \"CHEBI:22984\"\n  \"CHEBI:4031\"\n  \"CHEBI:27584\"\n  \"CHEBI:16243\"\n  \"CHEBI:9130\"\n  \"CHEBI:78543\"\n  \"CHEBI:15365\"\n  \"CHEMBL:CHEMBL62381\"\n  \"CHEBI:52717\"\n  \"CHEBI:175901\"\n  \"CHEBI:16113\"\n  \"CHEBI:29865\"\n  \"CHEBI:28748\"\n  \"CHEBI:5132\"\n  \"CHEBI:44423\"\n  \"CHEBI:45713\"\n  \"CHEBI:15738\"\n  \"CHEBI:16356\"\n  \"CHEBI:77986\"\n  \"CHEBI:3766\"\n  \"CHEBI:17489\"\n  \"CHEBI:8899\"\n  \"CHEBI:15355\"\n  \"CHEBI:3962\"\n  \"CHEBI:28088\"\n  \"CHEBI:76004\"\n  \"CHEBI:27656\"\n  \"CHEBI:77006\"\n  \"CHEMBL:CHEMBL504\"\n  \"CHEBI:8863\"\n  \"CHEBI:9150\"\n  \"CHEBI:31401\"\n  \"CHEBI:16330\"\n  \"CHEBI:44296\"\n  \"CHEBI:15930\"\n  \"CHEBI:17609\"\n  \"CHEBI:92413\"\n  \"CHEBI:47808\"\n  \"CHEMBL.COMPOUND:CHEMBL3545133\"\n  \"CHEMBL.COMPOUND:CHEMBL2109588\"\n  \"CHEBI:517248\"\n  \"CHEBI:28364\"\n  \"CHEBI:9786\"\n  \"CHEBI:3237\"\n  \"CHEMBL:CHEMBL1372588\"\n  \"CHEBI:135742\"\n  \"CHEBI:9241\"\n  \"CHEBI:6920\"\n  \"CHEMBL:CHEMBL305576\"\n  \"CHEBI:17712\"\n  \"CHEBI:5759\"\n  \"CHEBI:34892\"\n  \"CHEBI:15960\"\n  \"CHEBI:49040\"\n  \"GTPI:5965\"\n  \"CHEBI:8198\"\n  \"CHEBI:34935\"\n  \"CHEBI:52289\"\n  \"CHEBI:49668\"\n  \"CHEBI:34888\"\n  \"CHEBI:135736\"\n  \"CHEBI:138000\"\n  \"CHEBI:28940\"\n  \"CHEBI:29678\"\n  \"CHEBI:2666\"\n  \"CHEBI:35053\"\n  \"CHEMBL.COMPOUND:CHEMBL3707348\"\n  \"CHEBI:3763\"\n  \"CHEBI:50114\"\n  \"CHEMBL.COMPOUND:CHEMBL3545396\"\n  \"CHEBI:16412\"\n  \"CHEBI:88522\"\n  \"CHEBI:50694\"\n  \"CHEMBL:CHEMBL1903674\"\n  \"CHEBI:78373\"\n  \"CHEBI:28694\"\n  \"CHEBI:17578\"\n  \"CHEBI:30768\"\n  \"CHEBI:76612\"\n  \"CHEBI:338412\"\n  \"CHEBI:17823\"\n  \"CHEMBL:CHEMBL1371200\"\n  \"CHEBI:30740\"\n  \"CHEBI:107643\"\n  \"CHEBI:27385\"\n  \"CHEBI:15756\"\n  \"CHEBI:135949\"\n  \"CHEBI:15367\"\n  \"CHEBI:63954\"\n  \"GTPI:8492\"\n  \"CHEBI:137113\"\n  \"CHEBI:47495\"\n  \"CHEBI:28499\"\n  \"CHEBI:135735\"\n  \"CHEBI:566274\"\n  \"CHEBI:28112\"\n  \"CHEBI:76003\"\n  \"CHEBI:3655\"\n  \"CHEMBL:CHEMBL1221984\"\n  \"CHEMBL.COMPOUND:CHEMBL545315\"\n  \"CHEBI:49960\"\n  \"CHEMBL:CHEMBL1644699\"\n  \"CHEBI:28842\"\n  \"CHEBI:65310\"\n  \"CHEBI:8081\"\n  \"CHEMBL:CHEMBL8823\"\n  \"CHEMBL:CHEMBL1565107\"\n  \"CHEBI:30563\"\n  \"CHEBI:91452\"\n  \"CHEBI:4659\"\n  \"CHEBI:8062\"\n  \"CHEBI:16698\"\n  \"CHEBI:18388\"\n  \"CHEBI:28790\"\n  \"CHEMBL.COMPOUND:CHEMBL2105719\"\n  \"CHEBI:92843\"\n  \"CHEBI:18243\"\n  \"CHEBI:51450\"\n  \"CHEBI:90695\"\n  \"CHEBI:7590\"\n  \"CHEMBL.COMPOUND:CHEMBL499968\"\n  \"CHEBI:40303\"\n  \"CHEMBL.COMPOUND:CHEMBL3137331\"\n  \"CHEMBL.COMPOUND:CHEMBL356359\"\n  \"CHEBI:62825\"\n  \"CHEBI:2611\"\n  \"CHEBI:15553\"\n  \"CHEBI:132853\"\n  \"CHEBI:351346\"\n  \"CHEBI:17234\"\n  \"CHEBI:6402\"\n  \"CHEBI:39462\"\n  \"CHEBI:7465\"\n  \"CHEBI:34662\"\n  \"CHEMBL:CHEMBL2146125\"\n  \"CHEBI:31746\"\n  \"CHEBI:8382\"\n  \"CHEBI:18291\"\n  \"CHEBI:18152\"\n  \"CHEBI:95341\"\n  \"CHEBI:35456\"\n  \"CHEBI:18185\"\n  \"CHEBI:3385\"\n  \"CHEBI:6801\"\n  \"CHEBI:34076\"\n  \"CHEBI:6715\"\n  \"CHEBI:7735\"\n  \"CHEBI:45307\"\n  \"CHEBI:46024\"\n  \"CHEMBL:CHEMBL1981220\"\n  \"CHEBI:66917\"\n  \"CHEBI:556075\"\n  \"CHEBI:27363\"\n  \"CHEBI:15368\"\n  \"CHEBI:83732\"\n  \"CHEMBL.COMPOUND:CHEMBL1645462\"\n  \"CHEBI:4305\"\n  \"CHEBI:48045\"\n  \"CHEMBL:CHEMBL190083\"\n  \"CHEBI:65347\"\n  \"CHEBI:15343\"\n  \"CHEBI:86194\"\n  \"CHEBI:15940\"\n  \"CHEBI:38927\"\n  \"CHEBI:31561\"\n  \"CHEBI:6958\"\n  \"CHEBI:90939\"\n  \"CHEBI:32061\"\n  \"CHEBI:6842\"\n  \"CHEBI:6413\"\n  \"CHEMBL:CHEMBL7463\"\n  \"CHEBI:76607\"\n  \"CHEMBL.COMPOUND:CHEMBL2103884\"\n  \"CHEBI:35696\"\n  \"CHEMBL.COMPOUND:CHEMBL1709719\"\n  \"CHEBI:90948\"\n  \"CHEBI:4046\"\n  \"CHEBI:24814\"\n  \"CHEMBL.COMPOUND:CHEMBL587723\"\n  \"CHEBI:3084\"\n  \"CHEBI:34269\"\n  \"CHEBI:75253\"\n  \"CHEBI:61400\"\n  \"CHEBI:86345\"\n  \"CHEBI:34873\"\n  \"CHEBI:132268\"\n  \"GTPI:8145\"\n  \"CHEBI:43616\"\n  \"CHEBI:135590\"\n  \"CHEBI:15891\"\n  \"CHEMBL:CHEMBL1977579\"\n  \"CHEBI:50859\"\n  \"CHEBI:9635\"\n  \"CHEBI:101278\"\n  \"CHEBI:45652\"\n  \"CHEBI:3752\"\n  \"CHEBI:3175\"\n  \"CHEBI:44445\"\n  \"CHEBI:28680\"\n  \"CHEBI:39548\"\n  \"CHEMBL.COMPOUND:CHEMBL3545154\"\n  \"CHEBI:9908\"\n  \"CHEBI:92890\"\n  \"CHEBI:18145\"\n  \"CHEBI:134301\"\n  \"CHEMBL:CHEMBL499968\"\n  \"CHEBI:69581\"\n  \"CHEBI:39867\"\n  \"CHEBI:17997\"\n  \"CHEBI:17833\"\n  \"CHEBI:15843\"\n  \"CHEBI:45863\"\n  \"CHEBI:16118\"\n  \"CHEBI:61399\"\n  \"CHEBI:27638\"\n  \"CHEBI:28527\"\n  \"CHEBI:7565\"\n  \"CHEBI:61390\"\n  \"CHEBI:61057\"\n  \"CHEMBL:CHEMBL1201288\"\n  \"CHEBI:2814\"\n  \"CHEBI:91370\"\n  \"CHEBI:32020\"\n  \"CHEBI:8633\"\n  \"CHEMBL:CHEMBL378104\"\n  \"CHEBI:4460\"\n  \"CHEBI:67272\"\n  \"CHEBI:3440\"\n  \"CHEBI:17241\"\n  \"CHEBI:4042\"\n  \"CHEBI:23359\"))\n                                          \n(chemical->drug-filter strategy1_chemicals)\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/drug-ranker.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../../../medikanren/pieces-parts/query.rkt\"\n         racket/engine)\n;;not druggable \n#;(define all-hgncs\n  '(\"HGNC:894\"))\n\n;; HGNC:892, HGNC:1270 error in the constraint solver \n\n#;(define all-hgncs\n  (file->list \"/Users/michaelpatton/git/mediKanren/biolink/data/all-hgnc-curies.scm\"))\n\n#;(define ARDS-gene-ls\n  (map (lambda (x) (string-append \"HGNC:\" x))\n       (map number->string\n            '(4818\n              7516\n              8583\n              320\n              1936\n              2766\n              3655\n              5992\n              6000\n              6014\n              6018\n              5962\n              5973\n              5981\n              5986\n              16830\n              17020\n              6709\n              6922\n              7097\n              7797\n              8947\n              10798\n              10799\n              10803\n              11362\n              17192\n              11847\n              11892\n              11908\n              12036\n              3542\n              4443\n              21581\n              9052\n              12726\n              2707\n              333\n              338\n              3374\n              3763\n              5273\n              6363\n              6848\n              6858\n              7590\n              30092\n              12680\n              1232\n              3999\n              5013\n              5014\n              7782\n              2874\n              11181\n              11920\n              186\n              13633\n              348\n              600\n              1550\n              2595\n              2884\n              3553\n              9237\n              9386\n              12554\n              12698\n              4603\n              6027\n              4035\n              4053\n              51\n              290\n              17731\n              4095\n              4595\n              5293))))\n\n\n#|\n(define anti-coag-list\n  '(\"RXNORM:11289\"\n    \"CUI:C0043031\" \n    \"RXNORM:1546356\"\n    \"CUI:C2348066\" \n    \"RXNORM:1114195\"\n    \"CUI:C1739768\" \n    \"RXNORM:1364430\"\n    \"CUI:C1831808\" \n    \"RXNORM:1599538\"\n    \"CUI:C2975435\" \n    \"RXNORM:280611\"\n    \"CUI:C0916062\" \n    \"RXNORM:152610\"\n    \"CUI:C0592532\" \n    \"RXNORM:67109\"\n    \"CUI:C0206461\"\n    \"RXNORM:67108\"\n    \"CUI:C0206460\" \n    \"RXNORM:67031\"\n    \"CUI:C0206232\" \n    \"RXNORM:69528\"\n    \"CUI:C0215717\" \n    \"RXNORM:75960\"\n    \"CUI:C0254215\" \n    \"RXNORM:69646\"\n    \"CUI:C0216278\" \n    \"RXNORM:5224\"\n    \"CUI:C0019134\"))\n|#\n#|\n;; EWSR1 genes\n(define EWSR1-gene-ls\n  (map (lambda (x) (string-append \"HGNC:\" x))\n       (map number->string\n            '(38\n              14899\n              943\n              320\n              19990\n              489\n              490\n              2013\n              638\n              14103\n              15607\n              14872\n              974\n              24176\n              14343\n              1325\n              1389\n              1537\n              26295\n              1705\n              20455\n              2174\n              2191\n              22990\n              2333\n              24292\n              2498\n              2530\n              20348\n              2907\n              2908\n              2926\n              3010\n              3016\n              32188\n              19087\n              3154\n              27234\n              27683\n              30114\n              34236\n              3603\n              13590\n\n              3761\n              3800\n              3801\n              3817\n              25491\n              4092\n              4122\n              4131\n              4882\n              5141\n              17087\n              5466\n              25251\n              23236\n              48664\n              6617\n              6664\n              16895\n              17200\n              14575\n              17082\n              7159\n              7171\n              7514\n              7614\n              29832\n              13395\n              7746\n              7775\n              16191\n              19321\n              27106\n              7909\n              41983\n              7952\n              8126\n              8134\n              19316\n              8604\n              17270\n              16068\n              14180\n              27559\n              8890\n              8906\n              30065\n              19255\n              29037\n              14683\n\n              26303\n              20331\n              688\n              20457\n              13441\n              13655\n              24188\n              32455\n              18386\n              18387\n              10798\n              10799\n              10801\n              10802\n              10803\n              16192\n              11046\n              11049\n              11073\n              16698\n              15592\n              18065\n              15885\n              11568\n              11581\n              11595\n              20329\n              27916\n              11950\n              30887\n              20670\n              29315\n              15466\n              12769\n              19221\n              16804\n              13083))))\n\n|#\n\n\n\n\n#|proviral gene list for 2-hop|#\n;;\"HGNC:11876\" TMPRSS2\n;;\"HGNC:8568\" FURIN\n\n;; ANO1 for haley\n;; 21625 ano1\n;; 2244 = 24 genes\n#|\n(define pro-viral-gene-list\n  '())\n|#\n#|\n\"HGNC:15631\"\n    \"HGNC:15632\"\n    \"HGNC:11876\"\n    \"HGNC:8568\"\n    \"HGNC:13557\"\n    \"HGNC:3009\"\n|#\n\n\n#|\n;; alzheimer's genes                    ; ;\n(define pro-viral-gene-list             ; ;\n  (map symbol->string                   ; ;\n       '(HGNC:1052\n         HGNC:2095\n         HGNC:613\n         HGNC:37                        ; ;\n         HGNC:2334                      ; ;\n         HGNC:15514                     ; ;\n         HGNC:13375                     ; ;\n         HGNC:1659                      ; ;\n         HGNC:14284                     ; ;\n         HGNC:14258                     ; ;\n         HGNC:620                       ; ;\n         HGNC:6893                      ; ;\n         HGNC:9508                      ; ;\n         HGNC:9509                      ; ;\n         HGNC:17761)))                           ; ;\n|#\n\n\n#|\n(define pro-viral-gene-list             ; ;\n'(\"HGNC:11876\"                          ; ;\n\"HGNC:8568\"                             ; ;\n\"HGNC:7850\"                             ; ;\n\"HGNC:11320\"                            ; ;\n\"HGNC:8883\"                             ; ;\n\"HGNC:1776\"                             ; ;\n\"HGNC:2232\"                             ; ;\n\"HGNC:2537\"                             ; ;\n))                                      ; ;\n|#\n;; just TMPRSS2\n#;(define pro-viral-gene-list\n  '(\"HGNC:11876\"))\n#|\n(define pro-viral-gene-list\n  '(\"CHEBI:6887\"))\n|#\n\n#|\n#|\n;pro-viral kinases\nNME2\nABI1\nPFTK1\nCDK5R2\nCOPB2\nCTSL\n|#\n\n(define pro-viral-gene-list\n'(\"HGNC:7850\"\n\"HGNC:11320\"\n\"HGNC:8883\"\n\"HGNC:1776\"\n\"HGNC:2232\"\n\"HGNC:2537\"))\n|#\n\n#|\n;;anti-viral kinases\nCLK1\nMAP2K6\nCSNK1G1\nEPHA3\nCDK6\nAURKB\nGCK\nDGKD\n|#\n#|\n;; short 2hop \"HGNC:8122\"\n(define pro-viral-gene-list\n  '(\"HGNC:24591\"))\n|#\n#;(define pro-viral-gene-list\n  '(\"HGNC:24591\"\n    \"HGNC:19356\"\n    \"HGNC:10941\"\n    \"HGNC:51\"\n    \"HGNC:28756\"\n    \"HGNC:76\"\n    \"HGNC:2707\"\n    \"HGNC:13557\"\n    \"HGNC:7976\"\n    \"HGNC:338\"\n    \"HGNC:790\"\n    \"HGNC:868\"\n    \"HGNC:864\"\n    \"HGNC:13919\"\n    \"HGNC:990\"\n    \"HGNC:991\"\n    \"HGNC:992\"\n    \"HGNC:995\"\n    \"HGNC:1103\"\n    \"HGNC:1125\"\n    \"HGNC:25142\"\n    \"HGNC:1471\"\n    \"HGNC:1527\"\n    \"HGNC:1641\"\n    \"HGNC:1859\"\n    \"HGNC:24537\"\n    \"HGNC:2228\"\n    \"HGNC:2230\"\n    \"HGNC:2231\"\n    \"HGNC:2232\"\n    \"HGNC:2234\"\n    \"HGNC:2237\"\n    \"HGNC:2243\"\n    \"HGNC:9605\"\n    \"HGNC:7421\"\n    \"HGNC:52028\"\n    \"HGNC:2459\"\n    \"HGNC:2460\"\n    \"HGNC:2552\"\n    \"HGNC:2712\"\n    \"HGNC:28777\"\n    \"HGNC:2716\"\n    \"HGNC:2746\"\n    \"HGNC:2976\"\n    \"HGNC:3189\"\n    \"HGNC:3277\"\n    \"HGNC:3275\"\n    \"HGNC:3272\"\n    \"HGNC:3293\"\n    \"HGNC:3723\"\n    \"HGNC:18169\"\n    \"HGNC:3538\"\n    \"HGNC:23397\"\n    \"HGNC:3711\"\n    \"HGNC:33276\"\n    \"HGNC:8568\"\n    \"HGNC:14375\"\n    \"HGNC:4181\"\n    \"HGNC:19687\"\n    \"HGNC:4296\"\n    \"HGNC:4616\"\n    \"HGNC:14453\"\n    \"HGNC:4853\"\n    \"HGNC:4897\"\n    \"HGNC:5031\"\n    \"HGNC:24921\"\n    \"HGNC:5960\"\n    \"HGNC:6053\"\n    \"HGNC:6118\"\n    \"HGNC:6204\"\n    \"HGNC:6395\"\n    \"HGNC:29531\"\n    \"HGNC:25726\"\n    \"HGNC:6664\"\n    \"HGNC:29620\"\n    \"HGNC:3332\"\n    \"HGNC:6897\"\n    \"HGNC:6943\"\n    \"HGNC:18873\"\n    \"HGNC:7113\"\n    \"HGNC:7114\"\n    \"HGNC:3942\"\n    \"HGNC:7460\"\n    \"HGNC:7684\"\n    \"HGNC:18591\"\n    \"HGNC:25242\"\n    \"HGNC:7910\"\n    \"HGNC:16885\"\n    \"HGNC:8068\"\n    \"HGNC:3255\"\n    \"HGNC:8869\"\n    \"HGNC:8912\"\n    \"HGNC:9437\"\n    \"HGNC:9281\"\n    \"HGNC:14650\"\n    \"HGNC:9380\"\n    \"HGNC:9531\"\n    \"HGNC:17822\"\n    \"HGNC:9828\"\n    \"HGNC:3402\"\n    \"HGNC:10019\"\n    \"HGNC:10312\"\n    \"HGNC:10480\"\n    \"HGNC:18276\"\n    \"HGNC:1228\"\n    \"HGNC:10803\"\n    \"HGNC:8157\"\n    \"HGNC:10905\"\n    \"HGNC:13621\"\n    \"HGNC:30669\"\n    \"HGNC:30615\"\n    \"HGNC:11364\"\n    \"HGNC:11728\"\n    \"HGNC:11766\"\n    \"HGNC:11849\"\n    \"HGNC:16627\"\n    \"HGNC:2236\"\n    \"HGNC:6021\"\n    \"HGNC:11850\"\n    \"HGNC:11876\"\n    \"HGNC:12019\"\n    \"HGNC:12458\"\n    \"HGNC:12666\"\n    \"HGNC:23663\"\n    \"HGNC:12825\"\n    \"HGNC:11320\"\n    \"HGNC:171\"\n    \"HGNC:172\"\n    \"HGNC:19041\"\n    \"HGNC:375\"\n    \"HGNC:376\"\n    \"HGNC:52650\"\n    \"HGNC:1078\"\n    \"HGNC:33814\"\n    \"HGNC:1459\"\n    \"HGNC:1674\"\n    \"HGNC:1776\"\n    \"HGNC:15483\"\n    \"HGNC:1994\"\n    \"HGNC:19083\"\n    \"HGNC:2068\"\n    \"HGNC:2700\"\n    \"HGNC:2855\"\n    \"HGNC:3061\"\n    \"HGNC:3255\"\n    \"HGNC:24649\"\n    \"HGNC:3767\"\n    \"HGNC:4922\"\n    \"HGNC:18360\"\n    \"HGNC:6193\"\n    \"HGNC:6514\"\n    \"HGNC:6524\"\n    \"HGNC:6843\"\n    \"HGNC:6846\"\n    \"HGNC:19035\"\n    \"HGNC:7381\"\n    \"HGNC:7529\"\n    \"HGNC:7648\"\n    \"HGNC:9404\"\n    \"HGNC:9612\"\n    \"HGNC:9618\"\n    \"HGNC:9671\"\n    \"HGNC:11403\"\n    \"HGNC:11404\"\n    \"HGNC:11406\"\n    \"HGNC:11904\"\n    \"HGNC:9437\"))\n\n(define anti-viral-gene-list\n  '(\"HGNC:3009\"\n    \"HGNC:4617\"\n    \"HGNC:7114\"\n    \"HGNC:8984\"\n    \"HGNC:14650\"\n    \"HGNC:10819\"\n    \"HGNC:12458\"\n    \"HGNC:257\"\n    \"HGNC:289\"\n    \"HGNC:376\"\n    \"HGNC:14311\"\n    \"HGNC:11390\"\n    \"HGNC:913\"\n    \"HGNC:16902\"\n    \"HGNC:1057\"\n    \"HGNC:19341\"\n    \"HGNC:1492\"\n    \"HGNC:1678\"\n    \"HGNC:1777\"\n    \"HGNC:1782\"\n    \"HGNC:1786\"\n    \"HGNC:1791\"\n    \"HGNC:1991\"\n    \"HGNC:31736\"\n    \"HGNC:1995\"\n    \"HGNC:2071\"\n    \"HGNC:13659\"\n    \"HGNC:2363\"\n    \"HGNC:2454\"\n    \"HGNC:2455\"\n    \"HGNC:2457\"\n    \"HGNC:10637\"\n    \"HGNC:2674\"\n    \"HGNC:2676\"\n    \"HGNC:2704\"\n    \"HGNC:2849\"\n    \"HGNC:2850\"\n    \"HGNC:2851\"\n    \"HGNC:2857\"\n    \"HGNC:3070\"\n    \"HGNC:3071\"\n    \"HGNC:3091\"\n    \"HGNC:3386\"\n    \"HGNC:3387\"\n    \"HGNC:3388\"\n    \"HGNC:3389\"\n    \"HGNC:3431\"\n    \"HGNC:3655\"\n    \"HGNC:4036\"\n    \"HGNC:4119\"\n    \"HGNC:4195\"\n    \"HGNC:4291\"\n    \"HGNC:4545\"\n    \"HGNC:20565\"\n    \"HGNC:15566\"\n    \"HGNC:6171\"\n    \"HGNC:6307\"\n    \"HGNC:15719\"\n    \"HGNC:29798\"\n    \"HGNC:18608\"\n    \"HGNC:6840\"\n    \"HGNC:6847\"\n    \"HGNC:6849\"\n    \"HGNC:6850\"\n    \"HGNC:6871\"\n    \"HGNC:6886\"\n    \"HGNC:17574\"\n    \"HGNC:7110\"\n    \"HGNC:7111\"\n    \"HGNC:16243\"\n    \"HGNC:7601\"\n    \"HGNC:15576\"\n    \"HGNC:11399\"\n    \"HGNC:7850\"\n    \"HGNC:18981\"\n    \"HGNC:8883\"\n    \"HGNC:9529\"\n    \"HGNC:10251\"\n    \"HGNC:10812\"\n    \"HGNC:6773\"\n    \"HGNC:16852\"\n    \"HGNC:11394\"\n    \"HGNC:16835\"\n    \"HGNC:29259\"\n    \"HGNC:26160\"\n    \"HGNC:11847\"\n    \"HGNC:17995\"\n    \"HGNC:16473\"\n    \"HGNC:17797\"\n    \"HGNC:487\"\n    \"HGNC:2852\"))\n\n\n\n#|HELPER FUNCTIONS|#\n(define inner-loop/csv\n  (lambda (ls port)\n    (cond\n      ((null? ls) (void))\n      (else\n       (fprintf port \"~a~c\" (car ls) #\\,)\n       (inner-loop/csv (cdr ls) port)))))\n\n(define outer-loop/csv\n  (lambda (ls port)\n    (cond\n      ((null? ls)\n       (close-output-port port))\n      (else\n       (inner-loop/csv (car ls) port)\n       (fprintf port (format \"~c\" #\\newline))\n       (outer-loop/csv (cdr ls) port)))))\n\n(define export-column-headers/csv\n  (lambda (headers port path)\n    (cond \n      ((= (file-size path) 0)\n       (cond\n         ((null? headers)\n          (fprintf port \"~c\" #\\newline))\n         (else\n          (fprintf port \"~a~c\" (car headers) #\\,)\n          (export-column-headers/csv (cdr headers) port path))))\n      (else\n       (void)))))\n\n\n(define export-column-headers\n  (lambda (headers port path)\n    (cond \n      ((= (file-size path) 0)\n       (cond\n         ((null? headers)\n          (fprintf port \"~c\" #\\newline))\n         (else\n          (fprintf port \"~a~c\" (car headers) #\\tab)\n          (export-column-headers (cdr headers) port path))))\n      (else\n       (void)))))\n\n(define outer-loop\n  (lambda (ls port)\n    (cond\n      ((null? ls)\n       (close-output-port port))\n      (else\n       (inner-loop (car ls) port)\n       (fprintf port (format \"~c\" #\\newline))\n       (outer-loop (cdr ls) port)))))\n\n(define inner-loop\n  (lambda (ls port)\n    (cond\n      ((null? ls) (void))\n      (else\n       (fprintf port \"~a~c\" (car ls) #\\tab)\n       (inner-loop (cdr ls) port)))))\n\n\n\n(define atom?\n  (lambda (x)\n    (and (not (pair? x))\n         (not (list? x)))))\n\n(define member?\n  (lambda (x ls)\n    (cond\n      ((null? ls) #f)\n      (else \n       (or (equal? x (car ls))\n           (member? x (cdr ls)))))))\n\n(define union\n  (lambda (ls1 ls2)\n    (cond\n      ((null? ls1) ls2)\n      ((member? (car ls1) ls2)\n       (union (cdr ls1) ls2))\n      (else\n       (cons (car ls1)\n             (union (cdr ls1) ls2))))))\n\n(define intersect?\n  (lambda (ls1 ls2)\n    (cond\n      ((null? ls1) #f)\n      ((member? (car ls1) ls2) #t)\n      (else\n       (intersect? (cdr ls1) ls2)))))\n\n(define intersect\n  (lambda (ls1 ls2)\n    (cond\n      ((null? ls1) '())\n      ((member? (car ls1) ls2)\n       (cons (car ls1)\n             (intersect (cdr ls1) ls2)))\n      (else\n       (intersect (cdr ls1) ls2)))))\n\n#|ASSOCIATION-LIST KEYS/STRING LISTS FOR KNOWLEDGE GRAPH CONCEPTS|#\n(define robokop-concept-key/eq-id \"equivalent_identifiers\")\n(define robokop-xref-key \"equivalent_identifiers\")\n(define orange-concept-key/synonym \"synonym\")\n(define orange-concept-key/same-as \"same_as\")\n(define semmed-concept-key/xrefs \"xrefs\")\n(define semmed-concept-key/id \"id\")\n(define publication-key \"publications\")\n(define publication-key/pmids \"pmids\")\n(define drug-bank/key \"drugbank.groups\") \n(define drug-bank/withdrawn/key \"withdrawn_flag\")\n(define drug-bank/approved/key \"drugbank.approved\")\n(define drug-bank/therapeutic/key \"therapeutic_flag\")\n(define drug-bank/investigational/key \"drugbank.investigational\")\n(define umls-type-label/key \"umls_type_label\")\n(define umls-type/key \"umls_type\")\n(define PUBMED_URL_PREFIX \"https://www.ncbi.nlm.nih.gov/pubmed/\")\n\n(define decreases-pred-str/ls\n  '(\"negatively_regulates\"\n    \"negatively_regulates__entity_to_entity\"\n    \"decreases_molecular_interaction\"\n    \"decreases_secretion_of\"\n    \"decreases_localization_of\"\n    \"decreases_stability_of\"\n    \"decreases_synthesis_of\"\n    \"decreases_transport_of\"\n    \"decreases_uptake_of\"    \n    \"prevents\"\n    \"treats\"\n    \"disrupts\"\n    \"inhibits\"\n    \"inhibitor\"\n    \"binder\"\n    \"antagonist\"\n    \"blocker\"\n    \"increases_degradation_of\"\n    \"decreases_activity_of\"\n    \"decreases_expression_of\"))\n\n(define increases-pred-str/ls\n  '(\"positively_regulates\"\n     \"produces\"\n     \"agonist\"\n     \"causes\"\n     \"causes_condition\"\n     \"causally_related_to\"\n     \"contributes_to\"\n     \"gene_associated_with_condition\"\n     \"positively_regulates__entity_to_entity\"\n     \"gene_mutations_contribute_to\"\n     \"decreases_degradation_of\"\n     \"increases_activity_of\"\n     \"increases_expression_of\"\n     \"increases_molecular_interaction\"\n     \"increases_response_to\"\n     \"increases_secretion_of\"\n     \"increases_stability_of\"\n     \"increases_synthesis_of\"\n     \"increases_transport_of\"\n     \"increases_uptake_of\"\n     \"increases_localization_of\"\n     \"stimulates\"\n     \"activator\"))\n\n(define predicate-str/ls\n  '(\"physically_interacts_with\"\n    \"regulates\"\n    \"interacts_with\"\n    \"targets\"\n    \"modulator\"\n    \"directly_interacts_with\"\n    \"regulates_expression_of\"\n    \"affects_expression_of\"\n    \"affects\"\n    \"affects_activity_of\"\n    \"uses\"))\n\n(define allowable-predicates\n  '(\"negatively_regulates\"\n    \"negatively_regulates__entity_to_entity\"\n    \"decreases_molecular_interaction\"\n    \"decreases_secretion_of\"\n    \"decreases_localization_of\"\n    \"decreases_stability_of\"\n    \"decreases_synthesis_of\"\n    \"decreases_transport_of\"\n    \"decreases_uptake_of\"    \n    \"prevents\"\n    \"treats\"\n    \"disrupts\"\n    \"inhibits\"\n    \"inhibitor\"\n    \"binder\"\n    \"antagonist\"\n    \"blocker\"\n    \"increases_degradation_of\"\n    \"decreases_activity_of\"\n    \"decreases_expression_of\"\n    \"positively_regulates\"\n    \"produces\"\n    \"agonist\"\n    \"causes\"\n    \"causes_condition\"\n    \"causally_related_to\"\n    \"contributes_to\"\n    \"gene_associated_with_condition\"\n    \"positively_regulates__entity_to_entity\"\n    \"gene_mutations_contribute_to\"\n    \"decreases_degradation_of\"\n    \"increases_activity_of\"\n    \"increases_expression_of\"\n    \"increases_molecular_interaction\"\n    \"increases_response_to\"\n    \"increases_secretion_of\"\n    \"increases_stability_of\"\n    \"increases_synthesis_of\"\n    \"increases_transport_of\"\n    \"increases_uptake_of\"\n    \"increases_localization_of\"\n    \"stimulates\"\n    \"activator\"\n    \"physically_interacts_with\"\n    \"regulates\"\n    \"interacts_with\"\n    \"targets\"\n    \"modulator\"\n    \"directly_interacts_with\"\n    \"regulates_expression_of\"\n    \"affects_expression_of\"\n    \"affects\"\n    \"affects_activity_of\"\n    \"uses\"))\n\n(define substitute\n  (lambda (ls old new)\n    (cond \n      ((null? ls) '())\n      ((void? (car ls))\n       (substitute (cdr ls) old new))\n      ((boolean? (car ls))\n       (cons\n         (format \"~a\" (car ls))\n         (substitute (cdr ls) old new))) \n      ((equal? (car ls) old)\n       (cons new\n             (substitute (cdr ls) old new)))\n      (else\n       (cons (car ls)\n             (substitute (cdr ls) old new))))))\n\n(define str-converter\n  (lambda (ls)\n    (cond\n      ((null? ls)\n       (substitute ls '() \"NA\"))\n      ((or (boolean? (car ls))\n           (void? (car ls)))\n       (str-converter (cdr ls)))\n      (else \n       (if (symbol? (car ls))\n           (string-join (map symbol->string ls) \" \")\n           (string-join ls \" \"))))))\n\n(define append-predicate-symbol\n  (lambda (pred-str inc-pred dec-pred els)\n    (cond\n      ((null? pred-str) (car els))\n      ((or (boolean? (car pred-str))\n           (void? (car pred-str)))\n       (append-predicate-symbol\n        (cdr pred-str) inc-pred dec-pred els))\n      ((member? (car pred-str) inc-pred)\n       (append-predicate-symbol\n        (cdr pred-str)\n        inc-pred\n        dec-pred\n        (cons\n         \"1\" els)))\n      ((member? (car pred-str) dec-pred)\n        (append-predicate-symbol\n         (cdr pred-str)\n         inc-pred\n         dec-pred\n         (cons\n          \"-1\" els)))\n      ((not (member? (car pred-str) dec-pred))\n       (append-predicate-symbol\n        (cdr pred-str)\n         inc-pred\n         dec-pred\n         (cons\n          \"0\" els)))\n      (else\n       (error (format \"PREDICATE NOT A MEMBER OF GLOBAL VARIABLE:\\n ~a\" (car pred-str)))))))\n\n\n;;og\n#;(define filter/curie\n  (lambda (ls els curie)\n    (cond\n      ((null? ls) (set-union els))\n      ((string-prefix? (car ls) curie)\n       (filter/curie\n        (cdr ls)\n        (cons (car ls) els) curie))\n      (else\n       (filter/curie (cdr ls) els curie)))))\n;; test\n;; add clause \n(define filter/curie\n  (lambda (ls els curie)\n    (cond      \n      ((null? ls) els)\n      ((string-prefix? (car ls) curie)\n       (filter/curie\n        (cdr ls)\n        (cons (car ls) els) curie))\n      (else\n       (filter/curie (cdr ls) els curie)))))\n\n#|\n(define get-gene-synonyms-from-edge-subject-id\n  (lambda (subject-id/str)\n    (if (string-contains? subject-id/str \":\")\n        (set->list (curie-synonyms subject-id/str))\n        '())))\n|#\n(define remove-item\n  (lambda (x ls els)\n    (cond\n      ((null? ls) (reverse els))\n      ((or (boolean? (car ls))\n           (void? (car ls)))\n       (remove-item\n        x (cdr ls) els))\n      ((equal? x (car ls))\n       (remove-item x (cdr ls) els))\n      (else\n       (remove-item x (cdr ls)\n                    (cons (car ls) els))))))\n\n#|Gregs code for drug-info |#\n\n(define curie-to-anything\n  (lambda (curie predicate*)\n    ;;(printf \"starting curie-to-anything with curie ~s and preds ~s\\n\" curie predicate*)\n    (let ((val (query/graph\n                ( ;; concepts\n                 (X curie)\n                 (T #f))\n                ;; edges\n                ((X->T predicate*))\n                ;; paths      \n                (X X->T T))))\n      ;;(printf \"finished curie-to-anything with curie ~s and preds ~s\\n\" curie predicate*)\n      val)))\n\n(define curie-to-tradenames\n  (lambda (curie)\n    (curie-to-anything curie '(\"has_tradename\"))))\n\n(define curie-to-clinical-trials\n  (lambda (curie)\n    (curie-to-anything curie '(\"clinically_tested_terminated_phase_2\"\n                               \"clinically_tested_approved_unknown_phase\"\n                               \"clinically_tested_terminated_phase_2\"\n                               \"clinically_tested_terminated_phase_3\"\n                               \"clinically_tested_terminated_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2\"\n                               \"clinically_tested_suspended_phase_2\"\n                               \"clinically_tested_suspended_phase_3\"\n                               \"clinically_tested_suspended_phase_2_or_phase_3\"))))\n\n(define curie-to-indicated_for\n  (lambda (curie)\n    (curie-to-anything curie '(\"indicated_for\"))))\n\n(define curie-to-contraindicated_for\n  (lambda (curie)\n    (curie-to-anything curie '(\"contraindicated_for\"))))\n\n\n(define drug-info-for-curie\n  (lambda (curie)\n    ; (printf \"*** starting drug-info-for-curie ~s\\n\" curie)\n    (map\n     (lambda (l)\n       (match l\n         [`(,name . ,q)\n          ; (printf \"*** calculating curie-synonyms/names list for curie ~s\\n\" curie)\n          (let ((ls (map curie-synonyms/names (curies/query q 'T))))\n            ; (printf \"*** calculated curie-synonyms/names list for curie ~s\\n\" curie)\n            ; (printf \"*** ls length = ~s\\n\" (apply + (map length ls)))\n            (cons name ls))]))\n     (list \n      (cons 'tradenames (curie-to-tradenames curie))\n      (cons 'clinical-trials (curie-to-clinical-trials curie))\n      (cons 'indicated_for (curie-to-indicated_for curie))\n      (cons 'contraindicated_for (curie-to-contraindicated_for curie))))))\n\n\n\n\n\n;; og works\n#;(define get-canonical-curie-from-synonyms-ls\n  (lambda (ls)\n    (if (null? ls)\n        \"NA\"\n        (take ls 1))))\n\n;;testing\n(define get-canonical-curie-from-synonyms-ls\n  (lambda (x)\n    (cond\n      ((boolean? x)\n       \"NA\")\n      ((null? x) \"NA\")\n      (else\n       (car (take x 1))))))\n\n(define get-hgnc-symbol/take\n  (lambda (x)\n    (cond\n      ((or (equal? x '#f)\n           (boolean? x))\n       (take '(\"NA\") 1))\n      ((null? x)\n       (take '(\"NA\") 1))\n      (else\n       (car (string-split (car x) \" \"))))))\n\n(define get-fda-tag\n  (lambda (x)\n    (if (string-prefix? x \"RXNORM:\")\n        \"YES\"\n        \"NA\")))\n\n;; testing with edge match\n;;\n\n;; if an edge has subject/object that is a drug/gene\n;; we want to get a canonical identifier for that drug/gene\n;; drugs dont have a \"canonical 1-size-fits-all id\"\n;; but DRUGBANK:/RXNORM: is good for FDA approval\n;; and CHEBI is good for general molecules of biological interest\n\n(define gene-concept-in-synonyms-ls?\n  (lambda (synonyms-ls)\n    (cond      \n      ((null? synonyms-ls) #f)\n      (else\n       (or (string-prefix? (car synonyms-ls) \"HGNC:\")\n           (gene-concept-in-synonyms-ls? (cdr synonyms-ls)))))))\n\n(define drug-concept-in-synonyms-ls?\n  (lambda (synonyms-ls)\n    (cond      \n      ((null? synonyms-ls) #f)\n      (else\n       (or (string-prefix? (car synonyms-ls) \"CHEBI:\")\n           (drug-concept-in-synonyms-ls? (cdr synonyms-ls)))))))\n\n\n\n(define get-curie-synonyms-from-edge-subject/object-curie\n  (lambda (x)\n    (cond\n      ((string-contains? x \":\")\n       (let ((synonyms-ls (set->list (curie-synonyms x))))\n         (cond\n           ((gene-concept-in-synonyms-ls? synonyms-ls)\n            (get-canonical-curie-from-synonyms-ls\n             (filter/curie synonyms-ls '() \"HGNC:\")))\n           ((drug-concept-in-synonyms-ls? synonyms-ls) \n            (get-canonical-curie-from-synonyms-ls\n             (filter/curie synonyms-ls '() \"CHEBI:\")))\n           (else\n            \"NA\"))))\n      (else\n       \"NA\"))))\n\n(define extract-symbol-name-from-concept-or-edge\n  (lambda (query-ls els)\n    (cond\n      ((null? query-ls) (set-union els))\n      ((or (boolean? (car query-ls))\n           (void? (car query-ls)))\n       (extract-symbol-name-from-concept-or-edge\n        (cdr query-ls) els))\n      (else \n       (match (car query-ls)\n         [`(,db ,cui ,id ,name ,category ,properties-list)\n          (extract-symbol-name-from-concept-or-edge\n           (cdr query-ls)\n           (set-union\n            (list name) els))]\n         [`(,db ,edge-cui\n                (,subject-cui ,subject-id ,subject-name (,_ . ,subject-category) ,subject-props-assoc)\n                (,concept-cui ,concept-id ,concept-name (,_ . ,concept-category) ,concept-props-assoc)\n                (,_ . ,pred)\n                ,pred-props-assoc)\n          (extract-symbol-name-from-concept-or-edge (cdr query-ls)\n                                                    (set-union\n                                                     (list subject-name) els))])))))\n\n(define query-hgnc-curie-for-hgnc-symbol\n  (lambda (ls els)\n    (cond\n      ((null? ls)\n       (remove-duplicates (flatten els)))\n      ((or (boolean? (car ls))\n           (void? (car ls)))\n       (query-hgnc-curie-for-hgnc-symbol\n        (cdr ls) els))\n      ((string-contains? (car ls) \"HGNC:\")\n       (query-hgnc-curie-for-hgnc-symbol\n        (cdr ls)\n        (cons\n         (extract-symbol-name-from-concept-or-edge\n          (find-concepts #t (list (car ls))) '())\n         els)))\n      (else\n       (query-hgnc-curie-for-hgnc-symbol\n        (cdr ls) els)))))\n\n(define get-xrefs \n  (lambda (key properties-ls)\n    (cond \n      [(assoc key properties-ls)\n       => (lambda (assoc-ls)\n            (define x-refs (cdr assoc-ls))\n            (define in (open-input-string x-refs))\n            (cons (read in) '()))]\n      (else\n       '()))))\n\n(define get-rxnorm\n  (lambda (ls els)\n    (cond\n      ((null? ls) (set-union els))\n      ((or (boolean? (car ls))\n           (void? (car ls)))\n       (get-rxnorm (cdr ls)\n                   (cons \"NA\" els)))\n      ((atom? (car ls))\n       (cond\n         ((regexp-match #rx\"[Rr][Xx][Nn][Oo][Rr][Mm]:\" (car ls))\n          (get-rxnorm (cdr ls)\n                      (set-union\n                       (cons (car ls) els))))\n         (else\n          (get-rxnorm (cdr ls) els))))\n      (else\n       (set-union (get-rxnorm (car ls) els)\n                  (get-rxnorm (cdr ls) els))))))\n\n(define get-assoc-value\n  (lambda (key assoc-ls)\n    (cond\n      ((assoc key assoc-ls)\n       => (lambda (assoc-ls)\n            (let ((assoc-key (car assoc-ls))\n                  (assoc-value (cdr assoc-ls)))\n              (if (equal? assoc-key key)\n                  assoc-value\n                  \"NA\"))))\n      (else\n       '()))))\n\n\n(define match-edge/with-S/O-gene-linker-ids\n  (lambda (edges-ls els)\n    (cond\n      ((null? edges-ls) els)\n      (else \n       (match (car edges-ls)                       \n         [`(,db ,edge-cui\n                (,subject-cui ,subject-id ,subject-name (,_ . ,subject-category) ,subject-props-assoc)\n                (,object-cui ,object-id ,object-name (,_ . ,object-category) ,object-props-assoc)\n                (,_ . ,pred) ,pred-props-assoc)\n          (match-edge/with-S/O-gene-linker-ids           \n           (cdr edges-ls)\n           (cons\n            (substitute\n             (list\n              edge-cui ;; 0 edge-id\n              db                        ;; 1 kg id\n              (get-canonical-curie-from-synonyms-ls\n               (query-hgnc-curie-for-hgnc-symbol\n                (list (get-curie-synonyms-from-edge-subject/object-curie subject-id)) '())) ;; 2 linker_curie_nameS\n              (get-curie-synonyms-from-edge-subject/object-curie subject-id) ;; 3 linker_curie_idS\n              (append-predicate-symbol (list pred) increases-pred-str/ls decreases-pred-str/ls '()) ;; 4 symbol_pred\n              (get-fda-tag\n               (get-canonical-curie-from-synonyms-ls\n               (flatten                 \n                (get-rxnorm\n                 (substitute\n                  (flatten\n                   (list (get-xrefs semmed-concept-key/xrefs subject-props-assoc)\n                         (get-xrefs robokop-concept-key/eq-id subject-props-assoc)\n                         (set->list (curie-synonyms subject-id)))                   \n                   ) \"#f\" \"NA\") '()))))              \n              (get-canonical-curie-from-synonyms-ls\n               (query-hgnc-curie-for-hgnc-symbol\n                (list (get-curie-synonyms-from-edge-subject/object-curie object-id)) '())) ;;5 linker_curie_nameO\n              (get-curie-synonyms-from-edge-subject/object-curie object-id) ;; 6 linker_curie_nameO              \n              subject-name\n              subject-id\n              subject-category\n              pred               \n              object-name\n              object-id\n              object-category\n              (get-canonical-curie-from-synonyms-ls\n               (flatten                 \n                (get-rxnorm\n                 (substitute\n                  (flatten\n                   (list (get-xrefs semmed-concept-key/xrefs subject-props-assoc)\n                         (get-xrefs robokop-concept-key/eq-id subject-props-assoc)\n                         (set->list (curie-synonyms subject-id)))                   \n                   ) \"#f\" \"NA\") '())))\n              (length (pubmed-ids-from-edge-props pred-props-assoc))              \n              (string-join\n               (map (lambda (pubmed)\n                      (string-append PUBMED_URL_PREFIX (~a pubmed)))\n                    (pubmed-ids-from-edge-props pred-props-assoc)) \" \")                           \n              ) '() \"NA\")\n            els))])))))\n\n\n#|\n\n(str-converter\n                 (flatten\n                  (list \n                   (get-xrefs drug-bank/key drug-props-assoc))))\n|#\n#|\n;;og\n(define match-edge/with-S/O-gene-linker-ids\n  (lambda (edges-ls els)\n    (cond\n      ((null? edges-ls) els)\n      (else \n       (match (car edges-ls)                       \n         [`(,db ,edge-cui\n                (,subject-cui ,subject-id ,subject-name (,_ . ,subject-category) ,subject-props-assoc)\n                (,object-cui ,object-id ,object-name (,_ . ,object-category) ,object-props-assoc)\n                (,_ . ,pred) ,pred-props-assoc)\n          (match-edge/with-S/O-gene-linker-ids           \n           (cdr edges-ls)\n           (cons\n            (substitute\n             (list              \n              db\nsubject-name\n              subject-id\n              (get-curie-synonyms-from-edge-subject/object-curie subject-id) ;;3rd\n              subject-category\n              pred\n              (append-predicate-symbol (list pred) increases-pred-str/ls decreases-pred-str/ls '())\n              object-name\n              object-id\n              (get-curie-synonyms-from-edge-subject/object-curie object-id) ;;9th\n              object-category\n              (length (pubmed-ids-from-edge-props pred-props-assoc))\n              (string-join\n               (map (lambda (pubmed)\n                      (string-append PUBMED_URL_PREFIX (~a pubmed)))\n                    (pubmed-ids-from-edge-props pred-props-assoc)) \" \")\n              ) '() \"NA\")\n            els))])))))\n\n|#\n#|\n|#\n\n\n#|\n#;(get-canonical-curie-from-synonyms-ls\n(filter/curie (set->list (curie-synonyms subject-id)) '() \"HGNC:\")) ;; subject 3rd\n;;  (get-canonical-curie-from-synonyms-ls\n(filter/curie (set->list (curie-synonyms object-id)) '() \"HGNC:\")) ;; object 9th\n|#\n\n\n\n(define 1-hop-gene-lookup\n  (lambda (target-gene-ls els)\n    (define 1-hop/query\n      (lambda (target-gene)\n        (printf \"\\nQUERY/GRAPH RUNNING ON:   ~a\\n\" target-gene)\n        (cond\n          ((null? target-gene)\n           (cons \"NO_QUERY_CONCEPT\" els))\n          (else\n           (time (query/graph\n               ((X #f)\n                (TG target-gene))\n               ((X->TG #f))\n               (X X->TG TG)))))))\n    (cond\n      ((null? target-gene-ls) els)\n      (else\n       (1-hop-gene-lookup\n        (cdr target-gene-ls)\n        (cons\n         (edges/query (1-hop/query (car target-gene-ls)) 'X->TG)\n         els))))))\n\n(define 1-hop-gene-lookup/allowable-predicates\n  (lambda (target-gene-ls els predicates)\n    (define 1-hop/query\n      (lambda (target-gene)\n        (printf \"\\nQUERY/GRAPH RUNNING ON:   ~a\\n\" target-gene)\n        (time (query/graph\n               ((X #f)\n                (TG target-gene))\n               ((X->TG predicates))\n               (X X->TG TG)))))\n    (cond\n      ((null? target-gene-ls) els)\n      (else\n       (1-hop-gene-lookup/allowable-predicates\n        (cdr target-gene-ls)\n        (cons\n         (edges/query (1-hop/query (car target-gene-ls)) 'X->TG)\n         els)\n        predicates)))))\n\n(define 1-hop-drug-lookup/allowable-predicates/drug-->X\n  (lambda (target-curie-ls els predicates)\n    (define 1-hop/query\n      (lambda (target-concept)\n        (printf \"\\nQUERY/GRAPH RUNNING ON:   ~a\\n\" target-concept)\n        (time (query/graph\n               ((X #f)\n                (TC target-concept))\n               ((TC-->X predicates))\n               (TC TC-->X X)))))\n    (cond\n      ((null? target-curie-ls) els)\n      (else\n       (1-hop-drug-lookup/allowable-predicates/drug-->X\n        (cdr target-curie-ls)\n        (cons\n         (edges/query (1-hop/query (car target-curie-ls)) 'TC-->X)\n         els\n         )\n        predicates)))))\n\n#|\n;;; here \n(define 1hop-gene-lookup/1-HOP-AFFECTOR-GENE--ALLp-->ALL-GENES\n  (lambda (1hop-gene-ls els)\n    (define 1-hop/query\n      (lambda (1hop-gene)\n        (printf \"\\nQUERY/GRAPH RUNNING ON:   ~a\\n\" target-gene)\n        (time (query/graph\n               ((X #f)\n                (1H-GENE 1hop-gene))\n               ((X->TG #f))\n               (X X->TG TG)))))\n    (cond\n      ((null? target-gene-ls) els)\n      (else\n       (1-hop-gene-lookup\n        (cdr target-gene-ls)\n        (cons\n         (edges/query (1-hop/query (car target-gene-ls)) 'X->TG)\n         els))))))\n|#\n(define 2-hop-gene-lookup\n  (lambda (target-gene-ls els)\n    (define 1-hop/query\n      (lambda (target-gene)\n        (printf \"\\nQUERY/GRAPH RUNNING ON:   ~a\\n\" target-gene)\n        (time (query/graph\n               ((X #f)\n                (TG target-gene))\n               ((X->TG #f))\n               (X X->TG TG)))))\n    (let* ((1-hop-affector-genes/HGNC*\n            (synonyms/query (1-hop/query (car target-gene-ls)) 'X))\n           (1-hop-affector-genes/HGNC*\n            (flatten\n             (remove-item\n              '()\n              (map\n               (lambda (ls) (filter/curie ls '() \"HGNC:\"))\n               (map\n                set->list\n                1-hop-affector-genes/HGNC*))\n              '()))))\n      (printf \"\\n\\n~a 1-HOP AFFECTOR GENE CONCEPTS FOUND!\\n\" (length 1-hop-affector-genes/HGNC*))\n      (printf \"\\n\\n~a 1-HOP AFFECTOR GENES HGNC-IDs FOUND!\\n\\n~a\" (length 1-hop-affector-genes/HGNC*) 1-hop-affector-genes/HGNC*)\n      (cond\n        ((null? target-gene-ls) els)\n        (else\n         (displayln (format \"\\n\\nPREPARING 1-HOP AFFECTOR GENES FOR 2-HOP QUERY!\\n\\n\"))\n         (let ((2-hop-affector-gene/edges (let loop ((1-hop-affector-genes/HGNC* 1-hop-affector-genes/HGNC*))\n                                            (cond\n                                              ((null? 1-hop-affector-genes/HGNC*) '())\n                                              (else\n                                               (cons\n                                                (edges/query (1-hop/query (car 1-hop-affector-genes/HGNC*)) 'X->TG)\n                                                (loop\n                                                  (cdr 1-hop-affector-genes/HGNC*))))))))\n           (append* 2-hop-affector-gene/edges els)))))))\n\n\n(define 2-hop-gene-lookup/allowable-predicates\n  (lambda (target-gene-ls els predicates)\n    (define 1-hop/query\n      (lambda (target-gene)\n        (printf \"\\nQUERY/GRAPH RUNNING ON:   ~a\\n\" target-gene)\n        (time (query/graph\n               ((X #f)\n                (TG target-gene))\n               ((X->TG predicates))\n               (X X->TG TG)))))\n    (let* ((1-hop-affector-genes/HGNC*\n            (synonyms/query (1-hop/query (car target-gene-ls)) 'X))\n           (1-hop-affector-genes/HGNC*\n            (flatten\n             (remove-item\n              '()\n              (map\n               (lambda (ls) (filter/curie ls '() \"HGNC:\"))\n               (map\n                set->list\n                1-hop-affector-genes/HGNC*))\n              '()))))\n      (printf \"\\n\\n~a 1-HOP AFFECTOR GENE CONCEPTS FOUND!\\n\" (length 1-hop-affector-genes/HGNC*))\n      (printf \"\\n\\n~a 1-HOP AFFECTOR GENES HGNC-IDs FOUND!\\n\\n~a\" (length 1-hop-affector-genes/HGNC*) 1-hop-affector-genes/HGNC*)\n      (cond\n        ((null? target-gene-ls) els)\n        (else\n         (displayln (format \"\\n\\nPREPARING 1-HOP AFFECTOR GENES FOR 2-HOP QUERY!\\n\\n\"))\n         (let ((2-hop-affector-gene/edges (let loop ((1-hop-affector-genes/HGNC* 1-hop-affector-genes/HGNC*))\n                                            (cond\n                                              ((null? 1-hop-affector-genes/HGNC*) '())\n                                              (else\n                                               (cons\n                                                (edges/query (1-hop/query (car 1-hop-affector-genes/HGNC*)) 'X->TG)\n                                                (loop\n                                                  (cdr 1-hop-affector-genes/HGNC*))))))))\n           (append* 2-hop-affector-gene/edges els)))))))\n\n\n\n#|\n(define gene-concept?\n  (lambda (x)\n    (or\n     (boolean? (car x))\n     (string-prefix? (car x) \"HGNC:\")\n     (string-prefix? (car x) \"ENSEMBL:\")\n     (string-prefix? (car x) \"UniProtKB:\")\n     (string-prefix? (car x) \"NCBIGene:\")\n     (string-prefix? (car x) \"NCBIGENE:\"))))\n|#\n\n(define gene-concept?\n  (lambda (x)\n    (or\n     (string-prefix? x \"HGNC:\")\n     (string-prefix? x \"ENSEMBL:\")\n     (string-prefix? x \"UniProtKB:\")\n     (string-prefix? x \"NCBIGene:\")\n     (string-prefix? x \"NCBIGENE:\"))))\n\n#|\n(define drug-concept?\n  (lambda (x)\n    (or (boolean? (car x))\n        (string-prefix? (car x) \"CHEBI:\")\n        (string-prefix? (car x) \"CHEMBL:\")\n        (string-prefix? (car x) \"CHEMBL.\")\n        (string-prefix? (car x) \"KEGG:\")\n        (string-prefix? (car x) \"KEGG.\")\n        (string-prefix? (car x) \"DRUGBANK:\")\n        (string-prefix? (car x) \"RXNORM:\"))))\n|#\n\n(define drug-concept?\n  (lambda (x)\n    (or (string-prefix? x \"CHEBI:\")\n        (string-prefix? x \"CHEMBL:\")\n        (string-prefix? x \"CHEMBL.\")\n        (string-prefix? x \"KEGG:\")\n        (string-prefix? x \"KEGG.\")\n        (string-prefix? x \"DRUGBANK:\")\n        (string-prefix? x \"RXNORM:\"))))\n\n(define lat?\n  (lambda (ls)\n    (cond\n      ((null? ls) #t)\n      ((atom? (car ls))\n       (lat? (cdr ls)))\n      (else\n       #f))))\n\n(define get-export-edges\n  (lambda (ls)\n    (cond\n      ((null? ls) '())\n      ((lat? (car ls))\n       (cons (car ls)\n             (get-export-edges (cdr ls))))\n      (else\n       (set-union (get-export-edges (car ls))\n                  (get-export-edges (cdr ls)))))))\n\n\n\n#|\n(define affector-gene-edge?\n  (lambda (ls)\n    (match (car ls)\n      [`(,db ,edge-cui\n             (,subject-cui ,subject-id ,subject-name (,_ . ,subject-category) ,subject-props-assoc)\n             (,object-cui ,object-id ,object-name (,_ . ,object-category) ,object-props-assoc)\n             (,_ . ,pred)\n             ,pred-props-assoc)\n       (cond\n         ((gene-concept? `(,subject-id))\n          (list (car ls)))\n         (else\n          #f))])))\n|#\n\n(define filter-edges-by-affector-type\n  (lambda (ls els-gene els-drug)\n    (cond\n      ((null? ls)\n       (cons els-gene els-drug))\n      (else\n       (match (car ls)\n      [`(,db ,edge-cui\n             (,subject-cui ,subject-id ,subject-name (,_ . ,subject-category) ,subject-props-assoc)\n             (,object-cui ,object-id ,object-name (,_ . ,object-category) ,object-props-assoc)\n             (,_ . ,pred)\n             ,pred-props-assoc)\n       (cond\n         ((ormap drug-concept? (set->list (curie-synonyms subject-id)))\n          (filter-edges-by-affector-type\n           (cdr ls)\n           els-gene\n           (cons (car ls) els-drug)))\n         ((ormap gene-concept? (set->list (curie-synonyms subject-id)))\n          (filter-edges-by-affector-type\n           (cdr ls)\n           (cons (car ls) els-gene)\n           els-drug))\n         (else\n          (filter-edges-by-affector-type\n           (cdr ls)\n           els-gene\n           els-drug)))])))))\n\n(define get-subject-HGNC-from-edge \n  (lambda (edge)\n    (car (filter/curie (set->list (curie-synonyms (list-ref edge 2))) '() \"HGNC:\"))))\n\n#|MAKE 2HOP PATH|#\n(define get-object-synonyms-from-edge\n  (lambda (edge)\n    (set->list (curie-synonyms (list-ref edge 7)))))\n;;testing \n(define find-1-hop/2-hop-link\n  (lambda (1-hop-edge 2-hop-edge-ls)\n    (cond\n      ((null? 2-hop-edge-ls) '())\n      (else\n       (let ((2-hop-edge (car 2-hop-edge-ls))\n             (1-hop-subject-HGNC (list-ref 1-hop-edge 3)))\n         (let ((2-hop-edge-object-synonyms (set->list (curie-synonyms (list-ref 2-hop-edge 7)))))                 \n           (cond\n             ((member? 1-hop-subject-HGNC 2-hop-edge-object-synonyms)\n              (cons\n               (list 2-hop-edge 1-hop-edge)\n               (find-1-hop/2-hop-link\n                1-hop-edge\n                (cdr 2-hop-edge-ls))))\n             (else\n              (find-1-hop/2-hop-link\n               1-hop-edge\n               (cdr 2-hop-edge-ls))))))))))\n\n;; export edges! (NOT BIOLINK EDGES)\n(define make-2hop-path\n  (lambda (1-hop-edge-ls 2-hop-edge-ls)\n    (cond\n      ((null? 1-hop-edge-ls) '())\n      (else\n       (cons\n        (find-1-hop/2-hop-link (car 1-hop-edge-ls) 2-hop-edge-ls)\n        (make-2hop-path (cdr 1-hop-edge-ls) 2-hop-edge-ls))))))\n\n;;function takes list of 2hop paths and makes 2hop edges for export\n;; arg here is a list of all paths for a particular gene synonym @ 1hop gene\n\n;; a 2-hop-path\n(define make-single-2hop-path-export\n  (lambda (path)\n    (cond\n      ((and (pair? path)\n            (lat? (car path))\n            (lat? (cadr path)))\n       (append (car path) (cadr path)))\n      (else\n       (error (format \"EXPORT ERROR WITH EDGE: ~a\\n\" path))))))\n\n(define column-headers/1hop\n  '(\"edge_id\"\n    \"db\"\n    \"subject_linker_name\"              \n    \"subject_linker_curie\"\n    \"predicate_symbol\"\n    \"fda_approved\"\n    \"target_object_linker_name\"\n    \"target_object_linker_curie\"\n    \"subject_name\"\n    \"subject_curie\" \n    \"subject_category\"\n    \"predicate\"              \n    \"target_object_name\"\n    \"target_object_curie\"\n    \"target_object_category\"\n    \"rxnorm_drug_id\"\n    \"pubmed_number\"\n    \"pub_urls\"                            \n    ))\n\n(define get-2hop-paths-for-single-1hop-affector-gene\n  (lambda (all-2hop-paths-for-single-affector-gene)\n    (cond\n      ((null? all-2hop-paths-for-single-affector-gene) '())\n      (else\n       (cons\n        (make-single-2hop-path-export (car all-2hop-paths-for-single-affector-gene))\n        (get-2hop-paths-for-single-1hop-affector-gene (cdr all-2hop-paths-for-single-affector-gene)))))))  \n\n(define make-2hop-path/export\n  (lambda (2hop-paths-ls)\n    (cond\n      ((null? 2hop-paths-ls) '())\n      (else\n       (cons\n        (get-2hop-paths-for-single-1hop-affector-gene (car 2hop-paths-ls))\n        (make-2hop-path/export (cdr 2hop-paths-ls)))))))\n\n\n(define start-function\n  (lambda (gene-ls gene-ls-name)\n    (cond\n      ((null? gene-ls) (void))\n      (else\n       (handle-2hop-query (car gene-ls) gene-ls-name)\n       (start-function (cdr gene-ls) gene-ls-name)))))\n\n(define export-date\n  (format \"~a_~a_~a\" \n          (number->string (date-month (seconds->date (current-seconds))))\n          (number->string (date-day (seconds->date (current-seconds))))\n          (number->string (date-year (seconds->date (current-seconds))))))\n\n(define export-path\n  \"/Users/michaelpatton/git/automated_medikanren_queries/covid19/proviral_genes/\")\n\n(define export-path/antiviral\n  \"/Users/michaelpatton/git/automated_medikanren_queries/covid19/antiviral_gene_2hop/\")\n\n(define directory-path \n  (format \"~a~a/\" export-path export-date))\n        \n(define make-export-directory/proviral\n  (if (directory-exists? directory-path)\n      (error (format \"CHECK FILE, IT MAY EXIST\"))\n      (make-directory directory-path)))\n\n(define handle-2hop-query\n  (time\n   (lambda (curie gene-ls-name)\n     (cond\n       ((null? curie) (void))\n       (else\n        (let* ()\n          \n          (define curie-synonyms/CURIE\n            (curie-synonyms/names curie))\n\n          (define get-gene-curie-symbol-for-export\n            (lambda (curie)\n              (filter string?\n                      (map (lambda (x)\n                             (if (or (string-prefix? (car x) \"HGNC:\")\n                                     (string-prefix? (car x) \"CHEBI:\"))\n                                 (cdr x)\n                                 #f))\n                           (curie-synonyms/names curie)))))\n          \n          (define curie-str/EXPORT\n            (car (get-gene-curie-symbol-for-export curie)))\n                    \n          (printf \"\\nBEGINNING 1-HOP LOOKUP ON CONCEPT: ~a aka ~a\\n\" curie curie-str/EXPORT)\n\n          (printf \"\\n~a aka ~a SYNONYMS GATHERED FROM ALL KNOWLEDGE-GRAPHS:\\n\\n~a\\n\\n\" curie curie-str/EXPORT curie-synonyms/CURIE)\n          \n          \n          #|          \n          (define 1-hop-affector/BIOLINK-edges\n            (1-hop-gene-lookup (list curie) '()))\n          |#\n\n          #|\n          ;;; DRUG-LOOKUP!\n          (define 1-hop-affector-drug/BIOLINK-edges\n            (1-hop-drug-lookup/allowable-predicates/drug-->X (list curie) '() allowable-predicates))\n\n          \n          \n          ;; #### DRUG LOOKUP FILES\n          (define drug--pred-->X/path\n            (format \"~a~a--ALLp-->X.tsv\" directory-path gene-ls-name))\n          (define drug--pred-->X/port\n            (open-output-file drug--pred-->X/path #:exists 'append))\n\n          (export-column-headers\n           column-headers/1hop\n           drug--pred-->X/port\n           drug--pred-->X/path)\n\n          (outer-loop\n           1-hop-affector-drug/EXPORT-edges           \n           drug--pred-->X/port)\n        \n          \n          ;; #### DRUG LOOKUP FILES\n\n          |#\n          \n          \n          ;;GENE-LOOKUP!\n          (printf \"\\n1-hop-affector/BIOLINK-edges\\n\")\n          (define 1-hop-affector/BIOLINK-edges\n            (1-hop-gene-lookup/allowable-predicates (list curie) '() allowable-predicates))\n\n          \n   \n                             \n          ;;trying predicate bumpers\n          (printf \"\\n1-hop-affector-drug+gene/BIOLINK-edges\\n\")\n          (define 1-hop-affector-drug+gene/BIOLINK-edges\n            (remove-item '() (map (lambda (ls) (filter-edges-by-affector-type ls '() '())) 1-hop-affector/BIOLINK-edges) '()))\n          \n          (printf \"\\n1-hop-affector-gene/BIOLINK-edges\\n\")\n          (define 1-hop-affector-gene/BIOLINK-edges\n            (remove-item '() (map car 1-hop-affector-drug+gene/BIOLINK-edges) '()))\n\n          \n          (printf \"\\n1-hop-affector-drug/BIOLINK-edges\\n\")\n          (define 1-hop-affector-drug/BIOLINK-edges\n            (remove-item '() (map cdr 1-hop-affector-drug+gene/BIOLINK-edges) '()))\n          \n          (printf \"\\n1-hop-affector-gene/EXPORT-edges\\n\")\n          (define 1-hop-affector-gene/EXPORT-edges\n            (get-export-edges\n             (remove-item\n              '()\n              (map (lambda (x) (match-edge/with-S/O-gene-linker-ids x '())) 1-hop-affector-gene/BIOLINK-edges)\n              '())))\n          \n          \n          \n          (printf \"\\n1-hop-affector-drug/EXPORT-edges\\n\")\n          (define 1-hop-affector-drug/EXPORT-edges\n            (get-export-edges\n             (remove-item\n              '()\n              (map (lambda (x) (match-edge/with-S/O-gene-linker-ids x '())) 1-hop-affector-drug/BIOLINK-edges)\n              '())\n             ))\n          \n          ;;(pretty-print (car 1-hop-affector-drug/EXPORT-edges))\n\n          (printf \"\\n1-HOP LOOKUP FOR ~a COMPLETE!\\n\" curie-str/EXPORT)\n  \n          (define 1-hop-affector-gene/path\n            (format \"~a1HOP-AFFECTOR-GENES--ALLp-->~a.tsv\" directory-path gene-ls-name))\n          (define 1-hop-affector-drug/path\n            (format \"~a1HOP-AFFECTOR-DRUGS--ALLp-->~a.tsv\" directory-path gene-ls-name))\n        \n          (define 1-hop-affector-gene/port\n            (open-output-file 1-hop-affector-gene/path #:exists 'append))\n          (define 1-hop-affector-drug/port\n            (open-output-file 1-hop-affector-drug/path #:exists 'append))\n                             \n          \n          (export-column-headers\n           column-headers/1hop\n           1-hop-affector-gene/port\n           1-hop-affector-gene/path)\n\n          (outer-loop\n           1-hop-affector-gene/EXPORT-edges\n           1-hop-affector-gene/port)\n        \n          (export-column-headers\n           column-headers/1hop\n           1-hop-affector-drug/port\n           1-hop-affector-drug/path)\n\n          (outer-loop\n           1-hop-affector-drug/EXPORT-edges\n           1-hop-affector-drug/port)\n          \n          (printf \"\\n1-HOP EXPORT COMPLETE:\\nAFFECTOR-GENES-->ALL-PREDICATES-->~a\\n\" curie-str/EXPORT) \n          (printf \"\\n1-HOP EXPORT COMPLETE:\\nAFFECTOR-DRUGS-->ALL-PREDICATES-->~a\\n\" curie-str/EXPORT)\n                   \n          #|START 2-HOP LOOKUP|#\n          (printf \"\\nBEGINNING 2-HOP LOOKUP ON CONCEPT: ~a aka ~a\\n\" curie curie-str/EXPORT)\n          \n          #|\n          (define 2-hop-affector/BIOLINK-edges\n            (time\n             (2-hop-gene-lookup (list curie) '())))\n          |#\n          #|\n          ;; trying predicate bumpers\n          (printf \"\\n2-hop-affector/BIOLINK-edges\\n\")\n          (define 2-hop-affector/BIOLINK-edges\n            (time\n             (2-hop-gene-lookup/allowable-predicates (list curie) '() allowable-predicates)))\n          \n          (printf \"\\n2-hop-affector-drug+gene/BIOLINK-edges\\n\")\n          (define 2-hop-affector-drug+gene/BIOLINK-edges\n            (time\n             (remove-item\n              '()\n              (map (lambda (ls) (filter-edges-by-affector-type ls '() '())) 2-hop-affector/BIOLINK-edges)\n              '())\n             ))      \n\n          (printf \"\\n2-hop-affector-gene/BIOLINK-edges\\n\")\n          (define 2-hop-affector-gene/BIOLINK-edges  \n            (time (map car 2-hop-affector-drug+gene/BIOLINK-edges)))\n          \n          (printf \"\\n2-hop-affector-drug/BIOLINK-edges\\n\")\n          (define 2-hop-affector-drug/BIOLINK-edges            \n            (time\n             (map cdr 2-hop-affector-drug+gene/BIOLINK-edges)))\n\n          (printf \"\\n2-hop-affector-drug/EXPORT-edges\\n\")\n          (define 2-hop-affector-drug/EXPORT-edges\n            (time (get-export-edges\n                   (remove-item\n                    '()\n                    (map (lambda (x) (match-edge/with-S/O-gene-linker-ids x '())) 2-hop-affector-drug/BIOLINK-edges)\n                    '())\n                   )))\n\n                    \n          (define 2-hop-affector-drug/path\n            (format \"~a2HOP-AFFECTOR-DRUGS--ALLp-->1HOP-AFFECTOR-GENES-->ALLp-->~a.tsv\" directory-path gene-ls-name))\n          (define 2-hop-affector-drug/port\n            (open-output-file 2-hop-affector-drug/path #:exists 'append))\n\n          (export-column-headers\n           column-headers/1hop\n           2-hop-affector-drug/port\n           2-hop-affector-drug/path)\n\n          (outer-loop\n           2-hop-affector-drug/EXPORT-edges\n           2-hop-affector-drug/port)\n\n          \n          #|\n          ;; comment this out for now, don't need 2-hop affector genes until 3-hop affector drugs are computed\n          (printf \"\\n2-hop-affector-gene/EXPORT-edges\\n\")\n          (define 2-hop-affector-gene/EXPORT-edges\n            (time (get-export-edges (map (lambda (x) (match-edge/with-S/O-gene-linker-ids x '())) 2-hop-affector-gene/BIOLINK-edges))))\n          |#                    \n          #|\n          (define 2-hop-affector-drug-specific/path\n            (format \"~a2HOP-AFFECTOR-DRUGS--ALLp-->~a.tsv\" directory-path curie-str/EXPORT))\n          (define 2-hop-affector-drug-specific/port\n            (open-output-file 2-hop-affector-drug-specific/path #:exists 'append))\n          \n          (export-column-headers\n           column-headers/1hop\n           2-hop-affector-drug-specific/port\n           2-hop-affector-drug-specific/path)\n          (outer-loop\n           2-hop-affector-drug/EXPORT-edges\n           2-hop-affector-drug-specific/port)\n          \n          (printf \"\\n2-HOP EXPORT COMPLETE:\\nAFFECTOR-DRUGS--ALL-PREDICATES-->1-HOP-AFFECTOR GENE of ~a\\n\" curie-str/EXPORT)\n          |#\n          \n\n           #|        \n          (printf \"\\n\\n2-HOP PATH:\\n2-HOP-AFFECTOR-DRUG--ALL-PREDICATES-->1-HOP-AFFECTOR-GENE--ALL-PREDICATES-->~a\\n\\n\" curie-str/EXPORT)\n          |#\n          #|\n          (printf \"\\n2-hop-path/drug--predicate-->1hop-gene--predicate-->target-gene/EXPORT-edges\\n\")\n          (define 2-hop-path/drug--predicate-->1hop-gene--predicate-->target-gene/EXPORT-edges\n            (time\n             (get-export-edges\n              (make-2hop-path/export\n               (make-2hop-path\n                 1-hop-affector-gene/EXPORT-edges\n                 2-hop-affector-drug/EXPORT-edges)))))\n          \n          (define 2-hop-affector-drug-->1hop-gene-->target-gene-paths/path\n            (format \"~a2HOP-AFFECTOR-DRUGS--ALLp-->1HOP-AFFECTOR-GENES--ALLp-->PROVIRAL-GENES.tsv\" directory-path))\n          (define 2-hop-affector-drug-->1hop-gene-->target-gene-paths/port\n            (open-output-file 2-hop-affector-drug-->1hop-gene-->target-gene-paths/path #:exists 'append))\n\n          (define column-headers/2hop\n            '(\"edge_id\"\n              \"db\"\n              \"subject_linker_name\"              \n              \"subject_linker_curie\"\n              \"predicate_symbol\"\n              \"fda_approved\"\n              \"target_object_linker_name\"\n              \"target_object_linker_curie\"\n              \"subject_name\"\n              \"subject_curie\" \n              \"subject_category\"\n              \"predicate\"              \n              \"target_object_name\"\n              \"target_object_curie\"\n              \"target_object_category\"\n              \"rxnorm_drug_id\"\n              \"pubmed_number\"\n              \"pub_urls\"\n              \"edge_id\"\n              \"db\"\n              \"subject_linker_name\"              \n              \"subject_linker_curie\"\n              \"predicate_symbol\"\n              \"fda_approved\"\n              \"target_object_linker_name\"\n              \"target_object_linker_curie\"\n              \"subject_name\"\n              \"subject_curie\" \n              \"subject_category\"\n              \"predicate\"              \n              \"target_object_name\"\n              \"target_object_curie\"\n              \"target_object_category\"\n              \"rxnorm_drug_id\"\n              \"pubmed_number\"\n              \"pub_urls\"))\n\n          (export-column-headers\n           column-headers/2hop\n           2-hop-affector-drug-->1hop-gene-->target-gene-paths/port\n           2-hop-affector-drug-->1hop-gene-->target-gene-paths/path)\n\n          (outer-loop\n           2-hop-path/drug--predicate-->1hop-gene--predicate-->target-gene/EXPORT-edges\n           2-hop-affector-drug-->1hop-gene-->target-gene-paths/port)\n          \n          (export-column-headers\n           column-headers/2hop\n           2-hop-affector-drug-->1hop-gene-->target-gene-paths-specific/port\n           2-hop-affector-drug-->1hop-gene-->target-gene-paths-specific/path)\n\n          (outer-loop\n           2-hop-path/drug--predicate-->1hop-gene--predicate-->target-gene/EXPORT-edges\n           2-hop-affector-drug-->1hop-gene-->target-gene-paths-specific/port)\n          |#\n\n          |#\n          )\n        \n        (pretty-print \"QUERY FINISHED!\")\n\n        )))))\n\n(start-function all-hgncs \"HUMAN-GENOME\")\n\n\n          #|\n\n          (define 2-hop-affector-drug-->1hop-gene-->target-gene-paths-specific/path\n          (format \"~a2HOP-AFFECTOR-GENES--ALLp-->1HOP-AFFECTOR-GENES--ALLp-->~a.tsv\" directory-path curie-str/EXPORT))\n          (define 2-hop-affector-drug-->1hop-gene-->target-gene-paths-specific/port\n            (open-output-file 2-hop-affector-drug-->1hop-gene-->target-gene-paths-specific/path  #:exists 'append))          \n\n          \n          (printf \"\\nBUILDING 2-HOP GENE PATHS FOR CONCEPT: ~a aka ~a\\n\\n\" curie curie-str/EXPORT)\n          (printf \"\\n\\n2-HOP PATH:\\n2-HOP-AFFECTOR-GENE--ALL-PREDICATES-->1-HOP-AFFECTOR-GENE--ALL-PREDICATES-->~a\\n\\n\" curie-str/EXPORT)\n          ;;test without remove-item\n          (printf \"\\n2-hop-gene-path/EXPORT-edges\\n\")\n          (define 2-hop-gene-path/EXPORT-edges\n            (time\n             (make-2hop-path\n               1-hop-affector-gene/EXPORT-edges\n               2-hop-affector-gene/EXPORT-edges)))\n\n          (printf \"\\n2-hop-gene-paths-connected/EXPORT-edges\\n\")\n          (define 2-hop-gene-paths-connected/EXPORT-edges\n            (time\n             (get-export-edges\n             (make-2hop-path/export\n              2-hop-gene-path/EXPORT-edges))))\n\n          (define 2-hop-affector-gene-paths/path\n            (format \"~a2HOP-AFFECTOR-GENES--ALLp-->1HOP-AFFECTOR-GENES--ALLp-->PROVIRAL-GENES.tsv\" directory-path))\n          (define 2-hop-affector-gene-paths/port\n            (open-output-file 2-hop-affector-gene-paths/path #:exists 'append))\n          \n          (define column-headers/2hop\n            '(\"2hop_db\"\n              \"2hop_subject_name\"\n              \"2hop_subject_curie\"\n              \"2hop_subject_canonical_curie\"\n              \"2hop_subject_category\"\n              \"2hop_predicate\"\n              \"2hop_predicate_symbol\"\n              \"2hop_object_name\"\n              \"2hop_object_curie\"\n              \"2hop_object_canonical_curie\"\n              \"2hop_object_category\"\n              \"2hop_pubmed_number\"\n              \"2hop_pub_URLs\"\n              \"1hop_db\"\n              \"1hop_subject_name\"\n              \"1hop_subject_curie\"\n              \"1hop_subject_canonical_curie\"\n              \"1hop_subject_category\"\n              \"1hop_predicate\"\n              \"1hop_predicate_symbol\"\n              \"target_object_name\"\n              \"target_object_curie\"\n              \"target_object_canonical_curie\"\n              \"1hop_target_object_category\"\n              \"1hop_pubmed_number\"\n              \"1hop_pubmed_URLs\"))\n\n          (export-column-headers\n           column-headers/2hop\n           2-hop-affector-gene-paths/port\n           2-hop-affector-gene-paths/path)\n\n          (outer-loop\n           2-hop-gene-paths-connected/EXPORT-edges\n           2-hop-affector-gene-paths/port)\n          \n          (define 2-hop-affector-gene-paths-specific/path\n          (format \"~a2HOP-AFFECTOR-GENES--ALLp-->1HOP-AFFECTOR-GENES--ALLp-->~a.tsv\" directory-path curie-str/EXPORT))\n          (define 2-hop-affector-gene-paths-specific/port\n            (open-output-file 2-hop-affector-gene-paths-specific/path #:exists 'append))\n          \n          (export-column-headers\n           column-headers/2hop\n           2-hop-affector-gene-paths-specific/port\n           2-hop-affector-gene-paths-specific/path)\n\n          (outer-loop\n           2-hop-gene-paths-connected/EXPORT-edges\n           2-hop-affector-gene-paths-specific/port)\n          |#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/etl_for_new_KGs/xmlparse.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require xml)\n\n#lang racket\n(provide (all-defined-out))\n(require xml)\n(require net/http-client)\n \n;; download xml for national clinical trials found here: https://clinicaltrials.gov/\n(define all_nct_xml_dir\n  \"git/KG_creation/data/raw/AllPublicXML\")\n\n(define nct-https\n  (http-conn-open\n   \"clinicaltrials.gov\"\n   #:ssl? #t))\n\n;;\"https://clinicaltrials.gov/\"\n;; bytes? http 200 = ok request, 400 = bad request, 500 = server error, 404 = page not found\n;; lob? info of transaction \n;; ip? input-port we can read data from \n(define nct-data-files\n  (let-values (((bytes? lob? ip?)\n                (http-sendrecv\n                 \"clinicaltrials.gov\"\n                 \"/ct2/show/NCT03478891?displayxml=true\"\n                 ;;\"AllPublicXML.zip\"\n                 #:ssl? #t\n                 )))\n    (list bytes? lob? ip?)))\n\n#|\nxexpr conversion of xml\n(root\n  (parent-element                         \n     (element (attribute) <\"data\">)))         \n|#\n(define nct-data\n  (xml->xexpr\n   (document-element\n    (read-xml\n     (list-ref nct-data-files 2)))))\n\n\n(define test\n  (xml->xexpr\n    (document-element\n     (read-xml\n      (open-input-file\n       (car nct-xml-file-paths))))))\n\n\n(xml->xexpr\n    (document-element\n     (read-xml\n      (open-input-file\n       (car nct-xml-file-paths)))))\n\n\n(ftp-establish-connection\n \"https://clinicaltrials.gov/AllPublicXML.zip\"\t \t \t \t \n 21\t \t \t \t \n ;user\t \t \t \t \n ;passwd\n )\n\n\n\n(define user-home-path/str\n  (path->string (find-system-path 'home-dir)))\n\n(define nct_dir\n  (string-append user-home-path/str all_nct_xml_dir))\n\n(define nct-xml-file-paths\n  (filter\n   (lambda (x)\n     (and (path-has-extension? x \".xml\")\n          (regexp-match #rx\"^NCT[0-9]+.xml$\" (path->string (file-name-from-path x)))))\n          (sequence->list (in-directory nct_dir))))\n\n;; NCT03478891\n\n\n(define test\n  (xexpr->string\n   (xml->xexpr\n    (document-element\n     (read-xml\n      (open-input-file\n       (car nct-xml-file-paths)))))))\n\n\n#;(define t\n  (filter\n   (lambda (x) (and (not (null? x))\n                   (not (string? x))))\n   (xml->xexpr\n    (document-element\n     (read-xml\n      (open-input-file\n       (car nct-xml-file-paths)))))))\n\n\n#|\n;; list of all file paths \n(define paths-to-unichem-files\n  (filter\n   (lambda (x)\n     (and (path-has-extension? x \".txt\")\n          (regexp-match #rx\"^src[0-9]+src[0-9]+.txt$\" (path->string (file-name-from-path x)))))\n          (sequence->list (in-directory path-unichem))))\n\n\n(define xml_raw_files\n  (parse_xml_files nct_dir))\n\n\n\n(define parse_xml_files\n  (lambda (path)\n    (for/fold\n     ([ls '()])\n     ([f (in-directory path)] #:when (path-has-extension? f \".xml\"))     \n     (define xml-file-paths  (sequence->list f))\n     #;(define parsed-xml-file (read-xml (open-input-file f)))\n     (pretty-print xml-file-paths))))\n|#\n\n\n(define all_nct_xml_dir\n  \"git/KG_creation/data/raw/AllPublicXML\")\n\n(define user-home-path/str\n  (path->string (find-system-path 'home-dir)))\n\n(define nct_dir\n  (string-append user-home-path/str all_nct_xml_dir))\n\n(define nct-xml-file-paths\n  (filter\n   (lambda (x)\n     (and (path-has-extension? x \".xml\")\n          (regexp-match #rx\"^NCT[0-9]+.xml$\" (path->string (file-name-from-path x)))))\n          (sequence->list (in-directory nct_dir))))\n\n(define test\n  (xexpr->string\n   (xml->xexpr\n    (document-element\n     (read-xml\n      (open-input-file\n       (car nct-xml-file-paths)))))))\n\n\n(define t\n  (filter\n   (lambda (x) (and (not (null? x))\n                   (not (string? x))))\n   (xml->xexpr\n    (document-element\n     (read-xml\n      (open-input-file\n       (car nct-xml-file-paths)))))))\n\n\n#|\n;; list of all file paths \n(define paths-to-unichem-files\n  (filter\n   (lambda (x)\n     (and (path-has-extension? x \".txt\")\n          (regexp-match #rx\"^src[0-9]+src[0-9]+.txt$\" (path->string (file-name-from-path x)))))\n          (sequence->list (in-directory path-unichem))))\n\n\n(define xml_raw_files\n  (parse_xml_files nct_dir))\n\n\n\n(define parse_xml_files\n  (lambda (path)\n    (for/fold\n     ([ls '()])\n     ([f (in-directory path)] #:when (path-has-extension? f \".xml\"))     \n     (define xml-file-paths  (sequence->list f))\n     #;(define parsed-xml-file (read-xml (open-input-file f)))\n     (pretty-print xml-file-paths))))\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/example-2-hop-rhobtb2-drug-safe.rkt",
    "content": "(displayln \"\\nRunning 2-hop rhobtb2 query with drug safety constraint:\")\n(define q3 (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\")\n                   (T       #f))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates)\n                   ;; You can instead limit X to drugs with a tradename:\n                   ;(X->T       '(\"has_tradename\"))\n                   ;; Just comment this line out if you choose to.\n                   (X->T       drug-safe)\n                   )\n                  (X X->Y Y Y->rhobtb2 rhobtb2)\n                  (X X->T T))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q3)))\n\n#|\n=>\n\n((concepts: (X 11) (Y 1) (rhobtb2 1) (T 900))\n (edges: (X->Y 27) (Y->rhobtb2 2) (X->T 1019)))\n|#\n\n(displayln \"\\nRanking paths:\")\n(define ranked3 (time (ranked-paths q3)))\n(pretty-ranked (take ranked3 1))\n\n#|\n=>\n\n(path: 11 (X X->Y Y Y->rhobtb2 rhobtb2))\n((0.925\n  ((\"CUI:C0052416\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Arsenic trioxide\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:29073\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"L-ascorbic acid\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:41423\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"celecoxib\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0069717\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Oxaliplatin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:7553\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Niclosamide\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:66964\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Delta(9)-tetrahydrocannabinol\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:40303\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"lovastatin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:103210\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"hexahydrophthalic anhydride\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:49603\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"lapatinib\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:3181\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"bromocriptine\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:50924\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"sorafenib\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\"))))\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/example-2-hop-rhobtb2.rkt",
    "content": "(displayln \"\\nRunning 2-hop rhobtb2 query with concept categories:\")\n(define q (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates))\n                  (X X->Y Y Y->rhobtb2 rhobtb2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q)))\n\n#|\n=>\n\n((concepts: (X 52) (Y 1) (rhobtb2 1)) (edges: (X->Y 125) (Y->rhobtb2 2)))\n|#\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q)))\n(pretty-ranked ranked)\n\n#|\n=>\n\n(path: 52 (X X->Y Y Y->rhobtb2 rhobtb2))\n((0.925\n  ((\"CUI:C0936225\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Inorganic arsenic\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0008546\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Chromatin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0909265\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"pifithrin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0669391\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Keratin-14 [Chemical/Ingredient]\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0052416\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Arsenic trioxide\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0243192\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"agonists\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C1435338\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"nutlin 3\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0005456\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Binding Sites\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0033259\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Prodigiosin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0600508\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Response Elements\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:4917\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"eugenol\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0048451\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"4-Methoxyamphetamine\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:29073\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"L-ascorbic acid\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C1514727\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Ras Inhibitor\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0034424\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Quinolines [Chemical/Ingredient]\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C1443643\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Proteasome inhibitor\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:41423\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"celecoxib\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C1099354\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"RNA, Small Interfering [Chemical/Ingredient]\"\n    .\n    \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:137113\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Jq1\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C1101610\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"MicroRNAs [Chemical/Ingredient]\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0012854\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Deoxyribonucleic acid\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0066084\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"methaneselenol\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0078375\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Alpha tocopherol succinate\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0069717\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Oxaliplatin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:7553\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Niclosamide\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0013227\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Pharmaceutical / biologic product\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:66964\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Delta(9)-tetrahydrocannabinol\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEMBL:CHEMBL62381\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Sodium Butyrate\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:3962\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"curcumin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0003211\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Nonsteroidal Anti-inflammatory Drugs\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:32243\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"tolfenamic acid\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:40303\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"lovastatin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:63959\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"celastrol\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C1516312\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Caspase Inhibitor\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:103210\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"hexahydrophthalic anhydride\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CUI:C0006632\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Cadmium\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.925\n  ((\"CHEBI:49\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"(+)-Tetrandrine\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.85\n  ((\"MESH:C000602704\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"UF010 compound\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.85\n  ((\"MESH:C028031\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"cadmium acetate\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.85\n  ((\"CHEBI:30621\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"diarsenic trioxide\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:49603\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"lapatinib\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:3181\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"bromocriptine\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CUI:C0950721\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"7-hydroxystaurosporine\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:9516\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"thapsigargin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:50924\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"sorafenib\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:223316\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"(+)-artemisinin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CHEBI:338412\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"(-)-anisomycin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CUI:C0084178\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Prohibitin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CUI:C0010572\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Cycloheximide\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CUI:C0035668\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Ribonucleic acid\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CUI:C0961324\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"penetratin\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\")))\n (0.7\n  ((\"CUI:C0173532\" . \"CUI:C0812258\") (\"CUI:C0812258\" . \"CUI:C1425762\"))\n  ((\"Cyclin D3 [Chemical/Ingredient]\" . \"E2f transcription factor 1\")\n   (\"E2f transcription factor 1\"\n    .\n    \"Rho-related btb domain-containing protein 2\"))))\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/example-2-hop-tmprss2.rkt",
    "content": "(displayln \"\\nRunning 2-hop tmprss2 down-up query with concept categories:\")\n(define q1 (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (tmprss2 \"UMLS:C1336641\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->tmprss2 positively-regulates))\n                  (X X->Y Y Y->tmprss2 tmprss2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q1)))\n\n#|\n=>\n\n((concepts: (X 701) (Y 7) (tmprss2 1)) (edges: (X->Y 1570) (Y->tmprss2 10)))\n|#\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q1)))\n(pretty-ranked ranked)\n\n#|\n=>\n\n(path: 1010 (X X->Y Y Y->tmprss2 tmprss2))\n((0.8340624999999999\n  ((\"CHEBI:3347\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"candesartan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.8340624999999999\n  ((\"CHEBI:5959\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"irbesartan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.818125\n  ((\"CHEBI:7573\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"nilutamide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.818125\n  ((\"CHEBI:27732\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"caffeine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.818125\n  ((\"CHEBI:91372\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"2-(4-morpholinyl)-6-(1-thianthrenyl)-4-pyranone\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.818125\n  ((\"CHEBI:31932\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Olmesartan medoxomil\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0135693\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Pd 123319\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:6541\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"losartan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0006684\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Calcium channel blockers\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:9241\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"spironolactone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0009325\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Collagen\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C1257987\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Thiazolidinedione\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:17609\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"cortisol 21-acetate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:91739\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"2,2-diphenyl-N-[2,2,2-trichloro-1-[[(4-fluoro-3-nitroanilino)-sulfanylidenemethyl]amino]ethyl]acetamide\"\n    .\n    \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C1123005\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"fulvestrant\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:18357\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"(R)-noradrenaline\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0521942\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Angiotensin II Receptor Antagonists\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C1320169\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Nonsteroidal antiandrogen\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:9927\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"valsartan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0014939\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Estrogens\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0002842\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Antiandrogens\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0004504\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"Azole\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0591237\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Casodex\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0013227\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Pharmaceutical / biologic product\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0003015\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Ace inhibitors\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0285590\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Bicalutamide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0012789\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Dithiothreitol [Chemical/Ingredient]\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:41879\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"dexamethasone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:17347\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"testosterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:17347\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"testosterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0022625\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ketoconazole\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEMBL:CHEMBL491\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"HYDROXYFLUTAMIDE\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:39548\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"atorvastatin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CUI:C0001645\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Beta-adrenergic Blocking Agents\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.78625\n  ((\"CHEBI:41879\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"dexamethasone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0117234\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Fadrozole [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene 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(0.7224999999999999\n  ((\"CHEBI:27584\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"aldosterone\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0065374\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Lisinopril\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0015684\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Fatty acid\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:31394\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Chlormadinone acetate\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene 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\"CUI:C1336641\"))\n  ((\"Pharmaceutical / biologic product\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0815016\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"releasing hormones\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0079925\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Antisense oligonucleotide\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0302837\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Vitamin supplementation\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0031705\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Phosphorus\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0065321\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Ly 53857\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0022245\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Isoproterenol\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0754775\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Kr 31080\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0243077\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"antagonists & inhibitors\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0667047\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"oleoyl-estrone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0044965\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"17 alpha-ethinyl-3-isopropylsulfonyloxyestradiol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0285590\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Bicalutamide\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:521033\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"dutasteride\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1318898\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"5-alpha Reductase Inhibitor [EPC]\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0014594\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Epitestosterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:24536\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"hexachlorocyclohexane\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0028128\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Nitric oxide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0667225\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Krh 594\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:93368\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"2-(1-piperazinyl)quinoline\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5132\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"flutamide\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0163305\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"pyrrolidine dithiocarbamic acid\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0600334\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Silibinin\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0023755\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Linuron\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:41774\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"tamoxifen\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEMBL:CHEMBL1355736\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Theophylline [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:6715\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"medroxyprogesterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEMBL:CHEMBL550495\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Methylene blue\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5132\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"flutamide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0036800\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Serum Globulins [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0301818\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Steroid hormone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5120\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"fluoxymesterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0040135\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Thyroid hormone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0017890\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Glycine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 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\"CUI:C1336641\"))\n  ((\"catalpol\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0054036\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Brefeldin A [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0728964\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ethinyl Estradiol/Norgestrel\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0593802\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Aromatase inhibitor\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1099354\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"RNA, Small Interfering [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0008838\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Cisplatin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:74125\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"losartan carboxylic acid\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0064113\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Itraconazole\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:4868\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"estramustine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0038785\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Sulfuric Acid Esters [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0284825\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"6-anilino-5,8-quinolinedione\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:65329\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Ly294002\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:17609\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"cortisol 21-acetate\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0289313\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Rosiglitazone\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0309049\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"favor\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0647210\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"monooxyethylene trimethylolpropane tristearate\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0010505\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Cyanide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian 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(0.7224999999999999\n  ((\"CUI:C0014939\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Estrogens\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:47808\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"(R)-sulforaphane\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16330\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"17beta-hydroxy-5alpha-androstan-3-one\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:24814\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"indole-3-methanol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:3766\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"clozapine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0025175\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Megestrol\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0072063\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"procymidone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0033497\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Propranolol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28077\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"rifampicin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0667961\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Th 142177\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0209211\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Lanreotide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0591237\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Casodex\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0162772\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Reactive Oxygen Species [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:22984\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"calcium atom\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0009906\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"oral contraceptive pill\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0022020\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Ionomycin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16069\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"1H-imidazole\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0237795\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"pressors\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0000661\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"8-Bromo Cyclic Adenosine Monophosphate [Chemical/Ingredient]\"\n    .\n    \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0043505\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ziram product\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0055474\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"chlorpyrifos-methyl\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:49662\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"indomethacin\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:39421\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"perfluorooctane-1-sulfonic acid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0220853\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Hydroxide Ion\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0299755\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"fonsartan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1328699\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ogx-011\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16422\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"androst-4-ene-3,17-dione\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0026814\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Muscarine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0006684\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Calcium channel blockers\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16356\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"3',5'-cyclic GMP\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0033607\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Peptide hydrolase inhibitor product\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0085885\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Lathyrus poison\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:47499\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"imipramine\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0078245\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"vinclozolin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0025685\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Methoxychlor\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:44185\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"methotrexate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0002555\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Aminoglutethimide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus 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(0.7224999999999999\n  ((\"CHEBI:16973\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"11-deoxycorticosterone\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0003364\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Hypotensive agent\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28088\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"genistein\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0049144\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"5-dihydro-19-nortestosterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0033307\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Synthetic progestogen\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:50095\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"bucladesine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0012798\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Diuretics\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:77006\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"17beta-estradiol 3-benzoate\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1318898\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"5-alpha Reductase Inhibitor [EPC]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5062\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"finasteride\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0567415\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Atom\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0247955\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"3-((2'-carboxybiphenyl-4-yl)methyl)-2-cyclopropyl-7-methyl-3H-imidazo(4,5-b)pyridine\"\n    .\n    \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:41922\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"diethylstilbestrol\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0872893\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Estrogenic substances\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0527379\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Candesartan cilexetil\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0950793\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"osaterone acetate\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:17252\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"17alpha-hydroxyprogesterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0243192\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"agonists\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0701303\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"mifepristone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0631746\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"pregnane-20-one\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0033671\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Protein Synthesis Inhibitors\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0007004\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Carbohydrate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0600434\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Peroxisome Proliferators\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:18145\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"(+)-alpha-tocopherol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0756836\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ym 116\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0596922\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"methyl group\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:4911\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"etoposide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0360714\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"HMG-CoA reductase inhibitor product\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:63716\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"tenofovir hydrate\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0030817\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Penicillamine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0026160\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Mineralocorticoids\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1289975\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"androgenic steroid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:37537\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"phorbol 13-acetate 12-myristate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1514555\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Protein Kinase C Inhibitor\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0017725\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Glucose\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0812407\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Glucuronide\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:131184\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"2-aminoethoxydiphenylborane\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0812407\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Glucuronide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:15948\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"lycopene\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0010572\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Cycloheximide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16469\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"17beta-estradiol\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0677666\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Soy protein isolate\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:59809\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"docetaxel trihydrate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:32260\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"trilostane\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:41922\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"diethylstilbestrol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0049205\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"5-hydroxy-2-N,N-dipropylaminotetralin\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:2704\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"anastrozole\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:3181\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"bromocriptine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:4903\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"17alpha-ethynylestradiol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:3757\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"clonidine (imino form)\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0002844\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Androgens\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:52717\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"bortezomib\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0172006\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Ono 3805\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:88200\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"benazeprilat\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0090052\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"11-hydroxytestosterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0043031\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Warfarin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0521966\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Calcium ionophore A23187\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:138000\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"3-(1-methylpyrrolidin-2-yl)pyridine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:119486\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"efavirenz\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28088\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"genistein\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0291375\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"4,7beta-dimethyl-4-azacholestan-3-one\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0027415\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"narcotic\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0070915\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"phosphoramidon\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0019932\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Hormone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0012854\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Deoxyribonucleic acid\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0664210\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"7-hydroxytestosterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0090050\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"11-beta Hydroxyandrostenedione\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0286256\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Cgp 42112a\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5692\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"hexachlorobenzene\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0038317\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Steroid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16881\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"1H-indole\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16243\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"quercetin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0003765\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Arginine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0109641\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"2,2,5,7,8-pentamethyl-1-hydroxychroman\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0035339\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Retinoids\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0297076\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"4-(3-(3-(bis(4-isobutylphenyl)methylamino)benzoyl)-1H-indol-1-yl)butyric acid\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0052201\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Apolipoprotein E4\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0059497\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Equol [Chemical/Ingredient]\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0001645\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Beta-adrenergic Blocking Agents\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:88522\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Monobutylphthalate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0020393\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Hydroxysteroids [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:41879\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"dexamethasone\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0023755\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Linuron\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:8364\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"prazosin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0005456\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Binding Sites\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16962\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"cortisone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0600334\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Silibinin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0950211\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"oxendolone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1100708\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"3,3-diindolymethane\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1611640\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"therapeutic agent\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0012854\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Deoxyribonucleic acid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0603200\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"1,2-di-(4-sulfamidophenyl)-4-butylpyrazolidine-3,5-dione\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0768712\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"8-prenylnaringenin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0120107\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Goserelin product\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0003308\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"Antifungals\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0392419\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Fungicide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:27584\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"aldosterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0032458\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Polycyclic Aromatic Hydrocarbons [Chemical/Ingredient]\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:50742\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"cyproterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0577749\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Phytochemical product\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:17026\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"progesterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0728965\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ethinyl Estradiol-Norgestrel Combination\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0028128\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Nitric oxide\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:3757\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"clonidine (imino form)\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0014594\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Epitestosterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28748\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"doxorubicin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0010124\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Corticosterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:8107\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"phenytoin\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:50729\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"mitoxantrone\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28940\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"calciol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0036884\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Sex hormone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:7590\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"nitrofen\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0657318\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"lysyl-arginyl-alanyl-lysyl-alanyl-lysyl-threonyl-threonyl-lysyl-lysyl-arginine\"\n    .\n    \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0024467\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Magnesium\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0017725\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Glucose\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1101610\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"MicroRNAs [Chemical/Ingredient]\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0257337\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"17 beta-benzoyl-4-aza-5 alpha-androst-1-ene-3-one\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0013832\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Electrolytes\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0002845\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Anabolic Steroids\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0136082\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"perchlorate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:3647\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"chlorpromazine\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEMBL:CHEMBL187460\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"CRYPTOTANSHINONE\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0289313\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Rosiglitazone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:4532\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"diethylstilbestrol diphosphate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:8434\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"prochloraz\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0700620\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Losartan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5775\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"hydralazine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:17883\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"hydrogen chloride\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16422\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"androst-4-ene-3,17-dione\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:18220\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"isoflavone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0304497\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Cytotoxic\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16503\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"selane\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0243076\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"antagonists & inhibitors\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:27543\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"9H-carbazole\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0004147\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Atenolol\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0486333\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Androstanediol\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0032447\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Polychlorinated biphenyl\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28820\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"9-phenanthrol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:31189\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Allylestrenol\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:41774\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"tamoxifen\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:45713\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"trans-resveratrol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0053526\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Bethanechol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0252643\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Bosentan\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0772394\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Lepirudin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0034085\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Lung surfactant\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEMBL:CHEMBL170630\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"ETHANE\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0301818\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Steroid hormone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0075116\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"Src peptide\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:6715\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"medroxyprogesterone\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0073667\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"11,17-dihydroxy-6-methyl-17-(1-propynyl)androsta-1,4,6-triene-3-one\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0010124\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"Corticosterone\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0878412\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Calcimycin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1514972\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Steroidal Estrogen\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28324\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"11-deoxycortisol\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:2666\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"amitriptyline\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0057277\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Dehydroepiandrosterone sulfate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:39867\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"valproic acid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:5001\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"fenofibrate\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:58987\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"sildenafil citrate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0083966\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Pd 123177\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0149473\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Zoladex\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0076180\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"testosterone 17 beta-carboxylic acid\"\n    .\n    \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0163951\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"androstan-3-one\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0006456\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Buserelin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:26836\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"sulfuric acid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:15367\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"all-trans-retinoic acid\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0071649\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Polyphenol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0040615\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Antipsychotics\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:8707\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"quetiapine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0043481\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Zinc\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:28368\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"novobiocin\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:15379\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"oxygen\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0070455\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Permethrin\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0351241\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Androgens+anabolic steroids\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0127279\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Plomestane\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0009148\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Cobalt\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0028910\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Oils,essential\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0037343\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Autacoids [Chemical/Ingredient]\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0003765\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Arginine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:3699\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"cimetidine\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0035696\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Messenger RNA\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0034595\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Radioactive Isotopes\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1257954\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Cox-2 inhibitor\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:31186\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"alfacalcidol\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:34849\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"mibolerone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0213165\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Fr 139317\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:15367\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"all-trans-retinoic acid\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:45951\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"trifluoperazine\" . \"Androgens\")\n   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. \"CUI:C1336641\"))\n  ((\"RNA, Small Interfering [Chemical/Ingredient]\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0082608\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Fluvastatin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:27974\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"estriol\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0043791\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Diglyceride\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0071642\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"polypeptide C\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0360528\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Dexamethasone in oral dosage form\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1337263\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"hamster protein\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0028005\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Nicardipine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:17747\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"bis(2-ethylhexyl) phthalate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 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((\"Peptide product\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:35297\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"acene\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:135735\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"delapril\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0002842\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Antiandrogens\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0673767\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Kr 31080\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian 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((\"Corticosterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:4910\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"etomidate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0009905\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"oral contraceptive\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1446539\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Tegafur and uracil product\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0030956\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Peptide product\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian 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erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0169911\" . \"CUI:C0599295\") (\"CUI:C0599295\" . \"CUI:C1336641\"))\n  ((\"messenger protein\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")\n   (\"V-ets avian erythroblastosis virus e26 oncogene homolog\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0020616\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Hypoglycemic agent\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0376202\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Pregnanolone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0304402\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Stimulant\" . \"Androgens\")\n   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\"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Estrogens,conjugated\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0699161\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"norethindrone acetate\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:45081\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"pentamidine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0003402\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"antioxidant\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0017710\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Glucocorticoids\" . \"Androgens\")\n   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\"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0010572\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Cycloheximide\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0038734\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"Sulfhydryls\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:16118\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"berberine\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:50885\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  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((\"dehydroepiandrosterone\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0018282\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"Growth Inhibitors\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C1312096\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"15-deoxyprostaglandin J2\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0037239\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:4814\" . \"CUI:C0919524\") 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\"CUI:C1336641\"))\n  ((\"2-morpholin-4-yl-6-thianthren-1-yl-pyran-4-one\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:32020\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"pitavastatin\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0025219\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Melatonin\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:37941\" . \"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"clopidogrel\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:7553\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Niclosamide\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian 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\"CUI:C0919524\") (\"CUI:C0919524\" . \"CUI:C1336641\"))\n  ((\"cyclo(Trp-Asp-Pro-Val-Leu)\" . \"Atm\")\n   (\"Atm\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0022640\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Ketosteroids [Chemical/Ingredient]\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CHEBI:45906\" . \"CHEBI:16330\") (\"CHEBI:16330\" . \"CUI:C1336641\"))\n  ((\"suramin\" . \"17beta-hydroxy-5alpha-androstan-3-one\")\n   (\"17beta-hydroxy-5alpha-androstan-3-one\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.7224999999999999\n  ((\"CUI:C0162758\" . \"CUI:C0002844\") (\"CUI:C0002844\" . \"CUI:C1336641\"))\n  ((\"Serotonin Uptake Inhibitors\" . \"Androgens\")\n   (\"Androgens\" . \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.595\n  ((\"CUI:C0599786\" . 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 \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0243192\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"agonists\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:15367\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"all-trans-retinoic acid\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:65329\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Ly294002\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0210353\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"N-(2(R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl)-L-tryptophan methylamide\"\n    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((\"Protein Phosphatase Inhibitor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0302837\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Vitamin supplementation\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0001617\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Adrenal corticosteriods\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:6402\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"leflunomide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0013227\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Pharmaceutical / biologic product\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0012854\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Deoxyribonucleic acid\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:28364\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"all-cis-5,8,11,14,17-icosapentaenoic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0536128\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Xanthohumol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0079925\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Antisense oligonucleotide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:44215\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"NAD zwitterion\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1099354\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"RNA, Small Interfering [Chemical/Ingredient]\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:27584\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"aldosterone\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0244104\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Pyruvate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16240\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"hydrogen peroxide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1565237\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"2-morpholin-4-yl-6-thianthren-1-yl-pyran-4-one\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:50924\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"sorafenib\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1328709\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"siplizumab\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0060397\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"fisetin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0667961\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Th 142177\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0603200\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"1,2-di-(4-sulfamidophenyl)-4-butylpyrazolidine-3,5-dione\"\n    .\n    \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0071642\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"polypeptide C\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEMBL:CHEMBL92484\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Aptiganel\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0002520\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Amino acids\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0028005\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Nicardipine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0599740\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"pharmacophore\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1134434\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Ag 1879\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17045\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"dinitrogen oxide\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1176007\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Piceatannol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0030493\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Paraquat\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0971797\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"halenaquinol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0051936\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"ansamycin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0600434\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Peroxisome Proliferators\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1566074\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"salubrinal\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:30740\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"ethylene glycol bis(2-aminoethyl)tetraacetic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0243076\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"antagonists & inhibitors\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:28088\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"genistein\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:4948\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Evodiamine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:45863\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"paclitaxel\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16933\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"ergosterol\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:15367\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"all-trans-retinoic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0002007\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Aldosterone receptor antagonist\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:40303\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"lovastatin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEMBL:CHEMBL1742441\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"EMBUSARTAN\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0010592\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Cyclosporine\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0174494\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"candesartan cilexetil\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0028128\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Nitric oxide\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:5292\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"geldanamycin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17097\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"biphenyl\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0028910\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Oils,essential\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0017890\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Glycine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0054130\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"bromopyruvate\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:89642\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Gestrinone\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:8364\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"prazosin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:88200\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"benazeprilat\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0037907\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Sphingosine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0070913\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Phosphoramide Mustard\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:9908\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"ursolic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0012968\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Docosahexaenoic Acids [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:63616\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"pemetrexed\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0443985\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Flinders medical center-7 marker\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0029904\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Ouabain\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0298346\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"MEK Inhibitor PD-98059\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0718263\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Adenosine-5\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0162772\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Reactive Oxygen Species [Chemical/Ingredient]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0043791\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Diglyceride\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:114785\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"erlotinib\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:50729\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"mitoxantrone\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0301067\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Cyclohexamide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:103210\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"hexahydrophthalic anhydride\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0000641\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide [Chemical/Ingredient]\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0069535\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Oncostatin M [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0033497\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Propranolol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0754775\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Kr 31080\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:8890\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"(S)-ropivacaine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1099354\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"RNA, Small Interfering [Chemical/Ingredient]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0047611\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"3-methylquercetin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:28088\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"genistein\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:103210\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"hexahydrophthalic anhydride\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:4806\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"epigallocatechin gallate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0034407\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Quinazoline\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0243042\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Mediator of inflammation\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0003402\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"antioxidant\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0078433\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Nerve agent VX\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0005372\" . \"CUI:C1705846\") (\"CUI:C1705846\" . 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\"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0034325\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Pyrrole\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0038734\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Sulfhydryls\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:8899\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"rottlerin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:175901\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"gemcitabine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis 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Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:46345\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"5-fluorouracil\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:4814\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"eprosartan\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0769339\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Kf-25706\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0008466\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Chondroitin sulfate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0124673\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Kn 93\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:18243\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"dopamine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1328819\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Absolute Genomic Position\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0597298\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Protein Isoforms [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   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((\"Amine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:65408\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"andrographolide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:3962\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"curcumin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:6541\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"losartan\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:39112\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"bosutinib\" . \"SRC wt Allele\")\n 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.\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0033607\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Peptide hydrolase inhibitor product\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1097641\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"2-cyclopentyl-5-(5-isoquinolylsulfonyl)-6-nitro-1H-benzo(D)imidazole\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0360714\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"HMG-CoA reductase inhibitor product\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0732611\" . \"CUI:C1705997\") (\"CUI:C1705997\" 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avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0768581\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"4-ethoxymethylene-2-phenyl-2-oxazoline-5-one\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:135737\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"lacidipine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:27617\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"monensin A\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0020282\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Hydrogen sulfide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0009325\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Collagen\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0521966\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Calcium ionophore A23187\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0755562\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"U-0126\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0029984\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Oxadiazoles [Chemical/Ingredient]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17241\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"1H-pyrazole\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEMBL:CHEMBL475584\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"1-(4-(4-amino-5-(3-methoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)phenethyl)piperidin-4-ol\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0021966\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Iodide salt\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0618845\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"N-formyl-13-dihydrocarminomycin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:135735\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"delapril\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0023779\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Lipid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEMBL:CHEMBL62381\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Sodium Butyrate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1377705\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"preservative free\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0008864\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Citrulline\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0009325\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Collagen\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0022245\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Isoproterenol\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16227\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"pyridine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:6801\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"metformin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1572759\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Monohydrate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17362\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"quinoline\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0297666\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Sb 203580\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0256547\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"anacardic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0025405\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Tiopronin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0657318\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"lysyl-arginyl-alanyl-lysyl-alanyl-lysyl-threonyl-threonyl-lysyl-lysyl-arginine\"\n    .\n    \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0034136\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Purine nucleoside product\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:15864\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"luteolin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0246694\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Mg-132\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0008240\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Chlorogenic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0247955\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"3-((2'-carboxybiphenyl-4-yl)methyl)-2-cyclopropyl-7-methyl-3H-imidazo(4,5-b)pyridine\"\n    .\n    \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0003316\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Epitope\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1443643\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Proteasome inhibitor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0252643\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Bosentan\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0567415\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Atom\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16469\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"17beta-estradiol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0079925\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Antisense oligonucleotide\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0031453\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Phenylalanine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:9241\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"spironolactone\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0213165\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Fr 139317\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:9434\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"telmisartan\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1567637\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Rpr260243\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0175000\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"catalpol\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0286256\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Cgp 42112a\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0879551\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Visilizumab\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:76004\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"dimethyl fumarate\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0037874\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Spermine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0069035\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"norvaline\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:41879\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"dexamethasone\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0178528\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"carboxylate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1097828\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"denbinobin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0597128\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"ocular hypotensive\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0010738\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Cytochalasin D [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0001047\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Acetylcysteine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0391142\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"N-beta-alanyl-5-S-glutathionyl-3,4-dihydroxyphenylalanine\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0022020\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Ionomycin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1101610\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"MicroRNAs [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:30563\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"silicon dioxide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1328819\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Absolute Genomic Position\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0035696\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Messenger RNA\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0878412\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Calcimycin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1514555\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Protein Kinase C Inhibitor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0813872\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Dizocilpine Maleate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0005456\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Binding Sites\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0082608\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Fluvastatin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0008015\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Macrophage chemotactic factor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0700620\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Losartan\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0080124\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"antisense-RNA\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0058079\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"dihydroguaiaretic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0043791\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Diglyceride\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:119486\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"efavirenz\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:18388\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"apigenin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0027388\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Naphthoquinone\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1565238\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"2-morpholin-4-yl-6-thianthren-1-yl-pyran-4-one\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:556075\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"radicicol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0006521\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Butyrates [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0967397\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"halenaquinone\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEMBL:CHEMBL7463\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"GF-109203\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17303\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"morphine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0004147\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Atenolol\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0280038\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Purine antagonist\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:27584\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"aldosterone\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0013832\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Electrolytes\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0083966\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Pd 123177\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1564139\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Mutant Proteins [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16118\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"berberine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:31932\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Olmesartan medoxomil\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:46081\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"fluconazole\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0027415\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"narcotic\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1608746\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"4-quinazolinamine, N-(2-chloro-5-methoxyphenyl)-6-methoxy-7-((1-methyl-4-piperidinyl) methoxy)\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0040880\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Triazole\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0010737\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Cytochalasin B [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0619285\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"1,4-dioxin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0005456\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Binding Sites\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1257987\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Thiazolidinedione\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0000254\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"2-Amino-5-phosphonovalerate [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1120337\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"tyrphostin AG 1024\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0379142\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"cyclo(Trp-Asp-Pro-Val-Leu)\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0007412\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Catecholamine product\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0075116\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Src peptide\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:49960\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"vandetanib\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0037239\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-benzazepine\"\n    .\n    \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0003402\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"antioxidant\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:28364\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"all-cis-5,8,11,14,17-icosapentaenoic acid\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0729218\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"tacrolimus\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17793\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"calycosin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:5001\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"fenofibrate\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0034140\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Purines [Chemical/Ingredient]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0066801\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"morin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1519952\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Vanilloid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0283149\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"ophiocordin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0169911\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"messenger protein\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0010803\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Cytokeratin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:90695\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"anthra[1,9-cd]pyrazol-6(2H)-one\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:28901\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"busulfan\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1095795\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"EGb761\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0298346\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"MEK Inhibitor PD-98059\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1277078\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Human red blood cells, blood product\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0168957\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"halenaquinol sulfate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0032172\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Platelet activating factor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:22984\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"calcium atom\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0005456\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Binding Sites\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0025646\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Methionine\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:566274\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"malonaldehyde\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0053065\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Beauvericin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0035696\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Messenger RNA\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0165117\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"jasplakinolide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:5601\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"(+)-haematoxylin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0962522\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Su 6656\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0005050\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Benzimidazoles [Chemical/Ingredient]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0218197\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"cardiotoxin III, Naja naja atra\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0075116\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Src peptide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17939\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"puromycin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:9168\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"rapamycin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:15551\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"prostaglandin E2\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:6456\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"lidocaine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0037343\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Autacoids [Chemical/Ingredient]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0647210\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"monooxyethylene trimethylolpropane tristearate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:39867\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"valproic acid\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:28088\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"genistein\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:15422\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Atp\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0034424\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Quinolines [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0001771\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Agar\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16356\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"3',5'-cyclic GMP\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0597220\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"phospholipase inhibitor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEMBL:CHEMBL1977579\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Streptozocin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:131184\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"2-aminoethoxydiphenylborane\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:9287\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"streptonigrin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0021528\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Inosine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0378018\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"astragaloside A\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1449702\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Protein kinase inhibitor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0030956\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Peptide product\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0008838\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Cisplatin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0008838\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Cisplatin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:49603\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"lapatinib\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:74125\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"losartan carboxylic acid\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0038836\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Superoxides [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0070610\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"phenyl-2-aminoethyl sulfide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0906802\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"imatinib mesylate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1099354\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"RNA, Small Interfering [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0003364\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Hypotensive agent\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0162772\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Reactive Oxygen Species [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0527379\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Candesartan cilexetil\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0765885\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"beta-hydroxyisovalerylshikonin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0010934\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Dactinomycin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0597217\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"phosphatase inhibitor\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:16113\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"cholesterol\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:6570\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"lupeol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0289313\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Rosiglitazone\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0961045\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Ekb-569\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0682957\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"amine derivatives\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0964758\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Ws 1442\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0971473\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"cilengitide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0065374\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Lisinopril\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:38912\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Ro 31-8220\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:27732\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"caffeine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0063340\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Ifenprodil\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0070915\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"phosphoramidon\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:65329\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Ly294002\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0062565\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Herbimycin A\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:9516\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"thapsigargin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:80025\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Salinomycin\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0237795\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"pressors\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0006684\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Calcium channel blockers\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0029366\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Vanadates\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:8062\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"phenethyl caffeate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1566558\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"natural product\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:31536\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"emtricitabine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0013879\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Chemical element\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0042305\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Vanadates [Chemical/Ingredient]\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0045246\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"2,2'-azino-di-(3-ethylbenzothiazoline)-6-sulfonic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:59809\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"docetaxel trihydrate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0175000\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"catalpol\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0038317\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Steroid\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:47495\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0001645\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Beta-adrenergic Blocking Agents\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0772394\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Lepirudin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:27732\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"caffeine\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:46024\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"trichostatin A\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0914738\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"benzocycloheptapyridine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0012544\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Bisphosphonate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0033497\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"Propranolol\" . \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:8774\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"ramipril\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C1171350\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Kinase Inhibitor [EPC]\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:63618\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"pravastatin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0699251\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"acetylcysteine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0042010\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Uridine triphosphate\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0020349\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Hydroxyeicosatetraenoic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:52289\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"wortmannin\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:17154\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"nicotinamide\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:92413\" . \"CUI:C1705964\") (\"CUI:C1705964\" . \"CUI:C1336641\"))\n  ((\"5-[(2,5-dihydroxyphenyl)methyl-[(2-hydroxyphenyl)methyl]amino]-2-hydroxybenzoic acid\"\n    .\n    \"ERG wt Allele\")\n   (\"ERG wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0291658\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"Mk 996\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0048451\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"4-Methoxyamphetamine\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0040270\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"1,2-Dihydroxybenzene-3,5-Disulfonic Acid Disodium Salt [Chemical/Ingredient]\"\n    .\n    \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0013227\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Pharmaceutical / biologic product\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0014939\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Estrogens\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:15843\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"arachidonic acid\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CUI:C0042523\" . \"CUI:C1705997\") (\"CUI:C1705997\" . \"CUI:C1336641\"))\n  ((\"Verapamil\" . \"SRC wt Allele\")\n   (\"SRC wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\")))\n (0.48999999999999994\n  ((\"CHEBI:52289\" . \"CUI:C1705846\") (\"CUI:C1705846\" . \"CUI:C1336641\"))\n  ((\"wortmannin\" . \"ATM wt Allele\")\n   (\"ATM wt Allele\"\n    .\n    \"V-ets avian erythroblastosis virus e26 oncogene homolog\"))))\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/example-ontology.rkt",
    "content": ";; Expected outputs are block-commented after each expression.\n\n;; find ancestors of \"substance with phytoestrogen role\" in OBO:GOCHE ontology:\n(get-all-OBO:GOCHE-ancestors (keep 1 (find-concepts #t (list \"OBO:GOCHE_76989\"))))\n\n#|\n=>\n\n(set\n '(rtx2\n   5606341\n   \"OBO:GOCHE_52210\"\n   \"substance with pharmacological role role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_52210\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_52210\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5088598\n   \"OBO:GOCHE_24432\"\n   \"substance with biological role role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_24432\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_24432\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   885146\n   \"OBO:GOCHE_24621\"\n   \"substance with hormone role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_24621\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_24621\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5610174\n   \"OBO:GOCHE_33280\"\n   \"substance with molecular messenger role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_33280\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_33280\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5611882\n   \"OBO:GOCHE_50112\"\n   \"substance with sex hormone role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_50112\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_50112\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5611724\n   \"OBO:GOCHE_50906\"\n   \"substance with role role\"\n   (2 . \"http://w3id.org/biolink/vocab/NamedThing\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_50906\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"named_thing\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_50906\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5606343\n   \"OBO:GOCHE_48705\"\n   \"substance with agonist role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_48705\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_48705\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   947710\n   \"OBO:GOCHE_50114\"\n   \"substance with estrogen role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_50114\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_50114\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\"))))\n|#\n\n\n;; find descendants of \"substance with estrogen role\" in OBO:GOCHE ontology:\n(get-all-OBO:GOCHE-descendants (keep 1 (find-concepts #t (list \"OBO:GOCHE_50114\"))))\n\n#|\n=>\n\n(set\n '(rtx2\n   5606174\n   \"OBO:GOCHE_76989\"\n   \"substance with phytoestrogen role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_76989\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_76989\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5606175\n   \"OBO:GOCHE_76988\"\n   \"substance with xenoestrogen role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_76988\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_76988\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\"))))\n|#\n\n\n\n;; Examples finding the fixed-point of ancestor concepts in GO\n;; ontology.  (GO has multiple inheritance, which makes finding the\n;; fixed-point important.)\n\n;; Lymphangiogenesis\n(define S1 (keep 1 (find-concepts #t (list \"GO:0001946\"))))\n(define A1 (get-all-GO-ancestors S1))\n(pretty-print (get-curies/names-from-concepts A1))\n\n#|\n=>\n\n'((\"GO:0009653\" \"anatomical structure morphogenesis\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0048646\" \"anatomical structure formation involved in morphogenesis\")\n  (\"GO:0032502\" \"developmental process\"))\n|#\n\n;; negative regulation of cell migration involved in sprouting angiogenesis\n(define S2 (keep 1 (find-concepts #t (list \"GO:0090051\"))))\n(define A2 (get-all-GO-ancestors S2))\n(pretty-print (get-curies/names-from-concepts A2))\n\n#|\n=>\n\n'((\"GO:0010633\" \"negative regulation of epithelial cell migration\")\n  (\"GO:0065007\" \"biological regulation\")\n  (\"GO:0030334\" \"regulation of cell migration\")\n  (\"GO:0045765\" \"regulation of angiogenesis\")\n  (\"GO:0048523\" \"negative regulation of cellular process\")\n  (\"GO:0032879\" \"regulation of localization\")\n  (\"GO:0016525\" \"negative regulation of angiogenesis\")\n  (\"GO:0040013\" \"negative regulation of locomotion\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0043537\" \"negative regulation of blood vessel endothelial cell migration\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0030336\" \"negative regulation of cell migration\")\n  (\"GO:0010632\" \"regulation of epithelial cell migration\")\n  (\"GO:0051239\" \"regulation of multicellular organismal process\")\n  (\"GO:2000145\" \"regulation of cell motility\")\n  (\"GO:1901342\" \"regulation of vasculature development\")\n  (\"GO:0022603\" \"regulation of anatomical structure morphogenesis\")\n  (\"GO:0050793\" \"regulation of developmental process\")\n  (\"GO:0051271\" \"negative regulation of cellular component movement\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0043535\" \"regulation of blood vessel endothelial cell migration\")\n  (\"GO:2000026\" \"regulation of multicellular organismal development\")\n  (\"GO:0010594\" \"regulation of endothelial cell migration\")\n  (\"GO:0051270\" \"regulation of cellular component movement\")\n  (\"GO:0048519\" \"negative regulation of biological process\")\n  (\"GO:0051241\" \"negative regulation of multicellular organismal process\")\n  (\"GO:1901343\" \"negative regulation of vasculature development\")\n  (\"GO:2000181\" \"negative regulation of blood vessel morphogenesis\")\n  (\"GO:1903671\" \"negative regulation of sprouting angiogenesis\")\n  (\"GO:0051093\" \"negative regulation of developmental process\")\n  (\"GO:0010596\" \"negative regulation of endothelial cell migration\")\n  (\"GO:0090049\" \"regulation of cell migration involved in sprouting angiogenesis\")\n  (\"GO:2000146\" \"negative regulation of cell motility\")\n  (\"GO:1903670\" \"regulation of sprouting angiogenesis\")\n  (\"GO:0040012\" \"regulation of locomotion\"))\n|#\n\n;; positive regulation of execution phase of apoptosis\n(define S3 (keep 1 (find-concepts #t (list \"GO:1900119\"))))\n(define A3 (get-all-GO-ancestors S3))\n(pretty-print (get-curies/names-from-concepts A3))\n\n#|\n=>\n\n'((\"GO:0065007\" \"biological regulation\")\n  (\"GO:0042981\" \"regulation of apoptotic process\")\n  (\"GO:1900117\" \"regulation of execution phase of apoptosis\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0043067\" \"regulation of programmed cell death\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0048522\" \"positive regulation of cellular process\")\n  (\"GO:0043065\" \"positive regulation of apoptotic process\")\n  (\"GO:0010942\" \"positive regulation of cell death\")\n  (\"GO:0048518\" \"positive regulation of biological process\")\n  (\"GO:0010941\" \"regulation of cell death\")\n  (\"GO:0043068\" \"positive regulation of programmed cell death\"))\n|#\n\n;; positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis\n(define S4 (keep 1 (find-concepts #t (list \"GO:2001272\"))))\n(define A4 (get-all-GO-ancestors S4))\n(pretty-print (get-curies/names-from-concepts A4))\n\n#|\n=>\n\n'((\"GO:0065007\" \"biological regulation\")\n  (\"GO:0042981\" \"regulation of apoptotic process\")\n  (\"GO:0044093\" \"positive regulation of molecular function\")\n  (\"GO:0009893\" \"positive regulation of metabolic process\")\n  (\"GO:0019222\" \"regulation of metabolic process\")\n  (\"GO:0052547\" \"regulation of peptidase activity\")\n  (\"GO:0045862\" \"positive regulation of proteolysis\")\n  (\"GO:0051336\" \"regulation of hydrolase activity\")\n  (\"GO:0032270\" \"positive regulation of cellular protein metabolic process\")\n  (\"GO:1900117\" \"regulation of execution phase of apoptosis\")\n  (\"GO:2001056\" \"positive regulation of cysteine-type endopeptidase activity\")\n  (\"GO:0051171\" \"regulation of nitrogen compound metabolic process\")\n  (\"GO:0060255\" \"regulation of macromolecule metabolic process\")\n  (\"GO:0010950\" \"positive regulation of endopeptidase activity\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0043067\" \"regulation of programmed cell death\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0010604\" \"positive regulation of macromolecule metabolic process\")\n  (\"GO:0052548\" \"regulation of endopeptidase activity\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0048522\" \"positive regulation of cellular process\")\n  (\"GO:0051247\" \"positive regulation of protein metabolic process\")\n  (\"GO:0043065\" \"positive regulation of apoptotic process\")\n  (\"GO:0010942\" \"positive regulation of cell death\")\n  (\"GO:0010952\" \"positive regulation of peptidase activity\")\n  (\"GO:0031323\" \"regulation of cellular metabolic process\")\n  (\"GO:2000116\" \"regulation of cysteine-type endopeptidase activity\")\n  (\"GO:0051173\" \"positive regulation of nitrogen compound metabolic process\")\n  (\"GO:0048518\" \"positive regulation of biological process\")\n  (\"GO:0043085\" \"positive regulation of catalytic activity\")\n  (\"GO:0050790\" \"regulation of catalytic activity\")\n  (\"GO:0051246\" \"regulation of protein metabolic process\")\n  (\"GO:0051345\" \"positive regulation of hydrolase activity\")\n  (\"GO:0032268\" \"regulation of cellular protein metabolic process\")\n  (\"GO:0043280\" \"positive regulation of cysteine-type endopeptidase activity involved in apoptotic process\")\n  (\"GO:0010941\" \"regulation of cell death\")\n  (\"GO:2001270\" \"regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis\")\n  (\"GO:0043281\" \"regulation of cysteine-type endopeptidase activity involved in apoptotic process\")\n  (\"GO:0065009\" \"regulation of molecular function\")\n  (\"GO:0031325\" \"positive regulation of cellular metabolic process\")\n  (\"GO:1900119\" \"positive regulation of execution phase of apoptosis\")\n  (\"GO:0080090\" \"regulation of primary metabolic process\")\n  (\"GO:0030162\" \"regulation of proteolysis\")\n  (\"GO:0043068\" \"positive regulation of programmed cell death\"))\n|#\n\n;; cysteine-type endopeptidase activity involved in execution phase of apoptosis\n(define S5 (keep 1 (find-concepts #t (list \"GO:0097200\"))))\n(define A5 (get-all-GO-ancestors S5))\n(pretty-print (get-curies/names-from-concepts A5))\n\n#|\n=>\n\n'((\"GO:0097153\"\n   \"cysteine-type endopeptidase activity involved in apoptotic process\"))\n|#\n\n;; activation of JUN kinase activity\n(define S6 (keep 1 (find-concepts #t (list \"GO:0007257\"))))\n(define A6 (get-all-GO-ancestors S6))\n(pretty-print (get-curies/names-from-concepts A6))\n\n#|\n=>\n\n'((\"GO:0065007\" \"biological regulation\")\n  (\"GO:0043405\" \"regulation of MAP kinase activity\")\n  (\"GO:0044093\" \"positive regulation of molecular function\")\n  (\"GO:0023056\" \"positive regulation of signaling\")\n  (\"GO:0009893\" \"positive regulation of metabolic process\")\n  (\"GO:0019222\" \"regulation of metabolic process\")\n  (\"GO:0071900\" \"regulation of protein serine/threonine kinase activity\")\n  (\"GO:0032872\" \"regulation of stress-activated MAPK cascade\")\n  (\"GO:0080134\" \"regulation of response to stress\")\n  (\"GO:0032270\" \"positive regulation of cellular protein metabolic process\")\n  (\"GO:0045937\" \"positive regulation of phosphate metabolic process\")\n  (\"GO:0070304\" \"positive regulation of stress-activated protein kinase signaling cascade\")\n  (\"GO:0080135\" \"regulation of cellular response to stress\")\n  (\"GO:0001934\" \"positive regulation of protein phosphorylation\")\n  (\"GO:0051171\" \"regulation of nitrogen compound metabolic process\")\n  (\"GO:0060255\" \"regulation of macromolecule metabolic process\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0046328\" \"regulation of JNK cascade\")\n  (\"GO:0071902\" \"positive regulation of protein serine/threonine kinase activity\")\n  (\"GO:0031399\" \"regulation of protein modification process\")\n  (\"GO:0048583\" \"regulation of response to stimulus\")\n  (\"GO:0070302\" \"regulation of stress-activated protein kinase signaling cascade\")\n  (\"GO:0010604\" \"positive regulation of macromolecule metabolic process\")\n  (\"GO:0051338\" \"regulation of transferase activity\")\n  (\"GO:0001932\" \"regulation of protein phosphorylation\")\n  (\"GO:0010562\" \"positive regulation of phosphorus metabolic process\")\n  (\"GO:0051174\" \"regulation of phosphorus metabolic process\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0048522\" \"positive regulation of cellular process\")\n  (\"GO:0009966\" \"regulation of signal transduction\")\n  (\"GO:0023051\" \"regulation of signaling\")\n  (\"GO:0051347\" \"positive regulation of transferase activity\")\n  (\"GO:0043549\" \"regulation of kinase activity\")\n  (\"GO:0043410\" \"positive regulation of MAPK cascade\")\n  (\"GO:0043506\" \"regulation of JUN kinase activity\")\n  (\"GO:0000187\" \"activation of MAPK activity\")\n  (\"GO:0051247\" \"positive regulation of protein metabolic process\")\n  (\"GO:0045859\" \"regulation of protein kinase activity\")\n  (\"GO:0042325\" \"regulation of phosphorylation\")\n  (\"GO:1902531\" \"regulation of intracellular signal transduction\")\n  (\"GO:0033674\" \"positive regulation of kinase activity\")\n  (\"GO:0032147\" \"activation of protein kinase activity\")\n  (\"GO:0031323\" \"regulation of cellular metabolic process\")\n  (\"GO:0043507\" \"positive regulation of JUN kinase activity\")\n  (\"GO:0051173\" \"positive regulation of nitrogen compound metabolic process\")\n  (\"GO:1902533\" \"positive regulation of intracellular signal transduction\")\n  (\"GO:0048518\" \"positive regulation of biological process\")\n  (\"GO:0043085\" \"positive regulation of catalytic activity\")\n  (\"GO:0048584\" \"positive regulation of response to stimulus\")\n  (\"GO:0050790\" \"regulation of catalytic activity\")\n  (\"GO:0051246\" \"regulation of protein metabolic process\")\n  (\"GO:0046330\" \"positive regulation of JNK cascade\")\n  (\"GO:0032268\" \"regulation of cellular protein metabolic process\")\n  (\"GO:0043408\" \"regulation of MAPK cascade\")\n  (\"GO:0010647\" \"positive regulation of cell communication\")\n  (\"GO:0031401\" \"positive regulation of protein modification process\")\n  (\"GO:0043406\" \"positive regulation of MAP kinase activity\")\n  (\"GO:0032874\" \"positive regulation of stress-activated MAPK cascade\")\n  (\"GO:0065009\" \"regulation of molecular function\")\n  (\"GO:0031325\" \"positive regulation of cellular metabolic process\")\n  (\"GO:0042327\" \"positive regulation of phosphorylation\")\n  (\"GO:0009967\" \"positive regulation of signal transduction\")\n  (\"GO:0010646\" \"regulation of cell communication\")\n  (\"GO:0080090\" \"regulation of primary metabolic process\")\n  (\"GO:0045860\" \"positive regulation of protein kinase activity\")\n  (\"GO:0019220\" \"regulation of phosphate metabolic process\"))\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/example-synonymize.rkt",
    "content": ";; Find CURIE synonyms (and their descriptive names, for convenience) for the\n;; given CURIE.\n\n\n;; celecoxib\n(curie-synonyms/names \"CHEBI:41423\")\n;; This expression will give the same result because it's a synonym.\n;; The same should hold for all CURIE synonyms.\n;(curie-synonyms/names \"UMLS:C0538927\")\n\n#|\n=>\n\n((\"MTHSPL:JCX84Q7J1L\" . \"Celecoxib\")\n (\"CHEMBL.COMPOUND:CHEMBL118\" . \"CELECOXIB\")\n (\"DrugBank:DB00482\" . \"Celecoxib\")\n (\"CUI:C0538927\" . \"Celecoxib\")\n (\"MeSH:C105934\" . \"Celecoxib\")\n (\"CHEMBL:CHEMBL118\" . \"Celecoxib\")\n (\"NDFRT:N0000007233\" . \"Celecoxib [Chemical/Ingredient]\")\n (\"HMDB:HMDB0005014\" . \"Celecoxib\")\n (\"DRUGBANK:DB00482\" . \"Celecoxib\")\n (\"CHEBI:41423\" . \"celecoxib\")\n (\"RXNORM:140587\" . \"celecoxib\")\n (\"PUBCHEM:2662\" . \"Celecoxib\")\n (\"NDFRT:N0000148596\" . \"Celecoxib\")\n (\"UMLS:C0538927\" . \"celecoxib\"))\n|#\n\n\n;; e2f1\n(curie-synonyms/names \"UMLS:C0812258\")\n\n#|\n=>\n\n((\"UMLS:C0812258\" . \"E2F1 gene\")\n (\"OMIM:189971\" . \"E2f transcription factor 1\")\n (\"NCI:C18379\" . \"E2F1 gene\")\n (\"UniProtKB:Q9BSD8\" . \"E2F1 gene\")\n (\"HGNC:3113\" . \"E2F1 (human)\")\n (\"NCIT:C18379\" . \"E2F1 Gene\")\n (\"NCBIGene:1869\" . \"E2F transcription factor 1\")\n (\"UniProtKB:Q01094\" . \"E2F-1;\")\n (\"ENSEMBL:ENSG00000101412\"\n  .\n  \"E2F transcription factor 1 [Source:HGNC Symbol;Acc:HGNC:3113]\")\n (\"CUI:C0812258\" . \"E2f transcription factor 1\")\n (\"NCBIGENE:1869\" . \"E2F1 gene\"))\n\"query.rkt\">\n|#\n\n\n;; rhobtb2\n(curie-synonyms/names \"UMLS:C1425762\")\n\n#|\n=>\n\n((\"UniProtKB:Q9BYZ6\" . \"RHOBTB2\")\n (\"UniProtKB:E5RI44\" . \"RHOBTB2\")\n (\"UMLS:C1425762\" . \"RHOBTB2 gene\")\n (\"NCBIGene:23221\" . \"Rho related BTB domain containing 2\")\n (\"HGNC:18756\" . \"RHOBTB2 (human)\")\n (\"NCBIGENE:23221\" . \"RHOBTB2\")\n (\"OMIM:607352\" . \"Rho-related btb domain-containing protein 2\")\n (\"ENSEMBL:ENSG00000008853\"\n  .\n  \"Rho related BTB domain containing 2 [Source:HGNC Symbol;Acc:HGNC:18756]\")\n (\"CUI:C1425762\" . \"Rho-related btb domain-containing protein 2\"))\n\"query.rkt\">\n|#\n\n\n;; failure to thrive\n(curie-synonyms/names \"HP:0001508\")\n\n#|\n=>\n\n((\"MEDDRA:10047897\" . \"Weight gain poor\")\n (\"CUI:C0231246\" . \"Failure to gain weight\")\n (\"UMLS:C0231246\" . \"Failure to gain weight\")\n (\"CUI:C2315100\" . \"Pediatric failure to thrive\")\n (\"MEDDRA:10036164\" . \"Poor weight gain\")\n (\"UMLS:C2315100\" . \"Weight gain poor\")\n (\"HP:0001508\" . \"failure to thrive\"))\n|#\n\n\n;; bcr\n(curie-synonyms/names \"UMLS:C0812385\")\n\n#|\n=>\n\n((\"UniProtKB:H0Y554\" . \"BCR gene\")\n (\"UMLS:C0812385\" . \"BCR gene\")\n (\"NCBIGene:613\" . \"BCR activator of RhoGEF and GTPase\")\n (\"NCI:C18455\" . \"BCR gene\")\n (\"ENSEMBL:ENSG00000186716\"\n  .\n  \"BCR activator of RhoGEF and GTPase [Source:HGNC Symbol;Acc:HGNC:1014]\")\n (\"Orphanet:119016\" . \"BCR activator of RhoGEF and GTPase\")\n (\"NCBIGENE:613\" . \"BCR gene\")\n (\"NCIT:C18455\" . \"BCR Gene\")\n (\"UniProtKB:P11274\" . \"BCR\")\n (\"HGNC:1014\" . \"Bcr\")\n (\"OMIM:151410\" . \"Breakpoint cluster region\")\n (\"CUI:C0812385\" . \"Breakpoint cluster region\"))\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/gene-budging.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../../../medikanren/pieces-parts/query.rkt\"\n          racket/engine)\n\n(define make-directly-regulate-gene\n  (lambda (regulation-predicates)\n    (lambda (gene-curie)\n      (displayln \"\\nRunning 1-hop up query with concept categories\")\n      (define q (query/graph\n                 (\n                  ;; concepts\n                  (X       drug)\n                  (my-gene gene-curie)\n\t\t  )\n                 ;; edges\n                 ((X->my-gene regulation-predicates))\n                 ;; paths\n                 (X X->my-gene my-gene)))\n      q)))\n\n(define directly-upregulate-gene (make-directly-regulate-gene positively-regulates))\n(define directly-downregulate-gene (make-directly-regulate-gene negatively-regulates))\n\n\n\n(define curie-to-anything\n  (lambda (curie predicate*)\n    ;;(printf \"starting curie-to-anything with curie ~s and preds ~s\\n\" curie predicate*)\n    (let ((val (query/graph\n                ( ;; concepts\n                 (X curie)\n                 (T #f))\n                ;; edges\n                ((X->T predicate*))\n                ;; paths      \n                (X X->T T))))\n      ;;(printf \"finished curie-to-anything with curie ~s and preds ~s\\n\" curie predicate*)\n      val)))\n\n(define curie-to-tradenames\n  (lambda (curie)\n    (curie-to-anything curie '(\"has_tradename\"))))\n\n(define curie-to-clinical-trials\n  (lambda (curie)\n    (curie-to-anything curie '(\"clinically_tested_approved_unknown_phase\"\n                               \"clinically_tested_terminated_phase_2\"\n                               \"clinically_tested_terminated_phase_3\"\n                               \"clinically_tested_terminated_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2\"\n                               \"clinically_tested_suspended_phase_2\"\n                               \"clinically_tested_suspended_phase_3\"\n                               \"clinically_tested_suspended_phase_2_or_phase_3\"))))\n\n(define curie-to-indicated_for\n  (lambda (curie)\n    (curie-to-anything curie '(\"indicated_for\"))))\n\n(define curie-to-contraindicated_for\n  (lambda (curie)\n    (curie-to-anything curie '(\"contraindicated_for\"))))\n\n\n(define pubmed-URLs-from-composite-edge\n  (lambda (composite-edge)\n    ;;(printf \"starting pubmed-URLs-from-composite-edge\\n\")\n    (define concrete-edges (list-ref composite-edge 2))\n    ;;(printf \"concrete-edges length = ~s\\n\" (length concrete-edges))\n    (let ((url-ls (map pubmed-URLs-from-edge concrete-edges)))\n      ;;(printf \"url-ls = ~s\\n\" url-ls)\n      (remove-duplicates (append* url-ls)))))\n\n\n(define drug-info-for-curie\n  (lambda (curie)\n    ; (printf \"*** starting drug-info-for-curie ~s\\n\" curie)\n    (map\n     (lambda (l)\n       (match l\n         [`(,name . ,q)\n          ; (printf \"*** calculating curie-synonyms/names list for curie ~s\\n\" curie)\n          (let ((ls (map curie-synonyms/names (curies/query q 'T))))\n            ; (printf \"*** calculated curie-synonyms/names list for curie ~s\\n\" curie)\n            ; (printf \"*** ls length = ~s\\n\" (apply + (map length ls)))\n            (cons name ls))]))\n     (list \n      (cons 'tradenames (curie-to-tradenames curie))\n      (cons 'clinical-trials (curie-to-clinical-trials curie))\n      (cons 'indicated_for (curie-to-indicated_for curie))\n      (cons 'contraindicated_for (curie-to-contraindicated_for curie))))))\n\n\n(define drug-info-from-composite-edge\n  (lambda (composite-edge)    \n    (define curie (caar composite-edge))\n    ; (printf \"*** drug-info-from-composite-edge for curie = ~s\\n\" curie)\n    (define pubmed-URLs (pubmed-URLs-from-composite-edge composite-edge))\n    ; (printf \"*** calculating curie-synonyms/names\\n\")\n    (define synonyms/names (curie-synonyms/names curie))\n    ; (printf \"*** calculated curie-synonyms/names of length ~s\\n\" (length synonyms/names))\n    (append\n     (list (cons 'curie curie))\n     (list (cons 'curie-synonyms/names synonyms/names))\n     (drug-info-for-curie curie)\n     (list (cons 'pubmeds pubmed-URLs)))))\n\n(define drug-info-for-tsv-from-composite-edge\n  (lambda (composite-edge)\n    (match composite-edge\n      (`((,composite-subject . ,composite-object) ,score ,edges)\n        (define subject-info (map cdr (drug-info-for-curie composite-subject)))\n        (append*\n          (map (lambda (edge)\n                 (define pub-info (publications-info-alist-from-edge edge))\n                 (define pub-urls (pubmed-URLs-from-edge edge))\n                 (match edge\n                   [`(,db\n                       ,edge-id\n                       (,_ ,subject-curie ,subject-name (,_ . ,subject-cat) . ,_)\n                       (,_ ,object-curie ,object-name (,_ . ,object-cat) . ,_)\n                       (,_ . ,predicate) . ,_)\n                     (define (entry pubmed-url pub-date sentence)\n                       (append\n                         (list db\n                               subject-curie subject-cat subject-name\n                               predicate\n                               object-name object-cat object-curie\n                               pubmed-url pub-date sentence)\n                         subject-info))\n                     (cond ((pair? pub-info)\n                            (map (lambda (info)\n                                   (match info\n                                     [`(,pubmed-url ,pub-date ,subject-score ,object-score ,sentence)\n                                       (entry pubmed-url pub-date sentence)]))\n                                 pub-info))\n                           ((pair? pub-urls)\n                            (map (lambda (url) (entry url \"\" \"\")) pub-urls))\n                           (else (list (entry \"\" \"\" \"\"))))]))\n               edges))))))\n\n\n(define (make-dr-query1-up/down direction directly-up/down-regulate-gene)\n  (lambda (the-gene-curie the-gene-symbol)\n\n    ; (printf \"*** getting directly ~s for gene CURIE ~s\\n\" direction the-gene-curie)\n    \n    (define directly-up/down (directly-up/down-regulate-gene the-gene-curie))\n    ;; returns the set of all query results (for X, for gene, for edges X->my-gene, etc.)\n\n    ;; unused\n    ;; (define directly-up/down-Xs (curies/query directly-up/down 'X))\n\n    ; (printf \"*** getting edges/X->directly-~s for gene CURIE ~s\\n\" direction the-gene-curie)\n  \n    ;; each edge corresponds to an X in Xs\n    (define edges/X->directly-up/down (edges/ranked (ranked-paths directly-up/down) 0 0))\n\n    (printf \"*** getting directly-~s-drug-info for gene CURIE ~s\\n\" direction the-gene-curie)\n  \n    (define directly-up/down-drug-info (map drug-info-from-composite-edge edges/X->directly-up/down))\n\n    (printf \"*** getting directly-~s-drug-info-for-tsv for gene CURIE ~s\\n\" direction the-gene-curie)\n  \n    (define directly-up/down-drug-info-for-tsv (map drug-info-for-tsv-from-composite-edge edges/X->directly-up/down))\n\n    (printf \"*** finished getting directly-~s-drug-info-for-tsv for gene CURIE ~s\\n\" direction the-gene-curie)\n\n    directly-up/down-drug-info-for-tsv\n        \n    ))\n\n(define dr-query1-up (make-dr-query1-up/down 'up directly-upregulate-gene))\n\n(define dr-query1-down (make-dr-query1-up/down 'down directly-downregulate-gene))\n\n\n(define (dr-query1 the-gene-curie)\n\n  (printf \"*** dr-query1 called for gene CURIE ~s\\n\" the-gene-curie)\n\n  (printf \"*** getting gene symbol for gene CURIE ~s\\n\" the-gene-curie)\n  \n  (define the-gene-symbol (concept->name (car (find-concepts #t (list the-gene-curie)))))\n  \n  (printf \"*** found gene symbol ~s for gene CURIE ~s\\n\" the-gene-symbol the-gene-curie)\n\n  (printf \"*** finding up-regulators for gene CURIE ~s\\n\" the-gene-curie)\n\n  (define up-query-results (dr-query1-up the-gene-curie the-gene-symbol))\n    \n  ; (printf \"*** finding down-regulators for gene CURIE ~s\\n\" the-gene-curie)\n\n  (define down-query-results (dr-query1-down the-gene-curie the-gene-symbol))\n  \n  (define my-query-result (append up-query-results down-query-results))\n  \n  (define output-file-name (format \"~a-budging.tsv\" (string-replace the-gene-symbol \"/\" \"-\")))\n  \n  ; (printf \"*** writing results for gene CURIE ~s to file ~s\\n\" the-gene-curie output-file-name)\n  \n  (with-output-to-file output-file-name\n    (tsv-for the-gene-curie the-gene-symbol my-query-result)\n    #:exists 'replace)\n\n  ; (printf \"*** finished processing gene CURIE ~s\\n\" the-gene-curie)\n\n  'finished\n  )\n\n(define (dr-query gene-curies)\n  (for-each\n    (lambda (curie)\n      ;; 10 minute timeout per curie\n      (define timeout-ms (* 10 60 1000))\n      ; (printf \"@@@ dr-query creating engine for curie ~s\\n\" curie)\n      (define eng (engine (lambda (p)\n                            (dr-query1 curie))))\n      ; (printf \"@@@ dr-query running engine for ~s ms for curie ~s\\n\" timeout-ms curie)\n      (engine-run timeout-ms eng)\n      ; (printf \"@@@ dr-query engine for curie ~s finished\\n\" curie)\n      ; (if (engine-result eng)\n      ;   (printf \"@@@ dr-query engine for curie ~s ran to completion\\n\" curie)\n      ;   (printf \"@@@ dr-query engine for curie ~s timed out!!\\n\" curie))\n      ;(printf \"@@@ dr-query killing engine for curie ~s\\n\" curie)\n      (engine-kill eng)\n      ;(printf \"@@@ dr-query killed engine for curie ~s\\n\" curie)\n      )\n    gene-curies))\n\n(define (tsv-for gene-curie gene-symbol infos)\n  (lambda ()\n    (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n            \"gene CURIE\"\n            \"gene symbol\"\n            \"db\"\n            \"subject CURIE\" \"subject category\" \"subject\"\n            \"predicate\"\n            \"object\" \"object category\" \"object CURIE\"\n            \"pub URL\" \"pub date\" \"pub sentence\"\n            \"tradenames\" \"clinical trials\" \"indicated for\" \"contraindicated for\")\n    (for-each (lambda (xs)\n                (for-each (lambda (x)\n                            (apply printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n                                   gene-curie gene-symbol x))\n                          xs))\n              infos)))\n\n\n\n\n; (define the-gene-curies (list \"HGNC:11390\" \"HGNC:13557\" \"HGNC:2537\"))\n; (define the-gene-curies (list \"HGNC:29079\" \"HGNC:11390\" \"HGNC:13557\" \"HGNC:2537\"))\n\n; kdm1a\n; (define the-gene-curies (list \"HGNC:29079\"))\n\n; ACE2\n;(define the-gene-curies (list \"HGNC:13557\"))\n\n; CTSL\n;(define the-gene-curies (list \"HGNC:2537\"))\n\n;; TMPRSS2\n#|\n(define the-gene-curies  (list \"HGNC:11876\"))\n(map curie-synonyms-raw the-gene-curies)\n(map curie-synonyms/names the-gene-curies)\n(define alt-gene-curies  (list \"UMLS:C1336641\"))\n(dr-query the-gene-curies)\n|#\n\n#|\n;; aurkb\n(define aurkb-directly-up (directly-upregulate-gene \"HGNC:11390\"))\n;; returns the set of all query results (for X, for gene, for edges X->my-gene, etc.)\n\n(define aurkb-directly-up-Xs (curies/query aurkb-directly-up 'X))\n\n;; each edge corresponds to an X in aurkb-Xs\n(define edges/X->aurkb-directly-up (edges/ranked (ranked-paths aurkb-directly-up) 0 0))\n\n(define aurkb-directly-up-drug-info (map drug-info-from-composite-edge edges/X->aurkb-directly-up))\n|#\n\n#|\n(printf \"starting downregulation...\\n\")\n\n(define kdm1a-directly-down (directly-downregulate-gene \"HGNC:29079\"))\n;; returns the set of all query results (for X, for gene, for edges X->my-gene, etc.)\n\n(define kdm1a-directly-down-Xs (curies/query kdm1a-directly-down 'X))\n\n;; each edge corresponds to an X in kdm1a-Xs\n(define edges/X->kdm1a-directly-down (edges/ranked (ranked-paths kdm1a-directly-down) 0 0))\n\n;; \n(define kdm1a-directly-down-drug-info (map drug-info-from-composite-edge edges/X->kdm1a-directly-down))\n|#\n\n\n\n;;; 2-hop\n\n;; ACE2   HGNC:13557\n\n;; CTSL   HGNC:2537\n\n;; include semmed sentences, when possible  (date would be nice)\n\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/lib.rkt",
    "content": "(define (filter-edges a-drug predicates)\n  (define q\n    (time\n     (query/graph\n      ((X a-drug)\n       (O #f))\n      ((X->O predicates))\n      (X X->O O))))\n  (map curie-synonyms/names (curies/query q 'O)))\n\n(define (side-effects a-drug)\n  (filter-edges a-drug (list \"causes\" \"contributes_to\")))\n\n(define (counterindications a-drug)\n  (filter-edges a-drug (list \"contraindicated_with_disease\")))\n\n;;(side-effects imatinib)\n;;(counterindications imatinib)\n\n(define (all-predicates start)\n(define q\n  (time\n   (query/graph\n    ((X start)\n     (O #f))\n    ((X->O #f))\n    (X X->O O))))\n(sort (remove-duplicates (map (lambda (e) (cdr (list-ref e 4))) (edges/query q 'X->O))) string<=?)\n)\n;;(all-predicates imatinib)\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/make-map-fast.rkt",
    "content": "#lang racket\n\n(require\n racket/date\n racket/runtime-path)\n\n#|\n\nGenerate tab-separed value (TSV) files describing the mappings between\nconcepts for a specified Knowledge Graph (KG).\n\n\nHere are the tab-sepated columns for each of the generated TSV files.\n\nCURIE-prefix to CURIE-prefix mapping:\n\nsubject concept CURIE-prefix\nobject concept CURIE-prefix\npredicate string\nedge counts\n\n\n\nconcept-category to concept-category mapping:\n\nsubject concept category\nobject concept category\npredicate string\nedge counts\n\n\n\n**CAUTION**\n\nThis implementation reads from the KG's raw data files to reduce the\nrunning time and (especially) to reduce the (RAM) memory footprint.\nAs a result, this code makes assumptions about the formats of the raw\n'biolink' KG files, which is fragile.  This code would need to be\nmodified to work with the 'biolink2' KG file format, for\nexample (although rewriting the code to take advantage of the\n'biolink2' improvements may make more sense).\n\n|#\n\n\n\n;; *** Change this string to match the name of the KG you want to map! ***\n;(define kg-name \"chemstructure\")\n;(define kg-name \"co-occur\")\n;(define kg-name \"covid19\")\n;(define kg-name \"orange\")\n;(define kg-name \"pr-owl\")\n;(define kg-name \"robokop\")\n(define kg-name \"rtx2_2020_09_16\")\n;(define kg-name \"semmed\")\n;(define kg-name \"sri-reference-kg-0.2.0\")\n;(define kg-name \"sri_semmeddb\")\n;(define kg-name \"textminingprovider\")\n;(define kg-name \"umlsmeta\")\n;(define kg-name \"unichem\")\n\n\n#|\nDefine paths to the critical data files for the given KG.\n|#\n(define-runtime-path path:root \"..\")\n(define (path/root relative-path)   (build-path path:root relative-path))\n(define path:data                   (path/root \"data\"))\n(define (path/data relative-path)   (build-path path:data kg-name relative-path))\n(define path:kg-maps                (build-path path:root \"kg-maps\"))\n(define path:kg-maps/kg-name        (build-path path:kg-maps kg-name))\n(define (path/kg-map/kg-name relative-path) (build-path path:kg-maps/kg-name relative-path))\n\n(define predicates-file-path (path/data \"predicates.scm\"))\n(define categories-file-path (path/data \"categories.scm\"))\n(define concepts-file-path   (path/data \"concepts.scm\"))\n(define edges-file-path      (path/data \"edges.scm\"))\n\n\n;; Create the directories to hold the KG maps, if they do not exist already\n(unless (directory-exists? path:kg-maps)\n  (printf \"directory ~s not found\\ncreating directory ~s\\n\" path:kg-maps path:kg-maps)\n  (make-directory path:kg-maps))\n\n(unless (directory-exists? path:kg-maps/kg-name)\n  (printf \"directory ~s not found\\ncreating directory ~s\\n\" path:kg-maps/kg-name path:kg-maps/kg-name)\n  (make-directory path:kg-maps/kg-name))\n\n\n#|\nDefine file names and paths for the output TSV files.\n|#\n(define TSV-file-name-suffix \".tsv\")\n\n(define CURIE-prefix_to_CURIE-prefix-file-name-prefix \"subject-prefix_object-prefix_predicate_count\")\n(define CURIE-prefix_to_CURIE-prefix-file-name\n  (string-append CURIE-prefix_to_CURIE-prefix-file-name-prefix TSV-file-name-suffix))\n(define CURIE-prefix_to_CURIE-prefix-file-path\n  (path/kg-map/kg-name CURIE-prefix_to_CURIE-prefix-file-name))\n\n(define category_to_category-file-name-prefix \"subject-category_object-category_predicate_count\")\n(define category_to_category-file-name\n  (string-append category_to_category-file-name-prefix TSV-file-name-suffix))\n(define category_to_category-file-path\n  (path/kg-map/kg-name category_to_category-file-name))\n\n;; Represents a CURIE that does not conform to the standard : CURIE format.\n(define NON-STANDARD-CURIE-STRING \"*non-standard CURIE*\")\n\n\n\n#|\nTakes a Racket date object and returns a string containing the\nhour:minute:second + date in a pretty format.\n|#\n(define date->pretty-time/date\n  (lambda (d)\n    (let ((h (date-hour d))\n          (m (date-minute d))\n          (s (date-second d)))\n      (let ((num->pretty-string\n             (lambda (n)\n               (if (< n 10)\n                   (string-append \"0\" (number->string n))\n                   (number->string n)))))\n        (format \"~a:~a:~a ~a\"\n                (num->pretty-string h)\n                (num->pretty-string m)\n                (num->pretty-string s)\n                (date->string d))))))\n\n\n(printf \"\\n\\nProcessing KG ~s\\n\" kg-name)\n(printf \"started processing at ~s\\n\" (date->pretty-time/date (current-date)))\n(define start-seconds (current-seconds))\n\n#|\nOpen a text file with the given file path, reading in each row, and\nreturning a vector of those values. Closes the file automatically.\n|#\n(define file->vector\n  (lambda (file-path)\n    (with-input-from-file file-path\n      (lambda ()\n        (let loop ((ls '())\n                   (x (read)))\n          (cond\n            ((eof-object? x) (list->vector (reverse ls)))\n            (else (loop (cons x ls) (read))))))\n      #:mode 'text)))\n\n#|\nVector containing all the predicate strings for the given KG,\nin the same order as in the KG's 'predicates.scm' file.\n|#\n(define predicates-vector (file->vector predicates-file-path))\n(printf \"created predicates vector with ~s entries\\n\" (vector-length predicates-vector))\n\n#|\nVector containing all the category strings for the given KG,\nin the same order as in the KG's 'categories.scm' file.\n|#\n(define categories-vector (file->vector categories-file-path))\n(printf \"created categories vector with ~s entries\\n\" (vector-length categories-vector))\n\n\n#|\nReturns the number of rows in a file.\n|#\n(define count-number-of-rows\n  (lambda (file-path)\n    (printf \"counting the number of rows in file ~s\\n\" file-path)\n    (time\n     (with-input-from-file file-path\n       (lambda () (let loop ((i 0) (x (read-char)))\n                    (cond\n                      [(eof-object? x) i]\n                      [(char=? x #\\newline) (loop (add1 i) (read-char))]\n                      [else (loop i (read-char))])))\n       #:mode 'text))))\n\n\n#|\nTakes a string representing a CURIE.\n\nIf the string is a \"standard\" CURIE of the form\n\n:\n\nthen 'get-curie-prefix' returns the string .\n\nOtherwise, the string is not a CURIE in the standard format,\nin which case 'get-curie-prefix' returns #f.\n|#\n(define get-curie-prefix\n  (lambda (curie)\n    (cond\n      [(string-contains? curie \":\")\n       (let ((curie-prefix (car (string-split curie \":\" #:trim? #f))))\n         curie-prefix)]\n      [else #t])))\n\n#|\nNumber of distinct concepts in the KG.\n|#\n(define num-concepts (count-number-of-rows concepts-file-path))\n(printf \"KG ~s contains ~s distinct concepts\\n\" kg-name num-concepts)\n\n\n#|\nVector that maps concept indices (natural numbers) to CURIE prefixes.\n\nTo find the CURIE prefix for the concept with index N, reference the\nNth entry in 'concept->curie-prefix-vector'.  For example, this\nexpression will return the CURIE prefix for concept 7:\n\n(vector-ref concept->curie-prefix-vector 7)\n\nIf the CURIE string for a concept does not match the standard\n: format, the vector will instead contain the special\nstring bound to the NON-STANDARD-CURIE-STRING constant.\n|#\n(define concept->curie-prefix-vector (make-vector num-concepts))\n\n#|\nVector that maps concept indices (natural numbers) to category indices (natural numbers).\n\nTo find the category index for the concept with index N, reference the\nNth entry in 'concept->category-vector'.  For example, this expression\nwill return the category index for concept 7:\n\n(vector-ref concept->category-vector 7)\n\nTo map the category index to the category name, reference the category\nindex in 'categories-vector':\n\n(vector-ref categories-vector (vector-ref concept->category-vector 7))\n|#\n(define concept->category-vector (make-vector num-concepts))\n\n(time\n (with-input-from-file concepts-file-path\n   (lambda ()\n     (let loop ((i 0) ;; number of concepts read in\n                (good-curie-count 0) ;; number of CURIEs in the standard : format\n                (non-standard-curie-count 0) ;; number of CURIEs that don't match the standard format\n                (x (read)))\n       (when (zero? (modulo i (expt 10 5)))\n         (printf \"read ~s concepts, with ~s good CURIES and ~s non-standard CURIES so far...\\n\"\n                 i good-curie-count non-standard-curie-count))\n       (cond\n         ((eof-object? x)\n          (printf \"finished reading all ~s concepts, with \\n~s good CURIES and ~s non-standard CURIES\\n\"\n                  i good-curie-count non-standard-curie-count)\n          (void))\n         (else\n          (let ((concept-vec x))\n            (let ((curie (vector-ref concept-vec 0))\n                  (category (vector-ref concept-vec 1)))\n              (begin\n                ;; set the category for the current concept in the\n                ;; 'concept->category-vector' vector\n                (vector-set! concept->category-vector i category)\n                (let ((curie-prefix (get-curie-prefix curie)))\n                  (cond\n                    [curie-prefix ;; We were able to get the prefix of the CURIE string\n                     (begin\n                       (vector-set! concept->curie-prefix-vector i curie-prefix)\n                       (loop (add1 i)\n                             (add1 good-curie-count)\n                             non-standard-curie-count\n                             (read)))]\n                    [else ;; the CURIE string does not match the standard : format\n                     (begin\n                       (vector-set! concept->curie-prefix-vector i NON-STANDARD-CURIE-STRING)\n                       (loop (add1 i)\n                             good-curie-count\n                             (add1 non-standard-curie-count)\n                             (read)))])))))))))\n   #:mode 'text))\n\n(printf \"populated concept->curie-prefix-vector with ~s entries\\n\" (vector-length concept->curie-prefix-vector))\n(printf \"populated concept->category-vector with ~s entries\\n\" (vector-length concept->category-vector))\n\n\n;; functions that map ids (natural numbers) to strings\n(define identity (lambda (x) x))\n(define concept-id->curie-prefix (lambda (x) (vector-ref concept->curie-prefix-vector x)))\n(define category-id->category-name (lambda (x) (vector-ref categories-vector x)))\n(define predicate-id->predicate-name (lambda (x) (vector-ref predicates-vector x)))\n\n\n#|\nHash table containing a mapping between the key:\n\n(list subject-id object-id predicate-id)\n\nand:\n\nedge-count\n\nwhere 'edge-count' is the number of entries in the hash-table\nthat match the key.\n|#\n(define subject-prefix/object-prefix/predicate-id-hash (make-hash))\n\n#|\nHash table containing a mapping between the key:\n\n(list subject-category-id object-category-id predicate-id)\n\nand:\n\nedge-count\n\nwhere 'edge-count' is the number of entries in the hash-table\nthat match the key.\n|#\n(define subject-category-id/object-category-id/predicate-id-hash (make-hash))\n\n(time\n (with-input-from-file edges-file-path\n   (lambda ()\n     (let loop ((i 0)\n                (x (read)))\n       (when (zero? (modulo i (expt 10 5)))\n         (printf \"read \\n~s edges so far...\\n\" i))\n       (cond\n         ((eof-object? x) (void))\n         (else\n          (let ((edge-vec x))\n            (let ((subject-id (vector-ref edge-vec 0))\n                  (predicate-id (vector-ref edge-vec 1))\n                  (object-id (vector-ref edge-vec 2)))\n              (let ((subject-prefix (concept-id->curie-prefix subject-id))\n                    (object-prefix (concept-id->curie-prefix object-id))\n                    (subject-category-id (vector-ref concept->category-vector subject-id))\n                    (object-category-id (vector-ref concept->category-vector object-id)))\n                (let ((subject-prefix/object-prefix/predicate-id-key\n                       (list subject-prefix object-prefix predicate-id))\n                      (subject-category-id/object-category-id/predicate-id-key\n                       (list subject-category-id object-category-id predicate-id)))\n                  (let ((subject-prefix/object-prefix/predicate-id-edge-count\n                         (let ((c (hash-ref subject-prefix/object-prefix/predicate-id-hash\n                                            subject-prefix/object-prefix/predicate-id-key\n                                            #f)))\n                           (if c (add1 c) 1)))\n                        (subject-category-id/object-category-id/predicate-id-edge-count\n                         (let ((c (hash-ref subject-category-id/object-category-id/predicate-id-hash\n                                            subject-category-id/object-category-id/predicate-id-key\n                                            #f)))\n                           (if c (add1 c) 1))))\n                    (begin\n                      ;;\n                      (hash-set! subject-prefix/object-prefix/predicate-id-hash\n                                 subject-prefix/object-prefix/predicate-id-key\n                                 subject-prefix/object-prefix/predicate-id-edge-count)\n                      ;;\n                      (hash-set! subject-category-id/object-category-id/predicate-id-hash\n                                 subject-category-id/object-category-id/predicate-id-key\n                                 subject-category-id/object-category-id/predicate-id-edge-count)\n                      ;;\n                      (loop (add1 i) (read))))))))))))\n   #:mode 'text))\n\n\n(printf \"populated subject-prefix/object-prefix/predicate-id-hash hash table with ~s entries\\n\"\n        (hash-count subject-prefix/object-prefix/predicate-id-hash))\n(printf \"subject-prefix/object-prefix/predicate-id-hash hash table: ~s\\n\"\n        subject-prefix/object-prefix/predicate-id-hash)\n\n(printf \"populated subject-category-id/object-category-id/predicate-id-hash hash table with ~s entries\\n\"\n        (hash-count subject-category-id/object-category-id/predicate-id-hash))\n(printf \"subject-category-id/object-category-id/predicate-id-hash hash table: ~s\\n\"\n        subject-category-id/object-category-id/predicate-id-hash)\n\n\n\n#|\n'print-tab-separated-line' takes a list of values, and prints each\nvalue in the list, separated by tab characters. A newline-character,\ninstead of a tab character, is printed after the last value in the\nlist.\n|#\n(define print-tab-separated-line\n  (lambda (args)\n    (cond\n      ((null? args) (newline))\n      ((null? (cdr args))\n       (begin\n         (display (car args))\n         (print-tab-separated-line (cdr args))))\n      (else\n       (begin\n         (display (car args))\n         (display #\\tab)\n         (print-tab-separated-line (cdr args)))))))\n\n#|\nSorts and writes the hash-table information to a TSV file,\nwith the \"prettified\" values in the 'key' list written first,\nfollowed by the edge counts.\n\n'tsv-file-path' is the path to the TSV file to be written\n\n'map-hash-table' is the hash table whose prettified information is to\nbe written to the TSV\n\n'column-names-string' must be a format string\n\n'prettify-functions' must be a list of functions, the same length as 'key'\n|#\n(define sort-and-write-map-hash-table-to-tsv-file\n  (lambda (tsv-file-path map-hash-table column-names-string prettify-functions)\n    (printf \"writing output to ~s...\\n\" tsv-file-path)\n    (let ((list-of-list-of-strings\n           (map\n            (lambda (key)\n              (let ((pretty-values (map (lambda (f a) (f a)) prettify-functions key))\n                    (edge-count-string (format \"~s\" (hash-ref map-hash-table key))))\n                (let ((string-ls (append pretty-values (list edge-count-string))))\n                  string-ls)))\n            (hash-keys map-hash-table))))\n      (let ((sorted-list-of-list-of-strings\n             (sort\n              list-of-list-of-strings\n              (lambda (los1 los2)\n                (cond\n                  [(and\n                    (string? (car los1))\n                    (string? (car los2))\n                    (string-cipredicate-name))\n\n#|\nGenerate TSV file with the subject concept category, object concept\ncategory, predicate, and edge counts\n|#\n(sort-and-write-map-hash-table-to-tsv-file\n category_to_category-file-path\n subject-category-id/object-category-id/predicate-id-hash\n \"subject category\\tobject category\\tpredicate\\tedge count\\n\"\n (list\n  category-id->category-name\n  category-id->category-name\n  predicate-id->predicate-name))\n\n(define end-seconds (current-seconds))\n\n(printf \"Finished processing KG ~s\\n\" kg-name)\n(printf \"finished processing at ~s\\n\" (date->pretty-time/date (current-date)))\n(printf \"~s seconds elapsed wall-time\\n\\n\" (- end-seconds start-seconds))\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/make-map.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/repr.rkt\"\n  \"../../../medikanren/pieces-parts/common.rkt\"\n  )\n\n(define db (cdr (car (databases))))\n\n;; gets all edges\n(define result (time (run* (e) (edgeo e))))\n\n\n;; gets the prefix for a certain concept (i.e. \"MONDO\")\n(define (concept->prefix concept)\n  (car (string-split (concept->curie concept) \":\" #:trim? #f))\n  )\n\n;; creates a set of all unique edges ordered by subject, object, and predicate\n(define graph\n  (foldl\n   (lambda (e s)\n     (let ((subject-prefix (concept->prefix (edge->subject e)))\n           (predicate (cdr (edge->pred e)))\n           (object-prefix (concept->prefix (edge->object e))))\n       (set-add s (list subject-prefix object-prefix predicate))))\n   (set) result))\n\n#|\nOutputs the edges into dot format in a file\n\nThe entire dot graph can then be copied and pasted into a vis.js file and parsed as a DOT network. \n|#\n(define out (open-output-file \"orange_graph.dot\" #:exists 'replace))\n(fprintf out \"digraph{graph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, fontsize=12 ]; node [ fontname=Arial, fontcolor=blue, fontsize=11]; edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ]; splines=\\\"FALSE\\\"; rankdir=\\\"LR\\\";\")\n(set-for-each\n graph\n (lambda (t)\n   (apply fprintf out \"\\t~s -> ~s [label=~s]; \" t)))\n(fprintf out \"}\")\n(close-output-port out)\n\n\n\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/make-provenance-map-fast.rkt",
    "content": "#lang racket\n\n(require\n  racket/runtime-path)\n\n;; Creates a map of the provenance of the edges of a KG, using the \"provided_by\" edge attribute.\n;; Fast, since we read directly from the raw data files.\n\n;; *** Change this string to match the name of the KG you want to map! ***\n;(define kg-name \"rtx2_2020_09_16\")\n;(define kg-name \"textminingprovider\")\n;(define kg-name \"pr-owl\")\n;(define kg-name \"co-occur\")\n;(define kg-name \"orange\")\n\n(define-runtime-path path:root \"..\")\n(define (path/root relative-path) (build-path path:root relative-path))\n(define path:data                 (path/root \"data\"))\n(define (path/data relative-path) (build-path path:data kg-name relative-path))\n\n(define edges-file-path (path/data \"edges.scm\"))\n\n\n(define edge-provenance-hash\n  (time\n   (with-input-from-file\n       edges-file-path\n     (lambda ()\n       (let ((ht (make-hash)))\n         (let loop ((i 0)\n                    (x (read)))\n           (when (= (modulo i 100000) 0)\n             (printf \"read \\n~s edges so far...\\n\" i)\n             ;(printf \"ht: ~s\\n\" ht)\n             )\n           (cond\n             ((eof-object? x) ht)\n             (else\n              (let ((edge-properties-alist (vector-ref x 3)))\n                (let ((provided_by-entry (assoc \"provided_by\" edge-properties-alist)))\n                  (let ((key (if provided_by-entry\n                                 (cdr provided_by-entry)\n                                 '__no-provided-by-info__)))\n                    (let ((count (hash-ref ht key #f)))\n                      (begin\n                        (if count\n                            (hash-set! ht key (add1 count))\n                            (hash-set! ht key 1))\n                        (loop (add1 i) (read))))))))))))\n     #:mode 'text)))\n\n(printf \"created edge-provenance hash table with ~s entries\\n\" (hash-count edge-provenance-hash))\n(printf \"edge-provenance hash table: ~s\\n\" edge-provenance-hash)\n\n\n(define sorted-provenance-counts\n  (sort\n   (map (lambda (key) (cons key (hash-ref edge-provenance-hash key)))\n        (hash-keys edge-provenance-hash))\n   (lambda (e1 e2) (> (cdr e1) (cdr e2)))))\n\n#|\nGenerate TSV file with the provenance, and counts\n|#\n(with-output-to-file (string-append kg-name \"-provenance_count\" \".tsv\")\n  (lambda ()\n    (printf \"provenance\\tedge count\\n\")\n    (for-each\n      (lambda (key/count)\n        (let ((key (car key/count))\n              (count (cdr key/count)))\n          (printf \"~a\\t~a\\n\" key count)))\n      sorted-provenance-counts))\n  #:mode 'text\n  #:exists 'replace)\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/new-query-lang/select.rkt",
    "content": "#lang racket\n\n(require\n  (only-in \"query.rkt\"\n           query/graph edges/ranked)\n  )\n\n(define-syntax query\n  (syntax-parser\n    [(_ (select s:selector-exp ...+)\n        (concepts c:concept-decl ...+)\n        (edges e:edge-decl ...))\n     #'(let ([res\n              (query/graph\n                ([c.id c.category-expr] ...)\n                ([e.id e.predicate-list-expr])\n                [e.subject e.id e.object]\n                ...)])\n         (query-runtime\n           res\n           (lambda (c.id ... e.id ...)\n             (row-runtime\n               (lambda () s)\n               ...))))]))\n\n; ranked-paths output format:\n; (listof\n;   (list score\n;         (listof (cons subject object))))\n(define (query-runtime query-result selection-f)\n\n  )\n\n(define (row-runtime . selector-thunks)\n  (apply\n    append\n    (for/list ([t selector-thunks])\n      (call-with-values t list))))\n\n\n;(define (db concept-or-edge)\n  ;)\n\n;(define (property concept-or-edge symbol)\n  ;)\n\n;(define (curie concept)\n  ;)\n\n;(define (name concept)\n  ;)\n\n;(define (category concept)\n  ;)\n\n;(define (predicate edge)\n  ;)\n\n;(define (pubmed edge parts)\n  ;)\n\n(module+ main\n  ; example query\n  (query\n    (select\n      (db E) (curie D) (name D) (category D) (curie G) (name G)\n      (predicate E) (pubmed E '(url keyword symbol)))\n    (concepts\n      [D drug]\n      [G gene])\n    (edges\n      [E : D regulates G]))\n  )\n\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/non_drug_filter.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/pieces-parts/query.rkt\")\n\n;; define a number of helper functions for the function drug-info-for-curie\n(define curie-to-anything\n  (lambda (curie predicate*)\n    ;;(printf \"starting curie-to-anything with curie ~s and preds ~s\\n\" curie predicate*)\n    (let ((val (query/graph\n                ( ;; concepts\n                 (X curie)\n                 (T #f))\n                ;; edges\n                ((X->T predicate*))\n                ;; paths      \n                (X X->T T))))\n      ;;(printf \"finished curie-to-anything with curie ~s and preds ~s\\n\" curie predicate*)\n      val)))\n\n(define curie-to-tradenames\n  (lambda (curie)\n    (curie-to-anything curie '(\"has_tradename\")))) \n\n(define curie-to-clinical-trials\n  (lambda (curie)\n    (curie-to-anything curie '(\"clinically_tested_terminated_phase_2\"\n                               \"clinically_tested_approved_unknown_phase\"\n                               \"clinically_tested_terminated_phase_2\"\n                               \"clinically_tested_terminated_phase_3\"\n                               \"clinically_tested_terminated_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2\"\n                               \"clinically_tested_suspended_phase_2\"\n                               \"clinically_tested_suspended_phase_3\"\n                               \"clinically_tested_suspended_phase_2_or_phase_3\"))))\n\n(define curie-to-indicated_for\n  (lambda (curie)\n    (curie-to-anything curie '(\"indicated_for\"))))\n\n(define curie-to-contraindicated_for\n  (lambda (curie)\n    (curie-to-anything curie '(\"contraindicated_for\"))))\n\n(define drug-info-for-curie\n  (lambda (curie)\n    ; (printf \"*** starting drug-info-for-curie ~s\\n\" curie)\n    (map\n     (lambda (l)\n       (match l\n         [`(,name . ,q)\n          ; (printf \"*** calculating curie-synonyms/names list for curie ~s\\n\" curie)\n          (let ((ls (map curie-synonyms/names (curies/query q 'T))))\n            ; (printf \"*** calculated curie-synonyms/names list for curie ~s\\n\" curie)\n            ; (printf \"*** ls length = ~s\\n\" (apply + (map length ls)))\n            (cons name ls))]))\n     (list \n      (cons 'tradenames (curie-to-tradenames curie))\n      (cons 'clinical-trials (curie-to-clinical-trials curie))\n      (cons 'indicated_for (curie-to-indicated_for curie))\n      (cons 'contraindicated_for (curie-to-contraindicated_for curie))))))\n\n\n\n\n;; List of chemicals:\n;; These chemicals are the results of queries to up or down-regulate a number of genes of interest\n;; based on the CHAMP1 RNA sequencing data.\n\n\n(define strategy1_chemicals\n  '(\"CHEBI:28119\"\n  \"CHEBI:16469\"\n  \"CHEBI:37537\"\n  \"CHEBI:41879\"\n  \"CHEBI:17026\"\n  \"CHEBI:6541\"\n  \"CHEBI:4903\"\n  \"CHEBI:33216\"\n  \"CHEBI:9168\"\n  \"CHEBI:41774\"\n  \"CHEBI:65329\"\n  \"CHEBI:17347\"\n  \"CHEMBL:CHEMBL460433\"\n  \"CHEBI:17747\"\n  \"CHEBI:49662\"\n  \"CHEBI:22984\"\n  \"CHEBI:4031\"\n  \"CHEBI:27584\"\n  \"CHEBI:16243\"\n  \"CHEBI:9130\"\n  \"CHEBI:78543\"\n  \"CHEBI:15365\"\n  \"CHEMBL:CHEMBL62381\"\n  \"CHEBI:52717\"\n  \"CHEBI:175901\"\n  \"CHEBI:16113\"\n  \"CHEBI:29865\"\n  \"CHEBI:28748\"\n  \"CHEBI:5132\"\n  \"CHEBI:44423\"\n  \"CHEBI:45713\"\n  \"CHEBI:15738\"\n  \"CHEBI:16356\"\n  \"CHEBI:77986\"\n  \"CHEBI:3766\"\n  \"CHEBI:17489\"\n  \"CHEBI:8899\"\n  \"CHEBI:15355\"\n  \"CHEBI:3962\"\n  \"CHEBI:28088\"\n  \"CHEBI:76004\"\n  \"CHEBI:27656\"\n  \"CHEBI:77006\"\n  \"CHEMBL:CHEMBL504\"\n  \"CHEBI:8863\"\n  \"CHEBI:9150\"\n  \"CHEBI:31401\"\n  \"CHEBI:16330\"\n  \"CHEBI:44296\"\n  \"CHEBI:15930\"\n  \"CHEBI:17609\"\n  \"CHEBI:92413\"\n  \"CHEBI:47808\"\n  \"CHEMBL.COMPOUND:CHEMBL3545133\"\n  \"CHEMBL.COMPOUND:CHEMBL2109588\"\n  \"CHEBI:517248\"\n  \"CHEBI:28364\"\n  \"CHEBI:9786\"\n  \"CHEBI:3237\"\n  \"CHEMBL:CHEMBL1372588\"\n  \"CHEBI:135742\"\n  \"CHEBI:9241\"\n  \"CHEBI:6920\"\n  \"CHEMBL:CHEMBL305576\"\n  \"CHEBI:17712\"\n  \"CHEBI:5759\"\n  \"CHEBI:34892\"\n  \"CHEBI:15960\"\n  \"CHEBI:49040\"\n  \"GTPI:5965\"\n  \"CHEBI:8198\"\n  \"CHEBI:34935\"\n  \"CHEBI:52289\"\n  \"CHEBI:49668\"\n  \"CHEBI:34888\"\n  \"CHEBI:135736\"\n  \"CHEBI:138000\"\n  \"CHEBI:28940\"\n  \"CHEBI:29678\"\n  \"CHEBI:2666\"\n  \"CHEBI:35053\"\n  \"CHEMBL.COMPOUND:CHEMBL3707348\"\n  \"CHEBI:3763\"\n  \"CHEBI:50114\"\n  \"CHEMBL.COMPOUND:CHEMBL3545396\"\n  \"CHEBI:16412\"\n  \"CHEBI:88522\"\n  \"CHEBI:50694\"\n  \"CHEMBL:CHEMBL1903674\"\n  \"CHEBI:78373\"\n  \"CHEBI:28694\"\n  \"CHEBI:17578\"\n  \"CHEBI:30768\"\n  \"CHEBI:76612\"\n  \"CHEBI:338412\"\n  \"CHEBI:17823\"\n  \"CHEMBL:CHEMBL1371200\"\n  \"CHEBI:30740\"\n  \"CHEBI:107643\"\n  \"CHEBI:27385\"\n  \"CHEBI:15756\"\n  \"CHEBI:135949\"\n  \"CHEBI:15367\"\n  \"CHEBI:63954\"\n  \"GTPI:8492\"\n  \"CHEBI:137113\"\n  \"CHEBI:47495\"\n  \"CHEBI:28499\"\n  \"CHEBI:135735\"\n  \"CHEBI:566274\"\n  \"CHEBI:28112\"\n  \"CHEBI:76003\"\n  \"CHEBI:3655\"\n  \"CHEMBL:CHEMBL1221984\"\n  \"CHEMBL.COMPOUND:CHEMBL545315\"\n  \"CHEBI:49960\"\n  \"CHEMBL:CHEMBL1644699\"\n  \"CHEBI:28842\"\n  \"CHEBI:65310\"\n  \"CHEBI:8081\"\n  \"CHEMBL:CHEMBL8823\"\n  \"CHEMBL:CHEMBL1565107\"\n  \"CHEBI:30563\"\n  \"CHEBI:91452\"\n  \"CHEBI:4659\"\n  \"CHEBI:8062\"\n  \"CHEBI:16698\"\n  \"CHEBI:18388\"\n  \"CHEBI:28790\"\n  \"CHEMBL.COMPOUND:CHEMBL2105719\"\n  \"CHEBI:92843\"\n  \"CHEBI:18243\"\n  \"CHEBI:51450\"\n  \"CHEBI:90695\"\n  \"CHEBI:7590\"\n  \"CHEMBL.COMPOUND:CHEMBL499968\"\n  \"CHEBI:40303\"\n  \"CHEMBL.COMPOUND:CHEMBL3137331\"\n  \"CHEMBL.COMPOUND:CHEMBL356359\"\n  \"CHEBI:62825\"\n  \"CHEBI:2611\"\n  \"CHEBI:15553\"\n  \"CHEBI:132853\"\n  \"CHEBI:351346\"\n  \"CHEBI:17234\"\n  \"CHEBI:6402\"\n  \"CHEBI:39462\"\n  \"CHEBI:7465\"\n  \"CHEBI:34662\"\n  \"CHEMBL:CHEMBL2146125\"\n  \"CHEBI:31746\"\n  \"CHEBI:8382\"\n  \"CHEBI:18291\"\n  \"CHEBI:18152\"\n  \"CHEBI:95341\"\n  \"CHEBI:35456\"\n  \"CHEBI:18185\"\n  \"CHEBI:3385\"\n  \"CHEBI:6801\"\n  \"CHEBI:34076\"\n  \"CHEBI:6715\"\n  \"CHEBI:7735\"\n  \"CHEBI:45307\"\n  \"CHEBI:46024\"\n  \"CHEMBL:CHEMBL1981220\"\n  \"CHEBI:66917\"\n  \"CHEBI:556075\"\n  \"CHEBI:27363\"\n  \"CHEBI:15368\"\n  \"CHEBI:83732\"\n  \"CHEMBL.COMPOUND:CHEMBL1645462\"\n  \"CHEBI:4305\"\n  \"CHEBI:48045\"\n  \"CHEMBL:CHEMBL190083\"\n  \"CHEBI:65347\"\n  \"CHEBI:15343\"\n  \"CHEBI:86194\"\n  \"CHEBI:15940\"\n  \"CHEBI:38927\"\n  \"CHEBI:31561\"\n  \"CHEBI:6958\"\n  \"CHEBI:90939\"\n  \"CHEBI:32061\"\n  \"CHEBI:6842\"\n  \"CHEBI:6413\"\n  \"CHEMBL:CHEMBL7463\"\n  \"CHEBI:76607\"\n  \"CHEMBL.COMPOUND:CHEMBL2103884\"\n  \"CHEBI:35696\"\n  \"CHEMBL.COMPOUND:CHEMBL1709719\"\n  \"CHEBI:90948\"\n  \"CHEBI:4046\"\n  \"CHEBI:24814\"\n  \"CHEMBL.COMPOUND:CHEMBL587723\"\n  \"CHEBI:3084\"\n  \"CHEBI:34269\"\n  \"CHEBI:75253\"\n  \"CHEBI:61400\"\n  \"CHEBI:86345\"\n  \"CHEBI:34873\"\n  \"CHEBI:132268\"\n  \"GTPI:8145\"\n  \"CHEBI:43616\"\n  \"CHEBI:135590\"\n  \"CHEBI:15891\"\n  \"CHEMBL:CHEMBL1977579\"\n  \"CHEBI:50859\"\n  \"CHEBI:9635\"\n  \"CHEBI:101278\"\n  \"CHEBI:45652\"\n  \"CHEBI:3752\"\n  \"CHEBI:3175\"\n  \"CHEBI:44445\"\n  \"CHEBI:28680\"\n  \"CHEBI:39548\"\n  \"CHEMBL.COMPOUND:CHEMBL3545154\"\n  \"CHEBI:9908\"\n  \"CHEBI:92890\"\n  \"CHEBI:18145\"\n  \"CHEBI:134301\"\n  \"CHEMBL:CHEMBL499968\"\n  \"CHEBI:69581\"\n  \"CHEBI:39867\"\n  \"CHEBI:17997\"\n  \"CHEBI:17833\"\n  \"CHEBI:15843\"\n  \"CHEBI:45863\"\n  \"CHEBI:16118\"\n  \"CHEBI:61399\"\n  \"CHEBI:27638\"\n  \"CHEBI:28527\"\n  \"CHEBI:7565\"\n  \"CHEBI:61390\"\n  \"CHEBI:61057\"\n  \"CHEMBL:CHEMBL1201288\"\n  \"CHEBI:2814\"\n  \"CHEBI:91370\"\n  \"CHEBI:32020\"\n  \"CHEBI:8633\"\n  \"CHEMBL:CHEMBL378104\"\n  \"CHEBI:4460\"\n  \"CHEBI:67272\"\n  \"CHEBI:3440\"\n  \"CHEBI:17241\"\n  \"CHEBI:4042\"\n  \"CHEBI:23359\"))\n                                          \n  \n(define strategy2_chemicals\n  '(\"CHEBI:39867\"\n    \"CHEBI:46024\"\n    \"CHEBI:2666\"\n    \"CHEBI:4031\"\n    \"CHEBI:9150\"\n    \"CHEBI:31252\"\n    \"CHEBI:37537\"\n    \"CHEBI:41879\"\n    \"CHEBI:33216\"\n    \"CHEBI:16469\"\n    \"CHEBI:44915\"\n    \"CHEBI:2504\"\n    \"CHEBI:42944\"\n    \"CHEBI:34714\"\n    \"CHEBI:32315\"\n    \"CHEBI:16069\"\n    \"CHEBI:76591\"\n    \"CHEBI:16330\"\n    \"CHEBI:16243\"\n    \"CHEBI:6908\"\n    \"CHEBI:17609\"\n    \"CHEBI:17941\"\n    \"CHEBI:9130\"\n    \"CHEBI:28741\"\n    \"CHEMBL:CHEMBL455560\"\n    \"CHEBI:6762\"\n    \"CHEBI:24852\"\n    \"CHEBI:7575\"\n    \"CHEBI:27827\"\n    \"CHEBI:82160\"\n    \"CHEBI:8461\"\n    \"CHEBI:135742\"\n    \"CHEBI:63681\"\n    \"CHEBI:15864\"\n    \"CHEBI:6920\"\n    \"CHEBI:53188\"\n    \"CHEBI:32061\"\n    \"CHEBI:92811\"\n    \"CHEBI:81297\"\n    \"CHEBI:38845\"\n    \"CHEBI:251412\"\n    \"CHEBI:15960\"\n    \"CHEBI:609247\"\n    \"CHEBI:47499\"\n    \"CHEBI:31404\"\n    \"CHEBI:47426\"\n    \"CHEMBL:CHEMBL2002549\"\n    \"CHEMBL:CHEMBL2140710\"\n    \"GTPI:4589\"\n    \"CHEBI:27919\"\n    \"CHEBI:24814\"\n    \"CHEBI:18145\"\n    \"CHEBI:8062\"\n    \"CHEMBL:CHEMBL1929421\"\n    \"CHEBI:30114\"\n    \"CHEBI:29150\"\n    \"CHEMBL.COMPOUND:CHEMBL215645\"\n    \"CHEBI:35622\"\n    \"CHEBI:135935\"\n    \"CHEBI:134884\"\n    \"CHEBI:7459\"\n    \"CHEBI:140422\"\n    \"CHEBI:7071\"\n    \"CHEBI:16412\"\n    \"CHEBI:8107\"\n    \"CHEBI:28216\"\n    \"CHEMBL:CHEMBL33051\"\n    \"CHEBI:135464\"\n    \"CHEBI:8428\"\n    \"CHEBI:41774\"\n    \"CHEBI:28694\"\n    \"CHEBI:36560\"\n    \"CHEBI:59719\"\n    \"CHEBI:338412\"\n    \"CHEBI:45863\"\n    \"CHEBI:15422\"\n    \"CHEBI:45980\"\n    \"CHEBI:49662\"\n    \"CHEBI:32168\"\n    \"CHEBI:135804\"\n    \"CHEBI:2555\"\n    \"CHEBI:68478\"\n    \"CHEBI:2700\"\n    \"CHEBI:16526\"\n    \"CHEBI:17750\"\n    \"CHEBI:28499\"\n    \"CHEBI:36946\"\n    \"CHEBI:141474\"\n    \"CHEBI:4868\"\n    \"CHEBI:28593\"\n    \"CHEBI:34631\"\n    \"CHEBI:143794\"\n    \"CHEBI:7907\"\n    \"CHEBI:8459\"\n    \"CHEBI:27375\"\n    \"CHEBI:15379\"\n    \"CHEBI:8354\"\n    \"CHEBI:72449\"\n    \"CHEBI:2673\"\n    \"CHEBI:34905\"\n    \"CHEBI:33070\"\n    \"CHEBI:28119\"\n    \"CHEBI:18388\"\n    \"CHEBI:17097\"\n    \"CHEBI:45652\"\n    \"CHEBI:52010\"\n    \"CHEMBL:CHEMBL533841\"\n    \"CHEBI:31425\"\n    \"CHEBI:30563\"\n    \"CHEMBL:CHEMBL2163791\"\n    \"CHEBI:38093\"\n    \"CHEBI:15354\"\n    \"CHEBI:8874\"\n    \"CHEMBL:CHEMBL1233973\"\n    \"CHEBI:9741\"\n    \"CHEBI:4948\"\n    \"CHEBI:32988\"\n    \"CHEBI:8024\"\n    \"CHEBI:25944\"\n    \"CHEBI:18049\"\n    \"CHEBI:40303\"\n    \"CHEMBL:CHEMBL26505\"\n    \"CHEBI:87649\"\n    \"CHEBI:3213\"\n    \"CHEBI:8666\"\n    \"CHEBI:82142\"\n    \"CHEBI:31618\"\n    \"CHEBI:34036\"\n    \"CHEBI:39462\"\n    \"CHEMBL:CHEMBL2272837\"\n    \"CHEBI:53289\"\n    \"CHEBI:9195\"\n    \"CHEBI:38746\"\n    \"CHEBI:6060\"\n    \"CHEMBL:CHEMBL494887\"\n    \"CHEBI:251408\"\n    \"CHEBI:8382\"\n    \"CHEBI:18152\"\n    \"CHEBI:4791\"\n    \"CHEBI:18009\"\n    \"CHEBI:6931\"\n    \"CHEBI:29865\"\n    \"CHEBI:17051\"\n    \"CHEBI:48883\"\n    \"CHEBI:4806\"\n    \"CHEBI:41934\"\n    \"CHEBI:52741\"\n    \"CHEBI:94848\"\n    \"CHEBI:59514\"\n    \"CHEBI:16716\"\n    \"CHEMBL:CHEMBL444970\"\n    \"CHEBI:553827\"\n    \"CHEBI:17790\"\n    \"CHEBI:37931\"\n    \"CHEMBL:CHEMBL157912\"\n    \"CHEBI:16737\"\n    \"CHEBI:125392\"\n    \"CHEBI:38624\"\n    \"CHEBI:8102\"\n    \"CHEBI:28794\"\n    \"CHEBI:31622\"\n    \"CHEBI:9711\"\n    \"CHEBI:34761\"\n    \"CHEBI:83533\"\n    \"CHEBI:34611\"\n    \"CHEBI:6801\"\n    \"CHEBI:31561\"\n    \"CHEBI:102166\"\n    \"CHEBI:3390\"\n    \"CHEBI:3374\"\n    \"CHEBI:24536\"\n    \"CHEMBL:CHEMBL284328\"\n    \"CHEBI:30336\"\n    \"CHEBI:4753\"\n    \"CHEBI:27928\"\n    \"CHEBI:31687\"\n    \"CHEBI:5128\"\n    \"CHEMBL:CHEMBL190083\"\n    \"CHEBI:3766\"\n    \"CHEBI:35038\"\n    \"CHEBI:27953\"\n    \"CHEBI:3387\"\n    \"CHEBI:8230\"\n    \"CHEBI:9449\"\n    \"CHEBI:75701\"\n    \"CHEBI:75372\"\n    \"CHEBI:63716\"\n    \"CHEMBL.COMPOUND:CHEMBL997\"\n    \"CHEBI:28821\"\n    \"CHEBI:247956\"\n    \"CHEMBL:CHEMBL460433\"\n    \"CHEBI:32223\"\n    \"CHEBI:6758\"\n    \"CHEBI:39447\"\n    \"CHEBI:4527\"\n    \"CHEBI:28374\"\n    \"CHEBI:31302\"\n    \"CHEBI:43616\"\n    \"CHEBI:5706\"\n    \"CHEBI:2791\"\n    \"CHEBI:8665\"\n    \"CHEBI:50859\"\n    \"CHEBI:16881\"\n    \"CHEBI:9635\"\n    \"CHEMBL:CHEMBL26115\"\n    \"CHEMBL:CHEMBL3181798\"\n    \"CHEBI:8712\"\n    \"CHEBI:3175\"\n    \"CHEBI:313639\"\n    \"CHEBI:7601\"\n    \"CHEBI:27958\"\n    \"CHEBI:32250\"\n    \"CHEBI:135387\"\n    \"CHEBI:7581\"\n    \"CHEBI:31823\"\n    \"CHEBI:6015\"\n    \"CHEBI:49575\"\n    \"CHEBI:7514\"\n    \"CHEBI:63616\"\n    \"CHEBI:22984\"\n    \"CHEBI:135720\"\n    \"CHEBI:41423\"\n    \"CHEBI:125612\"\n    \"CHEBI:28885\"\n    \"CHEBI:28527\"\n    \"CHEBI:17230\"\n    \"CHEBI:4636\"\n    \"CHEBI:15355\"\n    \"CHEBI:3962\"\n    \"CHEBI:34682\"\n    \"CHEMBL:CHEMBL310934\"\n    \"CHEBI:8774\"\n    \"CHEBI:38721\"\n    \"CHEBI:59849\"\n    \"CHEBI:8025\"\n    \"CHEBI:34690\"\n    \"CHEBI:28088\"\n    \"CHEBI:6601\"\n    \"CHEMBL:CHEMBL430266\"\n    \"CHEBI:48981\"\n    \"CHEBI:15854\"\n    \"CHEMBL.COMPOUND:CHEMBL1677\"\n    \"CHEBI:23359\"))\n\n\n(define strategy3_chemicals '(\"CHEBI:39867\"\n  \"CHEBI:16469\"\n  \"CHEBI:17026\"\n  \"CHEBI:65329\"\n  \"CHEBI:41879\"\n  \"CHEBI:45713\"\n  \"CHEBI:6801\"\n  \"CHEBI:49662\"\n  \"CHEBI:16330\"\n  \"CHEBI:16118\"\n  \"CHEBI:16243\"\n  \"CHEBI:6541\"\n  \"CHEBI:15365\"\n  \"CHEBI:137113\"\n  \"CHEBI:15379\"\n  \"CHEBI:9168\"\n  \"CHEBI:3962\"\n  \"CHEBI:16113\"\n  \"CHEBI:9150\"\n  \"CHEMBL:CHEMBL504\"\n  \"CHEBI:8382\"\n  \"CHEBI:17609\"\n  \"CHEBI:44915\"\n  \"CHEBI:18145\"\n  \"CHEBI:78543\"\n  \"CHEBI:4903\"\n  \"CHEBI:52717\"\n  \"CHEBI:47426\"\n  \"CHEBI:41774\"\n  \"CHEBI:30740\"\n  \"CHEBI:2666\"\n  \"CHEBI:8107\"\n  \"CHEBI:17347\"\n  \"CHEBI:50694\"\n  \"CHEBI:28748\"\n  \"CHEBI:15367\"\n  \"CHEBI:18152\"\n  \"CHEBI:39548\"\n  \"CHEBI:18388\"\n  \"CHEBI:28918\"\n  \"CHEBI:28527\"\n  \"CHEBI:7565\"\n  \"CHEBI:16335\"\n  \"CHEBI:175901\"\n  \"CHEBI:28790\"\n  \"CHEBI:8024\"\n  \"CHEBI:40303\"\n  \"CHEBI:3213\"\n  \"CHEBI:15553\"\n  \"CHEBI:42944\"\n  \"CHEBI:6402\"\n  \"CHEBI:44445\"\n  \"CHEBI:39462\"\n  \"CHEBI:15544\"\n  \"CHEBI:61057\"\n  \"CHEBI:2639\"\n  \"CHEBI:68558\"\n  \"CHEMBL:CHEMBL2146125\"\n  \"CHEBI:6060\"\n  \"CHEBI:15552\"\n  \"CHEBI:17263\"\n  \"CHEBI:18291\"\n  \"CHEMBL:CHEMBL692\"\n  \"CHEBI:9334\"\n  \"CHEBI:17997\"\n  \"CHEMBL:CHEMBL33051\"\n  \"CHEBI:45951\"\n  \"CHEBI:17941\"\n  \"CHEBI:4917\"\n  \"CHEBI:31252\"\n  \"CHEBI:37931\"\n  \"CHEBI:7735\"\n  \"CHEBI:4806\"\n  \"CHEBI:15864\"\n  \"CHEBI:42191\"\n  \"CHEBI:5132\"\n  \"CHEBI:17230\"\n  \"CHEBI:94848\"\n  \"CHEBI:135742\"\n  \"CHEBI:9241\"\n  \"CHEBI:18332\"\n  \"CHEBI:44423\"\n  \"CHEBI:17790\"\n  \"CHEBI:31547\"\n  \"CHEMBL:CHEMBL117649\"\n  \"CHEBI:34892\"\n  \"CHEBI:49040\"\n  \"CHEBI:47499\"\n  \"CHEBI:27584\"\n  \"CHEBI:125392\"\n  \"CHEBI:9667\"\n  \"CHEBI:28794\"\n  \"CHEBI:3423\"\n  \"CHEBI:15940\"\n  \"CHEBI:41423\"\n  \"CHEBI:8062\"\n  \"CHEBI:15854\"\n  \"CHEBI:16898\"\n  \"CHEBI:3390\"\n  \"CHEBI:3374\"\n  \"CHEBI:24536\"\n  \"CHEBI:76004\"\n  \"CHEBI:7459\"\n  \"CHEBI:16881\"\n  \"CHEBI:8459\"\n  \"CHEBI:7071\"\n  \"CHEBI:16412\"\n  \"CHEBI:2038\"\n  \"CHEMBL:CHEMBL41631\"\n  \"CHEBI:3766\"\n  \"CHEBI:28593\"\n  \"CHEBI:27953\"\n  \"CHEBI:3387\"\n  \"CHEBI:46195\"\n  \"CHEMBL:CHEMBL264373\"\n  \"CHEBI:30768\"\n  \"CHEBI:45980\"\n  \"CHEBI:28821\"\n  \"CHEBI:61033\"\n  \"CHEBI:37941\"\n  \"CHEBI:17823\"\n  \"CHEBI:63716\"\n  \"CHEBI:3440\"\n  \"CHEBI:32020\"\n  \"CHEBI:135949\"\n  \"CHEBI:15422\"\n  \"CHEBI:9588\"\n  \"CHEBI:16526\"\n  \"CHEBI:17750\"\n  \"CHEBI:78741\"\n  \"CHEBI:3286\"\n  \"CHEBI:8665\"\n  \"CHEBI:18295\"\n  \"CHEBI:101278\"\n  \"CHEBI:566274\"\n  \"CHEBI:68478\"\n  \"CHEBI:8354\"\n  \"CHEBI:7907\"\n  \"CHEBI:16240\"\n  \"CHEBI:9908\"\n  \"CHEBI:9139\"\n  \"CHEBI:69581\"\n  \"CHEBI:6762\"\n  \"CHEBI:8899\"\n  \"CHEBI:7514\"\n  \"CHEBI:63616\"\n  \"CHEBI:45652\"\n  \"CHEBI:27958\"\n  \"CHEBI:86345\"\n  \"CHEBI:49575\"\n  \"CHEBI:4659\"\n  \"CHEBI:15355\"\n  \"CHEMBL:CHEMBL1201288\"\n  \"CHEBI:15354\"\n  \"CHEBI:76607\"\n  \"CHEBI:18243\"\n  \"CHEBI:8774\"\n  \"CHEBI:2700\"\n  \"CHEBI:50730\"\n  \"CHEBI:29150\"\n  \"CHEMBL:CHEMBL62381\"\n  \"CHEBI:135804\"\n  \"CHEBI:313639\"\n  \"CHEBI:17303\"\n  \"CHEBI:4636\"\n  \"CHEBI:28364\"\n  \"CHEBI:8378\"\n  \"CHEBI:119915\"\n  \"CHEBI:9130\"))\n\n\n\n;; From the list of chemicals, extract the non-drugs members with drugs are defined\n;; as having either tradenames, clinical trials, indicated for and contraindicated for predicates\n;; Chemicals that don't have any of these predicates are defined as non-drugs.\n;; They could be supplements, which are likely to be safe, chemicals that are synthesized in chemical labs\n;; to be used in several laboratory assays (these are unsafe until proven otherwise)\n;; They could be investigational compounds that are also unsafe until proven otherwise.\n;; They could be endogenous substances that are naturally produced in the human body by cells, DNA, RNA\n;; but for some reason they are not being tested by FDA to be approved as therapies.\n;; For non-drugs categories, unfortunately, I haven't found a mediKanren's way to group them into these different\n;; groups so I'll do this categorization manually.\n\n(define strategy1-non-drugs (filter\n                             (lambda (x)\n                               (equal? (drug-info-for-curie x)\n                                       (list '(tradenames) '(clinical-trials) '(indicated_for) '(contraindicated_for))))\n                             strategy1_chemicals))\n(define strategy2-non-drugs (filter\n                             (lambda (x)\n                               (equal? (drug-info-for-curie x)\n                                       (list '(tradenames) '(clinical-trials) '(indicated_for) '(contraindicated_for))))\n                             strategy2_chemicals))\n\n(define strategy3-non-drugs (filter\n                             (lambda (x)\n                               (equal? (drug-info-for-curie x)\n                                       (list '(tradenames) '(clinical-trials) '(indicated_for) '(contraindicated_for))))\n                             strategy3_chemicals))\n\n(define strategy1-non-drugs-names (map car (map curie-synonyms/names strategy1-non-drugs)))\n(define strategy2-non-drugs-names (map car (map curie-synonyms/names strategy2-non-drugs)))\n(define strategy3-non-drugs-names (map car (map curie-synonyms/names strategy3-non-drugs)))\n\n;; For the drugs, we need to assess if they have a lot of side effects\n;; First, extract drug members:\n(define strategy1-drugs (filter\n (lambda (x)\n   (not (equal? (drug-info-for-curie x)\n                (list '(tradenames) '(clinical-trials) '(indicated_for) '(contraindicated_for)))))\n strategy1_chemicals))\n\n(define strategy2-drugs (filter\n (lambda (x)\n   (not (equal? (drug-info-for-curie x)\n                (list '(tradenames) '(clinical-trials) '(indicated_for) '(contraindicated_for)))))\n strategy2_chemicals))\n\n(define strategy3-drugs (filter\n (lambda (x)\n   (not (equal? (drug-info-for-curie x)\n                (list '(tradenames) '(clinical-trials) '(indicated_for) '(contraindicated_for)))))\n strategy3_chemicals))\n\n;; Take a look at their names:\n(define strategy1-drugs-names (map car (map curie-synonyms/names strategy1-drugs)))\n(define strategy2-drugs-names (map car (map curie-synonyms/names strategy2-drugs)))\n(define strategy3-drugs-names (map car (map curie-synonyms/names strategy3-drugs)))\n\n;; Helper functions:\n(define side-effect-preds (list \"causes\"\n                                \"contributes_to\"\n                                \"contraindicated_for\"))\n\n\n(define (sort-assoc lst)\n  (sort lst\n   >\n   #:key (lambda (x) (length (cdr x)))))\n\n(define ((edge/db? db) e) (eq? db (car e)))\n\n\n;; sort-side-effects takes a list of drug-curies and sort them in descending order the number of side effects\n;; This results aren't that useful for drug prioritizations, however. This is due to the biased in our knowledge graphs\n;; because not all drugs have the same information density about their properties. Therefore, sorting drugs\n;; by their side-effects accidentally sorting drugs by how much information/knowledge and data we have about the\n;; particular drugs. This is not that useful in practice.\n(define (sort-side-effects drug-curies)\n  (sort-assoc\n   (map\n    (lambda (d)\n      (define qdrug (time (query/graph\n                           ((X d)\n                            (O #f))\n                           ((X->O side-effect-preds (edge/db? 'rtx2)))\n                           (X X->O O))))\n      (cons (assoc d (curie-synonyms/names d))\n            (map (lambda (s) (assoc s (curie-synonyms/names s))) (curies/query qdrug 'O))))\n     drug-curies)))\n\n(define sort-strategy1-drugs-by-side-effects (sort-side-effects strategy1-drugs))"
  },
  {
    "path": "contrib/medikanren/pieces-parts/postquery.rkt",
    "content": "#lang racket/base\n\n(provide (all-defined-out))\n(require \"../../../medikanren/pieces-parts/query.rkt\")\n(require  racket/list)\n(require (for-syntax racket/base syntax/parse racket/syntax syntax/transformer))\n\n;; different notions of consistency\n;; arc: across 1-hop\n;; path: across entire path\n;; global: between multiple paths that might share nodes\n\n;; global consistency\n;; X -> Y\n;; X -> Z\n;; Y -> Z\n;; need to find X -> Y -> Z\n;; but imagine that X, Y, Z are sets\n;; need the individual elements to be related\n\n;; query/graph\n;; returns an association list from the concept and edge names defined to their result\n\n(define (all-consistent query-result)\n  (define paths       (car query-result))\n  (define named-cells (cdr query-result))\n  (define kvs (map (lambda (nc) (cons (car nc) ((cdr nc) 'ref)))\n                   named-cells))\n  (define csets (filter (lambda (kv) (eq? (cadr kv) 'concept)) kvs))\n  (define esets (filter (lambda (kv) (eq? (cadr kv) 'edge))    kvs))\n\n  ;; symbolic: capital\n  ;; concrete: lower case\n\n  (define E=>sgs\n    (foldl (lambda (path e=>s)\n             (foldl (lambda (edge e=>s)\n                      (define ename (cadr  edge))\n                      (define sname (car   edge))\n                      (hash-set e=>s ename (cddr (assoc sname csets))))\n                    e=>s (path->edges path)))\n           (hash) paths))\n  (define E=>ogs\n    (foldl (lambda (path e=>o)\n             (foldl (lambda (edge e=>o)\n                      (define ename (cadr  edge))\n                      (define oname (caddr edge))\n                      (hash-set e=>o ename (cddr (assoc oname csets))))\n                    e=>o (path->edges path)))\n           (hash) paths))\n\n\n  (define (augment sgs ogs es)\n    (map (lambda (kv)\n           (define key (car kv))\n           (define es  (cdr kv))\n           (list key es))\n         (hash->list\n           (foldl (lambda (e acc)\n                    (define snorm (curie-norm sgs (cadr (caddr  e))))\n                    (define onorm (curie-norm ogs (cadr (cadddr e))))\n                    (define key (cons snorm onorm))\n                    (define existing (hash-ref acc key #f))\n                    (hash-set acc key (if existing (cons e existing) (list e))))\n                  (hash) es))))\n  (define E=>aes\n    (make-immutable-hash\n      (map (lambda (kv)\n             (define sgs (hash-ref E=>sgs (car kv)))\n             (define ogs (hash-ref E=>ogs (car kv)))\n             (define aes (augment sgs ogs (cddr kv)))\n             (cons (car kv) aes))\n           esets)))\n\n  (define (C=>Es f)\n    (foldl (lambda (path c=>e)\n             (foldl (lambda (edge c=>e)\n                      (define ename (cadr  edge))\n                      (define cname (f   edge))\n                      (hash-update c=>e cname\n                                   (lambda (old) (cons ename old))\n                                   '()))\n                    c=>e (path->edges path)))\n           (hash) paths))\n\n  (define S=>Es (C=>Es car))\n\n  (define O=>Es (C=>Es caddr))\n\n  (define (revert-C=>Es C=>Es)\n    (make-immutable-hash\n      (append*\n        (hash-map\n          C=>Es\n          (lambda (C Es)\n            (map (lambda (E)\n                   (cons E C))\n                 Es))))))\n\n  (define E=>S (revert-C=>Es S=>Es))\n  (define E=>O (revert-C=>Es O=>Es))\n\n  (define all-concepts (map car csets))\n  (define all-edges (map car esets))\n\n  (define (global-instances edges substitution)\n    (if (null? edges)\n      (list substitution)\n      (let* ((E (car edges))\n             (aes (hash-ref E=>aes E))\n             (S (hash-ref E=>S E))\n             (O (hash-ref E=>O E))\n             (s (hash-ref substitution S #f))\n             (o (hash-ref substitution O #f)))\n        (append*\n          (for/list ((ae aes))\n            (let* ((snorm (caar ae))\n                   (onorm (cdar ae))\n                   (edge-consistent?\n                     (and (or (not s) (equal? snorm s))\n                          (or (not o) (equal? onorm o)))))\n              (if edge-consistent?\n                (let ((substitution^ (hash-set (hash-set (hash-set substitution E ae)  S snorm) O onorm)))\n                  (global-instances (cdr edges)\n                                    substitution^))\n                '())))))))\n\n  (global-instances all-edges (hash))\n  )\n\n(define-syntax-rule (query/graph/consistent\n                      ((concept-name initial) ...)\n                      ((edge-name edge-constraints ...) ...)\n                      path ...)\n  (let ((q (query/graph\n             ((concept-name initial) ...)\n             ((edge-name edge-constraints ...) ...)\n             path ...)))\n    (all-consistent q)))\n\n(begin-for-syntax\n (struct selector-rep (runtime arg-count)\n         #:property prop:procedure\n         (lambda (self stx)\n           ((make-variable-like-transformer\n             (selector-rep-runtime self))\n            stx)))\n (define-syntax-class edge-decl\n   #:description \"edge declaration\"\n   (pattern (subject:id\n             predicate:expr\n             object:id\n             (~optional (~seq #:as name:id)\n                        #:defaults ([name (generate-temporary\n                                            (format-id #f \"~a->~a\" #'subject #'object))])))))\n\n (define-syntax-class concept-decl\n   #:description \"concept declaration\"\n   (pattern (name:id predicate:expr)))\n (define-syntax-class selector-id\n   #:description \"selector name\"\n   #:opaque\n   (pattern _:id))\n (define-syntax-class selector-exp\n   #:description \"selector expression\"\n   #:datum-literals (rkt)\n   (pattern e:id)\n   (pattern (s:selector-id arg:id ...+)\n            #:do [(define env-v (syntax-local-value #'s))]\n            #:fail-unless (selector-rep? env-v)\n            \"expected a selector\"\n            #:fail-unless (= (selector-rep-arg-count env-v)\n                             (length (syntax->list #'(arg ...))))\n            \"wrong number of arguments\"\n            #:attr e #`(#,(selector-rep-runtime env-v)\n                        arg ...))\n   (pattern (rkt e:expr)))\n)\n\n(define (query-runtime keys results f)\n  (for/list ([result results])\n            (apply f (for/list ([key keys]) (hash-ref result key)))))\n\n(define-syntax define-selector\n  (syntax-parser\n   [(_ (name:id arg:id ...+) body ...+)\n    (define arg-count\n      (length (syntax->list #'(arg ...))))\n    #`(begin\n        (define (runtime arg ...) body ...)\n        (define-syntax name\n          (selector-rep #'runtime #,arg-count)))]))\n\n(define-syntax query\n  (syntax-parser\n   #:datum-literals (select concepts edges)\n   [(_ (select s:selector-exp ...+)\n       (concepts c:concept-decl ...+)\n       (edges e:edge-decl ...))\n    #'(let ([res\n             (query/graph/consistent\n              ([c.name c.predicate] ...)\n              ([e.name e.predicate] ...)\n              [e.subject e.name e.object]\n              ...)])\n        (query-runtime\n         '(c.name ... e.name ...)\n         res\n         (lambda (c.name ... e.name ...)\n           (list\n            s.e\n            ...))))]))\n\n(define-selector (curie x) x)\n\n(module+\n test\n (require rackunit)\n (define q (time (query/graph/consistent\n                  ((X       drug-concept?)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates))\n                  (X X->Y Y Y->rhobtb2 rhobtb2))))\n\n (check-true (< 0 (length q)))\n (define q2\n   (query\n    (select (curie X) (curie Y) (rkt ((lambda (x) x) X)) (rkt (((lambda (x) x) curie) X)))\n    (concepts\n     (X       drug-concept?)\n     (Y       gene-or-protein)\n     (rhobtb2 \"UMLS:C1425762\"))\n    (edges\n     (X negatively-regulates Y #:as X->Y)\n     (Y positively-regulates rhobtb2))))\n (check-true (< 0 (length q2)))\n )\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/pub-clustering.rkt",
    "content": "#lang racket\n(require \"../../../medikanren/pieces-parts/query.rkt\")\n                 \n(define spike-covid19 \"UniProtKB:P0DTC2\")\n\n(define spike-sars \"UniProtKB:P59594\")\n\n(define ace2 \"UMLS:C1422064\")\n\n(define covid19 \"MONDO:0100096\")\n\n(define sars \"CUI:C1175743\")\n\n(define mers \"CUI:C3698360\")\n\n(define (sort-pubs pubs)\n  (sort\n   (hash-map pubs (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (set-count (cdr x)))))\n\n(define (sort-count c)\n  (sort\n   (hash-map c (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (cdr x))))\n\n#|\ntakes: a curie of interest (c), a list of type labels (eg. from query.rkt: drug, gene, etc.) (result-filter) - enter #f if no filter\nq1 does query C-\"biolink:related_to\"->P where C is the curie of interest (c), and P is a publication concept.\nq2 does a separate query C-\"biolink:related_to\"->P where C is either open (#f) or filtered by result-filter, and\nP is the list of publication curies resulting from the P in q1.\npurpose: shows the frequency of co-occurrence between different concepts in publications, this gives a sense of\n         what concept curies are often mentioned together in biomedical literature\nreturns: an association list where the keys are concept curies (x) (filtered by result-filter), and the values are sets of all\n         publications that mention both the concept curie (x) and the curie of interest (c). The assoc list is sorted (high->low)\n         by the number of publications in which the concept curie (x) and the curie of interest (c) co-occur\n|#\n(define (cluster-concepts-by-pubs c result-filter)\n  (define q1 (query/graph\n              ((C c)\n               (P #f))\n              ((C->P  '(\"biolink:related_to\")))\n              (C C->P P)))\n  (define related-pubs (curies/query q1 'P))\n  (define publications (make-hash))\n  (define (step2 p)\n    (define q2 (time (query/graph\n                      ((C result-filter)\n                       (P p))\n                      ((C->P  '(\"biolink:related_to\")))\n                      (C C->P P))))\n    (define related-concepts (curies/query q2 'C))\n    (for-each\n     (lambda (x)\n       (unless (equal? x c) \n         (hash-update! publications x (lambda (s) (set-add s p)) (set))\n         )\n       )\n     related-concepts)\n    )\n  (for-each step2 related-pubs)\n  (sort-pubs publications)\n  )\n#|Examples\n;;quick examples: these curies have fewer \"biolink:related_to\" edges, so they take a lot less time to finish running\n(cluster-concepts-by-pubs \"NCBIGene:3852\" #f))\n(cluster-concepts-by-pubs \"CUI:C1418795\" #f))\n\n;;longer, covid related examples:\n\n;;finds all curies (no filter) that are mentioned in the same publication as the sars spike protein and all\n  the publications in which this occurs\n(define sars-spike-gene-cluster (cluster-concepts-by-pubs \"UniProtKB:P59594\" #f))\n\n(define spike-covid19 \"UniProtKB:P0DTC2\")\n(define covid-spike-gene-cluster (cluster-concepts-by-pubs spike-covid19 gene))\n\n(define ace2-drug-cluster (cluster-concepts-by-pubs \"CUI:C1422064\" drug))\n|#\n\n#|\ntakes: the association list returned by cluster-concepts-by-pred\nreturns: a sorted assoc list where the value is just the count of the number of publications rather than a set\n         of the actual publication curies\n|#\n(define (pubs->count cluster)\n  (map\n   (lambda (x)\n     (cons (car x) (set-count (cdr x)))\n     )\n   cluster\n   )\n  )\n#|Examples\n(pubs->count sars-spike-gene-cluster)\n(pubs->count covid-spike-gene-cluster)\n(pubs->count ace2-drug-cluster)\n|#"
  },
  {
    "path": "contrib/medikanren/pieces-parts/rank-regulators-exe.rkt",
    "content": "#lang racket\n(require \"rank-regulators.rkt\"\n         \"rank-regulators-gene-lists.rkt\")\n#|\nPurpose: The purpose of this program is to find genes that have the most influence over a user inputted\n         list of genes of interest.\n\nMethods: It does this by using two separate methods of querying the knowledge graphs: (1) querying the GO\n         ontology and (2) using a 1-hop query. The relationships found through the GO query are looser \n         because the indirect, multi-hop query requires that we make bigger inferences. However, we have\n         more confidence in the information in GO. The 1-hop query looks for more direct relationships\n         and interactions between genes and proteins, but the information that that query returns could\n         be inaccurate due to inaccuracies in NLP generated knowledge graphs. After using both querying\n         methods, we compare the two results to find intersections between them. The results that are \n         common between both methods are held in higher confidence, but that is not to say that results\n         that don't lie in the overlap are inaccurate.\n\nInput/Output: Takes a list of the curies of genes of interest and outputs a sorted association list of\n              gene to regulated gene relationships. The association list is sorted from most to least\n              by the number of other genes/gene products that a gene regulates.\n\nInformation in Output: Contained within the sorted association list that is returned is a pair made from\n                       cons-ing the regulator gene's (G) curie and name. These (G curie. G name) pairs are\n                       the keys of the assoc list. The value is a list of lists that contains the regulated\n                       genes (rG) that the regulator gene (G) regulates along with additional information.\n                       Each element in the value is a list that contains the rG's curie, name, the presumed\n                       direction of regulation (told by predicates), and provenance for the edges in the form\n                       of pubmed ids. The functions 1-hop-query/report and find-intersections also include\n                       a boolean that indicates whether or not the G and rG directly interact with each other\n                       in the body (#t if yes) and provenance for that information also in the form of pubmed\n                       ids.\n\nNote: The functions called in this file are more extensively documented in rank-regulators.rkt\n|#\n\n#|\nThe following calls are an example based off an ARDS gene list, defined as ards-genes. There are 517 ENSEMBL\ngene curies on that list, and they yield 468 uniprot curies.\n\nNote: runtimes given in comments below are based off a 2020 MacBook Pro (2 GHz Quad-Core Intel Core i5,\n      16G RAM). They are meant to give an idea of which calls take a lot longer to finish.\n|#\n\n#|\nTurns the inputted gene list of interest into a list of uniprot curies in order to be passed\ninto the GO query.\nruntime: < 30s\n|#\n;;function call: genes->uniprots | takes: list of gene curies | returns: list of uniprot curies\n(define uniprots (time (genes->uniprots ards-genes)))\n\n#|\nThe next two statements 1) run the GO query and 2) reports the results of the query in an association list.\nruntime:\n    GO-query-edges: ~5 min\n    go-query-results: just under 2 hrs\n|#\n;;function call: query-GO | takes: list of uniprot curies | returns: list of three edge hashes\n(define GO-query-edges (time (query-GO uniprots)))\n\n;;function call: report-GO-queries | takes: list of three edge hashes | returns: sorted assoc list\n(define go-query-results (time (report-GO-queries GO-query-edges)))\n\n#|\nRuns and reports the 1-hop query.\nruntime: ~ 20 min\n|#\n;;function call: 1-hop-query/report | takes: list of uniprot curies | returns: sorted assoc list\n(define 1-hop-results (time (1-hop-query/report uniprots)))\n\n#|\nFinds the intersections between the GO query findings and 1-hop query findings.\n|#\n;;function call: find-intersections | takes: sorted assoc list returned by report-GO-queries, sorted\n;;assoc list returned by 1-hop-query/report | returns: sorted assoc list\n;; NOTE: CURRENTLY THROWS ERROR\n;;(define intersections (time (find-intersections go-query-results 1-hop-results)))\n\n;;function call: find-expression-locations | takes: list of gene/protein curies | returns: hash that maps cell/tissue type to list of gene/proteins\n;;runtime: ~25 min\n(define cell/tissue-types (time (find-expression-locations (set-union (map caar go-query-results) (map caar 1-hop-results) uniprots))))\n\n;;function call: sort-cell/tissue-types-by-G-and-rG | takes: hash returned by find-expression-locations | returns: sorted assoc list\n(define cell/tissue-types-sorted-by-G-or-rG (time (sort-cell/tissue-types-by-G-and-rG cell/tissue-types)))\n\n;;function call: sort-cell/tissue-types-by-rG | takes: hash returned by find-expression-locations | returns: sorted assoc list\n(define cell/tissue-types-sorted-by-rG (time (sort-cell/tissue-types-by-rG cell/tissue-types (map curie->curie/name uniprots))))\n\n#|\nGives a ranked list of G's with the count of the number of relationships they have with an rG. The same rG\ncan be counted twice if the nature of the relationship between the G and rG (ie. the direction or direct\ninteraction) is different.\nFirst is for go query results, second is for 1-hop-results\n|#\n(define go-ranked-Gs-indistinct (map (lambda (x) (cons (car x) (length (cdr x)))) go-query-results))\n(define 1-hop-ranked-Gs-indistinct (map (lambda (x) (cons (car x) (length (cdr x)))) 1-hop-results))\n\n#|\nGives a ranked list of G's with the count of the number of distinct rG's they regulate. The same rG cannot be\ncounted twice.\nFirst is for go query results, second is for 1-hop-results\n|#\n(define go-ranked-Gs-distinct (sort\n                               (map\n                                (lambda (g=>rg)\n                                  (cons (car g=>rg)\n                                        (length (group-by (lambda (rg/info) (caar rg/info)) (cdr g=>rg))))\n                                  )\n                                go-query-results\n                                )\n                               >\n                               #:key (lambda (x) (cdr x))))\n(define 1-hop-ranked-Gs-distinct (sort\n                                  (map\n                                   (lambda (g=>rg)\n                                     (cons (car g=>rg)\n                                           (length (group-by (lambda (rg/info) (caar rg/info)) (cdr g=>rg))))\n                                     )\n                                   1-hop-results\n                                   )\n                                  >\n                                  #:key (lambda (x) (cdr x))))\n\n#|\nGives the top 10 ranked G's that are also on ARDS gene list\n|#\n(define go-top-10-Gs-on-ards-list (map curie->curie/name (take (set-intersect (map caar go-ranked-Gs-distinct) uniprots) 10)))"
  },
  {
    "path": "contrib/medikanren/pieces-parts/rank-regulators-gene-lists.rkt",
    "content": "#lang racket\n(provide ards-genes\n         NGLY1-underexpressed\n         NGLY1-overexpressed)\n\n(define ards-genes '(\"ENSEMBL:ENSG00000167972\"\n                     \"ENSEMBL:ENSG00000198691\"\n                     \"ENSEMBL:ENSG00000175164\"\n                     \"ENSEMBL:ENSG00000278540\"\n                     \"ENSEMBL:ENSG00000100412\"\n                     \"ENSEMBL:ENSG00000162104\"\n                     \"ENSEMBL:ENSG00000204305\"\n                     \"ENSEMBL:ENSG00000135744\"\n                     \"ENSEMBL:ENSG00000144891\"\n                     \"ENSEMBL:ENSG00000180772\"\n                     \"ENSEMBL:ENSG00000142208\"\n                     \"ENSEMBL:ENSG00000148218\"\n                     \"ENSEMBL:ENSG00000163631\"\n                     \"ENSEMBL:ENSG00000085662\"\n                     \"ENSEMBL:ENSG00000154188\"\n                     \"ENSEMBL:ENSG00000091879\"\n                     \"ENSEMBL:ENSG00000182718\"\n                     \"ENSEMBL:ENSG00000134982\"\n                     \"ENSEMBL:ENSG00000132703\"\n                     \"ENSEMBL:ENSG00000023445\"\n                     \"ENSEMBL:ENSG00000142515\"\n                     \"ENSEMBL:ENSG00000026103\"\n                     \"ENSEMBL:ENSG00000117560\"\n                     \"ENSEMBL:ENSG00000240583\"\n                     \"ENSEMBL:ENSG00000161798\"\n                     \"ENSEMBL:ENSG00000006756\"\n                     \"ENSEMBL:ENSG00000117601\"\n                     \"ENSEMBL:ENSG00000149311\"\n                     \"ENSEMBL:ENSG00000164904\"\n                     \"ENSEMBL:ENSG00000171791\"\n                     \"ENSEMBL:ENSG00000101144\"\n                     \"ENSEMBL:ENSG00000010671\"\n                     \"ENSEMBL:ENSG00000100300\"\n                     \"ENSEMBL:ENSG00000149131\"\n                     \"ENSEMBL:ENSG00000171860\"\n                     \"ENSEMBL:ENSG00000106804\"\n                     \"ENSEMBL:ENSG00000197405\"\n                     \"ENSEMBL:ENSG00000149823\"\n                     \"ENSEMBL:ENSG00000063180\"\n                     \"ENSEMBL:ENSG00000164305\"\n                     \"ENSEMBL:ENSG00000121691\"\n                     \"ENSEMBL:ENSG00000105974\"\n                     \"ENSEMBL:ENSG00000124813\"\n                     \"ENSEMBL:ENSG00000149257\"\n                     \"ENSEMBL:ENSG00000134057\"\n                     \"ENSEMBL:ENSG00000170458\"\n                     \"ENSEMBL:ENSG00000121594\"\n                     \"ENSEMBL:ENSG00000101017\"\n                     \"ENSEMBL:ENSG00000102245\"\n                     \"ENSEMBL:ENSG00000026508\"\n                     \"ENSEMBL:ENSG00000085063\"\n                     \"ENSEMBL:ENSG00000129226\"\n                     \"ENSEMBL:ENSG00000179776\"\n                     \"ENSEMBL:ENSG00000100526\"\n                     \"ENSEMBL:ENSG00000170835\"\n                     \"ENSEMBL:ENSG00000001626\"\n                     \"ENSEMBL:ENSG00000133019\"\n                     \"ENSEMBL:ENSG00000196811\"\n                     \"ENSEMBL:ENSG00000099622\"\n                     \"ENSEMBL:ENSG00000122705\"\n                     \"ENSEMBL:ENSG00000183813\"\n                     \"ENSEMBL:ENSG00000188153\"\n                     \"ENSEMBL:ENSG00000115966\"\n                     \"ENSEMBL:ENSG00000167193\"\n                     \"ENSEMBL:ENSG00000132693\"\n                     \"ENSEMBL:ENSG00000118231\"\n                     \"ENSEMBL:ENSG00000112062\"\n                     \"ENSEMBL:ENSG00000101439\"\n                     \"ENSEMBL:ENSG00000118523\"\n                     \"ENSEMBL:ENSG00000168036\"\n                     \"ENSEMBL:ENSG00000100448\"\n                     \"ENSEMBL:ENSG00000166347\"\n                     \"ENSEMBL:ENSG00000140465\"\n                     \"ENSEMBL:ENSG00000140505\"\n                     \"ENSEMBL:ENSG00000138061\"\n                     \"ENSEMBL:ENSG00000160870\"\n                     \"ENSEMBL:ENSG00000106258\"\n                     \"ENSEMBL:ENSG00000196730\"\n                     \"ENSEMBL:ENSG00000011465\"\n                     \"ENSEMBL:ENSG00000159640\"\n                     \"ENSEMBL:ENSG00000164825\"\n                     \"ENSEMBL:ENSG00000197766\"\n                     \"ENSEMBL:ENSG00000181019\"\n                     \"ENSEMBL:ENSG00000213918\"\n                     \"ENSEMBL:ENSG00000197635\"\n                     \"ENSEMBL:ENSG00000164330\"\n                     \"ENSEMBL:ENSG00000213694\"\n                     \"ENSEMBL:ENSG00000078401\"\n                     \"ENSEMBL:ENSG00000138798\"\n                     \"ENSEMBL:ENSG00000197561\"\n                     \"ENSEMBL:ENSG00000021355\"\n                     \"ENSEMBL:ENSG00000066044\"\n                     \"ENSEMBL:ENSG00000116016\"\n                     \"ENSEMBL:ENSG00000133216\"\n                     \"ENSEMBL:ENSG00000120915\"\n                     \"ENSEMBL:ENSG00000130427\"\n                     \"ENSEMBL:ENSG00000157554\"\n                     \"ENSEMBL:ENSG00000157557\"\n                     \"ENSEMBL:ENSG00000180210\"\n                     \"ENSEMBL:ENSG00000117525\"\n                     \"ENSEMBL:ENSG00000198734\"\n                     \"ENSEMBL:ENSG00000117480\"\n                     \"ENSEMBL:ENSG00000166147\"\n                     \"ENSEMBL:ENSG00000151422\"\n                     \"ENSEMBL:ENSG00000140285\"\n                     \"ENSEMBL:ENSG00000160867\"\n                     \"ENSEMBL:ENSG00000111206\"\n                     \"ENSEMBL:ENSG00000115414\"\n                     \"ENSEMBL:ENSG00000170345\"\n                     \"ENSEMBL:ENSG00000154727\"\n                     \"ENSEMBL:ENSG00000163288\"\n                     \"ENSEMBL:ENSG00000128683\"\n                     \"ENSEMBL:ENSG00000141448\"\n                     \"ENSEMBL:ENSG00000168621\"\n                     \"ENSEMBL:ENSG00000134812\"\n                     \"ENSEMBL:ENSG00000265107\"\n                     \"ENSEMBL:ENSG00000173221\"\n                     \"ENSEMBL:ENSG00000147437\"\n                     \"ENSEMBL:ENSG00000186810\"\n                     \"ENSEMBL:ENSG00000167701\"\n                     \"ENSEMBL:ENSG00000113580\"\n                     \"ENSEMBL:ENSG00000082701\"\n                     \"ENSEMBL:ENSG00000132518\"\n                     \"ENSEMBL:ENSG00000145649\"\n                     \"ENSEMBL:ENSG00000100453\"\n                     \"ENSEMBL:ENSG00000148702\"\n                     \"ENSEMBL:ENSG00000084754\"\n                     \"ENSEMBL:ENSG00000019991\"\n                     \"ENSEMBL:ENSG00000100644\"\n                     \"ENSEMBL:ENSG00000189403\"\n                     \"ENSEMBL:ENSG00000100292\"\n                     \"ENSEMBL:ENSG00000125798\"\n                     \"ENSEMBL:ENSG00000135486\"\n                     \"ENSEMBL:ENSG00000257017\"\n                     \"ENSEMBL:ENSG00000113905\"\n                     \"ENSEMBL:ENSG00000176387\"\n                     \"ENSEMBL:ENSG00000204389\"\n                     \"ENSEMBL:ENSG00000204388\"\n                     \"ENSEMBL:ENSG00000170606\"\n                     \"ENSEMBL:ENSG00000070614\"\n                     \"ENSEMBL:ENSG00000041982\"\n                     \"ENSEMBL:ENSG00000090339\"\n                     \"ENSEMBL:ENSG00000185745\"\n                     \"ENSEMBL:ENSG00000171855\"\n                     \"ENSEMBL:ENSG00000111537\"\n                     \"ENSEMBL:ENSG00000006652\"\n                     \"ENSEMBL:ENSG00000017427\"\n                     \"ENSEMBL:ENSG00000146674\"\n                     \"ENSEMBL:ENSG00000167779\"\n                     \"ENSEMBL:ENSG00000104365\"\n                     \"ENSEMBL:ENSG00000115008\"\n                     \"ENSEMBL:ENSG00000125538\"\n                     \"ENSEMBL:ENSG00000115594\"\n                     \"ENSEMBL:ENSG00000136689\"\n                     \"ENSEMBL:ENSG00000109471\"\n                     \"ENSEMBL:ENSG00000134460\"\n                     \"ENSEMBL:ENSG00000113520\"\n                     \"ENSEMBL:ENSG00000136244\"\n                     \"ENSEMBL:ENSG00000168685\"\n                     \"ENSEMBL:ENSG00000169429\"\n                     \"ENSEMBL:ENSG00000136634\"\n                     \"ENSEMBL:ENSG00000169194\"\n                     \"ENSEMBL:ENSG00000112115\"\n                     \"ENSEMBL:ENSG00000150782\"\n                     \"ENSEMBL:ENSG00000169245\"\n                     \"ENSEMBL:ENSG00000125347\"\n                     \"ENSEMBL:ENSG00000005884\"\n                     \"ENSEMBL:ENSG00000169896\"\n                     \"ENSEMBL:ENSG00000160255\"\n                     \"ENSEMBL:ENSG00000115474\"\n                     \"ENSEMBL:ENSG00000128052\"\n                     \"ENSEMBL:ENSG00000171345\"\n                     \"ENSEMBL:ENSG00000172037\"\n                     \"ENSEMBL:ENSG00000148346\"\n                     \"ENSEMBL:ENSG00000115850\"\n                     \"ENSEMBL:ENSG00000131981\"\n                     \"ENSEMBL:ENSG00000138039\"\n                     \"ENSEMBL:ENSG00000105370\"\n                     \"ENSEMBL:ENSG00000226979\"\n                     \"ENSEMBL:ENSG00000160932\"\n                     \"ENSEMBL:ENSG00000183918\"\n                     \"ENSEMBL:ENSG00000277443\"\n                     \"ENSEMBL:ENSG00000166949\"\n                     \"ENSEMBL:ENSG00000165471\"\n                     \"ENSEMBL:ENSG00000143384\"\n                     \"ENSEMBL:ENSG00000014641\"\n                     \"ENSEMBL:ENSG00000110492\"\n                     \"ENSEMBL:ENSG00000095015\"\n                     \"ENSEMBL:ENSG00000240972\"\n                     \"ENSEMBL:ENSG00000138755\"\n                     \"ENSEMBL:ENSG00000087245\"\n                     \"ENSEMBL:ENSG00000149968\"\n                     \"ENSEMBL:ENSG00000100985\"\n                     \"ENSEMBL:ENSG00000005381\"\n                     \"ENSEMBL:ENSG00000130830\"\n                     \"ENSEMBL:ENSG00000125148\"\n                     \"ENSEMBL:ENSG00000087250\"\n                     \"ENSEMBL:ENSG00000171100\"\n                     \"ENSEMBL:ENSG00000210195\"\n                     \"ENSEMBL:ENSG00000185499\"\n                     \"ENSEMBL:ENSG00000215182\"\n                     \"ENSEMBL:ENSG00000136997\"\n                     \"ENSEMBL:ENSG00000172936\"\n                     \"ENSEMBL:ENSG00000109063\"\n                     \"ENSEMBL:ENSG00000065534\"\n                     \"ENSEMBL:ENSG00000116044\"\n                     \"ENSEMBL:ENSG00000109320\"\n                     \"ENSEMBL:ENSG00000100906\"\n                     \"ENSEMBL:ENSG00000001167\"\n                     \"ENSEMBL:ENSG00000089250\"\n                     \"ENSEMBL:ENSG00000164867\"\n                     \"ENSEMBL:ENSG00000161270\"\n                     \"ENSEMBL:ENSG00000135318\"\n                     \"ENSEMBL:ENSG00000111331\"\n                     \"ENSEMBL:ENSG00000112038\"\n                     \"ENSEMBL:ENSG00000089041\"\n                     \"ENSEMBL:ENSG00000185624\"\n                     \"ENSEMBL:ENSG00000007168\"\n                     \"ENSEMBL:ENSG00000117450\"\n                     \"ENSEMBL:ENSG00000106366\"\n                     \"ENSEMBL:ENSG00000126759\"\n                     \"ENSEMBL:ENSG00000197249\"\n                     \"ENSEMBL:ENSG00000124102\"\n                     \"ENSEMBL:ENSG00000121879\"\n                     \"ENSEMBL:ENSG00000051382\"\n                     \"ENSEMBL:ENSG00000171608\"\n                     \"ENSEMBL:ENSG00000105851\"\n                     \"ENSEMBL:ENSG00000170890\"\n                     \"ENSEMBL:ENSG00000188257\"\n                     \"ENSEMBL:ENSG00000116711\"\n                     \"ENSEMBL:ENSG00000118495\"\n                     \"ENSEMBL:ENSG00000011422\"\n                     \"ENSEMBL:ENSG00000115896\"\n                     \"ENSEMBL:ENSG00000075651\"\n                     \"ENSEMBL:ENSG00000178209\"\n                     \"ENSEMBL:ENSG00000266964\"\n                     \"ENSEMBL:ENSG00000115138\"\n                     \"ENSEMBL:ENSG00000186951\"\n                     \"ENSEMBL:ENSG00000122862\"\n                     \"ENSEMBL:ENSG00000100030\"\n                     \"ENSEMBL:ENSG00000107643\"\n                     \"ENSEMBL:ENSG00000169032\"\n                     \"ENSEMBL:ENSG00000115718\"\n                     \"ENSEMBL:ENSG00000184500\"\n                     \"ENSEMBL:ENSG00000189002\"\n                     \"ENSEMBL:ENSG00000135406\"\n                     \"ENSEMBL:ENSG00000041357\"\n                     \"ENSEMBL:ENSG00000197170\"\n                     \"ENSEMBL:ENSG00000011304\"\n                     \"ENSEMBL:ENSG00000073756\"\n                     \"ENSEMBL:ENSG00000169398\"\n                     \"ENSEMBL:ENSG00000105894\"\n                     \"ENSEMBL:ENSG00000081237\"\n                     \"ENSEMBL:ENSG00000113456\"\n                     \"ENSEMBL:ENSG00000069974\"\n                     \"ENSEMBL:ENSG00000080823\"\n                     \"ENSEMBL:ENSG00000112619\"\n                     \"ENSEMBL:ENSG00000173039\"\n                     \"ENSEMBL:ENSG00000143839\"\n                     \"ENSEMBL:ENSG00000102032\"\n                     \"ENSEMBL:ENSG00000163914\"\n                     \"ENSEMBL:ENSG00000067900\"\n                     \"ENSEMBL:ENSG00000149489\"\n                     \"ENSEMBL:ENSG00000196218\"\n                     \"ENSEMBL:ENSG00000196154\"\n                     \"ENSEMBL:ENSG00000163220\"\n                     \"ENSEMBL:ENSG00000031698\"\n                     \"ENSEMBL:ENSG00000111319\"\n                     \"ENSEMBL:ENSG00000108691\"\n                     \"ENSEMBL:ENSG00000108688\"\n                     \"ENSEMBL:ENSG00000163735\"\n                     \"ENSEMBL:ENSG00000110876\"\n                     \"ENSEMBL:ENSG00000168878\"\n                     \"ENSEMBL:ENSG00000168484\"\n                     \"ENSEMBL:ENSG00000133661\"\n                     \"ENSEMBL:ENSG00000064651\"\n                     \"ENSEMBL:ENSG00000197208\"\n                     \"ENSEMBL:ENSG00000166311\"\n                     \"ENSEMBL:ENSG00000075618\"\n                     \"ENSEMBL:ENSG00000125835\"\n                     \"ENSEMBL:ENSG00000142168\"\n                     \"ENSEMBL:ENSG00000112096\"\n                     \"ENSEMBL:ENSG00000109610\"\n                     \"ENSEMBL:ENSG00000125398\"\n                     \"ENSEMBL:ENSG00000100883\"\n                     \"ENSEMBL:ENSG00000168610\"\n                     \"ENSEMBL:ENSG00000126561\"\n                     \"ENSEMBL:ENSG00000173757\"\n                     \"ENSEMBL:ENSG00000087586\"\n                     \"ENSEMBL:ENSG00000067715\"\n                     \"ENSEMBL:ENSG00000231925\"\n                     \"ENSEMBL:ENSG00000006638\"\n                     \"ENSEMBL:ENSG00000118526\"\n                     \"ENSEMBL:ENSG00000120156\"\n                     \"ENSEMBL:ENSG00000164362\"\n                     \"ENSEMBL:ENSG00000003436\"\n                     \"ENSEMBL:ENSG00000105329\"\n                     \"ENSEMBL:ENSG00000198959\"\n                     \"ENSEMBL:ENSG00000178726\"\n                     \"ENSEMBL:ENSG00000116001\"\n                     \"ENSEMBL:ENSG00000102265\"\n                     \"ENSEMBL:ENSG00000136352\"\n                     \"ENSEMBL:ENSG00000137462\"\n                     \"ENSEMBL:ENSG00000164342\"\n                     \"ENSEMBL:ENSG00000136869\"\n                     \"ENSEMBL:ENSG00000127324\"\n                     \"ENSEMBL:ENSG00000149809\"\n                     \"ENSEMBL:ENSG00000232810\"\n                     \"ENSEMBL:ENSG00000118503\"\n                     \"ENSEMBL:ENSG00000067182\"\n                     \"ENSEMBL:ENSG00000118194\"\n                     \"ENSEMBL:ENSG00000131747\"\n                     \"ENSEMBL:ENSG00000111669\"\n                     \"ENSEMBL:ENSG00000128311\"\n                     \"ENSEMBL:ENSG00000125482\"\n                     \"ENSEMBL:ENSG00000155657\"\n                     \"ENSEMBL:ENSG00000136810\"\n                     \"ENSEMBL:ENSG00000198431\"\n                     \"ENSEMBL:ENSG00000149021\"\n                     \"ENSEMBL:ENSG00000174607\"\n                     \"ENSEMBL:ENSG00000111424\"\n                     \"ENSEMBL:ENSG00000112715\"\n                     \"ENSEMBL:ENSG00000146469\"\n                     \"ENSEMBL:ENSG00000110799\"\n                     \"ENSEMBL:ENSG00000158125\"\n                     \"ENSEMBL:ENSG00000164924\"\n                     \"ENSEMBL:ENSG00000121966\"\n                     \"ENSEMBL:ENSG00000146070\"\n                     \"ENSEMBL:ENSG00000106305\"\n                     \"ENSEMBL:ENSG00000050327\"\n                     \"ENSEMBL:ENSG00000083168\"\n                     \"ENSEMBL:ENSG00000118972\"\n                     \"ENSEMBL:ENSG00000206561\"\n                     \"ENSEMBL:ENSG00000184381\"\n                     \"ENSEMBL:ENSG00000069764\"\n                     \"ENSEMBL:ENSG00000108528\"\n                     \"ENSEMBL:ENSG00000117461\"\n                     \"ENSEMBL:ENSG00000134107\"\n                     \"ENSEMBL:ENSG00000136908\"\n                     \"ENSEMBL:ENSG00000171720\"\n                     \"ENSEMBL:ENSG00000176170\"\n                     \"ENSEMBL:ENSG00000111602\"\n                     \"ENSEMBL:ENSG00000173805\"\n                     \"ENSEMBL:ENSG00000131023\"\n                     \"ENSEMBL:ENSG00000157456\"\n                     \"ENSEMBL:ENSG00000162889\"\n                     \"ENSEMBL:ENSG00000103671\"\n                     \"ENSEMBL:ENSG00000133116\"\n                     \"ENSEMBL:ENSG00000181092\"\n                     \"ENSEMBL:ENSG00000100351\"\n                     \"ENSEMBL:ENSG00000136156\"\n                     \"ENSEMBL:ENSG00000102230\"\n                     \"ENSEMBL:ENSG00000057663\"\n                     \"ENSEMBL:ENSG00000134318\"\n                     \"ENSEMBL:ENSG00000117592\"\n                     \"ENSEMBL:ENSG00000187608\"\n                     \"ENSEMBL:ENSG00000103335\"\n                     \"ENSEMBL:ENSG00000165733\"\n                     \"ENSEMBL:ENSG00000079999\"\n                     \"ENSEMBL:ENSG00000044090\"\n                     \"ENSEMBL:ENSG00000117020\"\n                     \"ENSEMBL:ENSG00000105835\"\n                     \"ENSEMBL:ENSG00000105246\"\n                     \"ENSEMBL:ENSG00000131477\"\n                     \"ENSEMBL:ENSG00000127528\"\n                     \"ENSEMBL:ENSG00000167315\"\n                     \"ENSEMBL:ENSG00000140092\"\n                     \"ENSEMBL:ENSG00000101000\"\n                     \"ENSEMBL:ENSG00000100591\"\n                     \"ENSEMBL:ENSG00000160999\"\n                     \"ENSEMBL:ENSG00000162493\"\n                     \"ENSEMBL:ENSG00000048740\"\n                     \"ENSEMBL:ENSG00000173083\"\n                     \"ENSEMBL:ENSG00000196843\"\n                     \"ENSEMBL:ENSG00000126264\"\n                     \"ENSEMBL:ENSG00000137959\"\n                     \"ENSEMBL:ENSG00000269821\"\n                     \"ENSEMBL:ENSG00000083807\"\n                     \"ENSEMBL:ENSG00000167114\"\n                     \"ENSEMBL:ENSG00000129465\"\n                     \"ENSEMBL:ENSG00000136110\"\n                     \"ENSEMBL:ENSG00000256525\"\n                     \"ENSEMBL:ENSG00000142082\"\n                     \"ENSEMBL:ENSG00000096717\"\n                     \"ENSEMBL:ENSG00000136859\"\n                     \"ENSEMBL:ENSG00000172828\"\n                     \"ENSEMBL:ENSG00000123415\"\n                     \"ENSEMBL:ENSG00000025800\"\n                     \"ENSEMBL:ENSG00000154589\"\n                     \"ENSEMBL:ENSG00000177663\"\n                     \"ENSEMBL:ENSG00000034677\"\n                     \"ENSEMBL:ENSG00000196141\"\n                     \"ENSEMBL:ENSG00000004142\"\n                     \"ENSEMBL:ENSG00000113249\"\n                     \"ENSEMBL:ENSG00000007952\"\n                     \"ENSEMBL:ENSG00000086232\"\n                     \"ENSEMBL:ENSG00000138744\"\n                     \"ENSEMBL:ENSG00000163106\"\n                     \"ENSEMBL:ENSG00000138375\"\n                     \"ENSEMBL:ENSG00000086991\"\n                     \"ENSEMBL:ENSG00000219430\"\n                     \"ENSEMBL:ENSG00000138303\"\n                     \"ENSEMBL:ENSG00000126524\"\n                     \"ENSEMBL:ENSG00000167772\"\n                     \"ENSEMBL:ENSG00000165682\"\n                     \"ENSEMBL:ENSG00000101916\"\n                     \"ENSEMBL:ENSG00000172458\"\n                     \"ENSEMBL:ENSG00000124731\"\n                     \"ENSEMBL:ENSG00000011426\"\n                     \"ENSEMBL:ENSG00000135766\"\n                     \"ENSEMBL:ENSG00000241635\"\n                     \"ENSEMBL:ENSG00000104835\"\n                     \"ENSEMBL:ENSG00000185480\"\n                     \"ENSEMBL:ENSG00000110075\"\n                     \"ENSEMBL:ENSG00000079691\"\n                     \"ENSEMBL:ENSG00000171109\"\n                     \"ENSEMBL:ENSG00000151849\"\n                     \"ENSEMBL:ENSG00000126970\"\n                     \"ENSEMBL:ENSG00000169241\"\n                     \"ENSEMBL:ENSG00000074842\"\n                     \"ENSEMBL:ENSG00000185115\"\n                     \"ENSEMBL:ENSG00000136688\"\n                     \"ENSEMBL:ENSG00000115350\"\n                     \"ENSEMBL:ENSG00000111666\"\n                     \"ENSEMBL:ENSG00000198074\"\n                     \"ENSEMBL:ENSG00000283122\"\n                     \"ENSEMBL:ENSG00000139946\"\n                     \"ENSEMBL:ENSG00000175482\"\n                     \"ENSEMBL:ENSG00000117569\"\n                     \"ENSEMBL:ENSG00000130234\"\n                     \"ENSEMBL:ENSG00000198026\"\n                     \"ENSEMBL:ENSG00000132429\"\n                     \"ENSEMBL:ENSG00000114745\"\n                     \"ENSEMBL:ENSG00000060237\"\n                     \"ENSEMBL:ENSG00000262246\"\n                     \"ENSEMBL:ENSG00000104518\"\n                     \"ENSEMBL:ENSG00000153395\"\n                     \"ENSEMBL:ENSG00000146094\"\n                     \"ENSEMBL:ENSG00000125779\"\n                     \"ENSEMBL:ENSG00000197496\"\n                     \"ENSEMBL:ENSG00000169612\"\n                     \"ENSEMBL:ENSG00000138496\"\n                     \"ENSEMBL:ENSG00000169962\"\n                     \"ENSEMBL:ENSG00000130363\"\n                     \"ENSEMBL:ENSG00000103510\"\n                     \"ENSEMBL:ENSG00000106125\"\n                     \"ENSEMBL:ENSG00000131653\"\n                     \"ENSEMBL:ENSG00000145794\"\n                     \"ENSEMBL:ENSG00000163702\"\n                     \"ENSEMBL:ENSG00000100410\"\n                     \"ENSEMBL:ENSG00000137691\"\n                     \"ENSEMBL:ENSG00000160188\"\n                     \"ENSEMBL:ENSG00000151148\"\n                     \"ENSEMBL:ENSG00000137033\"\n                     \"ENSEMBL:ENSG00000178473\"\n                     \"ENSEMBL:ENSG00000162711\"\n                     \"ENSEMBL:ENSG00000161544\"\n                     \"ENSEMBL:ENSG00000153391\"\n                     \"ENSEMBL:ENSG00000205359\"\n                     \"ENSEMBL:ENSG00000168724\"\n                     \"ENSEMBL:ENSG00000229140\"\n                     \"ENSEMBL:ENSG00000165953\"\n                     \"ENSEMBL:ENSG00000172967\"\n                     \"ENSEMBL:ENSG00000163803\"\n                     \"ENSEMBL:ENSG00000197272\"\n                     \"ENSEMBL:ENSG00000175311\"\n                     \"ENSEMBL:ENSG00000170782\"\n                     \"ENSEMBL:ENSG00000189195\"\n                     \"ENSEMBL:ENSG00000161911\"\n                     \"ENSEMBL:ENSG00000197448\"\n                     \"ENSEMBL:ENSG00000251562\"\n                     \"ENSEMBL:ENSG00000187258\"\n                     \"ENSEMBL:ENSG00000248131\"\n                     \"ENSEMBL:ENSG00000284520\"\n                     \"ENSEMBL:ENSG00000199133\"\n                     \"ENSEMBL:ENSG00000284440\"\n                     \"ENSEMBL:ENSG00000199161\"\n                     \"ENSEMBL:ENSG00000207608\"\n                     \"ENSEMBL:ENSG00000207625\"\n                     \"ENSEMBL:ENSG00000207782\"\n                     \"ENSEMBL:ENSG00000283904\"\n                     \"ENSEMBL:ENSG00000283815\"\n                     \"ENSEMBL:ENSG00000284204\"\n                     \"ENSEMBL:ENSG00000207607\"\n                     \"ENSEMBL:ENSG00000199038\"\n                     \"ENSEMBL:ENSG00000207702\"\n                     \"ENSEMBL:ENSG00000207590\"\n                     \"ENSEMBL:ENSG00000207798\"\n                     \"ENSEMBL:ENSG00000207870\"\n                     \"ENSEMBL:ENSG00000284567\"\n                     \"ENSEMBL:ENSG00000199075\"\n                     \"ENSEMBL:ENSG00000199121\"\n                     \"ENSEMBL:ENSG00000207808\"\n                     \"ENSEMBL:ENSG00000207864\"\n                     \"ENSEMBL:ENSG00000207827\"\n                     \"ENSEMBL:ENSG00000207582\"\n                     \"ENSEMBL:ENSG00000284357\"\n                     \"ENSEMBL:ENSG00000207638\"\n                     \"ENSEMBL:ENSG00000199059\"\n                     \"ENSEMBL:ENSG00000199151\"\n                     \"ENSEMBL:ENSG00000199104\"\n                     \"ENSEMBL:ENSG00000198982\"\n                     \"ENSEMBL:ENSG00000199020\"\n                     \"ENSEMBL:ENSG00000208001\"\n                     \"ENSEMBL:ENSG00000202569\"\n                     \"ENSEMBL:ENSG00000194717\"\n                     \"ENSEMBL:ENSG00000207731\"\n                     \"ENSEMBL:ENSG00000122852\"\n                     \"ENSEMBL:ENSG00000207571\"\n                     \"ENSEMBL:ENSG00000185303\"\n                     \"ENSEMBL:ENSG00000211590\"\n                     \"ENSEMBL:ENSG00000285427\"\n                     \"ENSEMBL:ENSG00000228750\"\n                     \"ENSEMBL:ENSG00000280634\"\n                     \"ENSEMBL:ENSG00000243438\"\n                     \"ENSEMBL:ENSG00000201796\"\n                     \"ENSEMBL:ENSG00000240160\"))\n\n(define NGLY1-overexpressed '(\"ENSEMBL:ENSG00000183044\"\n                              \"ENSEMBL:ENSG00000179869\"\n                              \"ENSEMBL:ENSG00000167972\"\n                              \"ENSEMBL:ENSG00000198691\"\n                              \"ENSEMBL:ENSG00000085563\"\n                              \"ENSEMBL:ENSG00000005471\"\n                              \"ENSEMBL:ENSG00000166016\"\n                              \"ENSEMBL:ENSG00000120437\"\n                              \"ENSEMBL:ENSG00000176244\"\n                              \"ENSEMBL:ENSG00000114739\"\n                              \"ENSEMBL:ENSG00000145808\"\n                              \"ENSEMBL:ENSG00000155897\"\n                              \"ENSEMBL:ENSG00000078549\"\n                              \"ENSEMBL:ENSG00000075340\"\n                              \"ENSEMBL:ENSG00000135298\"\n                              \"ENSEMBL:ENSG00000173698\"\n                              \"ENSEMBL:ENSG00000162618\"\n                              \"ENSEMBL:ENSG00000164199\"\n                              \"ENSEMBL:ENSG00000198221\"\n                              \"ENSEMBL:ENSG00000135439\"\n                              \"ENSEMBL:ENSG00000126878\"\n                              \"ENSEMBL:ENSG00000230042\"\n                              \"ENSEMBL:ENSG00000140057\"\n                              \"ENSEMBL:ENSG00000171094\"\n                              \"ENSEMBL:ENSG00000189292\"\n                              \"ENSEMBL:ENSG00000165566\"\n                              \"ENSEMBL:ENSG00000181754\"\n                              \"ENSEMBL:ENSG00000185046\"\n                              \"ENSEMBL:ENSG00000103723\"\n                              \"ENSEMBL:ENSG00000154856\"\n                              \"ENSEMBL:ENSG00000171388\"\n                              \"ENSEMBL:ENSG00000134817\"\n                              \"ENSEMBL:ENSG00000100336\"\n                              \"ENSEMBL:ENSG00000178878\"\n                              \"ENSEMBL:ENSG00000137727\"\n                              \"ENSEMBL:ENSG00000179361\"\n                              \"ENSEMBL:ENSG00000122644\"\n                              \"ENSEMBL:ENSG00000169126\"\n                              \"ENSEMBL:ENSG00000172379\"\n                              \"ENSEMBL:ENSG00000099889\"\n                              \"ENSEMBL:ENSG00000102048\"\n                              \"ENSEMBL:ENSG00000139352\"\n                              \"ENSEMBL:ENSG00000162174\"\n                              \"ENSEMBL:ENSG00000141431\"\n                              \"ENSEMBL:ENSG00000168874\"\n                              \"ENSEMBL:ENSG00000158321\"\n                              \"ENSEMBL:ENSG00000168646\"\n                              \"ENSEMBL:ENSG00000109956\"\n                              \"ENSEMBL:ENSG00000135454\"\n                              \"ENSEMBL:ENSG00000164929\"\n                              \"ENSEMBL:ENSG00000007516\"\n                              \"ENSEMBL:ENSG00000171791\"\n                              \"ENSEMBL:ENSG00000133169\"\n                              \"ENSEMBL:ENSG00000133134\"\n                              \"ENSEMBL:ENSG00000281406\"\n                              \"ENSEMBL:ENSG00000101144\"\n                              \"ENSEMBL:ENSG00000251079\"\n                              \"ENSEMBL:ENSG00000169594\"\n                              \"ENSEMBL:ENSG00000174672\"\n                              \"ENSEMBL:ENSG00000151136\"\n                              \"ENSEMBL:ENSG00000204347\"\n                              \"ENSEMBL:ENSG00000162817\"\n                              \"ENSEMBL:ENSG00000179902\"\n                              \"ENSEMBL:ENSG00000239887\"\n                              \"ENSEMBL:ENSG00000112539\"\n                              \"ENSEMBL:ENSG00000137434\"\n                              \"ENSEMBL:ENSG00000285312\"\n                              \"ENSEMBL:ENSG00000112936\"\n                              \"ENSEMBL:ENSG00000204711\"\n                              \"ENSEMBL:ENSG00000225626\"\n                              \"ENSEMBL:ENSG00000165118\"\n                              \"ENSEMBL:ENSG00000118298\"\n                              \"ENSEMBL:ENSG00000104267\"\n                              \"ENSEMBL:ENSG00000178538\"\n                              \"ENSEMBL:ENSG00000157782\"\n                              \"ENSEMBL:ENSG00000006283\"\n                              \"ENSEMBL:ENSG00000075461\"\n                              \"ENSEMBL:ENSG00000105605\"\n                              \"ENSEMBL:ENSG00000142408\"\n                              \"ENSEMBL:ENSG00000104327\"\n                              \"ENSEMBL:ENSG00000070808\"\n                              \"ENSEMBL:ENSG00000164076\"\n                              \"ENSEMBL:ENSG00000076826\"\n                              \"ENSEMBL:ENSG00000237436\"\n                              \"ENSEMBL:ENSG00000087589\"\n                              \"ENSEMBL:ENSG00000130940\"\n                              \"ENSEMBL:ENSG00000102924\"\n                              \"ENSEMBL:ENSG00000183287\"\n                              \"ENSEMBL:ENSG00000163081\"\n                              \"ENSEMBL:ENSG00000198003\"\n                              \"ENSEMBL:ENSG00000198865\"\n                              \"ENSEMBL:ENSG00000203952\"\n                              \"ENSEMBL:ENSG00000267909\"\n                              \"ENSEMBL:ENSG00000117477\"\n                              \"ENSEMBL:ENSG00000177875\"\n                              \"ENSEMBL:ENSG00000015133\"\n                              \"ENSEMBL:ENSG00000091972\"\n                              \"ENSEMBL:ENSG00000272398\"\n                              \"ENSEMBL:ENSG00000185275\"\n                              \"ENSEMBL:ENSG00000174059\"\n                              \"ENSEMBL:ENSG00000019582\"\n                              \"ENSEMBL:ENSG00000112149\"\n                              \"ENSEMBL:ENSG00000101542\"\n                              \"ENSEMBL:ENSG00000179776\"\n                              \"ENSEMBL:ENSG00000129596\"\n                              \"ENSEMBL:ENSG00000064309\"\n                              \"ENSEMBL:ENSG00000007129\"\n                              \"ENSEMBL:ENSG00000278565\"\n                              \"ENSEMBL:ENSG00000159409\"\n                              \"ENSEMBL:ENSG00000143126\"\n                              \"ENSEMBL:ENSG00000166582\"\n                              \"ENSEMBL:ENSG00000147869\"\n                              \"ENSEMBL:ENSG00000163075\"\n                              \"ENSEMBL:ENSG00000188596\"\n                              \"ENSEMBL:ENSG00000143375\"\n                              \"ENSEMBL:ENSG00000070748\"\n                              \"ENSEMBL:ENSG00000106153\"\n                              \"ENSEMBL:ENSG00000016391\"\n                              \"ENSEMBL:ENSG00000100604\"\n                              \"ENSEMBL:ENSG00000276781\"\n                              \"ENSEMBL:ENSG00000101938\"\n                              \"ENSEMBL:ENSG00000175344\"\n                              \"ENSEMBL:ENSG00000160716\"\n                              \"ENSEMBL:ENSG00000125931\"\n                              \"ENSEMBL:ENSG00000166165\"\n                              \"ENSEMBL:ENSG00000150048\"\n                              \"ENSEMBL:ENSG00000166509\"\n                              \"ENSEMBL:ENSG00000153132\"\n                              \"ENSEMBL:ENSG00000146352\"\n                              \"ENSEMBL:ENSG00000118432\"\n                              \"ENSEMBL:ENSG00000122756\"\n                              \"ENSEMBL:ENSG00000184144\"\n                              \"ENSEMBL:ENSG00000187955\"\n                              \"ENSEMBL:ENSG00000139219\"\n                              \"ENSEMBL:ENSG00000197565\"\n                              \"ENSEMBL:ENSG00000112280\"\n                              \"ENSEMBL:ENSG00000158270\"\n                              \"ENSEMBL:ENSG00000047457\"\n                              \"ENSEMBL:ENSG00000135678\"\n                              \"ENSEMBL:ENSG00000196353\"\n                              \"ENSEMBL:ENSG00000148204\"\n                              \"ENSEMBL:ENSG00000178662\"\n                              \"ENSEMBL:ENSG00000169862\"\n                              \"ENSEMBL:ENSG00000163131\"\n                              \"ENSEMBL:ENSG00000180891\"\n                              \"ENSEMBL:ENSG00000111249\"\n                              \"ENSEMBL:ENSG00000154639\"\n                              \"ENSEMBL:ENSG00000145824\"\n                              \"ENSEMBL:ENSG00000121966\"\n                              \"ENSEMBL:ENSG00000019186\"\n                              \"ENSEMBL:ENSG00000146233\"\n                              \"ENSEMBL:ENSG00000276644\"\n                              \"ENSEMBL:ENSG00000126733\"\n                              \"ENSEMBL:ENSG00000187323\"\n                              \"ENSEMBL:ENSG00000011465\"\n                              \"ENSEMBL:ENSG00000232093\"\n                              \"ENSEMBL:ENSG00000204580\"\n                              \"ENSEMBL:ENSG00000229767\"\n                              \"ENSEMBL:ENSG00000137332\"\n                              \"ENSEMBL:ENSG00000230456\"\n                              \"ENSEMBL:ENSG00000234078\"\n                              \"ENSEMBL:ENSG00000223680\"\n                              \"ENSEMBL:ENSG00000215522\"\n                              \"ENSEMBL:ENSG00000109832\"\n                              \"ENSEMBL:ENSG00000204624\"\n                              \"ENSEMBL:ENSG00000262001\"\n                              \"ENSEMBL:ENSG00000198719\"\n                              \"ENSEMBL:ENSG00000275555\"\n                              \"ENSEMBL:ENSG00000173253\"\n                              \"ENSEMBL:ENSG00000158856\"\n                              \"ENSEMBL:ENSG00000122735\"\n                              \"ENSEMBL:ENSG00000225808\"\n                              \"ENSEMBL:ENSG00000088538\"\n                              \"ENSEMBL:ENSG00000101134\"\n                              \"ENSEMBL:ENSG00000175497\"\n                              \"ENSEMBL:ENSG00000121570\"\n                              \"ENSEMBL:ENSG00000157851\"\n                              \"ENSEMBL:ENSG00000162490\"\n                              \"ENSEMBL:ENSG00000110042\"\n                              \"ENSEMBL:ENSG00000133878\"\n                              \"ENSEMBL:ENSG00000120875\"\n                              \"ENSEMBL:ENSG00000264364\"\n                              \"ENSEMBL:ENSG00000007968\"\n                              \"ENSEMBL:ENSG00000282899\"\n                              \"ENSEMBL:ENSG00000129173\"\n                              \"ENSEMBL:ENSG00000136160\"\n                              \"ENSEMBL:ENSG00000114654\"\n                              \"ENSEMBL:ENSG00000108947\"\n                              \"ENSEMBL:ENSG00000138798\"\n                              \"ENSEMBL:ENSG00000206120\"\n                              \"ENSEMBL:ENSG00000198759\"\n                              \"ENSEMBL:ENSG00000164318\"\n                              \"ENSEMBL:ENSG00000196361\"\n                              \"ENSEMBL:ENSG00000186998\"\n                              \"ENSEMBL:ENSG00000183798\"\n                              \"ENSEMBL:ENSG00000163064\"\n                              \"ENSEMBL:ENSG00000164778\"\n                              \"ENSEMBL:ENSG00000168913\"\n                              \"ENSEMBL:ENSG00000151023\"\n                              \"ENSEMBL:ENSG00000136960\"\n                              \"ENSEMBL:ENSG00000159023\"\n                              \"ENSEMBL:ENSG00000129595\"\n                              \"ENSEMBL:ENSG00000234690\"\n                              \"ENSEMBL:ENSG00000229153\"\n                              \"ENSEMBL:ENSG00000285468\"\n                              \"ENSEMBL:ENSG00000154928\"\n                              \"ENSEMBL:ENSG00000178568\"\n                              \"ENSEMBL:ENSG00000149564\"\n                              \"ENSEMBL:ENSG00000092820\"\n                              \"ENSEMBL:ENSG00000158769\"\n                              \"ENSEMBL:ENSG00000164434\"\n                              \"ENSEMBL:ENSG00000184731\"\n                              \"ENSEMBL:ENSG00000121104\"\n                              \"ENSEMBL:ENSG00000150510\"\n                              \"ENSEMBL:ENSG00000130054\"\n                              \"ENSEMBL:ENSG00000154319\"\n                              \"ENSEMBL:ENSG00000185442\"\n                              \"ENSEMBL:ENSG00000140067\"\n                              \"ENSEMBL:ENSG00000273533\"\n                              \"ENSEMBL:ENSG00000258584\"\n                              \"ENSEMBL:ENSG00000281032\"\n                              \"ENSEMBL:ENSG00000111879\"\n                              \"ENSEMBL:ENSG00000104059\"\n                              \"ENSEMBL:ENSG00000273564\"\n                              \"ENSEMBL:ENSG00000188732\"\n                              \"ENSEMBL:ENSG00000084444\"\n                              \"ENSEMBL:ENSG00000283329\"\n                              \"ENSEMBL:ENSG00000166492\"\n                              \"ENSEMBL:ENSG00000144152\"\n                              \"ENSEMBL:ENSG00000130475\"\n                              \"ENSEMBL:ENSG00000214814\"\n                              \"ENSEMBL:ENSG00000149557\"\n                              \"ENSEMBL:ENSG00000114279\"\n                              \"ENSEMBL:ENSG00000102466\"\n                              \"ENSEMBL:ENSG00000174721\"\n                              \"ENSEMBL:ENSG00000261308\"\n                              \"ENSEMBL:ENSG00000155816\"\n                              \"ENSEMBL:ENSG00000122176\"\n                              \"ENSEMBL:ENSG00000171956\"\n                              \"ENSEMBL:ENSG00000129654\"\n                              \"ENSEMBL:ENSG00000206262\"\n                              \"ENSEMBL:ENSG00000164946\"\n                              \"ENSEMBL:ENSG00000150893\"\n                              \"ENSEMBL:ENSG00000172159\"\n                              \"ENSEMBL:ENSG00000114541\"\n                              \"ENSEMBL:ENSG00000147234\"\n                              \"ENSEMBL:ENSG00000188738\"\n                              \"ENSEMBL:ENSG00000134363\"\n                              \"ENSEMBL:ENSG00000172461\"\n                              \"ENSEMBL:ENSG00000104290\"\n                              \"ENSEMBL:ENSG00000166206\"\n                              \"ENSEMBL:ENSG00000268089\"\n                              \"ENSEMBL:ENSG00000175229\"\n                              \"ENSEMBL:ENSG00000119514\"\n                              \"ENSEMBL:ENSG00000171766\"\n                              \"ENSEMBL:ENSG00000168505\"\n                              \"ENSEMBL:ENSG00000111846\"\n                              \"ENSEMBL:ENSG00000285222\"\n                              \"ENSEMBL:ENSG00000184344\"\n                              \"ENSEMBL:ENSG00000130055\"\n                              \"ENSEMBL:ENSG00000228175\"\n                              \"ENSEMBL:ENSG00000165113\"\n                              \"ENSEMBL:ENSG00000178445\"\n                              \"ENSEMBL:ENSG00000242797\"\n                              \"ENSEMBL:ENSG00000087258\"\n                              \"ENSEMBL:ENSG00000128266\"\n                              \"ENSEMBL:ENSG00000168243\"\n                              \"ENSEMBL:ENSG00000282972\"\n                              \"ENSEMBL:ENSG00000238105\"\n                              \"ENSEMBL:ENSG00000150625\"\n                              \"ENSEMBL:ENSG00000046653\"\n                              \"ENSEMBL:ENSG00000183150\"\n                              \"ENSEMBL:ENSG00000164604\"\n                              \"ENSEMBL:ENSG00000211445\"\n                              \"ENSEMBL:ENSG00000141449\"\n                              \"ENSEMBL:ENSG00000158055\"\n                              \"ENSEMBL:ENSG00000155511\"\n                              \"ENSEMBL:ENSG00000152208\"\n                              \"ENSEMBL:ENSG00000273079\"\n                              \"ENSEMBL:ENSG00000198822\"\n                              \"ENSEMBL:ENSG00000144366\"\n                              \"ENSEMBL:ENSG00000145649\"\n                              \"ENSEMBL:ENSG00000173805\"\n                              \"ENSEMBL:ENSG00000170961\"\n                              \"ENSEMBL:ENSG00000143630\"\n                              \"ENSEMBL:ENSG00000263324\"\n                              \"ENSEMBL:ENSG00000138622\"\n                              \"ENSEMBL:ENSG00000138646\"\n                              \"ENSEMBL:ENSG00000144485\"\n                              \"ENSEMBL:ENSG00000112972\"\n                              \"ENSEMBL:ENSG00000134709\"\n                              \"ENSEMBL:ENSG00000120094\"\n                              \"ENSEMBL:ENSG00000120068\"\n                              \"ENSEMBL:ENSG00000170689\"\n                              \"ENSEMBL:ENSG00000180806\"\n                              \"ENSEMBL:ENSG00000116983\"\n                              \"ENSEMBL:ENSG00000002587\"\n                              \"ENSEMBL:ENSG00000182601\"\n                              \"ENSEMBL:ENSG00000185352\"\n                              \"ENSEMBL:ENSG00000176387\"\n                              \"ENSEMBL:ENSG00000164070\"\n                              \"ENSEMBL:ENSG00000168830\"\n                              \"ENSEMBL:ENSG00000157423\"\n                              \"ENSEMBL:ENSG00000283022\"\n                              \"ENSEMBL:ENSG00000090339\"\n                              \"ENSEMBL:ENSG00000174498\"\n                              \"ENSEMBL:ENSG00000137142\"\n                              \"ENSEMBL:ENSG00000085552\"\n                              \"ENSEMBL:ENSG00000185811\"\n                              \"ENSEMBL:ENSG00000123496\"\n                              \"ENSEMBL:ENSG00000144730\"\n                              \"ENSEMBL:ENSG00000160712\"\n                              \"ENSEMBL:ENSG00000143195\"\n                              \"ENSEMBL:ENSG00000148798\"\n                              \"ENSEMBL:ENSG00000163362\"\n                              \"ENSEMBL:ENSG00000161896\"\n                              \"ENSEMBL:ENSG00000269837\"\n                              \"ENSEMBL:ENSG00000177508\"\n                              \"ENSEMBL:ENSG00000176842\"\n                              \"ENSEMBL:ENSG00000101230\"\n                              \"ENSEMBL:ENSG00000164171\"\n                              \"ENSEMBL:ENSG00000135424\"\n                              \"ENSEMBL:ENSG00000144668\"\n                              \"ENSEMBL:ENSG00000105855\"\n                              \"ENSEMBL:ENSG00000078596\"\n                              \"ENSEMBL:ENSG00000180347\"\n                              \"ENSEMBL:ENSG00000280780\"\n                              \"ENSEMBL:ENSG00000154721\"\n                              \"ENSEMBL:ENSG00000111262\"\n                              \"ENSEMBL:ENSG00000129159\"\n                              \"ENSEMBL:ENSG00000234233\"\n                              \"ENSEMBL:ENSG00000082482\"\n                              \"ENSEMBL:ENSG00000075043\"\n                              \"ENSEMBL:ENSG00000281151\"\n                              \"ENSEMBL:ENSG00000128052\"\n                              \"ENSEMBL:ENSG00000165185\"\n                              \"ENSEMBL:ENSG00000130294\"\n                              \"ENSEMBL:ENSG00000139116\"\n                              \"ENSEMBL:ENSG00000168280\"\n                              \"ENSEMBL:ENSG00000276734\"\n                              \"ENSEMBL:ENSG00000126259\"\n                              \"ENSEMBL:ENSG00000163884\"\n                              \"ENSEMBL:ENSG00000231160\"\n                              \"ENSEMBL:ENSG00000162755\"\n                              \"ENSEMBL:ENSG00000213160\"\n                              \"ENSEMBL:ENSG00000122550\"\n                              \"ENSEMBL:ENSG00000230658\"\n                              \"ENSEMBL:ENSG00000154655\"\n                              \"ENSEMBL:ENSG00000101680\"\n                              \"ENSEMBL:ENSG00000078081\"\n                              \"ENSEMBL:ENSG00000119862\"\n                              \"ENSEMBL:ENSG00000153012\"\n                              \"ENSEMBL:ENSG00000064042\"\n                              \"ENSEMBL:ENSG00000131914\"\n                              \"ENSEMBL:ENSG00000245526\"\n                              \"ENSEMBL:ENSG00000233237\"\n                              \"ENSEMBL:ENSG00000214381\"\n                              \"ENSEMBL:ENSG00000277147\"\n                              \"ENSEMBL:ENSG00000259134\"\n                              \"ENSEMBL:ENSG00000261455\"\n                              \"ENSEMBL:ENSG00000244041\"\n                              \"ENSEMBL:ENSG00000260343\"\n                              \"ENSEMBL:ENSG00000282706\"\n                              \"ENSEMBL:ENSG00000229743\"\n                              \"ENSEMBL:ENSG00000280744\"\n                              \"ENSEMBL:ENSG00000248441\"\n                              \"ENSEMBL:ENSG00000269416\"\n                              \"ENSEMBL:ENSG00000229891\"\n                              \"ENSEMBL:ENSG00000270164\"\n                              \"ENSEMBL:ENSG00000280540\"\n                              \"ENSEMBL:ENSG00000228459\"\n                              \"ENSEMBL:ENSG00000180869\"\n                              \"ENSEMBL:ENSG00000233684\"\n                              \"ENSEMBL:ENSG00000264345\"\n                              \"ENSEMBL:ENSG00000228271\"\n                              \"ENSEMBL:ENSG00000257986\"\n                              \"ENSEMBL:ENSG00000203688\"\n                              \"ENSEMBL:ENSG00000248869\"\n                              \"ENSEMBL:ENSG00000230269\"\n                              \"ENSEMBL:ENSG00000272549\"\n                              \"ENSEMBL:ENSG00000101670\"\n                              \"ENSEMBL:ENSG00000175445\"\n                              \"ENSEMBL:ENSG00000121207\"\n                              \"ENSEMBL:ENSG00000081479\"\n                              \"ENSEMBL:ENSG00000204950\"\n                              \"ENSEMBL:ENSG00000179796\"\n                              \"ENSEMBL:ENSG00000128594\"\n                              \"ENSEMBL:ENSG00000183908\"\n                              \"ENSEMBL:ENSG00000181350\"\n                              \"ENSEMBL:ENSG00000131951\"\n                              \"ENSEMBL:ENSG00000146006\"\n                              \"ENSEMBL:ENSG00000198739\"\n                              \"ENSEMBL:ENSG00000176204\"\n                              \"ENSEMBL:ENSG00000105699\"\n                              \"ENSEMBL:ENSG00000176956\"\n                              \"ENSEMBL:ENSG00000274488\"\n                              \"ENSEMBL:ENSG00000147676\"\n                              \"ENSEMBL:ENSG00000197769\"\n                              \"ENSEMBL:ENSG00000171533\"\n                              \"ENSEMBL:ENSG00000109339\"\n                              \"ENSEMBL:ENSG00000116141\"\n                              \"ENSEMBL:ENSG00000132031\"\n                              \"ENSEMBL:ENSG00000053524\"\n                              \"ENSEMBL:ENSG00000198948\"\n                              \"ENSEMBL:ENSG00000138111\"\n                              \"ENSEMBL:ENSG00000071073\"\n                              \"ENSEMBL:ENSG00000167889\"\n                              \"ENSEMBL:ENSG00000225783\"\n                              \"ENSEMBL:ENSG00000254377\"\n                              \"ENSEMBL:ENSG00000199036\"\n                              \"ENSEMBL:ENSG00000215386\"\n                              \"ENSEMBL:ENSG00000141854\"\n                              \"ENSEMBL:ENSG00000288191\"\n                              \"ENSEMBL:ENSG00000100427\"\n                              \"ENSEMBL:ENSG00000108960\"\n                              \"ENSEMBL:ENSG00000100985\"\n                              \"ENSEMBL:ENSG00000138722\"\n                              \"ENSEMBL:ENSG00000120162\"\n                              \"ENSEMBL:ENSG00000135097\"\n                              \"ENSEMBL:ENSG00000170873\"\n                              \"ENSEMBL:ENSG00000138823\"\n                              \"ENSEMBL:ENSG00000129422\"\n                              \"ENSEMBL:ENSG00000205277\"\n                              \"ENSEMBL:ENSG00000116990\"\n                              \"ENSEMBL:ENSG00000134323\"\n                              \"ENSEMBL:ENSG00000233718\"\n                              \"ENSEMBL:ENSG00000041515\"\n                              \"ENSEMBL:ENSG00000095777\"\n                              \"ENSEMBL:ENSG00000128833\"\n                              \"ENSEMBL:ENSG00000145911\"\n                              \"ENSEMBL:ENSG00000186462\"\n                              \"ENSEMBL:ENSG00000185818\"\n                              \"ENSEMBL:ENSG00000104490\"\n                              \"ENSEMBL:ENSG00000130287\"\n                              \"ENSEMBL:ENSG00000124479\"\n                              \"ENSEMBL:ENSG00000078114\"\n                              \"ENSEMBL:ENSG00000103154\"\n                              \"ENSEMBL:ENSG00000277586\"\n                              \"ENSEMBL:ENSG00000104722\"\n                              \"ENSEMBL:ENSG00000184613\"\n                              \"ENSEMBL:ENSG00000166342\"\n                              \"ENSEMBL:ENSG00000107954\"\n                              \"ENSEMBL:ENSG00000163531\"\n                              \"ENSEMBL:ENSG00000066248\"\n                              \"ENSEMBL:ENSG00000145506\"\n                              \"ENSEMBL:ENSG00000276920\"\n                              \"ENSEMBL:ENSG00000196338\"\n                              \"ENSEMBL:ENSG00000157064\"\n                              \"ENSEMBL:ENSG00000109255\"\n                              \"ENSEMBL:ENSG00000101746\"\n                              \"ENSEMBL:ENSG00000198929\"\n                              \"ENSEMBL:ENSG00000007171\"\n                              \"ENSEMBL:ENSG00000204301\"\n                              \"ENSEMBL:ENSG00000238196\"\n                              \"ENSEMBL:ENSG00000235396\"\n                              \"ENSEMBL:ENSG00000232339\"\n                              \"ENSEMBL:ENSG00000223355\"\n                              \"ENSEMBL:ENSG00000206312\"\n                              \"ENSEMBL:ENSG00000234876\"\n                              \"ENSEMBL:ENSG00000139910\"\n                              \"ENSEMBL:ENSG00000104967\"\n                              \"ENSEMBL:ENSG00000151322\"\n                              \"ENSEMBL:ENSG00000169418\"\n                              \"ENSEMBL:ENSG00000106236\"\n                              \"ENSEMBL:ENSG00000119508\"\n                              \"ENSEMBL:ENSG00000091129\"\n                              \"ENSEMBL:ENSG00000154146\"\n                              \"ENSEMBL:ENSG00000021645\"\n                              \"ENSEMBL:ENSG00000198400\"\n                              \"ENSEMBL:ENSG00000148053\"\n                              \"ENSEMBL:ENSG00000140876\"\n                              \"ENSEMBL:ENSG00000132182\"\n                              \"ENSEMBL:ENSG00000198088\"\n                              \"ENSEMBL:ENSG00000174145\"\n                              \"ENSEMBL:ENSG00000197822\"\n                              \"ENSEMBL:ENSG00000273814\"\n                              \"ENSEMBL:ENSG00000149635\"\n                              \"ENSEMBL:ENSG00000115758\"\n                              \"ENSEMBL:ENSG00000197444\"\n                              \"ENSEMBL:ENSG00000177468\"\n                              \"ENSEMBL:ENSG00000082556\"\n                              \"ENSEMBL:ENSG00000085840\"\n                              \"ENSEMBL:ENSG00000257950\"\n                              \"ENSEMBL:ENSG00000233639\"\n                              \"ENSEMBL:ENSG00000124171\"\n                              \"ENSEMBL:ENSG00000135903\"\n                              \"ENSEMBL:ENSG00000007372\"\n                              \"ENSEMBL:ENSG00000125618\"\n                              \"ENSEMBL:ENSG00000189223\"\n                              \"ENSEMBL:ENSG00000238197\"\n                              \"ENSEMBL:ENSG00000280623\"\n                              \"ENSEMBL:ENSG00000251321\"\n                              \"ENSEMBL:ENSG00000102290\"\n                              \"ENSEMBL:ENSG00000099715\"\n                              \"ENSEMBL:ENSG00000150275\"\n                              \"ENSEMBL:ENSG00000136099\"\n                              \"ENSEMBL:ENSG00000250120\"\n                              \"ENSEMBL:ENSG00000255408\"\n                              \"ENSEMBL:ENSG00000113248\"\n                              \"ENSEMBL:ENSG00000113209\"\n                              \"ENSEMBL:ENSG00000253873\"\n                              \"ENSEMBL:ENSG00000253731\"\n                              \"ENSEMBL:ENSG00000253953\"\n                              \"ENSEMBL:ENSG00000169174\"\n                              \"ENSEMBL:ENSG00000115252\"\n                              \"ENSEMBL:ENSG00000123360\"\n                              \"ENSEMBL:ENSG00000152270\"\n                              \"ENSEMBL:ENSG00000184588\"\n                              \"ENSEMBL:ENSG00000162493\"\n                              \"ENSEMBL:ENSG00000242265\"\n                              \"ENSEMBL:ENSG00000139946\"\n                              \"ENSEMBL:ENSG00000181195\"\n                              \"ENSEMBL:ENSG00000177614\"\n                              \"ENSEMBL:ENSG00000130517\"\n                              \"ENSEMBL:ENSG00000056487\"\n                              \"ENSEMBL:ENSG00000168490\"\n                              \"ENSEMBL:ENSG00000107242\"\n                              \"ENSEMBL:ENSG00000179761\"\n                              \"ENSEMBL:ENSG00000087842\"\n                              \"ENSEMBL:ENSG00000166473\"\n                              \"ENSEMBL:ENSG00000057294\"\n                              \"ENSEMBL:ENSG00000100078\"\n                              \"ENSEMBL:ENSG00000122861\"\n                              \"ENSEMBL:ENSG00000114805\"\n                              \"ENSEMBL:ENSG00000154822\"\n                              \"ENSEMBL:ENSG00000284017\"\n                              \"ENSEMBL:ENSG00000180287\"\n                              \"ENSEMBL:ENSG00000166689\"\n                              \"ENSEMBL:ENSG00000120278\"\n                              \"ENSEMBL:ENSG00000008323\"\n                              \"ENSEMBL:ENSG00000117598\"\n                              \"ENSEMBL:ENSG00000136040\"\n                              \"ENSEMBL:ENSG00000240694\"\n                              \"ENSEMBL:ENSG00000277531\"\n                              \"ENSEMBL:ENSG00000128567\"\n                              \"ENSEMBL:ENSG00000184486\"\n                              \"ENSEMBL:ENSG00000198914\"\n                              \"ENSEMBL:ENSG00000196767\"\n                              \"ENSEMBL:ENSG00000106536\"\n                              \"ENSEMBL:ENSG00000175175\"\n                              \"ENSEMBL:ENSG00000163590\"\n                              \"ENSEMBL:ENSG00000198729\"\n                              \"ENSEMBL:ENSG00000101445\"\n                              \"ENSEMBL:ENSG00000135447\"\n                              \"ENSEMBL:ENSG00000158528\"\n                              \"ENSEMBL:ENSG00000156475\"\n                              \"ENSEMBL:ENSG00000119698\"\n                              \"ENSEMBL:ENSG00000278326\"\n                              \"ENSEMBL:ENSG00000057657\"\n                              \"ENSEMBL:ENSG00000112238\"\n                              \"ENSEMBL:ENSG00000152784\"\n                              \"ENSEMBL:ENSG00000188783\"\n                              \"ENSEMBL:ENSG00000124126\"\n                              \"ENSEMBL:ENSG00000046889\"\n                              \"ENSEMBL:ENSG00000116690\"\n                              \"ENSEMBL:ENSG00000162409\"\n                              \"ENSEMBL:ENSG00000126583\"\n                              \"ENSEMBL:ENSG00000007062\"\n                              \"ENSEMBL:ENSG00000117707\"\n                              \"ENSEMBL:ENSG00000183248\"\n                              \"ENSEMBL:ENSG00000130032\"\n                              \"ENSEMBL:ENSG00000112812\"\n                              \"ENSEMBL:ENSG00000166450\"\n                              \"ENSEMBL:ENSG00000225706\"\n                              \"ENSEMBL:ENSG00000106278\"\n                              \"ENSEMBL:ENSG00000250337\"\n                              \"ENSEMBL:ENSG00000179331\"\n                              \"ENSEMBL:ENSG00000152932\"\n                              \"ENSEMBL:ENSG00000127328\"\n                              \"ENSEMBL:ENSG00000218358\"\n                              \"ENSEMBL:ENSG00000131831\"\n                              \"ENSEMBL:ENSG00000091428\"\n                              \"ENSEMBL:ENSG00000136237\"\n                              \"ENSEMBL:ENSG00000106538\"\n                              \"ENSEMBL:ENSG00000172575\"\n                              \"ENSEMBL:ENSG00000101265\"\n                              \"ENSEMBL:ENSG00000203867\"\n                              \"ENSEMBL:ENSG00000167771\"\n                              \"ENSEMBL:ENSG00000198771\"\n                              \"ENSEMBL:ENSG00000121039\"\n                              \"ENSEMBL:ENSG00000165731\"\n                              \"ENSEMBL:ENSG00000178882\"\n                              \"ENSEMBL:ENSG00000080298\"\n                              \"ENSEMBL:ENSG00000111783\"\n                              \"ENSEMBL:ENSG00000102760\"\n                              \"ENSEMBL:ENSG00000147509\"\n                              \"ENSEMBL:ENSG00000182732\"\n                              \"ENSEMBL:ENSG00000141314\"\n                              \"ENSEMBL:ENSG00000131941\"\n                              \"ENSEMBL:ENSG00000166405\"\n                              \"ENSEMBL:ENSG00000101098\"\n                              \"ENSEMBL:ENSG00000255794\"\n                              \"ENSEMBL:ENSG00000172602\"\n                              \"ENSEMBL:ENSG00000108830\"\n                              \"ENSEMBL:ENSG00000267128\"\n                              \"ENSEMBL:ENSG00000141622\"\n                              \"ENSEMBL:ENSG00000180537\"\n                              \"ENSEMBL:ENSG00000108375\"\n                              \"ENSEMBL:ENSG00000243742\"\n                              \"ENSEMBL:ENSG00000241370\"\n                              \"ENSEMBL:ENSG00000241779\"\n                              \"ENSEMBL:ENSG00000241863\"\n                              \"ENSEMBL:ENSG00000243009\"\n                              \"ENSEMBL:ENSG00000239865\"\n                              \"ENSEMBL:ENSG00000242726\"\n                              \"ENSEMBL:ENSG00000239927\"\n                              \"ENSEMBL:ENSG00000177519\"\n                              \"ENSEMBL:ENSG00000072133\"\n                              \"ENSEMBL:ENSG00000198208\"\n                              \"ENSEMBL:ENSG00000025039\"\n                              \"ENSEMBL:ENSG00000111834\"\n                              \"ENSEMBL:ENSG00000182010\"\n                              \"ENSEMBL:ENSG00000139970\"\n                              \"ENSEMBL:ENSG00000103449\"\n                              \"ENSEMBL:ENSG00000165821\"\n                              \"ENSEMBL:ENSG00000177570\"\n                              \"ENSEMBL:ENSG00000145284\"\n                              \"ENSEMBL:ENSG00000226549\"\n                              \"ENSEMBL:ENSG00000153253\"\n                              \"ENSEMBL:ENSG00000166257\"\n                              \"ENSEMBL:ENSG00000175356\"\n                              \"ENSEMBL:ENSG00000007908\"\n                              \"ENSEMBL:ENSG00000250722\"\n                              \"ENSEMBL:ENSG00000153993\"\n                              \"ENSEMBL:ENSG00000082684\"\n                              \"ENSEMBL:ENSG00000188488\"\n                              \"ENSEMBL:ENSG00000063015\"\n                              \"ENSEMBL:ENSG00000163935\"\n                              \"ENSEMBL:ENSG00000145423\"\n                              \"ENSEMBL:ENSG00000189410\"\n                              \"ENSEMBL:ENSG00000140600\"\n                              \"ENSEMBL:ENSG00000162105\"\n                              \"ENSEMBL:ENSG00000148082\"\n                              \"ENSEMBL:ENSG00000187902\"\n                              \"ENSEMBL:ENSG00000237515\"\n                              \"ENSEMBL:ENSG00000138944\"\n                              \"ENSEMBL:ENSG00000180592\"\n                              \"ENSEMBL:ENSG00000139737\"\n                              \"ENSEMBL:ENSG00000158296\"\n                              \"ENSEMBL:ENSG00000163053\"\n                              \"ENSEMBL:ENSG00000108932\"\n                              \"ENSEMBL:ENSG00000036565\"\n                              \"ENSEMBL:ENSG00000187714\"\n                              \"ENSEMBL:ENSG00000110436\"\n                              \"ENSEMBL:ENSG00000105143\"\n                              \"ENSEMBL:ENSG00000137266\"\n                              \"ENSEMBL:ENSG00000235064\"\n                              \"ENSEMBL:ENSG00000173262\"\n                              \"ENSEMBL:ENSG00000181856\"\n                              \"ENSEMBL:ENSG00000288174\"\n                              \"ENSEMBL:ENSG00000196376\"\n                              \"ENSEMBL:ENSG00000050438\"\n                              \"ENSEMBL:ENSG00000157103\"\n                              \"ENSEMBL:ENSG00000165349\"\n                              \"ENSEMBL:ENSG00000092068\"\n                              \"ENSEMBL:ENSG00000100678\"\n                              \"ENSEMBL:ENSG00000137491\"\n                              \"ENSEMBL:ENSG00000154760\"\n                              \"ENSEMBL:ENSG00000187122\"\n                              \"ENSEMBL:ENSG00000086300\"\n                              \"ENSEMBL:ENSG00000171243\"\n                              \"ENSEMBL:ENSG00000182968\"\n                              \"ENSEMBL:ENSG00000143842\"\n                              \"ENSEMBL:ENSG00000181449\"\n                              \"ENSEMBL:ENSG00000242808\"\n                              \"ENSEMBL:ENSG00000125285\"\n                              \"ENSEMBL:ENSG00000227640\"\n                              \"ENSEMBL:ENSG00000134595\"\n                              \"ENSEMBL:ENSG00000217236\"\n                              \"ENSEMBL:ENSG00000104450\"\n                              \"ENSEMBL:ENSG00000182957\"\n                              \"ENSEMBL:ENSG00000171722\"\n                              \"ENSEMBL:ENSG00000107742\"\n                              \"ENSEMBL:ENSG00000262655\"\n                              \"ENSEMBL:ENSG00000196220\"\n                              \"ENSEMBL:ENSG00000125046\"\n                              \"ENSEMBL:ENSG00000184005\"\n                              \"ENSEMBL:ENSG00000140557\"\n                              \"ENSEMBL:ENSG00000113532\"\n                              \"ENSEMBL:ENSG00000130413\"\n                              \"ENSEMBL:ENSG00000015592\"\n                              \"ENSEMBL:ENSG00000068781\"\n                              \"ENSEMBL:ENSG00000140022\"\n                              \"ENSEMBL:ENSG00000165730\"\n                              \"ENSEMBL:ENSG00000173320\"\n                              \"ENSEMBL:ENSG00000145087\"\n                              \"ENSEMBL:ENSG00000122012\"\n                              \"ENSEMBL:ENSG00000110975\"\n                              \"ENSEMBL:ENSG00000143858\"\n                              \"ENSEMBL:ENSG00000134207\"\n                              \"ENSEMBL:ENSG00000011347\"\n                              \"ENSEMBL:ENSG00000144834\"\n                              \"ENSEMBL:ENSG00000176907\"\n                              \"ENSEMBL:ENSG00000092850\"\n                              \"ENSEMBL:ENSG00000158246\"\n                              \"ENSEMBL:ENSG00000087510\"\n                              \"ENSEMBL:ENSG00000105825\"\n                              \"ENSEMBL:ENSG00000129028\"\n                              \"ENSEMBL:ENSG00000151090\"\n                              \"ENSEMBL:ENSG00000144229\"\n                              \"ENSEMBL:ENSG00000173825\"\n                              \"ENSEMBL:ENSG00000169989\"\n                              \"ENSEMBL:ENSG00000100234\"\n                              \"ENSEMBL:ENSG00000007350\"\n                              \"ENSEMBL:ENSG00000163762\"\n                              \"ENSEMBL:ENSG00000149809\"\n                              \"ENSEMBL:ENSG00000167619\"\n                              \"ENSEMBL:ENSG00000249242\"\n                              \"ENSEMBL:ENSG00000178233\"\n                              \"ENSEMBL:ENSG00000205269\"\n                              \"ENSEMBL:ENSG00000206432\"\n                              \"ENSEMBL:ENSG00000125355\"\n                              \"ENSEMBL:ENSG00000147027\"\n                              \"ENSEMBL:ENSG00000125895\"\n                              \"ENSEMBL:ENSG00000167874\"\n                              \"ENSEMBL:ENSG00000176040\"\n                              \"ENSEMBL:ENSG00000158164\"\n                              \"ENSEMBL:ENSG00000123610\"\n                              \"ENSEMBL:ENSG00000164761\"\n                              \"ENSEMBL:ENSG00000049249\"\n                              \"ENSEMBL:ENSG00000103460\"\n                              \"ENSEMBL:ENSG00000146242\"\n                              \"ENSEMBL:ENSG00000283085\"\n                              \"ENSEMBL:ENSG00000134253\"\n                              \"ENSEMBL:ENSG00000206557\"\n                              \"ENSEMBL:ENSG00000083067\"\n                              \"ENSEMBL:ENSG00000167723\"\n                              \"ENSEMBL:ENSG00000106025\"\n                              \"ENSEMBL:ENSG00000158457\"\n                              \"ENSEMBL:ENSG00000223756\"\n                              \"ENSEMBL:ENSG00000205838\"\n                              \"ENSEMBL:ENSG00000170703\"\n                              \"ENSEMBL:ENSG00000167614\"\n                              \"ENSEMBL:ENSG00000276537\"\n                              \"ENSEMBL:ENSG00000276887\"\n                              \"ENSEMBL:ENSG00000275650\"\n                              \"ENSEMBL:ENSG00000137285\"\n                              \"ENSEMBL:ENSG00000250366\"\n                              \"ENSEMBL:ENSG00000176912\"\n                              \"ENSEMBL:ENSG00000168671\"\n                              \"ENSEMBL:ENSG00000136014\"\n                              \"ENSEMBL:ENSG00000162738\"\n                              \"ENSEMBL:ENSG00000171724\"\n                              \"ENSEMBL:ENSG00000134215\"\n                              \"ENSEMBL:ENSG00000136451\"\n                              \"ENSEMBL:ENSG00000128564\"\n                              \"ENSEMBL:ENSG00000169085\"\n                              \"ENSEMBL:ENSG00000166483\"\n                              \"ENSEMBL:ENSG00000127578\"\n                              \"ENSEMBL:ENSG00000165238\"\n                              \"ENSEMBL:ENSG00000169884\"\n                              \"ENSEMBL:ENSG00000002745\"\n                              \"ENSEMBL:ENSG00000108379\"\n                              \"ENSEMBL:ENSG00000277626\"\n                              \"ENSEMBL:ENSG00000277641\"\n                              \"ENSEMBL:ENSG00000154342\"\n                              \"ENSEMBL:ENSG00000162552\"\n                              \"ENSEMBL:ENSG00000179314\"\n                              \"ENSEMBL:ENSG00000113645\"\n                              \"ENSEMBL:ENSG00000206579\"\n                              \"ENSEMBL:ENSG00000122121\"\n                              \"ENSEMBL:ENSG00000166793\"\n                              \"ENSEMBL:ENSG00000109906\"\n                              \"ENSEMBL:ENSG00000119703\"\n                              \"ENSEMBL:ENSG00000177108\"\n                              \"ENSEMBL:ENSG00000136367\"\n                              \"ENSEMBL:ENSG00000152977\"\n                              \"ENSEMBL:ENSG00000043355\"\n                              \"ENSEMBL:ENSG00000156925\"\n                              \"ENSEMBL:ENSG00000174963\"\n                              \"ENSEMBL:ENSG00000139800\"\n                              \"ENSEMBL:ENSG00000171649\"\n                              \"ENSEMBL:ENSG00000165061\"\n                              \"ENSEMBL:ENSG00000131849\"\n                              \"ENSEMBL:ENSG00000197279\"\n                              \"ENSEMBL:ENSG00000187595\"\n                              \"ENSEMBL:ENSG00000186496\"\n                              \"ENSEMBL:ENSG00000180855\"\n                              \"ENSEMBL:ENSG00000196653\"\n                              \"ENSEMBL:ENSG00000281448\"\n                              \"ENSEMBL:ENSG00000237149\"\n                              \"ENSEMBL:ENSG00000198795\"\n                              \"ENSEMBL:ENSG00000167555\"\n                              \"ENSEMBL:ENSG00000269834\"\n                              \"ENSEMBL:ENSG00000198597\"\n                              \"ENSEMBL:ENSG00000198028\"\n                              \"ENSEMBL:ENSG00000180626\"\n                              \"ENSEMBL:ENSG00000177842\"\n                              \"ENSEMBL:ENSG00000197472\"\n                              \"ENSEMBL:ENSG00000196081\"\n                              \"ENSEMBL:ENSG00000213967\"\n                              \"ENSEMBL:ENSG00000197128\"\n                              \"ENSEMBL:ENSG00000196466\"\n                              \"ENSEMBL:ENSG00000180233\"\n                              \"ENSEMBL:ENSG00000183579\"\n                              \"ENSEMBL:ENSG00000162415\"))\n\n(define NGLY1-underexpressed '(\"ENSEMBL:ENSG00000128274\"\n                               \"ENSEMBL:ENSG00000173210\"\n                               \"ENSEMBL:ENSG00000157766\"\n                               \"ENSEMBL:ENSG00000144476\"\n                               \"ENSEMBL:ENSG00000102575\"\n                               \"ENSEMBL:ENSG00000005187\"\n                               \"ENSEMBL:ENSG00000107796\"\n                               \"ENSEMBL:ENSG00000180139\"\n                               \"ENSEMBL:ENSG00000169067\"\n                               \"ENSEMBL:ENSG00000159251\"\n                               \"ENSEMBL:ENSG00000145536\"\n                               \"ENSEMBL:ENSG00000140873\"\n                               \"ENSEMBL:ENSG00000154736\"\n                               \"ENSEMBL:ENSG00000049192\"\n                               \"ENSEMBL:ENSG00000121281\"\n                               \"ENSEMBL:ENSG00000020181\"\n                               \"ENSEMBL:ENSG00000272734\"\n                               \"ENSEMBL:ENSG00000120907\"\n                               \"ENSEMBL:ENSG00000171873\"\n                               \"ENSEMBL:ENSG00000150594\"\n                               \"ENSEMBL:ENSG00000135744\"\n                               \"ENSEMBL:ENSG00000185567\"\n                               \"ENSEMBL:ENSG00000106546\"\n                               \"ENSEMBL:ENSG00000063438\"\n                               \"ENSEMBL:ENSG00000006534\"\n                               \"ENSEMBL:ENSG00000180318\"\n                               \"ENSEMBL:ENSG00000139211\"\n                               \"ENSEMBL:ENSG00000167772\"\n                               \"ENSEMBL:ENSG00000154122\"\n                               \"ENSEMBL:ENSG00000148677\"\n                               \"ENSEMBL:ENSG00000011201\"\n                               \"ENSEMBL:ENSG00000122359\"\n                               \"ENSEMBL:ENSG00000163697\"\n                               \"ENSEMBL:ENSG00000240583\"\n                               \"ENSEMBL:ENSG00000128805\"\n                               \"ENSEMBL:ENSG00000138639\"\n                               \"ENSEMBL:ENSG00000150347\"\n                               \"ENSEMBL:ENSG00000105643\"\n                               \"ENSEMBL:ENSG00000140450\"\n                               \"ENSEMBL:ENSG00000180801\"\n                               \"ENSEMBL:ENSG00000108684\"\n                               \"ENSEMBL:ENSG00000174939\"\n                               \"ENSEMBL:ENSG00000206190\"\n                               \"ENSEMBL:ENSG00000074370\"\n                               \"ENSEMBL:ENSG00000277297\"\n                               \"ENSEMBL:ENSG00000081923\"\n                               \"ENSEMBL:ENSG00000104043\"\n                               \"ENSEMBL:ENSG00000156273\"\n                               \"ENSEMBL:ENSG00000168398\"\n                               \"ENSEMBL:ENSG00000176697\"\n                               \"ENSEMBL:ENSG00000183092\"\n                               \"ENSEMBL:ENSG00000123095\"\n                               \"ENSEMBL:ENSG00000168487\"\n                               \"ENSEMBL:ENSG00000164619\"\n                               \"ENSEMBL:ENSG00000101425\"\n                               \"ENSEMBL:ENSG00000130303\"\n                               \"ENSEMBL:ENSG00000222009\"\n                               \"ENSEMBL:ENSG00000119280\"\n                               \"ENSEMBL:ENSG00000173918\"\n                               \"ENSEMBL:ENSG00000197927\"\n                               \"ENSEMBL:ENSG00000171860\"\n                               \"ENSEMBL:ENSG00000234511\"\n                               \"ENSEMBL:ENSG00000197261\"\n                               \"ENSEMBL:ENSG00000074410\"\n                               \"ENSEMBL:ENSG00000100314\"\n                               \"ENSEMBL:ENSG00000165995\"\n                               \"ENSEMBL:ENSG00000138172\"\n                               \"ENSEMBL:ENSG00000042493\"\n                               \"ENSEMBL:ENSG00000159753\"\n                               \"ENSEMBL:ENSG00000249669\"\n                               \"ENSEMBL:ENSG00000105974\"\n                               \"ENSEMBL:ENSG00000105971\"\n                               \"ENSEMBL:ENSG00000177469\"\n                               \"ENSEMBL:ENSG00000170955\"\n                               \"ENSEMBL:ENSG00000141668\"\n                               \"ENSEMBL:ENSG00000166510\"\n                               \"ENSEMBL:ENSG00000149201\"\n                               \"ENSEMBL:ENSG00000188549\"\n                               \"ENSEMBL:ENSG00000185972\"\n                               \"ENSEMBL:ENSG00000271503\"\n                               \"ENSEMBL:ENSG00000274233\"\n                               \"ENSEMBL:ENSG00000150637\"\n                               \"ENSEMBL:ENSG00000026508\"\n                               \"ENSEMBL:ENSG00000196352\"\n                               \"ENSEMBL:ENSG00000013725\"\n                               \"ENSEMBL:ENSG00000163814\"\n                               \"ENSEMBL:ENSG00000071991\"\n                               \"ENSEMBL:ENSG00000062038\"\n                               \"ENSEMBL:ENSG00000138395\"\n                               \"ENSEMBL:ENSG00000117266\"\n                               \"ENSEMBL:ENSG00000147883\"\n                               \"ENSEMBL:ENSG00000000971\"\n                               \"ENSEMBL:ENSG00000205403\"\n                               \"ENSEMBL:ENSG00000138135\"\n                               \"ENSEMBL:ENSG00000123989\"\n                               \"ENSEMBL:ENSG00000181072\"\n                               \"ENSEMBL:ENSG00000174343\"\n                               \"ENSEMBL:ENSG00000160161\"\n                               \"ENSEMBL:ENSG00000163347\"\n                               \"ENSEMBL:ENSG00000249035\"\n                               \"ENSEMBL:ENSG00000158258\"\n                               \"ENSEMBL:ENSG00000143786\"\n                               \"ENSEMBL:ENSG00000130176\"\n                               \"ENSEMBL:ENSG00000018236\"\n                               \"ENSEMBL:ENSG00000154529\"\n                               \"ENSEMBL:ENSG00000283378\"\n                               \"ENSEMBL:ENSG00000182871\"\n                               \"ENSEMBL:ENSG00000124749\"\n                               \"ENSEMBL:ENSG00000172752\"\n                               \"ENSEMBL:ENSG00000206384\"\n                               \"ENSEMBL:ENSG00000144810\"\n                               \"ENSEMBL:ENSG00000092758\"\n                               \"ENSEMBL:ENSG00000198756\"\n                               \"ENSEMBL:ENSG00000160471\"\n                               \"ENSEMBL:ENSG00000128510\"\n                               \"ENSEMBL:ENSG00000178773\"\n                               \"ENSEMBL:ENSG00000139117\"\n                               \"ENSEMBL:ENSG00000109846\"\n                               \"ENSEMBL:ENSG00000112297\"\n                               \"ENSEMBL:ENSG00000242193\"\n                               \"ENSEMBL:ENSG00000147408\"\n                               \"ENSEMBL:ENSG00000173546\"\n                               \"ENSEMBL:ENSG00000260139\"\n                               \"ENSEMBL:ENSG00000170373\"\n                               \"ENSEMBL:ENSG00000101160\"\n                               \"ENSEMBL:ENSG00000107562\"\n                               \"ENSEMBL:ENSG00000169429\"\n                               \"ENSEMBL:ENSG00000166394\"\n                               \"ENSEMBL:ENSG00000051523\"\n                               \"ENSEMBL:ENSG00000186684\"\n                               \"ENSEMBL:ENSG00000134716\"\n                               \"ENSEMBL:ENSG00000108669\"\n                               \"ENSEMBL:ENSG00000146122\"\n                               \"ENSEMBL:ENSG00000057019\"\n                               \"ENSEMBL:ENSG00000197410\"\n                               \"ENSEMBL:ENSG00000284227\"\n                               \"ENSEMBL:ENSG00000165507\"\n                               \"ENSEMBL:ENSG00000058866\"\n                               \"ENSEMBL:ENSG00000211448\"\n                               \"ENSEMBL:ENSG00000231672\"\n                               \"ENSEMBL:ENSG00000107984\"\n                               \"ENSEMBL:ENSG00000164741\"\n                               \"ENSEMBL:ENSG00000185559\"\n                               \"ENSEMBL:ENSG00000144355\"\n                               \"ENSEMBL:ENSG00000115844\"\n                               \"ENSEMBL:ENSG00000105880\"\n                               \"ENSEMBL:ENSG00000197959\"\n                               \"ENSEMBL:ENSG00000272636\"\n                               \"ENSEMBL:ENSG00000272670\"\n                               \"ENSEMBL:ENSG00000206052\"\n                               \"ENSEMBL:ENSG00000176978\"\n                               \"ENSEMBL:ENSG00000189212\"\n                               \"ENSEMBL:ENSG00000184845\"\n                               \"ENSEMBL:ENSG00000134762\"\n                               \"ENSEMBL:ENSG00000171451\"\n                               \"ENSEMBL:ENSG00000262102\"\n                               \"ENSEMBL:ENSG00000143507\"\n                               \"ENSEMBL:ENSG00000158560\"\n                               \"ENSEMBL:ENSG00000135636\"\n                               \"ENSEMBL:ENSG00000164176\"\n                               \"ENSEMBL:ENSG00000078401\"\n                               \"ENSEMBL:ENSG00000151617\"\n                               \"ENSEMBL:ENSG00000115380\"\n                               \"ENSEMBL:ENSG00000172638\"\n                               \"ENSEMBL:ENSG00000166897\"\n                               \"ENSEMBL:ENSG00000118985\"\n                               \"ENSEMBL:ENSG00000049540\"\n                               \"ENSEMBL:ENSG00000164035\"\n                               \"ENSEMBL:ENSG00000138185\"\n                               \"ENSEMBL:ENSG00000168032\"\n                               \"ENSEMBL:ENSG00000261150\"\n                               \"ENSEMBL:ENSG00000177106\"\n                               \"ENSEMBL:ENSG00000065361\"\n                               \"ENSEMBL:ENSG00000115363\"\n                               \"ENSEMBL:ENSG00000283632\"\n                               \"ENSEMBL:ENSG00000126218\"\n                               \"ENSEMBL:ENSG00000181104\"\n                               \"ENSEMBL:ENSG00000164251\"\n                               \"ENSEMBL:ENSG00000148541\"\n                               \"ENSEMBL:ENSG00000204442\"\n                               \"ENSEMBL:ENSG00000248429\"\n                               \"ENSEMBL:ENSG00000166147\"\n                               \"ENSEMBL:ENSG00000116661\"\n                               \"ENSEMBL:ENSG00000161243\"\n                               \"ENSEMBL:ENSG00000156804\"\n                               \"ENSEMBL:ENSG00000088340\"\n                               \"ENSEMBL:ENSG00000138675\"\n                               \"ENSEMBL:ENSG00000140285\"\n                               \"ENSEMBL:ENSG00000176971\"\n                               \"ENSEMBL:ENSG00000168386\"\n                               \"ENSEMBL:ENSG00000176692\"\n                               \"ENSEMBL:ENSG00000251493\"\n                               \"ENSEMBL:ENSG00000176678\"\n                               \"ENSEMBL:ENSG00000179772\"\n                               \"ENSEMBL:ENSG00000070404\"\n                               \"ENSEMBL:ENSG00000177283\"\n                               \"ENSEMBL:ENSG00000163288\"\n                               \"ENSEMBL:ENSG00000131386\"\n                               \"ENSEMBL:ENSG00000136542\"\n                               \"ENSEMBL:ENSG00000139629\"\n                               \"ENSEMBL:ENSG00000180447\"\n                               \"ENSEMBL:ENSG00000233695\"\n                               \"ENSEMBL:ENSG00000141448\"\n                               \"ENSEMBL:ENSG00000187210\"\n                               \"ENSEMBL:ENSG00000156466\"\n                               \"ENSEMBL:ENSG00000143869\"\n                               \"ENSEMBL:ENSG00000164949\"\n                               \"ENSEMBL:ENSG00000146013\"\n                               \"ENSEMBL:ENSG00000099998\"\n                               \"ENSEMBL:ENSG00000179855\"\n                               \"ENSEMBL:ENSG00000109738\"\n                               \"ENSEMBL:ENSG00000156049\"\n                               \"ENSEMBL:ENSG00000138678\"\n                               \"ENSEMBL:ENSG00000164850\"\n                               \"ENSEMBL:ENSG00000166073\"\n                               \"ENSEMBL:ENSG00000169508\"\n                               \"ENSEMBL:ENSG00000170775\"\n                               \"ENSEMBL:ENSG00000119714\"\n                               \"ENSEMBL:ENSG00000125675\"\n                               \"ENSEMBL:ENSG00000182771\"\n                               \"ENSEMBL:ENSG00000164418\"\n                               \"ENSEMBL:ENSG00000183454\"\n                               \"ENSEMBL:ENSG00000198785\"\n                               \"ENSEMBL:ENSG00000152822\"\n                               \"ENSEMBL:ENSG00000179603\"\n                               \"ENSEMBL:ENSG00000113070\"\n                               \"ENSEMBL:ENSG00000099822\"\n                               \"ENSEMBL:ENSG00000164683\"\n                               \"ENSEMBL:ENSG00000019991\"\n                               \"ENSEMBL:ENSG00000127124\"\n                               \"ENSEMBL:ENSG00000136630\"\n                               \"ENSEMBL:ENSG00000146151\"\n                               \"ENSEMBL:ENSG00000275410\"\n                               \"ENSEMBL:ENSG00000276194\"\n                               \"ENSEMBL:ENSG00000171476\"\n                               \"ENSEMBL:ENSG00000253293\"\n                               \"ENSEMBL:ENSG00000106006\"\n                               \"ENSEMBL:ENSG00000078399\"\n                               \"ENSEMBL:ENSG00000173083\"\n                               \"ENSEMBL:ENSG00000196639\"\n                               \"ENSEMBL:ENSG00000106211\"\n                               \"ENSEMBL:ENSG00000173641\"\n                               \"ENSEMBL:ENSG00000135312\"\n                               \"ENSEMBL:ENSG00000102468\"\n                               \"ENSEMBL:ENSG00000148680\"\n                               \"ENSEMBL:ENSG00000166033\"\n                               \"ENSEMBL:ENSG00000170801\"\n                               \"ENSEMBL:ENSG00000146674\"\n                               \"ENSEMBL:ENSG00000163395\"\n                               \"ENSEMBL:ENSG00000147255\"\n                               \"ENSEMBL:ENSG00000152580\"\n                               \"ENSEMBL:ENSG00000095752\"\n                               \"ENSEMBL:ENSG00000163701\"\n                               \"ENSEMBL:ENSG00000168685\"\n                               \"ENSEMBL:ENSG00000122641\"\n                               \"ENSEMBL:ENSG00000188487\"\n                               \"ENSEMBL:ENSG00000120645\"\n                               \"ENSEMBL:ENSG00000262607\"\n                               \"ENSEMBL:ENSG00000005884\"\n                               \"ENSEMBL:ENSG00000115221\"\n                               \"ENSEMBL:ENSG00000149596\"\n                               \"ENSEMBL:ENSG00000132854\"\n                               \"ENSEMBL:ENSG00000182255\"\n                               \"ENSEMBL:ENSG00000131398\"\n                               \"ENSEMBL:ENSG00000152049\"\n                               \"ENSEMBL:ENSG00000055118\"\n                               \"ENSEMBL:ENSG00000184185\"\n                               \"ENSEMBL:ENSG00000157551\"\n                               \"ENSEMBL:ENSG00000104783\"\n                               \"ENSEMBL:ENSG00000269821\"\n                               \"ENSEMBL:ENSG00000250423\"\n                               \"ENSEMBL:ENSG00000066735\"\n                               \"ENSEMBL:ENSG00000162849\"\n                               \"ENSEMBL:ENSG00000281216\"\n                               \"ENSEMBL:ENSG00000127528\"\n                               \"ENSEMBL:ENSG00000149243\"\n                               \"ENSEMBL:ENSG00000128422\"\n                               \"ENSEMBL:ENSG00000171345\"\n                               \"ENSEMBL:ENSG00000135480\"\n                               \"ENSEMBL:ENSG00000167767\"\n                               \"ENSEMBL:ENSG00000240871\"\n                               \"ENSEMBL:ENSG00000171435\"\n                               \"ENSEMBL:ENSG00000115919\"\n                               \"ENSEMBL:ENSG00000130702\"\n                               \"ENSEMBL:ENSG00000196878\"\n                               \"ENSEMBL:ENSG00000213626\"\n                               \"ENSEMBL:ENSG00000122367\"\n                               \"ENSEMBL:ENSG00000143768\"\n                               \"ENSEMBL:ENSG00000108679\"\n                               \"ENSEMBL:ENSG00000214269\"\n                               \"ENSEMBL:ENSG00000143355\"\n                               \"ENSEMBL:ENSG00000128342\"\n                               \"ENSEMBL:ENSG00000072163\"\n                               \"ENSEMBL:ENSG00000232931\"\n                               \"ENSEMBL:ENSG00000186369\"\n                               \"ENSEMBL:ENSG00000233117\"\n                               \"ENSEMBL:ENSG00000185904\"\n                               \"ENSEMBL:ENSG00000231711\"\n                               \"ENSEMBL:ENSG00000246100\"\n                               \"ENSEMBL:ENSG00000240476\"\n                               \"ENSEMBL:ENSG00000228495\"\n                               \"ENSEMBL:ENSG00000233621\"\n                               \"ENSEMBL:ENSG00000234840\"\n                               \"ENSEMBL:ENSG00000258754\"\n                               \"ENSEMBL:ENSG00000259518\"\n                               \"ENSEMBL:ENSG00000253161\"\n                               \"ENSEMBL:ENSG00000268941\"\n                               \"ENSEMBL:ENSG00000226476\"\n                               \"ENSEMBL:ENSG00000204460\"\n                               \"ENSEMBL:ENSG00000244649\"\n                               \"ENSEMBL:ENSG00000259847\"\n                               \"ENSEMBL:ENSG00000261175\"\n                               \"ENSEMBL:ENSG00000258616\"\n                               \"ENSEMBL:ENSG00000256268\"\n                               \"ENSEMBL:ENSG00000234155\"\n                               \"ENSEMBL:ENSG00000223764\"\n                               \"ENSEMBL:ENSG00000241288\"\n                               \"ENSEMBL:ENSG00000174482\"\n                               \"ENSEMBL:ENSG00000136153\"\n                               \"ENSEMBL:ENSG00000163431\"\n                               \"ENSEMBL:ENSG00000129038\"\n                               \"ENSEMBL:ENSG00000261801\"\n                               \"ENSEMBL:ENSG00000184574\"\n                               \"ENSEMBL:ENSG00000172061\"\n                               \"ENSEMBL:ENSG00000128606\"\n                               \"ENSEMBL:ENSG00000033122\"\n                               \"ENSEMBL:ENSG00000049323\"\n                               \"ENSEMBL:ENSG00000168056\"\n                               \"ENSEMBL:ENSG00000153714\"\n                               \"ENSEMBL:ENSG00000187398\"\n                               \"ENSEMBL:ENSG00000150556\"\n                               \"ENSEMBL:ENSG00000133800\"\n                               \"ENSEMBL:ENSG00000181541\"\n                               \"ENSEMBL:ENSG00000204103\"\n                               \"ENSEMBL:ENSG00000189221\"\n                               \"ENSEMBL:ENSG00000069535\"\n                               \"ENSEMBL:ENSG00000101460\"\n                               \"ENSEMBL:ENSG00000197442\"\n                               \"ENSEMBL:ENSG00000156265\"\n                               \"ENSEMBL:ENSG00000152601\"\n                               \"ENSEMBL:ENSG00000076706\"\n                               \"ENSEMBL:ENSG00000140563\"\n                               \"ENSEMBL:ENSG00000151376\"\n                               \"ENSEMBL:ENSG00000102802\"\n                               \"ENSEMBL:ENSG00000134138\"\n                               \"ENSEMBL:ENSG00000163975\"\n                               \"ENSEMBL:ENSG00000105976\"\n                               \"ENSEMBL:ENSG00000182050\"\n                               \"ENSEMBL:ENSG00000283530\"\n                               \"ENSEMBL:ENSG00000285137\"\n                               \"ENSEMBL:ENSG00000111341\"\n                               \"ENSEMBL:ENSG00000276365\"\n                               \"ENSEMBL:ENSG00000247095\"\n                               \"ENSEMBL:ENSG00000282810\"\n                               \"ENSEMBL:ENSG00000196611\"\n                               \"ENSEMBL:ENSG00000166670\"\n                               \"ENSEMBL:ENSG00000099953\"\n                               \"ENSEMBL:ENSG00000275365\"\n                               \"ENSEMBL:ENSG00000137745\"\n                               \"ENSEMBL:ENSG00000198598\"\n                               \"ENSEMBL:ENSG00000125966\"\n                               \"ENSEMBL:ENSG00000149968\"\n                               \"ENSEMBL:ENSG00000079931\"\n                               \"ENSEMBL:ENSG00000135324\"\n                               \"ENSEMBL:ENSG00000179832\"\n                               \"ENSEMBL:ENSG00000178860\"\n                               \"ENSEMBL:ENSG00000235531\"\n                               \"ENSEMBL:ENSG00000013364\"\n                               \"ENSEMBL:ENSG00000162576\"\n                               \"ENSEMBL:ENSG00000198336\"\n                               \"ENSEMBL:ENSG00000065534\"\n                               \"ENSEMBL:ENSG00000101605\"\n                               \"ENSEMBL:ENSG00000229647\"\n                               \"ENSEMBL:ENSG00000177791\"\n                               \"ENSEMBL:ENSG00000138347\"\n                               \"ENSEMBL:ENSG00000134369\"\n                               \"ENSEMBL:ENSG00000166833\"\n                               \"ENSEMBL:ENSG00000158747\"\n                               \"ENSEMBL:ENSG00000164100\"\n                               \"ENSEMBL:ENSG00000242242\"\n                               \"ENSEMBL:ENSG00000163491\"\n                               \"ENSEMBL:ENSG00000050030\"\n                               \"ENSEMBL:ENSG00000162614\"\n                               \"ENSEMBL:ENSG00000101096\"\n                               \"ENSEMBL:ENSG00000162599\"\n                               \"ENSEMBL:ENSG00000237928\"\n                               \"ENSEMBL:ENSG00000163293\"\n                               \"ENSEMBL:ENSG00000172548\"\n                               \"ENSEMBL:ENSG00000188580\"\n                               \"ENSEMBL:ENSG00000103024\"\n                               \"ENSEMBL:ENSG00000166741\"\n                               \"ENSEMBL:ENSG00000089250\"\n                               \"ENSEMBL:ENSG00000086991\"\n                               \"ENSEMBL:ENSG00000168743\"\n                               \"ENSEMBL:ENSG00000113389\"\n                               \"ENSEMBL:ENSG00000221890\"\n                               \"ENSEMBL:ENSG00000164128\"\n                               \"ENSEMBL:ENSG00000151623\"\n                               \"ENSEMBL:ENSG00000123572\"\n                               \"ENSEMBL:ENSG00000170091\"\n                               \"ENSEMBL:ENSG00000185652\"\n                               \"ENSEMBL:ENSG00000140538\"\n                               \"ENSEMBL:ENSG00000133636\"\n                               \"ENSEMBL:ENSG00000275074\"\n                               \"ENSEMBL:ENSG00000104044\"\n                               \"ENSEMBL:ENSG00000277361\"\n                               \"ENSEMBL:ENSG00000145247\"\n                               \"ENSEMBL:ENSG00000118733\"\n                               \"ENSEMBL:ENSG00000162745\"\n                               \"ENSEMBL:ENSG00000183715\"\n                               \"ENSEMBL:ENSG00000116329\"\n                               \"ENSEMBL:ENSG00000144645\"\n                               \"ENSEMBL:ENSG00000180914\"\n                               \"ENSEMBL:ENSG00000174944\"\n                               \"ENSEMBL:ENSG00000099260\"\n                               \"ENSEMBL:ENSG00000137819\"\n                               \"ENSEMBL:ENSG00000152931\"\n                               \"ENSEMBL:ENSG00000138650\"\n                               \"ENSEMBL:ENSG00000184226\"\n                               \"ENSEMBL:ENSG00000154678\"\n                               \"ENSEMBL:ENSG00000172572\"\n                               \"ENSEMBL:ENSG00000113448\"\n                               \"ENSEMBL:ENSG00000197461\"\n                               \"ENSEMBL:ENSG00000145431\"\n                               \"ENSEMBL:ENSG00000154553\"\n                               \"ENSEMBL:ENSG00000165966\"\n                               \"ENSEMBL:ENSG00000112378\"\n                               \"ENSEMBL:ENSG00000067057\"\n                               \"ENSEMBL:ENSG00000119630\"\n                               \"ENSEMBL:ENSG00000102174\"\n                               \"ENSEMBL:ENSG00000181649\"\n                               \"ENSEMBL:ENSG00000274538\"\n                               \"ENSEMBL:ENSG00000109132\"\n                               \"ENSEMBL:ENSG00000175287\"\n                               \"ENSEMBL:ENSG00000153823\"\n                               \"ENSEMBL:ENSG00000100100\"\n                               \"ENSEMBL:ENSG00000158683\"\n                               \"ENSEMBL:ENSG00000135549\"\n                               \"ENSEMBL:ENSG00000189129\"\n                               \"ENSEMBL:ENSG00000138193\"\n                               \"ENSEMBL:ENSG00000149527\"\n                               \"ENSEMBL:ENSG00000276429\"\n                               \"ENSEMBL:ENSG00000115896\"\n                               \"ENSEMBL:ENSG00000100558\"\n                               \"ENSEMBL:ENSG00000169499\"\n                               \"ENSEMBL:ENSG00000196155\"\n                               \"ENSEMBL:ENSG00000102007\"\n                               \"ENSEMBL:ENSG00000203805\"\n                               \"ENSEMBL:ENSG00000130300\"\n                               \"ENSEMBL:ENSG00000161381\"\n                               \"ENSEMBL:ENSG00000120594\"\n                               \"ENSEMBL:ENSG00000221866\"\n                               \"ENSEMBL:ENSG00000132000\"\n                               \"ENSEMBL:ENSG00000288195\"\n                               \"ENSEMBL:ENSG00000132429\"\n                               \"ENSEMBL:ENSG00000133110\"\n                               \"ENSEMBL:ENSG00000224897\"\n                               \"ENSEMBL:ENSG00000132170\"\n                               \"ENSEMBL:ENSG00000086717\"\n                               \"ENSEMBL:ENSG00000119938\"\n                               \"ENSEMBL:ENSG00000061455\"\n                               \"ENSEMBL:ENSG00000166501\"\n                               \"ENSEMBL:ENSG00000027075\"\n                               \"ENSEMBL:ENSG00000138669\"\n                               \"ENSEMBL:ENSG00000171864\"\n                               \"ENSEMBL:ENSG00000184838\"\n                               \"ENSEMBL:ENSG00000150687\"\n                               \"ENSEMBL:ENSG00000146250\"\n                               \"ENSEMBL:ENSG00000165186\"\n                               \"ENSEMBL:ENSG00000125384\"\n                               \"ENSEMBL:ENSG00000073756\"\n                               \"ENSEMBL:ENSG00000134242\"\n                               \"ENSEMBL:ENSG00000054356\"\n                               \"ENSEMBL:ENSG00000151490\"\n                               \"ENSEMBL:ENSG00000115828\"\n                               \"ENSEMBL:ENSG00000228492\"\n                               \"ENSEMBL:ENSG00000041353\"\n                               \"ENSEMBL:ENSG00000276600\"\n                               \"ENSEMBL:ENSG00000128340\"\n                               \"ENSEMBL:ENSG00000132359\"\n                               \"ENSEMBL:ENSG00000100302\"\n                               \"ENSEMBL:ENSG00000152689\"\n                               \"ENSEMBL:ENSG00000198774\"\n                               \"ENSEMBL:ENSG00000163694\"\n                               \"ENSEMBL:ENSG00000159200\"\n                               \"ENSEMBL:ENSG00000134533\"\n                               \"ENSEMBL:ENSG00000256650\"\n                               \"ENSEMBL:ENSG00000117152\"\n                               \"ENSEMBL:ENSG00000186479\"\n                               \"ENSEMBL:ENSG00000206712\"\n                               \"ENSEMBL:ENSG00000198963\"\n                               \"ENSEMBL:ENSG00000047936\"\n                               \"ENSEMBL:ENSG00000181031\"\n                               \"ENSEMBL:ENSG00000262334\"\n                               \"ENSEMBL:ENSG00000282013\"\n                               \"ENSEMBL:ENSG00000147655\"\n                               \"ENSEMBL:ENSG00000188643\"\n                               \"ENSEMBL:ENSG00000188015\"\n                               \"ENSEMBL:ENSG00000197956\"\n                               \"ENSEMBL:ENSG00000180739\"\n                               \"ENSEMBL:ENSG00000187634\"\n                               \"ENSEMBL:ENSG00000164483\"\n                               \"ENSEMBL:ENSG00000205413\"\n                               \"ENSEMBL:ENSG00000171951\"\n                               \"ENSEMBL:ENSG00000149575\"\n                               \"ENSEMBL:ENSG00000166396\"\n                               \"ENSEMBL:ENSG00000135919\"\n                               \"ENSEMBL:ENSG00000107819\"\n                               \"ENSEMBL:ENSG00000108823\"\n                               \"ENSEMBL:ENSG00000102683\"\n                               \"ENSEMBL:ENSG00000118473\"\n                               \"ENSEMBL:ENSG00000118515\"\n                               \"ENSEMBL:ENSG00000104205\"\n                               \"ENSEMBL:ENSG00000164023\"\n                               \"ENSEMBL:ENSG00000104611\"\n                               \"ENSEMBL:ENSG00000172985\"\n                               \"ENSEMBL:ENSG00000259863\"\n                               \"ENSEMBL:ENSG00000125089\"\n                               \"ENSEMBL:ENSG00000129946\"\n                               \"ENSEMBL:ENSG00000185634\"\n                               \"ENSEMBL:ENSG00000178343\"\n                               \"ENSEMBL:ENSG00000185187\"\n                               \"ENSEMBL:ENSG00000170577\"\n                               \"ENSEMBL:ENSG00000221955\"\n                               \"ENSEMBL:ENSG00000141526\"\n                               \"ENSEMBL:ENSG00000146477\"\n                               \"ENSEMBL:ENSG00000185052\"\n                               \"ENSEMBL:ENSG00000162241\"\n                               \"ENSEMBL:ENSG00000139209\"\n                               \"ENSEMBL:ENSG00000138449\"\n                               \"ENSEMBL:ENSG00000148942\"\n                               \"ENSEMBL:ENSG00000115665\"\n                               \"ENSEMBL:ENSG00000131389\"\n                               \"ENSEMBL:ENSG00000183023\"\n                               \"ENSEMBL:ENSG00000065923\"\n                               \"ENSEMBL:ENSG00000174640\"\n                               \"ENSEMBL:ENSG00000184347\"\n                               \"ENSEMBL:ENSG00000184564\"\n                               \"ENSEMBL:ENSG00000120693\"\n                               \"ENSEMBL:ENSG00000179256\"\n                               \"ENSEMBL:ENSG00000271824\"\n                               \"ENSEMBL:ENSG00000198732\"\n                               \"ENSEMBL:ENSG00000112562\"\n                               \"ENSEMBL:ENSG00000120833\"\n                               \"ENSEMBL:ENSG00000246985\"\n                               \"ENSEMBL:ENSG00000109610\"\n                               \"ENSEMBL:ENSG00000061656\"\n                               \"ENSEMBL:ENSG00000166145\"\n                               \"ENSEMBL:ENSG00000167642\"\n                               \"ENSEMBL:ENSG00000134668\"\n                               \"ENSEMBL:ENSG00000196104\"\n                               \"ENSEMBL:ENSG00000118785\"\n                               \"ENSEMBL:ENSG00000116096\"\n                               \"ENSEMBL:ENSG00000171621\"\n                               \"ENSEMBL:ENSG00000070182\"\n                               \"ENSEMBL:ENSG00000179954\"\n                               \"ENSEMBL:ENSG00000172830\"\n                               \"ENSEMBL:ENSG00000115525\"\n                               \"ENSEMBL:ENSG00000148488\"\n                               \"ENSEMBL:ENSG00000144681\"\n                               \"ENSEMBL:ENSG00000115107\"\n                               \"ENSEMBL:ENSG00000104435\"\n                               \"ENSEMBL:ENSG00000148175\"\n                               \"ENSEMBL:ENSG00000198829\"\n                               \"ENSEMBL:ENSG00000137573\"\n                               \"ENSEMBL:ENSG00000198203\"\n                               \"ENSEMBL:ENSG00000109193\"\n                               \"ENSEMBL:ENSG00000099994\"\n                               \"ENSEMBL:ENSG00000173705\"\n                               \"ENSEMBL:ENSG00000197321\"\n                               \"ENSEMBL:ENSG00000234814\"\n                               \"ENSEMBL:ENSG00000162520\"\n                               \"ENSEMBL:ENSG00000078269\"\n                               \"ENSEMBL:ENSG00000204176\"\n                               \"ENSEMBL:ENSG00000139973\"\n                               \"ENSEMBL:ENSG00000142765\"\n                               \"ENSEMBL:ENSG00000147041\"\n                               \"ENSEMBL:ENSG00000115353\"\n                               \"ENSEMBL:ENSG00000158710\"\n                               \"ENSEMBL:ENSG00000253676\"\n                               \"ENSEMBL:ENSG00000135111\"\n                               \"ENSEMBL:ENSG00000204219\"\n                               \"ENSEMBL:ENSG00000282941\"\n                               \"ENSEMBL:ENSG00000118526\"\n                               \"ENSEMBL:ENSG00000110719\"\n                               \"ENSEMBL:ENSG00000183508\"\n                               \"ENSEMBL:ENSG00000226674\"\n                               \"ENSEMBL:ENSG00000137203\"\n                               \"ENSEMBL:ENSG00000105329\"\n                               \"ENSEMBL:ENSG00000119699\"\n                               \"ENSEMBL:ENSG00000120708\"\n                               \"ENSEMBL:ENSG00000178726\"\n                               \"ENSEMBL:ENSG00000136114\"\n                               \"ENSEMBL:ENSG00000127666\"\n                               \"ENSEMBL:ENSG00000142910\"\n                               \"ENSEMBL:ENSG00000223573\"\n                               \"ENSEMBL:ENSG00000038295\"\n                               \"ENSEMBL:ENSG00000137462\"\n                               \"ENSEMBL:ENSG00000183160\"\n                               \"ENSEMBL:ENSG00000164484\"\n                               \"ENSEMBL:ENSG00000196932\"\n                               \"ENSEMBL:ENSG00000121900\"\n                               \"ENSEMBL:ENSG00000105696\"\n                               \"ENSEMBL:ENSG00000165548\"\n                               \"ENSEMBL:ENSG00000187783\"\n                               \"ENSEMBL:ENSG00000136842\"\n                               \"ENSEMBL:ENSG00000120659\"\n                               \"ENSEMBL:ENSG00000120337\"\n                               \"ENSEMBL:ENSG00000116147\"\n                               \"ENSEMBL:ENSG00000111907\"\n                               \"ENSEMBL:ENSG00000259498\"\n                               \"ENSEMBL:ENSG00000159713\"\n                               \"ENSEMBL:ENSG00000102871\"\n                               \"ENSEMBL:ENSG00000056558\"\n                               \"ENSEMBL:ENSG00000211818\"\n                               \"ENSEMBL:ENSG00000132481\"\n                               \"ENSEMBL:ENSG00000121236\"\n                               \"ENSEMBL:ENSG00000069018\"\n                               \"ENSEMBL:ENSG00000144481\"\n                               \"ENSEMBL:ENSG00000187688\"\n                               \"ENSEMBL:ENSG00000134198\"\n                               \"ENSEMBL:ENSG00000100300\"\n                               \"ENSEMBL:ENSG00000180543\"\n                               \"ENSEMBL:ENSG00000265972\"\n                               \"ENSEMBL:ENSG00000215218\"\n                               \"ENSEMBL:ENSG00000156687\"\n                               \"ENSEMBL:ENSG00000145390\"\n                               \"ENSEMBL:ENSG00000150630\"\n                               \"ENSEMBL:ENSG00000206538\"\n                               \"ENSEMBL:ENSG00000261373\"\n                               \"ENSEMBL:ENSG00000146530\"\n                               \"ENSEMBL:ENSG00000103175\"\n                               \"ENSEMBL:ENSG00000156076\"\n                               \"ENSEMBL:ENSG00000188064\"\n                               \"ENSEMBL:ENSG00000255282\"\n                               \"ENSEMBL:ENSG00000189420\"\n                               \"ENSEMBL:ENSG00000251003\"\n                               \"ENSEMBL:ENSG00000144331\"\n                               \"ENSEMBL:ENSG00000225614\"\n                               \"ENSEMBL:ENSG00000183779\"\n                               \"ENSEMBL:ENSG00000170396\"))\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/rank-regulators.rkt",
    "content": "#lang racket\n(require \"../../../medikanren/pieces-parts/query.rkt\"\n         \"rank-regulators-gene-lists.rkt\"\n         racket/hash)\n(provide (all-defined-out)\n         (all-from-out \"../../../medikanren/pieces-parts/query.rkt\"\n                       \"rank-regulators-gene-lists.rkt\"\n                       racket/hash))\n\n#|\nMeaning of symbols/variable names\n\nG: a regulator gene or group of regulator genes. It can be any gene in the human genome that's contained in the\n   knowledge graphs. It doesn't have to be on gene list of interest, but it can be.\nrG: a regulated gene or group of regulated genes. These are constrained to the gene list of interest, so they must\n    be on the list of interest, but may be given in a different curie.\nM: a middleman. It is a GO: Biological Process concept. A redundancy in GO requires we go through this node in the\n   query to get to X.\nX: a GO: Biological Process that rGs are linked to via the \"involved_in\" predicate.\nC: a cell or tissue type. Usually given by a GO: or UBERON: curie.\n|#\n\n(define direct-interaction-preds '(\"regulates\"\n                                   \"directly_regulates\"\n                                   \"physically_interacts_with\"\n                                   \"directly_interacts_with\"\n                                   \"directly_positively_regulates\"\n                                   \"directly_negatively_regulates\"\n                                   \"biolink:directly_negatively_regulates\"\n                                   \"biolink:directly_positively_regulates\"\n                                   \"biolink:positively_regulates\"\n                                   \"biolink:directly_regulates\"\n                                   \"actively_involved_in\"))\n\n(define involved_in (keep 1 (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"involved_in\")))))\n(define subclass_of (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"subclass_of\"))))\n(define positively_regulates (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"positively_regulates\"))))\n(define negatively_regulates (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"negatively_regulates\"))))\n\n(define (uniprot-curie? curie)\n  (string-prefix? curie \"UniProtKB:\"))\n\n(define (gene-curie? curie)\n  (string-prefix? curie \"HGNC:\")\n  (string-prefix? curie \"ENSEMBL:\")\n  (string-prefix? curie \"NCBIGene:\"))\n\n(define (rtx2-concept? concept)\n  (equal? 'rtx2 (concept->dbname concept)))\n\n#|\nTakes two curies and determines if they are synonymous using curie-synonyms/names.\nCorrectness depends on the synonymization available in mediKanren.\n|#\n(define (synonymous-curies? curie1 curie2)\n  (assoc curie1 (curie-synonyms/names curie2)))\n\n#|\nChecks if a curie is an HGNC or NGBIGene curie. These two gene curies are currently the only two synonymized\nwith UniProtKB curies (as of 12/4/2020).\n|#\n(define (synonymized-gene-curie? curie)\n  (string-prefix? curie \"HGNC:\")\n  (string-prefix? curie \"NCBIGene:\"))\n\n#|\nTakes a concept and returns a pair with the concept's curie and its name.\nReturns: (curie . name)\n|#\n(define (concept->curie/name concept)\n  (cons (concept->curie concept) (concept->name concept)))\n\n#|\nTakes a curie and returns itself cons its name.\nReturns: (curie . name)\n|#\n(define (curie->curie/name curie)\n  (assoc curie (curie-synonyms/names curie)))\n\n#|\nTakes a list and \"unwraps\" the outer layer of parenthesis of each element in the list. If an element is an atom, it does\nnothing to it and retains its relative position in the list. If the input is not a list, unwrap just returns the input.\n|#\n(define (unwrap lst)\n  (cond [(or (null? lst) (not (list? lst))) lst]\n        [(list? (car lst)) (append (car lst) (unwrap (cdr lst)))]\n        [else (cons (car lst) (unwrap (cdr lst)))]))\n\n\n(define (hash-edges/curies edges)\n  (let ((edge-hash (make-hash)))\n    (for-each\n     (lambda (e)\n       (let ((subj-curie (concept->curie (edge->subject e)))\n             (obj-curie (concept->curie (edge->object e))))\n         (hash-update! edge-hash subj-curie (lambda (v) (set-add v obj-curie)) '())\n         )\n       )\n     edges\n     )\n    edge-hash\n    )\n  )\n\n(define (hash-edges/curies-reverse edges)\n  (let ((edge-hash (make-hash)))\n    (for-each\n     (lambda (e)\n       (let ((subj-curie (concept->curie (edge->subject e)))\n             (obj-curie (concept->curie (edge->object e))))\n         (hash-update! edge-hash obj-curie (lambda (v) (set-add v subj-curie)) '())\n         )\n       )\n     edges\n     )\n    edge-hash\n    )\n  )\n\n(define (link-edges/curies edges1 edges2)\n  (let ((linked-edges (make-hash))\n        (edges1-hash (hash-edges/curies edges1))\n        (edges2-hash (hash-edges/curies edges2)))\n    (hash-for-each edges1-hash\n                   (lambda (k1 v1)\n                     (hash-update! linked-edges k1 (lambda (v) (set-union v (hash-ref edges2-hash v1 '()))) '())\n                     )\n                   )\n    linked-edges\n    )\n  )\n\n(define (link-edges/curies-reverse edges1 edges2)\n  (let ((linked-edges (make-hash))\n        (edges1-hash (hash-edges/curies-reverse edges1))\n        (edges2-hash (hash-edges/curies-reverse edges2)))\n    (hash-for-each edges2-hash\n                   (lambda (k2 v2)\n                     (hash-update! linked-edges k2 (lambda (v) (set-union v (hash-ref edges1-hash v2 '()))) '())\n                     )\n                   )\n    linked-edges\n    )\n  )\n\n(define (gene-key->uniprot-key gene-key)\n  (define direction (cadr gene-key))\n  (map (lambda (y) (cons y direction)) (remove-duplicates (filter (lambda (x) (string-prefix? (car x) \"UniProtKB\"))\n                                                                  (curie-synonyms/names (caaar gene-key))))))\n\n#|\nTakes a list of gene curies and converts them to their uniprot curies.\nReturns: list of uniprot curies\n|#\n(define (genes->uniprots gene-list)\n  (define non-synonymized-gene-curies (filter (lambda (x) (not (synonymized-gene-curie? x))) gene-list))\n  (define synonymized-gene-curies (set-subtract gene-list non-synonymized-gene-curies))\n  (define non-synonymized-gene-concepts (filter rtx2-concept? (find-concepts #t non-synonymized-gene-curies)))\n  (define same-as (find-exact-predicates '(\"same_as\")))\n  (define has-gene-product (find-exact-predicates '(\"has_gene_product\")))\n\n  ;;This run/graph converts ENSEMBL:, UMLS:, etc. (curies that don't have edges going to UniProtKB: curies) into\n  ;;HGNC and NCBIGene curies.\n  (match-define\n    (list name=>concepts name=>edges)\n    (run/graph\n     ((N non-synonymized-gene-concepts)\n      (S #f))\n     ((N->S same-as))\n     (N N->S S)))\n\n  ;;synonymized-gene-concepts is a list of HGNC and NCBIGene concepts, which are the only gene concepts that have \"hash_gene_product\"\n  ;;predicate to UniProtKB concepts (as of 12/8/2020)\n  (define synonymized-gene-concepts (set-union (filter rtx2-concept? (find-concepts #t synonymized-gene-curies))\n                                               (hash-ref name=>concepts 'S)))\n\n  ;;This run/graph takes HGNC and NCBIGene concepts and finds their UniprotKB products\n  (match-define\n    (list name=>concepts2 name=>edges2)\n    (run/graph\n     ((G synonymized-gene-concepts)\n      (U #f))\n     ((G->U has-gene-product))\n     (G G->U U)))\n  \n  (map concept->curie (hash-ref name=>concepts2 'U))\n  )\n\n;;Currrently throws error\n(define (hash-uniprots=>genes gene-list)\n  (define uniprots=>genes (make-hash))\n  \n  (define non-synonymized-gene-curies (filter (lambda (x) (not (synonymized-gene-curie? x))) gene-list))\n  (define non-synonymized-gene-concepts (filter rtx2-concept? (find-concepts #t non-synonymized-gene-curies)))\n  \n  (define synonymized-gene-curies (set-subtract gene-list non-synonymized-gene-curies))\n  (define synonymized-gene-concepts (filter rtx2-concept? (find-concepts #t synonymized-gene-curies)))\n  \n  (define same_as (find-exact-predicates '(\"same_as\")))\n  (define has_gene_product (find-exact-predicates '(\"has_gene_product\")))\n\n  ;;run/graphs may be able to be combined\n  (match-define\n    (list name=>concepts name=>edges)\n    (run/graph\n     ((G non-synonymized-gene-concepts)\n      (M #f)\n      (U #f))\n     ((G->M same_as)\n      (M->U has_gene_product))\n     (G G->M M)\n     (M M->U U)))\n    \n  (match-define\n    (list name=>concepts2 name=>edges2)\n    (run/graph\n     ((G synonymized-gene-concepts)\n      (U #f))\n     ((G->U has_gene_product))\n     (G G->U U)))\n\n  (hash-union (link-edges/curies-reverse (hash-ref name=>edges 'G->M) (hash-ref name=>edges 'M->U))\n              (hash-edges/curies-reverse (hash-ref name=>edges2 'G->U)))\n  )\n\n#|\nTakes a list of uniprot curies.\nThese uniprots (once translated into concepts) become the input (rG) to a 3-hop query through GO.\nThe query has 2 parts, G->M->X and rG->X, but each hop is run as a separate run/graph for efficiency.\n\nReturns a list of 3 hashes that contain all of the edges from each run/graph\n|#\n(define (query-GO uniprot-list)\n  (define U (filter (lambda (x) (equal? (car x) 'rtx2)) (find-concepts #t uniprot-list)))\n\n  ;; rG->X hop\n  (match-define\n    (list rG/X=>concepts rG/X=>edges)\n    (time (run/graph\n           ((rG U)\n            (X #f))\n           ((rG->X involved_in))\n           (rG rG->X X))))\n\n  ;; M->X hop\n  (match-define\n    (list M/X=>concepts M/X=>edges)\n    (time (run/graph\n           ((M #f)\n            (X (hash-ref rG/X=>concepts 'X)))\n           ((M->X (set-union positively_regulates negatively_regulates subclass_of)))\n           (M M->X X))))\n\n  ;; G->M hop\n  (define Ms-in-GO (filter (lambda (m) (string-prefix? (concept->curie m) \"GO:\")) (hash-ref M/X=>concepts 'M)))\n  (match-define\n    (list G/M=>concepts G/M=>edges)\n    (time (run/graph\n           ((G #f)\n            (M Ms-in-GO))\n           ((G->M involved_in))\n           (G G->M M))))\n\n  ;; returns a list of the three edge hashes, one from each run/graph\n  (list rG/X=>edges M/X=>edges G/M=>edges)\n  )\n\n#|\nTakes the hash tables that contain the edges returned by the 3 run/graphs in the query-GO function.\nreport-GO-queries takes these edge hashes and returns a sorted association list with the following format:\n\nReturns assoc list (key value): '('(G-curie . G-name) '('('(rG-curie . rG-name) direction) M->X-pubmeds))\n\nIn the value, direction is either +1, -1, or 0, and it represents the direction in which G regulates rG, as\nindicated by what predicate the edge between them has.\nIn the value, M->X-pubmeds is a list of the pubmed IDs of the M->X edge (from the second query in the query-GO\nfunction) because that edge is the one that has the directional predicates.\n|#\n(define (report-GO-queries edge-hashes)\n  (match-define (list rG/X=>edges M/X=>edges G/M=>edges) edge-hashes)\n  (match-define (list X=>rG M=>X/info G=>rG) (list (make-hash) (make-hash) (make-hash)))\n\n  (time (for-each\n         (lambda (e)\n           (hash-update! X=>rG (concept->curie (edge->object e))\n                         (lambda (v) (set-add v (concept->curie (edge->subject e)))) '())\n           )\n         (hash-ref rG/X=>edges 'rG->X)\n         ))\n  \n  (time (for-each\n         (lambda (e)\n           (unless (not (string-prefix? (concept->curie (edge->subject e)) \"GO:\"))\n             (define direction 0)\n             (cond\n               [(set-member? (map cddr positively_regulates) (cdr (edge->pred e))) (set! direction 1)]\n               [(set-member? (map cddr negatively_regulates) (cdr (edge->pred e))) (set! direction -1)])\n             (hash-update! M=>X/info (concept->curie (edge->subject e))\n                           (lambda (v) (set-add v (list (concept->curie (edge->object e))\n                                                        direction\n                                                        (pubmed-ids-from-edge e))))\n                           '())\n             )\n           )\n         (hash-ref M/X=>edges 'M->X)\n         ))\n\n  (time (for-each\n         (lambda (g->m)\n           (for-each\n            (lambda (x/info)\n              (match-define (list x direction pubmeds) x/info)\n              (for-each\n               (lambda (rg)\n                 (define g (edge->subject g->m))\n                 (define new-val (list (cons (curie->curie/name rg) direction) pubmeds))\n                 (hash-update! G=>rG\n                               (concept->curie/name g)\n                               (lambda (v)\n                                 (cond\n                                   [(assoc (car new-val) v) => (lambda (a)\n                                                                 (set-add (set-remove v a)\n                                                                          (list (car a)\n                                                                                (set-union (cadr a) pubmeds))))]\n                                   [else (set-add v new-val)])) '())\n                 )\n               (hash-ref X=>rG x)\n               )\n              )\n            (hash-ref M=>X/info (concept->curie (edge->object g->m)))\n            )\n           )\n         (hash-ref G/M=>edges 'G->M)\n         ))\n  \n  ;;sort list by the number of regulated genes, rG, a gene, G, influences (most to least)\n  (sort\n   (hash-map G=>rG cons)\n   >\n   #:key (lambda (x) (length (cdr x))))\n  )\n\n#|\nThis function takes a list of uniprot curies and runs and reports a 1 hop query where the argument is the input to the query.\nThe 1-hop query is from G->rG, where the value passed into uniprot-list is rG. The G->rG edge is partitioned by 3 groups of\npredicates that indicate positive regulation, negative regulation, or direct interaction between the G and rG.\n\nThe function returns a sorted association list similar to that returned by report-GO-queries, but with more elements of information.\n\nReturns assoc list (key value): '('(G-curie . G-name) '('('(rG-curie . rG-name) direction) G->rG-pubmeds (direct-interaction? interaction-pubmeds)))\n\nIn the value, direction is either +1, -1, or 0, and it represents the direction in which G regulates rG, as\nindicated by what predicate the edge between them has.\nIn the value, G->rG-pubmeds is a list of the pubmed IDs for the edge between particular G and rG concepts.\nIn the value, direct-interaction? is a boolean that is only #t if there is an edge between the G and rG whose\npredicate indicates direct-interaction between the G and rG.\nIn the value, interaction-pubmeds is a list of the pubmed IDs for the edge that indicates direct interaction\nbetween a G and rG. If direct-interaction? is #f, then interaction-pubmeds is and empty list '().\n|#\n(define (1-hop-query/report uniprot-list)\n  (define 1-hop-hash (make-hash))\n  (for-each\n   (lambda (rg)\n     (define q (time (query/graph\n                      ((G+ gene-or-protein)\n                       (G- gene-or-protein)\n                       (G gene-or-protein)\n                       (rG-on-list rg))\n                      ((G+-pos->rG-on-list positively-regulates)\n                       (G--neg->rG-on-list negatively-regulates)\n                       (G->rG-on-list direct-interaction-preds))\n                      (G+ G+-pos->rG-on-list rG-on-list)\n                      (G- G--neg->rG-on-list rG-on-list)\n                      (G G->rG-on-list rG-on-list))))\n     \n     ;;This function takes a list of edges from the 1-hop-query above and populates the hash table\n     (define (1-hop-edges->hash edges direction)\n       (for-each\n        (lambda (e)\n          (define g (concept->curie (edge->subject e)))\n          ;;record whether the predicate indicates direct interaction between the two entities (#t if yes)\n          (define direct-interaction? (set-member? direct-interaction-preds (edge->pred  e)))\n          ;;record provenance\n          (define direction-pubmeds (pubmed-ids-from-edge e))\n          (define direct-interaction-pubmeds (pubmed-ids-from-edge e))\n          ;;add information to the hash\n          (hash-update! 1-hop-hash\n                        (curie->curie/name g)\n                        (lambda (v)\n                          (cond\n                            [(and (assoc (cons (curie->curie/name rg) direction) v)\n                                  (not (empty? direction-pubmeds)))\n                             (define rg/info (assoc (cons (curie->curie/name rg) direction) v))\n                             (set-add (set-remove v rg/info)\n                                      (list (car rg/info)\n                                            (set-union (cadr rg/info) direction-pubmeds)\n                                            (cons direct-interaction? direct-interaction-pubmeds)))]\n                            [else (set-add v (list (cons (curie->curie/name rg) direction)\n                                                   direction-pubmeds\n                                                   (cons direct-interaction? direct-interaction-pubmeds)))])\n                          ) '())\n          )\n        edges\n        )\n       )\n     \n     (1-hop-edges->hash (edges/query q 'G+-pos->rG-on-list) 1)\n     (1-hop-edges->hash (edges/query q 'G--neg->rG-on-list) -1)\n     (1-hop-edges->hash (edges/query q 'G->rG-on-list) 0)\n     )\n   uniprot-list\n   )\n  \n  ;;sort list by the number of regulated genes, rG, a gene, G, influences (most to least)\n  (sort\n   (hash-map 1-hop-hash cons)\n   >\n   #:key (lambda (x) (length (cdr x))))\n  )\n\n#|\nTakes the results returned by the report-GO-queries and 1-hop-query/report and finds intersection points\nbetween them to coroborate and increase confidence in the information at those intersection points.\n\nAn intersection point is qualified as an element from the GO query results and one from the 1-hop query results\nthat have synonymous Gs and rGs and have the same direction.\n\nReturns an association list of the intersecting G and rG relationships with all of the direction, direct interaction,\nand provenance information combined from the GO query results and the 1-hop auery results.\n\nReturns assoc list (key value): '('(G-curie . G-name) '('('(rG-curie . rG-name) direction) direction-pubmeds (direct-interaction? interaction-pubmeds)))\n|#\n(define (find-intersections go-query-results 1-hop-query-results)\n  (define intersections (make-hash))\n  (define 1-hop-keys (map car 1-hop-query-results))\n  (define 1-hop-uniprot-keys (filter (lambda (x) (uniprot-curie? (car x))) 1-hop-keys))\n  (define 1-hop-U=>G-hash (hash-uniprots=>genes (map car (set-subtract 1-hop-keys 1-hop-uniprot-keys))))\n  (define intersecting-Gs-uniprot-curies/names (set-intersect (map car go-query-results)\n                                                              1-hop-uniprot-keys\n                                                              (map curie->curie/name (hash-keys 1-hop-U=>G-hash))))\n  (print \"~v\\n\" (length intersecting-Gs-uniprot-curies/names))\n  (for-each\n   (lambda (u)\n     (let ((1-hop-value (cond [(hash-ref 1-hop-U=>G-hash (car u)) => (lambda (gene-curie)\n                                                                       (cadr (assoc (curie->curie/name (car gene-curie))\n                                                                                    1-hop-query-results)))]\n                              [else (cadr (assoc u 1-hop-query-results))]))\n           (go-query-value (cadr (assoc u go-query-results))))\n       (cond [(equal? (car 1-hop-value) (car go-query-value))\n              (let ((value (list (car go-query-value)\n                                 (set-union (cadr go-query-value) (cadr 1-hop-value))\n                                 (cadr 1-hop-value))))\n                    (hash-set! intersections u value '()))\n              ])\n       )\n     (print \".\\n\")\n     )\n   intersecting-Gs-uniprot-curies/names\n   )\n  \n  ;;sort list by the number of regulated genes, rG, a gene, G, influences (most to least)\n  (sort\n   (hash-map intersections cons)\n   >\n   #:key (lambda (x) (length (cdr x))))\n  )\n\n#|\nTakes a list of the curies of all of the genes/proteins found by the previous GO queries and 1-hop queries.\nRuns a query to find where all of the genes/protiens are expressed.\nReturns: a hash table that hashes the (curie .  name) of a cell/tissue type to a list of all of the genes/proteins,\nalso reported as (curie . name), expressed in that cell/tissue type.\n|#\n(define (find-expression-locations genes-and-proteins)\n  (define expression-location (make-hash))\n  (for-each\n   (lambda (g)\n     (define q (query/graph\n                ((G-or-rG g)\n                 (C #f))\n                ((G-or-rG->C '(\"expressed_in\")))\n                (G-or-rG G-or-rG->C C)))\n     (for-each\n      (lambda (e)\n        (define g-or-rg (concept->curie (edge->subject e)))\n        (define t (concept->curie (edge->object e)))\n        (hash-update! expression-location (curie->curie/name t) (lambda (v) (set-add v (curie->curie/name g-or-rg))) '())\n        )\n      (edges/query q 'G-or-rG->C)\n      )\n     )\n   genes-and-proteins\n   )\n  expression-location\n  )\n\n#|\nTakes the hash returned by find-expression-locations and returns an assoc list sorted most to least by the number\nof gene/proteins expressed in a cell/tissue type (a.k.a. the length of the value).\n|#\n(define (sort-cell/tissue-types-by-G-and-rG cell/tissue-type-hash)\n  (sort\n   (hash-map cell/tissue-type-hash cons)\n   >\n   #:key (lambda (x) (length (cdr x))))\n  )\n\n#|\nTakes the hash returned by find-expression-locations and returns an assoc list sorted most to least by the number\nof genes from the original list of interest expressed in a cell/tissue type (a.k.a. the length of the value intersected\nwith the gene list of interest).\n|#\n(define (sort-cell/tissue-types-by-rG cell/tissue-type-hash uniprots/names)\n  (sort\n   (hash-map cell/tissue-type-hash (lambda (k v) (cons k (set-intersect v uniprots/names))))\n   >\n   #:key (lambda (x) (length (cdr x))))\n  )\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/rank-side-effects.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/pieces-parts/query.rkt\")\n\n#|\ntakes: a drug curie as a string (a-drug), a list of predicates of interest (predicates)\nDoes query X->O where X is a-drug and the edges are filtered by predicates\nreturns: a list of the curies O from the X->O query\n|#\n(define (filter-edges a-drug predicates)\n  (define q\n    (time\n     (query/graph\n      ((X a-drug)\n       (O #f))\n      ((X->O predicates))\n      (X X->O O))))\n  (curies/query q 'O))\n\n;;predicates that indicate a side effect\n(define side-effect-preds (list \"causes\"\n                                \"contributes_to\"\n                                \"contraindicated_for\"))\n\n#|\ntakes: a disease curie as a string (disease-curie), a set of patient symptoms/phenotypes (empty set if none) (patient-phenos)\nRanks the drugs related to the disease-curie by the nature and number of side effects they cause\nreturns: A list of 3 lists. These lists contain all of the drug curies resulting from a drug->disease-curie query sorted as follows:\n         The last list contains the drugs that aggravate any pre-existing patient symptom.\n         The middle list contains the drugs that would further aggravate any symptoms caused by the disease (disease-curie)\n         The first list contains the rest of the drugs not in the 2nd or 3rd list that have a drug->disease (disease-curie) relationship.\n         The drugs within all three lists are sorted (least to most) by the number of side effects they have.\n|#\n(define (rank-drugs-related-to disease-curie patient-phenos)\n  ;;D->O, a query where D is any drug that has an edge to the disease-curie, O.\n  (define qtreats (query/graph\n                   ((D drug)\n                    (O disease-curie))\n                   ((D->O #f))\n                   (D D->O O)))\n  (define drugs (curies/query qtreats 'D))\n  ;;a query to get all of the symptoms/phenotypes of the given disease-curie, + the disease-curie itself\n  (define qphenos (query/graph\n                   ((S disease-curie)\n                    (P phenotype))\n                   ((S->P #f))\n                   (S S->P P)))\n  (define disease-phenos (set-add (list->set (map curie-synonyms/names (curies/query qphenos 'P))) disease-curie))\n  \n  ;;a hash of all the drugs to a set of their side effects\n  (define drug->side-effects (make-hash))\n  (for-each\n   (lambda (d)\n     (hash-set! drug->side-effects d (list->set (filter-edges d side-effect-preds)))\n     )\n   drugs)\n  ;;determines whether a given drug (drg) exacerbates any phenotype in a set of phenotypes (ph), returns a bool\n  (define (exacerbates? drg ph)\n    (not (set-empty? (set-intersect (hash-ref drug->side-effects drg) ph))))\n  \n  (define exacerbates-patient (mutable-set))\n  (define exacerbates-disease (mutable-set))\n  (define top-rank (mutable-set))\n  (for-each\n   (lambda (d)\n     (cond\n       [(exacerbates? d patient-phenos) (set-add! exacerbates-patient d)]\n       [(exacerbates? d disease-phenos) (set-add! exacerbates-disease d)]\n       [else (set-add! top-rank d)]\n       )\n     )\n   drugs)\n  ;;function to sort by number of side effects\n  (define (rank-num-side-effects drgs)\n    (sort (set->list drgs)\n          >\n          #:key (lambda (d) (set-count (hash-ref drug->side-effects d))))\n    )\n  (list (rank-num-side-effects top-rank) (rank-num-side-effects exacerbates-disease) (rank-num-side-effects exacerbates-patient))\n  )\n#|Examples\nHemophilia A, no pre-existing patient symptoms\n(rank-drugs-related-to \"MONDO:0010602\" (set))\nHemophilia A, patient also has liver disease and anemia\n(rank-drugs-related-to \"MONDO:0010602\" (set \"MONDO:0005154\" \"HP:0001903\"))\n|#"
  },
  {
    "path": "contrib/medikanren/pieces-parts/synonymization_algorithm.rkt",
    "content": "#lang racket\n(provide HGNC-CURIE->synonymized-concepts\n         curie-aliases curie-synonyms curie-synonyms-raw curie-synonyms/names\n         curie->name curie->concepts\n         (all-from-out \"../common.rkt\" \"../mk-db.rkt\"))\n(require \"../common.rkt\" \"../mk-db.rkt\" \"../db.rkt\" racket/runtime-path)\n\n\n\n#|\n\n\n\n\n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/test-propagator.rkt",
    "content": "#lang racket\n(provide\n  (all-from-out \"../../../medikanren/pieces-parts/common.rkt\")\n  (all-from-out \"../../../medikanren/pieces-parts/mk-db.rkt\")\n  (all-from-out \"../../../medikanren/pieces-parts/propagator.rkt\")\n  (all-defined-out))\n(require \"../../../medikanren/common.rkt\" \"../../../medikanren/mk-db.rkt\" \"../../../medikanren/pieces-parts/propagator.rkt\")\n(load-databases #t)\n\n(define positively-regulates '(\"causes\"))\n(define negatively-regulates '(\"negatively_regulates\"))\n\n(define imatinib \"UMLS:C0935989\")\n(define asthma   \"UMLS:C0004096\")\n\n(define S (concept/curie imatinib))\n(define X (concept/any))\n(define O (concept/curie asthma))\n\n(define S->X (edge/predicate negatively-regulates S X))\n(define X->O (edge/predicate positively-regulates X O))\n\n(displayln 'running:)\n(time (run!))\n\n(displayln 'S)\n(length (cdr (S 'ref)))\n\n(displayln 'O)\n(length (cdr (O 'ref)))\n\n(displayln 'X)\n(length (cdr (X 'ref)))\n\n(displayln 'S->X)\n(length (cdr (S->X 'ref)))\n\n(displayln 'X->O)\n(length (cdr (X->O 'ref)))\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/trace-pathways-by-tissue-type.rkt",
    "content": "#lang racket\n(require \"../../../medikanren/pieces-parts/query.rkt\")\n\n(define gene-list (list->set '(\"ENSEMBL:ENSG00000167972\"\n                               \"ENSEMBL:ENSG00000198691\"\n                               \"ENSEMBL:ENSG00000175164\"\n                               \"ENSEMBL:ENSG00000278540\"\n                               \"ENSEMBL:ENSG00000100412\"\n                               \"ENSEMBL:ENSG00000162104\"\n                               \"ENSEMBL:ENSG00000204305\"\n                               \"ENSEMBL:ENSG00000135744\"\n                               \"ENSEMBL:ENSG00000144891\"\n                               \"ENSEMBL:ENSG00000180772\"\n                               \"ENSEMBL:ENSG00000142208\"\n                               \"ENSEMBL:ENSG00000148218\"\n                               \"ENSEMBL:ENSG00000163631\"\n                               \"ENSEMBL:ENSG00000085662\"\n                               \"ENSEMBL:ENSG00000154188\"\n                               \"ENSEMBL:ENSG00000091879\"\n                               \"ENSEMBL:ENSG00000182718\"\n                               \"ENSEMBL:ENSG00000134982\"\n                               \"ENSEMBL:ENSG00000132703\"\n                               \"ENSEMBL:ENSG00000023445\"\n                               \"ENSEMBL:ENSG00000142515\"\n                               \"ENSEMBL:ENSG00000026103\"\n                               \"ENSEMBL:ENSG00000117560\"\n                               \"ENSEMBL:ENSG00000240583\"\n                               \"ENSEMBL:ENSG00000161798\"\n                               \"ENSEMBL:ENSG00000006756\"\n                               \"ENSEMBL:ENSG00000117601\"\n                               \"ENSEMBL:ENSG00000149311\"\n                               \"ENSEMBL:ENSG00000164904\"\n                               \"ENSEMBL:ENSG00000171791\"\n                               \"ENSEMBL:ENSG00000101144\"\n                               \"ENSEMBL:ENSG00000010671\"\n                               \"ENSEMBL:ENSG00000100300\"\n                               \"ENSEMBL:ENSG00000149131\"\n                               \"ENSEMBL:ENSG00000171860\"\n                               \"ENSEMBL:ENSG00000106804\"\n                               \"ENSEMBL:ENSG00000197405\"\n                               \"ENSEMBL:ENSG00000149823\"\n                               \"ENSEMBL:ENSG00000063180\"\n                               \"ENSEMBL:ENSG00000164305\"\n                               \"ENSEMBL:ENSG00000121691\"\n                               \"ENSEMBL:ENSG00000105974\"\n                               \"ENSEMBL:ENSG00000124813\"\n                               \"ENSEMBL:ENSG00000149257\"\n                               \"ENSEMBL:ENSG00000134057\"\n                               \"ENSEMBL:ENSG00000170458\"\n                               \"ENSEMBL:ENSG00000121594\"\n                               \"ENSEMBL:ENSG00000101017\"\n                               \"ENSEMBL:ENSG00000102245\"\n                               \"ENSEMBL:ENSG00000026508\"\n                               \"ENSEMBL:ENSG00000085063\"\n                               \"ENSEMBL:ENSG00000129226\"\n                               \"ENSEMBL:ENSG00000179776\"\n                               \"ENSEMBL:ENSG00000100526\"\n                               \"ENSEMBL:ENSG00000170835\"\n                               \"ENSEMBL:ENSG00000001626\"\n                               \"ENSEMBL:ENSG00000133019\"\n                               \"ENSEMBL:ENSG00000196811\"\n                               \"ENSEMBL:ENSG00000099622\"\n                               \"ENSEMBL:ENSG00000122705\"\n                               \"ENSEMBL:ENSG00000183813\"\n                               \"ENSEMBL:ENSG00000188153\"\n                               \"ENSEMBL:ENSG00000115966\"\n                               \"ENSEMBL:ENSG00000167193\"\n                               \"ENSEMBL:ENSG00000132693\"\n                               \"ENSEMBL:ENSG00000118231\"\n                               \"ENSEMBL:ENSG00000112062\"\n                               \"ENSEMBL:ENSG00000101439\"\n                               \"ENSEMBL:ENSG00000118523\"\n                               \"ENSEMBL:ENSG00000168036\"\n                               \"ENSEMBL:ENSG00000100448\"\n                               \"ENSEMBL:ENSG00000166347\"\n                               \"ENSEMBL:ENSG00000140465\"\n                               \"ENSEMBL:ENSG00000140505\"\n                               \"ENSEMBL:ENSG00000138061\"\n                               \"ENSEMBL:ENSG00000160870\"\n                               \"ENSEMBL:ENSG00000106258\"\n                               \"ENSEMBL:ENSG00000196730\"\n                               \"ENSEMBL:ENSG00000011465\"\n                               \"ENSEMBL:ENSG00000159640\"\n                               \"ENSEMBL:ENSG00000164825\"\n                               \"ENSEMBL:ENSG00000197766\"\n                               \"ENSEMBL:ENSG00000181019\"\n                               \"ENSEMBL:ENSG00000213918\"\n                               \"ENSEMBL:ENSG00000197635\"\n                               \"ENSEMBL:ENSG00000164330\"\n                               \"ENSEMBL:ENSG00000213694\"\n                               \"ENSEMBL:ENSG00000078401\"\n                               \"ENSEMBL:ENSG00000138798\"\n                               \"ENSEMBL:ENSG00000197561\"\n                               \"ENSEMBL:ENSG00000021355\"\n                               \"ENSEMBL:ENSG00000066044\"\n                               \"ENSEMBL:ENSG00000116016\"\n                               \"ENSEMBL:ENSG00000133216\"\n                               \"ENSEMBL:ENSG00000120915\"\n                               \"ENSEMBL:ENSG00000130427\"\n                               \"ENSEMBL:ENSG00000157554\"\n                               \"ENSEMBL:ENSG00000157557\"\n                               \"ENSEMBL:ENSG00000180210\"\n                               \"ENSEMBL:ENSG00000117525\"\n                               \"ENSEMBL:ENSG00000198734\"\n                               \"ENSEMBL:ENSG00000117480\"\n                               \"ENSEMBL:ENSG00000166147\"\n                               \"ENSEMBL:ENSG00000151422\"\n                               \"ENSEMBL:ENSG00000140285\"\n                               \"ENSEMBL:ENSG00000160867\"\n                               \"ENSEMBL:ENSG00000111206\"\n                               \"ENSEMBL:ENSG00000115414\"\n                               \"ENSEMBL:ENSG00000170345\"\n                               \"ENSEMBL:ENSG00000154727\"\n                               \"ENSEMBL:ENSG00000163288\"\n                               \"ENSEMBL:ENSG00000128683\"\n                               \"ENSEMBL:ENSG00000141448\"\n                               \"ENSEMBL:ENSG00000168621\"\n                               \"ENSEMBL:ENSG00000134812\"\n                               \"ENSEMBL:ENSG00000265107\"\n                               \"ENSEMBL:ENSG00000173221\"\n                               \"ENSEMBL:ENSG00000147437\"\n                               \"ENSEMBL:ENSG00000186810\"\n                               \"ENSEMBL:ENSG00000167701\"\n                               \"ENSEMBL:ENSG00000113580\"\n                               \"ENSEMBL:ENSG00000082701\"\n                               \"ENSEMBL:ENSG00000132518\"\n                               \"ENSEMBL:ENSG00000145649\"\n                               \"ENSEMBL:ENSG00000100453\"\n                               \"ENSEMBL:ENSG00000148702\"\n                               \"ENSEMBL:ENSG00000084754\"\n                               \"ENSEMBL:ENSG00000019991\"\n                               \"ENSEMBL:ENSG00000100644\"\n                               \"ENSEMBL:ENSG00000189403\"\n                               \"ENSEMBL:ENSG00000100292\"\n                               \"ENSEMBL:ENSG00000125798\"\n                               \"ENSEMBL:ENSG00000135486\"\n                               \"ENSEMBL:ENSG00000257017\"\n                               \"ENSEMBL:ENSG00000113905\"\n                               \"ENSEMBL:ENSG00000176387\"\n                               \"ENSEMBL:ENSG00000204389\"\n                               \"ENSEMBL:ENSG00000204388\"\n                               \"ENSEMBL:ENSG00000170606\"\n                               \"ENSEMBL:ENSG00000070614\"\n                               \"ENSEMBL:ENSG00000041982\"\n                               \"ENSEMBL:ENSG00000090339\"\n                               \"ENSEMBL:ENSG00000185745\"\n                               \"ENSEMBL:ENSG00000171855\"\n                               \"ENSEMBL:ENSG00000111537\"\n                               \"ENSEMBL:ENSG00000006652\"\n                               \"ENSEMBL:ENSG00000017427\"\n                               \"ENSEMBL:ENSG00000146674\"\n                               \"ENSEMBL:ENSG00000167779\"\n                               \"ENSEMBL:ENSG00000104365\"\n                               \"ENSEMBL:ENSG00000115008\"\n                               \"ENSEMBL:ENSG00000125538\"\n                               \"ENSEMBL:ENSG00000115594\"\n                               \"ENSEMBL:ENSG00000136689\"\n                               \"ENSEMBL:ENSG00000109471\"\n                               \"ENSEMBL:ENSG00000134460\"\n                               \"ENSEMBL:ENSG00000113520\"\n                               \"ENSEMBL:ENSG00000136244\"\n                               \"ENSEMBL:ENSG00000168685\"\n                               \"ENSEMBL:ENSG00000169429\"\n                               \"ENSEMBL:ENSG00000136634\"\n                               \"ENSEMBL:ENSG00000169194\"\n                               \"ENSEMBL:ENSG00000112115\"\n                               \"ENSEMBL:ENSG00000150782\"\n                               \"ENSEMBL:ENSG00000169245\"\n                               \"ENSEMBL:ENSG00000125347\"\n                               \"ENSEMBL:ENSG00000005884\"\n                               \"ENSEMBL:ENSG00000169896\"\n                               \"ENSEMBL:ENSG00000160255\"\n                               \"ENSEMBL:ENSG00000115474\"\n                               \"ENSEMBL:ENSG00000128052\"\n                               \"ENSEMBL:ENSG00000171345\"\n                               \"ENSEMBL:ENSG00000172037\"\n                               \"ENSEMBL:ENSG00000148346\"\n                               \"ENSEMBL:ENSG00000115850\"\n                               \"ENSEMBL:ENSG00000131981\"\n                               \"ENSEMBL:ENSG00000138039\"\n                               \"ENSEMBL:ENSG00000105370\"\n                               \"ENSEMBL:ENSG00000226979\"\n                               \"ENSEMBL:ENSG00000160932\"\n                               \"ENSEMBL:ENSG00000183918\"\n                               \"ENSEMBL:ENSG00000277443\"\n                               \"ENSEMBL:ENSG00000166949\"\n                               \"ENSEMBL:ENSG00000165471\"\n                               \"ENSEMBL:ENSG00000143384\"\n                               \"ENSEMBL:ENSG00000014641\"\n                               \"ENSEMBL:ENSG00000110492\"\n                               \"ENSEMBL:ENSG00000095015\"\n                               \"ENSEMBL:ENSG00000240972\"\n                               \"ENSEMBL:ENSG00000138755\"\n                               \"ENSEMBL:ENSG00000087245\"\n                               \"ENSEMBL:ENSG00000149968\"\n                               \"ENSEMBL:ENSG00000100985\"\n                               \"ENSEMBL:ENSG00000005381\"\n                               \"ENSEMBL:ENSG00000130830\"\n                               \"ENSEMBL:ENSG00000125148\"\n                               \"ENSEMBL:ENSG00000087250\"\n                               \"ENSEMBL:ENSG00000171100\"\n                               \"ENSEMBL:ENSG00000210195\"\n                               \"ENSEMBL:ENSG00000185499\"\n                               \"ENSEMBL:ENSG00000215182\"\n                               \"ENSEMBL:ENSG00000136997\"\n                               \"ENSEMBL:ENSG00000172936\"\n                               \"ENSEMBL:ENSG00000109063\"\n                               \"ENSEMBL:ENSG00000065534\"\n                               \"ENSEMBL:ENSG00000116044\"\n                               \"ENSEMBL:ENSG00000109320\"\n                               \"ENSEMBL:ENSG00000100906\"\n                               \"ENSEMBL:ENSG00000001167\"\n                               \"ENSEMBL:ENSG00000089250\"\n                               \"ENSEMBL:ENSG00000164867\"\n                               \"ENSEMBL:ENSG00000161270\"\n                               \"ENSEMBL:ENSG00000135318\"\n                               \"ENSEMBL:ENSG00000111331\"\n                               \"ENSEMBL:ENSG00000112038\"\n                               \"ENSEMBL:ENSG00000089041\"\n                               \"ENSEMBL:ENSG00000185624\"\n                               \"ENSEMBL:ENSG00000007168\"\n                               \"ENSEMBL:ENSG00000117450\"\n                               \"ENSEMBL:ENSG00000106366\"\n                               \"ENSEMBL:ENSG00000126759\"\n                               \"ENSEMBL:ENSG00000197249\"\n                               \"ENSEMBL:ENSG00000124102\"\n                               \"ENSEMBL:ENSG00000121879\"\n                               \"ENSEMBL:ENSG00000051382\"\n                               \"ENSEMBL:ENSG00000171608\"\n                               \"ENSEMBL:ENSG00000105851\"\n                               \"ENSEMBL:ENSG00000170890\"\n                               \"ENSEMBL:ENSG00000188257\"\n                               \"ENSEMBL:ENSG00000116711\"\n                               \"ENSEMBL:ENSG00000118495\"\n                               \"ENSEMBL:ENSG00000011422\"\n                               \"ENSEMBL:ENSG00000115896\"\n                               \"ENSEMBL:ENSG00000075651\"\n                               \"ENSEMBL:ENSG00000178209\"\n                               \"ENSEMBL:ENSG00000266964\"\n                               \"ENSEMBL:ENSG00000115138\"\n                               \"ENSEMBL:ENSG00000186951\"\n                               \"ENSEMBL:ENSG00000122862\"\n                               \"ENSEMBL:ENSG00000100030\"\n                               \"ENSEMBL:ENSG00000107643\"\n                               \"ENSEMBL:ENSG00000169032\"\n                               \"ENSEMBL:ENSG00000115718\"\n                               \"ENSEMBL:ENSG00000184500\"\n                               \"ENSEMBL:ENSG00000189002\"\n                               \"ENSEMBL:ENSG00000135406\"\n                               \"ENSEMBL:ENSG00000041357\"\n                               \"ENSEMBL:ENSG00000197170\"\n                               \"ENSEMBL:ENSG00000011304\"\n                               \"ENSEMBL:ENSG00000073756\"\n                               \"ENSEMBL:ENSG00000169398\"\n                               \"ENSEMBL:ENSG00000105894\"\n                               \"ENSEMBL:ENSG00000081237\"\n                               \"ENSEMBL:ENSG00000113456\"\n                               \"ENSEMBL:ENSG00000069974\"\n                               \"ENSEMBL:ENSG00000080823\"\n                               \"ENSEMBL:ENSG00000112619\"\n                               \"ENSEMBL:ENSG00000173039\"\n                               \"ENSEMBL:ENSG00000143839\"\n                               \"ENSEMBL:ENSG00000102032\"\n                               \"ENSEMBL:ENSG00000163914\"\n                               \"ENSEMBL:ENSG00000067900\"\n                               \"ENSEMBL:ENSG00000149489\"\n                               \"ENSEMBL:ENSG00000196218\"\n                               \"ENSEMBL:ENSG00000196154\"\n                               \"ENSEMBL:ENSG00000163220\"\n                               \"ENSEMBL:ENSG00000031698\"\n                               \"ENSEMBL:ENSG00000111319\"\n                               \"ENSEMBL:ENSG00000108691\"\n                               \"ENSEMBL:ENSG00000108688\"\n                               \"ENSEMBL:ENSG00000163735\"\n                               \"ENSEMBL:ENSG00000110876\"\n                               \"ENSEMBL:ENSG00000168878\"\n                               \"ENSEMBL:ENSG00000168484\"\n                               \"ENSEMBL:ENSG00000133661\"\n                               \"ENSEMBL:ENSG00000064651\"\n                               \"ENSEMBL:ENSG00000197208\"\n                               \"ENSEMBL:ENSG00000166311\"\n                               \"ENSEMBL:ENSG00000075618\"\n                               \"ENSEMBL:ENSG00000125835\"\n                               \"ENSEMBL:ENSG00000142168\"\n                               \"ENSEMBL:ENSG00000112096\"\n                               \"ENSEMBL:ENSG00000109610\"\n                               \"ENSEMBL:ENSG00000125398\"\n                               \"ENSEMBL:ENSG00000100883\"\n                               \"ENSEMBL:ENSG00000168610\"\n                               \"ENSEMBL:ENSG00000126561\"\n                               \"ENSEMBL:ENSG00000173757\"\n                               \"ENSEMBL:ENSG00000087586\"\n                               \"ENSEMBL:ENSG00000067715\"\n                               \"ENSEMBL:ENSG00000231925\"\n                               \"ENSEMBL:ENSG00000006638\"\n                               \"ENSEMBL:ENSG00000118526\"\n                               \"ENSEMBL:ENSG00000120156\"\n                               \"ENSEMBL:ENSG00000164362\"\n                               \"ENSEMBL:ENSG00000003436\"\n                               \"ENSEMBL:ENSG00000105329\"\n                               \"ENSEMBL:ENSG00000198959\"\n                               \"ENSEMBL:ENSG00000178726\"\n                               \"ENSEMBL:ENSG00000116001\"\n                               \"ENSEMBL:ENSG00000102265\"\n                               \"ENSEMBL:ENSG00000136352\"\n                               \"ENSEMBL:ENSG00000137462\"\n                               \"ENSEMBL:ENSG00000164342\"\n                               \"ENSEMBL:ENSG00000136869\"\n                               \"ENSEMBL:ENSG00000127324\"\n                               \"ENSEMBL:ENSG00000149809\"\n                               \"ENSEMBL:ENSG00000232810\"\n                               \"ENSEMBL:ENSG00000118503\"\n                               \"ENSEMBL:ENSG00000067182\"\n                               \"ENSEMBL:ENSG00000118194\"\n                               \"ENSEMBL:ENSG00000131747\"\n                               \"ENSEMBL:ENSG00000111669\"\n                               \"ENSEMBL:ENSG00000128311\"\n                               \"ENSEMBL:ENSG00000125482\"\n                               \"ENSEMBL:ENSG00000155657\"\n                               \"ENSEMBL:ENSG00000136810\"\n                               \"ENSEMBL:ENSG00000198431\"\n                               \"ENSEMBL:ENSG00000149021\"\n                               \"ENSEMBL:ENSG00000174607\"\n                               \"ENSEMBL:ENSG00000111424\"\n                               \"ENSEMBL:ENSG00000112715\"\n                               \"ENSEMBL:ENSG00000146469\"\n                               \"ENSEMBL:ENSG00000110799\"\n                               \"ENSEMBL:ENSG00000158125\"\n                               \"ENSEMBL:ENSG00000164924\"\n                               \"ENSEMBL:ENSG00000121966\"\n                               \"ENSEMBL:ENSG00000146070\"\n                               \"ENSEMBL:ENSG00000106305\"\n                               \"ENSEMBL:ENSG00000050327\"\n                               \"ENSEMBL:ENSG00000083168\"\n                               \"ENSEMBL:ENSG00000118972\"\n                               \"ENSEMBL:ENSG00000206561\"\n                               \"ENSEMBL:ENSG00000184381\"\n                               \"ENSEMBL:ENSG00000069764\"\n                               \"ENSEMBL:ENSG00000108528\"\n                               \"ENSEMBL:ENSG00000117461\"\n                               \"ENSEMBL:ENSG00000134107\"\n                               \"ENSEMBL:ENSG00000136908\"\n                               \"ENSEMBL:ENSG00000171720\"\n                               \"ENSEMBL:ENSG00000176170\"\n                               \"ENSEMBL:ENSG00000111602\"\n                               \"ENSEMBL:ENSG00000173805\"\n                               \"ENSEMBL:ENSG00000131023\"\n                               \"ENSEMBL:ENSG00000157456\"\n                               \"ENSEMBL:ENSG00000162889\"\n                               \"ENSEMBL:ENSG00000103671\"\n                               \"ENSEMBL:ENSG00000133116\"\n                               \"ENSEMBL:ENSG00000181092\"\n                               \"ENSEMBL:ENSG00000100351\"\n                               \"ENSEMBL:ENSG00000136156\"\n                               \"ENSEMBL:ENSG00000102230\"\n                               \"ENSEMBL:ENSG00000057663\"\n                               \"ENSEMBL:ENSG00000134318\"\n                               \"ENSEMBL:ENSG00000117592\"\n                               \"ENSEMBL:ENSG00000187608\"\n                               \"ENSEMBL:ENSG00000103335\"\n                               \"ENSEMBL:ENSG00000165733\"\n                               \"ENSEMBL:ENSG00000079999\"\n                               \"ENSEMBL:ENSG00000044090\"\n                               \"ENSEMBL:ENSG00000117020\"\n                               \"ENSEMBL:ENSG00000105835\"\n                               \"ENSEMBL:ENSG00000105246\"\n                               \"ENSEMBL:ENSG00000131477\"\n                               \"ENSEMBL:ENSG00000127528\"\n                               \"ENSEMBL:ENSG00000167315\"\n                               \"ENSEMBL:ENSG00000140092\"\n                               \"ENSEMBL:ENSG00000101000\"\n                               \"ENSEMBL:ENSG00000100591\"\n                               \"ENSEMBL:ENSG00000160999\"\n                               \"ENSEMBL:ENSG00000162493\"\n                               \"ENSEMBL:ENSG00000048740\"\n                               \"ENSEMBL:ENSG00000173083\"\n                               \"ENSEMBL:ENSG00000196843\"\n                               \"ENSEMBL:ENSG00000126264\"\n                               \"ENSEMBL:ENSG00000137959\"\n                               \"ENSEMBL:ENSG00000269821\"\n                               \"ENSEMBL:ENSG00000083807\"\n                               \"ENSEMBL:ENSG00000167114\"\n                               \"ENSEMBL:ENSG00000129465\"\n                               \"ENSEMBL:ENSG00000136110\"\n                               \"ENSEMBL:ENSG00000256525\"\n                               \"ENSEMBL:ENSG00000142082\"\n                               \"ENSEMBL:ENSG00000096717\"\n                               \"ENSEMBL:ENSG00000136859\"\n                               \"ENSEMBL:ENSG00000172828\"\n                               \"ENSEMBL:ENSG00000123415\"\n                               \"ENSEMBL:ENSG00000025800\"\n                               \"ENSEMBL:ENSG00000154589\"\n                               \"ENSEMBL:ENSG00000177663\"\n                               \"ENSEMBL:ENSG00000034677\"\n                               \"ENSEMBL:ENSG00000196141\"\n                               \"ENSEMBL:ENSG00000004142\"\n                               \"ENSEMBL:ENSG00000113249\"\n                               \"ENSEMBL:ENSG00000007952\"\n                               \"ENSEMBL:ENSG00000086232\"\n                               \"ENSEMBL:ENSG00000138744\"\n                               \"ENSEMBL:ENSG00000163106\"\n                               \"ENSEMBL:ENSG00000138375\"\n                               \"ENSEMBL:ENSG00000086991\"\n                               \"ENSEMBL:ENSG00000219430\"\n                               \"ENSEMBL:ENSG00000138303\"\n                               \"ENSEMBL:ENSG00000126524\"\n                               \"ENSEMBL:ENSG00000167772\"\n                               \"ENSEMBL:ENSG00000165682\"\n                               \"ENSEMBL:ENSG00000101916\"\n                               \"ENSEMBL:ENSG00000172458\"\n                               \"ENSEMBL:ENSG00000124731\"\n                               \"ENSEMBL:ENSG00000011426\"\n                               \"ENSEMBL:ENSG00000135766\"\n                               \"ENSEMBL:ENSG00000241635\"\n                               \"ENSEMBL:ENSG00000104835\"\n                               \"ENSEMBL:ENSG00000185480\"\n                               \"ENSEMBL:ENSG00000110075\"\n                               \"ENSEMBL:ENSG00000079691\"\n                               \"ENSEMBL:ENSG00000171109\"\n                               \"ENSEMBL:ENSG00000151849\"\n                               \"ENSEMBL:ENSG00000126970\"\n                               \"ENSEMBL:ENSG00000169241\"\n                               \"ENSEMBL:ENSG00000074842\"\n                               \"ENSEMBL:ENSG00000185115\"\n                               \"ENSEMBL:ENSG00000136688\"\n                               \"ENSEMBL:ENSG00000115350\"\n                               \"ENSEMBL:ENSG00000111666\"\n                               \"ENSEMBL:ENSG00000198074\"\n                               \"ENSEMBL:ENSG00000283122\"\n                               \"ENSEMBL:ENSG00000139946\"\n                               \"ENSEMBL:ENSG00000175482\"\n                               \"ENSEMBL:ENSG00000117569\"\n                               \"ENSEMBL:ENSG00000130234\"\n                               \"ENSEMBL:ENSG00000198026\"\n                               \"ENSEMBL:ENSG00000132429\"\n                               \"ENSEMBL:ENSG00000114745\"\n                               \"ENSEMBL:ENSG00000060237\"\n                               \"ENSEMBL:ENSG00000262246\"\n                               \"ENSEMBL:ENSG00000104518\"\n                               \"ENSEMBL:ENSG00000153395\"\n                               \"ENSEMBL:ENSG00000146094\"\n                               \"ENSEMBL:ENSG00000125779\"\n                               \"ENSEMBL:ENSG00000197496\"\n                               \"ENSEMBL:ENSG00000169612\"\n                               \"ENSEMBL:ENSG00000138496\"\n                               \"ENSEMBL:ENSG00000169962\"\n                               \"ENSEMBL:ENSG00000130363\"\n                               \"ENSEMBL:ENSG00000103510\"\n                               \"ENSEMBL:ENSG00000106125\"\n                               \"ENSEMBL:ENSG00000131653\"\n                               \"ENSEMBL:ENSG00000145794\"\n                               \"ENSEMBL:ENSG00000163702\"\n                               \"ENSEMBL:ENSG00000100410\"\n                               \"ENSEMBL:ENSG00000137691\"\n                               \"ENSEMBL:ENSG00000160188\"\n                               \"ENSEMBL:ENSG00000151148\"\n                               \"ENSEMBL:ENSG00000137033\"\n                               \"ENSEMBL:ENSG00000178473\"\n                               \"ENSEMBL:ENSG00000162711\"\n                               \"ENSEMBL:ENSG00000161544\"\n                               \"ENSEMBL:ENSG00000153391\"\n                               \"ENSEMBL:ENSG00000205359\"\n                               \"ENSEMBL:ENSG00000168724\"\n                               \"ENSEMBL:ENSG00000229140\"\n                               \"ENSEMBL:ENSG00000165953\"\n                               \"ENSEMBL:ENSG00000172967\"\n                               \"ENSEMBL:ENSG00000163803\"\n                               \"ENSEMBL:ENSG00000197272\"\n                               \"ENSEMBL:ENSG00000175311\"\n                               \"ENSEMBL:ENSG00000170782\"\n                               \"ENSEMBL:ENSG00000189195\"\n                               \"ENSEMBL:ENSG00000161911\"\n                               \"ENSEMBL:ENSG00000197448\"\n                               \"ENSEMBL:ENSG00000251562\"\n                               \"ENSEMBL:ENSG00000187258\"\n                               \"ENSEMBL:ENSG00000248131\"\n                               \"ENSEMBL:ENSG00000284520\"\n                               \"ENSEMBL:ENSG00000199133\"\n                               \"ENSEMBL:ENSG00000284440\"\n                               \"ENSEMBL:ENSG00000199161\"\n                               \"ENSEMBL:ENSG00000207608\"\n                               \"ENSEMBL:ENSG00000207625\"\n                               \"ENSEMBL:ENSG00000207782\"\n                               \"ENSEMBL:ENSG00000283904\"\n                               \"ENSEMBL:ENSG00000283815\"\n                               \"ENSEMBL:ENSG00000284204\"\n                               \"ENSEMBL:ENSG00000207607\"\n                               \"ENSEMBL:ENSG00000199038\"\n                               \"ENSEMBL:ENSG00000207702\"\n                               \"ENSEMBL:ENSG00000207590\"\n                               \"ENSEMBL:ENSG00000207798\"\n                               \"ENSEMBL:ENSG00000207870\"\n                               \"ENSEMBL:ENSG00000284567\"\n                               \"ENSEMBL:ENSG00000199075\"\n                               \"ENSEMBL:ENSG00000199121\"\n                               \"ENSEMBL:ENSG00000207808\"\n                               \"ENSEMBL:ENSG00000207864\"\n                               \"ENSEMBL:ENSG00000207827\"\n                               \"ENSEMBL:ENSG00000207582\"\n                               \"ENSEMBL:ENSG00000284357\"\n                               \"ENSEMBL:ENSG00000207638\"\n                               \"ENSEMBL:ENSG00000199059\"\n                               \"ENSEMBL:ENSG00000199151\"\n                               \"ENSEMBL:ENSG00000199104\"\n                               \"ENSEMBL:ENSG00000198982\"\n                               \"ENSEMBL:ENSG00000199020\"\n                               \"ENSEMBL:ENSG00000208001\"\n                               \"ENSEMBL:ENSG00000202569\"\n                               \"ENSEMBL:ENSG00000194717\"\n                               \"ENSEMBL:ENSG00000207731\"\n                               \"ENSEMBL:ENSG00000122852\"\n                               \"ENSEMBL:ENSG00000207571\"\n                               \"ENSEMBL:ENSG00000185303\"\n                               \"ENSEMBL:ENSG00000211590\"\n                               \"ENSEMBL:ENSG00000285427\"\n                               \"ENSEMBL:ENSG00000228750\"\n                               \"ENSEMBL:ENSG00000280634\"\n                               \"ENSEMBL:ENSG00000243438\"\n                               \"ENSEMBL:ENSG00000201796\"\n                               \"ENSEMBL:ENSG00000240160\")))\n\n(define (unwrap lst)\n  (if (null? lst) lst\n      (append (car lst) (unwrap (cdr lst)))))\n\n(define (predicate e)\n  (cdr (list-ref e 4)))\n\n(define (summary-obj edge-sum)\n  (car (list-ref edge-sum 4)))\n\n(define (summary-subj edge-sum)\n  (car (list-ref edge-sum 3)))\n\n(define ((edge/db? db) e) (eq? db (car e)))\n\n(define (sort-inner-hash h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (set-count (cdr x)))))\n\n(define (sort-outer-hash h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (length (cdr x)))))\n\n(define (sort-counter h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (cdr x))))\n\n#|getting uniprots using run/graph\n(define encodes (find-predicates '(\"encodes\")))\n(define gene-curie?\n  (lambda (x)\n    (or\n     (string-prefix? x \"HGNC:\")\n     (string-prefix? x \"ENSEMBL:\")\n     (string-prefix? x \"NCBIGene:\"))))\n\n(define encodes-us (remove-duplicates (unwrap (filter (lambda (x) (not (null? x))) (set-map gene-list\n                                                                         (lambda (g) (time\n                                                                                      (define S (filter (lambda (x) (eq? (car x) 'rtx2)) (find-concepts #t (filter gene-curie? (map car (curie-synonyms/names g))))))\n                                                                                      (match-define\n                                                                                        (list name=>concepts name=>edges)\n                                                                                        (run/graph\n                                                                                         ((G S)\n                                                                                          (U #f))\n                                                                                         ((G->U encodes))\n                                                                                         (G G->U U)))\n                                                                                      (map concept->curie (hash-ref name=>concepts 'U))\n                                                                                      ))\n                                                                         )))))\n|#\n\n(define uniprot-curie?\n  (lambda (x)\n    (string-prefix? x \"UniProtKB:\")))\n\n;;Converting ENSEMBL curies to UniProtKB curies using synonymization in order to pass into count-downstream\n(define uniprots (remove-duplicates (filter uniprot-curie? (map car (unwrap (set-map gene-list curie-synonyms/names))))))\n\n#|\ntakes: list of UniProt curies (prot-list), list of GO predicates** (preds)\n** note: preds should only contain \"positively_regulates\", \"negatively_regulates\", \"subclass_of\", or any combination\n**       of those three predicates depending on what type of relationshion you want to count\n\nreturns: a list of the hash tables in this order: go-processes, go-process-members, cell-expression-hash, regulated-cell-expression-hash\n         The contents of these hashes are documented inside the function\n|#\n(define (count-downstream prot-list preds)\n  ;;maps each Uniprot curie (key) in prot-list -> a set of all GO pathways (value) that the UniProt (key) regulates\n  (define go-processes (make-hash))\n  ;;maps GO pathway curies (key) -> a set of all UniProts (value) that are members of the GO pathway (key) (not intersected with prot-list)\n  (define go-process-members (make-hash))\n  ;;maps each Uniprot in prot-list (key) -> a set of cell/tissue types (value) they're expressed in\n  (define cell-expression-hash (make-hash))\n  ;;maps each regulated gene (key) found from the 2-hop query -> a set of cell/tissue types (value) they're expressed in\n  (define regulated-genes-cell-expression-hash (make-hash))\n  (define involved_in (keep 1 (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"involved_in\")))))\n  (define regulators (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates preds)))\n  (define expressed_in (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"expressed_in\"))))\n  (for-each\n   (lambda (u)\n     (define S (filter (lambda (x) (equal? (car x) 'rtx2)) (find-concepts #t (list u))))\n     ;;G->M->X 1.1 + 1.3\n     ;;G->C - 1.2\n     ;;rG->X - 1.4\n     ;;rG->rC - 1.5\n     (unless (empty? S)\n       (match-define\n         (list name=>concepts name=>edges)\n         (time (run/graph\n                ((G S)\n                 (M #f)\n                 (X #f)\n                 (C #f)\n                 (rG #f)\n                 (rC #f))\n                ((G->M involved_in)\n                 (G->C expressed_in)\n                 (M->X regulators)\n                 (rG->X involved_in)\n                 (rG->rC expressed_in))\n                (G G->M M)\n                (G G->C C)\n                (M M->X X)\n                (rG rG->X X)\n                (rG rG->rC rC))))\n       ;;go-processes (k=>v): G=>X\n       (hash-set! go-processes u (list->set (map concept->curie (hash-ref name=>concepts 'X))))\n       ;;cell-expression-hash (k=>v): G=>C\n       (hash-set! cell-expression-hash u (list->set (filter (lambda (x) (string-prefix? x \"UBERON:\")) (map concept->curie (hash-ref name=>concepts 'C)))))\n       ;;regulated-genes-cell-expression-hash (k=>v): rG=>rC\n       (for-each\n        (lambda (e)\n          (unless (not (string-prefix? (concept->curie (edge->object e)) \"UBERON:\"))\n            (hash-update! regulated-genes-cell-expression-hash (concept->curie (edge->subject e)) (lambda (v) (set-add v (concept->curie (edge->object e)))) (set))\n            )\n          )\n        (hash-ref name=>edges 'rG->rC)\n        )\n       ;;go-process-members (k=>v): X=>rG\n       (for-each\n        (lambda (e)\n          (unless (set-member? S (concept->curie (edge->subject e)))\n            (hash-update! go-process-members (concept->curie (edge->object e)) (lambda (v) (set-add v (concept->curie (edge->subject e)))) (set))\n            )\n          )\n        (hash-ref name=>edges 'rG->X)\n        )\n       )\n     )\n   prot-list\n   )\n  (list go-processes go-process-members cell-expression-hash regulated-genes-cell-expression-hash)\n  )\n#|Examples\n(define ards-pos-reg (count-downstream uniprots '(\"positively_regulates\")))\n(define ards-neg-reg (count-downstream uniprots '(\"negatively_regulates\")))\n(define ards-subclass_of (count-downstream uniprots '(\"subclass_of\")))\n(define ards-all-regulation (count-downstream uniprots '(\"positively_regulates\" \"negatively_regulates\" \"subclass_of\")))\n|#\n\n\n#|\ntakes: a list of 4 hash tables returned by the count-downstream function above\n\nManipulates the given hash tables to provide a ranked list of the genes of interest (given as argument prot-list in count-downstream function) by the number of\nother genes they regulate within each cell/tissue type thet they're expressed in. Also gives a ranked list of the cell/tissue types by the number of the genes\nof interest that are expressed in them. This is to make finding possible cells/tissues of interest easier.\n\nreturns: A list of 2 assoc lists - overview of the structure: (list\n                                                                (list (C' . int)\n                                                                      (C\" . int)\n                                                                        ...\n                                                                  )\n                                                                (list (C' (G . (set rG's))\n                                                                          (G . (set rG's))\n                                                                           ...\n                                                                        )\n                                                                      (C\" (G . (set rG's))\n                                                                          (G . (set rG's))\n                                                                           ...\n                                                                        )\n                                                                       ...\n                                                                  )\n                                                                )\nThe first assoc list (key . value): the key is the cell/tissue type (C), the value is (int) the number of genes of interest that are expressed in that\n                                    cell/tissue type. The first assoc is sorted from highest to lowest int\nThe second assoc list (key . (key . value)): the first key is the cell/tissue type (C), the value is another assoc list where the keys are the genes of interest (G)\n  (a nested assoc list)                      expressed in the cell/tissue type (C) and the values are sets of other genes (rG) that are expressed in the cell/tissue type (C)\n                                             AND regulated by the gene of interest (G)\n                                             The inner assoc list is sorted (high->low) by the number of regulated genes (rG). The outer assoc list is given in the same order as\n                                             the first assoc list above.\n|#\n(define (count-by-cell-expressed-in count-downstream-results)\n  (define G=>X (list-ref count-downstream-results 0))\n  (define X=>rG (list-ref count-downstream-results 1))\n  (define G=>C (list-ref count-downstream-results 2))\n  (define rG=>rC (list-ref count-downstream-results 3))\n  (define cell-expression-ranks (make-hash))\n  (define counter (make-hash))\n  ;;populate cell-expression-ranks\n  (hash-for-each\n   G=>X\n   (lambda (G X)\n     (set-for-each\n      X\n      (lambda (x)\n        (set-for-each\n         (set-intersect (hash-ref X=>rG x (set)) (list->set uniprots));;filters for just ARDS genes, remove set-intersect for no filter\n         (lambda (rg)\n           (set-for-each\n            (set-intersect (hash-ref G=>C G (set)) (hash-ref rG=>rC rg (set)))\n            (lambda (c)\n              (hash-update! cell-expression-ranks c\n                            (lambda (h)\n                              (hash-update! h G (lambda (v) (set-add v rg)) (set))\n                              h\n                              )\n                            (make-hash)\n                            )\n              )\n            )\n           )\n         )\n        )\n      )\n     )\n   )\n  (hash-for-each cell-expression-ranks\n                 (lambda (k v)\n                   (hash-set! cell-expression-ranks k (sort-inner-hash v))\n                   (hash-set! counter k (hash-count v))\n                   )\n                 )\n  (list (sort-counter counter) (sort-outer-hash cell-expression-ranks))\n  )\n#|Examples\n(define ards-cell-type-count (count-by-cell-expressed-in ards-pos-reg))\n\n(car ards-cell-type-count) ;;gives the ranked count of the number of genes expressed in each cell type\n(cadr ards-cell-type-count) ;;gives the second (more meaningful) assoc list\n\n;;To get the ranked assoc list of regulating genes for the liver (\"UBERON:0002107\")\n(define liver-genes (cdr (assoc \"UBERON:0002107\" (cadr ards-cell-type-count))))\n;;for the lung (\"UBERON:0002048\")\n(define lung-genes (cdr (assoc \"UBERON:0002048\" (cadr ards-cell-type-count))))\n|#\n\n#|\n(make-hash 'ARDS-Genelist\n           (make-hash 'Gene1-ARDS\n                      (make-hash 'Gene1-UBERON-cell-location\n                                 (make-hash 'pos-reg-GO1\n                                            (make-hash 'GO1\n                                                       (make-hash 'GO1-members\n                                                                  (make-hash 'GO1-member-UBERON-Cell-locations\n                                                                             (make-hash 'GO1-ARDS-members)\n                                                                             )))))))\n|#"
  },
  {
    "path": "contrib/medikanren/pieces-parts/trace-pathways-mjp.rkt",
    "content": "#lang racket\n(require \"../../../medikanren/pieces-parts/query.rkt\")\n\n(define gene-list (list->set '(\"ENSEMBL:ENSG00000167972\"\n                               \"ENSEMBL:ENSG00000198691\"\n                               \"ENSEMBL:ENSG00000175164\"\n                               \"ENSEMBL:ENSG00000278540\"\n                               \"ENSEMBL:ENSG00000100412\"\n                               \"ENSEMBL:ENSG00000162104\"\n                               \"ENSEMBL:ENSG00000204305\"\n                               \"ENSEMBL:ENSG00000135744\"\n                               \"ENSEMBL:ENSG00000144891\"\n                               \"ENSEMBL:ENSG00000180772\"\n                               \"ENSEMBL:ENSG00000142208\"\n                               \"ENSEMBL:ENSG00000148218\"\n                               \"ENSEMBL:ENSG00000163631\"\n                               \"ENSEMBL:ENSG00000085662\"\n                               \"ENSEMBL:ENSG00000154188\"\n                               \"ENSEMBL:ENSG00000091879\"\n                               \"ENSEMBL:ENSG00000182718\"\n                               \"ENSEMBL:ENSG00000134982\"\n                               \"ENSEMBL:ENSG00000132703\"\n                               \"ENSEMBL:ENSG00000023445\"\n                               \"ENSEMBL:ENSG00000142515\"\n                               \"ENSEMBL:ENSG00000026103\"\n                               \"ENSEMBL:ENSG00000117560\"\n                               \"ENSEMBL:ENSG00000240583\"\n                               \"ENSEMBL:ENSG00000161798\"\n                               \"ENSEMBL:ENSG00000006756\"\n                               \"ENSEMBL:ENSG00000117601\"\n                               \"ENSEMBL:ENSG00000149311\"\n                               \"ENSEMBL:ENSG00000164904\"\n                               \"ENSEMBL:ENSG00000171791\"\n                               \"ENSEMBL:ENSG00000101144\"\n                               \"ENSEMBL:ENSG00000010671\"\n                               \"ENSEMBL:ENSG00000100300\"\n                               \"ENSEMBL:ENSG00000149131\"\n                               \"ENSEMBL:ENSG00000171860\"\n                               \"ENSEMBL:ENSG00000106804\"\n                               \"ENSEMBL:ENSG00000197405\"\n                               \"ENSEMBL:ENSG00000149823\"\n                               \"ENSEMBL:ENSG00000063180\"\n                               \"ENSEMBL:ENSG00000164305\"\n                               \"ENSEMBL:ENSG00000121691\"\n                               \"ENSEMBL:ENSG00000105974\"\n                               \"ENSEMBL:ENSG00000124813\"\n                               \"ENSEMBL:ENSG00000149257\"\n                               \"ENSEMBL:ENSG00000134057\"\n                               \"ENSEMBL:ENSG00000170458\"\n                               \"ENSEMBL:ENSG00000121594\"\n                               \"ENSEMBL:ENSG00000101017\"\n                               \"ENSEMBL:ENSG00000102245\"\n                               \"ENSEMBL:ENSG00000026508\"\n                               \"ENSEMBL:ENSG00000085063\"\n                               \"ENSEMBL:ENSG00000129226\"\n                               \"ENSEMBL:ENSG00000179776\"\n                               \"ENSEMBL:ENSG00000100526\"\n                               \"ENSEMBL:ENSG00000170835\"\n                               \"ENSEMBL:ENSG00000001626\"\n                               \"ENSEMBL:ENSG00000133019\"\n                               \"ENSEMBL:ENSG00000196811\"\n                               \"ENSEMBL:ENSG00000099622\"\n                               \"ENSEMBL:ENSG00000122705\"\n                               \"ENSEMBL:ENSG00000183813\"\n                               \"ENSEMBL:ENSG00000188153\"\n                               \"ENSEMBL:ENSG00000115966\"\n                               \"ENSEMBL:ENSG00000167193\"\n                               \"ENSEMBL:ENSG00000132693\"\n                               \"ENSEMBL:ENSG00000118231\"\n                               \"ENSEMBL:ENSG00000112062\"\n                               \"ENSEMBL:ENSG00000101439\"\n                               \"ENSEMBL:ENSG00000118523\"\n                               \"ENSEMBL:ENSG00000168036\"\n                               \"ENSEMBL:ENSG00000100448\"\n                               \"ENSEMBL:ENSG00000166347\"\n                               \"ENSEMBL:ENSG00000140465\"\n                               \"ENSEMBL:ENSG00000140505\"\n                               \"ENSEMBL:ENSG00000138061\"\n                               \"ENSEMBL:ENSG00000160870\"\n                               \"ENSEMBL:ENSG00000106258\"\n                               \"ENSEMBL:ENSG00000196730\"\n                               \"ENSEMBL:ENSG00000011465\"\n                               \"ENSEMBL:ENSG00000159640\"\n                               \"ENSEMBL:ENSG00000164825\"\n                               \"ENSEMBL:ENSG00000197766\"\n                               \"ENSEMBL:ENSG00000181019\"\n                               \"ENSEMBL:ENSG00000213918\"\n                               \"ENSEMBL:ENSG00000197635\"\n                               \"ENSEMBL:ENSG00000164330\"\n                               \"ENSEMBL:ENSG00000213694\"\n                               \"ENSEMBL:ENSG00000078401\"\n                               \"ENSEMBL:ENSG00000138798\"\n                               \"ENSEMBL:ENSG00000197561\"\n                               \"ENSEMBL:ENSG00000021355\"\n                               \"ENSEMBL:ENSG00000066044\"\n                               \"ENSEMBL:ENSG00000116016\"\n                               \"ENSEMBL:ENSG00000133216\"\n                               \"ENSEMBL:ENSG00000120915\"\n                               \"ENSEMBL:ENSG00000130427\"\n                               \"ENSEMBL:ENSG00000157554\"\n                               \"ENSEMBL:ENSG00000157557\"\n                               \"ENSEMBL:ENSG00000180210\"\n                               \"ENSEMBL:ENSG00000117525\"\n                               \"ENSEMBL:ENSG00000198734\"\n                               \"ENSEMBL:ENSG00000117480\"\n                               \"ENSEMBL:ENSG00000166147\"\n                               \"ENSEMBL:ENSG00000151422\"\n                               \"ENSEMBL:ENSG00000140285\"\n                               \"ENSEMBL:ENSG00000160867\"\n                               \"ENSEMBL:ENSG00000111206\"\n                               \"ENSEMBL:ENSG00000115414\"\n                               \"ENSEMBL:ENSG00000170345\"\n                               \"ENSEMBL:ENSG00000154727\"\n                               \"ENSEMBL:ENSG00000163288\"\n                               \"ENSEMBL:ENSG00000128683\"\n                               \"ENSEMBL:ENSG00000141448\"\n                               \"ENSEMBL:ENSG00000168621\"\n                               \"ENSEMBL:ENSG00000134812\"\n                               \"ENSEMBL:ENSG00000265107\"\n                               \"ENSEMBL:ENSG00000173221\"\n                               \"ENSEMBL:ENSG00000147437\"\n                               \"ENSEMBL:ENSG00000186810\"\n                               \"ENSEMBL:ENSG00000167701\"\n                               \"ENSEMBL:ENSG00000113580\"\n                               \"ENSEMBL:ENSG00000082701\"\n                               \"ENSEMBL:ENSG00000132518\"\n                               \"ENSEMBL:ENSG00000145649\"\n                               \"ENSEMBL:ENSG00000100453\"\n                               \"ENSEMBL:ENSG00000148702\"\n                               \"ENSEMBL:ENSG00000084754\"\n                               \"ENSEMBL:ENSG00000019991\"\n                               \"ENSEMBL:ENSG00000100644\"\n                               \"ENSEMBL:ENSG00000189403\"\n                               \"ENSEMBL:ENSG00000100292\"\n                               \"ENSEMBL:ENSG00000125798\"\n                               \"ENSEMBL:ENSG00000135486\"\n                               \"ENSEMBL:ENSG00000257017\"\n                               \"ENSEMBL:ENSG00000113905\"\n                               \"ENSEMBL:ENSG00000176387\"\n                               \"ENSEMBL:ENSG00000204389\"\n                               \"ENSEMBL:ENSG00000204388\"\n                               \"ENSEMBL:ENSG00000170606\"\n                               \"ENSEMBL:ENSG00000070614\"\n                               \"ENSEMBL:ENSG00000041982\"\n                               \"ENSEMBL:ENSG00000090339\"\n                               \"ENSEMBL:ENSG00000185745\"\n                               \"ENSEMBL:ENSG00000171855\"\n                               \"ENSEMBL:ENSG00000111537\"\n                               \"ENSEMBL:ENSG00000006652\"\n                               \"ENSEMBL:ENSG00000017427\"\n                               \"ENSEMBL:ENSG00000146674\"\n                               \"ENSEMBL:ENSG00000167779\"\n                               \"ENSEMBL:ENSG00000104365\"\n                               \"ENSEMBL:ENSG00000115008\"\n                               \"ENSEMBL:ENSG00000125538\"\n                               \"ENSEMBL:ENSG00000115594\"\n                               \"ENSEMBL:ENSG00000136689\"\n                               \"ENSEMBL:ENSG00000109471\"\n                               \"ENSEMBL:ENSG00000134460\"\n                               \"ENSEMBL:ENSG00000113520\"\n                               \"ENSEMBL:ENSG00000136244\"\n                               \"ENSEMBL:ENSG00000168685\"\n                               \"ENSEMBL:ENSG00000169429\"\n                               \"ENSEMBL:ENSG00000136634\"\n                               \"ENSEMBL:ENSG00000169194\"\n                               \"ENSEMBL:ENSG00000112115\"\n                               \"ENSEMBL:ENSG00000150782\"\n                               \"ENSEMBL:ENSG00000169245\"\n                               \"ENSEMBL:ENSG00000125347\"\n                               \"ENSEMBL:ENSG00000005884\"\n                               \"ENSEMBL:ENSG00000169896\"\n                               \"ENSEMBL:ENSG00000160255\"\n                               \"ENSEMBL:ENSG00000115474\"\n                               \"ENSEMBL:ENSG00000128052\"\n                               \"ENSEMBL:ENSG00000171345\"\n                               \"ENSEMBL:ENSG00000172037\"\n                               \"ENSEMBL:ENSG00000148346\"\n                               \"ENSEMBL:ENSG00000115850\"\n                               \"ENSEMBL:ENSG00000131981\"\n                               \"ENSEMBL:ENSG00000138039\"\n                               \"ENSEMBL:ENSG00000105370\"\n                               \"ENSEMBL:ENSG00000226979\"\n                               \"ENSEMBL:ENSG00000160932\"\n                               \"ENSEMBL:ENSG00000183918\"\n                               \"ENSEMBL:ENSG00000277443\"\n                               \"ENSEMBL:ENSG00000166949\"\n                               \"ENSEMBL:ENSG00000165471\"\n                               \"ENSEMBL:ENSG00000143384\"\n                               \"ENSEMBL:ENSG00000014641\"\n                               \"ENSEMBL:ENSG00000110492\"\n                               \"ENSEMBL:ENSG00000095015\"\n                               \"ENSEMBL:ENSG00000240972\"\n                               \"ENSEMBL:ENSG00000138755\"\n                               \"ENSEMBL:ENSG00000087245\"\n                               \"ENSEMBL:ENSG00000149968\"\n                               \"ENSEMBL:ENSG00000100985\"\n                               \"ENSEMBL:ENSG00000005381\"\n                               \"ENSEMBL:ENSG00000130830\"\n                               \"ENSEMBL:ENSG00000125148\"\n                               \"ENSEMBL:ENSG00000087250\"\n                               \"ENSEMBL:ENSG00000171100\"\n                               \"ENSEMBL:ENSG00000210195\"\n                               \"ENSEMBL:ENSG00000185499\"\n                               \"ENSEMBL:ENSG00000215182\"\n                               \"ENSEMBL:ENSG00000136997\"\n                               \"ENSEMBL:ENSG00000172936\"\n                               \"ENSEMBL:ENSG00000109063\"\n                               \"ENSEMBL:ENSG00000065534\"\n                               \"ENSEMBL:ENSG00000116044\"\n                               \"ENSEMBL:ENSG00000109320\"\n                               \"ENSEMBL:ENSG00000100906\"\n                               \"ENSEMBL:ENSG00000001167\"\n                               \"ENSEMBL:ENSG00000089250\"\n                               \"ENSEMBL:ENSG00000164867\"\n                               \"ENSEMBL:ENSG00000161270\"\n                               \"ENSEMBL:ENSG00000135318\"\n                               \"ENSEMBL:ENSG00000111331\"\n                               \"ENSEMBL:ENSG00000112038\"\n                               \"ENSEMBL:ENSG00000089041\"\n                               \"ENSEMBL:ENSG00000185624\"\n                               \"ENSEMBL:ENSG00000007168\"\n                               \"ENSEMBL:ENSG00000117450\"\n                               \"ENSEMBL:ENSG00000106366\"\n                               \"ENSEMBL:ENSG00000126759\"\n                               \"ENSEMBL:ENSG00000197249\"\n                               \"ENSEMBL:ENSG00000124102\"\n                               \"ENSEMBL:ENSG00000121879\"\n                               \"ENSEMBL:ENSG00000051382\"\n                               \"ENSEMBL:ENSG00000171608\"\n                               \"ENSEMBL:ENSG00000105851\"\n                               \"ENSEMBL:ENSG00000170890\"\n                               \"ENSEMBL:ENSG00000188257\"\n                               \"ENSEMBL:ENSG00000116711\"\n                               \"ENSEMBL:ENSG00000118495\"\n                               \"ENSEMBL:ENSG00000011422\"\n                               \"ENSEMBL:ENSG00000115896\"\n                               \"ENSEMBL:ENSG00000075651\"\n                               \"ENSEMBL:ENSG00000178209\"\n                               \"ENSEMBL:ENSG00000266964\"\n                               \"ENSEMBL:ENSG00000115138\"\n                               \"ENSEMBL:ENSG00000186951\"\n                               \"ENSEMBL:ENSG00000122862\"\n                               \"ENSEMBL:ENSG00000100030\"\n                               \"ENSEMBL:ENSG00000107643\"\n                               \"ENSEMBL:ENSG00000169032\"\n                               \"ENSEMBL:ENSG00000115718\"\n                               \"ENSEMBL:ENSG00000184500\"\n                               \"ENSEMBL:ENSG00000189002\"\n                               \"ENSEMBL:ENSG00000135406\"\n                               \"ENSEMBL:ENSG00000041357\"\n                               \"ENSEMBL:ENSG00000197170\"\n                               \"ENSEMBL:ENSG00000011304\"\n                               \"ENSEMBL:ENSG00000073756\"\n                               \"ENSEMBL:ENSG00000169398\"\n                               \"ENSEMBL:ENSG00000105894\"\n                               \"ENSEMBL:ENSG00000081237\"\n                               \"ENSEMBL:ENSG00000113456\"\n                               \"ENSEMBL:ENSG00000069974\"\n                               \"ENSEMBL:ENSG00000080823\"\n                               \"ENSEMBL:ENSG00000112619\"\n                               \"ENSEMBL:ENSG00000173039\"\n                               \"ENSEMBL:ENSG00000143839\"\n                               \"ENSEMBL:ENSG00000102032\"\n                               \"ENSEMBL:ENSG00000163914\"\n                               \"ENSEMBL:ENSG00000067900\"\n                               \"ENSEMBL:ENSG00000149489\"\n                               \"ENSEMBL:ENSG00000196218\"\n                               \"ENSEMBL:ENSG00000196154\"\n                               \"ENSEMBL:ENSG00000163220\"\n                               \"ENSEMBL:ENSG00000031698\"\n                               \"ENSEMBL:ENSG00000111319\"\n                               \"ENSEMBL:ENSG00000108691\"\n                               \"ENSEMBL:ENSG00000108688\"\n                               \"ENSEMBL:ENSG00000163735\"\n                               \"ENSEMBL:ENSG00000110876\"\n                               \"ENSEMBL:ENSG00000168878\"\n                               \"ENSEMBL:ENSG00000168484\"\n                               \"ENSEMBL:ENSG00000133661\"\n                               \"ENSEMBL:ENSG00000064651\"\n                               \"ENSEMBL:ENSG00000197208\"\n                               \"ENSEMBL:ENSG00000166311\"\n                               \"ENSEMBL:ENSG00000075618\"\n                               \"ENSEMBL:ENSG00000125835\"\n                               \"ENSEMBL:ENSG00000142168\"\n                               \"ENSEMBL:ENSG00000112096\"\n                               \"ENSEMBL:ENSG00000109610\"\n                               \"ENSEMBL:ENSG00000125398\"\n                               \"ENSEMBL:ENSG00000100883\"\n                               \"ENSEMBL:ENSG00000168610\"\n                               \"ENSEMBL:ENSG00000126561\"\n                               \"ENSEMBL:ENSG00000173757\"\n                               \"ENSEMBL:ENSG00000087586\"\n                               \"ENSEMBL:ENSG00000067715\"\n                               \"ENSEMBL:ENSG00000231925\"\n                               \"ENSEMBL:ENSG00000006638\"\n                               \"ENSEMBL:ENSG00000118526\"\n                               \"ENSEMBL:ENSG00000120156\"\n                               \"ENSEMBL:ENSG00000164362\"\n                               \"ENSEMBL:ENSG00000003436\"\n                               \"ENSEMBL:ENSG00000105329\"\n                               \"ENSEMBL:ENSG00000198959\"\n                               \"ENSEMBL:ENSG00000178726\"\n                               \"ENSEMBL:ENSG00000116001\"\n                               \"ENSEMBL:ENSG00000102265\"\n                               \"ENSEMBL:ENSG00000136352\"\n                               \"ENSEMBL:ENSG00000137462\"\n                               \"ENSEMBL:ENSG00000164342\"\n                               \"ENSEMBL:ENSG00000136869\"\n                               \"ENSEMBL:ENSG00000127324\"\n                               \"ENSEMBL:ENSG00000149809\"\n                               \"ENSEMBL:ENSG00000232810\"\n                               \"ENSEMBL:ENSG00000118503\"\n                               \"ENSEMBL:ENSG00000067182\"\n                               \"ENSEMBL:ENSG00000118194\"\n                               \"ENSEMBL:ENSG00000131747\"\n                               \"ENSEMBL:ENSG00000111669\"\n                               \"ENSEMBL:ENSG00000128311\"\n                               \"ENSEMBL:ENSG00000125482\"\n                               \"ENSEMBL:ENSG00000155657\"\n                               \"ENSEMBL:ENSG00000136810\"\n                               \"ENSEMBL:ENSG00000198431\"\n                               \"ENSEMBL:ENSG00000149021\"\n                               \"ENSEMBL:ENSG00000174607\"\n                               \"ENSEMBL:ENSG00000111424\"\n                               \"ENSEMBL:ENSG00000112715\"\n                               \"ENSEMBL:ENSG00000146469\"\n                               \"ENSEMBL:ENSG00000110799\"\n                               \"ENSEMBL:ENSG00000158125\"\n                               \"ENSEMBL:ENSG00000164924\"\n                               \"ENSEMBL:ENSG00000121966\"\n                               \"ENSEMBL:ENSG00000146070\"\n                               \"ENSEMBL:ENSG00000106305\"\n                               \"ENSEMBL:ENSG00000050327\"\n                               \"ENSEMBL:ENSG00000083168\"\n                               \"ENSEMBL:ENSG00000118972\"\n                               \"ENSEMBL:ENSG00000206561\"\n                               \"ENSEMBL:ENSG00000184381\"\n                               \"ENSEMBL:ENSG00000069764\"\n                               \"ENSEMBL:ENSG00000108528\"\n                               \"ENSEMBL:ENSG00000117461\"\n                               \"ENSEMBL:ENSG00000134107\"\n                               \"ENSEMBL:ENSG00000136908\"\n                               \"ENSEMBL:ENSG00000171720\"\n                               \"ENSEMBL:ENSG00000176170\"\n                               \"ENSEMBL:ENSG00000111602\"\n                               \"ENSEMBL:ENSG00000173805\"\n                               \"ENSEMBL:ENSG00000131023\"\n                               \"ENSEMBL:ENSG00000157456\"\n                               \"ENSEMBL:ENSG00000162889\"\n                               \"ENSEMBL:ENSG00000103671\"\n                               \"ENSEMBL:ENSG00000133116\"\n                               \"ENSEMBL:ENSG00000181092\"\n                               \"ENSEMBL:ENSG00000100351\"\n                               \"ENSEMBL:ENSG00000136156\"\n                               \"ENSEMBL:ENSG00000102230\"\n                               \"ENSEMBL:ENSG00000057663\"\n                               \"ENSEMBL:ENSG00000134318\"\n                               \"ENSEMBL:ENSG00000117592\"\n                               \"ENSEMBL:ENSG00000187608\"\n                               \"ENSEMBL:ENSG00000103335\"\n                               \"ENSEMBL:ENSG00000165733\"\n                               \"ENSEMBL:ENSG00000079999\"\n                               \"ENSEMBL:ENSG00000044090\"\n                               \"ENSEMBL:ENSG00000117020\"\n                               \"ENSEMBL:ENSG00000105835\"\n                               \"ENSEMBL:ENSG00000105246\"\n                               \"ENSEMBL:ENSG00000131477\"\n                               \"ENSEMBL:ENSG00000127528\"\n                               \"ENSEMBL:ENSG00000167315\"\n                               \"ENSEMBL:ENSG00000140092\"\n                               \"ENSEMBL:ENSG00000101000\"\n                               \"ENSEMBL:ENSG00000100591\"\n                               \"ENSEMBL:ENSG00000160999\"\n                               \"ENSEMBL:ENSG00000162493\"\n                               \"ENSEMBL:ENSG00000048740\"\n                               \"ENSEMBL:ENSG00000173083\"\n                               \"ENSEMBL:ENSG00000196843\"\n                               \"ENSEMBL:ENSG00000126264\"\n                               \"ENSEMBL:ENSG00000137959\"\n                               \"ENSEMBL:ENSG00000269821\"\n                               \"ENSEMBL:ENSG00000083807\"\n                               \"ENSEMBL:ENSG00000167114\"\n                               \"ENSEMBL:ENSG00000129465\"\n                               \"ENSEMBL:ENSG00000136110\"\n                               \"ENSEMBL:ENSG00000256525\"\n                               \"ENSEMBL:ENSG00000142082\"\n                               \"ENSEMBL:ENSG00000096717\"\n                               \"ENSEMBL:ENSG00000136859\"\n                               \"ENSEMBL:ENSG00000172828\"\n                               \"ENSEMBL:ENSG00000123415\"\n                               \"ENSEMBL:ENSG00000025800\"\n                               \"ENSEMBL:ENSG00000154589\"\n                               \"ENSEMBL:ENSG00000177663\"\n                               \"ENSEMBL:ENSG00000034677\"\n                               \"ENSEMBL:ENSG00000196141\"\n                               \"ENSEMBL:ENSG00000004142\"\n                               \"ENSEMBL:ENSG00000113249\"\n                               \"ENSEMBL:ENSG00000007952\"\n                               \"ENSEMBL:ENSG00000086232\"\n                               \"ENSEMBL:ENSG00000138744\"\n                               \"ENSEMBL:ENSG00000163106\"\n                               \"ENSEMBL:ENSG00000138375\"\n                               \"ENSEMBL:ENSG00000086991\"\n                               \"ENSEMBL:ENSG00000219430\"\n                               \"ENSEMBL:ENSG00000138303\"\n                               \"ENSEMBL:ENSG00000126524\"\n                               \"ENSEMBL:ENSG00000167772\"\n                               \"ENSEMBL:ENSG00000165682\"\n                               \"ENSEMBL:ENSG00000101916\"\n                               \"ENSEMBL:ENSG00000172458\"\n                               \"ENSEMBL:ENSG00000124731\"\n                               \"ENSEMBL:ENSG00000011426\"\n                               \"ENSEMBL:ENSG00000135766\"\n                               \"ENSEMBL:ENSG00000241635\"\n                               \"ENSEMBL:ENSG00000104835\"\n                               \"ENSEMBL:ENSG00000185480\"\n                               \"ENSEMBL:ENSG00000110075\"\n                               \"ENSEMBL:ENSG00000079691\"\n                               \"ENSEMBL:ENSG00000171109\"\n                               \"ENSEMBL:ENSG00000151849\"\n                               \"ENSEMBL:ENSG00000126970\"\n                               \"ENSEMBL:ENSG00000169241\"\n                               \"ENSEMBL:ENSG00000074842\"\n                               \"ENSEMBL:ENSG00000185115\"\n                               \"ENSEMBL:ENSG00000136688\"\n                               \"ENSEMBL:ENSG00000115350\"\n                               \"ENSEMBL:ENSG00000111666\"\n                               \"ENSEMBL:ENSG00000198074\"\n                               \"ENSEMBL:ENSG00000283122\"\n                               \"ENSEMBL:ENSG00000139946\"\n                               \"ENSEMBL:ENSG00000175482\"\n                               \"ENSEMBL:ENSG00000117569\"\n                               \"ENSEMBL:ENSG00000130234\"\n                               \"ENSEMBL:ENSG00000198026\"\n                               \"ENSEMBL:ENSG00000132429\"\n                               \"ENSEMBL:ENSG00000114745\"\n                               \"ENSEMBL:ENSG00000060237\"\n                               \"ENSEMBL:ENSG00000262246\"\n                               \"ENSEMBL:ENSG00000104518\"\n                               \"ENSEMBL:ENSG00000153395\"\n                               \"ENSEMBL:ENSG00000146094\"\n                               \"ENSEMBL:ENSG00000125779\"\n                               \"ENSEMBL:ENSG00000197496\"\n                               \"ENSEMBL:ENSG00000169612\"\n                               \"ENSEMBL:ENSG00000138496\"\n                               \"ENSEMBL:ENSG00000169962\"\n                               \"ENSEMBL:ENSG00000130363\"\n                               \"ENSEMBL:ENSG00000103510\"\n                               \"ENSEMBL:ENSG00000106125\"\n                               \"ENSEMBL:ENSG00000131653\"\n                               \"ENSEMBL:ENSG00000145794\"\n                               \"ENSEMBL:ENSG00000163702\"\n                               \"ENSEMBL:ENSG00000100410\"\n                               \"ENSEMBL:ENSG00000137691\"\n                               \"ENSEMBL:ENSG00000160188\"\n                               \"ENSEMBL:ENSG00000151148\"\n                               \"ENSEMBL:ENSG00000137033\"\n                               \"ENSEMBL:ENSG00000178473\"\n                               \"ENSEMBL:ENSG00000162711\"\n                               \"ENSEMBL:ENSG00000161544\"\n                               \"ENSEMBL:ENSG00000153391\"\n                               \"ENSEMBL:ENSG00000205359\"\n                               \"ENSEMBL:ENSG00000168724\"\n                               \"ENSEMBL:ENSG00000229140\"\n                               \"ENSEMBL:ENSG00000165953\"\n                               \"ENSEMBL:ENSG00000172967\"\n                               \"ENSEMBL:ENSG00000163803\"\n                               \"ENSEMBL:ENSG00000197272\"\n                               \"ENSEMBL:ENSG00000175311\"\n                               \"ENSEMBL:ENSG00000170782\"\n                               \"ENSEMBL:ENSG00000189195\"\n                               \"ENSEMBL:ENSG00000161911\"\n                               \"ENSEMBL:ENSG00000197448\"\n                               \"ENSEMBL:ENSG00000251562\"\n                               \"ENSEMBL:ENSG00000187258\"\n                               \"ENSEMBL:ENSG00000248131\"\n                               \"ENSEMBL:ENSG00000284520\"\n                               \"ENSEMBL:ENSG00000199133\"\n                               \"ENSEMBL:ENSG00000284440\"\n                               \"ENSEMBL:ENSG00000199161\"\n                               \"ENSEMBL:ENSG00000207608\"\n                               \"ENSEMBL:ENSG00000207625\"\n                               \"ENSEMBL:ENSG00000207782\"\n                               \"ENSEMBL:ENSG00000283904\"\n                               \"ENSEMBL:ENSG00000283815\"\n                               \"ENSEMBL:ENSG00000284204\"\n                               \"ENSEMBL:ENSG00000207607\"\n                               \"ENSEMBL:ENSG00000199038\"\n                               \"ENSEMBL:ENSG00000207702\"\n                               \"ENSEMBL:ENSG00000207590\"\n                               \"ENSEMBL:ENSG00000207798\"\n                               \"ENSEMBL:ENSG00000207870\"\n                               \"ENSEMBL:ENSG00000284567\"\n                               \"ENSEMBL:ENSG00000199075\"\n                               \"ENSEMBL:ENSG00000199121\"\n                               \"ENSEMBL:ENSG00000207808\"\n                               \"ENSEMBL:ENSG00000207864\"\n                               \"ENSEMBL:ENSG00000207827\"\n                               \"ENSEMBL:ENSG00000207582\"\n                               \"ENSEMBL:ENSG00000284357\"\n                               \"ENSEMBL:ENSG00000207638\"\n                               \"ENSEMBL:ENSG00000199059\"\n                               \"ENSEMBL:ENSG00000199151\"\n                               \"ENSEMBL:ENSG00000199104\"\n                               \"ENSEMBL:ENSG00000198982\"\n                               \"ENSEMBL:ENSG00000199020\"\n                               \"ENSEMBL:ENSG00000208001\"\n                               \"ENSEMBL:ENSG00000202569\"\n                               \"ENSEMBL:ENSG00000194717\"\n                               \"ENSEMBL:ENSG00000207731\"\n                               \"ENSEMBL:ENSG00000122852\"\n                               \"ENSEMBL:ENSG00000207571\"\n                               \"ENSEMBL:ENSG00000185303\"\n                               \"ENSEMBL:ENSG00000211590\"\n                               \"ENSEMBL:ENSG00000285427\"\n                               \"ENSEMBL:ENSG00000228750\"\n                               \"ENSEMBL:ENSG00000280634\"\n                               \"ENSEMBL:ENSG00000243438\"\n                               \"ENSEMBL:ENSG00000201796\"\n                               \"ENSEMBL:ENSG00000240160\")))\n\n(define (unwrap lst)\n  (if (null? lst) lst\n      (append (car lst) (unwrap (cdr lst)))))\n\n(define (predicate e)\n  (cdr (list-ref e 4)))\n\n(define (summary-obj edge-sum)\n  (car (list-ref edge-sum 4)))\n\n(define (summary-subj edge-sum)\n  (car (list-ref edge-sum 3)))\n\n(define ((edge/db? db) e) (eq? db (car e)))\n\n(define (sort-count c)\n  (sort\n   (hash-map c (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (cdr x))))\n\n(define (sort-by-length h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (length (cdr x)))))\n\n#|getting uniprots using run/graph\n(define encodes (find-predicates '(\"encodes\")))\n(define gene-curie?\n  (lambda (x)\n    (or\n     (string-prefix? x \"HGNC:\")\n     (string-prefix? x \"ENSEMBL:\")\n     (string-prefix? x \"NCBIGene:\"))))\n\n(define encodes-us (remove-duplicates (unwrap (filter (lambda (x) (not (null? x))) (set-map gene-list\n                                                                         (lambda (g) (time\n                                                                                      (define S (filter (lambda (x) (eq? (car x) 'rtx2)) (find-concepts #t (filter gene-curie? (map car (curie-synonyms/names g))))))\n                                                                                      (match-define\n                                                                                        (list name=>concepts name=>edges)\n                                                                                        (run/graph\n                                                                                         ((G S)\n                                                                                          (U #f))\n                                                                                         ((G->U encodes))\n                                                                                         (G G->U U)))\n                                                                                      (map concept->curie (hash-ref name=>concepts 'U))\n                                                                                      ))\n                                                                         )))))\n|#\n\n(define uniprot-curie?\n  (lambda (x)\n    (string-prefix? x \"UniProtKB:\")))\n\n;;Converting ENSEMBL curies to UniProtKB curies using synonymization in order to pass into count-downstream\n(define uniprots (remove-duplicates (filter uniprot-curie? (map car (unwrap (set-map gene-list curie-synonyms/names))))))\n\n#|\ntakes: list of UniProt curies (prot-list), list of GO predicates** (preds)\n** note: preds should only contain \"positively_regulates\", \"negatively_regulates\", \"subclass_of\", or any combination\n**       of those three predicates depending on what type of relationshion you want to count\nreturns: sorted (high->low) assoc list of a count of the number of other proteins in prot-list that each prot in prot-list regulates\n|#\n(define cell-expression-hash\n  (make-hash))\n\n(define regulated-genes-cell-expression-hash\n  (make-hash))\n\n(define (count-downstream prot-list preds)\n  ;;hash that maps each Uniprot curie (key) in prot-list -> set of all GO pathways (value) that the UniProt (key) regulates\n  (define go-processes (make-hash))\n  ;;hash that maps GO pathway curie (key) -> set of all UniProts (value) that are members of the GO pathway (key) AND in the prot-list\n  (define go-process-members (make-hash))\n  (define counter (make-hash))\n  (define involved_in (keep 1 (filter (lambda (x) (equal? (car x) 'rtx_2020)) (find-exact-predicates '(\"involved_in\")))))\n  (define regulators (filter (lambda (x) (equal? (car x) 'rtx_2020)) (find-exact-predicates preds)))\n  (define expressed_in (filter (lambda (x) (equal? (car x) 'rtx_2020)) (find-exact-predicates '(\"expressed_in\"))))\n  (for-each\n   (lambda (u)\n     (define S (filter (lambda (x) (equal? (car x) 'rtx_2020)) (find-concepts #t (list u))))\n     ;;this run/graph contains 2-hop query (G->M->X) and 1-hop query (P->X)\n     ;;2-hop (G->M->X): Finds the GO pathways (X) that UniProt (G) regulates\n     ;;1-hop (P->X): Finds the UniProts (P) that are members of the GO pathway (X)\n     (match-define\n       (list name=>concepts name=>edges)\n       (time (run/graph\n              ((G S)\n               (M #f)\n               (X #f)\n               (P #f)\n               (C #f)\n               (rG #f)\n               (rC #f))\n              ((G->M involved_in)\n               (G->C expressed_in)\n               (M->X regulators)\n               (P->X involved_in)\n               (rG->C expressed_in))\n              (G G->M M)\n              (G G->C C)\n              (M M->X X)\n              (P P->X X)\n              (rG rG->C rC))))\n     ;;populates go-processes values with the GO pathways, X, gotten from the 2-hop query G->M->X\n     (hash-set! go-processes u (list->set (map concept->curie (hash-ref name=>concepts 'X))))\n     (hash-set! cell-expression-hash u (list->set (map concept->curie (hash-ref name=>concepts 'C))))\n     (hash-set! regulated-genes-cell-expression-hash u (list->set (map concept->curie (hash-ref name=>concepts 'C))))\n     (for-each\n      (lambda (e)\n        ;;populates go-process-members values with the member UniProts, P, gotten from the 1-hop query P->X\n        (hash-update! go-process-members (concept->curie (edge->object e)) (lambda (v) (set-add v (concept->curie (edge->subject e)))) (set))\n        )\n      (hash-ref name=>edges 'P->X)\n      )\n     )\n   prot-list\n   )\n  ;;counting\n  (hash-for-each go-processes\n                 (lambda (k v)\n                   (define members (mutable-set))\n                   (set-for-each v\n                                 (lambda (g)\n                                   (set-union! members (set-intersect (list->set prot-list) (hash-ref go-process-members g (set))))\n                                   ))\n                   (hash-set! counter k (set-count members))\n                   )\n                 )\n  (sort-count counter)\n  )\n(count-downstream uniprots '(\"positively_regulates\"))\n\n\n(make-hash 'ARDS-Genelist\n           (make-hash 'Gene1-ARDS\n                      (make-hash 'Gene1-UBERON-cell-location\n                                 (make-hash 'pos-reg-GO1\n                                            (make-hash 'GO1\n                                                       (make-hash 'GO1-members\n                                                                  (make-hash 'GO1-member-UBERON-Cell-locations\n                                                                             (make 'GO1-ARDS-members)\n                                                                             )))))))\n\n\n;; which gene regulates the most amount of other genes on the list in a given tissue type\n;; backtrace\n\n\n(define q2hop (query/graph\n               ((G \"UniProtKB:P15692\")\n                (M #f)\n                (X (lambda (c) (string-prefix? c \"GO:\")))\n                (rG #f))\n               ((G->M '(\"involved_in\"))\n                (M->X '(\"positively_regulates\"))\n                (rG->X '(\"expressed_in\")))\n               (G G->M M)\n               (M M->X X)\n               (rG rG->X X)))\n\n(define q2hop (query/graph\n               ((G \"UniProtKB:P15692\")\n                (M #f))\n               ((G->M '(\"expressed_in\")))\n               (G G->M M)))\n\n\n#|2-hop query using query/graph\n(for-each\n (lambda (x) (time\n              (define q2hop (query/graph\n                             ((G x)\n                              (M #f)\n                              (X (lambda (c) (string-prefix? c \"GO:\"))))\n                             ((G->M '(\"involved_in\"))\n                              (M->X go-regulators))\n                             (G G->M M)\n                             (M M->X X)))\n              (hash-set! go-processes x (curies/query q2hop 'X))\n              ))\n uniprots\n )\n|#\n\n#|\n(define (uniprot->ensembl uni)\n  (set-intersect (set->list gene-list) (map car (curie-synonyms/names uni)))\n  )\n\n(define top10 (remove-duplicates (flatten (map uniprot->ensembl (map car (take (sort-count counter) 10))))))\n\n(define member-of (make-hash))\n(hash-for-each go-process-members\n               (lambda (k v)\n                 (set-for-each v\n                               (lambda (u)\n                                 (hash-update! member-of u (lambda (x) (cons k x)) '())\n                                 )\n                               )\n                 )\n               )\n(sort-by-length member-of)\n\n(define regulates-go (make-hash))\n(hash-for-each go-processes\n               (lambda (k v)\n                 (set-for-each v\n                               (lambda (p)\n                                 (hash-update! regulates-go p (lambda (x) (cons k x)) '())\n                                 )\n                               )\n                 )\n               )\n(sort-by-length regulates-go)\n|#\n\n(define preds-of-interest '(\"negatively_regulates\"\n                            \"physically_interacts_with\"\n                            \"positively_regulates\"\n                            \"regulates\"\n                            \"regulates_activity_of\"\n                            \"regulates_expression_of\"\n                            \"stimulates\"\n                            \"inhibits\"))\n\n(define seen (mutable-set))\n(define g-of-interest (mutable-set \"ENSEMBL:ENSG00000136689\"))\n\n(define (backtrace cur-genes g-list)\n  (define all-upstreams (mutable-set))\n  (set-for-each cur-genes\n                (lambda (g)\n                  (define q (query/graph\n                             ((S #f)\n                              (G g))\n                             ((S->G preds-of-interest))\n                             (S S->G G)))\n                  (define all-synons (list->set (map car (unwrap (map curie-synonyms/names (curies/query q 'S))))))\n                  (define upstream (set-remove (set-intersect g-list all-synons) g))\n                  ;;(printf \"~v\\n\" upstream)\n                  (printf \"~v . ~v\\n\" g (set-count upstream)) \n                  (set-union! all-upstreams upstream)\n                  )\n                )\n  ;;update seen list\n  (set-union! seen cur-genes)\n  (set-subtract! all-upstreams seen)\n  (printf \"~v\\n\\n\" (set-count all-upstreams))\n  (if (eq? (set-count all-upstreams) 0) cur-genes\n      (backtrace all-upstreams g-list))\n  )\n  \n#;(backtrace g-of-interest gene-list)\n\n#|\n(define endpoints (mutable-set))\n(define prots-seen (mutable-set))\n\n(define (backtrace-by-go cur-prot)\n  (set-add! prots-seen cur-prot)\n  (define all-gos (hash-ref member-of cur-prot '()))\n  (define all-upstreams (mutable-set))\n  (for-each\n   (lambda (gp)\n     (set-union! all-upstreams (list->mutable-set (hash-ref regulates-go gp '())))\n     )\n   all-gos\n   )\n  (if (set-empty? all-upstreams) (set-add! endpoints cur-prot)\n      ((printf \"~v : ~v\\n\" cur-prot (set-count all-upstreams))\n       (set-subtract! all-upstreams prots-seen)\n       (set-for-each all-upstreams\n                     (lambda (u)\n                       (backtrace-by-go u)\n                       )\n                     )    )    \n      )\n  )\n\n(set-clear! endpoints)\n(backtrace-by-go \"UniProtKB:P01137\")\n|#\n#|\nTop10 from count-downstream of ARDS gene-list\n\n\"ENSEMBL:ENSG00000105329\"\n  \"ENSEMBL:ENSG00000112715\"\n  \"ENSEMBL:ENSG00000078401\"\n  \"ENSEMBL:ENSG00000100644\"\n  \"ENSEMBL:ENSG00000168610\"\n  \"ENSEMBL:ENSG00000125538\"\n  \"ENSEMBL:ENSG00000136689\"\n  \"ENSEMBL:ENSG00000100292\"\n  \"ENSEMBL:ENSG00000087250\"\n  \"ENSEMBL:ENSG00000105974\"\n  \"ENSEMBL:ENSG00000166949\"\n|#\n\n#|\nBacktrace results\nInput:\"ENSEMBL:ENSG00000105329\"\nOutput: \n\"ENSEMBL:ENSG00000208001\" . 0\n\"ENSEMBL:ENSG00000171109\" . 3\n\"ENSEMBL:ENSG00000063180\" . 2\n\"ENSEMBL:ENSG00000199038\" . 0\n\"ENSEMBL:ENSG00000199133\" . 0\n\"ENSEMBL:ENSG00000277443\" . 9\n\"ENSEMBL:ENSG00000211590\" . 0\n\"ENSEMBL:ENSG00000100410\" . 2\n\"ENSEMBL:ENSG00000109063\" . 7\n\"ENSEMBL:ENSG00000166347\" . 4\n\"ENSEMBL:ENSG00000162104\" . 2\n\"ENSEMBL:ENSG00000198982\" . 0\n\"ENSEMBL:ENSG00000125779\" . 1\n\"ENSEMBL:ENSG00000153391\" . 1\n\"ENSEMBL:ENSG00000103510\" . 2\n\"ENSEMBL:ENSG00000207590\" . 0\n\"ENSEMBL:ENSG00000207731\" . 0\n\"ENSEMBL:ENSG00000198026\" . 3\n\"ENSEMBL:ENSG00000083807\" . 4\n\"ENSEMBL:ENSG00000115718\" . 3\n\"ENSEMBL:ENSG00000199020\" . 0\n\"ENSEMBL:ENSG00000284520\" . 0\n\"ENSEMBL:ENSG00000163702\" . 5\n\"ENSEMBL:ENSG00000145649\" . 1\n\"ENSEMBL:ENSG00000153395\" . 1\n\"ENSEMBL:ENSG00000167315\" . 4\n\"ENSEMBL:ENSG00000160932\" . 0\n\"ENSEMBL:ENSG00000266964\" . 2\n\"ENSEMBL:ENSG00000165682\" . 3\n\"ENSEMBL:ENSG00000173805\" . 9\n\"ENSEMBL:ENSG00000125482\" . 4\n\"ENSEMBL:ENSG00000145794\" . 8\n\"ENSEMBL:ENSG00000163803\" . 1\n\"ENSEMBL:ENSG00000105370\" . 6\n\nInput:\"ENSEMBL:ENSG00000168610\"\nOutput: 29\n\"ENSEMBL:ENSG00000208001\" . 0\n\"ENSEMBL:ENSG00000063180\" . 2\n\"ENSEMBL:ENSG00000199038\" . 0\n\"ENSEMBL:ENSG00000199133\" . 0\n\"ENSEMBL:ENSG00000211590\" . 0\n\"ENSEMBL:ENSG00000100410\" . 2\n\"ENSEMBL:ENSG00000162104\" . 2\n\"ENSEMBL:ENSG00000198982\" . 0\n\"ENSEMBL:ENSG00000138744\" . 4\n\"ENSEMBL:ENSG00000125779\" . 1\n\"ENSEMBL:ENSG00000187258\" . 4\n\"ENSEMBL:ENSG00000153391\" . 1\n\"ENSEMBL:ENSG00000103510\" . 2\n\"ENSEMBL:ENSG00000207590\" . 0\n\"ENSEMBL:ENSG00000048740\" . 4\n\"ENSEMBL:ENSG00000198026\" . 3\n\"ENSEMBL:ENSG00000083807\" . 4\n\"ENSEMBL:ENSG00000137959\" . 3\n\"ENSEMBL:ENSG00000115850\" . 4\n\"ENSEMBL:ENSG00000115718\" . 3\n\"ENSEMBL:ENSG00000199020\" . 0\n\"ENSEMBL:ENSG00000174607\" . 1\n\"ENSEMBL:ENSG00000145649\" . 1\n\"ENSEMBL:ENSG00000167315\" . 4\n\"ENSEMBL:ENSG00000173805\" . 9\n\"ENSEMBL:ENSG00000196843\" . 1\n\"ENSEMBL:ENSG00000125482\" . 4\n\"ENSEMBL:ENSG00000145794\" . 8\n\"ENSEMBL:ENSG00000105370\" . 6\n\nInput:\"ENSEMBL:ENSG00000112715\"\nOutput: 1\n\"ENSEMBL:ENSG00000153391\" . 1\n\nInput: \"ENSEMBL:ENSG00000136689\"\nOutput: 41\n\"ENSEMBL:ENSG00000208001\" . 0\n\"ENSEMBL:ENSG00000171109\" . 3\n\"ENSEMBL:ENSG00000063180\" . 2\n\"ENSEMBL:ENSG00000133019\" . 5\n\"ENSEMBL:ENSG00000199038\" . 0\n\"ENSEMBL:ENSG00000199133\" . 0\n\"ENSEMBL:ENSG00000179776\" . 15\n\"ENSEMBL:ENSG00000021355\" . 5\n\"ENSEMBL:ENSG00000133661\" . 1\n\"ENSEMBL:ENSG00000207827\" . 1\n\"ENSEMBL:ENSG00000211590\" . 0\n\"ENSEMBL:ENSG00000100410\" . 2\n\"ENSEMBL:ENSG00000118194\" . 2\n\"ENSEMBL:ENSG00000109063\" . 7\n\"ENSEMBL:ENSG00000117569\" . 2\n\"ENSEMBL:ENSG00000162104\" . 2\n\"ENSEMBL:ENSG00000198982\" . 0\n\"ENSEMBL:ENSG00000138744\" . 4\n\"ENSEMBL:ENSG00000125779\" . 1\n\"ENSEMBL:ENSG00000085063\" . 14\n\"ENSEMBL:ENSG00000103510\" . 2\n\"ENSEMBL:ENSG00000207590\" . 0\n\"ENSEMBL:ENSG00000207731\" . 0\n\"ENSEMBL:ENSG00000284204\" . 0\n\"ENSEMBL:ENSG00000164330\" . 9\n\"ENSEMBL:ENSG00000101000\" . 6\n\"ENSEMBL:ENSG00000137959\" . 3\n\"ENSEMBL:ENSG00000115718\" . 3\n\"ENSEMBL:ENSG00000199020\" . 0\n\"ENSEMBL:ENSG00000284520\" . 0\n\"ENSEMBL:ENSG00000163702\" . 5\n\"ENSEMBL:ENSG00000167315\" . 4\n\"ENSEMBL:ENSG00000160932\" . 0\n\"ENSEMBL:ENSG00000070614\" . 3\n\"ENSEMBL:ENSG00000266964\" . 2\n\"ENSEMBL:ENSG00000165682\" . 3\n\"ENSEMBL:ENSG00000196843\" . 1\n\"ENSEMBL:ENSG00000125482\" . 4\n\"ENSEMBL:ENSG00000145794\" . 8\n\"ENSEMBL:ENSG00000163803\" . 1\n\"ENSEMBL:ENSG00000105370\" . 6 \n|#\n"
  },
  {
    "path": "contrib/medikanren/pieces-parts/trace-pathways.rkt",
    "content": "#lang racket\n(require \"../../../medikanren/pieces-parts/query.rkt\")\n\n(define gene-list (list->set '(\"ENSEMBL:ENSG00000167972\"\n                               \"ENSEMBL:ENSG00000198691\"\n                               \"ENSEMBL:ENSG00000175164\"\n                               \"ENSEMBL:ENSG00000278540\"\n                               \"ENSEMBL:ENSG00000100412\"\n                               \"ENSEMBL:ENSG00000162104\"\n                               \"ENSEMBL:ENSG00000204305\"\n                               \"ENSEMBL:ENSG00000135744\"\n                               \"ENSEMBL:ENSG00000144891\"\n                               \"ENSEMBL:ENSG00000180772\"\n                               \"ENSEMBL:ENSG00000142208\"\n                               \"ENSEMBL:ENSG00000148218\"\n                               \"ENSEMBL:ENSG00000163631\"\n                               \"ENSEMBL:ENSG00000085662\"\n                               \"ENSEMBL:ENSG00000154188\"\n                               \"ENSEMBL:ENSG00000091879\"\n                               \"ENSEMBL:ENSG00000182718\"\n                               \"ENSEMBL:ENSG00000134982\"\n                               \"ENSEMBL:ENSG00000132703\"\n                               \"ENSEMBL:ENSG00000023445\"\n                               \"ENSEMBL:ENSG00000142515\"\n                               \"ENSEMBL:ENSG00000026103\"\n                               \"ENSEMBL:ENSG00000117560\"\n                               \"ENSEMBL:ENSG00000240583\"\n                               \"ENSEMBL:ENSG00000161798\"\n                               \"ENSEMBL:ENSG00000006756\"\n                               \"ENSEMBL:ENSG00000117601\"\n                               \"ENSEMBL:ENSG00000149311\"\n                               \"ENSEMBL:ENSG00000164904\"\n                               \"ENSEMBL:ENSG00000171791\"\n                               \"ENSEMBL:ENSG00000101144\"\n                               \"ENSEMBL:ENSG00000010671\"\n                               \"ENSEMBL:ENSG00000100300\"\n                               \"ENSEMBL:ENSG00000149131\"\n                               \"ENSEMBL:ENSG00000171860\"\n                               \"ENSEMBL:ENSG00000106804\"\n                               \"ENSEMBL:ENSG00000197405\"\n                               \"ENSEMBL:ENSG00000149823\"\n                               \"ENSEMBL:ENSG00000063180\"\n                               \"ENSEMBL:ENSG00000164305\"\n                               \"ENSEMBL:ENSG00000121691\"\n                               \"ENSEMBL:ENSG00000105974\"\n                               \"ENSEMBL:ENSG00000124813\"\n                               \"ENSEMBL:ENSG00000149257\"\n                               \"ENSEMBL:ENSG00000134057\"\n                               \"ENSEMBL:ENSG00000170458\"\n                               \"ENSEMBL:ENSG00000121594\"\n                               \"ENSEMBL:ENSG00000101017\"\n                               \"ENSEMBL:ENSG00000102245\"\n                               \"ENSEMBL:ENSG00000026508\"\n                               \"ENSEMBL:ENSG00000085063\"\n                               \"ENSEMBL:ENSG00000129226\"\n                               \"ENSEMBL:ENSG00000179776\"\n                               \"ENSEMBL:ENSG00000100526\"\n                               \"ENSEMBL:ENSG00000170835\"\n                               \"ENSEMBL:ENSG00000001626\"\n                               \"ENSEMBL:ENSG00000133019\"\n                               \"ENSEMBL:ENSG00000196811\"\n                               \"ENSEMBL:ENSG00000099622\"\n                               \"ENSEMBL:ENSG00000122705\"\n                               \"ENSEMBL:ENSG00000183813\"\n                               \"ENSEMBL:ENSG00000188153\"\n                               \"ENSEMBL:ENSG00000115966\"\n                               \"ENSEMBL:ENSG00000167193\"\n                               \"ENSEMBL:ENSG00000132693\"\n                               \"ENSEMBL:ENSG00000118231\"\n                               \"ENSEMBL:ENSG00000112062\"\n                               \"ENSEMBL:ENSG00000101439\"\n                               \"ENSEMBL:ENSG00000118523\"\n                               \"ENSEMBL:ENSG00000168036\"\n                               \"ENSEMBL:ENSG00000100448\"\n                               \"ENSEMBL:ENSG00000166347\"\n                               \"ENSEMBL:ENSG00000140465\"\n                               \"ENSEMBL:ENSG00000140505\"\n                               \"ENSEMBL:ENSG00000138061\"\n                               \"ENSEMBL:ENSG00000160870\"\n                               \"ENSEMBL:ENSG00000106258\"\n                               \"ENSEMBL:ENSG00000196730\"\n                               \"ENSEMBL:ENSG00000011465\"\n                               \"ENSEMBL:ENSG00000159640\"\n                               \"ENSEMBL:ENSG00000164825\"\n                               \"ENSEMBL:ENSG00000197766\"\n                               \"ENSEMBL:ENSG00000181019\"\n                               \"ENSEMBL:ENSG00000213918\"\n                               \"ENSEMBL:ENSG00000197635\"\n                               \"ENSEMBL:ENSG00000164330\"\n                               \"ENSEMBL:ENSG00000213694\"\n                               \"ENSEMBL:ENSG00000078401\"\n                               \"ENSEMBL:ENSG00000138798\"\n                               \"ENSEMBL:ENSG00000197561\"\n                               \"ENSEMBL:ENSG00000021355\"\n                               \"ENSEMBL:ENSG00000066044\"\n                               \"ENSEMBL:ENSG00000116016\"\n                               \"ENSEMBL:ENSG00000133216\"\n                               \"ENSEMBL:ENSG00000120915\"\n                               \"ENSEMBL:ENSG00000130427\"\n                               \"ENSEMBL:ENSG00000157554\"\n                               \"ENSEMBL:ENSG00000157557\"\n                               \"ENSEMBL:ENSG00000180210\"\n                               \"ENSEMBL:ENSG00000117525\"\n                               \"ENSEMBL:ENSG00000198734\"\n                               \"ENSEMBL:ENSG00000117480\"\n                               \"ENSEMBL:ENSG00000166147\"\n                               \"ENSEMBL:ENSG00000151422\"\n                               \"ENSEMBL:ENSG00000140285\"\n                               \"ENSEMBL:ENSG00000160867\"\n                               \"ENSEMBL:ENSG00000111206\"\n                               \"ENSEMBL:ENSG00000115414\"\n                               \"ENSEMBL:ENSG00000170345\"\n                               \"ENSEMBL:ENSG00000154727\"\n                               \"ENSEMBL:ENSG00000163288\"\n                               \"ENSEMBL:ENSG00000128683\"\n                               \"ENSEMBL:ENSG00000141448\"\n                               \"ENSEMBL:ENSG00000168621\"\n                               \"ENSEMBL:ENSG00000134812\"\n                               \"ENSEMBL:ENSG00000265107\"\n                               \"ENSEMBL:ENSG00000173221\"\n                               \"ENSEMBL:ENSG00000147437\"\n                               \"ENSEMBL:ENSG00000186810\"\n                               \"ENSEMBL:ENSG00000167701\"\n                               \"ENSEMBL:ENSG00000113580\"\n                               \"ENSEMBL:ENSG00000082701\"\n                               \"ENSEMBL:ENSG00000132518\"\n                               \"ENSEMBL:ENSG00000145649\"\n                               \"ENSEMBL:ENSG00000100453\"\n                               \"ENSEMBL:ENSG00000148702\"\n                               \"ENSEMBL:ENSG00000084754\"\n                               \"ENSEMBL:ENSG00000019991\"\n                               \"ENSEMBL:ENSG00000100644\"\n                               \"ENSEMBL:ENSG00000189403\"\n                               \"ENSEMBL:ENSG00000100292\"\n                               \"ENSEMBL:ENSG00000125798\"\n                               \"ENSEMBL:ENSG00000135486\"\n                               \"ENSEMBL:ENSG00000257017\"\n                               \"ENSEMBL:ENSG00000113905\"\n                               \"ENSEMBL:ENSG00000176387\"\n                               \"ENSEMBL:ENSG00000204389\"\n                               \"ENSEMBL:ENSG00000204388\"\n                               \"ENSEMBL:ENSG00000170606\"\n                               \"ENSEMBL:ENSG00000070614\"\n                               \"ENSEMBL:ENSG00000041982\"\n                               \"ENSEMBL:ENSG00000090339\"\n                               \"ENSEMBL:ENSG00000185745\"\n                               \"ENSEMBL:ENSG00000171855\"\n                               \"ENSEMBL:ENSG00000111537\"\n                               \"ENSEMBL:ENSG00000006652\"\n                               \"ENSEMBL:ENSG00000017427\"\n                               \"ENSEMBL:ENSG00000146674\"\n                               \"ENSEMBL:ENSG00000167779\"\n                               \"ENSEMBL:ENSG00000104365\"\n                               \"ENSEMBL:ENSG00000115008\"\n                               \"ENSEMBL:ENSG00000125538\"\n                               \"ENSEMBL:ENSG00000115594\"\n                               \"ENSEMBL:ENSG00000136689\"\n                               \"ENSEMBL:ENSG00000109471\"\n                               \"ENSEMBL:ENSG00000134460\"\n                               \"ENSEMBL:ENSG00000113520\"\n                               \"ENSEMBL:ENSG00000136244\"\n                               \"ENSEMBL:ENSG00000168685\"\n                               \"ENSEMBL:ENSG00000169429\"\n                               \"ENSEMBL:ENSG00000136634\"\n                               \"ENSEMBL:ENSG00000169194\"\n                               \"ENSEMBL:ENSG00000112115\"\n                               \"ENSEMBL:ENSG00000150782\"\n                               \"ENSEMBL:ENSG00000169245\"\n                               \"ENSEMBL:ENSG00000125347\"\n                               \"ENSEMBL:ENSG00000005884\"\n                               \"ENSEMBL:ENSG00000169896\"\n                               \"ENSEMBL:ENSG00000160255\"\n                               \"ENSEMBL:ENSG00000115474\"\n                               \"ENSEMBL:ENSG00000128052\"\n                               \"ENSEMBL:ENSG00000171345\"\n                               \"ENSEMBL:ENSG00000172037\"\n                               \"ENSEMBL:ENSG00000148346\"\n                               \"ENSEMBL:ENSG00000115850\"\n                               \"ENSEMBL:ENSG00000131981\"\n                               \"ENSEMBL:ENSG00000138039\"\n                               \"ENSEMBL:ENSG00000105370\"\n                               \"ENSEMBL:ENSG00000226979\"\n                               \"ENSEMBL:ENSG00000160932\"\n                               \"ENSEMBL:ENSG00000183918\"\n                               \"ENSEMBL:ENSG00000277443\"\n                               \"ENSEMBL:ENSG00000166949\"\n                               \"ENSEMBL:ENSG00000165471\"\n                               \"ENSEMBL:ENSG00000143384\"\n                               \"ENSEMBL:ENSG00000014641\"\n                               \"ENSEMBL:ENSG00000110492\"\n                               \"ENSEMBL:ENSG00000095015\"\n                               \"ENSEMBL:ENSG00000240972\"\n                               \"ENSEMBL:ENSG00000138755\"\n                               \"ENSEMBL:ENSG00000087245\"\n                               \"ENSEMBL:ENSG00000149968\"\n                               \"ENSEMBL:ENSG00000100985\"\n                               \"ENSEMBL:ENSG00000005381\"\n                               \"ENSEMBL:ENSG00000130830\"\n                               \"ENSEMBL:ENSG00000125148\"\n                               \"ENSEMBL:ENSG00000087250\"\n                               \"ENSEMBL:ENSG00000171100\"\n                               \"ENSEMBL:ENSG00000210195\"\n                               \"ENSEMBL:ENSG00000185499\"\n                               \"ENSEMBL:ENSG00000215182\"\n                               \"ENSEMBL:ENSG00000136997\"\n                               \"ENSEMBL:ENSG00000172936\"\n                               \"ENSEMBL:ENSG00000109063\"\n                               \"ENSEMBL:ENSG00000065534\"\n                               \"ENSEMBL:ENSG00000116044\"\n                               \"ENSEMBL:ENSG00000109320\"\n                               \"ENSEMBL:ENSG00000100906\"\n                               \"ENSEMBL:ENSG00000001167\"\n                               \"ENSEMBL:ENSG00000089250\"\n                               \"ENSEMBL:ENSG00000164867\"\n                               \"ENSEMBL:ENSG00000161270\"\n                               \"ENSEMBL:ENSG00000135318\"\n                               \"ENSEMBL:ENSG00000111331\"\n                               \"ENSEMBL:ENSG00000112038\"\n                               \"ENSEMBL:ENSG00000089041\"\n                               \"ENSEMBL:ENSG00000185624\"\n                               \"ENSEMBL:ENSG00000007168\"\n                               \"ENSEMBL:ENSG00000117450\"\n                               \"ENSEMBL:ENSG00000106366\"\n                               \"ENSEMBL:ENSG00000126759\"\n                               \"ENSEMBL:ENSG00000197249\"\n                               \"ENSEMBL:ENSG00000124102\"\n                               \"ENSEMBL:ENSG00000121879\"\n                               \"ENSEMBL:ENSG00000051382\"\n                               \"ENSEMBL:ENSG00000171608\"\n                               \"ENSEMBL:ENSG00000105851\"\n                               \"ENSEMBL:ENSG00000170890\"\n                               \"ENSEMBL:ENSG00000188257\"\n                               \"ENSEMBL:ENSG00000116711\"\n                               \"ENSEMBL:ENSG00000118495\"\n                               \"ENSEMBL:ENSG00000011422\"\n                               \"ENSEMBL:ENSG00000115896\"\n                               \"ENSEMBL:ENSG00000075651\"\n                               \"ENSEMBL:ENSG00000178209\"\n                               \"ENSEMBL:ENSG00000266964\"\n                               \"ENSEMBL:ENSG00000115138\"\n                               \"ENSEMBL:ENSG00000186951\"\n                               \"ENSEMBL:ENSG00000122862\"\n                               \"ENSEMBL:ENSG00000100030\"\n                               \"ENSEMBL:ENSG00000107643\"\n                               \"ENSEMBL:ENSG00000169032\"\n                               \"ENSEMBL:ENSG00000115718\"\n                               \"ENSEMBL:ENSG00000184500\"\n                               \"ENSEMBL:ENSG00000189002\"\n                               \"ENSEMBL:ENSG00000135406\"\n                               \"ENSEMBL:ENSG00000041357\"\n                               \"ENSEMBL:ENSG00000197170\"\n                               \"ENSEMBL:ENSG00000011304\"\n                               \"ENSEMBL:ENSG00000073756\"\n                               \"ENSEMBL:ENSG00000169398\"\n                               \"ENSEMBL:ENSG00000105894\"\n                               \"ENSEMBL:ENSG00000081237\"\n                               \"ENSEMBL:ENSG00000113456\"\n                               \"ENSEMBL:ENSG00000069974\"\n                               \"ENSEMBL:ENSG00000080823\"\n                               \"ENSEMBL:ENSG00000112619\"\n                               \"ENSEMBL:ENSG00000173039\"\n                               \"ENSEMBL:ENSG00000143839\"\n                               \"ENSEMBL:ENSG00000102032\"\n                               \"ENSEMBL:ENSG00000163914\"\n                               \"ENSEMBL:ENSG00000067900\"\n                               \"ENSEMBL:ENSG00000149489\"\n                               \"ENSEMBL:ENSG00000196218\"\n                               \"ENSEMBL:ENSG00000196154\"\n                               \"ENSEMBL:ENSG00000163220\"\n                               \"ENSEMBL:ENSG00000031698\"\n                               \"ENSEMBL:ENSG00000111319\"\n                               \"ENSEMBL:ENSG00000108691\"\n                               \"ENSEMBL:ENSG00000108688\"\n                               \"ENSEMBL:ENSG00000163735\"\n                               \"ENSEMBL:ENSG00000110876\"\n                               \"ENSEMBL:ENSG00000168878\"\n                               \"ENSEMBL:ENSG00000168484\"\n                               \"ENSEMBL:ENSG00000133661\"\n                               \"ENSEMBL:ENSG00000064651\"\n                               \"ENSEMBL:ENSG00000197208\"\n                               \"ENSEMBL:ENSG00000166311\"\n                               \"ENSEMBL:ENSG00000075618\"\n                               \"ENSEMBL:ENSG00000125835\"\n                               \"ENSEMBL:ENSG00000142168\"\n                               \"ENSEMBL:ENSG00000112096\"\n                               \"ENSEMBL:ENSG00000109610\"\n                               \"ENSEMBL:ENSG00000125398\"\n                               \"ENSEMBL:ENSG00000100883\"\n                               \"ENSEMBL:ENSG00000168610\"\n                               \"ENSEMBL:ENSG00000126561\"\n                               \"ENSEMBL:ENSG00000173757\"\n                               \"ENSEMBL:ENSG00000087586\"\n                               \"ENSEMBL:ENSG00000067715\"\n                               \"ENSEMBL:ENSG00000231925\"\n                               \"ENSEMBL:ENSG00000006638\"\n                               \"ENSEMBL:ENSG00000118526\"\n                               \"ENSEMBL:ENSG00000120156\"\n                               \"ENSEMBL:ENSG00000164362\"\n                               \"ENSEMBL:ENSG00000003436\"\n                               \"ENSEMBL:ENSG00000105329\"\n                               \"ENSEMBL:ENSG00000198959\"\n                               \"ENSEMBL:ENSG00000178726\"\n                               \"ENSEMBL:ENSG00000116001\"\n                               \"ENSEMBL:ENSG00000102265\"\n                               \"ENSEMBL:ENSG00000136352\"\n                               \"ENSEMBL:ENSG00000137462\"\n                               \"ENSEMBL:ENSG00000164342\"\n                               \"ENSEMBL:ENSG00000136869\"\n                               \"ENSEMBL:ENSG00000127324\"\n                               \"ENSEMBL:ENSG00000149809\"\n                               \"ENSEMBL:ENSG00000232810\"\n                               \"ENSEMBL:ENSG00000118503\"\n                               \"ENSEMBL:ENSG00000067182\"\n                               \"ENSEMBL:ENSG00000118194\"\n                               \"ENSEMBL:ENSG00000131747\"\n                               \"ENSEMBL:ENSG00000111669\"\n                               \"ENSEMBL:ENSG00000128311\"\n                               \"ENSEMBL:ENSG00000125482\"\n                               \"ENSEMBL:ENSG00000155657\"\n                               \"ENSEMBL:ENSG00000136810\"\n                               \"ENSEMBL:ENSG00000198431\"\n                               \"ENSEMBL:ENSG00000149021\"\n                               \"ENSEMBL:ENSG00000174607\"\n                               \"ENSEMBL:ENSG00000111424\"\n                               \"ENSEMBL:ENSG00000112715\"\n                               \"ENSEMBL:ENSG00000146469\"\n                               \"ENSEMBL:ENSG00000110799\"\n                               \"ENSEMBL:ENSG00000158125\"\n                               \"ENSEMBL:ENSG00000164924\"\n                               \"ENSEMBL:ENSG00000121966\"\n                               \"ENSEMBL:ENSG00000146070\"\n                               \"ENSEMBL:ENSG00000106305\"\n                               \"ENSEMBL:ENSG00000050327\"\n                               \"ENSEMBL:ENSG00000083168\"\n                               \"ENSEMBL:ENSG00000118972\"\n                               \"ENSEMBL:ENSG00000206561\"\n                               \"ENSEMBL:ENSG00000184381\"\n                               \"ENSEMBL:ENSG00000069764\"\n                               \"ENSEMBL:ENSG00000108528\"\n                               \"ENSEMBL:ENSG00000117461\"\n                               \"ENSEMBL:ENSG00000134107\"\n                               \"ENSEMBL:ENSG00000136908\"\n                               \"ENSEMBL:ENSG00000171720\"\n                               \"ENSEMBL:ENSG00000176170\"\n                               \"ENSEMBL:ENSG00000111602\"\n                               \"ENSEMBL:ENSG00000173805\"\n                               \"ENSEMBL:ENSG00000131023\"\n                               \"ENSEMBL:ENSG00000157456\"\n                               \"ENSEMBL:ENSG00000162889\"\n                               \"ENSEMBL:ENSG00000103671\"\n                               \"ENSEMBL:ENSG00000133116\"\n                               \"ENSEMBL:ENSG00000181092\"\n                               \"ENSEMBL:ENSG00000100351\"\n                               \"ENSEMBL:ENSG00000136156\"\n                               \"ENSEMBL:ENSG00000102230\"\n                               \"ENSEMBL:ENSG00000057663\"\n                               \"ENSEMBL:ENSG00000134318\"\n                               \"ENSEMBL:ENSG00000117592\"\n                               \"ENSEMBL:ENSG00000187608\"\n                               \"ENSEMBL:ENSG00000103335\"\n                               \"ENSEMBL:ENSG00000165733\"\n                               \"ENSEMBL:ENSG00000079999\"\n                               \"ENSEMBL:ENSG00000044090\"\n                               \"ENSEMBL:ENSG00000117020\"\n                               \"ENSEMBL:ENSG00000105835\"\n                               \"ENSEMBL:ENSG00000105246\"\n                               \"ENSEMBL:ENSG00000131477\"\n                               \"ENSEMBL:ENSG00000127528\"\n                               \"ENSEMBL:ENSG00000167315\"\n                               \"ENSEMBL:ENSG00000140092\"\n                               \"ENSEMBL:ENSG00000101000\"\n                               \"ENSEMBL:ENSG00000100591\"\n                               \"ENSEMBL:ENSG00000160999\"\n                               \"ENSEMBL:ENSG00000162493\"\n                               \"ENSEMBL:ENSG00000048740\"\n                               \"ENSEMBL:ENSG00000173083\"\n                               \"ENSEMBL:ENSG00000196843\"\n                               \"ENSEMBL:ENSG00000126264\"\n                               \"ENSEMBL:ENSG00000137959\"\n                               \"ENSEMBL:ENSG00000269821\"\n                               \"ENSEMBL:ENSG00000083807\"\n                               \"ENSEMBL:ENSG00000167114\"\n                               \"ENSEMBL:ENSG00000129465\"\n                               \"ENSEMBL:ENSG00000136110\"\n                               \"ENSEMBL:ENSG00000256525\"\n                               \"ENSEMBL:ENSG00000142082\"\n                               \"ENSEMBL:ENSG00000096717\"\n                               \"ENSEMBL:ENSG00000136859\"\n                               \"ENSEMBL:ENSG00000172828\"\n                               \"ENSEMBL:ENSG00000123415\"\n                               \"ENSEMBL:ENSG00000025800\"\n                               \"ENSEMBL:ENSG00000154589\"\n                               \"ENSEMBL:ENSG00000177663\"\n                               \"ENSEMBL:ENSG00000034677\"\n                               \"ENSEMBL:ENSG00000196141\"\n                               \"ENSEMBL:ENSG00000004142\"\n                               \"ENSEMBL:ENSG00000113249\"\n                               \"ENSEMBL:ENSG00000007952\"\n                               \"ENSEMBL:ENSG00000086232\"\n                               \"ENSEMBL:ENSG00000138744\"\n                               \"ENSEMBL:ENSG00000163106\"\n                               \"ENSEMBL:ENSG00000138375\"\n                               \"ENSEMBL:ENSG00000086991\"\n                               \"ENSEMBL:ENSG00000219430\"\n                               \"ENSEMBL:ENSG00000138303\"\n                               \"ENSEMBL:ENSG00000126524\"\n                               \"ENSEMBL:ENSG00000167772\"\n                               \"ENSEMBL:ENSG00000165682\"\n                               \"ENSEMBL:ENSG00000101916\"\n                               \"ENSEMBL:ENSG00000172458\"\n                               \"ENSEMBL:ENSG00000124731\"\n                               \"ENSEMBL:ENSG00000011426\"\n                               \"ENSEMBL:ENSG00000135766\"\n                               \"ENSEMBL:ENSG00000241635\"\n                               \"ENSEMBL:ENSG00000104835\"\n                               \"ENSEMBL:ENSG00000185480\"\n                               \"ENSEMBL:ENSG00000110075\"\n                               \"ENSEMBL:ENSG00000079691\"\n                               \"ENSEMBL:ENSG00000171109\"\n                               \"ENSEMBL:ENSG00000151849\"\n                               \"ENSEMBL:ENSG00000126970\"\n                               \"ENSEMBL:ENSG00000169241\"\n                               \"ENSEMBL:ENSG00000074842\"\n                               \"ENSEMBL:ENSG00000185115\"\n                               \"ENSEMBL:ENSG00000136688\"\n                               \"ENSEMBL:ENSG00000115350\"\n                               \"ENSEMBL:ENSG00000111666\"\n                               \"ENSEMBL:ENSG00000198074\"\n                               \"ENSEMBL:ENSG00000283122\"\n                               \"ENSEMBL:ENSG00000139946\"\n                               \"ENSEMBL:ENSG00000175482\"\n                               \"ENSEMBL:ENSG00000117569\"\n                               \"ENSEMBL:ENSG00000130234\"\n                               \"ENSEMBL:ENSG00000198026\"\n                               \"ENSEMBL:ENSG00000132429\"\n                               \"ENSEMBL:ENSG00000114745\"\n                               \"ENSEMBL:ENSG00000060237\"\n                               \"ENSEMBL:ENSG00000262246\"\n                               \"ENSEMBL:ENSG00000104518\"\n                               \"ENSEMBL:ENSG00000153395\"\n                               \"ENSEMBL:ENSG00000146094\"\n                               \"ENSEMBL:ENSG00000125779\"\n                               \"ENSEMBL:ENSG00000197496\"\n                               \"ENSEMBL:ENSG00000169612\"\n                               \"ENSEMBL:ENSG00000138496\"\n                               \"ENSEMBL:ENSG00000169962\"\n                               \"ENSEMBL:ENSG00000130363\"\n                               \"ENSEMBL:ENSG00000103510\"\n                               \"ENSEMBL:ENSG00000106125\"\n                               \"ENSEMBL:ENSG00000131653\"\n                               \"ENSEMBL:ENSG00000145794\"\n                               \"ENSEMBL:ENSG00000163702\"\n                               \"ENSEMBL:ENSG00000100410\"\n                               \"ENSEMBL:ENSG00000137691\"\n                               \"ENSEMBL:ENSG00000160188\"\n                               \"ENSEMBL:ENSG00000151148\"\n                               \"ENSEMBL:ENSG00000137033\"\n                               \"ENSEMBL:ENSG00000178473\"\n                               \"ENSEMBL:ENSG00000162711\"\n                               \"ENSEMBL:ENSG00000161544\"\n                               \"ENSEMBL:ENSG00000153391\"\n                               \"ENSEMBL:ENSG00000205359\"\n                               \"ENSEMBL:ENSG00000168724\"\n                               \"ENSEMBL:ENSG00000229140\"\n                               \"ENSEMBL:ENSG00000165953\"\n                               \"ENSEMBL:ENSG00000172967\"\n                               \"ENSEMBL:ENSG00000163803\"\n                               \"ENSEMBL:ENSG00000197272\"\n                               \"ENSEMBL:ENSG00000175311\"\n                               \"ENSEMBL:ENSG00000170782\"\n                               \"ENSEMBL:ENSG00000189195\"\n                               \"ENSEMBL:ENSG00000161911\"\n                               \"ENSEMBL:ENSG00000197448\"\n                               \"ENSEMBL:ENSG00000251562\"\n                               \"ENSEMBL:ENSG00000187258\"\n                               \"ENSEMBL:ENSG00000248131\"\n                               \"ENSEMBL:ENSG00000284520\"\n                               \"ENSEMBL:ENSG00000199133\"\n                               \"ENSEMBL:ENSG00000284440\"\n                               \"ENSEMBL:ENSG00000199161\"\n                               \"ENSEMBL:ENSG00000207608\"\n                               \"ENSEMBL:ENSG00000207625\"\n                               \"ENSEMBL:ENSG00000207782\"\n                               \"ENSEMBL:ENSG00000283904\"\n                               \"ENSEMBL:ENSG00000283815\"\n                               \"ENSEMBL:ENSG00000284204\"\n                               \"ENSEMBL:ENSG00000207607\"\n                               \"ENSEMBL:ENSG00000199038\"\n                               \"ENSEMBL:ENSG00000207702\"\n                               \"ENSEMBL:ENSG00000207590\"\n                               \"ENSEMBL:ENSG00000207798\"\n                               \"ENSEMBL:ENSG00000207870\"\n                               \"ENSEMBL:ENSG00000284567\"\n                               \"ENSEMBL:ENSG00000199075\"\n                               \"ENSEMBL:ENSG00000199121\"\n                               \"ENSEMBL:ENSG00000207808\"\n                               \"ENSEMBL:ENSG00000207864\"\n                               \"ENSEMBL:ENSG00000207827\"\n                               \"ENSEMBL:ENSG00000207582\"\n                               \"ENSEMBL:ENSG00000284357\"\n                               \"ENSEMBL:ENSG00000207638\"\n                               \"ENSEMBL:ENSG00000199059\"\n                               \"ENSEMBL:ENSG00000199151\"\n                               \"ENSEMBL:ENSG00000199104\"\n                               \"ENSEMBL:ENSG00000198982\"\n                               \"ENSEMBL:ENSG00000199020\"\n                               \"ENSEMBL:ENSG00000208001\"\n                               \"ENSEMBL:ENSG00000202569\"\n                               \"ENSEMBL:ENSG00000194717\"\n                               \"ENSEMBL:ENSG00000207731\"\n                               \"ENSEMBL:ENSG00000122852\"\n                               \"ENSEMBL:ENSG00000207571\"\n                               \"ENSEMBL:ENSG00000185303\"\n                               \"ENSEMBL:ENSG00000211590\"\n                               \"ENSEMBL:ENSG00000285427\"\n                               \"ENSEMBL:ENSG00000228750\"\n                               \"ENSEMBL:ENSG00000280634\"\n                               \"ENSEMBL:ENSG00000243438\"\n                               \"ENSEMBL:ENSG00000201796\"\n                               \"ENSEMBL:ENSG00000240160\")))\n\n(define (unwrap lst)\n  (if (null? lst) lst\n      (append (car lst) (unwrap (cdr lst)))))\n\n(define (predicate e)\n  (cdr (list-ref e 4)))\n\n(define (summary-obj edge-sum)\n  (car (list-ref edge-sum 4)))\n\n(define (summary-subj edge-sum)\n  (car (list-ref edge-sum 3)))\n\n(define ((edge/db? db) e) (eq? db (car e)))\n\n(define (sort-count c)\n  (sort\n   (hash-map c (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (cdr x))))\n\n(define (sort-by-length h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (length (cdr x)))))\n\n#|getting uniprots using run/graph\n(define encodes (find-predicates '(\"encodes\")))\n(define gene-curie?\n  (lambda (x)\n    (or\n     (string-prefix? x \"HGNC:\")\n     (string-prefix? x \"ENSEMBL:\")\n     (string-prefix? x \"NCBIGene:\"))))\n\n(define encodes-us (remove-duplicates (unwrap (filter (lambda (x) (not (null? x))) (set-map gene-list\n                                                                         (lambda (g) (time\n                                                                                      (define S (filter (lambda (x) (eq? (car x) 'rtx2)) (find-concepts #t (filter gene-curie? (map car (curie-synonyms/names g))))))\n                                                                                      (match-define\n                                                                                        (list name=>concepts name=>edges)\n                                                                                        (run/graph\n                                                                                         ((G S)\n                                                                                          (U #f))\n                                                                                         ((G->U encodes))\n                                                                                         (G G->U U)))\n                                                                                      (map concept->curie (hash-ref name=>concepts 'U))\n                                                                                      ))\n                                                                         )))))\n|#\n\n(define uniprot-curie?\n  (lambda (x)\n    (string-prefix? x \"UniProtKB:\")))\n\n;;Converting ENSEMBL curies to UniProtKB curies using synonymization in order to pass into count-downstream\n(define uniprots (remove-duplicates (filter uniprot-curie? (map car (unwrap (set-map gene-list curie-synonyms/names))))))\n\n#|\ntakes: list of UniProt curies (prot-list), list of GO predicates** (preds)\n** note: preds should only contain \"positively_regulates\", \"negatively_regulates\", \"subclass_of\", or any combination\n**       of those three predicates depending on what type of relationshion you want to count\nreturns: sorted (high->low) assoc list of a count of the number of other proteins in prot-list that each prot in prot-list regulates\n|#\n(define (count-downstream prot-list preds)\n  ;;hash that maps each Uniprot curie (key) in prot-list -> set of all GO pathways (value) that the UniProt (key) regulates\n  (define go-processes (make-hash))\n  ;;hash that maps GO pathway curie (key) -> set of all UniProts (value) that are members of the GO pathway (key) AND in the prot-list\n  (define go-process-members (make-hash))\n  (define counter (make-hash))\n  (define involved_in (keep 1 (filter (lambda (x) (eq? (car x) 'rtx2)) (find-predicates '(\"involved_in\")))))\n  (define regulators (filter (lambda (x) (eq? (car x) 'rtx2)) (find-predicates preds)))\n  (for-each\n   (lambda (u)\n     (define S (filter (lambda (x) (eq? (car x) 'rtx2)) (find-concepts #t (list u))))\n     ;;this run/graph contains 2-hop query (G->M->X) and 1-hop query (P->X)\n     ;;2-hop (G->M->X): Finds the GO pathways (X) that UniProt (G) regulates\n     ;;1-hop (P->X): Finds the UniProts (P) that are members of the GO pathway (X)\n     (match-define\n       (list name=>concepts name=>edges)\n       (time (run/graph\n              ((G S)\n               (M #f)\n               (X #f)\n               (P #f))\n              ((G->M involved_in)\n               (M->X regulators)\n               (P->X involved_in))\n              (G G->M M)\n              (M M->X X)\n              (P P->X X))))\n     ;;populates go-processes values with the GO pathways, X, gotten from the 2-hop query G->M->X\n     (hash-set! go-processes u (list->set (map concept->curie (hash-ref name=>concepts 'X))))\n     (for-each\n      (lambda (e)\n        ;;populates go-process-members values with the member UniProts, P, gotten from the 1-hop query P->X\n        (hash-update! go-process-members (concept->curie (edge->object e)) (lambda (v) (set-add v (concept->curie (edge->subject e)))) (set))\n        )\n      (hash-ref name=>edges 'P->X)\n      )\n     )\n   prot-list\n   )\n  ;;counting\n  (hash-for-each go-processes\n                 (lambda (k v)\n                   (define members (mutable-set))\n                   (set-for-each v\n                                 (lambda (g)\n                                   (set-union! members (set-intersect (list->set prot-list) (hash-ref go-process-members g (set))))\n                                   ))\n                   (hash-set! counter k (set-count members))\n                   )\n                 )\n  (sort-count counter)\n  )\n\n#|2-hop query using query/graph\n(for-each\n (lambda (x) (time\n              (define q2hop (query/graph\n                             ((G x)\n                              (M #f)\n                              (X (lambda (c) (string-prefix? c \"GO:\"))))\n                             ((G->M '(\"involved_in\"))\n                              (M->X go-regulators))\n                             (G G->M M)\n                             (M M->X X)))\n              (hash-set! go-processes x (curies/query q2hop 'X))\n              ))\n uniprots\n )\n|#\n\n#|\n(define (uniprot->ensembl uni)\n  (set-intersect (set->list gene-list) (map car (curie-synonyms/names uni)))\n  )\n\n(define top10 (remove-duplicates (flatten (map uniprot->ensembl (map car (take (sort-count counter) 10))))))\n\n(define member-of (make-hash))\n(hash-for-each go-process-members\n               (lambda (k v)\n                 (set-for-each v\n                               (lambda (u)\n                                 (hash-update! member-of u (lambda (x) (cons k x)) '())\n                                 )\n                               )\n                 )\n               )\n(sort-by-length member-of)\n\n(define regulates-go (make-hash))\n(hash-for-each go-processes\n               (lambda (k v)\n                 (set-for-each v\n                               (lambda (p)\n                                 (hash-update! regulates-go p (lambda (x) (cons k x)) '())\n                                 )\n                               )\n                 )\n               )\n(sort-by-length regulates-go)\n|#\n\n(define preds-of-interest '(\"negatively_regulates\"\n                            \"physically_interacts_with\"\n                            \"positively_regulates\"\n                            \"regulates\"\n                            \"regulates_activity_of\"\n                            \"regulates_expression_of\"\n                            \"stimulates\"\n                            \"inhibits\"))\n\n(define seen (mutable-set))\n(define g-of-interest (mutable-set \"ENSEMBL:ENSG00000136689\"))\n\n(define (backtrace cur-genes g-list)\n  (define all-upstreams (mutable-set))\n  (set-for-each cur-genes\n                (lambda (g)\n                  (define q (query/graph\n                             ((S #f)\n                              (G g))\n                             ((S->G preds-of-interest))\n                             (S S->G G)))\n                  (define all-synons (list->set (map car (unwrap (map curie-synonyms/names (curies/query q 'S))))))\n                  (define upstream (set-remove (set-intersect g-list all-synons) g))\n                  ;;(printf \"~v\\n\" upstream)\n                  (printf \"~v . ~v\\n\" g (set-count upstream)) \n                  (set-union! all-upstreams upstream)\n                  )\n                )\n  ;;update seen list\n  (set-union! seen cur-genes)\n  (set-subtract! all-upstreams seen)\n  (printf \"~v\\n\\n\" (set-count all-upstreams))\n  (if (eq? (set-count all-upstreams) 0) cur-genes\n      (backtrace all-upstreams g-list))\n  )\n  \n;;(backtrace g-of-interest gene-list)\n\n#|\n(define endpoints (mutable-set))\n(define prots-seen (mutable-set))\n\n(define (backtrace-by-go cur-prot)\n  (set-add! prots-seen cur-prot)\n  (define all-gos (hash-ref member-of cur-prot '()))\n  (define all-upstreams (mutable-set))\n  (for-each\n   (lambda (gp)\n     (set-union! all-upstreams (list->mutable-set (hash-ref regulates-go gp '())))\n     )\n   all-gos\n   )\n  (if (set-empty? all-upstreams) (set-add! endpoints cur-prot)\n      ((printf \"~v : ~v\\n\" cur-prot (set-count all-upstreams))\n       (set-subtract! all-upstreams prots-seen)\n       (set-for-each all-upstreams\n                     (lambda (u)\n                       (backtrace-by-go u)\n                       )\n                     )    )    \n      )\n  )\n\n(set-clear! endpoints)\n(backtrace-by-go \"UniProtKB:P01137\")\n|#\n#|\nTop10 from count-downstream of ARDS gene-list\n\n\"ENSEMBL:ENSG00000105329\"\n  \"ENSEMBL:ENSG00000112715\"\n  \"ENSEMBL:ENSG00000078401\"\n  \"ENSEMBL:ENSG00000100644\"\n  \"ENSEMBL:ENSG00000168610\"\n  \"ENSEMBL:ENSG00000125538\"\n  \"ENSEMBL:ENSG00000136689\"\n  \"ENSEMBL:ENSG00000100292\"\n  \"ENSEMBL:ENSG00000087250\"\n  \"ENSEMBL:ENSG00000105974\"\n  \"ENSEMBL:ENSG00000166949\"\n|#\n\n#|\nBacktrace results\nInput:\"ENSEMBL:ENSG00000105329\"\nOutput: \n\"ENSEMBL:ENSG00000208001\" . 0\n\"ENSEMBL:ENSG00000171109\" . 3\n\"ENSEMBL:ENSG00000063180\" . 2\n\"ENSEMBL:ENSG00000199038\" . 0\n\"ENSEMBL:ENSG00000199133\" . 0\n\"ENSEMBL:ENSG00000277443\" . 9\n\"ENSEMBL:ENSG00000211590\" . 0\n\"ENSEMBL:ENSG00000100410\" . 2\n\"ENSEMBL:ENSG00000109063\" . 7\n\"ENSEMBL:ENSG00000166347\" . 4\n\"ENSEMBL:ENSG00000162104\" . 2\n\"ENSEMBL:ENSG00000198982\" . 0\n\"ENSEMBL:ENSG00000125779\" . 1\n\"ENSEMBL:ENSG00000153391\" . 1\n\"ENSEMBL:ENSG00000103510\" . 2\n\"ENSEMBL:ENSG00000207590\" . 0\n\"ENSEMBL:ENSG00000207731\" . 0\n\"ENSEMBL:ENSG00000198026\" . 3\n\"ENSEMBL:ENSG00000083807\" . 4\n\"ENSEMBL:ENSG00000115718\" . 3\n\"ENSEMBL:ENSG00000199020\" . 0\n\"ENSEMBL:ENSG00000284520\" . 0\n\"ENSEMBL:ENSG00000163702\" . 5\n\"ENSEMBL:ENSG00000145649\" . 1\n\"ENSEMBL:ENSG00000153395\" . 1\n\"ENSEMBL:ENSG00000167315\" . 4\n\"ENSEMBL:ENSG00000160932\" . 0\n\"ENSEMBL:ENSG00000266964\" . 2\n\"ENSEMBL:ENSG00000165682\" . 3\n\"ENSEMBL:ENSG00000173805\" . 9\n\"ENSEMBL:ENSG00000125482\" . 4\n\"ENSEMBL:ENSG00000145794\" . 8\n\"ENSEMBL:ENSG00000163803\" . 1\n\"ENSEMBL:ENSG00000105370\" . 6\n\nInput:\"ENSEMBL:ENSG00000168610\"\nOutput: 29\n\"ENSEMBL:ENSG00000208001\" . 0\n\"ENSEMBL:ENSG00000063180\" . 2\n\"ENSEMBL:ENSG00000199038\" . 0\n\"ENSEMBL:ENSG00000199133\" . 0\n\"ENSEMBL:ENSG00000211590\" . 0\n\"ENSEMBL:ENSG00000100410\" . 2\n\"ENSEMBL:ENSG00000162104\" . 2\n\"ENSEMBL:ENSG00000198982\" . 0\n\"ENSEMBL:ENSG00000138744\" . 4\n\"ENSEMBL:ENSG00000125779\" . 1\n\"ENSEMBL:ENSG00000187258\" . 4\n\"ENSEMBL:ENSG00000153391\" . 1\n\"ENSEMBL:ENSG00000103510\" . 2\n\"ENSEMBL:ENSG00000207590\" . 0\n\"ENSEMBL:ENSG00000048740\" . 4\n\"ENSEMBL:ENSG00000198026\" . 3\n\"ENSEMBL:ENSG00000083807\" . 4\n\"ENSEMBL:ENSG00000137959\" . 3\n\"ENSEMBL:ENSG00000115850\" . 4\n\"ENSEMBL:ENSG00000115718\" . 3\n\"ENSEMBL:ENSG00000199020\" . 0\n\"ENSEMBL:ENSG00000174607\" . 1\n\"ENSEMBL:ENSG00000145649\" . 1\n\"ENSEMBL:ENSG00000167315\" . 4\n\"ENSEMBL:ENSG00000173805\" . 9\n\"ENSEMBL:ENSG00000196843\" . 1\n\"ENSEMBL:ENSG00000125482\" . 4\n\"ENSEMBL:ENSG00000145794\" . 8\n\"ENSEMBL:ENSG00000105370\" . 6\n\nInput:\"ENSEMBL:ENSG00000112715\"\nOutput: 1\n\"ENSEMBL:ENSG00000153391\" . 1\n\nInput: \"ENSEMBL:ENSG00000136689\"\nOutput: 41\n\"ENSEMBL:ENSG00000208001\" . 0\n\"ENSEMBL:ENSG00000171109\" . 3\n\"ENSEMBL:ENSG00000063180\" . 2\n\"ENSEMBL:ENSG00000133019\" . 5\n\"ENSEMBL:ENSG00000199038\" . 0\n\"ENSEMBL:ENSG00000199133\" . 0\n\"ENSEMBL:ENSG00000179776\" . 15\n\"ENSEMBL:ENSG00000021355\" . 5\n\"ENSEMBL:ENSG00000133661\" . 1\n\"ENSEMBL:ENSG00000207827\" . 1\n\"ENSEMBL:ENSG00000211590\" . 0\n\"ENSEMBL:ENSG00000100410\" . 2\n\"ENSEMBL:ENSG00000118194\" . 2\n\"ENSEMBL:ENSG00000109063\" . 7\n\"ENSEMBL:ENSG00000117569\" . 2\n\"ENSEMBL:ENSG00000162104\" . 2\n\"ENSEMBL:ENSG00000198982\" . 0\n\"ENSEMBL:ENSG00000138744\" . 4\n\"ENSEMBL:ENSG00000125779\" . 1\n\"ENSEMBL:ENSG00000085063\" . 14\n\"ENSEMBL:ENSG00000103510\" . 2\n\"ENSEMBL:ENSG00000207590\" . 0\n\"ENSEMBL:ENSG00000207731\" . 0\n\"ENSEMBL:ENSG00000284204\" . 0\n\"ENSEMBL:ENSG00000164330\" . 9\n\"ENSEMBL:ENSG00000101000\" . 6\n\"ENSEMBL:ENSG00000137959\" . 3\n\"ENSEMBL:ENSG00000115718\" . 3\n\"ENSEMBL:ENSG00000199020\" . 0\n\"ENSEMBL:ENSG00000284520\" . 0\n\"ENSEMBL:ENSG00000163702\" . 5\n\"ENSEMBL:ENSG00000167315\" . 4\n\"ENSEMBL:ENSG00000160932\" . 0\n\"ENSEMBL:ENSG00000070614\" . 3\n\"ENSEMBL:ENSG00000266964\" . 2\n\"ENSEMBL:ENSG00000165682\" . 3\n\"ENSEMBL:ENSG00000196843\" . 1\n\"ENSEMBL:ENSG00000125482\" . 4\n\"ENSEMBL:ENSG00000145794\" . 8\n\"ENSEMBL:ENSG00000163803\" . 1\n\"ENSEMBL:ENSG00000105370\" . 6 \n|#"
  },
  {
    "path": "contrib/medikanren/pieces-parts/tutorial.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/db.rkt\"\n  \"../../../medikanren/pieces-parts/query.rkt\")\n\n#|\nThis line binds the identifier S to the result of the following expression,\nwhich takes the first concept containing the curie string \"UniProtKB:P51587.\"\n\nFunctions Used:\nkeep: returns the first n elements of a list, documented in common.rkt\nfind-concepts: finds all concepts connected to a list of curie strings, documented in common.rkt\n|#\n(define S (keep 1 (find-concepts #t (list \"UniProtKB:P51587\"))))\n\n#|\nThese lines run the knowledge graph to find edges that use S as a subject and returns the associated concepts and edges as\nname=>concepts and name=>edges.\n\nFunctions Used:\nmatch-define: takes a list of names and an expression and binds each name to its corresponding value in the expressions, documented in Racket Documentation\nrun/graph: \n|#\n(match-define\n  (list name=>concepts name=>edges)\n  (run/graph\n   ((S S)\n    (O #f))\n   ((S->O #f))\n   (S S->O O)))\n\n#|\n
Defines Es as the list of edges retrieved from name=>edges (associated with S, which is the concept associated with the curie \"UniProtKB:P51587.\")\nname=>edges was defined using match-define,
and it contains the edges that correspond to the subject concept defined above.\n\nFunctions used:\nhash-ref: from racket,returns value for the key ('S->O) in hash (name=>edges)\n|#\n\n(define Es (hash-ref name=>edges 'S->O))\n\n#|\nNext, we sought to find concepts that specifically came from the GO ontology. In order to do this, we had to\nextract the provider from a list of edges.\n\nFunctions Used:\ndefine: in this case, define is being used to create a procedure (named \"provider\"), documented in Racket Documentation\nassoc: assoc takes in a variable and a list and returns the first element of the list whose value is equal to the varaible,\ndocumented in Racket Documentation\n\n|#\n(define (provider e)\n  (let ((a (assoc \"provided_by\" (list-ref e 5))))\n    (if a\n        (cdr a)\n        a)))\n\n;; This line uses sort and remove-duplicates, as well as the provider function above, to get all the provider names from the edges in Es\n(sort (remove-duplicates (map provider Es)) string<=?)\n\n;; This line filters out the edges in Es that have the GO ontology (gene_ontology) as a provider\n;; (define goEs (filter (lambda (e) (string=? \"gene_ontology\" (provider e))) Es))\n\n(define go-provider-string \"(\\\"http://purl.obolibrary.org/obo/go-plus.owl\\\")\")\n\n(define goEs (filter (lambda (e) (string=? go-provider-string (provider e))) Es))\n\n;; This line checks the number of such edges using length\n(length (filter (lambda (e) (string=? go-provider-string (provider e))) Es))\n\n;; This line binds the identifier E to the first edge in Es that has the GO ontology as a provider\n(define E (car (filter (lambda (e) (string=? go-provider-string (provider e))) Es)))\n\n\n#|\n
This function takes an edge and gets the subject concept and object concept that the edge relates along\nwith the predicate associated with the edge and returns them in a list that is formatted to show the relationship.\n
returns: (subject-concept-name edge-predicate object-concept-name)\n\n
Functions Used:\nconcept->name, edge->subject, edge->pred, edge->object, documented in common.rkt\n|#
\n(define (story E)\n  (list\n   (concept->name (edge->subject E))\n   (cdr (edge->pred E))\n   (concept->name (edge->object E))))\n\n(story E)\n;; maps the story function onto all of the individual edges in the list Es\n(map story Es)\n;; maps the story function onto all individual edges in the list goES\n(map story goEs)\n;; creates an anonymous function that takes the cdr of the predicate of an edge\n;; which finds all of the possible predicate names (i.e. physically_interacts_with, participates_in)\n;; then, this line maps that function onto all the edges in Es\n(remove-duplicates (map (lambda (E) (cdr (edge->pred E))) Es))\n\n#|\n
This creates a mutable hash table and sets it to *counters*\n\nFunctions Used:\nmake-hash: creates a hashtable, documented in Racket Documentation\n|#\n(define *counters* (make-hash))\n(define (inc-count! key)\n  (hash-update! *counters*\n\t\tkey\n\t\t(lambda (x) (+ x 1))\n\t\t(lambda () 1)))\n\n;; This line defines f and sets it equal to the file opened by the open-input-file function\n(define f (open-input-file \"../data/rtx2/edges.scm\"))\n(define e (read f))\n\n#|\nThis reads through the file defined as f and counts the number of \"provided_by\" predicates that appear in the file\n\nFunctions used:\nflush-output, read, eof-object?, begin, close-input-port: This reads through the file defined as f and counts\nthe number of \"provided_by\" predicates that appear in the file, documented in Racket Documentation\n\n(let loop ((n 0))\n  (when (= 0 (modulo n 10000))\n    (display \".\")\n    (flush-output))\n  (let ((r (read f)))\n    (if (eof-object? r)\n\t(begin\n\t  (close-input-port f)\n\t  *counters*)\n\t(begin\n\t  (inc-count! (cdr (assoc \"provided_by\" (vector-ref r 3))))\n\t  (loop (+ 1 n))))))\n|#\n\n;; We can also use a miniKanren query instead:\n(define edges (run 1000 (e) (edgeo e)))\n(remove-duplicates (map provider edges))\n(define (edge-relation e)\n  (let ((a (assoc \"relation\" (list-ref e 5))))\n    (if a\n        (cdr a)\n        a)))\n(define (predicate e)\n  (cdr (list-ref e 4)))\n(remove-duplicates (map edge-relation edges))\n(remove-duplicates (map predicate edges))\n\n#|\nThis defines qb as the query/graph subsequently defined\nThe query/graph is defined with an arbitrary subject concept (X), an object concept (rhobtb2) that corresponds with\nthe CURIE \"UMLS:C1425762\", any edges (X->rhobtb2) that relate any subject concept to the rhobtb2 object concept, and the pathway\nthat encompasses the (subject edge object) relationship\n\nFunctions Used:\nquery/graph: runs the query graph given subject and object concepts, documented in query.rkt\n|#\n(define qb (time (query/graph\n                  ((X       #f)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->rhobtb2 #f))\n                  (X X->rhobtb2 rhobtb2))))\n\n\n#|\nThis defines qo as the run of the query/graph\nThe query/graph is defined with a subject concept (S) that corresponds with the CURIE \"UniProtKB:P51587\", an arbitrary\nobject concept (O), any edges (S->O) that relate the S subject concept to any object concept, and the pathway\nthat encompasses the (subject edge object) relationship.\n\nThe query answers: What are all the concepts reachable from this one gene in 1-hop?\n\nFunctions Used:\nquery/graph: runs the query graph given subject and object concepts, documented in query.rkt\n|#\n(define qo (time (query/graph\n\t\t (\n\t\t  (S \"UniProtKB:P51587\")\n\t\t  (O #f)\n\t\t  )\n\t\t ((S->O #f))\n\t\t (S S->O O))))\n(pretty-print (time (report/query qo)))\n;;(pretty-print (time (ranked-paths qo)))\n\n\n;; defines a list of the providers that indicate the GO ontology\n(define go-providers\n  (list\n   \"(\\\"http://purl.obolibrary.org/obo/go-plus.owl\\\")\"\n   \"(\\\"http://purl.bioontology.org/ontology/OMIM\\\")\"))\n\n\n;; function that takes in a provider and checks if it is a GO provider using the list defined above (go-providers)\n(define (edge/go-provider? e)\n  (member (provider e) go-providers))\n\n;; function that takes in a provider and checks if it is not a GO provider\n(define (edge/not-go-provider? e)\n  (not (edge/go-provider? e)))\n\n#|\nThis defines qa as the run of the query/graph subsequently defined, which found two different paths from subject to object,\nseparating them them based on whether the edges in between were provided by the GO ontology or not.\n\nThe query/graph is defined with a subject concept (S) that corresponds with the CURIE \"UniProtKB:P51587\", an arbitrary\nobject concept (O), any edges (S-1>O) that relate the S subject concept to any object concept provided that the edges\nare of the GO ontology, and any edges (S-2>O) that relate the S subject concept to any object concept provided that the\nedges are not of the GO ontology.\n\nThis query answers: What are all the concepts related to the initial gene that go through the GO provider and also not through the GO provider? There has to be two 1-hop ways to get through the concept.\n\nFunctions Used:\nquery/graph: runs the query graph given subject and object concepts, documented in query.rkt\n|#\n(define qa (time (query/graph\n\t\t (\n\t\t  (S \"UniProtKB:P51587\")\n\t\t  (O #f)\n\t\t  )\n\t\t ((S-1>O #f edge/not-go-provider?)\n\t\t  (S-2>O #f edge/go-provider?))\n\t\t (S S-1>O O)\n\t\t (S S-2>O O))))\n\n;; prints a report of the queries from the run of the query graph stored in qa\n(pretty-print (time (report/query qa)))\n;; prints the ranked paths in qa\n;;(pretty-print (time (ranked-paths qa)))\n\n#|\nThis defines q as the run of the query/graph subsequently defined, which found two different paths from subject to object,\nseparating them them based on whether the edges in between were provided by the GO ontology or not.\n\nThe query/graph is defined with a subject concept (S) that corresponds with the CURIE \"UniProtKB:P51587\", arbitrary\nobject concepts (O1/O2), any edges (S->O1) that relate the S subject concept to any object concept provided that the edges\nare of the GO ontology, and any edges (S->O2) that relate the S subject concept to any object concept provided that the\nedges are not of the GO ontology.\n\nThis query relaxes the previous query so that the final concepts can be different.\n\nFunctions Used:\nquery/graph: runs the query graph given subject and object concepts, documented in query.rkt\n|#\n(define q (time (query/graph\n\t\t (\n\t\t  (S \"UniProtKB:P51587\")\n\t\t  (O1 #f)\n\t\t  (O2 #f)\n\t\t  )\n\t\t ((S->O1 #f edge/not-go-provider?)\n\t\t  (S->O2 #f edge/go-provider?))\n\t\t (S S->O1 O1)\n\t\t (S S->O2 O2))))\n(pretty-print (time (report/query q)))\n\n#|\nThis function checks whether the relation in a pathway is \"involved-in,\" which\nwould indicate that the relationship is part of the GO ontology\n|#\n(define go-pathway '(\"involved_in\"))\n\n(define (unique-gene? g)\n  (not (string=? \"UniProtKB:P51587\" g)))\n\n#|\nThis defines qc as the run of the query/graph subsequently defined, which found two different paths from subject to object,\nseparating them them based on whether the edges in between were provided by the GO ontology or not.\n\nThe query/graph is defined with a subject concept (S1) that corresponds with the CURIE \"UniProtKB:P51587\", arbitrary\nobject concept O, gene subject concept S2, any edges (S1->O) that relate the S subject concept to any object concept,\nand any edges (S2->O) that relate the S2 gene concept to any object concept provided that these paths are go pathways.\n\nThis query answers: What are other genes in the same pathway?\n\nFunctions Used:\nquery/graph: runs the query graph given subject and object concepts, documented in query.rkt\n|#\n;; TODO: create a variant where the sources are different. --> this is left as is because it is difficult to do\n(define qc (time (query/graph\n\t\t (\n\t\t  (S1 \"UniProtKB:P51587\")\n\t\t  (O #f)\n\t\t  (S2 gene)\n\t\t  )\n\t\t ((S1->O go-pathway)\n\t\t  (S2->O go-pathway))\n\t\t (S1 S1->O O)\n\t\t (S2 S2->O O))))\n\n;; prints a report of the queries from the run of the query graph stored in qc\n(pretty-print (time (report/query qc)))\n\n(define qd (time (query/graph\n\t\t (\n\t\t  (S1 \"UniProtKB:P51587\")\n\t\t  (O #f)\n\t\t  (S2 gene)\n\t\t  )\n\t\t ((S1->O go-pathway)\n\t\t  (S2->O go-pathway))\n\t\t (S1 S1->O O)\n\t\t (S2 S2->O O))))\n(pretty-print (time (report/query qd)))\n\n#|\n
Each edge is given a score based on a set of parameters, and every edge with the same score is put in a composite edge that can be identified by that score.\nThe function then returns a list of these composite edges organized by score, with the highest scoring composite edge is first.\nThis line defines r as the list returned by (ranked-paths qc)\n\n
Functions Used: \nranked-paths: ranked-paths takes a query/graph and uses a ranking system to return a list of composite edges from query/graph ranked by confidence, documented in query.rkt\n|#\n(define r (ranked-paths qc))\n;;(cadr r)\n;; prints the ranked-paths\n;;(pretty-print (time (ranked-paths qc)))\n\n;; finds the edges from qc that are S2->O\n;;(edges/query qc 'S2->O)\n;; finds the the number of genes that are in the same pathway\n(length (curies/query qc 'S2))\n(length (edges/query qc 'S2->O))\n\n\n#|\nThis defines qcomp as a query/graph
.\nThe query/graph is defined with a subject concept (S) that corresponds with the CURIE \"UniProtKB:P51587\", an\nobject concept (O) that must be a gene, any edges (S->O) that relate the S subject concept to any gene object concept, and\n
the pathway that encompasses the (subject edge object) relationship\n\nFunctions Used:\nquery/graph: runs the query graph given subject and object concepts, documented in query.rkt\n|#\n(define qcomp (time (query/graph\n\t\t (\n\t\t  (S \"UniProtKB:P51587\")\n\t\t  (O gene)\n\t\t  )\n\t\t ((S->O #f))\n\t\t (S S->O O))))\n\n;; prints the queries and the ranked paths\n(pretty-print (time (report/query qcomp)))\n(define rcomp (ranked-paths qcomp))\n;;rcomp\n\npositively-regulates\n;; low-level 1-hop query\n(define rhobtb2-curie \"UMLS:C1425762\")\n(run* (q)\n  (fresh (db edge eid subject object pred eprops\n             scid scui sname sdetails\n             pred-id pred-name\n             ocid ocui oname odetails)\n     (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n     (== pred `(,pred-id . ,pred-name))\n     (conde\n      ((== pred-name \"positively_regulates\"))\n      ((== pred-name \"negatively_regulates\")))\n     (~cui-concepto rhobtb2-curie `(,db . ,object))\n     (edgeo `(,db . ,edge))\n     (== `(,scid ,scui ,sname . ,sdetails) subject)\n     (== `(,ocid ,ocui ,oname . ,odetails) object)\n     (== q `(,db ,sname ,pred-name ,oname))))\n\n;; let's find that TMPRSS is negatively regulated by estrogens\n;; in 2 hops: estrogens -decreases-> androgens -increases-> TMPRSS2\n\n(define tmprss2-curie \"UMLS:C1336641\")\n(define androgens-curie \"UMLS:C0002844\")\n\n;; the second hop in a low level queryb\n(run* (q)\n      (fresh (db edge eid subject object pred eprops\n                 scid scui sname sdetails\n                 pred-id pred-name\n                 ocid ocui oname odetails)\n            (== `(,eid ,subject ,object ,pred . ,eprops) edge)\n            (== pred `(,pred-id . ,pred-name))\n            (conde\n             ((== pred-name \"positively_regulates\"))\n             ((== pred-name \"negatively_regulates\")))\n            (~cui-concepto tmprss2-curie `(,db . ,object))\n            (edgeo `(,db . ,edge))\n            (== `(,scid ,scui ,sname . ,sdetails) subject)\n            (== `(,ocid ,ocui ,oname . ,odetails) object)\n            (== q `(,db ,sname ,pred-name ,oname))))\n\n(define (pretty-edges q edge-label)\n  (map (lambda (e)\n       (list\n        ;;(edge->eid e)\n        (edge->dbname e)\n        ;;(concept->curie (edge->subject e))\n        (concept->name (edge->subject e))\n        (cdr (edge->pred e))\n        ;;(concept->curie (edge->object e))\n        (concept->name (edge->object e))))\n     (edges/query q edge-label)))\n;; second hop in a high-level query\n\n(define q_hop2r\n  (query/graph\n   (;; concepts\n    (O rhobtb2-curie)\n    (S #f))\n   (;; edges\n    (S->O (list \"positively_regulates\" \"negatively_regulates\")))\n   ;; paths\n   (S S->O O)))\n(report/query q_hop2r)\n(pretty-edges q_hop2r 'S->O)\n\n(define q_hop2\n  (query/graph\n   (;; concepts\n    (O tmprss2-curie)\n    (S #f))\n   (;; edges\n    (S->O (list \"positively_regulates\" \"negatively_regulates\")))\n   ;; paths\n   (S S->O O)))\n(report/query q_hop2)\n;; we can find androgens\n(pretty-edges q_hop2 'S->O)\n\n(define q_hop1\n  (query/graph\n   (;; concepts\n    (O androgens-curie)\n    (S #f))\n   (;; edges\n    (S->O (list \"negatively_regulates\")))\n   ;; paths\n   (S S->O O)))\n(report/query q_hop1)\n;; we can find estrogen\n(pretty-edges q_hop1 'S->O)\n\n(define q_2hops\n  (query/graph\n   (;; concepts\n    (O tmprss2-curie)\n    (S #f)\n    (R #f))\n   (;; edges\n    (R->S (list \"negatively_regulates\"))\n    (S->O (list \"positively_regulates\")))\n   ;; paths\n   (R R->S S)\n   (S S->O O)))\n;; explosion of results\n(report/query q_2hops)\n"
  },
  {
    "path": "contrib/medikanren/query-graph.rkt",
    "content": "#lang racket/base\n(provide\n  ? help\n  graph path\n  C P T\n  show hide count unmodify\n  graph? path? C? P? T? show? hide? count? except?\n  except\n  inote iref aref untag)\n(require \"common.rkt\" \"mk.rkt\")\n\n(define help \"Use (?) or (? ) for more information.\")\n(define (? . _) \"TODO: define ?.\")\n\n(define (aref alist key)\n  (define kv (assoc key alist))\n  (unless kv (error \"missing association list key:\" key alist))\n  (cdr kv))\n(define (tagged? tag x)\n  (and (vector? x) (= 2 (vector-length x)) (eqv? tag (vector-ref x 0))))\n(define (tag t x)  (vector t x))\n(define (tagref x) (vector-ref x 0))\n(define (untag x)  (vector-ref x 1))\n\n;; Selectors\n(define (except x)  (tag 'except x))\n(define (except? x) (tagged? 'except x))\n;; Modifiers\n(define (show x)    (tag 'show  (unmodify x)))\n(define (hide x)    (tag 'hide  (unmodify x)))\n(define (count x)   (tag 'count (unmodify x)))\n(define (show? x)   (tagged? 'show x))\n(define (hide? x)   (tagged? 'hide x))\n(define (count? x)  (tagged? 'count x))\n(define (unmodify x)\n  (if (or (show? x) (hide? x) (count? x)) (untag x) x))\n;; Graph sets\n(define (graph? x)  (tagged? 'graph (unmodify x)))\n(define (path? x)   (tagged? 'path  (unmodify x)))\n;; Element sets: ((dbname id . data) ...)\n(define (C? x)      (tagged? 'concept     (unmodify x))) ;; data = (cui name)\n(define (P? x)      (tagged? 'predicate   (unmodify x))) ;; data = name\n(define (T? x)      (tagged? 'concep-type (unmodify x))) ;; data = name\n\n(define (inote x)\n  (define xs (untag (unmodify x)))\n  (map cons (range (length xs)) xs))\n(define (iref x . args)\n  (define u (unmodify x))\n  (define t (tagref u))\n  (define xs (untag u))\n  (define (iref? x) (and (integer? x) (<= 0 x)))\n  (define ixs\n    (foldl (lambda (arg ixs)\n             (cond ((iref? arg) (cons arg ixs))\n                   ((and (list? arg) (andmap iref? arg)) (append arg ixs))\n                   (else (error \"invalid iref argument:\" arg args))))\n           '() args))\n  (define new\n    (reverse (caddr (foldl (lambda (i acc)\n                             (define offset    (car acc))\n                             (define xs        (cadr acc))\n                             (define kept      (caddr acc))\n                             (define remaining (drop (- i offset) xs))\n                             (list i remaining (cons (car remaining) kept)))\n                           (list 0 xs '()) (sort ixs <)))))\n  (tag t new))\n\n;; These assumes unique pairing of dbname and id.\n(define (element=3? xs) (and (pair? xs) (pair? (cdr xs)) (pair? (cddr xs))))\n  (tag 'path\n       (let loop ((args args) (edges '()))\n         (cond ((null? args) edges)\n               ((l>=3? args)\n                (define e (edge (car args) (cadr args) (caddr args)))\n                (loop (cddr args) (cons e edges)))))))\n\n;; TODO: define this as syntax.\n(define (graph element-bindings components)\n  )\n\n"
  },
  {
    "path": "contrib/medikanren/simple-query.rkt",
    "content": "#lang racket\n\n(provide\n  (all-from-out \"../../medikanren/mk.rkt\")\n  (all-from-out \"../../medikanren/db.rkt\")\n  (all-from-out \"../../medikanren/mk-db.rkt\")\n  (all-from-out \"../../medikanren/common.rkt\")\n  (all-from-out racket/date)\n  (all-defined-out))\n\n(require\n  \"../../medikanren/mk.rkt\"\n  \"../../medikanren/db.rkt\"\n  \"../../medikanren/mk-db.rkt\"\n  \"../../medikanren/common.rkt\"\n  \"../../attic/medikanren/create-all-hashtables.rkt\"\n  racket/date\n  (except-in racket/match ==))\n\n#|\nconcept format (subject or object), without dbname at front:\n\n`(,cid ,cui ,name (,catid . ,cat) . ,props)\n\nconcept format (subject or object), with dbname at front (as used in fuzzy-concepto):\n\n`(,dbname ,cid ,cui ,name (,catid . ,cat) . ,props)\n\n\nedge format, without dbname at front:\n\n`(,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n       (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n       (,pid . ,pred) . ,eprops)\n\nedge format, with dbname at front (as used in edgeo):\n\n`(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n               (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n               (,pid . ,pred) . ,eprops)\n|#\n\n\n(displayln \"loading semmed knowledge graph\")\n(define semmed (make-db \"../../medikanren/data/semmed\"))\n\n(printf \"\\n\\nfull semmed edge:\\n\")\n(run 1 (edge) (db:edgeo semmed edge))\n\n(printf \"\\n\\nTyped query 1:\\n\")\n(run 1 (q)\n  (fresh (edge1\n          eid1 scid1 scui1 sname1 scatid1 scat1 sprops1\n          ocid1 ocui1 oname1 ocatid1 ocat1 oprops1\n          pid1 pred1 eprops1)\n    (== `(,eid1 (,scid1 ,scui1 ,sname1 (,scatid1 . ,scat1) . ,sprops1)\n                (,ocid1 ,ocui1 ,oname1 (,ocatid1 . ,ocat1) . ,oprops1)\n                (,pid1 . ,pred1) . ,eprops1)\n        edge1)\n    (== `(,sname1 ,pred1 ,oname1) q)\n    (db:edgeo semmed edge1)))\n\n(printf \"\\n\\nTyped query 2:\\n\")\n(run 1 (q)\n  (fresh (edge1\n          eid1 scid1 scui1 sname1 scatid1 scat1 sprops1\n          ocid1 ocui1 oname1 ocatid1 ocat1 oprops1\n          pid1 pred1 eprops1)\n    (== `(,eid1 (,scid1 ,scui1 ,sname1 (,scatid1 . ,scat1) . ,sprops1)\n                (,ocid1 ,ocui1 ,oname1 (,ocatid1 . ,ocat1) . ,oprops1)\n                (,pid1 . ,pred1) . ,eprops1)\n        edge1)\n    (== '(5 . \"chemical_substance\") `(,scatid1 . ,scat1))\n    (== `(,sname1 ,pred1 ,oname1) q)\n    (db:edgeo semmed edge1)))\n\n(printf \"\\n\\nTyped query 3:\\n\")\n(run 1 (q)\n  (fresh (edge1\n          eid1 scid1 scui1 sname1 scatid1 scat1 sprops1\n          ocid1 ocui1 oname1 ocatid1 ocat1 oprops1\n          pid1 pred1 eprops1)\n    (== `(,eid1 (,scid1 ,scui1 ,sname1 (,scatid1 . ,scat1) . ,sprops1)\n                (,ocid1 ,ocui1 ,oname1 (,ocatid1 . ,ocat1) . ,oprops1)\n                (,pid1 . ,pred1) . ,eprops1)\n        edge1)\n    (== '(5 . \"chemical_substance\") `(,scatid1 . ,scat1))\n    (== '(1 . \"treats\") `(,pid1 . ,pred1))\n    (== `(,sname1 ,pred1 ,oname1) q)\n    (db:edgeo semmed edge1)))\n"
  },
  {
    "path": "contrib/medikanren/test-web-server.rkt",
    "content": "#lang racket\n(require net/http-client)\n\n(define (read/string s) (with-input-from-string s (lambda () (read))))\n(define (write/string datum) (with-output-to-string (lambda () (write datum))))\n(define (pretty/string datum)\n  (with-output-to-string (lambda () (pretty-print datum))))\n\n(define (query sdatum)\n  (define-values (bstatus headers in)\n    (http-sendrecv \"localhost\" \"/query\"\n                   #:port 8000\n                   #:ssl? #f\n                   #:version \"1.1\"\n                   #:method \"POST\"\n                   #:data (write/string sdatum)))\n  (define status (bytes->string/utf-8 bstatus))\n  (define response (port->string in))\n  (close-input-port in)\n  (cond ((string-suffix? status \"200 OK\") (read/string response))\n        (else (printf \"~a\\n\" response)\n              (error \"Query failed:\" status (map bytes->string/utf-8 headers)\n                     response))))\n\n(define (decreases? p)\n  (member (cddr p) '(\"negatively_regulates\"\n                     \"prevents\"\n                     \"treats\"\n                     \"disrupts\"\n                     \"increases_degradation_of\"\n                     \"decreases_activity_of\"\n                     \"decreases_expression_of\")))\n(define (increases? p)\n  (member (cddr p) '(\"positively_regulates\"\n                     \"produces\"\n                     \"causes\"\n                     \"causes_condition\"\n                     \"causally_related_to\"\n                     \"contributes_to\"\n                     \"gene_associated_with_condition\"\n                     \"gene_mutations_contribute_to\"\n                     \"decreases_degradation_of\"\n                     \"increases_activity_of\"\n                     \"increases_expression_of\")))\n\n(define SP (map (lambda (cp)\n                  (define c (car cp))\n                  (define pS (cadr cp))\n                  (list c (filter decreases? pS) #f))\n                (take (query '(concept #t #f 0 #f (\"imatin\"))) 1)))\n\n(define OP (map (lambda (cp)\n                  (define c (car cp))\n                  (define pO (caddr cp))\n                  (list c #f (filter increases? pO)))\n                (take (query '(concept #f #t 0 #f (\"asthma\"))) 1)))\n\n(displayln \"Imatinib:\")\n(pretty-print SP)\n(newline)\n(displayln \"Asthma:\")\n(pretty-print OP)\n\n(define X (query `(X ,SP ,OP)))\n(define x-bcr\n  (car (filter (lambda (x) (equal? (cadddr (car x)) \"BCR gene\")) X)))\n\n(newline)\n(displayln 'X:)\n(pretty-print (car x-bcr))\n(newline)\n(displayln 'S-edges:)\n(pretty-print (cadr x-bcr))\n(newline)\n(displayln 'O-edges:)\n(pretty-print (caddr x-bcr))\n"
  },
  {
    "path": "contrib/medikanren/use-cases/CHAMP1_RNA_seq.rkt",
    "content": "#lang racket\n(require\n  \"../../../medikanren/pieces-parts/query.rkt\"\n  \"../pieces-parts/Thi-useful-functions.rkt\")\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*********GENERAL SEARCH********;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; *** Data Sources:\n;; - Processed CHAMP1 RNAseq data from outside of mediKanren\n;; - RNA was obtained from patients or control\n;;  cultured fibroblasts derived from skin biopsies\n;;\n;; *** Objective:\n;; Repurpose drugs for CHAMP1 genetic disorder using RNAseq data from patients-derived skin fibroblasts\n;;\n;; *** Please find the case presentation at\n;; First, I'm doing exploratory searches for the disease information related to CHAMP1 genes:\n;; Find disease conditions that are related to CHAMP1 genes\n(curie-synonyms/names \"HGNC:20311\")\n(define CHAMP1 \"HGNC:20311\")\n;; Check the diseases and conditions associted with the CHAMP1 gene\n(define q-disease-CHAMP1 (time (query/graph\n                     ((S disease)\n                      (O CHAMP1))\n                     ((S->O #f))\n                     (S S->O O))))\n\n(define disease-CHAMP1-edges (edges/query q-disease-CHAMP1 'S->O))\n\n;; The results show that CHAMP1 gene (chromosome alignment-maintaining phosphoprotein, is a protein-coding gene,\n;; a member of the zinc fingers C2H2-types protein, located on chromosome 13q34)\n;; is associated with certain disease conditions such as\n;; mental retardation (autosomal dominant), rare (non-syndromic) intellectual disability, monogenic genetic\n;; central nervous system disorder, mental disorder, and psychiatric disorder. \n\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******STRATEGY NUMBER 1*******;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; In this strategy, we want to find drugs that target the genes that belong to enriched functional categories\n;; such as cell cycle and cell senescence, retinol metabolism (which are results from gene set enrichemnet analysis (GSEA) performed\n;; outside of medikanren).\n;; GSEA has identified a number of genes that are upregulated in CHAMP1 fibroblasts compared to control fibroblasts.\n\n;; First, find HGNC CURIEs (\"HGNC:\") of each gene from the gene name (either by using\n;; genecards database \"https://www.genecards.org/\" or using mediKanren's find-concepts\n;; ,then check if they are synonymized.\n;; If the CURIE is synonymized, we use it to define the gene/protein in query/graph\n;; eg:\n\n(find-concepts #f (list \"VIM\"))\n(curie-synonyms/names \"HGNC:1583\")\n\n\n;; genes that are altered in the cell cycle pathway:\n(define CCND2 \"HGNC:1583\") ;; cell cycle up-regulated\n(define TUBA1A \"HGNC:20766\") ;; cell cycle down-regulated\n;; cell senescence pathway:\n;(define CCND2 \"HGNC:1583\") ;; up-regulated\n(define RASSF5 \"HGNC:17609\") ;; up-regulated\n;; DNA replication| apoptosis \n(define PSMA5 \"HGNC:9534\");; up-regulated\n;; Oocyte meiosis | progesterone-mediated oocyte maturation| calcium signaling\n(define ADCY4 \"HGNC:235\");; up-regulate\n;; retinol metabolism:\n(define ALDH1A1 \"HGNC:402\");; up-regulated\n;; ABC transporter:\n(define ABCA13 \"HGNC:14638\");; up-regulated\n;; HIV infection| calcium\n(define PTK2B \"HGNC:9612\");; up-regulated\n(define AP1G2 \"HGNC:556\");; up-regulated\n;; amyotropic lateral sclerosis | apoptosis\n(define TNFRSF1B \"HGNC:11917\");; down-regulated\n;; regulation of actin cytoskeleton:\n(define FGF10 \"HGNC:3666\");;  up-regulated\n(define CHRM2 \"HGNC:1951\");; down-regulated\n;; Gonadotropin hormone-releasing\n(define KCNN4 \"HGNC:6293\");; down-regulated\n;; ECM receptor interaction:\n(define CD36 \"HGNC:1663\");;  up-regulated\n;; Neuroactive ligand-receptor interaction | calcium\n(define EDNRB \"HGNC:3180\") ;;  up-regulated\n(define LHB \"HGNC:6584\");; down-regulated\n;; mRNA surveillance:\n(define MSI2 \"HGNC:18585\") ;; down-regulated\n;; calcium\n;(define ADCY4 \"HGNC:235\");; up-regulated\n;(define PTK2B \"HGNC:9612\");; up-regulated\n(define ERBB4 \"HGNC:3432\");; up-regulated\n;(define CHRM2 \"HGNC:1951\");; down-regulated\n;(define EDNRB \"HGNC:3180\") ;;  up-regulated\n;; apoptosis:\n(define VIM \"HGNC:12692\");; down-regulated\n\n\n;; All selected upregulated genes in enriched functional categories are:\n(define functional-cat-up (list CCND2 RASSF5 PSMA5 ADCY4 ALDH1A1 ABCA13 PTK2B\n                                AP1G2 FGF10 CD36 EDNRB EDNRB ERBB4))\n(define functional-cat-down (list TUBA1A TNFRSF1B CHRM2 KCNN4 LHB MSI2 VIM))\n\n\n(define results-CHAMP1-functional-cat-down (find-drugs-for-genes functional-cat-up positively-regulates))\n(define results-CHAMP1-functional-cat-up (find-drugs-for-genes functional-cat-up negatively-regulates))\n;;extract drug=>gene hash-table:\n(define drug=>gene-CHAMP1-functional-cat-down (car results-CHAMP1-functional-cat-down))\n(define drug=>gene-CHAMP1-functional-cat-up (car results-CHAMP1-functional-cat-up))\n;;extract gene=>drug hash-table:\n(define gene=>drug-CHAMP1-functional-cat-down (cadr results-CHAMP1-functional-cat-down))\n(define gene=>drug-CHAMP1-functional-cat-up (car results-CHAMP1-functional-cat-up))\n(define drug=>gene-strategy1 (merge-assoc-lists (list drug=>gene-CHAMP1-functional-cat-down drug=>gene-CHAMP1-functional-cat-up)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******STRATEGY NUMBER 2*******;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n\n;; Based on literature research, we identifed 5 different disease conditions that are associated with CHAMP1 genetic disorder:\n\n(define hypotonia-concepts (find-concepts #f (list \"hypotonia\")))\n(define cerebral-palsy-concepts (find-concepts #f (list \"cerebral palsy\")))\n(define autism-concepts (find-concepts #f (list \"autism\")))\n(define dev-delay-concepts (find-concepts #f (list \"developmental delay\")))\n(define epilepsy-concepts (find-concepts #f (list \"epilepsy\")))\n\n\n;; In this 2nd strategy, we first search for all the genes that are associated with the five CHAMP1\n;; disease associated conditions using run/graph\n\n(match-define\n  (list name=>concepts name=>edges)\n  (run/graph\n   ((S #f)\n    (O (set-union hypotonia-concepts\n                  cerebral-palsy-concepts\n                  autism-concepts\n                  dev-delay-concepts\n                  epilepsy-concepts)))\n   ((S->O gene-to-disease-preds))\n   (S S->O O)))\n\n;; filter the subjects to retain only genes or proteins and get their names:\n(map (lambda (y) (cons (concept->curie y) (concept->name y)))\n     (filter (lambda (x)\n               (gene/protein-concept? (concept->curie x))) (hash-ref name=>concepts 'S)))\n\n;; This filter results in 1397 genes/proteins that are related to CHAMP1 patients' phenotypes.\n;; I then cleaned the data, converted it to .csv and mapped different gene/protein identifers to HGNC symbols\n;; then I removed duplicates and NA.\n;; This resulted in 934 genes.\n;; Using these genes, I plot a volcano plot that show differences in expression levels between\n;; CHAMP1 patients fibroblasts vs control fibroblasts.\n;; This visualisation shows genes that are statistically significantly altered between these\n;; two conditions. These genes become our drug targets.\n\n\n;; Now we want to find drugs that reverse the directions of DEG genes (which are genes found to be associated\n;; with CHAMP1 patients' phenotypes- the results from the run/graph above.\n;; Directionality is provided by gene expression values (determined by experiments on CHAMP1 patients' fibroblasts).\n;; For genes that are significantly upregulated, we want to find drugs that decrease their expression, and vice versa.\n\n\n;; Abstract genes that are upregulated:\n(define CACNB4 \"HGNC:1404\")\n(define PRICKLE1 \"HGNC:17019\")\n(define DMD \"HGNC:2928\")\n(define SHANK2 \"HGNC:14295\")\n(define MAP2 \"HGNC:6839\")\n(define H19 \"HGNC:4713\")\n(define BCHE \"HGNC:983\")\n(define EFNA5 \"HGNC:3225\")\n(define CNTNAP2 \"HGNC:13830\")\n(define ANKH \"HGNC:15492\")\n(define SLC12A6 \"HGNC:10914\")\n(define CHAMP1-phenotype-RNA-up\n  (list CACNB4 PRICKLE1 DMD SHANK2 MAP2 H19 BCHE EFNA5 CNTNAP2 ANKH SLC12A6))\n\n;; Alternatively, for genes that are significantly downregulatated, we want to find drugs that increase their expression: \n(define GABRA5 \"HGNC:4079\")\n;(define TNFRSF1B \"HGNC:11917\")\n(define STX1B \"HGNC:18539\")\n(define RBFA \"HGNC:26120\")\n(define CHAMP1-phenotype-RNA-down\n  (list GABRA5 TNFRSF1B STX1B RBFA))\n\n\n\n;; Now we use the function find-drugs-for-genes in Thi's-useful-functions:\n(define results-CHAMP1-phenotype-RNA-up (find-drugs-for-genes CHAMP1-phenotype-RNA-up negatively-regulates))\n(define drug=>gene-CHAMP1-phenotype-RNA-up (car results-CHAMP1-phenotype-RNA-up))\n(define gene=>drug-CHAMP1-phenotype-RNA-up (cadr results-CHAMP1-phenotype-RNA-up))\n\n(define results-CHAMP1-phenotype-RNA-down (find-drugs-for-genes CHAMP1-phenotype-RNA-down positively-regulates))\n(define drug=>gene-CHAMP1-phenotype-RNA-down (car results-CHAMP1-phenotype-RNA-down))\n(define gene=>drug-CHAMP1-phenotype-RNA-down (cadr results-CHAMP1-phenotype-RNA-down))\n\n;; use the get-num-values function in Thi's-useful-functions:\n(define drug=>gene-CHAMP1-phenotype-RNA-up-with-stats (get-num-values drug=>gene-CHAMP1-phenotype-RNA-up))\n(define gene=>drug-CHAMP1-phenotype-RNA-up-with-stats (get-num-values gene=>drug-CHAMP1-phenotype-RNA-up))\n\n(define drug=>gene-CHAMP1-phenotype-RNA-down-with-stats (get-num-values drug=>gene-CHAMP1-phenotype-RNA-down))\n(define gene=>drug-CHAMP1-phenotype-RNA-down-with-stats (get-num-values gene=>drug-CHAMP1-phenotype-RNA-down))\n\n(define merged_strategy2 (merge-2-assoc-list drug=>gene-CHAMP1-phenotype-RNA-up drug=>gene-CHAMP1-phenotype-RNA-down))\n(define merged_trategy2_count (get-num-values (car merged_strategy2)))\n\n(define merged_strategy2_genes (merge-2-assoc-list gene=>drug-CHAMP1-phenotype-RNA-up gene=>drug-CHAMP1-phenotype-RNA-down))\n(define merged_trategy2_genes_count (get-num-values (car merged_strategy2_genes)))\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******************************;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*******STRATEGY NUMBER 3*******;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; 2-edge queries to find drugs that treat the CHAMP1 disease conditions and reverse the gene expression directions:\n;; These are all significantly altered genes in differential expression analyses performed outside of mediKanren\n\n(define CHAMP1-DE-RNA-up (list \"ENSEMBL:ENSG00000228630\"\n                               \"ENSEMBL:ENSG00000261340\"\n                               \"ENSEMBL:ENSG00000083937\"\n                               \"ENSEMBL:ENSG00000143106\"\n                               \"ENSEMBL:ENSG00000140199\"\n                               \"ENSEMBL:ENSG00000065357\"\n                               \"ENSEMBL:ENSG00000129480\"\n                               \"ENSEMBL:ENSG00000162688\"\n                               \"ENSEMBL:ENSG00000180818\"\n                               \"ENSEMBL:ENSG00000136478\"\n                               \"ENSEMBL:ENSG00000065413\"\n                               \"ENSEMBL:ENSG00000167394\"\n                               \"ENSEMBL:ENSG00000163249\"\n                               \"ENSEMBL:ENSG00000118762\"\n                               \"ENSEMBL:ENSG00000185070\"\n                               \"ENSEMBL:ENSG00000089060\"\n                               \"ENSEMBL:ENSG00000173221\"\n                               \"ENSEMBL:ENSG00000175040\"\n                               \"ENSEMBL:ENSG00000112964\"\n                               \"ENSEMBL:ENSG00000111670\"\n                               \"ENSEMBL:ENSG00000119986\"\n                               \"ENSEMBL:ENSG00000106415\"\n                               \"ENSEMBL:ENSG00000038427\"\n                               \"ENSEMBL:ENSG00000154122\"\n                               \"ENSEMBL:ENSG00000176531\"\n                               \"ENSEMBL:ENSG00000121413\"\n                               \"ENSEMBL:ENSG00000176809\"\n                               \"ENSEMBL:ENSG00000165804\"\n                               \"ENSEMBL:ENSG00000198948\"\n                               \"ENSEMBL:ENSG00000012171\"\n                               \"ENSEMBL:ENSG00000267454\"\n                               \"ENSEMBL:ENSG00000182379\"\n                               \"ENSEMBL:ENSG00000213983\"\n                               \"ENSEMBL:ENSG00000169313\"\n                               \"ENSEMBL:ENSG00000137573\"\n                               \"ENSEMBL:ENSG00000174469\"\n                               \"ENSEMBL:ENSG00000189129\"\n                               \"ENSEMBL:ENSG00000112378\"\n                               \"ENSEMBL:ENSG00000136048\"\n                               \"ENSEMBL:ENSG00000101134\"\n                               \"ENSEMBL:ENSG00000176928\"\n                               \"ENSEMBL:ENSG00000184916\"\n                               \"ENSEMBL:ENSG00000162643\"\n                               \"ENSEMBL:ENSG00000266094\"\n                               \"ENSEMBL:ENSG00000150540\"\n                               \"ENSEMBL:ENSG00000176771\"\n                               \"ENSEMBL:ENSG00000138772\"\n                               \"ENSEMBL:ENSG00000115271\"\n                               \"ENSEMBL:ENSG00000250133\"\n                               \"ENSEMBL:ENSG00000179104\"\n                               \"ENSEMBL:ENSG00000145390\"\n                               \"ENSEMBL:ENSG00000184349\"\n                               \"ENSEMBL:ENSG00000101605\"\n                               \"ENSEMBL:ENSG00000205002\"\n                               \"ENSEMBL:ENSG00000198133\"\n                               \"ENSEMBL:ENSG00000205835\"\n                               \"ENSEMBL:ENSG00000165113\"\n                               \"ENSEMBL:ENSG00000172403\"\n                               \"ENSEMBL:ENSG00000120899\"\n                               \"ENSEMBL:ENSG00000174600\"\n                               \"ENSEMBL:ENSG00000099260\"\n                               \"ENSEMBL:ENSG00000137727\"\n                               \"ENSEMBL:ENSG00000136160\"\n                               \"ENSEMBL:ENSG00000182901\"\n                               \"ENSEMBL:ENSG00000112981\"\n                               \"ENSEMBL:ENSG00000242600\"\n                               \"ENSEMBL:ENSG00000115604\"\n                               \"ENSEMBL:ENSG00000144229\"\n                               \"ENSEMBL:ENSG00000151623\"\n                               \"ENSEMBL:ENSG00000165023\"\n                               \"ENSEMBL:ENSG00000152804\"\n                               \"ENSEMBL:ENSG00000112379\"\n                               \"ENSEMBL:ENSG00000082497\"\n                               \"ENSEMBL:ENSG00000144645\"\n                               \"ENSEMBL:ENSG00000196208\"\n                               \"ENSEMBL:ENSG00000228495\"\n                               \"ENSEMBL:ENSG00000135919\"\n                               \"ENSEMBL:ENSG00000211448\"\n                               \"ENSEMBL:ENSG00000141449\"\n                               \"ENSEMBL:ENSG00000203727\"\n                               \"ENSEMBL:ENSG00000013588\"\n                               \"ENSEMBL:ENSG00000130600\"\n                               \"ENSEMBL:ENSG00000126861\"\n                               \"ENSEMBL:ENSG00000165084\"\n                               \"ENSEMBL:ENSG00000179869\"\n                               \"ENSEMBL:ENSG00000114200\"\n                               \"ENSEMBL:ENSG00000143028\"\n                               \"ENSEMBL:ENSG00000164106\"\n                               \"ENSEMBL:ENSG00000138449\"\n                               \"ENSEMBL:ENSG00000110723\"\n                               \"ENSEMBL:ENSG00000162687\"\n                               \"ENSEMBL:ENSG00000183775\"\n                               \"ENSEMBL:ENSG00000106538\"\n                               \"ENSEMBL:ENSG00000064225\"\n                               \"ENSEMBL:ENSG00000086289\"\n                               \"ENSEMBL:ENSG00000070193\"\n                               \"ENSEMBL:ENSG00000116183\"\n                               \"ENSEMBL:ENSG00000102109\"\n                               \"ENSEMBL:ENSG00000078018\"\n                               \"ENSEMBL:ENSG00000099864\"\n                               \"ENSEMBL:ENSG00000173391\"\n                               \"ENSEMBL:ENSG00000198947\"\n                               \"ENSEMBL:ENSG00000139174\"\n                               \"ENSEMBL:ENSG00000165092\"\n                               \"ENSEMBL:ENSG00000162105\"\n                               \"ENSEMBL:ENSG00000137672\"\n                               \"ENSEMBL:ENSG00000178568\"\n                               \"ENSEMBL:ENSG00000064042\"\n                               \"ENSEMBL:ENSG00000135218\"\n                               \"ENSEMBL:ENSG00000126785\"\n                               \"ENSEMBL:ENSG00000240694\"\n                               \"ENSEMBL:ENSG00000248874\"\n                               \"ENSEMBL:ENSG00000118971\"\n                               \"ENSEMBL:ENSG00000182389\"\n                               \"ENSEMBL:ENSG00000129467\"\n                               \"ENSEMBL:ENSG00000106483\"\n                               \"ENSEMBL:ENSG00000123572\"))\n\n\n(define CHAMP1-DE-RNA-down (list   \"EMSEMBL:ENSG00000204792\"\n                                   \"EMSEMBL:ENSG00000166796\"\n                                   \"EMSEMBL:ENSG00000186297\"\n                                   \"EMSEMBL:ENSG00000005379\"\n                                   \"EMSEMBL:ENSG00000234465\"\n                                   \"EMSEMBL:ENSG00000165887\"\n                                   \"EMSEMBL:ENSG00000115648\"\n                                   \"EMSEMBL:ENSG00000102575\"\n                                   \"EMSEMBL:ENSG00000175084\"\n                                   \"EMSEMBL:ENSG00000145824\"\n                                   \"EMSEMBL:ENSG00000213030\"\n                                   \"EMSEMBL:ENSG00000132639\"\n                                   \"EMSEMBL:ENSG00000006606\"\n                                   \"EMSEMBL:ENSG00000101017\"\n                                   \"EMSEMBL:ENSG00000154451\"\n                                   \"EMSEMBL:ENSG00000169429\"\n                                   \"EMSEMBL:ENSG00000104826\"\n                                   \"EMSEMBL:ENSG00000163618\"\n                                   \"EMSEMBL:ENSG00000147573\"\n                                   \"EMSEMBL:ENSG00000171517\"\n                                   \"EMSEMBL:ENSG00000130720\"\n                                   \"EMSEMBL:ENSG00000157557\"\n                                   \"EMSEMBL:ENSG00000178882\"\n                                   \"EMSEMBL:ENSG00000156453\"\n                                   \"EMSEMBL:ENSG00000148803\"\n                                   \"EMSEMBL:ENSG00000107611\"\n                                   \"EMSEMBL:ENSG00000175294\"\n                                   \"EMSEMBL:ENSG00000181072\"\n                                   \"EMSEMBL:ENSG00000104783\"\n                                   \"EMSEMBL:ENSG00000128285\"\n                                   \"EMSEMBL:ENSG00000080823\"\n                                   \"EMSEMBL:ENSG00000167889\"\n                                   \"EMSEMBL:ENSG00000124191\"\n                                   \"EMSEMBL:ENSG00000163701\"\n                                   \"EMSEMBL:ENSG00000076706\"\n                                   \"EMSEMBL:ENSG00000144354\"\n                                   \"EMSEMBL:ENSG00000103034\"\n                                   \"EMSEMBL:ENSG00000164929\"\n                                   \"EMSEMBL:ENSG00000204103\"\n                                   \"EMSEMBL:ENSG00000242265\"\n                                   \"EMSEMBL:ENSG00000196460\"\n                                   \"EMSEMBL:ENSG00000138395\"\n                                   \"EMSEMBL:ENSG00000225968\"\n                                   \"EMSEMBL:ENSG00000028137\"\n                                   \"EMSEMBL:ENSG00000091622\"\n                                   \"EMSEMBL:ENSG00000125968\"\n                                   \"EMSEMBL:ENSG00000173848\"\n                                   \"EMSEMBL:ENSG00000239332\"\n                                   \"EMSEMBL:ENSG00000139278\"\n                                   \"EMSEMBL:ENSG00000137563\"\n                                   \"EMSEMBL:ENSG00000163814\"\n                                   \"EMSEMBL:ENSG00000121904\"\n                                   \"EMSEMBL:ENSG00000186847\"\n                                   \"EMSEMBL:ENSG00000099365\"\n                                   \"EMSEMBL:ENSG00000136490\"\n                                   \"EMSEMBL:ENSG00000100181\"\n                                   \"EMSEMBL:ENSG00000079462\"\n                                   \"EMSEMBL:ENSG00000026025\"\n                                   \"EMSEMBL:ENSG00000105255\"\n                                   \"EMSEMBL:ENSG00000188064\"\n                                   \"EMSEMBL:ENSG00000103449\"\n                                   \"EMSEMBL:ENSG00000235162\"\n                                   \"EMSEMBL:ENSG00000074410\"\n                                   \"EMSEMBL:ENSG00000170961\"\n                                   \"EMSEMBL:ENSG00000140280\"\n                                   \"EMSEMBL:ENSG00000187583\"\n                                   \"EMSEMBL:ENSG00000205683\"\n                                   \"EMSEMBL:ENSG00000109062\"\n                                   \"EMSEMBL:ENSG00000159231\"\n                                   \"EMSEMBL:ENSG00000183077\"\n                                   \"EMSEMBL:ENSG00000173588\"\n                                   \"EMSEMBL:ENSG00000167552\"\n                                   \"EMSEMBL:ENSG00000243156\"\n                                   \"EMSEMBL:ENSG00000166886\"\n                                   \"EMSEMBL:ENSG00000153944\"\n                                   \"EMSEMBL:ENSG00000196912\"\n                                   \"EMSEMBL:ENSG00000183506\"\n                                   \"EMSEMBL:ENSG00000156535\"\n                                   \"EMSEMBL:ENSG00000087266\"\n                                   \"EMSEMBL:ENSG00000170921\"\n                                   \"EMSEMBL:ENSG00000185052\"\n                                   \"EMSEMBL:ENSG00000089486\"\n                                   \"EMSEMBL:ENSG00000196155\"\n                                   \"EMSEMBL:ENSG00000101546\"\n                                   \"EMSEMBL:ENSG00000038382\"\n                                   \"EMSEMBL:ENSG00000167460\"\n                                   \"EMSEMBL:ENSG00000186281\"\n                                   \"EMSEMBL:ENSG00000130309\"\n                                   \"EMSEMBL:ENSG00000054523\"\n                                   \"EMSEMBL:ENSG00000100097\"\n                                   \"EMSEMBL:ENSG00000142892\"\n                                   \"EMSEMBL:ENSG00000231419\"\n                                   \"EMSEMBL:ENSG00000163687\"))\n\n;; define CHAMP1 disease related conditions:\n(define dev-delay \"HP:0001263\")\n(define hypotonia \"HP:0001252\")\n(define cerebral-palsy \"HP:0100021\")\n(define autism \"MONDO:0005260\")\n(define epilepsy \"MONDO:0005027\")\n\n;; The function find-drug-for-condition takes a disease condition, a gene list (derived from RNA-seq DEG results)\n;; a list of drug-to-gene predicates that we want the drug to modulate.\n;; This function will run a query/graph that does a 2-edge query which find drugs that modify the disease condition\n;; while also modulate the gene in the gene list\n;; this function will return a list which contains 2 hash-tables which are sorted based on the number\n;; of genes or drugs available:\n\n; Use the find-drug-for-condition from Thi-useful-functions.rkt:\n(define dev-delay-drug-results-RNA-up (find-drug-for-condition dev-delay CHAMP1-DE-RNA-up negatively-regulates))\n(define dev-delay-drug-results-RNA-down (find-drug-for-condition dev-delay CHAMP1-DE-RNA-down positively-regulates))\n\n(define hypotonia-drug-results-RNA-up (find-drug-for-condition hypotonia CHAMP1-DE-RNA-up negatively-regulates))\n(define hypotonia-drug-results-RNA-down (find-drug-for-condition hypotonia CHAMP1-DE-RNA-up negatively-regulates))\n\n(define cerebral-palsy-drug-results-RNA-up (find-drug-for-condition cerebral-palsy CHAMP1-DE-RNA-up negatively-regulates))\n(define cerebral-palsy-drug-results-RNA-down (find-drug-for-condition cerebral-palsy CHAMP1-DE-RNA-down positively-regulates))\n\n(define autism-drug-results-RNA-up (find-drug-for-condition autism CHAMP1-DE-RNA-up negatively-regulates))\n(define autism-drug-results-RNA-down (find-drug-for-condition autism CHAMP1-DE-RNA-down positively-regulates))\n\n(define epilepsy-drug-results-RNA-up (find-drug-for-condition epilepsy CHAMP1-DE-RNA-up negatively-regulates))\n(define epilepsy-drug-results-RNA-down (find-drug-for-condition epilepsy CHAMP1-DE-RNA-down positively-regulates))\n\n;; Extract gene=>drug and drug=>gene tables:\n\n(define drug=>gene-dev-delay-drug-results-RNA-up (car dev-delay-drug-results-RNA-up))\n(define gene=>drug-dev-delay-drug-results-RNA-up (cadr dev-delay-drug-results-RNA-up))\n(define drug=>gene-dev-delay-drug-results-RNA-down (car dev-delay-drug-results-RNA-down))\n(define gene=>drug-dev-delay-drug-results-RNA-down (cadr dev-delay-drug-results-RNA-down))\n\n(define drug=>gene-hypotonia-drug-results-RNA-up (car hypotonia-drug-results-RNA-up))\n(define gene=>drug-hypotonia-drug-results-RNA-up (cadr hypotonia-drug-results-RNA-up))\n(define drug=>gene-hypotonia-drug-results-RNA-down (car hypotonia-drug-results-RNA-down))\n(define gene=>drug-hypotonia-drug-results-RNA-down (cadr hypotonia-drug-results-RNA-down))\n\n(define drug=>gene-cerebral-palsy-drug-results-RNA-up (car cerebral-palsy-drug-results-RNA-up))\n(define gene=>drug-cerebral-palsy-drug-results-RNA-up (cadr cerebral-palsy-drug-results-RNA-up))\n(define drug=>gene-cerebral-palsy-drug-results-RNA-down (car cerebral-palsy-drug-results-RNA-down))\n(define gene=>drug-cerebral-palsy-drug-results-RNA-down (cadr cerebral-palsy-drug-results-RNA-down))\n\n(define drug=>gene-autism-drug-results-RNA-up (car autism-drug-results-RNA-up))\n(define gene=>drug-autism-drug-results-RNA-up (cadr autism-drug-results-RNA-up))\n(define drug=>gene-autism-drug-results-RNA-down (car autism-drug-results-RNA-down))\n(define gene=>drug-autism-drug-results-RNA-down (cadr autism-drug-results-RNA-down))\n\n(define drug=>gene-epilepsy-drug-results-RNA-up (car epilepsy-drug-results-RNA-up))\n(define gene=>drug-epilepsy-drug-results-RNA-up (cadr epilepsy-drug-results-RNA-up))\n(define drug=>gene-epilepsy-drug-results-RNA-down (car epilepsy-drug-results-RNA-down))\n(define gene=>drug-epilepsy-drug-results-RNA-down (cadr epilepsy-drug-results-RNA-down))\n\n; combine 10 association lists:\n(define strategy3_results\n  (merge-assoc-lists\n   (list drug=>gene-dev-delay-drug-results-RNA-up\n         drug=>gene-dev-delay-drug-results-RNA-down\n         drug=>gene-hypotonia-drug-results-RNA-up \n         drug=>gene-hypotonia-drug-results-RNA-down\n         drug=>gene-cerebral-palsy-drug-results-RNA-up\n         drug=>gene-cerebral-palsy-drug-results-RNA-down\n         drug=>gene-autism-drug-results-RNA-up\n         drug=>gene-autism-drug-results-RNA-down\n         drug=>gene-epilepsy-drug-results-RNA-up\n         drug=>gene-epilepsy-drug-results-RNA-down)))\n\n\n(define strategy3_genes_results\n  (merge-assoc-lists\n   (list gene=>drug-dev-delay-drug-results-RNA-up\n         gene=>drug-dev-delay-drug-results-RNA-down\n         gene=>drug-hypotonia-drug-results-RNA-up \n         gene=>drug-hypotonia-drug-results-RNA-down\n         gene=>drug-cerebral-palsy-drug-results-RNA-up\n         gene=>drug-cerebral-palsy-drug-results-RNA-down\n         gene=>drug-autism-drug-results-RNA-up\n         gene=>drug-autism-drug-results-RNA-down\n         gene=>drug-epilepsy-drug-results-RNA-up\n         gene=>drug-epilepsy-drug-results-RNA-down)))\n\n; sort them by the values:\n(define strategy3_results-count (get-num-values (car strategy3_results)))\n(define strategy3_results-genes-count (get-num-values (car strategy3_genes_results)))\n\n"
  },
  {
    "path": "contrib/medikanren/use-cases/PMI-20-10-Il1R1-case-reviews.rkt",
    "content": "#lang racket\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;*****Application of mediKanren in case review*****;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n\n;; Here I'm demonstrating how I used mediKanren for the PMI-20-10 case.\n;; Date: 08/19/2020\n;; For the case presentation, please check the file PMI-20-10.pdf\n\n;; Participant is a 18 yo male who was diagnosed with Ulcerative Colitis at 3 yo. For the next 10 years, he was in\n;; remission but his colitis flared again when he was 13.\n;; For this case, there are many molecular data available such as Whole Exome Sequencing data (trio), microarray\n;; gene expression data and in-vitro macrophage stimulation assay. Subject Matter Experts (SME) in molecular biology\n;; , immunology and computational biology have looked at this case in details and hypothesized the mechanism\n;; of disease: participant's IL1R1 variant may lead to aberrant IL1R signaling in T cells and result in his colitis\n;; phenotype. Therefore, in this case, we used mediKanren to find drugs that target IL1R and IL1R signaling pathway.\n\n\n;; First, load all data sources into RAM\n(require \"../../../medikanren/pieces-parts/query.rkt\" \"../pieces-parts/Thi-useful-functions.rkt\")\n                       \n;; Find IL1R1 gene CURIE by looking up the identifiers in the GeneCards database\n(define IL-1R1 \"HGNC:5993\")\n\n;; Check if this CURIE has been synonymized in our Knowledge Graphs (KGs)\n(curie-synonyms \"HGNC:5993\")\n\n;; define the deccreases predicates to be used in run/graph drug->gene queries\n(define decreases '(\"prevents\"\n                    \"negatively_regulates\"\n                    \"negatively_regulates__entity_to_entity\"\n                    \"directly_negatively_regulates\"\n                    \"biolink:negatively_regulates\"\n                    \"biolink:negatively_regulates_entity_to_entity\"\n                    \"biolink:directly_negatively_regulates\"\n                    \"decreases_secretion_of\"\n                    \"decreases_transport_of\"\n                    \"decreases_activity_of\"\n                    \"decreases_synthesis_of\"\n                    \"decreases_expression_of\"\n                    \"increases_degradation_of\"\n                    \"disrupts\"\n                    \"biolink:disease_disrupts\"\n                    \"inhibits\"\n                    \"inhibitor\"\n                    \"antisense_inhibitor\"\n                    \"gating_inhibitor\"\n                    \"channel_blocker\"\n                    \"treats\"))\n;; define drug\n(define drug '(;; semmed\n              \"chemical_substance\"\n              ;; robokop\n              \"(\\\"named_thing\\\" \\\"chemical_substance\\\")\"\n              ;; orange?\n              ;; rtx2\n              \"http://w3id.org/biolink/vocab/Drug\"\n              \"http://w3id.org/biolink/vocab/ChemicalSubstance\"\n              \"http://w3id.org/biolink/vocab/Chemical_Substance\"\n              ))\n\n;; construct a query/graph to find drugs that targets/inhibits IL-1R1\n\n(define q-IL-1R1 (query/graph ;; query/graph is an interface that alows us to query our data\n                  ((S drug);; define the subject (S) to be drugs\n                   (C IL-1R1));; define the object (C) to be IL1R1\n                  ((S->C decreases));; define the verb/relationship between the subject and object\n                  (S S->C C)));; define the pathway (i.e. direction of the story).\n                              ;; This is where the subject is distinguished from the objects.\n\n\n#|\n***Please note that query/graph performs concept-synonymization/normalization under the hood.\n\nConcept normalization allows traversal of different knowledge graphs and databases without\nknowing all the equivalent CURIEs from different knowledge sources. This allows expansion\nof one single CURIE which belongs to a single database to multiple equivalent CURIEs from\nother databases, from where there may be productive search results for finding drugs.\n|#\n\n;; check the results of the query/graph output:\n(report/query q-IL-1R1)\n\n#| Output:\n\n'((concepts: (S 10) (C 1)) (edges: (S->C 16)))\n\n At a glance, there are 10 drugs that inhibit IL1R1 and there are 16 different stories.\n Edges not only contain subject and object information, they also contain the details about the story, especially\n information such as provenance via Pubmed IDs.\n\n|#\n\n;; extract the drugs:\n(define q-IL-1R1-drugs (curies/query q-IL-1R1 'S))\n\n#|\nOutput:\n\n'(\"CHEBI:15367\"\n  \"CHEBI:28918\"\n  \"CUI:C0002658\"\n  \"CUI:C0012854\"\n  \"CUI:C0022614\"\n  \"CUI:C0035339\"\n  \"CUI:C0041385\"\n  \"CUI:C0084183\"\n  \"CUI:C0376202\"\n  \"CUI:C0684163\")\n|#\n\n;; get the drug names from the drug curies\n(map curie-synonyms/names q-IL-1R1-drugs)\n\n#|\nIf we just want to map a CURIE to a name, we need to work with the list output:\n\n(map car (map curie-synonyms/names q-IL-1R1-drugs))\n\nOutput:\n\n'((\"UMLS:C0022265\" . \"Isotretinoin\")\n  (\"PUBCHEM:5816\" . \"Epinephrine\")\n  (\"RXNORM:725\" . \"Amphetamine\")\n  (\"UMLS:C0012854\" . \"DNA\")\n  (\"MTHSPL:690G0D6V8H\" . \"Ketamine\")\n  (\"NDFRT:N0000007700\" . \"Retinoids\")\n  (\"CUI:C0041385\" . \"Tunicamycin\")\n  (\"CUI:C0084183\" . \"prolinedithiocarbamate\")\n  (\"CUI:C0376202\" . \"Sepranolone\")\n  (\"UMLS:C0684163\" . \"membrane-bound receptors\"))\n|#\n\n;; We can also take a look at the edges, which contains a lot more information about the relationship between the subject and the object\n(define q-IL-1R1-edges (edges/query q-IL-1R1 'S->C))\n\n;; get pubmed-ids from the eges:\n(map pubmed-ids-from-edge q-IL-1R1-edges)\n\n#|\nOutput:\n\n'((\"23351058\")\n  (\"19746721\")\n  (\"9515014\")\n  (\"7780141\")\n  (\"16586090\")\n  (\"16586090\")\n  (\"23351058\")\n  (\"2341487\")\n  (\"7780141\")\n  (\"9515014\")\n  (\"15176475\")\n  (\"19746721\")\n  (\"7780141\")\n  (\"2341487\")\n  (\"23351058\")\n  (\"31191315\"))\n|#\n\n\n#|\n  The next strategy to solve this case is to target the IL-1R signaling pathway.\n\nILR-1 signaling pathway is a concept available in the GO database: (define IL-1R1-signaling \"GO:0070498\")\n\nIt would have been nice to be able to write a simple query to find drugs that target IL-1R signaling pathway.\n\n***However, currently our KGs don't have a direct connection from GO to a drug database, so a mediKanren\nquery for drug that target a pathway would yield no results.\n\nHere I'm manually define a pathway as a list of proteins belonging to that pathway.\n|#\n\n(define myD88 \"HGNC:7562\")\n(define TAK1 \"HGNC:6859\")\n(define NEMO \"HGNC:5961\")\n(define IRAK1 \"HGNC:6112\")\n(define IRAK2 \"HGNC:6113\")\n(define TRAF6 \"HGNC:12036\")\n(define MEK1 \"HGNC:6848\")\n(define MEK3 \"HGNC:6843\")\n(define MEK6 \"HGNC:6846\")\n(define NFkB \"HGNC:7794\")\n(define JNK \"HGNC:6861\")\n(define p38 \"HGNC:6876\")\n(define c-JNK \"HGNC:6881\")\n\n(define IL1R-pathway (list myD88 TAK1 NEMO IRAK1 IRAK2 TRAF6 MEK1 MEK3 MEK6 NFkB JNK p38 c-JNK))\n\n#|\nNext I'm using a pre-defined find-drugs-for-genes function from Thi-useful-functions. This function, built upon a simple query/graph\nsuch as the one above, will iterates through the list of subjects (i.e. genes to target in the IL1R-pathway).\n\n;; Function description:\n\nfind-drugs-for-genes takes a gene-list and a list of drug-gene predicates (direction that we\nwant the drugs to influence on the genes, one gene at a time) and returns a list of two hash-tables: a sorted drug=>gene table and\na sorted gene=>drug table, which is sorted by the number of genes that have drugs available to modify them or\nthe number of drugs that can are available to target multiple genes.\n\n|#\n(define target-IL1R-pathway-results (find-drugs-for-genes IL1R-pathway negatively-regulates))\n\n;; extract drug=>gene hash-table:\n(define drug=>gene-IL1R-pathway (car target-IL1R-pathway-results))\n\n#|\nThe output is a hash table with drug as key and genes as values.\n\nThis hashtable is sorted by how many genes the particular drug/chemical target.\n\n'(((\"CHEBI:3962\" . \"curcumin\")\n   (\"HGNC:6881\" . \"mitogen-activated protein kinase 8\")\n   (\"HGNC:6876\" . \"mitogen-activated protein kinase 14\")\n   (\"HGNC:7794\" . \"nuclear factor kappa B subunit 1\")\n   (\"HGNC:6846\" . \"mitogen-activated protein kinase kinase 6\")\n   (\"HGNC:6848\" . \"mitogen-activated protein kinase kinase kinase 1\")\n   (\"HGNC:6859\" . \"mitogen-activated protein kinase kinase kinase 7\")\n   (\"HGNC:7562\" . \"MYD88 innate immune signal transduction adaptor\"))\n  ((\"CHEBI:16243\" . \"quercetin\")\n   (\"HGNC:6881\" . \"mitogen-activated protein kinase 8\")\n   (\"HGNC:6876\" . \"mitogen-activated protein kinase 14\")\n   (\"HGNC:7794\" . \"nuclear factor kappa B subunit 1\")\n   (\"HGNC:12036\" . \"TNF receptor associated factor 6\")\n   (\"HGNC:6859\" . \"mitogen-activated protein kinase kinase kinase 7\")\n   (\"HGNC:7562\" . \"MYD88 innate immune signal transduction adaptor\"))\n  ((\"CHEBI:39867\" . \"valproic acid\")\n   (\"HGNC:6881\" . \"mitogen-activated protein kinase 8\")\n   (\"HGNC:7794\" . \"nuclear factor kappa B subunit 1\")\n   (\"HGNC:6846\" . \"mitogen-activated protein kinase kinase 6\")\n   (\"HGNC:6112\" . \"interleukin 1 receptor associated kinase 1\")\n   (\"HGNC:7562\" . \"MYD88 innate immune signal transduction adaptor\"))\n[...]\n|#\n\n;; To summarize the results, we count the length of the table and the values for each drug-key\n\n(length (map car drug=>gene-IL1R-pathway))\n\n;; The results show that there are 444 drugs that target more than one members of the IL1R signaling pathway,\n;; with the top 15 drugs target more than 5 members in this pathway. For example, curcumin targets 7 members (JNK,\n;; p38, NFkB, MEK6, MEK1, TRAF6, myD88), quercetin targets 6 (JNK, p38, NFkB, TRAF6, MEK3, myD88)\n;; members of the pathway.\n\n\n;; extract gene=>drug hash-table:\n(define gene=>drug-IL1R-pathway (cadr target-IL1R-pathway-results))\n;; Similarly, the output of this gene=>drug table is a also hash table with gene as the key and drug as the value.\n;; This table is also sorted by how many drugs available to target that gene.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"
  },
  {
    "path": "contrib/medikanren2/README.md",
    "content": "# Synopsis\n\nContributions for medikanren version 2 go in this directory.\n\n"
  },
  {
    "path": "contrib/medikanren2/Thi/CHAMP1-drug-repurpose-June-15-2021.rkt",
    "content": "#lang racket\n\n(require \"../../../medikanren2/common.rkt\")\n(require \"../../../medikanren2/db/rtx2-20210204.rkt\")\n(require \"../../../medikanren2/lw-reasoning.rkt\")\n(require \"../../../medikanren2/synonyms.rkt\")\n(require \"Hakon-DEG-list.rkt\")\n(require \"Hakon-DEG-syns.rkt\")\n\n\n; Date: June 15, 2021\n; Query: Find drugs that up or down-regulate a list of genes while treat the phenotypes\n\n; The list of genes were stored in Hakon-DEG-list.rkt\n; The list of synonymized genes were stored in Hakon-DEG-syns.rkt\n\n; First, look for synonyms of these genes using the synonym relation\n\n(time (map\n       (lambda (x)\n         (run*/set/steps 500 a\n                         (synonym a x)))\n       Hakon-CHAMP1-RNA-up))\n\n; the Hakon-CHAMP1-RNA-up contains 132 genes\n; time: 154062 real time: 177755 gc time: 1053\n; ~ 3 min\n; save the results in a .rkt file\n\n(length  Hakon-CHAMP1-RNA-up-syns)\n; 760 synonyms for RNA-up\n\n\n(time (map\n       (lambda (x)\n         (run*/set/steps 500 a\n                         (synonym a x)))\n       Hakon-CHAMP1-RNA-down))\n\n(length  Hakon-CHAMP1-RNA-down-syns)\n\n; the Hakon-CHAMP1-RNA-down contains  genes\n; cpu time: 388297 real time: 427985 gc time: 2749\n; 8 mins\n; 2036 synonyms for RNA-down\n\n\n\n\n\n;; These are PMI-18-04 phenotypes that we want to look for drugs to treat these conditions\n\n(define hypotonia \"HP:0001252\")\n(define impaired-convergence \"HP:0000619\")\n(define short-attention-span \"HP:0007018\")\n(define speech-apraxia \"HP:0011098\")\n(define autism \"MONDO:0005260\")\n(define cerebral-palsy \"HP:0100021\")\n(define constipation \"HP:0002019\")\n(define fatigue \"HP:0012378\")\n(define gas-reflux \"HP:0002020\")\n(define ID \"HP:0001249\")\n(define speech-delay \"HP:0000750\")\n\n\n; get the phenotype synonyms using the cached and indexed kgx-syn KG\n\n(define hypotonia-syn (set->list (run*/set x (kgx-synonym x hypotonia))))\n\n(get-names-ls hypotonia-syn)\n'((\"UMLS:C4049521\" \"Generalised atony\")\n  (\"UMLS:C0541791\" \"Atonia\")\n  (\"UMLS:C0541791\" \"Atonia\")\n  (\"UMLS:C0026827\" \"Poor muscle tone\")\n  (\"UMLS:C0026827\" \"Muscle hypotonia\")\n  (\"MEDDRA:10058909\" \"Muscle relaxant therapy\")\n  (\"UMLS:C0857516\" \"Floppy\")\n  (\"UMLS:C0857516\" \"Floppy\")\n  (\"UMLS:C1142135\" \"Muscle relaxant therapy\")\n  (\"HP:0001252\" \"Muscular hypotonia\")\n  (\"UMLS:C0541792\" \"Skeletal muscle atony\")\n  (\"UMLS:C0541792\" \"Skeletal muscle atony\")\n  (\"UMLS:C0859331\" \"Abdominal flaccidity\")\n  (\"UMLS:C0857388\" \"Non-depolarising relaxant\")\n  (\"MEDDRA:10021118\" \"Hypotonia\")\n  (\"UMLS:C0857388\" \"Non-depolarising relaxant\")\n  (\"NCIT:C87070\" \"Hypotonia\"))\n; 17 names with synonyms but only 14 unique curies\n\n; note that there are duplicates when we look for names\n; 14 synonyms for hypotonia\n\n\n\n\n\n#|\n; could try to do query expansion in the future\n(time (run* hypotonia-subclasses\n        (fresh (x)\n          (subclass-of* hypotonia-subclasses x)\n          (membero x hypotonia-syn))))\n|#\n\n\n\n\n\n; build main query to find drugs that inhibit genes and treat one phenotype, eg., hypotonia\n\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run* (d dname drug->gene-pred g gname disease disease-name drug->disease-pred)\n     (fresh (id1 id2 drug)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (cprop d \"name\" dname)\n       (cprop g \"name\" gname)\n       (cprop disease \"name\" disease-name)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (membero drug drug-categories)\n       (membero g Hakon-CHAMP1-RNA-up-syns)\n       (membero drug->gene-pred inhibit-preds)\n       (membero disease hypotonia-syn)\n       (membero drug->disease-pred inhibit-preds)))))\n\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run 1 (d dname drug->gene-pred g gname disease disease-name drug->disease-pred)\n     (fresh (id1 id2 drug)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (cprop d \"name\" dname)\n       (cprop g \"name\" gname)\n       (cprop disease \"name\" disease-name)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (membero drug drug-categories)\n       (membero g Hakon-CHAMP1-RNA-up-syns)\n       (membero drug->gene-pred inhibit-preds)\n       (membero disease hypotonia-syn)\n       (membero drug->disease-pred inhibit-preds)))))\n\n; this query terminates\n\n; cpu time: 17156 real time: 24444 gc time: 226\n\n\n; I tried this query without asking for drug/gene/disease names and it terminated.\n; First, try with run 1\n; According to Greg, if run 1 terminates, the query will eventually terminate so it\n; is good to check run 1 first.\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run 1 (d g disease)\n     (fresh (id1 id2 drug drug->gene-pred drug->disease-pred)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (membero drug drug-categories)\n       (membero g Hakon-CHAMP1-RNA-up-syns)\n       (membero drug->gene-pred inhibit-preds)\n       (membero disease hypotonia-syn)\n       (membero drug->disease-pred inhibit-preds)))))\n\n; cpu time: 9583 real time: 12312 gc time: 36\n; '((\"UMLS:C0013227\" \"UMLS:C0812307\" \"UMLS:C0026827\"))\n\n\n\n; If we don't look for names, this query looped though 14 disease curies and ~ 200 genes\n; to find drugs that inhibit both. This terminated in ~ 8 mins.\n\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run* (d g disease)\n     (fresh (id1 id2 drug drug->gene-pred drug->disease-pred)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (membero drug drug-categories)\n       (membero g Hakon-CHAMP1-RNA-up-syns)\n       (membero drug->gene-pred inhibit-preds)\n       (membero disease hypotonia-syn)\n       (membero drug->disease-pred inhibit-preds)))))\n\n\n\n\n; cpu time: 404819 real time: 445583 gc time: 2925\n; Hakon-drugs-hypotonia-RNA-up\n'((\"UMLS:C0013227\" \"UMLS:C0812307\" \"UMLS:C0026827\")\n  (\"UMLS:C0040616\" \"UMLS:C0812307\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"UMLS:C0812307\" \"UMLS:C0026827\")\n  (\"UMLS:C0040616\" \"UMLS:C0812307\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"UMLS:C0812307\" \"UMLS:C0541791\")\n  (\"UMLS:C0022614\" \"NCBIGene:4773\" \"UMLS:C0026827\")\n  (\"UMLS:C0028128\" \"NCBIGene:7351\" \"UMLS:C0026827\")\n  (\"UMLS:C0724441\" \"NCBIGene:7351\" \"UMLS:C0026827\")\n  (\"UMLS:C0008286\" \"NCBIGene:2149\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"UMLS:C1366449\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"UMLS:C1366449\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"UMLS:C1366449\" \"UMLS:C0541791\")\n  (\"UMLS:C0013227\" \"NCBIGene:26033\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:26033\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:26033\" \"UMLS:C0541791\")\n  (\"UMLS:C0013227\" \"NCBIGene:1021\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:1021\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:1021\" \"UMLS:C0541791\")\n  (\"UMLS:C0006644\" \"NCBIGene:5984\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:29126\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:29126\" \"UMLS:C0026827\")\n  (\"UMLS:C0030054\" \"NCBIGene:29126\" \"UMLS:C0026827\")\n  (\"UMLS:C0013227\" \"NCBIGene:29126\" \"UMLS:C0541791\")\n  (\"UMLS:C0012010\" \"NCBIGene:3977\" \"UMLS:C0026827\")\n  (\"UMLS:C0012010\" \"NCBIGene:3977\" \"UMLS:C0026827\")\n  (\"UMLS:C0026549\" \"NCBIGene:3977\" \"UMLS:C0026827\")\n  (\"UMLS:C0724441\" \"NCBIGene:3977\" \"UMLS:C0026827\")\n  (\"UMLS:C0033554\" \"NCBIGene:5733\" \"UMLS:C0541791\"))\n\n\n\n; Jeff suggested trying to the relation/table in place of membero to see if it speeds up the code\n(define (Hakon-drugs-hypotonia-RNA-up)\n  (time\n   (define-relation/table (rel-drug arg1)\n     'source-stream (map list drug-categories))\n   (define-relation/table (rel-Hakon arg1)\n     'source-stream (map list Hakon-CHAMP1-RNA-up-syns))\n   (define-relation/table (rel-drug-gene-inhibit arg1)\n     'source-stream (map list  inhibit-preds))\n   (define-relation/table (rel-hypotonia-syn arg1)\n     'source-stream (map list hypotonia-syn))\n   (define-relation/table (rel-drug-disease-inhibit arg1)\n     'source-stream (map list inhibit-preds))\n   (run* (d g disease)\n     (fresh (id1 id2 drug drug->gene-pred drug->disease-pred)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (rel-drug drug)           ;(membero drug drug-categories)\n       (rel-Hakon g)             ;(membero g Hakon-CHAMP1-RNA-up-syns)\n       (rel-drug-gene-inhibit drug->gene-pred) ;(membero drug->gene-pred inhibit-preds)\n       (rel-hypotonia-syn disease)    ;(membero disease hypotonia-syn)\n       (rel-drug-disease-inhibit  drug->disease-pred) ; (membero drug->disease-pred inhibit-preds)\n       ))))\n\n\n(define (Hakon-drugs-hypotonia-RNA-up)\n  (time\n   (define-relation/table (rel-drug arg1)\n     'source-stream (map list drug-categories))\n   (define-relation/table (rel-Hakon arg1)\n     'source-stream (map list Hakon-CHAMP1-RNA-up-syns))\n   (define-relation/table (rel-drug-gene-inhibit arg1)\n     'source-stream (map list  inhibit-preds))\n   (define-relation/table (rel-hypotonia-syn arg1)\n     'source-stream (map list hypotonia-syn))\n   (define-relation/table (rel-drug-disease-inhibit arg1)\n     'source-stream (map list inhibit-preds))\n   (run 1 (d g disease)\n     (fresh (id1 id2 drug drug->gene-pred drug->disease-pred)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (rel-drug drug)           ;(membero drug drug-categories)\n       (rel-Hakon g)             ;(membero g Hakon-CHAMP1-RNA-up-syns)\n       (rel-drug-gene-inhibit drug->gene-pred) ;(membero drug->gene-pred inhibit-preds)\n       (rel-hypotonia-syn disease)    ;(membero disease hypotonia-syn)\n       (rel-drug-disease-inhibit  drug->disease-pred) ; (membero drug->disease-pred inhibit-preds)\n       ))))\n\n; This approach doesn't speed up the code for some reason and it may creates infinite loop\n; => bugs in mediKanren2 or?\n\n; Greg mentioned it is a query planning issue\n\n; Jeff will take a look at this, June 15th, 2021.\n\n\n\n\n\n\n; Next time, try the map in place of membero to see if it helps\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n; Here are a few work-around approaches that Greg wrote back in May 2021\n\n(define-relation/table (inhibit-pred predicate)\n  'source-stream (map list inhibit-preds))\n\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run 1 (d dname drug->gene-pred g gname disease drug->disease-pred disease-name)\n     (fresh (id1 id2 drug)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (inhibit-pred drug->gene-pred)\n       (inhibit-pred drug->disease-pred)\n       (membero g Hakon-CHAMP1-RNA-up-syn)\n       (membero drug drug-categories)\n       (membero disease hypotonia-syn)\n       (:== dname (d) (car (run 1 name (cprop d \"name\" name))))\n       (:== gname (g) (car (run 1 name (cprop g \"name\" name))))\n       (:== disease-name (disease) (car (run 1 name (cprop disease \"name\" name))))))))\n\n; cpu time: 34497 real time: 42562 gc time: 197\n\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run 1 (d dname drug->gene-pred g gname disease drug->disease-pred disease-name)\n     (fresh (id1 id2 drug)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (cprop d \"category\" drug)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (inhibit-pred drug->gene-pred)\n       (inhibit-pred drug->disease-pred)\n       (membero g Hakon-CHAMP1-RNA-up-syn)\n       (membero drug drug-categories)\n       (membero disease hypotonia-syn)\n       (:== dname (d g disease) (car (run 1 name (cprop d \"name\" name))))\n       (:== gname (d g disease) (car (run 1 name (cprop g \"name\" name))))\n       (:== disease-name (d g disease) (car (run 1 name (cprop disease \"name\" name))))))))\n\n;cpu time: 27237 real time: 27446 gc time: 179\n\n(define-relation/table (drug-category category)\n  'source-stream (map list drug-categories))\n\n\n(define Hakon-drugs-hypotonia-RNA-up\n  (time\n   (run 1 (d dname drug->gene-pred g gname disease drug->disease-pred disease-name)\n     (fresh (id1 id2 drug)\n       (cprop d \"category\" drug)\n       (drug-category drug)\n       (edge id1 d g)\n       (edge id2 d disease)\n       (eprop id1 \"predicate\" drug->gene-pred)\n       (eprop id2 \"predicate\" drug->disease-pred)\n       (inhibit-pred drug->gene-pred)\n       (inhibit-pred drug->disease-pred)\n       (membero g Hakon-CHAMP1-RNA-up-syn)\n       (membero disease hypotonia-syn)\n       (:== dname (d g disease) (car (run 1 name (cprop d \"name\" name))))\n       (:== gname (d g disease) (car (run 1 name (cprop g \"name\" name))))\n       (:== disease-name (d g disease) (car (run 1 name (cprop disease \"name\" name))))\n))))\n\n\n; cpu time: 34839 real time: 35367 gc time: 196\n\n\n\n\n(define Hakon-drugs-RNA-up\n  (time\n   (run* (d drug->gene-pred g)\n     (fresh (id drug-cat)\n       (cprop d \"category\" drug-cat)\n       (drug-category drug-cat)\n       (edge id d g)\n       (eprop id \"predicate\" drug->gene-pred)\n       (inhibit-pred drug->gene-pred)\n       (membero g Hakon-CHAMP1-RNA-up-syn)))))\n\n;cpu time: 404819 real time: 445583 gc time: 2925\n\n\n\n\n\n;cpu time: 88185 real time: 100392 gc time: 579\n\n(write-list-to-tsv\n (list \"drug\" \"pred\" \"gene\")\n Hakon-drugs-RNA-up\n \"Hakon-drugs-RNA-up.tsv\")\n\n(define Hakon-drugs-disease\n  (time\n   (run* (d drug->disease-pred disease)\n     (fresh (id drug-cat)\n       (cprop d \"category\" drug-cat)\n       (drug-category drug-cat)\n       (edge id d disease)\n       (eprop id \"predicate\" drug->disease-pred)\n       (inhibit-pred drug->disease-pred)\n       (membero disease hypotonia-syn)))))\n\n\n(write-list-to-tsv\n (list \"drug\" \"pred\" \"disease\")\n Hakon-drugs-disease\n \"Hakon-drugs-hypononia.tsv\")\n\n\n(define-relation/table (Hakon-drug curie)\n  'source-stream\n    (run^ (d)\n      (fresh (id drug-cat drug->disease-pred disease)\n       (cprop d \"category\" drug-cat)\n       (drug-category drug-cat)\n       (edge id d disease)\n       (eprop id \"predicate\" drug->disease-pred)\n       (inhibit-pred drug->disease-pred)\n       (membero disease hypotonia-syn))))\n\n\n"
  },
  {
    "path": "contrib/medikanren2/Thi/Hakon-DEG-list.rkt",
    "content": "#lang racket\n\n(provide (all-defined-out))\n\n(provide Hakon-CHAMP1-RNA-up\n         Hakon-CHAMP1-RNA-down)\n\n\n;; Here are the lists of DEG genes from Dr. Hakonarson's CHAMP1 vs control samples\n\n(define Hakon-CHAMP1-RNA-up (list \"ENSEMBL:ENSG00000096746\"\n                                  \"ENSEMBL:ENSG00000144635\"\n                                  \"ENSEMBL:ENSG00000131873\"\n                                  \"ENSEMBL:ENSG00000116127\"\n                                  \"ENSEMBL:ENSG00000134318\"\n                                  \"ENSEMBL:ENSG00000145604\"\n                                  \"ENSEMBL:ENSG00000152684\"\n                                  \"ENSEMBL:ENSG00000115159\"\n                                  \"ENSEMBL:ENSG00000122779\"\n                                  \"ENSEMBL:ENSG00000206053\"\n                                  \"ENSEMBL:ENSG00000125249\"\n                                  \"ENSEMBL:ENSG00000178177\"\n                                  \"ENSEMBL:ENSG00000120137\"\n                                  \"ENSEMBL:ENSG00000128641\"\n                                  \"ENSEMBL:ENSG00000112972\"\n                                  \"ENSEMBL:ENSG00000152952\"\n                                  \"ENSEMBL:ENSG00000105810\"\n                                  \"ENSEMBL:ENSG00000052802\"\n                                  \"ENSEMBL:ENSG00000129675\"\n                                  \"ENSEMBL:ENSG00000134668\"\n                                  \"ENSEMBL:ENSG00000206560\"\n                                  \"ENSEMBL:ENSG00000182963\"\n                                  \"ENSEMBL:ENSG00000065882\"\n                                  \"ENSEMBL:ENSG00000084070\"\n                                  \"ENSEMBL:ENSG00000112183\"\n                                  \"ENSEMBL:ENSG00000113594\"\n                                  \"ENSEMBL:ENSG00000163918\"\n                                  \"ENSEMBL:ENSG00000172167\"\n                                  \"ENSEMBL:ENSG00000129680\"\n                                  \"ENSEMBL:ENSG00000143815\"\n                                  \"ENSEMBL:ENSG00000144218\"\n                                  \"ENSEMBL:ENSG00000049130\"\n                                  \"ENSEMBL:ENSG00000126803\"\n                                  \"ENSEMBL:ENSG00000178425\"\n                                  \"ENSEMBL:ENSG00000243927\"\n                                  \"ENSEMBL:ENSG00000112312\"\n                                  \"ENSEMBL:ENSG00000137941\"\n                                  \"ENSEMBL:ENSG00000156011\"\n                                  \"ENSEMBL:ENSG00000144824\"\n                                  \"ENSEMBL:ENSG00000118473\"\n                                  \"ENSEMBL:ENSG00000150540\"\n                                  \"ENSEMBL:ENSG00000164211\"\n                                  \"ENSEMBL:ENSG00000114739\"\n                                  \"ENSEMBL:ENSG00000095015\"\n                                  \"ENSEMBL:ENSG00000159433\"\n                                  \"ENSEMBL:ENSG00000120217\"\n                                  \"ENSEMBL:ENSG00000021826\"\n                                  \"ENSEMBL:ENSG00000176641\"\n                                  \"ENSEMBL:ENSG00000107796\"\n                                  \"ENSEMBL:ENSG00000029993\"\n                                  \"ENSEMBL:ENSG00000130164\"\n                                  \"ENSEMBL:ENSG00000157557\"\n                                  \"ENSEMBL:ENSG00000109861\"\n                                  \"ENSEMBL:ENSG00000180801\"\n                                  \"ENSEMBL:ENSG00000141198\"\n                                  \"ENSEMBL:ENSG00000169439\"\n                                  \"ENSEMBL:ENSG00000162892\"\n                                  \"ENSEMBL:ENSG00000151474\"\n                                  \"ENSEMBL:ENSG00000171208\"\n                                  \"ENSEMBL:ENSG00000155966\"\n                                  \"ENSEMBL:ENSG00000172164\"\n                                  \"ENSEMBL:ENSG00000277149\"\n                                  \"ENSEMBL:ENSG00000173546\"\n                                  \"ENSEMBL:ENSG00000166974\"\n                                  \"ENSEMBL:ENSG00000204131\"\n                                  \"ENSEMBL:ENSG00000163909\"\n                                  \"ENSEMBL:ENSG00000160111\"\n                                  \"ENSEMBL:ENSG00000150048\"\n                                  \"ENSEMBL:ENSG00000103196\"\n                                  \"ENSEMBL:ENSG00000076706\"\n                                  \"ENSEMBL:ENSG00000149970\"\n                                  \"ENSEMBL:ENSG00000131471\"\n                                  \"ENSEMBL:ENSG00000172322\"\n                                  \"ENSEMBL:ENSG00000198743\"\n                                  \"ENSEMBL:ENSG00000104435\"\n                                  \"ENSEMBL:ENSG00000054654\"\n                                  \"ENSEMBL:ENSG00000151320\"\n                                  \"ENSEMBL:ENSG00000175567\"\n                                  \"ENSEMBL:ENSG00000151617\"\n                                  \"ENSEMBL:ENSG00000116678\"\n                                  \"ENSEMBL:ENSG00000186854\"\n                                  \"ENSEMBL:ENSG00000106003\"\n                                  \"ENSEMBL:ENSG00000197442\"\n                                  \"ENSEMBL:ENSG00000104290\"\n                                  \"ENSEMBL:ENSG00000204397\"\n                                  \"ENSEMBL:ENSG00000187323\"\n                                  \"ENSEMBL:ENSG00000162654\"\n                                  \"ENSEMBL:ENSG00000171522\"\n                                  \"ENSEMBL:ENSG00000254087\"\n                                  \"ENSEMBL:ENSG00000106031\"\n                                  \"ENSEMBL:ENSG00000133392\"\n                                  \"ENSEMBL:ENSG00000196569\"\n                                  \"ENSEMBL:ENSG00000170891\"\n                                  \"ENSEMBL:ENSG00000181104\"\n                                  \"ENSEMBL:ENSG00000092969\"\n                                  \"ENSEMBL:ENSG00000165105\"\n                                  \"ENSEMBL:ENSG00000110852\"\n                                  \"ENSEMBL:ENSG00000137872\"\n                                  \"ENSEMBL:ENSG00000211445\"\n                                  \"ENSEMBL:ENSG00000165895\"\n                                  \"ENSEMBL:ENSG00000050628\"\n                                  \"ENSEMBL:ENSG00000150636\"\n                                  \"ENSEMBL:ENSG00000007944\"\n                                  \"ENSEMBL:ENSG00000069122\"\n                                  \"ENSEMBL:ENSG00000172159\"\n                                  \"ENSEMBL:ENSG00000151150\"\n                                  \"ENSEMBL:ENSG00000091879\"\n                                  \"ENSEMBL:ENSG00000101096\"\n                                  \"ENSEMBL:ENSG00000145287\"\n                                  \"ENSEMBL:ENSG00000118777\"\n                                  \"ENSEMBL:ENSG00000137501\"\n                                  \"ENSEMBL:ENSG00000142910\"\n                                  \"ENSEMBL:ENSG00000221818\"\n                                  \"ENSEMBL:ENSG00000150471\"\n                                  \"ENSEMBL:ENSG00000138795\"\n                                  \"ENSEMBL:ENSG00000076641\"\n                                  \"ENSEMBL:ENSG00000140030\"\n                                  \"ENSEMBL:ENSG00000006747\"\n                                  \"ENSEMBL:ENSG00000124749\"\n                                  \"ENSEMBL:ENSG00000196611\"\n                                  \"ENSEMBL:ENSG00000169129\"\n                                  \"ENSEMBL:ENSG00000115468\"\n                                  \"ENSEMBL:ENSG00000154451\"\n                                  \"ENSEMBL:ENSG00000107518\"\n                                  \"ENSEMBL:ENSG00000132688\"\n                                  \"ENSEMBL:ENSG00000046889\"\n                                  \"ENSEMBL:ENSG00000153404\"\n                                  \"ENSEMBL:ENSG00000149292\"\n                                  \"ENSEMBL:ENSG00000135218\"\n                                  \"ENSEMBL:ENSG00000069188\"\n                                  \"ENSEMBL:ENSG00000188393\"\n                                  \"ENSEMBL:ENSG00000106511\"))\n\n\n(define Hakon-CHAMP1-RNA-down (list \"ENSEMBL:ENSG00000109061\"\n                                    \"ENSEMBL:ENSG00000040731\"\n                                    \"ENSEMBL:ENSG00000104332\"\n                                    \"ENSEMBL:ENSG00000120885\"\n                                    \"ENSEMBL:ENSG00000198959\"\n                                    \"ENSEMBL:ENSG00000121361\"\n                                    \"ENSEMBL:ENSG00000069431\"\n                                    \"ENSEMBL:ENSG00000145526\"\n                                    \"ENSEMBL:ENSG00000169218\"\n                                    \"ENSEMBL:ENSG00000197614\"\n                                    \"ENSEMBL:ENSG00000138650\"\n                                    \"ENSEMBL:ENSG00000166669\"\n                                    \"ENSEMBL:ENSG00000176532\"\n                                    \"ENSEMBL:ENSG00000184408\"\n                                    \"ENSEMBL:ENSG00000103034\"\n                                    \"ENSEMBL:ENSG00000169946\"\n                                    \"ENSEMBL:ENSG00000111452\"\n                                    \"ENSEMBL:ENSG00000153132\"\n                                    \"ENSEMBL:ENSG00000143196\"\n                                    \"ENSEMBL:ENSG00000145423\"\n                                    \"ENSEMBL:ENSG00000164483\"\n                                    \"ENSEMBL:ENSG00000184922\"\n                                    \"ENSEMBL:ENSG00000156466\"\n                                    \"ENSEMBL:ENSG00000062282\"\n                                    \"ENSEMBL:ENSG00000162105\"\n                                    \"ENSEMBL:ENSG00000178568\"\n                                    \"ENSEMBL:ENSG00000017427\"\n                                    \"ENSEMBL:ENSG00000079841\"\n                                    \"ENSEMBL:ENSG00000139174\"\n                                    \"ENSEMBL:ENSG00000140563\"\n                                    \"ENSEMBL:ENSG00000135919\"\n                                    \"ENSEMBL:ENSG00000169184\"\n                                    \"ENSEMBL:ENSG00000095637\"\n                                    \"ENSEMBL:ENSG00000134317\"\n                                    \"ENSEMBL:ENSG00000067715\"\n                                    \"ENSEMBL:ENSG00000175745\"\n                                    \"ENSEMBL:ENSG00000165092\"\n                                    \"ENSEMBL:ENSG00000163618\"\n                                    \"ENSEMBL:ENSG00000007237\"\n                                    \"ENSEMBL:ENSG00000153162\"\n                                    \"ENSEMBL:ENSG00000205002\"\n                                    \"ENSEMBL:ENSG00000128710\"\n                                    \"ENSEMBL:ENSG00000147642\"\n                                    \"ENSEMBL:ENSG00000121989\"\n                                    \"ENSEMBL:ENSG00000077420\"\n                                    \"ENSEMBL:ENSG00000121743\"\n                                    \"ENSEMBL:ENSG00000131459\"\n                                    \"ENSEMBL:ENSG00000135472\"\n                                    \"ENSEMBL:ENSG00000125730\"\n                                    \"ENSEMBL:ENSG00000144339\"\n                                    \"ENSEMBL:ENSG00000241945\"\n                                    \"ENSEMBL:ENSG00000183578\"\n                                    \"ENSEMBL:ENSG00000121552\"\n                                    \"ENSEMBL:ENSG00000165124\"\n                                    \"ENSEMBL:ENSG00000127329\"\n                                    \"ENSEMBL:ENSG00000165995\"\n                                    \"ENSEMBL:ENSG00000148082\"\n                                    \"ENSEMBL:ENSG00000129465\"\n                                    \"ENSEMBL:ENSG00000261221\"\n                                    \"ENSEMBL:ENSG00000198816\"\n                                    \"ENSEMBL:ENSG00000119714\"\n                                    \"ENSEMBL:ENSG00000156427\"\n                                    \"ENSEMBL:ENSG00000136002\"\n                                    \"ENSEMBL:ENSG00000128573\"\n                                    \"ENSEMBL:ENSG00000101986\"\n                                    \"ENSEMBL:ENSG00000111199\"\n                                    \"ENSEMBL:ENSG00000138193\"\n                                    \"ENSEMBL:ENSG00000179104\"\n                                    \"ENSEMBL:ENSG00000132357\"\n                                    \"ENSEMBL:ENSG00000137033\"\n                                    \"ENSEMBL:ENSG00000134470\"\n                                    \"ENSEMBL:ENSG00000102174\"\n                                    \"ENSEMBL:ENSG00000177106\"\n                                    \"ENSEMBL:ENSG00000102265\"\n                                    \"ENSEMBL:ENSG00000065320\"\n                                    \"ENSEMBL:ENSG00000138821\"\n                                    \"ENSEMBL:ENSG00000008394\"\n                                    \"ENSEMBL:ENSG00000091656\"\n                                    \"ENSEMBL:ENSG00000125414\"\n                                    \"ENSEMBL:ENSG00000184349\"\n                                    \"ENSEMBL:ENSG00000149633\"\n                                    \"ENSEMBL:ENSG00000198113\"\n                                    \"ENSEMBL:ENSG00000138131\"\n                                    \"ENSEMBL:ENSG00000158555\"\n                                    \"ENSEMBL:ENSG00000071242\"\n                                    \"ENSEMBL:ENSG00000189129\"\n                                    \"ENSEMBL:ENSG00000158292\"\n                                    \"ENSEMBL:ENSG00000065717\"\n                                    \"ENSEMBL:ENSG00000137463\"\n                                    \"ENSEMBL:ENSG00000152217\"\n                                    \"ENSEMBL:ENSG00000142684\"\n                                    \"ENSEMBL:ENSG00000042493\"\n                                    \"ENSEMBL:ENSG00000142798\"\n                                    \"ENSEMBL:ENSG00000177697\"\n                                    \"ENSEMBL:ENSG00000137857\"\n                                    \"ENSEMBL:ENSG00000117122\"\n                                    \"ENSEMBL:ENSG00000214595\"\n                                    \"ENSEMBL:ENSG00000077942\"\n                                    \"ENSEMBL:ENSG00000197635\"\n                                    \"ENSEMBL:ENSG00000168056\"\n                                    \"ENSEMBL:ENSG00000167123\"\n                                    \"ENSEMBL:ENSG00000173801\"\n                                    \"ENSEMBL:ENSG00000013297\"\n                                    \"ENSEMBL:ENSG00000065268\"\n                                    \"ENSEMBL:ENSG00000100336\"\n                                    \"ENSEMBL:ENSG00000091831\"\n                                    \"ENSEMBL:ENSG00000116183\"\n                                    \"ENSEMBL:ENSG00000104213\"\n                                    \"ENSEMBL:ENSG00000113389\"\n                                    \"ENSEMBL:ENSG00000233927\"\n                                    \"ENSEMBL:ENSG00000177674\"\n                                    \"ENSEMBL:ENSG00000178031\"\n                                    \"ENSEMBL:ENSG00000159069\"\n                                    \"ENSEMBL:ENSG00000107281\"\n                                    \"ENSEMBL:ENSG00000170381\"\n                                    \"ENSEMBL:ENSG00000186654\"\n                                    \"ENSEMBL:ENSG00000132837\"\n                                    \"ENSEMBL:ENSG00000121039\"\n                                    \"ENSEMBL:ENSG00000134247\"\n                                    \"ENSEMBL:ENSG00000130479\"\n                                    \"ENSEMBL:ENSG00000186088\"\n                                    \"ENSEMBL:ENSG00000131669\"\n                                    \"ENSEMBL:ENSG00000049540\"\n                                    \"ENSEMBL:ENSG00000138061\"\n                                    \"ENSEMBL:ENSG00000159714\"\n                                    \"ENSEMBL:ENSG00000154096\"\n                                    \"ENSEMBL:ENSG00000104976\"\n                                    \"ENSEMBL:ENSG00000110697\"\n                                    \"ENSEMBL:ENSG00000177542\"\n                                    \"ENSEMBL:ENSG00000214063\"\n                                    \"ENSEMBL:ENSG00000064042\"\n                                    \"ENSEMBL:ENSG00000275074\"\n                                    \"ENSEMBL:ENSG00000103152\"\n                                    \"ENSEMBL:ENSG00000136732\"\n                                    \"ENSEMBL:ENSG00000023191\"\n                                    \"ENSEMBL:ENSG00000176978\"\n                                    \"ENSEMBL:ENSG00000126458\"\n                                    \"ENSEMBL:ENSG00000162241\"\n                                    \"ENSEMBL:ENSG00000107821\"\n                                    \"ENSEMBL:ENSG00000160323\"\n                                    \"ENSEMBL:ENSG00000177030\"\n                                    \"ENSEMBL:ENSG00000119559\"\n                                    \"ENSEMBL:ENSG00000105701\"\n                                    \"ENSEMBL:ENSG00000163874\"\n                                    \"ENSEMBL:ENSG00000107404\"\n                                    \"ENSEMBL:ENSG00000116663\"\n                                    \"ENSEMBL:ENSG00000100300\"\n                                    \"ENSEMBL:ENSG00000185803\"\n                                    \"ENSEMBL:ENSG00000164176\"\n                                    \"ENSEMBL:ENSG00000064932\"\n                                    \"ENSEMBL:ENSG00000101439\"\n                                    \"ENSEMBL:ENSG00000103888\"\n                                    \"ENSEMBL:ENSG00000006282\"\n                                    \"ENSEMBL:ENSG00000169760\"\n                                    \"ENSEMBL:ENSG00000198774\"\n                                    \"ENSEMBL:ENSG00000160932\"\n                                    \"ENSEMBL:ENSG00000091986\"\n                                    \"ENSEMBL:ENSG00000198542\"\n                                    \"ENSEMBL:ENSG00000011347\"\n                                    \"ENSEMBL:ENSG00000164484\"\n                                    \"ENSEMBL:ENSG00000188112\"\n                                    \"ENSEMBL:ENSG00000166166\"\n                                    \"ENSEMBL:ENSG00000130529\"\n                                    \"ENSEMBL:ENSG00000183098\"\n                                    \"ENSEMBL:ENSG00000137809\"\n                                    \"ENSEMBL:ENSG00000168528\"\n                                    \"ENSEMBL:ENSG00000177700\"\n                                    \"ENSEMBL:ENSG00000172270\"\n                                    \"ENSEMBL:ENSG00000104881\"\n                                    \"ENSEMBL:ENSG00000146072\"\n                                    \"ENSEMBL:ENSG00000105223\"\n                                    \"ENSEMBL:ENSG00000172725\"\n                                    \"ENSEMBL:ENSG00000122707\"\n                                    \"ENSEMBL:ENSG00000143369\"\n                                    \"ENSEMBL:ENSG00000099817\"\n                                    \"ENSEMBL:ENSG00000100284\"\n                                    \"ENSEMBL:ENSG00000177666\"\n                                    \"ENSEMBL:ENSG00000116525\"\n                                    \"ENSEMBL:ENSG00000107140\"\n                                    \"ENSEMBL:ENSG00000170801\"\n                                    \"ENSEMBL:ENSG00000165915\"\n                                    \"ENSEMBL:ENSG00000169692\"\n                                    \"ENSEMBL:ENSG00000167930\"\n                                    \"ENSEMBL:ENSG00000002330\"\n                                    \"ENSEMBL:ENSG00000115641\"\n                                    \"ENSEMBL:ENSG00000176101\"\n                                    \"ENSEMBL:ENSG00000172638\"\n                                    \"ENSEMBL:ENSG00000100241\"\n                                    \"ENSEMBL:ENSG00000162576\"\n                                    \"ENSEMBL:ENSG00000128713\"\n                                    \"ENSEMBL:ENSG00000011009\"\n                                    \"ENSEMBL:ENSG00000168936\"\n                                    \"ENSEMBL:ENSG00000106683\"\n                                    \"ENSEMBL:ENSG00000136877\"\n                                    \"ENSEMBL:ENSG00000100299\"\n                                    \"ENSEMBL:ENSG00000110717\"\n                                    \"ENSEMBL:ENSG00000093072\"\n                                    \"ENSEMBL:ENSG00000013364\"\n                                    \"ENSEMBL:ENSG00000139178\"\n                                    \"ENSEMBL:ENSG00000067221\"\n                                    \"ENSEMBL:ENSG00000131435\"\n                                    \"ENSEMBL:ENSG00000183077\"\n                                    \"ENSEMBL:ENSG00000197858\"\n                                    \"ENSEMBL:ENSG00000173264\"\n                                    \"ENSEMBL:ENSG00000174886\"\n                                    \"ENSEMBL:ENSG00000155011\"\n                                    \"ENSEMBL:ENSG00000171533\"\n                                    \"ENSEMBL:ENSG00000198892\"\n                                    \"ENSEMBL:ENSG00000133243\"\n                                    \"ENSEMBL:ENSG00000164040\"\n                                    \"ENSEMBL:ENSG00000099337\"\n                                    \"ENSEMBL:ENSG00000160360\"\n                                    \"ENSEMBL:ENSG00000127191\"\n                                    \"ENSEMBL:ENSG00000186501\"\n                                    \"ENSEMBL:ENSG00000093010\"\n                                    \"ENSEMBL:ENSG00000078808\"\n                                    \"ENSEMBL:ENSG00000140285\"\n                                    \"ENSEMBL:ENSG00000141985\"\n                                    \"ENSEMBL:ENSG00000131408\"\n                                    \"ENSEMBL:ENSG00000165655\"\n                                    \"ENSEMBL:ENSG00000068001\"\n                                    \"ENSEMBL:ENSG00000136878\"\n                                    \"ENSEMBL:ENSG00000197122\"\n                                    \"ENSEMBL:ENSG00000131899\"\n                                    \"ENSEMBL:ENSG00000143774\"\n                                    \"ENSEMBL:ENSG00000104805\"\n                                    \"ENSEMBL:ENSG00000131165\"\n                                    \"ENSEMBL:ENSG00000163703\"\n                                    \"ENSEMBL:ENSG00000123143\"\n                                    \"ENSEMBL:ENSG00000128591\"\n                                    \"ENSEMBL:ENSG00000107738\"\n                                    \"ENSEMBL:ENSG00000148343\"\n                                    \"ENSEMBL:ENSG00000114853\"\n                                    \"ENSEMBL:ENSG00000167967\"\n                                    \"ENSEMBL:ENSG00000197136\"\n                                    \"ENSEMBL:ENSG00000198853\"\n                                    \"ENSEMBL:ENSG00000148341\"\n                                    \"ENSEMBL:ENSG00000135441\"\n                                    \"ENSEMBL:ENSG00000267534\"\n                                    \"ENSEMBL:ENSG00000139567\"\n                                    \"ENSEMBL:ENSG00000186635\"\n                                    \"ENSEMBL:ENSG00000122515\"\n                                    \"ENSEMBL:ENSG00000181690\"\n                                    \"ENSEMBL:ENSG00000049239\"\n                                    \"ENSEMBL:ENSG00000206395\"\n                                    \"ENSEMBL:ENSG00000141959\"\n                                    \"ENSEMBL:ENSG00000176845\"\n                                    \"ENSEMBL:ENSG00000175756\"\n                                    \"ENSEMBL:ENSG00000185201\"\n                                    \"ENSEMBL:ENSG00000185215\"\n                                    \"ENSEMBL:ENSG00000137332\"\n                                    \"ENSEMBL:ENSG00000116260\"\n                                    \"ENSEMBL:ENSG00000102678\"\n                                    \"ENSEMBL:ENSG00000100379\"\n                                    \"ENSEMBL:ENSG00000185561\"\n                                    \"ENSEMBL:ENSG00000186111\"\n                                    \"ENSEMBL:ENSG00000088280\"\n                                    \"ENSEMBL:ENSG00000186716\"\n                                    \"ENSEMBL:ENSG00000107223\"\n                                    \"ENSEMBL:ENSG00000114841\"\n                                    \"ENSEMBL:ENSG00000082781\"\n                                    \"ENSEMBL:ENSG00000102030\"\n                                    \"ENSEMBL:ENSG00000164619\"\n                                    \"ENSEMBL:ENSG00000167815\"\n                                    \"ENSEMBL:ENSG00000125734\"\n                                    \"ENSEMBL:ENSG00000067829\"\n                                    \"ENSEMBL:ENSG00000197381\"\n                                    \"ENSEMBL:ENSG00000142186\"\n                                    \"ENSEMBL:ENSG00000110046\"\n                                    \"ENSEMBL:ENSG00000213398\"\n                                    \"ENSEMBL:ENSG00000035664\"\n                                    \"ENSEMBL:ENSG00000125733\"\n                                    \"ENSEMBL:ENSG00000180879\"\n                                    \"ENSEMBL:ENSG00000140092\"\n                                    \"ENSEMBL:ENSG00000116786\"\n                                    \"ENSEMBL:ENSG00000168899\"\n                                    \"ENSEMBL:ENSG00000115325\"\n                                    \"ENSEMBL:ENSG00000061938\"\n                                    \"ENSEMBL:ENSG00000241878\"\n                                    \"ENSEMBL:ENSG00000153406\"\n                                    \"ENSEMBL:ENSG00000167671\"\n                                    \"ENSEMBL:ENSG00000130706\"\n                                    \"ENSEMBL:ENSG00000123395\"\n                                    \"ENSEMBL:ENSG00000175573\"\n                                    \"ENSEMBL:ENSG00000177239\"\n                                    \"ENSEMBL:ENSG00000142733\"\n                                    \"ENSEMBL:ENSG00000005486\"\n                                    \"ENSEMBL:ENSG00000164081\"\n                                    \"ENSEMBL:ENSG00000005882\"\n                                    \"ENSEMBL:ENSG00000175220\"\n                                    \"ENSEMBL:ENSG00000238227\"\n                                    \"ENSEMBL:ENSG00000008441\"\n                                    \"ENSEMBL:ENSG00000166313\"\n                                    \"ENSEMBL:ENSG00000105221\"\n                                    \"ENSEMBL:ENSG00000005007\"\n                                    \"ENSEMBL:ENSG00000164543\"\n                                    \"ENSEMBL:ENSG00000110651\"\n                                    \"ENSEMBL:ENSG00000068724\"\n                                    \"ENSEMBL:ENSG00000091592\"\n                                    \"ENSEMBL:ENSG00000142459\"\n                                    \"ENSEMBL:ENSG00000176248\"\n                                    \"ENSEMBL:ENSG00000030419\"\n                                    \"ENSEMBL:ENSG00000084207\"\n                                    \"ENSEMBL:ENSG00000111371\"\n                                    \"ENSEMBL:ENSG00000197226\"\n                                    \"ENSEMBL:ENSG00000161091\"\n                                    \"ENSEMBL:ENSG00000126561\"\n                                    \"ENSEMBL:ENSG00000159842\"\n                                    \"ENSEMBL:ENSG00000100243\"\n                                    \"ENSEMBL:ENSG00000177156\"\n                                    \"ENSEMBL:ENSG00000079999\"\n                                    \"ENSEMBL:ENSG00000160209\"\n                                    \"ENSEMBL:ENSG00000095321\"\n                                    \"ENSEMBL:ENSG00000167674\"\n                                    \"ENSEMBL:ENSG00000063660\"\n                                    \"ENSEMBL:ENSG00000090565\"\n                                    \"ENSEMBL:ENSG00000134030\"\n                                    \"ENSEMBL:ENSG00000174903\"\n                                    \"ENSEMBL:ENSG00000106665\"\n                                    \"ENSEMBL:ENSG00000172890\"\n                                    \"ENSEMBL:ENSG00000099917\"\n                                    \"ENSEMBL:ENSG00000160211\"\n                                    \"ENSEMBL:ENSG00000140264\"\n                                    \"ENSEMBL:ENSG00000109065\"\n                                    \"ENSEMBL:ENSG00000041880\"\n                                    \"ENSEMBL:ENSG00000141503\"\n                                    \"ENSEMBL:ENSG00000171067\"\n                                    \"ENSEMBL:ENSG00000140553\"\n                                    \"ENSEMBL:ENSG00000072422\"\n                                    \"ENSEMBL:ENSG00000172057\"\n                                    \"ENSEMBL:ENSG00000088256\"\n                                    \"ENSEMBL:ENSG00000101152\"\n                                    \"ENSEMBL:ENSG00000100413\"\n                                    \"ENSEMBL:ENSG00000148331\"\n                                    \"ENSEMBL:ENSG00000141736\"\n                                    \"ENSEMBL:ENSG00000124067\"\n                                    \"ENSEMBL:ENSG00000137207\"\n                                    \"ENSEMBL:ENSG00000126391\"\n                                    \"ENSEMBL:ENSG00000131446\"\n                                    \"ENSEMBL:ENSG00000185359\"\n                                    \"ENSEMBL:ENSG00000134590\"\n                                    \"ENSEMBL:ENSG00000162512\"\n                                    \"ENSEMBL:ENSG00000167118\"\n                                    \"ENSEMBL:ENSG00000169851\"\n                                    \"ENSEMBL:ENSG00000196961\"\n                                    \"ENSEMBL:ENSG00000135924\"\n                                    \"ENSEMBL:ENSG00000135631\"\n                                    \"ENSEMBL:ENSG00000129250\"\n                                    \"ENSEMBL:ENSG00000129103\"\n                                    \"ENSEMBL:ENSG00000197694\"))\n\n\n\n"
  },
  {
    "path": "contrib/medikanren2/Thi/Hakon-DEG-syns.rkt",
    "content": "#lang racket\n\n(provide (all-defined-out))\n\n(provide Hakon-CHAMP1-RNA-up-syns\n         Hakon-CHAMP1-RNA-down-syns)\n\n(define Hakon-CHAMP1-RNA-up-syns\n  (list\n   \"ENSEMBL:ENSG00000115468\"\n   \"ENSEMBL:ENSG00000171208\"\n   \"UMLS:C1538790\"\n   \"HGNC:17198\"\n   \"UniProtKB:Q8NFY4\"\n   \"ENSEMBL:LRG_50\"\n   \"PR:Q9NPG1\"\n   \"ENSEMBL:ENSG00000132688\"\n   \"ENSEMBL:ENSG00000163918\"\n   \"HGNC:2053\"\n   \"UniProtKB:Q5EG05\"\n   \"UMLS:C2240136\"\n   \"HGNC:11168\"\n   \"NCBIGene:80243\"\n   \"HGNC:4280\"\n   \"HGNC:6343\"\n   \"ENSEMBL:ENSG00000254087\"\n   \"HGNC:485\"\n   \"ENSEMBL:ENSG00000166974\"\n   \"UniProtKB:Q99683\"\n   \"UniProtKB:P50135\"\n   \"UMLS:C1333585\"\n   \"NCBIGene:23362\"\n   \"UniProtKB:P31271\"\n   \"UMLS:C2239668\"\n   \"HGNC:12518\"\n   \"NCBIGene:7042\"\n   \"UMLS:C0812307\"\n   \"PR:Q9NZQ7\"\n   \"NCBIGene:134429\"\n   \"ENSEMBL:ENSG00000091879\"\n   \"ENSEMBL:ENSG00000144635\"\n   \"NCBIGene:26508\"\n   \"HGNC:10252\"\n   \"HGNC:6597\"\n   \"HGNC:25491\"\n   \"PR:Q9Y6U3\"\n   \"HGNC:2528\"\n   \"UMLS:C1424695\"\n   \"ENSEMBL:ENSG00000206053\"\n   \"NCBIGene:153478\"\n   \"NCBIGene:3209\"\n   \"ENSEMBL:ENSG00000126803\"\n   \"NCBIGene:4773\"\n   \"PR:P43304\"\n   \"UniProtKB:Q8NC67\"\n   \"ENSEMBL:ENSG00000150471\"\n   \"UniProtKB:Q8WY64\"\n   \"UniProtKB:Q9Y6G9\"\n   \"PR:Q6UVK1\"\n   \"HGNC:9082\"\n   \"HGNC:6848\"\n   \"ENSEMBL:ENSG00000109861\"\n   \"UniProtKB:Q5TFE4\"\n   \"ENSEMBL:ENSG00000137501\"\n   \"NCBIGene:7351\"\n   \"PR:A2A2Y4\"\n   \"NCBIGene:1075\"\n   \"UMLS:C1415074\"\n   \"PR:Q8WXH0\"\n   \"ENSEMBL:ENSG00000169129\"\n   \"ENSEMBL:ENSG00000112183\"\n   \"UniProtKB:Q9H892\"\n   \"UMLS:C1540292\"\n   \"ENSEMBL:ENSG00000054654\"\n   \"PR:P50135\"\n   \"NCBIGene:6502\"\n   \"NCBIGene:29116\"\n   \"NCBIGene:1464\"\n   \"HGNC:17493\"\n   \"NCBIGene:51267\"\n   \"HGNC:6547\"\n   \"ENSEMBL:ENSG00000131471\"\n   \"PR:Q68D86\"\n   \"NCBIGene:4162\"\n   \"HGNC:6554\"\n   \"UMLS:C1420593\"\n   \"UniProtKB:P01130\"\n   \"PR:Q13469\"\n   \"UniProtKB:Q8N4X5\"\n   \"PR:Q86SQ0\"\n   \"PR:P61812\"\n   \"NCBIGene:22866\"\n   \"UMLS:C1419269\"\n   \"NCBIGene:2149\"\n   \"ENSEMBL:ENSG00000198743\"\n   \"ENSEMBL:ENSG00000128641\"\n   \"PR:P48357\"\n   \"HGNC:22950\"\n   \"NCBIGene:90853\"\n   \"HGNC:2323\"\n   \"ENSEMBL:ENSG00000065882\"\n   \"HGNC:11578\"\n   \"PR:Q14739\"\n   \"HGNC:4456\"\n   \"HGNC:7776\"\n   \"HGNC:376\"\n   \"PR:Q6UVW9\"\n   \"NCBIGene:4430\"\n   \"ENSEMBL:ENSG00000104435\"\n   \"PR:Q86V40\"\n   \"NCBIGene:4254\"\n   \"NCBIGene:7976\"\n   \"PR:O15084\"\n   \"HGNC:6560\"\n   \"UMLS:C3543895\"\n   \"PR:Q9H0B8\"\n   \"PR:Q9UNQ0\"\n   \"ENSEMBL:ENSG00000134318\"\n   \"NCBIGene:129293\"\n   \"NCBIGene:64744\"\n   \"ENSEMBL:ENSG00000157557\"\n   \"HGNC:3776\"\n   \"UMLS:C1539762\"\n   \"ENSEMBL:ENSG00000129680\"\n   \"PR:P03956\"\n   \"UMLS:C1428873\"\n   \"UMLS:C2239938\"\n   \"UMLS:C1422375\"\n   \"UniProtKB:P55851\"\n   \"PR:Q9NQ87\"\n   \"UMLS:C1366449\"\n   \"ENSEMBL:ENSG00000143815\"\n   \"NCBIGene:23224\"\n   \"UniProtKB:Q13884\"\n   \"PR:Q9GZM7\"\n   \"NCBIGene:6641\"\n   \"ENSEMBL:ENSG00000006747\"\n   \"NCBIGene:3189\"\n   \"UMLS:C1417695\"\n   \"PR:Q96PP9\"\n   \"ENSEMBL:ENSG00000120217\"\n   \"HGNC:7014\"\n   \"UMLS:C1419063\"\n   \"NCBIGene:81578\"\n   \"HGNC:6551\"\n   \"NCBIGene:54843\"\n   \"UMLS:C1417014\"\n   \"UniProtKB:Q96DR4\"\n   \"HGNC:10545\"\n   \"NCBIGene:441250\"\n   \"UniProtKB:Q9P2Q2\"\n   \"ENSEMBL:ENSG00000007944\"\n   \"PR:Q96PP8\"\n   \"HGNC:11038\"\n   \"NCBIGene:160364\"\n   \"PR:Q9H910\"\n   \"UMLS:C1825519\"\n   \"PR:Q8N8N0\"\n   \"NCBIGene:221294\"\n   \"NCBIGene:3949\"\n   \"ENSEMBL:ENSG00000165895\"\n   \"ENSEMBL:ENSG00000112312\"\n   \"ENSEMBL:ENSG00000151617\"\n   \"ENSEMBL:ENSG00000134668\"\n   \"PR:Q6ZMY3\"\n   \"PR:P51816\"\n   \"UniProtKB:Q86SQ0\"\n   \"PR:P24043\"\n   \"PR:P62736\"\n   \"ENSEMBL:ENSG00000145604\"\n   \"PR:Q13233\"\n   \"ENSEMBL:ENSG00000118777\"\n   \"ENSEMBL:ENSG00000277149\"\n   \"UMLS:C1539087\"\n   \"NCBIGene:6383\"\n   \"NCBIGene:3955\"\n   \"UniProtKB:P50222\"\n   \"NCBIGene:2820\"\n   \"PR:Q9P2P6\"\n   \"ENSEMBL:ENSG00000116127\"\n   \"PR:Q9BUP0\"\n   \"UniProtKB:P16671\"\n   \"HGNC:4882\"\n   \"ENSEMBL:ENSG00000172322\"\n   \"UMLS:C1826479\"\n   \"HGNC:5004\"\n   \"ENSEMBL:ENSG00000141198\"\n   \"HGNC:4517\"\n   \"PR:P36383\"\n   \"PR:Q9P2Q2\"\n   \"UniProtKB:P35408\"\n   \"HGNC:26242\"\n   \"HGNC:550\"\n   \"HGNC:25901\"\n   \"UniProtKB:P53634\"\n   \"ENSEMBL:ENSG00000130164\"\n   \"ENSEMBL:ENSG00000187323\"\n   \"UMLS:C1332797\"\n   \"UMLS:C1419892\"\n   \"ENSEMBL:ENSG00000151474\"\n   \"UniProtKB:Q96PX9\"\n   \"ENSEMBL:ENSG00000170891\"\n   \"HGNC:14137\"\n   \"UniProtKB:P62736\"\n   \"UMLS:C1539745\"\n   \"UniProtKB:Q9H999\"\n   \"ENSEMBL:ENSG00000163909\"\n   \"UMLS:C1419064\"\n   \"HGNC:19030\"\n   \"NCBIGene:79646\"\n   \"NCBIGene:3953\"\n   \"UMLS:C1425966\"\n   \"UniProtKB:Q96PP9\"\n   \"PR:Q86X52\"\n   \"UniProtKB:Q8NC01\"\n   \"PR:P25101\"\n   \"PR:Q5HYW2\"\n   \"UMLS:C1427370\"\n   \"NCBIGene:55691\"\n   \"NCBIGene:83716\"\n   \"ENSEMBL:ENSG00000050628\"\n   \"HGNC:19168\"\n   \"HGNC:23228\"\n   \"HGNC:24435\"\n   \"PR:P21583\"\n   \"HGNC:10901\"\n   \"UniProtKB:Q5QGZ9\"\n   \"HGNC:33701\"\n   \"UniProtKB:Q8WU79\"\n   \"NCBIGene:51053\"\n   \"HGNC:33737\"\n   \"UniProtKB:Q9UJU2\"\n   \"HGNC:25742\"\n   \"HGNC:17635\"\n   \"UniProtKB:Q9NWQ8\"\n   \"UMLS:C1824630\"\n   \"HGNC:24125\"\n   \"UMLS:C1426119\"\n   \"PR:Q5EG05\"\n   \"ENSEMBL:ENSG00000118473\"\n   \"PR:P35249\"\n   \"PR:P15036\"\n   \"ENSEMBL:ENSG00000138795\"\n   \"NCBIGene:3149\"\n   \"ENSEMBL:LRG_991\"\n   \"NCBIGene:26033\"\n   \"ENSEMBL:LRG_781\"\n   \"UMLS:C1415644\"\n   \"ENSEMBL:ENSG00000178425\"\n   \"UMLS:C1418455\"\n   \"ENSEMBL:ENSG00000096746\"\n   \"PR:Q15052\"\n   \"HGNC:10577\"\n   \"UniProtKB:Q9HCH5\"\n   \"ENSEMBL:ENSG00000188393\"\n   \"PR:Q8TCU4\"\n   \"ENSEMBL:ENSG00000144218\"\n   \"HGNC:5043\"\n   \"PR:Q93045\"\n   \"ENSEMBL:ENSG00000181104\"\n   \"UniProtKB:P10114\"\n   \"ENSEMBL:ENSG00000107518\"\n   \"PR:Q9NRR1\"\n   \"UniProtKB:Q8NES3\"\n   \"NCBIGene:5352\"\n   \"HGNC:18745\"\n   \"UniProtKB:P48357\"\n   \"UMLS:C1538784\"\n   \"HGNC:26286\"\n   \"NCBIGene:90102\"\n   \"UniProtKB:P43146\"\n   \"PR:Q8WY64\"\n   \"ENSEMBL:LRG_283\"\n   \"NCBIGene:53918\"\n   \"UMLS:C1823488\"\n   \"UniProtKB:Q9HAR2\"\n   \"NCBIGene:9976\"\n   \"UMLS:C1428204\"\n   \"ENSEMBL:ENSG00000204397\"\n   \"HGNC:174\"\n   \"PR:P25116\"\n   \"PR:Q96DY7\"\n   \"HGNC:30776\"\n   \"ENSEMBL:ENSG00000221818\"\n   \"HGNC:3179\"\n   \"UniProtKB:Q9H0B8\"\n   \"NCBIGene:10982\"\n   \"UniProtKB:Q13023\"\n   \"PR:P31327\"\n   \"UMLS:C1428625\"\n   \"PR:Q8IZ41\"\n   \"ENSEMBL:LRG_336\"\n   \"UniProtKB:Q9NZF1\"\n   \"ENSEMBL:ENSG00000151320\"\n   \"NCBIGene:11009\"\n   \"UniProtKB:Q5HYW2\"\n   \"HGNC:6518\"\n   \"HGNC:9595\"\n   \"UniProtKB:P53794\"\n   \"NCBIGene:257019\"\n   \"ENSEMBL:ENSG00000145287\"\n   \"PR:P34741\"\n   \"UniProtKB:Q9NQ87\"\n   \"ENSEMBL:ENSG00000029993\"\n   \"ENSEMBL:ENSG00000076706\"\n   \"PR:Q8N4X5\"\n   \"ENSEMBL:ENSG00000069188\"\n   \"UMLS:C1417112\"\n   \"HGNC:10659\"\n   \"UniProtKB:Q13309\"\n   \"PR:Q70Z35\"\n   \"NCBIGene:4629\"\n   \"NCBIGene:4312\"\n   \"HGNC:25412\"\n   \"ENSEMBL:ENSG00000162892\"\n   \"NCBIGene:392490\"\n   \"UniProtKB:Q9NZQ7\"\n   \"NCBIGene:5911\"\n   \"NCBIGene:79739\"\n   \"ENSEMBL:ENSG00000152952\"\n   \"UniProtKB:Q6ZMY3\"\n   \"UniProtKB:P21583\"\n   \"PR:P82932\"\n   \"UniProtKB:Q01581\"\n   \"HGNC:23700\"\n   \"UniProtKB:Q8WXH0\"\n   \"UMLS:C1417411\"\n   \"ENSEMBL:ENSG00000276480\"\n   \"UniProtKB:Q9NPG1\"\n   \"HGNC:130\"\n   \"PR:A6NI28\"\n   \"PR:O15347\"\n   \"NCBIGene:80031\"\n   \"HGNC:6482\"\n   \"ENSEMBL:ENSG00000243927\"\n   \"ENSEMBL:ENSG00000176641\"\n   \"UniProtKB:Q6UVW9\"\n   \"HGNC:9596\"\n   \"HGNC:20974\"\n   \"UMLS:C1825085\"\n   \"UMLS:C1427805\"\n   \"HGNC:30043\"\n   \"HGNC:9972\"\n   \"UniProtKB:Q9UNQ0\"\n   \"PR:Q6ZT98\"\n   \"ENSEMBL:ENSG00000095015\"\n   \"PR:Q8NC01\"\n   \"ENSEMBL:ENSG00000112972\"\n   \"NCBIGene:3930\"\n   \"UMLS:C1415616\"\n   \"UMLS:C1426053\"\n   \"HGNC:1777\"\n   \"UMLS:C1417679\"\n   \"PR:Q5QGZ9\"\n   \"UniProtKB:Q8IZ41\"\n   \"UniProtKB:Q9H910\"\n   \"PR:Q92478\"\n   \"PR:Q9Y6G9\"\n   \"NCBIGene:79642\"\n   \"NCBIGene:85477\"\n   \"HGNC:8829\"\n   \"UniProtKB:Q9BX46\"\n   \"ENSEMBL:ENSG00000159433\"\n   \"HGNC:18058\"\n   \"UMLS:C1412318\"\n   \"UMLS:C1823542\"\n   \"ENSEMBL:ENSG00000152684\"\n   \"UMLS:C0812202\"\n   \"NCBIGene:80303\"\n   \"PR:Q58EX2\"\n   \"UniProtKB:O15164\"\n   \"NCBIGene:6307\"\n   \"ENSEMBL:ENSG00000129675\"\n   \"UniProtKB:Q9P2P6\"\n   \"PR:Q6NUM6\"\n   \"ENSEMBL:ENSG00000150048\"\n   \"PR:P35408\"\n   \"NCBIGene:9475\"\n   \"UMLS:C1425271\"\n   \"PR:Q9BX46\"\n   \"PR:Q5TFE4\"\n   \"HGNC:29399\"\n   \"HGNC:27013\"\n   \"HGNC:29573\"\n   \"UniProtKB:P82932\"\n   \"ENSEMBL:ENSG00000113594\"\n   \"UniProtKB:Q00534\"\n   \"UniProtKB:Q9BQI5\"\n   \"HGNC:2701\"\n   \"ENSEMBL:ENSG00000172167\"\n   \"PR:Q8IYL9\"\n   \"HGNC:11983\"\n   \"HGNC:19701\"\n   \"UniProtKB:Q13705\"\n   \"PR:Q13309\"\n   \"UniProtKB:O00469\"\n   \"PR:Q9H999\"\n   \"PR:P53794\"\n   \"PR:Q9NYI0\"\n   \"UniProtKB:Q8N8N0\"\n   \"UniProtKB:P42702\"\n   \"PR:Q13884\"\n   \"UMLS:C2239823\"\n   \"UniProtKB:P07948\"\n   \"NCBIGene:23243\"\n   \"ENSEMBL:ENSG00000069122\"\n   \"NCBIGene:27085\"\n   \"UMLS:C1708616\"\n   \"NCBIGene:1909\"\n   \"PR:Q86TI0\"\n   \"NCBIGene:2878\"\n   \"UMLS:C1420855\"\n   \"HGNC:428\"\n   \"UniProtKB:Q8IYL9\"\n   \"PR:Q8IZF2\"\n   \"NCBIGene:105374836\"\n   \"UniProtKB:Q15052\"\n   \"ENSEMBL:ENSG00000076641\"\n   \"PR:Q9HAR2\"\n   \"PR:O15123\"\n   \"UniProtKB:A6NI28\"\n   \"ENSEMBL:ENSG00000124749\"\n   \"PR:P01130\"\n   \"HGNC:5007\"\n   \"HGNC:19308\"\n   \"PR:O75496\"\n   \"NCBIGene:22856\"\n   \"UniProtKB:P51816\"\n   \"UMLS:C1539139\"\n   \"NCBIGene:2334\"\n   \"ENSEMBL:ENSG00000120137\"\n   \"UniProtKB:P31327\"\n   \"UniProtKB:Q92478\"\n   \"UMLS:C1427702\"\n   \"UMLS:C1538565\"\n   \"UMLS:C1366521\"\n   \"UniProtKB:Q58EX2\"\n   \"UMLS:C1366529\"\n   \"UniProtKB:Q15555\"\n   \"PR:Q9H892\"\n   \"PR:P48681\"\n   \"HGNC:3489\"\n   \"ENSEMBL:LRG_274\"\n   \"ENSEMBL:LRG_741\"\n   \"NCBIGene:114769\"\n   \"UniProtKB:A2A2Y4\"\n   \"HGNC:6473\"\n   \"ENSEMBL:ENSG00000144824\"\n   \"PR:O75674\"\n   \"UniProtKB:Q9NRR1\"\n   \"PR:Q5VV63\"\n   \"NCBIGene:3899\"\n   \"NCBIGene:3306\"\n   \"HGNC:24355\"\n   \"ENSEMBL:ENSG00000122779\"\n   \"UniProtKB:P34741\"\n   \"ENSEMBL:ENSG00000162654\"\n   \"NCBIGene:51316\"\n   \"HGNC:25248\"\n   \"HGNC:19365\"\n   \"UniProtKB:Q8WXI2\"\n   \"UniProtKB:Q6UVK1\"\n   \"ENSEMBL:ENSG00000172164\"\n   \"ENSEMBL:ENSG00000164211\"\n   \"NCBIGene:4223\"\n   \"ENSEMBL:ENSG00000106003\"\n   \"ENSEMBL:ENSG00000104290\"\n   \"HGNC:16770\"\n   \"NCBIGene:254251\"\n   \"ENSEMBL:ENSG00000149970\"\n   \"NCBIGene:10763\"\n   \"UniProtKB:Q96PP8\"\n   \"UniProtKB:O75674\"\n   \"PR:Q8WU79\"\n   \"NCBIGene:59\"\n   \"PR:O00469\"\n   \"ENSEMBL:ENSG00000103196\"\n   \"NCBIGene:6526\"\n   \"UniProtKB:P35749\"\n   \"UniProtKB:Q8TCU4\"\n   \"ENSEMBL:ENSG00000114739\"\n   \"NCBIGene:3176\"\n   \"NCBIGene:143872\"\n   \"UMLS:C1335831\"\n   \"PR:O75116\"\n   \"UniProtKB:P54652\"\n   \"NCBIGene:81831\"\n   \"UniProtKB:Q9HAK2\"\n   \"HGNC:21695\"\n   \"ENSEMBL:ENSG00000153404\"\n   \"NCBIGene:1021\"\n   \"NCBIGene:10052\"\n   \"UniProtKB:Q9Y6U3\"\n   \"PR:Q8IWC1\"\n   \"UMLS:C2239783\"\n   \"NCBIGene:10040\"\n   \"UniProtKB:Q12955\"\n   \"HGNC:19090\"\n   \"UniProtKB:Q14739\"\n   \"NCBIGene:3157\"\n   \"ENSEMBL:ENSG00000172159\"\n   \"NCBIGene:3908\"\n   \"ENSEMBL:ENSG00000204131\"\n   \"HGNC:19093\"\n   \"UMLS:C1825802\"\n   \"HGNC:15585\"\n   \"PR:P54652\"\n   \"ENSEMBL:ENSG00000173546\"\n   \"HGNC:14051\"\n   \"NCBIGene:8477\"\n   \"NCBIGene:1373\"\n   \"UniProtKB:Q13007\"\n   \"UniProtKB:P48681\"\n   \"NCBIGene:220441\"\n   \"NCBIGene:55824\"\n   \"HGNC:19254\"\n   \"ENSEMBL:ENSG00000142910\"\n   \"NCBIGene:5984\"\n   \"UMLS:C1412431\"\n   \"ENSEMBL:ENSG00000106511\"\n   \"PR:Q8NFY4\"\n   \"HGNC:3537\"\n   \"UniProtKB:Q93045\"\n   \"NCBIGene:93\"\n   \"UMLS:C1415251\"\n   \"UniProtKB:Q5VV63\"\n   \"ENSEMBL:ENSG00000116678\"\n   \"UniProtKB:O15084\"\n   \"UniProtKB:O75496\"\n   \"NCBIGene:5734\"\n   \"HGNC:29063\"\n   \"PR:P43146\"\n   \"UniProtKB:Q8IWC1\"\n   \"PR:Q16853\"\n   \"PR:P51826\"\n   \"PR:Q15555\"\n   \"HGNC:19895\"\n   \"NCBIGene:64129\"\n   \"PR:P10114\"\n   \"UMLS:C1825008\"\n   \"ENSEMBL:ENSG00000165105\"\n   \"PR:Q9HCH5\"\n   \"NCBIGene:54360\"\n   \"UniProtKB:O75116\"\n   \"PR:Q01581\"\n   \"HGNC:31713\"\n   \"ENSEMBL:ENSG00000131873\"\n   \"HGNC:17025\"\n   \"UniProtKB:Q86X52\"\n   \"PR:P42702\"\n   \"NCBIGene:27151\"\n   \"ENSEMBL:ENSG00000052802\"\n   \"PR:P07948\"\n   \"HGNC:6857\"\n   \"ENSEMBL:ENSG00000156011\"\n   \"PR:P43115\"\n   \"PR:Q8N3X6\"\n   \"HGNC:26811\"\n   \"NCBIGene:288\"\n   \"UniProtKB:Q15800\"\n   \"HGNC:20480\"\n   \"NCBIGene:8639\"\n   \"HGNC:26464\"\n   \"UniProtKB:P24043\"\n   \"HGNC:21539\"\n   \"HGNC:685\"\n   \"PR:Q13705\"\n   \"ENSEMBL:ENSG00000150636\"\n   \"HGNC:11768\"\n   \"NCBIGene:221662\"\n   \"ENSEMBL:ENSG00000206560\"\n   \"ENSEMBL:ENSG00000196569\"\n   \"ENSEMBL:ENSG00000105810\"\n   \"UMLS:C1539216\"\n   \"UMLS:C2681322\"\n   \"NCBIGene:29126\"\n   \"PR:O15164\"\n   \"UMLS:C1427216\"\n   \"UMLS:C1426964\"\n   \"NCBIGene:84251\"\n   \"HGNC:7756\"\n   \"PR:Q96P44\"\n   \"PR:Q8WXI2\"\n   \"PR:P53634\"\n   \"ENSEMBL:ENSG00000135218\"\n   \"UMLS:C1420202\"\n   \"UMLS:C1426193\"\n   \"UniProtKB:O43795\"\n   \"UniProtKB:Q9GZM7\"\n   \"HGNC:26545\"\n   \"NCBIGene:3977\"\n   \"PR:P31271\"\n   \"PR:Q8IZJ3\"\n   \"UniProtKB:Q16853\"\n   \"UniProtKB:P15036\"\n   \"ENSEMBL:ENSG00000115159\"\n   \"UniProtKB:P25101\"\n   \"UniProtKB:Q9BRX2\"\n   \"UMLS:C1428345\"\n   \"NCBIGene:4217\"\n   \"NCBIGene:340527\"\n   \"UMLS:C1539846\"\n   \"UniProtKB:P25116\"\n   \"ENSEMBL:ENSG00000180801\"\n   \"NCBIGene:79649\"\n   \"ENSEMBL:ENSG00000160111\"\n   \"UMLS:C1426155\"\n   \"PR:Q9NWQ8\"\n   \"HGNC:5028\"\n   \"HGNC:21556\"\n   \"HGNC:21155\"\n   \"ENSEMBL:ENSG00000186854\"\n   \"PR:Q96DR4\"\n   \"PR:Q00534\"\n   \"PR:Q9UJU2\"\n   \"UniProtKB:Q13233\"\n   \"ENSEMBL:ENSG00000137941\"\n   \"NCBIGene:158158\"\n   \"UniProtKB:O15123\"\n   \"UMLS:C1422809\"\n   \"UniProtKB:Q70Z35\"\n   \"ENSEMBL:ENSG00000149292\"\n   \"HGNC:14644\"\n   \"UniProtKB:Q86V40\"\n   \"NCBIGene:90861\"\n   \"UMLS:C1428878\"\n   \"PR:Q99683\"\n   \"PR:Q9NZF1\"\n   \"HGNC:6735\"\n   \"UniProtKB:Q6ZT98\"\n   \"ENSEMBL:ENSG00000151150\"\n   \"HGNC:24191\"\n   \"HGNC:4041\"\n   \"UniProtKB:P22352\"\n   \"UniProtKB:Q8IZF2\"\n   \"UMLS:C2828634\"\n   \"UMLS:C1417559\"\n   \"UniProtKB:P51826\"\n   \"UMLS:C1426006\"\n   \"PR:P22352\"\n   \"ENSEMBL:ENSG00000169439\"\n   \"HGNC:26295\"\n   \"ENSEMBL:ENSG00000107796\"\n   \"PR:Q15800\"\n   \"PR:P31942\"\n   \"UMLS:C1539106\"\n   \"NCBIGene:948\"\n   \"UniProtKB:P43304\"\n   \"ENSEMBL:ENSG00000049130\"\n   \"UMLS:C1428783\"\n   \"PR:P55851\"\n   \"PR:Q13023\"\n   \"NCBIGene:57519\"\n   \"NCBIGene:4214\"\n   \"PR:Q96PX9\"\n   \"PR:P16671\"\n   \"HGNC:5235\"\n   \"UMLS:C1419850\"\n   \"PR:O43795\"\n   \"NCBIGene:387836\"\n   \"UMLS:C1823280\"\n   \"HGNC:33908\"\n   \"UniProtKB:Q5FYB0\"\n   \"UniProtKB:Q96P44\"\n   \"NCBIGene:8805\"\n   \"ENSEMBL:LRG_409\"\n   \"UniProtKB:P61812\"\n   \"UniProtKB:P43115\"\n   \"ENSEMBL:ENSG00000110852\"\n   \"UMLS:C1415526\"\n   \"NCBIGene:7840\"\n   \"ENSEMBL:ENSG00000155966\"\n   \"UniProtKB:Q96DY7\"\n   \"NCBIGene:115361\"\n   \"UMLS:C1426511\"\n   \"HGNC:6891\"\n   \"UniProtKB:O15347\"\n   \"UniProtKB:Q9NYI0\"\n   \"NCBIGene:221395\"\n   \"ENSEMBL:ENSG00000211445\"\n   \"HGNC:494\"\n   \"UMLS:C1332089\"\n   \"UMLS:C1428531\"\n   \"UniProtKB:Q8IZJ3\"\n   \"UMLS:C1415277\"\n   \"ENSEMBL:ENSG00000154451\"\n   \"NCBIGene:9429\"\n   \"NCBIGene:9459\"\n   \"PR:Q9BRX2\"\n   \"UniProtKB:P31942\"\n   \"UMLS:C1419351\"\n   \"UniProtKB:Q13469\"\n   \"HGNC:29556\"\n   \"NCBIGene:64641\"\n   \"UMLS:C1428778\"\n   \"HGNC:74\"\n   \"UniProtKB:P35249\"\n   \"UniProtKB:Q6NUM6\"\n   \"ENSEMBL:ENSG00000084070\"\n   \"HGNC:7417\"\n   \"ENSEMBL:ENSG00000137872\"\n   \"ENSEMBL:ENSG00000046889\"\n   \"UMLS:C1420297\"\n   \"UMLS:C1423595\"\n   \"ENSEMBL:ENSG00000150540\"\n   \"UMLS:C1538736\"\n   \"NCBIGene:11075\"\n   \"PR:P50222\"\n   \"ENSEMBL:ENSG00000106031\"\n   \"PR:Q13007\"\n   \"HGNC:7596\"\n   \"HGNC:1663\"\n   \"HGNC:4555\"\n   \"NCBIGene:23284\"\n   \"NCBIGene:9472\"\n   \"ENSEMBL:ENSG00000196611\"\n   \"NCBIGene:84632\"\n   \"NCBIGene:64968\"\n   \"ENSEMBL:ENSG00000178177\"\n   \"NCBIGene:51176\"\n   \"NCBIGene:1630\"\n   \"PR:P35749\"\n   \"NCBIGene:115362\"\n   \"ENSEMBL:ENSG00000197442\"\n   \"NCBIGene:23216\"\n   \"ENSEMBL:ENSG00000140030\"\n   \"HGNC:25082\"\n   \"NCBIGene:4067\"\n   \"NCBIGene:2114\"\n   \"PR:Q5FYB0\"\n   \"HGNC:7569\"\n   \"HGNC:29024\"\n   \"HGNC:2466\"\n   \"ENSEMBL:ENSG00000125249\"\n   \"NCBIGene:51143\"\n   \"PR:Q12955\"\n   \"ENSEMBL:ENSG00000101096\"\n   \"ENSEMBL:ENSG00000133392\"\n   \"UniProtKB:Q9BUP0\"\n   \"ENSEMBL:ENSG00000092969\"\n   \"NCBIGene:54970\"\n   \"HGNC:5102\"\n   \"UniProtKB:Q8N3X6\"\n   \"UniProtKB:P03956\"\n   \"NCBIGene:5733\"\n   \"HGNC:7155\"\n   \"UMLS:C1415758\"\n   \"ENSEMBL:ENSG00000171522\"\n   \"PR:Q8NES3\"\n   \"HGNC:26338\"\n   \"PR:Q9HAK2\"\n   \"HGNC:17084\"\n   \"NCBIGene:54549\"\n   \"UniProtKB:Q68D86\"\n   \"NCBIGene:285\"\n   \"HGNC:19162\"\n   \"UMLS:C1419598\"\n   \"ENSEMBL:ENSG00000175567\"\n   \"PR:Q8NC67\"\n   \"NCBIGene:79839\"\n   \"UniProtKB:Q86TI0\"\n   \"HGNC:9861\"\n   \"ENSEMBL:ENSG00000182963\"\n   \"PR:Q9BQI5\"\n   \"HGNC:11812\"\n   \"HGNC:11346\"\n   \"ENSEMBL:ENSG00000021826\"\n   \"UniProtKB:P36383\"\n   \"UMLS:C1539088\"))\n\n\n(define Hakon-CHAMP1-RNA-down-syns\n  (list\n   \"HGNC:14163\"\n   \"NCBIGene:22871\"\n   \"ENSEMBL:ENSG00000160932\"\n   \"UniProtKB:Q92900\"\n   \"PR:Q8N2Y8\"\n   \"UniProtKB:Q04725\"\n   \"NCBIGene:55643\"\n   \"PR:Q8N6G6\"\n   \"PR:Q16774\"\n   \"UMLS:C1419973\"\n   \"ENSEMBL:ENSG00000063660\"\n   \"ENSEMBL:ENSG00000229767\"\n   \"HGNC:14565\"\n   \"UMLS:C1366777\"\n   \"UMLS:C1414259\"\n   \"ENSEMBL:ENSG00000281244\"\n   \"HGNC:2481\"\n   \"HGNC:13875\"\n   \"NCBIGene:7089\"\n   \"UniProtKB:P12882\"\n   \"UMLS:C1420714\"\n   \"NCBIGene:6423\"\n   \"UMLS:C1419756\"\n   \"UMLS:C1428332\"\n   \"UMLS:C1539903\"\n   \"HGNC:21288\"\n   \"ENSEMBL:ENSG00000228128\"\n   \"ENSEMBL:ENSG00000160209\"\n   \"UMLS:C1538701\"\n   \"ENSEMBL:ENSG00000213398\"\n   \"UMLS:C1538571\"\n   \"PR:Q9UIK5\"\n   \"NCBIGene:26056\"\n   \"ENSEMBL:ENSG00000198959\"\n   \"PR:P27037\"\n   \"PR:P03372\"\n   \"PR:P41227\"\n   \"ENSEMBL:ENSG00000176101\"\n   \"NCBIGene:7076\"\n   \"NCBIGene:3728\"\n   \"PR:P19388\"\n   \"ENSEMBL:ENSG00000101986\"\n   \"NCBIGene:23761\"\n   \"HGNC:9601\"\n   \"HGNC:29832\"\n   \"PR:O43854\"\n   \"ENSEMBL:ENSG00000172270\"\n   \"NCBIGene:92949\"\n   \"UniProtKB:Q13361\"\n   \"NCBIGene:2254\"\n   \"UMLS:C1417015\"\n   \"PR:Q6KF10\"\n   \"UMLS:C1417519\"\n   \"ENSEMBL:LRG_142\"\n   \"PR:P17858\"\n   \"HGNC:15985\"\n   \"HGNC:8951\"\n   \"ENSEMBL:ENSG00000162576\"\n   \"PR:P48509\"\n   \"ENSEMBL:ENSG00000101439\"\n   \"HGNC:6868\"\n   \"NCBIGene:6714\"\n   \"NCBIGene:9294\"\n   \"NCBIGene:51279\"\n   \"NCBIGene:822\"\n   \"NCBIGene:79734\"\n   \"NCBIGene:7186\"\n   \"UMLS:C1427969\"\n   \"ENSEMBL:ENSG00000005007\"\n   \"PR:P04216\"\n   \"PR:P01040\"\n   \"HGNC:5978\"\n   \"UniProtKB:Q9H7M9\"\n   \"UniProtKB:Q9HBA0\"\n   \"UniProtKB:P35613\"\n   \"NCBIGene:1312\"\n   \"ENSEMBL:ENSG00000178568\"\n   \"NCBIGene:1893\"\n   \"HGNC:17158\"\n   \"UMLS:C1420441\"\n   \"NCBIGene:7052\"\n   \"NCBIGene:80149\"\n   \"UniProtKB:P84101\"\n   \"UniProtKB:Q9H3H3\"\n   \"UniProtKB:Q9NS15\"\n   \"UniProtKB:Q9P212\"\n   \"HGNC:20910\"\n   \"PR:P10301\"\n   \"UMLS:C1539047\"\n   \"ENSEMBL:ENSG00000134317\"\n   \"NCBIGene:151887\"\n   \"ENSEMBL:ENSG00000175573\"\n   \"ENSEMBL:ENSG00000131669\"\n   \"HGNC:8029\"\n   \"UniProtKB:O15041\"\n   \"UMLS:C1428140\"\n   \"UniProtKB:Q08289\"\n   \"PR:P78562\"\n   \"ENSEMBL:ENSG00000067221\"\n   \"ENSEMBL:LRG_246\"\n   \"NCBIGene:8636\"\n   \"HGNC:4638\"\n   \"UMLS:C1418552\"\n   \"NCBIGene:54863\"\n   \"NCBIGene:51816\"\n   \"NCBIGene:284207\"\n   \"PR:Q13261\"\n   \"PR:Q9HBA0\"\n   \"ENSEMBL:ENSG00000126458\"\n   \"NCBIGene:347735\"\n   \"UniProtKB:P13489\"\n   \"PR:Q8NBJ7\"\n   \"ENSEMBL:ENSG00000121989\"\n   \"NCBIGene:2647\"\n   \"UniProtKB:Q9UPQ0\"\n   \"PR:P01024\"\n   \"UniProtKB:Q14938\"\n   \"UniProtKB:Q9Y6H8\"\n   \"UniProtKB:O60869\"\n   \"PR:O43292\"\n   \"ENSEMBL:ENSG00000165655\"\n   \"HGNC:3084\"\n   \"UniProtKB:P18084\"\n   \"UniProtKB:O95183\"\n   \"UniProtKB:Q15269\"\n   \"ENSEMBL:ENSG00000181690\"\n   \"NCBIGene:9817\"\n   \"ENSEMBL:ENSG00000069431\"\n   \"PR:Q6ZMW3\"\n   \"HGNC:30594\"\n   \"UniProtKB:Q8N6K7\"\n   \"UniProtKB:O15409\"\n   \"NCBIGene:4061\"\n   \"UMLS:C1427470\"\n   \"ENSEMBL:ENSG00000173801\"\n   \"NCBIGene:84674\"\n   \"ENSEMBL:ENSG00000115325\"\n   \"ENSEMBL:ENSG00000164484\"\n   \"PR:P07093\"\n   \"PR:Q5U623\"\n   \"UniProtKB:O95248\"\n   \"NCBIGene:9263\"\n   \"UniProtKB:O95865\"\n   \"UniProtKB:Q9Y572\"\n   \"NCBIGene:8566\"\n   \"NCBIGene:2950\"\n   \"PR:Q96F45\"\n   \"NCBIGene:51196\"\n   \"NCBIGene:5157\"\n   \"UniProtKB:Q8WW38\"\n   \"HGNC:3169\"\n   \"PR:P10589\"\n   \"HGNC:35412\"\n   \"PR:Q9Y535\"\n   \"NCBIGene:51586\"\n   \"ENSEMBL:ENSG00000078808\"\n   \"HGNC:11731\"\n   \"UniProtKB:Q9UKX2\"\n   \"ENSEMBL:ENSG00000214595\"\n   \"UMLS:C1825270\"\n   \"NCBIGene:57575\"\n   \"HGNC:14867\"\n   \"ENSEMBL:ENSG00000177239\"\n   \"ENSEMBL:ENSG00000177666\"\n   \"HGNC:226\"\n   \"UMLS:C1823388\"\n   \"PR:Q01629\"\n   \"HGNC:30649\"\n   \"HGNC:7715\"\n   \"NCBIGene:727910\"\n   \"UniProtKB:Q9BR76\"\n   \"UniProtKB:Q96SA4\"\n   \"HGNC:3219\"\n   \"ENSEMBL:ENSG00000185215\"\n   \"HGNC:8659\"\n   \"UniProtKB:Q10571\"\n   \"UniProtKB:Q9NZI5\"\n   \"UniProtKB:Q13634\"\n   \"ENSEMBL:ENSG00000152217\"\n   \"ENSEMBL:ENSG00000141503\"\n   \"ENSEMBL:ENSG00000107821\"\n   \"HGNC:38705\"\n   \"UMLS:C2681258\"\n   \"UniProtKB:Q9BXP8\"\n   \"ENSEMBL:ENSG00000116183\"\n   \"ENSEMBL:ENSG00000175220\"\n   \"UMLS:C1826719\"\n   \"UMLS:C1826712\"\n   \"HGNC:23790\"\n   \"HGNC:12619\"\n   \"NCBIGene:80832\"\n   \"ENSEMBL:ENSG00000017427\"\n   \"PR:Q96JB6\"\n   \"UniProtKB:Q96CN4\"\n   \"HGNC:1749\"\n   \"HGNC:25679\"\n   \"PR:Q8WTR4\"\n   \"PR:O75154\"\n   \"UMLS:C1419185\"\n   \"NCBIGene:4620\"\n   \"HGNC:14295\"\n   \"NCBIGene:29800\"\n   \"UniProtKB:Q9Y625\"\n   \"PR:Q02818\"\n   \"HGNC:6823\"\n   \"UniProtKB:Q9ULT0\"\n   \"NCBIGene:90120\"\n   \"UniProtKB:O00764\"\n   \"ENSEMBL:LRG_724\"\n   \"UMLS:C1823452\"\n   \"HGNC:9199\"\n   \"UniProtKB:Q8WUF5\"\n   \"HGNC:1402\"\n   \"ENSEMBL:ENSG00000103152\"\n   \"ENSEMBL:LRG_543\"\n   \"UMLS:C1824747\"\n   \"NCBIGene:23130\"\n   \"NCBIGene:3601\"\n   \"HGNC:21265\"\n   \"ENSEMBL:ENSG00000090565\"\n   \"UniProtKB:Q9UJX6\"\n   \"ENSEMBL:ENSG00000137809\"\n   \"HGNC:6136\"\n   \"UMLS:C1426120\"\n   \"UMLS:C1414689\"\n   \"ENSEMBL:ENSG00000160211\"\n   \"HGNC:13177\"\n   \"UniProtKB:Q14315\"\n   \"HGNC:24987\"\n   \"UniProtKB:Q6ZVK8\"\n   \"HGNC:6738\"\n   \"UniProtKB:Q86Y39\"\n   \"UniProtKB:P50479\"\n   \"HGNC:4379\"\n   \"HGNC:26259\"\n   \"UMLS:C1419145\"\n   \"NCBIGene:78987\"\n   \"UniProtKB:Q2MKA7\"\n   \"ENSEMBL:ENSG00000103888\"\n   \"PR:P21964\"\n   \"NCBIGene:10581\"\n   \"PR:O94808\"\n   \"PR:Q76M96\"\n   \"UniProtKB:Q9NWX5\"\n   \"ENSEMBL:ENSG00000285112\"\n   \"UMLS:C1538171\"\n   \"PR:Q8NF64\"\n   \"UniProtKB:Q7Z4V5\"\n   \"HGNC:13469\"\n   \"UniProtKB:P32119\"\n   \"UMLS:C1333246\"\n   \"UMLS:C1537434\"\n   \"ENSEMBL:ENSG00000128573\"\n   \"UniProtKB:Q9NR46\"\n   \"UMLS:C1424947\"\n   \"ENSEMBL:ENSG00000095637\"\n   \"UMLS:C1425765\"\n   \"HGNC:11283\"\n   \"UniProtKB:Q5U623\"\n   \"ENSEMBL:ENSG00000183077\"\n   \"ENSEMBL:ENSG00000198542\"\n   \"NCBIGene:387509\"\n   \"ENSEMBL:LRG_1287\"\n   \"NCBIGene:50488\"\n   \"UniProtKB:P31751\"\n   \"NCBIGene:5251\"\n   \"NCBIGene:115708\"\n   \"UMLS:C1420273\"\n   \"PR:Q9UP95\"\n   \"UniProtKB:P51571\"\n   \"ENSEMBL:ENSG00000176845\"\n   \"UniProtKB:P27487\"\n   \"PR:Q9BXF6\"\n   \"PR:Q9P2D7\"\n   \"PR:Q9H936\"\n   \"NCBIGene:6857\"\n   \"NCBIGene:975\"\n   \"HGNC:9405\"\n   \"NCBIGene:79751\"\n   \"PR:P23467\"\n   \"UMLS:C1413275\"\n   \"UMLS:C2239563\"\n   \"UniProtKB:O15120\"\n   \"PR:Q9UEE5\"\n   \"NCBIGene:7127\"\n   \"UniProtKB:P01040\"\n   \"PR:P62875\"\n   \"UMLS:C1421398\"\n   \"NCBIGene:4135\"\n   \"ENSEMBL:ENSG00000139174\"\n   \"ENSEMBL:ENSG00000131459\"\n   \"ENSEMBL:ENSG00000117122\"\n   \"NCBIGene:81876\"\n   \"UniProtKB:Q12979\"\n   \"NCBIGene:399909\"\n   \"UMLS:C1537686\"\n   \"UMLS:C1422757\"\n   \"NCBIGene:2006\"\n   \"HGNC:2675\"\n   \"ENSEMBL:ENSG00000134590\"\n   \"PR:P15289\"\n   \"PR:Q6ZVK8\"\n   \"NCBIGene:5099\"\n   \"UMLS:C1419743\"\n   \"PR:Q8IV08\"\n   \"NCBIGene:51368\"\n   \"ENSEMBL:ENSG00000064932\"\n   \"ENSEMBL:ENSG00000186501\"\n   \"ENSEMBL:ENSG00000142733\"\n   \"UMLS:C1420775\"\n   \"ENSEMBL:ENSG00000071242\"\n   \"HGNC:24845\"\n   \"PR:Q16553\"\n   \"UMLS:C1424585\"\n   \"ENSEMBL:ENSG00000167123\"\n   \"PR:Q9NWX5\"\n   \"ENSEMBL:ENSG00000141959\"\n   \"NCBIGene:216\"\n   \"HGNC:33842\"\n   \"ENSEMBL:LRG_27\"\n   \"NCBIGene:2356\"\n   \"UMLS:C1417239\"\n   \"PR:Q9HAB3\"\n   \"ENSEMBL:ENSG00000011347\"\n   \"HGNC:2569\"\n   \"UMLS:C1823243\"\n   \"NCBIGene:148223\"\n   \"HGNC:11395\"\n   \"HGNC:21296\"\n   \"ENSEMBL:ENSG00000275074\"\n   \"PR:O15409\"\n   \"HGNC:9756\"\n   \"UniProtKB:Q9H936\"\n   \"UMLS:C1425110\"\n   \"UMLS:C1423031\"\n   \"PR:Q9NRD1\"\n   \"UniProtKB:P60033\"\n   \"ENSEMBL:ENSG00000142459\"\n   \"UniProtKB:P04180\"\n   \"UniProtKB:Q9H6A9\"\n   \"ENSEMBL:ENSG00000093010\"\n   \"ENSEMBL:ENSG00000165995\"\n   \"UniProtKB:O75398\"\n   \"HGNC:7945\"\n   \"ENSEMBL:ENSG00000107140\"\n   \"UniProtKB:Q16678\"\n   \"ENSEMBL:ENSG00000135919\"\n   \"PR:Q9BTM9\"\n   \"HGNC:16038\"\n   \"HGNC:12646\"\n   \"ENSEMBL:ENSG00000176532\"\n   \"ENSEMBL:ENSG00000135924\"\n   \"NCBIGene:22904\"\n   \"PR:Q14145\"\n   \"HGNC:6164\"\n   \"ENSEMBL:ENSG00000168936\"\n   \"HGNC:9045\"\n   \"UMLS:C1836668\"\n   \"HGNC:10074\"\n   \"UniProtKB:Q8NF64\"\n   \"PR:Q96JE9\"\n   \"ENSEMBL:ENSG00000100241\"\n   \"ENSEMBL:ENSG00000204580\"\n   \"NCBIGene:26086\"\n   \"PR:Q9UBU2\"\n   \"UniProtKB:Q07507\"\n   \"HGNC:1174\"\n   \"ENSEMBL:ENSG00000274684\"\n   \"UMLS:C1427621\"\n   \"PR:Q5T4B2\"\n   \"UniProtKB:Q96HD1\"\n   \"NCBIGene:79987\"\n   \"NCBIGene:441376\"\n   \"PR:Q9Y2K6\"\n   \"PR:Q9H6A9\"\n   \"HGNC:402\"\n   \"UniProtKB:Q76LX8\"\n   \"UniProtKB:Q8TB22\"\n   \"PR:Q969U6\"\n   \"ENSEMBL:ENSG00000168899\"\n   \"NCBIGene:30008\"\n   \"UniProtKB:Q9Y2K6\"\n   \"HGNC:25460\"\n   \"NCBIGene:6196\"\n   \"UniProtKB:P11413\"\n   \"ENSEMBL:ENSG00000162241\"\n   \"NCBIGene:1191\"\n   \"ENSEMBL:ENSG00000173264\"\n   \"NCBIGene:59341\"\n   \"UMLS:C1428620\"\n   \"UniProtKB:P51553\"\n   \"UMLS:C1421975\"\n   \"UMLS:C1412520\"\n   \"NCBIGene:11047\"\n   \"UniProtKB:B1AH88\"\n   \"ENSEMBL:ENSG00000163874\"\n   \"PR:Q6NTF9\"\n   \"PR:Q9UFB7\"\n   \"NCBIGene:11093\"\n   \"HGNC:4897\"\n   \"HGNC:23177\"\n   \"HGNC:25981\"\n   \"UMLS:C1823924\"\n   \"NCBIGene:2192\"\n   \"UniProtKB:Q4LEZ3\"\n   \"NCBIGene:5822\"\n   \"PR:Q9Y6I9\"\n   \"HGNC:1366\"\n   \"HGNC:1014\"\n   \"UniProtKB:Q92934\"\n   \"UniProtKB:Q07960\"\n   \"NCBIGene:54461\"\n   \"UniProtKB:O95382\"\n   \"UniProtKB:O43896\"\n   \"UniProtKB:Q4LDE5\"\n   \"HGNC:3011\"\n   \"NCBIGene:5211\"\n   \"NCBIGene:4054\"\n   \"UniProtKB:Q8N394\"\n   \"PR:Q9UKS7\"\n   \"UniProtKB:Q9UKS7\"\n   \"ENSEMBL:ENSG00000109065\"\n   \"ENSEMBL:ENSG00000072422\"\n   \"UMLS:C1426912\"\n   \"ENSEMBL:LRG_148\"\n   \"NCBIGene:160\"\n   \"HGNC:10447\"\n   \"PR:P00352\"\n   \"NCBIGene:2995\"\n   \"ENSEMBL:ENSG00000164619\"\n   \"PR:O15041\"\n   \"HGNC:18370\"\n   \"NCBIGene:29841\"\n   \"PR:Q9BXP8\"\n   \"UMLS:C1416483\"\n   \"NCBIGene:6888\"\n   \"UMLS:C1418629\"\n   \"PR:O76093\"\n   \"HGNC:1474\"\n   \"UniProtKB:Q9NRD9\"\n   \"PR:Q5JYT7\"\n   \"HGNC:5134\"\n   \"HGNC:6160\"\n   \"UMLS:C2239652\"\n   \"PR:Q9H2H9\"\n   \"NCBIGene:53838\"\n   \"HGNC:3164\"\n   \"HGNC:2940\"\n   \"UMLS:C1421422\"\n   \"NCBIGene:23671\"\n   \"NCBIGene:23770\"\n   \"NCBIGene:783\"\n   \"ENSEMBL:ENSG00000121039\"\n   \"HGNC:7180\"\n   \"NCBIGene:54587\"\n   \"NCBIGene:284654\"\n   \"ENSEMBL:ENSG00000169946\"\n   \"PR:Q15743\"\n   \"UMLS:C1823888\"\n   \"NCBIGene:7106\"\n   \"ENSEMBL:ENSG00000107404\"\n   \"NCBIGene:9945\"\n   \"HGNC:2342\"\n   \"NCBIGene:126328\"\n   \"NCBIGene:9064\"\n   \"ENSEMBL:ENSG00000164543\"\n   \"HGNC:29028\"\n   \"PR:Q9HBL8\"\n   \"UMLS:C1420753\"\n   \"NCBIGene:4728\"\n   \"HGNC:8043\"\n   \"ENSEMBL:ENSG00000023191\"\n   \"ENSEMBL:ENSG00000136878\"\n   \"ENSEMBL:ENSG00000124067\"\n   \"ENSEMBL:ENSG00000154096\"\n   \"UniProtKB:Q13261\"\n   \"ENSEMBL:ENSG00000079999\"\n   \"PR:Q9NPR9\"\n   \"UniProtKB:O95479\"\n   \"PR:O75509\"\n   \"UMLS:C1429017\"\n   \"HGNC:14630\"\n   \"PR:P21579\"\n   \"ENSEMBL:ENSG00000142684\"\n   \"NCBIGene:9600\"\n   \"UniProtKB:P29992\"\n   \"PR:Q9NWT8\"\n   \"UniProtKB:P21964\"\n   \"HGNC:684\"\n   \"UMLS:C2239907\"\n   \"ENSEMBL:ENSG00000186111\"\n   \"UniProtKB:P31277\"\n   \"PR:Q9BVG3\"\n   \"PR:Q9NR46\"\n   \"UniProtKB:Q9NXH8\"\n   \"UMLS:C1418594\"\n   \"UniProtKB:P11274\"\n   \"NCBIGene:4883\"\n   \"PR:Q9NZI5\"\n   \"PR:P26572\"\n   \"HGNC:4519\"\n   \"PR:Q9NZK5\"\n   \"HGNC:11859\"\n   \"ENSEMBL:ENSG00000197136\"\n   \"ENSEMBL:ENSG00000153406\"\n   \"HGNC:60\"\n   \"UniProtKB:O00562\"\n   \"NCBIGene:3931\"\n   \"HGNC:30943\"\n   \"PR:Q9NXH8\"\n   \"PR:P35052\"\n   \"UMLS:C2681454\"\n   \"ENSEMBL:ENSG00000189129\"\n   \"HGNC:5321\"\n   \"NCBIGene:57418\"\n   \"ENSEMBL:ENSG00000132837\"\n   \"UMLS:C1422509\"\n   \"PR:Q9Y6N8\"\n   \"UMLS:C3147060\"\n   \"HGNC:10418\"\n   \"HGNC:11345\"\n   \"PR:Q15642\"\n   \"ENSEMBL:ENSG00000110046\"\n   \"PR:O00217\"\n   \"ENSEMBL:ENSG00000093072\"\n   \"UMLS:C2678557\"\n   \"UMLS:C1417778\"\n   \"ENSEMBL:ENSG00000125734\"\n   \"HGNC:10431\"\n   \"UniProtKB:Q5T4B2\"\n   \"UMLS:C1540066\"\n   \"HGNC:26711\"\n   \"ENSEMBL:ENSG00000148341\"\n   \"UMLS:C1414602\"\n   \"UniProtKB:Q7L4E1\"\n   \"PR:Q15119\"\n   \"PR:Q96I82\"\n   \"UniProtKB:Q6RW13\"\n   \"ENSEMBL:ENSG00000148331\"\n   \"UniProtKB:P01034\"\n   \"ENSEMBL:ENSG00000131165\"\n   \"HGNC:1839\"\n   \"NCBIGene:56654\"\n   \"NCBIGene:23017\"\n   \"NCBIGene:9672\"\n   \"ENSEMBL:ENSG00000196961\"\n   \"ENSEMBL:ENSG00000165124\"\n   \"UniProtKB:O14964\"\n   \"NCBIGene:6050\"\n   \"ENSEMBL:ENSG00000136877\"\n   \"PR:Q15842\"\n   \"HGNC:21075\"\n   \"UMLS:C1824365\"\n   \"UniProtKB:Q9BRK3\"\n   \"PR:O95382\"\n   \"HGNC:5133\"\n   \"PR:O60331\"\n   \"PR:Q9Y625\"\n   \"ENSEMBL:ENSG00000137033\"\n   \"NCBIGene:22801\"\n   \"UniProtKB:P04626\"\n   \"NCBIGene:3479\"\n   \"HGNC:4795\"\n   \"NCBIGene:26270\"\n   \"UniProtKB:P14923\"\n   \"UniProtKB:Q969U6\"\n   \"NCBIGene:84858\"\n   \"UMLS:C1425135\"\n   \"UMLS:C1418441\"\n   \"HGNC:18704\"\n   \"NCBIGene:2700\"\n   \"ENSEMBL:ENSG00000198892\"\n   \"NCBIGene:116985\"\n   \"ENSEMBL:ENSG00000197858\"\n   \"PR:Q7Z5R6\"\n   \"ENSEMBL:ENSG00000166313\"\n   \"UMLS:C1422080\"\n   \"ENSEMBL:ENSG00000067715\"\n   \"NCBIGene:11253\"\n   \"NCBIGene:10085\"\n   \"ENSEMBL:ENSG00000179104\"\n   \"NCBIGene:647024\"\n   \"NCBIGene:140459\"\n   \"HGNC:10777\"\n   \"UMLS:C1423930\"\n   \"HGNC:15573\"\n   \"UniProtKB:Q08345\"\n   \"ENSEMBL:ENSG00000156466\"\n   \"PR:Q9H6S3\"\n   \"ENSEMBL:ENSG00000134470\"\n   \"PR:Q9BWQ8\"\n   \"ENSEMBL:ENSG00000102678\"\n   \"HGNC:19989\"\n   \"NCBIGene:115704\"\n   \"PR:Q9Y6X0\"\n   \"HGNC:14615\"\n   \"NCBIGene:83786\"\n   \"HGNC:6207\"\n   \"NCBIGene:149345\"\n   \"UniProtKB:P00387\"\n   \"HGNC:16089\"\n   \"HGNC:3153\"\n   \"PR:Q7L4E1\"\n   \"UMLS:C1412101\"\n   \"NCBIGene:55616\"\n   \"HGNC:33522\"\n   \"HGNC:1073\"\n   \"HGNC:21574\"\n   \"HGNC:3225\"\n   \"ENSEMBL:ENSG00000126561\"\n   \"HGNC:10727\"\n   \"ENSEMBL:ENSG00000156427\"\n   \"PR:Q15569\"\n   \"PR:Q9H0X4\"\n   \"ENSEMBL:ENSG00000049239\"\n   \"PR:Q9NX95\"\n   \"HGNC:19975\"\n   \"ENSEMBL:ENSG00000041880\"\n   \"NCBIGene:215\"\n   \"NCBIGene:79581\"\n   \"PR:O95865\"\n   \"NCBIGene:1047\"\n   \"ENSEMBL:ENSG00000100300\"\n   \"PR:Q14318\"\n   \"ENSEMBL:ENSG00000102265\"\n   \"NCBIGene:8434\"\n   \"UniProtKB:O14640\"\n   \"PR:O95479\"\n   \"PR:P51553\"\n   \"NCBIGene:10060\"\n   \"ENSEMBL:ENSG00000233076\"\n   \"UniProtKB:Q15569\"\n   \"PR:O95965\"\n   \"ENSEMBL:ENSG00000169692\"\n   \"UniProtKB:Q9UI17\"\n   \"UniProtKB:Q8N413\"\n   \"PR:Q5D1E8\"\n   \"ENSEMBL:ENSG00000275246\"\n   \"UniProtKB:Q66K74\"\n   \"HGNC:11321\"\n   \"HGNC:17181\"\n   \"UniProtKB:Q9BV38\"\n   \"ENSEMBL:ENSG00000104976\"\n   \"HGNC:30247\"\n   \"PR:Q9ULP0\"\n   \"UniProtKB:O75056\"\n   \"ENSEMBL:ENSG00000129103\"\n   \"PR:P52803\"\n   \"UniProtKB:Q16774\"\n   \"NCBIGene:718\"\n   \"ENSEMBL:ENSG00000127191\"\n   \"HGNC:13447\"\n   \"ENSEMBL:ENSG00000148343\"\n   \"PR:O95372\"\n   \"PR:Q9BX70\"\n   \"HGNC:23618\"\n   \"NCBIGene:392255\"\n   \"UMLS:C1415897\"\n   \"NCBIGene:392\"\n   \"UniProtKB:Q15743\"\n   \"HGNC:18838\"\n   \"NCBIGene:84895\"\n   \"PR:Q92900\"\n   \"NCBIGene:64847\"\n   \"HGNC:24114\"\n   \"UniProtKB:P23142\"\n   \"ENSEMBL:ENSG00000185803\"\n   \"PR:P78537\"\n   \"NCBIGene:9961\"\n   \"HGNC:9192\"\n   \"PR:P10620\"\n   \"UniProtKB:Q9BWQ8\"\n   \"UniProtKB:Q9P2D7\"\n   \"ENSEMBL:ENSG00000164081\"\n   \"HGNC:4446\"\n   \"UniProtKB:Q9UBX5\"\n   \"NCBIGene:81621\"\n   \"NCBIGene:9723\"\n   \"HGNC:3756\"\n   \"UniProtKB:Q8WTR4\"\n   \"UMLS:C1420468\"\n   \"UMLS:C1416944\"\n   \"UMLS:C1418194\"\n   \"PR:Q96MT3\"\n   \"ENSEMBL:ENSG00000276230\"\n   \"NCBIGene:51148\"\n   \"HGNC:3685\"\n   \"NCBIGene:60676\"\n   \"NCBIGene:23564\"\n   \"NCBIGene:55223\"\n   \"HGNC:4449\"\n   \"UMLS:C1825943\"\n   \"UniProtKB:O14967\"\n   \"NCBIGene:51042\"\n   \"ENSEMBL:ENSG00000241945\"\n   \"UniProtKB:Q5T0Z8\"\n   \"UniProtKB:O95466\"\n   \"UniProtKB:Q99704\"\n   \"UniProtKB:P98160\"\n   \"ENSEMBL:ENSG00000035664\"\n   \"ENSEMBL:ENSG00000178031\"\n   \"PR:P28358\"\n   \"NCBIGene:10188\"\n   \"UMLS:C1823600\"\n   \"NCBIGene:6305\"\n   \"UMLS:C1413623\"\n   \"UMLS:C1422106\"\n   \"PR:P11274\"\n   \"ENSEMBL:ENSG00000119714\"\n   \"PR:Q9NR80\"\n   \"HGNC:28299\"\n   \"UniProtKB:Q6ZMW3\"\n   \"UniProtKB:O00391\"\n   \"UMLS:C1425202\"\n   \"UniProtKB:P09211\"\n   \"ENSEMBL:ENSG00000282825\"\n   \"ENSEMBL:ENSG00000101152\"\n   \"NCBIGene:126321\"\n   \"ENSEMBL:ENSG00000261221\"\n   \"PR:Q96F05\"\n   \"HGNC:8740\"\n   \"HGNC:21023\"\n   \"HGNC:23133\"\n   \"PR:Q6NV75\"\n   \"UniProtKB:Q8TDB4\"\n   \"UMLS:C1414058\"\n   \"PR:Q9UBI4\"\n   \"HGNC:15715\"\n   \"NCBIGene:84171\"\n   \"PR:P27487\"\n   \"UniProtKB:O00488\"\n   \"HGNC:11509\"\n   \"UniProtKB:Q96FX7\"\n   \"HGNC:17171\"\n   \"NCBIGene:3237\"\n   \"HGNC:9353\"\n   \"ENSEMBL:ENSG00000275338\"\n   \"PR:P32119\"\n   \"PR:Q8N6K7\"\n   \"UniProtKB:P37837\"\n   \"HGNC:2716\"\n   \"HGNC:17019\"\n   \"UMLS:C1335625\"\n   \"PR:Q07507\"\n   \"HGNC:7567\"\n   \"NCBIGene:3421\"\n   \"UniProtKB:Q9H2H9\"\n   \"UMLS:C1538712\"\n   \"NCBIGene:23207\"\n   \"HGNC:14987\"\n   \"UniProtKB:Q8IV08\"\n   \"HGNC:29191\"\n   \"PR:O15120\"\n   \"ENSEMBL:ENSG00000143369\"\n   \"ENSEMBL:ENSG00000100284\"\n   \"UniProtKB:O60706\"\n   \"ENSEMBL:ENSG00000197226\"\n   \"ENSEMBL:ENSG00000160323\"\n   \"UMLS:C1423010\"\n   \"UMLS:C1538324\"\n   \"HGNC:20371\"\n   \"PR:P17342\"\n   \"ENSEMBL:ENSG00000079841\"\n   \"UniProtKB:Q96MT3\"\n   \"PR:A6NGC4\"\n   \"ENSEMBL:ENSG00000168528\"\n   \"UMLS:C1424802\"\n   \"NCBIGene:53905\"\n   \"NCBIGene:57407\"\n   \"PR:Q04725\"\n   \"ENSEMBL:ENSG00000064042\"\n   \"NCBIGene:2767\"\n   \"ENSEMBL:ENSG00000107223\"\n   \"ENSEMBL:ENSG00000164483\"\n   \"NCBIGene:114801\"\n   \"HGNC:175\"\n   \"UMLS:C1428224\"\n   \"UniProtKB:Q9BZV1\"\n   \"ENSEMBL:LRG_870\"\n   \"HGNC:10776\"\n   \"ENSEMBL:ENSG00000007237\"\n   \"PR:Q14938\"\n   \"UMLS:C1413268\"\n   \"UniProtKB:Q9BXF6\"\n   \"NCBIGene:682\"\n   \"PR:O94844\"\n   \"UniProtKB:A4D1B5\"\n   \"ENSEMBL:ENSG00000123143\"\n   \"ENSEMBL:ENSG00000197614\"\n   \"NCBIGene:56904\"\n   \"NCBIGene:5976\"\n   \"ENSEMBL:ENSG00000133243\"\n   \"NCBIGene:50649\"\n   \"NCBIGene:3984\"\n   \"PR:O95782\"\n   \"NCBIGene:6618\"\n   \"ENSEMBL:ENSG00000107738\"\n   \"PR:Q9NZV8\"\n   \"UniProtKB:O75154\"\n   \"NCBIGene:94\"\n   \"UMLS:C1333348\"\n   \"NCBIGene:8692\"\n   \"UniProtKB:O43581\"\n   \"HGNC:18083\"\n   \"PR:Q9BRK3\"\n   \"ENSEMBL:ENSG00000172890\"\n   \"NCBIGene:400954\"\n   \"PR:P23142\"\n   \"NCBIGene:2987\"\n   \"HGNC:2475\"\n   \"UniProtKB:P41227\"\n   \"HGNC:3121\"\n   \"NCBIGene:1384\"\n   \"PR:Q4LDE5\"\n   \"UniProtKB:Q8N4C8\"\n   \"NCBIGene:64787\"\n   \"ENSEMBL:ENSG00000176248\"\n   \"ENSEMBL:ENSG00000042493\"\n   \"HGNC:20620\"\n   \"HGNC:15504\"\n   \"NCBIGene:10791\"\n   \"UMLS:C1416599\"\n   \"UniProtKB:P83110\"\n   \"HGNC:17858\"\n   \"UMLS:C1335875\"\n   \"HGNC:25462\"\n   \"PR:Q9H0R3\"\n   \"NCBIGene:10580\"\n   \"NCBIGene:80700\"\n   \"PR:Q13487\"\n   \"NCBIGene:56834\"\n   \"ENSEMBL:ENSG00000278788\"\n   \"HGNC:4057\"\n   \"NCBIGene:5324\"\n   \"HGNC:6522\"\n   \"UniProtKB:Q13487\"\n   \"UniProtKB:Q76M96\"\n   \"HGNC:29372\"\n   \"ENSEMBL:ENSG00000139178\"\n   \"HGNC:11514\"\n   \"ENSEMBL:ENSG00000110717\"\n   \"PR:Q96KG9\"\n   \"UMLS:C1853361\"\n   \"PR:P01034\"\n   \"HGNC:17175\"\n   \"PR:O95136\"\n   \"HGNC:9711\"\n   \"UniProtKB:Q5JTB6\"\n   \"UniProtKB:Q9H0R3\"\n   \"HGNC:2586\"\n   \"ENSEMBL:ENSG00000165092\"\n   \"PR:Q8TD43\"\n   \"PR:Q9UPX8\"\n   \"NCBIGene:84709\"\n   \"PR:Q9H3H3\"\n   \"ENSEMBL:ENSG00000183098\"\n   \"HGNC:29213\"\n   \"ENSEMBL:ENSG00000137463\"\n   \"UMLS:C1418591\"\n   \"NCBIGene:8817\"\n   \"NCBIGene:92\"\n   \"UniProtKB:P04216\"\n   \"NCBIGene:9424\"\n   \"PR:Q9BSB4\"\n   \"UniProtKB:Q6DJT9\"\n   \"HGNC:5386\"\n   \"NCBIGene:57104\"\n   \"HGNC:11135\"\n   \"NCBIGene:10555\"\n   \"UniProtKB:Q13813\"\n   \"HGNC:11820\"\n   \"NCBIGene:10043\"\n   \"PR:O75508\"\n   \"PR:Q9P2E7\"\n   \"UniProtKB:P0CJ78\"\n   \"HGNC:21679\"\n   \"UniProtKB:Q6QNK2\"\n   \"NCBIGene:2817\"\n   \"ENSEMBL:ENSG00000177700\"\n   \"PR:O14967\"\n   \"NCBIGene:93986\"\n   \"UMLS:C1825628\"\n   \"NCBIGene:9811\"\n   \"PR:P85299\"\n   \"UMLS:C1413108\"\n   \"NCBIGene:5585\"\n   \"UniProtKB:Q03169\"\n   \"PR:P21781\"\n   \"UniProtKB:Q9H3U1\"\n   \"PR:A4D1B5\"\n   \"UniProtKB:Q8N5Z5\"\n   \"NCBIGene:29\"\n   \"UniProtKB:Q8N6G6\"\n   \"UniProtKB:Q9Y257\"\n   \"PR:Q63HM1\"\n   \"PR:Q86Y39\"\n   \"PR:Q9HD42\"\n   \"HGNC:17916\"\n   \"PR:O95183\"\n   \"ENSEMBL:ENSG00000146072\"\n   \"HGNC:8918\"\n   \"ENSEMBL:ENSG00000284137\"\n   \"PR:Q96H72\"\n   \"ENSEMBL:ENSG00000121361\"\n   \"PR:O00213\"\n   \"ENSEMBL:ENSG00000099337\"\n   \"PR:Q14764\"\n   \"HGNC:17379\"\n   \"UniProtKB:Q6NTF9\"\n   \"PR:Q8TDY4\"\n   \"HGNC:11895\"\n   \"UMLS:C0242957\"\n   \"UMLS:C1539894\"\n   \"UniProtKB:Q12933\"\n   \"ENSEMBL:LRG_1010\"\n   \"ENSEMBL:ENSG00000138650\"\n   \"NCBIGene:322\"\n   \"UniProtKB:P78562\"\n   \"NCBIGene:57175\"\n   \"NCBIGene:55615\"\n   \"NCBIGene:104\"\n   \"NCBIGene:8721\"\n   \"UMLS:C1416501\"\n   \"NCBIGene:1008\"\n   \"HGNC:17956\"\n   \"ENSEMBL:ENSG00000122707\"\n   \"HGNC:14680\"\n   \"NCBIGene:54998\"\n   \"HGNC:673\"\n   \"UMLS:C1420854\"\n   \"NCBIGene:25981\"\n   \"HGNC:14632\"\n   \"PR:Q9UI17\"\n   \"NCBIGene:54518\"\n   \"NCBIGene:6234\"\n   \"UniProtKB:Q9NPR9\"\n   \"HGNC:18181\"\n   \"PR:P10909\"\n   \"PR:P04921\"\n   \"ENSEMBL:ENSG00000145423\"\n   \"UniProtKB:Q15349\"\n   \"HGNC:16940\"\n   \"UniProtKB:Q66K14\"\n   \"NCBIGene:92999\"\n   \"UMLS:C1415880\"\n   \"UniProtKB:P10909\"\n   \"NCBIGene:55784\"\n   \"UniProtKB:Q9H0X4\"\n   \"NCBIGene:9853\"\n   \"PR:P78563\"\n   \"HGNC:11982\"\n   \"ENSEMBL:ENSG00000197381\"\n   \"HGNC:20415\"\n   \"HGNC:14560\"\n   \"PR:Q15198\"\n   \"UMLS:C1413483\"\n   \"ENSEMBL:ENSG00000158555\"\n   \"UMLS:C1414141\"\n   \"HGNC:8514\"\n   \"ENSEMBL:ENSG00000068724\"\n   \"ENSEMBL:ENSG00000233927\"\n   \"NCBIGene:3751\"\n   \"ENSEMBL:ENSG00000282712\"\n   \"UniProtKB:Q63HM1\"\n   \"UMLS:C1415193\"\n   \"UniProtKB:Q99961\"\n   \"HGNC:6858\"\n   \"UniProtKB:P52803\"\n   \"HGNC:16925\"\n   \"NCBIGene:410\"\n   \"PR:Q9P2B2\"\n   \"ENSEMBL:ENSG00000225635\"\n   \"NCBIGene:94103\"\n   \"PR:Q66K74\"\n   \"NCBIGene:84717\"\n   \"HGNC:25363\"\n   \"NCBIGene:3236\"\n   \"ENSEMBL:ENSG00000165915\"\n   \"UMLS:C1418750\"\n   \"UniProtKB:Q86UP3\"\n   \"NCBIGene:2274\"\n   \"PR:Q86VY9\"\n   \"ENSEMBL:ENSG00000040731\"\n   \"PR:Q9BTE0\"\n   \"UniProtKB:Q9C0K1\"\n   \"NCBIGene:8933\"\n   \"NCBIGene:22861\"\n   \"NCBIGene:3300\"\n   \"PR:Q8WUJ3\"\n   \"UMLS:C1334353\"\n   \"NCBIGene:2066\"\n   \"NCBIGene:9322\"\n   \"ENSEMBL:ENSG00000186088\"\n   \"NCBIGene:8260\"\n   \"UniProtKB:Q15842\"\n   \"PR:Q2MKA7\"\n   \"ENSEMBL:ENSG00000160360\"\n   \"ENSEMBL:ENSG00000104881\"\n   \"ENSEMBL:ENSG00000062282\"\n   \"NCBIGene:22807\"\n   \"UniProtKB:O60245\"\n   \"NCBIGene:54103\"\n   \"NCBIGene:5441\"\n   \"HGNC:14466\"\n   \"ENSEMBL:ENSG00000130706\"\n   \"PR:O14640\"\n   \"HGNC:2597\"\n   \"HGNC:1116\"\n   \"ENSEMBL:LRG_992\"\n   \"UniProtKB:Q92529\"\n   \"ENSEMBL:ENSG00000008441\"\n   \"ENSEMBL:ENSG00000102174\"\n   \"UniProtKB:P78563\"\n   \"ENSEMBL:ENSG00000136002\"\n   \"NCBIGene:10169\"\n   \"PR:A0AVI4\"\n   \"UniProtKB:Q9NWT8\"\n   \"UMLS:C2680379\"\n   \"PR:Q8IWE5\"\n   \"PR:Q9NS15\"\n   \"NCBIGene:8076\"\n   \"HGNC:17565\"\n   \"NCBIGene:6237\"\n   \"ENSEMBL:ENSG00000177697\"\n   \"NCBIGene:84649\"\n   \"PR:Q99704\"\n   \"UniProtKB:O95631\"\n   \"UniProtKB:P78537\"\n   \"UniProtKB:P21980\"\n   \"ENSEMBL:LRG_1217\"\n   \"PR:Q12933\"\n   \"HGNC:28801\"\n   \"UMLS:C1416505\"\n   \"PR:Q9UFG5\"\n   \"NCBIGene:27123\"\n   \"HGNC:4277\"\n   \"ENSEMBL:ENSG00000177106\"\n   \"NCBIGene:1946\"\n   \"NCBIGene:208\"\n   \"PR:Q96HD1\"\n   \"PR:P53667\"\n   \"UniProtKB:P53667\"\n   \"ENSEMBL:ENSG00000159842\"\n   \"PR:P37023\"\n   \"HGNC:29097\"\n   \"NCBIGene:55191\"\n   \"PR:Q96P48\"\n   \"PR:Q96N19\"\n   \"UMLS:C1823776\"\n   \"PR:O60869\"\n   \"ENSEMBL:ENSG00000184408\"\n   \"HGNC:8819\"\n   \"ENSEMBL:ENSG00000278741\"\n   \"ENSEMBL:ENSG00000169218\"\n   \"HGNC:7033\"\n   \"UMLS:C1413907\"\n   \"ENSEMBL:ENSG00000167671\"\n   \"HGNC:17829\"\n   \"PR:Q9UBX5\"\n   \"HGNC:23621\"\n   \"PR:Q9H0U4\"\n   \"UMLS:C1423535\"\n   \"UMLS:C1135159\"\n   \"UniProtKB:P01033\"\n   \"PR:P15502\"\n   \"NCBIGene:6748\"\n   \"UniProtKB:Q8NBJ7\"\n   \"PR:O75901\"\n   \"PR:Q86UP3\"\n   \"UniProtKB:Q96KG9\"\n   \"NCBIGene:10039\"\n   \"NCBIGene:8618\"\n   \"ENSEMBL:ENSG00000139567\"\n   \"ENSEMBL:ENSG00000082781\"\n   \"HGNC:14928\"\n   \"UMLS:C2240105\"\n   \"ENSEMBL:ENSG00000013297\"\n   \"NCBIGene:1855\"\n   \"ENSEMBL:LRG_401\"\n   \"HGNC:11867\"\n   \"UniProtKB:O00217\"\n   \"UMLS:C1412873\"\n   \"ENSEMBL:ENSG00000278032\"\n   \"HGNC:22229\"\n   \"UniProtKB:Q9NW07\"\n   \"UMLS:C1823521\"\n   \"UniProtKB:Q9P2E7\"\n   \"UMLS:C1413940\"\n   \"PR:Q9UKX2\"\n   \"UMLS:C1412530\"\n   \"UniProtKB:P21579\"\n   \"PR:Q96HF1\"\n   \"NCBIGene:7376\"\n   \"NCBIGene:23061\"\n   \"UMLS:C1417133\"\n   \"ENSEMBL:ENSG00000128591\"\n   \"ENSEMBL:ENSG00000121743\"\n   \"ENSEMBL:ENSG00000186654\"\n   \"HGNC:10913\"\n   \"UniProtKB:Q9UKX5\"\n   \"NCBIGene:81544\"\n   \"HGNC:7044\"\n   \"ENSEMBL:ENSG00000142186\"\n   \"UniProtKB:Q9NX95\"\n   \"UMLS:C1414252\"\n   \"UniProtKB:P10301\"\n   \"ENSEMBL:ENSG00000008394\"\n   \"UniProtKB:Q96JB6\"\n   \"PR:P13489\"\n   \"PR:P31751\"\n   \"PR:Q8N474\"\n   \"HGNC:7211\"\n   \"NCBIGene:27242\"\n   \"NCBIGene:55898\"\n   \"PR:O43581\"\n   \"ENSEMBL:ENSG00000113389\"\n   \"NCBIGene:125061\"\n   \"UniProtKB:Q9Y6N8\"\n   \"HGNC:2873\"\n   \"UMLS:C1416387\"\n   \"NCBIGene:29958\"\n   \"NCBIGene:8522\"\n   \"NCBIGene:7461\"\n   \"UniProtKB:P25686\"\n   \"UMLS:C1412441\"\n   \"ENSEMBL:ENSG00000164176\"\n   \"UMLS:C1826353\"\n   \"NCBIGene:3339\"\n   \"HGNC:6628\"\n   \"UniProtKB:Q96JE9\"\n   \"UMLS:C1418880\"\n   \"PR:Q12891\"\n   \"UMLS:C1332427\"\n   \"HGNC:2892\"\n   \"UMLS:C1826343\"\n   \"NCBIGene:10868\"\n   \"PR:Q8IZV5\"\n   \"NCBIGene:26151\"\n   \"HGNC:6716\"\n   \"ENSEMBL:ENSG00000030419\"\n   \"NCBIGene:105372824\"\n   \"PR:Q9UHL4\"\n   \"UMLS:C1537465\"\n   \"ENSEMBL:ENSG00000186716\"\n   \"UMLS:C1421999\"\n   \"HGNC:4242\"\n   \"PR:Q16678\"\n   \"HGNC:13613\"\n   \"ENSEMBL:ENSG00000099817\"\n   \"NCBIGene:64115\"\n   \"ENSEMBL:ENSG00000141985\"\n   \"UniProtKB:Q9UG56\"\n   \"HGNC:7572\"\n   \"PR:Q96DD7\"\n   \"UMLS:C1413514\"\n   \"PR:H0YL14\"\n   \"PR:O60706\"\n   \"UniProtKB:Q14192\"\n   \"NCBIGene:5738\"\n   \"UniProtKB:Q9BX66\"\n   \"ENSEMBL:ENSG00000167118\"\n   \"ENSEMBL:ENSG00000153132\"\n   \"UMLS:C1415826\"\n   \"HGNC:9962\"\n   \"UniProtKB:P03372\"\n   \"UMLS:C1417811\"\n   \"ENSEMBL:ENSG00000100336\"\n   \"UMLS:C1414630\"\n   \"PR:Q8N138\"\n   \"NCBIGene:3764\"\n   \"HGNC:26194\"\n   \"HGNC:3173\"\n   \"UMLS:C1539950\"\n   \"HGNC:5273\"\n   \"PR:Q9BZV1\"\n   \"PR:Q5T0Z8\"\n   \"UMLS:C1824334\"\n   \"UniProtKB:Q96RN5\"\n   \"UniProtKB:Q9NZP8\"\n   \"NCBIGene:94031\"\n   \"PR:O14817\"\n   \"UniProtKB:Q16186\"\n   \"UniProtKB:O60784\"\n   \"UMLS:C1706636\"\n   \"ENSEMBL:ENSG00000175756\"\n   \"PR:Q96FX7\"\n   \"PR:Q13813\"\n   \"UniProtKB:Q9UEE5\"\n   \"ENSEMBL:ENSG00000170381\"\n   \"ENSEMBL:ENSG00000129465\"\n   \"UniProtKB:O60331\"\n   \"ENSEMBL:ENSG00000091592\"\n   \"HGNC:2253\"\n   \"HGNC:3724\"\n   \"UniProtKB:O95372\"\n   \"UniProtKB:Q9ULU8\"\n   \"ENSEMBL:ENSG00000197694\"\n   \"ENSEMBL:ENSG00000120885\"\n   \"NCBIGene:26040\"\n   \"ENSEMBL:ENSG00000106665\"\n   \"PR:Q4LEZ3\"\n   \"UniProtKB:Q15303\"\n   \"HGNC:30224\"\n   \"PR:Q9UG56\"\n   \"ENSEMBL:ENSG00000137857\"\n   \"UniProtKB:A6ZKI3\"\n   \"HGNC:29969\"\n   \"UniProtKB:Q96I82\"\n   \"UMLS:C1415367\"\n   \"UniProtKB:Q9GZM5\"\n   \"ENSEMBL:ENSG00000100243\"\n   \"UniProtKB:P48509\"\n   \"UMLS:C1416871\"\n   \"ENSEMBL:ENSG00000155011\"\n   \"PR:P22004\"\n   \"ENSEMBL:ENSG00000132357\"\n   \"NCBIGene:85449\"\n   \"PR:P98160\"\n   \"UMLS:C1539370\"\n   \"HGNC:936\"\n   \"PR:Q08345\"\n   \"ENSEMBL:ENSG00000128713\"\n   \"UniProtKB:Q8IV56\"\n   \"PR:O43805\"\n   \"HGNC:10830\"\n   \"PR:Q6DN12\"\n   \"ENSEMBL:ENSG00000184922\"\n   \"ENSEMBL:ENSG00000131899\"\n   \"NCBIGene:977\"\n   \"UMLS:C2239463\"\n   \"HGNC:1757\"\n   \"HGNC:2060\"\n   \"NCBIGene:5119\"\n   \"NCBIGene:8572\"\n   \"NCBIGene:7070\"\n   \"ENSEMBL:ENSG00000131408\"\n   \"ENSEMBL:ENSG00000102030\"\n   \"PR:Q9GZM5\"\n   \"ENSEMBL:ENSG00000163703\"\n   \"PR:P43155\"\n   \"NCBIGene:57085\"\n   \"PR:Q8N394\"\n   \"UniProtKB:Q5JYT7\"\n   \"HGNC:5228\"\n   \"NCBIGene:3693\"\n   \"UMLS:C1823603\"\n   \"UniProtKB:Q9C000\"\n   \"HGNC:11273\"\n   \"UMLS:C3470119\"\n   \"PR:P60033\"\n   \"HGNC:30349\"\n   \"ENSEMBL:ENSG00000049540\"\n   \"ENSEMBL:ENSG00000143774\"\n   \"HGNC:17923\"\n   \"UMLS:C1418491\"\n   \"HGNC:61\"\n   \"PR:O95248\"\n   \"PR:Q86YR5\"\n   \"ENSEMBL:ENSG00000161091\"\n   \"ENSEMBL:ENSG00000138193\"\n   \"UMLS:C1422760\"\n   \"UniProtKB:Q6IA69\"\n   \"NCBIGene:1796\"\n   \"NCBIGene:4237\"\n   \"UniProtKB:Q9NZK5\"\n   \"PR:P00387\"\n   \"PR:Q9NRD9\"\n   \"NCBIGene:1877\"\n   \"UniProtKB:Q8WTX9\"\n   \"UMLS:C0919507\"\n   \"ENSEMBL:ENSG00000177674\"\n   \"NCBIGene:9727\"\n   \"PR:Q16186\"\n   \"ENSEMBL:ENSG00000170801\"\n   \"UniProtKB:Q02818\"\n   \"PR:P33897\"\n   \"ENSEMBL:ENSG00000126391\"\n   \"UniProtKB:Q9BZ67\"\n   \"NCBIGene:25870\"\n   \"ENSEMBL:ENSG00000213722\"\n   \"UniProtKB:O95980\"\n   \"NCBIGene:4245\"\n   \"ENSEMBL:ENSG00000223680\"\n   \"NCBIGene:7016\"\n   \"PR:Q9Y6F1\"\n   \"PR:O95967\"\n   \"HGNC:6613\"\n   \"PR:Q16610\"\n   \"ENSEMBL:ENSG00000119559\"\n   \"ENSEMBL:ENSG00000088280\"\n   \"UMLS:C1420688\"\n   \"NCBIGene:6422\"\n   \"UMLS:C1424245\"\n   \"ENSEMBL:ENSG00000163618\"\n   \"PR:Q8N2Q7\"\n   \"UMLS:C1417145\"\n   \"UniProtKB:Q16610\"\n   \"ENSEMBL:ENSG00000226634\"\n   \"UniProtKB:Q9Y6I9\"\n   \"ENSEMBL:ENSG00000284400\"\n   \"PR:O00391\"\n   \"UniProtKB:P10589\"\n   \"NCBIGene:283130\"\n   \"UniProtKB:Q96P48\"\n   \"PR:Q15334\"\n   \"ENSEMBL:ENSG00000135441\"\n   \"ENSEMBL:ENSG00000109061\"\n   \"HGNC:1158\"\n   \"ENSEMBL:ENSG00000065320\"\n   \"UniProtKB:Q16512\"\n   \"HGNC:6281\"\n   \"UMLS:C1825595\"\n   \"UniProtKB:P30536\"\n   \"PR:O00764\"\n   \"ENSEMBL:LRG_1150\"\n   \"HGNC:3062\"\n   \"NCBIGene:5434\"\n   \"UniProtKB:Q9BRK5\"\n   \"UniProtKB:Q6NUT3\"\n   \"UniProtKB:Q9H0U4\"\n   \"PR:Q03169\"\n   \"ENSEMBL:ENSG00000159069\"\n   \"ENSEMBL:ENSG00000138131\"\n   \"ENSEMBL:ENSG00000077420\"\n   \"HGNC:6269\"\n   \"NCBIGene:10522\"\n   \"PR:Q9P212\"\n   \"HGNC:14374\"\n   \"UniProtKB:P22004\"\n   \"NCBIGene:4924\"\n   \"UMLS:C1537393\"\n   \"ENSEMBL:LRG_1323\"\n   \"NCBIGene:654\"\n   \"NCBIGene:2252\"\n   \"HGNC:5413\"\n   \"HGNC:26125\"\n   \"NCBIGene:222171\"\n   \"UMLS:C1538766\"\n   \"PR:Q15303\"\n   \"UniProtKB:O43292\"\n   \"HGNC:3674\"\n   \"UniProtKB:Q9ULP0\"\n   \"HGNC:9003\"\n   \"HGNC:8999\"\n   \"NCBIGene:23646\"\n   \"HGNC:17224\"\n   \"UniProtKB:Q9Y6F1\"\n   \"UniProtKB:Q9NQX5\"\n   \"ENSEMBL:ENSG00000159714\"\n   \"HGNC:18738\"\n   \"PR:Q9NZP8\"\n   \"HGNC:13585\"\n   \"UniProtKB:P01024\"\n   \"HGNC:4693\"\n   \"UniProtKB:Q8TD43\"\n   \"HGNC:25137\"\n   \"PR:P12931\"\n   \"HGNC:4704\"\n   \"NCBIGene:56927\"\n   \"PR:P42229\"\n   \"ENSEMBL:ENSG00000130529\"\n   \"UniProtKB:Q9UP95\"\n   \"UMLS:C1417022\"\n   \"UMLS:C1428164\"\n   \"ENSEMBL:ENSG00000168056\"\n   \"PR:P09211\"\n   \"ENSEMBL:ENSG00000167967\"\n   \"ENSEMBL:ENSG00000197635\"\n   \"PR:Q8TB22\"\n   \"ENSEMBL:ENSG00000148082\"\n   \"ENSEMBL:ENSG00000198113\"\n   \"PR:Q641Q3\"\n   \"NCBIGene:6709\"\n   \"PR:O95760\"\n   \"UniProtKB:P27037\"\n   \"HGNC:30802\"\n   \"HGNC:7899\"\n   \"NCBIGene:9886\"\n   \"UniProtKB:Q8N138\"\n   \"UniProtKB:Q9BX70\"\n   \"ENSEMBL:ENSG00000110651\"\n   \"HGNC:4200\"\n   \"NCBIGene:1475\"\n   \"UMLS:C1823913\"\n   \"UMLS:C1423694\"\n   \"NCBIGene:22941\"\n   \"UniProtKB:Q96PD7\"\n   \"NCBIGene:388121\"\n   \"ENSEMBL:ENSG00000234078\"\n   \"ENSEMBL:ENSG00000198853\"\n   \"ENSEMBL:ENSG00000177030\"\n   \"PR:O95466\"\n   \"UMLS:C1417217\"\n   \"HGNC:3600\"\n   \"PR:Q08289\"\n   \"UMLS:C1969051\"\n   \"UniProtKB:Q9NRD1\"\n   \"ENSEMBL:ENSG00000011009\"\n   \"UniProtKB:Q9H3Z4\"\n   \"NCBIGene:1805\"\n   \"ENSEMBL:ENSG00000128710\"\n   \"ENSEMBL:ENSG00000005882\"\n   \"HGNC:3703\"\n   \"ENSEMBL:ENSG00000145526\"\n   \"ENSEMBL:ENSG00000171533\"\n   \"ENSEMBL:ENSG00000177156\"\n   \"UMLS:C1419112\"\n   \"UMLS:C1823091\"\n   \"HGNC:27442\"\n   \"ENSEMBL:ENSG00000105221\"\n   \"PR:Q8TDB4\"\n   \"HGNC:7542\"\n   \"UniProtKB:Q96H72\"\n   \"PR:O60245\"\n   \"NCBIGene:29952\"\n   \"UMLS:C1420029\"\n   \"PR:P50479\"\n   \"UniProtKB:P62875\"\n   \"PR:P83110\"\n   \"PR:Q9H3Z4\"\n   \"ENSEMBL:ENSG00000174886\"\n   \"PR:Q6NUT3\"\n   \"NCBIGene:1545\"\n   \"UniProtKB:O43310\"\n   \"HGNC:20859\"\n   \"NCBIGene:100507290\"\n   \"ENSEMBL:ENSG00000153162\"\n   \"UniProtKB:Q641Q3\"\n   \"HGNC:2095\"\n   \"PR:P12882\"\n   \"ENSEMBL:ENSG00000267534\"\n   \"ENSEMBL:ENSG00000110697\"\n   \"UniProtKB:P62857\"\n   \"PR:Q15349\"\n   \"ENSEMBL:ENSG00000275031\"\n   \"UniProtKB:Q96AD5\"\n   \"UMLS:C1420093\"\n   \"PR:Q9Y6H8\"\n   \"NCBIGene:613\"\n   \"ENSEMBL:ENSG00000167674\"\n   \"UniProtKB:P00352\"\n   \"ENSEMBL:ENSG00000276016\"\n   \"PR:Q12979\"\n   \"ENSEMBL:ENSG00000127329\"\n   \"PR:Q96RN5\"\n   \"ENSEMBL:ENSG00000140092\"\n   \"ENSEMBL:ENSG00000116663\"\n   \"NCBIGene:10424\"\n   \"UniProtKB:A0AVI4\"\n   \"NCBIGene:11035\"\n   \"ENSEMBL:ENSG00000013364\"\n   \"UniProtKB:Q9UBI4\"\n   \"PR:P11413\"\n   \"ENSEMBL:LRG_544\"\n   \"ENSEMBL:ENSG00000114853\"\n   \"ENSEMBL:ENSG00000091831\"\n   \"PR:P21980\"\n   \"NCBIGene:9182\"\n   \"NCBIGene:9066\"\n   \"UMLS:C1422006\"\n   \"NCBIGene:4619\"\n   \"UniProtKB:O75901\"\n   \"ENSEMBL:ENSG00000084207\"\n   \"HGNC:16235\"\n   \"UniProtKB:P33897\"\n   \"UniProtKB:Q2TAZ0\"\n   \"HGNC:16501\"\n   \"NCBIGene:10082\"\n   \"HGNC:273\"\n   \"HGNC:28378\"\n   \"HGNC:13404\"\n   \"UMLS:C1822680\"\n   \"HGNC:25440\"\n   \"ENSEMBL:ENSG00000095321\"\n   \"HGNC:325\"\n   \"NCBIGene:23604\"\n   \"ENSEMBL:ENSG00000144339\"\n   \"NCBIGene:1727\"\n   \"HGNC:23625\"\n   \"ENSEMBL:ENSG00000136732\"\n   \"PR:Q9BRK5\"\n   \"UniProtKB:O94844\"\n   \"ENSEMBL:ENSG00000091986\"\n   \"HGNC:7975\"\n   \"NCBIGene:54795\"\n   \"UniProtKB:Q9NZV8\"\n   \"HGNC:6238\"\n   \"ENSEMBL:ENSG00000171067\"\n   \"UniProtKB:Q6NV75\"\n   \"NCBIGene:171568\"\n   \"UMLS:C1414143\"\n   \"HGNC:25705\"\n   \"ENSEMBL:ENSG00000111371\"\n   \"UniProtKB:P31371\"\n   \"HGNC:20397\"\n   \"PR:Q8WUF5\"\n   \"UMLS:C1823459\"\n   \"UniProtKB:Q86YR5\"\n   \"UniProtKB:P12931\"\n   \"PR:Q8N5Z5\"\n   \"UniProtKB:Q8N474\"\n   \"UniProtKB:O76093\"\n   \"PR:Q9BX69\"\n   \"UMLS:C1412459\"\n   \"UniProtKB:Q15198\"\n   \"PR:Q96SA4\"\n   \"NCBIGene:84065\"\n   \"HGNC:22310\"\n   \"ENSEMBL:ENSG00000106683\"\n   \"HGNC:24188\"\n   \"PR:P0CJ78\"\n   \"UniProtKB:Q9BPW4\"\n   \"UMLS:C1822616\"\n   \"UniProtKB:P23467\"\n   \"PR:P01033\"\n   \"UMLS:C1422803\"\n   \"UniProtKB:Q96F45\"\n   \"ENSEMBL:LRG_1018\"\n   \"PR:P18084\"\n   \"ENSEMBL:ENSG00000140285\"\n   \"HGNC:581\"\n   \"UniProtKB:P37023\"\n   \"HGNC:11366\"\n   \"PR:Q86UR5\"\n   \"PR:Q9H7M9\"\n   \"HGNC:12304\"\n   \"ENSEMBL:ENSG00000197122\"\n   \"ENSEMBL:ENSG00000114841\"\n   \"NCBIGene:10516\"\n   \"ENSEMBL:ENSG00000138821\"\n   \"ENSEMBL:ENSG00000006282\"\n   \"UniProtKB:P05019\"\n   \"PR:Q6RW13\"\n   \"UniProtKB:P26572\"\n   \"NCBIGene:57414\"\n   \"PR:Q9BR76\"\n   \"NCBIGene:9399\"\n   \"UniProtKB:Q9Y6X0\"\n   \"NCBIGene:1471\"\n   \"UMLS:C1419987\"\n   \"PR:O95980\"\n   \"PR:O00562\"\n   \"UniProtKB:Q9HAB3\"\n   \"PR:Q13361\"\n   \"HGNC:30939\"\n   \"ENSEMBL:ENSG00000115641\"\n   \"ENSEMBL:ENSG00000131446\"\n   \"HGNC:27139\"\n   \"UniProtKB:Q9UHL4\"\n   \"PR:Q66K89\"\n   \"NCBIGene:6560\"\n   \"HGNC:2730\"\n   \"UniProtKB:Q9UDT6\"\n   \"UMLS:C1414179\"\n   \"UniProtKB:H0YL14\"\n   \"HGNC:392\"\n   \"NCBIGene:4330\"\n   \"HGNC:11326\"\n   \"ENSEMBL:LRG_723\"\n   \"UniProtKB:O95965\"\n   \"PR:Q8N4C8\"\n   \"UniProtKB:O43805\"\n   \"ENSEMBL:ENSG00000164040\"\n   \"PR:Q92982\"\n   \"UMLS:C1417874\"\n   \"HGNC:31682\"\n   \"UniProtKB:O95967\"\n   \"PR:Q8N8U9\"\n   \"ENSEMBL:ENSG00000176978\"\n   \"UniProtKB:Q14318\"\n   \"HGNC:30085\"\n   \"UniProtKB:O15255\"\n   \"HGNC:1630\"\n   \"UMLS:C2680471\"\n   \"ENSEMBL:ENSG00000172638\"\n   \"ENSEMBL:ENSG00000067829\"\n   \"ENSEMBL:ENSG00000185561\"\n   \"UMLS:C0812385\"\n   \"ENSEMBL:ENSG00000061938\"\n   \"PR:O95631\"\n   \"UMLS:C2681227\"\n   \"PR:O75398\"\n   \"UMLS:C1412216\"\n   \"HGNC:1701\"\n   \"NCBIGene:90865\"\n   \"PR:Q76LX8\"\n   \"ENSEMBL:ENSG00000185359\"\n   \"UniProtKB:P10620\"\n   \"ENSEMBL:ENSG00000116260\"\n   \"ENSEMBL:ENSG00000140553\"\n   \"ENSEMBL:ENSG00000134247\"\n   \"PR:Q5JTB6\"\n   \"HGNC:19954\"\n   \"PR:Q9UJX6\"\n   \"NCBIGene:4257\"\n   \"ENSEMBL:ENSG00000162105\"\n   \"UMLS:C1823598\"\n   \"HGNC:19297\"\n   \"HGNC:27584\"\n   \"PR:Q9ULT0\"\n   \"HGNC:3602\"\n   \"UMLS:C1425479\"\n   \"HGNC:7531\"\n   \"UMLS:C1825141\"\n   \"NCBIGene:752\"\n   \"UMLS:C1425748\"\n   \"UMLS:C1423113\"\n   \"HGNC:25574\"\n   \"NCBIGene:57410\"\n   \"NCBIGene:22998\"\n   \"PR:P25686\"\n   \"PR:O00488\"\n   \"UniProtKB:O00213\"\n   \"HGNC:19893\"\n   \"ENSEMBL:ENSG00000169851\"\n   \"HGNC:17993\"\n   \"NCBIGene:4784\"\n   \"NCBIGene:2099\"\n   \"UMLS:C1415685\"\n   \"HGNC:11801\"\n   \"NCBIGene:83986\"\n   \"NCBIGene:4814\"\n   \"PR:000036451\"\n   \"NCBIGene:22999\"\n   \"HGNC:19750\"\n   \"PR:P84101\"\n   \"ENSEMBL:ENSG00000134030\"\n   \"ENSEMBL:ENSG00000123395\"\n   \"PR:P14923\"\n   \"HGNC:23723\"\n   \"UMLS:C1823957\"\n   \"PR:Q9Y257\"\n   \"ENSEMBL:ENSG00000227317\"\n   \"NCBIGene:79873\"\n   \"PR:Q92934\"\n   \"HGNC:10021\"\n   \"HGNC:11838\"\n   \"ENSEMBL:ENSG00000183578\"\n   \"UMLS:C1420798\"\n   \"UniProtKB:Q5GJ75\"\n   \"UniProtKB:Q8WUJ3\"\n   \"PR:Q9UKX5\"\n   \"UMLS:C1426586\"\n   \"UMLS:C1367459\"\n   \"NCBIGene:83638\"\n   \"UniProtKB:A6NGC4\"\n   \"ENSEMBL:ENSG00000198774\"\n   \"PR:Q99961\"\n   \"PR:Q96PD7\"\n   \"NCBIGene:5164\"\n   \"UniProtKB:O95760\"\n   \"NCBIGene:9423\"\n   \"PR:Q16512\"\n   \"PR:Q9H3U1\"\n   \"ENSEMBL:ENSG00000184349\"\n   \"ENSEMBL:ENSG00000068001\"\n   \"HGNC:23925\"\n   \"ENSEMBL:ENSG00000088256\"\n   \"ENSEMBL:ENSG00000138061\"\n   \"HGNC:3432\"\n   \"UniProtKB:P40121\"\n   \"PR:Q9BZ67\"\n   \"ENSEMBL:ENSG00000172725\"\n   \"UMLS:C1538581\"\n   \"NCBIGene:160335\"\n   \"NCBIGene:283383\"\n   \"ENSEMBL:ENSG00000131435\"\n   \"UniProtKB:P19388\"\n   \"UniProtKB:P07093\"\n   \"HGNC:9665\"\n   \"UniProtKB:Q9UIK5\"\n   \"HGNC:7824\"\n   \"HGNC:81\"\n   \"PR:Q9UPQ0\"\n   \"ENSEMBL:ENSG00000100299\"\n   \"PR:Q9Y2G9\"\n   \"PR:Q05932\"\n   \"ENSEMBL:ENSG00000105701\"\n   \"NCBIGene:83637\"\n   \"HGNC:6317\"\n   \"NCBIGene:706\"\n   \"NCBIGene:57217\"\n   \"UniProtKB:Q9P2B2\"\n   \"ENSEMBL:ENSG00000158292\"\n   \"HGNC:14892\"\n   \"UniProtKB:Q05932\"\n   \"NCBIGene:219348\"\n   \"PR:Q9UIK4\"\n   \"UMLS:C1826443\"\n   \"HGNC:8810\"\n   \"UMLS:C1419069\"\n   \"NCBIGene:23414\"\n   \"HGNC:7788\"\n   \"HGNC:8996\"\n   \"HGNC:23082\"\n   \"UMLS:C1822754\"\n   \"HGNC:20862\"\n   \"UMLS:C1424721\"\n   \"ENSEMBL:ENSG00000198816\"\n   \"PR:Q9C0K1\"\n   \"UniProtKB:O43854\"\n   \"HGNC:10660\"\n   \"UMLS:C1424794\"\n   \"ENSEMBL:ENSG00000180879\"\n   \"ENSEMBL:ENSG00000175745\"\n   \"UniProtKB:Q15642\"\n   \"ENSEMBL:ENSG00000116786\"\n   \"UMLS:C1826491\"\n   \"PR:Q8IV56\"\n   \"HGNC:29131\"\n   \"PR:Q13634\"\n   \"PR:Q8N413\"\n   \"UniProtKB:Q15334\"\n   \"NCBIGene:60673\"\n   \"PR:O60784\"\n   \"HGNC:5464\"\n   \"UniProtKB:Q16553\"\n   \"UMLS:C1415047\"\n   \"UMLS:C1423708\"\n   \"PR:Q9UDT6\"\n   \"UMLS:C1824605\"\n   \"NCBIGene:57214\"\n   \"NCBIGene:1016\"\n   \"ENSEMBL:ENSG00000125414\"\n   \"ENSEMBL:ENSG00000241878\"\n   \"UniProtKB:Q9UPX8\"\n   \"ENSEMBL:ENSG00000125733\"\n   \"HGNC:713\"\n   \"HGNC:8805\"\n   \"ENSEMBL:ENSG00000238227\"\n   \"ENSEMBL:ENSG00000104805\"\n   \"UniProtKB:O75508\"\n   \"ENSEMBL:ENSG00000143196\"\n   \"UniProtKB:Q92982\"\n   \"UniProtKB:P17342\"\n   \"UMLS:C1366450\"\n   \"PR:O43310\"\n   \"UniProtKB:O75509\"\n   \"HGNC:1426\"\n   \"ENSEMBL:ENSG00000122515\"\n   \"UMLS:C1412906\"\n   \"NCBIGene:7001\"\n   \"UMLS:C1418293\"\n   \"UniProtKB:Q86UR5\"\n   \"ENSEMBL:ENSG00000166669\"\n   \"UMLS:C1825403\"\n   \"UniProtKB:Q9Y535\"\n   \"UniProtKB:Q96DD7\"\n   \"UMLS:C1418743\"\n   \"NCBIGene:6455\"\n   \"NCBIGene:6776\"\n   \"UMLS:C1538768\"\n   \"NCBIGene:9146\"\n   \"HGNC:14677\"\n   \"HGNC:15759\"\n   \"PR:O43896\"\n   \"NCBIGene:3996\"\n   \"HGNC:14372\"\n   \"UMLS:C1413079\"\n   \"PR:Q2TAZ0\"\n   \"PR:P29372\"\n   \"NCBIGene:5270\"\n   \"UniProtKB:Q9UKM7\"\n   \"ENSEMBL:ENSG00000130479\"\n   \"NCBIGene:92305\"\n   \"PR:Q92529\"\n   \"ENSEMBL:ENSG00000107281\"\n   \"HGNC:3430\"\n   \"NCBIGene:80063\"\n   \"PR:P04180\"\n   \"NCBIGene:5768\"\n   \"UniProtKB:Q14764\"\n   \"ENSEMBL:ENSG00000135631\"\n   \"NCBIGene:780\"\n   \"NCBIGene:8111\"\n   \"UniProtKB:Q96HF1\"\n   \"UniProtKB:Q66K89\"\n   \"UniProtKB:P15502\"\n   \"ENSEMBL:ENSG00000129250\"\n   \"HGNC:3687\"\n   \"UMLS:C1825589\"\n   \"UniProtKB:P85299\"\n   \"ENSEMBL:ENSG00000205002\"\n   \"UniProtKB:P29372\"\n   \"NCBIGene:7025\"\n   \"NCBIGene:79776\"\n   \"HGNC:16028\"\n   \"HGNC:31009\"\n   \"UniProtKB:Q15119\"\n   \"UniProtKB:Q9UFB7\"\n   \"UniProtKB:Q9BTM9\"\n   \"HGNC:3824\"\n   \"PR:P31371\"\n   \"UMLS:C1333206\"\n   \"NCBIGene:9563\"\n   \"PR:Q66K14\"\n   \"ENSEMBL:ENSG00000099917\"\n   \"PR:Q96AD5\"\n   \"UMLS:C1414304\"\n   \"ENSEMBL:ENSG00000100379\"\n   \"PR:Q07960\"\n   \"ENSEMBL:ENSG00000005486\"\n   \"NCBIGene:168667\"\n   \"ENSEMBL:ENSG00000166166\"\n   \"UniProtKB:Q01629\"\n   \"NCBIGene:157506\"\n   \"ENSEMBL:ENSG00000147642\"\n   \"ENSEMBL:ENSG00000206395\"\n   \"HGNC:16838\"\n   \"HGNC:25636\"\n   \"UniProtKB:Q9HBL8\"\n   \"UniProtKB:P04921\"\n   \"NCBIGene:9358\"\n   \"HGNC:11559\"\n   \"HGNC:2228\"\n   \"UMLS:C1540084\"\n   \"ENSEMBL:ENSG00000214063\"\n   \"PR:000047670\"\n   \"HGNC:24300\"\n   \"ENSEMBL:ENSG00000174903\"\n   \"ENSEMBL:ENSG00000104332\"\n   \"UniProtKB:Q07912\"\n   \"PR:P37837\"\n   \"UniProtKB:Q9UBU2\"\n   \"ENSEMBL:ENSG00000167930\"\n   \"HGNC:17067\"\n   \"UniProtKB:Q8N2Y8\"\n   \"NCBIGene:1803\"\n   \"NCBIGene:29882\"\n   \"UMLS:C1417534\"\n   \"PR:Q9ULU8\"\n   \"NCBIGene:53358\"\n   \"UniProtKB:P43155\"\n   \"UniProtKB:P17858\"\n   \"NCBIGene:55201\"\n   \"HGNC:14248\"\n   \"PR:Q15269\"\n   \"UMLS:C1426509\"\n   \"ENSEMBL:ENSG00000103034\"\n   \"HGNC:18760\"\n   \"PR:Q14315\"\n   \"HGNC:16700\"\n   \"PR:Q6IA69\"\n   \"UMLS:C1423970\"\n   \"PR:Q9BV38\"\n   \"HGNC:3327\"\n   \"UniProtKB:Q9UIK4\"\n   \"UMLS:C1420728\"\n   \"ENSEMBL:ENSG00000104213\"\n   \"UMLS:C1418308\"\n   \"UniProtKB:P35052\"\n   \"ENSEMBL:ENSG00000116525\"\n   \"UniProtKB:Q8IWE5\"\n   \"UniProtKB:Q9BSB4\"\n   \"HGNC:7061\"\n   \"HGNC:173\"\n   \"ENSEMBL:ENSG00000177542\"\n   \"UMLS:C1417127\"\n   \"HGNC:29673\"\n   \"UniProtKB:O95782\"\n   \"ENSEMBL:ENSG00000162512\"\n   \"UMLS:C1422548\"\n   \"UMLS:C1420427\"\n   \"NCBIGene:10749\"\n   \"HGNC:12032\"\n   \"ENSEMBL:ENSG00000142798\"\n   \"HGNC:6727\"\n   \"NCBIGene:23396\"\n   \"HGNC:23589\"\n   \"NCBIGene:5787\"\n   \"HGNC:14291\"\n   \"HGNC:10757\"\n   \"HGNC:28804\"\n   \"UniProtKB:Q9BX69\"\n   \"HGNC:10542\"\n   \"UMLS:C1538336\"\n   \"UMLS:C1335822\"\n   \"ENSEMBL:ENSG00000077942\"\n   \"UniProtKB:Q6KF10\"\n   \"NCBIGene:51150\"\n   \"UniProtKB:Q6DN12\"\n   \"ENSEMBL:ENSG00000111199\"\n   \"UMLS:C1417509\"\n   \"HGNC:16394\"\n   \"UniProtKB:Q5D1E8\"\n   \"PR:Q9C000\"\n   \"UniProtKB:O14817\"\n   \"UniProtKB:O95136\"\n   \"UniProtKB:Q7Z5R6\"\n   \"UniProtKB:Q8N2Q7\"\n   \"UMLS:C1417728\"\n   \"PR:O75056\"\n   \"PR:P40121\"\n   \"NCBIGene:91252\"\n   \"ENSEMBL:ENSG00000065717\"\n   \"UMLS:C1419986\"\n   \"PR:P62857\"\n   \"PR:P31277\"\n   \"UMLS:C1538659\"\n   \"UniProtKB:P42229\"\n   \"UMLS:C1424640\"\n   \"UniProtKB:Q12891\"\n   \"UMLS:C1336675\"\n   \"PR:Q14192\"\n   \"ENSEMBL:ENSG00000141736\"\n   \"PR:P04626\"\n   \"UMLS:C1537698\"\n   \"UniProtKB:Q9H6S3\"\n   \"HGNC:26011\"\n   \"HGNC:13539\"\n   \"NCBIGene:154075\"\n   \"PR:Q5GJ75\"\n   \"UMLS:C1822659\"\n   \"PR:P51571\"\n   \"PR:Q9BX66\"\n   \"NCBIGene:11313\"\n   \"UniProtKB:Q9NR80\"\n   \"ENSEMBL:ENSG00000188112\"\n   \"HGNC:19255\"\n   \"ENSEMBL:ENSG00000135472\"\n   \"ENSEMBL:ENSG00000125730\"\n   \"NCBIGene:4350\"\n   \"HGNC:561\"\n   \"NCBIGene:144165\"\n   \"UMLS:C1412333\"\n   \"HGNC:11778\"\n   \"ENSEMBL:ENSG00000002330\"\n   \"UniProtKB:Q8N8U9\"\n   \"PR:P35613\"\n   \"PR:Q9BPW4\"\n   \"UniProtKB:O94808\"\n   \"ENSEMBL:ENSG00000230456\"\n   \"NCBIGene:2318\"\n   \"ENSEMBL:ENSG00000186635\"\n   \"ENSEMBL:ENSG00000282854\"\n   \"PR:Q07912\"\n   \"UniProtKB:P55001\"\n   \"HGNC:17282\"\n   \"ENSEMBL:ENSG00000285379\"\n   \"PR:Q10571\"\n   \"PR:Q96CN4\"\n   \"HGNC:3467\"\n   \"PR:O14964\"\n   \"UMLS:C1824302\"\n   \"ENSEMBL:ENSG00000137332\"\n   \"ENSEMBL:ENSG00000091656\"\n   \"NCBIGene:81605\"\n   \"NCBIGene:140467\"\n   \"UniProtKB:Q86VY9\"\n   \"UniProtKB:Q9UFG5\"\n   \"ENSEMBL:ENSG00000167815\"\n   \"UMLS:C1423061\"\n   \"PR:Q6DJT9\"\n   \"UniProtKB:P28358\"\n   \"UniProtKB:P15289\"\n   \"HGNC:2990\"\n   \"PR:Q8WTX9\"\n   \"ENSEMBL:ENSG00000140264\"\n   \"HGNC:28042\"\n   \"HGNC:24475\"\n   \"PR:O15173\"\n   \"ENSEMBL:ENSG00000149633\"\n   \"PR:Q9Y572\"\n   \"UniProtKB:Q9HD42\"\n   \"UniProtKB:P21781\"\n   \"NCBIGene:5010\"\n   \"UMLS:C1426576\"\n   \"PR:Q6QNK2\"\n   \"UMLS:C1333547\"\n   \"ENSEMBL:ENSG00000105223\"\n   \"HGNC:29158\"\n   \"UniProtKB:Q14145\"\n   \"ENSEMBL:ENSG00000111452\"\n   \"HGNC:3009\"\n   \"PR:P29992\"\n   \"UMLS:C1420025\"\n   \"HGNC:30464\"\n   \"ENSEMBL:ENSG00000185201\"\n   \"PR:Q8WW38\"\n   \"NCBIGene:65009\"\n   \"ENSEMBL:ENSG00000169760\"\n   \"UMLS:C1422049\"\n   \"ENSEMBL:ENSG00000140563\"\n   \"HGNC:24154\"\n   \"NCBIGene:25844\"\n   \"NCBIGene:81539\"\n   \"ENSEMBL:LRG_377\"\n   \"UMLS:C4320396\"\n   \"UMLS:C1366514\"\n   \"HGNC:4221\"\n   \"ENSEMBL:LRG_364\"\n   \"UMLS:C1539559\"\n   \"NCBIGene:2539\"\n   \"ENSEMBL:ENSG00000137207\"\n   \"PR:P05019\"\n   \"UniProtKB:Q9BVG3\"\n   \"UniProtKB:Q8IZV5\"\n   \"HGNC:10834\"\n   \"NCBIGene:10848\"\n   \"UniProtKB:Q9Y2G9\"\n   \"UniProtKB:Q8TDY4\"\n   \"UniProtKB:Q96F05\"\n   \"HGNC:1318\"\n   \"ENSEMBL:ENSG00000169184\"\n   \"NCBIGene:55638\"\n   \"HGNC:26955\"\n   \"ENSEMBL:ENSG00000065268\"\n   \"PR:Q9NQX5\"\n   \"NCBIGene:64116\"\n   \"ENSEMBL:ENSG00000172057\"\n   \"UMLS:C1414230\"\n   \"PR:P55001\"\n   \"UniProtKB:Q9BTE0\"\n   \"HGNC:1212\"\n   \"HGNC:4454\"\n   \"UniProtKB:Q96N19\"\n   \"PR:Q9NW07\"\n   \"UMLS:C1825955\"\n   \"NCBIGene:572\"\n   \"ENSEMBL:ENSG00000100413\"\n   \"HGNC:8876\"\n   \"UMLS:C1826843\"\n   \"NCBIGene:80331\"\n   \"UMLS:C1427198\"\n   \"HGNC:30406\"\n   \"UniProtKB:O15173\"\n   \"ENSEMBL:ENSG00000215522\"\n   \"UMLS:C1334342\"\n   \"HGNC:23231\"\n   \"UMLS:C1425173\"\n   \"HGNC:15739\"\n   \"NCBIGene:2064\"\n   \"NCBIGene:8733\"\n   \"ENSEMBL:ENSG00000121552\"\n   \"UMLS:C1427465\"\n   \"PR:Q9UKM7\"))\n"
  },
  {
    "path": "contrib/medikanren2/Thi/IL1R1-med2-translate-rtx2-only-June-15-2021.rkt",
    "content": "#lang racket\n\n(require \"../../../medikanren2/common.rkt\")\n(require \"../../../medikanren2/db/rtx2-20210204.rkt\")\n(require \"../../../medikanren2/lw-reasoning.rkt\")\n(require \"../../../medikanren2/synonyms.rkt\")\n\n\n; Date: June 15, 2021\n; Goal: translate some  medikanren1 common queries into medikanren2\n\n\n\n; Query 1 : find drugs that inhibits IL1R1\n\n\n; first, sanity check the curie\n\n(run* (k v)\n  (cprop  \"HGNC:5993\" k v))\n\n(define IL1R1 \"HGNC:5993\")\n\n; find synonyms of this HGNC curie using the synonym relation defined in synonyms.rkt\n; this approach uses the information in rtx2 to get synonyms. I prefer this for gene/protein.\n\n\n;(run*/set/steps 1000 x (synonym x IL1R1))\n\n; July 12th, working on the branch origin/prune-cyclic-calls\n(time (run*/set x (synonym x IL1R1)))\n; doens't terminate\n\n\n\n;(run*/set x (kgx-synonym x IL1R1))\n; results:\n(set\n \"NCBIGene:3554\"\n \"PR:P14778\"\n \"UniProtKB:P14778\"\n \"UMLS:C1416395\"\n \"HGNC:5993\"\n \"ENSEMBL:ENSG00000115594\")\n\n(define IL1R1-syns (list\n                    \"NCBIGene:3554\"\n                    \"PR:P14778\"\n                    \"UniProtKB:P14778\"\n                    \"UMLS:C1416395\"\n                    \"HGNC:5993\"\n                    \"ENSEMBL:ENSG00000115594\"))\n\n\n#;(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:negatively_regulates\"\n                        \"biolink:negatively_regulates,_entity_to_entity\"\n                        \"biolink:negatively_regulates,_process_to_process\"\n                        \"biolink:treats\"\n                        \"negatively_regulates\" ; semmed\n                        \"treats\" ; semmed\n                        ))\n\n; main query to find drugs that inhibit ILR1- synonyms\n\n(define IL1R1-drugs (time (run* (s sname p o)\n                            (fresh (id drug)\n                              (edge id s o)\n                              (cprop s \"category\" drug)\n                              (cprop s \"name\" sname)\n                              (eprop id \"predicate\" p)\n                              (membero o IL1R1-syns)\n                              (membero p inhibit-preds)\n                              (membero drug drug-categories)))))\n\n\n;cpu time: 10731 real time: 10909 gc time: 107\n\n; export the results\n(write-list-to-tsv\n (list \"id\" \"drug-name\" \"pred\" \"gene\")\n IL1R1-drugs\n \"IL1R1-drugs.tsv\")\n\n\n;; Query 2: find drugs that inhibit IL1R1 signaling pathway\n\n\n(define myD88 \"HGNC:7562\")\n(define TAK1 \"HGNC:6859\")\n(define NEMO \"HGNC:5961\")\n(define IRAK1 \"HGNC:6112\")\n(define IRAK2 \"HGNC:6113\")\n(define TRAF6 \"HGNC:12036\")\n(define MEK1 \"HGNC:6848\")\n(define MEK3 \"HGNC:6843\")\n(define MEK6 \"HGNC:6846\")\n(define NFkB \"HGNC:7794\")\n(define JNK \"HGNC:6861\")\n(define p38 \"HGNC:6876\")\n(define c-JNK \"HGNC:6881\")\n\n(define IL1R-pathway (list myD88 TAK1 NEMO IRAK1 IRAK2 TRAF6 MEK1 MEK3 MEK6 NFkB JNK p38 c-JNK))\n\n; find the synonyms for each of the IL1R-pathway genes\n(time (map\n       (lambda (x)\n         (run*/set/steps 500 a\n                         (synonym a x)))\n       IL1R-pathway))\n\n; point-free style way of writing the above code, i.e. no variables here, just apply functions on function's output\n\n(time (set->list (apply set-union (map\n                                   (lambda (x)\n                                     (run*/set/steps 500 a\n                                                     (synonym a x)))\n                                   IL1R-pathway))))\n\n\n; alternatively I can make the code easier to ready by using let to give names to function's output\n\n(time (let* ((set-of-syn* (map\n                           (lambda (x)\n                             (run*/set/steps 500 a\n                                             (synonym a x)))\n                           IL1R-pathway))\n             (set-of-syn (apply set-union set-of-syn*))\n             (syn* (set->list set-of-syn)))\n        syn*))\n\n; from this, I can make a reusable function to take a list of HGNC curies genes and return the list of combined synonyms\n\n\n\n\n(define IL1R1-pathway-syns (set->list (set-union\n                                       (set\n                                        \"ENSEMBL:ENSG00000172936\"\n                                        \"ENSEMBL:LRG_157\"\n                                        \"NCBIGene:4615\"\n                                        \"HGNC:7562\"\n                                        \"UniProtKB:Q99836\"\n                                        \"PR:Q99836\")\n                                       (set\n                                        \"ENSEMBL:ENSG00000135341\"\n                                        \"HGNC:6859\"\n                                        \"NCBIGene:6885\"\n                                        \"PR:O43318\"\n                                        \"UniProtKB:O43318\")\n                                       (set\n                                        \"UniProtKB:Q9Y6K9\"\n                                        \"ENSEMBL:ENSG00000269335\"\n                                        \"NCBIGene:8517\"\n                                        \"ENSEMBL:LRG_70\"\n                                        \"HGNC:5961\"\n                                        \"PR:Q9Y6K9\")\n                                       (set\n                                        \"HGNC:6112\"\n                                        \"NCBIGene:3654\"\n                                        \"UMLS:C1334134\"\n                                        \"PR:P51617\"\n                                        \"UniProtKB:P51617\"\n                                        \"ENSEMBL:ENSG00000184216\")\n                                       (set\n                                        \"UniProtKB:O43187\"\n                                        \"UMLS:C1334135\"\n                                        \"HGNC:6113\"\n                                        \"PR:O43187\"\n                                        \"NCBIGene:3656\"\n                                        \"ENSEMBL:ENSG00000134070\")\n                                       (set\n                                        \"HGNC:12036\"\n                                        \"ENSEMBL:ENSG00000175104\"\n                                        \"NCBIGene:7189\"\n                                        \"UMLS:C1336666\"\n                                        \"UniProtKB:Q9Y4K3\"\n                                        \"PR:Q9Y4K3\")\n                                       (set\n                                        \"HGNC:6848\"\n                                        \"PR:Q13233\"\n                                        \"ENSEMBL:ENSG00000095015\"\n                                        \"UniProtKB:Q13233\"\n                                        \"NCBIGene:4214\")\n                                       (set\n                                        \"PR:P46734\"\n                                        \"HGNC:6843\"\n                                        \"NCBIGene:5606\"\n                                        \"UniProtKB:P46734\"\n                                        \"ENSEMBL:ENSG00000034152\"\n                                        \"UMLS:C1456386\")\n                                       (set\n                                        \"ENSEMBL:ENSG00000108984\"\n                                        \"UMLS:C1334475\"\n                                        \"UniProtKB:P52564\"\n                                        \"NCBIGene:5608\"\n                                        \"HGNC:6846\"\n                                        \"PR:P52564\")\n                                       (set\n                                        \"UniProtKB:P19838\"\n                                        \"ENSEMBL:ENSG00000109320\"\n                                        \"NCBIGene:4790\"\n                                        \"HGNC:7794\"\n                                        \"PR:P19838\"\n                                        \"ENSEMBL:LRG_1316\")\n                                       (set\n                                        \"HGNC:6861\"\n                                        \"NCBIGene:4293\"\n                                        \"PR:P80192\"\n                                        \"UMLS:C1417016\"\n                                        \"UniProtKB:P80192\"\n                                        \"ENSEMBL:ENSG00000006432\")\n                                       (set\n                                        \"NCBIGene:1432\"\n                                        \"HGNC:6876\"\n                                        \"ENSEMBL:ENSG00000112062\"\n                                        \"UniProtKB:Q16539\"\n                                        \"UMLS:C1366876\"\n                                        \"PR:Q16539\")\n                                       (set\n                                        \"ENSEMBL:ENSG00000107643\"\n                                        \"UMLS:C1367731\"\n                                        \"PR:P45983\"\n                                        \"HGNC:6881\"\n                                        \"UniProtKB:P45983\"\n                                        \"NCBIGene:5599\"))))\n\n; 76 synonyms\n\n\n\n\n\n(define IL1R1-pathway-drugs (time (run* (s sname p o oname)\n                                    (fresh (id drug)\n                                      (edge id s o)\n                                      (cprop s \"category\" drug)\n                                      (cprop s \"name\" sname)\n                                      (cprop o \"name\" oname)\n                                      (eprop id \"predicate\" p)\n                                      (membero o IL1R1-pathway-syns)\n                                      (membero p inhibit-preds)\n                                      (membero drug drug-categories)))))\n\n; run time to run through 76 synonymized IL1R pathway members\n\n\n(write-list-to-tsv\n (list \"drug-id\" \"drug-name\" \"pred\" \"gene-id\" \"gene-name\")\n  IL1R1-pathway-drugs\n \"IL1R1-pathway-drugs_June15_2021.tsv\")\n\n; cpu time: 680250 real time: 825991 gc time: 5140\n; ~15 mins\n; once I have this table exported, I can use R to count duplicate drugs for different gene-id\n; that way I can rank drugs that inhibit the most genes\n\n\n; Next steps: we can test these queries in ARS \n"
  },
  {
    "path": "contrib/medikanren2/Thi/IL1R1-med2-translate.rkt",
    "content": "#lang racket\n\n(require \"../../../medikanren2/common.rkt\")\n(require \"../../../medikanren2/db/rtx2-20210204.rkt\")\n\n\n; Goal: translate some  medikanren1 common queries into medikanren2\n; note: just try rtx2 first\n\n; Query: find drugs that inhibits IL1R1\n\n#|\n; first, sanity check the curie\n(run* (k v)\n    (cprop \"HGNC:5993\" k v))\n|#\n\n(define IL1R1 \"HGNC:5993\")\n\n(define IL1R1-drugs (time (run 10 (s sname p o)\n                            (fresh (id drug)\n                              (edge id s o)\n                              (cprop s \"category\" drug)\n                              (cprop s \"name\" sname)\n                              (eprop id \"predicate\" p)\n                              (membero o IL1R1-synonyms)\n                              (membero p inhibit-preds)\n                              (membero drug drug-categories)))))\n\n(write-list-to-tsv\n (list \"id\" \"drug-name\" \"pred\" \"gene\")\n IL1R1-drugs\n \"IL1R1-drugs.tsv\")\n\n\n(define drug-categories '(\"biolink:ChemicalSubstance\"\n                          \"biolink:ClinicalIntervention\"\n                          \"biolink:ClinicalModifier\"\n                          \"biolink:Drug\"\n                          \"biolink:Treatment\"))\n\n\n\n;; look for all strings that key for eprop tables\n\n(run* eprop_key\n  (fresh (id value)\n    (eprop id eprop_key value)))\n\n#|\n;; all keys in the eprop table\n '(\"negated\"\n  \"object\"\n  \"predicate\"\n  \"predicate_label\"\n  \"provided_by\"\n  \"publications\"\n  \"publications_info\"\n  \"relation\"\n  \"relation_label\"\n  \"subject\"\n  \"update_date\")\n|#\n\n\n; define a lists of inhibit predicates (chem->decrease->genes)\n\n; check all predicates in our data:\n(run* pred_name\n  (fresh (id)\n    (eprop id \"predicate\" pred_name)))\n\n\n; look for all cprop keys\n\n(run* key\n  (fresh (id value)\n    (cprop id key value)))\n\n#|\n; all cprop keys\n\n '(\"category\"\n  \"category_label\"\n  \"creation_date\"\n  \"deprecated\"\n  \"description\"\n  \"full_name\"\n  \"id\"\n  \"iri\"\n  \"name\"\n  \"provided_by\"\n  \"publications\"\n  \"replaced_by\"\n  \"synonym\"\n  \"update_date\")\n|#\n\n; look for all cprop values\n\n(run* value\n  (fresh (id)\n   (cprop id \"category\" value)))\n\n#|\n; all cprop values\n '(\"biolink:Activity\"\n  \"biolink:Agent\"\n  \"biolink:AnatomicalEntity\"\n  \"biolink:Attribute\"\n  \"biolink:BiologicalEntity\"\n  \"biolink:BiologicalProcess\"\n  \"biolink:BiologicalProcessOrActivity\"\n  \"biolink:Carbohydrate\"\n  \"biolink:Cell\"\n  \"biolink:CellularComponent\"\n  \"biolink:ChemicalSubstance\"\n  \"biolink:ClinicalIntervention\"\n  \"biolink:ClinicalModifier\"\n  \"biolink:DataFile\"\n  \"biolink:Device\"\n  \"biolink:Disease\"\n  \"biolink:DiseaseOrPhenotypicFeature\"\n  \"biolink:Drug\"\n  \"biolink:EnvironmentalFeature\"\n  \"biolink:EnvironmentalProcess\"\n  \"biolink:Exon\"\n  \"biolink:ExposureEvent\"\n  \"biolink:FrequencyValue\"\n  \"biolink:Gene\"\n  \"biolink:GeneFamily\"\n  \"biolink:GeneProduct\"\n  \"biolink:GenomicEntity\"\n  \"biolink:GeographicLocation\"\n  \"biolink:GrossAnatomicalStructure\"\n  \"biolink:IndividualOrganism\"\n  \"biolink:InformationContentEntity\"\n  \"biolink:LifeStage\"\n  \"biolink:MacromolecularComplex\"\n  \"biolink:MaterialSample\"\n  \"biolink:Metabolite\"\n  \"biolink:MolecularActivity\"\n  \"biolink:MolecularEntity\"\n  \"biolink:NamedThing\"\n  \"biolink:OntologyClass\"\n  \"biolink:OrganismTaxon\"\n  \"biolink:OrganismalEntity\"\n  \"biolink:Pathway\"\n  \"biolink:Phenomenon\"\n  \"biolink:PhenotypicFeature\"\n  \"biolink:PhysicalEntity\"\n  \"biolink:PhysiologicalProcess\"\n  \"biolink:PopulationOfIndividualOrganisms\"\n  \"biolink:Procedure\"\n  \"biolink:Protein\"\n  \"biolink:Publication\"\n  \"biolink:QuantityValue\"\n  \"biolink:RelationshipType\"\n  \"biolink:Treatment\")\n|#\n\n\n#|\n; all preds in rtx2  \n\n'(\"biolink:actively_involved_in\"\n  \"biolink:affects\"\n  \"biolink:affects_activity_of\"\n  \"biolink:affects_degradation_of\"\n  \"biolink:affects_localization_of\"\n  \"biolink:affects_transport_of\"\n  \"biolink:biomarker_for\"\n  \"biolink:capable_of\"\n  \"biolink:causes\"\n  \"biolink:chemically_similar_to\"\n  \"biolink:close_match\"\n  \"biolink:coexists_with\"\n  \"biolink:colocalizes_with\"\n  \"biolink:contraindicated_for\"\n  \"biolink:contributes_to\"\n  \"biolink:correlated_with\"\n  \"biolink:decreases_activity_of\"\n  \"biolink:decreases_expression_of\"\n  \"biolink:derives_from\"\n  \"biolink:derives_into\"\n  \"biolink:develops_from\"\n  \"biolink:directly_interacts_with\"\n  \"biolink:disease_has_basis_in\"\n  \"biolink:disrupts\"\n  \"biolink:enables\"\n  \"biolink:expressed_in\"\n  \"biolink:expresses\"\n  \"biolink:gene_associated_with_condition\"\n  \"biolink:has_attribute\"\n  \"biolink:has_attribute_type\"\n  \"biolink:has_completed\"\n  \"biolink:has_count\"\n  \"biolink:has_decreased_amount\"\n  \"biolink:has_gene_product\"\n  \"biolink:has_increased_amount\"\n  \"biolink:has_input\"\n  \"biolink:has_molecular_consequence\"\n  \"biolink:has_not_completed\"\n  \"biolink:has_output\"\n  \"biolink:has_part\"\n  \"biolink:has_participant\"\n  \"biolink:has_phenotype\"\n  \"biolink:has_quantitative_value\"\n  \"biolink:has_route\"\n  \"biolink:has_unit\"\n  \"biolink:homologous_to\"\n  \"biolink:in_taxon\"\n  \"biolink:increases_activity_of\"\n  \"biolink:increases_degradation_of\"\n  \"biolink:increases_expression_of\"\n  \"biolink:increases_metabolic_processing_of\"\n  \"biolink:increases_stability_of\"\n  \"biolink:interacts_with\"\n  \"biolink:is_sequence_variant_of\"\n  \"biolink:lacks_part\"\n  \"biolink:located_in\"\n  \"biolink:location_of\"\n  \"biolink:manifestation_of\"\n  \"biolink:model_of\"\n  \"biolink:molecularly_interacts_with\"\n  \"biolink:negatively_regulates\"\n  \"biolink:negatively_regulates,_entity_to_entity\"\n  \"biolink:negatively_regulates,_process_to_process\"\n  \"biolink:occurs_in\"\n  \"biolink:overlaps\"\n  \"biolink:part_of\"\n  \"biolink:participates_in\"\n  \"biolink:physically_interacts_with\"\n  \"biolink:positively_regulates\"\n  \"biolink:positively_regulates,_entity_to_entity\"\n  \"biolink:positively_regulates,_process_to_process\"\n  \"biolink:preceded_by\"\n  \"biolink:precedes\"\n  \"biolink:predisposes\"\n  \"biolink:prevents\"\n  \"biolink:produces\"\n  \"biolink:quantifier_qualifier\"\n  \"biolink:regulates\"\n  \"biolink:regulates,_process_to_process\"\n  \"biolink:related_to\"\n  \"biolink:same_as\"\n  \"biolink:subclass_of\"\n  \"biolink:synonym\"\n  \"biolink:temporally_related_to\"\n  \"biolink:treats\")\n|#\n\n(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:negatively_regulates\"\n                        \"biolink:negatively_regulates,_entity_to_entity\"\n                        \"biolink:negatively_regulates,_process_to_process\"\n                        \"biolink:treats\"))\n\n(define synonyms-preds '(\"biolink:same_as\"\n                         \"biolink:close_match\"\n                         \"biolink:has_gene_product\"))\n\n(define-relation (direct-synonym a b)\n  (fresh (id sp)\n    (edge id a b)\n    (eprop id \"predicate\" sp)\n    (membero sp synonyms-preds)))\n\n(define-relation (direct-synonym+ a b)\n  (conde ((direct-synonym a b))\n         ((fresh (mid)\n            (direct-synonym a mid)\n            (direct-synonym+ mid b)))))\n\n(define-relation (synonym a b)\n  (conde ((direct-synonym a b))\n         ((direct-synonym b a))\n         ((fresh (mid)\n            (direct-synonym a mid)\n            (synonym mid b)))\n         ((fresh (mid)\n            (direct-synonym b mid)\n            (synonym mid a)))))\n\n(remove-duplicates (run*/steps 500 s (synonym \"HGNC:5993\" s)))\n\n(define IL1R1-synonyms '(\"UMLS:C1416395\"\n                         \"ENSEMBL:ENSG00000115594\"\n                         \"NCBIGene:3554\"\n                         \"PR:P14778\"\n                         \"UniProtKB:P14778\"\n                         \"NCBIGene:3554\"))\n\n(define-relation/table (IL1R1-synonym curie)\n  'source-stream (run*/steps 500 (s) (synonym \"HGNC:5993\" s)))\n\n(define-relation/table (inhibit-pred predicate)\n  'source-stream (map list inhibit-preds))\n\n(define-relation/table (drug-category category)\n  'source-stream (map list drug-categories))\n\n;; instead of using membero, we can use relation/table to decrease run times (with source-stream), but still need some more tweaks\n\n(define IL1R1-drugs2 (time (run 10 (s sname p o)\n                             (fresh (id drug)\n                               (edge id s o)\n                               (cprop s \"category\" drug)\n                               (cprop s \"name\" sname)\n                               (eprop id \"predicate\" p)\n                               ;(IL1R1-synonym o)\n                               (inhibit-pred p)\n                               (drug-category drug)\n                               (membero o IL1R1-synonyms)\n                               ;(membero p inhibit-preds)\n                               ;(membero drug drug-categories)\n                              ))))\n"
  },
  {
    "path": "contrib/medikanren2/Thi/PMI-21-34-NEXMIF-2hop.rkt",
    "content": "#lang racket\n\n(require \"../../../medikanren2/common.rkt\")\n(require \"../../../medikanren2/db/rtx2-20210204.rkt\")\n(require \"../../../medikanren2/lw-reasoning.rkt\")\n(require \"../../../medikanren2/synonyms.rkt\")\n\n; Real use case PMI-21-34 for 2-hop query\n\n; Find drugs/chemicals that inhibit certain gene/proteins that inhibit NEXMIF\n\n; First, sanity check the curie for NEXMIF\n\n(run* (k v)\n  (cprop \"HGNC:29433\" k v))\n\n\n\n\n; use the function get-synonyms-ls to get the list of synonyms for the curie\n(get-synonyms-ls '(\"HGNC:29433\"))\n\n(define NEXMIF-syns '(\"HGNC:29433\"\n                      \"UniProtKB:Q5QGS0\"\n                      \"PR:Q5QGS0\"\n                      \"NCBIGene:340533\"\n                      \"ENSEMBL:ENSG00000050030\"))\n\n\n(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:negatively_regulates\"\n                        \"biolink:negatively_regulates,_entity_to_entity\"\n                        \"biolink:negatively_regulates,_process_to_process\"\n                        \"biolink:treats\"\n                        \"negatively_regulates\" ; semmed\n                        \"treats\" ; semmed\n                        ))\n\n(define drug-categories '(\"biolink:ChemicalSubstance\"\n                          \"biolink:ClinicalIntervention\"\n                          \"biolink:ClinicalModifier\"\n                          \"biolink:Drug\"\n                          \"biolink:Treatment\"))\n\n(define gene-protein-cats '(\"biolink:Gene\"\n                            \"biolink:GeneFamily\"\n                            \"biolink:GeneProduct\"\n                            \"biolink:GenomicEntity\"\n                            \"biolink:MolecularEntity\"\n                            \"biolink:Protein\"))\n\n\n(define NEXMIF-drugs-2hop (time (run* (d p1 g1 p2 g2)\n                                  (fresh (id1 id2 drug gene)\n                                    (edge id1 d g1)\n                                    (edge id2 g1 g2)\n                                    (cprop d \"category\" drug)\n                                    (cprop g1 \"category\" gene)\n                                    (cprop g2 \"category\" gene)\n                                    (eprop id1 \"predicate\" p1)\n                                    (eprop id2 \"predicate\" p2)\n                                    (membero drug drug-categories)\n                                    (membero gene gene-protein-cats)\n                                    (membero g2 NEXMIF-syns)\n                                    (membero p1 inhibit-preds)\n                                    (membero p2 inhibit-preds)))))\n\n(define NEXMIF-drugs-2hop (time (run 1 (d p1 g1 p2 g2)\n                                  (fresh (id1 id2 drug gene)\n                                    (edge id1 d g1)\n                                    (edge id2 g1 g2)\n                                    (cprop d \"category\" drug)\n                                    (cprop g1 \"category\" gene)\n                                    (cprop g2 \"category\" gene)\n                                    (eprop id1 \"predicate\" p1)\n                                    (eprop id2 \"predicate\" p2)\n                                    (membero drug drug-categories)\n                                    (membero gene gene-protein-cats)\n                                    (membero g2 NEXMIF-syns)\n                                    (membero p1 inhibit-preds)\n                                    (membero p2 inhibit-preds)))))\n"
  },
  {
    "path": "contrib/medikanren2/Thi/SLC16A11-explore.rkt",
    "content": "#lang racket\n\n(require \"../../../medikanren2/common.rkt\")\n; only load rtx2 data in config.scm\n\n(define hispanic \"UMLS:C0086409\")\n\n; a use case: Find all genes/proteins that are one-hop away from this hispanic curie\n; Subject = gene-or-protein (can be defined with concepts' categories)\n; Object = a particular curie\n; predicate = #f\n\n; use the \"run\"  (minikanren's interface) to find anything related to this curie (limit to 10 entries)\n(run 10 (id s)\n  (edge id s hispanic))\n\n;; define the gene-or-protein categories with biolink categories\n\n(define gene-or-protein '(\"biolink:Gene\"\n                          \"biolink:GeneFamily\"\n                          \"biolink:GeneProduct\"\n                          \"biolink:GenomicEntity\"\n                          \"biolink:MacromolecularComplex\"\n                          \"biolink:MolecularEntity\"\n                          \"biolink:Protein\"))\n\n;; helper functions:\n\n(define (properties->hash kvs)\n  (make-immutable-hash\n   (map (lambda (kv) (cons (car kv) (cadr kv)))\n        kvs)))\n\n\n(define-relation (concept/category curie categories)\n  (fresh (category)\n    (cprop curie \"category\" category)\n    (membero category categories)))\n\n(define-relation (edge/properties s s->o o)\n  (fresh (s->o:id)\n    (edge s->o:id s o)\n    (:== s->o (s->o:id)\n         (run* (key value)\n           (eprop s->o:id key value)))))\n\n#;(define (makeshift-query/graph s o)\n  (map properties->hash\n       (run 10 s->o:properties\n         (fresh (s o)\n           (== o hispanic)\n           (constrain/categories s gene-or-protein)\n           (edge/properties s->o:properties s o)\n           ))))\n\n\n;;(define list-of-curies (list \"HGNC:10928\" \"HGNC:23093\" \"HGNC:10922\"))\n\n;; WISH-list: a higher level function that takes inputs: could be S, O (either curies, or list of curies\n;; or a list of categories, or #f) or S->O (single predicate, list of predicates, or #f)\n;; Output: 1/summary of results (it could be count of entries, count of S, O and Edges, such as report/query in medikanren1.\n;; or it could be a tsv export for medium-level summary) 2/verbose results so that we can look at the details if needed\n\n\n;; this function could be generalized\n\n(define gene-hispanic\n  (time (map (lambda (row)\n               (match-define (list s->o s:name o:name) row)\n               (hash-set (hash-set (properties->hash s->o)\n                                   'subject-name s:name)\n                         'object-name o:name))\n             (run* (s->o s:name o:name)\n               (fresh (s o)\n                                        ;(== o hispanic)\n                 (membero o list-of-curies)\n                 (concept/category s gene-or-protein)\n                 (cprop o \"name\" o:name)\n                 (cprop s \"name\" s:name)\n                 (edge/properties s s->o o))))))\n\n\n\n(length gene-hispanic)\n\n(length (remove-duplicates (map (lambda (ans) (hash-ref ans \"subject\")) gene-hispanic)))\n\n(map (lambda (ans) (hash-ref ans \"predicate\")) gene-hispanic)\n(map (lambda (ans) (hash-ref ans 'subject-name)) gene-hispanic)\n\n(run* (key value) (cprop \"HGNC:23093\" key value))\n\n\n\n"
  },
  {
    "path": "contrib/medikanren2/Thi/build-kgx-synonym.rkt",
    "content": "#lang racket/base\n(require \"../../../medikanren2/dbk/dbk/io.rkt\"\n         \"../../../medikanren2/dbk/dbk/data.rkt\"\n         \"../../../medikanren2/dbk/dbk/stream.rkt\"\n         racket/runtime-path)\n\n(define-runtime-path path.here \".\")\n\n(define db (database (build-path path.here \"kgx-synonym.db\")))\n\n(unless (database-relation-has? db '(kgx-synonym edge))\n  (database-relation-add!\n    db '(kgx-synonym edge)\n    'attributes '(subject object source)\n    'type       '(string  string string)\n    'source     (s-map (lambda (row)\n                         (map (lambda (key) (hash-ref row key))\n                              '(subject object source_database)))\n                       (in:file \"KGX-NN-data/KGX_NN_data_2021-03-11_edges.jsonl\"))))\n\n(database-compact! db)\n\n(define r.edge (database-relation db '(kgx-synonym edge)))\n\n(relation-index-add! r.edge\n                     '(subject object)\n                     '(object  subject)\n                     '(source))\n"
  },
  {
    "path": "contrib/medikanren2/Thi/build-rtx-kg2.rkt",
    "content": "#lang racket/base\n(require\n  \"../../../medikanren2/dbk/dbk/io.rkt\"\n  \"../../../medikanren2/dbk/dbk/data.rkt\"\n  \"../../../medikanren2/dbk/dbk/stream.rkt\"\n  racket/runtime-path)\n\n(define-runtime-path path.here \".\")\n\n(define db (database (build-path path.here \"rtx-kg2_20210204.db\")))\n\n(unless (database-relation-has? db '(rtx-kg2 cprop))\n  (database-relation-add!\n    db '(rtx-kg2 cprop)\n    'attributes '(curie  key    value)\n    'type       '(string string string)\n    'source     (in:file \"rtx_kg2.nodeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))))\n\n(unless (database-relation-has? db '(rtx-kg2 edge))\n  (database-relation-add!\n    db '(rtx-kg2 edge)\n    'attributes '(eid subject object)\n    'type       '(nat string  string)\n    'source     (s-map (lambda (row) (cons (string->number (car row)) (cdr row)))\n                       (in:file \"rtx_kg2.edge.tsv\"     'header '(\":ID\" \":START\" \":END\")))))\n\n(unless (database-relation-has? db '(rtx-kg2 eprop))\n  (database-relation-add!\n    db '(rtx-kg2 eprop)\n    'attributes '(eid key    value)\n    'type       '(nat string string)\n    'source     (s-map (lambda (row) (cons (string->number (car row)) (cdr row)))\n                       (in:file \"rtx_kg2.edgeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\")))))\n\n(define cprop (database-relation db '(rtx-kg2 cprop)))\n(define edge  (database-relation db '(rtx-kg2 edge)))\n(define eprop (database-relation db '(rtx-kg2 eprop)))\n\n(database-compact! db)\n\n(relation-index-add! cprop\n                     '(curie key)\n                     '(key value))\n(relation-index-add! edge\n                     '(eid)\n                     '(subject object)\n                     '(subject eid)\n                     '(object  eid))\n(relation-index-add! eprop\n                     '(eid key)\n                     '(key value))\n"
  },
  {
    "path": "contrib/medikanren2/Thi/example-one-hop-IL1R1-drugs.rkt",
    "content": "#lang racket/base\n(require\n  \"query-low-level.rkt\"\n  racket/pretty)\n\n(define drug-categories '(\"biolink:ChemicalSubstance\"\n                          \"biolink:ClinicalIntervention\"\n                          \"biolink:ClinicalModifier\"\n                          \"biolink:Drug\"\n                          \"biolink:Treatment\"))\n\n(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:negatively_regulates\"\n                        \"biolink:negatively_regulates,_entity_to_entity\"\n                        \"biolink:negatively_regulates,_process_to_process\"\n                        \"biolink:treats\"))\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; find drugs that inhibit IL1R1 ;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define IL1R1-synonyms '(\"NCBIGene:3554\"\n                         \"PR:P14778\"\n                         \"UniProtKB:P14778\"\n                         \"UMLS:C1416395\"\n                         \"HGNC:5993\"\n                         \"ENSEMBL:ENSG00000115594\"))\n\n;; This use of query:X->Known is analogous to this miniKanren query:\n;(run* (s sname p o oname)\n;  (fresh (id drug)\n;    (edge id s o)\n;    (cprop s \"category\" drug)\n;    (cprop s \"name\"  sname)\n;    (cprop o \"oname\" oname)\n;    (eprop id \"predicate\" p)\n;    (membero o IL1R1-synonyms)\n;    (membero p inhibit-preds)\n;    (membero drug drug-categories)))))\n\n(newline)\n(define IL1R1-drugs (query:X->Known drug-categories inhibit-preds IL1R1-synonyms))\n\n(pretty-write `(IL1R1-drugs count: ,(length IL1R1-drugs)))\n(pretty-write IL1R1-drugs)\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Find drugs that inhibit IL1R1 signalling pathway ;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define IL1R1-pathway-synonyms '(\"ENSEMBL:ENSG00000172936\"\n                                 \"ENSEMBL:LRG_157\"\n                                 \"NCBIGene:4615\"\n                                 \"HGNC:7562\"\n                                 \"UniProtKB:Q99836\"\n                                 \"PR:Q99836\"\n                                 \"ENSEMBL:ENSG00000135341\"\n                                 \"HGNC:6859\"\n                                 \"NCBIGene:6885\"\n                                 \"PR:O43318\"\n                                 \"UniProtKB:O43318\"\n                                 \"UniProtKB:Q9Y6K9\"\n                                 \"ENSEMBL:ENSG00000269335\"\n                                 \"NCBIGene:8517\"\n                                 \"ENSEMBL:LRG_70\"\n                                 \"HGNC:5961\"\n                                 \"PR:Q9Y6K9\"\n                                 \"HGNC:6112\"\n                                 \"NCBIGene:3654\"\n                                 \"UMLS:C1334134\"\n                                 \"PR:P51617\"\n                                 \"UniProtKB:P51617\"\n                                 \"ENSEMBL:ENSG00000184216\"\n                                 \"UniProtKB:O43187\"\n                                 \"UMLS:C1334135\"\n                                 \"HGNC:6113\"\n                                 \"PR:O43187\"\n                                 \"NCBIGene:3656\"\n                                 \"ENSEMBL:ENSG00000134070\"\n                                 \"HGNC:12036\"\n                                 \"ENSEMBL:ENSG00000175104\"\n                                 \"NCBIGene:7189\"\n                                 \"UMLS:C1336666\"\n                                 \"UniProtKB:Q9Y4K3\"\n                                 \"PR:Q9Y4K3\"\n                                 \"HGNC:6848\"\n                                 \"PR:Q13233\"\n                                 \"ENSEMBL:ENSG00000095015\"\n                                 \"UniProtKB:Q13233\"\n                                 \"NCBIGene:4214\"\n                                 \"PR:P46734\"\n                                 \"HGNC:6843\"\n                                 \"NCBIGene:5606\"\n                                 \"UniProtKB:P46734\"\n                                 \"ENSEMBL:ENSG00000034152\"\n                                 \"UMLS:C1456386\"\n                                 \"ENSEMBL:ENSG00000108984\"\n                                 \"UMLS:C1334475\"\n                                 \"UniProtKB:P52564\"\n                                 \"NCBIGene:5608\"\n                                 \"HGNC:6846\"\n                                 \"PR:P52564\"\n                                 \"UniProtKB:P19838\"\n                                 \"ENSEMBL:ENSG00000109320\"\n                                 \"NCBIGene:4790\"\n                                 \"HGNC:7794\"\n                                 \"PR:P19838\"\n                                 \"ENSEMBL:LRG_1316\"\n                                 \"HGNC:6861\"\n                                 \"NCBIGene:4293\"\n                                 \"PR:P80192\"\n                                 \"UMLS:C1417016\"\n                                 \"UniProtKB:P80192\"\n                                 \"ENSEMBL:ENSG00000006432\"\n                                 \"NCBIGene:1432\"\n                                 \"HGNC:6876\"\n                                 \"ENSEMBL:ENSG00000112062\"\n                                 \"UniProtKB:Q16539\"\n                                 \"UMLS:C1366876\"\n                                 \"PR:Q16539\"\n                                 \"ENSEMBL:ENSG00000107643\"\n                                 \"UMLS:C1367731\"\n                                 \"PR:P45983\"\n                                 \"HGNC:6881\"\n                                 \"UniProtKB:P45983\"\n                                 \"NCBIGene:5599\"))\n\n;; This use of query:X->Known is analogous to this miniKanren query:\n;(run* (s sname p o oname)\n;  (fresh (id drug)\n;    (edge id s o)\n;    (cprop s \"category\" drug)\n;    (cprop s \"name\" sname)\n;    (cprop o \"name\" oname)\n;    (eprop id \"predicate\" p)\n;    (membero o IL1R-pathway-synonyms)\n;    (membero p inhibit-preds)\n;    (membero drug drug-categories)))))\n\n(newline)\n(define IL1R1-pathway-drugs (query:X->Known drug-categories inhibit-preds IL1R1-pathway-synonyms))\n\n(pretty-write `(IL1R1-pathway-drugs count: ,(length IL1R1-pathway-drugs)))\n(pretty-write IL1R1-pathway-drugs)\n"
  },
  {
    "path": "contrib/medikanren2/Thi/example-one-hop-ORPHANET-ICD-9-10.rkt",
    "content": "#lang racket/base\n(require\n  \"query-low-level.rkt\"\n  racket/pretty)\n\n(define close-match-preds '(\"biolink:close_match\"))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Find ORPHANET curies that are close matches to ICD9 or ICD10 curies ;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define prefix.ORPHANET \"ORPHANET:\")\n(define prefix.ICD9     \"ICD9:\")\n(define prefix.ICD10    \"ICD10:\")\n\n(newline)\n(define ORPHANET-ICD9-matches (query:Prefix->Prefix prefix.ORPHANET close-match-preds prefix.ICD9))\n(pretty-write `(ORPHANET-ICD9-matches count: ,(length ORPHANET-ICD9-matches)))\n(pretty-write ORPHANET-ICD9-matches)\n\n(newline)\n(define ORPHANET-ICD10-matches (query:Prefix->Prefix prefix.ORPHANET close-match-preds prefix.ICD10))\n(pretty-write `(ORPHANET-ICD10-matches count: ,(length ORPHANET-ICD10-matches)))\n(pretty-write ORPHANET-ICD10-matches)\n"
  },
  {
    "path": "contrib/medikanren2/Thi/example-one-hop-UniProt-cause-OMIM.rkt",
    "content": "#lang racket/base\n(require\n  \"query-low-level.rkt\"\n  racket/pretty)\n\n(define disease-categories '(\"biolink:Disease\"\n                             \"biolink:PhenotypicFeature\"\n                             \"biolink:DiseaseOrPhenotypicFeature\"))\n\n(define cause-preds '(\"biolink:causes\"))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; find proteins implicated in a disease ;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define UniProt-to-Orphanet-curies '(\"UniProtKB:Q3MJ13\"\n                                     \"UniProtKB:Q9BZH6\"\n                                     \"UniProtKB:Q68DK2\"\n                                     \"UniProtKB:Q9ULM3\"\n                                     \"UniProtKB:O60315\"\n                                     \"UniProtKB:Q96JG9\"\n                                     \"UniProtKB:O14980\"\n                                     \"UniProtKB:Q8N8E2\"\n                                     \"UniProtKB:Q92610\"\n                                     \"UniProtKB:Q9UM01\"\n                                     \"UniProtKB:Q6PML9\"\n                                     \"UniProtKB:Q2M1K9\"\n                                     \"UniProtKB:Q8TBZ6\"\n                                     \"UniProtKB:Q6UX40\"\n                                     \"UniProtKB:P67936\"\n                                     \"UniProtKB:Q7L0Y3\"\n                                     \"UniProtKB:Q7Z4N2\"\n                                     \"UniProtKB:Q8TD43\"\n                                     \"UniProtKB:Q6DKK2\"\n                                     \"UniProtKB:Q70EL2\"\n                                     \"UniProtKB:Q9H869\"\n                                     \"UniProtKB:P35916\"\n                                     \"UniProtKB:P22309\"\n                                     \"UniProtKB:Q9Y484\"\n                                     \"UniProtKB:P56705\"\n                                     \"UniProtKB:Q8NEZ2\"\n                                     \"UniProtKB:Q9H9D4\"\n                                     \"UniProtKB:Q8NI36\"\n                                     \"UniProtKB:Q8NEZ3\"\n                                     \"UniProtKB:Q9NQH7\"\n                                     \"UniProtKB:P98170\"\n                                     \"UniProtKB:O95150\"\n                                     \"UniProtKB:P48023\"\n                                     \"UniProtKB:P09493\"\n                                     \"UniProtKB:O00300\"\n                                     \"UniProtKB:Q9NXH9\"\n                                     \"UniProtKB:P20333\"\n                                     \"UniProtKB:Q9H892\"\n                                     \"UniProtKB:Q9NUW8\"\n                                     \"UniProtKB:P23763\"\n                                     \"UniProtKB:Q9Y462\"\n                                     \"UniProtKB:Q9BZG2\"\n                                     \"UniProtKB:P31939\"\n                                     \"UniProtKB:Q9BZE2\"\n                                     \"UniProtKB:P51159\"\n                                     \"UniProtKB:Q9H082\"\n                                     \"UniProtKB:Q96NR8\"\n                                     \"UniProtKB:Q9H902\"\n                                     \"UniProtKB:Q5TAB7\"\n                                     \"UniProtKB:Q969S9\"\n                                     \"UniProtKB:P51531\"\n                                     \"UniProtKB:Q9P2R7\"\n                                     \"UniProtKB:Q9BX79\"\n                                     \"UniProtKB:P51692\"\n                                     \"UniProtKB:P08842\"\n                                     \"UniProtKB:Q14765\"\n                                     \"UniProtKB:P11277\"\n                                     \"UniProtKB:Q9NZD8\"\n                                     \"UniProtKB:Q9P2J5\"\n                                     \"UniProtKB:Q6IEE7\"\n                                     \"UniProtKB:P47897\"\n                                     \"UniProtKB:Q9UGM6\"\n                                     \"UniProtKB:P24821\"\n                                     \"UniProtKB:Q9NY65\"\n                                     \"UniProtKB:Q96BZ9\"\n                                     \"UniProtKB:P10586\"\n                                     \"UniProtKB:P63162\"\n                                     \"UniProtKB:Q13621\"\n                                     \"UniProtKB:O75845\"\n                                     \"UniProtKB:P31213\"\n                                     \"UniProtKB:P30531\"\n                                     \"UniProtKB:Q9BY12\"\n                                     \"UniProtKB:Q9Y3A5\"\n                                     \"UniProtKB:Q8IWT1\"\n                                     \"UniProtKB:P31639\"\n                                     \"UniProtKB:Q13424\"\n                                     \"UniProtKB:Q9NPD5\"\n                                     \"UniProtKB:P50452\"\n                                     \"UniProtKB:Q8TAQ2\"\n                                     \"UniProtKB:Q8TDD2\"\n                                     \"UniProtKB:Q96GM5\"\n                                     \"UniProtKB:Q658P3\"\n                                     \"UniProtKB:Q6Q759\"\n                                     \"UniProtKB:O43295\"\n                                     \"UniProtKB:Q9C004\"\n                                     \"UniProtKB:Q9NSD9\"\n                                     \"UniProtKB:P14868\"\n                                     \"UniProtKB:Q8N511\"\n                                     \"UniProtKB:P04350\"\n                                     \"UniProtKB:P12270\"\n                                     \"UniProtKB:Q8NET8\"\n                                     \"UniProtKB:O95292\"\n                                     \"UniProtKB:O15259\"\n                                     \"UniProtKB:O60313\"\n                                     \"UniProtKB:Q99572\"\n                                     \"UniProtKB:Q96FM1\"\n                                     \"UniProtKB:Q15042\"\n                                     \"UniProtKB:P35913\"\n                                     \"UniProtKB:P51160\"\n                                     \"UniProtKB:Q8IUD2\"\n                                     \"UniProtKB:P52945\"\n                                     \"UniProtKB:O43502\"\n                                     \"UniProtKB:O75771\"\n                                     \"UniProtKB:Q15120\"\n                                     \"UniProtKB:Q9UM63\"\n                                     \"UniProtKB:P00747\"\n                                     \"UniProtKB:P54277\"\n                                     \"UniProtKB:Q8NFJ6\"\n                                     \"UniProtKB:O60733\"\n                                     \"UniProtKB:Q8NBT0\"\n                                     \"UniProtKB:P57054\"\n                                     \"UniProtKB:Q9UBK2\"\n                                     \"UniProtKB:Q7L7X3\"\n                                     \"UniProtKB:P07101\"\n                                     \"UniProtKB:P40818\"\n                                     \"UniProtKB:P49810\"\n                                     \"UniProtKB:Q7Z5J4\"\n                                     \"UniProtKB:Q9UL12\"\n                                     \"UniProtKB:Q96E14\"\n                                     \"UniProtKB:O60930\"\n                                     \"UniProtKB:Q63HN8\"\n                                     \"UniProtKB:O95343\"\n                                     \"UniProtKB:P51532\"\n                                     \"UniProtKB:Q15427\"\n                                     \"UniProtKB:Q8IVB4\"\n                                     \"UniProtKB:O14656\"\n                                     \"UniProtKB:Q9BYW2\"\n                                     \"UniProtKB:Q9Y2M2\"\n                                     \"UniProtKB:Q16623\"\n                                     \"UniProtKB:Q15468\"\n                                     \"UniProtKB:P61764\"\n                                     \"UniProtKB:O95630\"\n                                     \"UniProtKB:P53597\"\n                                     \"UniProtKB:Q9NRP7\"\n                                     \"UniProtKB:Q15022\"\n                                     \"UniProtKB:O15020\"\n                                     \"UniProtKB:Q9BVA1\"\n                                     \"UniProtKB:Q9UBH6\"\n                                     \"UniProtKB:P50219\"\n                                     \"UniProtKB:P42898\"\n                                     \"UniProtKB:O75081\"\n                                     \"UniProtKB:Q86Y26\"\n                                     \"UniProtKB:Q92626\"\n                                     \"UniProtKB:P63000\"\n                                     \"UniProtKB:O43567\"\n                                     \"UniProtKB:P18577\"\n                                     \"UniProtKB:O94761\"\n                                     \"UniProtKB:O00584\"\n                                     \"UniProtKB:Q16518\"\n                                     \"UniProtKB:Q9NPC8\"\n                                     \"UniProtKB:A7XYQ1\"\n                                     \"UniProtKB:Q16650\"\n                                     \"UniProtKB:Q9Y5X0\"\n                                     \"UniProtKB:Q969G3\"\n                                     \"UniProtKB:Q12824\"\n                                     \"UniProtKB:Q92629\"\n                                     \"UniProtKB:O95363\"\n                                     \"UniProtKB:Q8IWV7\"\n                                     \"UniProtKB:Q9P0N9\"\n                                     \"UniProtKB:Q9UKE5\"\n                                     \"UniProtKB:Q9P0N5\"\n                                     \"UniProtKB:Q9HAV5\"\n                                     \"UniProtKB:Q96RJ3\"\n                                     \"UniProtKB:P53007\"\n                                     \"UniProtKB:Q8N427\"\n                                     \"UniProtKB:P07911\"\n                                     \"UniProtKB:P48651\"\n                                     \"UniProtKB:Q96IS3\"\n                                     \"UniProtKB:Q9Y4F9\"\n                                     \"UniProtKB:Q96AA3\"\n                                     \"UniProtKB:P27635\"\n                                     \"UniProtKB:Q5K651\"\n                                     \"UniProtKB:Q14108\"\n                                     \"UniProtKB:Q6P5W5\"\n                                     \"UniProtKB:O60880\"\n                                     \"UniProtKB:A6NNY8\"\n                                     \"UniProtKB:P25490\"\n                                     \"UniProtKB:P49459\"\n                                     \"UniProtKB:Q13432\"\n                                     \"UniProtKB:P04435\"\n                                     \"UniProtKB:Q9NPD8\"\n                                     \"UniProtKB:Q05086\"\n                                     \"UniProtKB:Q7Z3V4\"\n                                     \"UniProtKB:P17480\"\n                                     \"UniProtKB:Q08AM6\"\n                                     \"UniProtKB:P57082\"\n                                     \"UniProtKB:Q9UKZ4\"\n                                     \"UniProtKB:P07437\"\n                                     \"UniProtKB:Q9UJV3\"\n                                     \"UniProtKB:O75762\"\n                                     \"UniProtKB:Q9UHX1\"\n                                     \"UniProtKB:Q9NWF9\"\n                                     \"UniProtKB:P10301\"\n                                     \"UniProtKB:Q99720\"\n                                     \"UniProtKB:P54577\"\n                                     \"UniProtKB:Q0IIM8\"\n                                     \"UniProtKB:Q9ULP9\"\n                                     \"UniProtKB:P07478\"\n                                     \"UniProtKB:Q92889\"\n                                     \"UniProtKB:P42768\"\n                                     \"UniProtKB:Q6ISB3\"\n                                     \"UniProtKB:P10916\"\n                                     \"UniProtKB:Q99836\"\n                                     \"UniProtKB:Q7Z406\"\n                                     \"UniProtKB:P00387\"\n                                     \"UniProtKB:Q9UKX2\"\n                                     \"UniProtKB:O60890\"\n                                     \"UniProtKB:O00330\"\n                                     \"UniProtKB:P03999\"\n                                     \"UniProtKB:P04001\"\n                                     \"UniProtKB:Q86UR5\"\n                                     \"UniProtKB:P45378\"\n                                     \"UniProtKB:Q13114\"\n                                     \"UniProtKB:O14773\"\n                                     \"UniProtKB:P61960\"\n                                     \"UniProtKB:Q9UHD9\"\n                                     \"UniProtKB:Q3ZAQ7\"\n                                     \"UniProtKB:Q96HR9\"\n                                     \"UniProtKB:Q8IWN7\"\n                                     \"UniProtKB:P49247\"\n                                     \"UniProtKB:P56715\"\n                                     \"UniProtKB:Q9BQ52\"\n                                     \"UniProtKB:Q9NVW2\"\n                                     \"UniProtKB:Q15669\"\n                                     \"UniProtKB:P07949\"\n                                     \"UniProtKB:P40879\"\n                                     \"UniProtKB:P58743\"\n                                     \"UniProtKB:P41225\"\n                                     \"UniProtKB:Q16586\"\n                                     \"UniProtKB:Q14159\"\n                                     \"UniProtKB:P35270\"\n                                     \"UniProtKB:P28347\"\n                                     \"UniProtKB:P61812\"\n                                     \"UniProtKB:Q96Q05\"\n                                     \"UniProtKB:P51809\"\n                                     \"UniProtKB:Q8TAA9\"\n                                     \"UniProtKB:Q16572\"\n                                     \"UniProtKB:Q9H267\"\n                                     \"UniProtKB:Q96RL7\"\n                                     \"UniProtKB:Q9H091\"\n                                     \"UniProtKB:P01111\"\n                                     \"UniProtKB:O60673\"\n                                     \"UniProtKB:Q8N264\"\n                                     \"UniProtKB:Q52LW3\"\n                                     \"UniProtKB:O14593\"\n                                     \"UniProtKB:Q6ZVN8\"\n                                     \"UniProtKB:P57078\"\n                                     \"UniProtKB:P46777\"\n                                     \"UniProtKB:P23526\"\n                                     \"UniProtKB:Q92911\"\n                                     \"UniProtKB:Q9Y617\"\n                                     \"UniProtKB:Q13326\"\n                                     \"UniProtKB:Q3ZCQ8\"\n                                     \"UniProtKB:Q6ZVD7\"\n                                     \"UniProtKB:Q04837\"\n                                     \"UniProtKB:Q9UJ98\"\n                                     \"UniProtKB:P14410\"\n                                     \"UniProtKB:P46977\"\n                                     \"UniProtKB:Q5JPH6\"\n                                     \"UniProtKB:P49588\"\n                                     \"UniProtKB:Q15046\"\n                                     \"UniProtKB:Q99593\"\n                                     \"UniProtKB:Q92734\"\n                                     \"UniProtKB:Q9BQ65\"\n                                     \"UniProtKB:Q8NDX2\"\n                                     \"UniProtKB:Q9GZV5\"\n                                     \"UniProtKB:P08670\"\n                                     \"UniProtKB:Q9H6K4\"\n                                     \"UniProtKB:Q06710\"\n                                     \"UniProtKB:Q96QU1\"\n                                     \"UniProtKB:Q08499\"\n                                     \"UniProtKB:P16499\"\n                                     \"UniProtKB:Q75T13\"\n                                     \"UniProtKB:Q15198\"\n                                     \"UniProtKB:P00491\"\n                                     \"UniProtKB:P13797\"\n                                     \"UniProtKB:Q8NE79\"\n                                     \"UniProtKB:P16471\"\n                                     \"UniProtKB:Q3SYG4\"\n                                     \"UniProtKB:Q9BRK0\"\n                                     \"UniProtKB:Q96EP0\"\n                                     \"UniProtKB:P47804\"\n                                     \"UniProtKB:Q96KN7\"\n                                     \"UniProtKB:Q9BYT1\"\n                                     \"UniProtKB:P41440\"\n                                     \"UniProtKB:O60779\"\n                                     \"UniProtKB:Q9BZV2\"\n                                     \"UniProtKB:Q9Y3D3\"\n                                     \"UniProtKB:O95136\"\n                                     \"UniProtKB:Q01196\"\n                                     \"UniProtKB:Q13950\"\n                                     \"UniProtKB:P82650\"\n                                     \"UniProtKB:Q8WYR4\"\n                                     \"UniProtKB:Q08357\"\n                                     \"UniProtKB:Q9H1X1\"\n                                     \"UniProtKB:O76082\"\n                                     \"UniProtKB:Q9Y2B1\"\n                                     \"UniProtKB:Q96S37\"\n                                     \"UniProtKB:Q9Y2V3\"\n                                     \"UniProtKB:Q9NWS8\"\n                                     \"UniProtKB:Q9Y2P5\"\n                                     \"UniProtKB:O75792\"\n                                     \"UniProtKB:Q8IYW5\"\n                                     \"UniProtKB:Q9UQD0\"\n                                     \"UniProtKB:P78381\"\n                                     \"UniProtKB:Q9Y2D2\"\n                                     \"UniProtKB:P51168\"\n                                     \"UniProtKB:P21912\"\n                                     \"UniProtKB:O75880\"\n                                     \"UniProtKB:O43819\"\n                                     \"UniProtKB:Q9NTN3\"\n                                     \"UniProtKB:O43175\"\n                                     \"UniProtKB:P23246\"\n                                     \"UniProtKB:Q6FHJ7\"\n             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                              \"UniProtKB:Q9NP81\"\n                                     \"UniProtKB:Q8NFB2\"\n                                     \"UniProtKB:Q9BVV6\"\n                                     \"UniProtKB:Q96LT9\"\n                                     \"UniProtKB:Q92834\"\n                                     \"UniProtKB:P04843\"\n                                     \"UniProtKB:P51449\"\n                                     \"UniProtKB:Q9UGP8\"\n                                     \"UniProtKB:Q9NP59\"\n                                     \"UniProtKB:Q9Y5Y9\"\n                                     \"UniProtKB:Q9BZD2\"\n                                     \"UniProtKB:Q9UI33\"\n                                     \"UniProtKB:Q9Y2W3\"\n                                     \"UniProtKB:Q9UMX9\"\n                                     \"UniProtKB:P31040\"\n                                     \"UniProtKB:P00441\"\n                                     \"UniProtKB:Q9ULL8\"\n                                     \"UniProtKB:P60866\"\n                                     \"UniProtKB:Q96T21\"\n                                     \"UniProtKB:Q96DW6\"\n                                     \"UniProtKB:A6NNN8\"\n                                     \"UniProtKB:Q14524\"\n                                     \"UniProtKB:Q6P1M0\"\n                                     \"UniProtKB:Q96H72\"\n                                     \"UniProtKB:O75443\"\n                                     \"UniProtKB:Q04206\"\n                                     \"UniProtKB:P10827\"\n                                     \"UniProtKB:P10828\"\n                                     \"UniProtKB:Q9UGU0\"\n                                     \"UniProtKB:Q8WVM0\"\n                                     \"UniProtKB:Q8TF17\"\n                                     \"UniProtKB:Q8NDG6\"\n                                     \"UniProtKB:P13385\"\n                                     \"UniProtKB:O95455\"\n                                     \"UniProtKB:Q9NX18\"\n                                     \"UniProtKB:Q9NRF2\"\n                                     \"UniProtKB:Q9UQQ2\"\n                                     \"UniProtKB:Q9UHP9\"\n                                     \"UniProtKB:Q9UBP0\"\n                                     \"UniProtKB:Q9H5K3\"\n                                     \"UniProtKB:Q14BN4\"\n                                     \"UniProtKB:Q8IWL1\"\n                                     \"UniProtKB:P57727\"\n                                     \"UniProtKB:Q9NRS4\"\n                                     \"UniProtKB:O96008\"\n                                     \"UniProtKB:Q96Q45\"\n                                     \"UniProtKB:O43280\"\n                                     \"UniProtKB:Q8IU80\"\n                                     \"UniProtKB:Q3LXA3\"\n                                     \"UniProtKB:Q9UHF0\"\n                                     \"UniProtKB:Q8WZ04\"\n                                     \"UniProtKB:Q9NVV0\"\n                                     \"UniProtKB:O60220\"\n                                     \"UniProtKB:Q9NZC2\"\n                                     \"UniProtKB:P29401\"\n                                     \"UniProtKB:P48764\"\n                                     \"UniProtKB:Q92581\"\n                                     \"UniProtKB:Q9Y3D7\"\n                                     \"UniProtKB:Q13043\"\n                                     \"UniProtKB:Q7RTU9\"\n                                     \"UniProtKB:Q6ZRI0\"\n                                     \"UniProtKB:O75914\"\n                                     \"UniProtKB:P16234\"\n                                     \"UniProtKB:Q8IWS0\"\n                                     \"UniProtKB:Q13608\"\n                                     \"UniProtKB:Q96BD5\"\n                                     \"UniProtKB:O43924\"\n                                     \"UniProtKB:P16885\"\n                                     \"UniProtKB:Q8NAT1\"\n                                     \"UniProtKB:P29590\"\n                                     \"UniProtKB:P50336\"\n                                     \"UniProtKB:Q6P2Q9\"\n                                     \"UniProtKB:O94906\"\n                                     \"UniProtKB:O43490\"\n                                     \"UniProtKB:Q7Z3G6\"\n                                     \"UniProtKB:P62913\"\n                                     \"UniProtKB:Q7Z6L0\"\n                                     \"UniProtKB:P78527\"\n                                     \"UniProtKB:P12272\"\n                                     \"UniProtKB:Q96PU8\"\n                                     \"UniProtKB:P55895\"\n                                     \"UniProtKB:P15153\"\n                                     \"UniProtKB:P61313\"\n                                     \"UniProtKB:Q15043\"\n                                     \"UniProtKB:Q8TDP1\"\n                                     \"UniProtKB:Q5TBB1\"\n                                     \"UniProtKB:Q9H4F8\"\n                                     \"UniProtKB:Q9HB58\"\n                                     \"UniProtKB:Q16585\"\n                                     \"UniProtKB:Q9H5Y7\"\n                                     \"UniProtKB:Q9Y448\"\n                                     \"UniProtKB:P52788\"\n                                     \"UniProtKB:Q01130\"\n                                     \"UniProtKB:Q13586\"\n                                     \"UniProtKB:Q9UMX1\"\n                                     \"UniProtKB:Q8TC36\"\n                                     \"UniProtKB:Q8N3U4\"\n                                     \"UniProtKB:Q9ULZ2\"\n                                     \"UniProtKB:Q15526\"\n                                     \"UniProtKB:P34981\"\n                                     \"UniProtKB:O15269\"\n                                     \"UniProtKB:Q969V6\"\n                                     \"UniProtKB:P23409\"\n                                     \"UniProtKB:Q16633\"\n                                     \"UniProtKB:Q13702\"\n                                     \"UniProtKB:P42677\"\n                                     \"UniProtKB:P62854\"\n                                     \"UniProtKB:Q03519\"\n                                     \"UniProtKB:P08865\"\n                                     \"UniProtKB:Q5TD94\"\n                                     \"UniProtKB:O75298\"\n                                     \"UniProtKB:Q8IYM1\"\n                                     \"UniProtKB:P23975\"\n                                     \"UniProtKB:Q9Y345\"\n                                     \"UniProtKB:P48029\"\n                                     \"UniProtKB:Q9H1V8\"\n                                     \"UniProtKB:Q9Y6B6\"\n                                     \"UniProtKB:O75410\"\n                                     \"UniProtKB:Q9Y6A5\"\n                                     \"UniProtKB:P09758\"\n                                     \"UniProtKB:P37840\"\n                                     \"UniProtKB:Q9BSH4\"\n                                     \"UniProtKB:P40200\"\n                                     \"UniProtKB:P36897\"\n                                     \"UniProtKB:P56279\"\n                                     \"UniProtKB:P37173\"\n                                     \"UniProtKB:P55072\"\n                                     \"UniProtKB:Q15583\"\n                                     \"UniProtKB:P20062\"\n                                     \"UniProtKB:Q8NI27\"\n                                     \"UniProtKB:Q13428\"\n                                     \"UniProtKB:Q07699\"\n                                     \"UniProtKB:O60939\"\n                                     \"UniProtKB:Q8IVG5\"\n                                     \"UniProtKB:Q9Y3Z3\"\n                                     \"UniProtKB:Q495M3\"\n                                     \"UniProtKB:Q9H6I2\"\n                                     \"UniProtKB:P48431\"\n                                     \"UniProtKB:Q8TAP9\"\n                                     \"UniProtKB:Q8TAB3\"\n                                     \"UniProtKB:Q3MIW9\"\n                                     \"UniProtKB:Q15800\"\n                                     \"UniProtKB:Q96RE7\"\n                                     \"UniProtKB:Q15746\"\n                                     \"UniProtKB:Q9UPP1\"\n                                     \"UniProtKB:Q00872\"\n                                     \"UniProtKB:P00558\"\n                                     \"UniProtKB:P19878\"\n                                     \"UniProtKB:O15146\"\n                                     \"UniProtKB:O43676\"\n                                     \"UniProtKB:P36955\"\n                                     \"UniProtKB:O00567\"\n                                     \"UniProtKB:P19838\"\n                                     \"UniProtKB:Q330K2\"\n                                     \"UniProtKB:Q6VVB1\"\n                                     \"UniProtKB:P52952\"\n                                     \"UniProtKB:Q13563\"\n                                     \"UniProtKB:Q9NRD5\"\n                                     \"UniProtKB:Q08J23\"\n                                     \"UniProtKB:O95613\"\n                                     \"UniProtKB:Q9BZ23\"\n                                     \"UniProtKB:Q9NVE7\"\n                                     \"UniProtKB:P47712\"\n                                     \"UniProtKB:P40424\"\n                                     \"UniProtKB:P49585\"\n                                     \"UniProtKB:Q9BXM7\"\n                                     \"UniProtKB:Q8N490\"\n                                     \"UniProtKB:Q99959\"\n                                     \"UniProtKB:Q4J6C6\"\n                                     \"UniProtKB:Q9Y3E5\"\n                                     \"UniProtKB:P11686\"\n                                     \"UniProtKB:P42766\"\n                                     \"UniProtKB:P22033\"\n                                     \"UniProtKB:Q9NX14\"\n                                     \"UniProtKB:P20929\"\n                                     \"UniProtKB:Q9BU61\"\n                                     \"UniProtKB:Q9H9Q4\"\n                                     \"UniProtKB:Q8N183\"\n                                     \"UniProtKB:A6NCS4\"\n                                     \"UniProtKB:Q9Y697\"\n                                     \"UniProtKB:Q99608\"\n                                     \"UniProtKB:Q96NY8\"\n                                     \"UniProtKB:Q96E22\"\n                                     \"UniProtKB:Q9NPE3\"\n                                     \"UniProtKB:P56556\"\n                                     \"UniProtKB:Q15126\"\n                                     \"UniProtKB:Q9HC29\"\n                                     \"UniProtKB:Q9C000\"\n                                     \"UniProtKB:O15118\"\n                                     \"UniProtKB:O60936\"\n                                     \"UniProtKB:Q58EX7\"\n                                     \"UniProtKB:O94827\"\n                                     \"UniProtKB:Q8TC44\"\n                                     \"UniProtKB:Q08209\"\n                                     \"UniProtKB:Q9Y4G2\"\n                                     \"UniProtKB:Q9NP85\"\n                                     \"UniProtKB:Q8IWE5\"\n                                     \"UniProtKB:O00592\"\n                                     \"UniProtKB:Q8WVV4\"\n                                     \"UniProtKB:Q6NW34\"\n                                     \"UniProtKB:P03897\"\n                                     \"UniProtKB:Q9NUD9\"\n                                     \"UniProtKB:Q8TDX9\"\n                                     \"UniProtKB:Q92570\"\n                                     \"UniProtKB:Q96S44\"\n                                     \"UniProtKB:Q7Z494\"\n                                     \"UniProtKB:O75161\"\n                                     \"UniProtKB:Q96NG3\"\n                                     \"UniProtKB:P26367\"\n                                     \"UniProtKB:A6NGG8\"\n                                     \"UniProtKB:P11498\"\n                                     \"UniProtKB:Q9H3D4\"\n                                     \"UniProtKB:O15120\"\n                                     \"UniProtKB:P98161\"\n                                     \"UniProtKB:Q06124\"\n                                     \"UniProtKB:Q92781\"\n                                     \"UniProtKB:P51157\"\n                                     \"UniProtKB:Q9Y2R9\"\n                                     \"UniProtKB:Q9H2X9\"\n                                     \"UniProtKB:Q96RR1\"\n                                     \"UniProtKB:Q9Y6A1\"\n                                     \"UniProtKB:Q99575\"\n                                     \"UniProtKB:P42336\"\n                                     \"UniProtKB:Q9Y4D7\"\n                                     \"UniProtKB:P08F94\"\n                                     \"UniProtKB:Q6PCD5\"\n                                     \"UniProtKB:Q9BRB3\"\n                                     \"UniProtKB:Q9NQX1\"\n                                     \"UniProtKB:Q9NQX0\"\n                                     \"UniProtKB:O75360\"\n                                     \"UniProtKB:P54821\"\n                                     \"UniProtKB:Q8N3J5\"\n                                     \"UniProtKB:P62081\"\n                                     \"UniProtKB:Q2MKA7\"\n                                     \"UniProtKB:Q2I0M5\"\n                                     \"UniProtKB:A6NKG5\"\n                                     \"UniProtKB:Q86UC2\"\n                                     \"UniProtKB:Q8NB59\"\n                                     \"UniProtKB:P21579\"\n                                     \"UniProtKB:Q8NF91\"\n                                     \"UniProtKB:Q8WXH0\"\n                                     \"UniProtKB:Q8N9I0\"\n                                     \"UniProtKB:Q8N205\"\n                                     \"UniProtKB:O43426\"\n                                     \"UniProtKB:Q96I59\"\n                                     \"UniProtKB:P00734\"\n                                     \"UniProtKB:P31483\"\n                                     \"UniProtKB:P43007\"\n                                     \"UniProtKB:Q15437\"\n                                     \"UniProtKB:Q96AG3\"\n                                     \"UniProtKB:Q9Y6L6\"\n                                     \"UniProtKB:Q9BYJ1\"\n                                     \"UniProtKB:Q99677\"\n                                     \"UniProtKB:P43657\"\n                                     \"UniProtKB:Q14767\"\n                                     \"UniProtKB:Q8N2S1\"\n                                     \"UniProtKB:O14770\"\n                                     \"UniProtKB:O96007\"\n                                     \"UniProtKB:O60487\"\n                                     \"UniProtKB:Q00325\"\n                                     \"UniProtKB:Q9Y619\"\n                                     \"UniProtKB:Q9H1P3\"\n                                     \"UniProtKB:Q8N6M0\"\n                                     \"UniProtKB:P24386\"\n                                     \"UniProtKB:P08237\"\n                                     \"UniProtKB:P27169\"\n                                     \"UniProtKB:Q9NQV8\"\n                                     \"UniProtKB:P07737\"\n                                     \"UniProtKB:O75569\"\n                                     \"UniProtKB:Q03431\"\n                                     \"UniProtKB:P18077\"\n                                     \"UniProtKB:Q9H4B7\"\n                                     \"UniProtKB:Q9NZC9\"\n                                     \"UniProtKB:A1X283\"\n                                     \"UniProtKB:Q96MF2\"\n                                     \"UniProtKB:Q8WVM7\"\n                                     \"UniProtKB:P42226\"\n                                     \"UniProtKB:P61011\"\n                                     \"UniProtKB:Q13501\"))\n\n(newline)\n(define implicated-UniProts (query:Known->X UniProt-to-Orphanet-curies cause-preds disease-categories))\n\n(pretty-write `(implicated-UniProts count: ,(length implicated-UniProts)))\n(pretty-write implicated-UniProts)\n"
  },
  {
    "path": "contrib/medikanren2/Thi/example-two-hop-CHAMP1-drugs.rkt",
    "content": "#lang racket/base\n(require\n  \"query-low-level.rkt\"\n  racket/pretty)\n\n(define drug-categories '(\"biolink:ChemicalSubstance\"\n                          \"biolink:ClinicalIntervention\"\n                          \"biolink:ClinicalModifier\"\n                          \"biolink:Drug\"\n                          \"biolink:Treatment\"))\n\n(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:negatively_regulates\"\n                        \"biolink:negatively_regulates,_entity_to_entity\"\n                        \"biolink:negatively_regulates,_process_to_process\"\n                        \"biolink:treats\"))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Find drugs that up or down-regulate a list of genes while treating the phenotypes ;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define Hakon-CHAMP1-RNA-up-syns '(\"ENSEMBL:ENSG00000115468\"\n                                   \"ENSEMBL:ENSG00000171208\"\n                                   \"UMLS:C1538790\"\n                                   \"HGNC:17198\"\n                                   \"UniProtKB:Q8NFY4\"\n                                   \"ENSEMBL:LRG_50\"\n                                   \"PR:Q9NPG1\"\n                                   \"ENSEMBL:ENSG00000132688\"\n                                   \"ENSEMBL:ENSG00000163918\"\n                                   \"HGNC:2053\"\n                                   \"UniProtKB:Q5EG05\"\n                                   \"UMLS:C2240136\"\n                                   \"HGNC:11168\"\n                                   \"NCBIGene:80243\"\n                                   \"HGNC:4280\"\n                                   \"HGNC:6343\"\n                                   \"ENSEMBL:ENSG00000254087\"\n                                   \"HGNC:485\"\n                                   \"ENSEMBL:ENSG00000166974\"\n                                   \"UniProtKB:Q99683\"\n                                   \"UniProtKB:P50135\"\n                                   \"UMLS:C1333585\"\n                                   \"NCBIGene:23362\"\n                                   \"UniProtKB:P31271\"\n                                   \"UMLS:C2239668\"\n                                   \"HGNC:12518\"\n                                   \"NCBIGene:7042\"\n                                   \"UMLS:C0812307\"\n                                   \"PR:Q9NZQ7\"\n                                   \"NCBIGene:134429\"\n                                   \"ENSEMBL:ENSG00000091879\"\n                                   \"ENSEMBL:ENSG00000144635\"\n                                   \"NCBIGene:26508\"\n                                   \"HGNC:10252\"\n                                   \"HGNC:6597\"\n                                   \"HGNC:25491\"\n                                   \"PR:Q9Y6U3\"\n                                   \"HGNC:2528\"\n                                   \"UMLS:C1424695\"\n                                   \"ENSEMBL:ENSG00000206053\"\n                                   \"NCBIGene:153478\"\n                                   \"NCBIGene:3209\"\n                                   \"ENSEMBL:ENSG00000126803\"\n                                   \"NCBIGene:4773\"\n                                   \"PR:P43304\"\n                                   \"UniProtKB:Q8NC67\"\n                                   \"ENSEMBL:ENSG00000150471\"\n                                   \"UniProtKB:Q8WY64\"\n                                   \"UniProtKB:Q9Y6G9\"\n                                   \"PR:Q6UVK1\"\n                                   \"HGNC:9082\"\n                                   \"HGNC:6848\"\n                                   \"ENSEMBL:ENSG00000109861\"\n                                   \"UniProtKB:Q5TFE4\"\n                                   \"ENSEMBL:ENSG00000137501\"\n                                   \"NCBIGene:7351\"\n                                   \"PR:A2A2Y4\"\n                                   \"NCBIGene:1075\"\n                                   \"UMLS:C1415074\"\n                                   \"PR:Q8WXH0\"\n                                   \"ENSEMBL:ENSG00000169129\"\n                                   \"ENSEMBL:ENSG00000112183\"\n                                   \"UniProtKB:Q9H892\"\n                                   \"UMLS:C1540292\"\n                                   \"ENSEMBL:ENSG00000054654\"\n                                   \"PR:P50135\"\n                                   \"NCBIGene:6502\"\n                                   \"NCBIGene:29116\"\n                                   \"NCBIGene:1464\"\n                                   \"HGNC:17493\"\n                                   \"NCBIGene:51267\"\n                                   \"HGNC:6547\"\n                                   \"ENSEMBL:ENSG00000131471\"\n                                   \"PR:Q68D86\"\n                                   \"NCBIGene:4162\"\n                                   \"HGNC:6554\"\n                                   \"UMLS:C1420593\"\n                                   \"UniProtKB:P01130\"\n                                   \"PR:Q13469\"\n                                   \"UniProtKB:Q8N4X5\"\n                                   \"PR:Q86SQ0\"\n                                   \"PR:P61812\"\n                                   \"NCBIGene:22866\"\n                                   \"UMLS:C1419269\"\n                                   \"NCBIGene:2149\"\n                                   \"ENSEMBL:ENSG00000198743\"\n                                   \"ENSEMBL:ENSG00000128641\"\n                                   \"PR:P48357\"\n                                   \"HGNC:22950\"\n                                   \"NCBIGene:90853\"\n                                   \"HGNC:2323\"\n                                   \"ENSEMBL:ENSG00000065882\"\n                                   \"HGNC:11578\"\n                                   \"PR:Q14739\"\n                                   \"HGNC:4456\"\n                                   \"HGNC:7776\"\n                                   \"HGNC:376\"\n                                   \"PR:Q6UVW9\"\n                                   \"NCBIGene:4430\"\n                                   \"ENSEMBL:ENSG00000104435\"\n                                   \"PR:Q86V40\"\n                                   \"NCBIGene:4254\"\n                                   \"NCBIGene:7976\"\n                                   \"PR:O15084\"\n                                   \"HGNC:6560\"\n                                   \"UMLS:C3543895\"\n                                   \"PR:Q9H0B8\"\n                                   \"PR:Q9UNQ0\"\n                                   \"ENSEMBL:ENSG00000134318\"\n                                   \"NCBIGene:129293\"\n                                   \"NCBIGene:64744\"\n                                   \"ENSEMBL:ENSG00000157557\"\n                                   \"HGNC:3776\"\n                                   \"UMLS:C1539762\"\n                                   \"ENSEMBL:ENSG00000129680\"\n                                   \"PR:P03956\"\n                                   \"UMLS:C1428873\"\n                                   \"UMLS:C2239938\"\n                                   \"UMLS:C1422375\"\n                                   \"UniProtKB:P55851\"\n                                   \"PR:Q9NQ87\"\n                                   \"UMLS:C1366449\"\n                                   \"ENSEMBL:ENSG00000143815\"\n                                   \"NCBIGene:23224\"\n                                   \"UniProtKB:Q13884\"\n                                   \"PR:Q9GZM7\"\n                                   \"NCBIGene:6641\"\n                                   \"ENSEMBL:ENSG00000006747\"\n                                   \"NCBIGene:3189\"\n                                   \"UMLS:C1417695\"\n                                   \"PR:Q96PP9\"\n                                   \"ENSEMBL:ENSG00000120217\"\n                                   \"HGNC:7014\"\n                                   \"UMLS:C1419063\"\n                                   \"NCBIGene:81578\"\n                                   \"HGNC:6551\"\n                                   \"NCBIGene:54843\"\n                                   \"UMLS:C1417014\"\n                                   \"UniProtKB:Q96DR4\"\n                                   \"HGNC:10545\"\n                                   \"NCBIGene:441250\"\n                                   \"UniProtKB:Q9P2Q2\"\n                                   \"ENSEMBL:ENSG00000007944\"\n                                   \"PR:Q96PP8\"\n                                   \"HGNC:11038\"\n                                   \"NCBIGene:160364\"\n                                   \"PR:Q9H910\"\n                                   \"UMLS:C1825519\"\n                                   \"PR:Q8N8N0\"\n                                   \"NCBIGene:221294\"\n                                   \"NCBIGene:3949\"\n                                   \"ENSEMBL:ENSG00000165895\"\n                                   \"ENSEMBL:ENSG00000112312\"\n                                   \"ENSEMBL:ENSG00000151617\"\n                                   \"ENSEMBL:ENSG00000134668\"\n                                   \"PR:Q6ZMY3\"\n                                   \"PR:P51816\"\n                                   \"UniProtKB:Q86SQ0\"\n                                   \"PR:P24043\"\n                                   \"PR:P62736\"\n                                   \"ENSEMBL:ENSG00000145604\"\n                                   \"PR:Q13233\"\n                                   \"ENSEMBL:ENSG00000118777\"\n                                   \"ENSEMBL:ENSG00000277149\"\n                                   \"UMLS:C1539087\"\n                                   \"NCBIGene:6383\"\n                                   \"NCBIGene:3955\"\n                                   \"UniProtKB:P50222\"\n                                   \"NCBIGene:2820\"\n                                   \"PR:Q9P2P6\"\n                                   \"ENSEMBL:ENSG00000116127\"\n                                   \"PR:Q9BUP0\"\n                                   \"UniProtKB:P16671\"\n                                   \"HGNC:4882\"\n                                   \"ENSEMBL:ENSG00000172322\"\n                                   \"UMLS:C1826479\"\n                                   \"HGNC:5004\"\n                                   \"ENSEMBL:ENSG00000141198\"\n                                   \"HGNC:4517\"\n                                   \"PR:P36383\"\n                                   \"PR:Q9P2Q2\"\n                                   \"UniProtKB:P35408\"\n                                   \"HGNC:26242\"\n                                   \"HGNC:550\"\n                                   \"HGNC:25901\"\n                                   \"UniProtKB:P53634\"\n                                   \"ENSEMBL:ENSG00000130164\"\n                                   \"ENSEMBL:ENSG00000187323\"\n                                   \"UMLS:C1332797\"\n                                   \"UMLS:C1419892\"\n                                   \"ENSEMBL:ENSG00000151474\"\n                                   \"UniProtKB:Q96PX9\"\n                                   \"ENSEMBL:ENSG00000170891\"\n                                   \"HGNC:14137\"\n                                   \"UniProtKB:P62736\"\n                                   \"UMLS:C1539745\"\n                                   \"UniProtKB:Q9H999\"\n                                   \"ENSEMBL:ENSG00000163909\"\n                                   \"UMLS:C1419064\"\n                                   \"HGNC:19030\"\n                                   \"NCBIGene:79646\"\n                                   \"NCBIGene:3953\"\n                                   \"UMLS:C1425966\"\n                                   \"UniProtKB:Q96PP9\"\n                                   \"PR:Q86X52\"\n                                   \"UniProtKB:Q8NC01\"\n                                   \"PR:P25101\"\n                                   \"PR:Q5HYW2\"\n                                   \"UMLS:C1427370\"\n                                   \"NCBIGene:55691\"\n                                   \"NCBIGene:83716\"\n                                   \"ENSEMBL:ENSG00000050628\"\n                                   \"HGNC:19168\"\n                                   \"HGNC:23228\"\n                                   \"HGNC:24435\"\n                                   \"PR:P21583\"\n                                   \"HGNC:10901\"\n                                   \"UniProtKB:Q5QGZ9\"\n                                   \"HGNC:33701\"\n                                   \"UniProtKB:Q8WU79\"\n                                   \"NCBIGene:51053\"\n                                   \"HGNC:33737\"\n                                   \"UniProtKB:Q9UJU2\"\n                                   \"HGNC:25742\"\n                                   \"HGNC:17635\"\n                                   \"UniProtKB:Q9NWQ8\"\n                                   \"UMLS:C1824630\"\n                                   \"HGNC:24125\"\n                                   \"UMLS:C1426119\"\n                                   \"PR:Q5EG05\"\n                                   \"ENSEMBL:ENSG00000118473\"\n                                   \"PR:P35249\"\n                                   \"PR:P15036\"\n                                   \"ENSEMBL:ENSG00000138795\"\n                                   \"NCBIGene:3149\"\n                                   \"ENSEMBL:LRG_991\"\n                                   \"NCBIGene:26033\"\n                                   \"ENSEMBL:LRG_781\"\n                                   \"UMLS:C1415644\"\n                                   \"ENSEMBL:ENSG00000178425\"\n                                   \"UMLS:C1418455\"\n                                   \"ENSEMBL:ENSG00000096746\"\n                                   \"PR:Q15052\"\n                                   \"HGNC:10577\"\n                                   \"UniProtKB:Q9HCH5\"\n                                   \"ENSEMBL:ENSG00000188393\"\n                                   \"PR:Q8TCU4\"\n                                   \"ENSEMBL:ENSG00000144218\"\n                                   \"HGNC:5043\"\n                                   \"PR:Q93045\"\n                                   \"ENSEMBL:ENSG00000181104\"\n                                   \"UniProtKB:P10114\"\n                                   \"ENSEMBL:ENSG00000107518\"\n                                   \"PR:Q9NRR1\"\n                                   \"UniProtKB:Q8NES3\"\n                                   \"NCBIGene:5352\"\n                                   \"HGNC:18745\"\n                                   \"UniProtKB:P48357\"\n                                   \"UMLS:C1538784\"\n                                   \"HGNC:26286\"\n                                   \"NCBIGene:90102\"\n                                   \"UniProtKB:P43146\"\n                                   \"PR:Q8WY64\"\n                                   \"ENSEMBL:LRG_283\"\n                                   \"NCBIGene:53918\"\n                                   \"UMLS:C1823488\"\n                                   \"UniProtKB:Q9HAR2\"\n                                   \"NCBIGene:9976\"\n                                   \"UMLS:C1428204\"\n                                   \"ENSEMBL:ENSG00000204397\"\n                                   \"HGNC:174\"\n                                   \"PR:P25116\"\n                                   \"PR:Q96DY7\"\n                                   \"HGNC:30776\"\n                                   \"ENSEMBL:ENSG00000221818\"\n                                   \"HGNC:3179\"\n                                   \"UniProtKB:Q9H0B8\"\n                                   \"NCBIGene:10982\"\n                                   \"UniProtKB:Q13023\"\n                                   \"PR:P31327\"\n                                   \"UMLS:C1428625\"\n                                   \"PR:Q8IZ41\"\n                                   \"ENSEMBL:LRG_336\"\n                                   \"UniProtKB:Q9NZF1\"\n                                   \"ENSEMBL:ENSG00000151320\"\n                                   \"NCBIGene:11009\"\n                                   \"UniProtKB:Q5HYW2\"\n                                   \"HGNC:6518\"\n                                   \"HGNC:9595\"\n                                   \"UniProtKB:P53794\"\n                                   \"NCBIGene:257019\"\n                                   \"ENSEMBL:ENSG00000145287\"\n                                   \"PR:P34741\"\n                                   \"UniProtKB:Q9NQ87\"\n                                   \"ENSEMBL:ENSG00000029993\"\n                                   \"ENSEMBL:ENSG00000076706\"\n                                   \"PR:Q8N4X5\"\n                                   \"ENSEMBL:ENSG00000069188\"\n                                   \"UMLS:C1417112\"\n                                   \"HGNC:10659\"\n                                   \"UniProtKB:Q13309\"\n                                   \"PR:Q70Z35\"\n                                   \"NCBIGene:4629\"\n                                   \"NCBIGene:4312\"\n                                   \"HGNC:25412\"\n                                   \"ENSEMBL:ENSG00000162892\"\n                                   \"NCBIGene:392490\"\n                                   \"UniProtKB:Q9NZQ7\"\n                                   \"NCBIGene:5911\"\n                                   \"NCBIGene:79739\"\n                                   \"ENSEMBL:ENSG00000152952\"\n                                   \"UniProtKB:Q6ZMY3\"\n                                   \"UniProtKB:P21583\"\n                                   \"PR:P82932\"\n                                   \"UniProtKB:Q01581\"\n                                   \"HGNC:23700\"\n                                   \"UniProtKB:Q8WXH0\"\n                                   \"UMLS:C1417411\"\n                                   \"ENSEMBL:ENSG00000276480\"\n                                   \"UniProtKB:Q9NPG1\"\n                                   \"HGNC:130\"\n                                   \"PR:A6NI28\"\n                                   \"PR:O15347\"\n                                   \"NCBIGene:80031\"\n                                   \"HGNC:6482\"\n                                   \"ENSEMBL:ENSG00000243927\"\n                                   \"ENSEMBL:ENSG00000176641\"\n                                   \"UniProtKB:Q6UVW9\"\n                                   \"HGNC:9596\"\n                                   \"HGNC:20974\"\n                                   \"UMLS:C1825085\"\n                                   \"UMLS:C1427805\"\n                                   \"HGNC:30043\"\n                                   \"HGNC:9972\"\n                                   \"UniProtKB:Q9UNQ0\"\n                                   \"PR:Q6ZT98\"\n                                   \"ENSEMBL:ENSG00000095015\"\n                                   \"PR:Q8NC01\"\n                                   \"ENSEMBL:ENSG00000112972\"\n                                   \"NCBIGene:3930\"\n                                   \"UMLS:C1415616\"\n                                   \"UMLS:C1426053\"\n                                   \"HGNC:1777\"\n                                   \"UMLS:C1417679\"\n                                   \"PR:Q5QGZ9\"\n                                   \"UniProtKB:Q8IZ41\"\n                                   \"UniProtKB:Q9H910\"\n                                   \"PR:Q92478\"\n                                   \"PR:Q9Y6G9\"\n                                   \"NCBIGene:79642\"\n                                   \"NCBIGene:85477\"\n                                   \"HGNC:8829\"\n                                   \"UniProtKB:Q9BX46\"\n                                   \"ENSEMBL:ENSG00000159433\"\n                                   \"HGNC:18058\"\n                                   \"UMLS:C1412318\"\n                                   \"UMLS:C1823542\"\n                                   \"ENSEMBL:ENSG00000152684\"\n                                   \"UMLS:C0812202\"\n                                   \"NCBIGene:80303\"\n                                   \"PR:Q58EX2\"\n                                   \"UniProtKB:O15164\"\n                                   \"NCBIGene:6307\"\n                                   \"ENSEMBL:ENSG00000129675\"\n                                   \"UniProtKB:Q9P2P6\"\n                                   \"PR:Q6NUM6\"\n                                   \"ENSEMBL:ENSG00000150048\"\n                                   \"PR:P35408\"\n                                   \"NCBIGene:9475\"\n                                   \"UMLS:C1425271\"\n                                   \"PR:Q9BX46\"\n                                   \"PR:Q5TFE4\"\n                                   \"HGNC:29399\"\n                                   \"HGNC:27013\"\n                                   \"HGNC:29573\"\n                                   \"UniProtKB:P82932\"\n                                   \"ENSEMBL:ENSG00000113594\"\n                                   \"UniProtKB:Q00534\"\n                                   \"UniProtKB:Q9BQI5\"\n                                   \"HGNC:2701\"\n                                   \"ENSEMBL:ENSG00000172167\"\n                                   \"PR:Q8IYL9\"\n                                   \"HGNC:11983\"\n                                   \"HGNC:19701\"\n                                   \"UniProtKB:Q13705\"\n                                   \"PR:Q13309\"\n                                   \"UniProtKB:O00469\"\n                                   \"PR:Q9H999\"\n                                   \"PR:P53794\"\n                                   \"PR:Q9NYI0\"\n                                   \"UniProtKB:Q8N8N0\"\n                                   \"UniProtKB:P42702\"\n                                   \"PR:Q13884\"\n                                   \"UMLS:C2239823\"\n                                   \"UniProtKB:P07948\"\n                                   \"NCBIGene:23243\"\n                                   \"ENSEMBL:ENSG00000069122\"\n                                   \"NCBIGene:27085\"\n                                   \"UMLS:C1708616\"\n                                   \"NCBIGene:1909\"\n                                   \"PR:Q86TI0\"\n                                   \"NCBIGene:2878\"\n                                   \"UMLS:C1420855\"\n                                   \"HGNC:428\"\n                                   \"UniProtKB:Q8IYL9\"\n                                   \"PR:Q8IZF2\"\n                                   \"NCBIGene:105374836\"\n                                   \"UniProtKB:Q15052\"\n                                   \"ENSEMBL:ENSG00000076641\"\n                                   \"PR:Q9HAR2\"\n                                   \"PR:O15123\"\n                                   \"UniProtKB:A6NI28\"\n                                   \"ENSEMBL:ENSG00000124749\"\n                                   \"PR:P01130\"\n                                   \"HGNC:5007\"\n                                   \"HGNC:19308\"\n                                   \"PR:O75496\"\n                                   \"NCBIGene:22856\"\n                                   \"UniProtKB:P51816\"\n                                   \"UMLS:C1539139\"\n                                   \"NCBIGene:2334\"\n                                   \"ENSEMBL:ENSG00000120137\"\n                                   \"UniProtKB:P31327\"\n                                   \"UniProtKB:Q92478\"\n                                   \"UMLS:C1427702\"\n                                   \"UMLS:C1538565\"\n                                   \"UMLS:C1366521\"\n                                   \"UniProtKB:Q58EX2\"\n                                   \"UMLS:C1366529\"\n                                   \"UniProtKB:Q15555\"\n                                   \"PR:Q9H892\"\n                                   \"PR:P48681\"\n                                   \"HGNC:3489\"\n                                   \"ENSEMBL:LRG_274\"\n                                   \"ENSEMBL:LRG_741\"\n                                   \"NCBIGene:114769\"\n                                   \"UniProtKB:A2A2Y4\"\n                                   \"HGNC:6473\"\n                                   \"ENSEMBL:ENSG00000144824\"\n                                   \"PR:O75674\"\n                                   \"UniProtKB:Q9NRR1\"\n                                   \"PR:Q5VV63\"\n                                   \"NCBIGene:3899\"\n                                   \"NCBIGene:3306\"\n                                   \"HGNC:24355\"\n                                   \"ENSEMBL:ENSG00000122779\"\n                                   \"UniProtKB:P34741\"\n                                   \"ENSEMBL:ENSG00000162654\"\n                                   \"NCBIGene:51316\"\n                                   \"HGNC:25248\"\n                                   \"HGNC:19365\"\n                                   \"UniProtKB:Q8WXI2\"\n                                   \"UniProtKB:Q6UVK1\"\n                                   \"ENSEMBL:ENSG00000172164\"\n                                   \"ENSEMBL:ENSG00000164211\"\n                                   \"NCBIGene:4223\"\n                                   \"ENSEMBL:ENSG00000106003\"\n                                   \"ENSEMBL:ENSG00000104290\"\n                                   \"HGNC:16770\"\n                                   \"NCBIGene:254251\"\n                                   \"ENSEMBL:ENSG00000149970\"\n                                   \"NCBIGene:10763\"\n                                   \"UniProtKB:Q96PP8\"\n                                   \"UniProtKB:O75674\"\n                                   \"PR:Q8WU79\"\n                                   \"NCBIGene:59\"\n                                   \"PR:O00469\"\n                                   \"ENSEMBL:ENSG00000103196\"\n                                   \"NCBIGene:6526\"\n                                   \"UniProtKB:P35749\"\n                                   \"UniProtKB:Q8TCU4\"\n                                   \"ENSEMBL:ENSG00000114739\"\n                                   \"NCBIGene:3176\"\n                                   \"NCBIGene:143872\"\n                                   \"UMLS:C1335831\"\n                                   \"PR:O75116\"\n                                   \"UniProtKB:P54652\"\n                                   \"NCBIGene:81831\"\n                                   \"UniProtKB:Q9HAK2\"\n                                   \"HGNC:21695\"\n                                   \"ENSEMBL:ENSG00000153404\"\n                                   \"NCBIGene:1021\"\n                                   \"NCBIGene:10052\"\n                                   \"UniProtKB:Q9Y6U3\"\n                                   \"PR:Q8IWC1\"\n                                   \"UMLS:C2239783\"\n                                   \"NCBIGene:10040\"\n                                   \"UniProtKB:Q12955\"\n                                   \"HGNC:19090\"\n                                   \"UniProtKB:Q14739\"\n                                   \"NCBIGene:3157\"\n                                   \"ENSEMBL:ENSG00000172159\"\n                                   \"NCBIGene:3908\"\n                                   \"ENSEMBL:ENSG00000204131\"\n                                   \"HGNC:19093\"\n                                   \"UMLS:C1825802\"\n                                   \"HGNC:15585\"\n                                   \"PR:P54652\"\n                                   \"ENSEMBL:ENSG00000173546\"\n                                   \"HGNC:14051\"\n                                   \"NCBIGene:8477\"\n                                   \"NCBIGene:1373\"\n                                   \"UniProtKB:Q13007\"\n                                   \"UniProtKB:P48681\"\n                                   \"NCBIGene:220441\"\n                                   \"NCBIGene:55824\"\n                                   \"HGNC:19254\"\n                                   \"ENSEMBL:ENSG00000142910\"\n                                   \"NCBIGene:5984\"\n                                   \"UMLS:C1412431\"\n                                   \"ENSEMBL:ENSG00000106511\"\n                                   \"PR:Q8NFY4\"\n                                   \"HGNC:3537\"\n                                   \"UniProtKB:Q93045\"\n                                   \"NCBIGene:93\"\n                                   \"UMLS:C1415251\"\n                                   \"UniProtKB:Q5VV63\"\n                                   \"ENSEMBL:ENSG00000116678\"\n                                   \"UniProtKB:O15084\"\n                                   \"UniProtKB:O75496\"\n                                   \"NCBIGene:5734\"\n                                   \"HGNC:29063\"\n                                   \"PR:P43146\"\n                                   \"UniProtKB:Q8IWC1\"\n                                   \"PR:Q16853\"\n                                   \"PR:P51826\"\n                                   \"PR:Q15555\"\n                                   \"HGNC:19895\"\n                                   \"NCBIGene:64129\"\n                                   \"PR:P10114\"\n                                   \"UMLS:C1825008\"\n                                   \"ENSEMBL:ENSG00000165105\"\n                                   \"PR:Q9HCH5\"\n                                   \"NCBIGene:54360\"\n                                   \"UniProtKB:O75116\"\n                                   \"PR:Q01581\"\n                                   \"HGNC:31713\"\n                                   \"ENSEMBL:ENSG00000131873\"\n                                   \"HGNC:17025\"\n                                   \"UniProtKB:Q86X52\"\n                                   \"PR:P42702\"\n                                   \"NCBIGene:27151\"\n                                   \"ENSEMBL:ENSG00000052802\"\n                                   \"PR:P07948\"\n                                   \"HGNC:6857\"\n                                   \"ENSEMBL:ENSG00000156011\"\n                                   \"PR:P43115\"\n                                   \"PR:Q8N3X6\"\n                                   \"HGNC:26811\"\n                                   \"NCBIGene:288\"\n                                   \"UniProtKB:Q15800\"\n                                   \"HGNC:20480\"\n                                   \"NCBIGene:8639\"\n                                   \"HGNC:26464\"\n                                   \"UniProtKB:P24043\"\n                                   \"HGNC:21539\"\n                                   \"HGNC:685\"\n                                   \"PR:Q13705\"\n                                   \"ENSEMBL:ENSG00000150636\"\n                                   \"HGNC:11768\"\n                                   \"NCBIGene:221662\"\n                                   \"ENSEMBL:ENSG00000206560\"\n                                   \"ENSEMBL:ENSG00000196569\"\n                                   \"ENSEMBL:ENSG00000105810\"\n                                   \"UMLS:C1539216\"\n                                   \"UMLS:C2681322\"\n                                   \"NCBIGene:29126\"\n                                   \"PR:O15164\"\n                                   \"UMLS:C1427216\"\n                                   \"UMLS:C1426964\"\n                                   \"NCBIGene:84251\"\n                                   \"HGNC:7756\"\n                                   \"PR:Q96P44\"\n                                   \"PR:Q8WXI2\"\n                                   \"PR:P53634\"\n                                   \"ENSEMBL:ENSG00000135218\"\n                                   \"UMLS:C1420202\"\n                                   \"UMLS:C1426193\"\n                                   \"UniProtKB:O43795\"\n                                   \"UniProtKB:Q9GZM7\"\n                                   \"HGNC:26545\"\n                                   \"NCBIGene:3977\"\n                                   \"PR:P31271\"\n                                   \"PR:Q8IZJ3\"\n                                   \"UniProtKB:Q16853\"\n                                   \"UniProtKB:P15036\"\n                                   \"ENSEMBL:ENSG00000115159\"\n                                   \"UniProtKB:P25101\"\n                                   \"UniProtKB:Q9BRX2\"\n                                   \"UMLS:C1428345\"\n                                   \"NCBIGene:4217\"\n                                   \"NCBIGene:340527\"\n                                   \"UMLS:C1539846\"\n                                   \"UniProtKB:P25116\"\n                                   \"ENSEMBL:ENSG00000180801\"\n                                   \"NCBIGene:79649\"\n                                   \"ENSEMBL:ENSG00000160111\"\n                                   \"UMLS:C1426155\"\n                                   \"PR:Q9NWQ8\"\n                                   \"HGNC:5028\"\n                                   \"HGNC:21556\"\n                                   \"HGNC:21155\"\n                                   \"ENSEMBL:ENSG00000186854\"\n                                   \"PR:Q96DR4\"\n                                   \"PR:Q00534\"\n                                   \"PR:Q9UJU2\"\n                                   \"UniProtKB:Q13233\"\n                                   \"ENSEMBL:ENSG00000137941\"\n                                   \"NCBIGene:158158\"\n                                   \"UniProtKB:O15123\"\n                                   \"UMLS:C1422809\"\n                                   \"UniProtKB:Q70Z35\"\n                                   \"ENSEMBL:ENSG00000149292\"\n                                   \"HGNC:14644\"\n                                   \"UniProtKB:Q86V40\"\n                                   \"NCBIGene:90861\"\n                                   \"UMLS:C1428878\"\n                                   \"PR:Q99683\"\n                                   \"PR:Q9NZF1\"\n                                   \"HGNC:6735\"\n                                   \"UniProtKB:Q6ZT98\"\n                                   \"ENSEMBL:ENSG00000151150\"\n                                   \"HGNC:24191\"\n                                   \"HGNC:4041\"\n                                   \"UniProtKB:P22352\"\n                                   \"UniProtKB:Q8IZF2\"\n                                   \"UMLS:C2828634\"\n                                   \"UMLS:C1417559\"\n                                   \"UniProtKB:P51826\"\n                                   \"UMLS:C1426006\"\n                                   \"PR:P22352\"\n                                   \"ENSEMBL:ENSG00000169439\"\n                                   \"HGNC:26295\"\n                                   \"ENSEMBL:ENSG00000107796\"\n                                   \"PR:Q15800\"\n                                   \"PR:P31942\"\n                                   \"UMLS:C1539106\"\n                                   \"NCBIGene:948\"\n                                   \"UniProtKB:P43304\"\n                                   \"ENSEMBL:ENSG00000049130\"\n                                   \"UMLS:C1428783\"\n                                   \"PR:P55851\"\n                                   \"PR:Q13023\"\n                                   \"NCBIGene:57519\"\n                                   \"NCBIGene:4214\"\n                                   \"PR:Q96PX9\"\n                                   \"PR:P16671\"\n                                   \"HGNC:5235\"\n                                   \"UMLS:C1419850\"\n                                   \"PR:O43795\"\n                                   \"NCBIGene:387836\"\n                                   \"UMLS:C1823280\"\n                                   \"HGNC:33908\"\n                                   \"UniProtKB:Q5FYB0\"\n                                   \"UniProtKB:Q96P44\"\n                                   \"NCBIGene:8805\"\n                                   \"ENSEMBL:LRG_409\"\n                                   \"UniProtKB:P61812\"\n                                   \"UniProtKB:P43115\"\n                                   \"ENSEMBL:ENSG00000110852\"\n                                   \"UMLS:C1415526\"\n                                   \"NCBIGene:7840\"\n                                   \"ENSEMBL:ENSG00000155966\"\n                                   \"UniProtKB:Q96DY7\"\n                                   \"NCBIGene:115361\"\n                                   \"UMLS:C1426511\"\n                                   \"HGNC:6891\"\n                                   \"UniProtKB:O15347\"\n                                   \"UniProtKB:Q9NYI0\"\n                                   \"NCBIGene:221395\"\n                                   \"ENSEMBL:ENSG00000211445\"\n                                   \"HGNC:494\"\n                                   \"UMLS:C1332089\"\n                                   \"UMLS:C1428531\"\n                                   \"UniProtKB:Q8IZJ3\"\n                                   \"UMLS:C1415277\"\n                                   \"ENSEMBL:ENSG00000154451\"\n                                   \"NCBIGene:9429\"\n                                   \"NCBIGene:9459\"\n                                   \"PR:Q9BRX2\"\n                                   \"UniProtKB:P31942\"\n                                   \"UMLS:C1419351\"\n                                   \"UniProtKB:Q13469\"\n                                   \"HGNC:29556\"\n                                   \"NCBIGene:64641\"\n                                   \"UMLS:C1428778\"\n                                   \"HGNC:74\"\n                                   \"UniProtKB:P35249\"\n                                   \"UniProtKB:Q6NUM6\"\n                                   \"ENSEMBL:ENSG00000084070\"\n                                   \"HGNC:7417\"\n                                   \"ENSEMBL:ENSG00000137872\"\n                                   \"ENSEMBL:ENSG00000046889\"\n                                   \"UMLS:C1420297\"\n                                   \"UMLS:C1423595\"\n                                   \"ENSEMBL:ENSG00000150540\"\n                                   \"UMLS:C1538736\"\n                                   \"NCBIGene:11075\"\n                                   \"PR:P50222\"\n                                   \"ENSEMBL:ENSG00000106031\"\n                                   \"PR:Q13007\"\n                                   \"HGNC:7596\"\n                                   \"HGNC:1663\"\n                                   \"HGNC:4555\"\n                                   \"NCBIGene:23284\"\n                                   \"NCBIGene:9472\"\n                                   \"ENSEMBL:ENSG00000196611\"\n                                   \"NCBIGene:84632\"\n                                   \"NCBIGene:64968\"\n                                   \"ENSEMBL:ENSG00000178177\"\n                                   \"NCBIGene:51176\"\n                                   \"NCBIGene:1630\"\n                                   \"PR:P35749\"\n                                   \"NCBIGene:115362\"\n                                   \"ENSEMBL:ENSG00000197442\"\n                                   \"NCBIGene:23216\"\n                                   \"ENSEMBL:ENSG00000140030\"\n                                   \"HGNC:25082\"\n                                   \"NCBIGene:4067\"\n                                   \"NCBIGene:2114\"\n                                   \"PR:Q5FYB0\"\n                                   \"HGNC:7569\"\n                                   \"HGNC:29024\"\n                                   \"HGNC:2466\"\n                                   \"ENSEMBL:ENSG00000125249\"\n                                   \"NCBIGene:51143\"\n                                   \"PR:Q12955\"\n                                   \"ENSEMBL:ENSG00000101096\"\n                                   \"ENSEMBL:ENSG00000133392\"\n                                   \"UniProtKB:Q9BUP0\"\n                                   \"ENSEMBL:ENSG00000092969\"\n                                   \"NCBIGene:54970\"\n                                   \"HGNC:5102\"\n                                   \"UniProtKB:Q8N3X6\"\n                                   \"UniProtKB:P03956\"\n                                   \"NCBIGene:5733\"\n                                   \"HGNC:7155\"\n                                   \"UMLS:C1415758\"\n                                   \"ENSEMBL:ENSG00000171522\"\n                                   \"PR:Q8NES3\"\n                                   \"HGNC:26338\"\n                                   \"PR:Q9HAK2\"\n                                   \"HGNC:17084\"\n                                   \"NCBIGene:54549\"\n                                   \"UniProtKB:Q68D86\"\n                                   \"NCBIGene:285\"\n                                   \"HGNC:19162\"\n                                   \"UMLS:C1419598\"\n                                   \"ENSEMBL:ENSG00000175567\"\n                                   \"PR:Q8NC67\"\n                                   \"NCBIGene:79839\"\n                                   \"UniProtKB:Q86TI0\"\n                                   \"HGNC:9861\"\n                                   \"ENSEMBL:ENSG00000182963\"\n                                   \"PR:Q9BQI5\"\n                                   \"HGNC:11812\"\n                                   \"HGNC:11346\"\n                                   \"ENSEMBL:ENSG00000021826\"\n                                   \"UniProtKB:P36383\"\n                                   \"UMLS:C1539088\"))\n\n(define hypotonia-syn (map car '((\"UMLS:C4049521\" \"Generalised atony\")\n                                 (\"UMLS:C0541791\" \"Atonia\")\n                                 (\"UMLS:C0541791\" \"Atonia\")\n                                 (\"UMLS:C0026827\" \"Poor muscle tone\")\n                                 (\"UMLS:C0026827\" \"Muscle hypotonia\")\n                                 (\"MEDDRA:10058909\" \"Muscle relaxant therapy\")\n                                 (\"UMLS:C0857516\" \"Floppy\")\n                                 (\"UMLS:C0857516\" \"Floppy\")\n                                 (\"UMLS:C1142135\" \"Muscle relaxant therapy\")\n                                 (\"HP:0001252\" \"Muscular hypotonia\")\n                                 (\"UMLS:C0541792\" \"Skeletal muscle atony\")\n                                 (\"UMLS:C0541792\" \"Skeletal muscle atony\")\n                                 (\"UMLS:C0859331\" \"Abdominal flaccidity\")\n                                 (\"UMLS:C0857388\" \"Non-depolarising relaxant\")\n                                 (\"MEDDRA:10021118\" \"Hypotonia\")\n                                 (\"UMLS:C0857388\" \"Non-depolarising relaxant\")\n                                 (\"NCIT:C87070\" \"Hypotonia\"))))\n\n;; This use of query:Known<-X->Known is analogous to this miniKanren query:\n;(run* (g gname drug->gene-pred d dname drug->disease-pred disease disease-name)\n;  (fresh (id1 id2 drug)\n;    (edge id1 d g)\n;    (edge id2 d disease)\n;    (cprop d \"category\" drug)\n;    (cprop d \"name\" dname)\n;    (cprop g \"name\" gname)\n;    (cprop disease \"name\" disease-name)\n;    (eprop id1 \"predicate\" drug->gene-pred)\n;    (eprop id2 \"predicate\" drug->disease-pred)\n;    (membero drug drug-categories)\n;    (membero g Hakon-CHAMP1-RNA-up-syns)\n;    (membero drug->gene-pred inhibit-preds)\n;    (membero disease hypotonia-syn)\n;    (membero drug->disease-pred inhibit-preds)))\n\n(newline)\n(define Hakon-drugs-hypotonia-RNA-up (query:Known<-X->Known Hakon-CHAMP1-RNA-up-syns inhibit-preds drug-categories inhibit-preds hypotonia-syn))\n\n(pretty-write `(Hakon-drugs-hypotonia-RNA-up ,(length Hakon-drugs-hypotonia-RNA-up)))\n(pretty-write Hakon-drugs-hypotonia-RNA-up)\n"
  },
  {
    "path": "contrib/medikanren2/Thi/example-two-hop-PMI-21-34-NEXMIF.rkt",
    "content": "#lang racket/base\n(require\n  \"query-low-level.rkt\"\n  racket/pretty)\n\n(define drug-categories '(\"biolink:ChemicalSubstance\"\n                          \"biolink:ClinicalIntervention\"\n                          \"biolink:ClinicalModifier\"\n                          \"biolink:Drug\"\n                          \"biolink:Treatment\"))\n\n(define gene-protein-cats '(\"biolink:Gene\"\n                            \"biolink:GeneFamily\"\n                            \"biolink:GeneProduct\"\n                            \"biolink:GenomicEntity\"\n                            \"biolink:MolecularEntity\"\n                            \"biolink:Protein\"))\n\n(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:negatively_regulates\"\n                        \"biolink:negatively_regulates,_entity_to_entity\"\n                        \"biolink:negatively_regulates,_process_to_process\"\n                        \"biolink:treats\"))\n\n(define NEXMIF-syns '(\"HGNC:29433\"\n                      \"UniProtKB:Q5QGS0\"\n                      \"PR:Q5QGS0\"\n                      \"NCBIGene:340533\"\n                      \"ENSEMBL:ENSG00000050030\"))\n\n;; Reference query:\n;(define NEXMIF-drugs-2hop\n;  (time (run* (d p1 g1 p2 g2)\n;          (fresh (id1 id2 drug gene)\n;            (edge id1 d g1)\n;            (edge id2 g1 g2)\n;            (cprop d \"category\" drug)\n;            (cprop g1 \"category\" gene)\n;            (cprop g2 \"category\" gene)\n;            (eprop id1 \"predicate\" p1)\n;            (eprop id2 \"predicate\" p2)\n;            (membero drug drug-categories)\n;            (membero gene gene-protein-cats)\n;            (membero g2 NEXMIF-syns)\n;            (membero p1 inhibit-preds)\n;            (membero p2 inhibit-preds)))))\n\n(newline)\n(define NEXMIF-drugs-2hop (query:X->Y->Known\n                            drug-categories\n                            inhibit-preds\n                            gene-protein-cats\n                            inhibit-preds\n                            NEXMIF-syns))\n\n(pretty-write `(NEXMIF-drugs-2hop count: ,(length NEXMIF-drugs-2hop)))\n(pretty-write NEXMIF-drugs-2hop)\n"
  },
  {
    "path": "contrib/medikanren2/Thi/query-low-level.rkt",
    "content": "#lang racket/base\n(provide\n  query:Known->Known\n  query:Known->X\n  query:X->Known\n  query:Known<-X->Known\n  query:X->Y->Known\n  query:Prefix->Prefix\n  query:Concept\n  edge-properties\n  edge-property-values\n  concept-properties\n  concept-property-values\n  )\n(require\n  \"../../../medikanren2/dbk/dbk/data.rkt\"\n  \"../../../medikanren2/dbk/dbk/enumerator.rkt\"\n  \"../../../medikanren2/dbk/dbk/stream.rkt\"\n  racket/match\n  racket/runtime-path\n  racket/set\n  racket/string\n  )\n\n;; query:Known->X is analogous to a miniKanren-style query with this shape:\n; (run* (s sname p o oname)\n;   (fresh (id category)\n;     (edge id s o)\n;     (cprop o \"category\" category)\n;     (cprop s \"name\" sname)\n;     (cprop o \"name\" oname)\n;     (eprop id \"predicate\" p)\n;     (membero s subject-curies)\n;     (membero p predicates)\n;     (membero category object-categories)))\n\n(define (query:Known->X curies.K predicates.K->X categories.X)\n  (define (query yield)\n    (define ekey.predicate.id         (dict-select dict.string=>id \"predicate\"))\n    (define ckey.category.id          (dict-select dict.string=>id \"category\"))\n    (define ckey.name.id              (dict-select dict.string=>id \"name\"))\n    (define dict.curies.K             (strings->dict curies.K))\n    (define dict.predicates.K->X      (strings->dict predicates.K->X))\n    (define dict.categories.X         (strings->dict categories.X))\n    (define dict.eprop.eid.predicate  (dict-select dict.eprop.eid.value.key   ekey.predicate.id))\n    (define dict.cprop.curie.category (dict-select dict.cprop.curie.value.key ckey.category.id))\n    ((merge-join dict.curies.K dict.edge.object.eid.subject)\n     (lambda (id.K __ dict.edge.X.eid)\n       (define id.name.K ((dict-select (dict-select dict.cprop.value.key.curie id.K) ckey.name.id) 'min))\n       (define name.K    (dict-select dict.id=>string id.name.K))\n       (define K         (dict-select dict.id=>string id.K))\n       ((merge-join dict.predicates.K->X dict.eprop.eid.predicate)\n        (lambda (id.predicate.K->X __ dict.eprop.K->X)\n          (define predicate.K->X (dict-select dict.id=>string id.predicate.K->X))\n          ((merge-join dict.eprop.K->X dict.edge.X.eid)\n           (lambda (eid __ dict.edge.X)\n             (define props (edge-id->properties eid))\n             ((merge-join dict.categories.X dict.cprop.curie.category)\n              (lambda (__ ___ dict.cprop.X)\n                ((dict-join-ordered\n                   (lambda (yield)\n                     ((merge-join dict.cprop.X dict.edge.X)\n                      (lambda (id.X __ ___)\n                        (yield id.X '()))))\n                   dict.cprop.value.key.curie)\n                 (lambda (id.X __ dict.cprop.value.key)\n                   (define id.name.X ((dict-select dict.cprop.value.key ckey.name.id) 'min))\n                   (define name.X    (dict-select dict.id=>string id.name.X))\n                   (define X         (dict-select dict.id=>string id.X))\n                   (yield (list* K name.K predicate.K->X X name.X props)))))))))))))\n  (time (enumerator->rlist query)))\n\n;; query:X->Known is analogous to a miniKanren-style query with this shape:\n; (run* (s sname p o oname)\n;   (fresh (id category)\n;     (edge id s o)\n;     (cprop s \"category\" category)\n;     (cprop s \"name\" sname)\n;     (cprop o \"name\" oname)\n;     (eprop id \"predicate\" p)\n;     (membero o object-curies)\n;     (membero p predicates)\n;     (membero category subject-categories)))\n\n(define (query:X->Known categories.X predicates.X->K curies.K)\n  (define (query yield)\n    (define ekey.predicate.id         (dict-select dict.string=>id \"predicate\"))\n    (define ckey.category.id          (dict-select dict.string=>id \"category\"))\n    (define ckey.name.id              (dict-select dict.string=>id \"name\"))\n    (define dict.categories.X         (strings->dict categories.X))\n    (define dict.predicates.X->K      (strings->dict predicates.X->K))\n    (define dict.curies.K             (strings->dict curies.K))\n    (define dict.eprop.eid.predicate  (dict-select dict.eprop.eid.value.key   ekey.predicate.id))\n    (define dict.cprop.curie.category (dict-select dict.cprop.curie.value.key ckey.category.id))\n    ((merge-join dict.curies.K dict.edge.subject.eid.object)\n     (lambda (id.K __ dict.edge.X.eid)\n       (define id.name.K ((dict-select (dict-select dict.cprop.value.key.curie id.K) ckey.name.id) 'min))\n       (define name.K    (dict-select dict.id=>string id.name.K))\n       (define K         (dict-select dict.id=>string id.K))\n       ((merge-join dict.predicates.X->K dict.eprop.eid.predicate)\n        (lambda (id.predicate.X->K __ dict.eprop.X->K)\n          (define predicate.X->K (dict-select dict.id=>string id.predicate.X->K))\n          ((merge-join dict.eprop.X->K dict.edge.X.eid)\n           (lambda (eid __ dict.edge.X)\n             (define props (edge-id->properties eid))\n             ((merge-join dict.categories.X dict.cprop.curie.category)\n              (lambda (__ ___ dict.cprop.X)\n                ((dict-join-ordered\n                   (lambda (yield)\n                     ((merge-join dict.cprop.X dict.edge.X)\n                      (lambda (id.X __ ___)\n                        (yield id.X '()))))\n                   dict.cprop.value.key.curie)\n                 (lambda (id.X __ dict.cprop.value.key)\n                   (define id.name.X ((dict-select dict.cprop.value.key ckey.name.id) 'min))\n                   (define name.X    (dict-select dict.id=>string id.name.X))\n                   (define X         (dict-select dict.id=>string id.X))\n                   (yield (list* X name.X predicate.X->K K name.K props)))))))))))))\n  (time (enumerator->rlist query)))\n\n;; query:Known<-X->Known is analogous to a miniKanren-style query with this shape:\n;(run* (K1 name.K1 predicates.K1<-X X name.X predicates.X->K1 K2 name.K2)\n;  (fresh (id1 id2 category.X)\n;    (edge id1 X K1)\n;    (edge id2 X K2)\n;    (cprop X   \"category\" category.X)\n;    (cprop X   \"name\" name.X)\n;    (cprop K1  \"name\" name.K1)\n;    (cprop K2  \"name\" name.K2)\n;    (eprop id1 \"predicate\" K1<-X)\n;    (eprop id2 \"predicate\" X->K2)\n;    (membero category.X categories.X)\n;    (membero K1         curies.K1)\n;    (membero K1<-X      predicates.K1<-X)\n;    (membero K2         curies.K2)\n;    (membero X->K2      predicates.X->K2)))\n\n(define (query:Known<-X->Known curies.K1 predicates.K1<-X categories.X predicates.X->K2 curies.K2)\n  (define (candidates->dict candidates)\n    (define ordered (sort candidates (lambda (a b) (stringvector groups) caar))\n  (define candidates.X->K1 (query:X->Known categories.X predicates.K1<-X curies.K1))\n  (define candidates.X->K2 (query:X->Known categories.X predicates.X->K2 curies.K2))\n  (define dict.X->K1.X     (candidates->dict candidates.X->K1))\n  (define dict.X->K2.X     (candidates->dict candidates.X->K2))\n  (time (enumerator->list\n          (lambda (yield)\n            ((merge-join dict.X->K1.X dict.X->K2.X)\n             (lambda (X XK1s XK2s)\n               (for-each (lambda (XK1)\n                           (match-define (list* _ name.X X->K1 K1 name.K1 props1) XK1)\n                           (for-each (lambda (XK2)\n                                       (match-define (list* _ _ X->K2 K2 name.K2 props2) XK2)\n                                       (yield (append (list K1 name.K1 X->K1 X name.X X->K2 K2 name.K2)\n                                                      (append props1 props2))))\n                                     XK2s))\n                         XK1s)))))))\n\n(define (query:X->Y->Known categories.X predicates.X->Y categories.Y predicates.Y->K curies.K)\n  (define (results->dict key results)\n    (define ordered (sort results (lambda (a b) (stringvector groups) (lambda (x) (key (car x)))))\n  (define results.Y->K (query:X->Known categories.Y predicates.Y->K curies.K))\n  (define dict.Y->K.Y  (results->dict car results.Y->K))\n  (define curies.Y     (enumerator->list (dict.Y->K.Y 'enumerator)))\n  (define results.X->Y (query:X->Known categories.X predicates.X->Y curies.Y))\n  (define dict.X->Y.Y  (results->dict cadddr results.X->Y))\n  (time (enumerator->list\n          (lambda (yield)\n            ((merge-join dict.X->Y.Y dict.Y->K.Y)\n             (lambda (Y XYs YKs)\n               (for-each (lambda (XY)\n                           (match-define (list* X name.X X->Y _ name.Y props.X->Y) XY)\n                           (for-each (lambda (YK)\n                                       (match-define (list* _ _ Y->K K name.K props.Y->K) YK)\n                                       (yield (append (list X name.X X->Y Y name.Y Y->K K name.K)\n                                                      (append props.X->Y props.Y->K))))\n                                     YKs))\n                         XYs)))))))\n\n(define (query:Known->Known curies.S predicates.S->O curies.O)\n  (define dict.curies.S (strings->dict curies.S))\n  (define dict.curies.O (strings->dict curies.O))\n  (query:dict.Known->dict.Known dict.curies.S predicates.S->O dict.curies.O))\n\n(define (query:Prefix->Prefix prefix.S predicates.S->O prefix.O)\n  (define dict.curies.S (dict-string-prefix prefix.S))\n  (define dict.curies.O (dict-string-prefix prefix.O))\n  (query:dict.Known->dict.Known dict.curies.S predicates.S->O dict.curies.O))\n\n(define (query:dict.Known->dict.Known dict.curies.S predicates.S->O dict.curies.O)\n  (define (query yield)\n    (define ekey.predicate.id         (dict-select dict.string=>id \"predicate\"))\n    (define ckey.category.id          (dict-select dict.string=>id \"category\"))\n    (define ckey.name.id              (dict-select dict.string=>id \"name\"))\n    (define dict.predicates.S->O      (strings->dict predicates.S->O))\n    (define dict.eprop.eid.predicate  (dict-select dict.eprop.eid.value.key   ekey.predicate.id))\n    (define dict.cprop.curie.category (dict-select dict.cprop.curie.value.key ckey.category.id))\n    ((merge-join dict.curies.S dict.edge.object.eid.subject)\n     (lambda (id.S __ dict.edge.O.eid)\n       (define id.name.S ((dict-select (dict-select dict.cprop.value.key.curie id.S) ckey.name.id) 'min))\n       (define name.S    (dict-select dict.id=>string id.name.S))\n       (define S         (dict-select dict.id=>string id.S))\n       ((merge-join dict.predicates.S->O dict.eprop.eid.predicate)\n        (lambda (id.predicate.S->O __ dict.eprop.S->O)\n          (define predicate.S->O (dict-select dict.id=>string id.predicate.S->O))\n          ((merge-join dict.eprop.S->O dict.edge.O.eid)\n           (lambda (eid __ dict.edge.O)\n             (define props (edge-id->properties eid))\n             ((merge-join dict.curies.O dict.edge.O)\n              (lambda (id.O __ ___)\n                (define id.name.O ((dict-select (dict-select dict.cprop.value.key.curie id.O) ckey.name.id) 'min))\n                (define name.O    (dict-select dict.id=>string id.name.O))\n                (define O         (dict-select dict.id=>string id.O))\n                (yield (list* S name.S predicate.S->O O name.O props)))))))))))\n  (time (enumerator->rlist query)))\n\n(define (query:Concept curies)\n  (define (query yield)\n    (define dict.curie (strings->dict curies))\n    ((merge-join dict.curie dict.cprop.value.key.curie)\n     (lambda (id.curie _ dict.cprop.value.key)\n       (define curie (dict-select dict.id=>string id.curie))\n       ((dict.cprop.value.key 'enumerator/2)\n        (lambda (id.key dict.cprop.value)\n          (define key   (dict-select dict.id=>string id.key))\n          (define value (dict-select dict.id=>string (dict.cprop.value 'min)))\n          (yield (list curie key value)))))))\n  (time (enumerator->list query)))\n\n(define (concept-properties)          (enumerator->list\n                                        (lambda (yield)\n                                          ((merge-join dict.cprop.curie.value.key dict.id=>string)\n                                           (lambda (_ __ key)\n                                             (yield key))))))\n(define (edge-properties)             (enumerator->list\n                                        (lambda (yield)\n                                          ((merge-join dict.eprop.eid.value.key dict.id=>string)\n                                           (lambda (_ __ key)\n                                             (yield key))))))\n(define (concept-property-values key) (enumerator->list\n                                        (lambda (yield)\n                                          ((merge-join (dict-select dict.cprop.curie.value.key (dict-select dict.string=>id key))\n                                                       dict.id=>string)\n                                           (lambda (_ __ value) (yield value))))))\n(define (edge-property-values    key) (enumerator->list\n                                        (lambda (yield)\n                                          ((merge-join (dict-select dict.eprop.eid.value.key   (dict-select dict.string=>id key))\n                                                       dict.id=>string)\n                                           (lambda (_ __ value) (yield value))))))\n\n;;;;;;;;;;;;;;;\n;; Utilities ;;\n;;;;;;;;;;;;;;;\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n;; TODO: build small in-memory relations more easily\n(define (strings->dict strs)\n  (define vec.strs  (list->vector (sort (set->list (list->set strs)) stringvector\n                      (lambda (yield)\n                        ((merge-join dict.strs dict.string=>id)\n                         (lambda (__ ___ id) (yield id))))))\n  (dict:ordered (column:vector vec.ids) (column:const '()) 0 (vector-length vec.ids)))\n\n(define (dict-string-prefix prefix)\n  (define d.string=>id\n    ((dict.string=>id 'after (lambda (str) (stringid 'top))\n  (define end   (+ start (d.string=>id 'count)))\n  ((dict.id=>string '>= start) '< end))\n\n(define (edge-id->properties eid)\n  (define (get id default)\n    (eprops 'ref id\n            (lambda (dict.value) (dict-select dict.id=>string (dict.value 'min)))\n            (lambda ()           default)))\n  (define eprops       (dict-select dict.eprop.value.key.eid eid))\n  (define negated      (get id.negated \"\"))\n  (define provided-by  (get id.provided-by \"\"))\n  (define publications (get id.publications \"\"))\n  (list negated provided-by publications))\n\n(define-runtime-path path.here \".\")\n(define db      (database (path->string (build-path path.here \"rtx-kg2_20210204.db\"))))\n(define r.cprop (database-relation db '(rtx-kg2 cprop)))\n(define r.edge  (database-relation db '(rtx-kg2 edge)))\n(define r.eprop (database-relation db '(rtx-kg2 eprop)))\n\n(define domain-dicts                 (relation-domain-dicts r.cprop))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define dict.edge.object.eid.subject (relation-index-dict r.edge  '(subject eid object)))\n(define dict.edge.subject.eid.object (relation-index-dict r.edge  '(object eid subject)))\n(define dict.eprop.eid.value.key     (relation-index-dict r.eprop '(key value eid)))\n(define dict.eprop.value.key.eid     (relation-index-dict r.eprop '(eid key value)))\n(define dict.cprop.curie.value.key   (relation-index-dict r.cprop '(key value curie)))\n(define dict.cprop.value.key.curie   (relation-index-dict r.cprop '(curie key value)))\n\n(define id.negated      (dict-select dict.string=>id \"negated\"))\n(define id.provided-by  (dict-select dict.string=>id \"provided_by\"))\n(define id.publications (dict-select dict.string=>id \"publications\"))\n"
  },
  {
    "path": "contrib/medikanren2/Thi/synonym-low-level.rkt",
    "content": "#lang racket/base\n(provide curie->synonyms curies->synonyms)\n(require\n  \"../../../medikanren2/dbk/dbk/data.rkt\"\n  \"../../../medikanren2/dbk/dbk/enumerator.rkt\"\n  racket/runtime-path\n  racket/set)\n\n(define (curie->synonyms curie) (curies->synonyms (list curie)))\n\n(define (curies->synonyms curies)\n  (define (ids->dict ids)\n    (define vec.ids (list->vector (sort (set->list ids) <)))\n    (dict:ordered (column:vector vec.ids) (column:const '()) 0 (vector-length vec.ids)))\n  (define (step new)\n    (define (step/dict dict.edge.Y.X) (enumerator->rlist\n                                        (lambda (yield)\n                                          ((merge-join dict.new dict.edge.Y.X)\n                                           (lambda (id.curie _ dict.edge.Y)\n                                             ((dict.edge.Y 'enumerator) yield))))))\n    (define dict.new (ids->dict new))\n    (list->set (append (step/dict dict.edge.object.subject)\n                       (step/dict dict.edge.subject.object))))\n  (define ids.final (set-fixed-point (list->set (strings->ids curies)) step))\n  (enumerator->list\n    (lambda (yield)\n      ((merge-join (ids->dict ids.final) dict.id=>string)\n       (lambda (_ __ curie) (yield curie))))))\n\n;;;;;;;;;;;;;;;\n;; Utilities ;;\n;;;;;;;;;;;;;;;\n(define (set-fixed-point xs.initial step)\n  (let loop ((current (set))\n             (next    xs.initial))\n    (let ((new (set-subtract next current)))\n      (if (set-empty? new)\n        current\n        (loop (set-union current new)\n              (step      new))))))\n\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n;; TODO: build small in-memory relations more easily\n(define (strings->dict strs)\n  (define vec.strs  (list->vector (sort (set->list (list->set strs)) stringvector\n                      (lambda (yield)\n                        ((merge-join dict.strs dict.string=>id)\n                         (lambda (__ ___ id) (yield id))))))\n  (dict:ordered (column:vector vec.ids) (column:const '()) 0 (vector-length vec.ids)))\n\n(define (strings->ids strs) (enumerator->rlist ((strings->dict strs) 'enumerator)))\n\n(define-runtime-path path.here \".\")\n(define db     (database (path->string (build-path path.here \"kgx-synonym.db\"))))\n(define r.edge (database-relation db '(kgx-synonym edge)))\n\n(define domain-dicts                 (relation-domain-dicts r.edge))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define dict.edge.object.subject (relation-index-dict r.edge '(subject object)))\n(define dict.edge.subject.object (relation-index-dict r.edge '(object subject)))\n"
  },
  {
    "path": "contrib/medikanren2/draw.rkt",
    "content": "#lang racket/base\n;; may require manually installing graphviz, cairo, libjpeg\n\n(require \"../../medikanren2/common.rkt\" \n         racket/string racket/draw racket/format racket/list\n         graph\n         (prefix-in pict: pict)\n         (prefix-in graphviz: graphviz)\n         (prefix-in racket: racket)\n         )\n\n(define-relation (subclass-of a b)\n  (triple a \"biolink:subclass_of\" b))\n\n(define (draw-edges edges path)\n  (racket:send\n   (pict:pict->bitmap\n    (graphviz:dot->pict\n     (graphviz (directed-graph edges))))\n   save-file path 'png))\n\n(define (remove-prefix prefix str)\n  (string-replace str prefix \"\"))\n\n(define (remove-biolink-prefixes edges)\n  (let ((rem (lambda (e) (remove-prefix \"biolink:\" e))))\n    (map (lambda (pair)\n           (map rem pair))\n         edges)))\n\n(define (subtrees all-classes top-level-classes)\n  (filter (compose not null?)\n          (map (lambda (class)\n                 (cons class\n                       (let loop ((class class))\n                         (let* ((new-edges (filter (lambda (edge) (equal? (cadr edge) class))\n                                                   all-classes))\n                                (new-nodes (map car new-edges)))\n                           (append new-edges (apply append (map loop new-nodes)))))))\n               (map car top-level-classes))))\n\n(define (draw-subtrees subtrees)\n  (map (lambda (subtree)\n         (let ((label (car subtree))\n               (graph (cdr subtree)))\n           (when (not (null? subtree))\n             (draw-edges graph (~a \"drawings/\" label \".png\")))))\n       subtrees))\n\n(define all-ontology-classes\n  (remove-biolink-prefixes\n   (run* (s o)\n     (triple s \"biolink:subclass_of\" o) \n     (is-a s \"biolink:OntologyClass\")\n     (is-a o \"biolink:OntologyClass\")\n     (:== #t (s) (char-upper-case? (car (string->list (remove-prefix \"biolink:\" s)))))\n     (:== #t (o) (char-upper-case? (car (string->list (remove-prefix \"biolink:\" o)))))\n)))\n\n(define top-level-ontology-classes\n  (cons '(\"Annotation\")\n        (remove-biolink-prefixes\n         (run* (s) (subclass-of s \"biolink:Entity\")))))\n\n;; very strange -- let's hope this changes!\n(define all-predicates\n  (remove-biolink-prefixes\n   (run* (s o)\n     (triple s \"biolink:subclass_of\" o) \n     (is-a s \"biolink:OntologyClass\")\n     (is-a o \"biolink:OntologyClass\")\n     (:== #t (s) (char-lower-case? (car (string->list (remove-prefix \"biolink:\" s)))))\n     (:== #t (o) (char-lower-case? (car (string->list (remove-prefix \"biolink:\" o)))))\n)))\n\n(define top-level-predicates\n  (remove-biolink-prefixes\n   (run* (s) (subclass-of s \"biolink:related_to\"))))\n\n(draw-subtrees (subtrees all-ontology-classes top-level-ontology-classes))\n(draw-subtrees (subtrees all-predicates '((\"related_to\"))))\n(draw-subtrees (subtrees all-predicates top-level-predicates))\n"
  },
  {
    "path": "contrib/medikanren2/gregr/benchmark-nausea.rkt",
    "content": "#lang racket/base\n(require\n  \"../../../medikanren2/dbk/dbk.rkt\"\n  \"../../../medikanren2/dbk/dbk/data.rkt\"\n  \"../../../medikanren2/dbk/dbk/enumerator.rkt\"\n  racket/pretty\n  racket/runtime-path\n  racket/set)\n\n(define-relation/table (cprop curie key value)   'path \"../../../medikanren2/data/rtx2/20210204/cprop\")\n(define-relation/table (edge  id subject object) 'path \"../../../medikanren2/data/rtx2/20210204/edge\")\n(define-relation/table (eprop id key value)      'path \"../../../medikanren2/data/rtx2/20210204/eprop\")\n\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n(define-runtime-path path.here \".\")\n\n(define db      (database (path->string (build-path path.here \"rtx-kg2_20210204.db\"))))\n(define r.cprop (database-relation db '(rtx-kg2 cprop)))\n(define r.edge  (database-relation db '(rtx-kg2 edge)))\n(define r.eprop (database-relation db '(rtx-kg2 eprop)))\n\n(define dict.eprop.eid.value.key     (relation-index-dict r.eprop '(key value eid)))\n(define dict.edge.subject.eid.object (relation-index-dict r.edge  '(object eid subject)))\n(define dict.cprop.value.key.curie   (relation-index-dict r.cprop '(curie key value)))\n(define domain-dicts                 (relation-domain-dicts r.cprop))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define (string->id str) (dict-select dict.string=>id str))\n(define (id->string id)  (dict-select dict.id=>string id))\n\n(define (benchmark-find-treatments curie.target)\n  (define (run-query yield)\n    (define curie.nausea.id       (string->id curie.target))\n    (define ekey.predicate.id     (string->id \"predicate\"))\n    (define evalue.treats.id      (string->id \"biolink:treats\"))\n    (define ckey.category.id      (string->id \"category\"))\n    (define ckey.name.id          (string->id \"name\"))\n    (define dict.eprop.eid.value  (dict-select dict.eprop.eid.value.key     ekey.predicate.id))\n    (define dict.eprop.eid        (dict-select dict.eprop.eid.value         evalue.treats.id))\n    (define dict.edge.subject.eid (dict-select dict.edge.subject.eid.object curie.nausea.id))\n    ((merge-join dict.eprop.eid dict.edge.subject.eid)\n     (lambda (eid __ dict.edge.subject)\n       ((merge-join dict.edge.subject dict.cprop.value.key.curie)\n        (lambda (subject.id __ dict.cprop.value.key)\n          (define subject             (id->string subject.id))\n          (define dict.cprop.category (dict-select dict.cprop.value.key ckey.category.id))\n          (define dict.cprop.name     (dict-select dict.cprop.value.key ckey.name.id))\n          ((merge-join dict.cprop.category dict.id=>string)\n           (lambda (category.id __ category)\n             ((merge-join dict.cprop.name dict.id=>string)\n              (lambda (name.id __ name)\n                (yield (list subject category name)))))))))))\n  ;; Some nausea timings\n  ;; cpu time: 1485 real time: 1610 gc time: 19\n  ;; cpu time: 1539 real time: 1557 gc time: 15\n  ;; cpu time: 1538 real time: 1556 gc time: 24\n  (define results.old (time (run* (s cat name)\n                              (fresh (eid)\n                                (edge eid s curie.target)\n                                (cprop s \"category\" cat)\n                                (cprop s \"name\" name)\n                                (eprop eid \"predicate\" \"biolink:treats\")))))\n  ;; Some nausea timings\n  ;; cpu time: 27 real time: 27 gc time: 0\n  ;; cpu time: 31 real time: 31 gc time: 0\n  ;; cpu time: 30 real time: 31 gc time: 0\n  (define results.new (time (enumerator->rlist run-query)))\n  ;; 149 results\n  (pretty-write `(old:    ,(length results.old) ,results.old))\n  (pretty-write `(new:    ,(length results.new) ,results.new))\n  (pretty-write `(equal?: ,(equal? (list->set results.old) (list->set results.new)))))\n\n(define curie.nausea \"UMLS:C0520909\")\n(benchmark-find-treatments curie.nausea)\n"
  },
  {
    "path": "contrib/medikanren2/gregr/hao-demo.rkt",
    "content": "#lang racket/base\n(require \"dbk.rkt\")\n\n;;(define-relation (P x)\n;  ;(membero x '(1 2 3 4 5 6 7 8 9 10)))\n;;(define-relation (Q x)\n;  ;(membero x '(1 3 5 6 8 10)))\n;\n;(define-relation (P x)\n;  (conde ((== x 1))\n;         ((== x 2))\n;         ((== x 3))\n;         ((== x 4))\n;         ((== x 5))\n;         ((== x 6))\n;         ((== x 7))\n;         ((== x 8))\n;         ((== x 9))\n;         ((== x 10))))\n;\n;(define-relation (Q x)\n;  (conde ((== x 1))\n;         ((== x 3))\n;         ((== x 5))\n;         ((== x 6))\n;         ((== x 8))\n;         ((== x 10))))\n;\n;(define (frequency P Q)\n;  (caar (run* (p)\n;          (:== p ()\n;               (/ (length (run* (x) (P x) (Q x)))\n;                  (length (run* (x) (P x))))))))\n;\n;;(define (exists P Q) (fresh (x) (P x) (Q x))\n;\n;;(define (occurs p P Q)\n;  ;(:== #t () (<= p (frequency P Q))))\n;\n;(frequency P Q)\n;\n;(run* (_) (occurs .4 P Q))\n;\n;(run* (_) (occurs .8 P Q))\n;\n;\n;(define (forall P Q)\n;  (:== #t () (= (length (run* (x) (P x) (Q x)))\n;                (length (run* (x) (P x))))))\n;\n;(run* (_) (forall P Q))\n;\n;(run* (_) (forall Q P))\n;\n;\n;;; exists\n;(run* (x) (P x) (Q x))\n;\n;(run* (p y z)\n;  (fresh (y) (== z y))\n;  ;(== y z)\n;  (:== p ()\n;       (/ (length (run* (x) (P x) (Q x)))\n;          (length (run* (x) (P x))))))\n;\n;(define-relation (R x y)\n;  (conde ((== x 1)  (== y 111))\n;         ((== x 2)  (== y 111))\n;         ((== x 3)  (== y 111))\n;         ((== x 4)  (== y 111))\n;         ((== x 5)  (== y 111))\n;         ((== x 6)  (== y 111))\n;         ((== x 7)  (== y 111))\n;         ((== x 8)  (== y 111))\n;         ((== x 9)  (== y 111))\n;         ((== x 10) (== y 111))))\n;\n;;; forall x . (P x) -> (exists y . (R x y))\n;(run* (_)\n;  (:== #t () (= (length (run* (x) (P x)\n;                          (fresh (y) (R x y))))\n;                (length (run* (x) (P x))))))\n;\n;;; exists y . (forall x . (P x) -> (R x y))\n;(run* (y)\n;  (fresh (x) (R x y))\n;  (:== #t (y) (= (length (run* (x) (P x) (R x y)))\n;                 (length (run* (x) (P x))))))\n\n(define-relation (membero x xs)\n  (fresh (y ys)\n    (== `(,y . ,ys) xs)\n    (conde ((==  x y))\n           ((membero x ys)))))\n\n(define-syntax exists\n  (syntax-rules ()\n    ((_ y domain body ...) (fresh (y) domain body ...))))\n\n(define-syntax occurs\n  (syntax-rules ()\n    ((_ p y domain body ...)\n     (let ((P (lambda (y) domain))\n           (Q (lambda (y) body ...)))\n       (:== #t () (<= p (frequency P Q)))))))\n\n(define-syntax where\n  (syntax-rules ()\n    ((_ (deps ...) body ...)\n     (:== #t (deps ...) (pair? (run 1 (_) body ...))))))\n\n(define-syntax select\n  (syntax-rules ()\n    ((_ ((v domain) ...) body ...)\n     (run* (v ...) (domain v) ... body ...))))\n\n(define-syntax <-\n  (syntax-rules ()\n    ((_ x subquery body ...)\n     (fresh (x xs)\n       (:== xs () subquery)\n       (membero x xs)\n       body ...))))\n\n;; TODO: define all these relations\n; timepoint year< exposure-event stressor receptor individual-organism chemical-substance in has-phenotype\n\n(define-relation (exposed-to t y x)\n  (fresh (i)\n    (exposure-event t i)\n    (receptor i y)\n    (stressor i x)))\n\n(define-relation (asthma-cohort-organism y)\n  (individual-organism y)\n  (in y 'asthma-cohort))\n\n(define-relation (timepoint t)\n  (conde ((== t 2010))\n         ;; TODO: ...\n         ((== t 2019))))\n\n(run* (z)\n  (<- x (select ((x chemical-substance))\n                (where (x) ;(x exposed-to has-phenotype asthma-cohort-organism timepoint)\n                  (occurs\n                    p y asthma-cohort-organism\n                    (exists\n                      t1 timepoint\n                      (exposed-to t1 y x)\n                      (exists\n                        t2 timepoint\n                        (year< t1 t2)\n                        (has-phenotype t2 y 'asthma-exacerbation))))))\n      (target x z)))\n"
  },
  {
    "path": "contrib/medikanren2/gregr/notes-on-reasoning.md",
    "content": "# Notes on reasoning for Translator\n\nI'm interested in improving Translator's design to make sure it can support\nreal world use.  Specifically, I'm going to consider aspects of the design\nthat are related to reasoning.\n\n## Retrieval parameters\n\nSome retrieval parameters involving tradeoffs between precision and recall:\n- Facts only vs. facts and inferences\n  - Should we only consider ground-truth assertions coming directly from\n    knowledge sources, or should we also consider assertions derived from\n    reasoning about existing assertions?\n- Exact ontology matching vs. plausible ontology matching\n  - Should we only consider facts that are subtypes of what we are looking for?\n    Or can we also admit supertypes, which may not be what we're looking for,\n    but which we can't prove aren't what we're looking for?\n\nFull recall seems like the right default, as long as results include some\nmeasure of confidence.  Users and downstream systems can then make their own\nchoice of precision by filtering on confidence and other result structure.\n\nCurrently, Translator isn't designed for full recall:\n- It presupposes \"facts only\" mode (ironically).\n  - There is no formal way to express inference derivations in the Translator\n    Reasoner API!\n- It commits to exact ontology matching.\n  - https://github.com/NCATSTranslator/TranslatorArchitecture/blob/master/README.md\n    point 9 requires KPs to return identifiers and predicates that are a subtype of\n    what was asked for.\n\n## Ontology matching\n\nWe'll start with ontology matching since it's an easier issue to address.  For\ntractable support of both full recall and the option for more precision, KPs\nshould return both subtypes and supertypes of what was asked for.\n\nConsider the `regulates` predicate and its subtypes `negatively_regulates` and\n`positively_regulates`:\n\n- `A regulates B`\n  - `A negatively_regulates B`\n  - `A positively_regulates B`\n\nIf a user is interested in `A negatively_regulates B`, a KP is only allowed to\nreturn edges with predicate `negatively_regulates`.  Yet it is possible that a\nKP also contains less a specific edge claiming that `A regulates B`, possibly\nbecause it was sourced from natural language processing (NLP).  While it wasn't\npossible to determine the specific form of regulation involved in this claim,\nthe possibility that it is negative regulation can't be ruled out.  So this\nclaim could be one that the user is interested in!\n\nIf the user is interested in full recall, one workaround to consider is to have\nthe user ask for `A regulates B` instead of `A negatively_regulates B`.  In this\ncase a KP will return edges whose predicate is either `negatively_regulates` or\n`regulates`.  The problem with this is the KP will also return edges whose\npredicate is `positively_regulates`.  These edges are definitely not what the\nuser wants.\n\nSure, a user could filter these edges out, but consider what\nhappens with a taller ontology: given a complete binary-tree-shaped predicate\nontology of height `N`, asking for the most general predicate will return\nresults for `2^N` predicates.  If the user is only interested in one leaf\npredicate and its plausible substitutes (supertypes), this can involve an\nintractable amount of filtering.\n\nInstead, if KPs are allowed to return supertypes as well as subtypes, the user\ninterested in full recall can ask for the specific predicate they are interested\nin, and not have to do any filtering.  Alternatively, if the user is interested\nin precision, results will only be returned for `N` predicates, which is a\ntractable amount to filter.\n\n## Inferred claims\n\nThe specification for the Translator Reasoner API,\nhttps://github.com/NCATSTranslator/ReasonerAPI/blob/master/TranslatorReasonerAPI.yaml,\nprovides no formal mechanism for an ARA to describe a derived assertion that it\ncan infer from ground-truth assertions coming from KPs.  This description,\nwhere a reasoning system would \"show its work\", is needed so that users and\ndownstream systems can validate the assumptions behind the inference.  Although\nthe API provides a way to describe support for ground-truth assertions, this\nmechanism is not sufficient for describing inferences.  To properly describe an\ninference, it is necessary to refer to supporting assertions. Since assertions\nare graph edges, this means that the justification for an inferred edge needs to\nrefer to other edges.  Since inferences may be supported by other inferences,\nthis form of reference is recursive.\n\nInstead of allowing inferred claims, we could insist that the user ask for the\nexact graph structures they are interested in seeing results for.  This is what\nthe current design already insists.  But part of the value of Translator comes\nfrom providing ARAs that are capable of synthesizing new information from\nexisting knowledge.  In order for an interested user to fully utilize this\nsynthesized information, they would have to know what forms of reasoning were\navailable and understand how to structure their queries to access results coming\nfrom each form of reasoning.  This is a large burden to place on the user,\nespecially if they are non-technical.  It would be better to allow the user to\nask either naive or sophisticated questions, and automatically benefit from ARA\nreasoning in both cases.\n\nTo remedy this situation, the Reasoner API needs general structure for\nreasoning-based justification for inferred assertions, in addition to evidence\nand provenance for KP assertions.  We could adopt a structure analogous to\nproof-formation rules, where each step of inference would include an identifier\nfor the rule being invoked, and a list of sub-assertions that this rule depends\non.  These sub-assertions may be ground assertions, or may also be inferred,\ngiving justifications a tree-like structure.\n\n### Example justification rule\n\nFor example, you can imagine using two 1-hop claims with particular predicates\n`p0` and `p1` to justify belief in another 1-hop claim with predicate `p2`:\n\n```\nA-p0->B, B-p1->C\n---------------- some-rule-name:p0+p1=p2\nA-p2->C\n```\n\nHere are some instances of this 2 hops to 1 hop rule:\n```\np0                   | p1                   | p2\n------------------------------------------------------------------\npositively_regulates | positively_regulates | positively_regulates\nnegatively_regulates | positively_regulates | negatively_regulates\npositively_regulates | negatively_regulates | negatively_regulates\nnegatively_regulates | negatively_regulates | positively_regulates\n```\n\n### Normalization and conflation\n\nWith support for structured justification, inferences could even subsume\nnormalization.  If we treat normalization information as just another knowledge\ngraph containing equivalence edges, we can explicitly justify why we believe\nthat one concept identifier or predicate can stand in for another, and this\njustification can be validated externally.  Nobody would need to implicitly\ntrust the normalization data coming from a centralized service.  This also\nopens up the option for ARAs to perform selective conflation of concepts and\npredicates while communicating what it's doing and why.\n"
  },
  {
    "path": "contrib/medikanren2/gregr/old/graph-builder-explorer.rkt",
    "content": "#lang racket/base\n(provide\n\n  )\n\n(require\n  \"common.rkt\"\n  )\n\n(define-syntax define-record\n  (syntax-rules ()\n    ((_ name field ...) (struct name (field ...) #:prefab))))\n(define-syntax define-record*\n  (syntax-rules ()\n    ((_ (record-body ...) ...)\n     (begin (define-record record-body ...) ...))))\n\n(define-record*\n  (setdesc kind sources construction class text selections)\n  ;; kind: whether this is a concept or predicate set\n  ;; sources: choice of databases\n  ;; class: concept categories or relation parent classes\n  ;; construction: in terms of operations on other sets\n  ;; text: text search strings\n  ;; selections: explicitly chosen elements (referenced by CURIE/db-uid)\n\n  (metadata  uid attrs)\n  (workspace meta graph uid=>obj triples)\n  (graph     meta nodes edges subgraphs)\n  (node      meta concepts edges)\n  (edge      meta subject object predicates))\n\n;; maybe just represent these as s-expressions\n;(struct set-operation (op s1 s2))\n;(struct constraint    (cx s arg))\n;; category/class constraint\n;; text search constraint\n;; graph constraint\n;; user selection constraint\n\n;; TODO:\n;; workspace manipulators\n;;   track deltas to minimize recomputation of unknowns?\n;; computate unknowns/triples for workspace graphs\n\n;; union, intersection, difference\n\n(define fresh-uid (let ((uid -1)) (lambda () (set! uid (+ uid 1)) uid)))\n\n;(define (compute w)\n  ;(define uid=>obj (workspace-uid=>obj w))\n  ;(define seen     (set))\n  ;;(define pending  (set))\n  ;(define finished (hash))\n  ;(define failed   (set))\n\n  ;;(define unknowns '(()))\n\n  ;(define (uid->obj uid) (hash-ref uid=>obj uid))\n\n  ;(define (fail! obj->metadata obj)\n    ;(set! failed (set-add failed (obj->metadata obj)))\n    ;#f)\n\n  ;(define (seen?/add obj->metadata obj)\n    ;(define uid (metadata-uid (obj->metadata obj)))\n    ;(or (set-member? seen uid)\n        ;(begin (set! seen (set-add seen uid)) #f)))\n\n  ;(define (finished? uid) (hash-ref? finished uid #f))\n\n  ;(define (compute/graph g)\n    ;(or (seen?/add graph-meta g)\n        ;(unless\n          ;(and (for-each compute/node  (map uid->obj (graph-nodes g)))\n               ;(for-each compute/edge  (map uid->obj (graph-edges g)))\n               ;(for-each compute/graph (map uid->obj (graph-subgraphs g)))\n               ;(andmap (finished? node-meta)  (graph-nodes g))\n               ;(andmap (finished? edge-meta)  (graph-edges g))\n               ;(andmap (finished? graph-meta) (graph-subgraphs g)))\n          ;(fail! graph-meta g))))\n\n  ;(define (compute/edge e (query #f))\n    ;(unless (and (compute/predicates\n\n                   ;)\n\n              ;(compute/node (uid->obj subject))\n                 ;(compute/node (uid->obj object))\n                 ;((finished? node-meta) subject)\n                 ;((finished? node-meta) object))\n      ;(fail! edge-meta e)))\n\n  ;(define (compute/node n (query #f))\n    ;(define sd (node-concepts n))\n    ;(or (seen?/add node-meta n)\n        ;;; TODO: unknown or constructed?\n        ;(if (setdesc-construction sd)\n          ;;; TODO: construct concept set.\n\n          ;)\n\n        ;))\n\n\n\n  ;(define (compute/query\n\n            ;)\n\n    ;)\n\n  ;(compute/graph (workspace-graph w))\n\n\n  ;)\n"
  },
  {
    "path": "contrib/medikanren2/gregr/old/query-simple.rkt",
    "content": "#lang racket/base\n(provide\n\n  )\n(require\n\n  )\n\n; report\n; rrun\n; P T\n; C PO PS\n; patho ;; does this make PO PS unnecessary?\n\n;; include isa-related concepts\n;; concept: db cid cui category name\n;; predicate: -\n;; X: db cid cui category name max-pubmed-# min-pubmed-# path-length path-confidence\n;; Paths: db eid subject predicate object subj-cat obj-cat pubmed-#\n;;   grouped via --\n;; Properties: property value\n;; Pubmed: URL\n"
  },
  {
    "path": "contrib/medikanren2/gregr/old/query-tree.rkt",
    "content": "#lang racket/base\n(provide\n  ? help\n  graph path\n  C P T\n  show hide count unmodify\n  graph? path? C? P? T? show? hide? count? except?\n  except\n  inote iref aref untag\n  )\n(require \"common.rkt\" \"mk.rkt\")\n\n\n\n(define c1 (C (C (C \"imatinib\") '(db semmed)) '(cui \"...\")))\n;; ((db id cui name ()) ...)\n\n(define c2 (C (C (C \"asthma\") '(db semmed)) '(cui \"...\")))\n;; ((db id cui name ()) ...)\n\n(define p1 (P (subject 'Concept1 c1) \"decreases\"))\n;; #(subject Concept1\n;;   ((db id name) ...)\n;;   ((db id cui name ()) ...))\n\n(define p2 (P (object 'Concept2 c2) \"increases\"))\n;; #(object Concept2\n;;   ((db id name) ...)\n;;   ((db id cui name ()) ...))\n\n(define X (C p1 p2))\n;; ((db id cui name ((subject ((predicate . ((concept . edge-props) ...)) ...))\n;;                   (object  ((predicate . ((concept . edge-props) ...)) ...))) ...)\n\n(report (C X \"gene\"))  ;; edges? paths? pubs? sorting by pubcount or path confidence?\n"
  },
  {
    "path": "contrib/medikanren2/gregr/owlrl.rkt",
    "content": "#lang racket/base\n(provide (all-defined-out))\n;; TODO: This implementation won't work until we define =/=\n;(require \"basic-naive.rkt\")\n\n;; Based on a description logic reasoner sketch by Jim Balhoff\n\n(define RDF_TYPE \"\")\n(define RDF_FIRST \"\")\n(define RDF_REST \"\")\n(define RDF_NIL \"\")\n(define RDFS_SUBCLASS_OF \"\")\n(define RDFS_SUBPROPERTY_OF \"\")\n(define RDFS_DOMAIN \"\")\n(define RDFS_RANGE \"\")\n(define OWL_ANNOTATION_PROPERTY \"\")\n(define OWL_CLASS \"\")\n(define OWL_OBJECT_PROPERTY \"\")\n(define OWL_TRANSITIVE_PROPERTY \"\")\n(define OWL_FUNCTIONAL_PROPERTY \"\")\n(define OWL_INVERSE_FUNCTIONAL_PROPERTY \"\")\n(define OWL_IRREFLEXIVE_PROPERTY \"\")\n(define OWL_SYMMETRIC_PROPERTY \"\")\n(define OWL_ASYMMETRIC_PROPERTY \"\")\n(define OWL_INVERSE_OF \"\")\n(define OWL_EQUIVALENT_PROPERTY \"\")\n(define OWL_PROPERTY_DISJOINT_WITH \"\")\n(define OWL_ALL_DISJOINT_PROPERTIES \"\")\n(define OWL_NAMED_INDIVIDUAL \"\")\n(define OWL_PROPERTY_CHAIN_AXIOM \"\")\n(define OWL_ON_PROPERTY \"\")\n(define OWL_SOME_VALUES_FROM \"\")\n(define OWL_ALL_VALUES_FROM \"\")\n(define OWL_EQUIVALENT_CLASS \"\")\n(define OWL_SAME_AS \"\")\n(define OWL_INTERSECTION_OF \"\")\n(define OWL_UNION_OF \"\")\n(define OWL_COMPLEMENT_OF \"\")\n(define OWL_RESTRICTION \"\")\n(define OWL_MEMBERS \"\")\n(define OWL_DISJOINT_WITH \"\")\n(define OWL_ALL_DISJOINT_CLASSES \"\")\n(define OWL_HAS_SELF \"\")\n(define OWL_THING \"\")\n(define OWL_NOTHING \"\")\n(define OWL_SOURCE_INDIVIDUAL \"\")\n(define OWL_ASSERTION_PROPERTY \"\")\n(define OWL_TARGET_INDIVIDUAL \"\")\n(define OWL_TARGET_VALUE \"\")\n(define OWL_HAS_VALUE \"\")\n(define OWL_MAX_CARDINALITY \"\")\n(define OWL_ONE_OF \"\")\n(define XSD_TRUE \"\\\"true\\\"^^\")\n(define XSD_ZERO \"\\\"0\\\"^^\")\n(define XSD_ONE \"\\\"1\\\"^^\")\n(define SESAME_DIRECT_TYPE \"\")\n\n(define-relation (list-contains node.list item)\n  (conde ((rdf node.list RDF_FIRST item))\n         ((fresh (other)\n            (rdf node.list RDF_REST other)\n            (list-contains other item)))))\n\n(define-relation (chain s p o node.list)\n  (conde ((fresh (X P1 Y)\n            (rdf p OWL_PROPERTY_CHAIN_AXIOM X)\n            (rdf X RDF_FIRST P1)\n            (rdf s P1 o)\n            (rdf X RDF_REST node.list)\n            (=/= node.list RDF_NIL)))\n         ((fresh (X P1 O1)\n            (chain s p O1 X)\n            (rdf X RDF_FIRST P1)\n            (rdf O1 P1 o)\n            (rdf X RDF_REST node.list)\n            (=/= node.list RDF_NIL)))))\n\n(define-relation (ichain individual class node.list)\n  (conde ((fresh (X C1)\n            (rdf class OWL_INTERSECTION_OF X)\n            (rdf X RDF_FIRST C1)\n            (rdf individual RDF_TYPE C1)\n            (rdf X RDF_REST node.list)\n            (=/= node.list RDF_NIL)))\n         ((fresh (X C1)\n            (ichain individual class X)\n            (rdf X RDF_FIRST C1)\n            (rdf individual RDF_TYPE C1)\n            (rdf X RDF_REST node.list)\n            (=/= node.list RDF_NIL)))))\n\n(define-relation (rdf s p o)\n  (conde ((fresh (p.other ?)\n            (== p RDF_TYPE)\n            (rdf p.other RDFS_DOMAIN o)\n            (rdf s p.other ?)))\n         ((fresh (p.other ?)\n            (== p RDF_TYPE)\n            (rdf p.other RDFS_RANGE o)\n            (rdf ? p.other s)))\n         ((fresh (p.other x)\n            (== p OWL_SAME_AS)\n            (rdf p.other RDF_TYPE OWL_FUNCTIONAL_PROPERTY)\n            (rdf x p.other s)\n            (rdf x p.other o)))\n         ((fresh (p.other y)\n            (== p OWL_SAME_AS)\n            (rdf p.other RDF_TYPE OWL_INVERSE_FUNCTIONAL_PROPERTY)\n            (rdf s p.other y)\n            (rdf o p.other y)))\n         ((fresh (p.other)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf p.other RDF_TYPE OWL_IRREFLEXIVE_PROPERTY)\n            (rdf s p.other s)))\n         ((rdf p RDF_TYPE OWL_SYMMETRIC_PROPERTY)\n          (rdf o p s))\n         ((fresh (p.other y)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf p.other RDF_TYPE OWL_ASYMMETRIC_PROPERTY)\n            (rdf s p.other y)\n            (rdf y p.other s)))\n         ((fresh (y)\n            (rdf p RDF_TYPE OWL_TRANSITIVE_PROPERTY)\n            (rdf s p y)\n            (rdf y p o)))\n         ((fresh (p.other)\n            (rdf p.other RDFS_SUBPROPERTY_OF p)\n            (rdf s p.other o)))\n         ((fresh (X P1 O1)\n            (chain s p O1 X)\n            (rdf X RDF_FIRST P1)\n            (rdf O1 P1 o)\n            (rdf X RDF_REST RDF_NIL)))\n         ((fresh (P1)\n            (rdf P1 OWL_EQUIVALENT_PROPERTY p)\n            (rdf s P1 o)))\n         ((fresh (P1)\n            (rdf p OWL_EQUIVALENT_PROPERTY P1)\n            (rdf s P1 o)))\n         ((fresh (P1 P2 Y)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf P1 OWL_PROPERTY_DISJOINT_WITH P2)\n            (rdf s P1 Y)\n            (rdf s P2 Y)))\n         ((fresh (P1 P2 X)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf P1 OWL_PROPERTY_DISJOINT_WITH P2)\n            (rdf X P1 s)\n            (rdf X P2 s)))\n         ((fresh (V X Y P.i P.j)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf X RDF_TYPE OWL_ALL_DISJOINT_PROPERTIES)\n            (rdf X OWL_MEMBERS Y)\n            (list-contains Y P.i)\n            (list-contains Y P.j)\n            (=/= P.i P.j)\n            (rdf s P.i V)\n            (rdf s P.j V)))\n         ((fresh (U X Y P.i P.j)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf X RDF_TYPE OWL_ALL_DISJOINT_PROPERTIES)\n            (rdf X OWL_MEMBERS Y)\n            (list-contains Y P.i)\n            (list-contains Y P.j)\n            (=/= P.i P.j)\n            (rdf U P.i s)\n            (rdf U P.j s)))\n         ((fresh (P1)\n            (rdf P1 OWL_INVERSE_OF p)\n            (rdf o P1 s)))\n         ((fresh (P1)\n            (rdf p OWL_INVERSE_OF P1)\n            (rdf o P1 s)))\n         ((fresh (X P1 I2)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf X OWL_SOURCE_INDIVIDUAL s)\n            (rdf X OWL_ASSERTION_PROPERTY P1)\n            (rdf X OWL_TARGET_INDIVIDUAL I2)\n            (rdf s P1 I2)))\n         ((fresh (X P1 I1)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf X OWL_SOURCE_INDIVIDUAL I1)\n            (rdf X OWL_ASSERTION_PROPERTY P1)\n            (rdf X OWL_TARGET_INDIVIDUAL s)\n            (rdf I1 P1 s)))\n         ((fresh (X C1)\n            (== p RDF_TYPE)\n            (ichain s o X)\n            (rdf X RDF_FIRST C1)\n            (rdf s RDF_TYPE C1)\n            (rdf X RDF_REST RDF_NIL)))\n         ((fresh (C X)\n            (== p RDF_TYPE)\n            (rdf C OWL_INTERSECTION_OF X)\n            (list-contains X o)\n            (rdf s RDF_TYPE C)))\n         ((fresh (X C1)\n            (== p RDF_TYPE)\n            (rdf o OWL_UNION_OF X)\n            (list-contains X C1)\n            (rdf s RDF_TYPE C1)))\n         ((fresh (C1 C2)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf C1 OWL_COMPLEMENT_OF C2)\n            (rdf s RDF_TYPE C1)\n            (rdf s RDF_TYPE C2)))\n         ((fresh (Y P V)\n            (== p RDF_TYPE)\n            (rdf o OWL_SOME_VALUES_FROM Y)\n            (rdf o OWL_ON_PROPERTY P)\n            (rdf s P V)\n            (rdf V RDF_TYPE Y)))\n         ((fresh (P ?)\n            (== p RDF_TYPE)\n            (rdf o OWL_SOME_VALUES_FROM OWL_THING)\n            (rdf o OWL_ON_PROPERTY P)\n            (rdf s P ?)))\n         ((fresh (X P U)\n            (== p RDF_TYPE)\n            (rdf X OWL_THING o)\n            (rdf X OWL_ON_PROPERTY P)\n            (rdf U RDF_TYPE X)\n            (rdf U P s)))\n         ((fresh (X)\n            (rdf X OWL_HAS_VALUE o)\n            (rdf X OWL_ON_PROPERTY p)\n            (rdf s RDF_TYPE X)))\n         ((fresh (P Y)\n            (== P RDF_TYPE)\n            (rdf o OWL_HAS_VALUE Y)\n            (rdf o OWL_ON_PROPERTY P)\n            (rdf s P Y)))\n         ((fresh (X P ?)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf X OWL_MAX_CARDINALITY XSD_ZERO)\n            (rdf X OWL_ON_PROPERTY P)\n            (rdf s RDF_TYPE X)\n            (rdf s P ?)))\n         ((fresh (X P U)\n            (== p OWL_SAME_AS)\n            (rdf X OWL_MAX_CARDINALITY XSD_ONE)\n            (rdf X OWL_ON_PROPERTY P)\n            (rdf U RDF_TYPE X)\n            (rdf U P s)\n            (rdf U P o)))\n         ((fresh (X)\n            (== p RDF_TYPE)\n            (rdf o OWL_ONE_OF X)\n            (list-contains X s)))\n         ((fresh (C1)\n            (== p RDF_TYPE)\n            (rdf C1 RDFS_SUBCLASS_OF o)\n            (rdf s RDF_TYPE C1)))\n         ((fresh (C1)\n            (== p RDF_TYPE)\n            (rdf C1 OWL_EQUIVALENT_CLASS o)\n            (rdf s RDF_TYPE C1)))\n         ((fresh (C2)\n            (== p RDF_TYPE)\n            (rdf o OWL_EQUIVALENT_CLASS C2)\n            (rdf s RDF_TYPE C2)))\n         ((fresh (C1 C2)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf C1 OWL_DISJOINT_WITH C2)\n            (rdf s RDF_TYPE C1)\n            (rdf s RDF_TYPE C2)))\n         ((fresh (X Y C.i C.j)\n            (== p RDF_TYPE)\n            (== o OWL_NOTHING)\n            (rdf X RDF_TYPE OWL_ALL_DISJOINT_CLASSES)\n            (rdf X OWL_MEMBERS Y)\n            (list-contains Y C.i)\n            (list-contains Y C.j)\n            (=/= C.i C.j)\n            (rdf s RDF_TYPE C.i)\n            (rdf s RDF_TYPE C.j)))))\n"
  },
  {
    "path": "contrib/medikanren2/gregr/query-low-level.rkt",
    "content": "#lang racket/base\n(provide\n  query:Known->Known\n  query:Known->X\n  query:X->Known\n  query:Known<-X->Known\n  query:X->Y->Known\n  query:Prefix->Prefix\n  query:Concept\n  edge-properties\n  edge-property-values\n  concept-properties\n  concept-property-values\n  )\n(require\n  \"../../../medikanren2/dbk/dbk/data.rkt\"\n  \"../../../medikanren2/dbk/dbk/enumerator.rkt\"\n  \"../../../medikanren2/dbk/dbk/stream.rkt\"\n  racket/match\n  racket/runtime-path\n  racket/set\n  racket/string\n  )\n\n;;;;;;;;;;;;;;;\n;; Utilities ;;\n;;;;;;;;;;;;;;;\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n;; TODO: build small in-memory relations more easily\n(define (strings->dict strs)\n  (define vec.strs  (list->vector (sort (set->list (list->set strs)) stringvector\n                      (lambda (yield)\n                        ((merge-join dict.strs dict.string=>id)\n                         (lambda (__ ___ id) (yield id))))))\n  (dict:ordered (column:vector vec.ids) (column:const '()) 0 (vector-length vec.ids)))\n\n;; TODO: we don't need before and after, we can find a finite delimiter in the lexicographical ordering\n;; (integer->char (+ 1 (char->integer #\\:))) ==> #\\;\n(define (dict-string-prefix prefix)\n  (define d.string=>id\n    ((dict.string=>id 'after (lambda (str) (stringid 'top))\n  (define end   (+ start (d.string=>id 'count)))\n  ((dict.id=>string '>= start) '< end))\n\n;(define (edge-id->properties eid)\n  ;(define (get id default)\n    ;(eprops 'ref id\n            ;(lambda (dict.value) (dict-select dict.id=>string (dict.value 'min)))\n            ;(lambda ()           default)))\n  ;(define eprops       (dict-select dict.eprop:value.key.eid eid))\n  ;(define negated      (get id.negated \"\"))\n  ;(define provided-by  (get id.provided-by \"\"))\n  ;(define publications (get id.publications \"\"))\n  ;(list negated provided-by publications))\n\n(define-runtime-path path.here \".\")\n(define db      (database (path->string (build-path path.here \"rtx-kg2_20210204.db\"))))\n(define r.cprop (database-relation db '(rtx-kg2 cprop)))\n(define r.edge  (database-relation db '(rtx-kg2 edge)))\n(define r.eprop (database-relation db '(rtx-kg2 eprop)))\n\n(define domain-dicts                 (relation-domain-dicts r.cprop))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define dict.edge:object.eid.subject (relation-index-dict r.edge  '(subject eid object)))\n(define dict.edge:subject.eid.object (relation-index-dict r.edge  '(object eid subject)))\n(define dict.eprop:eid.value.key     (relation-index-dict r.eprop '(key value eid)))\n(define dict.eprop:value.key.eid     (relation-index-dict r.eprop '(eid key value)))\n(define dict.cprop:curie.value.key   (relation-index-dict r.cprop '(key value curie)))\n(define dict.cprop:value.key.curie   (relation-index-dict r.cprop '(curie key value)))\n\n(define id.negated      (dict-select dict.string=>id \"negated\"))\n(define id.provided-by  (dict-select dict.string=>id \"provided_by\"))\n(define id.publications (dict-select dict.string=>id \"publications\"))\n\n\n;; Testing\n\n(require racket/pretty)\n\n(define (f2 str.relation)\n  (define (query yield)\n    (define id.ekey              (dict-select dict.string=>id \"relation\"))\n    (define id.relation          (dict-select dict.string=>id str.relation))\n    (define dict.eprop:eid.value (dict-select dict.eprop:eid.value.key id.ekey))\n    (define dict.eprop:eid       (dict-select dict.eprop:eid.value     id.relation))\n    ((merge-join dict.eprop:eid dict.eprop:value.key.eid)\n     (lambda (eid __ dict.eprop:value.key)\n       (yield (list eid (enumerator->list\n                          (lambda (yield)\n                            ((dict.eprop:value.key 'enumerator/2)\n                             (lambda (id.key dict.eprop:value)\n                               (define str.key (dict-select dict.id=>string id.key))\n                               ((dict.eprop:value 'enumerator)\n                                (lambda (id.value)\n                                  (define str.value (dict-select dict.id=>string id.value))\n                                  (yield (cons str.key str.value)))))))))))))\n  (time (enumerator->rlist query)))\n\n(define results.f2 (f2 \"DGIdb:binder\"))\n\n(pretty-write (length results.f2))\n\n(read-line)\n(pretty-write results.f2)\n\n;; query:Known->X is analogous to a miniKanren-style query with this shape:\n; (run* (s sname p o oname)\n;   (fresh (id category)\n;     (edge id s o)\n;     (cprop o \"category\" category)\n;     (cprop s \"name\" sname)\n;     (cprop o \"name\" oname)\n;     (eprop id \"predicate\" p)\n;     (membero s subject-curies)\n;     (membero p predicates)\n;     (membero category object-categories)))\n\n(define (query:Known->X curies.K predicates.K->X categories.X)\n  (define (query yield)\n    (define ekey.predicate.id         (dict-select dict.string=>id \"predicate\"))\n    (define ckey.category.id          (dict-select dict.string=>id \"category\"))\n    (define ckey.name.id              (dict-select dict.string=>id \"name\"))\n    (define dict.curies.K             (strings->dict curies.K))\n    (define dict.predicates.K->X      (strings->dict predicates.K->X))\n    (define dict.categories.X         (strings->dict categories.X))\n    (define dict.eprop.eid.predicate  (dict-select dict.eprop.eid.value.key   ekey.predicate.id))\n    (define dict.cprop.curie.category (dict-select dict.cprop.curie.value.key ckey.category.id))\n    ((merge-join dict.curies.K dict.edge.object.eid.subject)\n     (lambda (id.K __ dict.edge.X.eid)\n       (define id.name.K ((dict-select (dict-select dict.cprop.value.key.curie id.K) ckey.name.id) 'min))\n       (define name.K    (dict-select dict.id=>string id.name.K))\n       (define K         (dict-select dict.id=>string id.K))\n       ((merge-join dict.predicates.K->X dict.eprop.eid.predicate)\n        (lambda (id.predicate.K->X __ dict.eprop.K->X)\n          (define predicate.K->X (dict-select dict.id=>string id.predicate.K->X))\n          ((merge-join dict.eprop.K->X dict.edge.X.eid)\n           (lambda (eid __ dict.edge.X)\n             (define props (edge-id->properties eid))\n             ((merge-join dict.categories.X dict.cprop.curie.category)\n              (lambda (__ ___ dict.cprop.X)\n                ((dict-join-ordered\n                   (lambda (yield)\n                     ((merge-join dict.cprop.X dict.edge.X)\n                      (lambda (id.X __ ___)\n                        (yield id.X '()))))\n                   dict.cprop.value.key.curie)\n                 (lambda (id.X __ dict.cprop.value.key)\n                   (define id.name.X ((dict-select dict.cprop.value.key ckey.name.id) 'min))\n                   (define name.X    (dict-select dict.id=>string id.name.X))\n                   (define X         (dict-select dict.id=>string id.X))\n                   (yield (list* K name.K predicate.K->X X name.X props)))))))))))))\n  (time (enumerator->rlist query)))\n\n;;; query:X->Known is analogous to a miniKanren-style query with this shape:\n;; (run* (s sname p o oname)\n;;   (fresh (id category)\n;;     (edge id s o)\n;;     (cprop s \"category\" category)\n;;     (cprop s \"name\" sname)\n;;     (cprop o \"name\" oname)\n;;     (eprop id \"predicate\" p)\n;;     (membero o object-curies)\n;;     (membero p predicates)\n;;     (membero category subject-categories)))\n\n;(define (query:X->Known categories.X predicates.X->K curies.K)\n  ;(define (query yield)\n    ;(define ekey.predicate.id         (dict-select dict.string=>id \"predicate\"))\n    ;(define ckey.category.id          (dict-select dict.string=>id \"category\"))\n    ;(define ckey.name.id              (dict-select dict.string=>id \"name\"))\n    ;(define dict.categories.X         (strings->dict categories.X))\n    ;(define dict.predicates.X->K      (strings->dict predicates.X->K))\n    ;(define dict.curies.K             (strings->dict curies.K))\n    ;(define dict.eprop.eid.predicate  (dict-select dict.eprop.eid.value.key   ekey.predicate.id))\n    ;(define dict.cprop.curie.category (dict-select dict.cprop.curie.value.key ckey.category.id))\n    ;((merge-join dict.curies.K dict.edge.subject.eid.object)\n     ;(lambda (id.K __ dict.edge.X.eid)\n       ;(define id.name.K ((dict-select (dict-select dict.cprop.value.key.curie id.K) ckey.name.id) 'min))\n       ;(define name.K    (dict-select dict.id=>string id.name.K))\n       ;(define K         (dict-select dict.id=>string id.K))\n       ;((merge-join dict.predicates.X->K dict.eprop.eid.predicate)\n        ;(lambda (id.predicate.X->K __ dict.eprop.X->K)\n          ;(define predicate.X->K (dict-select dict.id=>string id.predicate.X->K))\n          ;((merge-join dict.eprop.X->K dict.edge.X.eid)\n           ;(lambda (eid __ dict.edge.X)\n             ;(define props (edge-id->properties eid))\n             ;((merge-join dict.categories.X dict.cprop.curie.category)\n              ;(lambda (__ ___ dict.cprop.X)\n                ;((dict-join-ordered\n                   ;(lambda (yield)\n                     ;((merge-join dict.cprop.X dict.edge.X)\n                      ;(lambda (id.X __ ___)\n                        ;(yield id.X '()))))\n                   ;dict.cprop.value.key.curie)\n                 ;(lambda (id.X __ dict.cprop.value.key)\n                   ;(define id.name.X ((dict-select dict.cprop.value.key ckey.name.id) 'min))\n                   ;(define name.X    (dict-select dict.id=>string id.name.X))\n                   ;(define X         (dict-select dict.id=>string id.X))\n                   ;(yield (list* X name.X predicate.X->K K name.K props)))))))))))))\n  ;(time (enumerator->rlist query)))\n\n;;; query:Known<-X->Known is analogous to a miniKanren-style query with this shape:\n;;(run* (K1 name.K1 predicates.K1<-X X name.X predicates.X->K1 K2 name.K2)\n;;  (fresh (id1 id2 category.X)\n;;    (edge id1 X K1)\n;;    (edge id2 X K2)\n;;    (cprop X   \"category\" category.X)\n;;    (cprop X   \"name\" name.X)\n;;    (cprop K1  \"name\" name.K1)\n;;    (cprop K2  \"name\" name.K2)\n;;    (eprop id1 \"predicate\" K1<-X)\n;;    (eprop id2 \"predicate\" X->K2)\n;;    (membero category.X categories.X)\n;;    (membero K1         curies.K1)\n;;    (membero K1<-X      predicates.K1<-X)\n;;    (membero K2         curies.K2)\n;;    (membero X->K2      predicates.X->K2)))\n\n;(define (query:Known<-X->Known curies.K1 predicates.K1<-X categories.X predicates.X->K2 curies.K2)\n  ;(define (candidates->dict candidates)\n    ;(define ordered (sort candidates (lambda (a b) (stringvector groups) caar))\n  ;(define candidates.X->K1 (query:X->Known categories.X predicates.K1<-X curies.K1))\n  ;(define candidates.X->K2 (query:X->Known categories.X predicates.X->K2 curies.K2))\n  ;(define dict.X->K1.X     (candidates->dict candidates.X->K1))\n  ;(define dict.X->K2.X     (candidates->dict candidates.X->K2))\n  ;(time (enumerator->list\n          ;(lambda (yield)\n            ;((merge-join dict.X->K1.X dict.X->K2.X)\n             ;(lambda (X XK1s XK2s)\n               ;(for-each (lambda (XK1)\n                           ;(match-define (list* _ name.X X->K1 K1 name.K1 props1) XK1)\n                           ;(for-each (lambda (XK2)\n                                       ;(match-define (list* _ _ X->K2 K2 name.K2 props2) XK2)\n                                       ;(yield (append (list K1 name.K1 X->K1 X name.X X->K2 K2 name.K2)\n                                                      ;(append props1 props2))))\n                                     ;XK2s))\n                         ;XK1s)))))))\n\n;(define (query:X->Y->Known categories.X predicates.X->Y categories.Y predicates.Y->K curies.K)\n  ;(define (results->dict key results)\n    ;(define ordered (sort results (lambda (a b) (stringvector groups) (lambda (x) (key (car x)))))\n  ;(define results.Y->K (query:X->Known categories.Y predicates.Y->K curies.K))\n  ;(define dict.Y->K.Y  (results->dict car results.Y->K))\n  ;(define curies.Y     (enumerator->list (dict.Y->K.Y 'enumerator)))\n  ;(define results.X->Y (query:X->Known categories.X predicates.X->Y curies.Y))\n  ;(define dict.X->Y.Y  (results->dict cadddr results.X->Y))\n  ;(time (enumerator->list\n          ;(lambda (yield)\n            ;((merge-join dict.X->Y.Y dict.Y->K.Y)\n             ;(lambda (Y XYs YKs)\n               ;(for-each (lambda (XY)\n                           ;(match-define (list* X name.X X->Y _ name.Y props.X->Y) XY)\n                           ;(for-each (lambda (YK)\n                                       ;(match-define (list* _ _ Y->K K name.K props.Y->K) YK)\n                                       ;(yield (append (list X name.X X->Y Y name.Y Y->K K name.K)\n                                                      ;(append props.X->Y props.Y->K))))\n                                     ;YKs))\n                         ;XYs)))))))\n\n;(define (query:Known->Known curies.S predicates.S->O curies.O)\n  ;(define dict.curies.S (strings->dict curies.S))\n  ;(define dict.curies.O (strings->dict curies.O))\n  ;(query:dict.Known->dict.Known dict.curies.S predicates.S->O dict.curies.O))\n\n;(define (query:Prefix->Prefix prefix.S predicates.S->O prefix.O)\n  ;(define dict.curies.S (dict-string-prefix prefix.S))\n  ;(define dict.curies.O (dict-string-prefix prefix.O))\n  ;(query:dict.Known->dict.Known dict.curies.S predicates.S->O dict.curies.O))\n\n;(define (query:dict.Known->dict.Known dict.curies.S predicates.S->O dict.curies.O)\n  ;(define (query yield)\n    ;(define ekey.predicate.id         (dict-select dict.string=>id \"predicate\"))\n    ;(define ckey.category.id          (dict-select dict.string=>id \"category\"))\n    ;(define ckey.name.id              (dict-select dict.string=>id \"name\"))\n    ;(define dict.predicates.S->O      (strings->dict predicates.S->O))\n    ;(define dict.eprop.eid.predicate  (dict-select dict.eprop.eid.value.key   ekey.predicate.id))\n    ;(define dict.cprop.curie.category (dict-select dict.cprop.curie.value.key ckey.category.id))\n    ;((merge-join dict.curies.S dict.edge.object.eid.subject)\n     ;(lambda (id.S __ dict.edge.O.eid)\n       ;(define id.name.S ((dict-select (dict-select dict.cprop.value.key.curie id.S) ckey.name.id) 'min))\n       ;(define name.S    (dict-select dict.id=>string id.name.S))\n       ;(define S         (dict-select dict.id=>string id.S))\n       ;((merge-join dict.predicates.S->O dict.eprop.eid.predicate)\n        ;(lambda (id.predicate.S->O __ dict.eprop.S->O)\n          ;(define predicate.S->O (dict-select dict.id=>string id.predicate.S->O))\n          ;((merge-join dict.eprop.S->O dict.edge.O.eid)\n           ;(lambda (eid __ dict.edge.O)\n             ;(define props (edge-id->properties eid))\n             ;((merge-join dict.curies.O dict.edge.O)\n              ;(lambda (id.O __ ___)\n                ;(define id.name.O ((dict-select (dict-select dict.cprop.value.key.curie id.O) ckey.name.id) 'min))\n                ;(define name.O    (dict-select dict.id=>string id.name.O))\n                ;(define O         (dict-select dict.id=>string id.O))\n                ;(yield (list* S name.S predicate.S->O O name.O props)))))))))))\n  ;(time (enumerator->rlist query)))\n\n;(define (query:Concept curies)\n  ;(define (query yield)\n    ;(define dict.curie (strings->dict curies))\n    ;((merge-join dict.curie dict.cprop.value.key.curie)\n     ;(lambda (id.curie _ dict.cprop.value.key)\n       ;(define curie (dict-select dict.id=>string id.curie))\n       ;((dict.cprop.value.key 'enumerator/2)\n        ;(lambda (id.key dict.cprop.value)\n          ;(define key   (dict-select dict.id=>string id.key))\n          ;(define value (dict-select dict.id=>string (dict.cprop.value 'min)))\n          ;(yield (list curie key value)))))))\n  ;(time (enumerator->list query)))\n\n;(define (concept-properties)          (enumerator->list\n                                        ;(lambda (yield)\n                                          ;((merge-join dict.cprop.curie.value.key dict.id=>string)\n                                           ;(lambda (_ __ key)\n                                             ;(yield key))))))\n;(define (edge-properties)             (enumerator->list\n                                        ;(lambda (yield)\n                                          ;((merge-join dict.eprop.eid.value.key dict.id=>string)\n                                           ;(lambda (_ __ key)\n                                             ;(yield key))))))\n;(define (concept-property-values key) (enumerator->list\n                                        ;(lambda (yield)\n                                          ;((merge-join (dict-select dict.cprop.curie.value.key (dict-select dict.string=>id key))\n                                                       ;dict.id=>string)\n                                           ;(lambda (_ __ value) (yield value))))))\n;(define (edge-property-values    key) (enumerator->list\n                                        ;(lambda (yield)\n                                          ;((merge-join (dict-select dict.eprop.eid.value.key   (dict-select dict.string=>id key))\n                                                       ;dict.id=>string)\n                                           ;(lambda (_ __ value) (yield value))))))\n\n\n\n"
  },
  {
    "path": "contrib/medikanren2/gregr/test-dataflow-nausea.rkt",
    "content": "#lang racket/base\n(require\n  \"../dbk.rkt\"\n  \"../dbk/data.rkt\"\n  \"../dbk/enumerator.rkt\"\n  racket/pretty\n  racket/runtime-path\n  racket/set)\n\n(define-relation/table (cprop curie key value)   'path \"rtx2/20210204/cprop\")\n(define-relation/table (edge  id subject object) 'path \"rtx2/20210204/edge\")\n(define-relation/table (eprop id key value)      'path \"rtx2/20210204/eprop\")\n\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n(define-runtime-path path.here \".\")\n\n(define db      (database (path->string (build-path path.here \"rtx-kg2_20210204.db\"))))\n(define r.cprop (database-relation db '(rtx-kg2 cprop)))\n(define r.edge  (database-relation db '(rtx-kg2 edge)))\n(define r.eprop (database-relation db '(rtx-kg2 eprop)))\n\n(define dict.eprop.eid.value.key     (relation-index-dict r.eprop '(key value eid)))\n(define dict.edge.subject.eid.object (relation-index-dict r.edge  '(object eid subject)))\n(define dict.cprop.value.key.curie   (relation-index-dict r.cprop '(curie key value)))\n(define domain-dicts                 (relation-domain-dicts r.cprop))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define (string->id str) (dict-select dict.string=>id str))\n(define (id->string id)  (dict-select dict.id=>string id))\n\n(define (benchmark-find-treatments curie.target)\n  (define (run-query yield)\n    (define curie.nausea.id       (string->id curie.target))\n    (define ekey.predicate.id     (string->id \"predicate\"))\n    (define evalue.treats.id      (string->id \"biolink:treats\"))\n    (define ckey.category.id      (string->id \"category\"))\n    (define ckey.name.id          (string->id \"name\"))\n    (define dict.eprop.eid.value  (dict-select dict.eprop.eid.value.key     ekey.predicate.id))\n    (define dict.eprop.eid        (dict-select dict.eprop.eid.value         evalue.treats.id))\n    (define dict.edge.subject.eid (dict-select dict.edge.subject.eid.object curie.nausea.id))\n    ((merge-join dict.eprop.eid dict.edge.subject.eid)\n     (lambda (eid __ dict.edge.subject)\n       ((merge-join dict.edge.subject dict.cprop.value.key.curie)\n        (lambda (subject.id __ dict.cprop.value.key)\n          (define subject             (id->string subject.id))\n          (define dict.cprop.category (dict-select dict.cprop.value.key ckey.category.id))\n          (define dict.cprop.name     (dict-select dict.cprop.value.key ckey.name.id))\n          ((merge-join dict.cprop.category dict.id=>string)\n           (lambda (category.id __ category)\n             ((merge-join dict.cprop.name dict.id=>string)\n              (lambda (name.id __ name)\n                (yield (list subject category name)))))))))))\n  ;; Some nausea timings\n  ;; cpu time: 1485 real time: 1610 gc time: 19\n  ;; cpu time: 1539 real time: 1557 gc time: 15\n  ;; cpu time: 1538 real time: 1556 gc time: 24\n  (define results.old (time (run* (s cat name)\n                              (fresh (eid)\n                                (edge eid s curie.target)\n                                (cprop s \"category\" cat)\n                                (cprop s \"name\" name)\n                                (eprop eid \"predicate\" \"biolink:treats\")))))\n  ;; Some nausea timings\n  ;; cpu time: 27 real time: 27 gc time: 0\n  ;; cpu time: 31 real time: 31 gc time: 0\n  ;; cpu time: 30 real time: 31 gc time: 0\n  (define results.new (time (enumerator->rlist run-query)))\n  ;; 149 results\n  (pretty-write `(old:    ,(length results.old) ,results.old))\n  (pretty-write `(new:    ,(length results.new) ,results.new))\n  (pretty-write `(equal?: ,(equal? (list->set results.old) (list->set results.new)))))\n\n(define curie.nausea \"UMLS:C0520909\")\n(benchmark-find-treatments curie.nausea)\n"
  },
  {
    "path": "contrib/medikanren2/lw-reasoning-examples.rkt",
    "content": "#lang racket/base\n(provide trapi-response)\n(require\n \"../../medikanren2/common.rkt\"\n  \"../../medikanren2/lw-reasoning.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  json\n  )\n\n(define diabetes \"DOID:9351\")\n(define diabetes2 \"DOID:9352\")\n\n;; Reminder on 'semantic web'-style relations, defined in `medikanren2/common.rkt`\n\n;; `is-a` is a short-hand for the \"category\" property\n(run* c (is-a diabetes c))\n(run* c (cprop diabetes \"category\" c))\n\n;; and `triple` abstracts away the edge-id on triple relations\n(run 1 (s p o) (triple s p o))\n(run 1 (s p o) \n  (fresh (eid)\n    (edge eid s o)\n    (eprop eid \"predicate\" p)))\n\n;; Query subclasses in the Biolink Ontology directly using `subclass-of`, `subclass-of*`, `subclass-of+`\n(run* c (subclass-of+ c \"biolink:regulates\"))\n\n;; Subclass relations on concept category\n(run* c (is-a diabetes c))\n(run* (c c^) (is-a/subclass* diabetes c c^))\n\n;; Look for drugs that ameliorate (or a subclass thereof) diabetes\n(run* (drug p) (triple/subclass drug \"biolink:ameliorates\" p diabetes))\n\n;; ... or only subclasses thereof (mostly for testing)\n(run* (drug p) (triple/subclass+ drug \"biolink:ameliorates\" p diabetes))\n\n;; ... and drugs that ameliorate (or a subclass thereof) diabetes (or a subclass thereof)\n(run* (drug p^ diabetes^) \n  (triple/subclass drug \"biolink:ameliorates\" p^ diabetes^)\n  (subclass-of* diabetes^ diabetes))\n\n;; ... there is a single relation that does reasoning on all three elements\n;; but it can take a long time with run*\n(run 1 (drug drug^ p diabetes^) \n  (triple/reasoning drug drug^ \"biolink:ameliorates\" p diabetes diabetes^))\n\n(define gene \"NCBIGene:7422\")\n\n(run* o (triple gene \"biolink:regulates\" o))\n\n(run 10 (o p) (triple/subclass+ gene \"biolink:regulates\" p o))\n\n;; ;; From working with Thi\n;; (run* (graph drug d name) (quad graph drug \"biolink:treats\" d) (subclass-of+ d diabetes) (cprop drug \"name\" name))\n;; (run 1 (d name dc dcname) (is-a d \"biolink:Drug\") (subclass-of d dc) (cprop d \"name\" name) (cprop dc \"name\" dcname))\n;; (run 10 (d name dc dcname) (is-a d \"biolink:Drug\") (subclass-of d dc) (cprop d \"name\" name) (cprop dc \"name\" dcname))\n;; (run 10 (d name dc dcc dcname) (is-a d \"biolink:Drug\") (subclass-of d dc) (cprop d \"name\" name) (cprop dc \"name\" dcname) (is-a dc dcc))\n;; (run 10 (drug name dc dcc dcname) (is-a drug \"biolink:Drug\") (subclass-of drug dc) (cprop drug \"name\" name) (cprop dc \"name\" dcname) (is-a dc dcc))\n;; (run 10 (drug name dc dcc dcname) (is-a drug \"biolink:Drug\") (subclass-of drug dc) (cprop drug \"name\" name) (cprop dc \"name\" dcname) (is-a dc dcc))\n;; (run* (k v) (cprop    \"CHEBI:65259\" k v))\n;; (run* (drug name) (subclass-of+     \"CHEBI:65259\" drug) (cprop drug \"name\" name))\n;; \"../../medikanren2/lw-reasoning.rkt\"> (run* (drug name) (subclass-of+ drug    \"CHEBI:51374\") (cprop drug \"name\" name))\n;; (run* (drug name) (triple drug \"biolink:has_attribute\" \"CHEBI:65259\") (cprop drug \"name\" name))\n;; (run* (drug name) (triple drug \"biolink:subclass_of\" \"CHEBI:65259\") (cprop drug \"name\" name))\n\n\n\n(define gene-to-disease-preds '(\"biolink:affects\" ;rtx2_2021_02_04\n                                \"biolink:biomarker_for\" ;rtx2_2021_02_04\n                                \"biolink:causes\" ;rtx2_2021_02_04\n                                \"biolink:contributes_to\" ;rtx2_2021_02_04\n                                \"biolink:correlated_with\" ;rtx2_2021_02_04\n                                \"biolink:disrupts\" ;rtx2_2021_02_04\n                                \"biolink:gene_associated_with_condition\" ;rtx2_2021_02_04\n                                \"biolink:has_phenotype\" ;rtx2_2021_02_04\n                                \"biolink:manifestation_of\" ;rtx2_2021_02_04\n                                \"biolink:participates_in\" ;rtx2_2021_02_04\n                                \"biolink:predisposes\" ;rtx2_2021_02_04\n                                \"biolink:prevents\" ;rtx2_2021_02_04\n                                \"biolink:treats\" ;rtx2_2021_02_04\n                                \"biolink:contributes_to_morphology_of\" ;rtx2_2021_02_0\n                                ))\n\n(define gene-or-protein '(\"biolink:Gene\"\n                          \"biolink:GeneFamily\"\n                          \"biolink:GeneProduct\"\n                          \"biolink:GenomicEntity\"\n                          \"biolink:MacromolecularComplex\"\n                          \"biolink:MolecularEntity\"\n                          \"biolink:Protein\")) \n\n\n\n;; synonyms\n\n(define anxiety \"HP:0000739\")\n(define apnea \"HP:0002104\")\n(define epilepsy \"MONDO:0005027\")\n(define vomiting \"HP:0002013\")\n(define spasticity \"HP:0001257\")\n(define ID \"HP:0001249\")\n(define gas-reflux \"HP:0002020\")\n(define autism \"MONDO:0005260\")\n\n; some of the phenotypes are not actionable (no drugs)\n;(define feeding-diff \"HP:0011968\") ;; no drugs for this phenotype\n;(define flat-nose \"HP:0000457\")\n;(define loss-speech \"HP:0002371\")\n;(define low-set-ears \"HP:0000369\")\n;(define microcephaly \"HP:0000252\")\n;(define small-stature \"HP:0004322\")\n;(define small-teeth \"HP:0000691\")\n;(define speech-delay \"HP:0000750\")\n;(define global-dev-delay \"HP:0001263\")\n;(define episodic-vomit \"HP:0002572\")\n;(define nystagmus \"HP:0000639\")\n;(define strabismus \"HP:0000486\")\n\n(define anxiety \"HP:0000739\")\n(define anxieties (cons anxiety (run* a (direct-synonym anxiety a))))\n;; human-readable\n;; (run* (a name) \n;;   (fresh (syn)\n;;     (membero syn anxieties)\n;;     (subclass-of+ a syn)\n;;     (cprop a \"name\" name))))\n(define sub-anxieties\n  (remove-duplicates\n   (run* a \n     (fresh (syn) \n       (membero syn anxieties)\n       (subclass-of* a syn)))))\n(define sub-anxieties-synonyms\n  (remove-duplicates\n   (run* a\n     (fresh (anx)\n       (membero anx sub-anxieties)\n       (conde ((direct-synonym anx a))\n              ((direct-synonym a anx)))))))\n(define phens sub-anxieties-synonyms)\n;; why so long? (take out constraints, runs faster)\n(time (run 10 (gene name p phenotype pname) \n     (fresh (cat) \n       (triple gene p phenotype)\n       (membero cat gene-or-protein)\n       (membero phenotype phens)\n       (membero p gene-to-disease-preds)\n       (is-a gene cat)\n       (cprop gene \"name\" name)\n       (cprop phenotype \"name\" pname)\n       )))\n\n\n;; performance puzzle\n\n(time (length (run 100 (gene p phenotype ) \n         (triple gene p phenotype)\n       (membero phenotype phens)\n)))\n\n(time (length (run 100 (gene p phenotype ) \n         (triple gene p phenotype)\n       (membero phenotype phens)\n       (membero p gene-to-disease-preds))))\n\n(time (length (run 100 (gene p phenotype ) \n     (fresh (cat) \n       (triple gene p phenotype)\n       (membero cat gene-or-protein)\n       (membero phenotype phens)\n       (membero p gene-to-disease-preds)\n       ))))\n"
  },
  {
    "path": "contrib/medikanren2/neo/Andy/simple-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n(define (concept->name curie)\n  (let ((id-name-val\n         (remove-duplicates (filter (lambda (cl)\n                                      (and (equal? (car cl) curie)\n                                           (equal? (cadr cl) \"name\")))\n                                    (query:Concept (list curie))))))\n        (if (null? id-name-val)\n            curie\n            (caddar id-name-val))))\n\n(define (concept->category curie)\n  (let ((category (assoc \"category\" (curie->properties curie))))\n    (if category (cdr category) '())))\n\n(define (one-hop-results->jsexpr results)\n  (let loop ((results results)\n             (edges (set))\n             (nodes (set)))\n    (cond\n      ((null? results) (hasheq 'nodes (set->list nodes) 'edges (set->list edges)))\n      (else (let ((res (car results)))\n              (match res\n                (`(,subj ,pred ,obj . ,props)\n                 (loop (cdr results)\n                       (set-add edges (hasheq 'source subj 'target obj))\n                       (set-add (set-add nodes (hasheq 'id subj\n                                                       'label (concept->name subj)\n                                                       'category_label (concept->category subj)))\n                                (hasheq 'id obj\n                                        'label (concept->name obj)\n                                        'category_label (concept->category obj)))))))))))\n\n(define (two-hop-results->jsexpr results)\n  (let loop ((results results)\n             (edges (set))\n             (nodes (set)))\n    (cond\n      ((null? results) (hasheq 'nodes (set->list nodes) 'edges (set->list edges)))\n      (else (let ((res (car results)))\n              (match res\n                (`(,subj1 ,pred1 ,X ,pred2 ,obj2 . ,props)\n                 (loop (cdr results)\n                       (set-add (set-add edges (hasheq 'source subj1 'target X))\n                                (hasheq 'source X 'target obj2))\n                       (set-add (set-add (set-add nodes (hasheq 'id subj1\n                                                                'label (concept->name subj1)\n                                                                'category_label (concept->category subj1)))\n                                         (hasheq 'id obj2\n                                                 'label (concept->name obj2)\n                                                 'category_label (concept->category obj2)))\n                                (hasheq 'id X\n                                        'label (concept->name X)\n                                        'category_label (concept->category X)))))))))))\n\n\n\n\n(define regulates-EGFR\n  (time (query:X->Known\n         #f\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"HGNC:3236\")))))))\n\n#|\nThis is all that is required:\n{\n  \"nodes\": [\n    { \"id\": \"node1\", \"label\": \"Node 1\" },\n    { \"id\": \"node2\", \"label\": \"Node 2\" },\n    { \"id\": \"node3\", \"label\": \"Node 3\" }\n  ],\n  \"edges\": [\n    { \"source\": \"node1\", \"target\": \"node2\" },\n    { \"source\": \"node2\", \"target\": \"node3\" }\n  ]\n}\nI use the curie as the ID and the name as the label for nodes and get the categories as well.\nThen also get the predicate and qualifiers,  from the edge, but have not used that much. So, if It hard to break out then I can go without for now.\n|#\n\n\n(let ((op (open-output-file \"X-regulates-EGFR.json\" #:mode 'text #:exists 'replace)))\n  (write-json (one-hop-results->jsexpr regulates-EGFR) op)\n  (close-output-port op))\n\n\n\n#|\nGene1 - any node - Disease 1\n\nprobably should exclude `biolink:same_as` as a predicate\n|#\n\n(define (gene->any->disease gene disease)\n  (time (query:Known->X->Known\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list gene))))\n         (set->list\n          (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n           '(\"biolink:affects\"  \"biolink:interacts_with\")))\n         #f\n         (set->list\n          (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n           '(\"biolink:affects\"  \"biolink:interacts_with\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list disease)))))))\n\n;; BRCA2 and breast cancer\n(define BRCA2->any->breast-cancer\n  (gene->any->disease \"HGNC:1101\" \"MONDO:0007254\"))\n\n(let ((op (open-output-file \"BRCA2->any->breast-cancer.json\" #:mode 'text #:exists 'replace)))\n  (write-json (two-hop-results->jsexpr BRCA2->any->breast-cancer) op)\n  (close-output-port op))\n"
  },
  {
    "path": "contrib/medikanren2/neo/Kaiwen/auto-grow-example.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n racket/set)\n\n;; Numbers of the top bucket of the RoboKop KG, Text Mining KG, and RTX-KG2 KG.\n(define TOP_BUCKET_NUMBERS (list (list (get-highest-bucket-number-robokop))\n                                 (list (get-highest-bucket-number-text-mining))\n                                 (list (get-highest-bucket-number-rtx-kg2))))\n\n;; a comparison between one-hop query with or without using the bucket setting\n(define regulates-EGFR\n  (time (query:X->Known\n         #f\n         '(\"biolink:regulates\")\n         (curies->synonyms-in-db (list \"HGNC:3236\")))))\n(length regulates-EGFR)\n; 44\n\n(define regulates-EGFR-faster\n  (time (query:X->Known-scored\n         #f\n         '(\"biolink:regulates\")\n         (curies->synonyms-in-db (list \"HGNC:3236\"))\n         TOP_BUCKET_NUMBERS)))\n(length regulates-EGFR-faster)\n; 0\n\n;; There is a problem when we use the bucketing approach is that we might \n;; receive zero answer from the buckets that has a higer score (amount of supports).\n;; Hence, you can either manually decrease the bucket number and redo the\n;; query, or you may write a procedure to realize auto growing until reach\n;; the amount of answers you want, like the procedure auto-grow shown below.\n\n\n;; The procedure 1-hop-proc takes a list of bucket numbers.\n(define (1-hop-proc bucket*)\n  (query:X->Known-scored\n         #f\n         '(\"biolink:regulates\")\n         (curies->synonyms-in-db (list \"HGNC:3236\"))\n         bucket*))\n\n;; The procedure auto-grow takes a query procedure (how do you want to\n;; query against the mediKanren neo server?), a list of buket numbers to\n;; start with, and a number representing the least amount of anwers\n;; you expected to receive. It is possible you do not get 'enough'\n;; answers, it is because those are all the answers it can return\n;; from the KGs. You may try to modify the 1-hop-proc to get more:\n;; more input curies, taking the subclasses of it/them, etc. \n(define example (time (auto-grow 1-hop-proc TOP_BUCKET_NUMBERS 100)))\n(length example)\n; 44\n\n\n;; The implementation of auto-grow is constomized with the need of the\n;; mediKanren neo-server. So it starts querying with the given\n;; list of bucket numbers and decreases the level of confidency (score of\n;; the edge) each round. It does not have to behavior this way. You may\n;; write your own procedure to achieve a different goal.\n\n;; A trick to not query against a specific KG can be achived by manually\n;; set the bucket number to be #f, like (#f '(10) '(10)) which means\n;; 'I would not like answers from the robokop KG, and please querying\n;; text-mining KG and rtx-kg2 KG with the bucket 10 for each.'. As you\n;; may have noticed from the definition of TOP_BUCKET_NUMBERS, the bucket list\n;; represents the KGs in the order of robokop, text-mining, and rtx-kg2.\n(define regulates-EGFR-ramdom\n  (time (query:X->Known-scored\n         #f\n         '(\"biolink:regulates\")\n         (curies->synonyms-in-db (list \"HGNC:3236\"))\n         (list #f '(10) '(10)))))\n(length regulates-EGFR-ramdom)\n; 0\n"
  },
  {
    "path": "contrib/medikanren2/neo/Kaiwen/mayo-gene-list.rkt",
    "content": "#lang racket\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-command-line-interface/utils.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n )\n\n(define file-name \"gene_list_medikanren_merged.csv\")\n(define in (open-input-file file-name))\n\n(define genes\n  (let* ((header (read-line in 'any))\n         (header (string-split header \",\" #:trim? #f)))\n    (let loop ((line-str (read-line in 'any))\n               (genes '()))\n      (cond\n        ((eof-object? line-str)\n         (close-input-port in)\n         (printf \"finished processing gene curies\")\n         genes)\n        (else\n         (let* ((line (string-split line-str \",\" #:trim? #f))\n                (curie (cadr line))\n                (curie (string-append \"ENSEMBL:\" curie)))\n           (loop (read-line in 'any) (cons curie genes))))))))\n\n(define genes+ (curie->gene/protein-conflation (curies->synonyms genes)))\n\n(define (write-answers edge* path)\n  (write-list-to-tsv\n   '(\"subject_curie\"\n     \"subject_name\"\n     \"subject_categories\"\n     \"gene_curie\"\n     \"gene_name\"\n     \"predicate\"\n     \"qualified_predicate\"\n     \"object_aspect_qualifier\"\n     \"object_direction_qualifier\"\n     \"publications\"\n     \"publication_count\"\n     \"edge_source\"\n     )\n   (map (lambda (e)\n          (match e\n            [`(,sub ,pred ,obj . ,prop)\n             (let* ((qualified-pred (get-assoc \"qualified_predicate\" prop))\n                    (object-aspect-qualifier (get-assoc \"object_aspect_qualifier\" prop))\n                    (object-direction-qualifier (get-assoc \"object_direction_qualifier\" prop))\n                    (source (get-assoc \"primary_knowledge_source\" prop))\n                    (publications (get-publications prop))\n                    (publication-count (length publications))\n                    )\n               (list\n                sub\n                (curie->name-remember sub)\n                (curie->categories-remember sub)\n                obj\n                (curie->name-remember obj)\n                pred\n                (if qualified-pred qualified-pred \"not apply\")\n                (if object-aspect-qualifier object-aspect-qualifier \"not apply\")\n                (if object-direction-qualifier object-direction-qualifier \"not apply\")\n                publications\n                publication-count\n                source\n                ))]\n            [else '()]))\n        (remove-duplicates edge*))\n   path))\n\n(define (mediKanren-activates curie* path)\n  (write-answers\n   (filter\n    activate-edge-filter\n   (query:X->Known\n    (set->list (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db '(\"biolink:ChemicalOrDrugOrTreatment\")))\n    '(\"biolink:has_increased_amount\"\n      \"biolink:affects\"\n      \"biolink:produces\"\n      \"biolink:regulates\"\n      \"biolink:enables\"\n      ;\"biolink:treats\"\n      \"biolink:positively_correlated_with\"\n      ;\"biolink:ameliorates\"\n      )\n    curie*))\n   path))\n\n(define (mediKanren-inhibits curie* path)\n  (write-answers\n   (filter\n    inhibite-edge-filter\n    (query:X->Known\n     (set->list (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db '(\"biolink:ChemicalOrDrugOrTreatment\")))\n     '(\"biolink:prevents\"\n       \"biolink:affects\"\n       \"biolink:regulates\"\n       \"biolink:has_decreased_amount\"\n       \"biolink:disrupts\"\n       \"biolink:negatively_correlated_with\")\n     curie*))\n   path))\n\n;(time (mediKanren-activates genes+ \"drugmix_activate_genes.tsv\"))\n;(time (mediKanren-inhibits genes+ \"drugmix_inhibit_genes.tsv\"))"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/achromatopsia-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers.rkt\"\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n#|\nWhat treats achromatopsia (color blindness)?\n\nAn associated gene:\nCNGB3\n\nACHM3\n|#\n\n;; achromatopsia (DOID:13911)\n(define all-achromatopsia-curies\n  (get-descendent-curies*-in-db\n   (curies->synonyms-in-db\n    (list \"DOID:13911\"))))\n;; http://www.informatics.jax.org/disease/DOID:13911\n;; ICD10CM:H53.51, ICD9CM:368.54, MESH:D003117, NCI:C84528, ORDO:49382, UMLS_CUI:C0152200 \n'(\"DOID:0050679\"\n  \"UMLS:C0339537\"\n  \"MONDO:0014677\"\n  \"MESH:C536021\"\n  \"ORPHANET:16\"\n  \"DOID:13911\"\n  \"MONDO:0010563\"\n  \"ORPHANET:49382\"\n  \"NCIT:C84528\"\n  \"MONDO:0009003\"\n  \"HP:0011516\"\n  \"UMLS:C0152200\"\n  \"MONDO:0012398\"\n  \"DOID:0110009\"\n  \"DOID:0110007\"\n  \"DOID:0110008\"\n  \"DOID:0110010\"\n  \"MONDO:0013465\"\n  \"MONDO:0009875\"\n  \"UMLS:C0302129\"\n  \"MONDO:0018852\")\n\n;; achromatopsia 3 (DOID:0110008)\n(define all-achromatopsia3-curies\n  (get-descendent-curies*-in-db\n   (curies->synonyms-in-db\n    (list \"DOID:0110008\"))))\n;; http://www.informatics.jax.org/disease/DOID:0110008\n;; ACHM1; ACHM3; Pingelapese blindness; RMCH1; rod monochromacy 1; rod monochromatism 1 \n'(\"OMIM:262300\"\n \"OMIM:MTHU004637\"\n \"DOID:0110008\"\n \"MONDO:0009875\"\n \"OMIM:MTHU005722\"\n \"OMIM:MTHU028493\"\n \"OMIM:MTHU002321\"\n \"OMIM:MTHU023011\"\n \"OMIM:MTHU023012\"\n \"OMIM:MTHU023013\"\n \"OMIM:MTHU023014\"\n \"OMIM:MTHU036378\"\n \"UMLS:C1849792\"\n \"MESH:C536129\")\n\n\n;; What treats achromatopsia?\n(define achromatopsia-treatments\n  (query:X->Known\n   ;; Looking for any type of treatment\n   #f\n   ;; list of predicates\n   (set->list (get-predicate-descendents-in-db \"biolink:treats\"))\n   ;; list of known CURIES (for achromatopsia)\n   (set->list all-achromatopsia-curies)))\n;; =>\n'((\"UMLS:C0009836\"\n   \"Contact Lenses\"\n   \"biolink:treats\"\n   \"UMLS:C0302129\"\n   \"Achromatopsia 1\"\n   (\"id\" \"UMLS:C0009836---SEMMEDDB:treats---UMLS:C0302129---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0302129\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:315420\")\n   (\"publications_info\"\n    \"{\\\"PMID:315420\\\": {\\\"publication date\\\": \\\"1979 Jul\\\", \\\"sentence\\\": \\\"A young female rod monochromat is treated optometrically with binocular contact lenses to relieve light dazzlement and a monocular lens to improve hue discrimination.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 836}}\")\n   (\"subject\" \"UMLS:C0009836\"))\n  \n  (\"UMLS:C0012315\"\n   \"Dihydropyridines\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0012315---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:33827965\")\n   (\"publications_info\"\n    \"{\\\"PMID:33827965\\\": {\\\"publication date\\\": \\\"2021 Apr 07\\\", \\\"sentence\\\": \\\"Active compounds and our structure-activity correlated data for the dihydropyridine compound class may provide valuable information for developing a treatment of the trafficking defect in achromatopsia.\\\", \\\"subject score\\\": 851, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C0012315\"))\n  \n  (\"UMLS:C0220825\"\n   \"Evaluation\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0220825---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:32881472\")\n   (\"publications_info\"\n    \"{\\\"PMID:32881472\\\": {\\\"publication date\\\": \\\"2020 Aug 03\\\", \\\"sentence\\\": \\\"Methods: Affected members from three pedigrees with classical enhanced S-cone syndrome (ESCS; Pedigree 1), congenital stationary night blindness (CSNB; Pedigree 2), and achromatopsia (ACHM; Pedigree 3), respectively, underwent detailed ophthalmologic evaluation, optical coherence tomography, and electroretinography.\\\", \\\"subject score\\\": 851, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C0220825\"))\n  \n  (\"UMLS:C0699680\"\n   \"Metric (substance)\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0699680---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:25277229\")\n   (\"publications_info\"\n    \"{\\\"PMID:25277229\\\": {\\\"publication date\\\": \\\"2014 Oct 02\\\", \\\"sentence\\\": \\\"CONCLUSIONS: We present cone reflectivity as a metric that can be used to characterize cone structure in ACHM.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C0699680\"))\n  \n  (\"UMLS:C1261322\"\n   \"Evaluation procedure\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C1261322---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:25103266|PMID:28145975|PMID:30513534\")\n   (\"publications_info\"\n    \"{\\\"PMID:25103266\\\": {\\\"publication date\\\": \\\"2014 Aug 07\\\", \\\"sentence\\\": \\\"METHODS: Thirty-eight molecularly confirmed ACHM subjects underwent serial assessments, including spectral domain optical coherence tomography (SD-OCT), microperimetry, and fundus autofluorescence (FAF).\\\", \\\"subject score\\\": 872, \\\"object score\\\": 740}, \\\"PMID:28145975\\\": {\\\"publication date\\\": \\\"2017 Oct\\\", \\\"sentence\\\": \\\"REPEATABILITY AND LONGITUDINAL ASSESSMENT OF FOVEAL CONE STRUCTURE IN CNGB3-ASSOCIATED ACHROMATOPSIA.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 827}, \\\"PMID:30513534\\\": {\\\"publication date\\\": \\\"2018 Dec 03\\\", \\\"sentence\\\": \\\"Longitudinal Assessment of Retinal Structure in Achromatopsia Patients With Long-Term Follow-up.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 888}}\")\n   (\"subject\" \"UMLS:C1261322\"))\n  \n  (\"UMLS:C0021102\"\n   \"Implants\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0021102---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:26567794\")\n   (\"publications_info\"\n    \"{\\\"PMID:26567794\\\": {\\\"publication date\\\": \\\"2015 Oct\\\", \\\"sentence\\\": \\\"However, testing CNTF-releasing implant in human CNGB3 achromats failed to show benefit.\\\", \\\"subject score\\\": 868, \\\"object score\\\": 749}}\")\n   (\"subject\" \"UMLS:C0021102\"))\n  \n  (\"UMLS:C0009836\"\n   \"Contact Lenses\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0009836---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:17208670|PMID:17601566\")\n   (\"publications_info\"\n    \"{\\\"PMID:17601566\\\": {\\\"publication date\\\": \\\"2007 Jul\\\", \\\"sentence\\\": \\\"The use of tinted contact lenses in the management of achromatopsia.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 1000}, \\\"PMID:17208670\\\": {\\\"publication date\\\": \\\"2007 Jan\\\", \\\"sentence\\\": \\\"The use of tinted contact lenses in the management of achromatopsia.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C0009836\"))\n  \n  (\"UMLS:C0087111\"\n   \"Therapeutic procedure\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0087111---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:29926749|PMID:30289319\")\n   (\"publications_info\"\n    \"{\\\"PMID:29926749\\\": {\\\"publication date\\\": \\\"2018 Jul 30\\\", \\\"sentence\\\": \\\"The purpose of this study was to evaluate long-term efficacy and safety results of treatment, findings that hold great relevance for clinical trials that started recently in CNGA3 achromatopsia patients.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 790}, \\\"PMID:30289319\\\": {\\\"publication date\\\": \\\"2018 Dec\\\", \\\"sentence\\\": \\\"CONCLUSIONS: These novel variants expand the genotypes associated with ACHM and may help in future therapy development for ACHM.\\\", \\\"subject score\\\": 851, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C0087111\"))\n  \n  (\"UMLS:C0011900\"\n   \"Diagnosis\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0011900---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:29257187\")\n   (\"publications_info\"\n    \"{\\\"PMID:29257187\\\": {\\\"publication date\\\": \\\"2018 Mar 01\\\", \\\"sentence\\\": \\\"The purpose of this review was to survey the current knowledge on diagnosis and treatment options in achromatopsia.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C0011900\"))\n  \n  (\"UMLS:C1304648\"\n   \"Gene replacement therapy\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C1304648---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:26407004\")\n   (\"publications_info\"\n    \"{\\\"PMID:26407004\\\": {\\\"publication date\\\": \\\"2015\\\", \\\"sentence\\\": \\\"These newly characterized large animal models not only provide a valuable system for studying cone-specific CNG channel function in health and disease, but also represent prime candidates for proof-of-concept studies of CNGA3 gene replacement therapy for ACHM patients.\\\", \\\"subject score\\\": 923, \\\"object score\\\": 888}}\")\n   (\"subject\" \"UMLS:C1304648\"))\n  \n  (\"UMLS:C1533685\"\n   \"Injection procedure\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C1533685---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:28478700\")\n   (\"publications_info\"\n    \"{\\\"PMID:28478700\\\": {\\\"publication date\\\": \\\"2017 06\\\", \\\"sentence\\\": \\\"Safety and Efficacy Evaluation of rAAV2tYF-PR1.7-hCNGA3 Vector Delivered by Subretinal Injection in CNGA3 Mutant Achromatopsia Sheep.\\\", \\\"subject score\\\": 861, \\\"object score\\\": 775}}\")\n   (\"subject\" \"UMLS:C1533685\"))\n  \n  (\"UMLS:C1520007\"\n   \"Viral Vector\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C1520007---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:26603570\")\n   (\"publications_info\"\n    \"{\\\"PMID:26603570\\\": {\\\"publication date\\\": \\\"2016 Jan\\\", \\\"sentence\\\": \\\"These results have informed the design of an AAV vector for treatment of patients with achromatopsia.\\\", \\\"subject score\\\": 861, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C1520007\"))\n  \n  (\"UMLS:C1511790\"\n   \"Detection\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C1511790---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\" \"PMID:32531858|PMID:3486271\")\n   (\"publications_info\"\n    \"{\\\"PMID:3486271\\\": {\\\"publication date\\\": \\\"1986 Feb\\\", \\\"sentence\\\": \\\"Threshold detection for sine-wave grating stimuli of varying spatial and temporal frequency was used to investigate the nature of spatial and temporal post-receptoral sensitivity in the typical, complete achromat.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 740}, \\\"PMID:32531858\\\": {\\\"publication date\\\": \\\"2020 Jun 12\\\", \\\"sentence\\\": \\\"We achieved a molecular diagnostic rate of 35%-95%, depending on the clinical entities, with a high detection rate for achromatopsia, retinoschisis and choroideremia, and a low detection rate for central areolar choroidal dystrophy and macular dystrophy.\\\", \\\"subject score\\\": 851, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"UMLS:C1511790\"))\n  \n  (\"UMLS:C0017296\"\n   \"gene therapy\"\n   \"biolink:treats\"\n   \"UMLS:C0152200\"\n   \"Achromatopsia\"\n   (\"id\" \"UMLS:C0017296---SEMMEDDB:treats---UMLS:C0152200---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C0152200\")\n   (\"predicate\" \"biolink:treats\")\n   (\"publications\"\n    \"PMID:20378608|PMID:22882429|PMID:23141518|PMID:24658860|PMID:25616768|PMID:25855802|PMID:26087757|PMID:26196097|PMID:28095637|PMID:29259520|PMID:30324456|PMID:32352493|PMID:33528822|PMID:34006508\")\n   (\"publications_info\"\n    \"{\\\"PMID:24658860\\\": {\\\"publication date\\\": \\\"2014 Mar\\\", \\\"sentence\\\": \\\"The outstanding results derived from the animal model are the starting point for the first human translation of a gene therapy for achromatopsia in Germany.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:23141518\\\": {\\\"publication date\\\": \\\"2012 Aug\\\", \\\"sentence\\\": \\\"With the development of molecular genetics and the therapeutic gene replacement technology, the adeno-associated viral (AAV) vector-mediated gene therapy for achromatopsia in the preclinical animal experiments achieved encouraging progress in the past years.\\\", \\\"subject score\\\": 763, \\\"object score\\\": 1000}, \\\"PMID:22882429\\\": {\\\"publication date\\\": \\\"2012 Sep\\\", \\\"sentence\\\": \\\"Recent successes in using gene therapy to treat canine achromatopsia, X-linked progressive retinal atrophy (PRA) and the more severe rapid degenerations such as rod-cone dysplasia type 3 may lead also to the translation to human clinical trials.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 888}, \\\"PMID:20378608\\\": {\\\"publication date\\\": \\\"2010 Jul 01\\\", \\\"sentence\\\": \\\"Our results hold promise for future clinical trials of cone-directed gene therapy in achromatopsia and other cone-specific disorders.\\\", \\\"subject score\\\": 861, \\\"object score\\\": 1000}, \\\"PMID:29259520\\\": {\\\"publication date\\\": \\\"2017 12\\\", \\\"sentence\\\": \\\"The evidence to date suggests that gene therapy for achromatopsia will need to be applied early in childhood to be effective.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:25855802\\\": {\\\"publication date\\\": \\\"2015 Jul 01\\\", \\\"sentence\\\": \\\"Demonstration of gene therapy in a cone-dominant mouse model by IVit delivery provides a potential alternative vector delivery mode for safely transducing foveal cones in achromatopsia patients and in other human retinal diseases affecting foveal function.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 888}, \\\"PMID:26087757\\\": {\\\"publication date\\\": \\\"2015 Sep\\\", \\\"sentence\\\": \\\"The results support future application of subretinal AAV5-mediated gene-augmentation therapy in CNGA3 achromatopsia patients.\\\", \\\"subject score\\\": 803, \\\"object score\\\": 790}, \\\"PMID:28095637\\\": {\\\"publication date\\\": \\\"2017 Mar\\\", \\\"sentence\\\": \\\"Gene therapy for achromatopsia.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:30324456\\\": {\\\"publication date\\\": \\\"2019\\\", \\\"sentence\\\": \\\"One example is gene therapy for achromatopsia which affects daylight vision.\\\", \\\"subject score\\\": 812, \\\"object score\\\": 1000}, \\\"PMID:25616768\\\": {\\\"publication date\\\": \\\"2015 May\\\", \\\"sentence\\\": \\\"The present study took steps toward performing a trial of gene therapy in ACHM by characterizing the genetics of ACHM in Israel and the Palestinian Territories and analyzing retinal function and structure in CNGA3 ACHM patients from the Israeli-Palestinian population and US patients with other origins.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:26196097\\\": {\\\"publication date\\\": \\\"2015 Jul\\\", \\\"sentence\\\": \\\"The potential for the treatment of achromatopsia in humans with gene therapy shows great promise.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:32352493\\\": {\\\"publication date\\\": \\\"2020 Apr 30\\\", \\\"sentence\\\": \\\"Objective: To assess safety and vision outcomes of supplemental gene therapy with adeno-associated virus (AAV) encoding CNGA3 (AAV8.CNGA3) in patients with CNGA3-linked achromatopsia.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 840}, \\\"PMID:33528822\\\": {\\\"publication date\\\": \\\"2021 Feb 02\\\", \\\"sentence\\\": \\\"RESULTS: Various adenovirus vectors have been deployed to test the efficacy of gene therapy for achromatopsia in animals and humans.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:34006508\\\": {\\\"publication date\\\": \\\"2021 May 18\\\", \\\"sentence\\\": \\\"AIMS: To determine long-term safety and efficacy outcomes of a subretinal gene therapy for CNGA3-associated achromatopsia.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 802}}\")\n   (\"subject\" \"UMLS:C0017296\"))\n  )\n"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/alz-query-revisited-multi-db-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n;; Can we now answer the old Alz query?\n\n;; Which proteins with SH3 domains interact with tau protein in humans?\n\n;; tau protein has CURI UniProtKB:P10636\n\n;; find tau protein synonyms:\n(define tau-protein-synonyms\n  (curies->synonyms-in-db\n   (list \"UniProtKB:P10636\")))\n\ntau-protein-synonyms\n;;=>\n'(\"UMLS:C1446659\"\n  \"REACT:R-HSA-201574\"\n  \"REACT:R-HSA-9619519\"\n  \"ENSEMBL:ENSG00000186868\"\n  \"NCBIGene:4137\"\n  \"REACT:R-HSA-350628\"\n  \"HGNC:6893\"\n  \"PR:P10636\"\n  \"OMIM:157140\"\n  \"REACT:R-HSA-9619521\"\n  \"UniProtKB:P10636\"\n  \"REACT:R-HSA-350642\")\n\n(length tau-protein-synonyms)\n;; =>\n12\n\n\n;; We can get more CURIs by considering descendents of the synonyms:\n(define tau-protein-synonyms-and-descendents\n  (set->list\n   (get-descendent-curies*-in-db\n    (curies->synonyms-in-db\n     (list \"UniProtKB:P10636\")))))\n\n(length tau-protein-synonyms-and-descendents)\n;;=>\n141\n\n;; These synonyms include lots of Protein Ontology (PR) entries (not sure if all are human).\n;; Not sure if we want these descendent CURIs.\n\n;; We will want to see which proteins interact with tau proteins.\n;; The correct Biolink predicate seems to be:\n;; \"biolink:interacts_with\"\n\n;; We need to find proteins with SH3 domains.\n\n;; Let's find the concept(s) of 'SH3 domain', without including\n;; proteins with 'SH3' in the protein name.  We want proteins that\n;; include SH3 domains, rather than proteins with SH3 in their name\n;; (of course, there may be overlap!).\n\n;; Protein category:\n;; \"biolink:Protein\"\n\n;; Might also want to include gene.\n\n;; The mixin biolink:GeneOrGeneProduct seems most appropriate.\n;; Make sure that we handle biolink:GeneOrGeneProduct correctly.\n\n(get-non-deprecated-mixed-ins-and-descendent-classes*-in-db '(\"biolink:GeneOrGeneProduct\"))\n;; =>\n(set\n \"biolink:ProteinIsoform\"\n \"biolink:GeneProductIsoformMixin\"\n \"biolink:GeneOrGeneProduct\"\n \"biolink:Protein\"\n \"biolink:GeneProductMixin\"\n \"biolink:Gene\")\n\n#|\nprotein with SH3 domains\nInterPro IPR001452 (SH3 domain)\nhttp://www.ebi.ac.uk/interpro/entry/InterPro/IPR001452/?species=9606\nPfam PF00018 (SH3 domain)\nDo we have InterPro or Pfam info?  Neither \"Pfam:PF00018\" nor \"InterPro:IPR001452\" have any synonyms in the current KGs.  Do I have the right CURIs?\n|#\n\n;; Try the name resolver SRI service\n;; https://name-resolution-sri.renci.org/docs#/lookup/lookup_curies_lookup_post\n;; Lookup: \"SH3 domain\"\n\n;; Get back:\n#|\n\"NCIT:C13340\" (\"SH3 Domain\",\"SRC Homology Region 3 Domain\")\n\"UMLS:C0282535\" (\"SH3 Domain\",\"SH3 Domains\",\"SH Z 003 DOMAIN\",\"SRC Homology Region 3 Domain\")\n\"NCIT:C14109\" (\"SH3-Binding Domain\",\"SH3-Binding Motif\")\n\"GO:0017124\" (\"SH3 domain binding\")\n\"UMLS:C1519141\" (\"SH3-Binding Domain\",\"SH3-Binding Motif\")\n\"UMLS:C1149349\" (\"SH3 domain binding\"),\n\"PANTHER.FAMILY:PTHR15706\" (\"SH3 MULTIPLE DOMAIN\")\n|#\n\n(set->list\n (get-descendent-curies*-in-db\n  (curies->synonyms-in-db\n   (list \"NCIT:C13340\"\n         \"UMLS:C0282535\"\n         \"NCIT:C14109\"\n         \"GO:0017124\"\n         \"UMLS:C1519141\"\n         \"UMLS:C1149349\"\n         \"PANTHER.FAMILY:PTHR15706\"))))\n;;=>\n'(\"UMLS:C1519141\"\n  \"NCIT:C14109\"\n  \"NCIT:C14110\"\n  \"UMLS:C1149349\"\n  \"UMLS:C0282535\"\n  \"GO:0017124\"\n  \"NCIT:C13340\"\n  \"PANTHER.FAMILY:PTHR15706\")\n\n;; Need to find proteins with the SH3 domain that occur in humans, that are known to interact with tau protein\n\n;; \"biolink:related_to\" and subpredicates\n\n\n(define related-to-SH3-domain-1\n  (query:X->Known\n   #f\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:related_to\")))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"NCIT:C13340\"\n            \"UMLS:C0282535\"\n            \"NCIT:C14109\"\n            \"GO:0017124\"\n            \"UMLS:C1519141\"\n            \"UMLS:C1149349\"\n            \"PANTHER.FAMILY:PTHR15706\"))))))\n\n(define related-to-SH3-domain-2\n  (query:Known->X\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"NCIT:C13340\"\n            \"UMLS:C0282535\"\n            \"NCIT:C14109\"\n            \"GO:0017124\"\n            \"UMLS:C1519141\"\n            \"UMLS:C1149349\"\n            \"PANTHER.FAMILY:PTHR15706\"))))\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:related_to\")))\n   #f))\n\n(list->set (map (lambda (e) (match e\n                              [`(,a ,b ,c ,d ,e . ,rest)\n                               c]))\n                related-to-SH3-domain-1))\n;;=>\n(set\n \"biolink:disrupts\"\n \"biolink:related_to\"\n \"biolink:subclass_of\"\n \"biolink:coexists_with\"\n \"biolink:has_part\"\n \"biolink:regulates\"\n \"biolink:close_match\"\n \"biolink:affects\"\n \"biolink:enables\")\n\n;; Looks like \"biolink:has_part\" is the one we want.\n\n(list->set (map (lambda (e) (match e\n                              [`(,a ,b ,c ,d ,e . ,rest)\n                               c]))\n                related-to-SH3-domain-2))\n;;=>\n(set\n \"biolink:has_part\"\n \"biolink:occurs_in\"\n \"biolink:subclass_of\"\n \"biolink:actively_involved_in\"\n \"biolink:interacts_with\"\n \"biolink:located_in\"\n \"biolink:regulates\"\n \"biolink:close_match\"\n \"biolink:affects\"\n \"biolink:enables\")\n\n\n(filter (lambda (e) e)\n        (map (lambda (e) (match e\n                   [`(,a ,b ,c ,d ,e . ,rest)\n                    (if (equal? c \"biolink:has_part\")\n                        (list a b c e)\n                        #f)]))\n     related-to-SH3-domain-1))\n;;=>\n#|\n((\"NCIT:C20973\" \"Amphiphysin\" \"biolink:has_part\" \"SH3 Domain\")\n (\"NCIT:C28720\"\n  \"MYC Box-Dependent-Interacting Protein 1\"\n  \"biolink:has_part\"\n  \"SH3 Domain\")\n (\"NCIT:C30130\" \"Cdc42-Interacting Protein 4\" \"biolink:has_part\" \"SH3 Domain\")\n ...)\n|#\n\n(curies->synonyms-in-db\n (list \"NCIT:C28720\"))\n;;=>\n'(\"NCIT:C28720\")\n\n;; Hmm.  Are these NCI Thesaurus CURIs the same as UMLS?  No!!\n\n;; NCIT browser\n;; https://ncit.nci.nih.gov/ncitbrowser/pages/home.jsf?version=23.01e\n;; https://ncit.nci.nih.gov/ncitbrowser/pages/multiple_search.jsf?nav_type=terminologies\n\n;; According to the NCIT browser,\n\"NCIT:C28720\"\n;; which is 'MYC Box-Dependent-Interacting Protein 1',\n;; has synonyms:\n\"OMIM:601248\"\n\"UniProtKB:O00499\"\n\"UMLS:C0529765\"\n\n(curies->synonyms-in-db\n (list \"OMIM:601248\"))\n;; =>\n'(\"OMIM:601248\"\n  \"ENSEMBL:ENSG00000136717\"\n  \"ENSEMBL:LRG_873\"\n  \"UMLS:C4316932\"\n  \"HGNC:1052\"\n  \"PR:O00499\"\n  \"UniProtKB:O00499\"\n  \"UMLS:C1332412\"\n  \"NCBIGene:274\")\n\n(curies->synonyms-in-db\n (list \"UniProtKB:O00499\"))\n;; =>\n'(\"OMIM:601248\"\n  \"ENSEMBL:ENSG00000136717\"\n  \"UMLS:C4316932\"\n  \"REACT:R-HSA-8868265\"\n  \"HGNC:1052\"\n  \"PR:O00499\"\n  \"UniProtKB:O00499\"\n  \"UMLS:C1332412\"\n  \"NCBIGene:274\")\n\n(curies->synonyms-in-db\n (list \"UMLS:C0529765\"))\n;; =>\n'(\"UMLS:C0529765\")\n\n;; Sigh\n\n;; We don't get back the NCIT mapping, alas\n(curies->synonyms-in-db\n (list \"OMIM:601248\"\n       \"UniProtKB:O00499\"\n       \"UMLS:C0529765\"))\n;; =>\n'(\"UMLS:C0529765\"\n  \"UniProtKB:O00499\"\n  \"OMIM:601248\"\n  \"ENSEMBL:ENSG00000136717\"\n  \"ENSEMBL:LRG_873\"\n  \"UMLS:C4316932\"\n  \"REACT:R-HSA-8868265\"\n  \"HGNC:1052\"\n  \"PR:O00499\"\n  \"UMLS:C1332412\"\n  \"NCBIGene:274\")\n\n;; If we leave out \"UMLS:C0529765\"\n;; at least we get a couple of UMLSs, but not\n;; \"UMLS:C0529765\" as specified by NCIT.\n(set->list\n (get-descendent-curies*-in-db\n  (curies->synonyms-in-db\n   (list \"OMIM:601248\"\n         \"UniProtKB:O00499\"))))\n;; =>\n'(\"PR:000046483\"\n  \"UniProtKB:O00499\"\n  \"UniProtKB:O00499-6\"\n  \"UniProtKB:O00499-9\"\n  \"UMLS:C1706887\"\n  \"PR:O00499-5\"\n  \"PR:O00499-4\"\n  \"PR:O00499-7\"\n  \"PR:O00499-6\"\n  \"PR:O00499-1\"\n  \"PR:O00499-3\"\n  \"PR:O00499-2\"\n  \"PR:O00499-9\"\n  \"PR:O00499-8\"\n  \"UniProtKB:O00499-7\"\n  \"UniProtKB:O00499-8\"\n  \"ENSEMBL:ENSG00000136717\"\n  \"ENSEMBL:LRG_873\"\n  \"UniProtKB:O00499-3\"\n  \"UMLS:C4316932\"\n  \"UniProtKB:O00499-11\"\n  \"NCBIGene:274\"\n  \"UniProtKB:O00499-10\"\n  \"UniProtKB:O00499-4\"\n  \"UniProtKB:O00499-5\"\n  \"PR:O00499-11\"\n  \"UniProtKB:O00499-1\"\n  \"PR:O00499-10\"\n  \"OMIM:601248\"\n  \"UMLS:C1332412\"\n  \"REACT:R-HSA-8868265\"\n  \"HGNC:1052\"\n  \"UniProtKB:O00499-2\"\n  \"PR:O00499\")\n\n(set->list\n (get-descendent-curies*-in-db\n  (curies->synonyms-in-db\n   (list \"OMIM:601248\"\n         \"UniProtKB:O00499\"\n         \"UMLS:C0529765\"))))\n;; =>\n'(\"PR:000046483\"\n  \"UniProtKB:O00499\"\n  \"UniProtKB:O00499-6\"\n  \"UMLS:C0529765\"\n  \"UniProtKB:O00499-9\"\n  \"UMLS:C1706887\"\n  \"PR:O00499-5\"\n  \"PR:O00499-4\"\n  \"PR:O00499-7\"\n  \"PR:O00499-6\"\n  \"PR:O00499-1\"\n  \"PR:O00499-3\"\n  \"PR:O00499-2\"\n  \"PR:O00499-9\"\n  \"PR:O00499-8\"\n  \"UniProtKB:O00499-7\"\n  \"UniProtKB:O00499-8\"\n  \"ENSEMBL:ENSG00000136717\"\n  \"ENSEMBL:LRG_873\"\n  \"UniProtKB:O00499-3\"\n  \"UMLS:C4316932\"\n  \"UniProtKB:O00499-11\"\n  \"NCBIGene:274\"\n  \"UniProtKB:O00499-10\"\n  \"UniProtKB:O00499-4\"\n  \"UniProtKB:O00499-5\"\n  \"PR:O00499-11\"\n  \"UniProtKB:O00499-1\"\n  \"PR:O00499-10\"\n  \"OMIM:601248\"\n  \"UMLS:C1332412\"\n  \"REACT:R-HSA-8868265\"\n  \"HGNC:1052\"\n  \"UniProtKB:O00499-2\"\n  \"PR:O00499\")\n\n\n(curies->synonyms-in-db\n (map car\n      (filter (lambda (e) e)\n              (map (lambda (e) (match e\n                                 [`(,a ,b ,c ,d ,e . ,rest)\n                                  (if (equal? c \"biolink:has_part\")\n                                      (list a b c e)\n                                      #f)]))\n                   related-to-SH3-domain-1))))\n\n(curies->synonyms-in-db\n (map (lambda (NCIT-CURI)\n        (string-replace NCIT-CURI \"NCIT:\" \"UMLS:\"))\n      (map car\n           (filter (lambda (e) e)\n                   (map (lambda (e) (match e\n                                      [`(,a ,b ,c ,d ,e . ,rest)\n                                       (if (equal? c \"biolink:has_part\")\n                                           (list a b c e)\n                                           #f)]))\n                        related-to-SH3-domain-1)))))\n;;=>\n'()\n\n;; Sigh\n\n;; TODO\n;; Try NCIT CURIs in th online node normalizer\n;;\n;; https://nodenormalization-sri.renci.org/docs#/default/get_normalized_node_handler_get_normalized_nodes_get\n;;\n;; Seems like the node normalizer has NCIT equivalents for diseases (such as NCIT:C34373), but not for genes/proteins (such as NCIT:C20973, NCIT:C28720, NCIT:C30130).\n;;\n;; Ask Chris B. about this\n;;\n;; Also ask the SRI KG people if they have NCIT and UMLS mappings.\n;; See, for example,\n;; https://obofoundry.org/ontology/ncit\n;;\n;; In the worst case, can create our own KG with the NCIT mappings.  Annoying...\n\n;; TODO\n;; Ask for an up-to-date version of the SRI KG\n\n;; TODO\n;;\n;; find all human proteins that are known to interact with tau protein,\n;; then take set intersection of those proteins and the proteins with\n;; SH3 domains\n;;\n;; Is there a more direct way to express this query?\n;;\n;; The fact that we can't connect the NCIT CURIs to other CURIs in the\n;; KGs is a bummer...\n"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/genes-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n;; Problem encountered on 5 Dec 2022:\n;;\n;; * HGNC CURIES are not normalized to UMLS or NCBI or OMIM CURIES\n\n;; Hand-curated mappings of HGNC to UMLS mappings, since there doesn't\n;; seem to currently be a way to map HGNC CURIES to UMLS CURIES\n;; through RTX-KG2 or through the node normalization knowledge graph.\n(define symbol/HGNC/UMLS*-list\n  '((MAPK8IP3  HGNC:6884   C1417026 C1436798)\n    (VMA21     HGNC:22082  C2681112 C2715590)\n    (NTRK2     HGNC:8032   C1334909 C1704842 C3853697)\n    (SGO1      HGNC:25088  C1428445 C1565925 C3890006)\n    (TPI1      HGNC:12009  C1420871 C3887669 C3541335 C0041078)\n    (FKRP      HGNC:17997  C1425226 C1448221)\n    (PHETA1    HGNC:26509  C1825239 C2932936)\n    (SPOP      HGNC:11254  C1420368 C3540803 C0669183)\n    (YWHAZ     HGNC:12855  C1421564 C3492243 C2981740)\n    (JAK2      HGNC:6192   C1334291 C1527617 C0169661)\n    (GDAP1     HGNC:15968  C1423872 C1453327)\n    (ESCO2     HGNC:27230  C1539367 C1569535)\n    (ZMIZ1     HGNC:16493  C1823956 C1433857 C3889263)\n    (SBF1      HGNC:10542  C1419823 C1259214)\n    (PEX10     HGNC:8851   C1418470 C1449205)\n    (KIF5A     HGNC:6323   C1416638 C1569075)\n    (LAMA2     HGNC:6482   C1416776 C1569076)\n    (FOXG1     HGNC:3811   C0812297 C1705148)\n    (BANP      HGNC:13450  C1538317 C0961071)\n    (NEXMIF    HGNC:29433  C1845260 C4041927)\n    (TBCD      HGNC:11581  C1420596 C1447856)\n    (DHTKD1    HGNC:23537  C1428130 C3657993)\n    (PNPT1     HGNC:23166  C1427960 C1310854 C2984134)\n    (ALG2      HGNC:23159  C1427955)\n    (SETBP1    HGNC:15573  C1423585 C1309881 C3815268)))\n\n(define get-generic-synonym/descendent-curies\n  (lambda (curie)\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db (list curie)))))\n\n(define get-gene-synonym/descendent-curies\n  (lambda (curie)\n    (let ((related-curies (get-generic-synonym/descendent-curies curie))\n          (gene-synonym-predicates\n           (set->list\n            (apply set-union\n                   (map get-predicate-descendents-in-db\n                        '(\"biolink:same_as\"\n                          \"biolink:expresses\"\n                          \"biolink:has_gene_product\"\n                          \"biolink:has_gene_or_gene_product\"\n                          \"biolink:has_output\"\n                          \"biolink:exact_match\"\n                          \"biolink:mesh_terms\"\n                          ;; Beware of using 'xref', since it is a very loose predicate\n                          ;; \"biolink:xref\"\n                          ))))))\n      (set-union\n       related-curies\n       (list->set\n        (map (lambda (e) (list-ref e 3))\n             (query:Known->X\n              (set->list related-curies)\n              gene-synonym-predicates\n              #f)))\n       (list->set\n        (map car\n             (query:X->Known\n              #f\n              gene-synonym-predicates\n              (set->list related-curies))))))))\n\n(define process-gene\n  (lambda (curie)\n    (let ((gene-curies (get-gene-synonym/descendent-curies curie)))\n      (query:X->Known\n       ;; Looking for any type of chemical substance\n       #f\n       ;; list of predicates\n       (set->list\n        (apply set-union\n               (map get-predicate-descendents-in-db\n                    '(\"biolink:positively_regulates\"\n                      \"biolink:negatively_regulates\"\n                      ;;\n                      \"biolink:entity_positively_regulates_entity\"\n                      \"biolink:entity_negatively_regulates_entity\"\n                      ;;\n                      \"biolink:increased_amount_of\"\n                      \"biolink:increases_activity_of\"\n                      \"biolink:increases_amount_or_activity_of\"\n                      \"biolink:increases_abundance_of\"\n                      \"biolink:increases_expression_of\"\n                      \"biolink:increases_synthesis_of\"\n                      ;;\n                      \"biolink:decreased_amount_in\"\n                      \"biolink:decreases_abundance_of\"\n                      \"biolink:decreases_synthesis_of\"\n                      \"biolink:decreases_activity_of\"\n                      \"biolink:decreases_amount_or_activity_of\"\n                      \"biolink:decreases_expression_of\"))))\n       ;; list of known CURIES (for genes)\n       (set->list gene-curies)))))\n\n(define process-symbol/HGNC/UMLS*-list\n  (lambda (symbol/HGNC/UMLS*-list)\n    (let loop ((ls symbol/HGNC/UMLS*-list))\n      (match ls\n        ['() '()]\n        [`((,symbol ,hgnc-curie-symbol . ,cid-curie-symbols) . ,rest)\n         (let ((hgnc-curie (symbol->string hgnc-curie-symbol))\n               (cid-curies (map symbol->string cid-curie-symbols)))\n           (let ((umls-curies (map (lambda (c) (string-append \"UMLS:\" c)) cid-curies)))\n             (let ((answers (apply append (map process-gene (cons hgnc-curie umls-curies)))))\n               (cons `(,symbol (,hgnc-curie-symbol . ,umls-curies) ,answers)\n                     (loop rest)))))]))))\n\n(define answers (process-symbol/HGNC/UMLS*-list symbol/HGNC/UMLS*-list))\n\n\n\n\n\n#| Extract publication information from answers |#\n\n(define (python->json py)\n  (define len (string-length py))\n  (let loop ((i 0) (start 0))\n    (cond ((= i len) (if (= start 0) py (substring py start)))\n          ((eqv? (string-ref py i) #\\')\n           (string-append\n             (substring py start i) \"\\\"\"\n             (let requote ((i (+ i 1)) (start (+ i 1)))\n               (cond ((eqv? (string-ref py i) #\\')\n                      (string-append (substring py start i) \"\\\"\"\n                                     (loop (+ i 1) (+ i 1))))\n                     ((eqv? (string-ref py i) #\\\\)\n                      (if (eqv? (string-ref py (+ i 1)) #\\\")\n                        (requote (+ i 2) start)\n                        (string-append (substring py start i)\n                                       (requote (+ i 2) (+ i 1)))))\n                     ((eqv? (string-ref py i) #\\\")\n                      (string-append (substring py start i) \"\\\\\\\"\"\n                                     (requote (+ i 1) (+ i 1))))\n                     (else (requote (+ i 1) start))))))\n          ((eqv? (string-ref py i) #\\\")\n           (let skip ((i (+ i 1)) (start start))\n             (cond ((eqv? (string-ref py i) #\\\") (loop (+ i 1) start))\n                   ((eqv? (string-ref py i) #\\\\)\n                    (if (eqv? (string-ref py (+ i 1)) #\\\")\n                      (skip (+ i 2) start)\n                      (string-append (substring py start i)\n                                     (skip (+ i 2) (+ i 1)))))\n                   (else                         (skip (+ i 1) start)))))\n          (else (loop (+ i 1) start)))))\n\n(define (pubmed-ids-from-edge-props eprops)\n  (cond\n    [(assoc \"publications\" eprops)\n     => (lambda (pr)\n          (define pubs (cadr pr))\n          (if (not (string? pubs))\n            '()\n            (regexp-match* #rx\"PMID:([0-9]+)\" pubs #:match-select cadr)))]\n    [else '()]))\n(define (pubmed-ids-from-edge edge)\n  (remove-duplicates\n    (match edge\n      [`(,s-curie ,s-name ,pred ,o-curie ,o-name . ,eprops)\n        (pubmed-ids-from-edge-props eprops)])))\n(define PUBMED_URL_PREFIX \"https://www.ncbi.nlm.nih.gov/pubmed/\")\n(define (pubmed-URLs-from-edge edge)\n  (map (lambda (pubmed-id) (string-append PUBMED_URL_PREFIX (~a pubmed-id)))\n       (pubmed-ids-from-edge edge)))\n\n(define (publications-info-alist-from-edge-props eprops)\n  (cond\n    [(assoc \"publications_info\" eprops) ;; RTX2\n     => (lambda (pr)\n          (with-handlers ([exn:fail?\n                           (lambda (v)\n                             ((error-display-handler) (exn-message v) v)\n                             '())])\n            (define pubs (cadr pr))\n            ;;(printf \"pubs:\\n~s\\n\" pubs)\n            (define jason-ht (string->jsexpr (python->json pubs)))\n            ;;(printf \"jason-ht:\\n~s\\n\" jason-ht)\n            (let ((pub-info-ls\n                   (hash-map jason-ht (lambda (k v)\n                                        (let ((pubmed-num* (regexp-match* #rx\"([0-9]+)\"\n                                                                          (symbol->string k)\n                                                                          #:match-select cadr)))\n                                          (if (pair? pubmed-num*)\n                                              (let ((pubmed-url\n                                                     (string-append PUBMED_URL_PREFIX (car pubmed-num*))))\n                                                (cons pubmed-url\n                                                      (list (hash-ref v '|publication date| #f)\n                                                            (hash-ref v '|subject score| #f)\n                                                            (hash-ref v '|object score| #f)\n                                                            (regexp-replace*\n                                                             #rx\"([ ]+)\"\n                                                             (hash-ref v 'sentence #f)\n                                                             \" \"))))\n                                              ;; else, the JSON is malformed\n                                              #f))))))\n              ;; filter out any #f results from malformed JSON\n              (filter (lambda (v) v) pub-info-ls))))]\n    [else '()]))\n(define (publications-info-alist-from-edge edge)\n  ;; ((pubmed-URL . (publication-date subject-score object-score sentence)) ...)\n  (remove-duplicates\n    (match edge\n      [`(,s-curie ,s-name ,pred ,o-curie ,o-name . ,eprops)\n        (publications-info-alist-from-edge-props eprops)])))\n\n\n\n(define write-answer-to-TSV-file\n  (lambda (answer)\n    (match answer\n      [`(,gene-symbol (,hgnc-curie-symbol . ,umls-curies) ,answers)\n       (let ((op (open-output-file\n                  (string-append\n                    \"X regulates \"\n                    (symbol->string gene-symbol)\n                    \" \"\n                    (~a `(,hgnc-curie-symbol . ,umls-curies))\n                    \".tsv\")\n                  #:mode 'text\n                  #:exists 'error)))\n         (fprintf op\n                  \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t\\n\"\n                  \"Subject CURIE\"\n                  \"Subject Name\"\n                  \"Predicate\"\n                  \"Object CURIE\"\n                  \"Object Name\"\n                  \"Pubmed URL\"\n                  \"Publication Date\"\n                  \"Sentence\")\n         (let loop ((answers answers))\n           (match answers\n             [`() (close-output-port op)]\n             [`(,answer . ,rest)\n              (match answer\n                [`(,s-curie ,s-name ,pred ,o-curie ,o-name . ,eprops)\n                 ;;(printf \"calling publications-info-alist-from-edge on:\\n\")\n                 ;;(printf \"~s\\n\" `(,s-curie ,s-name ,pred ,o-curie ,o-name . ,eprops))\n                 (let ((pubs-alist (publications-info-alist-from-edge answer)))\n                   ;; ((pubmed-URL . (publication-date subject-score object-score sentence)) ...)\n                   ;;(printf \"pubs-alist:\\n~s\\n\" pubs-alist)\n                   (cond\n                     [(null? pubs-alist)\n                      (let ((pubmed-URLs (pubmed-URLs-from-edge answer)))\n                        (cond\n                          [(null? pubmed-URLs)\n                           (fprintf op\n                                    \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t\\n\"\n                                    s-curie\n                                    s-name\n                                    pred\n                                    o-curie\n                                    o-name\n                                    \"\"\n                                    \"\"\n                                    \"\")                           \n                           (loop rest)]\n                          [else\n                           (for-each\n                             (lambda (pubmed-URL)\n                               (fprintf op\n                                        \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t\\n\"\n                                        s-curie\n                                        s-name\n                                        pred\n                                        o-curie\n                                        o-name\n                                        pubmed-URL\n                                        \"\"\n                                        \"\"))\n                             pubmed-URLs)\n                           (loop rest)]))]\n                     [else\n                      (for-each\n                        (lambda (pub-info)\n                          (match pub-info\n                            [`(,pubmed-URL . (,publication-date ,subject-score ,object-score ,sentence))\n                             (fprintf op\n                                      \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t\\n\"\n                                      s-curie\n                                      s-name\n                                      pred\n                                      o-curie\n                                      o-name\n                                      pubmed-URL\n                                      publication-date\n                                      sentence)]))\n                        pubs-alist)\n                      (loop rest)]))])])))])))\n\n(for-each write-answer-to-TSV-file answers)\n"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/nfix-multi-db-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n;; gene ->regulates-> NFIX\n(define (gene->regulates->NFIX)\n  (query:X->Known\n  \n   ;; category*.X\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-classes*-in-db\n     (list \"biolink:Gene\")))\n   ;; predicate*.X->K\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:regulates\")))\n \n   ;; curie*.K\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"HGNC:7788\"))))\n   ))\n\n(gene->regulates->NFIX)\n;; =>\n'((\"NCBIGene:322\"\n   \"APBB1\"\n   \"biolink:regulates\"\n   \"NCBIGene:4784\"\n   \"NFIX\"\n   (\"id\"\n    \"NCBIGene:322---SEMMEDDB:stimulates---None---None---increased---NCBIGene:4784---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"NCBIGene:4784\")\n   (\"predicate\" \"biolink:regulates\")\n   (\"publications\" \"PMID:17170108\")\n   (\"publications_info\"\n    \"{\\\"PMID:17170108\\\": {\\\"publication date\\\": \\\"2007 Feb 16\\\", \\\"sentence\\\": \\\"RNAi silencing of Fe65 increased APP-CTF levels, although also decreasing Abeta levels in H4-FL-APP cells.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 850}}\")\n   (\"subject\" \"NCBIGene:322\"))\n  (\"NCBIGene:4782\"\n   \"NFIC\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   (\"id\"\n    \"NCBIGene:4782---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C1417707\")\n   (\"predicate\" \"biolink:regulates\")\n   (\"publications\" \"PMID:29106906\")\n   (\"publications_info\"\n    \"{\\\"PMID:29106906\\\": {\\\"publication date\\\": \\\"2017 12 15\\\", \\\"sentence\\\": \\\"Finally, we report that, in the absence of Nfia or Nfib, there is a marked reduction in the spinal cord expression of NFIX, and that NFIB can transcriptionally activate Nfix expression in vitro.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 888}}\")\n   (\"subject\" \"NCBIGene:4782\"))\n  (\"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   (\"id\"\n    \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C1417707\")\n   (\"predicate\" \"biolink:regulates\")\n   (\"publications\" \"PMID:30266829\")\n   (\"publications_info\"\n    \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"NCBIGene:2048\"))\n  (\"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   (\"id\"\n    \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n   (\"knowledge_source\" \"infores:semmeddb\")\n   (\"object\" \"UMLS:C1417707\")\n   (\"predicate\" \"biolink:regulates\")\n   (\"publications\" \"PMID:30266829\")\n   (\"publications_info\"\n    \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n   (\"subject\" \"NCBIGene:5594\")))\n\n\n(define (drug->regulates->NFIX)\n  (query:X->Known\n  \n   ;; category*.X\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-classes*-in-db\n     (list \"biolink:Drug\")))\n   ;; predicate*.X->K\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:regulates\")))\n \n   ;; curie*.K\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"NCBIGene:4782\"))))\n   ))\n\n(drug->regulates->NFIX)\n;; =>\n'()\n\n\n;; drug ->regulates-> gene ->regulates-> NFIX\n(define (drug->regulates->gene->regulates->NFIX)\n  (query:X->Y->Known\n   ;; category*.X \n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-classes*-in-db\n     (list \"biolink:Drug\")))\n   ;; predicate*.X->Y\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:regulates\")))\n  \n   ;; category*.Y\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-classes*-in-db\n     (list \"biolink:Gene\")))\n   ;; predicate*.Y->K\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:regulates\")))\n \n   ;; curie*.K\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"HGNC:7788\"))))\n   ))\n\n(drug->regulates->gene->regulates->NFIX)\n;; =>\n'((\"UMLS:C0017302\"\n   \"General anesthetic drugs\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0017302---SEMMEDDB:stimulates---None---None---increased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:26400403\")\n    (\"publications_info\"\n     \"{\\\"PMID:26400403\\\": {\\\"publication date\\\": \\\"2015 Dec\\\", \\\"sentence\\\": \\\"While all three general anesthetics effectively blocked nociceptive responses and activation of ERK in the rat ACC following formalin injection during anesthesia, only sevoflurane inhibited ERK activation in the spinal cord and ACC at 24 h post-injection.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0017302\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:2048\")))\n  (\"UMLS:C0304497\"\n   \"Cytotoxic agent (product)\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0304497---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:29507530\")\n    (\"publications_info\"\n     \"{\\\"PMID:29507530\\\": {\\\"publication date\\\": \\\"2018\\\", \\\"sentence\\\": \\\"Conclusion: Taken together, our data identified nilotinib as a cytotoxic drug that combined with ERK inhibitors deserves to be tested as a novel therapy for adrenocortical carcinoma.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 861}}\")\n    (\"subject\" \"UMLS:C0304497\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:2048\")))\n  (\"UMLS:C0597220\"\n   \"phospholipase inhibitor\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0597220---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:19048108\")\n    (\"publications_info\"\n     \"{\\\"PMID:19048108\\\": {\\\"publication date\\\": \\\"2008\\\", \\\"sentence\\\": \\\"A phospholipase Cgamma (PLCgamma) inhibitor and shRNA, as well as an Erk inhibitor, reduced ST6Gal1 and FUT9 mRNA levels and inhibited effects of L1 on neurite outgrowth and cell survival.\\\", \\\"subject score\\\": 913, \\\"object score\\\": 827}}\")\n    (\"subject\" \"UMLS:C0597220\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:2048\")))\n  (\"UMLS:C0040616\"\n   \"Anti-Anxiety Agents\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0040616---SEMMEDDB:stimulates---None---None---increased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30102992\")\n    (\"publications_info\"\n     \"{\\\"PMID:30102992\\\": {\\\"publication date\\\": \\\"2018 Nov 15\\\", \\\"sentence\\\": \\\"CONCLUSION: This study demonstrated that aqueous extracts from S. japonicus viscera are effective whitening and anti-aging agents that stimulate ERK signaling to inhibit melanin synthesis and promote collagen synthesis.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 861}}\")\n    (\"subject\" \"UMLS:C0040616\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:2048\")))\n  (\"UMLS:C0003211\"\n   \"Anti-Inflammatory Agents, Non-Steroidal\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0003211---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:16230075\")\n    (\"publications_info\"\n     \"{\\\"PMID:16230075\\\": {\\\"publication date\\\": \\\"2005 Oct\\\", \\\"sentence\\\": \\\"Exposure to NSAIDs inhibits Sp1 and ERK phosphorylation.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 861}}\")\n    (\"subject\" \"UMLS:C0003211\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:2048\")))\n  (\"UMLS:C1514713\"\n   \"Raf Kinase Inhibitor\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C1514713---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:18163502\")\n    (\"publications_info\"\n     \"{\\\"PMID:18163502\\\": {\\\"publication date\\\": \\\"2008 Jan\\\", \\\"sentence\\\": \\\"Components of the ERK pathway were inhibited by Raf-1 kinase inhibitor and the MEK inhibitor, PD98059.\\\", \\\"subject score\\\": 923, \\\"object score\\\": 861}}\")\n    (\"subject\" \"UMLS:C1514713\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:2048\")))\n  (\"UMLS:C0003385\"\n   \"Muscarinic Antagonists\"\n   \"biolink:regulates\"\n   \"NCBIGene:2048\"\n   \"EPHB2\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0003385---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:2048---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:2048\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:19533734\")\n    (\"publications_info\"\n     \"{\\\"PMID:19533734\\\": {\\\"publication date\\\": \\\"2009 Dec\\\", \\\"sentence\\\": \\\"These effects of fustin were reversed by treatment with dicyclomine, a muscarinic M1 receptor antagonist, and SL327, a selective ERK inhibitor, but not by chelerythrine, a pan-protein kinase C (PKC) inhibitor.\\\", \\\"subject score\\\": 880, \\\"object score\\\": 793}}\")\n    (\"subject\" \"UMLS:C0003385\"))\n   ((\"id\"\n     \"NCBIGene:2048---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    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{\\\"publication date\\\": \\\"2012 May 15\\\", \\\"sentence\\\": \\\"We further investigated the apoptotic mechanism demonstrating that E2, as well as ESR1 and GPER specific agonists, induced sustained ERK, c-Jun and p38 phosphorylation, Cytochrome c release, caspase 3 and endogenous substrate Poly (ADP-ribose) polymerase (PARP) activation and increased expression of cell cycle inhibitor p21.\\\", \\\"subject score\\\": 827, \\\"object score\\\": 694}, \\\"PMID:22796106\\\": {\\\"publication date\\\": \\\"2012 Nov\\\", \\\"sentence\\\": \\\"Blockade of glutamate release achieved by the mGluR2/3 agonist, LY354740 or the selective adenosine A1R agonist, CCPA as well as neurotoxic lesions of lateral entorhinal cortex reduced the ability of SKF81297 to induce ERK activation in the dentate gyrus.\\\", \\\"subject score\\\": 802, \\\"object score\\\": 1000}, \\\"PMID:19662020\\\": {\\\"publication date\\\": \\\"2009 Oct\\\", \\\"sentence\\\": \\\"Furthermore, the inverse agonist activity olmesartan exerts against stretch-induced ERK activation requires an additional drug-receptor interaction involving the tetrazole group of olmesartan and Gln(257) of the AT(1) receptor.\\\", \\\"subject score\\\": 833, \\\"object score\\\": 566}, \\\"PMID:19501623\\\": {\\\"publication date\\\": \\\"2009 Dec\\\", \\\"sentence\\\": \\\"Thus, in intact brain HB-EGF, known to be expressed in brain, may be the major EGF agonist released in response to stimulation of alpha(2)-adrenoceptors, the released agonist(s) activate(s) EGF receptors, and ERK(1/2) is phosphorylated as a conventional response to EGF receptor activation.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 1000}, \\\"PMID:27456816\\\": {\\\"publication date\\\": \\\"2016 07 26\\\", \\\"sentence\\\": \\\"We also demonstrate the ability of these new agonists to induce receptor internalization, ERK activation, and chemotaxis, all hallmarks of CXCR4 activation.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 1000}, 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\\\"sentence\\\": \\\"Furthermore, TLR agonists or live pathogen (S. aureus, P. aeruginosa, & C. albicans)-challenged Muller glia produced significantly higher levels of inflammatory mediators (TNF-alpha, IL-1beta, IL-6 and IL-8), concomitantly with the activation of NF-kappaB, p38 and Erk signaling.\\\", \\\"subject score\\\": 964, \\\"object score\\\": 861}, \\\"PMID:30455267\\\": {\\\"publication date\\\": \\\"2018 Dec 03\\\", \\\"sentence\\\": \\\"Mechanistically, TLR8, localizing in the endosomes and lysosomes, mediated ERK activation, inflammatory mediators' production, and neuronal hyperexcitability after SNL.\\\", \\\"subject score\\\": 877, \\\"object score\\\": 627}}\")\n    (\"subject\" \"UMLS:C0243042\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" 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\\\"sentence\\\": \\\"In contrast, psychostimulants activate ERK and induce hyperactivity in normal animals.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0304403\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C1519313\"\n   \"Signal Transduction Inhibitor\"\n   \"biolink:regulates\"\n   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29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C1514555\"\n   \"Protein Kinase C Inhibitor\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C1514555---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:12676927|PMID:12745093|PMID:20477948|PMID:20600853\")\n    (\"publications_info\"\n     \"{\\\"PMID:12676927\\\": {\\\"publication date\\\": \\\"2003 Jun 27\\\", \\\"sentence\\\": \\\"Inhibition of the ERK and protein kinase C signaling pathways 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muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C1443775\"\n   \"Epidermal growth factor receptor inhibitor (product)\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C1443775---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\"\n     \"PMID:16211241|PMID:18636178|PMID:19127349|PMID:19154417|PMID:19854188|PMID:22033246|PMID:24021351\")\n    (\"publications_info\"\n     \"{\\\"PMID:24021351\\\": {\\\"publication date\\\": \\\"2013 Nov 15\\\", \\\"sentence\\\": \\\"The EGFR inhibitor also inhibited the B[a]PDE-induced MEK/ERK and Akt signaling pathways and subsequently, suppressed COX-2 expression and promoter activity, in addition to suppressing the transactivation of AP-1 and NF-kappaB.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 549}, \\\"PMID:16211241\\\": {\\\"publication date\\\": \\\"2005 Nov\\\", \\\"sentence\\\": \\\"Paclitaxel-induced ERK and AKT activity was inhibited by the EGFR inhibitor, PD153035; ERK inhibitor, U0126; and PI3 kinase inhibitor, LY294002, respectively.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 827}, \\\"PMID:18636178\\\": {\\\"publication date\\\": \\\"2008 Aug\\\", \\\"sentence\\\": \\\"PD153035, an EGFR inhibitor, and U0126, an ERK inhibitor, inhibit atRA-induced upregulation of AQP3.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 827}, \\\"PMID:19154417\\\": {\\\"publication date\\\": \\\"2009 Mar\\\", \\\"sentence\\\": \\\"In these three high-sensitivity cells, the ERK pathway was activated without ligand stimulation, which was inhibited by EGFR TKI.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 861}, \\\"PMID:19127349\\\": {\\\"publication date\\\": \\\"2009 Feb\\\", \\\"sentence\\\": \\\"The loss in countering capacity of leptin on the ethanol-induced cytotoxicity was attained with Src kinase inhibitor, PP2, and EGFR kinase inhibitor, AG1478, as well as ERK inhibitor, PD98059.\\\", \\\"subject score\\\": 938, \\\"object score\\\": 827}, \\\"PMID:22033246\\\": {\\\"publication date\\\": \\\"2012 Jan 28\\\", \\\"sentence\\\": \\\"EGF induced the phosphorylation of EGFR, smad3, ERK, and JNK, and MMP-9 expression was decreased by the EGFR inhibitor, AG1478.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:19854188\\\": {\\\"publication date\\\": \\\"2009 Nov 19\\\", \\\"sentence\\\": \\\"Signal analyses showed that evodiamine stimulated the phosphorylation of EGFR, PKCalpha, and ERK, all of which were reduced by an EGFR inhibitor.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C1443775\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C0243042\"\n   \"Inflammation Mediators\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0243042---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:25501336\")\n    (\"publications_info\"\n     \"{\\\"PMID:25501336\\\": {\\\"publication date\\\": \\\"2014 Dec 09\\\", \\\"sentence\\\": \\\"These results suggest that pheophytin a functions by down-regulating the transcriptional levels of inflammatory mediators and blocking the ERK and STAT-1 pathways.\\\", \\\"subject score\\\": 964, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0243042\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C0003211\"\n   \"Anti-Inflammatory Agents, Non-Steroidal\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0003211---SEMMEDDB:stimulates---None---None---increased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:25406016\")\n    (\"publications_info\"\n     \"{\\\"PMID:25406016\\\": {\\\"publication date\\\": \\\"2015 Feb\\\", \\\"sentence\\\": \\\"In growth plate chondrocytes, inhibition of proliferation and ERK activation by NSAIDs is reversed by forskolin, 8-bromoadenosine, 3',5'-cAMP and a prostacyclin analog, iloprost.\\\", \\\"subject score\\\": 988, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0003211\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C0003402\"\n   \"Antioxidants\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0003402---SEMMEDDB:stimulates---None---None---increased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\"\n     \"PMID:12682429|PMID:15698432|PMID:21344382|PMID:24534200|PMID:25485998|PMID:27916558|PMID:30481789\")\n    (\"publications_info\"\n     \"{\\\"PMID:24534200\\\": {\\\"publication date\\\": \\\"2014 Sep 01\\\", \\\"sentence\\\": \\\"Moreover, ERK activation induced by PFHxS was blocked by MK801 but not antioxidants.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 1000}, \\\"PMID:25485998\\\": {\\\"publication date\\\": \\\"2015 Apr\\\", \\\"sentence\\\": \\\"Several studies have suggested that ERK activation in lung cells has a protective effect in response to hyperoxia, through stimulation of DNA repair and antioxidant mechanisms, and prolonged cell survival.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 1000}, \\\"PMID:27916558\\\": {\\\"publication date\\\": \\\"2017 Feb 05\\\", \\\"sentence\\\": \\\"Therefore, the cardioprotective effects of CAR may be attributed to its antioxidant and antiapoptotic activities through activations of the MAPK/ERK and Akt/eNOS signaling pathways.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 694}, \\\"PMID:12682429\\\": {\\\"publication date\\\": \\\"2003 Feb\\\", \\\"sentence\\\": \\\"To determine whether reactive oxygen species (ROS) play a role in mediating ERK activation and 6-OHDA toxicity, we examined the effects of catalase, superoxide dismutase (SOD1), and metalloporphyrin antioxidants ('SOD mimetics') on 6-OHDA-treated cells.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 1000}, \\\"PMID:21344382\\\": {\\\"publication date\\\": \\\"2011 Dec\\\", \\\"sentence\\\": \\\"Our experimental results clearly demonstrated that induction of p-ERK and cell proliferation by arsenite is mediated via oxidative stress, since antioxidants can inhibit arsenite-induced cell transformation.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 861}, \\\"PMID:30481789\\\": {\\\"publication date\\\": \\\"2018 Nov 27\\\", \\\"sentence\\\": \\\"All the compounds reduced p38MAPK activation, but only the AEM, especially ebselen, and NAC, both potentiating the glutathione peroxidase pathway, also inhibited NFkB activation.\\\", \\\"subject score\\\": 851, \\\"object score\\\": 1000}, \\\"PMID:15698432\\\": {\\\"publication date\\\": \\\"2005 Mar\\\", \\\"sentence\\\": \\\"Activation of ERK in renal fibrosis after unilateral ureteral obstruction: modulation by antioxidants.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0003402\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C0013162\"\n   \"Drug Combinations\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0013162---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:23501104|PMID:25704960|PMID:28649441\")\n    (\"publications_info\"\n     \"{\\\"PMID:23501104\\\": {\\\"publication date\\\": \\\"2013 Apr 19\\\", \\\"sentence\\\": \\\"The enhanced therapeutic efficacy of the drug combination was achieved by a relatively transient blockade of the ERK pathway.\\\", \\\"subject score\\\": 966, \\\"object score\\\": 861}, \\\"PMID:28649441\\\": {\\\"publication date\\\": \\\"2017\\\", \\\"sentence\\\": \\\"Prospective simulations were then used to evaluate potential drug combinations and predictive biomarkers for increasing responsiveness to MEK/ERK inhibitors in these patients.\\\", \\\"subject score\\\": 901, \\\"object score\\\": 802}, \\\"PMID:25704960\\\": {\\\"publication date\\\": \\\"2015 Sep\\\", \\\"sentence\\\": \\\"The drug combination inactivated ERK, AKT, p70 S6K, and mTOR and activated JNK.\\\", \\\"subject score\\\": 966, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0013162\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C0026249\"\n   \"Mitogens\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0026249---SEMMEDDB:stimulates---None---None---increased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:18334532|PMID:20030620|PMID:24212659\")\n    (\"publications_info\"\n     \"{\\\"PMID:24212659\\\": {\\\"publication date\\\": \\\"2011 Mar 08\\\", \\\"sentence\\\": \\\"They also completely block the activity of mitogens such as epidermal growth factor's ability to stimulate ERK and Ras.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:18334532\\\": {\\\"publication date\\\": \\\"2008 May\\\", \\\"sentence\\\": \\\"In vivo, recruitment of ERK and MSK is stimulated by mitogens, correlates with histone H3 phosphorylation and is impaired by Elk-1 knockdown.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:20030620\\\": {\\\"publication date\\\": \\\"2010\\\", \\\"sentence\\\": \\\"They also completely block the activity of mitogens such as epidermal growth factor's ability to stimulate ERK.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"UMLS:C0026249\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\")))\n  (\"UMLS:C0013227\"\n   \"Pharmaceutical Preparations\"\n   \"biolink:regulates\"\n   \"NCBIGene:5594\"\n   \"MAPK1\"\n   \"biolink:regulates\"\n   \"UMLS:C1417707\"\n   \"NFIX gene\"\n   ((\"id\"\n     \"UMLS:C0013227---SEMMEDDB:inhibits---None---None---decreased---NCBIGene:5594---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"NCBIGene:5594\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\"\n     \"PMID:11408604|PMID:12543078|PMID:15843040|PMID:18223169|PMID:21251612|PMID:21879255|PMID:24559688|PMID:30482227\")\n    (\"publications_info\"\n     \"{\\\"PMID:24559688\\\": {\\\"publication date\\\": \\\"2014 May\\\", \\\"sentence\\\": \\\"The sensitivity to the drug was accompanied by a potent inhibition of both phospho-ERK and phospho-AKT, and a significant induction of apoptosis while absent in lines with intrinsic or acquired resistance.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:11408604\\\": {\\\"publication date\\\": \\\"2001 Jul\\\", \\\"sentence\\\": \\\"The Src-family tyrosine kinase inhibitor PP2 blocked MAPK activation by dopamine; however, this drug was also found to inhibit PDGF-BB-stimulated ERK activity and autophosphorylation of the PDGF receptor-beta.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 872}, \\\"PMID:12543078\\\": {\\\"publication date\\\": \\\"2002 Nov 24\\\", \\\"sentence\\\": \\\"Interestingly, all of the effective drugs inhibited the ERK activity, while the drugs had no effects on p38 MAPK activity and IkappaB degradation.\\\", \\\"subject score\\\": 888, \\\"object score\\\": 861}, \\\"PMID:18223169\\\": {\\\"publication date\\\": \\\"2008 Apr 01\\\", \\\"sentence\\\": \\\"Finally, CD38 stimulation of T2 B lymphocytes obtained from Btk-, Lyn-, or Fyn-deficient mice showed a defective differentiation; similarly, drugs interfering with PI3K or ERK decreased the proliferation or differentiation of this subset.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:15843040\\\": {\\\"publication date\\\": \\\"2005 Apr 15\\\", \\\"sentence\\\": \\\"While ERK1/2 activation was a general phenomenon, irrespective of the used cell type or antitumour drug, the MEK/ERK inhibitors only reduced cisplatin toxicity in human myeloid cells (THP-1, HL-60 and NB-4), but not in RAW 264.7 mouse macrophages and NRK-52E rat renal tubular cells; and failed to reduce the toxicity etoposide, camptothecin, melphalan and arsenic trioxide, in U-937 cells.\\\", \\\"subject score\\\": 861, \\\"object score\\\": 753}, \\\"PMID:21879255\\\": {\\\"publication date\\\": \\\"2012 Jan\\\", \\\"sentence\\\": \\\"Neither (ZEGFR:1907)2 nor any of the other             drugs were able to completely inactivate Akt or Erk.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}, \\\"PMID:21251612\\\": {\\\"publication date\\\": \\\"2011 Jan 18\\\", \\\"sentence\\\": \\\"These drugs thus selectively inhibit ERK signaling in tumors with BRAF mutation.\\\", \\\"subject score\\\": 861, \\\"object score\\\": 861}, \\\"PMID:30482227\\\": {\\\"publication date\\\": \\\"2018 Nov 27\\\", \\\"sentence\\\": \\\"BACKGROUND: Drugs that inhibit the MEK/ERK pathway have therapeutic benefit in bladder cancer treatment but responses vary with patients, for reasons that are still not very clear.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 802}}\")\n    (\"subject\" \"UMLS:C0013227\"))\n   ((\"id\"\n     \"NCBIGene:5594---SEMMEDDB:stimulates---None---None---increased---UMLS:C1417707---SEMMEDDB:\")\n    (\"knowledge_source\" \"infores:semmeddb\")\n    (\"object\" \"UMLS:C1417707\")\n    (\"predicate\" \"biolink:regulates\")\n    (\"publications\" \"PMID:30266829\")\n    (\"publications_info\"\n     \"{\\\"PMID:30266829\\\": {\\\"publication date\\\": \\\"2018 Oct 29\\\", \\\"sentence\\\": \\\"Notably, the role of ERK in the activation of Nfix is conserved postnatally in satellite cells, which represent the canonical myogenic stem cells of adult muscle.\\\", \\\"subject score\\\": 1000, \\\"object score\\\": 1000}}\")\n    (\"subject\" \"NCBIGene:5594\"))))\n"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/simple-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers.rkt\"\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n;; What diseases are caused by, or associated with, the BRCA2 gene?\n(define brca2diseases\n  (query:Known->X\n   ;; list of known CURIES (for genes in this case)\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"HGNC:1101\" ;; BRCA2 gene\n            ))))\n   ;; list of predicates\n   (set->list\n    (set-union\n     (get-predicate-descendents-in-db \"biolink:causes\")\n     (get-predicate-descendents-in-db \"biolink:gene_associated_with_condition\")))\n   ;; list of concept categories\n   (set->list (get-class-descendents-in-db \"biolink:Disease\"))))\n\n(define brca2disease-names\n  (map\n    (lambda (x) (list-ref x 4))\n    brca2diseases))\n\n\n(define top-level-diabetes-curies\n  (curies->synonyms-in-db\n   (list \"DOID:9351\")))\n\n(define doid-diabetes-curies\n  (get-descendent-curies*-in-db (list \"DOID:9351\")))\n\n(define all-diabetes-curies\n  (get-descendent-curies*-in-db\n   (curies->synonyms-in-db\n    (list \"DOID:9351\"))))\n"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/wills-new-multi-db-queries.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n(define kxk\n  (lambda (c1 c2)\n    (query:Known->X->Known\n     (set->list\n      (get-descendent-curies*-in-db\n       (curies->synonyms-in-db (list c1))))\n     '(\"biolink:same_as\")\n     #f\n     '(\"biolink:treats\")\n     (set->list\n      (get-descendent-curies*-in-db\n       (curies->synonyms-in-db (list c2)))))))\n\n;; imatinib ->biolink:same_as-> X ->biolink:treats-> gastrointestinal stromal tumor\n(define a (kxk \"UMLS:C0935989\" \"UMLS:C0238198\"))\n\n;; Example of a result for 'a' that spans KGs:\n\n#|\n(\"CHEBI:45783\"\n   \"imatinib\"\n   \"biolink:same_as\"\n   \"DRUGBANK:DB00619\"\n   \"Imatinib\"\n   \"biolink:treats\"\n   \"MONDO:0011719\"\n   \"gastrointestinal stromal tumor\"\n   (\"id\"\n    \"CHEBI:45783---owl:sameAs---None---None---None---DRUGBANK:DB00619---UNICHEM_source:\")\n   (\"knowledge_source\" \"infores:pathwhiz|infores:unichem\")\n   (\"object\" \"DRUGBANK:DB00619\")\n   (\"predicate\" \"biolink:same_as\")\n   (\"publications_info\" \"{}\")\n   (\"subject\" \"CHEBI:45783\")\n   (\"_attributes\"\n    \"[{\\\"attribute_type_id\\\": \\\"biolink:original_knowledge_source\\\", \\\"value\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"value_type_id\\\": \\\"biolink:InformationResource\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_data_source\\\", \\\"value\\\": \\\"infores:pubmed\\\", \\\"value_type_id\\\": \\\"biolink:InformationResource\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:has_evidence_count\\\", \\\"value\\\": 6116, \\\"value_type_id\\\": \\\"biolink:EvidenceCount\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:tmkp_confidence_score\\\", \\\"value\\\": 0.9959426746860693, \\\"value_type_id\\\": \\\"biolink:ConfidenceLevel\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document\\\", \\\"value\\\": \\\"PMC3636436|PMC5590134|PMC6786996|PMID:16204927|PMID:21387287\\\", \\\"value_type_id\\\": \\\"biolink:Publication\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_study_result\\\", \\\"value\\\": \\\"tmkp:65bcc14a34089bd25c3db4ddc71cf57164f4d38a05f36e012b32335d18223c50\\\", \\\"value_type_id\\\": \\\"biolink:TextMiningResult\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"biolink:supporting_text\\\", \\\"value\\\": \\\"Imatinib as adjuvant therapy for gastrointestinal stromal tumors: a systematic review\\\", \\\"value_type_id\\\": \\\"EDAM:data_3671\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document\\\", \\\"value\\\": \\\"PMC3636436\\\", \\\"value_type_id\\\": \\\"biolink:Publication\\\", \\\"value_url\\\": \\\"https://pubmed.ncbi.nlm.nih.gov/PMC3636436/\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_text_located_in\\\", \\\"value\\\": \\\"REF\\\", \\\"value_type_id\\\": \\\"IAO_0000314\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.9995431, \\\"value_type_id\\\": \\\"EDAM:data_1772\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:subject_location_in_text\\\", \\\"value\\\": \\\"0|8\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:object_location_in_text\\\", \\\"value\\\": \\\"33|64\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted \\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document_year\\\", \\\"value\\\": 2012, \\\"value_type_id\\\": \\\"UO:0000036\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}]}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_study_result\\\", \\\"value\\\": \\\"tmkp:bd0753f3583f2decb8013ae694183fa5dda87764b52ef92c930abd1d624236da\\\", \\\"value_type_id\\\": \\\"biolink:TextMiningResult\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"biolink:supporting_text\\\", \\\"value\\\": \\\"Imatinib as adjuvant therapy for gastrointestinal stromal tumors: a systematic review\\\", \\\"value_type_id\\\": \\\"EDAM:data_3671\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document\\\", \\\"value\\\": \\\"PMC5590134\\\", \\\"value_type_id\\\": \\\"biolink:Publication\\\", \\\"value_url\\\": \\\"https://pubmed.ncbi.nlm.nih.gov/PMC5590134/\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_text_located_in\\\", \\\"value\\\": \\\"REF\\\", \\\"value_type_id\\\": \\\"IAO_0000314\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.9995431, \\\"value_type_id\\\": \\\"EDAM:data_1772\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:subject_location_in_text\\\", \\\"value\\\": \\\"0|8\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:object_location_in_text\\\", \\\"value\\\": \\\"33|64\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted \\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document_year\\\", \\\"value\\\": 2017, \\\"value_type_id\\\": \\\"UO:0000036\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}]}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_study_result\\\", \\\"value\\\": \\\"tmkp:cf744da3e48412c6341b1a80e9b9fece28ff3a555d0a040eec8391e59d684427\\\", \\\"value_type_id\\\": \\\"biolink:TextMiningResult\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"biolink:supporting_text\\\", \\\"value\\\": \\\"Imatinib as adjuvant therapy for gastrointestinal stromal tumors: a systematic review\\\", \\\"value_type_id\\\": \\\"EDAM:data_3671\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document\\\", \\\"value\\\": \\\"PMC6786996\\\", \\\"value_type_id\\\": \\\"biolink:Publication\\\", \\\"value_url\\\": \\\"https://pubmed.ncbi.nlm.nih.gov/PMC6786996/\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_text_located_in\\\", \\\"value\\\": \\\"REF\\\", \\\"value_type_id\\\": \\\"IAO_0000314\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.9995431, \\\"value_type_id\\\": \\\"EDAM:data_1772\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:subject_location_in_text\\\", \\\"value\\\": \\\"0|8\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:object_location_in_text\\\", \\\"value\\\": \\\"33|64\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted \\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document_year\\\", \\\"value\\\": 2019, \\\"value_type_id\\\": \\\"UO:0000036\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}]}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_study_result\\\", \\\"value\\\": \\\"tmkp:921205bc03c6569adb4df892ee82cd938606be62661023435625b6f8de8a50b8\\\", \\\"value_type_id\\\": \\\"biolink:TextMiningResult\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"biolink:supporting_text\\\", \\\"value\\\": \\\"Imatinib mesylate as therapy for gastrointestinal stromal tumor.\\\", \\\"value_type_id\\\": \\\"EDAM:data_3671\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document\\\", \\\"value\\\": \\\"PMID:16204927\\\", \\\"value_type_id\\\": \\\"biolink:Publication\\\", \\\"value_url\\\": \\\"https://pubmed.ncbi.nlm.nih.gov/16204927/\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_text_located_in\\\", \\\"value\\\": \\\"title\\\", \\\"value_type_id\\\": \\\"IAO_0000314\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.99954236, \\\"value_type_id\\\": \\\"EDAM:data_1772\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:subject_location_in_text\\\", \\\"value\\\": \\\"0|8\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:object_location_in_text\\\", \\\"value\\\": \\\"33|63\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted \\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document_year\\\", \\\"value\\\": 2005, \\\"value_type_id\\\": \\\"UO:0000036\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}]}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_study_result\\\", \\\"value\\\": \\\"tmkp:11f292a42ef4384d1544ee6c7dd9b3d5c2fe803a7f71f26243eedee6443f6718\\\", \\\"value_type_id\\\": \\\"biolink:TextMiningResult\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"biolink:supporting_text\\\", \\\"value\\\": \\\"Imatinib as adjuvant therapy for gastrointestinal stromal tumors: a systematic review.\\\", \\\"value_type_id\\\": \\\"EDAM:data_3671\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document\\\", \\\"value\\\": \\\"PMID:21387287\\\", \\\"value_type_id\\\": \\\"biolink:Publication\\\", \\\"value_url\\\": \\\"https://pubmed.ncbi.nlm.nih.gov/21387287/\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_text_located_in\\\", \\\"value\\\": \\\"title\\\", \\\"value_type_id\\\": \\\"IAO_0000314\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.9995378, \\\"value_type_id\\\": \\\"EDAM:data_1772\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:subject_location_in_text\\\", \\\"value\\\": \\\"0|8\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:object_location_in_text\\\", \\\"value\\\": \\\"33|64\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted \\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document_year\\\", \\\"value\\\": 2011, \\\"value_type_id\\\": \\\"UO:0000036\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}]}]\")\n   (\"association_type\"\n    \"biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation\")\n   (\"confidence_score\" \"0.9959426746860693\")\n   (\"id\" \"cfcb7c55f657acae4e169566d0aab4d8e5e27ae861ee4d47aac5d30020afb539\")\n   (\"object_curie\" \"MONDO:0011719\")\n   (\"predicate\" \"biolink:treats\")\n   (\"subject_curie\" \"DRUGBANK:DB00619\")\n   (\"supporting_publication_identifiers\"\n    \"PMC3636436|PMC5590134|PMC6786996|PMID:16204927|PMID:21387287\")\n   (\"supporting_study_result_identifiers\"\n    \"tmkp:65bcc14a34089bd25c3db4ddc71cf57164f4d38a05f36e012b32335d18223c50|tmkp:bd0753f3583f2decb8013ae694183fa5dda87764b52ef92c930abd1d624236da|tmkp:cf744da3e48412c6341b1a80e9b9fece28ff3a555d0a040eec8391e59d684427|tmkp:921205bc03c6569adb4df892ee82cd938606be62661023435625b6f8de8a50b8|tmkp:11f292a42ef4384d1544ee6c7dd9b3d5c2fe803a7f71f26243eedee6443f6718\"))\n|#\n\n\n;; RTX KG2:\n;; (query:X->Known #f '(\"biolink:treats\") (list \"DOID:9351\"))\n\n;; RTX KG2:\n;; (query:X->Known #f '(\"biolink:subclass_of\") (list \"DOID:9351\"))\n\n;; Robokop:\n;; (query:X->Known #f '(\"biolink:subclass_of\") (list \"NCBITaxon:1748027\"))\n\n;; Text Mining\n;; (query:X->Known #f '(\"biolink:entity_negatively_regulates_entity\") (list \"UniProtKB:P47712\"))\n\n(define diabetes-treatments\n  (query:X->Known\n   #f\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:treats\")))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n(length diabetes-treatments)\n;; 20042\n\n\n(define diabetes-causes\n  (query:X->Known\n   #f\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:causes\")))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n(length diabetes-causes)\n;; =>\n9297\n\n(sort (remove-duplicates (map car diabetes-causes)) string<=?)\n\n(filter (lambda (e) (string=? \"water\" (cadr e))) diabetes-causes)\n"
  },
  {
    "path": "contrib/medikanren2/neo/Mayu/wills-new-rtx-kg2-queries.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n(define diabetes-treatments\n  (query:X->Known\n   #f\n   (set->list\n    (apply set-union\n           (map get-predicate-descendents-in-db\n                '(\"biolink:treats\"\n                  ))))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n(length diabetes-treatments)\n;; 17247\n\n\n(define diabetes-causes\n  (query:X->Known\n   #f\n   (set->list\n    (apply set-union\n           (map get-predicate-descendents-in-db\n                '(\"biolink:causes\"\n                  ))))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n(length diabetes-causes)\n\n(sort (remove-duplicates (map car diabetes-causes)) string<=?)\n\n(filter (lambda (e) (string=? \"water\" (cadr e))) diabetes-causes)\n"
  },
  {
    "path": "contrib/medikanren2/neo/Will/adverse-effects.rkt",
    "content": "#lang racket/base\n\n(provide\n )\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-server/neo-server-utils.rkt\"\n \"../../../../medikanren2/neo/neo-reasoning/neo-biolink-reasoning-low-level.rkt\"\n \"../utils.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n;; adverse affects for imatinib mesylate\n(query:Known->X\n '(\"CHEBI:45783\")\n '(\"biolink:causes\"\n   \"biolink:exacerbates\"\n   \"biolink:has_adverse_event\"\n   \"biolink:contributes_to\")\n #f)\n\n;; contraindications for imatinib mesylate\n(query:Known->X\n '(\"CHEBI:45783\")\n '(\"biolink:contraindicated_in\")\n #f)\n\n;; the variable `all-predicates` is bound to a list of all supported\n;; biolink predicates\n\n;; other biolink predicates that might be useful:\n#|\n\"biolink:contraindicated_in\"\n\"biolink:has_side_effect\"\n\"biolink:FDA_adverse_event_level\"\n\"biolink:adverse_event_of\"\n\"biolink:has_adverse_event\"\n\"biolink:highest_FDA_approval_status\"\n\"biolink:drug_regulatory_status_world_wide\"\n|#\n"
  },
  {
    "path": "contrib/medikanren2/neo/Will/chemical-affects-gene.rkt",
    "content": "#lang racket/base\n\n(provide\n chem-affects-gene\n chem-affects-gene-entries\n chem-affects-gene-TSV)\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-server/neo-server-utils.rkt\"\n \"../utils.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n;; finds a list of compounds that affect a provided set of genes\n(define (chem-affects-gene gene-list)\n  (time (remove-duplicates\n         (query:X->Known\n          (set->list\n           (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n            '(\"biolink:ChemicalEntity\")))\n          (set->list\n           (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n            '(\"biolink:affects\")))\n          (set->list (curie-synonyms-and-descendents gene-list))))))\n\n(define header\n  (list \"chemical CURIE\" \"chemical name\" \"predicate description\" \"object CURIE\" \"object name\" \"NCBITaxon\" \"PUBMEDs\" \"source\"))\n\n(define (create-entry result)\n  (match result\n    [`(,subj-curie ,pred ,obj-curie . ,props)\n     (list\n       subj-curie\n       (concept->name subj-curie)\n       (or (get-assoc \"description\" props)\n           (get-assoc \"predicate_label\" props)\n           (let ((qp (get-assoc \"qualified_predicate\" props)))\n             (if qp\n                 (string-append\n                  qp\n                  \" \"\n                  (or (get-assoc \"object_direction_qualifier\" props) \"\")\n                  \" \"\n                  (or (get-assoc \"object_aspect_qualifier\" props) \"\"))\n                 #f))\n           pred)\n       obj-curie\n       (concept->name obj-curie)\n       (let ((taxon (get-assoc \"NCBITaxon\" props)))\n         (cond\n           ((equal? \"9606\" taxon) (string-append taxon \" (Homo sapiens)\"))\n           ((equal? \"10090\" taxon) (string-append taxon \" (Mus musculus)\"))\n           (else (or taxon \"N/A\"))))\n       (string-join (get-pubs props) \",\")\n       (get-primary-knowledge-source props))]))\n\n(define (chem-affects-gene-entries gene-list)\n  (cons header\n        (remove-duplicates\n         (map create-entry\n              (chem-affects-gene gene-list)))))\n\n(define (chem-affects-gene-TSV file-name gene-list)\n  (write-answers-to-tsv\n   file-name\n   (chem-affects-gene-entries gene-list)))\n"
  },
  {
    "path": "contrib/medikanren2/neo/Will/simple-query.rkt",
    "content": "#lang racket/base\n\n(require\n \"../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n \"../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"\n json\n racket/format\n racket/list\n racket/match\n racket/set\n racket/pretty\n racket/string)\n\n(define robokop-top-bucket (list 5)) ;top/max bucket num of RoboKop KG\n(define text-mining-top-bucket (list 5)) ;top/max bucket num of Text Mining KG\n(define rtx-kg2-top-bucket (list 7)) ;top/max bucket num of RTX-KG2 KG\n\n; Numbers of the top buckets of RoboKop KG, Text Mining KG, and RTX-KG2 KG (in this order).\n; [The higer the bucket number, the higher amount of publications supporting the edge]\n(define TOP_BUCKET_NUMBERS (list robokop-top-bucket \n                                 text-mining-top-bucket \n                                 rtx-kg2-top-bucket \n                                 ))\n\n(define regulates-EGFR\n  (time (query:X->Known\n         #f\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"HGNC:3236\")))))))\n\n(define regulates-EGFR-faster\n  (time (query:X->Known-scored\n         #f\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"HGNC:3236\"))))\n         TOP_BUCKET_NUMBERS\n         )))\n;; There is a problem when we use the bucketing approach is that we might \n;; receive zero answer from the buckets that has a higer amount of supports.\n;; Hence, you can either manually decrease the bucket number and redo the\n;; query, or you may write a procedure to realize auto growing until reach\n;; the amount of answers you want.\n;; `auto-grow` used by mediKanren neo server:\n;; https://github.com/webyrd/mediKanren/blob/master/medikanren2/neo/neo-server/neo-server-utils.rkt#L80-L92\n\n; If I would like to start with 2 buckets from, for example, rtx-kg2:\n; [we can have 1 or 1 more bucker number as a list in each of the\n; element of the bukect list]\n(define regulates-EGFR-faster-2bks-from-kg2\n  (time (query:X->Known-scored\n         #f\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"HGNC:3236\"))))\n         (list (list 5) (list 5) (list 6 7))\n         )))\n\n; Or we do not want the top bucket at all, for example, from robokop KG:\n(define regulates-EGFR-faster-notop-robokop\n  (time (query:X->Known-scored\n         #f\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"HGNC:3236\"))))\n         (list (list 4) ;; robokop KG has the max bucket number 5\n               (list 5) (list 7))\n         )))\n\n; If I only want to get answers from, for example, the text mining KG:\n; [#f in the correspong index of the bucket list means not do query in\n; this specific KG]\n(define regulates-EGFR-faster-only-tm\n  (time (query:X->Known-scored\n         #f\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"HGNC:3236\"))))\n         (list #f (list 5) #f)\n         )))\n\n(define downregulates-EGFR\n  (filter\n   (lambda (e)\n     (match e\n       [`(,subj ,pred ,obj . ,props)\n        (and (member '(\"predicate\" \"biolink:regulates\") props)\n             (member '(\"object_direction_qualifier\" \"downregulated\") props))]))\n   (query:X->Known\n    #f\n    (set->list\n     (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n      '(\"biolink:affects\")))\n    (set->list\n     (get-descendent-curies*-in-db\n      (curies->synonyms-in-db (list \"HGNC:3236\")))))))\n\n(define diabetes-causes\n  (query:X->Known\n   #f\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:causes\")))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n(define diabetes-treatments\n  (query:X->Known\n   #f\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:treats\")))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n(curies->synonyms-in-db (list \"PUBCHEM.COMPOUND:5291\"))\n;; =>\n'(\"PUBCHEM.COMPOUND:5291\"\n  \"PUBCHEM.COMPOUND:123596\"\n  \"DRUGBANK:DB00619\")\n\n(define imatinib-regulates\n  (time (query:Known->X\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"PUBCHEM.COMPOUND:5291\"))))\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         #f)))\n\n(define imatinib-regulates-faster\n  (time (query:Known->X-scored\n         (set->list\n          (get-descendent-curies*-in-db\n           (curies->synonyms-in-db (list \"PUBCHEM.COMPOUND:5291\"))))\n         (set->list\n          (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n           '(\"biolink:regulates\")))\n         #f\n         TOP_BUCKET_NUMBERS)))\n\n; `query:Known->Known` has not support the faster version yet\n(define BCL2-affects-diabetes\n  (query:Known->Known\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"HGNC:990\"))))\n   (set->list\n    (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n     '(\"biolink:affects\")))\n   (set->list\n    (get-descendent-curies*-in-db\n     (curies->synonyms-in-db\n      (list \"DOID:9351\"))))))\n\n; --------------------\n\n(define Casein-Kinase-2-Alpha-1\n  (list \"HGNC:2457\"\n        \"NCBIGene:1457\"\n        \"ENSEMBL:ENSG00000101266\"\n        \"OMIM:115440\"\n        \"UniProtKB:P68400\"))\n\n(define Casein-Kinase-2-Alpha-1+\n  (remove-duplicates (curies-in-db (curies->synonyms Casein-Kinase-2-Alpha-1))))\n\n(define (gene*->protein* gene*)\n  (remove-duplicates\n   (map car\n        (query:X->Known-scored \n         (set->list\n          (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n           '(\"biolink:Protein\")))\n         #;'(\"biolink:Protein\")\n         '(\"biolink:gene_product_of\")\n         gene*\n         (list #f #f (list 0))))))\n\n(define Casein-Kinase-2-Alpha-1-protein (gene*->protein* Casein-Kinase-2-Alpha-1+))\n\n(define chem-regulate-Casein-Kinase-2-Alpha-1\n  (time (query:X->Known\n   (set->list\n    (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n     '(\"biolink:ChemicalEntity\")))\n   (set->list\n    (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n     '(\"biolink:affects\")))\n   (remove-duplicates (append Casein-Kinase-2-Alpha-1-protein Casein-Kinase-2-Alpha-1+)))))\n\n;; To see the predicates from the answers\n(remove-duplicates (map cadr chem-regulate-Casein-Kinase-2-Alpha-1))\n\n(define chem-up-regulates-Casein-Kinase-2-Alpha-1\n  (filter\n   (lambda (e)\n     (match e\n       [`(,subj ,pred ,obj . ,props)\n        (or (member '(\"object_direction_qualifier\" \"increased\") props)\n             (member '(\"object_direction_qualifier\" \"upregulated\") props))]))\n   chem-regulate-Casein-Kinase-2-Alpha-1))\n#|\n'((\"PUBCHEM.COMPOUND:15625\"\n   \"biolink:affects\"\n   \"NCBIGene:1457\"\n   (\"NCBITaxon\" \"10090\")\n   (\"biolink:primary_knowledge_source\" \"infores:ctd\")\n   (\"description\" \"increases molecular interaction with\")\n   (\"object\" \"NCBIGene:1457\")\n   (\"object_aspect_qualifier\" \"molecular_interaction\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"publications\" \"(PMID:19654925)\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"subject\" \"PUBCHEM.COMPOUND:15625\"))\n  (\"PUBCHEM.COMPOUND:15625\"\n   \"biolink:affects\"\n   \"NCBIGene:1457\"\n   (\"NCBITaxon\" \"10090\")\n   (\"biolink:primary_knowledge_source\" \"infores:ctd\")\n   (\"description\" \"increases molecular interaction with\")\n   (\"object\" \"NCBIGene:1457\")\n   (\"object_aspect_qualifier\" \"molecular_interaction\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"publications\" \"(PMID:19654925)\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"subject\" \"PUBCHEM.COMPOUND:15625\"))\n  (\"PUBCHEM.COMPOUND:15625\"\n   \"biolink:affects\"\n   \"NCBIGene:1457\"\n   (\"NCBITaxon\" \"10090\")\n   (\"biolink:primary_knowledge_source\" \"infores:ctd\")\n   (\"description\" \"increases molecular interaction with\")\n   (\"object\" \"NCBIGene:1457\")\n   (\"object_aspect_qualifier\" \"molecular_interaction\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"publications\" \"(PMID:19654925)\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"subject\" \"PUBCHEM.COMPOUND:15625\"))\n  (\"PUBCHEM.COMPOUND:5991\"\n   \"biolink:affects\"\n   \"NCBIGene:1457\"\n   (\"NCBITaxon\" \"10090\")\n   (\"biolink:primary_knowledge_source\" \"infores:ctd\")\n   (\"description\" \"increases expression of\")\n   (\"object\" \"NCBIGene:1457\")\n   (\"object_aspect_qualifier\" \"expression\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"publications\" \"(PMID:17942748 PMID:29097150 PMID:24096037)\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"subject\" \"PUBCHEM.COMPOUND:5991\"))\n  (\"PUBCHEM.COMPOUND:5991\"\n   \"biolink:affects\"\n   \"NCBIGene:1457\"\n   (\"NCBITaxon\" \"10090\")\n   (\"biolink:primary_knowledge_source\" \"infores:ctd\")\n   (\"description\" \"increases expression of\")\n   (\"object\" \"NCBIGene:1457\")\n   (\"object_aspect_qualifier\" \"expression\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"publications\" \"(PMID:17942748 PMID:29097150 PMID:24096037)\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"subject\" \"PUBCHEM.COMPOUND:5991\"))\n  (\"PUBCHEM.COMPOUND:5991\"\n   \"biolink:affects\"\n   \"NCBIGene:1457\"\n   (\"NCBITaxon\" \"10090\")\n   (\"biolink:primary_knowledge_source\" \"infores:ctd\")\n   (\"description\" \"increases expression of\")\n   (\"object\" \"NCBIGene:1457\")\n   (\"object_aspect_qualifier\" \"expression\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"publications\" \"(PMID:17942748 PMID:29097150 PMID:24096037)\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"subject\" \"PUBCHEM.COMPOUND:5991\"))\n  (\"DRUGBANK:DB03088\"\n   \"biolink:affects\"\n   \"UniProtKB:P68400\"\n   (\"assertion_id\"\n    \"128b76f85670ba85bb5b91cad9758237cc0886ac449739de46d906886b198350\")\n   (\"association_curie\" \"biolink:ChemicalToGeneAssociation\")\n   (\"json_attributes\"\n    \"[{\\\"attribute_type_id\\\": \\\"biolink:primary_knowledge_source\\\", \\\"value\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"value_type_id\\\": \\\"biolink:InformationResource\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_data_source\\\", \\\"value\\\": \\\"infores:pubmed\\\", \\\"value_type_id\\\": \\\"biolink:InformationResource\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:evidence_count\\\", \\\"value\\\": 1, \\\"value_type_id\\\": \\\"biolink:EvidenceCount\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.9163411100614833, \\\"value_type_id\\\": \\\"biolink:ConfidenceLevel\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:publications\\\", \\\"value\\\": [\\\"PMC:4631799\\\"], \\\"value_type_id\\\": \\\"biolink:Uriorcurie\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:has_supporting_study_result\\\", \\\"value\\\": \\\"tmkp:480d75d32bc72138b0593be1e14c0f0087ec2cc41b61f80110402e8ff7f34748\\\", \\\"value_type_id\\\": \\\"biolink:TextMiningResult\\\", \\\"value_url\\\": \\\"https://tmui.text-mining-kp.org/evidence/480d75d32bc72138b0593be1e14c0f0087ec2cc41b61f80110402e8ff7f34748\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"biolink:supporting_text\\\", \\\"value\\\": \\\"It should also be noted that AA PCa was associated with a large number of up-regulated oncogenes (such as ITGA5, PIK3CB, PIK3AP, ITPR2, STAT1, CSNK2A1, MKK4, 14-3-3\\\\u03b5, MTOR and MCL1) as well as dysregulated unpaired miRNAs that are unique to AA PCa (e.g.\\\", \\\"value_type_id\\\": \\\"EDAM:data_3671\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:publications\\\", \\\"value\\\": \\\"PMC:4631799\\\", \\\"value_type_id\\\": \\\"biolink:Uriorcurie\\\", \\\"value_url\\\": \\\"https://pubmed.ncbi.nlm.nih.gov/PMC4631799/\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_text_located_in\\\", \\\"value\\\": \\\"DISCUSS\\\", \\\"value_type_id\\\": \\\"IAO_0000314\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:extraction_confidence_score\\\", \\\"value\\\": 0.9163411100614833, \\\"value_type_id\\\": \\\"EDAM:data_1772\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:subject_location_in_text\\\", \\\"value\\\": \\\"32|35\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted\\\"}, {\\\"attribute_type_id\\\": \\\"biolink:object_location_in_text\\\", \\\"value\\\": \\\"143|150\\\", \\\"value_type_id\\\": \\\"SIO:001056\\\", \\\"attribute_source\\\": \\\"infores:text-mining-provider-targeted \\\"}, {\\\"attribute_type_id\\\": \\\"biolink:supporting_document_year\\\", \\\"value\\\": 2015, \\\"value_type_id\\\": \\\"UO:0000036\\\", \\\"attribute_source\\\": \\\"infores:pubmed\\\"}]}]\")\n   (\"object\" \"UniProtKB:P68400\")\n   (\"object_aspect_qualifier\" \"activity_or_abundance\")\n   (\"object_direction_qualifier\" \"increased\")\n   (\"predicate\" \"biolink:affects\")\n   (\"qualified_predicate\" \"biolink:causes\")\n   (\"score\" \"0.9163411100614833\")\n   (\"subject\" \"DRUGBANK:DB03088\")\n   (\"supporting_publications\" \"PMC:4631799\")\n   (\"supporting_study_results\"\n    \"tmkp:480d75d32bc72138b0593be1e14c0f0087ec2cc41b61f80110402e8ff7f34748\")))\n|#\n   \n"
  },
  {
    "path": "contrib/medikanren2/neo/utils.rkt",
    "content": "#lang racket/base\n\n(provide concept->name\n         concept->category\n\n         curie-synonyms-and-descendents\n\n         write-answers-to-tsv\n\n         get-pubs\n         get-primary-knowledge-source\n         \n         get-assoc\n         list-assoc\n         merge-list\n         merge-hash   \n         )\n\n(require racket/list\n         racket/math\n         racket/string\n         json\n         racket/match\n         \"../../../medikanren2/neo/neo-server/neo-server-utils.rkt\"\n         \"../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt\"\n         \"../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt\"         \n         \"../../../medikanren2/neo/neo-utils/neo-helpers-without-db.rkt\"\n         )\n\n(define (get-pubs props)\n  (if (zero? (num-pubs props))\n      '()\n      (hash-ref (get-publications props) 'value)))\n\n(define (get-primary-knowledge-source props)\n  (if (edge-has-source? props)\n      (hash-ref (get-source props) 'resource_id)\n      (error 'get-primary-knowledge-source (format \"no primary knowledge source in properties: ~s\" props))))\n\n\n\n\n\n(define (curie-synonyms-and-descendents curie-list)\n  (get-descendent-curies*-in-db\n   (curies->synonyms-in-db curie-list)))\n\n#;(define (concept->name curie)\n  (let ((id-name-val\n         (remove-duplicates (filter (lambda (cl)\n                                      (and (equal? (car cl) curie)\n                                           (equal? (cadr cl) \"name\")))\n                                    (query:Concept (list curie))))))\n        (if (null? id-name-val)\n            curie\n            (caddar id-name-val))))\n\n(define (concept->name curie)\n  (let ((name (assoc \"name\" (curie->properties curie))))\n    (if name (cadr name) curie)))\n\n(define (concept->category curie)\n  (let ((category (assoc \"category\" (curie->properties curie))))\n    (if category (cdr category) '())))\n\n(define (write-answers-to-tsv file-name lines)\n  (let ((op (open-output-file file-name #:mode 'text #:exists 'replace)))\n    (for-each\n      (lambda (line)\n        (fprintf op (string-join line \"\\t\"))\n        (fprintf op \"\\n\"))\n      lines)\n    (close-output-port op)))\n"
  },
  {
    "path": "contrib/medikanren2/profiling.rkt",
    "content": "#lang racket\n(provide\n run/progress\n )\n(require \"../../medikanren2/base.rkt\"\n         chk)\n\n\n;;;(run/progress numMax s)\n;; \n;;   Run a query while reporting statistics.  Query must first be converted to a\n;;   stream s.  Parameter numMax indicates the maximum desired number of\n;;   query results.  Setting numMax to -1 searches for all results, as in run*.\n;;   Statistics are printed to current-output-port.\n;; \n;;   Example:\n;; \n;;   (run/progress 1000\n;;                (query->stream\n;;                 (query (id)\n;;                        (fresh (p o)\n;;                               (nodes id p o)\n;;                               (:== #t (id) (string-prefix? id \"APO\"))\n;;                               ))))\n;; \n;; Statistics printed are:\n;; \n;;   num => the number of results obtained so far\n;;   w => the number of ticks expended so far\n;;   sec => the number of seconds elapsed so far\n;;   num/sec => the results per second found so far\n;; \n(define (run/progress numMax s)\n  (let ((t0 (current-milliseconds))\n        (t-prev -1)\n        (dt-min 5000))\n    (define (report i w t)\n      (let ((dt-prev (- t t-prev)))\n        (when (> dt-prev dt-min)\n          (let* (\n                 (dt (- t t0))\n                 (ips (exact->inexact (* 1000 (/ i (+ dt 1)))))\n                 (dtsec (exact->inexact (/ dt 1000)))\n                 )\n            (printf \"num=~a w=~a sec=~a num/sec=~a\\n\" i w dtsec ips)\n            (set! t-prev t)))))\n    (define (iter i w xs s)\n      (cond\n        ((and (>= numMax 0) (>= i numMax)) xs)\n        ((null? s) xs)\n        ((procedure? s)\n         (report i w (if (> (bitwise-and w 255) 0) 0 (current-milliseconds)))\n         (iter i (+ w 1) xs (s)))\n        ((pair? s)\n         (let* ((x (car s))\n                (t (current-milliseconds))\n                )\n           (report i w t)\n           (iter (+ i 1) (+ w 1) (cons x xs) ((cdr s)))))\n        (else (raise (format \"unexpected type: ~a\" s)))))\n    (reverse (iter 0 0 '() s))))\n\n(module+ test\n  (chk\n   (#:do\n    (define-relation/table (rel a b)\n      'source-stream '(\n                       (\"a\" 1)\n                       (\"b\" 2)\n                       (\"c\" 3)\n                       (\"d\" 4)\n                       (\"e\" 5))))\n\n   (#:= (run\n         10\n         (num)\n         (fresh (id)\n                (membero id '(\"b\" \"c\"))\n                (rel id num)))\n    '((2) (3)))\n   \n   (#:= (run/progress\n         10\n         (query->stream\n          (query             \n           (num)\n           (fresh (id)\n                  (membero id '(\"b\" \"c\"))\n                  (rel id num)))))\n    '((2) (3)))\n  ))\n"
  },
  {
    "path": "contrib/medikanren2/trapi-tests.rkt",
    "content": "#lang racket/base\n(provide trapi-response)\n(require\n  \"../../medikanren2/trapi.rkt\"\n  \"../../medikanren2/lw-reasoning.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  json\n  )\n\n;; Simple tests for TRAPI interpreter\n\n(define q (string->jsexpr #<jsexpr #<jsexpr #<jsexpr #<string results))\n  (printf \"\\nSize:~s\\n\" (length (hash-ref results 'results '()))))\n\n\n;; (lw-reasoning? #t)\n;; (define m1    (hash-ref q 'message))\n;; (define m2    (hash-ref q2 'message))\n;; (define m3 (hash-ref q3 'message))\n\n\n;; (define r (time (trapi-response m1)))\n;; (display (jsexpr->string r))\n;; (printf \"\\nSize:~s\\n\" (length  (hash-ref r 'results '())))\n;; (printf \"\\n=====\\n\")\n;; (define r2 (time (trapi-response m2)))\n;; (display (jsexpr->string r2))\n;; (printf \"\\nSize:~s\\n\" (length (hash-ref r2 'results '())))\n;; (printf \"\\n=====\\n\")\n;; (define r3 (time (trapi-response m3)))\n;; (display (jsexpr->string r3))\n;; (printf \"\\nSize:~s\\n\" (length (hash-ref r3 'results '())))\n\n\n\n\n\n"
  },
  {
    "path": "medikanren/.compile.sh",
    "content": "#!/bin/bash\nadirRepo=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && cd .. && pwd )\"\nadirMk=\"$adirRepo/medikanren\"\nadirArtifacts=\"$adirRepo/ci_artifacts\"\n\n\nstepname=medikanren1_compile_trapi\nif raco make \"$adirMk/apps/translator-web-server.rkt\"\nthen\n    echo \"$stepname\" > \"$adirArtifacts/status/pass/$stepname\"\nelse\n    echo \"$stepname\" > \"$adirArtifacts/status/fail/$stepname\"\nfi\n\nstepname=medikanren1_compile_gui\nif raco make \"$adirMk/apps/gui-simple-v2.rkt\"\nthen\n    echo \"$stepname\" > \"$adirArtifacts/status/pass/$stepname\"\nelse\n    echo \"$stepname\" > \"$adirArtifacts/status/fail/$stepname\"\nfi\n"
  },
  {
    "path": "medikanren/.gitignore",
    "content": "/data\n/config.scm\n/last.sx\n/last.txt\n/last.tsv\n"
  },
  {
    "path": "medikanren/.install_pkgs.sh",
    "content": "#!/bin/bash\n\n# TODO: raco pkg will stop and do nothing if you run\n# this command as-is and any of the packages have been previously installed.\n\n# Current workaround is to only install it once, from the medikanren2 directory.\n\n# raco pkg install --auto --batch --fail-fast \\\n#     chk \\\n#     shell-pipeline \\\n#     yaml \\\n#     memoize\n"
  },
  {
    "path": "medikanren/.run_ci.sh",
    "content": "#!/bin/bash\nadirRepo=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && cd .. && pwd )\"\nadirMk=\"$adirRepo/medikanren\"\nadirArtifacts=\"$adirRepo/ci_artifacts\"\n\nbash \"$adirMk/.compile.sh\"\n\n# TODO: Replace this way to run tests with a way that actually\n# discovers them.  The purpose of the current way only to show that\n# tests can be run in Github Actions against real data.\n\nif raco test \"$adirMk/configref.rkt\"\nthen\n    echo medikanren_run_ci > \"$adirArtifacts/status/pass/medikanren1_run_ci\"\nelse\n    echo medikanren_run_ci > \"$adirArtifacts/status/fail/medikanren1_run_ci\"\nfi\n\n\n"
  },
  {
    "path": "medikanren/README.md",
    "content": "# MediKanren\n\n## Directory Structure\n\n| Directory | Description |\n|---|---|\n|[apps](apps)| Web service and local GUI applications |\n|[util/data-import](util/data-import)| Import tools from external KG formats |\n|[open-api](open-api)| Module for integration with external KGs |\n|[pieces-parts](pieces-parts)| Extensions of core API |\n|[data](data)| Install KG data here (.gitignored) |\n|[test](test)| Collection of test code |\n|[test/unit](test/unit)| Tests without external dependencies |\n|[test/full-dbs](test/full-dbs)| Tests depending on full KG |\n|[test/external-http](test/external-http)| Tests depending on external http services |\n|[use-cases](use-cases)| Moved to [contrib/medikanren/use-cases](../contrib/medikanren/use-cases) |\n\n"
  },
  {
    "path": "medikanren/apps/gui-simple-v2.rkt",
    "content": "#lang racket\n\n(require\n  \"../common.rkt\"\n  racket/sandbox\n  racket/gui/base\n  framework\n  racket/engine\n  racket/date\n  racket/string\n  net/sendurl\n  \"../db.rkt\"\n  (except-in racket/match ==)\n  (only-in srfi/1 iota))\n\n(provide\n  launch-gui)\n\n(define MEDIKANREN_VERSION_STRING \"mediKanren Explorer 0.2.30\")\n\n(define argv (current-command-line-arguments))\n(define argv-optional '#(CONFIG_FILE))\n\n(when (not (<= (vector-length argv) (vector-length argv-optional)))\n  (error \"optional arguments ~s; given ~s\" argv-optional argv))\n\n(displayln \"Starting mediKanren Explorer...\")\n(newline)\n(displayln \"************************************************\")\n(displayln \"*** mediKanren is for research purposes only ***\")\n(displayln \"************************************************\")\n(newline)\n(displayln MEDIKANREN_VERSION_STRING)\n;; Loading will occur at first use if not explicitly forced like this.\n(load-config #t (and (<= 1 (vector-length argv)) (vector-ref argv 0)))\n(load-databases #t)\n\n;;; Query save file settings\n(define WRITE_QUERY_RESULTS_TO_FILE            (config-ref 'query-results.write-to-file?))\n(define QUERY_RESULTS_FILE_NAME                (config-ref 'query-results.file-name))\n(define HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name-human))\n(define SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME (config-ref 'query-results.file-name-spreadsheet))\n(define QUERY_RESULTS_FILE_MODE                (config-ref 'query-results.file-mode))\n\n;;; Initial window size\n(define HORIZ-SIZE (config-ref 'initial-window-size.horizontal))\n(define VERT-SIZE (config-ref 'initial-window-size.vertical))\n\n;;; Decreases/increases predicate names\n(define DECREASES_PREDICATE_NAMES (config-ref 'decreases-predicate-names))\n(define INCREASES_PREDICATE_NAMES (config-ref 'increases-predicate-names))\n\n\n#|\nconcept format (subject or object), without dbname at front:\n\n`(,cid ,cui ,name (,catid . ,cat) ,props)\n\nconcept format (subject or object), with dbname at front:\n\n`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)\n\n\nedge format, without dbname at front:\n\n`(,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n       (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n       (,pid . ,pred) ,eprops)\n\nedge format, with dbname at front (as used in edgeo):\n\n`(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n               (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n               (,pid . ,pred) ,eprops)\n|#\n\n(define (split-name-string name)\n  (string-split name #px\"\\\\s+\"))\n\n(define (empty-string? str)\n  (not (not (regexp-match #px\"^[\\\\s]*$\" str))))\n\n(define *verbose* #t)\n\n(define input-response-latency 50)\n\n(define MAX-CHAR-WIDTH 150)\n\n(define smart-column-width-list-box%\n  (class list-box%\n    (super-new)\n    (define (on-size width height)\n      (super on-size width height)\n      (set-default-column-widths this))\n    (override on-size)))\n\n(define (set-default-column-widths list-box)\n  (define label* (send list-box get-column-labels))\n  (define num-cols (length label*))\n  (define window-width (send list-box get-width))\n  (define min-width 5)\n  (define max-width 1000)\n  (define fudge-factor 4) ;; column divider width\n  (define width (min (max (- (floor (/ window-width num-cols)) fudge-factor)\n                          min-width)\n                     max-width))\n  (let loop ((col-num (sub1 num-cols)))\n    (cond\n      [(zero? col-num) (void)]\n      [else\n       (send list-box\n             set-column-width\n             col-num\n             width\n             min-width\n             max-width)\n       (loop (sub1 col-num))])))\n\n(define construct-predicate-label-string\n  (lambda (pred-string pred-name-list)\n    (~a\n     (string-append pred-string\n                   \"  (\"\n                   (foldr (lambda (str1 str2)\n                            (if (equal? \"\" str2)\n                                (string-append str1 \"\" str2)\n                                (string-append str1 \", \" str2)))\n                          \"\"\n                          pred-name-list)\n                   \")\")\n     #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")))\n\n(define DECREASES_PREDICATE_PREFIX_STRING \"decreases [synthetic]\")\n(define DECREASES_PREDICATE_STRING\n  (construct-predicate-label-string DECREASES_PREDICATE_PREFIX_STRING DECREASES_PREDICATE_NAMES))\n(define INCREASES_PREDICATE_PREFIX_STRING \"increases [synthetic]\")\n(define INCREASES_PREDICATE_STRING\n  (construct-predicate-label-string INCREASES_PREDICATE_PREFIX_STRING INCREASES_PREDICATE_NAMES))\n\n(define SYNTHETIC_PREDICATE_PREFIXES (list DECREASES_PREDICATE_PREFIX_STRING\n                                           INCREASES_PREDICATE_PREFIX_STRING\n                                           ))\n\n\n(define SORT_COLUMN_INCREASING 'sort-column-increasing)\n(define SORT_COLUMN_DECREASING 'sort-column-decreasing)\n\n(define *concept-1-column-sort-order*\n  (vector SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING))\n(define *last-concept-1-column-clicked-for-sorting* (box -1))\n\n(define *concept-2-column-sort-order*\n  (vector SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING))\n(define *last-concept-2-column-clicked-for-sorting* (box -1))\n\n(define *concept-X-column-sort-order*\n  (vector SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING))\n(define *last-concept-X-column-clicked-for-sorting* (box -1))\n\n\n(define *concept-1-name-string* (box \"\"))\n(define *concept-1-isa-flag* (box #f))\n(define *concept-1-choices* (box '()))\n(define *predicate-1-choices* (box '()))\n\n(define *concept-2-name-string* (box \"\"))\n(define *concept-2-isa-flag* (box #f))\n(define *concept-2-choices* (box '()))\n(define *predicate-2-choices* (box '()))\n\n(define *concept-X-choices* (box '()))\n(define *full-path-choices* (box '()))\n(define *pubmed-choices* (box '()))\n\n;; saved choices used to generate\n;; paths when clicking on a concept in the X list box.\n(define *solution-concept-1-name-string* (box \"\"))\n(define *solution-concept-2-name-string* (box \"\"))\n(define *solution-concept-1-isa-flag* (box #f))\n(define *solution-concept-2-isa-flag* (box #f))\n(define *solution-concept-1-choices* (box '()))\n(define *solution-concept-2-choices* (box '()))\n(define *solution-predicate-1-choices* (box '()))\n(define *solution-predicate-2-choices* (box '()))\n\n;; ((pubmed-URL . (publication-date subject-score object-score sentence)) ...)\n(define *publications-info-alist* (box '()))\n\n(define *populate-publication-fields*\n  (lambda args\n    (error '*populate-publication-fields* \"*populate-publication-fields* function not initialized\")))\n\n(define (scheduler dependents)\n  (define mk-thread #f)\n  (define (kill-and-run p)\n    (kill-current-thread)\n    (set! mk-thread (thread p)))\n  (define (kill-current-thread)\n    (and mk-thread (begin (kill-thread mk-thread)\n                          (set! mk-thread #f)))\n    (for-each (lambda (s) (s 'kill)) dependents))\n  (lambda (op . args)\n    (case op\n      ((run)  (apply kill-and-run args))\n      ((kill) (kill-current-thread))\n      (else   (error \"invalid scheduler operation:\" op args)))))\n\n(define S (scheduler '()))\n(define S:edges S)\n(define S:X     S)\n(define S:C1P   S)\n(define S:C2P   S)\n(define S:C1    S)\n(define S:C2    S)\n;; TODO: ideally we would tier schedulers so that independent processes could\n;; be run concurrently.  Unfortunately, the underlying database does not\n;; currently use its ports in a thread-safe manner.  Fix this.\n;(define S:edges (scheduler '()))\n;(define S:X     (scheduler (list S:edges)))\n;(define S:C1P   (scheduler (list S:X)))\n;(define S:C2P   (scheduler (list S:X)))\n;(define S:C1    (scheduler (list S:C1P)))\n;(define S:C2    (scheduler (list S:C2P)))\n\n(define handle-search-in-Xs\n  (lambda (search-in-Xs-field\n           concept-X-list-box\n           search-in-Xs-previous-button\n           search-in-Xs-next-button\n           . rest)\n    (define direction (if (and (list? rest) (= (length rest) 1)) (car rest) #f))\n    (define search-str (send search-in-Xs-field get-value))\n\n    (define current-selection (send concept-X-list-box get-selection))\n\n    (cond\n      [direction\n\n       (define count (send concept-X-list-box get-number))\n\n       (define add1/sub1 (case direction\n                           [(previous) sub1]\n                           [(next) add1]\n                           [else (error 'add1/sub1 \"unknown direction in inc/dec\")]))\n\n       (define found-selection\n         (and (> count 0)\n              (let loop ((i (add1/sub1 current-selection)))\n                (cond\n                  [(>= i count) (loop 0)]\n                  [(< i 0) (loop (- count 1))]\n                  [else\n                   (define data (send concept-X-list-box get-data i))\n                   (define name-str (list-ref data 3))\n                   (define matches?\n                     (smart-string-matches? #f\n                                            chars:ignore-typical\n                                            \"\"\n                                            (string-split search-str \" \")\n                                            name-str))\n                   (cond\n                     [matches? i]\n                     [(= i current-selection)\n                      ;; wrapped around without a match\n                      #f]\n                     [else (loop (add1/sub1 i))])]))))\n\n       (if found-selection\n           (when (not (equal? found-selection current-selection))\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))\n             (send concept-X-list-box select found-selection #t)\n             (send concept-X-list-box set-first-visible-item found-selection))\n           (begin\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))))]\n      [(empty-string? search-str)\n       (when current-selection\n         (send concept-X-list-box select current-selection #f))\n       (send search-in-Xs-previous-button enable #f)\n       (send search-in-Xs-next-button enable #f)]\n      [else\n       (define count (send concept-X-list-box get-number))\n       (define found-selection\n         (and (> count 0)\n              (let loop ((i 0))\n                (cond\n                  [(>= i count) #f]\n                  [else\n                   (define data (send concept-X-list-box get-data i))\n                   (define name-str (list-ref data 3))\n                   (define matches?\n                     (smart-string-matches? #f\n                                            chars:ignore-typical\n                                            \"\"\n                                            (string-split search-str \" \")\n                                            name-str))\n                   (if matches?\n                       i\n                       (loop (add1 i)))]))))\n\n       (if found-selection\n           (begin\n             (send search-in-Xs-previous-button enable #t)\n             (send search-in-Xs-next-button enable #t))\n           (begin\n             (send search-in-Xs-previous-button enable #f)\n             (send search-in-Xs-next-button enable #f)))\n\n       (if found-selection\n           (when (not (equal? found-selection current-selection))\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))\n             (send concept-X-list-box select found-selection #t)\n             (send concept-X-list-box set-first-visible-item found-selection))\n           (begin\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))))])))\n\n(define (convert-concept-1/2-to-list-box-format concept)\n  (match concept\n    [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)\n     (list (format \"~a\" dbname)\n           (format \"~a\" cid)\n           (~a cui #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (format \"~a\" `(,catid . ,cat))\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\"))]))\n\n(define (convert-X-concept-to-list-box-format concept)\n  (match concept\n    [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-length ,confidence)\n     (list (format \"~a\" dbname)\n           (format \"~a\" cid)\n           (~a cui #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (format \"~a\" `(,catid . ,cat))\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (format \"~a\" max-pubmed-count)\n           (format \"~a\" min-pubmed-count)\n           (string-join pred-names \", \")\n           (format \"~a\" path-length)\n           (format \"~a\" confidence))]))\n\n(define (convert-concept-1/2-to-column-sorting-format concept)\n  (match concept\n    [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)\n     (list (format \"~a\" dbname)\n           cid\n           (~a cui #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           catid\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\"))]))\n\n(define (convert-X-concept-to-column-sorting-format concept)\n  (match concept\n    [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-length ,confidence)\n     (list (format \"~a\" dbname)\n           cid\n           (~a cui #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           catid\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           max-pubmed-count\n           min-pubmed-count\n           (string-join pred-names \", \")\n           path-length\n           confidence)]))\n\n(define (make-send-concepts-to-concept-1/2-list-box concept-1/2-list-box-thunk)\n  (lambda (concepts)\n    (define concept-1/2-list-box (concept-1/2-list-box-thunk))\n    (define formatted-concepts (map convert-concept-1/2-to-list-box-format concepts))\n    (send concept-1/2-list-box\n          set\n          (map (lambda (e) (list-ref e 0)) formatted-concepts)\n          (map (lambda (e) (list-ref e 1)) formatted-concepts)\n          (map (lambda (e) (list-ref e 2)) formatted-concepts)\n          (map (lambda (e) (list-ref e 3)) formatted-concepts)\n          (map (lambda (e) (list-ref e 4)) formatted-concepts))))\n\n(define (make-send-concepts-to-concept-X-list-box concept-X-list-box)\n  (lambda (concepts)\n    (define formatted-concepts (map convert-X-concept-to-list-box-format concepts))\n    (send concept-X-list-box\n          set\n          (map (lambda (e) (list-ref e 0)) formatted-concepts)\n          (map (lambda (e) (list-ref e 1)) formatted-concepts)\n          (map (lambda (e) (list-ref e 2)) formatted-concepts)\n          (map (lambda (e) (list-ref e 3)) formatted-concepts)\n          (map (lambda (e) (list-ref e 4)) formatted-concepts)\n          (map (lambda (e) (list-ref e 5)) formatted-concepts)\n          (map (lambda (e) (list-ref e 6)) formatted-concepts)\n          (map (lambda (e) (list-ref e 7)) formatted-concepts)\n          (map (lambda (e) (list-ref e 8)) formatted-concepts)\n          (map (lambda (e) (list-ref e 9)) formatted-concepts))))\n\n(define (handle-sort-by-column-header-click event\n                                            list-box\n                                            last-column-clicked-for-sorting-box\n                                            column-sort-order-vector\n                                            choices-box\n                                            convert-values-to-column-sorting-format\n                                            send-values-to-list-box)\n\n  (printf \"handle-sort-by-column-header-click called\\n\")\n\n  ;; get previously selected choice's data, if any\n  (define current-selection (send list-box get-selection))\n  (printf \"current-selection: ~s\\n\" current-selection)\n  (define current-selection-data (and current-selection\n                                      (send list-box get-data current-selection)))\n  (printf \"current-selection-data: ~s\\n\" current-selection-data)\n\n  (when current-selection\n    (send list-box select current-selection #f))\n\n  ;; sort by column\n  (define column-clicked (send event get-column))\n  (define last-column-clicked (unbox last-column-clicked-for-sorting-box))\n\n  (define sort-order (vector-ref column-sort-order-vector column-clicked))\n\n  ;; swap sort order if user clicks on same column twice in a row\n  (when (= column-clicked last-column-clicked)\n    (set! sort-order\n          (if (eqv? sort-order SORT_COLUMN_INCREASING)\n              SORT_COLUMN_DECREASING\n              SORT_COLUMN_INCREASING))\n    (vector-set! column-sort-order-vector\n                 column-clicked\n                 sort-order))\n\n  (printf \"sorting by column ~s in ~s order\\n\" column-clicked sort-order)\n\n  (define choices (unbox choices-box))\n\n  (define sorted-choices (sort choices\n                               (lambda (c1 c2)\n                                 (let ((fc1 (convert-values-to-column-sorting-format c1))\n                                       (fc2 (convert-values-to-column-sorting-format c2)))\n                                   (let ((v1 (list-ref fc1 column-clicked))\n                                         (v2 (list-ref fc2 column-clicked)))\n                                     (let ((num-compare\n                                            (if (eqv? sort-order SORT_COLUMN_INCREASING)\n                                                <\n                                                >))\n                                           (string-compare\n                                            (if (eqv? sort-order SORT_COLUMN_INCREASING)\n                                                string?)))\n                                       (if (and (number? v1) (number? v2))\n                                           (num-compare v1 v2)\n                                           (string-compare (string-downcase v1)\n                                                           (string-downcase v2)))))))))\n\n  (set-box! last-column-clicked-for-sorting-box column-clicked)\n\n  (set-box! choices-box sorted-choices)\n\n  (send-values-to-list-box sorted-choices)\n\n  ;; add choice data to each list-box entry\n  (define len (length sorted-choices))\n  (let loop ((i 0)\n             (c* sorted-choices))\n    (cond\n      [(= len i) (void)]\n      [else\n       (send list-box set-data i (car c*))\n       (loop (add1 i)\n             (cdr c*))]))\n\n  ;; select previously selected choice in its new location, if any\n  (when (and current-selection current-selection-data)\n    (define count (send list-box get-number))\n    (printf \"count: ~s\\n\" count)\n    (define new-selection\n      (let loop ((i 0))\n        (cond\n          [(>= i count) #f]\n          [else\n           (let ((d (send list-box get-data i)))\n             (printf \"--------\\n\")\n             (printf \"d: ~s\\n\" d)\n             (printf \"(equal? d current-selection-data): ~s\\n\" (equal? d current-selection-data))\n             (if (equal? d current-selection-data)\n                 i\n                 (loop (add1 i))))])))\n    (printf \"new-selection: ~s\\n\" new-selection)\n    (when new-selection\n      (send list-box select new-selection #t)\n      (send list-box set-first-visible-item new-selection)))\n\n  (void))\n\n(define (concept-list parent\n                      parent-search/isa-panel\n                      parent-list-boxes-panel\n                      label\n                      name-string\n                      isa-flag\n                      choices\n                      predicate-list-box-thunk\n                      predicate-choices\n                      edge-type\n                      last-column-clicked-for-sorting-box\n                      column-sort-order-vector\n                      choices-box\n                      convert-values-to-column-sorting-format\n                      send-values-to-list-box\n                      S:C S:CP)\n  (define name-field (new text-field%\n                          (label label)\n                          (parent parent-search/isa-panel)\n                          (init-value \"\")\n                          (callback (lambda (self event)\n                                      (define name (send self get-value))\n                                      (set-box! name-string name)\n                                      (set-box! predicate-choices '())\n                                      (send (predicate-list-box-thunk) set '())\n                                      (handle)))))\n  (define isa-field (new check-box%\n                         (parent parent-search/isa-panel)\n                         (label \"Include ISA-related concepts\")\n                         (value #f)\n                         (callback (lambda (self event) (handle)))))\n  (define concept-listbox (new smart-column-width-list-box%\n                               (label label)\n                               (choices '())\n                               (columns '(\"KG\" \"CID\" \"CURIE\" \"Category\" \"Name\"))\n                               (parent parent-list-boxes-panel)\n                               (style '(column-headers clickable-headers reorderable-headers extended))\n                               (callback (lambda (self event)\n                                           (define event-type (send event get-event-type))\n                                           (cond\n                                             [(eqv? event-type 'list-box-column)\n                                              (handle-sort-by-column-header-click\n                                                event\n                                                concept-listbox\n                                                last-column-clicked-for-sorting-box\n                                                column-sort-order-vector\n                                                choices-box\n                                                convert-values-to-column-sorting-format\n                                                send-values-to-list-box)]\n                                             [else\n                                               (define selections (send self get-selections))\n                                               (define selected-concepts\n                                                 (foldr (lambda (i l) (cons (list-ref (unbox choices) i) l)) '() selections))\n                                               (when *verbose*\n                                                 (printf \"selected concepts:\\n~s\\n\" selected-concepts))\n                                               (S:CP 'run\n                                                     (thunk\n                                                       (define preds-by-concept\n                                                         (time (case edge-type\n                                                                 [(in-edge)  (map caddr (find-predicates/concepts #f #t selected-concepts))]\n                                                                 [(out-edge) (map cadr (find-predicates/concepts #t #f selected-concepts))]\n                                                                 [else       (error 'concept-listbox/predicates)])))\n                                                       (define predicates\n                                                         (sort (remove-duplicates (map cddr (append* preds-by-concept))) string Predicate 1 -> [X] -> Predicate 2 -> Concept 2\")))\n\n    (define concept-2-overall-pane (new vertical-pane%\n                                        (parent upper-pane)\n                                        (alignment '(left center))))\n\n    (define concept-2-search/isa-panel (new panel:horizontal-dragable%\n                                            (parent concept-2-overall-pane)\n                                            (alignment '(left center))\n                                            (stretchable-height #f)))\n    (define concept-2-list-boxes-panel (new panel:horizontal-dragable%\n                                            (parent concept-2-overall-pane)\n                                            (alignment '(left center))))\n    (define predicate-2-list-box (new list-box%\n                                      (label \"Predicate 2\")\n                                      (choices (unbox *predicate-2-choices*))\n                                      (columns '(\"Name\"))\n                                      (parent concept-2-list-boxes-panel)\n                                      (style '(extended))\n                                      (callback go-callback)))\n    (define concept-2-list-box (concept-list concept-2-overall-pane\n                                             concept-2-search/isa-panel\n                                             concept-2-list-boxes-panel\n                                             \"Concept 2\"\n                                             *concept-2-name-string*\n                                             *concept-2-isa-flag*\n                                             *concept-2-choices*\n                                             (lambda () predicate-2-list-box)\n                                             *predicate-2-choices*\n                                             'in-edge\n                                             *last-concept-2-column-clicked-for-sorting*\n                                             *concept-2-column-sort-order*\n                                             *concept-2-choices*\n                                             convert-concept-1/2-to-column-sorting-format\n                                             (make-send-concepts-to-concept-1/2-list-box (lambda () concept-2-list-box))\n                                             S:C2 S:C2P))\n\n    (define running-status-description/search-in-Xs-panel\n      (new\n       horizontal-panel%\n       (parent concept-2-overall-pane)\n       (alignment '(left center))\n       (stretchable-height #f)))\n\n    (define running-status-description (new message%\n                                            (parent running-status-description/search-in-Xs-panel)\n                                            (label \"                                                                \")))\n\n    (define search-in-Xs-field (new text-field%\n                                    (label \"Find in X's\")\n                                    (parent running-status-description/search-in-Xs-panel)\n                                    (init-value \"\")\n                                    (callback (lambda (self event)\n                                                (handle-search-in-Xs self\n                                                                     concept-X-list-box\n                                                                     search-in-Xs-previous-button\n                                                                     search-in-Xs-next-button\n                                                                     )))))\n\n    (define search-in-Xs-previous-button (new button%\n                                              (parent running-status-description/search-in-Xs-panel)\n                                              (label \"Previous\")\n                                              (callback (lambda (self event)\n                                                          (handle-search-in-Xs search-in-Xs-field\n                                                                               concept-X-list-box\n                                                                               search-in-Xs-previous-button\n                                                                               search-in-Xs-next-button\n                                                                               'previous)))))\n\n    (define search-in-Xs-next-button (new button%\n                                          (parent running-status-description/search-in-Xs-panel)\n                                          (label \"Next\")\n                                          (callback (lambda (self event)\n                                                      (handle-search-in-Xs search-in-Xs-field\n                                                                           concept-X-list-box\n                                                                           search-in-Xs-previous-button\n                                                                           search-in-Xs-next-button\n                                                                           'next)))))\n\n    (define concept-X-list-box (new smart-column-width-list-box%\n                                    (label \"X\")\n                                    (choices (unbox *concept-X-choices*))\n                                    (columns '(\"KG\" \"CID\" \"CURIE\" \"Category\" \"Name\" \"Max PubMed #\" \"Min PubMed #\" \"Predicates\" \"Path Length\" \"Path Confidence\"))\n                                    (parent lower-pane)\n                                    (style '(column-headers clickable-headers reorderable-headers single))\n                                    (callback (lambda (self event)\n                                                (define event-type (send event get-event-type))\n                                                (S:edges 'run\n                                                         (thunk\n                                                           (cond\n                                                             [(eqv? event-type 'list-box-column)\n                                                              (handle-sort-by-column-header-click\n                                                                event\n                                                                concept-X-list-box\n                                                                *last-concept-X-column-clicked-for-sorting*\n                                                                *concept-X-column-sort-order*\n                                                                *concept-X-choices*\n                                                                convert-X-concept-to-column-sorting-format\n                                                                (make-send-concepts-to-concept-X-list-box self))]\n                                                             [(eqv? event-type 'list-box-dclick)\n                                                              (printf \"double-click!! copy name of the concept to the clipboard\\n\")\n                                                              (define time-stamp (send event get-time-stamp))\n                                                              (printf \"time stamp: ~s\\n\" time-stamp)\n                                                              (define concept-name\n                                                                (let ((sel* (send concept-X-list-box get-selections)))\n                                                                  (if (= (length sel*) 1)\n                                                                    (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n                                                                      (match selected-X\n                                                                        [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-count ,confidence)\n                                                                          name]\n                                                                        [else \"\"]))\n                                                                    \"\")))\n                                                              (printf \"concept name: ~s\\n\" concept-name)\n                                                              (send the-clipboard set-clipboard-string concept-name time-stamp)]\n                                                             [else\n\n                                                               ;; empty the entries in the full-path-list-box\n                                                               (send full-path-list-box set '() '() '() '() '() '() '() '())\n\n                                                               ;; empty the entries in the properties list-boxes\n                                                               (send subject-properties-list-box set '() '())\n                                                               (send edge-properties-list-box set '() '())\n                                                               (send object-properties-list-box set '() '())\n\n                                                               ;; empty the entries in the pubmed-list-box\n                                                               (send pubmed-list-box set '())\n\n                                                               (let ((sel* (send concept-X-list-box get-selections)))\n                                                                 (when (= (length sel*) 1)\n                                                                   (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n                                                                     (let ((selected-X\n                                                                             (match selected-X\n                                                                               [`(,dbname ,cid ,cui ,name (,catid . ,cat) ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-count ,confidence)\n                                                                                 `(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)])))\n                                                                       (printf \"selected ~s\\n\" selected-X)\n                                                                       (define concept-1* (unbox *solution-concept-1-choices*))\n                                                                       (define concept-2* (unbox *solution-concept-2-choices*))\n                                                                       (printf \"concept-1* ~s\\n\" concept-1*)\n                                                                       (printf \"concept-2* ~s\\n\" concept-2*)\n                                                                       (define predicate-1* (unbox *solution-predicate-1-choices*))\n                                                                       (define predicate-2* (unbox *solution-predicate-2-choices*))\n                                                                       (printf \"predicate-1* ~s\\n\" predicate-1*)\n                                                                       (printf \"predicate-2* ~s\\n\" predicate-2*)\n\n                                                                       (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates (unbox *predicate-1-choices*) predicate-1*))\n                                                                       (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates (unbox *predicate-2-choices*) predicate-2*))\n\n                                                                       (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n                                                                       (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n                                                                       (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n                                                                       (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n\n                                                                       (define paths '())\n\n\n                                                                       (cond\n                                                                         [(and\n                                                                            (null?\n                                                                              (split-name-string\n                                                                                (unbox *solution-concept-1-name-string*)))\n                                                                            (null?\n                                                                              (split-name-string\n                                                                                (unbox *solution-concept-2-name-string*))))\n\n                                                                          (set! paths '())]\n                                                                         [(null? (split-name-string (unbox *solution-concept-1-name-string*)))\n\n                                                                          (set! paths '())\n                                                                          ;; run synthetic queries here\n                                                                          (set! paths\n                                                                            (remove-duplicates\n                                                                              (append paths\n                                                                                      (run* (q)\n                                                                                        (fresh (e dbname eid x o pid pred eprops)\n                                                                                          (== (list `(,dbname ,eid ,x ,o (,pid . ,pred) ,eprops)) q)\n                                                                                          (== `(,dbname . ,x) selected-X)\n                                                                                          (== `(,dbname ,eid ,x ,o (,pid . ,pred) ,eprops) e)\n                                                                                          (membero `(,dbname . ,o) concept-2*)\n                                                                                          (membero pred atomic-predicate-2*)\n                                                                                          (edgeo e))))))]\n                                                                         [(null? (split-name-string (unbox *solution-concept-2-name-string*)))\n\n                                                                          (set! paths '())\n                                                                          ;; run synthetic queries here\n                                                                          (set! paths\n                                                                            (remove-duplicates\n                                                                              (append paths\n                                                                                      (run* (q)\n                                                                                        (fresh (e dbname eid s x pid pred eprops)\n                                                                                          (== (list `(,dbname ,eid ,s ,x (,pid . ,pred) ,eprops)) q)\n                                                                                          (== `(,dbname . ,x) selected-X)\n                                                                                          (== `(,dbname ,eid ,s ,x (,pid . ,pred) ,eprops) e)\n                                                                                          (membero `(,dbname . ,s) concept-1*)\n                                                                                          (membero pred atomic-predicate-1*)\n                                                                                          (edgeo e))))))]\n                                                                         [else\n                                                                           (set! paths '())\n                                                                           ;; run synthetic queries here\n                                                                           (set! paths\n                                                                             (remove-duplicates\n                                                                               (append paths\n                                                                                       (run* (q)\n                                                                                         (fresh (e1 e2 dbname eid1 eid2 s x o pid1 pid2 p1 p2 eprops1 eprops2)\n                                                                                           (== `(,dbname . ,x) selected-X)\n                                                                                           (== (list\n                                                                                                 `(,dbname ,eid1 ,s ,x (,pid1 . ,p1) ,eprops1)\n                                                                                                 `(,dbname ,eid2 ,x ,o (,pid2 . ,p2) ,eprops2))\n                                                                                               q)\n                                                                                           (== `(,dbname ,eid1 ,s ,x (,pid1 . ,p1) ,eprops1) e1)\n                                                                                           (== `(,dbname ,eid2 ,x ,o (,pid2 . ,p2) ,eprops2) e2)\n                                                                                           (membero `(,dbname . ,s) concept-1*)\n                                                                                           (membero `(,dbname . ,o) concept-2*)\n                                                                                           (membero p1 atomic-predicate-1*)\n                                                                                           (membero p2 atomic-predicate-2*)\n                                                                                           (edgeo e1)\n                                                                                           (edgeo e2))))))])\n\n                                                                       (printf \"paths: ~s\\n\" paths)\n                                                                       (newline)\n\n                                                                       ;; This sorting affects the order of the \"Path\" list\n                                                                       ;; for the selected concept.\n                                                                       (set! paths (sort-paths paths))\n\n                                                                       (define flattened-paths\n                                                                         (let ((ls (foldr\n                                                                                     (lambda (p l)\n                                                                                       (cons\n                                                                                         'path-separator\n                                                                                         (append (reverse p) l)))\n                                                                                     '()\n                                                                                     paths)))\n                                                                           (if (null? ls)\n                                                                             ;; ls should never be null!\n                                                                             '()\n                                                                             (reverse (cdr ls)))))\n\n\n\n                                                                       (define full-path-dbname-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n                                                                                    (~a dbname)]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-eid-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n                                                                                    (~a eid)]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-subj-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n                                                                                    (~a subj #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-pred-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n                                                                                    (~a `(,pid . ,pred) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-obj-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj (,pid . ,pred) ,eprops)\n                                                                                    (~a obj #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-subj-cat-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid (,cid ,cui ,name (,catid . ,cat) ,props) ,obj (,pid . ,pred) ,eprops)\n                                                                                    (~a `(,catid . ,cat) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-obj-cat-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj (,cid ,cui ,name (,catid . ,cat) ,props) (,pid . ,pred) ,eprops)\n                                                                                    (~a `(,catid . ,cat) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-PubMed-count-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj (,cid ,cui ,name (,catid . ,cat) ,props) (,pid . ,pred) ,eprops)\n                                                                                    (~a (length (pubmed-URLs-from-edge x)))]))\n                                                                              flattened-paths))\n\n                                                                       (send full-path-list-box\n                                                                             set\n                                                                             full-path-dbname-list\n                                                                             full-path-eid-list\n                                                                             full-path-subj-list\n                                                                             full-path-pred-list\n                                                                             full-path-obj-list\n                                                                             full-path-subj-cat-list\n                                                                             full-path-obj-cat-list\n                                                                             full-path-PubMed-count-list\n                                                                             )\n\n                                                                       (set-box! *full-path-choices* flattened-paths)\n\n                                                                       ;; unselect all items\n                                                                       (for ([i (length flattened-paths)])\n                                                                            (send full-path-list-box select i #f))\n\n                                                                       ;; select first item\n                                                                       (send full-path-list-box select 0 #t)\n                                                                       (populate-selected-paths))))\n                                                                 (void))])))))))\n\n    (define (populate-selected-paths)\n      (when *verbose*\n        (printf \"(unbox *full-path-choices*):\\n~s\\n\" (unbox *full-path-choices*)))\n      (define selections (send full-path-list-box get-selections))\n      (when *verbose*\n        (printf \"selection for full path:\\n~s\\n\" selections))\n      (define selected-full-paths\n        (foldr (lambda (i l) (cons (list-ref (unbox *full-path-choices*) i) l))\n               '()\n               selections))\n      (for-each\n        (lambda (x)\n          (match x\n            ['path-separator\n             (send subject-properties-list-box set '() '())\n             (send edge-properties-list-box set '() '())\n             (send object-properties-list-box set '() '())]\n            [`(,dbname ,eid\n                       (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n                       (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n                       ,p\n                       ,eprops)\n              (define (set-properties-list-box prop-list-box props)\n                (send prop-list-box\n                      set\n                      (map\n                        (lambda (p)\n                          (~a (car p)\n                              #:max-width\n                              MAX-CHAR-WIDTH\n                              #:limit-marker\n                              \"...\"))\n                        props)\n                      (map\n                        (lambda (p)\n                          (~a (cdr p)\n                              #:max-width\n                              MAX-CHAR-WIDTH\n                              #:limit-marker\n                              \"...\"))\n                        props)))\n              (set-properties-list-box subject-properties-list-box sprops)\n              (set-properties-list-box edge-properties-list-box eprops)\n              (set-properties-list-box object-properties-list-box oprops)]))\n        selected-full-paths)\n      (for-each\n        (lambda (edge)\n          (let ((URLs (pubmed-URLs-from-edge edge)))\n            (set-box! *pubmed-choices* URLs)\n            (send pubmed-list-box set URLs)))\n        selected-full-paths)\n      (for-each\n        (lambda (edge)\n          (let ((publications-info-alist\n                  (publications-info-alist-from-edge edge)))\n            (set-box! *publications-info-alist* publications-info-alist)))\n        selected-full-paths)\n      (when *verbose*\n        (printf \"selected full path:\\n\")\n        (for-each\n          (lambda (x)\n            (match x\n              ['path-separator\n               (printf \"-----------------------\\n\")]\n              [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n                (pretty-print `(,dbname ,eid ,subj ,obj ,p ,eprops))]))\n          selected-full-paths)))\n\n    (define full-path-list-box (new smart-column-width-list-box%\n                                    (label \"Paths\")\n                                    (choices (unbox *full-path-choices*))\n                                    (columns '(\"KG\" \"EID\" \"Subject\" \"Predicate\" \"Object\" \"Subj Cat\" \"Obj Cat\" \"PubMed #\"))\n                                    (parent lower-pane)\n                                    (style '(column-headers reorderable-headers extended))\n                                    (callback (lambda (self event) (populate-selected-paths)))))\n\n    (define properties/pubmed-panel (new panel:horizontal-dragable%\n                                         (parent lower-pane)\n                                         (alignment '(left center))\n                                         (stretchable-height #t)))\n\n    (define subject-properties-list-box (new smart-column-width-list-box%\n                                             (label \"Subject\")\n                                             (choices '())\n                                             (columns '(\"Property\" \"Value\"))\n                                             (parent properties/pubmed-panel)\n                                             (style '(column-headers reorderable-headers extended))\n                                             (callback (lambda (self event)\n                                                         (void)))))\n\n    (define edge-properties-list-box (new smart-column-width-list-box%\n                                     (label \"Edge\")\n                                     (choices '())\n                                     (columns '(\"Property\" \"Value\"))\n                                     (parent properties/pubmed-panel)\n                                     (style '(column-headers reorderable-headers extended))\n                                     (callback (lambda (self event)\n                                                 (void)))))\n\n    (define object-properties-list-box (new smart-column-width-list-box%\n                                            (label \"Object\")\n                                            (choices '())\n                                            (columns '(\"Property\" \"Value\"))\n                                            (parent properties/pubmed-panel)\n                                            (style '(column-headers reorderable-headers extended))\n                                            (callback (lambda (self event)\n                                                        (void)))))\n\n    (define pubmed-list-box (new list-box%\n                                 (label \"Pubmed\")\n                                 (choices (unbox *pubmed-choices*))\n                                 (columns '(\"URL\"))\n                                 (parent properties/pubmed-panel)\n                                 (style '(column-headers reorderable-headers single))\n                                 (callback (lambda (self event)\n                                             (define event-type (send event get-event-type))\n                                             (define selections (send self get-selections))\n                                             (define selected-pubmeds\n                                               (foldr (lambda (i l) (cons (list-ref (unbox *pubmed-choices*) i) l))\n                                                      '()\n                                                      selections))\n                                             (for-each\n                                               (lambda (url)\n                                                 (printf \"url: ~s\\n\" url)\n\n                                                 (match (assoc url (unbox *publications-info-alist*))\n                                                   [`(,pubmed-URL . (,publication-date ,subject-score ,object-score ,sentence))\n                                                    (*populate-publication-fields* publication-date subject-score object-score sentence)]\n                                                   [#f (*populate-publication-fields* \"\" \"\" \"\" \"\")])\n\n                                                 (when (eqv? event-type 'list-box-dclick)\n                                                   ;; if the user double-clicked on the URL, open it in a web browser\n                                                   (send-url url)))\n                                               selected-pubmeds)))))\n\n    (define publication-info-panel (new panel:vertical-dragable%\n                                        (parent lower-pane)\n                                        (alignment '(left center))\n                                        (stretchable-height #t)))\n\n    (define publication-info-date/subject/object-panel (new horizontal-panel%\n                                                            (parent publication-info-panel)\n                                                            (alignment '(left center))\n                                                            (stretchable-height #f)))\n\n    (define publication-date (new text-field%\n                                  (label \"Publication Date\")\n                                  (parent publication-info-date/subject/object-panel)\n                                  (enabled #f)\n                                  (init-value \"\")))\n\n    (define subject-score (new text-field%\n                               (label \"Subject Score\")\n                               (parent publication-info-date/subject/object-panel)\n                               (enabled #f)\n                               (init-value \"\")))\n\n    (define object-score (new text-field%\n                              (label \"Object Score\")\n                              (parent publication-info-date/subject/object-panel)\n                              (enabled #f)\n                              (init-value \"\")))\n\n    (define publication-sentence-editor-canvas (new editor-canvas%\n                                                    (parent publication-info-panel)\n                                                    (enabled #f)\n                                                    (label \"Sentence\")))\n    (define publication-sentence-text (new text%))\n    (send publication-sentence-text insert \"\")\n    (send publication-sentence-editor-canvas set-editor publication-sentence-text)\n\n    (set! *populate-publication-fields*\n          (lambda (date subj-score obj-score sentence)\n            (send publication-date set-value date)\n            (send subject-score set-value (format \"~a\" subj-score))\n            (send object-score set-value (format \"~a\" obj-score))\n            (send publication-sentence-text erase)\n            (send publication-sentence-text insert sentence)))\n\n\n    ;; trigger reflowing of object sizes\n    (send frame reflow-container)\n\n    ;; disable previous and next buttons by default\n    (send search-in-Xs-previous-button enable #f)\n    (send search-in-Xs-next-button enable #f)\n\n    (set-default-column-widths concept-1-list-box)\n    (set-default-column-widths concept-2-list-box)\n    (set-default-column-widths concept-X-list-box)\n    (set-default-column-widths full-path-list-box)\n    (set-default-column-widths edge-properties-list-box)\n    (set-default-column-widths edge-properties-list-box)\n    (set-default-column-widths object-properties-list-box)\n\n    (send frame show #t)))\n\n(define (launch-gene-window)\n  (let ((frame (new frame%\n                    (label \"Gene Explorer\")\n                    (width HORIZ-SIZE)\n                    (height VERT-SIZE))))\n\n    (define gene-name-field (new text-field%\n                                 (label \"Gene Name\")\n                                 (parent frame)\n                                 (init-value \"\")\n                                 (callback (lambda (self event)\n                                             (void)))))\n\n    (define gene-listbox (new smart-column-width-list-box%\n                              (label \"Gene\")\n                              (choices '())\n                              (columns '(\"KG\" \"CID\" \"CURIE\" \"Category\" \"Name\"))\n                              (parent frame)\n                              (style '(column-headers reorderable-headers extended))\n                              (callback (lambda (self event)\n                                          (void)))))\n\n\n    (define current-gene-name \"\")\n\n    (send frame show #t)\n    ))\n\n\n(define (split-atomic/synthetic-predicates choices predicate*)\n  (define (synthetic? pred)\n    (memf (lambda (syn-prefix) (string-prefix? pred syn-prefix))\n          SYNTHETIC_PREDICATE_PREFIXES))\n\n  (define atomic-predicate* (filter-not synthetic? predicate*))\n  (define synthetic-predicate* (filter synthetic? predicate*))\n\n  (when (memf (lambda (pred) (string-prefix? pred DECREASES_PREDICATE_PREFIX_STRING))\n              synthetic-predicate*)\n    (set! atomic-predicate* (append DECREASES_PREDICATE_NAMES atomic-predicate*)))\n\n  (when (memf (lambda (pred) (string-prefix? pred INCREASES_PREDICATE_PREFIX_STRING))\n              synthetic-predicate*)\n    (set! atomic-predicate* (append INCREASES_PREDICATE_NAMES atomic-predicate*)))\n\n  (set! atomic-predicate* (set-intersect choices (remove-duplicates atomic-predicate*)))\n\n  (printf \"atomic-predicate*: ~s\\n\" atomic-predicate*)\n  (printf \"synthetic-predicate*: ~s\\n\" synthetic-predicate*)\n\n  (list atomic-predicate* synthetic-predicate*))\n\n\n(define (find-X-concepts concept-1* concept-2* predicate-1* predicate-2* predicate-1-choices predicate-2-choices concept-X-list-box running-status-description full-path-list-box subject-properties-list-box edge-properties-list-box object-properties-list-box pubmed-list-box search-in-Xs-field search-in-Xs-previous-button search-in-Xs-next-button)\n\n  (define start-time (current-milliseconds))\n  (printf \"\\nfinding concepts X for which\\n[C1] -> P1 -> [X] -> P2 -> [C2]\\n\")\n  (printf \"=============================\\n\")\n\n  (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates predicate-1-choices predicate-1*))\n  (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates predicate-2-choices predicate-2*))\n\n  (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n  (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n  (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n  (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n  (define all-X-concepts-with-edges '())\n\n  (printf \"atomic/synthetic-predicate-1*: ~s\\n\" atomic/synthetic-predicate-1*)\n  (printf \"atomic/synthetic-predicate-2*: ~s\\n\" atomic/synthetic-predicate-2*)\n  (newline)\n  (printf \"atomic-predicate-1*: ~s\\n\" atomic-predicate-1*)\n  (printf \"atomic-predicate-2*: ~s\\n\" atomic-predicate-2*)\n  (newline)\n  (printf \"synthetic-predicate-1*: ~s\\n\" synthetic-predicate-1*)\n  (printf \"synthetic-predicate-2*: ~s\\n\" synthetic-predicate-2*)\n  (newline)\n\n  (cond\n    [(and\n      (null?\n       (split-name-string\n        (unbox *concept-1-name-string*)))\n      (null?\n       (split-name-string\n        (unbox *concept-2-name-string*))))\n\n     (set! all-X-concepts-with-edges '())]\n    [(null? (split-name-string (unbox *concept-1-name-string*)))\n\n     (set! all-X-concepts-with-edges '())\n     (set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append all-X-concepts-with-edges\n                    (run* (q)\n                      (fresh (dbname eid s o pid pred eprops e)\n                        (== (list dbname s (list eprops) (list e)) q)\n                        (== `(,dbname ,eid ,s ,o (,pid . ,pred) ,eprops) e)\n                        (membero `(,dbname . ,o) concept-2*)\n                        (membero pred atomic-predicate-2*)\n                        (edgeo e))))))]\n    [(null? (split-name-string (unbox *concept-2-name-string*)))\n\n     (set! all-X-concepts-with-edges '())\n     ;; run synthetic queries here\n     (set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append all-X-concepts-with-edges\n                    (run* (q)\n                      (fresh (dbname eid s o pid pred eprops e)\n                        (== (list dbname o (list eprops) (list e)) q)\n                        (== `(,dbname ,eid ,s ,o (,pid . ,pred) ,eprops) e)\n                        (membero `(,dbname . ,s) concept-1*)\n                        (membero pred atomic-predicate-1*)\n                        (edgeo e))))))]\n    [else\n     (set! all-X-concepts-with-edges '())\n     ;; run synthetic queries here\n     (set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append all-X-concepts-with-edges\n                    (run* (q)\n                      (fresh (dbname eid1 eid2 s m o pid1 pid2 p1 p2 eprops1 eprops2 e1 e2)\n                        (== (list dbname m (list eprops1 eprops2) (list e1 e2)) q)\n                        (== `(,dbname ,eid1 ,s ,m (,pid1 . ,p1) ,eprops1) e1)\n                        (== `(,dbname ,eid2 ,m ,o (,pid2 . ,p2) ,eprops2) e2)\n                        (membero `(,dbname . ,s) concept-1*)\n                        (membero `(,dbname . ,o) concept-2*)\n                        (membero p1 atomic-predicate-1*)\n                        (membero p2 atomic-predicate-2*)\n                        (edgeo e1)\n                        (edgeo e2))))))])\n\n  (define end-time (current-milliseconds))\n\n  (define elapsed-time (- end-time start-time))\n\n  (printf \"elapsed query time: ~s seconds\\n\" (/ elapsed-time 1000.0))\n  (printf \"=============================\\n\")\n\n  ;; This sorting affects order of appearance in the \"X\" concept list\n  (set! all-X-concepts-with-edges\n    (sort\n      all-X-concepts-with-edges\n      (lambda (c1 c2)\n        (match (list c1 c2)\n          [`((,_ ,_ ,_ ,e1*) (,_ ,_ ,_ ,e2*))\n           (not (path-confidencestring (seconds->date (current-seconds)) #t))\n  (newline)\n\n\n  (define number-Xs-found (length all-X-concepts))\n  (define query-seconds (/ elapsed-time 1000.0))\n  (define query-time-format-string \"Found ~s X's after ~s seconds\")\n  (send running-status-description set-label (format query-time-format-string number-Xs-found query-seconds))\n  (printf query-time-format-string number-Xs-found query-seconds)\n  (newline)\n  (newline)\n\n\n  (set-box! *concept-X-choices* all-X-concepts)\n\n  (set-box! *solution-concept-1-name-string* (unbox *concept-1-name-string*))\n  (set-box! *solution-concept-2-name-string* (unbox *concept-2-name-string*))\n\n  (set-box! *solution-concept-1-isa-flag* (unbox *concept-1-isa-flag*))\n  (set-box! *solution-concept-2-isa-flag* (unbox *concept-2-isa-flag*))\n\n  (set-box! *solution-concept-1-choices* concept-1*)\n  (set-box! *solution-concept-2-choices* concept-2*)\n  (set-box! *solution-predicate-1-choices* predicate-1*)\n  (set-box! *solution-predicate-2-choices* predicate-2*)\n\n  (printf \"*solution-concept-1-name-string*:\\n~s\\n\" (unbox *solution-concept-1-name-string*))\n  (printf \"*solution-concept-1-isa-flag*:\\n~s\\n\" (unbox *solution-concept-1-isa-flag*))\n  (printf \"*solution-concept-1-choices*:\\n\")\n  (pretty-print (unbox *solution-concept-1-choices*))\n  (printf \"*solution-predicate-1-choices*:\\n\")\n  (pretty-print (unbox *solution-predicate-1-choices*))\n  (newline)\n\n  (printf \"*solution-concept-2-name-string*:\\n~s\\n\" (unbox *solution-concept-2-name-string*))\n  (printf \"*solution-concept-2-isa-flag*:\\n~s\\n\" (unbox *solution-concept-2-isa-flag*))\n  (printf \"*solution-concept-2-choices*:\\n\")\n  (pretty-print (unbox *solution-concept-2-choices*))\n  (printf \"*solution-predicate-2-choices*:\\n\")\n  (pretty-print (unbox *solution-predicate-2-choices*))\n  (newline)\n\n  (define pretty-print-X-concepts-with-edges\n    (lambda (file-name pretty-printer print-basic-header print-low-level-query-information X-concepts-with-edges)\n      (with-output-to-file\n          file-name\n          (lambda ()\n            (when print-basic-header\n              (printf \";; mediKanren query output\\n\")\n              (printf \";; ~a\\n\" MEDIKANREN_VERSION_STRING)\n              (printf \";; \\n\")\n              (let ((local-date (seconds->date (current-seconds))))\n                (printf \";; Query run at date/time: ~s ~s ~s  ~s:~s:~s   (Year Month Day  Hour:Minute:Second)\\n\"\n                        (date-year local-date)\n                        (date-month local-date)\n                        (date-day local-date)\n                        (date-hour local-date)\n                        (date-minute local-date)\n                        (date-second local-date)))\n              (printf \";; \\n\"))\n            (when print-low-level-query-information\n              (printf \";; ===================================================\\n\")\n              (printf \";; Low-level query information from the mediKanren GUI\\n\")\n              (printf \";; ===================================================\\n\")\n              (printf \";; \\n\")\n              (printf \";; *concept-1-name-string*: ~s\\n\" (unbox *concept-1-name-string*))\n              (printf \";; *solution-concept-1-name-string*: ~s\\n\" (unbox *solution-concept-1-name-string*))\n              (printf \";; *solution-concept-1-isa-flag*: ~s\\n\" (unbox *solution-concept-1-isa-flag*))\n              (printf \";; *solution-concept-1-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-concept-1-choices*))\n              (printf \"|#\\n\")\n              (printf \";; atomic/synthetic-predicate-1*: ~s\\n\" atomic/synthetic-predicate-1*)\n              (printf \";; atomic-predicate-1*: ~s\\n\" atomic-predicate-1*)\n              (printf \";; synthetic-predicate-1*: ~s\\n\" synthetic-predicate-1*)\n              (printf \";; *solution-predicate-1-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-predicate-1-choices*))\n              (printf \"|#\\n\")\n              (printf \";; \\n\")\n              (printf \";; \\n\")\n              (printf \";; \\n\")\n              (printf \";; atomic/synthetic-predicate-2*: ~s\\n\" atomic/synthetic-predicate-2*)\n              (printf \";; atomic-predicate-2*: ~s\\n\" atomic-predicate-2*)\n              (printf \";; synthetic-predicate-2*: ~s\\n\" synthetic-predicate-2*)\n              (printf \";; *solution-predicate-2-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-predicate-2-choices*))\n              (printf \"|#\\n\")\n              (printf \";; *concept-2-name-string*: ~s\\n\" (unbox *concept-2-name-string*))\n              (printf \";; *solution-concept-2-name-string*: ~s\\n\" (unbox *solution-concept-2-name-string*))\n              (printf \";; *solution-concept-2-isa-flag*: ~s\\n\" (unbox *solution-concept-2-isa-flag*))\n              (printf \";; *solution-concept-2-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-concept-2-choices*))\n              (printf \"|#\\n\")\n              (printf \"\\n\"))\n            (when print-basic-header\n              (printf \";; ======================================\\n\")\n              (printf \";; Query results (list of complete edges)\\n\")\n              (printf \";; ======================================\\n\"))\n            (pretty-printer X-concepts-with-edges))\n          #:mode 'text\n          #:exists QUERY_RESULTS_FILE_MODE)))\n\n  (define human-friendly-pretty-print-X-concepts-with-edges\n    (lambda (X-concepts-with-edges)\n      (for-each\n        (lambda (entry index)\n          (match entry\n            [`(,dbname\n                ,s\n                ,eprops*\n                ,edges)\n              (printf \"*** Edge group:\")\n              (for-each\n                (lambda (edge)\n                  (match edge\n                    [`(,dbname\n                       ,eid\n                       (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n                       (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n                       (,pid . ,pred) ,eprops)\n                     (let ((pubmed* (pubmed-URLs-from-edge edge)))\n                       (printf \"\\n~s\\t~s\\t~s\\t~s\\t~s\\t~s\\t~s\\t~s PubMed Entries\\n~s\\n\" index dbname sname scat pred oname ocat (length pubmed*) pubmed*))]))\n                edges)\n              (printf \"***\\n\\n\") ]))\n        X-concepts-with-edges\n        (iota (length X-concepts-with-edges) 1))))\n\n  (define spreadsheet-friendly-pretty-print-X-concepts-with-edges\n    (lambda (X-concepts-with-edges)\n      (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n              \"KG Name\"\n              \n              \"Subject Category\"\n              \"Subject Name\"\n\n              \"Predicate\"\n\n              \"Object Category\"\n              \"Object Name\"\n\n              \"PubMed URL\"\n\n              \"Pub Date\"\n\n              \"Sentence\")\n      (for-each\n        (lambda (entry index)\n          (match entry\n            [`(,dbname\n                ,s\n                ,eprops*\n                ,edges)\n              (for-each\n                (lambda (edge)\n                  (match edge\n                    [`(,dbname\n                       ,eid\n                       (,scid ,scui ,sname (,scatid . ,scat) . ,sprops)\n                       (,ocid ,ocui ,oname (,ocatid . ,ocat) . ,oprops)\n                       (,pid . ,pred) ,eprops)\n                     \n                     ;; Create list of\n                     ;;\n                     ;; (pub-url pub-date subj-score obj-score sentence)\n                     ;;\n                     ;; entries, containing as much publication\n                     ;; information as is available for the given\n                     ;; edge.\n                     (define publications-info-alist\n                       (let ((p* (publications-info-alist-from-edge edge)))\n                         (if (null? p*)\n                             (let ((pubmed* (pubmed-URLs-from-edge edge)))\n                               (if (null? pubmed*)\n                                   (list (list \"\" \"\" \"\" \"\" \"\"))\n                                   (map\n                                    (lambda (pub-url)\n                                      (list pub-url \"\" \"\" \"\" \"\"))\n                                    pubmed*)))\n                             p*)))\n                     \n                     (for-each\n                       (lambda (pub-info)\n                         (match pub-info\n                           [`(,pub-url ,pub-date ,subj-score ,obj-score ,sentence)\n                            (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n                                    dbname\n\n                                    scat\n                                    sname\n\n                                    pred\n\n                                    ocat\n                                    oname\n\n                                    pub-url\n\n                                    pub-date\n\n                                    sentence)]))\n                       publications-info-alist)]))\n                edges)]))\n        X-concepts-with-edges\n        (iota (length X-concepts-with-edges) 1))))\n\n  (when WRITE_QUERY_RESULTS_TO_FILE\n\n    (printf \"saving all-X-concepts-with-edges to '~a' file...\\n\"\n            QUERY_RESULTS_FILE_NAME)\n    (pretty-print-X-concepts-with-edges\n      QUERY_RESULTS_FILE_NAME\n      pretty-print\n      #t ;; print-basic-header flag\n      #t ;; print-low-level-query-information flag\n      all-X-concepts-with-edges)\n    (printf \"saved all-X-concepts-with-edges to '~a' file\\n\"\n            QUERY_RESULTS_FILE_NAME)\n\n    (printf \"saving human-friendly version of all-X-concepts-with-edges to '~a' file...\\n\"\n            HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n    (pretty-print-X-concepts-with-edges\n      HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME\n      human-friendly-pretty-print-X-concepts-with-edges\n      #t ;; print-basic-header flag\n      #f ;; print-low-level-query-information flag\n      all-X-concepts-with-edges)\n    (printf \"saved human-friendly version of all-X-concepts-with-edges to '~a' file\\n\"\n            HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n\n    (printf \"saving spreadsheet-friendly version of all-X-concepts-with-edges to '~a' file...\\n\"\n            SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n    (pretty-print-X-concepts-with-edges\n      SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME\n      spreadsheet-friendly-pretty-print-X-concepts-with-edges\n      #f ;; print-basic-header flag\n      #f ;; print-low-level-query-information flag\n      all-X-concepts-with-edges)\n    (printf \"saved spreadsheet-friendly version of all-X-concepts-with-edges to '~a' file\\n\"\n            SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n\n    )\n\n  (printf \"========== end query results =============\\n\")\n\n  ((make-send-concepts-to-concept-X-list-box concept-X-list-box) all-X-concepts)\n\n  ;; unselect all items\n  (for ([i (length all-X-concepts)])\n       (send concept-X-list-box select i #f))\n\n  ;; add X concept data for each list-box entry\n  (let loop ((i 0)\n             (c* all-X-concepts))\n    (cond\n      [(null? c*) (void)]\n      [else\n       (send concept-X-list-box set-data i (car c*))\n       (loop (add1 i)\n             (cdr c*))]))\n\n  ;; empty the search in X's field, and disable the previous/next buttons\n  (send search-in-Xs-field set-value \"\")\n  (send search-in-Xs-previous-button enable #f)\n  (send search-in-Xs-next-button enable #f)\n\n  ;; empty the entries in the full-path-list-box\n  (send full-path-list-box set '() '() '() '() '() '() '() '())\n\n  ;; empty the entries in the properties list-boxes\n  (send subject-properties-list-box set '() '())\n  (send edge-properties-list-box set '() '())\n  (send object-properties-list-box set '() '())\n\n  ;; empty the entries in the pubmed-list-box\n  (send pubmed-list-box set '())\n\n  )\n\n(displayln\n  \"Launching GUI\")\n\n(launch-gui)\n"
  },
  {
    "path": "medikanren/apps/translator-web-server.rkt",
    "content": "#lang racket/base\n(require\n  \"../common.rkt\"\n  \"../open-api/api-query.rkt\"\n  \"../pieces-parts/synonymize.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  json\n  web-server/servlet\n  web-server/servlet-env\n  web-server/managers/none\n  web-server/private/gzip\n  xml\n  )\n\n(define (alist-ref alist key default)\n  (define kv (assoc key alist))\n  (if kv (cdr kv) default))\n\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n(define argv (current-command-line-arguments))\n(define argv-optional '#(CONFIG_FILE))\n(when (not (<= (vector-length argv) (vector-length argv-optional)))\n  (error \"optional arguments ~s; given ~s\" argv-optional argv))\n;; Loading will occur at first use if not explicitly forced like this.\n(load-config #t (and (<= 1 (vector-length argv)) (vector-ref argv 0)))\n(load-databases #t)\n\n(define-runtime-path path:root \".\")\n(define (path/root relative-path) (build-path path:root relative-path))\n(define schema.json.txt\n  (file->string (path/root \"../open-api/TranslatorReasonersAPI.json\")))\n(define schema.yaml.txt\n  (file->string (path/root \"../open-api/TranslatorReasonersAPI.yaml\")))\n(define schema.html\n  (file->string (path/root \"../open-api/html/index.html\")))\n(define schema.html2\n  (file->string (path/root \"../open-api/html2/index.html\")))\n(define schema.json\n  (call-with-input-file (path/root \"../open-api/TranslatorReasonersAPI.json\")\n                        read-json))\n(pretty-print (list 'openapi:      (hash-ref schema.json 'openapi)))\n(pretty-print (list 'info:         (hash-ref schema.json 'info)))\n(pretty-print (list 'externalDocs: (hash-ref schema.json 'externalDocs)))\n(pretty-print (list 'tags:         (hash-ref schema.json 'tags)))\n(pretty-print (list 'paths:        (hash-keys (hash-ref schema.json 'paths))))\n(pretty-print (list 'components:   (hash-keys (hash-ref schema.json 'components))))\n\n(define (xexpr->html-string xe)\n  (string-append \"\" (xexpr->string xe)))\n(define mime:text (string->bytes/utf-8 \"text/plain;charset=utf-8\"))\n(define mime:html (string->bytes/utf-8 \"text/html; charset=utf-8\"))\n(define mime:js   (string->bytes/utf-8 \"text/javascript;charset=utf-8\"))\n(define mime:json (string->bytes/utf-8 \"application/json; charset=utf-8\"))\n(define index.js \"\nwindow.addEventListener('load', function(){\nvar query_result       = document.getElementById('query-result');\nvar query_result_clear = document.getElementById('query-result-clear');\nvar query_form         = document.getElementById('query-form');\nvar query_text         = document.getElementById('query-text');\nvar query_submit       = document.getElementById('query-submit');\nfunction pretty_json(json_text) {\n  try { return JSON.stringify(JSON.parse(json_text), null, 2); }\n  catch (_) { return json_text; }\n}\nfunction query(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ show('POST error'); });\n  xhr.open('POST', '/query');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction show(result)   { query_result.textContent = pretty_json(result); }\nfunction clear_result() { query_result.textContent = ''; }\n\nquery_text.textContent = pretty_json(query_text.textContent);\nquery_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  query(query_text.value);\n}, false);\nquery_result_clear.addEventListener('click', function(){\n  clear_result();\n}, false);\n});\")\n(define v2:index.js \"\nwindow.addEventListener('load', function(){\nvar find_concepts_form           = document.getElementById('find-concepts-form');\nvar find_concepts_text           = document.getElementById('find-concepts-text');\nvar find_concepts_submit         = document.getElementById('find-concepts-submit');\nvar find_concepts_result         = document.getElementById('find-concepts-result');\nvar find_concepts_result_clear   = document.getElementById('find-concepts-result-clear');\nvar find_categories_form         = document.getElementById('find-categories-form');\nvar find_categories_text         = document.getElementById('find-categories-text');\nvar find_categories_submit       = document.getElementById('find-categories-submit');\nvar find_categories_result       = document.getElementById('find-categories-result');\nvar find_categories_result_clear = document.getElementById('find-categories-result-clear');\nvar find_predicates_form         = document.getElementById('find-predicates-form');\nvar find_predicates_text         = document.getElementById('find-predicates-text');\nvar find_predicates_submit       = document.getElementById('find-predicates-submit');\nvar find_predicates_result       = document.getElementById('find-predicates-result');\nvar find_predicates_result_clear = document.getElementById('find-predicates-result-clear');\nvar query_result       = document.getElementById('query-result');\nvar query_result_clear = document.getElementById('query-result-clear');\nvar query_form         = document.getElementById('query-form');\nvar query_text         = document.getElementById('query-text');\nvar query_submit       = document.getElementById('query-submit');\nfunction pretty_json(json_text) {\n  try { return JSON.stringify(JSON.parse(json_text), null, 2); }\n  catch (_) { return json_text; }\n}\nfunction show(element, result) { element.textContent = pretty_json(result); }\n\nfunction find_concepts_show(result)     { show(find_concepts_result,   result); }\nfunction find_categories_show(result)   { show(find_categories_result, result); }\nfunction find_predicates_show(result)   { show(find_predicates_result, result); }\nfunction find_concepts_clear_result()   { find_concepts_result.textContent = ''; }\nfunction find_categories_clear_result() { find_categories_result.textContent = ''; }\nfunction find_predicates_clear_result() { find_predicates_result.textContent = ''; }\nfunction find_concepts(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ find_concepts_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ find_concepts_show('POST error'); });\n  xhr.open('POST', '/v2/find-concepts');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction find_categories(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ find_categories_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ find_categories_show('POST error'); });\n  xhr.open('POST', '/v2/find-categories');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction find_predicates(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ find_predicates_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ find_predicates_show('POST error'); });\n  xhr.open('POST', '/v2/find-predicates');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfind_concepts_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  find_concepts('\\\"'+find_concepts_text.value+'\\\"');\n}, false);\nfind_categories_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  find_categories('\\\"'+find_categories_text.value+'\\\"');\n}, false);\nfind_predicates_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  find_predicates('\\\"'+find_predicates_text.value+'\\\"');\n}, false);\nfind_concepts_result_clear.addEventListener('click', function(){\n  find_concepts_clear_result();\n}, false);\nfind_categories_result_clear.addEventListener('click', function(){\n  find_categories_clear_result();\n}, false);\nfind_predicates_result_clear.addEventListener('click', function(){\n  find_predicates_clear_result();\n}, false);\n\nfunction query(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ query_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ query_show('POST error'); });\n  xhr.open('POST', '/v2/query');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction query_show(result)   { show(query_result, result); }\nfunction query_clear_result() { query_result.textContent = ''; }\nquery_text.textContent = pretty_json(query_text.textContent);\nquery_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  query(query_text.value);\n}, false);\nquery_result_clear.addEventListener('click', function(){\n  query_clear_result();\n}, false);\n\n});\")\n(define (not-found.html uri)\n  `(html (head (title \"mediKanren: 404\"))\n         (body (h1 \"What are you looking for?\")\n               (p \"There was nothing found at\")\n               (pre ,uri))))\n(define index.html\n  `(html (head (title \"mediKanren Reasoner API\")\n               (script ((src \"/index.js\"))))\n         (body (h1 \"mediKanren Reasoner API\")\n               (p (a ((href \"https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI\"))\n                     \"NCATS Biomedical Translator Reasoners Standard API\"))\n               (ul (li (a ((href \"/schema.html\")) \"schema.html\"))\n                   (li (a ((href \"/schema.html2\")) \"schema.html2\"))\n                   (li (a ((href \"/schema.yaml\")) \"schema.yaml\"))\n                   (li (a ((href \"/schema.json\")) \"schema.json\")))\n               (p (a ((href \"/predicates\")) \"GET /predicates\"))\n               (form ((method \"post\") (action \"/query\") (id \"query-form\"))\n                     (div (textarea\n                            ((id \"query-text\"))\n                            \"{\n  \\\"message\\\": {\n    \\\"query_graph\\\": {\n      \\\"nodes\\\": {\n        \\\"n0\\\": { \\\"id\\\": \\\"UMLS:C0935989\\\" },\n        \\\"n1\\\": { \\\"category\\\": \\\"gene\\\" },\n        \\\"n2\\\": { \\\"id\\\": \\\"UMLS:C0004096\\\" }\n      },\n      \\\"edges\\\": {\n        \\\"e0\\\": {\n          \\\"predicate\\\": \\\"negatively_regulates\\\",\n          \\\"subject\\\": \\\"n0\\\",\n          \\\"object\\\": \\\"n1\\\"\n        },\n        \\\"e1\\\": {\n          \\\"predicate\\\": \\\"gene_associated_with_condition\\\",\n          \\\"subject\\\": \\\"n1\\\",\n          \\\"object\\\": \\\"n2\\\"\n        }\n      }\n    }\n  }\n}\"\n                            ))\n                     (div (button ((type \"submit\") (id \"query-submit\"))\n                                  \"POST /query\")))\n               (div (button ((id \"query-result-clear\")) \"Clear Result\"))\n               (div (pre ((id \"query-result\")) \"Result will appear here.\")))))\n\n(define v2:index.html\n  `(html (head (title \"mediKanren Reasoner API\")\n               (script ((src \"/v2/index.js\"))))\n         (body (h1 \"mediKanren Reasoner API\")\n               (p (a ((href \"https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI\"))\n                     \"NCATS Biomedical Translator Reasoners Standard API\"))\n               (ul (li (a ((href \"/schema.html\")) \"schema.html\"))\n                   (li (a ((href \"/schema.html2\")) \"schema.html2\"))\n                   (li (a ((href \"/schema.yaml\")) \"schema.yaml\"))\n                   (li (a ((href \"/schema.json\")) \"schema.json\")))\n               (form ((method \"post\") (id \"find-concepts-form\"))\n                     (div (input ((type \"text\")\n                                  (id \"find-concepts-text\")\n                                  (value \"UMLS:C0935989\"))))\n                     (div (button ((type \"submit\") (id \"find-concepts-submit\"))\n                                  \"Find concepts\")))\n               (div (button ((id \"find-concepts-result-clear\")) \"Clear\"))\n               (div (pre ((id \"find-concepts-result\")) \"Concepts will appear here.\"))\n               (form ((method \"post\") (id \"find-categories-form\"))\n                     (div (input ((type \"text\")\n                                  (id \"find-categories-text\")\n                                  (value \"gene\"))))\n                     (div (button ((type \"submit\") (id \"find-categories-submit\"))\n                                  \"Find categories\")))\n               (div (button ((id \"find-categories-result-clear\")) \"Clear\"))\n               (div (pre ((id \"find-categories-result\")) \"Categories will appear here.\"))\n               (form ((method \"post\") (id \"find-predicates-form\"))\n                     (div (input ((type \"text\")\n                                  (id \"find-predicates-text\")\n                                  (value \"negatively_regulates\"))))\n                     (div (button ((type \"submit\") (id \"find-predicates-submit\"))\n                                  \"Find predicates\")))\n               (div (button ((id \"find-predicates-result-clear\")) \"Clear\"))\n               (div (pre ((id \"find-predicates-result\")) \"Predicates will appear here.\"))\n               (p (a ((href \"/predicates\")) \"GET /predicates\"))\n               (form ((method \"post\") (action \"/v2/query\") (id \"query-form\"))\n                     (div (textarea\n                            ((id \"query-text\"))\n                            \"{\n  \\\"message\\\": {\n    \\\"query_graph\\\": {\n      \\\"nodes\\\": {\n        \\\"n0\\\": { \\\"id\\\": \\\"UMLS:C0935989\\\" },\n        \\\"n1\\\": { \\\"category\\\": \\\"gene\\\" },\n        \\\"n2\\\": { \\\"id\\\": \\\"UMLS:C0004096\\\" }\n      },\n      \\\"edges\\\": {\n        \\\"e0\\\": {\n          \\\"predicate\\\": \\\"negatively_regulates\\\",\n          \\\"subject\\\": \\\"n0\\\",\n          \\\"object\\\": \\\"n1\\\"\n        },\n        \\\"e1\\\": {\n          \\\"predicate\\\": \\\"gene_associated_with_condition\\\",\n          \\\"subject\\\": \\\"n1\\\",\n          \\\"object\\\": \\\"n2\\\"\n        }\n      }\n    }\n  }\n}\"\n                            ))\n                     (div (button ((type \"submit\") (id \"query-submit\"))\n                                  \"POST /v2/query\")))\n               (div (button ((id \"query-result-clear\")) \"Clear Result\"))\n               (div (pre ((id \"query-result\")) \"Result will appear here.\")))))\n\n(define hash-empty (hash))\n(define (str   v) (if (string? v) v (error \"invalid string:\" v)))\n(define (olift v) (if (hash?   v) v (error \"invalid object:\" v)))\n(define (slift v) (cond ((pair?   v) v)\n                        ((string? v) (list v))\n                        ((null?   v) '())\n                        (else        (error \"invalid string or list of strings:\" v))))\n\n(define (alist->attributes alist)\n  ;; TODO: provide standard types for\n  ;; * negated, publications, provided_by\n  ;; * ngd_score, association_type, id\n  ;; * update_date, publications_info\n  ;; * is_defined_by, pmids, n_pmids, SEMMED_PRED\n  (map (lambda (kv) (hash 'name  (car kv)\n                          'type  \"miscellaneous\"\n                          'value (cdr kv)))\n       alist))\n\n(define (concept->result c)\n  (define attrs\n    (alist->attributes\n      (cons (cons \"mediKanren-source\" (symbol->string (concept->dbname c)))\n            (concept->props c))))\n  (cons (string->symbol (concept->curie c))\n        (hash 'name       (concept->name c)\n              'category   (cdr (concept->category c))\n              'attributes attrs)))\n(define (edge->result e)\n  (define id (string-append (symbol->string (edge->dbname e)) \".\"\n                            (number->string (edge->eid e))))\n  (define props (make-immutable-hash (edge->props e)))\n  (define relation (hash-ref props \"relation\" #f))\n  (define attrs\n    (alist->attributes\n      (hash->list\n        (foldl (lambda (k ps) (hash-remove ps k)) props\n               '(\"relation\" \"subject\" \"object\"\n                 \"simplified_relation\" \"simplified_edge_label\")))))\n  (define obj\n    (hash 'predicate  (cdr (edge->pred e))\n          'subject    (concept->curie (edge->subject e))\n          'object     (concept->curie (edge->object e))\n          'attributes attrs))\n  (cons (string->symbol id) (if relation\n                              (hash-set obj 'relation relation)\n                              obj)))\n\n(define (message->response msg)\n  (define broad-results\n    (if (config-ref 'trapi-enable-external-requests?)\n      (let* (\n          (broad-response (time (api-query (string-append url.broad path.query)\n                                              (hash 'message msg))))\n          (broad-results (hash-ref broad-response 'response)))\n        (printf \"broad response:\\n~s\\n\" (hash-ref broad-response 'status))\n        (pretty-print (hash-ref broad-response 'headers))\n        broad-results)\n      '#hash()\n      ))\n  (printf \"broad result size: ~s\\n\" (js-count broad-results))\n  ;; NOTE: ignore 'results and 'knowledge_graph until we find a use for them.\n  (define qgraph (hash-ref msg 'query_graph hash-empty))\n  (define nodes\n    (filter-not\n      not\n      (map (lambda (id+n)\n             (let* ((id       (car id+n))\n                    (n        (cdr id+n))\n                    (curie    (slift (hash-ref n 'id       '())))\n                    (category (slift (hash-ref n 'category '()))))\n               ;; TODO: use a new find-concepts based on xrefo instead?\n               `(,id ',(cond ((pair? curie)    (find-concepts #t curie))\n                             ((pair? category) (find-categories category))\n                             (else             #f)))))\n           (hash->list (olift (hash-ref qgraph 'nodes hash-empty))))))\n  (define edges&paths\n    (filter-not\n      not\n      (map (lambda (id+e)\n             (let* ((id        (car id+e))\n                    (e         (cdr id+e))\n                    (predicate (slift (hash-ref e 'predicate '())))\n                    (subject   (str   (hash-ref e 'subject   #f)))\n                    (object    (str   (hash-ref e 'object    #f))))\n               (and subject object\n                    `((,id ',(and (pair? predicate)\n                                  (find-predicates predicate)))\n                      (,(string->symbol subject)\n                        ,id\n                        ,(string->symbol object))))))\n           (hash->list (olift (hash-ref qgraph 'edges hash-empty))))))\n  (define edges (map car  edges&paths))\n  (define paths (map cadr edges&paths))\n  (define runq #`(run/graph #,nodes #,edges . #,paths))\n  (displayln \"===============================================================\")\n  (pretty-print (syntax->datum runq))\n  (match-define (list name=>concepts name=>edges)\n    (if (null? paths)\n      (begin (displayln \"no paths were provided\")\n             (list hash-empty hash-empty))\n      (time (eval runq))))\n  (displayln \"result counts:\")\n  (pretty-print (hash-map name=>concepts (lambda (n xs) (cons n (length xs)))))\n  (pretty-print (hash-map name=>edges    (lambda (n xs) (cons n (length xs)))))\n  (define knodes\n    (append* (hash-map name=>concepts\n                       (lambda (name xs) (map concept->result xs)))))\n  (define kedges\n    (append* (hash-map name=>edges\n                       (lambda (name xs) (map edge->result xs)))))\n  (define local-results\n    (append* (map (lambda (p)\n                    (define qsubject (car p))\n                    (define qname    (cadr p))\n                    (define qobject  (caddr p))\n                    (map (lambda (e)\n                           (define id+r    (edge->result e))\n                           (define id      (symbol->string (car id+r)))\n                           (define r       (cdr id+r))\n                           (define subject (hash-ref r 'subject))\n                           (define object  (hash-ref r 'object))\n                           (hash 'edge_bindings (hash qname (list (hash 'id id)))\n                                 'node_bindings (make-immutable-hash\n                                                  (list (cons qsubject (list (hash 'id subject)))\n                                                        (cons qobject  (list (hash 'id object)))))))\n                         (hash-ref name=>edges qname)))\n                  paths)))\n  (merge-results\n    (list (hash-ref (olift broad-results) 'message hash-empty)\n          (hash 'results local-results\n                'knowledge_graph\n                (hash 'nodes (apply hash-union (hash)\n                                    (map (lambda (knode) (hash (car knode) (cdr knode)))\n                                         knodes)\n                                    #:combine\n                                    (lambda (c.0 c.1)\n                                      (hash-update\n                                        c.0 'attributes\n                                        (lambda (attrs)\n                                          (append (alist->attributes\n                                                    (list (cons \"extra-result\" c.1)))\n                                                  attrs)))))\n                      'edges (make-immutable-hash kedges))))))\n\n(define (merge-results rs)\n  (let loop ((rs rs) (results '()) (nodes '()) (edges '()))\n    (cond ((null? rs) (hash 'results         results\n                            'knowledge_graph (hash 'nodes (make-immutable-hash nodes)\n                                                   'edges (make-immutable-hash edges))))\n          (else (define r (car rs))\n                (define kg (hash-ref r 'knowledge_graph hash-empty))\n                (loop (cdr rs)\n                      (append (hash-ref r 'results '()) results)\n                      (append (hash->list (hash-ref kg 'nodes hash-empty))\n                              nodes)\n                      (append (hash->list (hash-ref kg 'edges hash-empty))\n                              edges))))))\n\n(define (predicates)\n  ;; TODO: at greater expense, we could restrict each list of predicates\n  ;; to those reflected by existing edges for the corresponding categories.\n  (define cs (run* (c) (categoryo c)))\n  (define ps (run* (p) (predicateo p)))\n  (define dbs (map car cs))\n  (make-immutable-hash\n    (append*\n      (map (lambda (db)\n             (define dcs\n               (filter-not\n                 not (map (lambda (c) (and (eq? (car c) db) (cddr c)))\n                          cs)))\n             (define dps\n               (filter-not\n                 not (map (lambda (p) (and (eq? (car p) db) (cddr p)))\n                          ps)))\n             (define dcps\n               (make-immutable-hash\n                 (map (lambda (c) (cons (string->symbol c) dps)) dcs)))\n             (map (lambda (c) (cons (string->symbol c) dcps)) dcs))\n           dbs))))\n(define predicates-cached (string->bytes/utf-8 (jsexpr->string (predicates))))\n(define predicates-cached-gzip (gzip/bytes predicates-cached))\n(define (query jsdata)\n  (cond ((or (eof-object? jsdata) (not (hash? jsdata))) 'null)\n        (else (hash 'message\n                    (message->response (olift (hash-ref (olift jsdata) 'message\n                                                        hash-empty)))))))\n(define (accepts-gzip? req)\n  (member \"gzip\" (map string-trim\n                      (string-split (alist-ref (request-headers req)\n                                               'accept-encoding \"\") \",\"))))\n(define (respond code message headers mime-type body)\n  (response/full code (string->bytes/utf-8 message)\n                 (current-seconds) mime-type headers\n                 (list body)))\n(define (OK req extra-headers mime-type body (body-gzipped? #f))\n  (define gzip? (accepts-gzip? req))\n  (define headers (if gzip? (cons (make-header #\"Content-Encoding\" #\"gzip\")\n                                  extra-headers)\n                    extra-headers))\n  (define bytes.body (if (string? body) (string->bytes/utf-8 body) body))\n  (define payload (if (and gzip? (not body-gzipped?)) (gzip/bytes bytes.body)\n                    bytes.body))\n  (respond 200 \"OK\" headers mime-type payload))\n(define (not-found req)\n  (respond 404 \"Not Found\" '() mime:html\n           (string->bytes/utf-8\n             (xexpr->html-string\n               (not-found.html (url->string (request-uri req)))))))\n(define (OK/jsexpr f req)\n  (define input (bytes->jsexpr (request-post-data/raw req)))\n  (define result (job (thunk (f input))))\n  (if (job-failure? result)\n    (respond 400 \"Bad Request\" '() mime:text\n             (string->bytes/utf-8 (job-failure-message result)))\n    (OK req '() mime:json (jsexpr->string result))))\n\n(define (/index req)\n  (pretty-print `(request-headers: ,(request-headers req)))\n  (OK req '() mime:html (xexpr->html-string index.html)))\n(define (/v2/index req)\n  (pretty-print `(request-headers: ,(request-headers req)))\n  (OK req '() mime:html (xexpr->html-string v2:index.html)))\n(define (/index.js     req) (OK req '() mime:js   index.js))\n(define (/schema.json  req) (OK req '() mime:text schema.json.txt))\n(define (/schema.yaml  req) (OK req '() mime:text schema.yaml.txt))\n(define (/schema.html  req) (OK req '() mime:html schema.html))\n(define (/schema.html2 req) (OK req '() mime:html schema.html2))\n(define (/predicates   req) (if (accepts-gzip? req)\n                              (OK req '() mime:json predicates-cached-gzip #t)\n                              (OK req '() mime:json predicates-cached #f)))\n(define (/query        req) (OK/jsexpr query req))\n\n(define (group-by-db xs)\n  (foldl (lambda (x db=>id)\n           (hash-update db=>id (car x) (lambda (xs) (cons (cdr x) xs)) '()))\n         (hash) xs))\n\n(define (pretty-synonyms ss)\n  (if (and (pair? ss) (not (cdar ss))) '()\n    (make-immutable-hash\n      (map (lambda (kv) (cons (string->symbol (car kv)) (cdr kv))) ss))))\n\n(define (find-concepts/any str)\n  (hash 'synonyms (pretty-synonyms (curie-synonyms/names str))\n        'concepts\n        (make-immutable-hash\n          (hash-map\n            (group-by-db\n              (map (lambda (c)\n                     (define r (concept->result c))\n                     (define attrs (hash-ref (cdr r) 'attributes))\n                     (define dbnames\n                       (map (lambda (attr) (hash-ref attr 'value))\n                            (filter (lambda (attr) (equal? (hash-ref attr 'name)\n                                                           \"mediKanren-source\"))\n                                    attrs)))\n                     (define dbname (if (null? dbnames) 'unknown\n                                      (string->symbol (car dbnames))))\n                     (cons dbname r))\n                   (append (find-concepts #t (list str))\n                           (find-concepts #f (list str)))))\n            (lambda (db cs) (cons db (make-immutable-hash cs)))))))\n\n(define ((find/db-id find) data)\n  (group-by-db (map (lambda (x) (cons (car x) (cddr x))) (find (list data)))))\n\n(define (/v2/index.js        req) (OK req '() mime:js v2:index.js))\n(define (/v2/query req)           (OK/jsexpr query                        req))\n(define (/v2/find-concepts   req) (OK/jsexpr find-concepts/any            req))\n(define (/v2/find-categories req) (OK/jsexpr (find/db-id find-categories) req))\n(define (/v2/find-predicates req) (OK/jsexpr (find/db-id find-predicates) req))\n\n(struct job-failure (message))\n\n(define (job work)\n  (define job-response (make-channel))\n  (channel-put job-request (cons job-response work))\n  (channel-get job-response))\n\n(define job-request (make-channel))\n\n(define worker\n  (thread\n    (thunk (let loop ()\n             (match-define (cons job-response work) (channel-get job-request))\n             (channel-put job-response\n                          (with-handlers ((exn:fail?\n                                            (lambda (v)\n                                              ((error-display-handler) (exn-message v) v)\n                                              (job-failure (exn-message v))))\n                                          ((lambda _ #t)\n                                           (lambda (v)\n                                             (define message\n                                               (string-append \"unknown error: \"\n                                                              (with-output-to-string (thunk (write v)))))\n                                             (pretty-write message)\n                                             (job-failure message))))\n                            (work)))\n             (loop)))))\n\n(define (start)\n  (define-values (dispatch _)\n    (dispatch-rules\n      ((\"\")                     #:method \"get\"  /index)\n      ((\"index.js\")             #:method \"get\"  /index.js)\n      ((\"schema.json\")          #:method \"get\"  /schema.json)\n      ((\"schema.yaml\")          #:method \"get\"  /schema.yaml)\n      ((\"schema.html\")          #:method \"get\"  /schema.html)\n      ((\"schema.html2\")         #:method \"get\"  /schema.html2)\n      ((\"predicates\")           #:method \"get\"  /predicates)\n      ((\"query\")                #:method \"post\" /query)\n      ((\"v2\")                   #:method \"get\"  /v2/index)\n      ((\"v2\" \"index.js\")        #:method \"get\"  /v2/index.js)\n      ((\"v2\" \"find-concepts\")   #:method \"post\" /v2/find-concepts)\n      ((\"v2\" \"find-categories\") #:method \"post\" /v2/find-categories)\n      ((\"v2\" \"find-predicates\") #:method \"post\" /v2/find-predicates)\n      ((\"v2\" \"query\")           #:method \"post\" /v2/query)\n      (else                                     not-found)))\n  (serve/servlet dispatch\n                 ;; none-manager for better performance:\n                 ;; only possible because we're not using web continuations.\n                 #:manager (create-none-manager #f)\n                 #:servlet-regexp #rx\"\"\n                 #:listen-ip #f  ;; comment this to disable external connection\n                 #:port 8080\n                 #:launch-browser? #f))\n\n(module+ main (start))\n"
  },
  {
    "path": "medikanren/biolink-types-examples.scm",
    "content": "With Chris Mungall (BioHackathon 2019, Fukuoka, Japan)\n\nYAML:\nhttps://github.com/biolink/biolink-model/blob/master/biolink-model.yaml\n\nRaw YAML:\nhttps://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml\n\nPredicates can be found in YAML file\n\n\n(run* (type)\n  (type-infero '(imatinib treats aspirin) type))\n=>\n()\nor\nAssociation\n\n(run* (type)\n  (type-infero '(imatinib treats cancer) type))\n=>\nChemicalToDiseaseOrPhenotypicFeatureAssociation\n\n(run* (disease)\n  (type-infero `(imatinib treats ,disease)\n               'ChemicalToDiseaseOrPhenotypicFeatureAssociation))\n\n(run* (X type)\n  (type-infero `(conj (imatinib treats ,X) (,X causes asthma))\n               type))\n=>\nthis is okay\n\n(run* (X Y type)\n  (type-infero `(conj (imatinib treats ,X) (,X orthologous-to ,Y))\n               type))\n=>\n()\n\n\nPay attention to domain and range:\n\n\n  increases expression of:\n    description: >-\n      holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest\n    is_a: affects expression of\n    in_subset:\n      - translator_minimal\n    domain: molecular entity\n    range: genomic entity\n"
  },
  {
    "path": "medikanren/common.rkt",
    "content": "#lang racket/base\n(provide\n  (all-from-out \"mk.rkt\")\n  find-concepts/name\n  find-concepts\n  find-isa-concepts\n  find-concepts/options\n  find-concepts/options/cui-infer\n  find-predicates/concepts\n  find-predicates\n  find-exact-predicates\n  find-categories\n  find-exact-categories\n  find-Xs\n  find-graph\n  run/graph\n\n  membero\n\n  concept->dbname\n  concept->cid\n  concept->curie\n  concept->name\n  concept->category\n  concept->props\n\n  edge->dbname\n  edge->eid\n  edge->subject\n  edge->object\n  edge->pred\n  edge->props\n\n  ~name*-concepto\n  ~cui*-concepto\n  ~cui-concepto\n  ~categoryo\n  ~predicateo\n  synonym-concepto\n  xref-concepto\n  category-concepto\n  concepto\n  categoryo\n  predicateo\n  edgeo\n  pmid-edgeo\n  subject-predicateo\n  object-predicateo\n  isao\n\n  pubmed-ids-from-edge-props\n  pubmed-ids-from-edge\n  pubmed-URLs-from-edge\n  pubmed-count\n\n  PUBMED_URL_PREFIX\n\n  publications-info-alist-from-edge\n  publications-info-alist-from-edge-props\n\n  path-confidence\n  path-confidencejson\n\n  write-list-to-tsv)\n\n(require\n  \"db.rkt\"\n  \"mk.rkt\"\n  \"mk-db.rkt\"\n  \"repr.rkt\"\n  \"configref.rkt\"\n  json\n  racket/format\n  racket/list\n  (except-in racket/match ==)\n  racket/runtime-path\n  racket/port\n  racket/set\n  racket/stream\n  racket/string)\n\n(define (keep n xs)\n  (if (or (and n (= n 0)) (null? xs)) '()\n    (cons (car xs) (keep (and n (- n 1)) (cdr xs)))))\n(define (read/file path)  (with-input-from-file  path (lambda () (read))))\n(define (read/string str) (with-input-from-string str (lambda () (read))))\n\n(define-runtime-path path:root \".\")\n(define (path/root relative-path) (build-path path:root relative-path))\n(define path:data                 (path/root \"data\"))\n(define (path/data relative-path) (build-path path:data relative-path))\n(define (path-simple path)        (path->string (simplify-path path)))\n\n\n(define box:databases (box #f))\n(define (databases)\n  (define dbs (unbox box:databases))\n  (cond (dbs dbs)\n        (else (load-databases #t)\n              (unbox box:databases))))\n(define (load-databases verbose?)\n  (define (load-dbs)\n    (filter (lambda (desc) desc)\n            (map (lambda (name)\n                   (define path (path/data (symbol->string name)))\n                   (define options (list (config-ref 'in-memory-names?)\n                                         (config-ref 'in-memory-cuis?)))\n                   (cond ((directory-exists? path)\n                          (when verbose? (printf \"loading ~a\\n\" name))\n                          (cons name (if verbose?\n                                       (time (apply make-db path options))\n                                       (apply make-db path options))))\n                         (else (when verbose?\n                                 (printf \"cannot load ~a; \" name)\n                                 (printf \"directory missing: ~a\\n\" path))\n                               #f)))\n                 (config-ref 'databases))))\n  (unless (unbox box:databases)\n    (when verbose? (displayln \"loading data sources...\"))\n    (define dbs (load-dbs))\n    (set-box! box:databases dbs)\n    (when verbose? (displayln \"finished loading data sources\"))))\n(define (conde/databases dbdesc->clause)\n  (foldr (lambda (desc rest)\n           (conde ((dbdesc->clause (car desc) (cdr desc))) (rest)))\n         (== #t #f) (databases)))\n\n;; list membership\n(define membero\n  (lambda (x ls)\n    (fresh (y rest)\n      (== `(,y . ,rest) ls)\n      (conde\n        [(== x y)]\n        [(=/= x y) (membero x rest)]))))\n\n#|\nconcept = `(,dbname ,cid ,cui ,name (,catid . ,cat) ,props)\n|#\n(define (concept->dbname concept) (car concept))\n(define (concept->cid concept) (cadr concept))\n(define (concept->curie concept) (caddr concept))\n(define (concept->name concept) (cadddr concept))\n(define (concept->category concept) (cadddr (cdr concept)))\n(define (concept->props concept) (cadddr (cddr concept)))\n\n#|\nedge = `(,dbname ,eid ,subject-concept ,object-concept (,pid . ,pred-name) ,props)\n|#\n(define (edge->dbname edge) (car edge))\n(define (edge->eid edge) (cadr edge))\n(define (edge->subject edge) (cons (edge->dbname edge) (caddr edge)))\n(define (edge->object edge) (cons (edge->dbname edge) (cadddr edge)))\n(define (edge->pred edge) (cadddr (cdr edge)))\n(define (edge->props edge) (cadddr (cddr edge)))\n\n\n(define (~name*-concepto ~name* concept)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c)\n        (== `(,dbname . ,c) concept)\n        (db:~name*-concepto/options\n          #f ;; case sensitivity flag\n          \"\" ;; ignored characters ('chars:ignore-typical' is pre-defined)\n          \"\" ;; characters to split target name on for exact matching ('chars:split-typical' is pre-defined)\n          db ~name* c)))))\n(define (~cui*-concepto ~cui* concept)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c) (== `(,dbname . ,c) concept)\n        (db:~cui*-concepto db ~cui* c)))))\n(define (~cui-concepto ~cui concept)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c) (== `(,dbname . ,c) concept)\n        (db:~cui-concepto db ~cui c)))))\n(define (synonym-concepto synonym concept)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c) (== `(,dbname . ,c) concept)\n        (db:synonym-concepto db synonym c)))))\n(define (xref-concepto xref concept)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c) (== `(,dbname . ,c) concept)\n        (db:xref-concepto db xref c)))))\n(define (category-concepto category concept)\n  (fresh (db cid cui name cat props)\n    (== category `(,db . ,cat))\n    (== concept `(,db ,cid ,cui ,name ,cat . ,props))\n    (concepto concept)))\n(define (concepto concept)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c)\n        (== `(,dbname . ,c) concept)\n        (db:concepto db c)))))\n\n(define (~categoryo ~category-name category)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c)\n        (== `(,dbname . ,c) category)\n        (db:~categoryo db ~category-name c)))))\n(define (~predicateo ~predicate-name predicate)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (p)\n        (== `(,dbname . ,p) predicate)\n        (db:~predicateo db ~predicate-name p)))))\n\n(define (categoryo category)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c)\n        (== `(,dbname . ,c) category)\n        (db:categoryo db c)))))\n(define (predicateo predicate)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (p)\n        (== `(,dbname . ,p) predicate)\n        (db:predicateo db p)))))\n\n#|\nedge = `(,dbname ,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n                      (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n                      (,pid . ,pred) ,eprops)\n|#\n(define (edgeo edge)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (e)\n        (== `(,dbname . ,e) edge)\n        (db:edgeo db e)))))\n(define (pmid-edgeo pmid edge)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (eid body)\n        (== `(,dbname ,eid . ,body) edge)\n        (db:pmid-eido db pmid eid)\n        (edgeo edge)))))\n\n(define (subject-predicateo concept predicate)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c p)\n        (== `(,dbname . ,c) concept)\n        (== `(,dbname . ,p) predicate)\n        (db:subject-predicateo db c p)))))\n(define (object-predicateo concept predicate)\n  (conde/databases\n    (lambda (dbname db)\n      (fresh (c p)\n        (== `(,dbname . ,c) concept)\n        (== `(,dbname . ,p) predicate)\n        (db:object-predicateo db c p)))))\n\n(define (isao s/db o/db)\n  (fresh (dbname s o eid pid eprops)\n    (== `(,dbname . ,o) o/db)\n    (== `(,dbname . ,s) s/db)\n    (edgeo `(,dbname ,eid ,s ,o (,pid . \"subclass_of\") ,eprops))))\n\n(define (pubmed-ids-from-edge-props eprops)\n  (cond\n    [(assoc \"pmids\" eprops)  ;; WEB the 'pmids' property is only used by semmed, I believe\n     => (lambda (pr) (regexp-split #rx\";\" (cdr pr)))]\n    [(assoc \"publications\" eprops)\n     => (lambda (pr)\n          (define pubs (cdr pr))\n          (if (not (string? pubs))\n            '()\n            (regexp-match* #rx\"PMID:([0-9]+)\" pubs #:match-select cadr)))]\n    [else '()]))\n(define (pubmed-ids-from-edge edge)\n  (remove-duplicates\n    (match edge\n      ['path-separator '()]\n      [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n        (pubmed-ids-from-edge-props eprops)])))\n(define PUBMED_URL_PREFIX \"https://www.ncbi.nlm.nih.gov/pubmed/\")\n(define (pubmed-URLs-from-edge edge)\n  (map (lambda (pubmed-id) (string-append PUBMED_URL_PREFIX (~a pubmed-id)))\n       (pubmed-ids-from-edge edge)))\n\n(define (pubmed-count e)\n  (length (pubmed-ids-from-edge e)))\n\n(define (python->json py)\n  (define len (string-length py))\n  (let loop ((i 0) (start 0))\n    (cond ((= i len) (if (= start 0) py (substring py start)))\n          ((eqv? (string-ref py i) #\\')\n           (string-append\n             (substring py start i) \"\\\"\"\n             (let requote ((i (+ i 1)) (start (+ i 1)))\n               (cond ((eqv? (string-ref py i) #\\')\n                      (string-append (substring py start i) \"\\\"\"\n                                     (loop (+ i 1) (+ i 1))))\n                     ((eqv? (string-ref py i) #\\\\)\n                      (if (eqv? (string-ref py (+ i 1)) #\\\")\n                        (requote (+ i 2) start)\n                        (string-append (substring py start i)\n                                       (requote (+ i 2) (+ i 1)))))\n                     ((eqv? (string-ref py i) #\\\")\n                      (string-append (substring py start i) \"\\\\\\\"\"\n                                     (requote (+ i 1) (+ i 1))))\n                     (else (requote (+ i 1) start))))))\n          ((eqv? (string-ref py i) #\\\")\n           (let skip ((i (+ i 1)) (start start))\n             (cond ((eqv? (string-ref py i) #\\\") (loop (+ i 1) start))\n                   ((eqv? (string-ref py i) #\\\\)\n                    (if (eqv? (string-ref py (+ i 1)) #\\\")\n                      (skip (+ i 2) start)\n                      (string-append (substring py start i)\n                                     (skip (+ i 2) (+ i 1)))))\n                   (else                         (skip (+ i 1) start)))))\n          (else (loop (+ i 1) start)))))\n\n(define (publications-info-alist-from-edge-props eprops)\n  (cond\n    [(assoc \"publications_info\" eprops) ;; RTX2\n     => (lambda (pr)\n          (with-handlers ([exn:fail?\n                           (lambda (v)\n                             ((error-display-handler) (exn-message v) v)\n                             '())])\n            (define pubs (cdr pr))\n            (define jason-ht (string->jsexpr (python->json pubs)))\n            (hash-map jason-ht (lambda (k v)\n                                 (cons (string-append\n                                        PUBMED_URL_PREFIX\n                                        (car (regexp-match* #rx\"([0-9]+)\" (symbol->string k) #:match-select cadr)))\n                                       (list (hash-ref v '|publication date| #f)\n                                             (hash-ref v '|subject score| #f)\n                                             (hash-ref v '|object score| #f)\n                                             (regexp-replace*\n                                              #rx\"([ ]+)\"\n                                              (hash-ref v 'sentence #f)\n                                              \" \")))))))]\n    [else '()]))\n(define (publications-info-alist-from-edge edge)\n  ;; ((pubmed-URL . (publication-date subject-score object-score sentence)) ...)\n  (remove-duplicates\n    (match edge\n      ['path-separator '()]\n      [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n        (publications-info-alist-from-edge-props eprops)])))\n\n(define (get-pred-names e*)\n  (let loop ([e* e*]\n             [pred-names '()])\n    (cond\n      [(null? e*) pred-names]\n      [else\n       (let ((edge (car e*))\n             (rest (cdr e*)))\n         (match edge\n           ['path-separator\n            (loop rest pred-names)]\n           [`(,dbname ,eid ,subj ,obj (,pid . ,p-name) ,eprops)\n            (loop rest (if (member p-name pred-names)\n                           pred-names\n                           (cons p-name pred-names)))]\n           [else (error 'get-pred-names (format \"unmatched edge ~s\\n\" edge))]))])))\n\n(define (path-confidence p)\n  (define (weight-linear+1 n) (+ 1 n))\n  (define (weight-exponential n) (expt 2 n))\n  ;; To experiment with sorting, try to only change the weight calculation\n  ;; being used.  Leave everything else the same.\n  (define weight weight-exponential)\n  (define (confidence/edge e) (- 1 (/ 1.0 (weight (pubmed-count e)))))\n  (foldl * 1 (map confidence/edge p)))\n(define (path-confidence max-pubmed-count1 max-pubmed-count2)))]\n             [(< min-pubmed-count1 min-pubmed-count2) #t]\n             [else #f])))]\n      [(< pc1 pc2) #t]\n      [else #f])))\n(define (sort-paths paths) (sort paths path-confidencestring (car a1)))\n                      (cui1 (caddr a1))\n                      (dbname2 (symbol->string (car a2)))\n                      (cui2 (caddr a2)))\n                  (or (string>? dbname1 dbname2)\n                      (and (string=? dbname1 dbname2)\n                           (stringlist X-groups)) groups))\n                       '() (hash->list groups))))\n  (define (groups-intersect gS gO)\n    (foldl (lambda (kv groups)\n             (define X          (car kv))\n             (define o-X-groups (cdr kv))\n             (define s-X-groups (hash-ref gS X #f))\n             (if s-X-groups\n               (cons (list X (hash->list s-X-groups) (hash->list o-X-groups))\n                     groups)\n               groups))\n           '() (hash->list gO)))\n  (define subject-edges?\n    (and subjects?\n         (group-by-X (run* (q)\n                       (fresh (dbname eid s m predicates p eprops _)\n                         (== (list dbname m s p eid eprops) q)\n                         (membero `((,dbname . ,s) ,predicates ,_) subjects?)\n                         (membero `(,dbname . ,p) predicates)\n                         (edgeo `(,dbname ,eid ,s ,m ,p ,eprops)))))))\n  (define object-edges?\n    (and objects?\n         (group-by-X (run* (q)\n                       (fresh (dbname eid o m predicates p eprops _)\n                         (== (list dbname m o p eid eprops) q)\n                         (membero `((,dbname . ,o) ,_ ,predicates) objects?)\n                         (membero `(,dbname . ,p) predicates)\n                         (edgeo `(,dbname ,eid ,m ,o ,p ,eprops)))))))\n  (if (and subject-edges? object-edges?)\n    (groups-intersect subject-edges? object-edges?)\n    (groups-flatten (or subject-edges? object-edges?))))\n\n(define (find-graph concept=>set concept=>cx predicate=>cx edges)\n  (define-syntax-rule (set!/combine hash-name key value default combine)\n                      (let* ((current (hash-ref hash-name key default))\n                             (new (if current (combine current value) value)))\n                        (set! hash-name (hash-set hash-name key new))\n                        (and (not (equal? current new)) new)))\n  (define-syntax-rule (set!/add hash-name key value)\n                      (set!/combine hash-name key value (set) set-add))\n  (define-syntax-rule (set!/intersect hash-name key value)\n                      (set!/combine hash-name key value #f set-intersect))\n  (define edge=>set      (hash))\n  (define concept=>edges (hash))\n  (define (concept->set   name) (hash-ref concept=>set   name #f))\n  (define (concept->cx    name) (hash-ref concept=>cx    name #f))\n  (define (predicate->cx  name) (hash-ref predicate=>cx  name #f))\n  (define (edge->set      name) (hash-ref edge=>set      name #f))\n  (define (concept->edges name) (hash-ref concept=>edges name (set)))\n\n  (define (?min x y) (or (and x (or (and y (min (set-count x) (set-count y)))\n                                    (set-count x)))\n                         (and y (set-count y))))\n  (define (?< x y)   (or (and x y (< x y)) x))\n  (define/match (edgeset s1) (concept->set o1)))\n     (define min2 (?min (concept->set s2) (concept->set o2)))\n     (or (?< min1 min2)\n         (and (not (?< min2 min1))\n              (let ((min1 (?min (concept->cx s1) (concept->cx o1)))\n                    (min2 (?min (concept->cx s2) (concept->cx o2))))\n                (or (?< min1 min2)\n                    (and (not (?< min2 min1))\n                         (let ((pcx1 (predicate->cx p1))\n                               (pcx2 (predicate->cx p2)))\n                           (?< (and pcx1 (set-count pcx1))\n                               (and pcx2 (set-count pcx2)))))))))))\n\n  (define (update-edge! e s o id-edges)\n    (define enew? (set!/intersect edge=>set e id-edges))\n    (when enew?\n      (define id-subjects\n        (list->set\n          (set-map enew?\n                   (match-lambda ((list dbname iedge isubject iobject)\n                                  (cons dbname isubject))))))\n      (define id-objects\n        (list->set\n          (set-map enew?\n                   (match-lambda ((list dbname iedge isubject iobject)\n                                  (cons dbname iobject))))))\n      (define snew? (set!/intersect concept=>set s id-subjects))\n      (define onew? (set!/intersect concept=>set o id-objects))\n      (define (propagate! c cnew?)\n        (when cnew?\n          (set-for-each\n            (concept->edges c)\n            (match-lambda ((list ename sname oname)\n                           (constrain-edge! ename sname oname))))))\n      (propagate! s snew?)\n      (propagate! o onew?)))\n  (define (constrain-edge! e s o)\n    (define sids (concept->set s))\n    (define oids (concept->set o))\n    (define id-edges\n      (list->set (filter (match-lambda\n                           ((list dbname iedge isubject iobject)\n                            (and (set-member? sids (cons dbname isubject))\n                                 (set-member? oids (cons dbname iobject)))))\n                         (set->list (edge->set e)))))\n    (update-edge! e s o id-edges))\n  (define (concepts->predicates cpo cs)\n    (constraints->set\n      (append* (map (lambda (c) (run* (p) (cpo (report-concept c) p)))\n                    (set->list cs)))))\n  (define (concept-predicate-intersect cpo pcx cs)\n    (if (and pcx cs (< (set-count cs) (set-count pcx)))\n      (let ((cpcx (concepts->predicates cpo cs)))\n        (set-intersect cpcx pcx))\n      pcx))\n\n  (let loop ((pending edges))\n    (unless (null? pending)\n      (define edges (sort pending edgeedges s edge)\n      (set!/add concept=>edges o edge)\n      (define ss  (concept->set s))\n      (define os  (concept->set o))\n      (define pcx (concept-predicate-intersect\n                    object-predicateo\n                    (concept-predicate-intersect\n                      subject-predicateo (predicate->cx e) ss)\n                    os))\n      (define (find-edges/db db stream-edges srcs pids cats dsts)\n        (define srcids\n          (sort\n            (if srcs srcs\n              (run* (src)\n                (fresh (cui cname catid catname cprops)\n                  (if cats (membero catid cats) (== #t #t))\n                  (db:concepto\n                    db `(,src ,cui ,cname (,catid . ,catname) ,cprops)))))\n            <))\n        (define (src->edges src)\n          (define (stream/pid pid)\n            (cond (dsts (append* (map (lambda (dst)\n                                        (stream->list\n                                          (stream-edges src pid #f dst)))\n                                      dsts)))\n                  (cats (append* (map (lambda (cat)\n                                        (stream->list\n                                          (stream-edges src pid cat #f)))\n                                      cats)))\n                  (else (stream->list (stream-edges src pid #f #f)))))\n          (if pids (append* (map stream/pid pids)) (stream/pid #f)))\n        (map (lambda (e)\n               (define eid (edge-eid e))\n               (define e/p (db:eid->edge db eid))\n               (list eid (edge/props-subject e/p) (edge/props-object e/p)))\n             (append* (map src->edges srcids))))\n      (define (find-edges stream-edges/db srcs cats dsts)\n        (append*\n          (map (lambda (dbdesc)\n                 (define dbname (car dbdesc))\n                 (define db     (cdr dbdesc))\n                 (define (filter/db xs)\n                   (map cdr (filter (lambda (x) (equal? dbname (car x))) xs)))\n                 (map (lambda (e) (cons dbname e))\n                      (find-edges/db\n                        db (lambda args (apply stream-edges/db db args))\n                        (and srcs (filter/db (set->list srcs)))\n                        (and pcx  (filter/db (set->list pcx)))\n                        (and cats (filter/db (set->list cats)))\n                        (and dsts (filter/db (set->list dsts))))))\n               (databases))))\n      (define id-edges\n        (if (and os (= (set-count os) (?min ss os)))\n          (find-edges db:object->edge-stream os (concept->cx s) ss)\n          (find-edges db:subject->edge-stream ss (concept->cx o) os)))\n      (update-edge! e s o (list->set id-edges))\n      (loop (cdr edges))))\n  (cons concept=>set edge=>set))\n\n(define (duplicates xs)\n  (remove-duplicates\n    (let loop ((xs xs))\n      (cond ((null? xs)                 '())\n            ((member (car xs) (cdr xs)) (cons (car xs) (loop (cdr xs))))\n            (else                       (loop (cdr xs)))))))\n(define (constraints? xs)\n  (or (not xs) (and (pair? xs)\n                    (not (list? (cdr (car xs))))\n                    (not (number? (cdr (car xs)))))))\n(define (constraints->set cxs)\n  (list->set (map (lambda (c) (cons (car c) (cadr c))) cxs)))\n(define (constraint-sets kvs)\n  (make-immutable-hash\n    (map (match-lambda ((cons name cxs) (cons name (constraints->set cxs))))\n         (filter (match-lambda\n                   ((cons name value) (and value (constraints? value))))\n                 kvs))))\n(define (path*->edges paths cnames enames)\n  (when (null? paths) (error \"no paths were provided\"))\n  (unless (list? paths) (error \"paths must be given as a list:\" paths))\n  (for-each\n    (lambda (path)\n      (unless (list? path) (error \"path must be a list:\" path))\n      (unless (<= 3 (length path))\n        (error \"path must contain at least one edge triple:\" path))\n      (let loop ((parts path))\n        (cond ((null? parts) (error \"missing concept at end of path:\" path))\n              ((not (member (car parts) cnames))\n               (error \"unknown path concept:\"\n                      path `(unknown-concept: ,(car parts))\n                      `(valid-concepts: ,cnames)))\n              ((and (pair? (cdr parts)) (not (member (cadr parts) enames)))\n               (error \"unknown path edge:\"\n                      path `(unknown-edge: ,(cadr parts))\n                      `(valid-edges: ,enames)))\n              ((pair? (cdr parts)) (loop (cddr parts))))))\n    paths)\n  (define (path->edges path)\n    (if (null? (cdr path)) '()\n      (cons (list (cadr path) (car path) (caddr path))\n            (path->edges (cddr path)))))\n  (append* (map path->edges paths)))\n(define (report-concept c)\n  (define dbname (car c))\n  (define cid (cdr c))\n  (car (run* (concept)\n          (fresh (cui name catid cat props)\n            (== concept `(,dbname ,cid ,cui ,name (,catid . ,cat) ,props))\n            (concepto concept)))))\n(define (report-edge e)\n  (define dbname (car e))\n  (define eid (cadr e))\n  (define scid (caddr e))\n  (define ocid (cadddr e))\n  (car (run* (edge)\n          (fresh (scui sname scatid scat sprops\n                      ocui oname ocatid ocat oprops\n                      pid pred eprops)\n            (== edge `(,dbname ,eid\n                       (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n                       (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n                       (,pid . ,pred) ,eprops))\n            (edgeo edge)))))\n(define (report report-x x=>set)\n  (make-immutable-hash\n    (map (lambda (kv)\n            (define name (car kv))\n            (cons name (map report-x (set->list (cdr kv)))))\n          (hash->list x=>set))))\n(define-syntax run/graph\n  (syntax-rules ()\n    ((_ ((cname cexpr) ...) ((ename pexpr) ...) path* ...)\n     (let* ((concepts (list (cons 'cname cexpr) ...))\n            (pedges   (list (cons 'ename pexpr) ...))\n            (paths    '(path* ...))\n            (cnames   (map car concepts))\n            (enames   (map car pedges))\n            (dup-concepts (duplicates cnames))\n            (dup-pedges   (duplicates enames))\n            (_ (unless (null? dup-concepts)\n                 (error \"duplicate concept bindings:\"\n                        dup-concepts '((cname cexpr) ...))))\n            (_ (unless (null? dup-pedges)\n                 (error \"duplicate edge bindings:\"\n                        dup-pedges '((ename pexpr) ...))))\n            (edges (path*->edges paths cnames enames))\n            (concept=>set\n              (make-immutable-hash\n                (map (match-lambda\n                       ((cons name concepts)\n                        (cons name (list->set\n                                     (map (lambda (c)\n                                            (cons (car c)\n                                                  (if (number? (cdr c)) (cdr c)\n                                                    (cadr c))))\n                                          concepts)))))\n                     (filter\n                       (match-lambda\n                         ((cons name value) (not (constraints? value))))\n                       concepts))))\n            (concept=>cx (constraint-sets concepts))\n            (predicate=>cx (constraint-sets pedges)))\n       (match-define (cons concept-sets edge=>set)\n                     (find-graph concept=>set concept=>cx predicate=>cx edges))\n       (list (report report-concept concept-sets)\n             (report report-edge    edge=>set))))))\n\n\n#|\nexample usage, where 'results' is bound to a list of lists:\n\n(write-list-to-tsv\n  (list \"db\" \"subject\" \"predicate\" \"object\")\n  results\n  \"my-tsv.tsv\")\n|#\n(define write-list-to-tsv\n  (lambda (header-ls lol path)\n    (with-output-to-file path\n      ;; thunk -- procedure that takes no arguments\n      (lambda ()\n        (for-each\n          (lambda (l)\n            (let loop ([l l])\n              (cond\n                ((null? l)\n                 (error 'output-to-tsv \"where's the data!?\"))\n                ((null? (cdr l)) ;; l contains exactly 1 element\n                 (display (car l))\n                 (display #\\newline))\n                (else\n                 (display (car l))\n                 (display #\\tab)\n                 (loop (cdr l))))))\n          (cons header-ls lol)))\n      #:mode 'text\n      #:exists 'replace)))\n"
  },
  {
    "path": "medikanren/config.defaults.scm",
    "content": ";; DO NOT EDIT THIS FILE!\n;; Instead, add overrides to: config.scm\n((databases . (\n               uab-pmi\n               semmed\n               orange\n               robokop\n               rtx\n               ))\n (cache-synonyms? . #t)\n\n (in-memory-names? . #t)\n (in-memory-cuis?  . #t)\n\n (query-results.write-to-file?  . #t)  ;; #t will write the query and results to file, #f will not\n (query-results.file-name       . \"last.sx\")\n (query-results.file-name-human . \"last.txt\")\n (query-results.file-name-spreadsheet . \"last.tsv\")\n ;; Uncomment exactly one of these:\n (query-results.file-mode       . replace)  ;; Clobber the save file each time you run a query.\n ;(query-results.file-mode       . append)  ;; Save all the queries.\n (initial-window-size.horizontal . 800)\n (initial-window-size.vertical . 400)\n (decreases-predicate-names\n  .\n  (\"negatively_regulates\"\n   \"prevents\"\n   \"treats\"\n   \"indicated_for\"\n   \"decreases_activity_of\"\n   \"decreases_expression_of\"\n   \"decreases_molecular_interaction\"\n   \"decreases_secretion_of\"\n   \"decreases_synthesis_of\"\n   \"decreases_transport_of\"\n   \"decreases_uptake_of\"\n   \"disrupts\"\n   \"increases_degradation_of\"\n   ;; \"negatively_regulates__entity_to_entity\"\n   ;; \"increases_metabolic_processing_of\"\n   ;; \"decreases_response_to\"\n   ;; \"decreases_localization_of\"\n   ;; \"decreases_molecular_modification_of\"\n   ))\n (increases-predicate-names\n  .\n  (\"positively_regulates\"\n   \"causes\"\n   \"produces\"\n   \"causes_condition\"\n   \"causally_related_to\"\n   \"contributes_to\"\n   \"causes_adverse_event\"\n   \"gene_associated_with_condition\"\n   \"gene_mutations_contribute_to\"\n   \"disease_to_gene_association\"\n   \"increases_activity_of\"\n   \"increases_expression_of\"\n   \"increases_molecular_interaction\"\n   \"increases_response_to\"\n   \"increases_secretion_of\"\n   \"increases_stability_of\"\n   \"increases_synthesis_of\"\n   \"increases_transport_of\"\n   \"increases_uptake_of\"\n   \"decreases_degradation_of\"\n   \"posetively_regulates\" ;;; robokop typo--now fixed, but keep it for compatibility with old data\n   ;; \"positively_regulates__entity_to_entity\"\n   ;; \"increases_molecular_modification_of\"\n   ;; \"increases_localization_of\"\n   ;; \"increases_splicing_of\"\n   ;; \"decreases_mutation_rate_of\"\n   ;; \"predisposes\"\n   ;; \"decreases_metabolic_processing_of\"\n   ))\n\n  ;; Disable this flag to prevent translator-web-server.rkt\n  ;; and open-api/ from making downstream HTTP requests.  Useful\n  ;; for functional CI tests, and for offline development.\n  (trapi-enable-external-requests?  . #f)\n\n ;; Add configuration options as new association pairs.\n )\n\n"
  },
  {
    "path": "medikanren/configref.rkt",
    "content": "#lang racket \n(require\n    racket/runtime-path\n)\n(provide\n    config\n    config-ref\n    load-config\n    override-config\n)\n\n(define (read/file path)  (with-input-from-file  path (lambda () (read))))\n\n(define-runtime-path path:root \".\")\n(define (path/root relative-path) (build-path path:root relative-path))\n(define (path-simple path)        (path->string (simplify-path path)))\n\n(define box:config-override (box '()))\n(define box:config (box #f))\n(define (config)\n  (define cfg (unbox box:config))\n  (cond (cfg cfg)\n        (else (load-config #t #f)\n              (unbox box:config))))\n;;; override-config\n;; Set a set of config keys with higher precidence than \"user config\" config.scm\n;; or \"config.defaults.scm\".  Primarily for use in the repl, secondarily for use\n;; in automated tests.  Use discouraged in applications.\n(define (override-config config)\n  (validate-config config)\n  (set-box! box:config-override config)\n  (set-box! box:config #f))\n(define (config-ref key #:testing-dict (dict-config (config)))\n  (define kv (assoc key dict-config))\n  (unless kv (error \"missing configuration key:\" key))\n  (cdr kv))\n(define (valid-entry? kv)\n  (and (pair? kv) (symbol? (car kv))))\n(define (validate-config config)\n  (unless (and (list? config) (andmap valid-entry? config))\n    (error \"invalid configuration:\" config))\n)\n;;; config-combine\n;; Default configs go last, and must contain a superset of all config keys.\n;; Could be faster, but intended to only be run once at startup.\n(define (config-combine . configs)\n  (define (find k configs)\n    (when (empty? configs)\n      (error \"config defaults must contain a superset of all other config keys\"))\n    (define kv (assoc k (car configs)))\n    (if kv\n      (cdr kv)\n      (find k (cdr configs))))\n  (define ks (map car (last configs)))\n  (map (lambda (k)\n    (cons k (find k configs)))\n    ks)\n)\n(define (path:config.user path:config) (or path:config (path/root \"config.scm\")))\n(define (path:config.defaults) (path/root \"config.defaults.scm\"))\n(define (load-config verbose? path:config)\n  (when verbose? (printf \"loading default configuration: ~a\\n\"\n                         (path-simple (path:config.defaults))))\n  (when verbose? (printf \"loading user configuration: ~a\\n\"\n                         (path-simple (path:config.user path:config))))\n  (define config.user     (if (file-exists? (path:config.user path:config))\n                            (read/file (path:config.user path:config))\n                            '()))\n  (define config.defaults (read/file (path:config.defaults)))\n  (validate-config config.user)\n  (set-box! box:config (config-combine (unbox box:config-override) config.user config.defaults)))\n\n(module+ test\n  ; has required package:\n  ;   raco pkg install chk\n  ;\n  ; how to run tests:\n  ;   (cd medikanren && raco test configref.rkt)\n\n  (require chk)\n\n  ; test config-ref\n  (chk\n      #:= (config-ref 'foo #:testing-dict '((foo . 1))) 1)\n  (chk\n      #:do (config-ref 'foo #:testing-dict '((foo . 1)))\n      #:t #t)\n  (chk\n      #:x (config-ref 'foo #:testing-dict '((bar . 1))) \"missing configuration key\")\n\n  ; test validate-config\n  (chk #:x (validate-config (vector)) \"invalid configuration\")\n  (chk #:x (validate-config '(())) \"invalid configuration\")\n  (chk #:x (validate-config '((\"foo\" . 1))) \"invalid configuration\")\n  (chk\n      #:do (validate-config '((foo . 1)))\n      #:t #t)\n  (chk\n      #:do (validate-config (read/file (path:config.defaults)))\n      #:t #t)\n\n\n  ; test config-combine\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '((foo . 1)) '((foo . 2)) ))\n    1)\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '((foo . 1)) '((foo . 2)) '((foo . 3)) ))\n    1)\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '() '((foo . 2)) ))\n    2)\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '((foo . 1)) '((foo . 2) (bar . 1)) ))\n    1)\n\n  ; test override-config\n  (chk\n    #:= (config-ref 'query-results.file-name-human) \"last.txt\"\n    )\n  (chk\n    #:do (override-config '())\n    #:= (config-ref 'query-results.file-name-human) \"last.txt\"\n    )\n  (chk\n    #:do (override-config '((query-results.file-name-human . \"bob\")))\n    #:= (config-ref 'query-results.file-name-human) \"bob\"\n    )\n)"
  },
  {
    "path": "medikanren/csv.rkt",
    "content": "#lang racket/base\n(provide\n  csv-records\n  set-field-separator!\n  )\n\n\n;; Informal CSV Grammar\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record ::= field | field FIELD-SEPARATOR record\n;field ::= \\\" inner-content* \\\" | CONTENT*\n;inner-content ::= CONTENT | \\\"\\\" | FIELD-SEPARATOR | WHITESPACE\n;; CONTENT includes anything other than double-quote, field separator, whitespace\n\n(define *field-separator* #\\,)\n(define (set-field-separator! ch) (set! *field-separator* ch))\n\n(define (end-of-record?! in)\n  (define ch (peek-char in))\n  (or (and (char=? #\\return ch)\n           (or (and (char=? #\\newline (peek-char in 1)) (read-string 2 in) #t)\n               (and (read-char in) #t)))\n      (and (char=? #\\newline ch) (read-char in) #t)\n      (eof-object? ch)))\n\n(define (field-separator?! in)\n  (define ch (peek-char in))\n  (and (char=? *field-separator* ch) (read-char in) #t))\n\n(define (end-of-field?! in)\n  (define ch (peek-char in))\n  (or (char=? *field-separator* ch)\n      (char=? #\\return ch) (char=? #\\newline ch) (eof-object? ch)))\n\n(define (field-quoted-begin?! in)\n  (define ch (peek-char in))\n  (and (char=? #\\\" ch) (read-char in) #t))\n\n(define (field-quoted-end?! in)\n  (define ch (peek-char in))\n  (and (char=? #\\\" ch) (read-char in) (not (char=? #\\\" (peek-char in)))))\n\n(define (csv-records in)\n  (define (next-record)\n    (and (not (eof-object? (peek-char in)))\n         (let record ((continue? #t))\n           (if continue?\n             (cons (list->string\n                     (let field ()\n                       (cond ((end-of-field?! in) '())\n                             ((field-quoted-begin?! in)\n                              (let field-quoted ()\n                                (if (field-quoted-end?! in) (field)\n                                  (cons (read-char in) (field-quoted)))))\n                             (else (cons (read-char in) (field))))))\n                   (record (field-separator?! in)))\n             (if (end-of-record?! in) '() (error \"malformed csv\"))))))\n  (define current #f)\n  (lambda (request)\n    (case request\n      ((current) current)\n      ((next) (set! current (next-record)) current)\n      (else (error \"invalid csv-records request:\" request)))))\n"
  },
  {
    "path": "medikanren/db.rkt",
    "content": "#lang racket/base\n(provide\n  make-db\n\n  db:category*\n  db:predicate*\n  db:concept-cui-corpus\n\n  db:catid->category\n  db:pid->predicate\n  db:catid->cid*\n  db:cid->concept\n  db:eid->edge\n  db:cid&concept-stream\n  db:eid&edge/props-stream\n  db:subject->pids\n  db:object->pids\n  db:subject->edge-stream\n  db:object->edge-stream\n  db:pmid->eid*\n  db:pmid&eid*-stream\n  db:synonym->cid*\n  db:xref->cid*\n\n  db:~category->catid&category*\n  db:~predicate->pid&predicate*\n  db:~cui*->cid&concept*\n  db:~cui->cid&concept*\n  db:~name*->cid&concept*/options\n  db:~name->cid&concept*\n\n  chars:ignore-typical\n  chars:split-typical\n\n  smart-string-matches?\n  )\n\n(require\n  \"repr.rkt\"\n  \"string-search.rkt\"\n  racket/file\n  racket/stream\n  racket/string\n  racket/vector)\n\n(define fnin-concepts             \"concepts.scm\")\n(define fnin-synonyms             \"synonyms.scm\")\n(define fnin-concepts-by-synonym  \"concepts-by-synonym.scm\")\n(define fnin-xrefs                \"xrefs.scm\")\n(define fnin-concepts-by-xref     \"concepts-by-xref.scm\")\n(define fnin-concept-cui-corpus   \"concept-cui-corpus.scm\")\n(define fnin-concept-cui-index    \"concept-cui-index.bytes\")\n(define fnin-concept-name-corpus  \"concept-name-corpus.scm\")\n(define fnin-concept-name-index   \"concept-name-index.bytes\")\n(define fnin-categories           \"categories.scm\")\n(define fnin-concepts-by-category \"concepts-by-category.scm\")\n(define fnin-edges                \"edges.scm\")\n(define fnin-predicates           \"predicates.scm\")\n(define fnin-edges-by-subject     \"edges-by-subject.bytes\")\n(define fnin-edges-by-object      \"edges-by-object.bytes\")\n(define fnin-pubmed-edges         \"pubmed-edges.scm\")\n(define (fname-offset fname) (string-append fname \".offset\"))\n\n(define (read-all in)\n  (define datum (read in))\n  (if (eof-object? datum) '() (cons datum (read-all in))))\n(define (read-all-from-file path) (call-with-input-file path read-all))\n\n;; TODO: incorporate a time/space tradeoff parameter.\n;; memory usage ranking:\n;;   2:\n;;     edges\n;;   1:\n;;     edge-by-X * 2\n;;   0:\n;;     concepts\n;;     cat->concepts\n;;     category*, predicate*\n\n;; memory-usage: 0 1 2 3\n(define (make-db db-dir (in-memory-names? #t) (in-memory-cuis? #t))\n  (define (db-path fname) (expand-user-path (build-path db-dir fname)))\n  (define (open-db-path fname) (open-input-file (db-path fname)))\n  (define (open-db-path/optional fname)\n    (if (file-exists? (db-path fname))\n        (open-db-path fname)\n        (if (file-exists? \"/dev/null\")\n            (open-input-file \"/dev/null\")\n            (open-input-file \"nul\"))))\n  (define in-concepts            (open-db-path fnin-concepts))\n  (define in-concepts-by-category (open-db-path fnin-concepts-by-category))\n  (define in-offset-concepts-by-category\n    (open-db-path (fname-offset fnin-concepts-by-category)))\n  (define in-concepts-by-synonym (open-db-path fnin-concepts-by-synonym))\n  (define in-offset-concepts-by-synonym\n    (open-db-path (fname-offset fnin-concepts-by-synonym)))\n  (define in-synonyms            (open-db-path fnin-synonyms))\n  (define in-offset-synonyms     (open-db-path (fname-offset fnin-synonyms)))\n  (define in-concepts-by-xref (open-db-path fnin-concepts-by-xref))\n  (define in-offset-concepts-by-xref\n    (open-db-path (fname-offset fnin-concepts-by-xref)))\n  (define in-xrefs               (open-db-path fnin-xrefs))\n  (define in-offset-xrefs        (open-db-path (fname-offset fnin-xrefs)))\n  (define in-concept-cui-index   (open-db-path fnin-concept-cui-index))\n  (define in-concept-name-corpus (open-db-path fnin-concept-name-corpus))\n  (define in-offset-concepts  (open-db-path (fname-offset fnin-concepts)))\n  (define in-edges            (open-db-path fnin-edges))\n  (define in-offset-edges     (open-db-path (fname-offset fnin-edges)))\n  (define in-edges-by-subject (open-db-path fnin-edges-by-subject))\n  (define in-edges-by-object  (open-db-path fnin-edges-by-object))\n  (define in-offset-edges-by-subject\n    (open-db-path (fname-offset fnin-edges-by-subject)))\n  (define in-offset-edges-by-object\n    (open-db-path (fname-offset fnin-edges-by-object)))\n  (define in-pubmed-edges (open-db-path/optional fnin-pubmed-edges))\n  (define in-offset-pubmed-edges\n    (open-db-path/optional (fname-offset fnin-pubmed-edges)))\n\n  (define category*\n    (list->vector (read-all-from-file (db-path fnin-categories))))\n  (define predicate*\n    (list->vector (read-all-from-file (db-path fnin-predicates))))\n\n  (define (get-cui-corpus/raw)\n    (call-with-input-file\n      (db-path fnin-concept-cui-corpus)\n      (lambda (in-concept-cui-corpus)\n        (displayln \"* cui-corpus:\")\n        (time (for/vector ((x (port->stream-offset&values in-concept-cui-corpus)))\n                (cdr x))))))\n  (define get-cui-corpus\n    (cond (in-memory-cuis? (define cui-corpus (get-cui-corpus/raw))\n                           (lambda () cui-corpus))\n          (else            get-cui-corpus/raw)))\n\n  (define cui*->cid*\n    (cond (in-memory-cuis?\n            (define cui-corpus (get-cui-corpus))\n            (define cui-index (port->string-keys in-concept-cui-index))\n            (close-input-port in-concept-cui-index)\n            (lambda (cui*) (string:corpus-find*      cui-corpus   cui-index            cui*)))\n          (else\n            (lambda (cui*) (string:corpus-find*/disk cid->concept in-concept-cui-index cui*)))))\n\n  (define ~name*->cid*\n    (cond (in-memory-names?\n            (displayln \"* name-corpus:\")\n            (define name-corpus\n              (time (for/vector ((x (port->stream-offset&values in-concept-name-corpus)))\n                      (cdr x))))\n            (displayln \"* name-index:\")\n            (define name-index (time (file->bytes (db-path fnin-concept-name-index))))\n            (lambda (~name*) (suffix:corpus-find*      name-corpus  name-index            ~name*)))\n          (else\n            (define in-concept-name-index (open-input-file (db-path fnin-concept-name-index)))\n            (lambda (~name*) (suffix:corpus-find*/disk cid->concept in-concept-name-index ~name*)))))\n  (close-input-port in-concept-name-corpus)\n\n  (define catid=>cid* (make-vector (vector-length category*) #f))\n  (for ((catid (in-range 0 (vector-length category*))))\n       (define cid* (detail-ref in-concepts-by-category\n                                in-offset-concepts-by-category catid))\n       (vector-set! catid=>cid* catid cid*))\n  (close-input-port in-concepts-by-category)\n  (close-input-port in-offset-concepts-by-category)\n\n  (define (synonym->cid* synonym)\n    (define id (detail-find-index in-synonyms in-offset-synonyms\n                                  (lambda (key)\n                                    (cond ((stringcid* xref)\n    (define xid (detail-find-index in-xrefs in-offset-xrefs\n                                   (lambda (key)\n                                     (cond ((stringcid* catid)  (vector-ref catid=>cid* catid))\n  (define (cid->concept cid)   (detail-ref in-concepts in-offset-concepts cid))\n  (define (cid&concept-stream) (port->stream-offset&values in-concepts))\n  (define (eid->edge eid)         (detail-ref in-edges in-offset-edges eid))\n  (define (eid&edge/props-stream) (port->stream-offset&values in-edges))\n\n  (define (subject->pids cid)\n    (edge-pids-by-X in-edges-by-subject in-offset-edges-by-subject cid))\n  (define (object->pids cid)\n    (edge-pids-by-X in-edges-by-object in-offset-edges-by-object cid))\n  (define (subject->edge-stream cid pid? cat? dst?)\n    (stream-edges-by-X in-edges-by-subject in-offset-edges-by-subject\n                       cid pid? cat? dst?))\n  (define (object->edge-stream cid pid? cat? dst?)\n    (stream-edges-by-X in-edges-by-object in-offset-edges-by-object\n                       cid pid? cat? dst?))\n  (define (pmid->eid* pmid)\n    (define pmid&eid*\n      (detail-find in-pubmed-edges in-offset-pubmed-edges\n                   (lambda (x)\n                     (define key (car x))\n                     (cond ((stringcid* ~name*->cid*\n          catid->cid* cid->concept eid->edge\n          cid&concept-stream eid&edge/props-stream\n          subject->edge-stream object->edge-stream\n          pmid->eid* pmid&eid*-stream subject->pids object->pids\n          synonym->cid* xref->cid*\n          get-cui-corpus))\n\n(define (db:category*             db)        (vector-ref db 0))\n(define (db:predicate*            db)        (vector-ref db 1))\n(define (db:cui*->cids            db   cui*) ((vector-ref db 2) cui*))\n(define (db:~name*->cids          db ~name*) ((vector-ref db 3) ~name*))\n(define (db:catid->cid*           db . args) (apply (vector-ref db 4) args))\n(define (db:cid->concept          db . args) (apply (vector-ref db 5) args))\n(define (db:eid->edge             db . args) (apply (vector-ref db 6) args))\n(define (db:cid&concept-stream    db)        ((vector-ref db 7)))\n(define (db:eid&edge/props-stream db)        ((vector-ref db 8)))\n(define (db:subject->edge-stream  db . args) (apply (vector-ref db 9) args))\n(define (db:object->edge-stream   db . args) (apply (vector-ref db 10) args))\n(define (db:pmid->eid*            db . args) (apply (vector-ref db 11) args))\n(define (db:pmid&eid*-stream      db)        ((vector-ref db 12)))\n(define (db:subject->pids         db . args) (apply (vector-ref db 13) args))\n(define (db:object->pids          db . args) (apply (vector-ref db 14) args))\n(define (db:synonym->cid*         db . args) (apply (vector-ref db 15) args))\n(define (db:xref->cid*            db . args) (apply (vector-ref db 16) args))\n(define (db:concept-cui-corpus    db)        ((vector-ref db 17)))\n\n(define (db:catid->category db catid) (vector-ref (db:category* db) catid))\n(define (db:pid->predicate db pid)    (vector-ref (db:predicate* db) pid))\n\n(define chars:ignore-typical \"-\")\n(define chars:split-typical \"\\t\\n\\v\\f\\r !\\\"#$%&'()*+,./:;<=>?@\\\\[\\\\\\\\\\\\]\\\\^_`{|}~\")\n\n(define (smart-string-matches? case-sensitive? chars:ignore chars:split str* hay)\n  (define re:ignore (and (non-empty-string? chars:ignore)\n                         (pregexp (string-append \"[\" chars:ignore \"]\"))))\n  (define re:split (and (non-empty-string? chars:split)\n                        (pregexp (string-append \"[\" chars:split \"]\"))))\n  (define (normalize s case-sensitive?)\n    (define pruned (if re:ignore (string-replace s re:ignore \"\") s))\n    (if case-sensitive? pruned (string-downcase pruned)))\n  (define (contains-upcase? s) (not (string=? s (string-downcase s))))\n  (define case-sensitive?*\n    (map (lambda (s) (or case-sensitive? (contains-upcase? s))) str*))\n  (define needles\n    (map (lambda (v case-sensitive?) (normalize v case-sensitive?))\n         str* case-sensitive?*))\n  (and hay\n       (andmap\n        (if re:split\n            (lambda (n case-sensitive?)\n              (ormap (lambda (s) (string=? s n))\n                     (string-split (normalize hay case-sensitive?) re:split)))\n            (lambda (n case-sensitive?)\n              (string-contains? (normalize hay case-sensitive?) n)))\n        needles case-sensitive?*)))\n\n(define (~string*->offset&value*\n          case-sensitive? chars:ignore chars:split offset&value* str* v->str)\n  (define (p? v)\n    (define hay (v->str (cdr v)))\n    (smart-string-matches? case-sensitive? chars:ignore chars:split str* hay))\n  (stream-filter p? offset&value*))\n\n(define (simple~string->offset&value* offset&value* str v->str)\n  (~string*->offset&value* #f \"\" \"\" offset&value* (list str) v->str))\n\n(define (db:~category->catid&category* db ~category)\n  (simple~string->offset&value*\n    (vector->stream-offset&values (db:category* db))\n    ~category (lambda (v) v)))\n(define (db:~predicate->pid&predicate* db ~predicate)\n  (simple~string->offset&value*\n    (vector->stream-offset&values (db:predicate* db))\n    ~predicate (lambda (v) v)))\n\n(define (db:~cui*->cid&concept* db ~cui*)\n  (define cids (db:cui*->cids db ~cui*))\n  (foldr (lambda (i cs) (stream-cons (cons i (db:cid->concept db i)) cs))\n         '() cids))\n(define (db:~cui->cid&concept* db ~cui)\n  (db:~cui*->cid&concept* db (list ~cui)))\n\n(define (db:~name*->cid&concept*/options\n          case-sensitive? chars:ignore chars:split db ~name*)\n  (define cids (db:~name*->cids db ~name*))\n  (define found (foldr (lambda (i cs)\n                         (stream-cons (cons i (db:cid->concept db i)) cs))\n                       '() cids))\n  (~string*->offset&value* case-sensitive? chars:ignore chars:split\n                           found ~name* concept-name))\n(define (db:~name->cid&concept* db ~name)\n  (simple~string->offset&value* (db:cid&concept-stream db) ~name concept-name))\n"
  },
  {
    "path": "medikanren/hgnc-ids.txt",
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  },
  {
    "path": "medikanren/mk-db.rkt",
    "content": "#lang racket/base\n(provide\n  (all-from-out \"mk.rkt\")\n  make-db\n\n  db:edgeo\n  db:concepto\n  db:categoryo\n  db:predicateo\n  db:pmid-eido\n  db:subject-predicateo\n  db:object-predicateo\n\n  db:~cui*-concepto\n  db:~cui-concepto\n  db:~name-concepto\n  db:~predicateo\n  db:~categoryo\n  db:~name*-concepto/options\n  db:synonym-concepto\n  db:xref-concepto\n\n  chars:ignore-typical\n  chars:split-typical\n  )\n\n(require\n  \"db.rkt\"\n  \"mk.rkt\"\n  \"repr.rkt\"\n  (except-in racket/match ==)\n  racket/stream\n  )\n\n(define (vconcept->details db v)\n  (define catid (concept-category v))\n  (list (concept-cui v)\n        (concept-name v)\n        (cons catid (vector-ref (db:category* db) catid))\n        (concept-props v)))\n(define ((i&v->i&d db) i&v) (cons (car i&v) (vconcept->details db (cdr i&v))))\n\n(define (stream-refo i&v* iv)\n  (let loop ((i&v* i&v*))\n    (if (stream-empty? i&v*) fail\n      (let* ((i&v (stream-first i&v*)))\n        (conde\n          ((== `(,(car i&v) . ,(cdr i&v)) iv))\n          ((loop (stream-rest i&v*))))))))\n\n(define (db:~cui*-concepto db ~cui* concept)\n  (project (~cui*)\n    (stream-refo\n      (stream-map (i&v->i&d db) (db:~cui*->cid&concept* db ~cui*)) concept)))\n(define (db:~cui-concepto db ~cui concept)\n  (project (~cui)\n    (stream-refo\n      (stream-map (i&v->i&d db) (db:~cui->cid&concept* db ~cui)) concept)))\n(define (db:~name-concepto db ~name concept)\n  (project (~name)\n    (stream-refo\n      (stream-map (i&v->i&d db) (db:~name->cid&concept* db ~name)) concept)))\n(define (db:~name*-concepto/options\n          case-sensitive? chars:ignore chars:split db ~name* concept)\n  (project (~name*)\n    (stream-refo\n      (stream-map (i&v->i&d db)\n                  (db:~name*->cid&concept*/options\n                    case-sensitive? chars:ignore chars:split db ~name*))\n      concept)))\n(define (db:~predicateo db ~predicate predicate)\n  (project (~predicate)\n    (stream-refo (db:~predicate->pid&predicate* db ~predicate) predicate)))\n(define (db:~categoryo db ~category category)\n  (project (~category)\n    (stream-refo (db:~category->catid&category* db ~category) category)))\n\n(define (db:synonym-concepto db synonym concept)\n  (project (synonym concept)\n    (match concept\n      (`(,(and cid (? integer?)) . ,_)\n        (fresh ()\n          (db:concepto db concept)\n          (let loop ((synonym* (concept->synonyms (db:cid->concept db cid))))\n            (if (null? synonym*) fail\n              (conde ((== (car synonym*) synonym))\n                     ((loop (cdr synonym*))))))))\n      (_ (cond ((not (var? synonym))\n                (let loop ((cid* (db:synonym->cid* db synonym)))\n                  (if (null? cid*) fail\n                    (let ((c (vconcept->details\n                               db (db:cid->concept db (car cid*)))))\n                      (conde ((== (cons (car cid*) c) concept))\n                             ((loop (cdr cid*))))))))\n               (else (fresh ()\n                       (db:concepto db concept)\n                       (db:synonym-concepto db synonym concept))))))))\n(define (db:xref-concepto db xref concept)\n  (project (xref concept)\n    (match concept\n      (`(,(and cid (? integer?)) . ,_)\n        (fresh ()\n          (db:concepto db concept)\n          (let loop ((xref* (concept->xrefs (db:cid->concept db cid))))\n            (if (null? xref*) fail\n              (conde ((== (car xref*) xref))\n                     ((loop (cdr xref*))))))))\n      (_ (cond ((not (var? xref))\n                (let loop ((cid* (db:xref->cid* db xref)))\n                  (if (null? cid*) fail\n                    (let ((c (vconcept->details\n                               db (db:cid->concept db (car cid*)))))\n                      (conde ((== (cons (car cid*) c) concept))\n                             ((loop (cdr cid*))))))))\n               (else (fresh ()\n                       (db:concepto db concept)\n                       (db:xref-concepto db xref concept))))))))\n\n(define (vector-refo e->v v* iv)\n  (when (not (vector? v*)) (error \"vector-refo vector must be ground:\" v* iv))\n  (project (iv)\n    (cond ((and (pair? iv) (integer? (car iv)))\n           (== (cons (car iv) (e->v (vector-ref v* (car iv)))) iv))\n          (else\n            (define len (vector-length v*))\n            (let loop ((i 0))\n              (if (<= len i) fail\n                (conde\n                  ((== (cons i (e->v (vector-ref v* i))) iv))\n                  ((loop (+ i 1))))))))))\n\n(define (db:predicateo db predicate)\n  (vector-refo (lambda (x) x) (db:predicate* db) predicate))\n\n(define (db:categoryo db category)\n  (vector-refo (lambda (x) x) (db:category* db) category))\n\n(define (db:concepto db concept)\n  (define (v->concept v) (vconcept->details db v))\n  (project (concept)\n    (match concept\n      (`(,(and cid (? integer?)) . ,_)\n        (== (cons cid (v->concept (db:cid->concept db cid))) concept))\n      (`(,_ ,_ ,_ (,(and catid (? integer?)) . ,_) . ,_)\n        (define cid* (db:catid->cid* db catid))\n        (define len (vector-length cid*))\n        (let loop ((i 0))\n          (if (<= len i) fail\n            (let ((cid (vector-ref cid* i)))\n              (conde\n                ((== (cons cid (v->concept (db:cid->concept db cid))) concept))\n                ((loop (+ i 1))))))))\n      (_ (let loop ((c&c* (db:cid&concept-stream db)))\n           (if (stream-empty? c&c*) fail\n             (let ((c&c (stream-first c&c*)))\n               (conde\n                 ((== (cons (car c&c) (v->concept (cdr c&c))) concept))\n                 ((loop (stream-rest c&c*)))))))))))\n\n(define (db:concept-predicateo db:concept->pids db concept predicate)\n  (fresh (cid cdetails pdetails)\n    (== `(,cid . ,cdetails) concept)\n    (db:concepto db concept)\n    (project (cid)\n      (foldr (lambda (pid others) (conde\n                                    ((== `(,pid . ,pdetails) predicate)\n                                     (db:predicateo db predicate))\n                                    (others)))\n             fail (db:concept->pids db cid)))))\n(define (db:subject-predicateo db concept predicate)\n  (db:concept-predicateo db:subject->pids db concept predicate))\n(define (db:object-predicateo db concept predicate)\n  (db:concept-predicateo db:object->pids db concept predicate))\n\n(define (db:edgeo db edge)\n  (define (edge-propso eid scid ocid pid eprops)\n    (define e/p (db:eid->edge db eid))\n    (fresh ()\n      (== (edge/props-subject e/p) scid)\n      (== (edge/props-object e/p) ocid)\n      (== (edge/props-pid e/p) pid)\n      (== (edge/props-props e/p) eprops)))\n  (define (edges-by-Xo cid->stream cid pid dcatid dcid eid)\n    (project (cid pid dcatid dcid eid)\n      (let loop ((e* (cid->stream db cid\n                                  (and (not (var? pid)) pid)\n                                  (and (not (var? dcatid)) dcatid)\n                                  (and (not (var? dcid)) dcid))))\n        (if (stream-empty? e*) fail\n          (conde\n            ((== (edge-eid (stream-first e*)) eid))\n            ((loop (stream-rest e*))))))))\n  (fresh (scid scui sname scatid scat sprops\n               ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n    (== `(,eid (,scid ,scui ,sname (,scatid . ,scat) ,sprops)\n               (,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)\n               (,pid . ,pred) ,eprops) edge)\n    (project (scid scui sname scatid scat sprops\n                   ocid ocui oname ocatid ocat oprops eid pid pred eprops)\n      (let* ((edges-by-subject\n               (edges-by-Xo db:subject->edge-stream scid pid ocatid ocid eid))\n             (edges-by-object\n               (edges-by-Xo db:object->edge-stream ocid pid scatid scid eid))\n             (subject (db:concepto\n                        db `(,scid ,scui ,sname (,scatid . ,scat) ,sprops)))\n             (object (db:concepto\n                       db `(,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops)))\n             (subject-edges (fresh () subject edges-by-subject))\n             (object-edges (fresh () object edges-by-object)))\n        (cond ((not (var? eid)) succeed)\n              ((not (var? scid)) edges-by-subject)\n              ((not (var? ocid)) edges-by-object)\n              ((not (var? scatid)) subject-edges)\n              ((not (var? ocatid)) object-edges)\n              ((not (var? scat))\n               (fresh () (db:categoryo db `(,scatid . ,scat)) subject-edges))\n              ((not (var? ocat))\n               (fresh () (db:categoryo db `(,ocatid . ,ocat)) object-edges))\n              ((not (andmap var? (list scui sname scat sprops))) subject-edges)\n              ((not (andmap var? (list ocui oname ocat oprops))) object-edges)\n              (else subject-edges))))\n    (project (eid) (edge-propso eid scid ocid pid eprops))\n    (db:predicateo db `(,pid . ,pred))\n    (db:concepto db `(,scid ,scui ,sname (,scatid . ,scat) ,sprops))\n    (db:concepto db `(,ocid ,ocui ,oname (,ocatid . ,ocat) ,oprops))))\n\n(define (db:pmid-eido db pmid eid)\n  (define (eid-loop eid*)\n    (if (null? eid*) fail\n      (conde\n        ((== (car eid*) eid))\n        ((eid-loop (cdr eid*))))))\n  (project (pmid)\n    (if (var? pmid)\n      (let loop ((pe* (db:pmid&eid*-stream db)))\n        (cond ((stream-empty? pe*) fail)\n              (else (define pe (stream-first pe*))\n                    (conde\n                      ((== (car pe) pmid) (eid-loop (cdr pe)))\n                      ((loop (stream-rest pe*)))))))\n      (eid-loop (db:pmid->eid* db pmid)))))\n"
  },
  {
    "path": "medikanren/mk.rkt",
    "content": "#lang racket/base\n\n(require racket/list\n         racket/include\n         racket/stream\n         )\n\n(provide\n  run run* run-stream\n  == =/=\n  fresh\n  conde\n  symbolo numbero\n  absento\n  project\n  var?\n  fail\n  succeed\n  choice\n  inc\n  unify\n  walk\n  walk*\n  mplus\n  mplus*\n  bind\n  bind*\n  take-stream\n  reify\n  )\n\n;; extra stuff for racket\n;; due mostly to samth\n(define (list-sort f l) (sort l f))\n\n(define (remp f l) (filter-not f l))\n\n(define (call-with-string-output-port f)\n  (define p (open-output-string))\n  (f p)\n  (get-output-string p))\n\n(define (exists f l) (ormap f l))\n\n(define for-all andmap)\n\n(define (find f l)\n  (cond [(memf f l) => car] [else #f]))\n\n(define memp memf)\n\n(define (var*? v) (var? (car v)))\n\n\n; Substitution representation\n\n(define empty-subst-map (hasheq))\n\n(define subst-map-length hash-count)\n\n; Returns #f if not found, or a pair of u and the result of the lookup.\n; This distinguishes between #f indicating absence and being the result.\n(define subst-map-lookup\n  (lambda (u S)\n    (hash-ref S u unbound)))\n\n(define (subst-map-add S var val)\n  (hash-set S var val))\n\n(define subst-map-eq? eq?)\n\n\n; Constraint store representation\n\n(define empty-C (hasheq))\n\n(define set-c\n  (lambda (v c st)\n    (state (state-S st) (hash-set (state-C st) v c))))\n\n(define lookup-c\n  (lambda (v st)\n    (hash-ref (state-C st) v empty-c)))\n\n(define remove-c\n  (lambda (v st)\n    (state (state-S st) (hash-remove (state-C st) v))))\n\n\n; Scope object.\n; Used to determine whether a branch has occured between variable creation\n; and unification to allow the set-var-val! optimization in subst-add. Both variables\n; and substitutions will contain a scope. When a substitution flows through a\n; conde it is assigned a new scope.\n\n; Creates a new scope that is not scope-eq? to any other scope\n(define new-scope\n  (lambda ()\n    (list 'scope)))\n\n; Scope used when variable bindings should always be made in the substitution,\n; as in disequality solving and reification. We don't want to set-var-val! a\n; variable when checking if a disequality constraint holds!\n(define nonlocal-scope\n  (list 'non-local-scope))\n\n(define scope-eq? eq?)\n\n\n; Logic variable object.\n; Contains:\n;   val - value for variable assigned by unification using set-var-val! optimization.\n;           unbound if not yet set or stored in substitution.\n;   scope - scope that the variable was created in.\n;   idx - unique numeric index for the variable. Used by the trie substitution representation.\n; Variable objects are compared by object identity.\n\n; The unique val for variables that have not yet been bound to a value\n; or are bound in the substitution\n(define unbound (list 'unbound))\n\n(define var\n  (let ((counter -1))\n    (lambda (scope)\n      (set! counter (+ 1 counter))\n      (vector unbound scope counter))))\n\n; Vectors are not allowed as terms, so terms that are vectors are variables.\n(define var?\n  (lambda (x)\n    (vector? x)))\n\n(define var-eq? eq?)\n\n(define var-val\n  (lambda (x)\n    (vector-ref x 0)))\n\n(define set-var-val!\n  (lambda (x v)\n    (vector-set! x 0 v)))\n\n(define var-scope\n  (lambda (x)\n    (vector-ref x 1)))\n\n(define var-idx\n  (lambda (x)\n    (vector-ref x 2)))\n\n\n; Substitution object.\n; Contains:\n;   map - mapping of variables to values\n;   scope - scope at current program point, for set-var-val! optimization. Updated at conde.\n;               Included in the substitution because it is required to fully define the substitution\n;               and how it is to be extended.\n;\n; Implementation of the substitution map depends on the Scheme used, as we need a map. See mk.rkt\n; and mk-vicare.scm.\n\n(define subst\n  (lambda (mapping scope)\n    (cons mapping scope)))\n\n(define subst-map car)\n\n(define subst-scope cdr)\n\n(define subst-length\n  (lambda (S)\n    (subst-map-length (subst-map S))))\n\n(define subst-with-scope\n  (lambda (S new-scope)\n    (subst (subst-map S) new-scope)))\n\n(define empty-subst (subst empty-subst-map (new-scope)))\n\n(define subst-add\n  (lambda (S x v)\n    ; set-var-val! optimization: set the value directly on the variable\n    ; object if we haven't branched since its creation\n    ; (the scope of the variable and the substitution are the same).\n    ; Otherwise extend the substitution mapping.\n    (if (scope-eq? (var-scope x) (subst-scope S))\n      (begin\n        (set-var-val! x v)\n        S)\n      (subst (subst-map-add (subst-map S) x v) (subst-scope S)))))\n\n(define subst-lookup\n  (lambda (u S)\n    ; set-var-val! optimization.\n    ; Tried checking the scope here to avoid a subst-map-lookup\n    ; if it was definitely unbound, but that was slower.\n    (if (not (eq? (var-val u) unbound))\n      (var-val u)\n      (subst-map-lookup u (subst-map S)))))\n\n; Association object.\n; Describes an association mapping the lhs to the rhs. Returned by unification\n; to describe the associations that were added to the substitution (whose representation\n; is opaque) and used to represent disequality constraints.\n\n(define lhs car)\n\n(define rhs cdr)\n\n; Constraint record object.\n;\n; Describes the constraints attached to a single variable.\n;\n; Contains:\n;   T - type constraint. 'symbolo 'numbero or #f to indicate no constraint\n;   D - list of disequality constraints. Each disequality is a list of associations.\n;           The constraint is violated if all associated variables are equal in the\n;           substitution simultaneously. D could contain duplicate constraints (created\n;           by distinct =/= calls). A given disequality constraint is only attached to\n;           one of the variables involved, as all components of the constraint must be\n;           violated to cause failure.\n;   A - list of absento constraints. Each constraint is a ground atom. The list contains\n;           no duplicates.\n\n(define empty-c `(#f () ()))\n\n(define c-T\n  (lambda (c)\n    (car c)))\n\n(define c-D\n  (lambda (c)\n    (cadr c)))\n\n(define c-A\n  (lambda (c)\n    (caddr c)))\n\n(define c-with-T\n  (lambda (c T)\n    (list T (c-D c) (c-A c))))\n\n(define c-with-D\n  (lambda (c D)\n    (list (c-T c) D (c-A c))))\n\n(define c-with-A\n  (lambda (c A)\n    (list (c-T c) (c-D c) A)))\n\n; Constraint store object.\n; Mapping of representative variable to constraint record. Constraints are\n; always on the representative element and must be moved / merged when that\n; element changes.\n\n; Implementation depends on the Scheme used, as we need a map. See mk.rkt\n; and mk-vicare.scm.\n\n; State object.\n; The state is the value that is monadically passed through the search.\n; Contains:\n;   S - the substitution\n;   C - the constraint store\n\n(define state\n  (lambda (S C)\n    (cons S C)))\n\n(define state-S (lambda (st) (car st)))\n(define state-C (lambda (st) (cdr st)))\n\n(define empty-state (state empty-subst empty-C))\n\n(define state-with-scope\n  (lambda (st new-scope)\n    (state (subst-with-scope (state-S st) new-scope) (state-C st))))\n\n; Unification\n\n(define walk\n  (lambda (u S)\n    (if (var? u)\n      (let ((val (subst-lookup u S)))\n        (if (eq? val unbound)\n          u\n          (walk val S)))\n      u)))\n\n(define occurs-check\n  (lambda (x v S)\n    (let ((v (walk v S)))\n      (cond\n        ((var? v) (var-eq? v x))\n        ((pair? v)\n         (or\n           (occurs-check x (car v) S)\n           (occurs-check x (cdr v) S)))\n        (else #f)))))\n\n(define ext-s-check\n  (lambda (x v S)\n    (cond\n      ((occurs-check x v S) (values #f #f))\n      (else (values (subst-add S x v) `((,x . ,v)))))))\n\n; Returns as values the extended substitution and a list of associations added\n; during the unification, or (values #f #f) if the unification failed.\n;\n; Right now appends the list of added values from sub-unifications. Alternatively\n; could be threaded monadically, which could be faster or slower.\n(define unify\n  (lambda (u v s)\n    (let ((u (walk u s))\n          (v (walk v s)))\n      (cond\n        ((eq? u v) (values s '()))\n        ((var? u) (ext-s-check u v s))\n        ((var? v) (ext-s-check v u s))\n        ((and (pair? u) (pair? v))\n         (let-values (((s added-car) (unify (car u) (car v) s)))\n           (if s\n             (let-values (((s added-cdr) (unify (cdr u) (cdr v) s)))\n               (values s (append added-car added-cdr)))\n             (values #f #f))))\n        ((equal? u v) (values s '()))\n        (else (values #f #f))))))\n\n(define unify*\n  (lambda (S+ S)\n    (unify (map lhs S+) (map rhs S+) S)))\n\n\n; Search\n\n; SearchStream: #f | Procedure | State | (Pair State (-> SearchStream))\n\n; SearchStream constructor types. Names inspired by the plus monad?\n\n; -> SearchStream\n(define mzero (lambda () #f))\n\n; c: State\n; -> SearchStream\n(define unit (lambda (c) c))\n\n; c: State\n; f: (-> SearchStream)\n; -> SearchStream\n;\n; f is a thunk to avoid unnecessary computation in the case that c is the\n; last answer needed to satisfy the query.\n(define choice (lambda (c f) (cons c f)))\n\n; e: SearchStream\n; -> (-> SearchStream)\n(define-syntax inc\n  (syntax-rules ()\n    ((_ e) (lambda () e))))\n\n; Goal: (State -> SearchStream)\n\n; e: SearchStream\n; -> Goal\n(define-syntax lambdag@\n  (syntax-rules ()\n    ((_ (st) e) (lambda (st) e))))\n\n; Match on search streams. The state type must not be a pair with a procedure\n; in its cdr.\n;\n; (() e0)     failure\n; ((f) e1)    inc for interleaving. separate from success or failure to ensure\n;               it goes all the way to the top of the tree.\n; ((c) e2)    single result. Used rather than (choice c (inc (mzero))) to avoid\n;               returning to search a part of the tree that will inevitably fail.\n; ((c f) e3)  multiple results.\n(define-syntax case-inf\n  (syntax-rules ()\n    ((_ e (() e0) ((f^) e1) ((c^) e2) ((c f) e3))\n     (let ((c-inf e))\n       (cond\n         ((not c-inf) e0)\n         ((procedure? c-inf)  (let ((f^ c-inf)) e1))\n         ((not (and (pair? c-inf)\n                 (procedure? (cdr c-inf))))\n          (let ((c^ c-inf)) e2))\n         (else (let ((c (car c-inf)) (f (cdr c-inf)))\n                 e3)))))))\n\n; c-inf: SearchStream\n;     f: (-> SearchStream)\n; -> SearchStream\n;\n; f is a thunk to avoid unnecesarry computation in the case that the first\n; answer produced by c-inf is enough to satisfy the query.\n(define mplus\n  (lambda (c-inf f)\n    (case-inf c-inf\n      (() (f))\n      ((f^) (inc (mplus (f) f^)))\n      ((c) (choice c f))\n      ((c f^) (choice c (inc (mplus (f) f^)))))))\n\n; c-inf: SearchStream\n;     g: Goal\n; -> SearchStream\n(define bind\n  (lambda (c-inf g)\n    (case-inf c-inf\n      (() (mzero))\n      ((f) (inc (bind (f) g)))\n      ((c) (g c))\n      ((c f) (mplus (g c) (inc (bind (f) g)))))))\n\n; Int, SearchStream -> (ListOf SearchResult)\n(define take\n  (lambda (n f)\n    (cond\n      ((and n (zero? n)) '())\n      (else\n       (case-inf (f)\n         (() '())\n         ((f) (take n f))\n         ((c) (cons c '()))\n         ((c f) (cons c\n                  (take (and n (- n 1)) f))))))))\n\n(define take-stream\n  (lambda (f)\n    (case-inf (f)\n              (() '())\n              ((f) (take-stream f))\n              ((c) (stream-cons c '()))\n              ((c f) (stream-cons c (take-stream f))))))\n\n; -> SearchStream\n(define-syntax bind*\n  (syntax-rules ()\n    ((_ e) e)\n    ((_ e g0 g ...) (bind* (bind e g0) g ...))))\n\n; -> SearchStream\n(define-syntax mplus*\n  (syntax-rules ()\n    ((_ e) e)\n    ((_ e0 e ...) (mplus e0\n                    (inc (mplus* e ...))))))\n\n; -> Goal\n(define-syntax fresh\n  (syntax-rules ()\n    ((_ (x ...) g0 g ...)\n     (lambdag@ (st)\n       ; this inc triggers interleaving\n       (inc\n         (let ((scope (subst-scope (state-S st))))\n           (let ((x (var scope)) ...)\n             (bind* (g0 st) g ...))))))))\n\n\n; -> Goal\n(define-syntax conde\n  (syntax-rules ()\n    ((_ (g0 g ...) (g1 g^ ...) ...)\n     (lambdag@ (st)\n       ; this inc triggers interleaving\n       (inc\n         (let ((st (state-with-scope st (new-scope))))\n           (mplus*\n             (bind* (g0 st) g ...)\n             (bind* (g1 st) g^ ...) ...)))))))\n\n(define-syntax run\n  (syntax-rules ()\n    ((_ n (q) g0 g ...)\n     (take n\n       (inc\n         ((fresh (q) g0 g ...\n            (lambdag@ (st)\n              (let ((st (state-with-scope st nonlocal-scope)))\n                (let ((z ((reify q) st)))\n                  (choice z (lambda () (lambda () #f)))))))\n          empty-state))))\n    ((_ n (q0 q1 q ...) g0 g ...)\n     (run n (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n(define-syntax run*\n  (syntax-rules ()\n    ((_ (q0 q ...) g0 g ...) (run #f (q0 q ...) g0 g ...))))\n\n(define-syntax run-stream\n  (syntax-rules ()\n    ((_ (q) g0 g ...)\n     (take-stream\n       (inc\n         ((fresh (q) g0 g ...\n            (lambdag@ (st)\n              (let ((st (state-with-scope st nonlocal-scope)))\n                (let ((z ((reify q) st)))\n                  (choice z (lambda () (lambda () #f)))))))\n          empty-state))))\n    ((_ (q0 q1 q ...) g0 g ...)\n     (run-stream (x) (fresh (q0 q1 q ...) g0 g ... (== `(,q0 ,q1 ,q ...) x))))))\n\n; Constraints\n; C refers to the constraint store map\n; c refers to an individual constraint record\n\n; Constraint: State -> #f | State\n;\n; (note that a Constraint is a Goal but a Goal is not a Constraint.\n;  Constraint implementations currently use this more restrained type. See `and-foldl`\n;  and `update-constraints`.)\n\n; Requirements for type constraints:\n; 1. Must be positive, not negative. not-pairo wouldn't work.\n; 2. Each type must have infinitely many possible values to avoid\n;      incorrectness in combination with disequality constraints, like:\n;      (fresh (x) (booleano x) (=/= x #t) (=/= x #f))\n(define type-constraint\n  (lambda (type-pred type-id)\n    (lambda (u)\n      (lambdag@ (st)\n        (let ((term (walk u (state-S st))))\n          (cond\n            ((type-pred term) st)\n            ((var? term)\n             (let* ((c (lookup-c term st))\n                   (T (c-T c)))\n               (cond\n                 ((eq? T type-id) st)\n                 ((not T) (set-c term (c-with-T c type-id) st))\n                 (else #f))))\n            (else #f)))))))\n\n(define symbolo (type-constraint symbol? 'symbolo))\n(define numbero (type-constraint number? 'numbero))\n\n(define (add-to-D st v d)\n  (let* ((c (lookup-c v st))\n         (c^ (c-with-D c (cons d (c-D c)))))\n    (set-c v c^ st)))\n\n(define =/=*\n  (lambda (S+)\n    (lambdag@ (st)\n      (let-values (((S added) (unify* S+ (subst-with-scope (state-S st) nonlocal-scope))))\n        (cond\n          ((not S) st)\n          ((null? added) #f)\n          (else\n            ; Choose one of the disequality elements (el) to attach the constraint to. Only\n            ; need to choose one because all must fail to cause the constraint to fail.\n            (let ((el (car added)))\n              (let ((st (add-to-D st (car el) added)))\n                (if (var? (cdr el))\n                  (add-to-D st (cdr el) added)\n                  st)))))))))\n\n(define =/=\n  (lambda (u v)\n    (=/=* `((,u . ,v)))))\n\n(define absento\n  (lambda (ground-atom term)\n    (lambdag@ (st)\n      (let ((term (walk term (state-S st))))\n        (cond\n          ((pair? term)\n           (let ((st^ ((absento ground-atom (car term)) st)))\n             (and st^ ((absento ground-atom (cdr term)) st^))))\n          ((eqv? term ground-atom) #f)\n          ((var? term)\n           (let* ((c (lookup-c term st))\n                  (A (c-A c)))\n             (if (memv ground-atom A)\n               st\n               (let ((c^ (c-with-A c (cons ground-atom A))))\n                 (set-c term c^ st)))))\n          (else st))))))\n\n; Fold lst with proc and initial value init. If proc ever returns #f,\n; return with #f immediately. Used for applying a series of constraints\n; to a state, failing if any operation fails.\n(define (and-foldl proc init lst)\n  (if (null? lst)\n    init\n    (let ([res (proc (car lst) init)])\n      (and res (and-foldl proc res (cdr lst))))))\n\n(define ==\n  (lambda (u v)\n    (lambdag@ (st)\n      (let-values (((S added) (unify u v (state-S st))))\n        (if S\n          (and-foldl update-constraints (state S (state-C st)) added)\n          #f)))))\n\n\n; Not fully optimized. Could do absento update with fewer hash-refs / hash-sets.\n(define update-constraints\n  (lambda (a st)\n    (let ([old-c (lookup-c (lhs a) st)])\n      (if (eq? old-c empty-c)\n        st\n        (let ((st (remove-c (lhs a) st)))\n         (and-foldl (lambda (op st) (op st)) st\n          (append\n            (if (eq? (c-T old-c) 'symbolo)\n              (list (symbolo (rhs a)))\n              '())\n            (if (eq? (c-T old-c) 'numbero)\n              (list (numbero (rhs a)))\n              '())\n            (map (lambda (atom) (absento atom (rhs a))) (c-A old-c))\n            (map (lambda (d) (=/=* d)) (c-D old-c)))))))))\n\n\n; Reification\n\n(define walk*\n  (lambda (v S)\n    (let ((v (walk v S)))\n      (cond\n        ((var? v) v)\n        ((pair? v)\n         (cons (walk* (car v) S) (walk* (cdr v) S)))\n        (else v)))))\n\n(define vars\n  (lambda (term acc)\n    (cond\n      ((var? term) (cons term acc))\n      ((pair? term)\n       (vars (cdr term) (vars (car term) acc)))\n      (else acc))))\n\n(define-syntax project\n  (syntax-rules ()\n    ((_ (x ...) g g* ...)\n     (lambdag@ (st)\n       (let ((x (walk* x (state-S st))) ...)\n         ((fresh () g g* ...) st))))))\n\n\n; Create a constraint store of the old representation from a state object,\n; so that we can use the old reifier. Only accumulates constraints related\n; to the variable being reified which makes things a bit faster.\n(define c-from-st\n  (lambda (st x)\n    (let ((vs (vars (walk* x (state-S st)) '())))\n      (foldl\n        (lambda (v c-store)\n          (let ((c (lookup-c v st)))\n            (let ((S (state-S st))\n                  (D (c->D c-store))\n                  (Y (c->Y c-store))\n                  (N (c->N c-store))\n                  (T (c->T c-store))\n                  (T^ (c-T c))\n                  (D^ (c-D c))\n                  (A^ (c-A c)))\n              `(,S\n                 ,(append D^ D)\n                 ,(if (eq? T^ 'symbolo)\n                    (cons v Y)\n                    Y)\n                 ,(if (eq? T^ 'numbero)\n                    (cons v N)\n                    N)\n                 ,(append\n                    (map (lambda (atom) (cons atom v)) A^)\n                    T)))))\n        `(,(state-S st) () () () ())\n        (remove-duplicates vs)))))\n\n(define reify\n  (lambda (x)\n    (lambda (st)\n      (let ((c (c-from-st st x)))\n        (let ((c (cycle c)))\n          (let* ((S (c->S c))\n                 (D (walk* (c->D c) S))\n                 (Y (walk* (c->Y c) S))\n                 (N (walk* (c->N c) S))\n                 (T (walk* (c->T c) S)))\n            (let ((v (walk* x S)))\n              (let ((R (reify-S v (subst empty-subst-map nonlocal-scope))))\n                (reify+ v R\n                        (let ((D (remp\n                                   (lambda (d)\n                                     (let ((dw (walk* d S)))\n                                       (anyvar? dw R)))\n                                   (rem-xx-from-d c))))\n                          (rem-subsumed D))\n                        (remp\n                          (lambda (y) (var? (walk y R)))\n                          Y)\n                        (remp\n                          (lambda (n) (var? (walk n R)))\n                          N)\n                        (remp (lambda (t)\n                                (anyvar? t R)) T))))))))))\n\n\n; Bits from the old constraint implementation, still used for reification.\n\n; In this part of the code, c refers to the\n; old constraint store with components:\n; S - substitution\n; D - disequality constraints\n; Y - symbolo\n; N - numbero\n; T - absento\n\n(define c->S (lambda (c) (car c)))\n(define c->D (lambda (c) (cadr c)))\n(define c->Y (lambda (c) (caddr c)))\n(define c->N (lambda (c) (cadddr c)))\n(define c->T (lambda (c) (cadddr (cdr c))))\n\n; Syntax for reification goal objects using the old constraint store\n(define-syntax lambdar@\n  (syntax-rules (:)\n    ((_ (c) e) (lambda (c) e))\n    ((_ (c : S D Y N T) e)\n     (lambda (c)\n       (let ((S (c->S c)) (D (c->D c)) (Y (c->Y c)) (N (c->N c)) (T (c->T c)))\n         e)))))\n\n(define tagged?\n  (lambda (S Y y^)\n    (exists (lambda (y) (eqv? (walk y S) y^)) Y)))\n\n(define untyped-var?\n  (lambda (S Y N t^)\n    (let ((in-type? (lambda (y) (var-eq? (walk y S) t^))))\n      (and (var? t^)\n           (not (exists in-type? Y))\n           (not (exists in-type? N))))))\n\n(define reify-S\n  (lambda (v S)\n    (let ((v (walk v S)))\n      (cond\n        ((var? v)\n         (let ((n (subst-length S)))\n           (let ((name (reify-name n)))\n             (subst-add S v name))))\n        ((pair? v)\n         (let ((S (reify-S (car v) S)))\n           (reify-S (cdr v) S)))\n        (else S)))))\n\n(define reify-name\n  (lambda (n)\n    (string->symbol\n      (string-append \"_\" \".\" (number->string n)))))\n\n(define drop-dot\n  (lambda (X)\n    (map (lambda (t)\n           (let ((a (lhs t))\n                 (d (rhs t)))\n             `(,a ,d)))\n         X)))\n\n(define sorter\n  (lambda (ls)\n    (list-sort lex<=? ls)))\n\n(define lex<=?\n  (lambda (x y)\n    (string<=? (datum->string x) (datum->string y))))\n\n(define datum->string\n  (lambda (x)\n    (call-with-string-output-port\n      (lambda (p) (display x p)))))\n\n(define anyvar?\n  (lambda (u r)\n    (cond\n      ((pair? u)\n       (or (anyvar? (car u) r)\n           (anyvar? (cdr u) r)))\n      (else (var? (walk u r))))))\n\n(define member*\n  (lambda (u v)\n    (cond\n      ((equal? u v) #t)\n      ((pair? v)\n       (or (member* u (car v)) (member* u (cdr v))))\n      (else #f))))\n\n(define drop-N-b/c-const\n  (lambdar@ (c : S D Y N T)\n    (let ((const? (lambda (n)\n                    (not (var? (walk n S))))))\n      (cond\n        ((find const? N) =>\n           (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n        (else c)))))\n\n(define drop-Y-b/c-const\n  (lambdar@ (c : S D Y N T)\n    (let ((const? (lambda (y)\n                    (not (var? (walk y S))))))\n      (cond\n        ((find const? Y) =>\n           (lambda (y) `(,S ,D ,(remq1 y Y) ,N ,T)))\n        (else c)))))\n\n(define remq1\n  (lambda (elem ls)\n    (cond\n      ((null? ls) '())\n      ((eq? (car ls) elem) (cdr ls))\n      (else (cons (car ls) (remq1 elem (cdr ls)))))))\n\n(define same-var?\n  (lambda (v)\n    (lambda (v^)\n      (and (var? v) (var? v^) (var-eq? v v^)))))\n\n(define find-dup\n  (lambda (f S)\n    (lambda (set)\n      (let loop ((set^ set))\n        (cond\n          ((null? set^) #f)\n          (else\n           (let ((elem (car set^)))\n             (let ((elem^ (walk elem S)))\n               (cond\n                 ((find (lambda (elem^^)\n                          ((f elem^) (walk elem^^ S)))\n                        (cdr set^))\n                  elem)\n                 (else (loop (cdr set^))))))))))))\n\n(define drop-N-b/c-dup-var\n  (lambdar@ (c : S D Y N T)\n    (cond\n      (((find-dup same-var? S) N) =>\n       (lambda (n) `(,S ,D ,Y ,(remq1 n N) ,T)))\n      (else c))))\n\n(define drop-Y-b/c-dup-var\n  (lambdar@ (c : S D Y N T)\n    (cond\n      (((find-dup same-var? S) Y) =>\n       (lambda (y)\n         `(,S ,D ,(remq1 y Y) ,N ,T)))\n      (else c))))\n\n(define var-type-mismatch?\n  (lambda (S Y N t1^ t2^)\n    (cond\n      ((num? S N t1^) (not (num? S N t2^)))\n      ((sym? S Y t1^) (not (sym? S Y t2^)))\n      (else #f))))\n\n(define term-ununifiable?\n  (lambda (S Y N t1 t2)\n    (let ((t1^ (walk t1 S))\n          (t2^ (walk t2 S)))\n      (cond\n        ((or (untyped-var? S Y N t1^) (untyped-var? S Y N t2^)) #f)\n        ((var? t1^) (var-type-mismatch? S Y N t1^ t2^))\n        ((var? t2^) (var-type-mismatch? S Y N t2^ t1^))\n        ((and (pair? t1^) (pair? t2^))\n         (or (term-ununifiable? S Y N (car t1^) (car t2^))\n             (term-ununifiable? S Y N (cdr t1^) (cdr t2^))))\n        (else (not (eqv? t1^ t2^)))))))\n\n(define T-term-ununifiable?\n  (lambda (S Y N)\n    (lambda (t1)\n      (let ((t1^ (walk t1 S)))\n        (letrec\n            ((t2-check\n              (lambda (t2)\n                (let ((t2^ (walk t2 S)))\n                  (if (pair? t2^)\n                    (and\n                       (term-ununifiable? S Y N t1^ t2^)\n                       (t2-check (car t2^))\n                       (t2-check (cdr t2^)))\n                    (term-ununifiable? S Y N t1^ t2^))))))\n          t2-check)))))\n\n(define num?\n  (lambda (S N n)\n    (let ((n (walk n S)))\n      (cond\n        ((var? n) (tagged? S N n))\n        (else (number? n))))))\n\n(define sym?\n  (lambda (S Y y)\n    (let ((y (walk y S)))\n      (cond\n        ((var? y) (tagged? S Y y))\n        (else (symbol? y))))))\n\n(define drop-T-b/c-Y-and-N\n  (lambdar@ (c : S D Y N T)\n    (let ((drop-t? (T-term-ununifiable? S Y N)))\n      (cond\n        ((find (lambda (t) ((drop-t? (lhs t)) (rhs t))) T) =>\n         (lambda (t) `(,S ,D ,Y ,N ,(remq1 t T))))\n        (else c)))))\n\n(define move-T-to-D-b/c-t2-atom\n  (lambdar@ (c : S D Y N T)\n    (cond\n      ((exists (lambda (t)\n               (let ((t2^ (walk (rhs t) S)))\n                 (cond\n                   ((and (not (untyped-var? S Y N t2^))\n                         (not (pair? t2^)))\n                    (let ((T (remq1 t T)))\n                      `(,S ((,t) . ,D) ,Y ,N ,T)))\n                   (else #f))))\n             T))\n      (else c))))\n\n(define terms-pairwise=?\n  (lambda (pr-a^ pr-d^ t-a^ t-d^ S)\n    (or\n     (and (term=? pr-a^ t-a^ S)\n          (term=? pr-d^ t-a^ S))\n     (and (term=? pr-a^ t-d^ S)\n          (term=? pr-d^ t-a^ S)))))\n\n(define T-superfluous-pr?\n  (lambda (S Y N T)\n    (lambda (pr)\n      (let ((pr-a^ (walk (lhs pr) S))\n            (pr-d^ (walk (rhs pr) S)))\n        (cond\n          ((exists\n               (lambda (t)\n                 (let ((t-a^ (walk (lhs t) S))\n                       (t-d^ (walk (rhs t) S)))\n                   (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S)))\n             T)\n           (for-all\n            (lambda (t)\n              (let ((t-a^ (walk (lhs t) S))\n                    (t-d^ (walk (rhs t) S)))\n                (or\n                 (not (terms-pairwise=? pr-a^ pr-d^ t-a^ t-d^ S))\n                 (untyped-var? S Y N t-d^)\n                 (pair? t-d^))))\n            T))\n          (else #f))))))\n\n(define drop-from-D-b/c-T\n  (lambdar@ (c : S D Y N T)\n    (cond\n      ((find\n           (lambda (d)\n             (exists\n                 (T-superfluous-pr? S Y N T)\n               d))\n         D) =>\n         (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n      (else c))))\n\n(define drop-t-b/c-t2-occurs-t1\n  (lambdar@ (c : S D Y N T)\n    (cond\n      ((find (lambda (t)\n               (let ((t-a^ (walk (lhs t) S))\n                     (t-d^ (walk (rhs t) S)))\n                 (mem-check t-d^ t-a^ S)))\n             T) =>\n             (lambda (t)\n               `(,S ,D ,Y ,N ,(remq1 t T))))\n      (else c))))\n\n(define split-t-move-to-d-b/c-pair\n  (lambdar@ (c : S D Y N T)\n    (cond\n      ((exists\n         (lambda (t)\n           (let ((t2^ (walk (rhs t) S)))\n             (cond\n               ((pair? t2^) (let ((ta `(,(lhs t) . ,(car t2^)))\n                                  (td `(,(lhs t) . ,(cdr t2^))))\n                              (let ((T `(,ta ,td . ,(remq1 t T))))\n                                `(,S ((,t) . ,D) ,Y ,N ,T))))\n               (else #f))))\n         T))\n      (else c))))\n\n(define find-d-conflict\n  (lambda (S Y N)\n    (lambda (D)\n      (find\n        (lambda (d)\n          (exists (lambda (pr)\n                    (term-ununifiable? S Y N (lhs pr) (rhs pr)))\n                  d))\n        D))))\n\n(define drop-D-b/c-Y-or-N\n  (lambdar@ (c : S D Y N T)\n    (cond\n      (((find-d-conflict S Y N) D) =>\n       (lambda (d) `(,S ,(remq1 d D) ,Y ,N ,T)))\n      (else c))))\n\n(define cycle\n  (lambdar@ (c)\n    (let loop ((c^ c)\n               (fns^ (LOF))\n               (n (length (LOF))))\n      (cond\n        ((zero? n) c^)\n        ((null? fns^) (loop c^ (LOF) n))\n        (else\n         (let ((c^^ ((car fns^) c^)))\n           (cond\n             ((not (eq? c^^ c^))\n              (loop c^^ (cdr fns^) (length (LOF))))\n             (else (loop c^ (cdr fns^) (sub1 n))))))))))\n\n(define mem-check\n  (lambda (u t S)\n    (let ((t (walk t S)))\n      (cond\n        ((pair? t)\n         (or (term=? u t S)\n             (mem-check u (car t) S)\n             (mem-check u (cdr t) S)))\n        (else (term=? u t S))))))\n\n(define term=?\n  (lambda (u t S)\n    (let-values (((S added) (unify u t (subst-with-scope S nonlocal-scope))))\n      (and S (null? added)))))\n\n(define ground-non-?\n  (lambda (pred)\n    (lambda (u S)\n      (let ((u (walk u S)))\n        (cond\n          ((var? u) #f)\n          (else (not (pred u))))))))\n\n(define ground-non-symbol?\n  (ground-non-? symbol?))\n\n(define ground-non-number?\n  (ground-non-? number?))\n\n(define succeed (== #f #f))\n\n(define fail (== #f #t))\n\n(define ==fail-check\n  (lambda (S0 D Y N T)\n    (let ([S0 (subst-with-scope S0 nonlocal-scope)])\n      (cond\n        ((atomic-fail-check S0 Y ground-non-symbol?) #t)\n        ((atomic-fail-check S0 N ground-non-number?) #t)\n        ((symbolo-numbero-fail-check S0 Y N) #t)\n        ((=/=-fail-check S0 D) #t)\n        ((absento-fail-check S0 T) #t)\n        (else #f)))))\n\n(define atomic-fail-check\n  (lambda (S A pred)\n    (exists (lambda (a) (pred (walk a S) S)) A)))\n\n(define symbolo-numbero-fail-check\n  (lambda (S A N)\n    (let ((N (map (lambda (n) (walk n S)) N)))\n      (exists (lambda (a) (exists (same-var? (walk a S)) N))\n        A))))\n\n(define absento-fail-check\n  (lambda (S T)\n    (exists (lambda (t) (mem-check (lhs t) (rhs t) S)) T)))\n\n(define =/=-fail-check\n  (lambda (S D)\n    (exists (d-fail-check S) D)))\n\n(define d-fail-check\n  (lambda (S)\n    (lambda (d)\n      (let-values (((S added) (unify* d S)))\n        (and S (null? added))))))\n\n(define reify+\n  (lambda (v R D Y N T)\n    (form (walk* v R)\n          (walk* D R)\n          (walk* Y R)\n          (walk* N R)\n          (rem-subsumed-T (walk* T R)))))\n\n(define form\n  (lambda (v D Y N T)\n    (let ((fd (sort-D D))\n          (fy (sorter Y))\n          (fn (sorter N))\n          (ft (sorter T)))\n      (let ((fd (if (null? fd) fd\n                    (let ((fd (drop-dot-D fd)))\n                      `((=/= . ,fd)))))\n            (fy (if (null? fy) fy `((sym . ,fy))))\n            (fn (if (null? fn) fn `((num . ,fn))))\n            (ft (if (null? ft) ft\n                    (let ((ft (drop-dot ft)))\n                      `((absento . ,ft))))))\n        (cond\n          ((and (null? fd) (null? fy)\n                (null? fn) (null? ft))\n           v)\n          (else (append `(,v) fd fn fy ft)))))))\n\n(define sort-D\n  (lambda (D)\n    (sorter\n     (map sort-d D))))\n\n(define sort-d\n  (lambda (d)\n    (list-sort\n       (lambda (x y)\n         (lex<=? (car x) (car y)))\n       (map sort-pr d))))\n\n(define drop-dot-D\n  (lambda (D)\n    (map drop-dot D)))\n\n(define lex<-reified-name?\n  (lambda (r)\n    (charstring r) 0)\n     #\\_)))\n\n(define sort-pr\n  (lambda (pr)\n    (let ((l (lhs pr))\n          (r (rhs pr)))\n      (cond\n        ((lex<-reified-name? r) pr)\n        ((lex<=? r l) `(,r . ,l))\n        (else pr)))))\n\n(define rem-subsumed\n  (lambda (D)\n    (let rem-subsumed ((D D) (d^* '()))\n      (cond\n        ((null? D) d^*)\n        ((or (subsumed? (car D) (cdr D))\n             (subsumed? (car D) d^*))\n         (rem-subsumed (cdr D) d^*))\n        (else (rem-subsumed (cdr D)\n                (cons (car D) d^*)))))))\n\n(define subsumed?\n  (lambda (d d*)\n    (cond\n      ((null? d*) #f)\n      (else\n        (let-values (((S ignore) (unify* d (subst empty-subst-map nonlocal-scope))))\n          (let-values (((S+ added) (unify* (car d*) S)))\n            (or\n              (and S+ (null? added))\n              (subsumed? d (cdr d*)))))))))\n\n\n\n(define rem-xx-from-d\n  (lambdar@ (c : S D Y N T)\n    (let ((D (walk* D S)))\n      (remp not\n            (map (lambda (d)\n                   (let-values (((S0 ignore) (unify* d S)))\n                     (cond\n                       ((not S0) #f)\n                       ((==fail-check S0 '() Y N T) #f)\n                       (else\n                         (let-values (((S added) (unify* d (subst empty-subst-map nonlocal-scope))))\n                           added)))))\n                 D)))))\n\n(define rem-subsumed-T\n  (lambda (T)\n    (let rem-subsumed ((T T) (T^ '()))\n      (cond\n        ((null? T) T^)\n        (else\n         (let ((lit (lhs (car T)))\n               (big (rhs (car T))))\n           (cond\n             ((or (subsumed-T? lit big (cdr T))\n                  (subsumed-T? lit big T^))\n              (rem-subsumed (cdr T) T^))\n             (else (rem-subsumed (cdr T)\n                     (cons (car T) T^))))))))))\n\n(define subsumed-T?\n  (lambda (lit big T)\n    (cond\n      ((null? T) #f)\n      (else\n       (let ((lit^ (lhs (car T)))\n             (big^ (rhs (car T))))\n         (or\n           (and (eq? big big^) (member* lit^ lit))\n           (subsumed-T? lit big (cdr T))))))))\n\n(define LOF\n  (lambda ()\n    `(,drop-N-b/c-const ,drop-Y-b/c-const ,drop-Y-b/c-dup-var\n      ,drop-N-b/c-dup-var ,drop-D-b/c-Y-or-N ,drop-T-b/c-Y-and-N\n      ,move-T-to-D-b/c-t2-atom ,split-t-move-to-d-b/c-pair\n      ,drop-from-D-b/c-T ,drop-t-b/c-t2-occurs-t1)))\n\n"
  },
  {
    "path": "medikanren/open-api/ISB-KG-api.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require net/url)\n(require net/http-client)\n(require json)\n\n(define api-query\n  (lambda (api-url)\n    (call/input-url\n     (string->url api-url)\n     get-pure-port\n     (lambda (port)\n       (string->jsexpr (port->string port))))))\n\n;; ISB KP\n(define url-ISB\n  \"https://biothings.ncats.io/tcga_mut_freq_kp/metadata/fields\")\n\n(define ISB-query1\n  \"https://biothings.ncats.io/drug_response_kp/query?q=subject.SYMBOL:EGFR%20AND%20association.effect_size:%3C0%20AND%20association.pvalue:%3C0.05%20AND%20association.median_ic50_mut:%3C0&size=1000\")\n\n(api-query ISB-query1)\n\n#|\nTODO: modify Greg's code below to query ISB with structured\ncontents Subject, Object, pvalue, ic50\n\n;; Broad Institute KP\n(define url.broad\n  \"https://translator.broadinstitute.org/molepro_reasoner\")\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n(define path.predicates\n  \"/predicates\")\n(define path.query\n  \"/query\")\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (define-values (status headers in)\n    (if (void? optional-post-jsexpr)\n      (http-sendrecv/url\n        (string->url url-string)\n        #:method \"GET\")\n      (http-sendrecv/url\n        (string->url url-string)\n        #:method \"POST\"\n        #:data (jsexpr->string optional-post-jsexpr)\n        #:headers '(\"Content-Type: application/json; charset=utf-8\"))))\n  (hash 'status status\n        'headers headers\n        'response (string->jsexpr (port->string in))))\n\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n;; test predicates available on Broad Institute KG\n;(pretty-print\n  ;(api-query (string-append url.broad path.predicates)))\n\n;(pretty-print\n  ;(api-query (string-append url.broad path.query)\n             ;(js-query (list (hash 'id        \"e00\"\n                                   ;'source_id \"n00\"\n                                   ;'target_id \"n01\"\n                                   ;'type      \"affects\"))\n                       ;(list (hash 'curie \"CID:2244\"\n                                   ;'id    \"n00\"\n                                   ;'type  \"chemical_substance\")\n                             ;(hash 'id    \"n01\"\n                                   ;'type  \"gene\")))))\n\n;(pretty-print\n  ;(api-query (string-append url.unsecret path.predicates)))\n\n(pretty-print\n  (api-query (string-append url.unsecret path.query)\n             (js-query (list (hash 'id        \"e00\"\n                                   'source_id \"n00\"\n                                   'target_id \"n01\"\n                                   'type      \"affects\"))\n                       (list (hash 'curie \"CHEBI:15365\"\n                                   'id    \"n00\"\n                                   'type  \"chemical_substance\")\n                             (hash 'id    \"n01\"\n                                   'type  \"gene\")))))\n\n\ndef buildQuery(genes):\n    # empty response\n    response = { \"query_graph\": dict(),\n                 \"knowledge_graph\": dict(),\n                 \"response\": dict()\n               }\n\n    # empty query graph\n    response[\"query_graph\"] = { \"edges\": [],\n                                \"nodes\": []\n                              }\n\n    # empty knowledge graph\n    response[\"knowledge_graph\"] = { \"edges\": [],\n                                    \"nodes\": []\n                                  }\n\n    # empty response graph\n    response[\"results\"] = { \"node_bindings\": [],\n                            \"edge_bindings\": []\n                          }\n\n    # nodes\n    nodeCount = 0\n    # edges\n    edgeCount = 0\n\n    # add in evidence genes\n    \n    for g in genes:\n        response['query_graph']['nodes'].append({ 'id':'n{}'.format(nodeCount),\n                                                  'type':'Gene',\n                                                  'name':'{}'.format(g[0]),\n                                                  'curie':'{}'.format(g[1])\n                                               })\n        nodeCount += 1\n\n    # grouping for genes\n    response['query_graph']['nodes'].append({ 'id':'n{}'.format(nodeCount),\n                                              'type':'gene_grouping'\n                                           })\n    nodeCount += 1\n    \n    # link genes over grouping\n    for n in response['query_graph']['nodes'][:-1]:\n        response['query_graph']['edges'].append({ 'id':'e{}'.format(edgeCount),\n                                                  'type':'part_of',\n                                                  'curie':['SEMMEDDB:PART_OF'],\n                                                  'source_id':n['id'],\n                                                  'target_id':'n{}'.format(nodeCount-1)\n                                               })\n        edgeCount += 1\n\n    # patient node\n    response['query_graph']['nodes'].append({ 'id':'n{}'.format(nodeCount),\n                                              'type':'patient',\n                                              'curie':['UMLSSC:T101']\n                                           })\n    nodeCount += 1\n\n    # link gene group to patient\n    response['query_graph']['edges'].append({ 'id':'e{}'.format(edgeCount),\n                                              'type':'expressed_in',\n                                              'curie':['RO:0002206'],\n                                              'source_id':'n{}'.format(nodeCount-2),\n                                              'target_id':'n{}'.format(nodeCount-1)\n                                           })\n    edgeCount += 1\n\n    # survival node\n    response['query_graph']['nodes'].append({ 'id': 'n{}'.format(nodeCount),\n                                              'type': 'PhenotypicFeature',\n                                              'curie': 'CHPDART:SURVIVAL',\n                                              'operator': '>=',\n                                              'value': '1000'\n                                           })\n    nodeCount += 1\n\n    # link patient to survival\n    response['query_graph']['edges'].append({ 'id':'e{}'.format(edgeCount),\n                                              'type':'has_phenotype',\n                                              'source_id':'n{}'.format(nodeCount-2),\n                                              'target_id':'n{}'.format(nodeCount-1)\n                                           })\n    edgeCount += 1\n\n    # BKB target\n    response['probability_targets'] = [('Survival_Time', '>=', 1000)]\n\n    return response\n\n\n\n\n\n\n|#\n"
  },
  {
    "path": "medikanren/open-api/TranslatorReasonersAPI.json",
    "content": "{\n    \"openapi\": \"3.0.1\",\n    \"info\": {\n        \"description\": \"OpenAPI for NCATS Biomedical Translator Reasoners\",\n        \"version\": \"1.0.0-beta\",\n        \"title\": \"OpenAPI for NCATS Biomedical Translator Reasoners\",\n        \"contact\": {\n            \"email\": \"edeutsch@systemsbiology.org\"\n        },\n        \"license\": {\n            \"name\": \"Apache 2.0\",\n            \"url\": \"http://www.apache.org/licenses/LICENSE-2.0.html\"\n        },\n        \"termsOfService\": \"INSERT-URL-HERE\"\n    },\n    \"externalDocs\": {\n        \"description\": \"Documentation for the NCATS Biomedical Translator Reasoners web services\",\n        \"url\": \"https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI\"\n    },\n    \"tags\": [\n        {\n            \"name\": \"predicates\",\n            \"description\": \"Get supported relationships by source and target\",\n            \"externalDocs\": {\n                \"description\": \"Documentation for the reasoner predicates function\",\n                \"url\": \"http://reasonerhost.ncats.io/overview.html#predicates\"\n            }\n        },\n        {\n            \"name\": \"query\",\n            \"description\": \"Query reasoner using a predefined question type\",\n            \"externalDocs\": {\n                \"description\": \"Documentation for the reasoner query function\",\n                \"url\": \"http://reasonerhost.ncats.io/overview.html#query\"\n            }\n        },\n        {\n            \"name\": \"translator\"\n        },\n        {\n            \"name\": \"reasoner\"\n        }\n    ],\n    \"paths\": {\n        \"/predicates\": {\n            \"get\": {\n                \"tags\": [\n                    \"predicates\"\n                ],\n                \"summary\": \"Get supported relationships by source and target\",\n                \"responses\": {\n                    \"200\": {\n                        \"description\": \"Predicates by source and target\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"description\": \"Source map\",\n                                    \"type\": \"object\",\n                                    \"additionalProperties\": {\n                                        \"description\": \"Target map\",\n                                        \"type\": \"object\",\n                                        \"additionalProperties\": {\n                                            \"description\": \"Array of predicates\",\n                                            \"type\": \"array\",\n                                            \"items\": {\n                                                \"type\": \"string\"\n                                            }\n                                        }\n                                    },\n                                    \"example\": {\n                                        \"biolink:ChemicalSubstance\": {\n                                            \"biolink:Gene\": [\n                                                \"biolink:directly_interacts_with\",\n                                                \"biolink:decreases_activity_of\"\n                                            ]\n                                        }\n                                    }\n                                }\n                            }\n                        }\n                    }\n                }\n            }\n        },\n        \"/query\": {\n            \"post\": {\n                \"tags\": [\n                    \"query\"\n                ],\n                \"summary\": \"Query reasoner via one of several inputs\",\n                \"description\": \"\",\n                \"operationId\": \"query\",\n                \"requestBody\": {\n                    \"description\": \"Query information to be submitted\",\n                    \"required\": true,\n                    \"content\": {\n                        \"application/json\": {\n                            \"schema\": {\n                                \"$ref\": \"#/components/schemas/Query\"\n                            }\n                        }\n                    }\n                },\n                \"responses\": {\n                    \"200\": {\n                        \"description\": \"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized.\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"$ref\": \"#/components/schemas/Response\"\n                                }\n                            }\n                        }\n                    },\n                    \"400\": {\n                        \"description\": \"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized).\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"type\": \"string\"\n                                }\n                            }\n                        }\n                    },\n                    \"500\": {\n                        \"description\": \"Internal server error.\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"type\": \"string\"\n                                }\n                            }\n                        }\n                    },\n                    \"501\": {\n                        \"description\": \"Not implemented.\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"type\": \"string\"\n                                }\n                            }\n                        }\n                    }\n                },\n                \"x-swagger-router-controller\": \"swagger_server.controllers.query_controller\"\n            }\n        }\n    },\n    \"components\": {\n        \"schemas\": {\n            \"Query\": {\n                \"description\": \"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.\",\n                \"x-body-name\": \"request_body\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"message\": {\n                        \"$ref\": \"#/components/schemas/Message\",\n                        \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"message\"\n                ]\n            },\n            \"Response\": {\n                \"type\": \"object\",\n                \"description\": \"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.\",\n                \"properties\": {\n                    \"message\": {\n                        \"description\": \"Contains the knowledge of the response (query graph, knowledge graph, and results).\",\n                        \"$ref\": \"#/components/schemas/Message\"\n                    },\n                    \"status\": {\n                        \"description\": \"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable\",\n                        \"type\": \"string\",\n                        \"example\": \"Success\",\n                        \"nullable\": true\n                    },\n                    \"description\": {\n                        \"description\": \"A brief human-readable description of the outcome\",\n                        \"type\": \"string\",\n                        \"example\": \"Success. 42 results found.\",\n                        \"nullable\": true\n                    },\n                    \"logs\": {\n                        \"description\": \"Log entries containing errors, warnings, debugging information, etc\",\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/LogEntry\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"message\"\n                ]\n            },\n            \"Message\": {\n                \"description\": \"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"results\": {\n                        \"description\": \"List of all returned Result objects for the query posed\",\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Result\"\n                        },\n                        \"nullable\": true\n                    },\n                    \"query_graph\": {\n                        \"type\": \"object\",\n                        \"description\": \"QueryGraph object that contains a serialization of a query in the form of a graph\",\n                        \"$ref\": \"#/components/schemas/QueryGraph\",\n                        \"nullable\": true\n                    },\n                    \"knowledge_graph\": {\n                        \"type\": \"object\",\n                        \"description\": \"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message\",\n                        \"$ref\": \"#/components/schemas/KnowledgeGraph\",\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": false\n            },\n            \"LogEntry\": {\n                \"description\": \"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"timestamp\": {\n                        \"type\": \"string\",\n                        \"format\": \"date-time\",\n                        \"description\": \"Timestamp in ISO 8601 format\",\n                        \"example\": \"2020-09-03T18:13:49+00:00\",\n                        \"nullable\": true\n                    },\n                    \"level\": {\n                        \"type\": \"string\",\n                        \"description\": \"Logging level\",\n                        \"enum\": [\n                            \"ERROR\",\n                            \"WARNING\",\n                            \"INFO\",\n                            \"DEBUG\"\n                        ],\n                        \"nullable\": true\n                    },\n                    \"code\": {\n                        \"type\": \"string\",\n                        \"description\": \"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed\",\n                        \"nullable\": true\n                    },\n                    \"message\": {\n                        \"type\": \"string\",\n                        \"description\": \"A human-readable log message\",\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true\n            },\n            \"Result\": {\n                \"type\": \"object\",\n                \"description\": \"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings).\",\n                \"properties\": {\n                    \"node_bindings\": {\n                        \"type\": \"object\",\n                        \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.\",\n                        \"additionalProperties\": {\n                            \"type\": \"array\",\n                            \"items\": {\n                                \"$ref\": \"#/components/schemas/NodeBinding\"\n                            }\n                        }\n                    },\n                    \"edge_bindings\": {\n                        \"type\": \"object\",\n                        \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple knowledge graph edges in the result.\",\n                        \"additionalProperties\": {\n                            \"type\": \"array\",\n                            \"items\": {\n                                \"$ref\": \"#/components/schemas/EdgeBinding\"\n                            }\n                        }\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"node_bindings\",\n                    \"edge_bindings\"\n                ]\n            },\n            \"NodeBinding\": {\n                \"type\": \"object\",\n                \"properties\": {\n                    \"id\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"description\": \"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation (such annotation is not yet fully standardized).\"\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"id\"\n                ]\n            },\n            \"EdgeBinding\": {\n                \"type\": \"object\",\n                \"description\": \"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized).\",\n                \"properties\": {\n                    \"id\": {\n                        \"type\": \"string\",\n                        \"description\": \"The key identifier of a specific KnowledgeGraph Edge.\"\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"id\"\n                ]\n            },\n            \"KnowledgeGraph\": {\n                \"type\": \"object\",\n                \"description\": \"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.\",\n                \"properties\": {\n                    \"nodes\": {\n                        \"type\": \"object\",\n                        \"description\": \"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/Node\"\n                        }\n                    },\n                    \"edges\": {\n                        \"type\": \"object\",\n                        \"description\": \"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/Edge\"\n                        }\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"nodes\",\n                    \"edges\"\n                ]\n            },\n            \"QueryGraph\": {\n                \"type\": \"object\",\n                \"description\": \"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.\",\n                \"properties\": {\n                    \"nodes\": {\n                        \"type\": \"object\",\n                        \"description\": \"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/QNode\"\n                        }\n                    },\n                    \"edges\": {\n                        \"type\": \"object\",\n                        \"description\": \"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/QEdge\"\n                        }\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"nodes\",\n                    \"edges\"\n                ]\n            },\n            \"QNode\": {\n                \"type\": \"object\",\n                \"description\": \"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.\",\n                \"properties\": {\n                    \"id\": {\n                        \"oneOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/CURIE\"\n                            },\n                            {\n                                \"type\": \"array\",\n                                \"items\": {\n                                    \"$ref\": \"#/components/schemas/CURIE\"\n                                }\n                            }\n                        ],\n                        \"example\": \"OMIM:603903\",\n                        \"description\": \"CURIE identifier for this node\",\n                        \"nullable\": true\n                    },\n                    \"category\": {\n                        \"oneOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/BiolinkEntity\"\n                            },\n                            {\n                                \"type\": \"array\",\n                                \"items\": {\n                                    \"$ref\": \"#/components/schemas/BiolinkEntity\"\n                                }\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"is_set\": {\n                        \"type\": \"boolean\",\n                        \"description\": \"Boolean that if set to true, indicates that this QNode MAY have multiple KnowledgeGraph Nodes bound to it within each Result. The nodes in a set should be considered as a set of independent nodes, rather than a set of dependent nodes, i.e., the answer would still be valid if the nodes in the set were instead returned individually. Multiple QNodes may have is_set=True. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=False, each n1 must be connected to n2. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True, each n1 must be connected to at least one n2.\",\n                        \"default\": false\n                    }\n                },\n                \"additionalProperties\": true\n            },\n            \"QEdge\": {\n                \"type\": \"object\",\n                \"description\": \"An edge in the QueryGraph used as an filter pattern specification in a query. If optional predicate or relation properties are not specified, they are assumed to be wildcard matches to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the terms provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate or relation term ('class'), or to a term which is a subclass of the QEdge specified term.\",\n                \"properties\": {\n                    \"predicate\": {\n                        \"oneOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n                            },\n                            {\n                                \"type\": \"array\",\n                                \"items\": {\n                                    \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n                                }\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"relation\": {\n                        \"type\": \"string\",\n                        \"example\": \"RO:0002447\",\n                        \"description\": \"Query constraint against the relationship type term of this edge, as originally specified by, or curated by inference from, the original external source of knowledge. Note that this should often be specified as predicate ontology term CURIE, although this may not be strictly enforced.\",\n                        \"nullable\": true\n                    },\n                    \"subject\": {\n                        \"type\": \"string\",\n                        \"example\": \"https://omim.org/entry/603903\",\n                        \"description\": \"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.\"\n                    },\n                    \"object\": {\n                        \"type\": \"string\",\n                        \"example\": \"https://www.uniprot.org/uniprot/P00738\",\n                        \"description\": \"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.\"\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"subject\",\n                    \"object\"\n                ]\n            },\n            \"Node\": {\n                \"type\": \"object\",\n                \"description\": \"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.\",\n                \"properties\": {\n                    \"name\": {\n                        \"type\": \"string\",\n                        \"example\": \"Haptoglobin\",\n                        \"description\": \"Formal name of the entity\",\n                        \"nullable\": true\n                    },\n                    \"category\": {\n                        \"oneOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/BiolinkEntity\"\n                            },\n                            {\n                                \"type\": \"array\",\n                                \"items\": {\n                                    \"$ref\": \"#/components/schemas/BiolinkEntity\"\n                                }\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of attributes describing the node\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Attribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": false\n            },\n            \"Attribute\": {\n                \"type\": \"object\",\n                \"description\": \"Generic attribute for a node or an edge that expands key-value pair concept by including a type of this attribute from a suitable ontology, a source of this attribute, and (optionally) a url with additional information about this attribute.\",\n                \"properties\": {\n                    \"name\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-readable name or label for the attribute. If appropriate, should be the name of the semantic type term.\",\n                        \"example\": \"PubMed Identifier\",\n                        \"nullable\": true\n                    },\n                    \"value\": {\n                        \"example\": 32529952,\n                        \"description\": \"Value of the attribute. May be any data type, including a list.\"\n                    },\n                    \"type\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"description\": \"CURIE of the semantic type of the attribute. For properties defined by the Biolink model this should be a biolink CURIE, otherwise, if possible, from the EDAM ontology. If a suitable identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n                        \"example\": \"EDAM:data_1187\"\n                    },\n                    \"url\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-consumable URL to link out and provide additional information about the attribute (not the node or the edge).\",\n                        \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n                        \"nullable\": true\n                    },\n                    \"source\": {\n                        \"type\": \"string\",\n                        \"description\": \"Source of the attribute, preferably as a CURIE prefix.\",\n                        \"example\": \"UniProtKB\",\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"type\",\n                    \"value\"\n                ],\n                \"additionalProperties\": false\n            },\n            \"Edge\": {\n                \"type\": \"object\",\n                \"description\": \"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \\\"thought\\\" graph resulting from a query upon the underlying knowledge source.\",\n                \"properties\": {\n                    \"predicate\": {\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"relation\": {\n                        \"type\": \"string\",\n                        \"example\": \"RO:0002447\",\n                        \"description\": \"The relationship type term of this edge, originally specified by, or curated by inference from, the original source of knowledge. This should generally be specified as predicate ontology CURIE.\",\n                        \"nullable\": true\n                    },\n                    \"subject\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"example\": \"OMIM:603903\",\n                        \"description\": \"Corresponds to the map key CURIE of the subject concept node of this relationship edge.\"\n                    },\n                    \"object\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"example\": \"UniProtKB:P00738\",\n                        \"description\": \"Corresponds to the map key CURIE of the object concept node of this relationship edge.\"\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of additional attributes for this edge\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Attribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": false,\n                \"required\": [\n                    \"subject\",\n                    \"object\"\n                ]\n            },\n            \"BiolinkEntity\": {\n                \"description\": \"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.\",\n                \"type\": \"string\",\n                \"pattern\": \"^biolink:[A-Z][a-zA-Z]*$\",\n                \"externalDocs\": {\n                    \"description\": \"Biolink model entities\",\n                    \"url\": \"https://biolink.github.io/biolink-model/docs/NamedThing.html\"\n                },\n                \"example\": \"biolink:PhenotypicFeature\"\n            },\n            \"BiolinkPredicate\": {\n                \"description\": \"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.\",\n                \"type\": \"string\",\n                \"pattern\": \"^biolink:[a-z][a-z_]*$\",\n                \"externalDocs\": {\n                    \"description\": \"Biolink model predicates\",\n                    \"url\": \"https://biolink.github.io/biolink-model/docs/related_to.html\"\n                },\n                \"example\": \"biolink:interacts_with\"\n            },\n            \"CURIE\": {\n                \"type\": \"string\",\n                \"description\": \"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.\",\n                \"externalDocs\": {\n                    \"url\": \"https://www.w3.org/TR/2010/NOTE-curie-20101216/\"\n                }\n            }\n        }\n    }\n}\n"
  },
  {
    "path": "medikanren/open-api/TranslatorReasonersAPI.yaml",
    "content": "openapi: 3.0.1\ninfo:\n  description: OpenAPI for NCATS Biomedical Translator Reasoners\n  version: 1.0.0-beta\n  title: OpenAPI for NCATS Biomedical Translator Reasoners\n  contact:\n    email: webyrd@gmail.com\n    name: William E. Byrd\n    url: https://github.com/webyrd\n  license:\n    name: Apache 2.0\n    url: http://www.apache.org/licenses/LICENSE-2.0.html\n  termsOfService: INSERT-URL-HERE\n  x-translator:\n    component: ARA\n    team:\n    - \"Unsecret Agent\"\nexternalDocs:\n  description: >-\n    Documentation for the NCATS Biomedical Translator Reasoners web services.\n  url: https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI\ntags:\n  - name: predicates\n    description: Get supported relationships by source and target\n    externalDocs:\n      description: Documentation for the reasoner predicates function\n      url: http://unsecret.ncats.io/overview.html#predicates\n  - name: query\n    description: Query reasoner using a predefined question type\n    externalDocs:\n      description: Documentation for the reasoner query function\n      url: http://unsecret.ncats.io/overview.html#query\n  - name: translator\n  - name: reasoner\npaths:\n  /predicates:\n    get:\n      tags:\n        - predicates\n      summary: Get supported relationships by source and target\n      responses:\n        '200':\n          description: Predicates by source and target\n          content:\n            application/json:\n              schema:\n                description: Source map\n                type: object\n                additionalProperties:\n                  description: Target map\n                  type: object\n                  additionalProperties:\n                    description: Array of predicates\n                    type: array\n                    items:\n                      type: string\n                example:\n                  'biolink:ChemicalSubstance':\n                    'biolink:Gene':\n                      - biolink:directly_interacts_with\n                      - biolink:decreases_activity_of\n  /query:\n    post:\n      tags:\n        - query\n      summary: Query reasoner via one of several inputs\n      description: ''\n      operationId: query\n      requestBody:\n        description: Query information to be submitted\n        required: true\n        content:\n          application/json:\n            schema:\n              $ref: '#/components/schemas/Query'\n      responses:\n        '200':\n          description: >-\n            OK. There may or may not be results. Note that some of the provided\n            identifiers may not have been recognized.\n          content:\n            application/json:\n              schema:\n                $ref: '#/components/schemas/Response'\n        '400':\n          description: >-\n            Bad request. The request is invalid according to this OpenAPI\n            schema OR a specific identifier is believed to be invalid somehow\n            (not just unrecognized).\n          content:\n            application/json:\n              schema:\n                type: string\n        '500':\n          description: >-\n            Internal server error.\n          content:\n            application/json:\n              schema:\n                type: string\n        '501':\n          description: >-\n            Not implemented.\n          content:\n            application/json:\n              schema:\n                type: string\n      x-swagger-router-controller: swagger_server.controllers.query_controller\ncomponents:\n  schemas:\n    Query:\n      description: >-\n        The Query class is used to package a user request for information. A\n        Query object consists of a required Message object with optional\n        additional properties. Additional properties are intended to convey\n        implementation-specific or query-independent parameters. For example,\n        an additional property specifying a log level could allow a user to\n        override the default log level in order to receive more fine-grained\n        log information when debugging an issue.\n      x-body-name: request_body\n      type: object\n      properties:\n        message:\n          $ref: '#/components/schemas/Message'\n          description: >-\n            The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For\n            example, the fill operation requires a non-empty query_graph field\n            as part of the Message, whereas other operations, e.g. overlay,\n            require non-empty results and knowledge_graph fields.\n      additionalProperties: true\n      required:\n        - message\n    Response:\n      type: object\n      description: >-\n        The Response object contains the main payload when a TRAPI query\n        endpoint interprets and responds to the submitted query successfully\n        (i.e., HTTP Status Code 200). The message property contains the\n        knowledge of the response (query graph, knowledge graph, and results).\n        The status, description, and logs properties provide additional details\n        about the response.\n      properties:\n        message:\n          description: >-\n            Contains the knowledge of the response (query graph, knowledge\n            graph, and results).\n          $ref: '#/components/schemas/Message'\n        status:\n          description: >-\n            One of a standardized set of short codes,\n            e.g. Success, QueryNotTraversable, KPsNotAvailable\n          type: string\n          example: Success\n          nullable: true\n        description:\n          description: A brief human-readable description of the outcome\n          type: string\n          example: Success. 42 results found.\n          nullable: true\n        logs:\n          description: >-\n            Log entries containing errors, warnings, debugging information, etc\n          type: array\n          items:\n            $ref: '#/components/schemas/LogEntry'\n          nullable: true\n      additionalProperties: true\n      required:\n        - message\n    Message:\n      description: >-\n        The message object holds the main content of a Query or a Response in\n        three properties: query_graph, results, and knowledge_graph.\n        The query_graph property contains the query configuration, the results\n        property contains any answers that are returned by the service,\n        and knowledge_graph property contains lists of edges and nodes in the\n        thought graph corresponding to this message. The content of these\n        properties is context-dependent to the encompassing object and\n        the TRAPI operation requested.\n      type: object\n      properties:\n        results:\n          description: >-\n            List of all returned Result objects for the query posed\n          type: array\n          items:\n            $ref: '#/components/schemas/Result'\n          nullable: true\n        query_graph:\n          type: object\n          description: >-\n            QueryGraph object that contains a serialization of a query in the\n            form of a graph\n          $ref: '#/components/schemas/QueryGraph'\n          nullable: true\n        knowledge_graph:\n          type: object\n          description: >-\n            KnowledgeGraph object that contains lists of nodes and edges\n            in the thought graph corresponding to the message\n          $ref: '#/components/schemas/KnowledgeGraph'\n          nullable: true\n      additionalProperties: false\n    LogEntry:\n      description: >-\n        The LogEntry object contains information useful for tracing\n        and debugging across Translator components.  Although an\n        individual component (for example, an ARA or KP) may have its\n        own logging and debugging infrastructure, this internal\n        information is not, in general, available to other components.\n        In addition to a timestamp and logging level, LogEntry\n        includes a string intended to be read by a human, along with\n        one of a standardized set of codes describing the condition of\n        the component sending the message.\n      type: object\n      properties:\n        timestamp:\n          type: string\n          format: date-time\n          description: Timestamp in ISO 8601 format\n          example: '2020-09-03T18:13:49+00:00'\n          nullable: true\n        level:\n          type: string\n          description: Logging level\n          enum:\n            - ERROR\n            - WARNING\n            - INFO\n            - DEBUG\n          nullable: true\n        code:\n          type: string\n          description: >-\n            One of a standardized set of short codes\n            e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed\n          nullable: true\n        message:\n          type: string\n          description: A human-readable log message\n          nullable: true\n      additionalProperties: true\n    Result:\n      type: object\n      description: >-\n        A Result object specifies the nodes and edges in the knowledge graph\n        that satisfy the structure or conditions of a user-submitted query\n        graph. It must contain a NodeBindings object (list of query graph node\n        to knowledge graph node mappings) and an EdgeBindings object (list of\n        query graph edge to knowledge graph edge mappings).\n      properties:\n        node_bindings:\n          type: object\n          description: >-\n            The dictionary of Input Query Graph to Result Knowledge Graph node\n            bindings where the dictionary keys are the key identifiers of the\n            Query Graph nodes and the associated values of those keys are\n            instances of NodeBinding schema type (see below). This value is an\n            array of NodeBindings since a given query node may have multiple\n            knowledge graph Node bindings in the result.\n          additionalProperties:\n            type: array\n            items:\n              $ref: '#/components/schemas/NodeBinding'\n        edge_bindings:\n          type: object\n          description: >-\n            The dictionary of Input Query Graph to Result Knowledge Graph edge\n            bindings where the dictionary keys are the key identifiers of the\n            Query Graph edges and the associated values of those keys are\n            instances of EdgeBinding schema type (see below). This value is an\n            array of EdgeBindings since a given query edge may resolve to\n            multiple knowledge graph edges in the result.\n          additionalProperties:\n            type: array\n            items:\n              $ref: '#/components/schemas/EdgeBinding'\n      additionalProperties: true\n      required:\n        - node_bindings\n        - edge_bindings\n    NodeBinding:\n      type: object\n      properties:\n        id:\n          $ref: '#/components/schemas/CURIE'\n          description: >-\n            An instance of NodeBinding is a single KnowledgeGraph Node mapping,\n            identified by the corresponding 'id' object key identifier of the\n            Node within the Knowledge Graph. Instances of NodeBinding may\n            include extra annotation (such annotation is not yet fully\n            standardized).\n      additionalProperties: true\n      required:\n        - id\n    EdgeBinding:\n      type: object\n      description: >-\n        A instance of EdgeBinding is a single KnowledgeGraph Edge mapping,\n        identified by the corresponding 'id' object key identifier of the\n        Edge within the Knowledge Graph. Instances of EdgeBinding may include\n        extra annotation (such annotation is not yet fully standardized).\n      properties:\n        id:\n          type: string\n          description: The key identifier of a specific KnowledgeGraph Edge.\n      additionalProperties: true\n      required:\n        - id\n    KnowledgeGraph:\n      type: object\n      description: >-\n        The knowledge graph associated with a set of results. The instances\n        of Node and Edge defining this graph represent instances of\n        biolink:NamedThing (concept nodes) and biolink:Association\n        (relationship edges) representing (Attribute) annotated knowledge\n        returned from the knowledge sources and inference agents wrapped by\n        the given TRAPI implementation.\n      properties:\n        nodes:\n          type: object\n          description: >-\n            Dictionary of Node instances used in the KnowledgeGraph,\n            referenced elsewhere in the TRAPI output by the dictionary key.\n          additionalProperties:\n            $ref: '#/components/schemas/Node'\n        edges:\n          type: object\n          description: >-\n            Dictionary of Edge instances used in the KnowledgeGraph,\n            referenced elsewhere in the TRAPI output by the dictionary key.\n          additionalProperties:\n            $ref: '#/components/schemas/Edge'\n      additionalProperties: true\n      required:\n        - nodes\n        - edges\n    QueryGraph:\n      type: object\n      description: >-\n        A graph representing a biomedical question. It serves as a template for\n        each result (answer), where each bound knowledge graph node/edge is\n        expected to obey the constraints of the associated query graph element.\n      properties:\n        nodes:\n          type: object\n          description: >-\n            The node specifications. The keys of this map are unique node\n            identifiers and the corresponding values include the constraints\n            on bound nodes.\n          additionalProperties:\n            $ref: '#/components/schemas/QNode'\n        edges:\n          type: object\n          description: >-\n            The edge specifications. The keys of this map are unique edge\n            identifiers and the corresponding values include the constraints\n            on bound edges, in addition to specifying the subject and object\n            QNodes.\n          additionalProperties:\n            $ref: '#/components/schemas/QEdge'\n      additionalProperties: true\n      required:\n        - nodes\n        - edges\n    QNode:\n      type: object\n      description: A node in the QueryGraph used to represent an entity in a\n        query. If a CURIE is not specified, any nodes matching the category\n        of the QNode will be returned in the Results.\n      properties:\n        id:\n          oneOf:\n            - $ref: '#/components/schemas/CURIE'\n            - type: array\n              items:\n                $ref: '#/components/schemas/CURIE'\n          example: OMIM:603903\n          description: CURIE identifier for this node\n          nullable: true\n        category:\n          oneOf:\n            - $ref: '#/components/schemas/BiolinkEntity'\n            - type: array\n              items:\n                $ref: '#/components/schemas/BiolinkEntity'\n          nullable: true\n        is_set:\n          type: boolean\n          description: >-\n            Boolean that if set to true, indicates that this QNode MAY have\n            multiple KnowledgeGraph Nodes bound to it within each Result.\n            The nodes in a set should be considered as a set of independent\n            nodes, rather than a set of dependent nodes, i.e., the answer\n            would still be valid if the nodes in the set were instead returned\n            individually. Multiple QNodes may have is_set=True. If a QNode\n            (n1) with is_set=True is connected to a QNode (n2) with\n            is_set=False, each n1 must be connected to n2. If a QNode (n1)\n            with is_set=True is connected to a QNode (n2) with is_set=True,\n            each n1 must be connected to at least one n2.\n          default: false\n      additionalProperties: true\n    QEdge:\n      type: object\n      description: >-\n        An edge in the QueryGraph used as an filter pattern specification in a\n        query. If optional predicate or relation properties are not specified,\n        they are assumed to be wildcard matches to the target knowledge space.\n        If specified, the ontological inheritance hierarchy associated with\n        the terms provided is assumed, such that edge bindings returned may be\n        an exact match to the given QEdge predicate or relation term ('class'),\n        or to a term which is a subclass of the QEdge specified term.\n      properties:\n        predicate:\n          oneOf:\n            - $ref: '#/components/schemas/BiolinkPredicate'\n            - type: array\n              items:\n                $ref: '#/components/schemas/BiolinkPredicate'\n          nullable: true\n        relation:\n          type: string\n          example: RO:0002447\n          description: >-\n            Query constraint against the relationship type term of this edge,\n            as originally specified by, or curated by inference from, the\n            original external source of knowledge. Note that this should\n            often be specified as predicate ontology term CURIE, although\n            this may not be strictly enforced.\n          nullable: true\n        subject:\n          type: string\n          example: https://omim.org/entry/603903\n          description: >-\n            Corresponds to the map key identifier of the\n            subject concept node anchoring the query filter\n            pattern for the query relationship edge.\n        object:\n          type: string\n          example: https://www.uniprot.org/uniprot/P00738\n          description: >-\n            Corresponds to the map key identifier of the\n            object concept node anchoring the query filter\n            pattern for the query relationship edge.\n      additionalProperties: true\n      required:\n        - subject\n        - object\n    Node:\n      type: object\n      description: >-\n        A node in the KnowledgeGraph which represents some biomedical\n        concept. Nodes are identified by the keys in the KnowledgeGraph\n        Node mapping.\n      properties:\n        name:\n          type: string\n          example: Haptoglobin\n          description: Formal name of the entity\n          nullable: true\n        category:\n          oneOf:\n            - $ref: '#/components/schemas/BiolinkEntity'\n            - type: array\n              items:\n                $ref: '#/components/schemas/BiolinkEntity'\n          nullable: true\n        attributes:\n          type: array\n          description: A list of attributes describing the node\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n      additionalProperties: false\n    Attribute:\n      type: object\n      description: >-\n        Generic attribute for a node or an edge that expands key-value pair\n        concept by including a type of this attribute from a suitable ontology,\n        a source of this attribute, and (optionally) a url with additional\n        information about this attribute.\n      properties:\n        name:\n          type: string\n          description: >-\n            Human-readable name or label for the attribute. If appropriate,\n            should be the name of the semantic type term.\n          example: PubMed Identifier\n          nullable: true\n        value:\n          example: 32529952\n          description: >-\n            Value of the attribute. May be any data type, including a list.\n        type:\n          $ref: '#/components/schemas/CURIE'\n          description: >-\n            CURIE of the semantic type of the attribute. For properties\n            defined by the Biolink model this should be a biolink CURIE,\n            otherwise, if possible, from the EDAM ontology. If a suitable\n            identifier does not exist, enter a descriptive phrase here and\n            submit the new type for consideration by the appropriate\n            authority.\n          example: EDAM:data_1187\n        url:\n          type: string\n          description: >-\n            Human-consumable URL to link out and provide additional information\n            about the attribute (not the node or the edge).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n        source:\n          type: string\n          description: Source of the attribute, preferably as a CURIE prefix.\n          example: UniProtKB\n          nullable: true\n      required:\n        - type\n        - value\n      additionalProperties: false\n    Edge:\n      type: object\n      description: >-\n        A specification of the semantic relationship linking two concepts\n        that are expressed as nodes in the knowledge \"thought\" graph\n        resulting from a query upon the underlying knowledge source.\n      properties:\n        predicate:\n          allOf:\n            - $ref: '#/components/schemas/BiolinkPredicate'\n          nullable: true\n        relation:\n          type: string\n          example: RO:0002447\n          description: >-\n            The relationship type term of this edge, originally specified by,\n            or curated by inference from, the original source of knowledge.\n            This should generally be specified as predicate ontology CURIE.\n          nullable: true\n        subject:\n          $ref: '#/components/schemas/CURIE'\n          example: OMIM:603903\n          description: >-\n            Corresponds to the map key CURIE of the\n            subject concept node of this relationship edge.\n        object:\n          $ref: '#/components/schemas/CURIE'\n          example: UniProtKB:P00738\n          description: >-\n            Corresponds to the map key CURIE of the\n            object concept node of this relationship edge.\n        attributes:\n          type: array\n          description: A list of additional attributes for this edge\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n      additionalProperties: false\n      required:\n        - subject\n        - object\n    BiolinkEntity:\n      description: >-\n        Compact URI (CURIE) for a Biolink class, biolink:NamedThing\n        or a child thereof. The CURIE must use the prefix 'biolink:'\n        followed by the PascalCase class name.\n      type: string\n      pattern: ^biolink:[A-Z][a-zA-Z]*$\n      externalDocs:\n        description: Biolink model entities\n        url: https://biolink.github.io/biolink-model/docs/NamedThing.html\n      example: biolink:PhenotypicFeature\n    BiolinkPredicate:\n      description: >-\n        CURIE for a Biolink 'predicate' slot, taken from the Biolink slot\n        ('is_a') hierarchy rooted in biolink:related_to (snake_case). This\n        predicate defines the Biolink relationship between the subject and\n        object nodes of a biolink:Association defining a knowledge graph edge.\n      type: string\n      pattern: ^biolink:[a-z][a-z_]*$\n      externalDocs:\n        description: Biolink model predicates\n        url: https://biolink.github.io/biolink-model/docs/related_to.html\n      example: biolink:interacts_with\n    CURIE:\n      type: string\n      description: >-\n        A Compact URI, consisting of a prefix and a reference separated\n        by a colon, such as UniProtKB:P00738. Via an external context\n        definition, the CURIE prefix and colon may be replaced by a URI\n        prefix, such as http://identifiers.org/uniprot/, to form a full\n        URI.\n      externalDocs:\n        url: https://www.w3.org/TR/2010/NOTE-curie-20101216/\n"
  },
  {
    "path": "medikanren/open-api/api-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../mk.rkt\" json net/url)\n(require \"../common.rkt\")\n\n(define (js-count js)\n  (cond ((pair? js) (foldl + 0 (map js-count js)))\n        ((hash? js) (foldl + 0 (hash-map js (lambda (k v) (js-count v)))))\n        (else       1)))\n\n;; BKB Pathway Provider (currently uses a non-standard query path)\n(define url.bkbp-query\n  \"http://chp.thayer.dartmouth.edu/submitQuery/\")\n\n;; Broad Institute KP\n(define url.broad\n  \"https://translator.broadinstitute.org/molepro/trapi/v1.0\")\n\n;; Broad Institute KP specific for CHEMBL queries\n(define url.broad_chembl\n  \"https://translator.broadinstitute.org/chembl\")\n\n(define chembl-drug-indications/transform\n  \"/indications/transform\")\n\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n(define path.predicates\n  \"/predicates\")\n(define path.query\n  \"/query\")\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (define-values (status headers in)\n    (time (if (void? optional-post-jsexpr)\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"GET\")\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"POST\"\n              #:data (jsexpr->string optional-post-jsexpr)\n              #:headers '(\"Content-Type: application/json; charset=utf-8\")))))\n  (define response-string (time (port->string in)))\n  ;(pretty-print `(,status ,headers ,response-string))\n  (hash 'status status\n        'headers headers\n        'response (string->jsexpr response-string)))\n\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n(define (js-query/bkbp edges nodes)\n  (hash 'query\n        (hash 'reasoner_id \"unsecret\"\n              'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n(define (bkbp-query edges nodes)\n  (api-query url.bkbp-query (js-query/bkbp edges nodes)))\n\n(define (bkbp-g2d e s o)  (hash 'id e  'type \"gene_to_disease_association\"      'source_id s 'target_id o))\n(define (bkbp-d2p e s o)  (hash 'id e  'type \"disease_to_phenotype_association\" 'source_id s 'target_id o 'value 1000))\n(define (bkbp-g id curie) (hash 'id id 'type \"Gene\"              'curie curie))\n(define (bkbp-d id curie) (hash 'id id 'type \"disease\"           'curie curie))\n(define (bkbp-p id curie) (hash 'id id 'type \"PhenotypicFeature\" 'curie curie))\n\n;{'query':\n;  {'query_graph':\n;    {'edges':\n;      [{'id': 'e0', 'type': 'gene_to_disease_association', 'source_id': 'n0', 'target_id': 'n2'},\n;       {'id': 'e1', 'type': 'gene_to_disease_association', 'source_id': 'n1', 'target_id': 'n2'},\n;       {'id': 'e2', 'type': 'disease_to_phenotype_association', 'value': 1000, 'source_id': 'n2', 'target_id': 'n3'}],\n;     'nodes':\n;      [{'id': 'n0', 'type': 'Gene', 'curie':              'ENSEMBL:ENSG00000132155'},\n;       {'id': 'n1', 'type': 'Gene', 'curie':              'ENSEMBL:ENSG00000073803'},\n;       {'id': 'n2', 'type': 'disease', 'curie':           'MONDO:0007254'},\n;       {'id': 'n3', 'type': 'PhenotypicFeature', 'curie': 'EFO:0000714'}]},\n;  'reasoner_id': 'unsecret'}}\n(define bkbp-edges\n  (list (bkbp-g2d \"e0\" \"n0\" \"n2\")\n        (bkbp-g2d \"e1\" \"n1\" \"n2\")\n        (bkbp-d2p \"e2\" \"n2\" \"n3\")))\n(define bkbp-nodes\n  (list (bkbp-g \"n0\" \"ENSEMBL:ENSG00000132155\")\n        (bkbp-g \"n1\" \"ENSEMBL:ENSG00000073803\")\n        (bkbp-d \"n2\" \"MONDO:0007254\")\n        (bkbp-p \"n3\" \"EFO:0000714\")))\n;(define response (bkbp-query bkbp-edges bkbp-nodes))\n\n;\n;{\"query\":\n;  {\"query_graph\":\n;    {\"edges\":\n;      [{\"target_id\":\"d00\",\"type\":\"gene_to_disease_association\",\"source_id\":\"g00\",\"id\":\"e00\"}],\n;     \"nodes\":\n;      [{\"type\":\"Gene\",\"curie\":\"ENSEMBLE:ENSG00000132155\",\"id\":\"g00\"},\n;       {\"type\":\"disease\",\"curie\":\"MONDO:0007254\",\"id\":\"d00\"}]},\n;  \"reasoner_id\": \"unsecret\"}}\n\n;; (define RAF1 (hash 'id \"g00\" 'type \"Gene\" 'curie \"ENSEMBLE:ENSG00000132155\"))\n;; (define (g2d e s o) (hash 'id e 'type \"gene_to_disease_association\" 'source_id s 'target_id o))\n;; (define breast-cancer (hash 'id \"d00\" 'type \"disease\" 'curie \"MONDO:0007254\"))\n;; (define MAP3K13 (hash 'id \"g01\" 'type \"Gene\" 'curie \"ENSEMBL:ENSG00000073803\"))\n;; (displayln (jsexpr->string (apply js-query/bkbp (reverse (list (list RAF1 breast-cancer) (list (g2d \"e00\" \"g00\" \"d00\")))))))\n;; (bkbp-query (list (g2d \"e00\" \"g00\" \"d00\") (list RAF1 breast-cancer))\n\n;(define (bkb-pathwayo subject subject-type verb object object-type)\n  ;(project (subject subject-type verb object object-type)\n    ;(let ()\n      ;(when (or (var? verb) (var? subject-type) (var? object-type)\n                ;(and (var? subject) (var? object)))\n        ;(error \"verb, types, and subject or object curie must be ground\"))\n      ;(define edges (list (hash 'id        \"e00\"\n                                ;'source_id \"n00\"\n                                ;'target_id \"n01\"\n                                ;'type      verb)))\n      ;(define subject-node\n        ;(make-immutable-hash\n          ;(append (if (var? subject) '() `((curie . ,subject)))\n                  ;`((id . \"n00\") (type . ,subject-type)))))\n      ;(define object-node\n        ;(make-immutable-hash\n          ;(append (if (var? object) '() `((curie . ,object)))\n                  ;`((id . \"n01\") (type . ,object-type)))))\n      ;(define nodes (list subject-node object-node))\n      ;(define results\n        ;(hash-ref\n          ;(hash-ref\n            ;(hash-ref (api-query (string-append url.broad path.query)\n                                 ;(js-query edges nodes))\n                      ;'response)\n            ;'knowledge_graph)\n          ;'edges))\n      ;;(pretty-print results)\n      ;;(pretty-print edges)\n      ;;(pretty-print nodes)\n      ;(let loop ((results results))\n        ;(if (null? results) (== #t #f)\n          ;(let ((e (car results)))\n            ;;; NOTE: this conditional equality constraint is due to the fact\n            ;;; that molepro doesn't return the same curies you put in.\n            ;(conde ((if (var? subject) (== subject (hash-ref e 'source_id))\n                      ;(== #t #t))\n                    ;(if (var? object) (== object  (hash-ref e 'target_id))\n                      ;(== #t #t)))\n                   ;((loop (cdr results))))))))))\n\n(define (molepro-edgeo subject subject-type verb object object-type)\n  (project (subject subject-type verb object object-type)\n    (let ()\n      (when (or (var? verb) (var? subject-type) (var? object-type)\n                (and (var? subject) (var? object)))\n        (error \"verb, types, and subject or object curie must be ground\"))\n      (define edges (list (hash 'id        \"e00\"\n                                'source_id \"n00\"\n                                'target_id \"n01\"\n                                'type      verb)))\n      (define subject-node\n        (make-immutable-hash\n          (append (if (var? subject) '() `((curie . ,subject)))\n                  `((id . \"n00\") (type . ,subject-type)))))\n      (define object-node\n        (make-immutable-hash\n          (append (if (var? object) '() `((curie . ,object)))\n                  `((id . \"n01\") (type . ,object-type)))))\n      (define nodes (list subject-node object-node))\n      (define results\n        (hash-ref\n          (hash-ref\n            (hash-ref (api-query (string-append url.broad path.query)\n                                 (js-query edges nodes))\n                      'response)\n            'knowledge_graph)\n          'edges))\n      ;(pretty-print results)\n      ;(pretty-print edges)\n      ;(pretty-print nodes)\n      (let loop ((results results))\n        (if (null? results) (== #t #f)\n          (let ((e (car results)))\n            ;; NOTE: this conditional equality constraint is due to the fact\n            ;; that molepro doesn't return the same curies you put in.\n            (conde ((if (var? subject) (== subject (hash-ref e 'source_id))\n                      (== #t #t))\n                    (if (var? object) (== object  (hash-ref e 'target_id))\n                      (== #t #t)))\n                   ((loop (cdr results))))))))))\n\n(module+ main\n  (pretty-print (api-query (string-append url.broad path.predicates)))\n\n  (run* (g) (molepro-edgeo \"CID:2244\" \"chemical_substance\" \"affects\" g \"gene\"))\n  ;(run 1 (g) (molepro-edgeo \"CHEBI:15365\" \"chemical_substance\" \"affects\" g \"gene\"))\n  ;(run 1 (c) (molepro-edgeo c \"chemical_substance\" \"affects\" \"HGNC:7645\" \"gene\"))\n  (run* (c) (molepro-edgeo \"HGNC:7645\" \"gene\" \"affected_by\" c \"chemical_substance\"))\n\n  ;(pretty-print\n     ;(api-query (string-append url.broad path.query)\n              ;(js-query (list (hash 'id        \"e00\"\n                                    ;'source_id \"n00\"\n                                    ;'target_id \"n01\"\n                                    ;'type      \"affects\"))\n                        ;(list (hash 'curie \"CID:2244\"\n                                    ;'id    \"n00\"\n                                    ;'type  \"chemical_substance\"\n                                    ;)\n                              ;(hash 'id    \"n01\"\n                                    ;'type  \"gene\")))))\n  )\n\n(module+ old-main\n  ;; test predicates available on Broad Institute KG\n #;(pretty-print\n   (api-query (string-append url.broad path.predicates)))\n\n  #;(pretty-print\n     (api-query (string-append url.broad path.query)\n              (js-query (list (hash 'id        \"e00\"\n                                    'source_id \"n00\"\n                                    'target_id \"n01\"\n                                    'type      \"affects\"))\n                        (list (hash 'curie \"CID:2244\"\n                                    'id    \"n00\"\n                                    'type  \"chemical_substance\")\n                              (hash 'id    \"n01\"\n                                    'type  \"gene\")))))\n\n  #;(js-count\n    (time (api-query (string-append url.unsecret path.predicates))))\n\n  #;(pretty-print\n    (time\n      (api-query (string-append url.unsecret path.query)\n                (js-query (list (hash 'id        \"e00\"\n                                       'source_id \"n00\"\n                                       'target_id \"n01\"\n                                       'type      \"causes\"))\n                           (list (hash 'curie \"UMLS:C0004096\"\n                                       'id    \"n01\"\n                                       'type  \"disease\")\n                                 (hash 'id    \"n00\"\n                                       'type  \"gene\"))))))\n\n  #;(pretty-print\n    (time\n       (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"causes\"))\n                            (list (hash 'curie \"UMLS:C0004096\"\n                                        'id    \"n01\"\n                                        'type  \"disease\")\n                                  (hash 'id    \"n00\"\n                                        'type  \"gene\"))))))\n\n  #;(pretty-print\n    (time (api-query (string-append url.unsecret path.query)\n                     (js-query (list (hash 'id        \"e00\"\n                                           'source_id \"n00\"\n                                           'target_id \"n01\"\n                                           'type      \"affects\"))\n                               (list (hash 'curie \"CID:2244\"\n                                           'id    \"n00\"\n                                           'type  \"chemical_substance\")\n                                     (hash 'id    \"n01\"\n                                           'type  \"gene\"))))))\n\n\n\n#|NOTES FOR SEPTEMBER 2020 RELAY API CALLS|#\n\n#|\n\n1. all \"NO-evidence/provenance\" queries are to the base broad.url\n\"https://translator.broadinstitute.org/molepro_reasoner\n\n2. all \"LIMITED evidence/provenance\" queries are to the chembl url\n\"https://translator.broadinstitute.org/chembl\"\n\n|#\n\n;;MOLEPRO drug --treats--> disease query w/ NO EVIDENCE\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"treats\"))\n                            (list (hash 'curie \"ChEMBL:CHEMBL25\"\n                                        'id    \"n00\"\n                                        'type  \"chemical_substance\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"disease\"))))))\n\n;; new query structure for chembl specific provenance/evidence queries\n(define (js-query/transform curie)\n  (hash 'collection\n        (list\n         (hash\n          'id \"\"\n          'identifiers\n          (hash\n           'chembl curie)))\n        'controls '()))\n\n#|\n;; {} = hash                            ;\n;; [] = list                            ;\n;; key:value                            ;\n                                        ;\nQUERY/TRANSFORM QUERY STRUCTURE         ;\n------------------------------\n\nquery = {\n    'collection': [{\n            'id':'',\n            'identifiers': {'chembl':'ChEMBL:CHEMBL25'}\n        }],\n    'controls':[]\n}\n|#\n\n;; addition provenance/evidence for drug indication query\n(when (config-ref 'trapi-enable-external-requests?)\n  (begin\n(pretty-print\n (time\n  (api-query\n   (string-append (string-append url.broad_chembl chembl-drug-indications/transform))\n   (js-query/transform\n    \"ChEMBL:CHEMBL25\"))))\n\n\n;; STRING gene->gene edge\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"related_to\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n\n;; CMAP gene-to-compound query\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"correlated_with\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"chemical_substance\"))))))\n\n;; CMAP gene-to-gene query\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"correlated_with\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n\n;; CMAP gene-to-gene query\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"correlated_with\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n))\n\n)\n"
  },
  {
    "path": "medikanren/open-api/html/.swagger-codegen/VERSION",
    "content": "3.0.14"
  },
  {
    "path": "medikanren/open-api/html/.swagger-codegen-ignore",
    "content": "# Swagger Codegen Ignore\n# Generated by swagger-codegen https://github.com/swagger-api/swagger-codegen\n\n# Use this file to prevent files from being overwritten by the generator.\n# The patterns follow closely to .gitignore or .dockerignore.\n\n# As an example, the C# client generator defines ApiClient.cs.\n# You can make changes and tell Swagger Codgen to ignore just this file by uncommenting the following line:\n#ApiClient.cs\n\n# You can match any string of characters against a directory, file or extension with a single asterisk (*):\n#foo/*/qux\n# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux\n\n# You can recursively match patterns against a directory, file or extension with a double asterisk (**):\n#foo/**/qux\n# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux\n\n# You can also negate patterns with an exclamation (!).\n# For example, you can ignore all files in a docs folder with the file extension .md:\n#docs/*.md\n# Then explicitly reverse the ignore rule for a single file:\n#!docs/README.md\n"
  },
  {
    "path": "medikanren/open-api/html/index.html",
    "content": "\n\n  \n    OpenAPI for NCATS Biomedical Translator Reasoners\n    \n  \n  \n  
OpenAPI for NCATS Biomedical Translator Reasoners
\n    
OpenAPI for NCATS Biomedical Translator Reasoners
\n    
More information: https://helloreverb.com
\n    
Contact Info: edeutsch@systemsbiology.org
\n    
Version: 0.9.2
\n\n    
Apache 2.0
\n    
http://www.apache.org/licenses/LICENSE-2.0.html
\n  
Access
\n\n  
Methods
\n  [ Jump to Models ]\n\n  
Table of Contents 
\n  
\n  
Predicates
\n  \n  
Query
\n  \n\n  
Predicates
\n  
\n    
\n    Up\n    
get /predicates
\n    
Get supported relationships by source and target (predicatesGet)
\n    
\n\n\n\n\n\n\n\n    
Return type
\n    
\n\n      map[String, map[String, array[String]]]\n    
\n\n    \n\n    
Example data
\n    
Content-Type: application/json
\n    
{\n  \"chemical_substance\" : {\n    \"gene\" : [ \"directly_interacts_with\", \"decreases_activity_of\" ]\n  }\n}
\n\n    
Produces
\n    This API call produces the following media types according to the Accept request header;\n    the media type will be conveyed by the Content-Type response header.\n    
    \n      
  • application/json
    • \n    
\n\n    
Responses
\n    
200
\n    Predicates by source and target\n\n  
 \n  
\n  
Query
\n  
\n    
\n    Up\n    
post /query
\n    
Query reasoner via one of several inputs (query)
\n    
\n\n\n    
Consumes
\n    This API call consumes the following media types via the Content-Type request header:\n    
    \n      
  • application/json
    • \n    
\n\n    
Request body
\n    
\n      
body map (required)
\n\n            
Body Parameter — Query information to be submitted 
\n                
  \n\n\n\n\n    
Return type
\n    
\n      Message\n\n    
\n\n    \n\n    
Example data
\n    
Content-Type: application/json
\n    
{\n  \"knowledge_graph\" : \"\",\n  \"results\" : [ {\n    \"edge_bindings\" : [ {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    }, {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    } ],\n    \"node_bindings\" : [ {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    }, {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    } ]\n  }, {\n    \"edge_bindings\" : [ {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    }, {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    } ],\n    \"node_bindings\" : [ {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    }, {\n      \"kg_id\" : \"\",\n      \"qg_id\" : \"qg_id\"\n    } ]\n  } ],\n  \"query_graph\" : {\n    \"nodes\" : [ {\n      \"curie\" : \"OMIM:603903\",\n      \"id\" : \"n00\",\n      \"type\" : \"\"\n    }, {\n      \"curie\" : \"OMIM:603903\",\n      \"id\" : \"n00\",\n      \"type\" : \"\"\n    } ],\n    \"edges\" : [ {\n      \"target_id\" : \"https://www.uniprot.org/uniprot/P00738\",\n      \"id\" : \"e00\",\n      \"source_id\" : \"https://omim.org/entry/603903\",\n      \"type\" : \"\"\n    }, {\n      \"target_id\" : \"https://www.uniprot.org/uniprot/P00738\",\n      \"id\" : \"e00\",\n      \"source_id\" : \"https://omim.org/entry/603903\",\n      \"type\" : \"\"\n    } ]\n  }\n}
\n\n    
Produces
\n    This API call produces the following media types according to the Accept request header;\n    the media type will be conveyed by the Content-Type response header.\n    
    \n      
  • application/json
    • \n    
\n\n    
Responses
\n    
200
\n    successful operation\n        Message\n    
400
\n    Invalid status value\n        \n  
 \n  
\n\n  
Models
\n  [ Jump to Methods ]\n\n  
Table of Contents
\n  
    \n    
  1. BiolinkEntity
    2. \n    
  2. BiolinkRelation
    3. \n    
  3. Credentials
    4. \n    
  4. Edge
    5. \n    
  5. EdgeBinding
    6. \n    
  6. KnowledgeGraph
    7. \n    
  7. Message
    8. \n    
  8. Node
    9. \n    
  9. NodeBinding
    10. \n    
  10. QEdge
    11. \n    
  11. QNode
    12. \n    
  12. Query
    13. \n    
  13. QueryGraph
    14. \n    
  14. RemoteKnowledgeGraph
    15. \n    
  15. Result
    16. \n  
\n\n  
\n    
BiolinkEntity Up
\n    
A subclass of named_thing (snake_case)
\n    
\n          
  \n  
\n  
\n    
BiolinkRelation Up
\n    
A relation, i.e. child of related_to (snake_case)
\n    
\n          
  \n  
\n  
\n    
Credentials Up
\n    
Credentials needed for programmatic access to the remote knowledge graph
\n    
\n          
  \n  
\n  
\n    
Edge Up
\n    
An edge in the thought subgraph linking two nodes
\n    
\n          
  \n  
\n  
\n    
EdgeBinding Up
\n\n    
\n      
qg_id 
String Query-graph edge id, i.e. the <code>edge_id</code> of a QEdge 
\n
kg_id 
 One or more knowledge-graph edge ids, i.e. the <code>id</code> of a KEdge 
\n    
  \n  
\n  
\n    
KnowledgeGraph Up
\n    
A thought graph associated with this result. This will commonly be a linear path subgraph from one concept to another, but related items aside of the path may be included.
\n    
\n          
  \n  
\n  
\n    
Message Up
\n\n    
\n          
  \n  
\n  
\n    
Node Up
\n    
A node in the thought subgraph
\n    
\n          
  \n  
\n  
\n    
NodeBinding Up
\n\n    
\n      
qg_id 
String Query-graph node id, i.e. the <code>node_id</code> of a QNode 
\n
kg_id 
 One or more knowledge-graph node ids, i.e. the <code>id</code> of a KNode 
\n    
  \n  
\n  
\n    
QEdge Up
\n    
An edge in the QueryGraph
\n    
\n          
  \n  
\n  
\n    
QNode Up
\n    
A node in the QueryGraph
\n    
\n          
  \n  
\n  
\n    
Query Up
\n\n    
\n          
  \n  
\n  
\n    
QueryGraph Up
\n    
A graph intended to be the thought path to be followed by a reasoner to answer the question. This graph is a representation of a question.
\n    
\n          
  \n  
\n  
\n    
RemoteKnowledgeGraph Up
\n    
A thought graph associated with this result that is not repeated here, but stored elsewhere in a way that can be remotely accessed by the reader of this Message
\n    
\n      
url 
String URL that provides programmatic access to the remote knowledge graph 
\n          
example: http://robokop.renci.org/api/kg
\n
credentials (optional)
array[Credentials] Credentials needed for programmatic access to the remote knowledge graph 
\n
protocol (optional)
String  
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Result Up
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One of potentially several results or answers for a query
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node_bindings 
array[NodeBinding] List of QNode-KNode bindings. 
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edge_bindings 
array[EdgeBinding] List of QEdge-KEdge bindings. 
\n    
  \n  
\n  \n\n"
  },
  {
    "path": "medikanren/open-api/html2/.swagger-codegen/VERSION",
    "content": "3.0.14"
  },
  {
    "path": "medikanren/open-api/html2/.swagger-codegen-ignore",
    "content": "# Swagger Codegen Ignore\n# Generated by swagger-codegen https://github.com/swagger-api/swagger-codegen\n\n# Use this file to prevent files from being overwritten by the generator.\n# The patterns follow closely to .gitignore or .dockerignore.\n\n# As an example, the C# client generator defines ApiClient.cs.\n# You can make changes and tell Swagger Codgen to ignore just this file by uncommenting the following line:\n#ApiClient.cs\n\n# You can match any string of characters against a directory, file or extension with a single asterisk (*):\n#foo/*/qux\n# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux\n\n# You can recursively match patterns against a directory, file or extension with a double asterisk (**):\n#foo/**/qux\n# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux\n\n# You can also negate patterns with an exclamation (!).\n# For example, you can ignore all files in a docs folder with the file extension .md:\n#docs/*.md\n# Then explicitly reverse the ignore rule for a single file:\n#!docs/README.md\n"
  },
  {
    "path": "medikanren/open-api/html2/index.html",
    "content": "\n\n\n  \n  OpenAPI for NCATS Biomedical Translator Reasoners\n  \n  \n  \n  \n  \n  \n  \n  \n  \n\n\n  \n\n  
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OpenAPI for NCATS Biomedical Translator Reasoners
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API and SDK Documentation
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Version: 0.9.2
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OpenAPI for NCATS Biomedical Translator Reasoners
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Predicates
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predicatesGet
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Get supported relationships by source and target
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/predicates
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Usage and SDK Samples
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curl -X GET \"//predicates\"
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import io.swagger.client.*;\nimport io.swagger.client.auth.*;\nimport io.swagger.client.model.*;\nimport io.swagger.client.api.PredicatesApi;\n\nimport java.io.File;\nimport java.util.*;\n\npublic class PredicatesApiExample {\n\n    public static void main(String[] args) {\n\n        PredicatesApi apiInstance = new PredicatesApi();\n        try {\n            map['String', map['String', array['String']]] result = apiInstance.predicatesGet();\n            System.out.println(result);\n        } catch (ApiException e) {\n            System.err.println(\"Exception when calling PredicatesApi#predicatesGet\");\n            e.printStackTrace();\n        }\n    }\n}
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import io.swagger.client.api.PredicatesApi;\n\npublic class PredicatesApiExample {\n\n    public static void main(String[] args) {\n        PredicatesApi apiInstance = new PredicatesApi();\n        try {\n            map['String', map['String', array['String']]] result = apiInstance.predicatesGet();\n            System.out.println(result);\n        } catch (ApiException e) {\n            System.err.println(\"Exception when calling PredicatesApi#predicatesGet\");\n            e.printStackTrace();\n        }\n    }\n}
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\nPredicatesApi *apiInstance = [[PredicatesApi alloc] init];\n\n// Get supported relationships by source and target\n[apiInstance predicatesGetWithCompletionHandler:\n              ^(map['String', map['String', array['String']]] output, NSError* error) {\n                            if (output) {\n                                NSLog(@\"%@\", output);\n                            }\n                            if (error) {\n                                NSLog(@\"Error: %@\", error);\n                            }\n                        }];\n
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var OpenApiForNcatsBiomedicalTranslatorReasoners = require('open_api_for_ncats_biomedical_translator_reasoners');\n\nvar api = new OpenApiForNcatsBiomedicalTranslatorReasoners.PredicatesApi()\nvar callback = function(error, data, response) {\n  if (error) {\n    console.error(error);\n  } else {\n    console.log('API called successfully. Returned data: ' + data);\n  }\n};\napi.predicatesGet(callback);\n
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using System;\nusing System.Diagnostics;\nusing IO.Swagger.Api;\nusing IO.Swagger.Client;\nusing IO.Swagger.Model;\n\nnamespace Example\n{\n    public class predicatesGetExample\n    {\n        public void main()\n        {\n\n            var apiInstance = new PredicatesApi();\n\n            try\n            {\n                // Get supported relationships by source and target\n                map['String', map['String', array['String']]] result = apiInstance.predicatesGet();\n                Debug.WriteLine(result);\n            }\n            catch (Exception e)\n            {\n                Debug.Print(\"Exception when calling PredicatesApi.predicatesGet: \" + e.Message );\n            }\n        }\n    }\n}\n
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<?php\nrequire_once(__DIR__ . '/vendor/autoload.php');\n\n$api_instance = new Swagger\\Client\\ApiPredicatesApi();\n\ntry {\n    $result = $api_instance->predicatesGet();\n    print_r($result);\n} catch (Exception $e) {\n    echo 'Exception when calling PredicatesApi->predicatesGet: ', $e->getMessage(), PHP_EOL;\n}\n?>
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use Data::Dumper;\nuse WWW::SwaggerClient::Configuration;\nuse WWW::SwaggerClient::PredicatesApi;\n\nmy $api_instance = WWW::SwaggerClient::PredicatesApi->new();\n\neval {\n    my $result = $api_instance->predicatesGet();\n    print Dumper($result);\n};\nif ($@) {\n    warn \"Exception when calling PredicatesApi->predicatesGet: $@\\n\";\n}
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from __future__ import print_statement\nimport time\nimport swagger_client\nfrom swagger_client.rest import ApiException\nfrom pprint import pprint\n\n# create an instance of the API class\napi_instance = swagger_client.PredicatesApi()\n\ntry:\n    # Get supported relationships by source and target\n    api_response = api_instance.predicates_get()\n    pprint(api_response)\nexcept ApiException as e:\n    print(\"Exception when calling PredicatesApi->predicatesGet: %s\\n\" % e)
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Parameters
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Responses
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 Status: 200 - Predicates by source and target 
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Query
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query
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Query reasoner via one of several inputs
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/query
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Usage and SDK Samples
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curl -X POST \"//query\"
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import io.swagger.client.*;\nimport io.swagger.client.auth.*;\nimport io.swagger.client.model.*;\nimport io.swagger.client.api.QueryApi;\n\nimport java.io.File;\nimport java.util.*;\n\npublic class QueryApiExample {\n\n    public static void main(String[] args) {\n\n        QueryApi apiInstance = new QueryApi();\n        map[String, Object] body = ; // map[String, Object] | Query information to be submitted\n        try {\n            Message result = apiInstance.query(body);\n            System.out.println(result);\n        } catch (ApiException e) {\n            System.err.println(\"Exception when calling QueryApi#query\");\n            e.printStackTrace();\n        }\n    }\n}
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import io.swagger.client.api.QueryApi;\n\npublic class QueryApiExample {\n\n    public static void main(String[] args) {\n        QueryApi apiInstance = new QueryApi();\n        map[String, Object] body = ; // map[String, Object] | Query information to be submitted\n        try {\n            Message result = apiInstance.query(body);\n            System.out.println(result);\n        } catch (ApiException e) {\n            System.err.println(\"Exception when calling QueryApi#query\");\n            e.printStackTrace();\n        }\n    }\n}
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map[String, Object] *body = ; // Query information to be submitted\n\nQueryApi *apiInstance = [[QueryApi alloc] init];\n\n// Query reasoner via one of several inputs\n[apiInstance queryWith:body\n              completionHandler: ^(Message output, NSError* error) {\n                            if (output) {\n                                NSLog(@\"%@\", output);\n                            }\n                            if (error) {\n                                NSLog(@\"Error: %@\", error);\n                            }\n                        }];\n
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var OpenApiForNcatsBiomedicalTranslatorReasoners = require('open_api_for_ncats_biomedical_translator_reasoners');\n\nvar api = new OpenApiForNcatsBiomedicalTranslatorReasoners.QueryApi()\nvar body = ; // {{map[String, Object]}} Query information to be submitted\n\nvar callback = function(error, data, response) {\n  if (error) {\n    console.error(error);\n  } else {\n    console.log('API called successfully. Returned data: ' + data);\n  }\n};\napi.query(body, callback);\n
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using System;\nusing System.Diagnostics;\nusing IO.Swagger.Api;\nusing IO.Swagger.Client;\nusing IO.Swagger.Model;\n\nnamespace Example\n{\n    public class queryExample\n    {\n        public void main()\n        {\n\n            var apiInstance = new QueryApi();\n            var body = new map[String, Object](); // map[String, Object] | Query information to be submitted\n\n            try\n            {\n                // Query reasoner via one of several inputs\n                Message result = apiInstance.query(body);\n                Debug.WriteLine(result);\n            }\n            catch (Exception e)\n            {\n                Debug.Print(\"Exception when calling QueryApi.query: \" + e.Message );\n            }\n        }\n    }\n}\n
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<?php\nrequire_once(__DIR__ . '/vendor/autoload.php');\n\n$api_instance = new Swagger\\Client\\ApiQueryApi();\n$body = ; // map[String, Object] | Query information to be submitted\n\ntry {\n    $result = $api_instance->query($body);\n    print_r($result);\n} catch (Exception $e) {\n    echo 'Exception when calling QueryApi->query: ', $e->getMessage(), PHP_EOL;\n}\n?>
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use Data::Dumper;\nuse WWW::SwaggerClient::Configuration;\nuse WWW::SwaggerClient::QueryApi;\n\nmy $api_instance = WWW::SwaggerClient::QueryApi->new();\nmy $body = WWW::SwaggerClient::Object::map[String, Object]->new(); # map[String, Object] | Query information to be submitted\n\neval {\n    my $result = $api_instance->query(body => $body);\n    print Dumper($result);\n};\nif ($@) {\n    warn \"Exception when calling QueryApi->query: $@\\n\";\n}
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from __future__ import print_statement\nimport time\nimport swagger_client\nfrom swagger_client.rest import ApiException\nfrom pprint import pprint\n\n# create an instance of the API class\napi_instance = swagger_client.QueryApi()\nbody =  # map[String, Object] | Query information to be submitted\n\ntry:\n    # Query reasoner via one of several inputs\n    api_response = api_instance.query(body)\n    pprint(api_response)\nexcept ApiException as e:\n    print(\"Exception when calling QueryApi->query: %s\\n\" % e)
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Parameters
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Body parameters
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NameDescription
body *\n\n\n                                \n                                
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Responses
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 Status: 200 - successful operation 
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 Status: 400 - Invalid status value 
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Suggestions, contact, support and error reporting;\n                  
Information URL: https://helloreverb.com
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Contact Info: edeutsch@systemsbiology.org
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Apache 2.0
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http://www.apache.org/licenses/LICENSE-2.0.html
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  },
  {
    "path": "medikanren/open-api/yaml-to-json.sh",
    "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\npython3 \"$here/yaml2json.py\" < \"$here/TranslatorReasonersAPI.yaml\" > \"$here/TranslatorReasonersAPI.json\"\n"
  },
  {
    "path": "medikanren/open-api/yaml2json.py",
    "content": "import sys, json, yaml\n\ndata = yaml.load(sys.stdin, Loader=yaml.SafeLoader)\nprint(json.dumps(data, indent=4))\n"
  },
  {
    "path": "medikanren/pieces-parts/NOTES-DB.md",
    "content": "- db.rkt exposes the data, and indexes.\n  - Only lookup what you need by offset.\n- mk-db.rkt bridges the gap between db and mk.\n- db:edgeo in mk-db.rkt\n  - db represents an entire database, that contains tables and indexes\n  - edge is miniKanren term to populate\n  - implementation not relational, escapes to Racket and uses indexes according to where the variables are\n- common.rkt provides conde/databases to lookup over all knowledge sources (databases). Uses tagging to disambiguate the knowledge source.\n- dbKanren would enable more things to be done relationally as in Datalog. Express fixpoint computations relationally instead of in Racket. Also will be able to mix top-down and bottom-up relations. Top-down queries prune the search space quickly.\n- propagators are for implementing finite joints.\n\n"
  },
  {
    "path": "medikanren/pieces-parts/NOTES.md",
    "content": "# Queries\n\n- mediKanren has connected lots of DB\n  - with a single query, I am hitting giant DBs to get back answers\n  - one giant query to get all the mk data!\n  - graph: you have to think of it a certain way\n  - vs tables\n  \n- druggable genome\n  - kinease very druggable\n  - protease druggable\n  - transcription factors not so druggable\n  - chemical reaction things are often more druggable\n  - can start with druggable genome\n  - experiment: knock out each gene in a list to see which with the virus survives\n  - allows to add genes \"just in case\" because we know they are druggable\n  - sophisticated intersection:\n    - these are genes involved in the pathways of the virus\n    - set of genes in each functional pathways\n    - complete the set with druggable genes\n    - can use GO ontology\n    - can use algorithms for 'gene enrichment' (the gene list sharpener)\n      - https://indigo.ncats.io/\n- gene interaction\n- tell me the genes associated with a phenotype for a type of disease or disorder\n- drug prioritzation:\n  - here are all the drugs that would buge the genes that would be pro and anti viral.\n  - lower the priority for testing if it exacerbates the disease.\n- bridge are the drugs:\n  - here's a list of drugs. without knowing the gene list, use counter indication information.\n  - this drug is bad for this disease, however it's related.\n- how do you find the drug/genes?\n  - we know the pathways it hijacks in the cell.\n  - virus need to escape detection.\n\n- What repeated queries would be useful?\n  - batch 2-hop query: drug - gene2 - gene1\n    set of gene1s\n  - predicates for upregulates\n  - predicates for downregulates\n  - another way to sort:\n    - strong relationship vs weaker/ambiguous relationship\n  - direction + strength (some tools use that, is it confidence, probability?)\n  - bio example:\n    - all the 1-hops have already been done, because a journal says this uprelates that. relationship is not novel.\n    - with 2-hops, we can know thing that have not been known before. nobody can do that in a way that we can look at 2-hops at the same time, and do the filtering.\n    - here is all the DFA approved drugs from 2-hop from these gene list.\n    - UI: build a gene list, and do things with it.\n    - if ..., filter it out\n    - 2-hop: many thousands of this\n- Understand what do we lose from a drug list that is FDA approved\n  - Resveratrol? FDA-approved\n  - FDA will put a \"generally recognized as safe\"\n  - e.g. tag GRAS: generally recognized as safe\n  - we can put filters, but doctors want to understand the filters\n  - maybe RX norm?\n  - diabetics are in trouble via glucose. in one gene, see evidence that sugar would be bad.\n\n- more exploratory data mining?\n  - as opposed to excel sheet\n\n- when doing up/down regulation, the information comes from semmed db\n  - check against other databases like GO\n- broad has hightroughput experiments\n  - cancer cells + thousands of drugs figuring out gene expression levels\n  - you get quantitive information, an entire profile\n  - can be 2 TB of data\n  - noisy data\n  - across tissue types\n- drug gene budger website\n  - use broad data\n  - to predict whether a drug up or down regulate this gene, with quantitative score\n\n- finding a 'safe' drug to regulate a gene\n  - this drug might have an effect on many genes\n  - look at 2-hop queries: drug -> gene -> gene, -> regulates.\n  - 2-hop queries are a tricky ranking problem\n  - you want to know the off target effects\n\n- at least two notions of ranking\n  - because data is incomplete, or contradictory, or wrong (because of bad NLP)\n  - one notion of ranking: what's the confidence you have this is true\n  - other notion: assuming it's true, how well does it work?\n  - how can you display a query where you express preferences\n  - trade-offs\n\n- goal: improving the ranking for 1- & 2-hop queries for gene budging\n\n- also: how to visualize it?\n\n- or better ways to determine whether a drug is safe\n\n- certain class of queries are really import for both COVID-19 and oncology\n  - set of genes we want to upregulate and set of genes we want to downregulate\n  - one drug can have several effects in the sets of genes, some in the wrong direction, some indirect effects\n\n- for COVID-19\n  - in the COVID universe of gene\n  - an interactome (genetic relation in knock out experiments where virus is impacted)\n  - what are the direct interactors\n  - how to group those in related pathways\n  - how can modulate a pathway?\n  - optimization problem with multiple genes to target\n  - priotization\n  - genetic set from COVID, predictions on the drugs, explanation\n  - other optimization: in vitro screening, say 40 hits, pick one drug per pathway\n  - use reactome to look at cellular pathway information\n  - genetic information: don't use this drug if patient has this gene\n    - https://www.pharmgkb.org/\n  - get the list of drugs that have been successful in fighting the replication of the virus\n    - to test our logic\n    - fights the mechanics of the replication, e.g. the hijacking of organelle, it's not a full human test!\n    - a hit means an attack of how to build a virus\n    \n\n- for Cancer:\n  - same spirit as COVID-19\n  - sequence the tumor, sequence the person, compare the two\n  - if i see a promoter in front of a gene that shouldnt be there,\n    - then targetting the promotor will not do what is expected\n    - drugs that normally have an effect on one gene(s), will have an effect on a totally different gene(s)\n  - experiment in vitro: cut tumor out, and test various drugs in wells for them\n  - done in leukemia\n    - tested every single FDA approved drugs against it\n    - narrowed it down to 300\n   - Are there datasets that showed tumor vs drug that worked?\n     - more machine learning, but maybe can combine with reasoning\n     - do the counting, and see if we get a similar answer\n\n- Recommended Books\n  - Molecular Biology Quick Start\n    https://www.cshlpress.com/default.tpl?cart=1592597073832848389&fromlink=T&linkaction=full&linksortby=oop_title&--eqSKUdatarq=1019\n  - A Genetic Switch, Phage Lambda Revisited\n    https://www.cshlpress.com/default.tpl?cart=1592597118832862691&fromlink=T&linkaction=full&linksortby=oop_title&--eqSKUdatarq=468\n\n# Propagators\n\nIf query structure is not a tree, then you can run into inconsistency.\n\nSituation were arc-consistency is not enough.\n\nA --- B\n \\ C /\n\n```\n(query\n  (concepts\n   (a A)\n   (b B)\n   (c C))\n  (edges\n    (a R1 b)\n    (b R2 c)\n    (c R3 a)))\n\nA: {a1, a2}\nB: {b1, b2}\nC: {c1, c2}\n\nR1: {(a1,b1) (a2,b2)}\nR2: {(b1,c2) (b2,c1)}\nR3: {(c1,a1) (c2,a2)}\n```\n\nWe're constrainting the sets A, B, C based on the edges.\n"
  },
  {
    "path": "medikanren/pieces-parts/new-query-lang/may2.txt",
    "content": "Query-defined concepts imply subqueries with existentials. To get this to work correctly in general, we need to implement a global consistency algorithm that is aware of whether each variable is part of the top-level, visible query.\n\nExample:\n\n(define-category (bar C)\n  (concepts\n    [A' baz]\n    [B' baz]\n    [C baz])\n  (edges\n    [e1 : A' foo B]\n    [e2 : B' foo C]\n    [e3 : C foo A]))\n\n(query\n  (concepts\n    [A bar]\n    [B bar]\n    [C bar])\n  (edges\n    [e1 : A foo B]\n    [e2 : B foo C]\n    [e3 : C foo A]))\n\nOr, safe-drug query. We only want one copy of the drug, though there are multiple diseases it safely treats.\n\nFor now we will pre-compute categories like safe-drug. To then use these precomputed categories, we need an extension to query/graph that accepts a list of curies.\n\nGreg:\n * add list of curies feature\n * add safe-drug and human-gene precomputed lists\n\nNext time:\n * write logic to get globally consistent results out of ranked-paths.\n\n"
  },
  {
    "path": "medikanren/pieces-parts/new-query-lang/michael-query-language-design.txt",
    "content": "(define-simple-predicate regulates\n  (upregulates downregulates))\n\n(define-predicate (regulates e)\n  (edges (e (primitive-predicate '(upregulates downregulates)))))\n\n(define-predicate (treats-safely e)\n  (edges\n    (e treats))\n  (where\n    (has-property e treats-safely-predicates))))\n\n(define-category (safe-drug drg)\n  (concepts (drg drug) (dis disease))\n  (edges\n    (drg -- e -- dis treats-safely))))\n\n(define-category (druggable-gene g)\n  (concepts (drg safe-drug) (g gene))\n  (edges\n    (drg -- g regulates))))\n\n(query\n  (select\n    (curie d) (name d) (curie g) (name g) (pubmed e))\n  (concepts\n    (d safe-drug)\n    (g druggable-gene))\n  (edges\n    (d -- e -- g regulates)))\n\n\n(query\n  (select (pubmed e1) (pubmed e2))\n  (concepts\n    (d safe-drug)\n    (g1 druggable-gene)\n    (g2 gene))\n  (edges\n    (d -- e1 -- g1 regulates)\n    (g1 -- e2 -- g2 regulates))\n  (limit 10))\n\n\n; this is a comment\n(define-concept (kinome g)\n  (concept\n    (g gene)\n    (h hgnc))\n  (where\n    (synonymous g h)\n    (in-list (hgnc-id h) kinome-list)))\n\n(query\n  (concept\n    (d (from-list precomputed-drugs) drug)))\n\n(query\n  (select (pubmed e1) (pubmed e2))\n  (concepts\n    (d safe-drug)\n    (g1 druggable-gene)\n    (g2 gene))\n  (edges\n    (e1 : d regulates g1))\n  (where\n    (has-pubmed e1))\n  (limit 10))\n\n\n(define-fragment (safely-upregulates-2hop d int g)\n  (concepts\n    (d safe-drug)\n    (int gene)\n    (g gene))\n  (edge\n    (e1 : d upregulates int)\n    (e2 : int upregulates g)))\n\n(query\n  (select (name d) (name g))\n  (safely-upregulates-2hop d int g)\n  (where\n    (in-list g gene-list)))\n\n\nCompilation:\n\n(concept\n  (id category))\n=>\n(fresh (id)\n  (concepto id)\n  (category id))\n\n\n\n\n(query\n  (select\n    (curie D) (name D) (predicate Eup) (curie D) (name D) (category D)\n    (pubmed Eup [#:url #:date #:sentence]))\n  (concepts\n   (D drug)\n   (G gene))\n  (edges\n   (Eup : D upregulates G)))\n\n\n; macros for select, concepts, edges, and where syntax\n\n(define-selector-syntax pubmed\n  (syntax-parser\n    [(_ [attr ...+] edge)\n     #'(select-lambda ((property edge \"pmid\") (property edge \"publication\"))\n         ??)]))\n\n(define upregulates-list '(?? ...))\n(define-predicate-syntax upregulates\n  (lambda (_)\n    #'(predicates upregulates-list)))\n\n(define drug-categories-list '(?? ...))\n(define-category-syntax drug\n  (lambda (_)\n    #'(categories drug-categories-list))\n\n(define-category-syntax FDA-approved-drug\n  (syntax-parser\n    [(C _)\n     #'(query-fragment\n         (concepts\n           (C (categories drug-categories)))\n         (where\n           (property C \"fda-approved\" #t)))]))\n"
  },
  {
    "path": "medikanren/pieces-parts/ontology.rkt",
    "content": "#lang racket\n(provide (all-defined-out)\n         (all-from-out \"../common.rkt\" \"../mk-db.rkt\"))\n(require \"../common.rkt\" \"../mk-db.rkt\")\n\n;; helper for pretty-printing concepts\n(define get-curies/names-from-concepts\n  (lambda (s)\n    (map (lambda (c)\n           (match c\n             [`(,db ,cid ,curie ,name (,catid . ,cat) ,props)\n              (list curie name)]\n             [else\n              (error 'get-curies/names-from-concepts (format \"c didn't match:\\n~s\\n\" c))]))\n         (set->list s))))\n\n(define make-get-all-ontology-ancestors\n  (lambda (subclass_of-pred-ls ontology-prefix-str)\n    (lambda (S)\n      (define get-all-ontology-ancestors\n        (lambda (S ancestors)\n          (match (run/graph\n                   ((S S)\n                    (O #f))\n                   ((S->O subclass_of-pred-ls))\n                   (S S->O O))\n            [(list name=>concepts name=>edges)\n             (let* ((c* (hash-ref name=>concepts 'O))\n                    (c* (filter (lambda (c) (not (set-member? ancestors c))) c*))\n                    (c* (filter (lambda (c) (string-prefix? (concept->curie c) ontology-prefix-str)) c*)))\n               (cond\n                 [(null? c*) ancestors]\n                 [else\n                  (let ((ancestors (let loop ((c* c*)\n                                              (ancestors ancestors))\n                                     (match c*\n                                       ['() ancestors]\n                                       [`(,c . ,c*)\n                                        (loop c* (set-add ancestors c))]))))\n                    (get-all-ontology-ancestors c* ancestors))]))])))\n      (get-all-ontology-ancestors S (set)))))\n\n(define get-all-GO-ancestors (make-get-all-ontology-ancestors '((rtx2 15 . \"subclass_of\")) \"GO:\"))\n(define get-all-OBO:GOCHE-ancestors (make-get-all-ontology-ancestors '((rtx2 15 . \"subclass_of\")) \"OBO:GOCHE\"))\n\n#|\n;; find ancestors of \"substance with phytoestrogen role\" in OBO:GOCHE ontology:\n(get-all-OBO:GOCHE-ancestors (keep 1 (find-concepts #t (list \"OBO:GOCHE_76989\"))))\n\n=>\n\n(set\n '(rtx2\n   5606341\n   \"OBO:GOCHE_52210\"\n   \"substance with pharmacological role role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_52210\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_52210\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5088598\n   \"OBO:GOCHE_24432\"\n   \"substance with biological role role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_24432\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_24432\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   885146\n   \"OBO:GOCHE_24621\"\n   \"substance with hormone role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_24621\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_24621\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5610174\n   \"OBO:GOCHE_33280\"\n   \"substance with molecular messenger role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_33280\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_33280\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5611882\n   \"OBO:GOCHE_50112\"\n   \"substance with sex hormone role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_50112\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_50112\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5611724\n   \"OBO:GOCHE_50906\"\n   \"substance with role role\"\n   (2 . \"http://w3id.org/biolink/vocab/NamedThing\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_50906\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"named_thing\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_50906\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5606343\n   \"OBO:GOCHE_48705\"\n   \"substance with agonist role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_48705\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_48705\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   947710\n   \"OBO:GOCHE_50114\"\n   \"substance with estrogen role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_50114\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_50114\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\"))))\n|#\n\n(define make-get-all-ontology-descendants\n  (lambda (subclass_of-pred-ls ontology-prefix-str)\n    (lambda (O)\n      (define get-all-ontology-descendants\n        (lambda (O descendants)\n          (match (run/graph\n                   ((S #f)\n                    (O O))\n                   ((S->O subclass_of-pred-ls))\n                   (S S->O O))\n            [(list name=>concepts name=>edges)\n             (let* ((c* (hash-ref name=>concepts 'S))\n                    (c* (filter (lambda (c) (not (set-member? descendants c))) c*))\n                    (c* (filter (lambda (c) (string-prefix? (concept->curie c) ontology-prefix-str)) c*)))\n               (cond\n                 [(null? c*) descendants]\n                 [else\n                  (let ((descendants (let loop ((c* c*)\n                                                (descendants descendants))\n                                       (match c*\n                                         ['() descendants]\n                                         [`(,c . ,c*)\n                                          (loop c* (set-add descendants c))]))))\n                    (get-all-ontology-descendants c* descendants))]))])))\n      (get-all-ontology-descendants O (set)))))\n\n(define get-all-GO-descendants (make-get-all-ontology-descendants '((rtx2 15 . \"subclass_of\")) \"GO:\"))\n(define get-all-OBO:GOCHE-descendants (make-get-all-ontology-descendants '((rtx2 15 . \"subclass_of\")) \"OBO:GOCHE\"))\n\n#|\n;; find descendants of \"substance with estrogen role\" in OBO:GOCHE ontology:\n(get-all-OBO:GOCHE-descendants (keep 1 (find-concepts #t (list \"OBO:GOCHE_50114\"))))\n\n=>\n\n(set\n '(rtx2\n   5606174\n   \"OBO:GOCHE_76989\"\n   \"substance with phytoestrogen role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_76989\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_76989\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\")))\n '(rtx2\n   5606175\n   \"OBO:GOCHE_76988\"\n   \"substance with xenoestrogen role\"\n   (4 . \"http://w3id.org/biolink/vocab/ChemicalSubstance\")\n   ((\"iri\" . \"http://purl.obolibrary.org/obo/GOCHE_76988\")\n    (\"synonym\" . \"[]\")\n    (\"category_label\" . \"chemical_substance\")\n    (\"deprecated\" . \"False\")\n    (\"provided_by\"\n     .\n     \"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl\")\n    (\"id\" . \"OBO:GOCHE_76988\")\n    (\"update_date\" . \"2019-08-02 18:27:55 GMT\")\n    (\"publications\" . \"[]\"))))\n|#\n\n\n\n;; Examples finding the fixed-point of ancestor concepts in GO\n;; ontology.  (GO has multiple inheritance, which makes finding the\n;; fixed-point important.)\n\n#|\n;; Lymphangiogenesis\n(define S1 (keep 1 (find-concepts #t (list \"GO:0001946\"))))\n(define A1 (get-all-GO-ancestors S1))\n(pretty-print (get-curies/names-from-concepts A1))\n\n=>\n\n'((\"GO:0009653\" \"anatomical structure morphogenesis\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0048646\" \"anatomical structure formation involved in morphogenesis\")\n  (\"GO:0032502\" \"developmental process\"))\n|#\n\n#|\n;; negative regulation of cell migration involved in sprouting angiogenesis\n(define S2 (keep 1 (find-concepts #t (list \"GO:0090051\"))))\n(define A2 (get-all-GO-ancestors S2))\n(pretty-print (get-curies/names-from-concepts A2))\n\n=>\n\n'((\"GO:0010633\" \"negative regulation of epithelial cell migration\")\n  (\"GO:0065007\" \"biological regulation\")\n  (\"GO:0030334\" \"regulation of cell migration\")\n  (\"GO:0045765\" \"regulation of angiogenesis\")\n  (\"GO:0048523\" \"negative regulation of cellular process\")\n  (\"GO:0032879\" \"regulation of localization\")\n  (\"GO:0016525\" \"negative regulation of angiogenesis\")\n  (\"GO:0040013\" \"negative regulation of locomotion\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0043537\" \"negative regulation of blood vessel endothelial cell migration\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0030336\" \"negative regulation of cell migration\")\n  (\"GO:0010632\" \"regulation of epithelial cell migration\")\n  (\"GO:0051239\" \"regulation of multicellular organismal process\")\n  (\"GO:2000145\" \"regulation of cell motility\")\n  (\"GO:1901342\" \"regulation of vasculature development\")\n  (\"GO:0022603\" \"regulation of anatomical structure morphogenesis\")\n  (\"GO:0050793\" \"regulation of developmental process\")\n  (\"GO:0051271\" \"negative regulation of cellular component movement\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0043535\" \"regulation of blood vessel endothelial cell migration\")\n  (\"GO:2000026\" \"regulation of multicellular organismal development\")\n  (\"GO:0010594\" \"regulation of endothelial cell migration\")\n  (\"GO:0051270\" \"regulation of cellular component movement\")\n  (\"GO:0048519\" \"negative regulation of biological process\")\n  (\"GO:0051241\" \"negative regulation of multicellular organismal process\")\n  (\"GO:1901343\" \"negative regulation of vasculature development\")\n  (\"GO:2000181\" \"negative regulation of blood vessel morphogenesis\")\n  (\"GO:1903671\" \"negative regulation of sprouting angiogenesis\")\n  (\"GO:0051093\" \"negative regulation of developmental process\")\n  (\"GO:0010596\" \"negative regulation of endothelial cell migration\")\n  (\"GO:0090049\" \"regulation of cell migration involved in sprouting angiogenesis\")\n  (\"GO:2000146\" \"negative regulation of cell motility\")\n  (\"GO:1903670\" \"regulation of sprouting angiogenesis\")\n  (\"GO:0040012\" \"regulation of locomotion\"))\n|#\n\n#|\n;; positive regulation of execution phase of apoptosis\n(define S3 (keep 1 (find-concepts #t (list \"GO:1900119\"))))\n(define A3 (get-all-GO-ancestors S3))\n(pretty-print (get-curies/names-from-concepts A3))\n\n=>\n\n'((\"GO:0065007\" \"biological regulation\")\n  (\"GO:0042981\" \"regulation of apoptotic process\")\n  (\"GO:1900117\" \"regulation of execution phase of apoptosis\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0043067\" \"regulation of programmed cell death\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0048522\" \"positive regulation of cellular process\")\n  (\"GO:0043065\" \"positive regulation of apoptotic process\")\n  (\"GO:0010942\" \"positive regulation of cell death\")\n  (\"GO:0048518\" \"positive regulation of biological process\")\n  (\"GO:0010941\" \"regulation of cell death\")\n  (\"GO:0043068\" \"positive regulation of programmed cell death\"))\n|#\n\n#|\n;; positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis\n(define S4 (keep 1 (find-concepts #t (list \"GO:2001272\"))))\n(define A4 (get-all-GO-ancestors S4))\n(pretty-print (get-curies/names-from-concepts A4))\n\n=>\n\n'((\"GO:0065007\" \"biological regulation\")\n  (\"GO:0042981\" \"regulation of apoptotic process\")\n  (\"GO:0044093\" \"positive regulation of molecular function\")\n  (\"GO:0009893\" \"positive regulation of metabolic process\")\n  (\"GO:0019222\" \"regulation of metabolic process\")\n  (\"GO:0052547\" \"regulation of peptidase activity\")\n  (\"GO:0045862\" \"positive regulation of proteolysis\")\n  (\"GO:0051336\" \"regulation of hydrolase activity\")\n  (\"GO:0032270\" \"positive regulation of cellular protein metabolic process\")\n  (\"GO:1900117\" \"regulation of execution phase of apoptosis\")\n  (\"GO:2001056\" \"positive regulation of cysteine-type endopeptidase activity\")\n  (\"GO:0051171\" \"regulation of nitrogen compound metabolic process\")\n  (\"GO:0060255\" \"regulation of macromolecule metabolic process\")\n  (\"GO:0010950\" \"positive regulation of endopeptidase activity\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0043067\" \"regulation of programmed cell death\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0010604\" \"positive regulation of macromolecule metabolic process\")\n  (\"GO:0052548\" \"regulation of endopeptidase activity\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0048522\" \"positive regulation of cellular process\")\n  (\"GO:0051247\" \"positive regulation of protein metabolic process\")\n  (\"GO:0043065\" \"positive regulation of apoptotic process\")\n  (\"GO:0010942\" \"positive regulation of cell death\")\n  (\"GO:0010952\" \"positive regulation of peptidase activity\")\n  (\"GO:0031323\" \"regulation of cellular metabolic process\")\n  (\"GO:2000116\" \"regulation of cysteine-type endopeptidase activity\")\n  (\"GO:0051173\" \"positive regulation of nitrogen compound metabolic process\")\n  (\"GO:0048518\" \"positive regulation of biological process\")\n  (\"GO:0043085\" \"positive regulation of catalytic activity\")\n  (\"GO:0050790\" \"regulation of catalytic activity\")\n  (\"GO:0051246\" \"regulation of protein metabolic process\")\n  (\"GO:0051345\" \"positive regulation of hydrolase activity\")\n  (\"GO:0032268\" \"regulation of cellular protein metabolic process\")\n  (\"GO:0043280\" \"positive regulation of cysteine-type endopeptidase activity involved in apoptotic process\")\n  (\"GO:0010941\" \"regulation of cell death\")\n  (\"GO:2001270\" \"regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis\")\n  (\"GO:0043281\" \"regulation of cysteine-type endopeptidase activity involved in apoptotic process\")\n  (\"GO:0065009\" \"regulation of molecular function\")\n  (\"GO:0031325\" \"positive regulation of cellular metabolic process\")\n  (\"GO:1900119\" \"positive regulation of execution phase of apoptosis\")\n  (\"GO:0080090\" \"regulation of primary metabolic process\")\n  (\"GO:0030162\" \"regulation of proteolysis\")\n  (\"GO:0043068\" \"positive regulation of programmed cell death\"))\n|#\n\n#|\n;; cysteine-type endopeptidase activity involved in execution phase of apoptosis\n(define S5 (keep 1 (find-concepts #t (list \"GO:0097200\"))))\n(define A5 (get-all-GO-ancestors S5))\n(pretty-print (get-curies/names-from-concepts A5))\n\n=>\n\n'((\"GO:0097153\"\n   \"cysteine-type endopeptidase activity involved in apoptotic process\"))\n|#\n\n#|\n;; activation of JUN kinase activity\n(define S6 (keep 1 (find-concepts #t (list \"GO:0007257\"))))\n(define A6 (get-all-GO-ancestors S6))\n(pretty-print (get-curies/names-from-concepts A6))\n\n=>\n\n'((\"GO:0065007\" \"biological regulation\")\n  (\"GO:0043405\" \"regulation of MAP kinase activity\")\n  (\"GO:0044093\" \"positive regulation of molecular function\")\n  (\"GO:0023056\" \"positive regulation of signaling\")\n  (\"GO:0009893\" \"positive regulation of metabolic process\")\n  (\"GO:0019222\" \"regulation of metabolic process\")\n  (\"GO:0071900\" \"regulation of protein serine/threonine kinase activity\")\n  (\"GO:0032872\" \"regulation of stress-activated MAPK cascade\")\n  (\"GO:0080134\" \"regulation of response to stress\")\n  (\"GO:0032270\" \"positive regulation of cellular protein metabolic process\")\n  (\"GO:0045937\" \"positive regulation of phosphate metabolic process\")\n  (\"GO:0070304\" \"positive regulation of stress-activated protein kinase signaling cascade\")\n  (\"GO:0080135\" \"regulation of cellular response to stress\")\n  (\"GO:0001934\" \"positive regulation of protein phosphorylation\")\n  (\"GO:0051171\" \"regulation of nitrogen compound metabolic process\")\n  (\"GO:0060255\" \"regulation of macromolecule metabolic process\")\n  (\"GO:0050789\" \"regulation of biological process\")\n  (\"GO:0008150\" \"biological_process\")\n  (\"GO:0046328\" \"regulation of JNK cascade\")\n  (\"GO:0071902\" \"positive regulation of protein serine/threonine kinase activity\")\n  (\"GO:0031399\" \"regulation of protein modification process\")\n  (\"GO:0048583\" \"regulation of response to stimulus\")\n  (\"GO:0070302\" \"regulation of stress-activated protein kinase signaling cascade\")\n  (\"GO:0010604\" \"positive regulation of macromolecule metabolic process\")\n  (\"GO:0051338\" \"regulation of transferase activity\")\n  (\"GO:0001932\" \"regulation of protein phosphorylation\")\n  (\"GO:0010562\" \"positive regulation of phosphorus metabolic process\")\n  (\"GO:0051174\" \"regulation of phosphorus metabolic process\")\n  (\"GO:0050794\" \"regulation of cellular process\")\n  (\"GO:0048522\" \"positive regulation of cellular process\")\n  (\"GO:0009966\" \"regulation of signal transduction\")\n  (\"GO:0023051\" \"regulation of signaling\")\n  (\"GO:0051347\" \"positive regulation of transferase activity\")\n  (\"GO:0043549\" \"regulation of kinase activity\")\n  (\"GO:0043410\" \"positive regulation of MAPK cascade\")\n  (\"GO:0043506\" \"regulation of JUN kinase activity\")\n  (\"GO:0000187\" \"activation of MAPK activity\")\n  (\"GO:0051247\" \"positive regulation of protein metabolic process\")\n  (\"GO:0045859\" \"regulation of protein kinase activity\")\n  (\"GO:0042325\" \"regulation of phosphorylation\")\n  (\"GO:1902531\" \"regulation of intracellular signal transduction\")\n  (\"GO:0033674\" \"positive regulation of kinase activity\")\n  (\"GO:0032147\" \"activation of protein kinase activity\")\n  (\"GO:0031323\" \"regulation of cellular metabolic process\")\n  (\"GO:0043507\" \"positive regulation of JUN kinase activity\")\n  (\"GO:0051173\" \"positive regulation of nitrogen compound metabolic process\")\n  (\"GO:1902533\" \"positive regulation of intracellular signal transduction\")\n  (\"GO:0048518\" \"positive regulation of biological process\")\n  (\"GO:0043085\" \"positive regulation of catalytic activity\")\n  (\"GO:0048584\" \"positive regulation of response to stimulus\")\n  (\"GO:0050790\" \"regulation of catalytic activity\")\n  (\"GO:0051246\" \"regulation of protein metabolic process\")\n  (\"GO:0046330\" \"positive regulation of JNK cascade\")\n  (\"GO:0032268\" \"regulation of cellular protein metabolic process\")\n  (\"GO:0043408\" \"regulation of MAPK cascade\")\n  (\"GO:0010647\" \"positive regulation of cell communication\")\n  (\"GO:0031401\" \"positive regulation of protein modification process\")\n  (\"GO:0043406\" \"positive regulation of MAP kinase activity\")\n  (\"GO:0032874\" \"positive regulation of stress-activated MAPK cascade\")\n  (\"GO:0065009\" \"regulation of molecular function\")\n  (\"GO:0031325\" \"positive regulation of cellular metabolic process\")\n  (\"GO:0042327\" \"positive regulation of phosphorylation\")\n  (\"GO:0009967\" \"positive regulation of signal transduction\")\n  (\"GO:0010646\" \"regulation of cell communication\")\n  (\"GO:0080090\" \"regulation of primary metabolic process\")\n  (\"GO:0045860\" \"positive regulation of protein kinase activity\")\n  (\"GO:0019220\" \"regulation of phosphate metabolic process\"))\n|#\n"
  },
  {
    "path": "medikanren/pieces-parts/orange_graph.dot",
    "content": "digraph{\ngraph [ bgcolor=lightgray, fontname=Arial, fontcolor=blue, \n                         fontsize=12 ];\n\n                 node [ fontname=Arial, fontcolor=blue, fontsize=11];\n\n                 edge [ fontname=Helvetica, fontcolor=red, fontsize=10, labeldistance=2, labelangle=-50 ];\n\n    splines=\"FALSE\";\n\n    rankdir=\"LR\";\n\t\"MONDO\" -> \"NCIT\" [label=\"related_to\"]\n\t\"ClinVarVariant\" -> \"MONDO\" [label=\"related_condition\"]\n\t\"MONDO\" -> \"HP\" [label=\"has_modifier\"]\n\t\"CL\" -> \"CL\" [label=\"subclass_of\"]\n\t\"ENSEMBL\" -> \"MONDO\" [label=\"causally_related_to\"]\n\t\"OMIM\" -> \"HP\" [label=\"has_disposition\"]\n\t\"OMIM\" -> \"GENO\" [label=\"subclass_of\"]\n\t\"ClinVarVariant\" -> \"MedGen\" [label=\"causes_condition\"]\n\t\"DECIPHER\" -> \"HP\" [label=\"has_disposition\"]\n\t\"ClinVarVariant\" -> \"MONDO\" [label=\"related_to\"]\n\t\"MONDO\" -> \"HP\" [label=\"has_disposition\"]\n\t\"BNODE\" -> \"OMIM\" [label=\"contributes_to\"]\n\t\"OMIM\" -> \"OMIM\" [label=\"causes_condition\"]\n\t\"BNODE\" -> \"MONDO\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"GO\" [label=\"related_to\"]\n\t\"OMIM\" -> \"OMIM\" [label=\"biomarker_for\"]\n\t\"NCBIGene\" -> \"MONDO\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"related_to\"]\n\t\"ClinVarVariant\" -> \"OMIM\" [label=\"related_condition\"]\n\t\"MONDO\" -> \"SO\" [label=\"has_modifier\"]\n\t\"UBERON\" -> \"BFO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"PR\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"PATO\" [label=\"causally_related_to\"]\n\t\"FOODON\" -> \"NCBITaxon\" [label=\"subclass_of\"]\n\t\"HGNC\" -> \"MONDO\" [label=\"biomarker_for\"]\n\t\"FOODON\" -> \"FOODON\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"OBO\" [label=\"causally_related_to\"]\n\t\"BNODE\" -> \"OMIM\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"OBO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"UBERON\" [label=\"related_to\"]\n\t\"ClinVarVariant\" -> \"OMIM\" [label=\"related_to\"]\n\t\"MONDO\" -> \"PATO\" [label=\"subclass_of\"]\n\t\"ENSEMBL\" -> \"SO\" [label=\"subclass_of\"]\n\t\"OMIM\" -> \"MONDO\" [label=\"subclass_of\"]\n\t\"Orphanet\" -> \"MONDO\" [label=\"biomarker_for\"]\n\t\"BNODE\" -> \"OMIM\" [label=\"biomarker_for\"]\n\t\"NCBIGene\" -> \"MONDO\" [label=\"has_phenotype\"]\n\t\"ClinVarVariant\" -> \"MedGen\" [label=\"related_condition\"]\n\t\"ClinVarVariant\" -> \"Orphanet\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"CHEBI\" [label=\"related_to\"]\n\t\"OMIM\" -> \"UPHENO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"MFOMD\" [label=\"related_to\"]\n\t\"MONDO\" -> \"NCBITaxon\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"MFOEM\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"HP\" [label=\"related_to\"]\n\t\"NCBIGene\" -> \"GENO\" [label=\"subclass_of\"]\n\t\"ClinVarVariant\" -> \"MedGen\" [label=\"related_to\"]\n\t\"HP\" -> \"HP\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"causally_related_to\"]\n\t\"BNODE\" -> \"Orphanet\" [label=\"causes_condition\"]\n\t\"HP\" -> \"UPHENO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"GO\" [label=\"causally_related_to\"]\n\t\"NCBIGene\" -> \"Orphanet\" [label=\"biomarker_for\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"subclass_of\"]\n\t\"NCBIGene\" -> \"OMIM\" [label=\"has_phenotype\"]\n\t\"MONDO\" -> \"NBO\" [label=\"related_to\"]\n\t\"ClinVarVariant\" -> \"Orphanet\" [label=\"related_condition\"]\n\t\"ClinVarVariant\" -> \"NCBIGene\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"UBERON\" [label=\"causally_related_to\"]\n\t\"BNODE\" -> \"MONDO\" [label=\"contributes_to\"]\n\t\"MONDO\" -> \"FOODON\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"BFO\" [label=\"subclass_of\"]\n\t\"NCBIGene\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"MONDO\" -> \"NCBITaxon\" [label=\"in_taxon\"]\n\t\"MONDO\" -> \"CL\" [label=\"causally_related_to\"]\n\t\"DOID\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"NCBIGene\" -> \"MONDO\" [label=\"contributes_to\"]\n\t\"MONDO\" -> \"OMIM\" [label=\"subclass_of\"]\n\t\"NCBIGene\" -> \"NCBIGene\" [label=\"contributes_to\"]\n\t\"NCBIGene\" -> \"CHR\" [label=\"is_subsequence_of\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"has_phenotype\"]\n\t\"MONDO\" -> \"CHEBI\" [label=\"causally_related_to\"]\n\t\"OMIM\" -> \"HP\" [label=\"subclass_of\"]\n\t\"Orphanet\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"BNODE\" -> \"MONDO\" [label=\"causes_condition\"]\n\t\"ENSEMBL\" -> \"MONDO\" [label=\"biomarker_for\"]\n\t\"OMIM\" -> \"OMIM\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"NCBITaxon\" [label=\"transmitted_by\"]\n\t\"OMIM\" -> \"MONDO\" [label=\"contributes_to\"]\n\t\"MONDO\" -> \"HP\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"NCIT\" [label=\"disease_has_feature\"]\n\t\"MONDO\" -> \"HGNC\" [label=\"causally_related_to\"]\n\t\"ClinVarVariant\" -> \"NCBIGene\" [label=\"related_condition\"]\n\t\"NCBIGene\" -> \"OMIM\" [label=\"contributes_to\"]\n\t\"ENSEMBL\" -> \"CHR\" [label=\"is_subsequence_of\"]\n\t\"HGNC\" -> \"MONDO\" [label=\"causally_related_to\"]\n\t\"NCBIGene\" -> \"MONDO\" [label=\"causes_condition\"]\n\t\"OMIM\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"NCBIGene\" -> \"NCBIGene\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"PATO\" [label=\"has_modifier\"]\n\t\"MONDO\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"CHR\" -> \"SO\" [label=\"subclass_of\"]\n\t\"NCBIGene\" -> \"MONDO\" [label=\"biomarker_for\"]\n\t\"MONDO\" -> \"ENSEMBL\" [label=\"causally_related_to\"]\n\t\"DECIPHER\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"MONDO\" -> \"NCIT\" [label=\"has_modifier\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"disease_has_feature\"]\n\t\"Orphanet\" -> \"MONDO\" [label=\"causally_related_to\"]\n\t\"OMIM\" -> \"MONDO\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"GO\" [label=\"disease_relationship\"]\n\t\"MONDO\" -> \"NBO\" [label=\"causally_related_to\"]\n\t\"NCBIGene\" -> \"NCBIGene\" [label=\"biomarker_for\"]\n\t\"NCBIGene\" -> \"OMIM\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"UBERON\" [label=\"disease_relationship\"]\n\t\"MONDO\" -> \"OBA\" [label=\"disease_has_feature\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"contributes_to\"]\n\t\"Orphanet\" -> \"SO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"CL\" [label=\"disease_relationship\"]\n\t\"MONDO\" -> \"ENVO\" [label=\"causally_related_to\"]\n\t\"HGNC\" -> \"CHR\" [label=\"is_subsequence_of\"]\n\t\"MONDO\" -> \"UPHENO\" [label=\"subclass_of\"]\n\t\"MESH\" -> \"HP\" [label=\"has_phenotype\"]\n\t\"NCBIGene\" -> \"OMIM\" [label=\"biomarker_for\"]\n\t\"HGNC\" -> \"SO\" [label=\"subclass_of\"]\n\t\"GO\" -> \"GO\" [label=\"subclass_of\"]\n\t\"NCBIGene\" -> \"HP\" [label=\"has_disposition\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"has_modifier\"]\n\t\"ClinVarVariant\" -> \"MONDO\" [label=\"causes_condition\"]\n\t\"NCBIGene\" -> \"Orphanet\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"HP\" [label=\"disease_has_feature\"]\n\t\"MONDO\" -> \"MONDO\" [label=\"causes_condition\"]\n\t\"BNODE\" -> \"SO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"NCBIGene\" [label=\"causally_related_to\"]\n\t\"OMIM\" -> \"SO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"UBERON\" [label=\"has_modifier\"]\n\t\"NCBIGene\" -> \"SO\" [label=\"subclass_of\"]\n\t\"MONDO\" -> \"CL\" [label=\"disease_has_location\"]\n\t\"ClinVarVariant\" -> \"OMIM\" [label=\"causes_condition\"]\n\t\"MONDO\" -> \"UBERON\" [label=\"disease_has_location\"]\n\t\"MONDO\" -> \"MF\" [label=\"causally_related_to\"]\n\t\"MONDO\" -> \"PO\" [label=\"causally_related_to\"]\n\t\"UBERON\" -> \"CARO\" [label=\"subclass_of\"]\n\t\"OMIM\" -> \"OMIM\" [label=\"contributes_to\"]\n}\n"
  },
  {
    "path": "medikanren/pieces-parts/propagator.rkt",
    "content": "#lang racket/base\n(provide group-curie group-curies group-categories group-concepts\n         concept/any concept/category concept/curie-filter concept/curie\n         edge/predicate edge/predicate/filter run!)\n(require \"synonymize.rkt\"\n         racket/function racket/list (except-in racket/match ==) racket/set)\n\n;; Simple OO\n;; TODO: () should summarize supported messages\n(define (method-unknown name . args) (error \"unknown method:\" name args))\n(define (method-except m names)\n  (lambda (name . args)\n    (apply (if (member name names) method-unknown m) name args)))\n(define (method-only m names)\n  (lambda (name . args)\n    (apply (if (member name names) m method-unknown) name args)))\n(define-syntax method-choose\n  (syntax-rules (else)\n    ((_ ((name ...) body ...) ... (else else-body ...))\n     (lambda (method-name . args)\n       (apply (case method-name\n                ((name ...) body ...) ...\n                (else       else-body ...))\n              method-name args)))\n    ((_ body ...) (method-choose body ... (else method-unknown)))))\n(define-syntax method-lambda\n  (syntax-rules (else)\n    ((_ ((name . param) body ...) ... (else else-body ...))\n     (method-choose ((name) (lambda (_ . param) body ...)) ... (else else-body ...)))\n    ((_ body ...) (method-lambda body ... (else method-unknown)))))\n\n;; TODO: priorities change and propagators are redundantly scheduled (though\n;; that might mitigate some of the priority changes).  Fix these issues by\n;; having propagators track their own scheduling and cost changes.\n;; Heap as priority queue\n(define (heap-top h) (vector-ref h 0))\n(define (heap! ? h end)\n  (let loop ((i (- (quotient end 2) 1)))\n    (when (<= 0 i) (heap-sink! ? h end i) (loop (- i 1)))))\n(define (heap-remove! ? h end)\n  (vector-set! h 0 (vector-ref h (- end 1))) (heap-sink! ? h (- end 1) 0))\n(define (heap-replace! ? h end top)\n  (vector-set! h 0 top)                      (heap-sink! ? h    end    0))\n(define (heap-sink! ? h end i)\n  (let loop ((i i))\n    (let ((ileft (+ i i 1)) (iright (+ i i 2)))\n      (cond ((<= end ileft))  ;; done\n            ((<= end iright)\n             (let ((p (vector-ref h i)) (l (vector-ref h ileft)))\n               (when (? l p) (vector-set! h i l) (vector-set! h ileft p))))\n            (else (let ((p (vector-ref h i))\n                        (l (vector-ref h ileft)) (r (vector-ref h iright)))\n                    (cond ((? l p) (cond ((? r l) (vector-set! h i r)\n                                                  (vector-set! h iright p)\n                                                  (loop iright))\n                                         (else (vector-set! h i l)\n                                               (vector-set! h ileft p)\n                                               (loop ileft))))\n                          ((? r p) (vector-set! h i r)\n                                   (vector-set! h iright p)\n                                   (loop iright)))))))))\n(define (heap-add! ? h end v)\n  (let loop ((i end))\n    (if (= i 0) (vector-set! h i v)\n      (let* ((iparent (- (quotient (+ i 1) 2) 1))\n             (pv      (vector-ref h iparent)))\n        (cond ((? v pv) (vector-set! h i pv) (loop iparent))\n              (else     (vector-set! h i v)))))))\n\n;; Propagators\n(define (pgroup curie)\n  (define synonyms (curie-synonyms curie))\n  (define curies (set->list synonyms))\n  (define first-curie (foldl string-min (car curies) (cdr curies)))\n  (define cs         #f)\n  (define categories #f)\n  (define (force!)\n    (unless cs\n      (set! cs (find-concepts #t (set->list synonyms)))\n      (set! categories\n        (list->set (map cons (map car cs)\n                        (map (lambda (c) (cadddr (cdr c))) cs))))))\n  (method-lambda\n    ((curie)      first-curie)\n    ((curies)     synonyms)\n    ((categories) (force!) categories)\n    ((concepts)   (force!) cs)))\n(define (curies->groups curies)\n  (sort (cdr (foldl (lambda (c acc)\n                      (let ((seen (car acc)) (groups (cdr acc)))\n                        (if (set-member? seen c) acc\n                          (let ((g (curie->group c)))\n                            (cons (set-union seen (group-curies g))\n                                  (cons g groups))))))\n                    (cons (set) '())\n                    curies))\n        groupset (map group-curie as))\n             (list->set (map group-curie bs))))\n    ;; TODO: if we ever find a way to reduce categories, this is not sound.\n    ((`(,tag-a . ,_) `(,tag-b . ,_))\n     (equal? tag-a tag-b))))\n\n(define (concept-intersect ca cb)\n  (if (eq? ca cb) ca\n    (match* (ca cb)\n      (('(any) _)      cb)\n      ((_ '(any)) ca)\n      ((`(concept . ,_) `(category     . ,_)) (concept-intersect cb ca))\n      ((`(concept . ,_) `(curie-filter . ,_)) (concept-intersect cb ca))\n      ((`(category . ,cats) `(concept  . ,groups))\n       (define (valid-group? g)\n         (ormap (lambda (cat) (set-member? (group-categories g) cat)) cats))\n       `(concept . ,(filter valid-group? groups)))\n      ((`(curie-filter . ,f) `(concept . ,groups))\n       (define (valid-group? g) (ormap f (set->list (group-curies g))))\n       `(concept . ,(filter valid-group? groups)))\n      ((`(concept . ,as) `(concept  . ,bs))\n       (define changed? #f)\n       (define result\n         (let loop ((as as) (bs bs))\n           (if (or (null? as) (null? bs)) '()\n             (let ((a (car as)) (b (car bs)))\n               (cond ((groupgroups curies)))\n      (`(category . ,cats)\n        (concept-intersect c `(concept . ,(curies->groups curies))))\n      (`(curie-filter . ,f)\n        (concept-intersect c `(concept . ,(curies->groups curies))))\n      (`(concept . ,gs)\n        (define (valid-group? g)\n          (ormap (lambda (curie) (group-member? g curie)) curies))\n        `(concept . ,(filter valid-group? gs))))\n    c))\n\n;; TODO: these should look at the object at the same time, to avoid including\n;; irrelevant edges when possible.\n(define (edge-constrain/subject e c)\n  (match c\n    ;; TODO: optionally find edges with only category/any constraints\n    ('(any)               e)\n    (`(category . ,_)     e)\n    (`(curie-filter . ,_) e)\n    (`(concept  . ,gs)\n      (match e\n        (`(edge . ,es)\n          (define (valid-eg? e)\n            (ormap (lambda (g) (group-member? g (cadr (caddr e)))) gs))\n          `(edge . ,(filter valid-eg? es)))\n        (`(predicate ,ps ,valid?)\n          (define cs (append* (map group-concepts gs)))\n          (define es0 (run* (e) (fresh (s o p db eid erest)\n                                  (== e `(,db ,eid ,s ,o ,p . ,erest))\n                                  (membero `(,db . ,s) cs)\n                                  (membero `(,db . ,p) ps)\n                                  (edgeo e))))\n          (define es (if valid? (filter valid? es0) es0))\n          `(edge . ,es))))))\n\n(define (edge-constrain/object e c)\n  (match c\n    ;; TODO: optionally find edges with only category/any constraints\n    ('(any)               e)\n    (`(category . ,_)     e)\n    (`(curie-filter . ,_) e)\n    (`(concept  . ,gs)\n      (match e\n        (`(edge . ,es)\n          (define (valid-eg? e)\n            (ormap (lambda (g) (group-member? g (cadr (cadddr e)))) gs))\n          `(edge . ,(filter valid-eg? es)))\n        (`(predicate ,ps ,valid?)\n          (define cs (append* (map group-concepts gs)))\n          (define es0 (run* (e) (fresh (s o p db eid erest)\n                                         (== e `(,db ,eid ,s ,o ,p . ,erest))\n                                         (membero `(,db . ,o) cs)\n                                         (membero `(,db . ,p) ps)\n                                         (edgeo e))))\n          (define es (if valid? (filter valid? es0) es0))\n          `(edge . ,es))))))\n\n(define (edge-subjects e)\n  (match e\n    (`(edge . ,es) (map (lambda (e) (cadr (caddr  e))) es))\n    (_             #f)))\n(define (edge-objects e)\n  (match e\n    (`(edge . ,es) (map (lambda (e) (cadr (cadddr e))) es))\n    (_             #f)))\n\n(define (concept-cost c)\n  (match c\n    (`(concept . ,gs) (foldl + 0 (map (lambda (g) (set-count (group-curies g)))\n                                      gs)))\n    (_                0)))\n(define (edge-cost e)\n  (match e\n    (`(edge . ,es) (length es))\n    (_             0)))\n\n(define (concept/any) (cell concept=? '(any)))\n(define (concept/category categories)\n  (cell concept=? (cons 'category (find-exact-categories categories))))\n(define (concept/curie curie)\n  (cell concept=? (cons 'concept (list (curie->group curie)))))\n(define (concept/curie-filter f) (cell concept=? (cons 'curie-filter f)))\n\n(define (edge/predicate predicates subject object)\n  (edge/predicate/filter #f predicates subject object))\n(define (edge/predicate/filter valid? predicates subject object)\n  (define ps (if predicates (find-exact-predicates predicates)\n               (run* (p) (predicateo p))))\n  (define edge (cell equal? (list 'predicate ps valid?)))\n  (propagator\n    (list subject)\n    (thunk (concept-cost (subject 'ref)))\n    (thunk\n     #|\n      (displayln `(running subject update: ,(concept-cost (subject 'ref))\n                           ,(car (subject 'ref))\n                           ,(length (cdr (subject 'ref)))))\n     |#\n      (edge 'set! (edge-constrain/subject (edge 'ref) (subject 'ref)))))\n  (propagator\n    (list object)\n    (thunk (concept-cost (object 'ref)))\n    (thunk\n     #|\n      (displayln `(running object update: ,(concept-cost (object 'ref))\n                           ,(car (object 'ref))\n                           ,(length (cdr (object 'ref)))))\n     |#\n      (edge 'set! (edge-constrain/object  (edge 'ref) (object  'ref)))))\n  (propagator\n    (list edge)\n    (thunk (edge-cost (edge 'ref)))\n    (thunk\n     #|\n      (displayln `(running edge update: ,(edge-cost (edge 'ref))\n                           ,(car (edge 'ref))))\n     |#\n      (define e (edge 'ref))\n      (subject 'set! (concept-constrain (subject 'ref) (edge-subjects e)))\n      (object  'set! (concept-constrain (object  'ref) (edge-objects  e)))))\n  edge)\n"
  },
  {
    "path": "medikanren/pieces-parts/query.rkt",
    "content": "#lang racket/base\n(provide summarize summarize/assoc query query/graph report/query\n         ranked-paths pretty-ranked edges/ranked\n         curies/query synonyms/query edges/query\n         positively-regulates negatively-regulates drug-safe\n         edges-between\n         gene drug disease phenotype\n         (all-defined-out)\n         (all-from-out \"../common.rkt\" \"../mk-db.rkt\"\n                       \"propagator.rkt\" \"synonymize.rkt\" \"ontology.rkt\"))\n(require \"../common.rkt\" \"../mk-db.rkt\" \"propagator.rkt\" \"synonymize.rkt\" \"ontology.rkt\"\n         racket/list (except-in racket/match ==) racket/pretty\n         racket/set racket/string)\n\n#|\n;; ** rtx2 neutral predicates -- do we want to include these somewhere? **\n\n\"regulates_expression_of\"\n\"regulates_activity_of\"\n\"targets\"\n|#\n\n(define gene/protein-concept?\n  (lambda (x)\n    (or\n     (string-prefix? x \"HGNC:\")\n     (string-prefix? x \"ENSEMBL:\")\n     (string-prefix? x \"UniProtKB:\")\n     (string-prefix? x \"NCBIGene:\")\n     (string-prefix? x \"NCBIGENE:\"))))\n\n(define drug-concept?\n  (lambda (x)\n    (or (string-prefix? x \"CHEBI:\")\n        (string-prefix? x \"CHEMBL:\")\n        (string-prefix? x \"CHEMBL.\")\n        (string-prefix? x \"KEGG:\")\n        (string-prefix? x \"KEGG.\")\n        (string-prefix? x \"DRUGBANK:\")\n        (string-prefix? x \"RXNORM:\"))))\n\n(define disease-concept?\n  (lambda (x)\n    (or (string-prefix? x \"OMIM:\")\n        (string-prefix? x \"DOID:\")\n        (string-prefix? x \"MONDO:\")\n        (string-prefix? x \"HP:\"))))\n\n(define positively-regulates '(;; common\n                               \"causes\" \"positively_regulates\" \"produces\"\n                               ;; robokop\n                               \"decreases_degradation_of\"\n                               \"increases_secretion_of\"\n                               \"increases_transport_of\"\n                               \"increases_activity_of\"\n                               \"increases_synthesis_of\"\n                               \"increases_expression_of\"\n                               \"positively_regulates__entity_to_entity\"\n                               ;; orange\n                               \"causes_condition\"\n                               \"contributes_to\"\n                               ;; rtx2\n                               \"directly_positively_regulates\"\n                               \"stimulates\"\n                               \"activator\"\n                               \"augments\"\n                               \"induces\"\n                               \"cause_of\"\n                               \"causes_or_contributes_to\"\n                               \"contributes_to_condition\"\n                               ))\n(define negatively-regulates '(;; common\n                               \"prevents\" \"negatively_regulates\"\n                               ;; semmed\n                               ;; robokop\n                               \"decreases_secretion_of\"\n                               \"decreases_transport_of\"\n                               \"decreases_activity_of\"\n                               \"decreases_synthesis_of\"\n                               \"decreases_expression_of\"\n                               \"increases_degradation_of\"\n                               \"negatively_regulates__entity_to_entity\"\n                               \"disrupts\"\n                               ;; orange\n                               ;; rtx2\n                               \"directly_negatively_regulates\"\n                               \"inhibits\"\n                               \"inhibitor\"\n                               \"channel_blocker\"\n                               \"treats\"\n                               \"disrupts\"\n                               \"may_inhibit_effect_of\"\n                               \"may_prevent\"\n                               \"may_treat\"\n                               ))\n(define drug-safe            '(;; rtx2\n                               \"clinically_tested_approved_unknown_phase\"\n                               \"clinically_tested_terminated_phase_2\"\n                               \"clinically_tested_terminated_phase_3\"\n                               \"clinically_tested_terminated_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2_or_phase_3\"\n                               \"clinically_tested_withdrawn_phase_2\"\n                               \"clinically_tested_suspended_phase_2\"\n                               \"clinically_tested_suspended_phase_3\"\n                               \"clinically_tested_suspended_phase_2_or_phase_3\"\n                               \"has_tradename\"\n                               ))\n(define gene      '(;; semmed\n                    \"gene\"\n                    ;; robokop\n                    \"(\\\"named_thing\\\" \\\"gene\\\")\"\n                    ;; orange\n                    \"(\\\"gene\\\")\"\n                    \"(\\\"genomic entity\\\" \\\"gene\\\")\"\n                    \"(\\\"gene\\\" \\\"genomic entity\\\")\"\n                    ;; rtx2\n                    \"http://w3id.org/biolink/vocab/Gene\"\n                    ))\n(define protein   '(;; semmed\n                    \"biological_entity\" ;; with \\\"Amino Acid, Peptide, or Protein\\\" in \"umls_type_label\"\n                    ;; robokop\n                    ;; orange\n                    \"(\\\"gene\\\" \\\"genomic entity\\\")\"\n                    ;; rtx2\n                    \"http://w3id.org/biolink/vocab/Protein\"\n                    ;; \"http://w3id.org/biolink/vocab/NamedThing\" ;; ugh\n                    ))\n(define gene-or-protein (set->list (set-union gene protein)))\n(define drug      '(;; semmed\n                    \"chemical_substance\"\n                    ;; robokop\n                    \"(\\\"named_thing\\\" \\\"chemical_substance\\\")\"\n                    ;; orange?\n                    ;; rtx2\n                    \"http://w3id.org/biolink/vocab/Drug\"\n                    \"http://w3id.org/biolink/vocab/ChemicalSubstance\"\n                    \"http://w3id.org/biolink/vocab/Chemical_Substance\"\n                    ))\n(define disease   '(;; semmed\n                    \"disease_or_phenotypic_feature\"\n                    ;; robokop\n                    \"(\\\"named_thing\\\" \\\"disease\\\")\"\n                    \"(\\\"named_thing\\\" \\\"genetic_condition\\\" \\\"disease\\\")\"\n                    \"(\\\"named_thing\\\" \\\"disease\\\" \\\"phenotypic_feature\\\")\"\n                    \"(\\\"named_thing\\\" \\\"genetic_condition\\\" \\\"disease\\\" \\\"phenotypic_feature\\\")\"\n                    ;; orange\n                    \"(\\\"disease\\\")\"\n                    ;; rtx2\n                    \"http://w3id.org/biolink/vocab/Disease\"\n                    ))\n(define phenotype '(;; semmed\n                    \"phenotypic_feature\"\n                    ;; robokop\n                    \"(\\\"named_thing\\\" \\\"phenotypic_feature\\\")\"\n                    ;; orange\n                    \"(\\\"phenotypic feature\\\")\"\n                    ;; rtx2\n                    \"http://w3id.org/biolink/vocab/PhenotypicFeature\"\n                    \"http://w3id.org/biolink/vocab/Phenotypic_Feature\"\n                    ))\n\n(define imatinib \"UMLS:C0935989\")\n(define asthma   \"UMLS:C0004096\")\n\n(define (edges-between c1 c2)\n  (define c1s (curie->concepts c1))\n  (define c2s (curie->concepts c2))\n  (run* (e) (fresh (s o p db eid erest)\n              (== e `(,db ,eid ,s ,o ,p . ,erest))\n              (membero `(,db . ,s) c1s)\n              (membero `(,db . ,o) c2s)\n              (edgeo e))))\n\n(define (path->edges path)\n  (if (and (pair? path) (null? (cdr path))) '()\n    (cons (take path 3) (path->edges (drop path 2)))))\n\n;; TODO: catch naming errors\n(define (query concepts edge-constraints paths)\n  (define edges (append* (map path->edges paths)))\n  (define csets (map cons (map car concepts)\n                     (map (lambda (c)\n                            (cond ((string? c)    (concept/curie c))\n                                  ((not c)        (concept/any))\n                                  ((procedure? c) (concept/curie-filter c))\n                                  (else           (concept/category c))))\n                          (map cdr concepts))))\n  (define esets\n    (map (lambda (e) (let* ((s       (car e))\n                            (p       (cadr e))\n                            (o       (caddr e))\n                            (scxs    (cdr (assoc s csets)))\n                            (ocxs    (cdr (assoc o csets)))\n                            (ecxs    (cdr (assoc p edge-constraints)))\n                            (preds   (car ecxs))\n                            (efilter (and (pair? (cdr ecxs)) (cadr ecxs))))\n                       (cons p (edge/predicate/filter efilter preds scxs ocxs))))\n         edges))\n  (cons paths (append csets esets)))\n\n(define (summarize-edge es)\n  (map (lambda (e) (list (car e) (cadr e) (car (cddddr e))\n                         (cons (cadr (caddr  e)) (caddr (caddr  e)))\n                         (cons (cadr (cadddr e)) (caddr (cadddr e)))))\n       es))\n(define (summarize-concept gs)\n  (map (lambda (curies) (map (lambda (c) (take c 4))\n                             (find-concepts #t curies)))\n       (map set->list (map group-curies gs))))\n(define (summarize cell)\n  (match (cell 'ref)\n    (`(edge    . ,es) `(edge    . ,(summarize-edge    es)))\n    (`(concept . ,gs) `(concept . ,(summarize-concept gs)))\n    (v                v)))\n(define (summarize/assoc named-cells)\n  (map cons (map car named-cells) (map summarize (map cdr named-cells))))\n\n(define-syntax-rule (query/graph ((concept-name initial) ...)\n                                 ((edge-name edge-constraints ...) ...)\n                                 path ...)\n  (let ((q (query `((concept-name . ,initial)   ...)\n                  `((edge-name ,edge-constraints ...) ...)\n                  '(path ...))))\n    (run!)\n    q))\n\n(define (curie-norm gs curie)\n  (group-curie (findf (lambda (g) (set-member? (group-curies g) curie)) gs)))\n\n(define (report/query q)\n  (define paths       (car q))\n  (define named-cells (cdr q))\n  (define kvs (map (lambda (nc) (cons (car nc) ((cdr nc) 'ref)))\n                   named-cells))\n  (define csets (filter (lambda (kv) (eq? (cadr kv) 'concept)) kvs))\n  (define esets (filter (lambda (kv) (eq? (cadr kv) 'edge))    kvs))\n  `((concepts: . ,(map (lambda (cset) `(,(car cset) ,(length (cddr cset))))\n                       csets))\n    (edges: . ,(map (lambda (eset) `(,(car eset) ,(length (cddr eset))))\n                    esets))))\n\n(define (ranked-paths q)\n  (define paths       (car q))\n  (define named-cells (cdr q))\n  (define kvs (map (lambda (nc) (cons (car nc) ((cdr nc) 'ref)))\n                   named-cells))\n  (define csets (filter (lambda (kv) (eq? (cadr kv) 'concept)) kvs))\n  (define esets (filter (lambda (kv) (eq? (cadr kv) 'edge))    kvs))\n  (define e=>s\n    (foldl (lambda (path e=>s)\n             (foldl (lambda (edge e=>s)\n                      (define ename (cadr  edge))\n                      (define sname (car   edge))\n                      (hash-set e=>s ename (cddr (assoc sname csets))))\n                    e=>s (path->edges path)))\n           (hash) paths))\n  (define e=>o\n    (foldl (lambda (path e=>o)\n             (foldl (lambda (edge e=>o)\n                      (define ename (cadr  edge))\n                      (define oname (caddr edge))\n                      (hash-set e=>o ename (cddr (assoc oname csets))))\n                    e=>o (path->edges path)))\n           (hash) paths))\n  (define (augment sgs ogs es)\n    (map (lambda (kv)\n           (define key (car kv))\n           (define es  (cdr kv))\n           (define sg (car key))\n           (define og (cdr key))\n           (list key (augmented-edge-confidence sg og es) es))\n         (hash->list\n           (foldl (lambda (e acc)\n                    (define snorm (curie-norm sgs (cadr (caddr  e))))\n                    (define onorm (curie-norm ogs (cadr (cadddr e))))\n                    (define key (cons snorm onorm))\n                    (define existing (hash-ref acc key #f))\n                    (hash-set acc key (if existing (cons e existing) (list e))))\n                  (hash) es))))\n  (define e=>aes\n    (make-immutable-hash\n      (map (lambda (kv)\n             (define sgs (hash-ref e=>s (car kv)))\n             (define ogs (hash-ref e=>o (car kv)))\n             (define aes (augment sgs ogs (cddr kv)))\n             (cons (car kv) aes))\n           esets)))\n  (define (path-instances path)\n    (let loop ((edges (path->edges path)) (lhs #f))\n      (if (null? edges) '(())\n        (let ((aes (hash-ref e=>aes (cadar edges))))\n          (append* (map (lambda (ae)\n                          (define key   (car   ae))\n                          (define snorm (car   key))\n                          (define onorm (cdr   key))\n                          (if (or (not lhs) (equal? lhs snorm))\n                            (map (lambda (suffix) (cons ae suffix))\n                                 (loop (cdr edges) onorm))\n                            '()))\n                        aes))))))\n  (define path-results\n    (map (lambda (path)\n           (cons path (sort (map (lambda (p) (cons (path-confidence p) p))\n                                 (path-instances path))\n                            (lambda (pa pb) (> (car pa) (car pb))))))\n         paths))\n  path-results)\n\n(define (take/n xs n)\n  (if (or (null? xs) (= n 0)) '() (cons (car xs) (take/n (cdr xs) (- n 1)))))\n\n(define (edges/ranked-with-key ranked path-pos edge-pos key)\n  (define path-report (list-ref ranked path-pos))\n  (define instances   (cdr path-report))\n  (list-ref (cdr (findf (lambda (i) (equal? (car (list-ref (cdr i) edge-pos)) key))\n                        instances))\n            edge-pos))\n\n(define (edges/ranked ranked path-pos edge-pos)\n  (define path-report (list-ref ranked path-pos))\n  (define instances   (cdr path-report))\n  (map (lambda (instance) (list-ref (cdr instance) edge-pos))\n       instances))\n\n(define (edges/query  q name) (cdr ((cdr (assoc name q)) 'ref)))\n(define (curies/query q name)\n  (map group-curie (cdr ((cdr (assoc name q)) 'ref))))\n(define (synonyms/query q name)\n  (map group-curies (cdr ((cdr (assoc name q)) 'ref))))\n\n(define (pretty-ranked ranked (n #f))\n  (for ((path-report ranked))\n       (define instances (cdr path-report))\n       (displayln `(path: ,(length instances) ,(car path-report)))\n       (pretty-print\n         (map (lambda (pi)\n                (define confidence          (car pi))\n                (define pes        (map car (cdr pi)))\n                (define npes (map (lambda (pe) (cons (curie->name (car pe))\n                                                     (curie->name (cdr pe))))\n                                  pes))\n                (list confidence pes npes))\n              (if n (take/n instances n) instances)))))\n\n;; TODO: do these values make sense?\n(define (base-edge-confidence edge)\n  (define (umls? curie) (or (string-prefix? curie \"UMLS:\")\n                            (string-prefix? curie \"CUI:\")))\n  (match edge\n    (`(uab-pmi . ,_) 1.0)\n    (`(semmed  . ,_) 0.4)\n    (`(,_ ,_ (,_ ,subject-curie . ,_) (,_ ,object-curie . ,_) . ,rest)\n      (if (or (umls? subject-curie) (umls? object-curie)) 0.4 0.7))))\n\n;; TODO: relevance ranking? drug safety?\n(define (edge-confidence edge)\n  (define base (base-edge-confidence edge))\n  ;; TODO: examine publications, subject/object scores, and other evidence\n  base)\n\n(define (augmented-edge-confidence sg og es)\n  ;(define (weight-linear+1 n) (+ 1 n))\n  (define (weight-exponential n) (expt 2 n))\n  (define weight weight-exponential)\n  (define support (- 1 (/ 1.0 (weight (length es)))))\n  (define base (apply max (map edge-confidence es)))\n  (+ base (* (- 1 base) support)))\n\n(define (path-confidence aes) (foldl * 1 (map cadr aes)))\n\n;; TODO: bayesian concept-based or edge-based reinforcement\n\n;; multiple edges (an edge set) between two synonym sets\n;;   take max base confidence + accumulate all pubs and evidence?\n\n;compute edge confidences:\n  ;(f (* edge-base subject-xref-base object-xref-base) pubs evidence)\n\n;;; multiply sub-path confidence between this concept and every other known concept node\n;;; intuition: if there is no path to an anchor node, that's confidence 0, and\n;;; multiplied by anything is 0, meaning this concept should not be included\n;compute concept confidences:\n  ;(* concept-xref-base\n     ;(apply * (map (apply max (map (path-confidence path)\n                                   ;(paths-to known-concept)))\n                   ;known-concepts)))\n\n;;; to rank edges, first rank solved unknown concepts\n;;; return best concept's best paths to each anchor node\n;;; gradually swap in lower-confidence edges and adjust best concept's confidence downward to match\n;;; if best concept is no longer best, swap in new best, and repeat until all edges are returned\n;;; ... or just let the upstream reporter report edges specific to selected unknown results\n\n\n(load-databases #t)\n\n\n;;;; RHOBTB2 Queries\n\n;; 1-hop\n#|\n(displayln \"\\nRunning 1-hop rhobtb2 query:\")\n(define q (time (query/graph\n                  ((X       #f)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->rhobtb2 negatively-regulates))\n                  (X X->rhobtb2 rhobtb2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q)))\n(pretty-ranked ranked)\n|#\n\n\n;; Unconstrained 2-hop\n#|\n(displayln \"\\nRunning 2-hop rhobtb2 query:\")\n(define q (time (query/graph\n                  ((X       #f)\n                   (Y       #f)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates))\n                  (X X->Y Y Y->rhobtb2 rhobtb2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q)))\n(pretty-ranked ranked)\n|#\n\n\n;; Constrained 2-hop\n#|\n(displayln \"\\nRunning 2-hop rhobtb2 query with concept categories:\")\n(define q (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates))\n                  (X X->Y Y Y->rhobtb2 rhobtb2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q)))\n(pretty-ranked ranked)\n|#\n\n#|\n(displayln \"\\nRunning 2-hop rhobtb2 query with concept categories via curie filter:\")\n(define q (time (query/graph\n                  ((X       drug-concept?)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates))\n                  (X X->Y Y Y->rhobtb2 rhobtb2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q)))\n(pretty-ranked ranked)\n|#\n\n#|\n(displayln \"\\nRunning 2-hop rhobtb2 query with concept categories w/ edge filter:\")\n(define ((edge/db? db) e) (eq? db (car e)))\n(define q (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\"))\n                  ((X->Y       negatively-regulates (edge/db? 'robokop))\n                   ;(X->Y       negatively-regulates (edge/db? 'semmed))\n                   (Y->rhobtb2 positively-regulates (edge/db? 'uab-pmi)))\n                  (X X->Y Y Y->rhobtb2 rhobtb2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q)))\n(pretty-ranked ranked)\n|#\n\n;; Drug safety constraint\n#|\n(displayln \"\\nRunning 2-hop rhobtb2 query with concept categories:\")\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q3)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked3 (time (ranked-paths q3)))\n(pretty-ranked (take ranked3 1))\n;(pretty-ranked (drop ranked3 1))\n|#\n\n\n;; has_tradename constraint\n#|\n(define q4 (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (rhobtb2 \"UMLS:C1425762\")\n                   (T       #f))\n                  ((X->Y       negatively-regulates)\n                   (Y->rhobtb2 positively-regulates)\n                   (X->T       '(\"has_tradename\")))\n                  (X X->Y Y Y->rhobtb2 rhobtb2)\n                  (X X->T T))))\n(define ranked4 (time (ranked-paths q4)))\n(pretty-ranked (take ranked4 1))\n\n;(pretty-ranked (drop ranked4 1))\n;(curies/query q4 'T)\n;(edges/query q4 'X->T)\n|#\n\n\n\n\n;;;; TMPRSS2 Queries\n\n;; 2-hop down-up\n#|\n(displayln \"\\nRunning 2-hop tmprss2 down-up query with concept categories:\")\n(define q1 (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (tmprss2 \"UMLS:C1336641\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->tmprss2 positively-regulates))\n                  (X X->Y Y Y->tmprss2 tmprss2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q1)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q1)))\n(pretty-ranked ranked)\n\n;(edges/ranked ranked 0 0 EDGE-KEY)\n|#\n\n\n;; 2-hop up-down\n#|\n(displayln \"\\nRunning 2-hop tmprss2 up-down query with concept categories:\")\n(define q2 (time (query/graph\n                  ((X       drug)\n                   (Y       gene-or-protein)\n                   (tmprss2 \"UMLS:C1336641\"))\n                  ((X->Y       positively-regulates)\n                   (Y->tmprss2 negatively-regulates))\n                  (X X->Y Y Y->tmprss2 tmprss2))))\n\n(displayln \"\\nBuilding report:\")\n(pretty-print (time (report/query q2)))\n\n(displayln \"\\nRanking paths:\")\n(define ranked (time (ranked-paths q2)))\n(pretty-ranked ranked)\n|#\n\n\n;; Writing unconstrained 2-hop edges to file\n#|\n(define qu (time (query/graph\n                  ((X       #f)\n                   (Y       #f)\n                   (tmprss2 \"UMLS:C1336641\"))\n                  ((X->Y       negatively-regulates)\n                   (Y->tmprss2 positively-regulates))\n                  (X X->Y Y Y->tmprss2 tmprss2))))\n\n(call-with-output-file \"newoutttt.scm\"\n  (lambda (op)\n    (pretty-write (edges/query qu 'X->Y) op)))\n|#\n\n\n\n\n;;;; Direct relationship example\n\n#|\n(define q (time (query/graph\n                  ((A \"UMLS:C0812258\") (B \"UMLS:C1425762\"))\n                  ((A->B #f))\n                  (A A->B B))))\n;; Ranking doesn't really make sense in this particular context.\n(define ranked (time (ranked-paths q)))\n;(pretty-ranked ranked)\n(map curie-synonyms/names (curies/query q 'A))\n|#\n\n\n#|\n(curie-synonyms/names \"UMLS:C0812258\")\n(curie-synonyms/names \"UMLS:C1425762\")\n(define es (edges-between \"UMLS:C0812258\" \"UMLS:C1425762\"))\n|#\n"
  },
  {
    "path": "medikanren/pieces-parts/synonymize.rkt",
    "content": "#lang racket\n(provide HGNC-CURIE->synonymized-concepts\n         curie-aliases curie-synonyms curie-synonyms-build curie-synonyms-raw curie-synonyms/names\n         curie->name curie->concepts\n         (all-from-out \"../common.rkt\" \"../mk-db.rkt\"))\n(require \"../common.rkt\" \"../mk-db.rkt\" \"../db.rkt\" racket/runtime-path)\n\n(define (curie->name? curie)\n  (define cs (find-concepts #t (list curie)))\n  (and (pair? cs) (cadddr (car cs))))\n(define (curie->name curie)\n  (define name? (curie->name? curie))\n  (or name? (ormap curie->name? (set->list (curie-synonyms curie)))))\n(define (curie->concepts curie)\n  (find-concepts #t (set->list (curie-synonyms curie))))\n(define (curie-synonyms/names curie)\n  ;; (printf \"curie-synonyms/names for curie ~s\\n\" curie)\n  (define css (set->list (curie-synonyms curie)))\n  ;; (printf \"css = ~s\\n\" css)\n  (map cons css (map curie->name css)))\n\n(define (curie-aliases curies)\n  (foldl (lambda (c acc)\n           (cond ((string-prefix? c \"UMLS:\")\n                  (cons (string-replace c \"UMLS:\" \"CUI:\") acc))\n                 ((string-prefix? c \"CUI:\")\n                  (cons (string-replace c \"CUI:\" \"UMLS:\") acc))\n                 ((string-prefix? c \"NCI:\")\n                  (cons (string-replace c \"NCI:\" \"NCIT:\") acc))\n                 ((string-prefix? c \"NCIT:\")\n                  (cons (string-replace c \"NCIT:\" \"NCI:\") acc))\n                 (else acc)))\n         curies curies))\n\n(define (curie-UMLS-gene? c)\n  (and (string-prefix? (caddr c) \"UMLS:\")\n       (string? (cdar (cddddr c)))\n       (string=? (cdar (cddddr c)) \"gene\")))\n(define (curie-UMLS-drug? c)\n  (and (string-prefix? (caddr c) \"UMLS:\")\n       (string? (cdar (cddddr c)))\n       (string=? (cdar (cddddr c)) \"chemical_substance\")))\n(define (curie-NCIT-gene? c)\n  (and (string-prefix? (caddr c) \"NCIT:\")\n       (string? (cdar (cddddr c)))\n       (string=? (cdar (cddddr c)) \"http://w3id.org/biolink/vocab/GeneSet\")))\n(define (curie-xref-gene? curie)\n  (ormap (lambda (pre) (string-prefix? curie pre))\n         '(\"NCI:\" \"HGNC:\")))\n(define (curie-xref-drug? curie)\n  (ormap (lambda (pre) (string-prefix? curie pre))\n         '(\"MTHSPL:\" \"NDFRT:\" \"RXNORM:\" \"CHEMBL:\")))\n(define ((curie-prefix? prefix) c) (string-prefix? (caddr c) prefix))\n(define curie-HGNC? (curie-prefix? \"HGNC:\"))\n(define curie-NCIT? (curie-prefix? \"NCIT:\"))\n(define curie-CUI?  (curie-prefix? \"CUI:\"))\n(define (any? x) #t)\n\n(define (curie-synonyms-raw curie)\n  (define max-synonyms 100)\n  (define same-as\n    (find-exact-predicates\n      (list ;; \"same_as\" ;; same_as in RTX2 seems too dangerous\n            \"biolink:same_as\"\n            \"equivalent_to\"\n            ;; \"encodes\" ;; obsolete? seems to have been remapped in RTX2\n            \"has_gene_product\"\n            \"gene_encodes_gene_product\"\n            \"biolink:has_gene_template*\")))\n  (define subclass-of (find-exact-predicates (list \"subclass_of\" \"biolink:subClassOf\" \"isa\")))\n  (define xref        (find-exact-predicates (list \"xref\")))\n  ;;;;;;;;;;;;;;;;;;;;;;;;;;\n  ;; Synonymization rules ;;\n  ;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n  ;; Equivalence predicates: add or remove individual rules to adjust\n  (define preds/filters\n    (list\n      (list same-as     any?        any?)\n      ; (list subclass-of curie-NCIT? curie-NCIT?)\n      ; (list xref        curie-NCIT-gene? curie-CUI?)\n      ))\n\n  ;; Concept name hacking: add or remove individual rules to adjust\n  (define suffixes/filters\n    (list\n      ;(list \" wt Allele\" curie-HGNC? curie-NCIT?)\n      ))\n\n  ;; Concept property equivalence lists to be used\n  (define use-synonym-concepto? #t)\n  (define use-xref-concepto?    #f)\n\n  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n  ;; It should rarely be necessary to change code below this point ;;\n  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n  (define (hack-names cs)\n    ;; If you want to change this behavior, adjust the suffixes/filters rules\n    (append*\n      (map (lambda (s/fs)\n             (match-define (list suffix before? after?) s/fs)\n             (define (add-suffix c)\n               (define n (cadddr c))\n               (and n (string-append n suffix)))\n             (define (remove-suffix c)\n               (define n (cadddr c))\n               (and n (string-suffix? n suffix)\n                    (substring n 0 (- (string-length n)\n                                      (string-length suffix)))))\n             (append\n               (filter after?\n                       (append*\n                         (map find-concepts/name\n                              (filter-not\n                                not (remove-duplicates\n                                      (map add-suffix (filter before? cs)))))))\n               (filter before?\n                       (append*\n                         (map find-concepts/name\n                              (filter-not\n                                not (remove-duplicates\n                                      (map remove-suffix\n                                           (filter after? cs)))))))))\n           suffixes/filters)))\n  (define (connect-edges cs)\n    ;; If you want to change this behavior, adjust the preds/filters rules\n    (append*\n      (map (lambda (p/fs)\n             (match-define (list preds s? o?) p/fs)\n             (append (filter o? (run* (x)\n                                  (fresh (s o p db eid erest)\n                                    (membero `(,db . ,s) (filter s? cs))\n                                    (== x `(,db . ,o))\n                                    (membero `(,db . ,p) preds)\n                                    (edgeo `(,db ,eid ,s ,o ,p . ,erest)))))\n                     (filter s? (run* (x)\n                                  (fresh (s o p db eid erest)\n                                    (membero `(,db . ,o) (filter o? cs))\n                                    (== x `(,db . ,s))\n                                    (membero `(,db . ,p) preds)\n                                    (edgeo `(,db ,eid ,s ,o ,p . ,erest)))))))\n           preds/filters)))\n  (define (xref-forward cs0)\n    ;; If you want to change this behavior, change use-xref-concepto?\n    (define cs-gene (filter (lambda (c) (curie-UMLS-gene? c)) cs0))\n    (define xs-gene (filter curie-xref-gene?\n                            (run* (x) (fresh (c)\n                                        (membero c cs-gene)\n                                        (xref-concepto x c)))))\n    (define cs-drug (filter (lambda (c) (curie-UMLS-drug? c)) cs0))\n    (define xs-drug (filter curie-xref-drug?\n                            (run* (x) (fresh (c)\n                                        (membero c cs-drug)\n                                        (xref-concepto x c)))))\n    (append xs-gene xs-drug))\n  (define (xref-backward ids0)\n    ;; If you want to change this behavior, change use-xref-concepto?\n    (define xs-gene\n      (filter (lambda (c) (curie-xref-gene? c)) ids0))\n    (define cs-gene (filter curie-UMLS-gene?\n                            (run* (c) (fresh (x)\n                                        (membero x xs-gene)\n                                        (xref-concepto x c)))))\n    (define xs-drug\n      (filter (lambda (c) (curie-xref-drug? c)) ids0))\n    (define cs-drug (filter curie-UMLS-drug?\n                            (run* (c) (fresh (x)\n                                        (membero x xs-drug)\n                                        (xref-concepto x c)))))\n    (map caddr (append cs-gene cs-drug)))\n\n  (define ids (curie-aliases (list curie)))\n  (let retry ((synonym-concepto? use-synonym-concepto?)\n              (xref-concepto?    use-xref-concepto?))\n    (let loop ((ids0 ids) (synonym-ids (list->set ids)))\n      (if (< max-synonyms (set-count synonym-ids))\n        (cond (synonym-concepto? (retry #f #t))\n              (xref-concepto?    (retry #f #f))\n              (else              (list->set ids)))\n        ;; (printf \"ids0 = ~s\\n\" ids0)\n        (let* ((cs0 (find-concepts #t ids0))\n               ;; Set use-synonym-concepto? to #f to disable\n               (ids (if synonym-concepto?\n                      (run* (curie)\n                        (fresh (c)\n                          (membero c cs0)\n                          (synonym-concepto curie c)))\n                      '()))\n               ;; Set use-synonym-concepto? to #f to disable\n               (cs  (if synonym-concepto?\n                      (run* (c)\n                        (fresh (curie)\n                          (membero curie ids0)\n                          (synonym-concepto curie c)))\n                      '()))\n               (ids (append ids\n                            (map caddr cs)\n                            (map caddr (connect-edges cs0))\n                            ;; Empty suffixes/filters to disable\n                            (map caddr (hack-names    cs0))\n                            ;; Set use-xref-concepto? to #f to disable\n                            (if xref-concepto?\n                              (append (xref-forward cs0) (xref-backward ids0))\n                              '())))\n               (ids (set-subtract (list->set (curie-aliases ids))\n                                  synonym-ids)))\n          (if (set-empty? ids) synonym-ids\n            (loop (set->list ids) (set-union synonym-ids ids))))))))\n\n(define-runtime-path path:data \"../data/\")\n(define (data-path path) (build-path path:data path))\n(define path:curie=>synonyms (data-path \"curie-to-synonyms.scm\"))\n(define path:synonyms        (data-path \"synonyms.scm\"))\n\n(define curie-synonyms\n  (if (and (config-ref 'cache-synonyms?)\n           (file-exists? path:curie=>synonyms) (file-exists? path:synonyms))\n    (let* ((_ (printf \"loading cached synonyms\\n\"))\n           (curie=>sid (time (call-with-input-file path:curie=>synonyms read)))\n           (synonyms   (time (call-with-input-file path:synonyms        read)))\n           (synonyms   (time (vector-map list->set synonyms))))\n      (printf \"loaded ~s synonym classes for ~s curies\\n\"\n              (vector-length synonyms) (hash-count curie=>sid))\n      (lambda (curie)\n        (define idx (hash-ref curie=>sid curie #f))\n        (if idx (vector-ref synonyms (hash-ref curie=>sid curie))\n          (curie-synonyms-raw curie))))\n    curie-synonyms-raw))\n\n(define (curie-synonyms-build)\n  (when (or (file-exists? path:curie=>synonyms) (file-exists? path:synonyms))\n    (error \"synonyms are already cached:\" path:curie=>synonyms path:synonyms))\n  (call-with-output-file\n    path:curie=>synonyms\n    (lambda (out:curie=>synonyms)\n      (call-with-output-file\n        path:synonyms\n        (lambda (out:synonyms)\n          (write-string \"#(\"     out:synonyms)\n          (write-string \"#hash(\" out:curie=>synonyms)\n          (time\n            (let db-loop ((dbs (databases)) (si 0) (seen (set)))\n              (printf \"~s\\n\" (seconds->date (current-seconds)))\n              (printf \"curies seen: ~s\\n\" (set-count seen))\n              (printf \"synonym classes formed: ~s\\n\" si)\n              (unless (null? dbs)\n                (define cs (db:concept-cui-corpus (cdar dbs)))\n                (printf \"finding synonyms for ~s curies in ~s\\n\"\n                        (vector-length cs) (caar dbs))\n                (let loop ((i 0) (si si) (seen seen))\n                  (cond ((= (vector-length cs) i)\n                         (db-loop (cdr dbs) si seen))\n                        ((set-member? seen (vector-ref cs i))\n                         (loop (+ i 1) si seen))\n                        (else\n                          (define ss (curie-synonyms-raw (vector-ref cs i)))\n                          (write (set->list ss) out:synonyms)\n                          (for ((c ss))\n                            (write `(,c . ,si) out:curie=>synonyms))\n                          (loop (+ i 1) (+ si 1) (set-union seen ss))))))))\n          (write-string \")\" out:synonyms)\n          (write-string \")\" out:curie=>synonyms))))))\n\n\n(define DEBUG-SYNONYMIZE #f)\n\n(define human-gene/protein-suffix-ls\n  (list \" protein, human\"\n        \" gene\"\n        \" Gene\"\n        \" wt Allele\"\n        \" (human)\"))\n\n(define animal-model/bacteria/plant-gene/protein-suffix-ls\n  (list \" protein, mouse\"\n        \" protein, rat\"\n        \" protein, zebrafish\"\n        \" protein, C elegans\"\n        \" protein, S cerevisiae\"\n        \" protein, Drosophila\"\n        \" protein, Arabidopsis\"\n        \" protein, E coli\"\n        \" protein, S pombe\"\n        \" protein, Xenopus\"\n        \" (mouse)\"\n        \" (rat)\"\n        \" (zebrafish)\"\n        \" (C elegans)\"\n        \" (S cerevisiae)\"\n        \" (Drosophila)\"\n        \" (Arabidopsis)\"\n        \" (E coli)\"\n        \" (S pombe)\"\n        \" (Xenopus)\"))\n\n;; TODO -- generalize to handle predicates better (really this is more\n;; of a KG standardization issue)\n;;\n;; (define equivalent_to (find-predicates (list \"equivalent_to\")))\n;; (define xref (find-predicates (list \"xref\")))\n;; (define subclass_of (find-predicates '(\"subclass_of\")))\n\n(define extract-name/curie/category-from-concept-ls\n  (lambda (query-ls els)\n    (cond\n      ((null? query-ls) els)\n      ((or (void? (car query-ls))\n           (boolean? (car query-ls)))\n       (extract-name/curie/category-from-concept-ls\n        (cdr query-ls) els))\n      (else\n       (match (car query-ls)\n         [`(,db ,cui ,id ,name ,category ,properties-list)\n          (extract-name/curie/category-from-concept-ls\n           (cdr query-ls)\n           (cons\n            (list db id name) els))])))))\n\n(define extract-concept-from-concept-ls\n  (lambda (query-ls els curie kg)\n    (cond\n      ((null? query-ls) (remove-duplicates els))\n      ((or (void? (car query-ls))\n           (boolean? (car query-ls)))\n       (extract-concept-from-concept-ls\n        (cdr query-ls) els curie kg))\n      (else\n       (match (car query-ls)\n         [`(,db ,cui ,id ,name ,category ,properties-list)\n          (cond\n            ((and (equal? db kg)\n                  (string-contains? id curie))\n             (extract-concept-from-concept-ls\n              (cdr query-ls)\n              (set-union\n               `(,db ,cui ,id ,name ,category ,properties-list) els) curie kg))\n            (else\n             (extract-concept-from-concept-ls\n                         (cdr query-ls)\n                         els curie kg)))])))))\n\n(define extract-curie-from-concept-ls\n  (lambda (query-ls els curie kg)\n    (cond\n      ((null? query-ls) (flatten (remove-duplicates els)))\n      ((or (void? (car query-ls))\n           (boolean? (car query-ls)))\n       (extract-curie-from-concept-ls\n        (cdr query-ls) els curie kg))\n      (else\n       (match (car query-ls)\n         [`(,db ,cui ,id ,name ,category ,properties-list)\n          (cond\n            ((and (equal? db kg)\n                  (string-contains? id curie))\n             (extract-curie-from-concept-ls\n              (cdr query-ls)\n              (cons\n               id els) curie kg))\n            (else\n             (extract-curie-from-concept-ls\n                         (cdr query-ls)\n                         els curie kg)))])))))\n\n(define extract-name-from-concept-ls\n  (lambda (query-ls els curie kg)\n    (cond\n      ((null? query-ls) (remove-duplicates els))\n      ((or (void? (car query-ls))\n           (boolean? (car query-ls)))\n       (extract-name-from-concept-ls\n        (cdr query-ls) els curie kg))\n      (else\n       (match (car query-ls)\n         [`(,db ,cui ,id ,name ,category ,properties-list)\n          (cond\n            ((and (equal? db kg)\n                  (string-contains? id curie))\n             (extract-name-from-concept-ls\n              (cdr query-ls)\n              (cons\n               name els) curie kg))\n            (else\n             (extract-name-from-concept-ls\n                         (cdr query-ls)\n                         els curie kg)))])))))\n\n\n\n\n(define HGNC-CURIE->synonymized-concepts\n  (lambda (hgnc-curie)\n    (define HGNC-gene-query (find-concepts #t (list hgnc-curie)))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln (format \"CONCEPTS FOUND RETURNED FROM INITIAL INPUT CURIE: ~a\" HGNC-gene-query))\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-gene-query '())))\n\n    (match-define\n      (list A-->HGNC-input-->B=>concepts\n            A-->HGNC-input-->B=>edges)\n      (run/graph\n        ((A #f)\n         (HGNC-input HGNC-gene-query)\n         (B #f))\n        ((--equivalent_to--> '((rtx2 57 . \"equivalent_to\")))\n         (--xref--> '((rtx2 3 . \"xref\"))))\n        (A --equivalent_to--> HGNC-input --xref--> B)))\n\n    (define A-->HGNC-input/concepts\n      (hash-ref A-->HGNC-input-->B=>concepts 'A))\n\n    (define HGNC-input-->B/concepts\n      (hash-ref A-->HGNC-input-->B=>concepts 'B))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --equivalent_to--> HGNC-input\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls A-->HGNC-input/concepts '()))\n      (newline)\n\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nHGNC-input --xref--> B\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-input-->B/concepts '()))\n      (newline))\n\n    (define HGNC-NCBIGene-ENSEMBL-CUIg-OMIM/concept-ls\n      (set-union\n       HGNC-gene-query\n       (set-union\n        A-->HGNC-input/concepts\n        HGNC-input-->B/concepts)))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --equivalent_to--> HGNC-input --xref--> B\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-NCBIGene-ENSEMBL-CUIg-OMIM/concept-ls '()))\n      (newline))\n\n    ;; get NCITg (if it exists), OMIM, and redundant HGNC\n    (match-define\n      (list A-->CUIg=>concepts\n            A-->CUIg=>edges)\n      (run/graph\n        ((A #f)\n         (CUIg HGNC-input-->B/concepts))\n        ((--xref--> '((rtx2 3 . \"xref\"))))\n        (A --xref--> CUIg)))\n\n    (define A-->CUIg/concept-ls\n      (hash-ref A-->CUIg=>concepts 'A))\n\n    (when DEBUG-SYNONYMIZE\n      ;; NCITg (if it exists), OMIM, and redundant HGNC\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --xref--> CUI gene\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls A-->CUIg/concept-ls '()))\n      (newline))\n\n    (define HGNC-NCBIGene-ENSEMBL-CUIg-NCITg/concept-ls\n      (set-union\n       HGNC-NCBIGene-ENSEMBL-CUIg-OMIM/concept-ls\n       A-->CUIg/concept-ls))\n\n\n    ;; TODO, filter specifically on the NCITg concept if it exists!!\n    (define NCITg-concept-ls\n      A-->CUIg/concept-ls)\n\n\n\n    ;;get NCIT wt Allele\n    (match-define\n      (list A-->NCITg=>concepts\n            A-->NCITg=>edges)\n      (run/graph\n        ((A #f)\n         (NCITg A-->CUIg/concept-ls))\n        ((--subclass_of--> '((rtx2 15 . \"subclass_of\"))))\n        (A --subclass_of--> NCITg)))\n\n    (define A-->NCITg/concept-ls\n      (hash-ref A-->NCITg=>concepts 'A))\n\n    (when DEBUG-SYNONYMIZE\n      ;;should have NCIT wt Allele\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --subclass_of--> NCIT gene:\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls A-->NCITg/concept-ls '()))\n      (newline))\n\n    (define HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt/concept-ls\n      (set-union\n       A-->NCITg/concept-ls\n       HGNC-NCBIGene-ENSEMBL-CUIg-NCITg/concept-ls))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --equivalent_to--> HGNC-input --xref--> B\\nA --xref--> CUI gene\\nA --subclass_of--> NCIT gene\\n\")\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt/concept-ls '()))\n      (newline))\n\n    (match-define\n      (list NCITwt-->A=>concepts\n            NCITwt-->A=>edges)\n      (run/graph\n        ((A #f)\n         (NCITwt A-->NCITg/concept-ls))\n        ((--xref--> '((rtx2 3 . \"xref\"))))\n        (NCITwt --xref--> A)))\n\n    (define NCITwt-->A/concept-ls\n      (hash-ref NCITwt-->A=>concepts 'A))\n\n    (when DEBUG-SYNONYMIZE\n      ;; should have CUI wt Allele\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nNCIT wt Allele --xref--> A\")\n      (pretty-print (extract-name/curie/category-from-concept-ls NCITwt-->A/concept-ls '()))\n      (newline))\n\n    (define HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt/concept-ls\n      (set-union\n       NCITwt-->A/concept-ls\n       HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt/concept-ls))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --equivalent_to--> HGNC-input --xref--> B\\nA --xref--> CUI gene\\nA --subclass_of--> NCIT gene\\nNCIT wt Allele --xref--> A\\n\" )\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt/concept-ls '()))\n      (newline))\n\n    (define NCBIGene-concept/rtx2\n      (extract-concept-from-concept-ls\n       HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt/concept-ls '() \"NCBIGene:\" 'rtx2))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"NCBIGene-concept/rtx2:\")\n      (newline)\n      (pretty-print NCBIGene-concept/rtx2)\n      (newline))\n\n    (define encodes (find-predicates (list \"encodes\")))\n\n    (match-define\n      (list NCBI-input-->Y=>concepts\n            NCBI-input-->Y=>edges)\n      (run/graph\n        ((Y #f)\n         (NCBIg (list NCBIGene-concept/rtx2)))\n        ((--encodes--> '((rtx2 775 . \"encodes\"))))\n        (NCBIg --encodes--> Y)\n        ))\n\n\n    ;; returns a redundant CUI for gene as well as desired CUI for protein\n    ;; has the CUIprotein concept\n    (define NCBI-input-->Y/concepts\n      (hash-ref NCBI-input-->Y=>concepts 'Y))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nNCBIGene --encodes--> B\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls NCBI-input-->Y/concepts '()))\n      (newline))\n\n    (match-define\n      (list A-->NCBI-input=>concepts\n            A-->NCBI-input=>edges)\n      (run/graph\n        ((A #f)\n         (NCBIg (list NCBIGene-concept/rtx2)))\n        ((--xref--> '((rtx2 3 . \"xref\"))))\n        (A --xref--> NCBIg)))\n\n    (define A-->NCBIGene/concepts\n      (hash-ref A-->NCBI-input=>concepts 'A))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --xref--> NCBIGene\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls A-->NCBIGene/concepts '()))\n      (newline))\n\n    (define NCBIGene-concept/orange\n      (find-concepts\n       #t\n       (extract-curie-from-concept-ls\n        HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt/concept-ls '() \"NCBIGene:\" 'rtx2)))\n\n\n    (define HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt-CUIp-UniProtKB/concept-ls\n      (set-union NCBIGene-concept/orange\n                 (set-union A-->NCBIGene/concepts\n                            (set-union\n                             NCBI-input-->Y/concepts\n                             HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt/concept-ls))))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --equivalent_to--> HGNC-input --xref--> B\\nA --xref--> CUI gene\\nA --subclass_of--> NCIT gene\\nNCIT wt Allele --xref--> A\\nA --xref--> NCBIGene\\nNCBIGene --encodes--> B\\n\" )\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt-CUIp-UniProtKB/concept-ls '()))\n      (newline))\n\n    (match-define\n      (list A-->CUIp-input=>concepts\n            A-->CUIp-input=>edges)\n      (run/graph\n        ((A #f)\n         (CUIp A-->NCBIGene/concepts))\n        ((--xref--> '((rtx2 3 . \"xref\"))))\n        (A --xref--> CUIp)))\n\n    ;; should have MESH protein id\n    (define A-->CUIp-input/concepts\n      (hash-ref A-->CUIp-input=>concepts 'A))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --xref--> CUI protein\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls A-->CUIp-input/concepts '()))\n      (newline))\n\n    (define HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt-CUIp-UniProtKB-MESHp/concept-ls\n      (set-union\n       A-->CUIp-input/concepts\n       HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt-CUIp-UniProtKB/concept-ls))\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPTS FROM:\\nA --equivalent_to--> HGNC-input --xref--> B\\nA --xref--> CUI gene\\nA --subclass_of--> NCIT gene\\nNCIT wt Allele --xref--> A\\nA --xref--> NCBIGene\\nNCBIGene --encodes--> B\\nA --xref--> CUI protein\\n\")\n      (newline)\n      (pretty-print (extract-name/curie/category-from-concept-ls HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt-CUIp-UniProtKB-MESHp/concept-ls '()))\n      (newline))\n\n    (define molecular-entity/concept-ls/sans-UMLS\n      HGNC-NCBIGene-ENSEMBL-CUIg-NCITg-NCITwt-CUIwt-CUIp-UniProtKB-MESHp/concept-ls)\n\n\n    (define molecular-entity/curie-ls/CUI-ONLY\n      (extract-curie-from-concept-ls molecular-entity/concept-ls/sans-UMLS '() \"CUI:\" 'rtx2))\n\n\n    (define molecular-entity/curie-ls/UMLS-ONLY\n      (map (lambda (curie)\n             (string-replace curie \"CUI:\" \"UMLS:\"))\n           molecular-entity/curie-ls/CUI-ONLY))\n\n    (define molecular-entity/concept-ls/UMLS-ONLY\n      (find-concepts #t molecular-entity/curie-ls/UMLS-ONLY))\n\n    ;; dangerous!  Not every HGNC in rtx2 is in robokop\n    #|\n    (define molecular-entity/curie-ls/HGNC-ONLY\n    (extract-name-from-concept-ls molecular-entity/concept-ls/sans-UMLS '() \"HGNC:\" 'robokop))\n    |#\n\n    (define molecular-entity/curie-ls/HGNC-ONLY\n      (list (cadr (regexp-match #px\"^HGNC:([0-9]+)\" hgnc-curie))))\n\n\n    ;; string append HGNC symbol to list of human suffixes\n    (define HGNC-string-with-human-gene/protein-suffix-ls\n      (map (lambda (str) (string-append (car molecular-entity/curie-ls/HGNC-ONLY) str)) human-gene/protein-suffix-ls))\n\n    ;; use this to filter find-concepts\n    (define HGNC-string-with-human-gene/protein-suffix-concept-ls\n      (remove-duplicates\n       (apply append\n              (map\n                (lambda (x) (find-concepts #f (list x)))\n                HGNC-string-with-human-gene/protein-suffix-ls))))\n\n    (define filtered-HGNC-string-with-human-gene/protein-suffix-concept-ls\n      (filter (lambda (c)\n                (member (concept->name c)\n                        HGNC-string-with-human-gene/protein-suffix-ls))\n              HGNC-string-with-human-gene/protein-suffix-concept-ls\n              ))\n\n    (define molecular-entity-concept-ls/complete\n      (set-union filtered-HGNC-string-with-human-gene/protein-suffix-concept-ls\n                 (set-union molecular-entity/concept-ls/sans-UMLS\n                            molecular-entity/concept-ls/UMLS-ONLY)))\n\n    (define human-gene/protein-concept-ls molecular-entity-concept-ls/complete)\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPT BUILDING FOR HGNC QUERY COMPLETE:\\n\")\n      (pretty-print (extract-name/curie/category-from-concept-ls human-gene/protein-concept-ls '()))\n      (newline))\n\n    (define HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-ls\n      (let ((hgnc-id-str (car molecular-entity/curie-ls/HGNC-ONLY)))\n        (map string-downcase\n             (map (lambda (x) (string-append hgnc-id-str x))\n                  animal-model/bacteria/plant-gene/protein-suffix-ls))))\n\n    (define HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-concept-ls\n      (remove-duplicates\n       (apply append\n              (map (lambda (x) (find-concepts #f (list x)))\n                   HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-ls))))\n\n    (define filtered-HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-concept-ls\n      (filter (lambda (c)\n                (member (string-downcase (concept->name c))\n                        HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-ls))\n              HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-concept-ls))\n\n    (define animal-genes/proteins-concept-ls filtered-HGNC-string-with-animal-model/bacteria/plant-gene/protein-suffix-concept-ls)\n\n    (when DEBUG-SYNONYMIZE\n      (newline)\n      (displayln \"CONCEPT BUILDING FOR ANIMAL MODEL QUERY COMPLETE:\\n\")\n      (pretty-print (extract-name/curie/category-from-concept-ls animal-genes/proteins-concept-ls '()))\n      (newline))\n\n    (define all-genes/proteins (set-union human-gene/protein-concept-ls\n                                          animal-genes/proteins-concept-ls))\n\n    (hash\n\n     'all-genes/proteins\n     all-genes/proteins\n\n     'human-genes/proteins\n     human-gene/protein-concept-ls\n\n     'animal-genes/proteins\n     animal-genes/proteins-concept-ls\n     )\n    ))\n\n\n\n;; RHOBTB2\n;; (define RHOBTB2-synonyms (HGNC-CURIE->synonymized-concepts \"HGNC:18756\"))\n\n;; E2F1\n;; (define E2F1-synonyms (HGNC-CURIE->synonymized-concepts \"HGNC:3113\"))\n"
  },
  {
    "path": "medikanren/pieces-parts/visjs.html",
    "content": "\n\n  Vis Network | Data | DOT Language\n\n  \n\n\n
\n  Network supports the DOT language.\n
\n
\n\n\n\n\n"
  },
  {
    "path": "medikanren/repr.rkt",
    "content": "#lang racket/base\n(provide\n  concept-cui\n  concept-category\n  concept-name\n  concept-props\n  concept->synonyms\n  concept->xrefs\n\n  edge/props-subject\n  edge/props-pid\n  edge/props-object\n  edge/props-props\n\n  edge-predicate\n  edge-dst-category\n  edge-dst\n  edge-eid\n  edge->bytes\n  bytes->edge\n\n  string-key->bytes\n  bytes->string-key\n  write-string-keys\n  port->string-keys\n  string-index->string-key\n  string-key-count\n\n  suffix-key-count\n  suffix-key-count/port\n  suffix-key-ref\n  suffix-key->bytes\n  write-suffix-keys\n  suffix-index->suffix-key\n\n  edge-pids-by-X\n  stream-edges-by-X\n  port->stream-offset&values\n  vector->stream-offset&values\n\n  write-scm\n  offset-write\n  offset-count\n  offset-ref\n  detail-find-index\n  detail-find\n  detail-ref\n  detail-next\n  detail-write\n  detail-stream)\n\n(require racket/list racket/port racket/set racket/stream racket/string)\n\n(define (read-list/string s)\n  (cond ((string-prefix? s \"(\")\n         (define datum (call-with-input-string s read))\n         (if (list? datum) datum '()))\n        (else (list s))))\n\n(define (concept-cui c)      (vector-ref c 0))\n(define (concept-category c) (vector-ref c 1))\n(define (concept-name c)     (vector-ref c 2))\n(define (concept-props c)    (vector-ref c 3))\n(define (concept->synonyms c)\n  (define props (concept-props c))\n  (define (dedup xs)\n    (cdr (reverse (foldl (lambda (part acc) (if (equal? part (car acc)) acc\n                                              (cons part acc)))\n                         '(#t) xs))))\n  (append* (map (lambda (key)\n                  (define rib (assoc key props))\n                  (if rib (map (lambda (curie)\n                                 (string-join (dedup (string-split curie \":\"))\n                                              \":\"))\n                               (read-list/string (cdr rib))) '()))\n                '(\"same_as\" \"equivalent_identifiers\"))))\n(define (concept->xrefs c)\n  (define props (concept-props c))\n  (define (dedup xs)\n    (cdr (reverse (foldl (lambda (part acc) (if (equal? part (car acc)) acc\n                                              (cons part acc)))\n                         '(#t) xs))))\n  (append* (map (lambda (key)\n                  (define rib (assoc key props))\n                  (if rib (map (lambda (curie)\n                                 (string-join (dedup (string-split curie \":\"))\n                                              \":\"))\n                               (read-list/string (cdr rib))) '()))\n                '(\"xrefs\"))))\n\n;; This is the edge representation for edges.scm, not for edges-by-X.detail.\n(define (edge/props-subject e) (vector-ref e 0))\n(define (edge/props-pid e)     (vector-ref e 1))\n(define (edge/props-object e)  (vector-ref e 2))\n(define (edge/props-props e)   (vector-ref e 3))\n\n;; This is the edge representation for edges-by-X.detail, not for edges.scm.\n(define (edge-predicate e)    (vector-ref e 0))\n(define (edge-dst-category e) (vector-ref e 1))\n(define (edge-dst e)          (vector-ref e 2))\n(define (edge-eid e)          (vector-ref e 3))\n\n(define (byte-at offset n) (bitwise-and 255 (arithmetic-shift n offset)))\n\n;; 2-byte predicate + 2-byte category + 3-byte concept-id + 4-byte eid\n(define edge-byte-size (+ 2 2 3 4))\n(define (edge->bytes e)\n  (define c   (edge-dst e))\n  (define pid (edge-predicate e))\n  (define cc  (edge-dst-category e))\n  (define eid (edge-eid e))\n  (bytes                                     (byte-at -8 pid) (byte-at 0 pid)\n                                             (byte-at -8 cc)  (byte-at 0 cc)\n                           (byte-at -16 c)   (byte-at -8 c)   (byte-at 0 c)\n         (byte-at -24 eid) (byte-at -16 eid) (byte-at -8 eid) (byte-at 0 eid)))\n(define (bytes->edge bs)\n  (define (bref pos) (bytes-ref bs pos))\n  (define (bref-to pos offset) (arithmetic-shift (bref pos) offset))\n  (vector (+                               (bref-to 0 8) (bref-to 1  0))\n          (+                               (bref-to 2 8) (bref-to 3  0))\n          (+                (bref-to 4 16) (bref-to 5 8) (bref-to 6  0))\n          (+ (bref-to 7 24) (bref-to 8 16) (bref-to 9 8) (bref-to 10 0))))\n(define (read-edge-bytes in) (read-bytes edge-byte-size in))\n\n(define string-key-byte-size 4)\n(define (string-key->bytes cid)\n  (bytes (byte-at -24 cid) (byte-at -16 cid) (byte-at -8 cid) (byte-at 0 cid)))\n(define (bytes->string-key bs)\n  (define (bref-to pos offset) (arithmetic-shift (bytes-ref bs pos) offset))\n  (+ (bref-to 0 24) (bref-to 1 16) (bref-to 2 8) (bref-to 3 0)))\n(define (read-string-key-bytes in) (read-bytes string-key-byte-size in))\n(define (write-string-keys out v)\n  (for ((s (in-vector v))) (write-bytes (string-key->bytes s) out)))\n(define (port->string-keys in)\n  (define end (begin (file-position in eof) (file-position in)))\n  (file-position in 0)\n  (for/vector ((_ (in-range (/ end string-key-byte-size))))\n              (bytes->string-key (read-string-key-bytes in))))\n(define (string-index->string-key in si)\n  (file-position in (* string-key-byte-size si))\n  (bytes->string-key (read-string-key-bytes in)))\n(define (string-key-count in)\n  (file-position in eof)\n  (/ (file-position in) string-key-byte-size))\n\n(define suffix-key-byte-size (+ 4 2))\n(define (suffix-key-count bs) (/ (bytes-length bs) suffix-key-byte-size))\n(define (suffix-key-count/port in)\n  (file-position in eof)\n  (/ (file-position in) suffix-key-byte-size))\n(define (suffix-key-ref index i) (bytes->suffix-key index i))\n(define (suffix-key->bytes s)\n  (define cid (car s))\n  (define pos (cdr s))\n  (bytes (byte-at -24 cid) (byte-at -16 cid) (byte-at -8 cid) (byte-at 0 cid)\n         (byte-at -8 pos) (byte-at 0 pos)))\n(define (bytes->suffix-key bs start)\n  (define i (* start suffix-key-byte-size))\n  (define (bref-to j offset) (arithmetic-shift (bytes-ref bs (+ i j)) offset))\n  (cons (+ (bref-to 0 24) (bref-to 1 16) (bref-to 2 8) (bref-to 3 0))\n        (+ (bref-to 4 8) (bref-to 5 0))))\n(define (read-suffix-key-bytes in) (read-bytes suffix-key-byte-size in))\n(define (write-suffix-keys out v)\n  (for ((s (in-vector v))) (write-bytes (suffix-key->bytes s) out)))\n(define (suffix-index->suffix-key in si)\n  (file-position in (* suffix-key-byte-size si))\n  (bytes->suffix-key (read-suffix-key-bytes in) 0))\n\n(define (edge-pids-by-X in in-offset src)\n  (define start (offset-ref in-offset src))\n  (define end   (offset-ref in-offset (+ src 1)))\n  (file-position in start)\n  (let loop ((n (/ (- end start) edge-byte-size)) (pids (set)))\n    (cond ((= n 0) (sort (set->list pids) <))\n          (else (define edge (bytes->edge (read-edge-bytes in)))\n                (loop (- n 1) (set-add pids (edge-predicate edge)))))))\n\n;; Stream edges-by-X by mask for a particular source concept, e.g.,\n;;   #(#f  #f         #f):     get all.\n;;   #(#f  dst-cat-id #f):     get all with some destination category, any pid.\n;;   #(#f  _          dst-id): get all with some destination, any pid.\n;;   #(pid #f         #f):     get all with some pid and any destination.\n;;   #(pid dst-cat-id #f):     get all with some pid and destination category.\n;;   #(pid _          dst-id): get all with some pid and destination.\n(define (stream-edges-by-X in in-offset src pid? cat? dst?)\n  ;; TODO: binary search for start of non-#f mask prefix.\n  (define end (offset-ref in-offset (+ src 1)))\n  (let loop ((pos (offset-ref in-offset src)) (set-pos? #t))\n    (cond ((= pos end) '())\n          (else (when set-pos? (file-position in pos))\n                (define bs (read-edge-bytes in))\n                (if (eof-object? bs) '()\n                  (let* ((edge (bytes->edge bs))\n                         (pos-next (+ pos edge-byte-size))\n                         (pid (edge-predicate edge)))\n                    (cond ((and pid? (> pid pid?)) '())\n                          ((and pid? (< pid pid?)) (loop pos-next #f))\n                          ((and cat? (not (= cat? (edge-dst-category edge))))\n                           (loop pos-next #f))\n                          ((and dst? (not (= dst? (edge-dst edge))))\n                           (loop pos-next #f))\n                          (else (stream-cons edge (loop pos-next #t))))))))))\n;; TODO: stream edges-by-X by pid set, equivalent to a union of pid-only masks.\n\n(define (port->stream-offset&values in)\n  (let loop ((offset 0) (pos 0))\n    (file-position in pos)\n    (define v (read in))\n    (define pos-next (file-position in))\n    (if (eof-object? v) '()\n      (stream-cons (cons offset v) (loop (+ offset 1) pos-next)))))\n\n(define (vector->stream-offset&values v*)\n  (define len (vector-length v*))\n  (let loop ((offset 0))\n    (if (<= len offset) '()\n      (stream-cons (cons offset (vector-ref v* offset)) (loop (+ offset 1))))))\n\n(define (write-scm out scm) (fprintf out \"~s\\n\" scm))\n\n(define offset-size 8)\n(define (offset->bytes o) (integer->integer-bytes o offset-size #f #f))\n(define (bytes->offset b) (integer-bytes->integer b #f #f 0 offset-size))\n(define (offset-write out offset) (write-bytes (offset->bytes offset) out))\n(define (offset-count in)\n  (file-position in eof)\n  (/ (file-position in) offset-size))\n(define (offset-ref in n)\n  (file-position in (* n offset-size))\n  (bytes->offset (read-bytes offset-size in)))\n\n(define (detail-write detail-out offset-out detail)\n  (when offset-out (offset-write offset-out (file-position detail-out)))\n  (write-scm detail-out detail))\n(define (detail-ref detail-in offset-in n)\n  (file-position detail-in (offset-ref offset-in n))\n  (read detail-in))\n(define (detail-next detail-in) (read detail-in))\n\n(define (detail-find-index detail-in offset-in compare)\n  (let loop ((start 0) (end (offset-count offset-in)) (best #f))\n    (cond ((< start end)\n           (define n (+ start (quotient (- end start) 2)))\n           (define detail (detail-ref detail-in offset-in n))\n           (case (compare detail)\n             ((-1) (loop (+ 1 n) end best))\n             (( 0) (loop start n n))\n             (( 1) (loop start n best))))\n          (else best))))\n\n(define (detail-find detail-in offset-in compare)\n  (let loop ((start 0) (end (offset-count offset-in)) (best #f))\n    (cond ((< start end)\n           (define n (+ start (quotient (- end start) 2)))\n           (define detail (detail-ref detail-in offset-in n))\n           (case (compare detail)\n             ((-1) (loop (+ 1 n) end best))\n             (( 0) (loop start n n))\n             (( 1) (loop start n best))))\n          (best (detail-ref detail-in offset-in best))\n          (else eof))))\n\n(define (detail-stream in)\n  (let loop ((pos 0))\n    (file-position in pos)\n    (define datum (detail-next in))\n    (define pos-next (file-position in))\n    (if (eof-object? datum) '() (stream-cons datum (loop pos-next)))))\n"
  },
  {
    "path": "medikanren/string-search.rkt",
    "content": "#lang racket/base\n(provide\n  string/searchable\n  suffix:corpus->index\n  suffix:corpus-find*\n  suffix:corpus-find*/disk\n  string:corpus->index\n  string:corpus-find*\n  string:corpus-find*/disk)\n(require\n  \"repr.rkt\"\n  racket/list\n  racket/match\n  racket/string\n  racket/unsafe/ops\n  racket/vector)\n\n(define (msd-radix-sort vs len dref vvector vs))\n  (define out (make-vector (vector-length vvs)))\n  (define pos-count 127)\n  (define pos (make-vector pos-count))\n  (define (++pos! i) (unsafe-vector*-set!\n                       pos i (+ 1 (unsafe-vector*-ref pos i))))\n  (let loop ((bi 0) (vi 0) (vend (vector-length vvs)) (vs vvs) (out out))\n    (cond\n      ((< (- vend vi) 100) (vector-sort! vs vinteger #\\0))\n(define i9              (char->integer #\\9))\n(define iA              (char->integer #\\A))\n(define iZ              (char->integer #\\Z))\n(define (searchable? c) (and (<= i0 c) (<= c iZ) (or (<= c i9) (<= iA c))))\n(define (string/searchable s)\n  (define cs (map char->integer (string->list (string-upcase s))))\n  (list->string (map integer->char (filter searchable? cs))))\n(define (suffix->string corpus s)\n  (substring (vector-ref corpus (car s)) (cdr s)))\n(define (suffix-string-length corpus s)\n  (- (string-length (vector-ref corpus (car s))) (cdr s)))\n(define (suffix-string-ref corpus s i)\n  (char->integer (string-ref (unsafe-vector*-ref corpus (car s))\n                             (+ (cdr s) i))))\n(define (string? (string-ref a ai) (string-ref b bi)) #f)\n          (else (loop (- k 1) (+ ai 1) (+ bi 1))))))\n(define (suffixindex corpus)\n  (define suffixes\n    (foldl (lambda (i all)\n             (foldl (lambda (j all) (cons (cons i j) all))\n                    all (range (string-length (vector-ref corpus i)))))\n           '() (range (vector-length corpus))))\n  (define (suffixstring corpus (suffix-key-ref index si)))\n    (cond ((string-prefix? hay needle) 0)\n          ((stringconcept in-index str)\n  (define needle (string/searchable str))\n  (define (compare si needle)\n    (match-define (cons cid pos) (suffix-index->suffix-key in-index si))\n    (define hay (substring (string/searchable (concept-name (cid->concept cid))) pos))\n    (cond ((string-prefix? hay needle) 0)\n          ((stringconcept in-index str*)\n  (define (rz r) (- (cdr r) (car r)))\n  (define rs (map (lambda (s) (suffix:corpus-find-range/disk cid->concept in-index s)) str*))\n  (define zmin (* 2 (if (null? rs) 0 (foldl (lambda (r z) (min z (rz r)))\n                                            (rz (car rs)) (cdr rs)))))\n  (nlist-intersection\n    (map (lambda (r) (dedup/< (map (lambda (i) (car (suffix-index->suffix-key in-index i)))\n                                   (range (car r) (cdr r)))))\n         (filter (lambda (r) (<= (rz r) zmin)) rs))))\n\n(define (string:corpus->index corpus)\n  (define ixs (range (vector-length corpus)))\n  (define (ixinteger (string-ref (vector-ref corpus ix) i)))\n  (msd-radix-sort ixs ix-length ix-ref ixconcept in-index needle)\n  (define (compare si needle)\n    (define cid (string-index->string-key in-index si))\n    (define hay (concept-cui (cid->concept cid)))\n    (cond ((string=? hay needle)  0)\n          ((stringstring-key in-index i))\n                                      (range rstart rend))))))\n          (else '()))))\n\n(define (string:corpus-find*/disk cid->concept in-index str*)\n  (remove-duplicates\n    (sort (append* (map (lambda (s) (string:corpus-find/disk cid->concept in-index s)) str*))\n          <)))\n"
  },
  {
    "path": "medikanren/test/external-http/2020_NCATS_relay/INTEGRATED-QUERY/integrated-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../../../../pieces-parts/query.rkt\"\n         \"../../open-api/api-query.rkt\"\n         ;\"../molepro-api-query.rkt\"\n         racket/engine)\n\n(define crosskg-mondo-disease-curies\n  '(\"MONDO:0016192\"\n    \"DOID:0050890\"\n    \"MONDO:0016153\"\n    \"MONDO:0016147\"    \n    \"MONDO:0016191\"\n    \"MONDO:0016196\"\n    \"MONDO:0016187\"))\n\n(define CHEBI--negatively-regulates-->PR-->MONDO\n  (curies/query\n   (time (query/graph\n          ((Drug #f)\n           (PR #f)\n           ;(Disease \"MONDO:0000510\")\n           (Disease \"MONDO:0016147\")\n           )\n          ((Drug->PR (list \"biolink:negatively_regulates_entity_to_entity\") (edge/db? 'textminingprovider)) \n           (PR->Disease\n            (list\n             \"gene_mapped_to_disease\"\n             \"gene_involved_in_pathogenesis_of_disease\"\n             \"gene_associated_with_disease\"\n             \"associated_with_disease\"\n             \"INVERTED:disease_has_basis_in_dysfunction_of\") (edge/db? 'rtx2_2020_09_16)))\n          (Drug Drug->PR PR)                         \n          (PR PR->Disease Disease)))\n   'Drug))\n\n(define CHEBI--postively-regulates-->PR-->MONDO\n  (curies/query\n   (time (query/graph\n          ((Drug #f)\n           (PR #f)\n           (Disease \"MONDO:0000510\"))\n          ((Drug->PR (list \"biolink:positively_regulates_entity_to_entity\") (edge/db? 'textminingprovider)) \n           (PR->Disease\n            (list\n             \"gene_mapped_to_disease\"\n             \"gene_involved_in_pathogenesis_of_disease\"\n             \"gene_associated_with_disease\"\n             \"associated_with_disease\"\n             \"INVERTED:disease_has_basis_in_dysfunction_of\") (edge/db? 'rtx2_2020_09_16)))\n          (Drug Drug->PR PR)               \n          (PR PR->Disease Disease)))\n   'Drug))\n\n#|\n(filter (lambda (x) (string-prefix? x \"CHEMBL:\"))\n        (flatten (map set->list (map curie-synonyms CHEBI--negatively-regulates-->PR-->MONDO))))\n\n\n|#\n\n\n\n\n#;(pretty-print\n CHEBI--postively-regulates-->PR-->MONDO)\n\n#;(pretty-print\n (time\n  (api-query\n   (string-append (string-append url.broad_chembl chembl-drug-indications/transform))\n   (js-query/transform\n    'chembl\n    \"ChEMBL:CHEMBL1433\"))))\n\n#|\n(define json->curie-ls\n  (lambda (json-str curie-prefix)\n    (map (lambda (ls) (string))\n         (map jsexpr->string json-str))))\n\n(define js\n  '{\"size\": 2731, \"severity\": {\"operator\": \"=\", \"value\": 0}, \"drugs\": [{\"drug\": \"Prednisone\", \"identifier\": \"CHEMBL:CHEMBL635\", \"frequency\": 282}, {\"drug\": \"Fluticasone\", \"identifier\": \"CHEMBL:CHEMBL1473\", \"frequency\": 79}, {\"drug\": \"Mometasone\", \"identifier\": \"CHEMBL:CHEMBL1161\", \"frequency\": 7}, {\"drug\": \"Budesonide\", \"identifier\": \"CHEMBL:CHEMBL1370\", \"frequency\": 36}, {\"drug\": \"Beclomethasone\", \"identifier\": \"CHEMBL:CHEMBL1586\", \"frequency\": 15}, {\"drug\": \"Ciclesonide\", \"identifier\": \"CHEMBL:CHEMBL2040682\", \"frequency\": 2}, {\"drug\": \"Flunisolide\", \"identifier\": \"CHEMBL:CHEMBL1512\", \"frequency\": 0}, {\"drug\": \"Albuterol\", \"identifier\": \"CHEMBL:CHEMBL1002\", \"frequency\": 515}, {\"drug\": \"Metaproterenol\", \"identifier\": \"PUBCHEM:4086\", \"frequency\": 0}, {\"drug\": \"Diphenhydramine\", \"identifier\": \"CHEMBL:CHEMBL657\", \"frequency\": 58}, {\"drug\": \"Fexofenadine\", \"identifier\": \"CHEMBL:CHEMBL914\", \"frequency\": 34}, {\"drug\": \"Cetirizine\", \"identifier\":\n\"CHEMBL:CHEMBL896\", \"frequency\": 69}, {\"drug\": \"Ipratropium\", \"identifier\": \"CHEMBL:CHEMBL1464005\", \"frequency\": 84}, {\"drug\": \"Salmeterol\", \"identifier\": \"CHEMBL:CHEMBL1263\", \"frequency\": 167}, {\"drug\": \"Arformoterol\", \"identifier\": \"CHEMBL:CHEMBL1363\", \"frequency\": 2}, {\"drug\": \"Formoterol\", \"identifier\": \"CHEMBL:CHEMBL605993\", \"frequency\": 32}, {\"drug\": \"Indacaterol\", \"identifier\": \"CHEMBL:CHEMBL1346\", \"frequency\": 0}, {\"drug\": \"Theophylline\", \"identifier\": \"CHEMBL:CHEMBL589251\", \"frequency\": 2}, {\"drug\": \"Omalizumab\", \"identifier\": \"CHEMBL:CHEMBL1201589\", \"frequency\": 0}, {\"drug\": \"Mepolizumab\", \"identifier\": \"CHEMBL:CHEMBL2108429\", \"frequency\": 0}, {\"drug\": \"Sertraline\", \"identifier\": \"RXCUI:155137\", \"frequency\": 0}, {\"drug\": \"Citalopram\", \"identifier\": \"RXCUI:221078\", \"frequency\": 0}, {\"drug\": \"Fluoxetine\", \"identifier\": \"RXCUI:227224\", \"frequency\": 0}, {\"drug\": \"Paroxetine\", \"identifier\": \"RXCUI:32937\", \"frequency\": 0}, {\"drug\": \"Trazodone\", \"identifier\": \"RXCUI:82112\", \"frequency\": 0}, {\"drug\": \"Escitalopram\", \"identifier\": \"RXCUI:353108\", \"frequency\": 0}, {\"drug\": \"Duloxetine\", \"identifier\": \"RXCUI:476250\", \"frequency\": 0}, {\"drug\": \"Venlafaxine\", \"identifier\": \"RXCUI:39786\", \"frequency\": 0}, {\"drug\": \"Propranolol\", \"identifier\": \"RXCUI:8787\", \"frequency\": 0}, {\"drug\": \"Hydroxyzine\", \"identifier\": \"RXCUI:5553\", \"frequency\": 0}, {\"drug\": \"Estradiol\", \"identifier\": \"RXCUI:4083\", \"frequency\": 0}, {\"drug\": \"Estropipate\", \"identifier\": \"RXCUI:33747\", \"frequency\": 0}, {\"drug\": \"Estrogen\", \"identifier\": \"RXCUI:4100\", \"frequency\": 0}, {\"drug\": \"Progesterone\", \"identifier\": \"RXCUI:8727\", \"frequency\": 0}, {\"drug\": \"Medroxyprogresterone\", \"identifier\": \"RXCUI:6691\", \"frequency\": 0}, {\"drug\": \"Testosterone\", \"identifier\": \"RXCUI:10379\", \"frequency\": 0}, {\"drug\": \"Androstenedione\", \"identifier\": \"RXCUI:784\", \"frequency\": 0}, {\"drug\": \"Nandrolone\", \"identifier\": \"RXCUI:7244\", \"frequency\": 0}, {\"drug\": \"Prasterone\", \"identifier\": \"RXCUI:3143\", \"frequency\": 0}, {\"drug\": \"Leuprolide\", \"identifier\": \"RXCUI:42375\", \"frequency\": 0}, {\"drug\": \"Goserelin\", \"identifier\": \"RXCUI:50610\", \"frequency\": 0}, {\"drug\": \"Triptorelin\", \"identifier\": \"RXCUI:38782\", \"frequency\": 0}, {\"drug\": \"Histrelin\", \"identifier\": \"RXCUI:50975\", \"frequency\": 0}, {\"drug\": \"Tamoxifen\", \"identifier\": \"RXCUI:10324\", \"frequency\": 0}]})\n\n|#\n"
  },
  {
    "path": "medikanren/test/external-http/2020_NCATS_relay/genetics-provider-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require json net/url\n         nested-hash)\n\n(define (js-count js)\n  (cond ((pair? js) (foldl + 0 (map js-count js)))\n        ((hash? js) (foldl + 0 (hash-map js (lambda (k v) (js-count v)))))\n        (else       1)))\n\n;; Broad Institute KP GENETICS PROVIDERS\n;; DATASETS: NOT SHOWN\n;; GENE (NCBI) <--> DISEASE (EFO)\n;; DISEASE --> PATHWAY . DISEASE AS 0 EDGE\n\n(define url.broad\n  \"https://translator.broadinstitute.org/genetics_data_provider\")\n\n;; Broad Institute KP specific for CHEMBL queries\n(define url.broad_chembl\n  \"https://translator.broadinstitute.org/chembl\")\n\n(define chembl-drug-indications/transform\n  \"/indications/transform\")\n\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n(define path.predicates\n  \"/predicates\")\n(define path.query\n  \"/query\")\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (define-values (status headers in)\n    (time (if (void? optional-post-jsexpr)\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"GET\")\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"POST\"\n              #:data (jsexpr->string optional-post-jsexpr)\n              #:headers '(\"Content-Type: application/json; charset=utf-8\")))))\n  (define response-string (time (port->string in)))\n  (displayln (string-length response-string))\n  (pretty-print headers)\n  (hash 'status status\n        'headers headers\n        'response (string->jsexpr response-string)))\n\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n\n;; X genes --associated--> Asthma EFO:0000270\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"associated\"))\n                            (list (hash 'curie \"EFO:0000270\"\n                                        'id    \"n00\"\n                                        'type  \"disease\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n\n(define geneticsprovider:disease->gene\n  (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"associated\"))\n                            (list (hash 'curie \"EFO:0000270\"\n                                        'id    \"n00\"\n                                        'type  \"disease\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n\n#|\n(define edges-from-geneticsprovider:disease->gene\n  (let* ((edges (nested-hash-ref* geneticsprovider:disease->gene '(response knowledge_graph edges)))\n        (subject (map (lambda (hasheq) (hash-ref hasheq 'source_id)) edges))\n        (predicate (map (lambda (hasheq) (hash-ref hasheq 'type)) edges))\n        (object (map (lambda (hasheq) (hash-ref hasheq 'target_id)) edges))\n        (evidence (map (lambda (hasheq) (hash-ref hasheq 'score)) edges))\n        (provinance (map (lambda (hasheq) (hash-ref hasheq 'score_name)) edges)))\n(list subject predicate object evidence provinance)))\n|#\n\n\n\n#|\n{\n  \"message\": {\n    \"query_graph\": {\n      \"edges\": [\n        {\n          \"id\": \"e00\",\n          \"source_id\": \"n00\",\n          \"target_id\": \"n01\",\n          \"type\": \"associated\"\n        }\n      ],\n      \"nodes\": [\n        {\n          \"curie\": \"EFO:0000270\",\n          \"id\": \"n00\",\n          \"type\": \"disease\"\n        },\n        {\n          \"id\": \"n01\",\n          \"type\": \"gene\"\n        }\n      ]\n    }\n  }\n}\n\n|#\n"
  },
  {
    "path": "medikanren/test/external-http/2020_NCATS_relay/molepro-api-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require json net/url)\n\n(define (js-count js)\n  (cond ((pair? js) (foldl + 0 (map js-count js)))\n        ((hash? js) (foldl + 0 (hash-map js (lambda (k v) (js-count v)))))\n        (else       1)))\n\n;; Broad Institute KP\n(define url.broad\n  \"https://translator.broadinstitute.org/molepro_reasoner\")\n\n;; Broad Institute KP specific for CHEMBL queries\n(define url.broad_chembl\n  \"https://translator.broadinstitute.org/chembl\")\n\n(define chembl-drug-indications/transform\n  \"/indications/transform\")\n\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n(define path.predicates\n  \"/predicates\")\n(define path.query\n  \"/query\")\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (define-values (status headers in)\n    (time (if (void? optional-post-jsexpr)\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"GET\")\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"POST\"\n              #:data (jsexpr->string optional-post-jsexpr)\n              #:headers '(\"Content-Type: application/json; charset=utf-8\")))))\n  (define response-string (time (port->string in)))\n  (displayln (string-length response-string))\n  (pretty-print headers)\n  (hash 'status status\n        'headers headers\n        'response (string->jsexpr response-string)))\n\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n\n#|\n;; {} = hash                            ;\n;; [] = list                            ;\n;; key:value                            ;\n                                        ;\nQUERY/TRANSFORM QUERY STRUCTURE         ;\n------------------------------\n\nquery = {\n    'collection': [{\n            'id':'',\n            'identifiers': {'chembl':'ChEMBL:CHEMBL25'}\n        }],\n    'controls':[]\n}\n|#\n\n\n(module+ main\n  ;; test predicates available on Broad Institute KG\n #;(pretty-print\n   (api-query (string-append url.broad path.predicates)))\n\n  #;\n\n(pretty-print\n     (api-query (string-append url.broad path.query)\n              (js-query (list (hash 'id        \"e00\"\n                                    'source_id \"n00\"\n                                    'target_id \"n01\"\n                                    'type      \"affects\"))\n                        (list (hash 'curie \"CID:2244\"\n                                    'id    \"n00\"\n                                    'type  \"chemical_substance\")\n                              (hash 'id    \"n01\"\n                                    'type  \"gene\")))))\n\n  #;(js-count\n    (time (api-query (string-append url.unsecret path.predicates))))\n\n  #;(pretty-print\n    (time\n      (api-query (string-append url.unsecret path.query)\n                (js-query (list (hash 'id        \"e00\"\n                                       'source_id \"n00\"\n                                       'target_id \"n01\"\n                                       'type      \"causes\"))\n                           (list (hash 'curie \"UMLS:C0004096\"\n                                       'id    \"n01\"\n                                       'type  \"disease\")\n                                 (hash 'id    \"n00\"\n                                       'type  \"gene\"))))))\n\n  #;(pretty-print\n    (time\n       (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"causes\"))\n                            (list (hash 'curie \"UMLS:C0004096\"\n                                        'id    \"n01\"\n                                        'type  \"disease\")\n                                  (hash 'id    \"n00\"\n                                        'type  \"gene\"))))))\n  \n  #;(pretty-print\n    (time (api-query (string-append url.unsecret path.query)\n                     (js-query (list (hash 'id        \"e00\"\n                                           'source_id \"n00\"\n                                           'target_id \"n01\"\n                                           'type      \"affects\"))\n                               (list (hash 'curie \"CID:2244\"\n                                           'id    \"n00\"\n                                           'type  \"chemical_substance\")\n                                     (hash 'id    \"n01\"\n                                           'type  \"gene\"))))))\n\n  ;;MOLEPRO drug --treats--> disease query w/ NO EVIDENCE\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"treats\"))\n                            (list (hash 'curie \"ChEMBL:CHEMBL25\"\n                                        'id    \"n00\"\n                                        'type  \"chemical_substance\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"disease\"))))))\n\n\n;; addition provenance/evidence for drug indication query\n(pretty-print\n (time\n  (api-query\n   (string-append (string-append url.broad_chembl chembl-drug-indications/transform))\n   (js-query/transform\n    \"ChEMBL:CHEMBL25\"))))\n\n\n;; STRING gene->gene edge\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"related_to\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n\n;; CMAP gene-to-compound query\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"correlated_with\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"chemical_substance\"))))))\n\n;; CMAP gene-to-gene query \n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"correlated_with\"))\n                            (list (hash 'curie \"HGNC:4556\"\n                                        'id    \"n00\"\n                                        'type  \"gene\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"gene\"))))))\n\n\n)\n\n\n\n#|\nall breast cancer curies currently supported by molepro api for disease--treated_by--> Drug X\nMalignant tumor of breast\tMONDO:0021100\tC0006142\t254837009\tDOID:1612\nHormone receptor positive malignant neoplasm of breast\tUMLS:C1562029\tC1562029\t417181009\t\nSecondary malignant neoplasm of female breast\tUMLS:C0346993\tC0346993\t94297009\t\nHER2-positive carcinoma of breast\tMONDO:0006244\tC1960398\t427685000\t\nHuman epidermal growth factor 2 negative carcinoma of breast\tUMLS:C2316304\tC2316304\t431396003\t\nCarcinoma of female breast\tMONDO:0004379\tC3163805\t447782002\t\nCarcinoma of breast\tMONDO:0004989\tC0678222\t254838004\tDOID:3459\nMetastatic Breast Carcinoma\t\t\t\t\nOsteolytic Bone Metastases of Breast Cancer\t\t\t\t\nAdvanced Breast Cancer Progression Post-Antiestrogen Therapy\t\t\t\t\nMetastatic Breast Cancer Progression Post-Antiestrogen Therapy\t\t\t\t\nBreastfeeding (mother)\tUMLS:C1623040\tC1623040\t413712001\t\nHER2 Positive Carcinoma of Breast\t\t\t\t\nEarly Breast Cancer Hormone Receptor Positive and Postmenopausal\t\t\t\t\nPrevention of Breast Carcinoma\t\t\t\t\nFibrocystic breast changes\tMONDO:0005219\tC0016034\t27431007\tDOID:10354\nInfiltrating duct carcinoma of breast\tMONDO:0005590\tC1134719\t408643008\tDOID:3008\n|#\n\n(pretty-print\n (time (api-query (string-append url.broad path.query)\n                  (js-query (list (hash 'id        \"e00\"\n                                        'source_id \"n00\"\n                                        'target_id \"n01\"\n                                        'type      \"treated_by\"))\n                            (list (hash 'curie \"MONDO:0021100\"\n                                        'id    \"n00\"\n                                        'type  \"disease\")\n                                  (hash 'id    \"n01\"\n                                        'type  \"chemical_substance\"))))))\n\n\n#| QUERY for presentation |#\n(define (js-query/transform curie-prefix/lower-case curie)\n  (hash 'collection\n        (list\n         (hash\n          'id \"\"\n          'identifiers\n          (hash\n           curie-prefix/lower-case curie)))     \n        'controls '()))\n\n#;(pretty-print\n (time\n  (api-query\n   (string-append (string-append url.broad_chembl chembl-drug-indications/transform))\n   (js-query/transform\n    'chembl\n    \"ChEMBL:CHEMBL25\"))))\n\n#|NOTES FOR SEPTEMBER 2020 RELAY API CALLS|#\n\n#|\n1. all \"NO-evidence/provenance\" queries are to the base broad.url\n\"https://translator.broadinstitute.org/molepro_reasoner\n\n2. all \"LIMITED evidence/provenance\" queries are to the chembl url\n\"https://translator.broadinstitute.org/chembl\"\n|#\n\n\n"
  },
  {
    "path": "medikanren/test/external-http/2020_NCATS_relay/multiomics-api-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require json net/url)\n\n(define (js-count js)\n  (cond ((pair? js) (foldl + 0 (map js-count js)))\n        ((hash? js) (foldl + 0 (hash-map js (lambda (k v) (js-count v)))))\n        (else       1)))\n\n;; drug response kg\n(define url.multiomics/drug-response\n  \"https://biothings.ncats.io/drug_response_kp\")\n\n;; cancer gene mutation frequnency \n(define url.multiomics/tcga-mut-freq\n  \"https://biothings.ncats.io/tcga_mut_freq_kp\")\n\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n\n(define path.predicates\n  \"/predicates\")\n\n(define path.query\n  \"/query\")\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (define-values (status headers in)\n    (time (if (void? optional-post-jsexpr)\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"GET\")\n            (http-sendrecv/url\n              (string->url url-string)\n              #:method \"POST\"\n              #:data (jsexpr->string optional-post-jsexpr)\n              #:headers '(\"Content-Type: application/json; charset=utf-8\")))))\n  (define response-string (time (port->string in)))\n  (displayln (string-length response-string))\n  (pretty-print headers)\n  (hash 'status status\n        'headers headers\n        'response (string->jsexpr response-string)))\n\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n;; query with gene and get back mutation prevalence by cancer-type\n(define tcga_query:Gene--has-mutation-prevalence-in-cancer-type->DiseaseX/pvalue=.05\n  (lambda (HGNC-gene-symbol)\n    (string-append\n     \"/query?q=association.freq_by_case:%3E0.05%20AND%20subject.SYMBOL:\"\n     (symbol->string HGNC-gene-symbol))))\n\n(pretty-print\n (time\n  (api-query\n   (string-append\n    url.multiomics/tcga-mut-freq\n    (tcga_query:Gene--has-mutation-prevalence-in-cancer-type->DiseaseX/pvalue=.05 'EGFR)))))\n\n\n\n(define tcga_query:GeneX--has-mutation-prevalence-in-cancer-type->Disease/pvalue=.05\n  (lambda (mondo-curie)\n    (string-append\n     \"/query?q=object.id:%22\"\n     (string-append mondo-curie \"%22%20AND%20association.freq_by_case:%3E0.03\"))))\n\n;; disease --> gene w/ frequency of mutation \n;; \"MONDO:0006256\" = invasive breast carcinoma\n(pretty-print\n (time\n  (api-query\n   \"https://biothings.ncats.io/tcga_mut_freq_kp/query?q=object.id:%22MONDO:0006256%22%20AND%20association.freq_by_case:%3E0.03&size=1000\"\n   #;(string-append\n    url.multiomics/tcga-mut-freq\n    (tcga_query:GeneX--has-mutation-prevalence-in-cancer-type->Disease/pvalue=.05 \"MONDO:0007254\"))\n   )))\n\n"
  },
  {
    "path": "medikanren/test/full-dbs/example-common.rkt",
    "content": "#lang racket\n(provide\n  (all-from-out \"../../common.rkt\")\n  (all-defined-out))\n(require \"../../common.rkt\")\n\n(displayln \"all categories:\")\n(pretty-print (run* (c) (categoryo c)))\n\n(newline)\n(displayln \"all predicates:\")\n(pretty-print (run* (p) (predicateo p)))\n\n(newline)\n(displayln \"some concepts:\")\n(pretty-print (run 10 (c) (concepto c)))\n\n(newline)\n(displayln \"some edges:\")\n(pretty-print (run 10 (e) (edgeo e)))\n\n(newline)\n(displayln \"fuzzy name search:\")\n(time (pretty-print\n        ;; Match names that include all listed fragments.\n        (run* (c) (~name*-concepto (list \"imatin\" \"400\") c))))\n\n(newline)\n(displayln \"CURIE search:\")\n(time (pretty-print\n        (run* (c)\n          (~cui*-concepto\n            ;; Match CURIEs that match any of the listed fragments.\n            (list \"UMLS:C0004096\" \"DOID:2841\" \"HP:0002099\" \"MONDO:0004979\")\n            c))))\n\n(newline)\n(displayln \"xref search:\")\n(time (pretty-print\n        (run* (xref c)\n          (membero xref '(\"DOID:2841\" \"HP:0002099\" \"MONDO:0004979\"))\n          (xref-concepto xref c))))\n\n(newline)\n(displayln \"finding pubmed ids and associated edges:\")\n(time (pretty-print (run 3 (pmid e) (pmid-edgeo pmid      e))))\n(displayln \"associating specific pubmed ids with edges:\")\n(time (pretty-print (run*       (e) (pmid-edgeo \"1000085\" e))))\n(time (pretty-print (run*       (e) (pmid-edgeo \"1000018\" e))))\n(time (pretty-print (run*       (e) (pmid-edgeo \"10000\"   e))))\n(time (pretty-print (run*       (e) (pmid-edgeo \"999999\"  e))))\n"
  },
  {
    "path": "medikanren/test/full-dbs/test-common.rkt",
    "content": "#lang racket\n(provide (all-defined-out)\n         (all-from-out \"../../common.rkt\"))\n(require \"../../common.rkt\")\n\n(define decreases\n  (find-predicates\n    '(\"negatively_regulates\"\n      \"prevents\"\n      \"treats\"\n      \"disrupts\"\n      \"increases_degradation_of\"\n      \"decreases_activity_of\"\n      \"decreases_expression_of\")))\n\n(define increases\n  (find-predicates\n    '(\"positively_regulates\"\n      \"produces\"\n      \"causes\"\n      \"causes_condition\"\n      \"causally_related_to\"\n      \"contributes_to\"\n      \"gene_associated_with_condition\"\n      \"gene_mutations_contribute_to\"\n      \"decreases_degradation_of\"\n      \"increases_activity_of\"\n      \"increases_expression_of\")))\n\n(define S (keep 1 (find-concepts #f (list \"imatin\"))))\n;; Alternatively, fuzzy search by name.\n;(define O (keep 1 (find-concepts #f (list \"asthma\"))))\n(define O (keep 1 (find-concepts #t (list \"UMLS:C0004096\"\n                                          \"DOID:2841\"\n                                          \"HP:0002099\"\n                                          \"MONDO:0004979\"))))\n\n(define gene (find-categories (list \"gene\")))\n\n(match-define\n  (list name=>concepts name=>edges)\n  (time\n    (run/graph\n      ;; Introduce concept names.  Optionally constrain them with lists of\n      ;; either concepts or categories.\n      ((X gene)  ;; To ask for all Xs instead, specify this as (X #f).\n       (S S)\n       (O O))\n\n      ;; Introduce edge names.  Optionally constrain them with predicate lists.\n      ((S->X decreases)\n       (X->O increases))\n\n      ;; Specify one or more directed paths.  Paths imply edges with subject on\n      ;; the left and object on the right.\n      (S S->X X X->O O)\n      ;; This path could also have been equivalently specified as two separate\n      ;; paths (in either order), each containing a single edge:\n      ;; (X X->O O)\n      ;; (S S->X X)\n      )))\n\n(displayln \"concepts by name:\")\n(pretty-print name=>concepts)\n(newline)\n(displayln \"edges by name:\")\n(pretty-print name=>edges)\n(newline)\n\n(define (summary name=>xs)\n  (hash-map name=>xs (lambda (name xs) (cons name (length xs)))))\n(displayln \"summary:\")\n(pretty-print `((concepts: . ,(summary name=>concepts))\n                (edges:    . ,(summary name=>edges))))\n\n\n;; Old testing of find-Xs\n(define (test-find-Xs)\n  (define (decreases? p)\n    (member (cddr p) '(\"negatively_regulates\"\n                       \"prevents\"\n                       \"treats\"\n                       \"disrupts\"\n                       \"increases_degradation_of\"\n                       \"decreases_activity_of\"\n                       \"decreases_expression_of\")))\n  (define (increases? p)\n    (member (cddr p) '(\"positively_regulates\"\n                       \"produces\"\n                       \"causes\"\n                       \"causes_condition\"\n                       \"causally_related_to\"\n                       \"contributes_to\"\n                       \"gene_associated_with_condition\"\n                       \"gene_mutations_contribute_to\"\n                       \"decreases_degradation_of\"\n                       \"increases_activity_of\"\n                       \"increases_expression_of\")))\n\n  (define S (keep 1 (find-concepts #f (list \"imatin\"))))\n  (define O (keep 1 (find-concepts #f (list \"asthma\"))))\n\n  (define SP (map (lambda (cp)\n                    (define c (car cp))\n                    (define pS (cadr cp))\n                    (list c (filter decreases? pS) #f))\n                  (find-predicates/concepts #t #f S)))\n  (define OP (map (lambda (cp)\n                    (define c (car cp))\n                    (define pO (caddr cp))\n                    (list c #f (filter increases? pO)))\n                  (find-predicates/concepts #f #t O)))\n\n  (define X (find-Xs SP OP))\n\n  (define x-bcr (car (filter (lambda (x) (equal? (cadddr (car x)) \"BCR gene\")) X)))\n\n  (displayln 'X:)\n  (pretty-print (car x-bcr))\n  (newline)\n  (displayln 'S-edges:)\n  (pretty-print (cadr x-bcr))\n  (newline)\n  (displayln 'O-edges:)\n  (pretty-print (caddr x-bcr)))\n"
  },
  {
    "path": "medikanren/test-behave.sh",
    "content": "#!/bin/bash\nset -euo pipefail\n\n## Usage: bash test-behave.sh PATH-TO-TRANSLATOR-TESTING-FRAMEWORK\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\n: ${output_path=\"$here/test-output.txt\"}\n: ${behave_path=\"$1\"}\n\nprintf 'output_path=%s\\n' \"$output_path\"\nprintf 'behave_path=%s\\n' \"$behave_path\"\n\ntrap 'jobs > /dev/null && kill $(jobs -p)' EXIT ERR\n\nwhile true; do\n  printf \"Tests running: %s\\n\" \"$(date)\"\n  cd \"$here\"\n  racket translator-web-server.rkt &> \"$output_path\" &\n  sleep 120\n  cd \"$behave_path\"\n  ( time behave -i features/medikanren-tests.feature --no-capture --no-capture-stderr\n  ) &>> \"$output_path\" || cat \"$output_path\"\n  printf 'Tests finished: %s\\n' \"$(date)\"\n  kill $(jobs -p) || true\n  sleep 60\ndone\n"
  },
  {
    "path": "medikanren/tmp/ignore",
    "content": ""
  },
  {
    "path": "medikanren/todo.txt",
    "content": "HIGH PRIORITY\n* Matt : 2-hop query--want to modify a target T;  may need to find X that modifies Y that modifies T\n(need to link concepts and synonyms across data sets)\n\n\n* update defaults for synthetic predicates\n* add blacklist to default config file, for things like 'Disease' in Semmeddb, etc.  Make sure this list is respected in *every* relevant 'run' expression (for example, need to filter before determining which predicates are available)\n* consider adding a mode for aggressively checking/pruning likely low quality/howler answers (for example, the innumerable incorrect answers in Semmeddb due to gene aliasing colliding with random short abbreviations for non-genes)\n* figure out what to do when concepts in more than one KG has an identical CUI (there can still be differences in the Category and Name, for example!)  For example, for 'X has_phentype SOX5', 'Robokop' and 'orange' each have a concept for SOX5 with MONDO:0017782 as the CUI, but with slightly different category and name info!\n* add ability to annotate queries/answers, or otherwise provide feedback for good/suspicious/missing answers (potentially send to some central place, or at least save locally)\n* create window for getting all info about a specified gene (run a bunch of standard mini-queries and display results/report)\n* create window for Workflow 1 and Workflow X modules\n* workflow builder\n* figure out how to make the deep blue selection color easier to read\n* add ability to import and use user data\n* be able to answer the SH3 / tau question\n\n\nStandardization\n* support emerging 9.1 input/output standard\n\n\nRefactoring/Generalization/Consistency\n* double-clicking on any property entry should copy the Value to the clipboard (what if the property's value is a URL?  what to do then?)\n* auto-select the first X entry once the X concept list is populated\n* be able to specify a gene, drug, etc., by standard IDs (ENSMBL, etc) (need to index by these IDs, etc)\n* add ability to find all edges with a given PubMed ID to interface (see find-edges-by-pubmed-id.rkt; will probably need to index Orange and RTX KGs as well)\n* consolidate/generalize code for outputting 'last.???' save files\n* generalize code for synthetic predicates, so user can add/override new synthetic predicates from config files\n* update the ISA checkbox to handle ontological connections in a more sophisticated way\n* be able to query between KGs in a single query (like in 'imatinib [decreases] X [increases] asthma')\n* add a simple query builder window, similar to ROBOKOP\n* be able to (efficiently?) find all edges for a given predicate/predicates\n\n\nPerformance/Responsiveness\n* add interruptible thread tech for when clicking on predicates, just like we have for concept string searches\n\n\nold TODOs\n\n====================================\n\n\n;;; TODO FIXME\n\n;;; NGLY1 in concept 2\n;;; semmed\n;;; interacts_with\n;;; FAF1 gene\n\n\n;;; Extract Pubmed ids from the alist of properties in the full path\n\n;;; semmed:\n;;; (\"pmids\" . \"27748395\")\n\n;;; rtx:\n;;;\n\n;;; monarch-lite:\n;;;\n\n;;; TODO FEATURES\n;;;\n;;; hotkeys for moving between panes, etc.--should be able to do everything from the keyboard\n\n;;; Improve sorting to take into account num of pub med entries\n\n;;; TODO\n;;;\n;;; recognize concept name containing only whitespace as being empty\n;;;\n;;; use a reasonable default sorting for the concepts\n;;;\n;;; add ability to sort concept columns by clicking on column titles\n;;;\n;;; speed up concept search--seems much slower than in the old mediKanren\n;;; (perhaps consider searching one DB exhaustively before moving to the next one)\n;;;\n;;; add ability to include only some of the data sources\n;;;\n;;; add ability to show and hide concept columns\n;;;\n;;; add ability to show date of data sources, and date/provenance for results\n;;;\n;;; add ability to specify/filter by data source or category\n\n\n;;; ISSUES\n;;;\n;;; Seem to be missing ' has_phenotype alacrima' entries for\n;;; HEXA and GBA, even though these seem to be in the Monarch website.\n;;; Why?\n;;;\n;;; Different data sources have what are effectively duplicate entries,\n;;; but it isn't always easy to tell.\n;;;\n;;; Different data sources have different category numbers for the\n;;; same CUI/entity.  For example, 'Imatinib mesylate' has the 'UMLS:C0939537'\n;;; CUI in both Semmed and Scigraph, yet the category is (5 . \"chemical_substance\")\n;;; for Semmed and (21 . \"chemical_substance\") for Scigraph.  Why?\n;;; (The concept IDs are different in this case)\n"
  },
  {
    "path": "medikanren/tsv.rkt",
    "content": "#lang racket/base\n(provide tsv-records)\n(require racket/string)\n\n;; Informal grammar for tab-separated values (no escapes supported)\n;FIELD-SEPARATOR  ::= \\t\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= CONTENT*\n;CONTENT includes anything other than \\t, \\n, \\r\n\n(define (tsv-records in)\n  (define (next-record)\n    (define l (read-line in 'any))\n    (and (not (eof-object? l)) (string-split l \"\\t\" #:trim? #f)))\n  (define current #f)\n  (lambda (request)\n    (case request\n      ((current) current)\n      ((next)    (set! current (next-record)) current)\n      (else      (error \"invalid tsv-records request:\" request)))))\n"
  },
  {
    "path": "medikanren/use-cases/README.md",
    "content": "\n# NOTICE: Change of directory structure\n\nContributed use cases, queries and applications are now located in a directory separate from medikanren itself:\n\n- [contrib/](../../contrib)\n\nThe use cases previously residing in this directory now reside in:\n\n- [contrib/medikanren/use-cases/](../../contrib/medikanren/use-cases)\n\n"
  },
  {
    "path": "medikanren/util/data-import/README.md",
    "content": "\n# Medikanren data import\n\n\n[Biolink model](https://biolink.github.io/biolink-model/)\n\n## Setup for data import\n\n* Install racket.\n* Install python3.\n* Clone this repo.\n* Clone the kgx repo: https://github.com/NCATS-Tangerine/kgx\n* Checkout the `source-sink` branch in kgx: `git checkout origin/source-sink`\n* Install dependencies via: `pip3 install -r requirements.txt`\n  * If `pip3` isn't found, try using `pip` instead\n\n\n## Using a local neo4j instance\n\nIf you were given a dump file instead of a remote neo4j instance to connect to, start here.\nOtherwise, skip to the ingestion section.\nFollow these instructions to set up a local instance using the dump file.  Then follow the usual ingestion instructions.\n\n### Download neo4J community server\n\nOn Mac: `brew install neo4j`\n\nComplete setup by running `neo4j start`, then once that suceeds, `neo4j stop`.  This will set up `var/neo4j/data/transaction`.\n\n### Start a local neo4j instance from a dump file\n\nAssuming `neo4j` is already stopped, convert a Robokop (or RTX) `X.dump` to TSV format via:\n\n```\nneo4j-admin load --from X.dump --database graph.db --force  # If this is your first time, remove the --force option.\nneo4j start\ncd YOUR-PATH-TO-NCATS-ROOT/ncats-translator/kgx\ncp config-robokop.yml config.yml\ntime python3 neo4j_download.py\nneo4j stop\n```\n\nThen follow the instructions for converting the TSVs to mediKanren format.\n\n(If you've just set neo4j up for the first time and kgx failed due to authorization, try visiting localhost:7474 in the browser, and logging in with username=neo4j password=neo4j.  You'll be prompted to set a new password.  Set it to be consistent with the password in your kgx config file.)\n\n### Freeing up space once you are finished\n\nIf you installed neo4j using homebrew:\n\n```\nneo4j stop\n# Your data might live here.\nrm -rf /usr/local/Cellar/neo4j/VERSION/libexec/data/databases/*\n# Or it might live here.\nrm -rf /usr/local/var/neo4j/data/databases/*\n```\n\nSupposedly this query should also work, but I get a memory error:\n\n```\nneo4j start\ncypher-shell -u YOURUSERNAME -p YOURPASSWORD --non-interactive 'MATCH(n) DETACH DELETE n'\nneo4j stop\n```\n\n\n## Ingesting new data sources\n\n### Downloading neo4j data in TSV format\n\n* Obtain username, password, host, and port of the neo4j instance.\n* `cd` to the kgx repo.\n* Modify `config.yml` to use the instance information you obtained.  Set the `outputname` here to describe your data source, e.g., `robokop`.\n* Run the download script via `python3`, likely with this command: `python3 neo4j_download.py` (For a typical data source, the download may take an hour or so.)\n  * If `python3` isn't found, try using `python` instead\n\n### Converting TSVs (or CSVs) to mediKanren format\n\n* `cd` to the `medikanren` subdirectory of the `medikanren` repo (which is this repo).\n* Move or copy the downloaded TSV (or CSV) files to an appropriately-named subdirectory of the `medikanren/data` directory.  We'll assume your datasource is named `NAME`, and will live at `medikanren/data/NAME`.\n* For TSV files, perform conversion by running: (For a typical data source, conversion may take an hour or so.)\n```\nracket tsv-graph-to-db.rkt data NAME\nracket build-string-index.rkt data NAME\n```\n* For CSV files, perform conversion by running: (For a typical data source, conversion may take an hour or so.)\n```\nracket csv-graph-to-db.rkt data NAME\nracket build-string-index.rkt data NAME\n```\n* Optionally, map pubmed ids to the edge ids that reference them: `racket build-pubmed-edges.rkt data NAME`\n* Given `(require \"mk-db.rkt\")` you should now be able to access the new db by evaluating `(make-db \"data/NAME\")`.\n\n### Verify data\n\nWithin racket, running this should produce sensible results:\n```\n(require \"mk-db.rkt\")\n(define NAME (make-db \"data/NAME\"))\n(run* (c) (db:categoryo NAME c)))\n(run* (p) (db:predicateo NAME p)))\n(run 10 (c) (db:concepto NAME c)))\n(run 10 (e) (db:edgeo NAME e)))\n```\n\n### Back up TSV (or CSV) source data\n\nIf TSVs are downloaded from a remote source, then after the TSVs are grouped in a directory, yet before running racket conversion scripts, first create a zip for backup:\n```\ncd data\nzip -r semmed.tsv.zip semmed\n```\n\nThis isn't necessary for neo4j dumps because the dump is a reliable source (though doing so could still save the self-download time).  Remote sources are not reliable.\n\nTo backup the TSV->mediKanren work:\n```\ncd data\nzip -r robokop.db.zip robokop\n```\n\n\n\n\n## TODO\n\n### High-level\n\n* queries we want to show during demo, common use cases\n* figure out what info we need and how to build an ontologyo (better name?) relation to relate concepts and classes for traversal in either direction\n* synonymization with max concept distance\n  * e.g., equivalent_to might be distance 0, encodes might be distance 1, etc.\n* figure out what scoring parameters to use, some possibilities are:\n  * confidence we're even referencing the right concepts\n  * confidence in the evidence of a claim (via publications, ontological traversal, etc.)\n    * avoid double-counting same ontological information from multiple sources\n  * confidence via presence in multiple knowledge graphs (RTX2 + sulab semmed)\n  * some notion of relevance: how interesting/useful is this result?\n    * safe drugs are more relevant than unsafe drugs\n\n\n### Graph queries\n\n* Given a query graph\n  * set of nodes\n    * known concepts with CURIEs\n    * unknown concepts, possibly with known category/type\n  * set of edges with known predicate/relation/type\n* Produce a result graph\n  * this is the query graph augmented with instantiations and their metadata\n  * unknown query nodes are bound to (possibly multiple) concepts with CURIEs\n    * contain other information? confidence (the right concept)? relevance?\n  * query edges are bound to (possibly multiple) result edges linking concepts\n    * subject, object\n    * type\n    * negated\n    * `provided_by`\n    * `has_evidence`\n    * publications\n    * `has_confidence_level` (how likely a result is to be true)\n    * `confidence_calculation` ?\n    * relevance (how important a result would be if true; not a biolink property)\n\n* Strategy for producing result graph\n  * synonymization, within and across knowledge graphs\n    * high confidence: `equivalent_to`\n    * low confidence: `xref`\n  * kg-specific base confidence in edges\n  * improving confidence when possible to double-check\n  * reasoning about contradictions (applying negated edges)\n  * determine relevance (e.g., drug is safe (approved or passed phase 1 trial))\n\n\n### UI\n\n* concept distance for (potentially cross-KG) synonyms (similar to ISA checkbox)\n* sorting results by different scoring parameters (confidence vs. relevance)\n* reimplement GUI result builder in terms of run/graph for consistency\n* display JSON version of input/output (need to map different forms of evidence to biolink model)\n* display a simple handmade graph visualization of query and results\n\n\n### Greg will do these\n\n* impose maximum on synonym sets, and gradually reduce allowed connections\n  * after each violation: stop synonym-concepto, then xrefs, then equivalent_to\n* filter for global consistency after propagation\n* improve edge constrainer to pay attention to both subject and object at once\n* separate composite edge construction from ranking\n\n* implement dbKanren\n  * reduce corpus load time\n    * reprocess corpus data using a flat binary format of length-encoded strings\n\n* index edges by predicate\n* index gene aliasing data\n\n* consolidate db generation with one script\n\n* reorganize directory structure\n  * lift medikanren to main directory, moving current main contents somewhere else\n  * keep configs, logs, and user programs (such as gui, web-server...) in main directory\n  * move library and data processing code to a new subdirectory\n  * move tests and examples into their own subdirectories\n\n* web interface\n  * webserver endpoints for lookup of:\n    * concepts/predicates (by name or CUI)\n    * Xs (by chosen concepts and predicates)\n  * web client corresponding to GUI\n\n\n### bottom-up explorer and graph builder ideas\n* organization\n  * all work persistsed in a single environment/repo/version-DAG\n  * workspaces: can have multiple pointers/views/HEADs into the environment\n    * expressed as separate workspaces/tabs/splits to support concurrent\n      activities\n      * not a perfect analogy since you might want multiple visual windows\n        into the same workspace for UI convenience\n    * manipulating multiple workspaces is analogous to branching\n      * opening a new empty workspace is analogous to creating a new branch\n        at the (empty) \"initial commit\"\n  * while \"branches\" are mutable in the sense that they update/repoint as\n    manipulations are performed, data itself is stateless/versionless: may\n    copy/reference data across worksapces\n  * environment is version-controlled at two levels\n    * fine-grained event log recording all user manipulations automatically\n      * raw diffs: show true manipulation history\n      * algebraically simplified diffs: show only effective manipulations\n        * if user flips back and forth between two states, cancel them out\n      * filtered diffs (raw or simplified): only show manipulations relevant\n        to a subset of workspace components\n    * course-grained commits/tags/bookmarks that the user explicitly creates\n    * support rebase/merge/cherry-picking, with optional component filtering\n\n* data\n  * concept sets\n    * unknown or union/intersection/difference of other sets\n    * filter if a text search query is given\n    * filter if known category\n    * filter if constrained as source/target with given predicates\n    * filter by user selections\n  * predicate sets (e.g., increases, decreases)\n    * unknown or union/intersection/difference of other sets\n    * filter if a text search query is given\n    * filter if known parent class(es)\n    * filter if constrained by given source/target concepts\n    * filter by user selections\n  * graphs\n    * nodes and edges\n      * nodes constrained by concept sets\n      * edges connect subject and object sets, constrained by predicate sets\n      * metadata: unique ID, optional name, UI, or visualization preferences\n      * knowns\n        * stratified concept/predicate set computation\n      * unknowns\n        * nodes collect solution sets of concepts\n        * edges collect solution sets of triples\n    * subgraphs\n      * used for organizational convenience\n      * metadata\n      * collection of nodes and edges\n      * may compute as union/intersection/difference of other subgraphs\n\n* computation\n  * stratified construction and constraint resolution\n    * topologically sort element sets along construction expression dependencies\n    * iteratively compute knowns and unknowns\n      * compute known concept and predicate sets\n        * construct new sets using dependencies\n        * filter elements by class, then text search, then selections\n        * validate element selections\n      * solve for unknowns used as subject/object, i.e., (== #f construction)\n        * filter subject/object by text search, then class, then selections\n        * find edge triples\n        * accumulate subject/object concepts from triples, making them known\n        * validate subject/object selections\n  * cache retrieved triples per workspace?\n\n* basic graph building manipulations\n  * update node/edge metadata\n    * node/edge attributes, UI position, other preferences\n  * create new node/edge\n  * duplicate subgraph\n    * alpha rename components (maintain unique ID invariant)\n    * retain dependencies on external component\n      * i.e., computations and constraints\n    * create new internal dependencies that preserve relationships between\n      subgraph components\n  * connect nodes and edges\n  * add/remove node/edge constraints\n    * choose a set of categories/predicate-classes\n    * compute any union/intersection/difference operations\n    * search for text (across name, CURIE, description, etc.)\n    * manually select entries from a list\n\n* more advanced graph building manipulation ideas\n  * multi-hop path-finding between concepts, discovering concepts in between\n  * concept discovery/introduction prioritized via relevance to a background\n    context\n    * background context specified with concept sets\n    * introduced concepts prioritized by the presence of more/better\n      connections to context concepts\n\n* UI\n  * a text-based interface usable from the command-line\n    * workspace could be a directory structure of subgraphs\n  * a (web-based?) graphical interface\n    * clicking/dragging and spatial visualization\n"
  },
  {
    "path": "medikanren/util/data-import/build-pubmed-edges.rkt",
    "content": "#lang racket/base\n(require\n  \"../../common.rkt\"\n  \"../../repr.rkt\"\n  (except-in racket/match ==)\n  racket/stream)\n\n;; Script to index edges of a mediKanren 1 knowledge graph (KG) by PUBMED identifier.\n;;\n;;\n;; Command-line usage:\n;;\n;; racket build-pubmed-edges.rkt  \n;;\n;;\n;; Example usage, on Will's laptop, for indexing rtx2_2021_02_04:\n;;\n;; racket build-pubmed-edges.rkt /Users/webyrd/github/mediKanren/medikanren/data rtx2_2021_02_04\n\n\n;; The script generates two files, 'edges.scm.offset' and 'edges.scm', in the directory of the KG being indexed.\n;;\n;; Once these files have been created, you can start Racket and load\n;; mediKanren 1 as usual.  Please make sure to require \"common.rkt\".\n;;\n;; To get a list of edges that contain the PUBMED id \"10022988\" (for example), you can use the expression:\n;;\n;; (run* (e) (pmid-edgeo \"10022988\" e)\n\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DATA_DIR GRAPH_DIR))\n\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define data-dir (vector-ref argv 0))\n(define graph-dir (vector-ref argv 1))\n(define (graph-path fname)\n  (expand-user-path (build-path data-dir graph-dir fname)))\n\n(define (call-with-?-files cw?f paths proc)\n  (let loop ((paths paths) (ports '()))\n    (if (null? paths) (apply proc (reverse ports))\n      (cw?f (car paths)\n            (lambda (port) (loop (cdr paths) (cons port ports)))))))\n(define (call-with-output-files paths proc)\n  (call-with-?-files call-with-output-file paths proc))\n\n(define (fname-offset fname) (string-append fname \".offset\"))\n(define fnin-edges         \"edges.scm\")\n(define fnout-pubmed-edges \"pubmed-edges.scm\")\n\n(define (process-pmids in-edges out-pubmed-edges out-offset-pubmed-edges)\n  (define pmid=>eid* (hash))\n  (let loop ((eid&edge-stream (port->stream-offset&values in-edges))\n             (edges-seen 0))\n    (cond ((stream-empty? eid&edge-stream)\n           (printf \"Found total ~s pmids\\n\" (hash-count pmid=>eid*))\n           (for ((pmid (in-list (sort (hash-keys pmid=>eid*) stringeid* pmid))\n                (detail-write out-pubmed-edges out-offset-pubmed-edges\n                              (cons pmid eid*)))\n           (flush-output out-pubmed-edges)\n           (flush-output out-offset-pubmed-edges))\n          (else\n           (define eid&edge (stream-first eid&edge-stream))\n           (define eid (car eid&edge))\n           (define props (edge/props-props (cdr eid&edge)))\n           (for-each\n             (lambda (pmid)\n               (set! pmid=>eid*\n                     (hash-set pmid=>eid* pmid\n                               (cons eid (hash-ref pmid=>eid* pmid '())))))\n             (pubmed-ids-from-edge-props props))\n\n           (when (= (modulo edges-seen 1000000) 0)\n             (printf \"seen ~s edges\\n\" edges-seen)\n             (printf \"found ~s pmids so far\\n\" (hash-count pmid=>eid*)))\n\n           (loop (stream-rest eid&edge-stream)\n                 (add1 edges-seen))))))\n\n(printf \"\\nMapping pmids to edges:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-edges)\n        (lambda (in-edges)\n          (call-with-output-files\n            (map graph-path (list fnout-pubmed-edges\n                                  (fname-offset fnout-pubmed-edges)))\n            (lambda out* (apply process-pmids in-edges out*))))))\n"
  },
  {
    "path": "medikanren/util/data-import/build-string-index.rkt",
    "content": "#lang racket/base\n(require\n  \"../repr.rkt\"\n  \"../string-search.rkt\"\n  racket/list\n  racket/set\n  racket/stream\n  racket/vector)\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DATA_DIR GRAPH_DIR))\n\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define data-dir (vector-ref argv 0))\n(define graph-dir (vector-ref argv 1))\n(define (graph-path fname)\n  (expand-user-path (build-path data-dir graph-dir fname)))\n(define (assert-file-absent! fnout)\n  (when (file-exists? (graph-path fnout))\n    (error \"file already exists:\"\n           (path->string (simplify-path (graph-path fnout))))))\n(define (output/filename fname out->)\n  (printf \"writing ~s\\n\" fname)\n  (time (call-with-output-file (graph-path fname) out->)))\n\n(define (fname-offset fname) (string-append fname \".offset\"))\n(define fnin-concepts             \"concepts.scm\")\n(define fnout-synonyms            \"synonyms.scm\")\n(define fnout-xrefs               \"xrefs.scm\")\n(define fnout-concept-synonym     \"concepts-by-synonym.scm\")\n(define fnout-concept-xref        \"concepts-by-xref.scm\")\n(define fnout-concept-cui-corpus  \"concept-cui-corpus.scm\")\n(define fnout-concept-cui-index   \"concept-cui-index.bytes\")\n(define fnout-concept-name-corpus \"concept-name-corpus.scm\")\n(define fnout-concept-name-index  \"concept-name-index.bytes\")\n(assert-file-absent! fnout-synonyms)\n(assert-file-absent! (fname-offset fnout-synonyms))\n(assert-file-absent! fnout-concept-synonym)\n(assert-file-absent! (fname-offset fnout-concept-synonym))\n(assert-file-absent! fnout-xrefs)\n(assert-file-absent! (fname-offset fnout-xrefs))\n(assert-file-absent! fnout-concept-xref)\n(assert-file-absent! (fname-offset fnout-concept-xref))\n(assert-file-absent! fnout-concept-cui-corpus)\n(assert-file-absent! fnout-concept-cui-index)\n(assert-file-absent! fnout-concept-name-corpus)\n(assert-file-absent! fnout-concept-name-index)\n\n(printf \"loading concepts...\\n\")\n(define concept*\n  (time (call-with-input-file\n          (graph-path fnin-concepts)\n          (lambda (in-concepts)\n            (list->vector\n              (stream->list\n                (stream-map cdr (port->stream-offset&values in-concepts))))))))\n(printf \"loaded ~a concepts\\n\" (vector-length concept*))\n\n(let ()\n  (printf \"gathering concept synonyms...\\n\")\n  (define synonym=>concepts\n    (time (let loop ((i 0) (synonym=>concepts (hash)))\n            (cond ((< i (vector-length concept*))\n                   (loop (+ 1 i)\n                         (foldl (lambda (synonym c=>cs)\n                                  (hash-update c=>cs synonym\n                                               (lambda (cs) (cons i cs)) '()))\n                                synonym=>concepts\n                                (concept->synonyms (vector-ref concept* i)))))\n                  (else synonym=>concepts)))))\n  (printf \"building synonym vector...\\n\")\n  (define synonyms (time (for/vector ((key (in-hash-keys synonym=>concepts)))\n                                     key)))\n  (printf \"found ~a synonyms\\n\" (vector-length synonyms))\n  (printf \"sorting synonyms...\\n\")\n  (time (vector-sort! synonyms stringlist (list->set (hash-ref synonym=>concepts\n                                                       synonym)))\n                       <))))))))\n\n(let ()\n  (printf \"gathering concept cross-references...\\n\")\n  (define xref=>concepts\n    (time (let loop ((i 0) (xref=>concepts (hash)))\n            (cond ((< i (vector-length concept*))\n                   (loop (+ 1 i)\n                         (foldl (lambda (xref c=>cs)\n                                  (hash-update c=>cs xref\n                                               (lambda (cs) (cons i cs)) '()))\n                                xref=>concepts\n                                (concept->xrefs (vector-ref concept* i)))))\n                  (else xref=>concepts)))))\n  (printf \"building xref vector...\\n\")\n  (define xrefs (time (for/vector ((key (in-hash-keys xref=>concepts))) key)))\n  (printf \"found ~a xrefs\\n\" (vector-length xrefs))\n  (printf \"sorting xrefs...\\n\")\n  (time (vector-sort! xrefs stringlist (list->set (hash-ref xref=>concepts xref)))\n                       <))))))))\n\n(let ()\n  (printf \"building CUI search corpus...\\n\")\n  (define cui-corpus\n    (time (vector-map (lambda (c) (or (concept-cui c) \"\")) concept*)))\n  (printf \"building CUI search index...\\n\")\n  (define cui-index (time (string:corpus->index cui-corpus)))\n  (printf \"indexed ~a CUIs\\n\" (vector-length cui-index))\n  (output/filename\n    fnout-concept-cui-corpus\n    (lambda (out) (for ((s (in-vector cui-corpus))) (write-scm out s))))\n  (output/filename\n    fnout-concept-cui-index\n    (lambda (out) (write-string-keys out cui-index))))\n\n(let ()\n  (printf \"building name search corpus...\\n\")\n  (define name-corpus\n    (time (vector-map (lambda (c) (let ((name (concept-name c)))\n                                    (if name (string/searchable name) \"\")))\n                      concept*)))\n  (printf \"building name search index...\\n\")\n  (define name-index (time (suffix:corpus->index name-corpus)))\n  (printf \"indexed ~a suffixes\\n\" (vector-length name-index))\n  (output/filename\n    fnout-concept-name-corpus\n    (lambda (out) (for ((s (in-vector name-corpus))) (write-scm out s))))\n  (output/filename\n    fnout-concept-name-index\n    (lambda (out) (write-suffix-keys out name-index))))\n"
  },
  {
    "path": "medikanren/util/data-import/csv-graph-to-db.rkt",
    "content": "#lang racket/base\n(require\n  \"../csv.rkt\"\n  \"../repr.rkt\"\n  json\n  racket/match\n  )\n\n(define (json-simplify json)\n  (if (and (string? json) (< 0 (string-length json))\n           (eqv? #\\\" (string-ref json 0))\n           (eqv? #\\\" (string-ref json (- (string-length json) 1))))\n    (string->jsexpr json)\n    json))\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DATA_DIR GRAPH_DIR))\n\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define data-dir (vector-ref argv 0))\n(define graph-dir (vector-ref argv 1))\n(define (graph-path fname)\n  (expand-user-path (build-path data-dir graph-dir fname)))\n\n;; Input\n;; We don't need anything from *.node.csv to build the DB.\n(define fnin-nodeprop (string-append graph-dir \".nodeprop.csv\"))\n(define fnin-edge     (string-append graph-dir \".edge.csv\"))\n(define fnin-edgeprop (string-append graph-dir \".edgeprop.csv\"))\n\n;; Output\n(define fnout-concepts             \"concepts.scm\")\n(define fnout-categories           \"categories.scm\")\n(define fnout-concepts-by-category \"concepts-by-category.scm\")\n(define fnout-edges                \"edges.scm\")\n(define fnout-predicates           \"predicates.scm\")\n(define fnout-edges-by-subject     \"edges-by-subject.bytes\")\n(define fnout-edges-by-object      \"edges-by-object.bytes\")\n(define (fname-offset fname) (string-append fname \".offset\"))\n\n(define nodeprop-header-expected \":ID,propname,value\")\n(define edgeprop-header-expected \":ID,propname,value\")\n(define edge-header-expected     \":ID,:START,:END\")\n(define (validate-header header-expected in)\n  (define header-found (read-line in 'any))\n  (when (not (equal? header-found header-expected))\n    (error \"unexpected CSV header:\" header-found header-expected)))\n\n(define cui=>id&cat (hash))\n\n(define (process-nodes in-nodeprop out-concepts out-offset-concepts\n                       out-categories out-concepts-by-category\n                       out-offset-concepts-by-category)\n  (define (flush)\n    (flush-output out-categories)\n    (flush-output out-concepts)\n    (flush-output out-offset-concepts))\n  (define category-count 0)\n  (define category=>id (hash))\n  (define cat-id=>concept-id* (hash))\n  (define add-concept\n    (let ((id 0))\n      (define (add-category category)\n        (cond ((not (hash-has-key? category=>id category))\n               (set! category=>id\n                 (hash-set category=>id category category-count))\n               (detail-write out-categories #f category)\n               (set! category-count (+ category-count 1))\n               (- category-count 1))\n              (else (hash-ref category=>id category))))\n      (lambda (cui props)\n        (define (required-prop props key)\n          (define kv (assoc key props))\n          (and kv (cdr kv)))\n        (define category (required-prop props \"category\"))\n        (define name (required-prop props \"name\"))\n        (define category-id (add-category category))\n        (define (other-key? kv)\n          (not (ormap (lambda (k) (equal? k (car kv))) '(\"category\" \"name\"))))\n        (set! cui=>id&cat (hash-set cui=>id&cat cui (cons id category-id)))\n        (set! cat-id=>concept-id*\n          (hash-set cat-id=>concept-id*\n                    category-id\n                    (cons id (hash-ref cat-id=>concept-id* category-id '()))))\n        (detail-write out-concepts out-offset-concepts\n                      (vector cui category-id name (filter other-key? props)))\n        (set! id (+ id 1)))))\n\n  (define nodeprops (csv-records in-nodeprop))\n  (define first-nodeprop (nodeprops 'next))\n  (when (not first-nodeprop) (error \"nodeprop file is empty\"))\n  (match-define (list cui key raw-val) first-nodeprop)\n\n  (let loop ((count 1) (current-cui cui))\n    (define props\n      (let loop-props ((row (nodeprops 'current)))\n        (match row\n          ((list (? (lambda (cui) (equal? current-cui cui))) key raw-val)\n           (cons (cons key (json-simplify raw-val))\n                 (loop-props (nodeprops 'next))))\n          (_ '()))))\n    (add-concept current-cui props)\n    (when (= 0 (remainder count 10000))\n      (printf \"Processed ~s nodes/concepts\\n\" count)\n      (flush))\n\n    (match (nodeprops 'current)\n      ((list cui _ _) (loop (+ 1 count) cui))\n      (#f (printf \"Found ~s concepts in ~s categories\\n\"\n                  (- count 1) category-count)\n       (flush)\n       (for ((cat-id (in-range 0 category-count)))\n            (define cids (sort (hash-ref cat-id=>concept-id* cat-id '()) <=))\n            (define vcids (list->vector cids))\n            (printf \"Category ~s: ~s concepts\\n\" cat-id (vector-length vcids))\n            (detail-write\n              out-concepts-by-category out-offset-concepts-by-category vcids)))\n      (_ (error \"malformed row:\" (nodeprops 'current))))))\n\n(define (process-edges in-edge in-edgeprop\n                       out-predicates\n                       out-edges out-offset-edges\n                       out-edges-by-subject out-offset-edges-by-subject\n                       out-edges-by-object  out-offset-edges-by-object)\n  (define (flush)\n    (flush-output out-predicates)\n    (flush-output out-edges)\n    (flush-output out-offset-edges))\n  (define predicate-count 0)\n  (define predicate=>id (hash))\n  (define subject=>edges (hash))\n  (define object=>edges (hash))\n  (define add-edge\n    (let ((id 0))\n      (define (add-predicate predicate)\n        (cond ((not (hash-has-key? predicate=>id predicate))\n               (set! predicate=>id\n                 (hash-set predicate=>id predicate predicate-count))\n               (detail-write out-predicates #f predicate)\n               (set! predicate-count (+ predicate-count 1))\n               (- predicate-count 1))\n              (else (hash-ref predicate=>id predicate))))\n      (lambda (subject-cui object-cui props)\n        (match-define (cons subject subject-category)\n                      (hash-ref cui=>id&cat subject-cui))\n        (match-define (cons object object-category)\n                      (hash-ref cui=>id&cat object-cui))\n        (define (required-prop props key)\n          (define kv (assoc key props))\n          (and kv (cdr kv)))\n        (define type (or (required-prop props \"edge_label\")\n                         (required-prop props \"type\")\n                         (required-prop props \"predicate\")\n                         (error \"missing required property:\" id props)))\n        (define pid (add-predicate type))\n        (define (other-key? kv)\n          (not (ormap (lambda (k) (equal? k (car kv))) '(\"type\" \"edge_label\"))))\n        ;(define (other-key? kv) (not (equal? \"type\" (car kv))))\n        (set! subject=>edges\n          (hash-set subject=>edges subject\n                    (cons (edge->bytes\n                            (vector pid object-category object id))\n                          (hash-ref subject=>edges subject '()))))\n        (set! object=>edges\n          (hash-set object=>edges object\n                    (cons (edge->bytes\n                            (vector pid subject-category subject id))\n                          (hash-ref object=>edges object '()))))\n        (detail-write out-edges out-offset-edges\n                      (vector subject pid object (filter other-key? props)))\n        (set! id (+ id 1)))))\n\n  (define edges (csv-records in-edge))\n  (define edgeprops (csv-records in-edgeprop))\n  (define first-edge (edges 'next))\n  (define first-edgeprop (edgeprops 'next))\n  (when (not (and first-edge first-edgeprop)) (error \"empty edge files\"))\n  (match-define (list eid0 subject-cui object-cui) first-edge)\n  (match-define (list eid key raw-val) first-edgeprop)\n  (when (not (equal? eid0 eid)) (error \"mismatching edge ids:\" eid0 eid))\n\n  (let loop ((count 1) (current-eid eid) (subject-cui subject-cui)\n                       (object-cui object-cui))\n    (define props\n      (let loop-props ((row (edgeprops 'current)))\n        (match row\n          ((list (? (lambda (eid) (equal? current-eid eid))) key raw-val)\n           (cons (cons key (json-simplify raw-val))\n                 (loop-props (edgeprops 'next))))\n          (_ '()))))\n    (add-edge subject-cui object-cui props)\n    (when (= 0 (remainder count 100000))\n      (printf \"Processed ~s edges\\n\" count)\n      (flush))\n\n    (match (cons (edges 'next) (edgeprops 'current))\n      ((cons (list eid0 subject-cui object-cui) (list eid _ _))\n       (when (not (equal? eid0 eid)) (error \"mismatching edge ids:\" eid0 eid))\n       (loop (+ 1 count) eid subject-cui object-cui))\n      ((cons #f #f)\n       (printf \"Found ~s edges involving ~s predicates\\n\"\n               (- count 1) predicate-count)\n       (flush)\n       (define max-edges/src 0)\n       (for ((src-id (in-range 0 (+ 1 (hash-count cui=>id&cat)))))\n            (when (= 0 (remainder src-id 10000))\n              (printf \"Processed edges for ~s concepts\\n\" src-id)\n              (flush-output out-edges-by-subject)\n              (flush-output out-offset-edges-by-subject)\n              (flush-output out-edges-by-object)\n              (flush-output out-offset-edges-by-object))\n            (define (write-edges-by-X X=>edges out out-offset)\n              (define edges/src 0)\n              (offset-write out-offset (file-position out))\n              (for ((edge (sort (hash-ref X=>edges src-id '()) bytesedges out-edges-by-subject out-offset-edges-by-subject)\n            (write-edges-by-X\n              object=>edges out-edges-by-object out-offset-edges-by-object)))\n      (_ (error \"malformed row(s):\" (edges 'current) (edgeprops 'current))))))\n\n(define (call-with-?-files cw?f paths proc)\n  (let loop ((paths paths) (ports '()))\n    (if (null? paths) (apply proc (reverse ports))\n      (cw?f (car paths)\n            (lambda (port) (loop (cdr paths) (cons port ports)))))))\n(define (call-with-output-files paths proc)\n  (call-with-?-files call-with-output-file paths proc))\n\n(printf \"Processing nodes:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-nodeprop)\n        (lambda (in-nodeprop)\n          (validate-header nodeprop-header-expected in-nodeprop)\n          (call-with-output-files\n            (map graph-path (list fnout-concepts\n                                  (fname-offset fnout-concepts)\n                                  fnout-categories\n                                  fnout-concepts-by-category\n                                  (fname-offset fnout-concepts-by-category)))\n            (lambda out* (apply process-nodes in-nodeprop out*))))))\n\n(printf \"\\nProcessing edges:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-edge)\n        (lambda (in-edge)\n          (validate-header edge-header-expected in-edge)\n          (call-with-input-file\n            (graph-path fnin-edgeprop)\n            (lambda (in-edgeprop)\n              (validate-header edgeprop-header-expected in-edgeprop)\n              (call-with-output-files\n                (map graph-path (list fnout-predicates\n                                      fnout-edges (fname-offset fnout-edges)\n                                      fnout-edges-by-subject\n                                      (fname-offset fnout-edges-by-subject)\n                                      fnout-edges-by-object\n                                      (fname-offset fnout-edges-by-object)))\n                (lambda out*\n                  (apply process-edges in-edge in-edgeprop out*))))))))\n"
  },
  {
    "path": "medikanren/util/data-import/edges-to-csv.rkt",
    "content": "#lang racket/base\n(require racket/set racket/string)\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DATA_DIR GRAPH_DIR))\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define data-dir  (vector-ref argv 0))\n(define graph-dir (vector-ref argv 1))\n(define (graph-path fname)\n  (expand-user-path (build-path data-dir graph-dir fname)))\n(define (graph-path/gname fname) (graph-path (string-append graph-dir fname)))\n\n(define (call/files fins fouts p)\n  (let loop ((fins fins) (ins '()))\n    (if (null? fins)\n      (let loop ((fouts fouts) (outs '()))\n        (if (null? fouts)\n          (apply p (append (reverse ins) (reverse outs)))\n          (call-with-output-file\n            (car fouts) (lambda (out) (loop (cdr fouts) (cons out outs))))))\n      (call-with-input-file\n        (car fins) (lambda (in) (loop (cdr fins) (cons in ins)))))))\n\n(define-syntax-rule (let/files ((in fin) ...) ((out fout) ...) body ...)\n  (call/files (list fin ...) (list fout ...)\n              (lambda (in ... out ...) body ...)))\n\n(define (csv-escape s)\n  (string-append \"\\\"\" (string-replace s \"\\\"\" \"\\\"\\\"\") \"\\\"\"))\n\n(let/files ((in-edges (graph-path \"edges.input.scm\")))\n  ((out-node     (graph-path/gname \".node.csv\"))\n   (out-nodeprop (graph-path/gname \".nodeprop.csv\"))\n   (out-edge     (graph-path/gname \".edge.csv\"))\n   (out-edgeprop (graph-path/gname \".edgeprop.csv\")))\n  (fprintf out-node     \":ID\\n\")\n  (fprintf out-nodeprop \":ID,propname,value\\n\")\n  (fprintf out-edge     \":ID,:START,:END\\n\")\n  (fprintf out-edgeprop \":ID,propname,value\\n\")\n  (let loop ((i 0) (concepts (set)))\n    (define (add-concept concepts c)\n      (define curie    (car    c))\n      (define name     (cadr   c))\n      (define category (caddr  c))\n      (define cprops   (cadddr c))\n      (cond ((set-member? concepts curie) concepts)\n            (else (fprintf out-node \"~a\\n\" curie)\n                  (fprintf out-nodeprop \"~a,~a,~a\\n\" curie \"name\"\n                           (csv-escape name))\n                  (fprintf out-nodeprop \"~a,~a,~a\\n\" curie \"category\"\n                           (csv-escape category))\n                  (for-each (lambda (kv)\n                              (fprintf out-nodeprop \"~a,~a,~a\\n\" curie\n                                       (car kv) (csv-escape (cdr kv))))\n                            cprops)\n                  (set-add concepts curie))))\n    (define e (read in-edges))\n    (unless (eof-object? e)\n      (define subject   (car    e))\n      (define object    (cadr   e))\n      (define predicate (caddr  e))\n      (define eprops    (cadddr e))\n      (fprintf out-edge \"~a,~a,~a\\n\" i (car subject) (car object))\n      (fprintf out-edgeprop \"~a,~a,~a\\n\" i \"edge_label\" predicate)\n      (for-each (lambda (kv) (fprintf out-edgeprop \"~a,~a,~a\\n\" i (car kv)\n                                      (csv-escape (cdr kv))))\n                eprops)\n      (loop (+ i 1) (add-concept (add-concept concepts subject) object)))))\n"
  },
  {
    "path": "medikanren/util/data-import/tsv-graph-to-db-lenient.rkt",
    "content": "#lang racket/base\n(require\n  \"../tsv.rkt\"\n  \"../repr.rkt\"\n  json\n  racket/match\n  )\n\n(define (json-simplify json)\n  (if (and (string? json) (< 0 (string-length json))\n           (eqv? #\\\" (string-ref json 0)))\n    (string->jsexpr json)\n    json))\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DATA_DIR GRAPH_DIR))\n\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define data-dir (vector-ref argv 0))\n(define graph-dir (vector-ref argv 1))\n(define (graph-path fname)\n  (expand-user-path (build-path data-dir graph-dir fname)))\n\n;; Input\n;; We don't need anything from *.node.tsv to build the DB.\n(define fnin-nodeprop (string-append graph-dir \".nodeprop.tsv\"))\n(define fnin-edge     (string-append graph-dir \".edge.tsv\"))\n(define fnin-edgeprop (string-append graph-dir \".edgeprop.tsv\"))\n\n;; Output\n(define fnout-concepts             \"concepts.scm\")\n(define fnout-categories           \"categories.scm\")\n(define fnout-concepts-by-category \"concepts-by-category.scm\")\n(define fnout-edges                \"edges.scm\")\n(define fnout-predicates           \"predicates.scm\")\n(define fnout-edges-by-subject     \"edges-by-subject.bytes\")\n(define fnout-edges-by-object      \"edges-by-object.bytes\")\n(define (fname-offset fname) (string-append fname \".offset\"))\n\n(define nodeprop-header-expected \":ID\\tpropname\\tvalue\")\n(define edgeprop-header-expected \":ID\\tpropname\\tvalue\")\n(define edge-header-expected     \":ID\\t:START\\t:END\")\n(define (validate-header header-expected in)\n  (define header-found (read-line in 'any))\n  (when (not (equal? header-found header-expected))\n    (error \"unexpected TSV header:\" header-found header-expected)))\n\n(define cui=>id&cat (hash))\n\n(define (process-nodes in-nodeprop out-concepts out-offset-concepts\n                       out-categories out-concepts-by-category\n                       out-offset-concepts-by-category)\n  (define (flush)\n    (flush-output out-categories)\n    (flush-output out-concepts)\n    (flush-output out-offset-concepts))\n  (define category-count 0)\n  (define category=>id (hash))\n  (define cat-id=>concept-id* (hash))\n  (define add-concept\n    (let ((id 0))\n      (define (add-category category)\n        (cond ((not (hash-has-key? category=>id category))\n               (set! category=>id\n                 (hash-set category=>id category category-count))\n               (detail-write out-categories #f category)\n               (set! category-count (+ category-count 1))\n               (- category-count 1))\n              (else (hash-ref category=>id category))))\n      (lambda (cui props)\n        (define (required-prop props key)\n          (define kv (assoc key props))\n          (and kv (cdr kv)))\n        (define category (required-prop props \"category\"))\n        (define name (required-prop props \"name\"))\n        (define category-id (add-category category))\n        (define (other-key? kv)\n          (not (ormap (lambda (k) (equal? k (car kv))) '(\"category\" \"name\"))))\n        (set! cui=>id&cat (hash-set cui=>id&cat cui (cons id category-id)))\n        (set! cat-id=>concept-id*\n          (hash-set cat-id=>concept-id*\n                    category-id\n                    (cons id (hash-ref cat-id=>concept-id* category-id '()))))\n        (detail-write out-concepts out-offset-concepts\n                      (vector cui category-id name (filter other-key? props)))\n        (set! id (+ id 1)))))\n\n  (define nodeprops (tsv-records in-nodeprop))\n  (define first-nodeprop (nodeprops 'next))\n  (when (not first-nodeprop) (error \"nodeprop file is empty\"))\n  (match-define (list cui key raw-val) first-nodeprop)\n\n  (let loop ((count 1) (current-cui cui))\n    (define props\n      (let loop-props ((row (nodeprops 'current)))\n        (match row\n          ((list (? (lambda (cui) (equal? current-cui cui))) key raw-val)\n           (cons (cons key (json-simplify raw-val))\n                 (loop-props (nodeprops 'next))))\n          (_ '()))))\n    (add-concept current-cui props)\n    (when (= 0 (remainder count 10000))\n      (printf \"Processed ~s nodes/concepts\\n\" count)\n      (flush))\n\n    (match (nodeprops 'current)\n      ((list cui _ _) (loop (+ 1 count) cui))\n      (#f (printf \"Found ~s concepts in ~s categories\\n\"\n                  (- count 1) category-count)\n       (flush)\n       (for ((cat-id (in-range 0 category-count)))\n            (define cids (sort (hash-ref cat-id=>concept-id* cat-id '()) <=))\n            (define vcids (list->vector cids))\n            (printf \"Category ~s: ~s concepts\\n\" cat-id (vector-length vcids))\n            (detail-write\n              out-concepts-by-category out-offset-concepts-by-category vcids)))\n      (_ (error \"malformed row:\" (nodeprops 'current))))))\n\n(define (process-edges in-edge in-edgeprop\n                       out-predicates\n                       out-edges out-offset-edges\n                       out-edges-by-subject out-offset-edges-by-subject\n                       out-edges-by-object  out-offset-edges-by-object)\n  (define (flush)\n    (flush-output out-predicates)\n    (flush-output out-edges)\n    (flush-output out-offset-edges))\n  (define predicate-count 0)\n  (define predicate=>id (hash))\n  (define subject=>edges (hash))\n  (define object=>edges (hash))\n  (define add-edge\n    (let ((id 0))\n      (define (add-predicate predicate)\n        (cond ((not (hash-has-key? predicate=>id predicate))\n               (set! predicate=>id\n                 (hash-set predicate=>id predicate predicate-count))\n               (detail-write out-predicates #f predicate)\n               (set! predicate-count (+ predicate-count 1))\n               (- predicate-count 1))\n              (else (hash-ref predicate=>id predicate))))\n      (lambda (subject-cui object-cui props)\n        (match-define (cons subject subject-category)\n                      (hash-ref cui=>id&cat subject-cui (cons #f #f)))\n        (match-define (cons object object-category)\n                      (hash-ref cui=>id&cat object-cui (cons #f #f)))\n\t(if (not (and subject object))\n\t    (begin\n\t      (printf \"skipping edge\\n\")\n\t      (unless subject\n\t\t(printf \"missing subject ~a\\n\" subject-cui))\n\t      (unless object\n\t\t(printf \"missing object ~a\\n\" object-cui))\n\t      )\n\t    (let ()\n        (define (required-prop props key)\n          (define kv (assoc key props))\n          (and kv (cdr kv)))\n        (define type (or (required-prop props \"edge_label\")\n                         (required-prop props \"type\")\n                         (error \"missing required property:\" id key)))\n        (define pid (add-predicate type))\n        (define (other-key? kv)\n          (not (ormap (lambda (k) (equal? k (car kv))) '(\"type\" \"edge_label\"))))\n        ;(define (other-key? kv) (not (equal? \"type\" (car kv))))\n        (set! subject=>edges\n          (hash-set subject=>edges subject\n                    (cons (edge->bytes\n                            (vector pid object-category object id))\n                          (hash-ref subject=>edges subject '()))))\n        (set! object=>edges\n          (hash-set object=>edges object\n                    (cons (edge->bytes\n                            (vector pid subject-category subject id))\n                          (hash-ref object=>edges object '()))))\n        (detail-write out-edges out-offset-edges\n                      (vector subject pid object (filter other-key? props)))\n        (set! id (+ id 1)))))))\n\n  (define edges (tsv-records in-edge))\n  (define edgeprops (tsv-records in-edgeprop))\n  (define first-edge (edges 'next))\n  (define first-edgeprop (edgeprops 'next))\n  (when (not (and first-edge first-edgeprop)) (error \"empty edge files\"))\n  (match-define (list eid0 subject-cui object-cui) first-edge)\n  (match-define (list eid key raw-val) first-edgeprop)\n  (when (not (equal? eid0 eid)) (error \"mismatching edge ids:\" eid0 eid))\n\n  (let loop ((count 1) (current-eid eid) (subject-cui subject-cui)\n                       (object-cui object-cui))\n    (define props\n      (let loop-props ((row (edgeprops 'current)))\n        (match row\n          ((list (? (lambda (eid) (equal? current-eid eid))) key raw-val)\n           (cons (cons key (json-simplify raw-val))\n                 (loop-props (edgeprops 'next))))\n          (_ '()))))\n    (add-edge subject-cui object-cui props)\n    (when (= 0 (remainder count 100000))\n      (printf \"Processed ~s edges\\n\" count)\n      (flush))\n\n    (match (cons (edges 'next) (edgeprops 'current))\n      ((cons (list eid0 subject-cui object-cui) (list eid _ _))\n       (when (not (equal? eid0 eid)) (error \"mismatching edge ids:\" eid0 eid))\n       (loop (+ 1 count) eid subject-cui object-cui))\n      ((cons #f #f)\n       (printf \"Found ~s edges involving ~s predicates\\n\"\n               (- count 1) predicate-count)\n       (flush)\n       (define max-edges/src 0)\n       (for ((src-id (in-range 0 (+ 1 (hash-count cui=>id&cat)))))\n            (when (= 0 (remainder src-id 10000))\n              (printf \"Processed edges for ~s concepts\\n\" src-id)\n              (flush-output out-edges-by-subject)\n              (flush-output out-offset-edges-by-subject)\n              (flush-output out-edges-by-object)\n              (flush-output out-offset-edges-by-object))\n            (define (write-edges-by-X X=>edges out out-offset)\n              (define edges/src 0)\n              (offset-write out-offset (file-position out))\n              (for ((edge (sort (hash-ref X=>edges src-id '()) bytesedges out-edges-by-subject out-offset-edges-by-subject)\n            (write-edges-by-X\n              object=>edges out-edges-by-object out-offset-edges-by-object)))\n      (_ (error \"malformed row(s):\" (edges 'current) (edgeprops 'current))))))\n\n(define (call-with-?-files cw?f paths proc)\n  (let loop ((paths paths) (ports '()))\n    (if (null? paths) (apply proc (reverse ports))\n      (cw?f (car paths)\n            (lambda (port) (loop (cdr paths) (cons port ports)))))))\n(define (call-with-output-files paths proc)\n  (call-with-?-files call-with-output-file paths proc))\n\n(printf \"Processing nodes:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-nodeprop)\n        (lambda (in-nodeprop)\n          (validate-header nodeprop-header-expected in-nodeprop)\n          (call-with-output-files\n            (map graph-path (list fnout-concepts\n                                  (fname-offset fnout-concepts)\n                                  fnout-categories\n                                  fnout-concepts-by-category\n                                  (fname-offset fnout-concepts-by-category)))\n            (lambda out* (apply process-nodes in-nodeprop out*))))))\n\n(printf \"\\nProcessing edges:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-edge)\n        (lambda (in-edge)\n          (validate-header edge-header-expected in-edge)\n          (call-with-input-file\n            (graph-path fnin-edgeprop)\n            (lambda (in-edgeprop)\n              (validate-header edgeprop-header-expected in-edgeprop)\n              (call-with-output-files\n                (map graph-path (list fnout-predicates\n                                      fnout-edges (fname-offset fnout-edges)\n                                      fnout-edges-by-subject\n                                      (fname-offset fnout-edges-by-subject)\n                                      fnout-edges-by-object\n                                      (fname-offset fnout-edges-by-object)))\n                (lambda out*\n                  (apply process-edges in-edge in-edgeprop out*))))))))\n"
  },
  {
    "path": "medikanren/util/data-import/tsv-graph-to-db.rkt",
    "content": "#lang racket/base\n(require\n  \"../tsv.rkt\"\n  \"../repr.rkt\"\n  json\n  racket/match\n  )\n\n(define (json-simplify json)\n  (if (and (string? json) (< 0 (string-length json))\n           (eqv? #\\\" (string-ref json 0))\n           (eqv? #\\\" (string-ref json (- (string-length json) 1))))\n    (string->jsexpr json)\n    json))\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DATA_DIR GRAPH_DIR))\n\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define data-dir (vector-ref argv 0))\n(define graph-dir (vector-ref argv 1))\n(define (graph-path fname)\n  (expand-user-path (build-path data-dir graph-dir fname)))\n\n;; Input\n;; We don't need anything from *.node.tsv to build the DB.\n(define fnin-nodeprop (string-append graph-dir \".nodeprop.tsv\"))\n(define fnin-edge     (string-append graph-dir \".edge.tsv\"))\n(define fnin-edgeprop (string-append graph-dir \".edgeprop.tsv\"))\n\n;; Output\n(define fnout-concepts             \"concepts.scm\")\n(define fnout-categories           \"categories.scm\")\n(define fnout-concepts-by-category \"concepts-by-category.scm\")\n(define fnout-edges                \"edges.scm\")\n(define fnout-predicates           \"predicates.scm\")\n(define fnout-edges-by-subject     \"edges-by-subject.bytes\")\n(define fnout-edges-by-object      \"edges-by-object.bytes\")\n(define (fname-offset fname) (string-append fname \".offset\"))\n\n(define nodeprop-header-expected \":ID\\tpropname\\tvalue\")\n(define edgeprop-header-expected \":ID\\tpropname\\tvalue\")\n(define edge-header-expected     \":ID\\t:START\\t:END\")\n(define (validate-header header-expected in)\n  (define header-found (read-line in 'any))\n  (when (not (equal? header-found header-expected))\n    (error \"unexpected TSV header:\" header-found header-expected)))\n\n(define cui=>id&cat (hash))\n\n(define (process-nodes in-nodeprop out-concepts out-offset-concepts\n                       out-categories out-concepts-by-category\n                       out-offset-concepts-by-category)\n  (define (flush)\n    (flush-output out-categories)\n    (flush-output out-concepts)\n    (flush-output out-offset-concepts))\n  (define category-count 0)\n  (define category=>id (hash))\n  (define cat-id=>concept-id* (hash))\n  (define add-concept\n    (let ((id 0))\n      (define (add-category category)\n        (cond ((not (hash-has-key? category=>id category))\n               (set! category=>id\n                 (hash-set category=>id category category-count))\n               (detail-write out-categories #f category)\n               (set! category-count (+ category-count 1))\n               (- category-count 1))\n              (else (hash-ref category=>id category))))\n      (lambda (cui props)\n        (define (required-prop props key)\n          (define kv (assoc key props))\n          (and kv (cdr kv)))\n        (define category (required-prop props \"category\"))\n        (define name (required-prop props \"name\"))\n        (define category-id (add-category category))\n        (define (other-key? kv)\n          (not (ormap (lambda (k) (equal? k (car kv))) '(\"category\" \"name\"))))\n        (set! cui=>id&cat (hash-set cui=>id&cat cui (cons id category-id)))\n        (set! cat-id=>concept-id*\n          (hash-set cat-id=>concept-id*\n                    category-id\n                    (cons id (hash-ref cat-id=>concept-id* category-id '()))))\n        (detail-write out-concepts out-offset-concepts\n                      (vector cui category-id name (filter other-key? props)))\n        (set! id (+ id 1)))))\n\n  (define nodeprops (tsv-records in-nodeprop))\n  (define first-nodeprop (nodeprops 'next))\n  (when (not first-nodeprop) (error \"nodeprop file is empty\"))\n  (match-define (list cui key raw-val) first-nodeprop)\n\n  (let loop ((count 1) (current-cui cui))\n    (define props\n      (let loop-props ((row (nodeprops 'current)))\n        (match row\n          ((list (? (lambda (cui) (equal? current-cui cui))) key raw-val)\n           (cons (cons key (json-simplify raw-val))\n                 (loop-props (nodeprops 'next))))\n          (_ '()))))\n    (add-concept current-cui props)\n    (when (= 0 (remainder count 10000))\n      (printf \"Processed ~s nodes/concepts\\n\" count)\n      (flush))\n\n    (match (nodeprops 'current)\n      ((list cui _ _) (loop (+ 1 count) cui))\n      (#f (printf \"Found ~s concepts in ~s categories\\n\"\n                  (- count 1) category-count)\n       (flush)\n       (for ((cat-id (in-range 0 category-count)))\n            (define cids (sort (hash-ref cat-id=>concept-id* cat-id '()) <=))\n            (define vcids (list->vector cids))\n            (printf \"Category ~s: ~s concepts\\n\" cat-id (vector-length vcids))\n            (detail-write\n              out-concepts-by-category out-offset-concepts-by-category vcids)))\n      (_ (error \"malformed row:\" (nodeprops 'current))))))\n\n(define (process-edges in-edge in-edgeprop\n                       out-predicates\n                       out-edges out-offset-edges\n                       out-edges-by-subject out-offset-edges-by-subject\n                       out-edges-by-object  out-offset-edges-by-object)\n  (define (flush)\n    (flush-output out-predicates)\n    (flush-output out-edges)\n    (flush-output out-offset-edges))\n  (define predicate-count 0)\n  (define predicate=>id (hash))\n  (define subject=>edges (hash))\n  (define object=>edges (hash))\n  (define add-edge\n    (let ((id 0))\n      (define (add-predicate predicate)\n        (cond ((not (hash-has-key? predicate=>id predicate))\n               (set! predicate=>id\n                 (hash-set predicate=>id predicate predicate-count))\n               (detail-write out-predicates #f predicate)\n               (set! predicate-count (+ predicate-count 1))\n               (- predicate-count 1))\n              (else (hash-ref predicate=>id predicate))))\n      (lambda (subject-cui object-cui props)\n        (match-define (cons subject subject-category)\n                      (hash-ref cui=>id&cat subject-cui))\n        (match-define (cons object object-category)\n                      (hash-ref cui=>id&cat object-cui))\n        (define (required-prop props key)\n          (define kv (assoc key props))\n          (and kv (cdr kv)))\n        (define type (or (required-prop props \"edge_label\")\n                         (required-prop props \"type\")\n                         (required-prop props \"predicate\")\n                         (error \"missing required property:\" id props)))\n        (define pid (add-predicate type))\n        (define (other-key? kv)\n          (not (ormap (lambda (k) (equal? k (car kv))) '(\"type\" \"edge_label\"))))\n        ;(define (other-key? kv) (not (equal? \"type\" (car kv))))\n        (set! subject=>edges\n          (hash-set subject=>edges subject\n                    (cons (edge->bytes\n                            (vector pid object-category object id))\n                          (hash-ref subject=>edges subject '()))))\n        (set! object=>edges\n          (hash-set object=>edges object\n                    (cons (edge->bytes\n                            (vector pid subject-category subject id))\n                          (hash-ref object=>edges object '()))))\n        (detail-write out-edges out-offset-edges\n                      (vector subject pid object (filter other-key? props)))\n        (set! id (+ id 1)))))\n\n  (define edges (tsv-records in-edge))\n  (define edgeprops (tsv-records in-edgeprop))\n  (define first-edge (edges 'next))\n  (define first-edgeprop (edgeprops 'next))\n  (when (not (and first-edge first-edgeprop)) (error \"empty edge files\"))\n  (match-define (list eid0 subject-cui object-cui) first-edge)\n  (match-define (list eid key raw-val) first-edgeprop)\n  (when (not (equal? eid0 eid)) (error \"mismatching edge ids:\" eid0 eid))\n\n  (let loop ((count 1) (current-eid eid) (subject-cui subject-cui)\n                       (object-cui object-cui))\n    (define props\n      (let loop-props ((row (edgeprops 'current)))\n        (match row\n          ((list (? (lambda (eid) (equal? current-eid eid))) key raw-val)\n           (cons (cons key (json-simplify raw-val))\n                 (loop-props (edgeprops 'next))))\n          (_ '()))))\n    (add-edge subject-cui object-cui props)\n    (when (= 0 (remainder count 100000))\n      (printf \"Processed ~s edges\\n\" count)\n      (flush))\n\n    (match (cons (edges 'next) (edgeprops 'current))\n      ((cons (list eid0 subject-cui object-cui) (list eid _ _))\n       (when (not (equal? eid0 eid)) (error \"mismatching edge ids:\" eid0 eid))\n       (loop (+ 1 count) eid subject-cui object-cui))\n      ((cons #f #f)\n       (printf \"Found ~s edges involving ~s predicates\\n\"\n               (- count 1) predicate-count)\n       (flush)\n       (define max-edges/src 0)\n       (for ((src-id (in-range 0 (+ 1 (hash-count cui=>id&cat)))))\n            (when (= 0 (remainder src-id 10000))\n              (printf \"Processed edges for ~s concepts\\n\" src-id)\n              (flush-output out-edges-by-subject)\n              (flush-output out-offset-edges-by-subject)\n              (flush-output out-edges-by-object)\n              (flush-output out-offset-edges-by-object))\n            (define (write-edges-by-X X=>edges out out-offset)\n              (define edges/src 0)\n              (offset-write out-offset (file-position out))\n              (for ((edge (sort (hash-ref X=>edges src-id '()) bytesedges out-edges-by-subject out-offset-edges-by-subject)\n            (write-edges-by-X\n              object=>edges out-edges-by-object out-offset-edges-by-object)))\n      (_ (error \"malformed row(s):\" (edges 'current) (edgeprops 'current))))))\n\n(define (call-with-?-files cw?f paths proc)\n  (let loop ((paths paths) (ports '()))\n    (if (null? paths) (apply proc (reverse ports))\n      (cw?f (car paths)\n            (lambda (port) (loop (cdr paths) (cons port ports)))))))\n(define (call-with-output-files paths proc)\n  (call-with-?-files call-with-output-file paths proc))\n\n(printf \"Processing nodes:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-nodeprop)\n        (lambda (in-nodeprop)\n          (validate-header nodeprop-header-expected in-nodeprop)\n          (call-with-output-files\n            (map graph-path (list fnout-concepts\n                                  (fname-offset fnout-concepts)\n                                  fnout-categories\n                                  fnout-concepts-by-category\n                                  (fname-offset fnout-concepts-by-category)))\n            (lambda out* (apply process-nodes in-nodeprop out*))))))\n\n(printf \"\\nProcessing edges:\\n\")\n(time (call-with-input-file\n        (graph-path fnin-edge)\n        (lambda (in-edge)\n          (validate-header edge-header-expected in-edge)\n          (call-with-input-file\n            (graph-path fnin-edgeprop)\n            (lambda (in-edgeprop)\n              (validate-header edgeprop-header-expected in-edgeprop)\n              (call-with-output-files\n                (map graph-path (list fnout-predicates\n                                      fnout-edges (fname-offset fnout-edges)\n                                      fnout-edges-by-subject\n                                      (fname-offset fnout-edges-by-subject)\n                                      fnout-edges-by-object\n                                      (fname-offset fnout-edges-by-object)))\n                (lambda out*\n                  (apply process-edges in-edge in-edgeprop out*))))))))\n"
  },
  {
    "path": "medikanren2/.clean.sh",
    "content": "#!/bin/bash\nadirRepo=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && cd .. && pwd )\"\nadirMk=\"$adirRepo/medikanren2\"\n\nset -o pipefail\ntouch \"$adirMk\"/junk.zo # avoid failure when already clean\nif ! find \"$adirMk\" -name \\*.zo | xargs -L1 rm\nthen\n  echo \"*** Warning *** .zo file deletion may not have been complete (e.g. due to spaces in filenames)\"\nfi\n"
  },
  {
    "path": "medikanren2/.compile.sh",
    "content": "#!/bin/bash\nif [ -z \"$adirRepo\" ]\nthen\n    echo -e \"*** ERROR ***\\n  Invoke with \\\".\\\" or \\\"source\\\" from another bash script\\n\" 1>&2\nelse\n    stepname=medikanren2_compile_trapi\n    if (cd \"$adirMk\" && raco make \"server.rkt\" ${rfileTests} )\n    then\n        echo \"$stepname\" > \"$adirArtifacts/status/pass/$stepname\"\n    else\n        echo \"$stepname\" > \"$adirArtifacts/status/fail/$stepname\"\n    fi\nfi"
  },
  {
    "path": "medikanren2/.data-directory-ci",
    "content": "etc/data-10GB-CI.yaml\n"
  },
  {
    "path": "medikanren2/.gitignore",
    "content": "/dbk/.git.backup\n/data\n/config.scm\n"
  },
  {
    "path": "medikanren2/.install_pkgs.sh",
    "content": "#!/bin/bash\n\nraco pkg install --auto --batch --fail-fast \\\n    chk \\\n    shell-pipeline \\\n    yaml \\\n    memoize \\\n    aws\n"
  },
  {
    "path": "medikanren2/.run_ci.sh",
    "content": "#!/bin/bash\nadirRepo=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && cd .. && pwd )\"\nadirMk=\"$adirRepo/medikanren2\"\nadirArtifacts=\"$adirRepo/ci_artifacts\"\n\n# Name files -spec.rkt to be auto-discovered as automated unit tests for the 10GB-CI run.\n\nrfileTests=$(cd \"$adirMk\" && \\\n    find . -name \\*-spec.rkt -a \\\n        \\( -path \\*/test/10GB-CI/\\* -o -not -path \\*/test/10GB-CI/\\* \\) )\n\nbash \"$adirMk/.clean.sh\"\n. \"$adirMk/.compile.sh\"\n\nfind \"$adirMk\" -name config\\*.scm\n\necho \"$adirMk/etc/config.installer.scm:\"\ncat \"$adirMk/etc/config.installer.scm\"\n\nif (cd \"$adirMk\" && env MK_STAGE=prod raco test ${rfileTests} )\nthen\n    echo medikanren_run_ci > \"$adirArtifacts/status/pass/medikanren2_run_ci\"\nelse\n    echo medikanren_run_ci > \"$adirArtifacts/status/fail/medikanren2_run_ci\"\nfi\n"
  },
  {
    "path": "medikanren2/base.rkt",
    "content": "#lang racket/base\n(provide cfg:config-ref cfg:load-config cfg:override-config\n         path-for-database source-path-for-database\n         (all-from-out \"dbk.rkt\") load-config\n         relation-name relation-definition-info relation-missing-data?\n         tagged-relation dynamic-relation relation-extensions database-extend-relations! database-load! database-unload!)\n(require\n  \"dbk.rkt\"\n  racket/list (except-in racket/match ==) racket/runtime-path racket/set\n  racket/dict racket/string\n  (prefix-in cfg: \"mkconfigref.rkt\"))\n\n(define-runtime-path path.root \".\")\n(define (path-simple path) (path->string (simplify-path path)))\n(define (path/root relative-path)\n  (path-simple (build-path path.root relative-path)))\n(define path.data (path/root \"data\"))\n(define (path/data relative-path)\n  (path-simple (build-path path.data relative-path)))\n\n(define (load-config (verbose? #t))\n  (cfg:load-config #t)\n  (cfg:override-dbkanren-defaults\n    (list (cons 'relation-root-path  path.data)\n          (cons 'temporary-root-path (path/data \"temporary\"))))\n  ;; populate configuration of dbKanren\n  (define config-for-dbkanren\n    (map (lambda (kv)\n      (define k (car kv))\n      (define v (cfg:config-ref k))\n      (cons k v))\n      (dict->list dbk:config.default)))\n  (dbk:current-config-set!/alist #;(dbk:current-config) config-for-dbkanren))\n\n(load-config #t)\n\n(define (version-for-database kgid)\n  (define version-for-database (cfg:config-ref 'version-for-database))\n  (if (dict-has-key? version-for-database kgid)\n    (dict-ref version-for-database kgid)\n    'ver-bogus  ;; Not a real version.  The system is designed to allow\n                ;; (require \"db/foodb.rkt\") without foodb actually being installed.\n                ;; Returning a bogus value will tell the system that the bogus\n                ;; database is not installed, which is ok.  Throwing an exception\n                ;; here will cause a crash if a database version is not specified,\n                ;; which is not ok.\n    ))\n\n(define (path-for-database kgid rel)\n  (define ver (version-for-database kgid))\n  (define path (string-join `(,(symbol->string kgid) ,(symbol->string ver) ,(symbol->string rel)) \"/\"))\n  path)\n\n(define (source-path-for-database kgid filename)\n  (define ver (version-for-database kgid))\n  (define path\n    (if filename\n      (string-join `(\"upstream\" ,(symbol->string kgid) ,(symbol->string ver) ,filename) \"/\")\n      (string-join `(\"upstream\" ,(symbol->string kgid) ,(symbol->string ver)) \"/\")))\n  path)\n\n(define (relation-name            r) (hash-ref (relations-ref r)            'name))\n(define (relation-definition-info r) (hash-ref (relations-ref r)            'definition-info))\n(define (relation-missing-data?   r) (hash-ref (relation-definition-info r) 'missing-data? #f))\n\n(define name.r=>tagged-relations   (hash))\n(define name.db=>name.r=>relations (hash))\n\n(define (database-extend-relations! name.db . extensions)\n  (define nr*s (plist->alist extensions))\n  (set! name.db=>name.r=>relations\n    (hash-update name.db=>name.r=>relations name.db\n                 (lambda (name=>relations)\n                   (foldl (lambda (name relation n=>rs)\n                            (hash-update n=>rs name\n                                         (lambda (rs) (cons relation rs))\n                                         '()))\n                          name=>relations (map car nr*s) (map cdr nr*s)))\n                 (hash))))\n\n(define (database-load! name.db)\n  (define name=>relations (hash-ref name.db=>name.r=>relations name.db\n                                    (lambda () (error \"unknown database:\" name.db))))\n  (define missing (filter-not not (append* (map (lambda (rs)\n                                                  (map (lambda (r)\n                                                         (and (relation-missing-data? r)\n                                                              (relation-name          r)))\n                                                       rs))\n                                                (hash-values name=>relations)))))\n  (unless (null? missing)\n    (error \"loaded database has relations that are missing data:\" name.db missing))\n  (define nr*s (hash->list name=>relations))\n  (set! name.r=>tagged-relations\n    (foldl (lambda (name relations n=>rs)\n             (define tagged-relations (list->set (map (lambda (r) (cons name.db r)) relations)))\n             (hash-update n=>rs name\n                          (lambda (rs) (set-union rs tagged-relations))\n                          (set)))\n           name.r=>tagged-relations (map car nr*s) (map cdr nr*s))))\n\n(define (database-unload! name.db)\n  (define name=>relations (hash-ref name.db=>name.r=>relations name.db\n                                    (lambda () (error \"unknown database:\" name.db))))\n  (define nr*s (hash->list name=>relations))\n  (set! name.r=>tagged-relations\n    (foldl (lambda (name relations n=>rs)\n             (define tagged-relations (list->set (map (lambda (r) (cons name.db r)) relations)))\n             (hash-update n=>rs name\n                          (lambda (rs) (set-subtract rs tagged-relations))\n                          (set)))\n           name.r=>tagged-relations (map car nr*s) (map cdr nr*s))))\n\n(define (relation-extensions name)\n  (set->list (hash-ref name.r=>tagged-relations name (set))))\n\n(define ((tagged-relation r tag . tag-positions) . args)\n  (let loop ((args args) (tag-positions tag-positions))\n    (match tag-positions\n      ('()                      (apply r args))\n      ((cons pos tag-positions) (fresh (x)\n                                  (== (list-ref args pos) (cons tag x))\n                                  (loop (list-set args pos x)\n                                        tag-positions))))))\n\n(define (dynamic-relation name . tag-positions)\n  (define extensions (relation-extensions name))\n  (define tagged-relations\n    (map (lambda (name.db r.db) (apply tagged-relation r.db name.db tag-positions))\n         (map car extensions)\n         (map cdr extensions)))\n  (lambda args\n    (foldl (lambda (r g)\n             (conde ((apply r args))\n                    (g)))\n           (== #f #t)\n           tagged-relations)))\n"
  },
  {
    "path": "medikanren2/chembl_sample_edge.rkt",
    "content": "- edge \n  :ID   :START                               :END\n  0     ''    ''\n  1     ...                                  ... \n\n- edgeprops \n  :ID   propname                  value\n  0     edge_label                ''\n  0     subject_curie             ''\n  0     subject_name              {'string_names' : {'preferred_chemical_name' : '' }\n                                                     'IUPAC_chemical_name' : '' }\n  0     subject_curie_synonyms    {...?curie-synonyms?...}\n  0     subject_ontology_parent   {'cross_mapped_ontology_parent' : {CHEBI_parent : }}>\n  0     object_curie              ''\n  0     object_name               ''\n  0     object_ontology_parent    {'cross_mapped_ontology_parent' : {...?UniProtKB:ProteinFamily?...}}>\n  0     object_curie_synonyms     {...?curie-synonyms?...}\n  0     simplified_edge_label     '<...?biolink-predicate?...>'\n  0     experimental_evidence     {'CHEMBL_27': {'assay_id' : ''},\n                                                {'assay_publication_info' : {'assay_PMID' : '',\n                                                                             'assay_DOI' : '',\n                                                                             'assay_description' : '',\n                                                                             'assay_curation_method' : '',\n                                                                             'assay_confidence_score' : '',\n                                                                             'assay_info_last_update' : '',\n                                                                             'assay_publication_date' : '',\n                                                                             'assay_publication_journal' : '',\n                                                                             'assay_publication_title' : '', \n                                                                             'assay_publication_authors' : '',\n                                                                             'assay_publication_abstract' : ''}},\n                                                {'assay_paramater_info' : {'assay_target_type' : '',\n                                                                           'assay_target_chembl_id' : '',\n                                                                           'assay_target_chembl_name' : '',\n                                                                           'assay_type' : '',\n                                                                           'assay_organism' : '',\n                                                                           'assay_organism_taxon_id' : '',\n                                                                           'assay_tissue_type' : '',\n                                                                           'assay_tissue_type_curies' : '',\n                                                                           'assay_cell_type' : '',\n                                                                           'assay_cell_taxon' : {''}\n                                                                           'assay_cell_type_curies' : {'',\n                                                                                                       '',\n                                                                                                       '',\n                                                                                                       '',\n                                                                                                       ''}}},\n                                                {'assay_experimental_data' : {'assay_measurement_type' : '',\n                                                                              'assay_measurment_relation' : ''\n                                                                              'assay_measurment_value' : ''\n                                                                              'assay_measurement_units' : '',\n                                                                              'assay_chembl_pvalue' : '',\n                                                                              'assay_measurement_type_BAO_name' : ''\n                                                                              'assay_measurement_type_BAO_curie' : ''\n                                                                              'assay_measurement_units_UO_curie' : ''\n                                                                              'assay_measurement_units_QUDT_id' : ''}}}\n"
  },
  {
    "path": "medikanren2/common.rkt",
    "content": "#lang racket/base\n(provide (all-from-out \"base.rkt\"\n                       \"db/semmed.rkt\"\n                       \"db/rtx2-20210204.rkt\"\n                       \"db/kgx-synonym.rkt\") ; workaround:\n                                             ; so long as KGX_synonym isn't specified in config.scm\n                                             ; this won't signal an error even if KGX isn't present\n         cprop edge eprop\n         triple quad triple/eid is-a is-a/quad triple-property\n         write-list-to-tsv)\n \n(require \"base.rkt\"\n         racket/dict\n         (prefix-in semmed: \"db/semmed.rkt\")\n         (prefix-in rtx:    \"db/rtx2-20210204.rkt\")\n         (prefix-in kgx:    \"db/kgx-synonym.rkt\"))\n\n(printf \"Configuration says to load these databases: ~s\\n\" (cfg:config-ref 'databases))\n(for ((kgid (cfg:config-ref 'databases)))\n  (unless (dict-has-key? (cfg:config-ref 'version-for-database) kgid)\n    (printf \"Warning: no version-for-database information for ~a (check etc/config.installer.scm)\\n\" kgid)))\n(for-each database-load! (cfg:config-ref 'databases))\n\n;; TODO: define higher-level relations over the db-specific relations\n\n(define cprop (dynamic-relation 'cprop))\n;; tag argument 0 (the edge id) with database name\n(define edge  (dynamic-relation 'edge  0))\n(define eprop (dynamic-relation 'eprop 0))\n\n;; Semantic-web flavored relations\n\n(define-relation (rtx:triple s p o)\n    (fresh (id)\n      (rtx:eprop id \"predicate\" p)\n      (rtx:edge id s o)))\n\n(define-relation (semmed:triple s p o)\n    (fresh (id)\n      (semmed:eprop id \"edge_label\" p)\n      (semmed:edge id s o)))\n\n(define-relation (triple s p o)\n  (conde ((rtx:triple s p o))\n         ((semmed:triple s p o))))\n\n(define-relation (quad graph s p o)\n  (fresh (id)\n    (conde ((== graph rtx:kgid)\n            (rtx:triple s p o))\n           ((== graph 'semmed)\n            (semmed:triple s p o)))))\n\n(define-relation (triple/eid eid s p o)\n  (fresh (id graph)\n    (== eid `(,graph . ,id))\n    (conde ((== graph rtx:kgid)\n            (rtx:eprop id \"predicate\" p)\n            (rtx:edge id s o))\n           ((== graph 'semmed)\n            (semmed:eprop id \"edge_label\" p)\n            (semmed:edge id s o)))))\n\n(define-relation (is-a s c)\n  (cprop s \"category\" c))\n\n(define-relation (is-a/quad graph s c)\n  (conde ((== graph rtx:kgid)\n          (rtx:cprop s \"category\" c))\n         ((== graph 'semmed)\n          (semmed:cprop s \"category\" c))))\n\n(define-relation (triple-property s p o k v)\n  (fresh (eid id graph)\n    (== eid `(,graph . ,id))\n    (conde ((== graph rtx:kgid)\n            (rtx:eprop id \"predicate\" p)\n            (rtx:edge id s o)\n            (rtx:eprop id k v))\n           ((== graph 'semmed)\n            (semmed:eprop id \"edge_label\" p)\n            (semmed:edge id s o)\n            (semmed:eprop id k v)))))\n\n(define-relation (edge-predicate eid p)\n  (eprop eid \"predicate\" p))\n\n;; usage:\n;(run*/set/steps 500 x (syn* \"HGNC:5993\" x))\n \n(define write-list-to-tsv\n  (lambda (header-ls lol path)\n    (with-output-to-file path\n      ;; thunk -- procedure that takes no arguments\n      (lambda ()\n        (for-each\n          (lambda (l)\n            (let loop ([l l])\n              (cond\n                ((null? l)\n                 (error 'output-to-tsv \"where's the data!?\"))\n                ((null? (cdr l)) ;; l contains exactly 1 element\n                 (display (car l))\n                 (display #\\newline))\n                (else\n                 (display (car l))\n                 (display #\\tab)\n                 (loop (cdr l))))))\n          (cons header-ls lol)))\n      #:mode 'text\n      #:exists 'replace)))\n"
  },
  {
    "path": "medikanren2/configref.rkt",
    "content": "#lang racket \n(require\n    racket/runtime-path\n)\n(provide\n    config-ref\n    refresh-config\n    validate-config\n    config-combine\n    configlayer-ref\n    expose-configlayer\n    set-build-thunk!\n)\n\n;; The configuration layers\n(define config-by-cbranch (make-hash))\n(define (configlayer-ref cb cb-default)\n  (hash-ref config-by-cbranch cb cb-default))\n\n;; The active configuration, or #f if configuration needs to be rebuilt\n(define box:config (box #f))\n(define box:build-config (box (lambda () '())))\n(define (set-build-thunk! build-config)\n  (set-box! box:build-config build-config))\n\n(define (config-current)\n  (define cfg (unbox box:config))\n  (cond (cfg cfg)\n        (else (refresh-config)\n              (unbox box:config))))\n(define ((expose-configlayer cbranch) config)\n  (validate-config config)\n  (hash-set! config-by-cbranch cbranch config)\n  (set-box! box:config #f))\n(define (config-ref key #:testing-dict (dict-config (config-current)))\n  (define kv (assoc key dict-config))\n  (unless kv (error \"missing configuration key:\" key))\n  (cdr kv))\n(define (valid-entry? kv)\n  (and (pair? kv) (symbol? (car kv))))\n(define (validate-config config)\n  (unless (and (list? config) (andmap valid-entry? config))\n    (error \"invalid configuration:\" config))\n)\n;;; config-combine\n;; Default configs go last, and must contain a superset of all config keys.\n;; Could be faster, but intended to only be run once at startup.\n(define (config-combine . configs)\n  (define (find k configs)\n    (when (empty? configs)\n      (error \"config defaults must contain a superset of all other config keys\"))\n    (define kv (assoc k (car configs)))\n    (if kv\n      (cdr kv)\n      (find k (cdr configs))))\n  (define ks (map car (last configs)))\n  (map (lambda (k)\n    (cons k (find k configs)))\n    ks)\n)\n\n(define (refresh-config)\n  (define config-new ((unbox box:build-config)))\n  ; (printf \"refresh-config:\\n\")\n  ; (pretty-write config-new)\n  (set-box! box:config config-new))\n\n(module+ test\n  ; has required package:\n  ;   raco pkg install chk\n  ;\n  ; how to run tests:\n  ;   (cd medikanren && raco test configref.rkt)\n\n  (require chk)\n\n  ; test config-ref\n  (chk\n      #:= (config-ref 'foo #:testing-dict '((foo . 1))) 1)\n  (chk\n      #:do (config-ref 'foo #:testing-dict '((foo . 1)))\n      #:t #t)\n  (chk\n      #:x (config-ref 'foo #:testing-dict '((bar . 1))) \"missing configuration key\")\n\n  ; test validate-config\n  (chk #:x (validate-config (vector)) \"invalid configuration\")\n  (chk #:x (validate-config '(())) \"invalid configuration\")\n  (chk #:x (validate-config '((\"foo\" . 1))) \"invalid configuration\")\n  (chk\n      #:do (validate-config '((foo . 1)))\n      #:t #t)\n\n\n  ; test config-combine\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '((foo . 1)) '((foo . 2)) ))\n    1)\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '((foo . 1)) '((foo . 2)) '((foo . 3)) ))\n    1)\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '() '((foo . 2)) ))\n    2)\n  (chk #:=\n    (config-ref 'foo #:testing-dict\n      (config-combine '((foo . 1)) '((foo . 2) (bar . 1)) ))\n    1)\n\n  ; test override-config\n  #;(chk\n    #:do ((expose-configlayer 'override-test) '())\n    #:do (override-config '((query-results.file-name-human . \"last.txt\")))\n    #:= (config-ref 'query-results.file-name-human) \"last.txt\"\n    )\n  #;(chk\n    #:do ((expose-configlayer 'override-test) '((query-results.file-name-human . \"last.txt\")))\n    #:do (override-config '())\n    #:= (config-ref 'query-results.file-name-human) \"last.txt\"\n    )\n  #;(chk\n    #:do ((expose-configlayer 'override-test) '((query-results.file-name-human . \"last.txt\")))\n    #:do (override-config '((query-results.file-name-human . \"bob\")))\n    #:= (config-ref 'query-results.file-name-human) \"bob\"\n    )\n)"
  },
  {
    "path": "medikanren2/connect_dbk_to_sql.rkt",
    "content": "#lang racket/base\n(require db\n         racket/sequence\n         racket/stream\n         racket/list\n         racket/string\n         db/util/datetime\n         srfi/19\n         )\n\n;; create sql connection object\n(define sql_server\n  (mysql-connect\n   #:user \"\"\n   #:database \"\"\n   #:server \"\"\n   #:port \n   #:password \"\"))\n\n;; #:fetch 1 = lazy\n;; #:fetch +inf.0 = entire table \n(define query-->stream\n  (lambda (db-conn query)\n    (sequence->stream\n     (in-query\n      db-conn\n      query\n      #:fetch +inf.0\n      ;;#:fetch 1 \n      ))))\n\n(define normalize-string-for-TSV-export\n  (lambda (row-item)\n    (string-normalize-spaces\n     (string-trim\n      (list->string\n       (remove #\\tab\n               (remove #\\newline\n                       (string->list row-item))))))))\n\n(define row-item-cleaner\n  (lambda (row-item)\n    (cond\n      ((boolean? row-item)\n       row-item)\n      ((sql-null? row-item) \n       \"NULL\")\n      ((sql-timestamp? row-item)\n       (date->string (sql-datetime->srfi-date row-item) \"~1\"))\n      ((string? row-item)\n       (cond\n         ((or (string-contains? row-item \"\\t\")\n              (string-contains? row-item \"\\n\"))\n          (normalize-string-for-TSV-export row-item))\n         (else\n          (string-normalize-spaces row-item))))      \n      (else\n       row-item))))\n\n(define print-table-row-to-TSV\n  (lambda (ls port)\n    (cond\n      ((null? ls)       \n       (fprintf port \"~c\" #\\newline)\n       (void))      \n      ((null? (cdr ls))\n       (fprintf port \"~a\" (row-item-cleaner (car ls)))\n       (print-table-row-to-TSV (cdr ls) port))\n      (else\n       (fprintf port \"~a~c\" (row-item-cleaner (car ls)) #\\tab)\n       (print-table-row-to-TSV (cdr ls) port)))))\n\n(define process-stream-to-TSV\n  (lambda (stream port)\n    (cond\n      ((stream-empty? stream)\n       (void))\n      (else\n       (begin\n         (print-table-row-to-TSV (call-with-values (lambda () (stream-first stream)) list) port)\n         (process-stream-to-TSV (stream-rest stream) port))))))\n\n\n(define get-table-col-names-from-table-list\n  (lambda (db-conn tbl-names/ls els)\n    (cond\n      ((null? tbl-names/ls)\n       (flatten els))\n      (else\n       (get-table-col-names-from-table-list\n        db-conn\n        (cdr tbl-names/ls)\n        (reverse (cons (map (lambda (x) (vector-ref x 0))\n                            (query-rows db-conn (string-append \"DESCRIBE \" (car tbl-names/ls)))) els)))))))\n\n\n(define export-query-result-to-TSV/with-table-names\n  (lambda (db-conn tbl-names/ls query)\n    (let* ((tbl-col-names (get-table-col-names-from-table-list db-conn tbl-names/ls '()))\n           (output-file (open-output-file\n                         (format\n                          (find-system-path 'home-dir)                          \n                          (string-join tbl-names/ls \"_join_\")\n                          ) #:exists 'replace))  \n           (stream (query-->stream db-conn query)))\n      (begin\n        (print-table-row-to-TSV tbl-col-names output-file)\n        (process-stream-to-TSV stream output-file)\n        (close-output-port output-file)))))\n\n;;(export-query-result-to-TSV/with-table-names sql_server '(\"\" \"\") \";\")\n\n"
  },
  {
    "path": "medikanren2/db/clinical_kg.rkt",
    "content": "#lang racket/base\n;; provide will load the materialized relation defined below\n(provide patient-clinical-data)\n(require \"../base.rkt\" (except-in racket/match ==))\n\n(define path-clinical-data )\n\n(define path-demographic-data )\n\n(define in (open-input-file path-clinical-data))\n\n\n(define-relation/table patient-clinical-data\n  'path               \"uab_emr_covid/patient_clinical_data\"\n  'source-file-path   path-clinical-data\n  'source-file-header '(\"patient_id\" \"date_time\" \"type_curie\" \"type_string\" \"type_value\" \"type_unit\")\n  'attribute-names    '(patient_id date_time type_curie type_string type_value type_unit)\n  ;; #f in the attrib-type means \"any\" type\n  'attribute-types    '(nat nat string string string string)\n  'map (value/syntax\n         (lambda (row)\n           (match-define (list patient_id date_time type_curie type_string type_value type_unit) row)\n           (list (string->number patient_id)\n                 (string->number date_time)\n                 type_curie\n                 type_string\n                 type_value\n                 type_unit)))\n  ;; if you know curie and value, you can get a pointer to all other data\n  'indexes '((type_curie type_value)\n             (patient_id type_curie type_value)\n             ))\n"
  },
  {
    "path": "medikanren2/db/kgx-synonym.rkt",
    "content": "#lang racket/base\n(provide synonym)\n\n(require json \"../base.rkt\" (except-in racket/match ==))\n\n\n(define edge-keys '(subject object predicate id source_database))\n\n;(define in-edge (open-input-file \"../data/KGX_NN_data_2021-03-11_edges.jsonl\"))\n\n(define kgid 'kgx-synonym)\n\n(define-relation/table synonym\n  'path                 (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          (path-for-database kgid 'synonym)\n                          \"kgx-synonym/010\")\n  'attribute-names edge-keys\n  'attribute-types '(string string string string string)\n  'indexes '((object subject))\n  #|'source-stream (value/syntax\n                  (let loop ()\n                    (lambda ()\n                      (define line (read-line (open-input-file \"../data/KGX_NN_data_2021-03-11_edges.jsonl\")))\n                      (cond ((eof-object? line) '())\n                            (else\n                             (define row-edge (string->jsexpr line))\n                             (cons (map (lambda (k) (hash-ref row-edge k)) edge-keys)\n                                   (loop)))))))|#\n  )\n\n(database-extend-relations!\n  'kgx-synonym\n  'synonym synonym)\n"
  },
  {
    "path": "medikanren2/db/rtx2-20210204.rkt",
    "content": "#lang racket/base\n(provide kgid concept cprop edge eprop\n         subclass-of subclass-of+ subclass-of*)\n(require \"../base.rkt\" (except-in racket/match ==))\n(require \"../string-search.rkt\")\n\n(define kgid\n  (if (cfg:config-ref 'migrated-to-new-db-versioning)\n      'rtx-kg2\n      'rtx2-20210204))\n\n;; TODO: this might be useful later\n;(define-relation/table concept\n  ;'path               \"rtx2/20210204/concept\"\n  ;'source-file-path   \"rtx2/20210204/rtx_kg2.node.tsv\"\n  ;'source-file-header '(\":ID\")\n  ;'attribute-names    '(curie)\n  ;'attribute-types    '(string))\n(define-relation (concept curie)\n  (fresh (k v)\n    (cprop curie k v)))\n\n(define-relation/table cprop\n  'path               (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          (path-for-database kgid 'cprop)\n                          \"rtx2/20210204/cprop\")\n  'source-file-path   (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          \"upstream/rtx-kg2/rtx_kg2.nodeprop.tsv\"          ; TODO kip: migrated-to-new-db-versioning\n                          \"rtx2/20210204/rtx_kg2.nodeprop.tsv\")\n  'source-file-header '(:ID propname value)\n  'attribute-names    '(curie key value)\n  'attribute-types    '(string string string)\n  'tables             '((curie key value))\n  'indexes            '((key value)))\n\n(string-search-init-rel cprop)\n\n(define-relation/table edge\n  'path               (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          (path-for-database kgid 'edge)\n                          \"rtx2/20210204/edge\")\n  'source-file-path   (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          \"upstream/rtx-kg2/rtx_kg2.edge.tsv\"              ; TODO kip: migrated-to-new-db-versioning\n                          \"rtx2/20210204/rtx_kg2.edge.tsv\")\n  'source-file-header '(\":ID\" \":START\" \":END\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id subject object) row)\n                          (list (string->number id) subject object)))\n  'attribute-names    '(id subject object)\n  'attribute-types    '(nat string string)\n  'indexes            '((subject object)\n                        (object subject)))\n\n(define-relation/table eprop\n  'path               (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          (path-for-database kgid 'eprop)\n                          \"rtx2/20210204/eprop\")\n  'source-file-path   (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          \"upstream/rtx-kg2/rtx_kg2.edgeprop.tsv\"          ; TODO kip: migrated-to-new-db-versioning\n                          \"rtx2/20210204/rtx_kg2.edgeprop.tsv\")\n  'source-file-header '(\":ID\" \"propname\" \"value\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id key value) row)\n                          (list (string->number id) key value)))\n  'attribute-names    '(id key value)\n  'attribute-types    '(nat string string)\n  'indexes            '((key value)))\n\n(define-relation (subclass-of a b)\n  (fresh (eid)\n    (eprop eid \"predicate\" \"biolink:subclass_of\")\n    (edge eid a b)))\n\n(define-relation (subclass-of+ a b)\n  (conde ((subclass-of a b))\n         ((fresh (mid)\n            (subclass-of mid b)\n            (subclass-of+ a mid)))))\n\n(define-relation (subclass-of* a b)\n  (conde ((== a b))\n         ((subclass-of+ a b))))\n\n(database-extend-relations!\n  kgid\n  'cprop cprop\n  'eprop eprop\n  'edge  edge)\n"
  },
  {
    "path": "medikanren2/db/rtx2-biolink_2_1_2021_07_28.rkt",
    "content": "#lang racket/base\n(provide concept cprop edge eprop\n         subclass-of subclass-of+ subclass-of*)\n(require \"../base.rkt\" (except-in racket/match ==))\n(require \"../string-search.rkt\")\n\n;; TODO: this might be useful later\n;(define-relation/table concept\n  ;'path               \"rtx2/biolink_2_1_2021_07_28/concept\"\n  ;'source-file-path   \"rtx2/biolink_2_1_2021_07_28/rtx_kg2.node.tsv\"\n  ;'source-file-header '(\":ID\")\n  ;'attribute-names    '(curie)\n  ;'attribute-types    '(string))\n(define-relation (concept curie)\n  (fresh (k v)\n    (cprop curie k v)))\n\n(define-relation/table cprop\n  'path               \"rtx2/biolink_2_1_2021_07_28/cprop\"\n  'source-file-path   \"rtx2/biolink_2_1_2021_07_28/rtx_kg2.nodeprop.tsv\"\n  'source-file-header '(:ID propname value)\n  'attribute-names    '(curie key value)\n  'attribute-types    '(string string string)\n  'tables             '((curie key value))\n  'indexes            '((key value)))\n\n(string-search-init-rel cprop)\n\n(define-relation/table edge\n  'path               \"rtx2/biolink_2_1_2021_07_28/edge\"\n  'source-file-path   \"rtx2/biolink_2_1_2021_07_28/rtx_kg2.edge.tsv\"\n  'source-file-header '(\":ID\" \":START\" \":END\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id subject object) row)\n                          (list (string->number id) subject object)))\n  'attribute-names    '(id subject object)\n  'attribute-types    '(nat string string)\n  'indexes            '((subject object)\n                        (object subject)))\n\n(define-relation/table eprop\n  'path               \"rtx2/biolink_2_1_2021_07_28/eprop\"\n  'source-file-path   \"rtx2/biolink_2_1_2021_07_28/rtx_kg2.edgeprop.tsv\"\n  'source-file-header '(\":ID\" \"propname\" \"value\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id key value) row)\n                          (list (string->number id) key value)))\n  'attribute-names    '(id key value)\n  'attribute-types    '(nat string string)\n  'indexes            '((key value)))\n\n(define-relation (subclass-of a b)\n  (fresh (eid)\n    (eprop eid \"predicate\" \"biolink:subclass_of\")\n    (edge eid a b)))\n\n(define-relation (subclass-of+ a b)\n  (conde ((subclass-of a b))\n         ((fresh (mid)\n            (subclass-of mid b)\n            (subclass-of+ a mid)))))\n\n(define-relation (subclass-of* a b)\n  (conde ((== a b))\n         ((subclass-of+ a b))))\n\n(database-extend-relations!\n  'rtx2-biolink_2_1_2021_07_28\n  'cprop cprop\n  'eprop eprop\n  'edge  edge)\n"
  },
  {
    "path": "medikanren2/db/rtx2-biolink_2_1_2021_08_04_condensed.rkt",
    "content": "#lang racket/base\n(provide concept cprop edge eprop\n         subclass-of subclass-of+ subclass-of*)\n(require \"../base.rkt\" (except-in racket/match ==))\n(require \"../string-search.rkt\")\n\n;; TODO: this might be useful later\n;(define-relation/table concept\n  ;'path               \"rtx2/biolink_2_1_2021_08_04_condensed/concept\"\n  ;'source-file-path   \"rtx2/biolink_2_1_2021_08_04_condensed/rtx_kg2.node.tsv\"\n  ;'source-file-header '(\":ID\")\n  ;'attribute-names    '(curie)\n  ;'attribute-types    '(string))\n(define-relation (concept curie)\n  (fresh (k v)\n    (cprop curie k v)))\n\n(define-relation/table cprop\n  'path               \"rtx2/biolink_2_1_2021_08_04_condensed/cprop\"\n  'source-file-path   \"rtx2/biolink_2_1_2021_08_04_condensed/rtx_kg2.nodeprop.tsv\"\n  'source-file-header '(:ID propname value)\n  'attribute-names    '(curie key value)\n  'attribute-types    '(string string string)\n  'tables             '((curie key value))\n  'indexes            '((key value)))\n\n(string-search-init-rel cprop)\n\n(define-relation/table edge\n  'path               \"rtx2/biolink_2_1_2021_08_04_condensed/edge\"\n  'source-file-path   \"rtx2/biolink_2_1_2021_08_04_condensed/rtx_kg2.edge.tsv\"\n  'source-file-header '(\":ID\" \":START\" \":END\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id subject object) row)\n                          (list (string->number id) subject object)))\n  'attribute-names    '(id subject object)\n  'attribute-types    '(nat string string)\n  'indexes            '((subject object)\n                        (object subject)))\n\n(define-relation/table eprop\n  'path               \"rtx2/biolink_2_1_2021_08_04_condensed/eprop\"\n  'source-file-path   \"rtx2/biolink_2_1_2021_08_04_condensed/rtx_kg2.edgeprop.tsv\"\n  'source-file-header '(\":ID\" \"propname\" \"value\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id key value) row)\n                          (list (string->number id) key value)))\n  'attribute-names    '(id key value)\n  'attribute-types    '(nat string string)\n  'indexes            '((key value)))\n\n(define-relation (subclass-of a b)\n  (fresh (eid)\n    (eprop eid \"predicate\" \"biolink:subclass_of\")\n    (edge eid a b)))\n\n(define-relation (subclass-of+ a b)\n  (conde ((subclass-of a b))\n         ((fresh (mid)\n            (subclass-of mid b)\n            (subclass-of+ a mid)))))\n\n(define-relation (subclass-of* a b)\n  (conde ((== a b))\n         ((subclass-of+ a b))))\n\n(database-extend-relations!\n  'rtx2-biolink_2_1_2021_08_04_condensed\n  'cprop cprop\n  'eprop eprop\n  'edge  edge)\n"
  },
  {
    "path": "medikanren2/db/semmed.rkt",
    "content": "#lang racket/base\n(provide concept cprop edge eprop)\n(require \"../base.rkt\" (except-in racket/match ==))\n(require \"../string-search.rkt\")\n\n;; TODO: this might be useful later\n;(define-relation/table concept\n  ;'path               \"semmed/concept\"\n  ;'source-file-path   \"semmed/semmed.node.csv\"\n  ;'source-file-header '(\":ID\")\n  ;'attribute-names    '(curie)\n  ;'attribute-types    '(string))\n(define-relation (concept curie)\n  (fresh (k v)\n    (cprop curie k v)))\n\n(define-relation/table cprop\n  'path               \"semmed/cprop\"\n  'source-file-path   \"semmed/semmed.nodeprop.csv\"\n  'source-file-header '(:ID propname value)\n  'attribute-names    '(curie key value)\n  'attribute-types    '(string string string)\n  'tables             '((curie key value))\n  'indexes            '((key value)\n                        (value))\n  ;; specifying retrieval-type is optional (default is disk)\n  'retrieval-type     'disk\n  ;'retrieval-type     'bytes\n  ;'retrieval-type     'scm\n  )\n\n(string-search-init-rel cprop)\n\n(define-relation/table edge\n  'path               \"semmed/edge\"\n  'source-file-path   \"semmed/semmed.edge.csv\"\n  'source-file-header '(\":ID\" \":START\" \":END\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id subject object) row)\n                          (list (string->number id) subject object)))\n  'attribute-names    '(id subject object)\n  'attribute-types    '(nat string string)\n  'indexes            '((subject object)\n                        (object subject)))\n\n(define-relation/table eprop\n  'path               \"semmed/eprop\"\n  'source-file-path   \"semmed/semmed.edgeprop.csv\"\n  'source-file-header '(\":ID\" \"propname\" \"value\")\n  'map                (value/syntax\n                        (lambda (row)\n                          (match-define (list id key value) row)\n                          (list (string->number id) key value)))\n  'attribute-names    '(id key value)\n  'attribute-types    '(nat string string)\n  'indexes            '((key value)\n                        (value)))\n\n(database-extend-relations!\n  'semmed\n  'cprop cprop\n  'eprop eprop\n  'edge  edge)\n"
  },
  {
    "path": "medikanren2/db/sri-reference-kg-0.3.0.rkt",
    "content": "#lang racket\n(provide nodes edges)\n(require \"../base.rkt\" (except-in racket/match ==))\n\n(define columns-of-nodes\n'(\n    id name category description xref ;0-4\n    provided_by synonym anonymous clique_leader comment ;5-9\n    created deprecated election_strategy gene_associated_with_condition genomic_sequence_localization_object\n    has_url has_value identifier in_taxon invalid_biolink_category ;15-19\n    iri mentions position same_as some_values_from ; 20-24\n    source_version subsets title type _invalid_category) ;25-29\n)\n(define stcolumns-of-nodes (map symbol->string columns-of-nodes))\n\n(define-relation/table nodes\n  'path               \"sri-reference/0.3.0/nodes\"\n  'source-file-path   \"sri-reference/0.3.0/sri-reference-kg-0.3.0_nodes_nocr.tsv\"\n  'source-file-header columns-of-nodes\n  'attribute-names    '(id subject object)\n  'attribute-types    '(string string string)\n  'map/append          (value/syntax\n                        (lambda (row)\n                          (define id (car row))\n                          (append-map\n                           (lambda (k v)\n                             (if (equal? v \"\")\n                                 '()\n                                 (list (list id k v))))\n                           (cdr stcolumns-of-nodes)\n                           (cdr row))))\n;  'tables             '((curie name value))\n;  'indexes            '((name value))\n  )\n\n(define columns-of-edges\n'(id subject edge_label object relation\n  provided_by assertion_confidence_score comment created_on description\n  frequency_of_phenotype has_evidence has_measurement_value has_quantifier has_sex_specificity\n  onset source type xref\n))\n(define stcolumns-of-edges (map symbol->string columns-of-edges))\n\n(define-relation/table edges\n  'path               \"sri-reference/0.3.0/edges\"\n  'source-file-path   \"sri-reference/0.3.0/sri-reference-kg-0.3.0_edges_nocr.tsv\"\n  'source-file-header columns-of-edges\n  'attribute-names    '(id subject object)\n  'attribute-types    '(string string string)\n  'map/append          (value/syntax\n                        (lambda (row)\n                          (define id (car row))\n                          (append-map\n                           (lambda (k v)\n                             (if (equal? v \"\")\n                                 '()\n                                 (list (list id k v))))\n                           (cdr stcolumns-of-edges)\n                           (cdr row))))\n  'indexes            '(                  ; default index is: id subject object\n                        (subject object)  ; implicit: lookup ending in id\n                        (object subject)) ; implicit: lookup ending in id\n)\n\n(database-extend-relations!\n  'sri-reference-kg-0.3.0\n  '???nodes nodes\n  '???edges edges)\n"
  },
  {
    "path": "medikanren2/db/yeast-micro-sri-reference-kg-0.3.0.rkt",
    "content": "#lang racket\n(provide\n  tabled-relations nodes edges\n)\n\n#|\n  Extract from source data and rebuild with:\n\n    time python medikanren2/util/storage-size-workaround/s-cerevisiae-kg-ref-ll.py && \\\n    rm -rf medikanren2/data/yeast-sri-reference && \\\n    time racket -l errortrace -u medikanren2/db/yeast-sri-reference-kg-0.3.0.rkt\n|#\n\n\n(require \"../base.rkt\" (except-in racket/match ==))\n(require \"../string-search.rkt\")\n\n(define columns-of-nodes \n'(\n    id name category description xref ;0-4\n    provided_by synonym anonymous clique_leader comment ;5-9\n    created deprecated election_strategy gene_associated_with_condition genomic_sequence_localization_object\n    has_url has_value identifier in_taxon invalid_biolink_category ;15-19\n    iri mentions position same_as some_values_from ; 20-24\n    source_version subsets title type _invalid_category) ;25-29\n)\n(define stcolumns-of-nodes (map symbol->string columns-of-nodes))\n\n(define-relation/table nodes\n  'path               \"yeast-micro-sri-reference/0.3.0c/nodes\"\n  'source-file-path   \"upstream/yeast-micro-sri-reference/0.3.0c/nodes.tsv\"\n  'source-file-header columns-of-nodes\n  'attribute-names    '(id subject object)\n  'attribute-types    '(string string string)\n  'map/append          (value/syntax\n                        (lambda (row)\n                          (define id (car row))\n                          (append-map\n                           (lambda (k v)\n                             (if (equal? v \"\")\n                                 '()\n                                 (list (list id k v))))\n                           (cdr stcolumns-of-nodes)\n                           (cdr row))))\n;  'tables             '((curie name value))\n;  'indexes            '((name value))\n  )\n\n(string-search-init-rel nodes)\n\n(define columns-of-edges\n'(id subject edge_label object relation\n  provided_by assertion_confidence_score comment created_on description\n  frequency_of_phenotype has_evidence has_measurement_value has_quantifier has_sex_specificity\n  onset source type xref\n))\n(define stcolumns-of-edges (map symbol->string columns-of-edges))\n\n(define-relation/table edges\n  'path               \"yeast-micro-sri-reference/0.3.0c/edges\"\n  'source-file-path   \"upstream/yeast-micro-sri-reference/0.3.0c/edges.tsv\"\n  'source-file-header columns-of-edges\n  'attribute-names    '(id subject object)\n  'attribute-types    '(string string string)\n  'map/append          (value/syntax\n                        (lambda (row)\n                          (define id (car row))\n                          (append-map\n                           (lambda (k v)\n                             (if (equal? v \"\")\n                                 '()\n                                 (list (list id k v))))\n                           (cdr stcolumns-of-edges)\n                           (cdr row))))\n  'indexes            '(                  ; default index is: id subject object\n                        (subject object)  ; implicit: lookup ending in id\n                        (object subject)) ; implicit: lookup ending in id\n)\n\n(define tabled-relations (list nodes edges))\n"
  },
  {
    "path": "medikanren2/db/yeast-sri-reference-kg-0.3.0.rkt",
    "content": "#lang racket\n(provide nodes edges)\n\n#|\n  Extract from source data and rebuild with:\n\n    time python medikanren2/util/storage-size-workaround/s-cerevisiae-kg-ref-ll.py && \\\n    rm -rf medikanren2/data/yeast-sri-reference && \\\n    time racket -l errortrace -u medikanren2/db/yeast-sri-reference-kg-0.3.0.rkt\n|#\n\n\n(require \"../base.rkt\" (except-in racket/match ==))\n(require \"../string-search.rkt\")\n\n(define columns-of-nodes\n'(\n    id name category description xref ;0-4\n    provided_by synonym anonymous clique_leader comment ;5-9\n    created deprecated election_strategy gene_associated_with_condition genomic_sequence_localization_object\n    has_url has_value identifier in_taxon invalid_biolink_category ;15-19\n    iri mentions position same_as some_values_from ; 20-24\n    source_version subsets title type _invalid_category) ;25-29\n)\n(define stcolumns-of-nodes (map symbol->string columns-of-nodes))\n\n(define kgid 'yeast-sri-reference)\n\n(define-relation/table nodes\n  'path               (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          (path-for-database kgid 'nodes)\n                          \"yeast-sri-reference/0.3.0b/nodes\")\n  'source-file-path   \"yeast-sri-reference/0.3.0b/simulation-of-upstream/sri-reference-kg-0.3.0_nodes_nocr.tsv\"\n  'source-file-header columns-of-nodes\n  'attribute-names    '(id subject object)\n  'attribute-types    '(string string string)\n  'map/append          (value/syntax\n                        (lambda (row)\n                          (define id (car row))\n                          (append-map\n                           (lambda (k v)\n                             (if (equal? v \"\")\n                                 '()\n                                 (list (list id k v))))\n                           (cdr stcolumns-of-nodes)\n                           (cdr row))))\n;  'tables             '((curie name value))\n;  'indexes            '((name value))\n  )\n\n(string-search-init-rel nodes)\n\n(define columns-of-edges\n'(id subject edge_label object relation\n  provided_by assertion_confidence_score comment created_on description\n  frequency_of_phenotype has_evidence has_measurement_value has_quantifier has_sex_specificity\n  onset source type xref\n))\n(define stcolumns-of-edges (map symbol->string columns-of-edges))\n\n(define-relation/table edges\n  'path               (if (cfg:config-ref 'migrated-to-new-db-versioning)\n                          (path-for-database kgid 'edges)\n                          \"yeast-sri-reference/0.3.0b/edges\")\n  'source-file-path   \"yeast-sri-reference/0.3.0b/simulation-of-upstream/sri-reference-kg-0.3.0_edges_nocr.tsv\"\n  'source-file-header columns-of-edges\n  'attribute-names    '(id subject object)\n  'attribute-types    '(string string string)\n  'map/append          (value/syntax\n                        (lambda (row)\n                          (define id (car row))\n                          (append-map\n                           (lambda (k v)\n                             (if (equal? v \"\")\n                                 '()\n                                 (list (list id k v))))\n                           (cdr stcolumns-of-edges)\n                           (cdr row))))\n  'indexes            '(                  ; default index is: id subject object\n                        (subject object)  ; implicit: lookup ending in id\n                        (object subject)) ; implicit: lookup ending in id\n)\n\n(database-extend-relations!\n  kgid\n  '???nodes nodes\n  '???edges edges)\n"
  },
  {
    "path": "medikanren2/dbk/LICENSE",
    "content": "The MIT License (MIT)\n\nCopyright (c) 2020 Gregory Rosenblatt\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n"
  },
  {
    "path": "medikanren2/dbk/README.md",
    "content": "# dbKanren\n\nThis implementation of Kanren supports defining, and efficiently querying,\nlarge-scale relations.\n\nTypical use:\n\n```\n(require \"PATH-TO-DBKANREN/dbk.rkt\")\n```\n\n\n## TODO\n\n* local relation definitions\n  * expressing subqueries by capturing other vars\n\n* a smaller extended syntax\n  * logical connectives (not, and, or)\n  * apply for relations\n  * anonymous vars\n\n* support void values? (have to stop overloading the meaning of void everywhere)\n\n* GOO join heuristic\n\n* implement checkpointing to avoid losing work with a long materialization process\n\n* `explain` for extracting the database subset needed to reproduce a query's results\n  * with each result, run an instrumented query to record supporting facts\n  * there may be redundancy (one result could be computed in multiple ways)\n\n* only register `c:table` with the subset of variables that are indexable\n* factor out table choosing\n\n* redesign tables, indexing, variable ordering heuristics\n  * to get array-based lookup, specify appropriate column constraints\n  * also, define tables that use column-oriented layout\n  * identify most-constrained-variable more appropriately\n    * simple cardinality (minimum-remaining-values) heuristic is not effective\n    * cardinality is innaccurate since we only track bounds and don't eagerly\n      maintain arc consistency\n    * instead of MRV heuristic, a better heuristic considers how variables\n      constrain relations\n      * ~~rank relation constraints by the ratio of rows `remaining/total`~~\n        * ~~a constraint's remaining rows are those whose first column value\n          falls within the constraint's corresponding variable's bounds~~\n        * smallest ratio wins, choose that constraint's first column variable\n      * it may also make sense to consider all the ratios a variable\n        participates in, and rank variables by some function on these ratios\n        * e.g., could take minimum (described above), could multiply, etc.\n    * we can speculatively compute a fixed number of members of a variable's\n      finite domain, working inward from its bounds, to improve accuracy\n      * helps accuracy of both MRV and most-constrained-relation heuristic\n    * maybe augment this heuristic with consideration of a variable's\n      index-path effectiveness (i.e., starting at this variable makes it easy\n      to efficiently use other indexes)\n      * see index-based path-finding below\n  * maybe support intra-table/inter-table selectivity hints\n    * intra: how many values of attr A do you get when setting attrs B, C, etc.?\n      * degree constraints\n      * could also declare that a column's values appear frequently\n        * if they appear frequently, constraints to that column should not\n          constrain other columns much\n    * inter: `(conj (P a b c) (Q c d e))`\n      * a form of join dependency\n      * what proportion of distinct values `c` from each of `P` and `Q` remain\n        after taking their intersection? e.g., maybe `(3/4 in P . 1/2 in Q)`\n  * analyze, simplify, and plan with query structure\n    * index-based path-finding to find candidate variable orderings\n      * stick with one variable choice order until invalidation is possible\n        * only long-distance constraints can invalidate assumptions\n          * this includes monotone dependencies\n      * when appropriate index paths aren't available, or query can be\n        decomposed, consider materializing/indexing results for subqueries\n    * articulation vertices for fast recognition of decomposable queries\n      * may store intermediate results per subquery for faster integration\n\n* redesign states, strategies to support adaptive analysis and optimization\n  * ~~hypothetical states for analyzing and transforming disjunction components~~\n    * should also use this approach for transforming arbitrary formulas\n    * ~~process a disjunct's constraints in the usual way, but retain simplified\n      residual constraints~~\n      * optionally expand user-defined relations\n    * may detect more opportunities for subsumption by reordering\n    * may drop constraints for eliminated disjunct-local variables\n      * e.g., simple equality constraints that have fully propagated\n    * extract shared constraints from disjunction components via lattice-join\n      * e.g., to implement efficient union of table constraints\n  * decorate unexpanded user-defined relation constraints with the chain of\n    already-expanded parent/caller relations that led to this constraint\n    * to identify nonterminating loops\n    * to help measure progress\n  * optional bottom-up evaluation strategy\n    * safety analysis of relations referenced during query/materialization\n  * randomized variants of interleaving or depth-first search\n\n* alternative variable ordering heuristic\n  * joined?, unique? (approximate w/ single-column-remaining?)\n    * or maybe specificity (via minimum relation cardinality?), cardinality\n    * not all non-joined variables will be reachable, but worry about this later\n\n* use small tables for finite domains\n* fixed point computation\n  * binding signatures with constraints\n    * share work by generalizing signatures\n\n* support hashes, sets, and procedures\n  * if not orderable, can't embed in tables, but that could be fine\n    * procedures probably aren't orderable, but sets and hashes could be\n    * set elements may not be logic variables?\n      * no, we can allow it\n    * hash keys may not be logic variables?\n      * no, we can allow it\n  * `set->list` and `hash->list` will sort elements for determinism\n    * implement them in terms of a numeric indexing operation\n      * map each `i` in `0 <= i < count` to the appropriate key in sorted order\n\n* improve bounds algebra by adding slightly-less and slightly-greater values for open interval endpoints\n  * define comparison operators, min, and max, over these values\n\n* simpler codec definition\n  * simplified extracting/inserting of fixed or variable-length bit vectors\n  * variable-length bit vectors may be encoded in a couple ways\n    * a prefix describing length\n      * if the prefix is itself fixed-size, this implies an upper bound on length\n    * a UTF-8 style encoding with no upper bound on length\n\n* place-based concurrency/parallelism?\n* thread-safe table retrieval\n* tee/piping output logs to file\n* background worker threads/places for materialization\n* documentation and examples\n  * small tsv data example for testing materialization\n  * LiveJournal, Orkut graph benchmark examples for\n    * https://github.com/frankmcsherry/blog/blob/master/posts/2019-09-06.md\n    * reachability\n    * connected components\n    * single-source shortest path\n    * http://yellowstone.cs.ucla.edu/papers/rasql.pdf\n    * http://pages.cs.wisc.edu/~aws/papers/vldb19.pdf\n* support an interactive stepping/user-choice \"strategy\"\n  * both for debugging and devising new strategies\n  * `run/interactive`\n    * same as a `run^` with `current-config` `search-strategy` set to `interactive`\n    * non-stream, first-order representation of strategy-independent states\n      * also support embedding and combining sub-states (hypothetical along a disjunct)\n        * states are just fancy representations of conjunctions, and should be\n          combinable/disolvable\n\n* how do we express columns of suffix type?\n  * it would have this representation type: `#(suffix count len)`\n  * but it would use a different comparison operator\n\n* relation compilation to remove interpretive overhead\n  * mode analysis\n  * represent low-level operation representation depending on mode\n    * e.g., == can act like an assignment, or a type/equality test\n      * likewise for other constraint evaluations\n  * partial evaluation\n    * e.g., unify on partially-known term structures can be unrolled\n    * constraint evaluations can be pre-simplified and reordered\n  * code generation\n\n* eventually, make sure relation metadata contains information for analysis\n  * e.g., degree constraints, fast column ordering, subsumption tag/rules\n  * descriptions used for subsumption\n    * #(,relation ,attributes-satisfied ,attributes-pending)\n    * within a relation, table constraint A subsumes B if\n      B's attributes-pending is a prefix of A's\n      AND\n      B does not have any attributes-satisfied that A does not have\n  * schema: heading, constraints, other dependencies\n    * heading: set of attributes and their types\n    * degree constraints (generalized functional dependencies)\n      * interpret degree constraints to find useful special cases\n        * functional dependency\n        * bijection (one-to-one mapping via opposing functional dependencies)\n        * uniqueness (functional dependency to full set of of attributes)\n    * maybe join and inclusion dependencies\n  * body: finite set of tuples\n\n* floating point numbers are not valid terms\n  * reordering operations endangers soundness\n  * detect float literals when doing so won't hurt performance\n\n\n### Data processing\n\n* types\n  * string/vector prefixes, suffixes, and slices\n    * represented as pairs or vectors of nats\n      * ID, start, end are all fixed-size nats\n    * prefix: `(ID . end)`\n    * suffix: `(ID . start)`\n    * slice:  `#(ID start end)`\n  * ~~binary/bytevector serialization format for compact storage and fast loading~~\n    * more efficient numbers: polymorphic, int, rat\n      * consider exponent-based representations when they would be more compact\n  * string (and suffix) full-text search via bytes rather than chars?\n    * and radix sorting\n\n* high-level relation specification for transforming stream\n  * high-level string transformation types: string, number, json, s-expression\n    * perform this with Racket computation via `:==`\n  * flattening of tuple/array (pair, vector) fields, increasing record arity\n    * supports compact columnarization of scalar-only fields\n  * generate helper relations for large or variable-length data columns\n    * positional ID generation and substitution\n    * replace strings/structures with unique IDs\n    * IDs given by logical or file position\n      * original value obtained by dereferencing ID appropriately\n    * leads to compact and uniform record representations\n  * job/task scheduler that automatically manages dependencies, validates\n    integrity, and parallelizes relational stream transformation/tabulation\n    * no need to manually coordinate stream processing tasks\n    * config option for fast-replay byte encoding of input streams that need\n      multiple passes\n\n* ingestion\n  * parsing: nq (n-quads)\n  * gathering statistics\n    * reservoir sampling\n    * optional column type inference\n    * per-type statistics for polymorphic columns\n    * count, min, max, sum, min-length, max-length\n    * histogram up to distinct element threshold\n    * range bucketing\n  * transformations specified relationally\n    * possibly involving embedded Racket computation\n\n* relational source data transformation\n  * ability to attach metadata to relations, describing:\n    * high-level column types, such as string suffix\n    * transient or persistent status\n    * memory usage budget/preferences\n\n\n### Database representation\n\n* metadata and data storage\n  * hierarchical directory structure (generalizing catalog/schema/table org)\n    * directories/relations are (un)loadable at runtime\n      * causes dynamic extension/retraction of dependent intensional relations\n      * later, support arbitrary insertion, deletion, and update\n        * describe via temporal rules\n  * record definition/dependency information in relation metadata\n  * support export and import (and mounting) of database fragments\n\n* intensional relations (user-level)\n  * search strategy: backward or forward chaining\n    * could be inferred\n  * forward-chaining supports stratified negation and aggregation\n  * materialization (caching/tabling)\n    * if materialized, may be populated on-demand or up-front\n    * partial materialization supported, specified per-rule\n  * optionally temporal\n    * each time-step, elements may be inserted or removed\n      * update is remove and insert\n      * some insertions may happen at non-deterministic times (async)\n\n* extensional relations (user-level)\n  * metadata\n    * constraints:\n      * degree (subsumes uniqueness, functional dependency, cardinality)\n        * in relation R, given (A B C), how many (D E F)s are there?\n          * lower and upper bounds, i.e., 0 to 2, exactly 1, at least 5, etc.\n        * maybe support more precise constraints given specific field values\n      * monotone dependencies\n        * e.g., C is nondecreasing when sorting by (A B C D)\n        * implies sorted rows for (C A B D) appear in same order as (A B C D)\n          * one index can support either ordering\n        * generalized: (sorted-columns (A B . C) (B . D) B) means:\n          * B is already nondecreasing\n          * C becomes nondecreasing once both A and B are chosen\n          * D becomes nondecreasing once B is chosen (regardless of A)\n    * statistics (derived from table statistics)\n\n* low-level tables with optional keys/indices (not user-level)\n  * disk/memory residence and memory structure reconfigurable at runtime\n  * other types of tables:\n    * suffix arrays: given order of the array describes sorted text\n  * high-level semantic types\n    * variable-width: logical position (ID) determined by offset table\n      * text:        `string`\n        * also possible to map text to a smaller alphabet for faster search\n    * fixed-width: logical position (ID) = file-position / width\n      * text suffix: `(ID . start-pos)`\n  * metadata\n    * ~~integrity/consistency checking~~\n      * ~~source files (csvs or otherwise) with their size/modification-time~~\n        * ~~element type/transformations~~\n        * maybe statistics about their content\n    * files/types and table dependencies\n      * text suffix:\n        * suffix file\n          * `(#(nat ,text-ID-size) . #(nat ,pos-size))`\n        * text column table\n    * statistics\n\n\n### Relational language for rules and queries\n\n* functional term sublanguage\n  * ~~atoms and constructors can be appear freely~~\n  * ~~other computation appears under `:==`~~\n    * ~~should be referentially transparent~~\n    * ~~e.g., subqueries used for aggregation, implicitly grouped by outer query~~\n  * maybe indicate monotonicity for efficient incremental update\n    * by default, `:==` will stratify based on dependencies\n\n* relations\n  * local relation definitions to share work (cached results) during aggregation\n    * `(let-relations (((name param ...) formula ...) ...) formula ...)`\n  * if `r` is a relation:\n    * `(r arg+ ...)` relates `arg+ ...` by `r`\n    * `(relations-ref r)` accesses a metaprogramming control structure\n      * configure persistence, representation, uniqueness and type constraints\n      * indicate evaluation preferences or hints, such as indexing\n      * dynamically disable/enable\n      * view source, statistics, configuration, preferences, other metadata\n  * data retention modes\n    * caching/persistence may be forced or performed lazily\n    * from most to least retention:\n      * persistent\n      * cached results\n      * cached constraint states\n      * cached analysis/plan\n      * recomputed from scratch\n\n* misc conveniences\n  * `apply` to supply a single argument/variable to an n-ary relation\n  * tuple-column/record-field keywords\n    * optional keyword argument calling convention for relations\n    * optional keyword projection of query results\n  * relation extension?\n\n* evaluation\n  * query evaluation\n    * precompute relevant persistent/cached safe relations via forward-chaining\n    * safe/finite results loop (mostly backward-chaining)\n      * prune search space top-down to shrink scale of bulk operations\n        * expand recursive relation calls while safe\n          * safety: at least one never-increasing parameter is decreasing\n            * this safety measure still allows polynomial-time computations\n            * may prefer restricting to linear-time computations\n            * or a resource budget to limit absolute cost for any complexity\n          * track call history to measure this\n          * recursive calls of exactly the same size are considered failures\n        * keep results of branching relation calls independent until join phase\n      * ~~maintain constraint satisfiability\n        * ~~constraint propagation loop: `state-enforce-local-consistency`~~\n          * ~~cheap first-pass via domain consistency, then arc consistency~~\n          * backjump and learn clauses when conflict is detected\n        * ~~then global satisfiability via search~~\n          * ~~choose candidate for the most-constrained variable~~\n            * ~~maybe the variable participating in largest number of constraints~~\n          * ~~interleave search candidate choice with cheap first-pass methods~~\n      * perform the (possibly multi-way) join with lowest estimated cost\n      * repeat until either all results computed or only unsafe calls remain\n    * perform unsafe interleaving until finished or safe calls reappear\n      * like typical miniKanren search\n      * if safe calls reappear, re-enter safe/finite results loop\n  * safety (and computation) categories for relations\n    * simple\n      * persistent (extensional or precomputed intensional)\n        * compute via retrieval\n      * nonrecursive\n        * compute via naive expansion\n      * \"safe\" in the datalog sense\n        * compute fixed point via semi-naive eval after top-down rewriting\n          * also be able to compute fixed point via DFS w/ repetition check\n        * all relations used in the body are safe\n        * all head parameter vars mentioned in positive position in body\n          * i.e., all head parameters will be bound to ground values\n        * no constructors containing vars in \"dangerous\" positions\n          * head parameters of recursive relation\n          * arguments to recursive relations in body\n        * aggregation is stratified\n      * \"unsafe\": top-down interleaving search\n        * no safety guarantees at all\n          * refutational incompleteness\n          * unlimited answers\n          * answers with unbound variables, possibly with constraints\n    * more complex alternatives\n      * \"safe\" for forward chaining only\n        * compute fixed point via semi-naive eval\n        * generalizes \"safe\" datalog slightly\n          * constructors w/ vars allowed as args to recursive relations in body\n      * \"safe\" for backward chaining only\n        * compute via DFS\n        * may or may not guarantee all variables are bound (groundness)\n        * termination guaranteed by structural recursion argument metric\n\n* mode analysis\n  * modes as binding patterns with result cardinalities\n    * parameter binding classes from least to most constraining\n      * f: free        (no guarantees of any kind)\n      * x: constrained (if it's a variable, it at least has some constraints)\n      * c: constructed (not a variable, but not necessarily fully ground)\n      * b: bound       (fully ground)\n    * appendo: (b f f) -> (0 1) (b f b)\n      * bound first param leads to 0 or 1 result with bound third param\n  * mode-specific safety\n    * appendo termination requires (c f f) or (f f c) at every recursive call\n  * mode-specific cost\n    * different parameter bindings determine effectiveness of indices\n\n* lazy population of text/non-atomic fields\n  * equality within the same shared-id column can be done by id\n    * also possible with foreign keys\n    * analogous to pointer address equality\n  * equality within the same nonshared-id column must be done by value\n    * equal if ids are the same, but may still be equal with different ids\n  * equality between incomparable columns must be done by value\n    * address spaces are different\n  * how is this integrated with mk search and query evaluation?\n    * can do this in general for functional dependencies\n      * `(conj (relate-function x a) (relate-function x b))` implies `(== a b)`\n  * would like similar \"efficient join\" behavior for text suffix indexes\n    * given multiple text constraints, find an efficient way to filter\n      * will involve intersecting a matching suffix list for each constraint\n      * one suffix list may be tiny, another may be huge\n        * rather than finding their intersection, it's likely more efficient\n          to just throw the huge one away and run the filter directly on the\n          strings for each member of the tiny suffix set\n    * how is this integrated with mk search and query evaluation?\n      * text search can be expressed with `string-appendo` constraints\n        * `(conj (string-appendo t1 needle t2) (string-appendo t2 t3 hay))`\n      * suffix index can be searched via\n        * `(string-appendo needle t1 hay-s)`\n      * multiple needles\n        * `(conj (string-appendo n1 t1 hay-s) (string-appendo n2 t2 hay-s))`\n      * maybe best done explicitly as aggregation via `:==`\n\n\n### Aggregation ideas\n\n* finite relations may relate their tuples to an extra position parameter\n  * `(apply-relation-position R pos tuple)`\n\n* aggregation via negation\n  * can this be done efficiently?\n  * edb: `(edge x y)`\n  * ```\n    (define-relation (1-hops x targets)\n      (=/= targets '())\n      (:== targets (query y (edge x y))))\n\n    or\n\n    (define-relation (1-hops x targets)\n      (=/= targets '())\n      (query== targets y (edge x y)))\n\n    vs.\n\n    (define-relation (1-hops-rest x prev targets)\n      (conde\n        ((== targets '())\n         (not (fresh (z)\n                (any< prev z)\n                (edge x z))))\n        ((fresh (y targets.rest)\n           (== targets (cons y targets.rest))\n           (edge x y)\n           (not (fresh (z)\n                  (any< prev z)\n                  (any< z y)\n                  (edge x z)))\n           (1-hops-rest x y targets.rest)))))\n    (define-relation (1-hops x targets)\n      (fresh (y targets.rest)\n        (== targets (cons y targets.rest))\n        (edge x y)\n        (not (fresh (z)\n               (any< z y)\n               (edge x z)))\n        (1-hops-rest x y targets.rest)))\n    ```\n\n    ```\n    (define-relation (max+o threshold x xs)\n      (conde ((== xs '()) (== x threshold))\n             ((fresh (y ys)\n                (== xs (cons y ys))\n                (conde ((any<= y threshold) (max+o threshold x ys))\n                       ((any<  threshold y) (max+o y         x ys)))))))\n    (define-relation (maxo x xs)\n      (fresh (y ys)\n        (== xs (cons y ys))\n        (max+o y x ys)))\n    (define-relation (edge-largest x largest)\n      (fresh (targets)\n        (query== targets y (edge x y))\n        (maxo largest targets)))\n\n    vs.\n\n    (define-relation (edge-largest x largest)\n      (edge x largest)\n      (not (fresh (y) (any< largest y) (edge x y))))\n    ```\n\n\n### Query planning and joins\n\nWe need some low-level language for transformation (not for humans or direct interpretation).  Is this the right one?\n- is there a more operational datalog-like notation? e.g., datalog + ordering hints?\n  - (and _ ...) and (or _ ...) can be used to specify specific join/union order and nesting\n  - but these seem hard, so this idea is probably not enough:\n    - what about specifying particular kinds of joins?\n    - what about projection and filtering?\n    - what about aggregation?\n    - how about sub-computation sharing and scope?\n\nInitial sketch of relational algebra language for lower-level optimization transformations:\n```\nposition ::= \ncount    ::= \nmerge-op ::= + | * | min | max | set-union | (min-union count) | (max-union count)\nop       ::= cons | vector | list->vector | car | cdr | vector-ref | vector-length | merge-op\nexpr     ::= (quote value) | (ref position position) | (app op expr ...)\ncmp      ::= == | any<= | any< | =/=\ncx       ::= (cmp expr expr) | (and cx ...) | (or cx ...)\nrelation ::= (quote   ((value ...) ...)) ; What operator does this correspond to? Does it assume sorting/deduping? Probably no assumptions, just enumerate raw tuples.\n           | (table   rid)               ; This corresponds to a basic table scan, use a different operator for more efficient access.\n           | (rvar    name)\n           | (filter  (lambda 1 cx) relation)\n           | (project (lambda 1 (expr ...)) relation)\n           | (union   relation ...)\n           | (subtract relation relation)\n           | (cross   relation ...)      ; TODO: replace with nested [for-]loop notation.\n\n;; How do we specify n-way join shared keys?\n;; New notation for join-key specification?\n;; Operators for sorting (with direction), deduplication.\n;; Operators for skipping (dropping), and limiting (taking).\n\n           | (agg     relation (lambda 1 (expr ...)) value (lambda 1 (expr ...)) (merge-op ...))  ; rel group init map merge (map exprs and merge ops must be same length)\n           | (let     ((name relation) ...) relation)  ; Relations are materialized, nesting describes stratification.\n           | (letrec  ((name relation) ...) relation)  ; Relations computed as fixed points, relations are materialized, nesting describes stratification.\n\n;; Let-bound relations should be specific about what physical tables/indexes are formed?\n\ndirection        ::= < | >\ndirection-suffix ::= () | #f\noffset           ::= \nlimit            ::=  | #f\nquery            ::= (query offset limit (direction ... . direction-suffix) relation)  ; Do we need this? Should we embed sorting, skipping, and limiting as operators instead?\n```\n\nExample query thought experiments:\n\nMaybe bounds feedback doesn't make sense, and should be part of the plan ordering, where bounds actually come from the bottom rather than the top?\ne.g., consider variable-centric plans for:\n```\n(run* (a b d e)\n  (exist (c)\n    (and (P a b c)\n         (Q c d e)\n         (R c d e))))\n\n- c then (c d e) then c: (P ((P Q) (P R)))  ; aka semijoins\n  - (join P [2] [1 2]\n          (join (join P [2] [] Q [0] [0 1 2]) [0 1 2] [1 2]  ; this is a semijoin\n                (join P [2] [] R [0] [0 1 2]) [0 1 2] [])    ; this is also a semijoin\n          [0] [1 2])\n\n- (c d e) then c: (P (Q R))\n  - (join P [2] [1 2]\n          (join Q [0 1 2] [1 2] R [0 1 2] [])  ; no semijoining performed\n          [0] [1 2])\n\nBut neither of these gives adaptive feedback ...\nUpstream and downstream can't communicate bounds with this approach.\nIdeally we would choose an ordering like:\n- c d e\nor\n- d e c\n\nBinary joins seem too inflexible here.\n```\n\nMulti-join GOO perspective:\n```\n- (run* (a c) (exist (b) (P a b) (Q b c)))\n  - max cardinality: (* (cardinality P a) (cardinality Q c))\n- (run* (a b c) (P a b) (Q b c))\n  - max cardinality: (min (* (cardinality P a)\n                             (cardinality Q b c))\n                          (* (cardinality Q c)\n                             (cardinality P a b))\n                          (* (cardinality P a)\n                             (cardinality Q c)\n                             (min (cardinality P b)\n                                  (cardinality Q b))))\n```\n\nNaive selectivity for join cardinality estimation:\n```\n- |S join.x T| ~= (/ (* |S||T|) (max (cardinality S x) (cardinality T x)))\n- can generalize for multi-way joins:\n  - if joining k relations\n    - numerator is a product of the k relation sizes\n    - denominator is a product of the (- k 1) largest join-column cardinalities\n```\n\nNon-materializing multi-way joins may be wasteful:\n```\n- (P a b) (Q b c) (R c d) (S d e)\n- joining variables: b c d\n  - for each choice of b, we learn a set of cs and repeat some of the work of joining (R c d) (S d e) on d\n  - the repeated work has two parts:\n    - finding values of c where a satisfying (d e) exists\n    - bisection revisitation overhead in enumerating these\n  - if the result cardinality of (R c d) (S d e) is small, materializing this sub-join may be better\n- semijoins as degenerate joins\n  - (P a b) (Q b c) where P is used to reduce the size of Q based on b\n  - equivalent to (P _ b) (Q b c)\n  - Q^  = (P  _ b) (Q   b c)\n  - R^  = (Q^ _ c) (R   c d)\n  - S^  = (R^ _ d) (S   d e)\n  - R^^ = (R^ c d) (S^  d _)\n  - Q^^ = (Q^ b c) (R^^ c _)\n  - P^  = (P  a b) (Q^^ b _)\n  - arc-constrained query: (P^ a b) (Q^^ b c) (R^^ c d) (S^ d e)\n    - benefit: increased cardinality estimation accuracy\n```\n\nMulti-way joins are not wasteful when all relations share the same join attributes (assuming proper indexes):\n```\n- (P x y a) (Q x b y) (R c y x)\n- can intersect on either (x y) or (y x), and simply enumerate crosses of the non-join attributes\n```\n\nMulti-way joins may improve over binary joins whose expected result cardinality is greater than the max cardinality of either input.\n\n\n### Database construction and management\n\nA string dictionary (domain) on disk could involve 3 data files (with metadata in a separate file):\n- metadata:\n  - names of constituent files\n  - number of strings in this dictionary\n- id=>str\n  - str.data: data file containing N variable-length strings\n    - hello|world|more\n    - N items\n    - not sorted\n    - no need to store string lengths (this is covered by the position file)\n  - str.data.pos: position file for referencing data file (N + 1 positions)\n    - 0|5|10|14\n    - N+1 items\n- str=>id\n  - id.data: data file containing N ids, sorted alphabetically by the strings they refer to\n  - N items\n  - sorted indirectly by id => str.data.pos =interval=> str.data\n    - lookup via binary search through this same indirection\n- instead of this logical id format, we could save an indirection by using file positions as ids\n\n- domains for variable-length-or-large-data\n  - lazy merging of domains\n  - write-ahead blocks maintain local domains until merged\n\n- fixed-width data does not need a domain\n  - null (but why?), bool, fixnat, fixint, fixrat, pair/fixed, tuple, fixarray (behaves like a tuple)\n\n- atomic batch updates\n  - single metadata file for entire database, providing a consistent view of the current state\n    - batch updates will commit to this metadata file (at the next checkpoint)\n  - not quite transactions, but good enough for now\n  - inserted/deleted tuples based on a consistent database snapshot\n  - insertion/deletion of single-relation blocks and domain+relation(s) write-ahead blocks\n    - file path, file size, (file checksum?), block layout\n    - garbage collection / export-of-current-db-state-snapshot\n\n- initial domain insertion\n  - should returned ids be the logical or the file positions?\n    - if we load into RAM, file positions will still work on bytevectors\n    - logical ids can save ~20% of single column memory if there are fewer than 4 billion strings\n      - relatively small savings given small size of data?\n      - may still be able to use other forms of compression on the non-logical ids\n      - but may be worth it if queries tend to not cross databases, and new string data is not frequently inserted\n  - domain sorting and possibly re-mapping ids\n    - can either index ids based on string order\n    - or maintain id assignment in string order directly\n      - provides monotonic ids, which are more efficient when crossing dbs or emitting sorted string output\n      - requires re-mapping the insertion ids to resulting monotonic ids in the original tuple data\n\n- merge-unioning domain blocks\n  - each block uses a different id basis, requiring id translation during merge\n  - first index or monotonize ids block-locally\n  - perform bisect/2-or-k-way merge-union, producing new domain column file\n    - insert new logical or file position into remapping hashes for each original block\n  - map the remapping tuple columns, producing new column files for each\n    - if monotonic ids are used, indexes should not need to be re-sorted\n\n- ideas for domain caching during block production, to minimize redundancy during sort and remap\n  - maintain two datum=>id hash tables for these two pools: multiple-refs and single-ref-so-far\n    - maybe parameterize a more general version: less-than-N-refs-so-far\n      - in this case, treat as LRU, where seeing a new ref pushes a datum back onto the queue to\n        preserve it for a little longer\n      - maybe also give special treatment to small datums, which are less expensive to preserve?\n  - treat single-ref-so-far as a fixed-size queue, where each datum&id pair is thrown away if\n    a second ref isn't found before it rolls off the end\n  - if a second ref is found for a datum in single-ref-so-far, it is promoted to multiple-refs, and\n    stored for the rest of the production\n\n- write-ahead block directory files:\n  - one data file per domain (e.g., variable-length bytes for text, bigint, bigrat, or fixed-width pair/any)\n    - pair/any is a 4-column table, where the car and cdr are annotated with type tags\n    - more generally, a logical column type of \"any\" is itself 2 physical columns, one for the type tag\n  - one position file per domain\n    - potentially-segregated starting positions + one final ending position\n  - one tuple file per update direction (insert or delete) per relation participating in update\n    - if only inserting or deleting, that means one file, and if both, then two files for that relation\n    - potentially-segregated fixed-width tuples that reference data positions\n    - any segregations are due to mistakes in column-byte-width-guessing\n  - metadata describing the contents of each of the other files\n    - particularly the byte-widths of the position and tuple files, for each segregation, along with the\n      segregation division locations\n\n- once the initial write-ahead block is complete, it is committed to the database metadata, to avoid losing progress\n  - each update is a transaction that either completely succeeds or fails\n\n- sort domains\n  - for each domain, this means producing a new file of sorted logical ids, which are themselves data file positions\n    - the sorted order of these ids is implicitly an id remapping table\n    - for each domain sorted, apply a checkpoint after that sorting process is finished\n      - if the domain is large enough to require external sorting, apply finer-grained checkpoints as well\n  - for each domain, merge into the database's main domain\n    - merging domains produces 3 files:\n      - new domain data file\n      - old position remapping file\n      - new (from the write-ahead block) position remapping file\n        - for full write-ahead remapping, compose this with the remapping table produced by write-ahead domain sorting\n    - checkpoint after each merge\n- for each relation-delete and relation-insert file, remap its ids\n  - checkpoint each of these\n- remap each main db relation table not participating in update\n  - checkpoint each of these remappings\n- remap-merge each main db relation table participating in update\n  - each of these is a 3-way merge between these sets: original, delete, insert\n    - the delete and insert sets have already been remapped\n    - tuples from the original set are remapped just-in-time\n      - just-in-time will make bisection harder, so maybe not a good idea? remap ahead of time instead?\n        - nah, this is probably fine\n  - checkpoint each of these remapping-merges\n- rebuild indexes for updated relations\n  - checkpoint each of these\n\n- to avoid manual code-commenting to deal with interrupted batch jobs, can also support a brute force insertion process\n  - this way a small update-history relation can be used to describe and check the progress of a job\n  - still single db consolidation, just brute-force read from the update-history relation\n\n- for simplicity, let's start with relation-creation-time-single-insertion with errors and manual code-commenting for checkpoints\n  - and single db consolidation, because the domains are shared\n\n\n## Naming conventions\n\n```\n_    = blank\nx-y  = x  y     ; for multi-word phrases, e.g., launch-all-missiles\nx/y  = x with y\nx^y  = x superscript y\nx.y  = x subscript y   ; emphasizing grouping by x\ny:x  = x subscript y   ; emphasizing grouping by y, the subscript; e.g., a type\n                       ; y with constructors x, or implementing a common\n                       ; interface of operations x, or other situations where\n                       ; if the context is clear, the y: could be dropped from\n                       ; the name\nx@y  = x at y          ; result of projection or access using address/key y\nx->y = x to y          ; procedure mapping type x to y\nx=>y = x to y          ; finite map (e.g., hash or vector) with key type x\nx&y  = x and y         ; a pair, or sometimes a 2-element list or vector\nx*   = 0 or more xs    ; (typically homogeneous) lists, sometimes vectors\nx?   = x huh           ; x is either a boolean(-ish) value itself, or a\n                       ; predicate (procedure returning a boolean(-ish) value)\nx!   = x bang          ; x may cause important side effects, such as mutation\n                       ; or throwing an error; I/O operations often don't use\n                       ; this convention\nx?!  = assert x        ; a predicate/guard that throws an error if false\n```\n\n\n## References\n\n- [miniKanren: an embedded DSL for logic programming](http://minikanren.org)\n- [Bloom Programming Language](http://bloom-lang.net/)\n- [Dedalus: Datalog in Time and Space](http://www2.eecs.berkeley.edu/Pubs/TechRpts/2009/EECS-2009-173.pdf)\n- [Datafun Programming Language](http://www.rntz.net/datafun/)\n- [Flix Programming Language](https://flix.dev/)\n\n### Datalog and Bottom-up Evaluation Techniques\n\n- [What You Always Wanted to Know About Datalog (And Never Dared to Ask)](https://personal.utdallas.edu/~gupta/courses/acl/papers/datalog-paper.pdf)\n- [Integrating Datalog and Constraint Solving](https://biblio.ugent.be/publication/5646054/file/5646069.pdf)\n- [Compilation Of Bottom-Up Evaluation For a Pure Logic Programming Language](https://researchcommons.waikato.ac.nz/bitstream/handle/10289/12882/thesis.pdf)\n- [Bottom-Up Evaluation](http://users.informatik.uni-halle.de/~brass/lp07/c6_botup.pdf)\n- [Magic Sets](http://users.informatik.uni-halle.de/~brass/lp07/c7_magic.pdf)\n\n### Recursive Relations\n\n- [A Cost Estimation Technique for Recursive Relational Algebra](https://hal.inria.fr/hal-03004218/document)\n- [On the Optimization of Recursive Relational Queries: Application to Graph Queries](http://pierre.geneves.net/papers/mura-sigmod20.pdf)\n- [Cost-Based Optimization for Magic: Algebra and Implementation](https://dsf.berkeley.edu/papers/sigmod96-magic.pdf)\n\n### Query Plans\n\n- [How Good Are Query Optimizers, Really?](https://www.vldb.org/pvldb/vol9/p204-leis.pdf)\n- [Cardinality Estimation Done Right: Index-Based Join Sampling](http://cidrdb.org/cidr2017/papers/p9-leis-cidr17.pdf)\n- [A New Heuristic for Optimizing Large Queries](http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.31.737)\n- [Looking Ahead Makes Query Plans Robust](http://www.vldb.org/pvldb/vol10/p889-zhu.pdf)\n- [Worst-case Optimal Join Algorithms](http://pages.cs.wisc.edu/~chrisre/papers/paper49.Ngo.pdf)\n\n### Low-level Efficiency\n\n- [Sort vs. Hash joins](http://www.vldb.org/pvldb/vol7/p85-balkesen.pdf)\n- [Efficiently Compiling Efficient Query Plans for Modern Hardware](http://www.vldb.org/pvldb/vol4/p539-neumann.pdf)\n- [Push vs. Pull-Based Loop Fusion in Query Engines](https://arxiv.org/pdf/1610.09166.pdf)\n- [How to Architect a Query Compiler, Revisited](https://www.cs.purdue.edu/homes/rompf/papers/tahboub-sigmod18.pdf)\n"
  },
  {
    "path": "medikanren2/dbk/SNAPSHOT",
    "content": "https://github.com/gregr/dbKanren\n5aa9af98dd7653312f03b85d9c10215cb12f5202"
  },
  {
    "path": "medikanren2/dbk/bcat.rkt",
    "content": "#lang racket/base\n(require \"dbk/codec.rkt\" racket/pretty racket/port)\n\n(module+ main\n  (define argv      (current-command-line-arguments))\n  (define arg-names '#(DATA-TYPE))\n  (unless (= (vector-length argv) (vector-length arg-names))\n    (error \"invalid arguments\" 'expected arg-names 'given argv))\n  (define type (with-input-from-string (vector-ref argv 0) read))\n  (define in   (current-input-port))\n  (define out  (current-output-port))\n  (with-handlers (((lambda (e)\n                     (and (exn:fail:filesystem:errno? e)\n                          (equal? (exn:fail:filesystem:errno-errno e)\n                                  '(32 . posix))))\n                   void))\n    (let loop ()\n      (unless (eof-object? (peek-byte in))\n        (pretty-write (decode in type))\n        (loop)))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/abstract-syntax.rkt",
    "content": "#lang racket/base\n(provide\n  f:query f:true f:false f:relate f:imply f:iff f:or f:and f:not f:exist f:all\n  t:query t:quote t:var t:prim t:app t:lambda t:if t:let\n  scm->term)\n(require \"misc.rkt\" (except-in racket/match ==) racket/set)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Abstract syntax\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-variant formula?\n  (f:query  result param f)  ; TODO: omit this class of formula?\n  (f:true)\n  (f:false)\n  ;; TODO: local relation definitions, to express subqueries\n  ;; but this may be macro-expressible without a dedicated AST node?\n  ;(f:letrec defs)  ; defs ::= list-of (name params f)\n  (f:relate relation args)  ; finite position built-in? #f for infinite relations\n  ;; TODO:\n  ;(f:relate relation arg)  ; switch to single argument for apply-relation, where variadic version is sugar\n\n  ;(f:meta thunk)\n\n  ;; or maybe just aggregate via forall/not-exists/any<=o enumeration\n  (f:imply  if then)\n  (f:iff    f1 f2)\n  (f:or     f1 f2)\n  (f:and    f1 f2)\n  (f:not    f)\n\n  ;; TODO: single-param versions of f:exist and f:all:\n  ;(f:exist  param body)\n  ;(f:all    param body)\n\n  (f:exist  params body)\n  (f:all    params body))\n\n(define-variant term?\n  ;; TODO: simplify, removing t:query, t:lambda, t:if, t:let, t:prim, t:app\n  ;; replace t:app with t:cons and t:vector\n  (t:query  name formula)\n  (t:quote  value)\n  (t:var    name)\n  (t:prim   name)\n  (t:app    proc args)\n  (t:lambda params body)\n  (t:if     c t f)\n  (t:let    bpairs body))\n\n(define (t:cons         a d) (t:app (t:prim 'cons)          (list a d)))\n(define (t:list->vector xs)  (t:app (t:prim 'list->vector)  (list xs)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Values and term conversion\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (atom? x)\n  (or (null? x) (boolean? x) (symbol? x) (string? x) (bytes? x) (and (real? x) (exact? x)) (void? x)))\n\n(define (scm->term x)\n  (cond ((term?         x)  x)\n        ((pair?         x)  (t:cons         (scm->term (car          x))\n                                            (scm->term (cdr          x))))\n        ((vector?       x)  (t:list->vector (scm->term (vector->list x))))\n        ((atom?         x)  (t:quote        x))\n        ((and (real?    x)\n              (inexact? x)) (scm->term (inexact->exact x)))\n        (else               (error \"invalid dbk value:\" x))))\n\n(define (f-relations f)\n  (match f\n    ((f:query   _ _ f)       (f-relations f))\n    ;; TODO: no need for t-relations* if we lift all uses of t:query\n    ;((f:relate  relation args) (set-add (t-relations* args) relation))\n    ((f:relate  relation _)  (set relation))\n    ((f:imply   f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:iff     f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:or      f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:and     f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:not     f)           (f-relations f))\n    ((f:exist   _ body)      (f-relations body))\n    ((f:all     _ body)      (f-relations body))\n    ((or (f:true) (f:false)) (set))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/codec.rkt",
    "content": "#lang racket/base\n(provide encode decode sizeof nat-type/max)\n(require racket/list racket/match)\n\n(define (exact-number? x) (and (number? x) (exact? x)))\n(define (<< i s) (arithmetic-shift i s))\n(define (>> i s) (arithmetic-shift i (- s)))\n(define (& a b)  (bitwise-and a b))\n(define (\\| a b) (bitwise-ior a b))\n(define (^ a b)  (bitwise-xor a b))\n\n(match-define (list t.bytes t.string t.symbol t.array t.pair\n                    t.true t.false t.null t.number\n                    ;; TODO: support more efficient numeric representations\n                    ;; is a separate rat type (for rationals) superfluous?\n                    t.nat t.int t.rat)\n  (range (length '(t.bytes t.string t.symbol t.array t.pair\n                   t.true t.false t.null t.number\n                   t.nat t.int t.rat))))\n\n(define (nat-type/max max-nat) `#(nat ,(- (sizeof 'nat max-nat) 1)))\n\n(define (sizeof type v)\n  (match type\n    (#f                (sizeof-any          v))\n    (`#(nat    ,size)  (sizeof-nat    size  v))\n    (`#(string ,len)   (sizeof-string len   v))\n    (`#(symbol ,len)   (sizeof-symbol len   v))\n    (`#(bytes  ,len)   (sizeof-bytes  len   v))\n    (`#(array ,len ,t) (sizeof-array  len t v))\n    (`#(list  ,len ,t) (sizeof-list   len t v))\n    (`#(tuple ,@ts)    (sizeof-tuple  ts    v))\n    (`(,ta . ,td)      (sizeof-pair   ta td v))\n    ('nat              (sizeof-nat    #f    v))\n    ('string           (sizeof-string #f    v))\n    ('symbol           (sizeof-symbol #f    v))\n    ('bytes            (sizeof-bytes  #f    v))\n    ('array            (sizeof-array  #f #f v))\n    ('list             (sizeof-list   #f #f v))\n    ('number           (sizeof-number       v))\n    ((or 'true 'false '()) 0)))\n(define (sizeof-any v)\n  (define value-size\n    (cond ((vector?       v) (sizeof-array  #f #f v))\n          ((string?       v) (sizeof-string #f    v))\n          ((bytes?        v) (sizeof-bytes  #f    v))\n          ((pair?         v) (sizeof-pair   #f #f v))\n          ((exact-number? v) (sizeof-number       v))\n          ((symbol?       v) (sizeof-symbol #f    v))\n          ((or (null? v) (eqv? #t v) (not v))      0)\n          ((void? v)                              #f)\n          (else (error \"sizeof-any; invalid type:\" v))))\n  (and value-size (+ 1 value-size)))\n(define (sizeof-nat size n)\n  (cond (size      size)\n        ((void? n) #f)\n        (else (+ 1 (cond ((< n (<< 1 32)) (if (< n (<< 1 16))\n                                            (if (< n (<< 1 8))  1 2)\n                                            (if (< n (<< 1 24)) 3 4)))\n                         ((< n (<< 1 40)) 5)\n                         ((< n (<< 1 48)) 6)\n                         ((< n (<< 1 56)) 7)\n                         ((< n (<< 1 64)) 8)\n                         (else (error \"sizeof-nat; too large:\" n)))))))\n;; TODO: consider exponent representations, which may be more compact\n(define (sizeof-number v)   (sizeof-string #f (if (void? v) v\n                                                (number->string v))))\n(define (sizeof-bytes l v)  (or l (and (not (void? v))\n                                       (let ((len (bytes-length v)))\n                                         (+ len (sizeof-nat #f len))))))\n(define (sizeof-symbol l v) (or l (sizeof-string l (if (void? v) v\n                                                     (symbol->string v)))))\n(define (sizeof-string l v) (or l (sizeof-bytes l (if (void? v) v\n                                                    (string->bytes/utf-8 v)))))\n(define (sizeof-pair ta td v) (let ((za (sizeof ta (if (void? v) v (car v))))\n                                    (zd (sizeof td (if (void? v) v (cdr v)))))\n                                (and za zd (+ za zd))))\n(define (sizeof-tuple ts v) (sizeof ts (if (void? v) v (vector->list v))))\n(define (sizeof-list l t v)\n  (if l (sizeof-tuple (make-list l t) v)\n    (and (not (void? v)) (let* ((l (length v))\n                                (z (sizeof-list l t v)))\n                           (and z (+ (sizeof-nat #f l) z))))))\n(define (sizeof-array l t v)\n  (if l (sizeof-tuple (make-list l t) v)\n    (and (not (void? v)) (let ((z (sizeof-array (vector-length v) t v)))\n                           (and z (+ (sizeof-nat #f (vector-length v)) z))))))\n\n(define (encode out type v)\n  (match type\n    (#f                (encode-any    out       v))\n    (`#(nat    ,size)  (encode-nat    out size  v))\n    (`#(string ,len)   (encode-string out len   v))\n    (`#(symbol ,len)   (encode-symbol out len   v))\n    (`#(bytes  ,len)   (encode-bytes  out len   v))\n    (`#(array ,len ,t) (encode-array  out len t v))\n    (`#(list  ,len ,t) (encode-list   out len t v))\n    (`#(tuple ,@ts)    (encode-tuple  out ts    v))\n    (`(,ta . ,td)      (encode-pair   out ta td v))\n    ('nat              (encode-nat    out #f    v))\n    ('int              (encode-int    out       v))\n    ('string           (encode-string out #f    v))\n    ('symbol           (encode-symbol out #f    v))\n    ('bytes            (encode-bytes  out #f    v))\n    ('array            (encode-array  out #f #f v))\n    ('list             (encode-list   out #f #f v))\n    ('number           (encode-number out       v))\n    ((or 'true 'false '()) 0)))\n(define (encode-any out v)\n  (define (tag t) (encode-nat out 1 t))\n  (cond ((vector? v)       (tag t.array)  (encode-array  out #f #f v))\n        ((string? v)       (tag t.string) (encode-string out #f    v))\n        ((bytes?  v)       (tag t.bytes)  (encode-bytes  out #f    v))\n        ((pair?   v)       (tag t.pair)   (encode-pair   out #f #f v))\n        ((exact-number? v) (tag t.number) (encode-number out       v))\n        ((symbol? v)       (tag t.symbol) (encode-symbol out #f    v))\n        ((null?   v)       (tag t.null))\n        ((eqv? #t v)       (tag t.true))\n        ((not     v)       (tag t.false))\n        (else (error \"encode-any; invalid type:\" v))))\n(define (encode-nat out size n)\n  (define (enc/size sz) (unless (= sz 0)\n                          (write-byte (& #xFF (>> n (* 8 (- sz 1)))) out)\n                          (enc/size (- sz 1))))\n  (define (enc sz) (encode-nat out 1 sz) (enc/size sz))\n  (cond (size (enc/size size))\n        ((< n (<< 1 32)) (if (< n (<< 1 16))\n                           (if (< n (<< 1 8))  (enc 1) (enc 2))\n                           (if (< n (<< 1 24)) (enc 3) (enc 4))))\n        ((< n (<< 1 40)) (enc 5))\n        ((< n (<< 1 48)) (enc 6))\n        ((< n (<< 1 56)) (enc 7))\n        ((< n (<< 1 64)) (enc 8))\n        (else (error \"encode-nat; too large:\" n))))\n(define (encode-int out v)\n  (encode-nat out #f (+ (<< v 1) (if (< v 0) 1 0))))\n;; TODO: consider exponent representations, which may be more compact\n(define (encode-number out n) (encode-string out #f (number->string n)))\n(define (encode-bytes out len bs)\n  (unless len (encode-nat out #f (bytes-length bs)))\n  (write-bytes bs out))\n(define (encode-symbol out len s) (encode-string out len (symbol->string s)))\n(define (encode-string out len s)\n  (encode-bytes out len (string->bytes/utf-8 s)))\n(define (encode-pair   out ta td v)\n  (encode out ta (car v)) (encode out td (cdr v)))\n(define (encode-tuple out ts v) (for ((t (in-list ts)) (v (in-vector v)))\n                                     (encode out t v)))\n(define (encode-list out l t v)\n  (unless l (encode-nat out #f (length v)))\n  (for ((v (in-list v))) (encode out t v)))\n(define (encode-array out l t v)\n  (unless l (encode-nat out #f (vector-length v)))\n  (for ((v (in-vector v))) (encode out t v)))\n\n(define (decode in type)\n  (match type\n    (#f                (decode-any    in))\n    (`#(nat    ,size)  (decode-nat    in size))\n    (`#(string ,len)   (decode-string in len))\n    (`#(symbol ,len)   (decode-symbol in len))\n    (`#(bytes  ,len)   (decode-bytes  in len))\n    (`#(array ,len ,t) (decode-array  in len t))\n    (`#(list  ,len ,t) (decode-list   in len t))\n    (`#(tuple ,@ts)    (decode-tuple  in ts))\n    (`(,ta . ,td)      (decode-pair   in ta td))\n    ('nat              (decode-nat    in #f))\n    ('int              (decode-int    in))\n    ('string           (decode-string in #f))\n    ('symbol           (decode-symbol in #f))\n    ('bytes            (decode-bytes  in #f))\n    ('array            (decode-array  in #f #f))\n    ('list             (decode-list   in #f #f))\n    ('number           (decode-number in))\n    ('true             #t)\n    ('false            #f)\n    ('()               '())))\n(define (decode-any in)\n  (define tag (decode-nat in 1))\n  (define (? t) (= tag t))\n  (cond ((? t.array)  (decode-array  in #f #f))\n        ((? t.string) (decode-string in #f))\n        ((? t.bytes)  (decode-bytes  in #f))\n        ((? t.pair)   (decode-pair   in #f #f))\n        ((? t.number) (decode-number in))\n        ((? t.symbol) (decode-symbol in #f))\n        ((? t.null)   '())\n        ((? t.true)   #t)\n        ((? t.false)  #f)\n        (else (error \"decode-any; invalid tag:\" tag))))\n(define (decode-nat in size)\n  (if size (let loop ((n 0) (sz size))\n             (if (= sz 0) n\n               (loop (+ (<< n 8) (read-byte in)) (- sz 1))))\n    (let ((size (decode-nat in 1))) (decode-nat in size))))\n(define (decode-int in)\n  (define nat (decode-nat in #f))\n  (* (if (odd? nat) -1 1) (>> nat 1)))\n;; TODO: consider exponent representations, which may be more compact\n(define (decode-number in)      (string->number (decode-string in #f)))\n(define (decode-bytes in l)     (if l (read-bytes l in)\n                                  (decode-bytes in (decode-nat in #f))))\n(define (decode-symbol in l)    (string->symbol (decode-string in l)))\n(define (decode-string in l)    (bytes->string/utf-8 (decode-bytes in l)))\n(define (decode-pair  in ta td) (cons (decode in ta) (decode in td)))\n(define (decode-tuple in ts)    (list->vector (decode in ts)))\n(define (decode-list  in l t)   (if l (decode in (make-list l t))\n                                  (decode-list in (decode-nat in #f) t)))\n(define (decode-array in l t)   (if l (decode-tuple in (make-list l t))\n                                  (decode-array in (decode-nat in #f) t)))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/common.rkt",
    "content": "#lang racket/base\n(provide symbolo numbero stringo byteso pairo vectoro booleano integero\n         not-symbolo not-numbero not-stringo not-byteso\n         not-pairo not-vectoro not-booleano not-integero\n         vector==listo bytes==listo <=o vector        (dbk:quasiquote/level level (q ...))))\n    ((_ level   quasiquote)                   (raise-syntax-error #f \"misplaced quasiquote\"       stx))\n    ((_ level   unquote)                      (raise-syntax-error #f \"misplaced unquote\"          stx))\n    ((_ level   unquote-splicing)             (raise-syntax-error #f \"misplaced unquote-splicing\" stx))\n    ((_ level   q)                            #'(dbk:term (quote q)))))\n\n(define-syntax-rule (dbk:quasiquote q) (dbk:quasiquote/level () q))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/concrete-syntax.rkt",
    "content": "#lang racket/base\n(provide\n  fresh-name with-fresh-names ??\n  (for-syntax current-vocabulary)\n  with-no-vocabulary with-formula-vocabulary with-term-vocabulary\n  conj disj imply iff ~ all exist fresh conde query== query\n  == =/= any<= any< flooro +o *o\n  vector-lengtho vector-refo bytes-lengtho bytes-refo symbol==stringo string==utf8-byteso\n  dbk:term dbk:app dbk:apply dbk:cons dbk:list->vector dbk:append dbk:not\n  dbk:map/merge dbk:map/append dbk:map dbk:filter dbk:filter-not\n  dbk:begin dbk:let dbk:let* dbk:lambda dbk:if dbk:when dbk:unless dbk:cond dbk:and dbk:or\n  apply-relation\n  relation-kind relation-arity relation-properties relation-properties-set!\n  relation-method relation-dirty! relation-clean!\n  define-relation define-relation/table define-relation/input\n  define-relations)\n(require \"abstract-syntax.rkt\" \"misc.rkt\" \"stream.rkt\"\n         (for-syntax racket/base) racket/list racket/struct racket/stxparam)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Names\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; TODO: this might belong in abstract-syntax.rkt\n\n(define fresh-name-count (make-parameter #f))\n\n(define (call-with-fresh-names thunk)\n  (if (fresh-name-count)\n    (thunk)\n    (parameterize ((fresh-name-count 0))\n      (thunk))))\n\n(define-syntax-rule (with-fresh-names body ...)\n  (call-with-fresh-names (lambda () body ...)))\n\n(define (fresh-name name)\n  (define uid.next (fresh-name-count))\n  (unless uid.next (error \"fresh name not available:\" name))\n  (fresh-name-count (+ uid.next 1))\n  (cons uid.next (if (pair? name) (cdr name) name)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Anonymous variables\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define anonymous-vars (make-parameter #f))\n\n(define (anonymous-var (sym '_))\n  (unless (anonymous-vars) (error \"misplaced anonymous variable\"))\n  (define name (fresh-name sym))\n  (anonymous-vars (cons name (anonymous-vars)))\n  (t:var name))\n\n(define-syntax formula/anonymous-vars\n  (syntax-rules ()\n    ((_ body ...) (parameterize ((anonymous-vars '()))\n                    (define f (let () body ...))\n                    (if (null? (anonymous-vars))\n                      f\n                      (f:exist (anonymous-vars) f))))))\n\n(define-syntax (?? stx)\n  (syntax-case stx ()\n    ((_ . args) (raise-syntax-error #f \"cannot apply anonymous variable\" stx))\n    (_          #'(anonymous-var '??))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Vocabularies\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-syntax-parameter stxparam.vocabulary #f)\n(begin-for-syntax (define-syntax-rule (current-vocabulary)\n                    (syntax-parameter-value #'stxparam.vocabulary)))\n\n(define-syntax-rule (with-no-vocabulary      body ...) (syntax-parameterize ((stxparam.vocabulary #f))       body ...))\n(define-syntax-rule (with-formula-vocabulary body ...) (syntax-parameterize ((stxparam.vocabulary 'formula)) body ...))\n(define-syntax-rule (with-term-vocabulary    body ...) (syntax-parameterize ((stxparam.vocabulary 'term))    body ...))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Relations\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (relation-apply r . args)\n  (define l.args  (length args))\n  (define l.extra (- (relation-arity r) (- l.args 1)))\n  (when (= l.args 0)\n    (error \"relation-apply requires at least one argument besides the relation:\" r args))\n  (when (< l.extra 0)\n    (error \"relation-apply number of arguments exceeds relation arity:\" r args))\n  (define rargs      (reverse args))\n  (define arg.last   (car rargs))\n  (define rargs.init (cdr rargs))\n  (define attrs      (hash-ref (relation-properties r) 'attributes (range (relation-arity r))))\n  (define names      (s-drop (- l.args 1) attrs))\n  (formula/anonymous-vars\n    (let* ((vars.last (map (lambda (n) (anonymous-var (vector 'apply n))) names))\n           (args.new  (foldl cons vars.last rargs.init)))\n      (conj (== arg.last vars.last)\n            (apply r args.new)))))\n\n(define (relation-kind            r)     (if (relation? r)\n                                           ((relation-method r) 'kind)\n                                           `(primitive ,r)))\n(define (relation-arity           r)     ((relation-method r) 'arity))\n(define (relation-properties      r)     ((relation-method r) 'properties))\n(define (relation-properties-set! r k v) ((relation-method r) 'properties-set! k v))\n(define (relation-dirty!          r)     ((relation-method r) 'dirty!))\n(define (relation-clean!          r)     ((relation-method r) 'clean!))\n\n;; TODO: maybe normalize definitions (axioms) to clausal form first, for stronger assumptions when analyzing safety\n\n;; TODO: Datalog safety check\n;; Due to mutual recursion, this will have to be run across multiple relations simultaneously, not individually.\n;(define (relation-finite? r)\n  ;(or (not (eq? 'rule (relation-kind r)))\n      ;(match-let (((f:all (f:imply f.body (f:relate _ vars.head))) ((relation-method r) 'formula)))\n        ;;; TODO:\n        ;;; all vars.head must be mentioned at least once in a positive position\n        ;;; all dependency relations must be finite (or the particular call to its args must be total)\n        ;;; all relations mentioned in subqueries must be stratified\n        ;;; all terms in recursive calls or assigned to head vars are non-function literals\n        ;;;   head vars can be function terms if this relation isn't recursive\n        ;(let loop ((f f.body) (fs.pending '()) (vars.pending (list->set vars.head)))\n          ;(match f\n            ;((f:relate r.f args.f)\n             ;;; TODO: also try totality checking\n             ;;; TODO: recognize mutual recursion\n             ;;; TODO: primitives need special handling\n             ;(and (relation-finite? r.f)\n                  ;;; TODO: what about compound/function literals?  these can violate safety\n                  ;;; TODO: look for subqueries and verify stratification\n                  ;(continue (set-subtract vars.pending (t-free-vars-positive* args.f)))))\n            ;((f:or f.1 f.2)\n             ;;; TODO: instead, reorganize finiteness checking to avoid redundant work\n             ;;; instead, we could determine what head vars are positively referenced in each of f.1 and f.2\n             ;;; taking their intersection, and subtracting that from the total\n             ;;; and if either fails to be finite locally, it can return #f to signal combined failure\n             ;(and (loop f.1 fs.pending vars.pending)\n                  ;(loop f.2 fs.pending vars.pending)))\n            ;((f:and f.1 f.2) (loop f.1 (cons f.2 fs.pending) vars.pending))\n            ;((f:not f)\n             ;;; TODO: negative polarity\n\n             ;)\n            ;((f:exist params.f body.f)\n             ;;; TODO: shadow? or is this not necessary?\n             ;(loop body.f fs.pending vars.pending))\n            ;(_ (error \"TODO: finiteness check for unhandled formula type:\" f)))))))\n\n;; TODO: should also return info about any change in arg groundness after this relation runs?\n;(define (relate-total? relation args)\n  ;)\n\n(struct relation (method)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (r) 'relation)\n             (lambda (r) (list (cons 'kind  (relation-kind       r))\n                               (cons 'arity (relation-arity      r))\n                               (relation-properties r))))))\n        #:property prop:procedure\n        (lambda (r . args)\n          (unless (= (relation-arity r) (length args))\n            (error \"relation called with invalid number of arguments\" args r))\n          (f:relate r (map scm->term args))))\n\n(define (make-relation kind arity parent->self)\n  (define properties (hash))\n  (relation\n    (parent->self\n      (method-lambda\n        ((kind)                   kind)\n        ((arity)                  arity)\n        ((properties)             properties)\n        ((properties-set!    k v) (when (eq? k 'attributes)\n                                    (unless (and (list? v) (= arity (length v)))\n                                      (error \"invalid number of attributes for arity:\" arity v)))\n                                  (set! properties (hash-set    properties k v)))\n        ((properties-remove! k)   (set! properties (hash-remove properties k)))\n        ((dirty!)                 (void))\n        ((clean!)                 (void))))))\n\n(define (relation/primitive arity name)\n  (make-relation\n    `(primitive ,name) arity\n    (lambda (parent) parent)))\n\n(define (relation/rule arity rule)\n  (define r\n    (make-relation\n      'rule arity\n      (lambda (parent)\n        (method-lambda\n          ((apply . args) (define len (length args))\n                          (unless (= len arity) (error \"invalid number of arguments:\" arity args))\n                          (apply rule args))\n          ((formula)      (define attrs  (hash-ref (relation-properties r) 'attributes (range arity)))\n                          (define params (map fresh-name attrs))\n                          (define vars   (map t:var      params))\n                          (f:all params (f:imply (apply rule vars) (apply r vars))))\n          (else           parent)))))\n  r)\n\n(define (relation/table arity path)\n  ;; TODO: if path is #f, use temporary storage\n  (make-relation\n    'table arity\n    (lambda (parent)\n      (method-lambda\n        ;; TODO:\n        ;; Define instantiation of table controllers that manage their own column constraints.\n        ;; A single query might instantiate multiple controllers for the same table, each with\n        ;; a different set of constraints/bounds.\n        ;; Controller interface provides:\n        ;; - retrieval of statistics:\n        ;;   - total tuple count\n        ;;   - per-column cardinality\n        ;;   - per-column bounds\n        ;; - update of per-column bounds\n        ;; - index descriptions\n\n        ;; TODO:\n        ;; Define an interface for updating table content.\n        ;; Maintain a log of insertions and deletions.\n        ;; Possibly support log subscriptions to allow other processes to observe changes.\n        ((path) path)\n        (else   parent)))))\n\n(define (relation/input arity produce)\n  (make-relation\n    'input arity\n    (lambda (parent)\n      (method-lambda\n        ((produce) (s-enumerate 0 (produce)))\n        (else      parent)))))\n\n(define-syntax apply-relation\n  (syntax-rules ()\n    ((_ r . args) (formula/anonymous-vars (with-term-vocabulary (relation-apply r . args))))))\n\n(define-syntax (define-relations stx)\n  (syntax-case stx ()\n    ((_ (kind (name.r param ...) body ...) ...)\n     (with-syntax (((r ...) (generate-temporaries #'(name.r ...))))\n       #'(begin (define-syntax (name.r stx)\n                  (syntax-case stx ()\n                    ((_ . args) #'(formula/anonymous-vars (with-term-vocabulary (r . args))))\n                    (_          #'r))) ...\n                (define-values (r ...)\n                  (values (defined-relation-value (kind (name.r param ...) body ...)) ...))\n                (begin (relation-properties-set! r 'name       'name.r)\n                       (relation-properties-set! r 'attributes '(param ...))) ...)))))\n\n(define-syntax defined-relation-value\n  (syntax-rules (primitive rule table input)\n    ((_ (rule      (name param ...) f ...))    (let ((r (relation/rule (length '(param ...))\n                                                                       (lambda (param ...)\n                                                                         (with-formula-vocabulary\n                                                                           (conj f ...))))))\n                                                 (relation-properties-set! r 'rule '((name param ...) :- f ...))\n                                                 r))\n    ((_ (table     (name param ...) body ...)) (relation/table     (length '(param ...)) body ...))\n    ((_ (input     (name param ...) body ...)) (relation/input     (length '(param ...)) body ...))\n    ((_ (primitive (name param ...)))          (relation/primitive (length '(param ...)) 'name))))\n\n(define-syntax-rule (define-relation           body ...) (define-relations (rule      body ...)))\n(define-syntax-rule (define-relation/table     body ...) (define-relations (table     body ...)))\n(define-syntax-rule (define-relation/input     body ...) (define-relations (input     body ...)))\n(define-syntax-rule (define-relation/primitive body ...) (define-relations (primitive body ...)))\n\n(define-syntax-rule (define-primitive-relations signature ...) (begin (define-relation/primitive signature) ...))\n\n(define-primitive-relations\n  (==                  t1 t2)\n  (=/=                 t1 t2)\n  (any<=               t1 t2)\n  (any<                t1 t2)\n  (flooro              t1 t2)\n  (+o                  t1 t2 t3)\n  (*o                  t1 t2 t3)\n  (vector-lengtho      t  l)\n  (vector-refo         t  i  x)\n  (bytes-lengtho       t  l)\n  (bytes-refo          t  i  x)\n  (symbol==stringo     t1 t2)\n  (string==utf8-byteso t1 t2))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Basic syntax for formulas and terms\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-syntax conj*\n  (syntax-rules ()\n    ((_)          f:true)\n    ((_ f)        f)\n    ((_ fs ... f) (f:and (conj* fs ...) f))))\n\n(define-syntax disj*\n  (syntax-rules ()\n    ((_)          f:false)\n    ((_ f)        f)\n    ((_ f fs ...) (f:or f (disj* fs ...)))))\n\n(define-syntax-rule (conj   fs ...)    (with-formula-vocabulary (conj*   fs ...)))\n(define-syntax-rule (disj   fs ...)    (with-formula-vocabulary (disj*   fs ...)))\n(define-syntax-rule (imply  f.h f.c)   (with-formula-vocabulary (f:imply f.h f.c)))\n(define-syntax-rule (iff    f.0 f ...) (with-formula-vocabulary (and (f:iff f.0 f) ...)))\n(define-syntax-rule (~      f)         (with-formula-vocabulary (f:not   f)))\n\n(define-syntax-rule (define-quantifier-syntax name f:quantifier)\n  (... (define-syntax (name stx)\n         (syntax-case stx ()\n           ((_ (x ...) body ...)\n            (with-syntax (((name.x ...) (generate-temporaries #'(x ...))))\n              #'(let ((name.x (fresh-name 'x)) ...)\n                  (let ((x (t:var name.x)) ...)\n                    (f:quantifier (list name.x ...) (conj body ...))))))))))\n\n(define-quantifier-syntax exist f:exist)\n(define-quantifier-syntax all   f:all)\n\n(define-syntax-rule (fresh (x ...) body ...) (exist (x ...) body ...))\n\n(define-syntax-rule (conde (f.0 fs.0 ...)\n                           (f   fs   ...) ...)\n  (disj (conj f.0 fs.0 ...)\n        (conj f   fs   ...) ...))\n\n(define-syntax query==\n  (syntax-rules ()\n    ((_ result (x ...) body ...) (query== result x.0 (exist (x ...)\n                                                       (== x.0 (list x ...))\n                                                       body ...)))\n    ((_ result x       body ...) (let* ((name.x (fresh-name 'q))\n                                        (x      (t:var      name.x)))\n                                   (f:query result name.x (conj body ...))))))\n\n;; TODO: can we auto-lift these terms via anonymous vars?\n(define-syntax query\n  (syntax-rules ()\n    ((_ (x ...) body ...) (query x.0 (exist (x ...)\n                                       (== x.0 (list x ...))\n                                       body ...)))\n    ((_ x       body ...) (with-fresh-names\n                            (let* ((name.x (fresh-name 'q))\n                                   (x      (t:var      name.x)))\n                              (t:query name.x (conj body ...)))))))\n\n(define (dbk:term         x)        (scm->term x))\n(define (dbk:app          p . args) (t:app (scm->term p) (map scm->term args)))\n(define (dbk:prim-app     p . args) (t:app (t:prim    p) (map scm->term args)))\n(define (dbk:cons         a d)      (dbk:prim-app 'cons         a d))\n(define (dbk:list->vector xs)       (dbk:prim-app 'list->vector xs))\n\n(define-syntax (dbk:apply stx)\n  (syntax-case stx ()\n    ((_ . args) #'(dbk:prim-app 'apply . args))\n    (_          #'(t:prim 'apply))))\n\n(define-syntax-rule (define-lambda (name . params) body)\n  (define-syntax (name stx)\n    (syntax-case stx ()\n      ((_ . args) #'(dbk:app (dbk:lambda params body) . args))\n      (_          #'(dbk:lambda params body)))))\n\n(define-lambda (dbk:not        x)                  (dbk:if x #f #t))\n(define-lambda (dbk:append     xs ys)              (dbk:prim-app   'append    xs ys))\n(define-lambda (dbk:map/merge  f merge default xs) (dbk:prim-app   'map/merge f merge default xs))\n(define-lambda (dbk:map/append f               xs) (dbk:map/merge  f (dbk:lambda (a b) (dbk:append a b)) '()            xs))\n(define-lambda (dbk:map        f               xs) (dbk:map/append (dbk:lambda (x) (list (dbk:app f x)))                xs))\n(define-lambda (dbk:filter     p               xs) (dbk:map/append (dbk:lambda (x) (dbk:if (dbk:app p x) (list x) '())) xs))\n(define-lambda (dbk:filter-not p               xs) (dbk:filter     (dbk:lambda (x) (dbk:not (dbk:app p x)))             xs))\n\n(define-syntax dbk:begin\n  (syntax-rules ()\n    ((_)          (dbk:term (void)))\n    ((_ e)        (dbk:term e))\n    ((_ e es ...) (dbk:let ((temp.begin (dbk:term e))) es ...))))\n\n(define-syntax dbk:let\n  (syntax-rules ()\n    ((_ ((x e) ...) body ...) (let ((name.x (fresh-name 'x)) ...)\n                                (let ((x (t:var name.x)) ...)\n                                  (with-term-vocabulary\n                                    (t:let (list (cons name.x (dbk:term e)) ...)\n                                           (dbk:begin body ...))))))))\n\n(define-syntax dbk:let*\n  (syntax-rules ()\n    ((_ ()                  body ...) (dbk:let ()                              body ...))\n    ((_ ((x e) (xs es) ...) body ...) (dbk:let ((x e)) (dbk:let* ((xs es) ...) body ...)))))\n\n(define-syntax (dbk:lambda stx)\n  (syntax-case stx ()\n    ((_ (x ...)     body ...)\n     (with-syntax (((name.x ...) (generate-temporaries #'(x ...))))\n       #'(let ((name.x (fresh-name 'x)) ...)\n           (let ((x (t:var name.x)) ...)\n             (with-term-vocabulary\n               (t:lambda (list  name.x ...)        (dbk:begin body ...)))))))\n    ((_ (x ... . y) body ...)\n     (with-syntax (((name.x ...) (generate-temporaries #'(x ...))))\n       #'(let ((name.y (fresh-name 'y)) (name.x (fresh-name 'x)) ...)\n           (let ((x (t:var name.x)) ...)\n             (with-term-vocabulary\n               (t:lambda (list* name.x ... name.y) (dbk:begin body ...)))))))))\n\n(define-syntax-rule (dbk:if     c t f)      (t:if (dbk:term c) (dbk:term t) (dbk:term f)))\n(define-syntax-rule (dbk:when   c body ...) (dbk:if c (dbk:begin body ...) (dbk:term (void))))\n(define-syntax-rule (dbk:unless c body ...) (dbk:if c (dbk:term (void))    (dbk:begin body ...)))\n\n(define-syntax (dbk:cond stx)\n  (syntax-case stx (else =>)\n    ((_)                      #'(dbk:term (void)))\n    ((_ (else e ...))         #'(dbk:begin e ...))\n    ((_ (else e ...) etc ...) (raise-syntax-error #f \"misplaced else\" stx))\n    ((_ (c => p) cs ...)      #'(dbk:let ((x c)) (dbk:if x (dbk:app   p c)   (dbk:cond cs ...))))\n    ((_ (c e ...) cs ...)     #'(                 dbk:if c (dbk:begin e ...) (dbk:cond cs ...)))\n    ((_ c cs ...)             #'(dbk:let ((x c)) (dbk:if x x                 (dbk:cond cs ...))))))\n\n(define-syntax dbk:and\n  (syntax-rules ()\n    ((_)          (dbk:term #t))\n    ((_ e)        (dbk:term e))\n    ((_ e es ...) (dbk:if e (dbk:and es ...) (dbk:term #f)))))\n\n(define-syntax dbk:or\n  (syntax-rules ()\n    ((_)          (dbk:term #f))\n    ((_ e)        (dbk:term e))\n    ((_ e es ...) (dbk:let ((temp.or e)) (dbk:if temp.or temp.or (dbk:or es ...))))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/config.rkt",
    "content": "#lang racket/base\n(provide current-config config.default file->config current-config-ref\n         current-config-set current-config-set/alist\n         current-config-set! current-config-set!/alist\n         current-config-relation-path config-ref config-set config-set/alist\n         policy-allow? logf logf/date)\n(require racket/date racket/string)\n\n(define config.default\n  (make-immutable-hash\n    '((relation-root-path         . #f) ;; root path for materialized relations\n      (temporary-root-path        . #f) ;; root path for temporary caches\n      (buffer-size                . 100000)\n      (progress-logging-threshold . 100000) ;; number of rows per log message\n      ;; interactive, always, never\n      (update-policy              . interactive) ;; rebuild stale tables\n      (cleanup-policy             . interactive) ;; remove unspecified indexes\n      (migrate-policy             . interactive) ;; migrate to new data format\n      (allow-missing-data-policy  . interactive) ;; ignore missing data\n      ;; biased-interleaving (default), depth-first\n      (search-strategy            . #f))))\n\n(define (valid-config?! cfg)\n  (define (valid-policy? policy) (member policy '(always never interactive)))\n  (define (valid-path?   p)      (or (not p) (string? p) (path? p)))\n  (define-syntax validate!\n    (syntax-rules ()\n      ((_ (test ... key) ...)\n       (begin (unless (test ... (hash-ref cfg 'key))\n                (error \"invalid config:\" 'key (hash-ref cfg 'key))) ...))))\n  (validate! (valid-path?   relation-root-path)\n             (valid-path?   temporary-root-path)\n             (< 0           buffer-size)\n             (< 0           progress-logging-threshold)\n             (valid-policy? update-policy)\n             (valid-policy? cleanup-policy)\n             (valid-policy? migrate-policy))\n  cfg)\n\n(define (config-ref cfg key)       (hash-ref cfg key))\n(define (config-set cfg key value) (valid-config?! (hash-set cfg key value)))\n(define (config-set/alist cfg kvs)\n  (valid-config?! (foldl (lambda (kv cfg) (hash-set cfg (car kv) (cdr kv)))\n                         cfg kvs)))\n(define (file->config path)\n  (config-set/alist config.default (with-input-from-file path read)))\n\n(define current-config (make-parameter config.default))\n(define (current-config-ref key)       (config-ref (current-config) key))\n(define (current-config-set key value) (config-set (current-config) key value))\n(define (current-config-set/alist kvs) (config-set/alist (current-config) kvs))\n(define (current-config-set! key value)\n  (current-config (current-config-set key value)))\n(define (current-config-set!/alist kvs)\n  (current-config (current-config-set/alist kvs)))\n(define (current-config-relation-path path)\n  (cond ((and (string? path) (string-prefix? path \"/\")) path)\n        (else (define relation-root-path\n                (current-config-ref 'relation-root-path))\n              (if relation-root-path\n                (path->string (build-path relation-root-path path))\n                path))))\n\n(define (policy-allow? policy describe prompt-message prompt-args)\n  (case policy\n    ((interactive)\n     (describe)\n     (apply printf (string-append prompt-message \" [y/n]: \") prompt-args)\n     (case (read)\n       ((y Y yes Yes YES) #t)\n       (else              #f)))\n    ((always) #t)\n    (else     #f)))\n\n(define (pad2 n) (let ((s (number->string n)))\n                   (if (<= 2 (string-length s)) s\n                     (string-append \"0\" s))))\n\n(define (logf/date message . args)\n  (define msg (string-append \"[~a/~a/~a - ~a:~a:~a] \" message))\n  (define d (current-date))\n  (define stamp (list (date-month d) (date-day d)\n                      (date-hour d) (date-minute d) (date-second d)))\n  (apply eprintf msg (date-year d) (append (map pad2 stamp) args)))\n\n(define (logf message . args)\n  (define msg (string-append \"[~a:~a:~a] \" message))\n  (define d (current-date))\n  (define stamp (list (date-hour d) (date-minute d) (date-second d)))\n  (apply eprintf msg (append (map pad2 stamp) args)))\n\n;; TODO: job system\n;; single worker thread\n;; jobs w/ independent loggers (port, file, in-memory, or null)\n\n;(define (thread/wait proc)\n;  (define t (thread proc))\n;  (plumber-add-flush! (current-plumber)\n;                      (lambda (h) (thread-wait t)))\n;  t)\n"
  },
  {
    "path": "medikanren2/dbk/dbk/constraint.rkt",
    "content": "#lang racket/base\n(provide bis:query->stream dfs:query->stream\n         relation/table define-relation/table)\n(require \"misc.rkt\" \"order.rkt\" \"stream.rkt\" \"syntax.rkt\" \"table.rkt\"\n         (except-in racket/match ==)\n         racket/function racket/list racket/set racket/vector)\n\n#| ;; Definitions for performance diagnostics\n(require racket/pretty)\n(define (pretty-var-bindings vbs)\n  (map (lambda (vb) (cons (var-name (car vb)) (cdr vb))) vbs))\n(define (state-var-bindings st)\n  (pretty-var-bindings\n    (filter (lambda (kv) (not (vcx? (cdr kv)))) (hash->list (state-var=>cx st)))))\n;|#\n\n;; TODO:\n;; extra solvers, beyond bounds checking/limiting for domains and arcs:\n;;   +o, *o:\n;;     for generality, could use a substitute and simplify model\n;;       if a + b = c, then replace c whenever it appears\n;;       still need some functional dependencies (only forward?)\n;;          e.g., a + b = c and a + b = d implies c = d\n;;          also true that a + b = c and a + d = c implies b = d\n;;          however, substituting for c and simplifying covers this:\n;;            a + b = a + d, and simplifying shows b = d\n;;          similar for *o, but case split with 0\n;;     in special cases, can do linear programming\n;;       incremental simplex\n;;       keep in mind: flooro, X-lengtho, X-refo introduce integer constraints\n;;     in other cases: difference equations, polynomials...\n;;     calculus for optimization\n;;     etc.\n;;   (uninterpreted) functional dependencies:\n;;     == propagation forward\n;;       e.g., if (f a b = c) and (f a b = d) then (== c d)\n;;     =/= propagation in reverse\n;;       e.g., if (f a b = c) and (f a d = e) and (c =/= e) then (b =/= d)\n;;         note: this is not a bi-implication unless the function is one-to-one\n;;         (expresssed as two opposing functional dependency constraints)\n;;     also can be used to encode some forms of subsumption checking\n;;   X-refo: maintain minimum length and partial mapping\n;;   string==byteso: look for impossible utf-8 bytes (possibly partial mapping)\n\n;; TODO:\n;; satisfiability loop for a variable constraint graph:\n;;   after propagation quiessence, attempt to divide and conquer\n;;     this is attempted once each time through the satisfiability loop because\n;;       new assignments may lead to disconnection, allowing more decomposition\n;;     decompose into subproblem per subgraph of connected variables\n;;       connection comes from dependency arcs implied by shared constraints\n;;       each subgraph can be satisfied independently\n;;       subgraph solutions can be enumerated and composed\n;;\n;;   for each variable constraint subgraph:\n;;     while there are unresolved variables with possible assignments:\n;;       choose variable with lowest assignment-set cardinality\n;;       choose an assignment for the variable\n;;         may introduce/expand new constraints by stepping into a disj branch\n;;       re-enter satisfiability loop with any new constraints\n;;       if enumerating or loop fails, choose the next assignment\n;;       if no more assignments are available, fail\n;;     once no more unresolved variables, succeed\n;;   compose subgraph solutions\n;;     if any subgraph failed completely, composition also fails\n\n;;; TODO: occurs check for vector-ref\n\n(define (uid:new) (gensym))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Interval bounds for describing a (potentially-infinite) set of terms\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (term-bounds st t.0)\n  (define t (walk st t.0))\n  (cond ((pair? t)\n         (define b.a (term-bounds st (car t)))\n         (define b.d (term-bounds st (cdr t)))\n         (apply bounds\n                (append\n                  (if (bounds-lb-inclusive? b.a)\n                    (list (cons (bounds-lb b.a) (bounds-lb b.d)) (bounds-lb-inclusive? b.d))\n                    (list (cons (bounds-lb b.a) term.max)        #f))\n                  (if (bounds-ub-inclusive? b.a)\n                    (list (cons (bounds-ub b.a) (bounds-ub b.d)) (bounds-ub-inclusive? b.d))\n                    (list (cons (bounds-ub b.a) term.min)        #f)))))\n        ((vector? t)\n         (define b (term-bounds st (vector->list t)))\n         (bounds (list->vector (bounds-lb b)) (bounds-lb-inclusive? b)\n                 (list->vector (bounds-ub b)) (bounds-ub-inclusive? b)))\n        ((var? t) (vcx-bounds (state-vcx-ref st t)))\n        (else     (bounds t #t t #t))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Variable constraints\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(record vcx (bounds simple table disj use) #:transparent)\n(define vcx.empty (vcx (bounds bounds.any)\n                       (simple (seteq)) (table (seteq)) (disj (seteq)) (use (seteq))))\n\n(define (vcx-bounds-set  x b) (vcx:set x (bounds b)))\n(define (vcx-simple-add  x c) (vcx:set x (simple (set-add (vcx-simple x) c))))\n(define (vcx-table-add   x c) (vcx:set x (table  (set-add (vcx-table  x) c))))\n(define (vcx-disj-add    x c) (vcx:set x (disj   (set-add (vcx-disj   x) c))))\n(define (vcx-use-add     x c) (vcx:set x (use    (set-add (vcx-use    x) c))))\n(define (vcx-cx-clear x)      (vcx-bounds-set vcx.empty (vcx-bounds x)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Work queue with recency-based prioritization\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(struct queue (recent high low))\n(define queue.empty (queue (seteq) '() '()))\n(define (queue-empty? q) (set-empty? (queue-recent q)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Partially-satisfied state of a query's constraints\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(record state (qterm vars proc-stack log var=>cx cx pending))\n(define (state:new qterm) (state (qterm qterm) (vars (term-vars qterm)) (proc-stack '()) (log '())\n                                 (var=>cx (hash)) (cx (hash)) (pending queue.empty)))\n\n(define (state-vars-simplify st)\n  (state:set st (vars (term-vars (walk* st (set->list (state-vars st)))))))\n\n(define (state-vcx-ref st x)                          (hash-ref (state-var=>cx st) x vcx.empty))\n(define (state-vcx-set st x t) (state:set st (var=>cx (hash-set (state-var=>cx st) x t))))\n\n(define (state-proc-stack-push st proc-frame)\n  (define proc    (car proc-frame))\n  (define args    (cdr proc-frame))\n  (define parents (state-proc-stack st))\n  (let*/and ((st (c-apply st #f (c:conj (map (lambda (p)\n                                               ;(displayln `(=/= ,args ,(cdr p)))\n\n                                               (c:=/= args (cdr p)))\n                                             (filter (lambda (p) (equal? proc (car p)))\n                                                     parents))))))\n    (state:set st (proc-stack (cons proc-frame parents)))))\n(define (state-proc-stack-pop st) (state:set st (proc-stack (cdr (state-proc-stack st)))))\n\n(define (state-log-add st c)\n  (define log (state-log st))\n  (state:set st (log (and log (cons c log)))))\n\n(define (state-cx-add st vars vcx-add uid? c)\n  (if (null? vars)\n    (state-log-add st c)\n    (let ((uid (or uid? (uid:new))))\n      (foldl (lambda (x st)\n               (state-vcx-set st x (vcx-add (state-vcx-ref st x) uid)))\n             (state:set (state-log-add st c)\n                        (cx (hash-set (state-cx st) uid c)))\n             (set->list vars)))))\n\n(define (state-cx-remove* st uids)\n  (state:set st (cx (foldl (lambda (uid uid=>c) (hash-remove uid=>c uid))\n                           (state-cx st) uids))))\n\n(define (state-cx-update* st uids)\n  (define uid=>c (state-cx st))\n  (define c* (map (lambda (uid) (hash-ref uid=>c uid #f)) uids))\n  (foldl/and (lambda (uid c st) (if c (c-apply st uid c) st))\n             (state-cx-remove* st uids) uids c*))\n\n(define (state-uses-empty?! st)\n  (define uses (filter c:use? (hash-values (state-cx st))))\n  (unless (null? uses)\n    (error \":== dependencies are not ground:\"\n           (map (lambda (u)\n                  (match-define `#s(c:use ,vs ,l ,deps ,r ,desc) u)\n                  (pretty (==/use (walk* st l) (walk* st deps) r desc))\n                  (error \":== dependencies are not ground:\"\n                         (pretty (==/use (walk* st l) (walk* st deps) r desc))))\n                uses))))\n\n(define (state-solve-lte-cycles st)\n  (define cs (map (lambda (c)\n                    (match-define (c:<= lhs rhs) c)\n                    (c:<= (walk* st lhs) (walk* st rhs)))\n                  (filter c:<=? (hash-values (state-cx st)))))\n  ;; Kosaraju's algorithm for simplicity\n  (define a<=b (foldl (lambda (c a<=b)\n                        (match-define (c:<= lhs rhs) c)\n                        (hash-update a<=b lhs (lambda (rhss) (cons rhs rhss)) '()))\n                      (hash) cs))\n  (define b>=a (foldl (lambda (c b>=a)\n                        (match-define (c:<= lhs rhs) c)\n                        (hash-update b>=a rhs (lambda (lhss) (cons lhs lhss)) '()))\n                      (hash) cs))\n  (define (dfs graph pending.0 order.0 source)\n    (cond ((set-member? pending.0 source)\n           (match-define (cons pending order)\n             (foldl (lambda (target p&o)\n                      (match-define (cons p o) p&o)\n                      (dfs graph p o target))\n                    (cons (set-remove pending.0 source) order.0)\n                    (hash-ref graph source)))\n           (cons pending (cons source order)))\n          (else (cons pending.0 order.0))))\n  (define order.<=\n    (let loop ((pending (list->set (hash-keys a<=b))) (order '()))\n      (if (set-empty? pending)\n        order\n        (match-let (((cons pending order) (dfs a<=b pending order (set-first pending))))\n          (loop pending order)))))\n  (define sccs\n    (let loop ((order order.<=) (pending (list->set (hash-keys b>=a))))\n      (if (null? order)\n        '()\n        (match-let (((cons pending scc) (dfs b>=a pending '() (car order))))\n          (define rest (loop (cdr order) pending))\n          (if (null? scc) rest (cons scc rest))))))\n  (foldl/and (lambda (scc st)\n               (define t.0 (car scc))\n               (foldl/and (lambda (t st) (unify st t t.0)) st (cdr scc)))\n             st sccs))\n\n(define (state-schedule-add-var st x)\n  (define (st/q recent high low) (state:set st (pending (queue recent high low))))\n  (match-define (queue recent high low) (state-pending st))\n  (cond ((or (member x high)\n             (member x low))    st)\n        ((set-member? recent x) (st/q          recent            high (cons x low)))\n        (else                   (st/q (set-add recent x) (cons x high)        low))))\n\n(define (state-schedule-run st)\n  (define (update-and-loop st x)\n    (define t (walk st x))\n    (let*/and ((st (if (var? t) (var-update st t) st)))\n      (state-schedule-run st)))\n  (match-define (queue recent high low) (state-pending st))\n  (cond ((not (null? high)) (update-and-loop\n                              (state:set st (pending (queue recent (cdr high)     low)))\n                              (car high)))\n        ((not (null? low))  (define high.new (reverse low))\n                            (update-and-loop\n                              (state:set st (pending (queue recent (cdr high.new) '())))\n                              (car high.new)))\n        (else               (state:set st (pending queue.empty)))))\n\n(define (state-schedule-empty? st) (queue-empty? (state-pending st)))\n\n;; TODO: include a parameter to specify the degree of locality\n(define (state-enforce-local-consistency st)\n  #| ;; Performance diagnostics\n  (pretty-write `(before: term: ,(walk* st (state-qterm st))\n                          vcxs: ,(state-var-bindings st)))\n  ;|#\n  (let*/and ((st (state-schedule-run     st))\n             (st (state-solve-lte-cycles st)))\n    #| ;; Performance diagnostics\n    (pretty-write `(after: term: ,(walk* st (state-qterm st))\n                           vcxs: ,(state-var-bindings st)))\n    ;|#\n    (if (state-schedule-empty? st)\n      st\n      (state-enforce-local-consistency st))))\n\n(define (state-enforce-global-consistency st k.fail k.succeed)\n  ;; TODO: preserve progress made while finding first satisfying state (see factoring TODO below)\n  (let loop ((s (state->satisfied-states st)))\n    (match (s-next s)\n      ((? procedure? s) (thunk (loop s)))\n      ('()              (k.fail))\n      ((cons _ _)       (k.succeed st)))))\n\n;; TODO: factor out table constraint satisfaction to support pre-branch global satisfiability checking\n;;       in cases where we want to split a disjunction before committing to all table constraints\n;;       (taking the first result from a state->satisfied-states stream is not sufficient: we want to\n;;        preserve any state simplification progress made while searching for that first satisfier)\n(define (state->satisfied-states st)\n  (define (dsatisfied-states st?) '()))\n    (define st (state-cx-remove* st.0 (list uid)))\n    (s-append        (k (c-apply st #f          (car cs)))\n                     ;; TODO: negate (car cs) if possible, for better subsumption\n              (thunk (k (c-apply st uid (c:disj (cdr cs)))))))\n  (define (choose-variable st xs.observable xss)\n    (define x=>c&s\n      (foldl (lambda (x=>s x=>c&s)\n               (foldl (lambda (x&s x=>c&s)\n                        (match-define (cons x s) x&s)\n                        (match (hash-ref x=>c&s x #f)\n                          (#f (hash-set x=>c&s x (cons 1 s)))\n                          ((cons count s.0)\n                           (hash-set x=>c&s x (cons (+ count 1)\n                                                    (statistics-intersect s.0 s))))))\n                      x=>c&s (hash->list x=>s)))\n             (hash) xss))\n    ;; TODO: also consider paths provided by available table indexes, maybe via\n    ;; prioritized topological sort of SCCs.\n    (define (xcs count.a count.b)\n                            (and (= count.a count.b)\n                                 (set-member? xs.observable x.a)\n                                 (not (set-member? xs.observable x.b)))))))))\n    (define xcss   (hash->list x=>c&s))\n    (define x.best (car (foldl (lambda (xcs xcs.min) (if (xcsc&s x.best)\n                              ,(vcx-bounds (state-vcx-ref st x.best))\n                              all-choices: ,(pretty-var-bindings xcss)\n                              term: ,(walk* st (state-qterm st))\n                              vcxs: ,(state-var-bindings st)))\n    ;(read-line)\n    ;|#\n\n    (define t (bounds-lb (vcx-bounds (state-vcx-ref st x.best))))\n    (define (k st?) (if st? (state->satisfied-states st?) '()))\n    (s-append        (k (var-assign    st    x.best t))\n              (thunk (k (var-disassign st #f x.best t)))))\n  (match (state-enforce-local-consistency st)\n    (#f '())\n    (st (define cxs (hash->list (state-cx st)))\n        (match (map c:table-t (filter c:table? (map cdr cxs)))\n          ;; If there are no more table constraints, pick a disjunction to split\n          ('() (match (map (lambda (uid&c) (cons (car uid&c) (c:disj-cs (cdr uid&c))))\n                           (filter (lambda (uid&c) (c:disj? (cdr uid&c))) cxs))\n                 ;; If there are no more disjunctions either, we should be done\n                 ('() (list st))\n                 (ds  (define d.min (foldl (lambda (d d.min) (if (dc f)\n  (match f\n    (`#s(conj ,f1 ,f2) (define (f->cs f) (match (f->c f)\n                                           ((c:conj cs) cs)\n                                           (c           (list c))))\n                       (c:conj (append (f->cs f1) (f->cs f2))))\n    (`#s(disj ,f1 ,f2) (define (f->cs f) (match (f->c f)\n                                           ((c:disj cs) cs)\n                                           (c           (list c))))\n                       (c:disj (append (f->cs f1) (f->cs f2))))\n    (`#s(==/use ,lhs ,args ,proc ,desc) (c:use args lhs args proc desc))\n    (`#s(constrain =/=    (,lhs ,rhs))  (c:=/=   lhs rhs))\n    (`#s(constrain ==     (,lhs ,rhs))  (c:==    lhs rhs))\n    (`#s(constrain any<=o (,lhs ,rhs))  (c:<=    lhs rhs))\n    (`#s(constrain ,proc  ,args)        (c:proc  proc args (set)))))\n\n(define (c->f c)\n  (match c\n    ((c:==  l r)                     (==     l r))\n    ((c:=/= l r)                     (=/=    l r))\n    ((c:<=  l r)                     (any<=o l r))\n    ((c:disj cs)                     (apply disj* (map c->f cs)))\n    ((c:conj cs)                     (apply conj* (map c->f cs)))\n    ((c:table t)                     (c->f (t 'constraint)))\n    ((c:proc proc args parents)      (relate proc args))\n    ((c:use vars lhs args proc desc) (==/use lhs args proc desc))))\n\n(define (c-success? c) (and (c:conj? c) (null? (c:conj-cs c))))\n\n(define (c-simplify st.0 effort? c)\n  (let*/and ((st (c-apply (state:set st.0 (log '()) (cx (hash)))\n                          #f c))\n             (st (if effort?\n                   (let*/and ((st (foldl/and (lambda (u&c st)\n                                               (match-define (cons uid? c) u&c)\n                                               (c-apply st uid? c))\n                                             st (hash->list (state-cx st.0)))))\n                     (state-enforce-local-consistency st))\n                   st)))\n    (let ((log (state-log st)))\n      (if (and (pair? log) (null? (cdr log)))\n        (car log)\n        (c:conj log)))))\n\n(define (c-apply st uid? c)\n  (match c\n    ((c:==  l r)                     (unify        st      l r))\n    ((c:=/= l r)                     (disunify     st uid? l r))\n    ((c:<=  l r)                     (ltunify      st uid? l r))\n    ((c:disj cs)                     (disjoin      st uid? cs))\n    ((c:conj cs)                     (conjoin      st      cs))\n    ((c:table t)                     (table-update st uid? t))\n    ((c:proc proc args parents)      (proc-apply   st uid? proc args parents))\n    ((c:use vars lhs args proc desc) (use          st uid? vars lhs args proc desc))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Constraint operations\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (unify st t1 t2)\n  (let ((t1 (walk st t1)) (t2 (walk st t2)))\n    (cond ((eqv? t1 t2) st)\n          ((var?    t1) (var-assign st t1 t2))\n          ((var?    t2) (var-assign st t2 t1))\n          ((pair?   t1) (and (pair? t2)\n                             (let ((st (unify st (car t1) (car t2))))\n                               (and st (unify st (cdr t1) (cdr t2))))))\n          ((vector? t1) (and (vector? t2) (= (vector-length t1)\n                                             (vector-length t2))\n                             (unify st (vector->list t1) (vector->list t2))))\n          ((equal? t1 t2) st)\n          (else           #f))))\n\n(define (disunify st uid? t1 t2)\n  (let ((t1 (walk st t1)) (t2 (walk st t2)))\n    (cond ((eqv? t1 t2) #f)\n          ((var?    t1) (var-disassign st uid? t1 t2))\n          ((var?    t2) (var-disassign st uid? t2 t1))\n          ((pair?   t1) (cond ((not (pair? t2)) st)\n                              (else (disjoin st #f (list (c:=/= (car t1) (car t2))\n                                                         (c:=/= (cdr t1) (cdr t2)))))))\n          ((vector? t1) (cond ((not (and (vector? t2))\n                                    (= (vector-length t1) (vector-length t2))) st)\n                              (else (disjoin st #f (map c:=/=\n                                                        (vector->list t1)\n                                                        (vector->list t2))))))\n          ((equal? t1 t2) #f)\n          (else           st))))\n\n(define (ltunify st uid? t1 t2)\n  (let ((t1 (walk st t1)) (t2 (walk st t2)))\n    (cond ((or (null? t1) (eq? #t t2) (eqv? t1 t2)) st)\n          ((or (var? t1) (var? t2))\n           (match-define (bounds lb.t1 lbi.t1 ub.t1 ubi.t1) (term-bounds st t1))\n           (match-define (bounds lb.t2 lbi.t2 ub.t2 ubi.t2) (term-bounds st t2))\n           (cond ((any<=?                                ub.t1 lb.t2) st)\n                 (((if (and lbi.t1 ubi.t2) anylist (set-union vs.t1 vs.t2)))))\n                           (state-cx-add st vs vcx-simple-add uid? (c:<= t1 t2)))))))\n          ((pair? t1)\n           (cond ((pair?   t2) (let*/and ((st (ltunify st #f (car t1) (car t2))))\n                                 (disjoin st #f (list (c:=/= (car t1) (car t2))\n                                                      (c:<=  (cdr t1) (cdr t2))))))\n                 ((vector? t2)                        st)\n                 (else (and (any<=? term.pair.max t2) st))))\n          ((vector? t1)\n           (cond ((vector? t2)\n                  (define len.t1 (vector-length t1))\n                  (define len.t2 (vector-length t2))\n                  (cond ((< len.t1 len.t2) st)\n                        ((> len.t1 len.t2) #f)\n                        (else (ltunify st #f (vector->list t1) (vector->list t2)))))\n                 ((pair? t2)                            #f)\n                 (else (and (any<=? term.vector.max t2) st))))\n          (else (and (any<=? t1 t2) st)))))\n\n(define (disjoin st uid? cs)\n  (define (c-vars c)\n    (match c\n      ((c:==  l r)        (set-union (term-vars l)     (term-vars r)))\n      ((c:=/= l r)        (set-union (term-vars l)     (term-vars r)))\n      ((c:<=  l r)        (set-union (term-vars l)     (term-vars r)))\n      ((c:disj cs)        (set-union (c-vars (car cs)) (c-vars (cadr cs))))\n      ((c:conj cs)        (apply set-union (seteq) (map c-vars cs)))\n      ((c:use vs _ _ _ _) (term-vars vs))\n      ((c:table t)        (table-vars t))\n      ((c:proc  _ args _) (term-vars args))))\n  (let loop ((cs cs) (cs.new '()))\n    (if (null? cs)\n      (match cs.new\n        ('()          #f)\n        ((list c.new) (c-apply st #f c.new))\n        (_            (define cx (c:disj (reverse cs.new)))\n                      (define vs (set->list (c-vars cx)))\n                      ;; TODO: in the future when a c:proc appears in a c:disj,\n                      ;; it is possible for vs to be empty even when the disj\n                      ;; has not been satisfied (because the proc hasn't been\n                      ;; allowed to expand yet).  Figure out how to resolve\n                      ;; this, possibly by adding a queue of cxs containing\n                      ;; procs that need to be expanded.\n                      (if (null? vs)\n                        (error \"TODO: unexpanded c:proc without vars:\" cx)\n                        (state-cx-add st vs vcx-disj-add uid? cx))))\n      (match (c-simplify st #f (car cs))\n        ;; TODO: if applicable, negate (car cs) in st while simplifying (cdr cs).\n        ;; This achieves some disjoint-ness across branches, reducing redundancy\n        ;; in the search space.  (Ideally we would also do the same in reverse,\n        ;; propagating negated constraints from later branches into earlier\n        ;; branches.)\n        (#f            (loop (cdr cs) cs.new))\n        ((c:conj '())  st)\n        ((c:disj cs.d) (loop (cdr cs) (foldl cons cs.new cs.d)))\n        (c             (loop (cdr cs) (cons c cs.new)))))))\n\n(define (conjoin st cs) (foldl/and (lambda (c st) (c-apply st #f c)) st cs))\n\n(define (use st uid? t.vs lhs args proc desc)\n  (define vars.pending (set->list (term-vars (walk* st t.vs))))\n  (if (null? vars.pending)\n    (unify st lhs (apply proc (walk* st args)))\n    (state-cx-add st vars.pending vcx-use-add uid?\n                  `#s(c:use ,vars.pending ,lhs ,args ,proc ,desc))))\n\n(define (proc-apply st uid? proc args parents)\n  ;; TODO: determine whether to expand instead of adding a c:proc\n  ;; TODO: without expanding, it is possible to infinite loop when no variables\n  ;; are present in args, since in that case, state-cx-add will c-apply again.\n  ;; Figure out how to resolve this, possibly by adding a queue of cxs that\n  ;; need to be expanded.\n  (state-cx-add st (term-vars args) vcx-simple-add uid? (c:proc proc args parents)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Table interaction\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (table-update     st uid? tc) (tc 'update st uid?))\n(define (table-vars               tc) (tc 'variables))\n(define (table-statistics st      tc) (tc 'variable-statistics st))\n\n(define (relation/table . pargs)\n  (match-define (list info thunk.t.0) (apply materialization pargs))\n  (define name             (hash-ref info 'relation-name))\n  (define attribute-names  (hash-ref info 'attribute-names))\n  (define primary-key-name (hash-ref info 'key-name))\n  ;; TODO: this is a workaround to make sure key column is tracked for update.\n  (define attrs\n    (if (member primary-key-name attribute-names)\n      attribute-names\n      (cons #t attribute-names)))\n  (define (app st args.0.0)\n    ;; TODO: this introduces a phantom variable for the key column update workaround.\n    ;; Is there a better solution?\n    (define args.0\n      (if (member primary-key-name attribute-names)\n        args.0.0\n        (cons (var #t) args.0.0)))\n    (define (update-state st t)\n      (define c=>b (t 'bounds))\n      (foldl/and (lambda (c a st)\n                   (c-apply st #f (c:bounds (hash-ref c=>b c bounds.any) a)))\n                 st attrs args.0))\n    (let*/and ((t.0 (thunk.t.0))\n               (st  (update-state st t.0)))\n      (define args (walk* st args.0))\n      (define tc\n        (let controller ((t  t.0)\n                         (vs (set->list (term-vars args))))\n          (method-lambda\n            ((constraint) (c:proc r args.0.0 (set)))\n            ((variables)  vs)\n            ((variable-statistics st)\n             (define c=>stats (t 'statistics))\n             (foldl (lambda (c a x=>stats)\n                      (match (hash-ref c=>stats c #f)\n                        (#f  x=>stats)\n                        (s.x (define (merge s.0) (statistics-intersect s.0 s.x))\n                             (foldl (lambda (x x=>stats) (hash-update x=>stats x merge s.x))\n                                    x=>stats (set->list (term-vars (walk* st a)))))))\n                    (hash) attrs args))\n            ((update st uid?)\n             (let*/and ((t (t 'update (map (lambda (c a) (cons c (term-bounds st a)))\n                                           attrs args))))\n               (update-state\n                 (if (t 'done?)\n                   st\n                   ;; TODO: we only want to register with the subset of variables that are indexable\n                   (let* ((vs (set->list (term-vars (walk* st vs))))\n                          (tc (controller t vs)))\n                     (if (null? vs)\n                       (tc 'update st uid?)\n                       (state-cx-add st vs vcx-table-add uid? (c:table tc)))))\n                 t))))))\n      (c-apply st #f (c:table tc))))\n  (define r (make-relation name attribute-names))\n  (relations-set! r 'definition-info info)\n  (relations-set! r 'apply           app)\n  r)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Variable-centric constraint operations\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (var-update st x)\n  (define vcx.x (state-vcx-ref st x))\n  (foldl/and (lambda (uids st) (state-cx-update* st (set->list uids)))\n             (state-vcx-set st x (vcx-cx-clear vcx.x))\n             (list (vcx-table  vcx.x)  ;; typically the strongest constraints\n                   (vcx-simple vcx.x)\n                   (vcx-disj   vcx.x)\n                   (vcx-use    vcx.x))))\n\n(define (var-assign st x t)\n  ;; could replace occurs check with: (set-member? (term-vars (walk* st t)) x)\n  (and (not (let occurs? ((t t))\n              (cond ((pair?   t) (or (occurs? (walk st (car t)))\n                                     (occurs? (walk st (cdr t)))))\n                    ((vector? t) (let vloop ((i (- (vector-length t) 1)))\n                                   (and (<= 0 i) (or (occurs? (walk st (vector-ref t i)))\n                                                     (vloop (- i 1))))))\n                    (else        (eq? x t)))))\n       (let* ((vcx.x              (state-vcx-ref st x))\n              (vcx.t (if (var? t) (state-vcx-ref st t) vcx.empty))\n              (st    (state-log-add st (c:== x t)))\n              (st    (state-vcx-set st x t)))\n         (foldl/and (lambda (uids st) (state-cx-update* st (set->list uids)))\n                    (c-apply st #f (c:bounds (vcx-bounds vcx.x) t))\n                    (list (vcx-simple vcx.x)  ;; the least expensive constraints\n                          ;; TODO: try disjs containing only simple cxs before tables.\n                          ;; It may only make sense to try the disjs that only\n                          ;; reference this var and no others.\n                          (vcx-table  vcx.x)\n                          ;; TODO: try other disjs after tables\n                          (vcx-disj   vcx.x)\n                          (vcx-use    vcx.x))))))\n\n(define (var-disassign st uid? x t)\n  (let* ((t    (walk* st t))\n         (vs.t (term-vars t)))\n    (define (add) (state-cx-add st (set->list (set-add vs.t x))\n                                vcx-simple-add uid? (c:=/= x t)))\n    (cond ((set-member? vs.t x) st)  ;; simple occurs check\n          ((set-empty?  vs.t)\n           (match-define (bounds lb lbi ub ubi) (term-bounds st x))\n           (define (assign-bounds c b) (var-assign-bounds (state-log-add st c) x b))\n           (cond ((and lbi (equal? t lb)) (define lb.inc (any-increment lb))\n                                          (if (eq? lb lb.inc)\n                                            (assign-bounds (c:=/= lb     x) (bounds lb     #f ub ubi))\n                                            (assign-bounds (c:<=  lb.inc x) (bounds lb.inc #t ub ubi))))\n                 ((and ubi (equal? t ub)) (define ub.dec (any-decrement ub))\n                                          (if (eq? ub ub.dec)\n                                            (assign-bounds (c:=/= x ub    ) (bounds lb lbi ub     #f))\n                                            (assign-bounds (c:<=  x ub.dec) (bounds lb lbi ub.dec #t))))\n                 ((or (any<=? t lb) (any<=? ub t)) st)\n                 (else                             (add))))\n          (else (match-define (bounds lb.x lbi.x ub.x ubi.x) (term-bounds st x))\n                (match-define (bounds lb.t lbi.t ub.t ubi.t) (term-bounds st t))\n                (if (or ((if (and lbi.t ubi.x) anycx (state-var=>cx st)))\n      (let loop ((x t))\n        (define val (hash-ref v=>cx x vcx.empty))\n        (cond ((var? val) (loop val))\n              ((vcx? val) x)\n              (else       val))))\n    t))\n(define (walk* st t)\n  (let loop ((term t))\n    (define t (walk st term))\n    (cond ((pair?   t) (cons (loop (car t)) (loop (cdr t))))\n          ((vector? t) (vector-map loop t))\n          (else        t))))\n\n(define (reify st.0)\n  (define (refine-bounds x st)\n    (define (=/=? x t) (not (let*/and ((st (var-assign st x t)))\n                              (pair? (s-force (state->satisfied-states st))))))\n    (define (trim x t) (refine-bounds x (c-apply st #f (c:=/= x t))))\n    (define vcx.x (state-vcx-ref st x))\n    (match-define (bounds lb lbi? ub ubi?) (vcx-bounds vcx.x))\n    (cond ((and lbi? (=/=? x lb)) (trim x lb))\n          ((and ubi? (=/=? x ub)) (trim x ub))\n          (else                   st)))\n  (define term (walk* st.0 (state-qterm st.0)))\n  (define xs   (set->list (term-vars term)))\n  ;; Refinement should never fail after global satisfaction\n  (define st   (foldl refine-bounds st.0 xs))\n  (cond ((null? xs) (pretty term))\n        (else (define b&uids\n                (map (lambda (x)\n                       (define vcx.x (state-vcx-ref st x))\n                       (cons (vcx-bounds vcx.x) (vcx-simple vcx.x)))\n                     xs))\n              (define uids (apply set-union (seteq) (map cdr b&uids)))\n              (define cxs  (walk* st (map c->f (filter-not\n                                                 not (map (lambda (uid) (hash-ref (state-cx st) uid #f))\n                                                          (set->list uids))))))\n              (define bs\n                (append* (map (lambda (x b)\n                                (if (equal? b bounds.any)\n                                  '()\n                                  (list (list (bounds-lb b)\n                                              (if (bounds-lb-inclusive? b) '<= '<)\n                                              x\n                                              (if (bounds-ub-inclusive? b) '<= '<)\n                                              (bounds-ub b)))))\n                              xs (map car b&uids))))\n              (match-define (cons t c) (pretty (cons term (append bs cxs))))\n              `#s(cx (term: ,t) (constraints: . ,(sort c termsatisfied-states st)))\n\n(define (bis:query->stream q)\n  (match-define `#s(query ,t ,f) q)\n  (s-append* (s-map enumerate-and-reify ((bis:goal f) (state:new t)))))\n(define (bis:bind s k)\n  (cond ((null?      s) '())\n        ((procedure? s) (thunk (bis:bind (s) k)))\n        (else           (s-append/interleaving (k (car s)) (thunk (bis:bind (cdr s) k))))))\n(define ((bis:apply/expand ex args) st)\n  ((bis:goal (apply ex (walk* st args))) st))\n(define ((bis:expand ex r args) st)\n  (define frame (cons r args))\n  (thunk (bis:bind (bis:return (state-proc-stack-push st frame))\n                   (lambda (st) (bis:bind ((bis:goal (apply ex args)) st)\n                                          (lambda (st) (bis:return (state-proc-stack-pop st))))))))\n\n(define (bis:goal f)\n  (match f\n    (`#s(conj ,f1 ,f2) (let ((k1 (bis:goal f1)) (k2 (bis:goal f2)))\n                         (lambda (st) (bis:bind (k1 st) k2))))\n    (`#s(disj ,f1 ,f2) (let ((k1 (bis:goal f1)) (k2 (bis:goal f2)))\n                         (lambda (st)\n                           (state-enforce-global-consistency\n                             st\n                             (lambda ()   '())\n                             (lambda (st) (s-append/interleaving (k1 st) (thunk (k2 st))))))))\n    (`#s(constrain ,(? procedure? proc) ,args)\n      (define r (relations-ref proc))\n      (define apply/bis    (hash-ref r 'apply/bis    #f))  ; strategy-specific application\n      (define apply.r      (hash-ref r 'apply        #f))  ; strategy-agnostic application\n      (define expand       (hash-ref r 'expand       #f))  ; pure expansion\n      (cond (apply/bis    (apply/bis args))\n            (apply.r      (lambda (st) (bis:return (apply.r st args))))\n            (expand       (bis:expand expand r args))\n            (else (error \"no interpretation for:\" proc args))))\n    (_ (define c (f->c f))\n       (lambda (st) (bis:return (c-apply st #f c))))))\n(define (bis:return st)         (if st (list st) '()))\n\n(define (dfs:query->stream q)\n  ((dfs:goal (query-formula q) enumerate-and-reify)\n   (state:new (query-term q))))\n(define ((dfs:mplus k1 k2) st)\n  (state-enforce-global-consistency\n    st\n    (lambda ()   '())\n    (lambda (st) (s-append (k1 st) (thunk (k2 st))))))\n(define ((dfs:expand ex r args k) st)\n  (define frame (cons r args))\n  (dfs:return (dfs:goal (apply ex args)\n                        (lambda (st) (dfs:return k (state-proc-stack-pop st))))\n              (state-proc-stack-push st frame)))\n\n(define (dfs:goal f k)\n  (define loop dfs:goal)\n  (match f\n    (`#s(conj ,f1 ,f2) (loop f1 (loop f2 k)))\n    (`#s(disj ,f1 ,f2) (dfs:mplus (loop f1 k) (loop f2 k)))\n    (`#s(constrain ,(? procedure? proc) ,args)\n      (define r (relations-ref proc))\n      (define apply/dfs    (hash-ref r 'apply/dfs    #f))  ; strategy-specific application\n      (define apply.r      (hash-ref r 'apply        #f))  ; strategy-agnostic application\n      (define expand       (hash-ref r 'expand       #f))  ; pure expansion\n      (cond (apply/dfs    (apply/dfs k args))\n            (apply.r      (lambda (st) (dfs:return k (apply.r st args))))\n            (expand       (dfs:expand expand r args k))\n            (else (error \"no interpretation for:\" proc args))))\n    (_ (define c (f->c f))\n       (lambda (st) (dfs:return k (c-apply st #f c))))))\n(define (dfs:return k st)      (if st (k st) '()))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Syntax definitions\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-syntax define-relation/table\n  (syntax-rules ()\n    ((_ (name attr ...) pargs ...)\n     (define name (relation/table 'relation-name   'name\n                                  'attribute-names '(attr ...)\n                                  pargs ...)))\n    ((_ name pargs ...)\n     (define name (relation/table 'relation-name 'name\n                                  pargs ...)))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/data.rkt",
    "content": "#lang racket/base\n(provide\n  column:const\n  column:identity\n  column:offset\n  column:vector\n  column:table\n  column:indirect\n  column:interval\n  column:bytes:nat\n  column:port\n  column:port-indirect\n  column:port-string\n  interval->dict:ordered\n  dict.empty\n  dict:integer\n  dict:ordered\n  dict:ordered:vector\n  dict:hash\n  enumerator-project\n  enumerator-filter\n  enumerator-sort\n  enumerator-dedup\n  enumerator->dict:ordered:vector-flat\n  enumerator->dict:ordered:vector-group\n  group-fold->hash\n  group-fold\n  group-fold-ordered\n  merge-key-union\n  merge-antijoin\n  merge-join\n  dict-join-unordered\n  dict-join-ordered\n  hash-join\n  dict-antijoin-unordered\n  dict-antijoin-ordered\n  hash-antijoin\n  dict-key-union-unordered\n  dict-key-union-ordered\n  dict-subtract-unordered\n  dict-subtract-ordered\n\n  database\n  database-path\n  database-metadata\n  database-relation\n  database-relation-names\n  database-relation-has?\n  database-relation-add!\n  database-relation-remove!\n  database-compact!\n  database-import!\n  database-export!\n\n  relation-name\n  relation-metadata\n  relation-copy!\n  relation-rename!\n  relation-delete!\n  relation-rename-attributes!\n  relation-index-add!\n  relation-index-remove!\n  relation-index-dict\n  relation-domain-dicts\n  relation-compact!\n  )\n(require \"codec.rkt\" \"enumerator.rkt\" \"heap.rkt\" \"misc.rkt\" \"order.rkt\" \"stream.rkt\"\n         racket/file racket/list racket/match racket/pretty racket/set racket/struct racket/vector)\n\n;; TODO:\n;bscm.rkt\n;bscm:read bscm:write ?\n;or favor a bytes-ref/bytes-set! style interface with bscm types?\n\n;; TODO: use these definitions to replace the logging defined in config.rkt\n(define (pretty-log/port out . args)\n  (define seconds (current-seconds))\n  (define d       (seconds->date seconds #f))\n  (define d-parts (list seconds 'UTC\n                        (date-year d) (date-month  d) (date-day    d)\n                        (date-hour d) (date-minute d) (date-second d)))\n  (pretty-write (cons d-parts args) out))\n\n(define (pretty-logf/port out message . args) (pretty-log/port out (apply format message args)))\n\n(define current-log-port (make-parameter (current-error-port)))\n\n(define (pretty-log  . args) (apply pretty-log/port  (current-log-port) args))\n(define (pretty-logf . args) (apply pretty-logf/port (current-log-port) args))\n\n(define-syntax-rule (time/pretty-log body ...)\n  (let-values (((results time.cpu time.real time.gc) (time-apply (lambda () body ...) '())))\n    (pretty-log `(time cpu ,time.cpu real ,time.real gc ,time.gc))\n    (apply values results)))\n\n;;;;;;;;;;;;;;;;;;;;;;;\n;;; Metadata format ;;;\n;;;;;;;;;;;;;;;;;;;;;;;\n;;\n;;desc.database\n;;(hash\n;;  'relations      (hash NAME desc.relation ...)\n;;  'current        (hash PATH desc.arbitrary ...)\n;;  'pending        (list JOB ...)\n;;  )\n;;\n;;;; supports copying by sharing table and index descriptions\n;;desc.relation\n;;(hash\n;;  'attributes (list attribute-names ...)\n;;  'type       (list high-level-types ...)\n;;  'tables     (list path.table ...)\n;;  'indexes    (hash ordering (list path.table-index ...) ...)\n;;  )\n;;\n;;desc.domain\n;;(hash\n;;  'text path-to-domain-text\n;;  ...\n;;  )\n;;\n;;desc.domain-text\n;;(hash\n;;  'count         num-elements\n;;  'size.position num-bytes\n;;  'index         optional-path-to-index\n;;  )\n;;\n;;TODO:\n;;desc.domain-text-index\n;;(hash\n;;  'domain path.domain\n;;  )\n;;\n;;desc.column\n;;(hash\n;;  'type   'int|'text\n;;  'count  num-elements\n;;  'size   nat-bytes\n;;  'min    _\n;;  'max    _\n;;  'offset _\n;;  )\n;;\n;;desc.table\n;;(hash\n;;  'direction 'insert|'delete\n;;  'domain    desc.domain\n;;  'count     tuple-count\n;;  'columns   (list desc.column ...)\n;;  )\n;;\n;;desc.table-index\n;;(hash\n;;  'table            path.table\n;;  'ordering         (list 3 1 2 etc.)\n;;  'columns.value    (list desc.column ...)\n;;  'columns.indirect (list desc.column ...)  ; length is (- (length columns) 1)\n;;  )\n\n(define fnsuffix.key        \".key\")\n(define fnsuffix.indirect   \".indirect\")\n(define fnsuffix.next       \".next\")\n(define fnsuffix.initial    \".initial\")\n(define fn.metadata         \"metadata.scm\")\n(define fn.value            \"value\")\n(define fn.pos              \"position\")\n(define fn.tuple            \"tuple\")\n(define fn.col              \"column\")\n(define fn.metadata.initial (string-append fn.metadata fnsuffix.initial))\n\n(define metadata-format-version \"0\")\n\n(define (write-metadata path.metadata metadata)\n  (let/files () ((out.metadata path.metadata))\n    (pretty-write\n      (hash-set metadata 'format-version metadata-format-version)\n      out.metadata)))\n\n(define desc.database.empty\n  (hash 'relations (hash)\n        'data      (hash)))\n\n;; TODO: store redundant metadata\n;; - for optional consistency checking\n;; - also for independent file/folder exploration (e.g., analyzing trash)\n;;   - file explorer:\n;;     - display both logical and physical values\n;;     - indicate min/max\n;;     - jump to row, jump to column\n;;       - absolute or relative\n;;     - search for logical/physical value\n;;       - local (fast), or various forms of global (slow)\n;;       - optionally use full-text search indexes\n;; - \"previous\" directory supports time travel as long as most recent groups are not deleted\n\n(define (valid-attributes?! attrs)\n  (unless (list? attrs)\n    (error \"attributes must be a list\" attrs))\n  (for-each (lambda (a) (unless (symbol? a) (error \"attribute must be a symbol\" a 'in attrs)))\n            attrs)\n  (unless (= (length attrs) (set-count (list->set attrs)))\n    (error \"attributes must be unique\" attrs)))\n\n(struct wrapped-database (controller)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (db) 'database)\n             (lambda (db) (list (database-path db)\n                                (hash-ref (database-metadata db) 'relations)))))))\n\n(struct wrapped-relation (controller)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (r) 'relation)\n             (lambda (r) (list (relation-name     r)\n                               (relation-metadata r)))))))\n\n;; Racket doesn't seem to have a weak-value hash table, so we\n;; suboptimally use a weak-key hash table as a self-cleaning list.\n(define all-databases (make-weak-hash))\n(define (database path.db)\n  (let ((path.db (normalize-path path.db)))\n    (or (ormap (lambda (db) (and (equal? path.db (database-path db)) db))\n               (hash-keys all-databases))\n        (let ((db (make-database path.db)))\n          (hash-set! all-databases db (void))\n          db))))\n\n(define (make-database path.db)\n  (define (db-path   name) (path->string (build-path path.db      name)))\n  (define (data-path name) (path->string (build-path path.current name)))\n\n  (define (relations-update! f) (set! metadata (hash-update metadata 'relations f)))\n  (define (data-update!      f) (set! metadata (hash-update metadata 'data      f)))\n\n  (define (reachable (relation-names #f))\n    (define data               (hash-ref metadata 'data))\n    (define name=>relation     (hash-ref metadata 'relations))\n    (define descs.relation     (if relation-names\n                                 (map (lambda (name) (hash-ref name=>relation name)) relation-names)\n                                 (hash-values name=>relation)))\n    (define lpaths.table       (list->set (append* (map (lambda (desc.r) (hash-ref desc.r 'tables))\n                                                        descs.relation))))\n    (define lpaths.table-index (list->set (append* (map (lambda (desc.r) (append* (hash-values (hash-ref desc.r 'indexes))))\n                                                        descs.relation))))\n    (define descs.table        (set-map lpaths.table (lambda (lp) (hash-ref data lp))))\n    (define lpaths.domain-text (list->set (map (lambda (desc.t) (hash-ref (hash-ref desc.t 'domain) 'text))\n                                               descs.table)))\n    (set-union lpaths.table lpaths.table-index lpaths.domain-text))\n\n  (define (clean!)\n    (define pending-previous   (path->string (build-path path.db          \"pending-previous\")))\n    (define metadata.previous  (path->string (build-path pending-previous fn.metadata)))\n    (define lpaths.old         (if (and (directory-exists? pending-previous)\n                                        (file-exists?      metadata.previous))\n                                 (list->set (hash-keys (hash-ref (call-with-input-file metadata.previous read)\n                                                                 'data)))\n                                 (set)))\n    (define lpaths.known       (set-union lpaths.old (list->set (hash-keys (hash-ref metadata 'data)))))\n    (define lpaths.reachable   (reachable))\n    (define lpaths.all         (list->set (map path->string (directory-list path.current))))\n    (define lpaths.trash       (set->list (set-subtract lpaths.all   lpaths.known)))\n    (define lpaths.unreachable (set->list (set-subtract lpaths.known lpaths.reachable)))\n    (unless (null? lpaths.unreachable)\n      (apply pretty-log '(archiving unreachable data) lpaths.unreachable)\n      (make-directory* pending-previous)\n      (for-each (lambda (lp)\n                  (define apath (data-path lp))\n                  (when (directory-exists? apath)\n                    (rename-file-or-directory apath (build-path pending-previous lp))))\n                lpaths.unreachable))\n    (when (directory-exists? pending-previous)\n      (define upath (unique-previous-path))\n      (pretty-log `(moving ,pending-previous to ,upath))\n      (rename-file-or-directory pending-previous upath))\n    (define pending-trash (path->string (build-path path.db \"pending-trash\")))\n    (when (file-exists? path.metadata.next)\n      (pretty-log '(moving interrupted checkpoint to trash) path.metadata.next)\n      (make-directory* pending-trash)\n      (rename-file-or-directory path.metadata.next\n                                (build-path pending-trash (string-append fn.metadata fnsuffix.next))))\n    (unless (null? lpaths.trash)\n      (apply pretty-log '(moving unknown data to trash) lpaths.trash)\n      (make-directory* pending-trash)\n      (for-each (lambda (lp) (rename-file-or-directory (data-path lp) (build-path pending-trash lp)))\n                lpaths.trash))\n    (when (directory-exists? pending-trash)\n      (define upath (unique-trash-path))\n      (pretty-log `(moving ,pending-trash to ,upath))\n      (rename-file-or-directory pending-trash upath)))\n\n  (define (checkpoint!)\n    (define metadata.previous (call-with-input-file path.metadata read))\n    (when   (equal? metadata metadata.previous) (pretty-log '(no checkpoint necessary)))\n    (unless (equal? metadata metadata.previous)\n      (define lpaths.known       (list->set (hash-keys (hash-ref metadata 'data))))\n      (define lpaths.reachable   (reachable))\n      (define lpaths.unreachable (set->list (set-subtract lpaths.known lpaths.reachable)))\n      (unless (null? lpaths.unreachable)\n        (data-update! (lambda (data) (foldl (lambda (lp data) (hash-remove data lp))\n                                            data lpaths.unreachable))))\n      (call-with-output-file path.metadata.next (lambda (out) (pretty-write metadata out)))\n      (define pending-previous (build-path path.db \"pending-previous\"))\n      (make-directory* pending-previous)\n      (pretty-log `(archiving ,path.metadata))\n      (rename-file-or-directory path.metadata (build-path pending-previous fn.metadata))\n      (pretty-log '(checkpointing metadata) metadata)\n      (rename-file-or-directory path.metadata.next path.metadata)\n      (clean!)))\n\n  ;; TODO: later, consolidate subsequent inserts/deletes\n  (define (compact!)\n    (pretty-log `(compacting ,path.db))\n    (define data           (hash-ref metadata 'data))\n    (define descs.relation (hash-values (hash-ref metadata 'relations)))\n    (match-define (list paths.table descs.table paths.domain-text/duplicates)\n      (let* ((paths.table       (append* (map (lambda (desc.relation) (hash-ref desc.relation 'tables))\n                                              descs.relation)))\n             (descs.table       (map (lambda (path.table) (hash-ref data path.table)) paths.table))\n             (paths.domain-text (map (lambda (d) (hash-ref (hash-ref d 'domain) 'text))\n                                     descs.table))\n             (pdps              (map (lambda (path.table desc.table path.domain-text)\n                                       (and path.domain-text (list path.table desc.table path.domain-text)))\n                                     paths.table descs.table paths.domain-text)))\n        (apply map list (filter-not not pdps))))\n    (define paths.domain-text (set->list (list->set paths.domain-text/duplicates)))\n    (unless (< 1 (length paths.domain-text)) (pretty-log '(no compaction necessary)))\n    (when (< 1 (length paths.domain-text))\n      (define (type=>id=>id path.domain-text)\n        (hash 'text (hash-ref path.domain-text=>id=>id path.domain-text)))\n      (define path.domain-text.new     (unique-path \"domain-text\"))\n      (define descs.domain-text        (map (lambda (p) (hash-ref data p)) paths.domain-text))\n      (define compaction               (compact-text-domains\n                                         (data-path path.domain-text.new)\n                                         (map data-path paths.domain-text)\n                                         descs.domain-text))\n      (define desc.domain-text.new     (hash-ref compaction 'domain-text))\n      (define path.domain-text=>id=>id (make-immutable-hash\n                                         (map cons paths.domain-text (hash-ref compaction 'remappings))))\n      (define paths.table.new          (map (lambda (path.table desc.table path.domain-text)\n                                              (if (remap-table? desc.table (type=>id=>id path.domain-text))\n                                                (unique-path \"table\")\n                                                path.table))\n                                            paths.table descs.table paths.domain-text/duplicates))\n      (define path.t=>path.t.new       (make-immutable-hash (map cons paths.table paths.table.new)))\n      (define descs.table.new\n        (map (lambda (path.table path.table.new desc.table path.domain-text)\n               (define desc.domain.new (hash 'text path.domain-text.new))\n               (if (equal? path.table path.table.new)\n                 (begin (pretty-log '(no need to remap table) path.table)\n                        (hash-set desc.table 'domain desc.domain.new))\n                 (remap-table (data-path path.table)\n                              (data-path path.table.new)\n                              desc.table\n                              desc.domain.new\n                              (type=>id=>id path.domain-text))))\n             paths.table paths.table.new descs.table paths.domain-text/duplicates))\n      (define paths.table-index\n        (append* (map (lambda (desc.relation)\n                        (filter (lambda (path.table-index)\n                                  (define desc.table-index (hash-ref data path.table-index))\n                                  (member (hash-ref desc.table-index 'table) paths.table))\n                                (append* (hash-values (hash-ref desc.relation 'indexes)))))\n                      descs.relation)))\n      (define descs.table-index     (map (lambda (path.ti) (hash-ref data path.ti)) paths.table-index))\n      (define paths.table-index.new (map (lambda (path.ti desc.ti)\n                                           (define path.table  (hash-ref desc.ti 'table))\n                                           (define desc.domain (hash-ref (hash-ref data path.table) 'domain))\n                                           (define path.dt     (hash-ref desc.domain 'text))\n                                           (if (remap-table-index? desc.ti (type=>id=>id path.dt))\n                                             (unique-path \"table-index\")\n                                             path.ti))\n                                         paths.table-index descs.table-index))\n      (define path.ti=>path.ti.new  (make-immutable-hash (map cons paths.table-index paths.table-index.new)))\n      (define (replace-p.ti p.ti) (hash-ref path.ti=>path.ti.new p.ti p.ti))\n      (define descs.table-index.new\n        (map (lambda (path.table-index path.table-index.new desc.table-index)\n               (define path.table       (hash-ref desc.table-index   'table))\n               (define path.table.new   (hash-ref path.t=>path.t.new path.table))\n               (define path.domain-text (hash-ref (hash-ref (hash-ref data path.table) 'domain) 'text))\n               (if (equal? path.table-index path.table-index.new)\n                 (begin (pretty-log '(no need to remap table index) path.table-index)\n                        desc.table-index)\n                 (remap-table-index (data-path path.table-index)\n                                    (data-path path.table-index.new)\n                                    desc.table-index\n                                    path.table.new\n                                    (type=>id=>id path.domain-text))))\n             paths.table-index paths.table-index.new descs.table-index))\n      (pretty-log '(installing remapped data))\n      (data-update!\n        (lambda (data)\n          (apply hash-set* data\n                 path.domain-text.new desc.domain-text.new\n                 (append (append* (map list paths.table.new       descs.table.new))\n                         (append* (map list paths.table-index.new descs.table-index.new))))))\n      (pretty-log '(updating relations with remapped data))\n      (relations-update!\n        (lambda (rs)\n          (make-immutable-hash\n            (hash-map rs (lambda (name.r desc.r)\n                           (let* ((desc.r (hash-update desc.r 'tables\n                                                       (lambda (paths.table)\n                                                         (map (lambda (p) (hash-ref path.t=>path.t.new   p p))\n                                                              paths.table))))\n                                  (desc.r (hash-update desc.r 'indexes\n                                                       (lambda (ordering=>paths.table-index)\n                                                         (make-immutable-hash\n                                                           (hash-map ordering=>paths.table-index\n                                                                     (lambda (o ps.ti)\n                                                                       (cons o (map replace-p.ti ps.ti)))))))))\n                             (cons name.r desc.r)))))))\n      (checkpoint!)))\n\n  (define (unique-path str.type)\n    (define data    (hash-ref metadata 'data))\n    (define seconds (number->string (current-seconds)))\n    (let loop ((id.local 0))\n      (define candidate (string-append str.type \"-\" seconds \"-\" (number->string id.local)))\n      (cond ((hash-has-key? data candidate) (loop (+ id.local 1)))\n            (else                           (make-directory* (data-path candidate))\n                                            (data-update! (lambda (data) (hash-set data candidate #f)))\n                                            candidate))))\n  (define (unique-directory path.root str.type)\n    (define seconds (number->string (current-seconds)))\n    (let loop ((id.local 0))\n      (define candidate (string-append str.type \"-\" seconds \"-\" (number->string id.local)))\n      (define apath (path->string (build-path path.root candidate)))\n      (cond ((directory-exists? apath) (loop (+ id.local 1)))\n            (else                      apath))))\n  (define (unique-previous-path) (unique-directory path.previous \"previous\"))\n  (define (unique-trash-path)    (unique-directory path.trash    \"trash\"))\n\n  (define (new-relation?! name) (when (hash-has-key? name=>relation name)\n                                  (error \"relation already exists\" name path.db)))\n\n  (define (make-relation name)\n    (define (description)           (hash-ref (hash-ref metadata 'relations) name))\n    (define (description-update! f) (relations-update! (lambda (rs) (hash-update rs name f))))\n    (define self\n      (method-lambda\n        ((name)                     name)\n        ((metadata)                 (description))\n        ((copy!   name.new)         (pretty-log `(copying relation ,name to ,name.new))\n                                    (new-relation?! name.new)\n                                    (set! name=>relation\n                                      (hash-set name=>relation name.new (hash-ref name=>relation name)))\n                                    (relations-update! (lambda (rs) (hash-set rs name.new (hash-ref rs name))))\n                                    (checkpoint!))\n        ((rename! name.new)         (pretty-log `(renaming relation ,name to ,name.new))\n                                    (new-relation?! name.new)\n                                    (set! name=>relation (let ((r    (hash-ref    name=>relation name))\n                                                               (n=>r (hash-remove name=>relation name)))\n                                                           (hash-set n=>r name.new r)))\n                                    (relations-update! (lambda (rs) (let* ((r  (hash-ref    rs name))\n                                                                           (rs (hash-remove rs name)))\n                                                                      (hash-set rs name.new r))))\n                                    (set! name name.new)\n                                    (checkpoint!))\n        ((delete!)                  (pretty-log `(deleting relation ,name))\n                                    (set! self           #f)\n                                    (set! name=>relation (hash-remove name=>relation name))\n                                    (relations-update! (lambda (rs) (hash-remove rs name)))\n                                    (checkpoint!))\n        ((rename-attributes! attrs) (pretty-log `(renaming ,name attributes)\n                                                `(old: ,(hash-ref (description) 'attributes))\n                                                `(new: ,attrs))\n                                    (valid-attributes?! attrs)\n                                    (let ((attrs.old (hash-ref (description) 'attributes)))\n                                      (unless (= (length attrs) (length attrs.old))\n                                        (error \"cannot change the number of attributes\"\n                                               name 'new attrs 'old attrs.old)))\n                                    (relations-update! (lambda (rs) (let* ((r (hash-ref rs name))\n                                                                           (r (hash-set r 'attributes attrs)))\n                                                                      (hash-set rs name r))))\n                                    (checkpoint!))\n        ((index-add!    signatures) (apply pretty-log `(adding indexes for ,name) signatures)\n                                    (let* ((desc         (description))\n                                           (data         (hash-ref metadata 'data))\n                                           (attrs        (hash-ref desc     'attributes))\n                                           (lpaths.table (hash-ref desc     'tables))\n                                           (descs.table  (map (lambda (lp) (hash-ref data lp)) lpaths.table))\n                                           (orderings    (map (attrs->signature->ordering attrs) signatures))\n                                           (orderings    (normalize-table-index-orderings (length attrs) orderings))\n                                           (ords.current (list->set (hash-keys (hash-ref desc 'indexes))))\n                                           (ords.skipped (set->list (set-intersect (list->set orderings) ords.current)))\n                                           (ords.new     (set->list (set-subtract  (list->set orderings) ords.current))))\n                                      (define (ords->sigs ords)\n                                        (map (lambda (ordering) (map (lambda (i) (list-ref attrs i))\n                                                                     (filter-not (lambda (i) (eq? #t i))\n                                                                                 ordering)))\n                                             ords))\n                                      (apply pretty-log '(normalizing table index signatures) (ords->sigs orderings))\n                                      (unless (null? ords.skipped)\n                                        (apply pretty-log '(skipping existing table indexes)\n                                               (ords->sigs ords.skipped)))\n                                      (when   (null? ords.new) (pretty-log '(no table indexes to build)))\n                                      (unless (null? ords.new)\n                                        (define lpaths*.ti\n                                          (apply map list\n                                                 (map (lambda (lpath.table desc.table)\n                                                        (define lpaths.ti (map (lambda (_) (unique-path \"table-index\")) ords.new))\n                                                        (define descs.ti  (build-table-indexes\n                                                                            path.current lpaths.ti lpath.table desc.table ords.new))\n                                                        (data-update!\n                                                          (lambda (data) (apply hash-set* data\n                                                                                (append* (map list lpaths.ti descs.ti)))))\n                                                        lpaths.ti)\n                                                      lpaths.table descs.table)))\n                                        (description-update!\n                                          (lambda (desc) (hash-update desc 'indexes\n                                                                      (lambda (ordering=>lps)\n                                                                        (apply hash-set* ordering=>lps\n                                                                               (append* (map list ords.new lpaths*.ti)))))))\n                                        (checkpoint!))))\n        ((index-remove! signatures) (apply pretty-log `(removing indexes for ,name) signatures)\n                                    (let* ((desc         (description))\n                                           (data         (hash-ref metadata 'data))\n                                           (attrs        (hash-ref desc     'attributes))\n                                           (orderings    (map (attrs->signature->ordering attrs) signatures))\n                                           (orderings    (normalize-table-index-orderings (length attrs) orderings))\n                                           (ords.current (list->set (hash-keys (hash-ref desc 'indexes))))\n                                           (ords.missing (set->list (set-subtract  (list->set orderings) ords.current)))\n                                           (ords.found   (set->list (set-intersect (list->set orderings) ords.current))))\n                                      (define (ords->sigs ords)\n                                        (map (lambda (ordering) (map (lambda (i) (list-ref attrs i))\n                                                                     (filter-not (lambda (i) (eq? #t i))\n                                                                                 ordering)))\n                                             ords))\n                                      (apply pretty-log '(normalizing table index signatures) (ords->sigs orderings))\n                                      (unless (null? ords.missing)\n                                        (apply pretty-log '(skipping table indexes that do not exist)\n                                               (ords->sigs ords.missing)))\n                                      (when   (null? ords.found) (pretty-log '(no table indexes to remove)))\n                                      (unless (null? ords.found)\n                                        (description-update!\n                                          (lambda (desc) (hash-update desc 'indexes\n                                                                      (lambda (ordering=>lps)\n                                                                        (foldl (lambda (o o=>lps) (hash-remove o=>lps o))\n                                                                               ordering=>lps ords.found)))))\n                                        (checkpoint!))))\n        ((index-dict signature)     (let* ((desc      (description))\n                                           (data      (hash-ref metadata 'data))\n                                           (attrs     (hash-ref desc     'attributes))\n                                           (ordering  ((attrs->signature->ordering attrs) signature))\n                                           (ordering  (car (normalize-table-index-orderings (length attrs) (list ordering))))\n                                           (lpaths.ti (hash-ref (hash-ref desc 'indexes) ordering\n                                                                (lambda () (error \"no relation index matches signature\"\n                                                                                  name signature)))))\n                                      (match lpaths.ti\n                                        ('() dict.empty)\n                                        ((list lpath.ti)\n                                         (define (descs->cols fnsuffix descs.col)\n                                           (map (lambda (j desc.col)\n                                                  (and desc.col\n                                                       (let ((size   (hash-ref desc.col 'size))\n                                                             (offset (hash-ref desc.col 'offset 0))) ; TODO: later, require this\n                                                         (column:offset\n                                                           (if (< 0 size)\n                                                             (let* ((fname (string-append \"column.\" (number->string j) fnsuffix))\n                                                                    (apath (build-path (data-path lpath.ti) fname)))\n                                                               (column:port (open-input-file apath) `#(nat ,size))\n                                                               ;; Optionally load index columns into memory instead\n                                                               ;(time (column:bytes:nat (file->bytes apath) (hash-ref desc.col 'size)))\n                                                               )\n                                                             column:identity)\n                                                           offset))))\n                                                (range (length descs.col)) descs.col))\n                                         (define desc.ti       (hash-ref data lpath.ti))\n                                         (define descs.col.key (hash-ref desc.ti 'columns.key))\n                                         (define cols.key      (descs->cols \".key\"      descs.col.key))\n                                         (define cols.indirect (descs->cols \".indirect\" (hash-ref desc.ti 'columns.indirect)))\n                                         (let loop ((start         0)\n                                                    (end           (hash-ref (car descs.col.key) 'count))\n                                                    (cols.key      cols.key)\n                                                    (cols.indirect cols.indirect))\n                                           (define (next start end) (loop start end (cdr cols.key) (cdr cols.indirect)))\n                                           (define i->key   (car cols.key))\n                                           (define i->value (if (null? cols.indirect)\n                                                              (column:const '())\n                                                              (let ((ci (car cols.indirect)))\n                                                                (if ci\n                                                                  (column:interval ci next)\n                                                                  (lambda (i) (next i (+ i 1)))))))\n                                           (dict:ordered i->key i->value start end)))\n                                        ;; TODO: multiple table-indexes, possibly with deletions\n                                        (_ (error \"multi-table indexes are not yet supported\" name lpaths.ti)))))\n        ;; TODO: share domain dicts when the domains are shared across relations\n        ((domain-dicts)             (let* ((desc         (description))\n                                           (data         (hash-ref metadata 'data))\n                                           (lpaths.table (hash-ref desc     'tables))\n                                           (descs.table  (map (lambda (lp) (hash-ref data lp)) lpaths.table))\n                                           (descs.domain (map (lambda (desc) (hash-ref desc 'domain)) descs.table)))\n                                      (define (domain->dict-pair.text desc.domain)\n                                        (define lpath.dt     (hash-ref desc.domain 'text))\n                                        (define desc.dt      (hash-ref data        lpath.dt))\n                                        (define size.pos     (hash-ref desc.dt     'size.position))\n                                        (define count        (hash-ref desc.dt     'count))\n                                        (define apath.dt     (data-path lpath.dt))\n                                        ;; TODO: should col.pos be shared like this, or duplicated across dicts for safety?\n                                        (define col.pos      (column:port (open-input-file (build-path apath.dt \"position\")) `#(nat ,size.pos)))\n                                        ;; Optionally load positions into memory instead\n                                        ;(define col.pos      (time (column:bytes:nat (file->bytes (build-path apath.dt \"position\")) size.pos)))\n                                        ;; TODO: properly support all text types: bytes, string, symbol\n                                        (define id->str      (column:port-string col.pos (open-input-file (build-path apath.dt \"value\"))))\n                                        (define dict.str=>id (dict:ordered id->str (lambda (id) id) 0 count))\n                                        (define dict.id=>str (dict:integer 0       id->str          0 count))\n                                        (cons dict.str=>id dict.id=>str))\n                                      (define dict-pairs.text (map domain->dict-pair.text descs.domain))\n                                      (cons (hash 'text (map car dict-pairs.text))\n                                            (hash 'text (map cdr dict-pairs.text)))))\n        ;; TODO: only spend effort compacting this relation\n        ((compact!)                 (compact!))))\n    (wrapped-relation (lambda args\n                        (unless self (error \"cannot use deleted relation\" name))\n                        (apply self args))))\n\n  (define path.current       (db-path \"current\"))\n  (define path.previous      (db-path \"previous\"))\n  (define path.trash         (db-path \"trash\"))\n  (define path.metadata      (db-path fn.metadata))\n  (define path.metadata.next (string-append path.metadata fnsuffix.next))\n  (for-each make-directory* (list path.db path.current path.previous path.trash))\n  (define metadata\n    (cond ((file-exists? path.metadata)      (call-with-input-file path.metadata read))\n          ((file-exists? path.metadata.next) (pretty-log '(checkpointing metadata after interrupted swap))\n                                             (rename-file-or-directory path.metadata.next path.metadata)\n                                             (call-with-input-file path.metadata read))\n          (else                              (pretty-log '(creating new database) path.db)\n                                             (call-with-output-file\n                                               path.metadata\n                                               (lambda (out) (pretty-write desc.database.empty out)))\n                                             desc.database.empty)))\n  (pretty-log '(loaded metadata for) path.db metadata)\n  ;; TODO: migrate metadata if format-version is old\n  (clean!)\n\n  (define name=>relation (make-immutable-hash\n                           (hash-map (hash-ref metadata 'relations)\n                                     (lambda (name desc.relation)\n                                       (pretty-log `(loading relation ,name) desc.relation)\n                                       (cons name (make-relation name))))))\n\n  (wrapped-database\n    (method-lambda\n      ((path)                              path.db)\n      ((metadata)                          metadata)\n      ((reachable names)                   (reachable names))\n      ((relation name)                     (hash-ref name=>relation name\n                                                     (lambda () (error \"unknown relation\" name path.db))))\n      ((relation-add! name attrs type src) (apply pretty-log `(creating relation ,name)\n                                                  (map (lambda (a t) `(,a : ,t)) attrs type))\n                                           (new-relation?! name)\n                                           (valid-attributes?! attrs)\n                                           (for-each (lambda (t) (unless (member t '(nat int bytes string symbol))\n                                                                   (error \"invalid attribute type\" t 'in type)))\n                                                     type)\n                                           (unless (= (length attrs) (length type))\n                                             (error \"number of attributes must match the relation type arity\"\n                                                    name attrs type))\n                                           (define path.domain-text (unique-path \"domain-text\"))\n                                           (define path.table       (unique-path \"table\"))\n                                           (define desc.ingest      (ingest-relation-source\n                                                                      path.current path.domain-text path.table type src))\n                                           (define desc.domain-text (hash-ref (hash-ref desc.ingest 'domain) 'text))\n                                           (define desc.table       (hash-ref desc.ingest 'table))\n                                           (define desc.relation    (hash 'attributes attrs\n                                                                          'type       type\n                                                                          'tables     (list path.table)\n                                                                          'indexes    (hash)))\n                                           (data-update!      (lambda (data) (hash-set* data\n                                                                                        path.domain-text desc.domain-text\n                                                                                        path.table       desc.table)))\n                                           (relations-update! (lambda (rs)   (hash-set  rs name desc.relation)))\n                                           (checkpoint!)\n                                           (set! name=>relation (hash-set name=>relation name (make-relation name))))\n      ((import! db.in names.in)            (pretty-log `(importing relations . ,names.in) 'from: (db.in 'path) 'into: path.db)\n                                           (define path.current.in   (path->string (build-path (db.in 'path) \"current\")))\n                                           (define name=>relation.in (hash-ref (db.in 'metadata) 'relations))\n                                           (define lpath=>data.in    (hash-ref (db.in 'metadata) 'data))\n                                           (define descs.relation.in (map (lambda (name)\n                                                                            (unless (hash-has-key? name=>relation.in name)\n                                                                              (error \"cannot import non-existent relation\"\n                                                                                     name (db.in 'path)))\n                                                                            (new-relation?! name)\n                                                                            (hash-ref name=>relation.in name))\n                                                                          names.in))\n                                           (define lpaths.reachable (set->list (db.in 'reachable names.in)))\n                                           (for-each (lambda (lpath)\n                                                       (define apath.in  (path->string (build-path path.current.in lpath)))\n                                                       (define apath.out (data-path lpath))\n                                                       ;; TODO: validate that skipped data is identical\n                                                       ;; TODO: support renaming paths when non-identical data collision occurs\n                                                       (cond ((directory-exists? apath.out) (pretty-log '(skipping import copy) apath.in apath.out))\n                                                             (else                          (pretty-log '(copying for import)   apath.in apath.out)\n                                                                                            (copy-directory/files apath.in apath.out\n                                                                                                                  #:keep-modify-seconds? #t))))\n                                                     lpaths.reachable)\n                                           (data-update!      (lambda (data)\n                                                                (foldl (lambda (lpath data)\n                                                                         (hash-set data lpath (hash-ref lpath=>data.in lpath)))\n                                                                       data lpaths.reachable)))\n                                           (relations-update! (lambda (rs)\n                                                                (foldl (lambda (name desc rs) (hash-set rs name desc))\n                                                                       rs names.in descs.relation.in)))\n                                           (checkpoint!))\n      ((compact!)                          (compact!)))))\n\n(define (database-path             db)              ((wrapped-database-controller db) 'path))\n(define (database-metadata         db)              ((wrapped-database-controller db) 'metadata))\n(define (database-relation         db name)         ((wrapped-database-controller db) 'relation         name))\n(define (database-relation-names   db)              (hash-keys     (hash-ref (database-metadata db) 'relations)))\n(define (database-relation-has?    db name)         (hash-has-key? (hash-ref (database-metadata db) 'relations) name))\n(define (database-relation-add!    db name . pargs) ((wrapped-database-controller db) 'relation-add!    name\n                                                                                      (plist-ref pargs 'attributes)\n                                                                                      (plist-ref pargs 'type)\n                                                                                      (plist-ref pargs 'source)))\n(define (database-relation-remove! db name)         (relation-delete! (database-relation db name)))\n(define (database-compact!         db)              ((wrapped-database-controller db) 'compact!))\n\n(define (database-import! db db.in    . relation-names.in)\n  ((wrapped-database-controller db) 'import! (wrapped-database-controller db.in) relation-names.in))\n(define (database-export! db path.out . relation-names.out)\n  (let ((path.out (normalize-path path.out)))\n    (when (or (file-exists? path.out) (directory-exists? path.out))\n      (error \"export destination already exists\" path.out))\n    (apply database-import! (database path.out) db relation-names.out)))\n\n(define (relation-name                r)              ((wrapped-relation-controller r) 'name))\n(define (relation-metadata            r)              ((wrapped-relation-controller r) 'metadata))\n(define (relation-copy!               r name.new)     ((wrapped-relation-controller r) 'copy!              name.new))\n(define (relation-rename!             r name.new)     ((wrapped-relation-controller r) 'rename!            name.new))\n(define (relation-delete!             r)              ((wrapped-relation-controller r) 'delete!))\n(define (relation-rename-attributes!  r attrs.new)    ((wrapped-relation-controller r) 'rename-attributes! attrs.new))\n(define (relation-index-add!          r . signatures) ((wrapped-relation-controller r) 'index-add!         signatures))\n(define (relation-index-remove!       r . signatures) ((wrapped-relation-controller r) 'index-remove!      signatures))\n(define (relation-index-dict          r signature)    ((wrapped-relation-controller r) 'index-dict         signature))\n(define (relation-domain-dicts        r)              ((wrapped-relation-controller r) 'domain-dicts))\n(define (relation-compact!            r)              ((wrapped-relation-controller r) 'compact!))\n\n;; TODO: in-place sorting of multiple columns\n(define (int-tuplestring\n                     (build-path path.table (string-append fn.col \".\" (number->string i)))))\n       column-ids))\n\n(define (ingest-relation-source apath.root lpath.domain-text lpath.table type s.in)\n  (define bytes=>id             (make-hash))\n  (define size.bytes            0)\n  (define count.tuples.initial  0)\n  (define apath.domain.value    (path->string (build-path apath.root lpath.domain-text fn.value)))\n  (define apath.domain.pos      (path->string (build-path apath.root lpath.domain-text fn.pos)))\n  (define apath*.column         (column-paths (build-path apath.root lpath.table) (range (length type))))\n  (define apath*.column.initial (map (lambda (p.c) (string-append p.c fnsuffix.initial))\n                                     apath*.column))\n  (define (insert-bytes! b)\n    (or (hash-ref bytes=>id b #f)\n        (let ((id (hash-count bytes=>id)))\n          (hash-set! bytes=>id b id)\n          (set! size.bytes (+ size.bytes (bytes-length b)))\n          id)))\n  (define row->tuple\n    (let ((col->num* (map\n                      (lambda (i t.col)\n\n                        #;(match t.col\n                          ('int    (lambda (x)\n                                     (unless (int?    x) (error \"invalid int\"    `(column: ,i) x))\n                                     x))\n                          ('nat    (lambda (x)\n                                     (unless (nat?    x) (error \"invalid nat\"    `(column: ,i) x))\n                                     x))\n                          ('bytes  (lambda (x)\n                                     (unless (bytes?  x) (error \"invalid bytes\"  `(column: ,i) x))\n                                     (insert-bytes!                                      x)))\n                          ('string (lambda (x)\n                                     (unless (string? x) (error \"invalid string\" `(column: ,i) x))\n                                     (insert-bytes! (string->bytes/utf-8                 x))))\n                          ('symbol (lambda (x)\n                                     (unless (symbol? x) (error \"invalid symbol\" `(column: ,i) x))\n                                     (insert-bytes! (string->bytes/utf-8 (symbol->string x)))))\n                          (_ (error \"(currently) unsupported type\"                `(column: ,i) t.col)))\n\n                        (case t.col\n                          ((int)    (lambda (x)\n                                     (unless (int?    x) (error \"invalid int\"    `(column: ,i) x))\n                                     x))\n                          ((nat)    (lambda (x)\n                                     (unless (nat?    x) (error \"invalid nat\"    `(column: ,i) x))\n                                     x))\n                          ((bytes)  (lambda (x)\n                                     (unless (bytes?  x) (error \"invalid bytes\"  `(column: ,i) x))\n                                     (insert-bytes!                                      x)))\n                          ((string) (lambda (x)\n                                     (unless (string? x) (error \"invalid string\" `(column: ,i) x))\n                                     (insert-bytes! (string->bytes/utf-8                 x))))\n                          ((symbol) (lambda (x)\n                                     (unless (symbol? x) (error \"invalid symbol\" `(column: ,i) x))\n                                     (insert-bytes! (string->bytes/utf-8 (symbol->string x)))))\n                          (else (error \"(currently) unsupported type\"                `(column: ,i) t.col)))\n\n                        )\n                      \n                          (range (length type))\n                          type)))\n      (lambda (row)\n        (set! count.tuples.initial (+ count.tuples.initial 1))\n        (let loop ((col* row) (col->num* col->num*))\n          (match* (col* col->num*)\n            (((cons col col*) (cons col->num col->num*)) (cons (col->num col) (loop col* col->num*)))\n            (('()             '())                       '())\n            ((_               _)                         (error \"incorrect number of columns\" row type)))))))\n\n  (apply pretty-log '(ingesting rows and writing initial tuple columns) apath*.column.initial)\n  (call/files\n    '() apath*.column.initial\n    (lambda outs.column.initial\n      (define type.tuple (map (lambda (_) 'int) type))\n      (define *row-num* 0)\n      (time/pretty-log\n        (s-each (lambda (row)\n                  (when (zero? (modulo *row-num* 100000))\n                    (printf \"processing row ~s\\n\" *row-num*))\n                  (set! *row-num* (add1 *row-num*))\n                  (for-each encode outs.column.initial type.tuple (row->tuple row)))\n                s.in))))\n\n  (define size.pos  (min-nat-bytes size.bytes))\n  (define count.ids (hash-count bytes=>id))\n  (define id=>id    (make-vector count.ids))\n  (pretty-log `(ingested ,count.tuples.initial tuples))\n  (pretty-log `(sorting ,(hash-count bytes=>id) strings -- ,size.bytes bytes total))\n  (let ((bytes&id*.sorted (time/pretty-log (sort (hash->list bytes=>id)\n                                                 (lambda (a b) (bytesbytes size.pos (file-position out.bytes.value)) out.bytes.pos))\n      (write-pos)\n      (time/pretty-log\n        (let loop ((i 0) (b&id* bytes&id*.sorted))\n          (unless (null? b&id*)\n            (let* ((b&id (car b&id*))\n                   (b    (car b&id))\n                   (id   (cdr b&id)))\n              (write-bytes b out.bytes.value)\n              (write-pos)\n              (vector-set! id=>id id i)\n              (loop (+ i 1) (cdr b&id*))))))))\n  (define desc.domain-text\n    (hash 'count         count.ids\n          'size.position size.pos))\n  (write-metadata (build-path apath.root lpath.domain-text fn.metadata.initial) desc.domain-text)\n\n  (pretty-log '(remapping columns))\n  (define column-vmms\n    (map (lambda (t.col apath.in)\n           (define col->col\n             (match t.col\n               ((or 'nat 'int)              (lambda (n)  n))\n               ((or 'bytes 'string 'symbol) (lambda (id) (vector-ref id=>id id)))))\n           (define (read-element in) (col->col (decode in 'int)))\n           (match-define (list vec.col min.col max.col)\n             (read-column/bounds apath.in count.tuples.initial read-element))\n           (pretty-log `(deleting ,apath.in))\n           (delete-file apath.in)\n           (list vec.col min.col max.col))\n         type apath*.column.initial))\n  (define columns (map car column-vmms))\n\n  (define tuples  (sorted-tuples count.tuples.initial columns))\n  (pretty-log '(deduplicating tuples))\n  (define (columns-set! j tuple) (for-each (lambda (vec.col value.col)\n                                             (vector-set! vec.col j value.col))\n                                           columns tuple))\n  (define count.tuples.unique\n    (time/pretty-log\n      (when (< 0 count.tuples.initial)\n        (define t0 (vector-ref tuples 0))\n        (columns-set! 0 t0)\n        (let loop ((prev t0) (i 1) (j 1))\n          (if (< i count.tuples.initial)\n            (let ((next (vector-ref tuples i)))\n              (cond ((equal? prev next) (loop prev (+ i 1) j))\n                    (else (columns-set! j next)\n                          (loop next (+ i 1) (+ j 1)))))\n            j)))))\n\n  (define column-descriptions\n    (map (lambda (t.col vec.col min.col max.col apath.out)\n           (match-define (cons size.col offset.col)\n             (write-column apath.out count.tuples.unique vec.col min.col max.col))\n           (hash 'type   (match t.col\n                           ((or 'nat 'int)              'int)\n                           ((or 'bytes 'string 'symbol) 'text))\n                 'count  count.tuples.unique\n                 'size   size.col\n                 'offset offset.col\n                 'min    min.col\n                 'max    max.col))\n         type columns (map cadr column-vmms) (map caddr column-vmms) apath*.column))\n  (define desc.table\n    (hash 'direction 'insert\n          'domain    (hash 'text lpath.domain-text)\n          'count     count.tuples.unique\n          'columns   column-descriptions))\n  (write-metadata (build-path apath.root lpath.table fn.metadata.initial) desc.table)\n\n  (hash 'domain (hash 'text desc.domain-text)\n        'table  desc.table))\n\n(define ((multi-merge vector gens))\n  (define end (vector-length h))\n  (heap! string (build-path apath.domain-text.new fn.value)))\n  (define apath.pos    (path->string (build-path apath.domain-text.new fn.pos)))\n  (define size.bytes   (sum (map (lambda (apath.in) (file-size (build-path apath.in fn.value)))\n                                 apaths.domain-text)))\n  (define size.pos     (min-nat-bytes size.bytes))\n  (define id=>ids      (map (lambda (desc.in) (make-vector (hash-ref desc.in 'count)))\n                            descs.domain-text))\n  (define custodian.gs (make-custodian))\n  (define gs           (parameterize ((current-custodian custodian.gs))\n                         (map (lambda (apath.in desc.in id=>id)\n                                (define count       (hash-ref desc.in 'count))\n                                (define size.pos    (hash-ref desc.in 'size.position))\n                                (define apath.value (build-path apath.in fn.value))\n                                (define apath.pos   (build-path apath.in fn.pos))\n                                (and (< 0 count)\n                                     (let ((in.value (open-input-file apath.value))\n                                           (in.pos   (open-input-file apath.pos)))\n                                       (define (read-pos) (bytes-nat-ref (read-bytes size.pos in.pos)\n                                                                         size.pos\n                                                                         0))\n                                       (let loop ((id 0) (pos.current (read-pos)))\n                                         (let ((pos.next (read-pos)))\n                                           (cons (read-bytes (- pos.next pos.current) in.value)\n                                                 (lambda (i)\n                                                   (vector-set! id=>id id i)\n                                                   (and (< (+ id 1) count)\n                                                        (loop (+ id 1) pos.next)))))))))\n                              apaths.domain-text descs.domain-text id=>ids)))\n  (pretty-log '(merging domains) (map cons apaths.domain-text descs.domain-text)\n              '(writing merge-sorted strings to) apath.value\n              '(writing positions to) apath.pos)\n  (define count.ids    (let/files () ((out.value apath.value)\n                                      (out.pos   apath.pos))\n                         (define (write-pos) (write-bytes (nat->bytes size.pos\n                                                                      (file-position out.value))\n                                                          out.pos))\n                         (write-pos)\n                         (time/pretty-log\n                           ((multi-merge (lambda (g.0 g.1) (bytesid)\n                              (let loop ((i (- (vector-length id=>id) 1)))\n                                (and (<= 0 i)\n                                     (if (= i (vector-ref id=>id i))\n                                       (loop (- i 1))\n                                       id=>id))))\n                            id=>ids))\n  (define desc.domain-text\n    (hash 'count         count.ids\n          'size.position size.pos))\n  (write-metadata (build-path apath.domain-text.new fn.metadata.initial) desc.domain-text)\n  (hash 'domain-text desc.domain-text\n        'remappings  remappings))\n\n(define ((attrs->signature->ordering attrs) signature)\n  (map (lambda (attr) (let ((i (index-of attrs attr)))\n                        (if i i (error \"invalid signature attribute\" attr signature))))\n       signature))\n\n(define (normalize-table-index-orderings count.columns orderings)\n  (for-each (lambda (ordering) (unless (and (not (null? ordering))\n                                            (list? ordering)\n                                            (andmap (lambda (i) (and (nat? i) (<= 0 i) (< i count.columns)))\n                                                    ordering)\n                                            (= (length ordering) (set-count (list->set ordering))))\n                                 (error \"invalid index\" ordering)))\n            orderings)\n  (remove-duplicates\n    (map (lambda (ordering)\n           (define len (length ordering))\n           (cond ((= (+ len 1) count.columns) (append ordering (set-subtract (range count.columns)\n                                                                             ordering)))\n                 ((<    len    count.columns) (append ordering '(#t)))\n                 (else                                ordering)))\n         orderings)))\n\n(define (build-table-indexes apath.root lpath*.index lpath.table desc.table orderings)\n  (define apath.root.table  (path->string (build-path apath.root lpath.table)))\n  (define apath*.root.index (map (lambda (lpath.index) (path->string (build-path apath.root lpath.index)))\n                                 lpath*.index))\n  (define count.tuples      (hash-ref desc.table 'count))\n  (define desc*.column      (hash-ref desc.table 'columns))\n  (define count.columns     (length desc*.column))\n  (pretty-log '(building indexes for) apath.root.table orderings desc.table apath*.root.index)\n  (define key-used?       (ormap (lambda (ordering) (member #t ordering))\n                                 orderings))\n  (define column-ids.used (set->list (set-remove (foldl (lambda (ordering col-ids)\n                                                          (set-union col-ids (list->set ordering)))\n                                                        (set) orderings)\n                                                 #t)))\n  (define size.pos        (min-nat-bytes (- count.tuples 1)))\n  (define i=>desc.col     (make-immutable-hash\n                            (append (if key-used?\n                                      (list (cons #t (hash 'type   'int\n                                                           'count  count.tuples\n                                                           'size   size.pos\n                                                           'offset 0\n                                                           'min    0\n                                                           'max    (- count.tuples 1))))\n                                      '())\n                                    (map cons (range count.columns) desc*.column))))\n  (define i=>col          (make-immutable-hash\n                            (append (if key-used?\n                                      (list (cons #t (let ((column.key (make-vector count.tuples)))\n                                                       (let loop ((i 0))\n                                                         (when (< i count.tuples)\n                                                           (vector-set! column.key i i)\n                                                           (loop (+ i 1))))\n                                                       column.key)))\n                                      '())\n                                    (map (lambda (i.col apath.in)\n                                           (cons i.col (read-column apath.in (hash-ref i=>desc.col i.col))))\n                                         column-ids.used\n                                         (column-paths apath.root.table column-ids.used)))))\n  (map (lambda (apath.root.index ordering)\n         (pretty-log '(building index) apath.root.index '(with ordering) ordering)\n         (define columns.used        (map (lambda (i.col) (hash-ref i=>col      i.col))   ordering))\n         (define descs.used          (map (lambda (i.col) (hash-ref i=>desc.col i.col))   ordering))\n         (define s&o*.used           (map (lambda (desc) (ideal-size-and-offset (hash-ref desc 'min)\n                                                                                (hash-ref desc 'max)))\n                                          descs.used))\n         (define sizes.used          (map car s&o*.used))\n         (define offsets.used        (map cdr s&o*.used))\n         (define tuples              (sorted-tuples count.tuples columns.used))\n         (define apath*.col.key      (map (lambda (apath.col) (string-append apath.col fnsuffix.key))\n                                          (column-paths apath.root.index (range    (length ordering)))))\n         (define apath*.col.indirect (map (lambda (apath.col) (string-append apath.col fnsuffix.indirect))\n                                          (column-paths apath.root.index (range (- (length ordering) 1)))))\n         (pretty-log '(writing index columns))\n         (define counts\n           (call/files\n             '()\n             apath*.col.key\n             (lambda out*.key\n               (call/files\n                 '()\n                 apath*.col.indirect\n                 (lambda out*.indirect\n                   (time/pretty-log\n                     (when (< 0 count.tuples)\n                       (for-each (lambda (out) (write-bytes (nat->bytes size.pos 0) out))\n                                 out*.indirect)\n                       (let loop.keys ((i*.key        (range (length ordering)))\n                                       (size*.key     sizes.used)\n                                       (offset*.key   offsets.used)\n                                       (out*.key      out*.key)\n                                       (out*.indirect out*.indirect)\n                                       (pos*          (make-list (length out*.key) 0))\n                                       (start         0)\n                                       (end           count.tuples))\n                         (let ((i.key      (car i*.key))\n                               (i*.key     (cdr i*.key))\n                               (size.key   (car size*.key))\n                               (offset.key (car offset*.key)))\n                           (define (key-ref i) (list-ref (vector-ref tuples i) i.key))\n                           (let ((out.key (car out*.key)))\n                             (define (write-key key) (write-bytes (nat->bytes size.key (- key offset.key)) out.key))\n                             (if (null? i*.key)\n                               (let loop.final ((i start))\n                                 (cond ((< i end) (write-key (key-ref i))\n                                                  (loop.final (+ i 1)))\n                                       (else      (list (+ (car pos*) (- i start))))))\n                               (let ((out.indirect (car out*.indirect)))\n                                 (let loop.key ((pos (car pos*)) (pos* (cdr pos*)) (start start) (end end))\n                                   (if (< start end)\n                                     (let ((key (key-ref start)))\n                                       (write-key key)\n                                       (let ((start.new (bisect-next start end (lambda (i) (<= (key-ref i) key)))))\n                                         (let ((pos* (loop.keys i*.key\n                                                                (cdr size*.key)\n                                                                (cdr offset*.key)\n                                                                (cdr out*.key)\n                                                                (cdr out*.indirect)\n                                                                pos*\n                                                                start\n                                                                start.new)))\n                                           (write-bytes (nat->bytes size.pos (car pos*)) out.indirect)\n                                           (loop.key (+ pos 1) pos* start.new end))))\n                                     (cons pos pos*)))))))))))))))\n         (define descs.column.key      (map (lambda (apath desc count size offset)\n                                              (let* ((desc (hash-set* desc 'count count 'size size 'offset offset)))\n                                                (cond ((column-consecutive? (lambda () (read-column apath desc))\n                                                                            count\n                                                                            (hash-ref desc 'min)\n                                                                            (hash-ref desc 'max))\n                                                       (delete-file apath)\n                                                       (hash-set* desc 'size 0 'offset (hash-ref desc 'min)))\n                                                      (else desc))))\n                                            apath*.col.key descs.used counts sizes.used offsets.used))\n         (define descs.column.indirect (map (lambda (apath.indirect count.current count.next)\n                                              (cond ((= count.current count.next)\n                                                     (pretty-log '(deleting identity indirection) apath.indirect)\n                                                     (delete-file apath.indirect)\n                                                     #f)\n                                                    (else (hash 'type  'int\n                                                                'count count.current\n                                                                'size  size.pos\n                                                                'min   0\n                                                                'max   count.next))))\n                                            apath*.col.indirect\n                                            (reverse (cdr (reverse counts)))\n                                            (cdr counts)))\n         (define desc.table-index      (hash 'table            lpath.table\n                                             'ordering         ordering\n                                             'columns.key      descs.column.key\n                                             'columns.indirect descs.column.indirect))\n         (write-metadata (build-path apath.root.index fn.metadata.initial) desc.table-index)\n         desc.table-index)\n       apath*.root.index orderings))\n\n(define (read-column/bounds apath.in count read-element)\n  ;; TODO: consider specialized vectors: https://docs.racket-lang.org/foreign/homogeneous-vectors.html\n  (define vec.col (make-vector count))\n  (pretty-log `(reading ,count elements and computing min/max from) apath.in)\n  (let/files ((in apath.in)) ()\n    (time/pretty-log\n      (let loop ((i 0) (min.col #f) (max.col 0))\n        (cond ((< i count)\n               (define value (read-element in))\n               (vector-set! vec.col i value)\n               (loop (+ i 1)\n                     (if min.col (min min.col value) value)\n                     (max max.col value)))\n              (else (list vec.col (or min.col 0) max.col)))))))\n\n(define (read-column apath.in desc.in)\n  (define count   (hash-ref desc.in 'count))\n  (define size    (hash-ref desc.in 'size))\n  (define offset  (hash-ref desc.in 'offset 0)) ; TODO: later, require this\n  ;; TODO: consider specialized vectors: https://docs.racket-lang.org/foreign/homogeneous-vectors.html\n  (define vec.col (make-vector count))\n  (cond ((< 0 size) (pretty-log `(reading ,count elements from) apath.in)\n                    (let/files ((in apath.in)) ()\n                      (time/pretty-log\n                        (let loop ((i 0))\n                          (cond ((< i count) (define v.in (bytes-nat-ref (read-bytes size in) size 0))\n                                             (vector-set! vec.col i (+ offset v.in))\n                                             (loop (+ i 1)))\n                                (else        vec.col))))))\n        (else       (pretty-log `(building ,count consecutive integers starting at ,offset)\n                                '(instead of reading from) apath.in)\n                    (let loop ((i 0))\n                      (cond ((< i count) (vector-set! vec.col i (+ offset i))\n                                         (loop (+ i 1)))\n                            (else        vec.col))))))\n\n(define (write-column apath.out count vec.col min.col max.col)\n  (if (column-consecutive? (lambda () vec.col) count min.col max.col)\n    (begin (pretty-log '(not writing column to file because column is consecutive)\n                       `(would have written ,count elements to) apath.out\n                       `(nat-size: ,0 offset: ,min.col min: ,min.col max: ,max.col))\n           (cons 0 min.col))\n    (match-let (((cons size.col offset.col) (ideal-size-and-offset min.col max.col)))\n      (pretty-log `(writing ,count elements to) apath.out\n                  `(nat-size: ,size.col offset: ,offset.col min: ,min.col max: ,max.col))\n      (let/files () ((out apath.out))\n        (time/pretty-log\n          (let loop ((i 0))\n            (when (< i count)\n              (write-bytes (nat->bytes size.col (- (vector-ref vec.col i) offset.col)) out)\n              (loop (+ i 1))))))\n      (cons size.col offset.col))))\n\n(define (ideal-size-and-offset min.col max.col)\n  (define diff.col  (- max.col min.col))\n  (define size.diff (min-nat-bytes diff.col))\n  (define size.max  (min-nat-bytes max.col))\n  (if (or (< min.col   0)\n          (< size.diff size.max))\n    (cons size.diff min.col)\n    (cons size.max  0)))\n\n(define (column-consecutive? ->vec count.col min.col max.col)\n  (and (= count.col (+ 1 (- max.col min.col)))\n       (let ((vec.col (->vec)))\n         (let loop ((i 0) (expected min.col))\n           (or (= i count.col)\n               (and (= expected (vector-ref vec.col i))\n                    (loop (+ i 1) (+ expected 1))))))))\n\n(define (remap-column?      desc.col   type=>id=>id) (not (not (hash-ref type=>id=>id (hash-ref desc.col 'type) #f))))\n(define (remap-table?       desc.table type=>id=>id) (ormap (lambda (desc.col) (remap-column? desc.col type=>id=>id))\n                                                            (hash-ref desc.table 'columns)))\n(define (remap-table-index? desc.ti    type=>id=>id) (ormap (lambda (desc.col) (remap-column? desc.col type=>id=>id))\n                                                            (hash-ref desc.ti 'columns.key)))\n\n(define (remap-column apath.in apath.out desc.in type=>id=>id)\n  (pretty-log `(remapping ,apath.in to ,apath.out) desc.in)\n  (define type    (hash-ref desc.in 'type))\n  (define count   (hash-ref desc.in 'count))\n  (define size.in (hash-ref desc.in 'size))\n  (define offset  (hash-ref desc.in 'offset 0)) ; TODO: later, require this\n  (define id=>id  (hash-ref type=>id=>id type #f))\n  (cond (id=>id (match-define (list vec.col min.col max.col)\n                  (if (< 0 size.in)\n                    (read-column/bounds apath.in count\n                                        (lambda (in)\n                                          (define v.in (bytes-nat-ref (read-bytes size.in in) size.in 0))\n                                          (vector-ref id=>id (+ offset v.in))))\n                    (let loop ((i 0))\n                      (cond ((< i count) (vector-set! vec.col i (+ offset i))\n                                         (loop (+ i 1)))\n                            (else        (list vec.col offset (+ offset (- count 1))))))))\n                (match-define (cons size.col offset.col)\n                  (write-column apath.out (vector-length vec.col) vec.col min.col max.col))\n                (hash-set* desc.in 'size size.col 'offset offset.col 'min min.col 'max max.col))\n        ((= 0 size.in) (pretty-log '(identity remapping on a consecutive integer sequence: nothing to do))\n                       desc.in)\n        (else          (pretty-log '(copying verbatim due to identity remapping))\n                       (time/pretty-log (copy-file apath.in apath.out))\n                       desc.in)))\n\n(define (remap-table apath.in apath.out desc.table.in desc.domain.new type=>id=>id)\n  (pretty-log `(remapping ,apath.in to ,apath.out) desc.table.in)\n  (define columns.in     (hash-ref desc.table.in 'columns))\n  (define columns.out    (map (lambda (apath.in.col apath.out.col desc.in.col)\n                                (remap-column apath.in.col apath.out.col desc.in.col type=>id=>id))\n                              (column-paths apath.in  (range (length columns.in)))\n                              (column-paths apath.out (range (length columns.in)))\n                              columns.in))\n  (define desc.table.out (hash 'domain  desc.domain.new\n                               'count   (hash-ref desc.table.in 'count)\n                               'columns columns.out))\n  (write-metadata (build-path apath.out fn.metadata.initial) desc.table.out)\n  desc.table.out)\n\n(define (remap-table-index apath.in apath.out desc.table-index.in lpath.table.new type=>id=>id)\n  (pretty-log `(remapping ,apath.in to ,apath.out) desc.table-index.in)\n  (define (remap fnsuffix desc*.in)\n    (map (lambda (apath.in.col apath.out.col desc.in.col)\n           (and desc.in.col (remap-column apath.in.col apath.out.col desc.in.col type=>id=>id)))\n         (map (lambda (apath.col) (string-append apath.col fnsuffix))\n              (column-paths apath.in  (range (length desc*.in))))\n         (map (lambda (apath.col) (string-append apath.col fnsuffix))\n              (column-paths apath.out (range (length desc*.in))))\n         desc*.in))\n  (define columns.key.in       (hash-ref desc.table-index.in 'columns.key))\n  (define columns.indirect.in  (hash-ref desc.table-index.in 'columns.indirect))\n  (define columns.key.out      (remap fnsuffix.key      columns.key.in))\n  (define columns.indirect.out (remap fnsuffix.indirect columns.indirect.in))\n  (define desc.table-index.out (hash-set* desc.table-index.in\n                                          'table            lpath.table.new\n                                          'columns.key      columns.key.out\n                                          'columns.indirect columns.indirect.out))\n  (write-metadata (build-path apath.out fn.metadata.initial) desc.table-index.out)\n  desc.table-index.out)\n\n\n;; TODO: benchmark a design based on streams/iterators for comparison\n\n;; TODO:\n;; simple edb-relations vs. idb-relations w/ fixed-point iteration materializations (current + next-delta + now-being-produced)\n\n(define (bisect start end i<)\n  (let loop ((start start) (end end))\n    (if (<= end start) end\n      (let ((i (+ start (quotient (- end start) 2))))\n        (if (i< i) (loop (+ 1 i) end) (loop start i))))))\n\n(define (bisect-next start end i<)\n  (define i (- start 1))\n  (let loop ((offset 1))\n    (define next (+ i offset))\n    (cond ((and (< next end) (i< next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (next (+ i o)))\n                    (cond ((= o 0)                      (+ i 1))\n                          ((and (< next end) (i< next)) (loop next o))\n                          (else                         (loop i    o)))))))))\n\n(define (bisect-prev start end i>)\n  (define i end)\n  (let loop ((offset 1))\n    (define next (- i offset))\n    (cond ((and (>= next start) (i> next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (n (- i o)))\n                    (cond ((= o 0)                   i)\n                          ((and (>= n start) (i> n)) (loop n o))\n                          (else                      (loop i o)))))))))\n\n;; TODO: remove tables, or at least reduce their scope?\n(define table.empty\n  (method-lambda\n    ((length)                         0)\n    ((subtable start.sub (end.sub 0)) table.empty)\n    ((columns  start.col (end.col 0)) table.empty)\n    ((copy)                           table.empty)\n    ((dedup)                          table.empty)\n    ((dedup!)                         (void))\n    ((sort)                           table.empty)\n    ((sort!)                          (void))))\n\n(define (table columns (start 0) (end (vector-length (vector-ref columns 0))))\n  (if (= 0 (vector-length columns))\n    table.empty\n    (let loop ((start start) (end end))\n      (define (self-length)         (- end start))\n      (define (self-width)          (vector-length columns))\n      (define (self-column col)     (vector-ref    columns           col))\n      (define (self-ref  col row)   (vector-ref    (self-column col) row))\n      (define (self-set! col row v) (vector-set!   (self-column col) row v))\n      (define (self-copy)           (table (vector-map (lambda (v.col) (vector-copy v.col start end))\n                                                       columns)))\n      (define (self-dedup!)\n        (define width (self-width))\n        (let dedup ((row.prev start) (row (+ start 1)))\n          (if (= row end)\n            (when (< (+ row.prev 1) end)\n              (set! end (+ row.prev 1)))\n            (if (let duplicate? ((col 0))\n                  (or (= col width)\n                      (let ((v.col (self-column col)))\n                        (and (equal? (vector-ref v.col row.prev)\n                                     (vector-ref v.col row))\n                             (duplicate? (+ col 1))))))\n              (dedup row.prev (+ row 1))\n              (let ((row.prev (+ row.prev 1)))\n                (unless (= row.prev row)\n                  (let swap! ((col 0))\n                    (when (< col width)\n                      (let ((v.col (self-column col)))\n                        (vector-set! v.col row.prev (vector-ref v.col row))\n                        (swap! (+ col 1))))))\n                (dedup row.prev (+ row 1)))))))\n      (if (<= end start)\n        table.empty\n        (method-lambda\n          ((width)                                      (self-width))\n          ((length)                                     (self-length))\n          ((ref  col row)                               (self-ref  col row))\n          ((set! col row v)                             (self-set! col row v))\n          ((subtable start.sub (end.sub (self-length))) (loop (+ start start.sub) (+ start end.sub)))\n          ((columns  start.col (end.col (self-width)))  (table (vector-copy columns start.col end.col) start end))\n          ((copy)                                       (self-copy))\n          ((dedup)                                      (let ((t (self-copy)))\n                                                          (t 'dedup!)\n                                                          t))\n          ((dedup!)                                     (self-dedup!))\n          ;; TODO:\n          ;((sort ))\n          ;((sort! ))\n          )))))\n\n(define (table-width    t)                              (t 'width))\n(define (table-length   t)                              (t 'length))\n(define (table-ref      t col row)                      (t 'ref      col row))\n(define (table-set!     t col row v)                    (t 'set!     col row v))\n(define (table-subtable t start (end (table-length t))) (t 'subtable start end))\n(define (table-columns  t start (end (table-width  t))) (t 'columns  start end))\n(define (table-dedup    t)                              (t 'dedup))\n(define (table-dedup!   t)                              (t 'dedup!))\n(define (table-sort     t)                              (t 'sort))\n(define (table-sort!    t)                              (t 'sort!))\n\n;; TODO: support a direct-scanning operator, rather than scanning via column indices\n;; TODO: columns with methods: 'ref for what it does now, and 'enumerator for efficient scanning?\n;; TODO: more flexible/efficient method-lambda\n\n(define (column:identity                           i) i)\n(define ((column:const     c)                      _) c)\n(define ((column:offset    column offset)          i) (+ (column i) offset))\n(define ((column:vector    rows)                   i) (vector-ref rows i))\n(define ((column:table     columns)                i) (map (lambda (col) (col i)) columns))\n(define ((column:indirect  column.pos column)      i) (column (column.pos i)))\n(define ((column:interval  column.pos interval->x) i) (interval->x (column.pos i) (column.pos (+ i 1))))\n(define ((column:bytes:nat bs size)                i) (bytes-nat-ref bs size (* i size)))\n\n;; TODO: specialize to fixed-size nat\n(define (column:port                     in type) (let ((size.type (sizeof type (void))))\n                                                    (lambda (i)\n                                                      (file-position in (* i size.type))\n                                                      (decode        in type))))\n(define (column:port-indirect column.pos in type)   (lambda (i)\n                                                      (file-position in (column.pos i))\n                                                      (decode        in type)))\n;; TODO: generalize to bytes\n(define (column:port-string   column.pos in)      (column:interval\n                                                    column.pos\n                                                    (lambda (pos.0 pos.1)\n                                                      (file-position in pos.0)\n                                                      (bytes->string/utf-8 (read-bytes (- pos.1 pos.0) in)))))\n\n(define ((interval->dict:ordered i->key i->value) start end) (dict:ordered i->key i->value start end))\n\n;; TODO: not needed?\n;(define (dict:ordered:trie start end)\n  ;)\n\n\n(define dict.empty\n  (method-lambda\n    ((count)                   0)\n    ((=/= _)                   dict.empty)\n    ((==  _)                   dict.empty)\n    ((<=  _)                   dict.empty)\n    ((<   _)                   dict.empty)\n    ((>=  _)                   dict.empty)\n    ((>   _)                   dict.empty)\n    ((bstr-prefix   _)         dict.empty)\n    ((bstr-contains _)         dict.empty)\n    ((has-key?      _)         #f)\n    ((ref _ k.found k.missing) (k.missing))\n    ((enumerator/2)            (lambda _ (void)))\n    ((enumerator)              (lambda _ (void)))))\n\n(define (dict:integer offset.key i->value start end)\n  (let loop ((start start) (end end))\n    (define self\n      (if (<= end start)\n        dict.empty\n        (method-lambda\n          ((pop)    (loop (+ start 1) end))\n          ((count)  (- end start))\n          ((top)    (i->value start))\n          ((max)    (+ offset.key (- end 1)))\n          ((min)    (+ offset.key start))\n          ((>= key) (loop (max start    (- key offset.key))    end))\n          ((>  key) (loop (max start (+ (- key offset.key) 1)) end))\n          ((<= key) (loop start                                (min end (+ (- key offset.key) 1))))\n          ((<  key) (loop start                                (min end    (- key offset.key))))\n          ((== key) ((self '>= key) '<= key))\n          ((has-key? key)              (let ((self (self '>= key)))\n                                         (and (< 0 (self 'count))\n                                              (equal? (self 'min) key))))\n          ((ref key k.found k.missing) (let ((self (self '>= key)))\n                                         (if (or (= 0 (self 'count))\n                                                 (not (equal? (self 'min) key)))\n                                           (k.missing)\n                                           (k.found (self 'top)))))\n          ((enumerator/2)              (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (+ i offset.key) (i->value i))\n                                             (loop (+ i 1))))))\n          ((enumerator)                (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (+ i offset.key))\n                                             (loop (+ i 1)))))))))\n    self))\n\n(define (dict:ordered i->key i->value start end)\n  (let loop ((start start) (end end))\n    (define (after  k<) (loop (bisect-next start end (lambda (i) (k< (i->key i)))) end))\n    (define (before k>) (loop start (bisect-prev start end (lambda (i) (k> (i->key i))))))\n    (define self\n      (if (<= end start)\n        dict.empty\n        (method-lambda\n          ((pop)       (loop (+ start 1) end))\n          ((count)     (- end start))\n          ((top)       (i->value start))\n          ((max)       (i->key   (- end 1)))\n          ((min)       (i->key   start))\n          ((after  k<) (after  k<))\n          ((before k>) (before k>))\n          ((>= key)    (after  (lambda (k) (any  key)    (after  (lambda (k) (any<=? k key))))\n          ((<= key)    (before (lambda (k) (any= key) '<= key))\n          ((has-key? key)              (let ((self (self '>= key)))\n                                         (and (< 0 (self 'count))\n                                              (equal? (self 'min) key))))\n          ((ref key k.found k.missing) (let ((self (self '>= key)))\n                                         (if (or (= 0 (self 'count))\n                                                 (not (equal? (self 'min) key)))\n                                           (k.missing)\n                                           (k.found (self 'top)))))\n          ((enumerator/2)              (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (i->key i) (i->value i))\n                                             (loop (+ i 1))))))\n          ((enumerator)                (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (i->key i))\n                                             (loop (+ i 1)))))))))\n    self))\n\n(define (dict:ordered:vector rows (t->key (lambda (t) t)) (start 0) (end (vector-length rows)))\n  (define (i->value i) (vector-ref rows i))\n  (define (i->key   i) (t->key (i->value i)))\n  (dict:ordered i->key i->value start end))\n\n(define (dict:hash k=>t)\n  (let loop ((k=>t k=>t))\n    (if (= (hash-count k=>t) 0)\n      dict.empty\n      (method-lambda\n        ((count)                     (hash-count k=>t))\n        ((=/= key)                   (loop (hash-remove k=>t key)))\n        ((==  key)                   (if (hash-has-key? k=>t key)\n                                       (loop (hash key (hash-ref k=>t key)))\n                                       dict.empty))\n        ((has-key? key)              (hash-has-key? k=>t key))\n        ((ref key k.found k.missing) (if (hash-has-key? k=>t key)\n                                       (k.found (hash-ref k=>t key))\n                                       (k.missing)))\n        ((enumerator/2)              (hash->enumerator/2 k=>t))\n        ((enumerator)                (lambda (yield)\n                                       (for ((k (in-hash-keys k=>t)))\n                                         (yield k))))))))\n\n(define ((merge-join A B) yield)\n  (when (and (< 0 (A 'count))\n             (< 0 (B 'count)))\n    (let loop ((A   A)\n               (k.A (A 'min))\n               (B   B)\n               (k.B (B 'min)))\n      (case (compare-any k.A k.B)\n        ((-1) (let ((A (A '>= k.B)))\n                (when (< 0 (A 'count))\n                  (loop A (A 'min) B k.B))))\n        (( 1) (let ((B (B '>= k.A)))\n                (when (< 0 (B 'count))\n                  (loop A k.A B (B 'min)))))\n        (else (let ((t.A (A 'top))\n                    (t.B (B 'top))\n                    (A   (A 'pop))\n                    (B   (B 'pop)))\n                (yield k.A t.A t.B)\n                (when (and (< 0 (A 'count))\n                           (< 0 (B 'count)))\n                  (loop A (A 'min) B (B 'min)))))))))\n\n(define ((merge-antijoin A B) yield)\n  ((dict-antijoin-ordered (A 'enumerator/2) B) yield))\n\n(define ((merge-key-union A B) yield)\n  ((dict-key-union-ordered (A 'enumerator) B) yield))\n\n(define (group-fold->hash en v.0 f)\n  (define k=>v (hash))\n  (en (lambda (k v) (set! k=>v (hash-update k=>v k\n                                            (lambda (v.current) (f v v.current))\n                                            v.0))))\n  k=>v)\n\n(define ((group-fold en v.0 f) yield)\n  ((hash->enumerator/2 (group-fold->hash en v.0 f)) yield))\n\n(define ((group-fold-ordered en v.0 f) yield)\n  (let ((first?    #t)\n        (k.current #f)\n        (v.current v.0))\n    (en (lambda (k v)\n          (cond (first?               (set! first?    #f)\n                                      (set! k.current k)\n                                      (set! v.current (f v v.0)))\n                ((equal? k k.current) (set! v.current (f v v.current)))\n                (else                 (yield k.current v.current)\n                                      (set! k.current k)\n                                      (set! v.current (f v v.0))))))\n    (unless first?\n      (yield k.current v.current))))\n\n(define ((enumerator-dedup en) yield)\n  (define first?     #t)\n  (define t.previous #f)\n  (en (lambda (t)\n        (cond (first?                      (set! first?     #f)\n                                           (set! t.previous t)\n                                           (yield t))\n              ((not (equal? t t.previous)) (set! t.previous t)\n                                           (yield t))))))\n\n(define ((enumerator-project en f) yield)\n  (en (lambda args (apply f yield args))))\n\n(define ((enumerator-filter en ?) yield)\n  (en (lambda (t) (when (? t) (yield t)))))\n\n(define ((enumerator-sort en enumerator (sort (enumerator->rlist en) dict:ordered:vector-flat en (t->key (lambda (t) t)))\n  (dict:ordered:vector\n    (enumerator->vector (enumerator-dedup (enumerator-sort en anykey))\n\n(define (enumerator->dict:ordered:vector-group en t->key)\n  (dict:ordered:vector\n    (enumerator->vector\n      (enumerator-project\n        (group-fold-ordered\n          (enumerator-project (enumerator-dedup (enumerator-sort en anykey t) t)))\n          '() cons)\n        (lambda (yield _ ts.reversed) (yield (reverse ts.reversed)))))\n    (lambda (ts) (t->key (car ts)))))\n\n(define ((hash-join en en.hash) yield)\n  ((dict-join-unordered en (dict:hash (group-fold->hash en.hash '() cons)))\n   (lambda (k t ts.hash)\n     (for ((t.hash (in-list (reverse ts.hash))))  ; is this reversal necessary?\n       (yield k t t.hash)))))\n\n(define ((hash-antijoin en en.hash) yield)\n  ((dict-antijoin-unordered en (dict:hash (group-fold->hash en.hash (void) (lambda _ (void)))))\n   yield))\n\n(define ((dict-join-unordered en d.index) yield)\n  (when (< 0 (d.index 'count))\n    (en (lambda (k v) (d.index 'ref k\n                               (lambda (v.index) (yield k v v.index))\n                               (lambda ()        (void)))))))\n\n(define ((dict-join-ordered en.ordered d.index) yield)\n  (when (< 0 (d.index 'count))\n    (en.ordered (lambda (k v)\n                  (set! d.index (d.index '>= k))\n                  (d.index 'ref k\n                           (lambda (v.index) (yield k v v.index))\n                           (lambda ()        (void)))))))\n\n(define ((dict-antijoin-unordered en d.index) yield)\n  (en (if (= 0 (d.index 'count))\n        yield\n        (lambda (k v) (unless (d.index 'has-key? k)\n                        (yield k v))))))\n\n(define ((dict-antijoin-ordered en.ordered d.index) yield)\n  (en.ordered (if (= 0 (d.index 'count))\n                yield\n                (lambda (k v)\n                  (set! d.index (d.index '>= k))\n                  (unless (d.index 'has-key? k)\n                    (yield k v))))))\n\n(define ((dict-subtract-unordered en d.index) yield)\n  (en (if (= 0 (d.index 'count))\n        yield\n        (lambda (k) (unless (d.index 'has-key? k)\n                      (yield k))))))\n\n(define ((dict-subtract-ordered en.ordered d.index) yield)\n  (en.ordered (if (= 0 (d.index 'count))\n                yield\n                (lambda (k)\n                  (set! d.index (d.index '>= k))\n                  (unless (d.index 'has-key? k)\n                    (yield k))))))\n\n(define ((hash-key-union en en.hash) yield)\n  (define d.index (dict:hash (let ((k=> (hash)))\n                               (en.hash (lambda (k) (set! k=> (hash-set k=> k (void)))))\n                               k=>)))\n  ((dict-key-union-unordered en d.index) yield))\n\n(define ((dict-key-union-unordered en d.index) yield)\n  ((dict-subtract-unordered en d.index) yield)\n  ((d.index 'enumerator)                yield))\n\n(define ((dict-key-union-ordered en.ordered d.index) yield)\n  (en.ordered (if (= 0 (d.index 'count))\n                yield\n                (lambda (k)\n                  (let loop ()\n                    (if (= 0 (d.index 'count))\n                      (yield k)\n                      (let ((k.d (d.index 'min)))\n                        (case (compare-any k k.d)\n                          ((-1) (yield k))\n                          (( 1) (set! d.index (d.index 'pop))\n                                (yield k.d)\n                                (loop))\n                          (else (set! d.index (d.index 'pop))\n                                (yield k))))))))))\n\n\n;; TODO: computing fixed points?\n;; - iteration: changed?\n;; - relation/variable: stable, next, to-add\n\n;; TODO: multiway-joins\n;; - extend-with\n;; - extend-anti\n;; - filter-with\n;; - filter-anti\n\n(module+ test\n  (require racket/pretty)\n\n  (define (test.0 yield.0)\n    (define (yield . args)\n      (pretty-write `(yielding: . ,args))\n      (apply yield.0 args))\n    (yield 0 1)\n    (yield 0 2)\n    (yield 0 3)\n    (yield 1 1)\n    (yield 1 2)\n    (yield 5 2)\n    (yield 5 7))\n\n  (define test.1 (enumerator->enumerator/2\n                   (vector->enumerator '#((0 . 1)\n                                          (0 . 2)\n                                          (0 . 3)\n                                          (1 . 1)\n                                          (1 . 2)\n                                          (5 . 2)\n                                          (5 . 7)))))\n\n  (displayln 'group-fold.0)\n  ((group-fold test.0 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'group-fold-ordered.0)\n  ((group-fold-ordered test.0 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'group-fold.1)\n  ((group-fold test.1 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'group-fold-ordered.1)\n  ((group-fold-ordered test.1 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'hash-join)\n  ((hash-join\n     (enumerator->enumerator/2 (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3))))\n     (enumerator->enumerator/2 (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (0 . 77) (8 . 3)))))\n   (lambda (k a b) (pretty-write (list k a b))))\n\n  (displayln 'merge-join)\n  ((merge-join\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (0 . 77) (8 . 3)))\n       car))\n   (lambda (k a b) (pretty-write (list k a b))))\n\n  (displayln 'hash-key-union)\n  ((hash-key-union\n     (list->enumerator (map car '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3))))\n     (list->enumerator (map car '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (0 . 77) (8 . 3)))))\n   pretty-write)\n\n  (displayln 'merge-key-union)\n  ((merge-key-union\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (0 . 77) (8 . 3)))\n       car))\n   pretty-write)\n\n  (displayln 'hash-antijoin)\n  ((hash-antijoin\n     (enumerator->enumerator/2 (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3))))\n     (enumerator->enumerator/2 (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (0 . 77) (8 . 3)))))\n   (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'merge-antijoin)\n  ((merge-antijoin\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (0 . 77) (8 . 3)))\n       car))\n   (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'table)\n  (let ((t (table (vector (vector  0  0  0  0  1  1  1  2  2  3  3  3  3  3  4)\n                          (vector 'a 'a 'a 'b 'a 'a 'b 'a 'a 'a 'b 'b 'c 'c 'a)\n                          (vector  0  1  1  1  0  1  1  2  2  1  1  1  1  1  7)))))\n    (for ((col (in-range (table-width t))))\n      (for ((row (in-range (table-length t))))\n        (printf \"~s \" (table-ref t col row)))\n      (newline))\n\n    (displayln 'table-dedup!)\n    (table-dedup! t)\n\n    (for ((col (in-range (table-width t))))\n      (for ((row (in-range (table-length t))))\n        (printf \"~s \" (table-ref t col row)))\n      (newline)))\n  )\n\n;; TODO:\n;join-many, need attribute order\n\n;extend-with/anti\n;filter-with/anti\n\n;;; TODO: these are analogous to operators: a set of tuples flowing through a particular program point\n;(struct idb-relation (done current new) #:prefab)\n\n;;; exponential search aka one-sided binary search\n;(define (join-tables t.0 t.1 k)\n  ;;; (k key v.0 v.1)\n;;key.0 key.1\n  ;)\n\n;;; NOTE: this semi-naive join does not correctly generalize to more than 2 relations\n;(define (join-idb-relations r.0 r.1 logic)\n  ;(append\n    ;(map (lambda (t.1)\n           ;(join-tables (idb-relation-current r.0)\n                        ;t.1\n                        ;;; TODO: no need to eta expand\n                        ;(lambda (k v.0 v.1)\n                          ;(logic k v.0 v.1))))\n         ;(idb-relation-done r.1))\n    ;(map (lambda (t.0)\n           ;(join-tables t.0\n                        ;(idb-relation-current r.1)\n                        ;(lambda (k v.0 v.1)\n                          ;(logic k v.0 v.1))))\n         ;(idb-relation-done r.0))\n    ;(join-tables (idb-relation-current r.0)\n                 ;(idb-relation-current r.1)\n                 ;(lambda (k v.0 v.1)\n                   ;(logic k v.0 v.1)))))\n\n;(define (idb-relation-step r)\n  ;(match-define (idb-relation done current new) r)\n  ;(let* ((done    (let loop ((done done) (current current))\n                    ;(match done\n                      ;('()             (list current))\n                      ;((cons top done) (if (<= (vector-length top)\n                                               ;(* 2 (vector-length current)))\n                                         ;(loop done (table-union current top))\n                                         ;(cons current (cons top done)))))))\n         ;(current (foldl (lambda (t.done next)\n                           ;(filter-not (lambda (tuple) (table-member? t.done)) next))\n                         ;(vector->list (match new\n                                         ;('()             (table '()))\n                                         ;((cons next new) (foldl table-union next new))))\n                         ;done)))\n    ;(idb-relation done current '())))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/dsv.rkt",
    "content": "#lang racket/base\n(provide tsv->stream dsv->stream csv->stream\n         path->format format->header/port->stream)\n(require \"../../neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-utils.rkt\"\n         racket/function racket/list racket/string)\n\n;; Informal grammar for tab-separated values (no escapes supported)\n;FIELD-SEPARATOR  ::= \\t\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= CONTENT*\n;CONTENT includes anything other than \\t, \\n, \\r\n\n(define (tsv->stream header? in)\n  (valid-header?! in header? \"\\t\")\n  (let loop () (thunk (define l (read-line in 'any))\n                      (if (eof-object? l) '()\n                        (cons (efficient-no-trim-tab-string-split l) (loop))))))\n\n;; Informal grammar for delimiter-separated values (escapes via double quote)\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= \\\" inner-content* \\\" | CONTENT*\n;inner-content    ::= CONTENT | \\\"\\\" | FIELD-SEPARATOR | WHITESPACE\n;CONTENT includes anything other than double-quote, field separator, whitespace\n\n(define (csv->stream header? in) (dsv->stream #\\, header? in))\n\n(define (dsv->stream field-separator header? in)\n  (define (field)\n    (define ch (peek-char in))\n    (cond ((eqv? ch field-separator) (read-char in) \"\")\n          ((or (eqv? ch #\\newline) (eqv? ch #\\return) (eof-object? ch)) \"\")\n          ((eqv? ch #\\\")\n           (read-char in)\n           (let loop ((i 0))\n             (define ch (peek-char in i))\n             (cond ((eqv? ch #\\\")\n                    (if (eqv? (peek-char in (+ i 1)) #\\\") (loop (+ i 2))\n                      (let ((qs (bytes->string/utf-8 (read-bytes i in))))\n                        (read-char in)\n                        (when (eqv? (peek-char in) field-separator)\n                          (read-char in))\n                        (string-replace qs \"\\\"\\\"\" \"\\\"\"))))\n                   (else (loop (+ i 1))))))\n          (else (let loop ((i 1))\n                  (define ch (peek-char in i))\n                  (cond ((eqv? ch field-separator)\n                         (define s (bytes->string/utf-8 (read-bytes i in)))\n                         (read-char in) s)\n                        ((or (eqv? ch #\\newline) (eqv? ch #\\return) (eof-object? ch))\n                         (bytes->string/utf-8 (read-bytes i in)))\n                        (else (loop (+ i 1))))))))\n  (define (record)\n    (cons (field)\n          (let ((ch (peek-char in)))\n            (cond ((eqv? ch #\\return) (read-char in)\n                                      (when (eqv? (peek-char in) #\\newline)\n                                        (read-char in))\n                                      '())\n                  ((eqv? ch #\\newline) (read-char in) '())\n                  ((eof-object? ch)                   '())\n                  (else                               (record))))))\n  (valid-header?! in header? (make-string 1 field-separator))\n  (let loop () (thunk (if (eof-object? (peek-char in)) '()\n                        (cons (record) (loop))))))\n\n(define (valid-header?! in header delimiter)\n  (define found    (and header (read-line in 'any)))\n  (define expected (and header (cond ((eq? header #t)  found)\n                                     ((string? header) header)\n                                     (else (string-join header delimiter)))))\n  (unless (equal? found expected)\n    (error \"invalid header:\" 'found: found 'expected: expected)))\n\n(define (path->format path)\n  (define fname (if (path? path) (path->string path) path))\n  (case (last (string-split fname \".\" #:trim? #f))\n    ((\"tsv\") 'tsv)\n    ((\"csv\") 'csv)\n    (else    #f)))\n\n(define (format->header/port->stream format)\n  (case format\n    ((tsv) tsv->stream)\n    ((csv) csv->stream)\n    (else  (error \"invalid format:\" format))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/enumerator.rkt",
    "content": "#lang racket/base\n(provide enumerator-append\n         list->enumerator enumerator->rlist enumerator->list\n         s->enumerator enumerator->s\n         vector->enumerator unsafe-vector->enumerator enumerator->rvector enumerator->vector\n         generator->enumerator\n         enumerator/2->enumerator\n         enumerator->enumerator/2\n         hash->enumerator/2)\n(require racket/control racket/unsafe/ops)\n\n(define ((enumerator-append e.0 e.1) yield)\n  (e.0 yield)\n  (e.1 yield))\n\n(define ((list->enumerator xs) yield) (for-each yield xs))\n\n(define (enumerator->rlist en)\n  (define xs '())\n  (en (lambda (x) (set! xs (cons x xs))))\n  xs)\n\n(define (enumerator->list en)\n  (reverse (enumerator->rlist en)))\n\n(define ((s->enumerator s) yield)\n  (let loop ((s s))\n    (cond ((null? s) (void))\n          ((pair? s) (yield (car s)) (loop (cdr s)))\n          (else      (loop (s))))))\n\n(define ((enumerator->s en))\n  (define tag (make-continuation-prompt-tag))\n  (reset-at tag\n            (en (lambda (x)\n                  (shift-at tag k (cons x (lambda () (k (void)))))))\n            '()))\n\n(define (enumerator->rvector en)\n  (list->vector (enumerator->rlist en)))\n\n(define (enumerator->vector en)\n  (list->vector (enumerator->list en)))\n\n(define (vector->enumerator v (start 0) (end (vector-length v)))\n  (define len (min end (vector-length v)))\n  (unsafe-vector->enumerator v (min start len) len))\n\n(define ((unsafe-vector->enumerator v (start 0) (end (unsafe-vector*-length v))) yield)\n  (let loop ((i start))\n    (when (unsafe-fx< i end)\n      (yield (unsafe-vector*-ref v i))\n      (loop (unsafe-fx+ i 1)))))\n\n(define ((generator->enumerator gen stop?) yield)\n  (let loop ()\n    (define x (gen))\n    (unless (stop? x)\n      (yield x)\n      (loop))))\n\n;; An enumerator/2 expects its iteratee to take two arguments\n(define ((enumerator/2->enumerator en) yield)\n  (en (lambda (a b) (yield (cons a b)))))\n\n(define ((enumerator->enumerator/2 en) yield)\n  (en (lambda (x&y) (yield (car x&y) (cdr x&y)))))\n\n(define ((hash->enumerator/2 kvs) yield) (hash-for-each kvs yield))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/example-concrete-syntax-extended.rkt",
    "content": "#lang racket/base\n;(provide foo bar)\n\n(require \"concrete-syntax-extended.rkt\")\n\n(define-relations\n  (rule  (foo x)      (== x 5) (bar x 1 2))\n  (table (bar id s o) \"somewhere/bar\"))\n\n((relation-method foo) 'apply 888)\nbar\n\n;(define-relation (foo x) (== x 5) (bar x 1 2))\n\n;(define-relation/table (bar id s o) \"somewhere/bar\")\n\n;(with-formula-vocabulary (foo 11))\n\n;(foo 'apply 12)\n\n;(== 1 2)\n;(with-formula-vocabulary (== 1 2))\n;==\n;;)\n"
  },
  {
    "path": "medikanren2/dbk/dbk/heap.rkt",
    "content": "#lang racket/base\n(provide\n  heap-top\n  heap!\n  heap-remove!\n  heap-replace!\n  heap-sink!\n  heap-add!\n  )\n\n(define (heap-top         h)         (vector-ref h 0))\n(define (heap!         format file-stats s-pop-header produce/pop-header\n         port-produce port-consume\n         out:port out:file\n         in:transform in:procedure in:port in:file\n         in:stream in:pop-header\n         jsonl:read jsonl:write json:read json:write\n         tsv:read tsv:write csv:read csv:write csv:escape)\n(require \"codec.rkt\" \"enumerator.rkt\" \"misc.rkt\" \"stream.rkt\"\n         \"../../neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-utils.rkt\"\n         json racket/list racket/match racket/port racket/string)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Utilities\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (path->format path.0)\n  (define path (if (path? path.0) (path->string path.0) path.0))\n  (case (last (string-split path \".\" #:trim? #f))\n    ((\"bscm\")  'bscm)\n    ((\"scm\")   'scm)\n    ((\"tsv\")   'tsv)\n    ((\"csv\")   'csv)\n    ((\"json\")  'json)\n    ((\"jsonl\") 'jsonl)\n    (else      #f)))\n\n(define (file-stats path)\n  (and (file-exists? path)\n       (hash 'size          (file-size path)\n             'time.modified (file-or-directory-modify-seconds path))))\n\n(define (s-pop-header ? expected s.0)\n  (define s (s-force s.0))\n  (unless (pair? s)   (error \"missing header:\" 'expected: expected))\n  (unless (? (car s)) (error \"invalid header:\" 'found: (car s) 'expected: expected))\n  (cdr s))\n\n(define (produce/pop-header produce header)\n  (define ((produce/pop ? h)) (s-pop-header ? h (produce)))\n  (match header\n    (#f produce)\n    (#t (produce/pop (lambda (x) #t)           #t))\n    (h  (produce/pop (lambda (x) (equal? x h)) h))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Producers and consumers\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (in:procedure  proc)           proc)\n(define (in:stream     s)              (lambda () s))\n(define (in:transform  produce f)      (cond (f    (lambda () (f (produce))))\n                                             (else produce)))\n(define (in:pop-header produce header) (produce/pop-header produce header))\n\n(define (in:port in . pargs)\n  (define kwargs (make-immutable-hash (plist->alist pargs)))\n  (define (produce) (port-produce in\n                                  (hash-ref kwargs 'close? #f)\n                                  (hash-ref kwargs 'format)\n                                  (hash-ref kwargs 'type #f)))\n  (in:transform (produce/pop-header produce (hash-ref kwargs 'header #f))\n                (hash-ref kwargs 'transform #f)))\n\n(define (in:file path.0 . pargs)\n  (define path   (if (path? path.0) (path->string path.0) path.0))\n  (define kwargs (make-immutable-hash (plist->alist pargs)))\n  (define format (hash-ref kwargs 'format (path->format path)))\n  (unless format            (error \"unknown format:\"     path))\n  (unless (file-stats path) (error \"missing input file:\" path))\n  (define (produce) (let ((in (open-input-file path)))\n                      (port-produce in (lambda () (close-input-port in))\n                                    format\n                                    (hash-ref kwargs 'type #f))))\n  (in:transform (produce/pop-header produce (hash-ref kwargs 'header #f))\n                (hash-ref kwargs 'transform #f)))\n\n(define (out:port out . pargs) (port-consume out\n                                             (plist-ref pargs 'format)\n                                             (plist-ref pargs 'type #f)))\n\n(define (out:file path.0 . pargs)\n  (define path   (if (path? path.0) (path->string path.0) path.0))\n  (define kwargs (make-immutable-hash (plist->alist pargs)))\n  (define exists (hash-ref kwargs 'exists 'error))\n  (define format (hash-ref kwargs 'format (path->format path)))\n  (unless format (error \"unknown format:\" path))\n  (let ((pargs (alist->plist (hash->list (hash-set kwargs 'format format)))))\n    (call-with-output-file path\n                           (lambda (out) (apply out:port out pargs))\n                           #:exists exists)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Port management\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (port-produce in close? format type)\n  (case format\n    ((json) (define data (vector->list (json:read in)))\n            (when close? (close?))\n            data)\n    (else   (define get\n              (case format\n                ((bscm)  (lambda () (if (eof-object? (peek-byte in)) eof (decode in type))))\n                ((scm)   (lambda () (read in)))\n                ((tsv)   (lambda () (tsv:read in)))\n                ((csv)   (lambda () (csv:read in)))\n                ((jsonl) (lambda () (jsonl:read in)))\n                (else    (error \"unsupported input format:\" format))))\n            (let loop ()\n              (lambda ()\n                (define datum (get))\n                (cond ((eof-object? datum) (when close? (close?))\n                                           '())\n                      (else                (cons datum (loop)))))))))\n\n(define (port-consume out format type)\n  (case format\n    ((json) (lambda (en) (json:write out (enumerator->list en))))\n    (else   (let ((yield (case format\n                           ((scm)   (lambda (x) (write x out) (write-char #\\newline out)))\n                           ((bscm)  (lambda (x) (encode      out type x)))\n                           ((tsv)   (lambda (x) (tsv:write   out      x)))\n                           ((csv)   (lambda (x) (csv:write   out      x)))\n                           ((jsonl) (lambda (x) (jsonl:write out      x)))\n                           (else    (error \"unsupported output format:\" format)))))\n              (lambda (en) (en yield))))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; JSON and JSONL formats\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (jsonl:read in)\n  (define s (read-line in 'any))\n  (if (eof-object? s) s (string->jsexpr s)))\n\n(define (jsonl:write out x)\n  (write-string (jsexpr->string x) out)\n  (write-char #\\newline out))\n\n(define (json:read  in)    (string->jsexpr (port->string in)))\n(define (json:write out x) (write-string (jsexpr->string x) out))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; TSV format\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Informal grammar for tab-separated values (no escapes supported)\n;FIELD-SEPARATOR  ::= \\t\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record [RECORD-SEPARATOR] EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= CONTENT*\n;CONTENT includes anything other than \\t, \\n, \\r\n\n(define (tsv:read in)\n  (define l (read-line in 'any))\n  (if (eof-object? l)\n    l\n    (let ((fields (efficient-no-trim-tab-string-split l)))\n      (if (null? fields)\n        '(\"\")\n        fields))))\n\n(define (tsv:write out x)\n  (write-string (string-join x \"\\t\" #:after-last \"\\n\") out))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; CSV format\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Informal grammar for delimiter-separated values (escapes via double quote)\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record [RECORD-SEPARATOR] EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= \\\" inner-content* \\\" | CONTENT*\n;inner-content    ::= CONTENT | \\\"\\\" | FIELD-SEPARATOR | WHITESPACE\n;CONTENT includes anything other than double-quote, field separator, whitespace\n\n(define (csv:read in)\n  (define (field)\n    (define ch (peek-char in))\n    (cond ((eqv? ch #\\,)           (read-char in)\n                                   \"\")\n          ((or (eqv? ch #\\newline)\n               (eqv? ch #\\return)\n               (eof-object? ch))   \"\")\n\n          ((eqv? ch #\\\")           (read-char in)\n                                   (let loop ((i 0))\n                                     (define ch (peek-char in i))\n                                     (cond ((eqv? ch #\\\") (if (eqv? (peek-char in (+ i 1)) #\\\")\n                                                            (loop (+ i 2))\n                                                            (let ((qs (bytes->string/utf-8 (read-bytes i in))))\n                                                              (read-char in)\n                                                              (when (eqv? (peek-char in) #\\,)\n                                                                (read-char in))\n                                                              (string-replace qs \"\\\"\\\"\" \"\\\"\"))))\n                                           (else          (loop (+ i 1))))))\n\n          (else                    (let loop ((i 1))\n                                     (define ch (peek-char in i))\n                                     (cond ((eqv? ch #\\,)           (define s (bytes->string/utf-8 (read-bytes i in)))\n                                                                    (read-char in)\n                                                                    s)\n                                           ((or (eqv? ch #\\newline)\n                                                (eqv? ch #\\return)\n                                                (eof-object? ch))   (bytes->string/utf-8 (read-bytes i in)))\n                                           (else                    (loop (+ i 1))))))))\n  (if (eof-object? (peek-char in))\n    eof\n    (let record ()\n      (cons (field)\n            (let ((ch (peek-char in)))\n              (cond ((eqv? ch #\\return)  (read-char in)\n                                         (when (eqv? (peek-char in) #\\newline)\n                                           (read-char in))\n                                         '())\n                    ((eqv? ch #\\newline) (read-char in)\n                                         '())\n                    ((eof-object? ch)    '())\n                    (else                (record))))))))\n\n(define (csv:write out x)\n  (write-string (string-join (map csv:escape x) \",\" #:after-last \"\\n\") out))\n\n(define (csv:escape s)\n  (if (ormap (lambda (x) (string-contains? s x)) '(\",\" \"\\\"\" \"\\n\" \"\\r\"))\n    (string-append \"\\\"\" (string-replace s \"\\\"\" \"\\\"\\\"\") \"\\\"\")\n    s))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/misc.rkt",
    "content": "#lang racket/base\n(provide simple-match simple-match-lambda record\n         method-lambda method-choose method-unknown method-except method-only\n         foldl/and let*/and define-variant\n         plist->alist plist-ref alist->plist alist-ref alist-remove alist-update alist-set\n         hash-remove*\n         call/files let/files\n         map/merge map/append\n         min-bits min-bytes min-bytes-power2 int? nat?\n         bytes-nat-ref bytes-nat-set! nat->bytes bytes->nat\n         sum\n         normalize-path)\n(require (for-syntax racket/base) racket/fixnum racket/list racket/match racket/set)\n\n(define-syntax simple-match-lambda\n  (syntax-rules ()\n    ((_ (params body ...) ...) (lambda args\n                                 (simple-match args\n                                   (params body ...) ...)))))\n\n(define-syntax simple-match\n  (syntax-rules ()\n    ((_ e) (error \"no matching pattern:\" e))\n    ((_ e (pattern body ...) clauses ...)\n     (let* ((x e)\n            (k.f (lambda () (simple-match x clauses ...))))\n       (simple-match-clause (let () body ...) (k.f) x pattern)))))\n\n(define-syntax simple-match-clause\n  (syntax-rules ()\n    ((_ k.t k.f x ())          (if (null? x) k.t k.f))\n    ((_ k.t k.f x (p.a . p.d)) (if (pair? x)\n                                 (let ((x.car (car x))\n                                       (x.cdr (cdr x)))\n                                   (simple-match-clause\n                                     (simple-match-clause k.t k.f x.cdr p.d)\n                                     k.f x.car p.a))\n                                 k.f))\n    ((_ k.t k.f x #(p ...))    (if (vector? x)\n                                 (let ((x (vector->list x)))\n                                   (simple-match-clause k.t k.f x (p ...)))\n                                 k.f))\n    ((_ k.t k.f x id)          (let ((id x)) k.t))))\n\n(begin-for-syntax\n  (define (syntax/context context stx)\n    (datum->syntax context (syntax->datum stx)))\n  (define (id/suffix id str)\n    (define str.id (symbol->string (syntax->datum id)))\n    (datum->syntax id (string->symbol (string-append str.id str))))\n  (define (syntax-permute keys stx.alist blame)\n    (define kvs\n      (syntax-case stx.alist ()\n        (((key . value) ...) (map cons\n                                  (syntax->datum #'(key ...))\n                                  (syntax->list #'((key . value) ...))))))\n    (map (lambda (k) (let ((kv (assoc k kvs)))\n                       (if kv (cdr kv)\n                         (error \"missing record field:\" k blame))))\n         keys))\n  (define-syntax with-syntax*\n    (syntax-rules ()\n      ((_ ()                  body ...) (with-syntax () body ...))\n      ((_ ((p0 e0) (p e) ...) body ...) (with-syntax ((p0 e0))\n                                          (with-syntax* ((p e) ...)\n                                            body ...))))))\n\n;; (record name (field ...) extra ...)\n;; produces these definitions:\n;; * struct:         (struct name:struct (field ...) extra ...)\n;; * predicate:      name?\n;; * constructor:    (name (field expr) ...)\n;; * setter:         (name:set expr (field expr) ...)\n;; * match-expander: (name:match (field pattern) ...)\n(define-syntax (record stx)\n  (syntax-case stx ()\n    ((_ name (field-name ...) extras ...)\n     (let* ((field-names     (syntax->datum #'(field-name ...)))\n            (field-name-strs (map symbol->string field-names)))\n       (with-syntax* ((id.struct  (id/suffix #'name \":struct\"))\n                      (id.ref     (id/suffix #'name \":ref\"))\n                      (id.set     (id/suffix #'name \":set\"))\n                      (id.?       (id/suffix #'name \"?\"))\n                      (id.struct? (id/suffix #'name \":struct?\"))\n                      (id.match   (id/suffix #'name \":match\"))\n                      (ids.field-names #'(field-name ...))\n                      ((id.accessor ...)\n                       (map (lambda (f) (id/suffix #'name\n                                                   (string-append \"-\" f)))\n                            field-name-strs))\n                      ((id.struct-accessor ...)\n                       (map (lambda (f) (id/suffix #'id.struct\n                                                   (string-append \"-\" f)))\n                            field-name-strs)))\n         #`(begin\n             (struct id.struct (field-name ...) extras ...)\n             (define id.?        id.struct?)\n             (define id.accessor id.struct-accessor) ...\n             (...\n               (begin\n                 (define-syntax (name stx)\n                   (syntax-case stx ()\n                     ((_ (f e) ...)\n                      (with-syntax ((((f e) ...) (syntax-permute\n                                                   'ids.field-names\n                                                   #'((f e) ...)\n                                                   stx)))\n                        #'(let ((f e) ...) (id.struct f ...))))))\n                 (define-syntax (id.set stx)\n                   (syntax-case stx ()\n                     ((_ r (f e) ...)\n                      (let ((field-names '#,field-names))\n                        #`(let ()\n                            (match-define (id.struct #,@field-names) r)\n                            (let #,(map list\n                                        (syntax->datum #'(f ...))\n                                        (syntax->list  #'(e ...)))\n                              (id.struct #,@field-names)))))))\n                 (define-match-expander id.match\n                   (lambda (stx)\n                     (syntax-case stx ()\n                       ((_ (f p) ...)\n                        #'(struct* id.struct ((f p) ...))))))))))))))\n\n(define (method-unknown name . args) (error \"unknown method:\" name args))\n(define (method-except m names)\n  (lambda (name . args)\n    (apply (if (member name names) method-unknown m) name args)))\n(define (method-only m names)\n  (lambda (name . args)\n    (apply (if (member name names) m method-unknown) name args)))\n\n(define-syntax method-choose\n  (syntax-rules (else)\n    ((_ ((name ...) body ...) ... (else else-body ...))\n     (lambda (method-name . args)\n       (apply (case method-name\n                ((name ...) body ...) ...\n                (else       else-body ...))\n              method-name args)))\n    ((_ body ...) (method-choose body ... (else method-unknown)))))\n\n(define-syntax method-lambda\n  (syntax-rules (else)\n    ((_ ((name . param) body ...) ... (else else-body ...))\n     (method-choose ((name) (lambda (_ . param) body ...)) ... (else else-body ...)))\n    ((_ body ...) (method-lambda body ... (else method-unknown)))))\n\n(define (foldl/and f acc xs . yss)\n  (let loop ((acc acc) (xs xs) (yss yss))\n    (if (null? xs)\n      acc\n      (and acc (loop (apply f (car xs) (append (map car yss) (list acc)))\n                     (cdr xs)\n                     (map cdr yss))))))\n\n(define-syntax let*/and\n  (syntax-rules ()\n    ((_ () body ...)                   (let () body ...))\n    ((_ ((lhs rhs) rest ...) body ...) (let ((lhs rhs))\n                                         (and lhs (let*/and (rest ...)\n                                                    body ...))))))\n\n(define-syntax define-variant\n  (syntax-rules ()\n    ((_ type? (struct-name fields ...) ...)\n     (begin (define (type? x)\n              (match x\n                ((struct-name fields ...) #t) ...\n                (_                        #f)))\n            (struct struct-name (fields ...) #:prefab) ...))))\n\n(define (plist->alist plist)\n  (match plist\n    ('()                     '())\n    ((cons k (cons v plist)) (cons (cons k v) (plist->alist plist)))))\n\n(define (plist-ref plist key (default (void)))\n  (let loop ((kvs plist))\n    (match kvs\n      ('()                   (if (void? default)\n                               (error \"missing key in property list:\" key plist)\n                               default))\n      ((cons k (cons v kvs)) (if (equal? k key)\n                               v\n                               (loop kvs))))))\n\n(define (alist->plist alist)\n  (match alist\n    ('()                     '())\n    ((cons (cons k v) alist) (cons k (cons v (alist->plist alist))))))\n\n(define (alist-ref alist key (default (void)))\n  (define kv (assoc key alist))\n  (cond (kv              (cdr kv))\n        ((void? default) (error \"missing key in association list:\" key alist))\n        (else            default)))\n\n(define (alist-remove alist key)\n  (filter (lambda (kv) (not (equal? (car kv) key))) alist))\n\n(define (alist-update alist key v->v (default (void)))\n  (let loop ((kvs alist) (prev '()))\n    (cond ((null?        kvs     )\n           (when (void? default) (error \"missing key in association list:\" key alist))\n           (cons (cons key (v->v default)) alist))\n          ((equal? (caar kvs) key) (foldl cons (cons (cons key (v->v (cdar kvs))) (cdr kvs)) prev))\n          (else                    (loop (cdr kvs) (cons (car kvs) prev))))))\n\n(define (alist-set alist key value)\n  (alist-update alist key (lambda (_) value) #f))\n\n(define (hash-remove* h keys)\n  (foldl (lambda (k h) (hash-remove h k)) h keys))\n\n(define (call/files fins fouts p)\n  (let loop ((fins fins) (ins '()))\n    (if (null? fins)\n      (let loop ((fouts fouts) (outs '()))\n        (if (null? fouts)\n          (apply p (append (reverse ins) (reverse outs)))\n          (call-with-output-file\n            (car fouts) (lambda (out) (loop (cdr fouts) (cons out outs))))))\n      (call-with-input-file\n        (car fins) (lambda (in) (loop (cdr fins) (cons in ins)))))))\n\n(define-syntax-rule (let/files ((in fin) ...) ((out fout) ...) body ...)\n  (call/files (list fin ...) (list fout ...)\n              (lambda (in ... out ...) body ...)))\n\n(define (map/merge f merge default xs)\n  (define ys (reverse (cond ((list?   xs) (map f               xs))\n                            ((vector? xs) (map f (vector->list xs)))\n                            ((set?    xs) (set-map  xs f))\n                            ((hash?   xs) (hash-map xs (lambda (k v) (f (cons k v)))))\n                            (else         (error \"invalid map/merge collection:\" xs)))))\n  (if (null? ys)\n    default\n    (foldl merge (car ys) (cdr ys))))\n\n(define (map/append f xs) (append* (map f xs)))\n\n(define (min-bits n)\n  (if (< 0 n)\n    (+ 1 (min-bits (fxrshift n 1)))\n    0))\n\n(define (min-bytes n)\n  (let ((min-bits (min-bits n)))\n    (+ (quotient min-bits 8)\n       (if (= 0 (remainder min-bits 8)) 0 1))))\n\n(define (min-bytes-power2 n)\n  (define c (min-bytes n))\n  (cond ((<= c 1) 1)\n        ((<= c 2) 2)\n        ((<= c 4) 4)\n        (else     8)))\n\n(define (int? x) (and (number? x) (exact? x) (integer? x)))\n(define (nat? x) (and (int? x) (<= 0 x)))\n\n(define (bytes-nat-set! bs size offset n)\n  ;(integer->integer-bytes n size #f #t bs offset) (void)\n  (let ((end (+ offset size)))\n    (let loop ((i offset) (shift (* 8 (- size 1))))\n      (cond ((< i end) (bytes-set! bs i (bitwise-and 255 (fxrshift n shift)))\n                       (loop (+ i 1) (- shift 8)))\n            (else      bs)))))\n\n(define (bytes-nat-ref bs size offset)\n  ;(integer-bytes->integer bs #f #t offset (+ offset size))\n  (let ((end (+ offset size)))\n    (let loop ((i offset) (n 0))\n      (cond ((< i end) (loop (+ i 1) (+ (fxlshift n 8)\n                                        (bytes-ref bs i))))\n            (else      n)))))\n\n(define (nat->bytes size n)  (let ((bs (make-bytes size 0)))\n                               (bytes-nat-set! bs size 0 n)\n                               bs))\n\n(define (bytes->nat bs size) (bytes-nat-ref bs size 0))\n\n(define (sum xs) (foldl + 0 xs))\n\n(define (normalize-path path) (path->string (simplify-path (resolve-path (simplify-path path)))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/mk.rkt",
    "content": "#lang racket/base\n(provide (all-from-out \"common.rkt\") (all-from-out \"syntax.rkt\")\n         (all-from-out \"constraint.rkt\")\n         query->stream\n         run^ run run* run/steps run*/steps\n         run/set run*/set run/set/steps run*/set/steps)\n(require \"common.rkt\" \"config.rkt\" \"constraint.rkt\" \"stream.rkt\" \"syntax.rkt\"\n         (except-in racket/match ==))\n\n(define (query->stream q)\n  ((match (or (current-config-ref 'search-strategy) 'biased-interleaving)\n     ('biased-interleaving bis:query->stream)\n     ('depth-first         dfs:query->stream)\n     (strategy (error \"invalid search strategy:\" strategy)))\n   q))\n\n(define-syntax run^\n  (syntax-rules () ((_   body ...) (query->stream (query  body ...)))))\n(define-syntax run\n  (syntax-rules () ((_ n body ...) (s-take n      (run^   body ...)))))\n(define-syntax run*\n  (syntax-rules () ((_   body ...)                (run #f body ...))))\n(define-syntax run/steps\n  (syntax-rules () ((_ steps n body ...) (s-take/steps steps n (run^               body ...)))))\n(define-syntax run*/steps\n  (syntax-rules () ((_ steps   body ...)                       (run/steps steps #f body ...))))\n\n(define-syntax run/set\n  (syntax-rules () ((_ n body ...) (s-take/set n (run^       body ...)))))\n(define-syntax run*/set\n  (syntax-rules () ((_   body ...)               (run/set #f body ...))))\n(define-syntax run/set/steps\n  (syntax-rules () ((_ steps n body ...) (s-take/set/steps steps n (run^                   body ...)))))\n(define-syntax run*/set/steps\n  (syntax-rules () ((_ steps   body ...)                           (run/set/steps steps #f body ...))))\n\n;; TODO: special case aggregation operators that could be implemented more\n;; efficiently than post-processing `run*` results:\n;; * run/min, run/max, run/count\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/abstract-syntax.rkt",
    "content": "#lang racket/base\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; TODO\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; input and output devices are specified and created using host language\n;; - may describe data coming from arbitrary input sources:\n;;   - filesystem, network, channels, events, etc.\n;;   - all sources are assumed to be unstable across time, reflecting a dynamic system\n;;   - include metadata that will be retained in process history\n;; - modules embed input and output device specifications in appropriate temporal relation declarations\n;;   - input relations may only appear on the RHS of rules\n;;   - output relations may only appear on the LHS of indeterminate inference rules\n;;     - i.e., `<<~` (asynchronous send)\n\n;; modules\n;; - optional precomputation with indexing choices and retrieval preferences\n;; - definitions for relations\n;;   - rules for immediate inference: `define-relation` and/or `extend-relation`\n;;     - deliver new facts during current time step, until fixed point is reached\n;;     - synonym for `extend-relation`, deliver during current timestep: <<=\n;;   - rules for next-step inference\n;;     - delete at next timestep: <<-\n;;     - insert at next timestep: <<+\n;;   - rules for indeterminate inference\n;;     - deliver at arbitrary (future?) timetep: <<~\n;;     - these will write to output devices for the host system to process\n;; - assertions: queries used for property/consistency checking or other validation\n;;   - can inform data representation choices and query optimization\n;;   - can use to infer:\n;;     - uniqueness/degrees/cardinalities\n;;     - value information (types, value ranges, frequencies)\n;;     - join dependencies\n;; - module linking\n;;   - by default, a module will export all definitions\n;;   - apply visibility modifiers (such as except, only, rename, prefix) to change a module's exports\n;;     - renamings apply to a process too, so that its database relations can be targeted by new rules\n;;     - support dependency shaking\n;;       - given a root set of terms/relations, throw away everything else\n;;   - combine compatible modules to produce a new module\n;;     - same module may be linked more than once, to produce different variations (mixin-style)\n;;       - for instance, this may be used to switch io devices\n\n;; process state (like a version control system commit):\n;; - reference to the dbms that manages this process state's database\n;; - database\n;;   - schemas\n;;   - current content of all persistent temporal relations\n;;     - i.e., (indexed) tables keyed by name\n;;   - pending work (incomplete indexes)\n;; - io device temporal relation bindings and buffers\n;; - current program, describing how the process evolves each time step\n;;   - mapping of public names to internal names\n;;   - mapping of internal names to devices\n;;   - mapping of internal names to tables\n;;   - hierarchically-named subprograms w/ enabled/disabled status\n;;   - in order to run, program must not have unresolved dependencies\n;;     - terms without definitions are unresolved\n;; - residual environment (when used as a library)\n;;   - module specs inheriting from this process will be parsed using this environment\n;; - history of database transitions\n;;   - program changes\n;;   - ingestion metadata per time step\n;; - how do we check source data consistency?\n;;   - processes allow data to change, so inconsistency with original sources may be intentional\n;;   - to check consistency as in the old approach, analyze the process history for data provenance\n;;     - particularly data io device bindings and their dependencies across time steps\n;;       - input device metadata should include real world time stamps, filesystem information, transformation code, possibly content hash\n;; - main operations:\n;;   - run a query over the current database\n;;   - change current program\n;;     - enable/disable subprograms\n;;     - rename/hide public names\n;;     - hierarchy rearrangement and linking\n;;     - nontemporal relations declared to be precomputed will be precomputed before returning\n;;     - will add a program diff to the history\n;;   - step, with a step/fuel count (`#f` to run continously)\n;;     - will return unused fuel if (temporary) quiessence is detected, otherwise `#f`\n;;     - if any work was performed, this will log a new database uid in the process history\n;;     - if input was produced by devices configured for snapshot, snapshots will be included in the history\n;;       - for replay reproducibility\n;;   - synchronizable event indicating more work can be performed\n;;     - e.g., if not even temporary quiessence has been achieved yet\n;;     - e.g., if temporary quiessence had been achieved, but new input has arrived\n;;     - `#f` if permanent quiessence has been reached\n;;       - only possible if no input devices are bound\n;;       - permanence w.r.t. the current program\n;;   - save/flush (to dbms filesystem, for later reloading)\n;;     - transitions should be continuously checkpointed and saved, so this may not be necessary\n;;       - if background saving ends up being asynchronous, this operation will wait until the flush catches up\n;;     - io devices cannot be directly restored from disk\n;;       - their metadata can still be saved, however\n;;       - when restoring such a process, io device rebindings must be provided\n\n;; process (like a version control system branch):\n;; - process state\n;; - db name for stable reference in later program runs\n;; - performing operations will update the current process\n;;   - produce new process state and reassign stable name to the new state\n;; - may spawn new process sharing the current process state\n;;   - can explore diverging transitions\n;;   - can save earlier state to later revisit\n;;   - explicit garbage collection and compaction can be used to retain only data that is directly-referenced by active processes\n;;     - can optionally preserve external data ingestion snapshots to support reproducing intermediate databases\n;; - may be packaged for export to another dbms\n;;   - dbms garbage collection and process export are similar activities\n\n;; dbms (database management system):\n;; - collection of named process databases\n;; - cached relation content keyed by history dependencies, to support sharing between similar processes\n;;   - includes content of temporal relations as well as nontemporal relations declared to be cached/precomputed\n;;   - cache may include term values that were expensive to compute\n;;   - processes evolving from a common ancestor will share content unless rule extensions lead to logical divergence\n;;     - extending a precomputed relation will require precomputing a new version to be consistent\n;;       - not an error, but maybe provide a warning\n;;       - progammer decides whether multiple precomputed versions of similar rules is worth the time/space trade off\n;;         - programmer organizes modules according to this decision\n\n;; modular stratification given a partial order on relation parameters\n;; - would be convenient to define a universal <= that respected point-wise monotonicity (any<= does not)\n;; - reachability example using equivalence classes reduces materialized space usage from O(n^2) to O(n):\n;;     (define-relation/source (node n)\n;;       ;; specify graph vertex data here\n;;       )\n;;     (define-relation/source (arc a b)\n;;       ;; specify graph connection data here\n;;       )\n;;\n;;     ;; original definition of reachable before optimization\n;;     ;; materialization could take O(n^2) space\n;;     (define-relation (reachable a b)\n;;       (conde\n;;         ((node a) (== a b))\n;;         ((fresh (mid)\n;;            (reachable a mid)\n;;            (conde ((arc mid b))\n;;                   ((arc b mid)))))))\n;;\n;;     ;; new definition of reachable after optimization\n;;     (define-relation (reachable a b)\n;;       (fresh (repr)\n;;         (reachable-class repr a)\n;;         (reachable-class repr b)))\n;;\n;;     ;; materialization will take O(n) space\n;;     (define-relation (reachable-class representative x)\n;;       (string<= representative x)  ;; not required, but does this improve performance?\n;;       ;; This negated condition ensures we represent each reachability class only once, to save space.\n;;       ;; self-recursion within negation is possible due to modular stratification by string<\n;;       ;; i.e., (reachable-class r x) only depends on knowing (reachable-class p _) for all (string< p r), giving us a safe evaluation order\n;;       (not (fresh (predecessor)\n;;              (string< predecessor representative)\n;;              (reachable-class predecessor representative)))\n;;       (conde\n;;         ((node representative) (== representative x))\n;;         ((fresh (mid)\n;;            (reachable-class representative mid)\n;;            (conde ((arc mid x))\n;;                   ((arc x mid)))))))\n\n;; ACILG hierarchy for analysis and optimization\n;; - associative, commutative, idempotent, has-least-element, has-greatest-element\n;; - comprehensions: map followed by combining mapped results\n;; - an operator having all the properties in a prefix of this list may support more optimization\n;; - associative: parallelism, but may need coordination for ordering\n;; - commutative: parallelism, no ordering coordination needed\n;; - idempotent:  fixed point computation without needing stratification; may need an initial value\n;; - has-least-element: natural choice of initial value already known\n;; - has-greatest-element: some computation may be stopped early, before all data is seen, if threshold is reached\n\n;; order-by for converting sets/dicts to sequences\n\n;; compact formulas as state component?\n;; - state is a strategy-agnostic compact formula, plus a strategy-specific component (including a work scheduler)\n;; - multi-pass strategy compilation: describe this state representation in the AST for the next pass's language\n\n;; In some untyped systems, term evaluation may produce side-conditions (formulas)\n;; - e.g., (car x) may introduce the formula (pair? x)\n\n;; complex terms should be replaced with fresh variables to avoid redundant computations\n\n;; more specific variable domain constraints:\n;; - constant\n;; - non-constant data construction (cons, vector, ...)\n;;   - shape may not be fully known (vector with unspecified length)\n;; - finite domain\n;;   - could be represented as a join of constants; probably better to use a small table\n;;   - could also include a representation for semi-joined table constraints\n;; - interval domain\n;;   - possibly with gaps/subtractions (negative finite domains)\n;; - join of domain constraints\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/example/base.rkt",
    "content": "#lang racket/base\n(provide m.base)\n\n(define-dbk m.base\n  (<<= (==    u u))\n  (<<= (=/=   u v) (not (== u u)))\n  (<<= (any<= u v) (== #t (any<= u v)))\n  (<<= (any<  u v) (=/= u v) (any<= u v))\n  (<<= (any>= u v) (any<= v u))\n  (<<= (any>  u v) (any<  v u))\n\n  (relation (member x ys)\n    modes ((ys)))  ;; this mode could be inferred\n  (<<= (member x (cons x ys)))\n  (<<= (member x (cons y ys))\n    (=/= x y) (member x ys))\n  ;; member can also be defined with a single rule:\n  ;(<<= (member x ys)\n  ;  (exist (a d)\n  ;    (== ys `(,a . ,d))\n  ;    (or (== x a)\n  ;        (and (=/= x a) (member x d)))))\n\n  (relation (append xs ys xsys)\n    modes ((xs) (xsys)))  ;; these modes could be inferred\n  (<<= (append '() ys ys))\n  (<<= (append `(,x . ,xs) ys `(,x . ,xsys))\n    (append xs ys xsys))\n\n  ;; Can this theorem be proven?\n  ;(assert (all (xs ys)\n  ;          (iff (append xs ys ys)\n  ;               (== xs '()))))\n  )\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/example/counters.rkt",
    "content": "#lang racket/base\n(provide dbk.counters)\n(require \"base.rkt\"\n\n(define-dbk dbk.counters\n  (module 'foo\n    (<<+ (foo (+ n 1)) (foo n)))\n  (module 'bar\n    (<<+ (bar (+ n 1)) (bar n)))\n  (module 'initialize\n    (<<+ (foo 0))\n    (<<+ (bar 0)))\n  (module 'clean\n    (<<- (foo n) (bar n))\n    (<<- (bar n) (foo n))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/example/path.rkt",
    "content": "#lang racket/base\n(provide m.path m.edge.acyclic m.edge.cycles)\n(require \"base.rkt\")\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Define program modules\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-dbk m.path\n  (relation (edge source target)\n    indexes ((target source)))\n\n  (<<= (path s t) (edge s t))\n  (<<= (path s t) (exist (mid)\n                    (edge s mid) (path mid t))))\n\n(define-dbk m.edge.acyclic\n  (link m.base)\n  (<<+ (edge s t) (member (list s t)\n                          '((1 2)\n                            (2 4)\n                            (1 3)\n                            (3 5)\n                            (2 6)\n                            (3 6)\n                            (6 4)))))\n\n(define-dbk m.edge.cycles\n  (link m.base)\n  (<<+ (edge s t) (member (list s t)\n                          '((1 1)\n                            (5 1)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Run example\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define p (process m.path))\n\n;; edge relation is empty\n(p 'eval '(query (s t) (path s t)))\n;; ==>\n;; ()\n\n;; insert acyclic edge data\n(p 'program-set! (link m.path m.edge.acyclic))\n(p 'tick!)\n(p 'program-set! m.path)\n\n(p 'eval '(query (s t) (path s t)))\n;; ==>\n;; ? TODO\n\n;; insert extra edges that form cycles\n(p 'program-set! (link m.path m.edge.cycles))\n(p 'tick!)\n(p 'program-set! m.path)\n\n(p 'eval '(query (s t) (path s t)))\n;; ==>\n;; ? TODO\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/example/quorum.rkt",
    "content": "#lang racket/base\n(provide m.quorum-vote)\n(require \"base.rkt\")\n\n;; Based on figures 2 and 3 in: Logic and Lattices for Distributed Programming\n;; https://dsf.berkeley.edu/papers/socc12-blooml.pdf\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Define program modules\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-dbk m.quorum-vote\n  (<<+ (vote id) (vote.in id))\n\n  ;; Demonstrate intermediate term definitions\n  (define vote-count (set-count (query id (vote id))))\n  (define quorum?    (<= quorum-size count))\n  (<<~ (result.out 'success) (== #t quorum?))\n\n  ;; This is what it looks like without intermediate definitions\n  ;(<<~ (result.out 'success)\n  ;  (== #t (<= quorum-size (set-count (query id (vote id))))))\n\n  ;; And this is an alternative where <= is used as a relation instead\n  ;(<<~ (result.out 'success)\n  ;  (<= quorum-size (set-count (query id (vote id)))))\n  )\n\n(define pipe.result (dbk:pipe))\n\n(define program\n  (link m.quorum-vote\n        ;; Factored out so that m.quorum-vote is reusable\n        (dbk\n          (parameter quorum-size 3)\n          (input     (vote.in    id) _)  ; TODO: fill _ with an actual input device\n          (output    (result.out x)  (out:pipe pipe.result)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Run example\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define p (process program))\n\n;; Loop until enough votes arrive (assumes vote.in input device is populated concurrently)\n(let loop ()\n  (unless (s-member '(success) (pipe-get pipe.result))\n    (p 'tick!)\n    (loop)))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/example/shortest-path.rkt",
    "content": "#lang racket/base\n(provide m.shortest-path)\n(require \"base.rkt\")\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Define program modules\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-dbk m.shortest-path\n  (link m.base)\n\n  (relation (edge source target distance)\n    indexes ((target source)))\n\n  ;; Guard against cyclic data\n  (<<= (reachable s t) (edge s t _))\n  (<<= (reachable s t) (exist (mid)\n                         (edge s mid _) (reachable mid t)))\n  (assert (not (exist (x) (reachable x x))))\n\n  ;; This relation will be infinitely large if edge describes a cyclic graph.\n  ;; To support cyclic data, we can rewrite this to stratify across time steps,\n  ;; stopping when there are no more improvements made during a single tick.\n  ;; TODO: It might be possible to avoid stratifying over time by expressing\n  ;; shortest-path directly using lattice operations for computing distance,\n  ;; allowing recursion within aggregation due to monotonicity.\n  (<<= (path s t d) (edge s t d))\n  (<<= (path s t (+ d.e d.p))\n    (exist (mid)\n      (edge s mid d.e)\n      (path mid t d.p)))\n\n  (<<= (shortest-path s t distance)\n    (=/= distance #f)\n    (== distance (merge min #f (query distance (path s t distance)))))\n\n  (<<= (edge s t distance)\n    (member (list s t distance)\n            '((a b 2)\n              (b c 5)\n              (b c 1)\n              (c d 3)\n              (c e 5)\n              (d e 1)\n              (e f 2)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Run examples\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define p (process m.shortest-path))\n\n(p 'eval '(query (s t c) (path s t c)))\n;; ==>\n;; ? TODO\n\n(p 'eval '(query (s t c) (shortest-path s t c)))\n;; ==>\n;; ? TODO\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/parse.rkt",
    "content": "#lang racket/base\n(provide\n  env.empty env:new env-ref env-ref* env-set env-set* env-remove env-remove* env-bind env-bind* env-union env-rename\n  m:named m:link m:term m:relation m:assert\n  f:const f:relate f:implies f:iff f:or f:and f:not f:exist f:all\n  f:any<= f:== f:=/=\n  t:query t:map/merge t:quote t:var t:prim t:app t:lambda t:if t:let t:letrec\n  t:apply t:cons t:car t:cdr t:vector t:list->vector t:vector-ref t:vector-length\n  t-free-vars f-free-vars t-free-vars* t-free-vars-first-order t-free-vars-first-order*\n  t-substitute f-substitute t-substitute* t-substitute-first-order t-substitute-first-order*\n  f-relations t-relations t-relations*\n  module-flatten module-ref module-add module-remove module-remove* module-wrap module-unwrap\n  program.empty program:new program:set program-module program-env program-flatten program-remove*\n  define-dbk dbk dbk-parse dbk-syntax link parameter input output\n  dbk-environment dbk-environment-update with-dbk-environment-update with-fresh-names\n  literal? literal simple-parser\n  parse:program parse:module parse:formula parse:term)\n(require \"misc.rkt\" racket/hash racket/list racket/match racket/set racket/struct)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Environments with vocabularies\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define env.empty (hash))\n\n(define (env-ref     env vocab n)     (hash-ref (hash-ref env n (hash)) vocab #f))\n(define (env-ref*    env vocab ns)    (map (lambda (n) (env-ref env vocab n)) ns))\n(define (env-set     env vocab n  v)  (let* ((vocab=>v (hash-ref env n (hash)))\n                                             (vocab=>v (if v\n                                                         (hash-set    vocab=>v vocab v)\n                                                         (hash-remove vocab=>v vocab))))\n                                        (if (hash-empty? vocab=>v)\n                                          (hash-remove env n)\n                                          (hash-set env n vocab=>v))))\n(define (env-set*    env vocab ns vs) (foldl (lambda (n v env) (env-set env vocab n v)) env ns vs))\n\n(define (env-remove  env       n)     (hash-remove env n))\n(define (env-remove* env       ns)    (foldl (lambda (n e) (env-remove env n)) env ns))\n\n(define (env-bind    env vocab n  v)  (env-set  (env-remove  env n)  vocab n  v))\n(define (env-bind*   env vocab ns vs) (env-set* (env-remove* env ns) vocab ns vs))\n\n(define (env-union   env . envs)      (foldl (lambda (e e.0)\n                                               (hash-union e.0 e #:combine\n                                                           (lambda (vocab=>v.0 vocab=>v)\n                                                             (hash-union vocab=>v.0 vocab=>v #:combine\n                                                                         (lambda (v.0 v) (if v v v.0))))))\n                                             env envs))\n\n(define (env-rename env n=>n)\n  (define (v-rename vocab v)    (cons vocab               (if (procedure? v)\n                                                            v\n                                                            (hash-ref n=>n v v))))\n  (define (n-rename n vocab=>v) (cons (hash-ref n=>n n n) (make-immutable-hash\n                                                            (hash-map vocab=>v v-rename))))\n  (make-immutable-hash (hash-map env n-rename)))\n\n(define (env:new vocab . args)\n  (define nvs (plist->alist args))\n  (env-set* env.empty vocab\n            (map car nvs)\n            (map cdr nvs)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Abstract syntax\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-variant formula?\n  (f:const   value)  ; can be thought of as a relation taking no arguments\n  (f:relate  relation args)\n  (f:implies if then)\n  (f:iff     f1 f2)\n  (f:or      f1 f2)\n  (f:and     f1 f2)\n  (f:not     f)\n  (f:exist   params body)\n  (f:all     params body))\n\n(define (f:any<= u v) (f:relate '(prim any<=) (list u v)))\n(define (f:any<  u v) (f:relate '(prim any<)  (list u v)))\n(define (f:==    u v) (f:relate '(prim ==)    (list u v)))\n(define (f:=/=   u v) (f:relate '(prim =/=)   (list u v)))\n\n;; lambda calculus extended with constants (quote), logical queries, map/merge comprehensions\n(define-variant term?\n  (t:query     name formula)\n  (t:map/merge proc.map proc.merge default xs)\n  (t:quote     value)\n  (t:var       name)\n  (t:prim      name)\n  (t:app       proc args)\n  (t:lambda    params body)\n  (t:if        c t f)\n  (t:let       bpairs body)\n  (t:letrec    bpairs body))\n\n(define (t:apply f . args)  (t:app (t:prim 'apply)         args))\n(define (t:cons a d)        (t:app (t:prim 'cons)          (list a d)))\n(define (t:car p)           (t:app (t:prim 'car)           (list p)))\n(define (t:cdr p)           (t:app (t:prim 'cdr)           (list p)))\n(define (t:vector . args)   (t:app (t:prim 'vector)        args))\n(define (t:list->vector xs) (t:app (t:prim 'list->vector)  (list xs)))\n(define (t:vector-ref v i)  (t:app (t:prim 'vector-ref)    (list v i)))\n(define (t:vector-length v) (t:app (t:prim 'vector-length) (list v)))\n\n;; TODO: use CPS yielding to efficiently support partial-answer variations\n(define (t-free-vars t (first-order? #f))\n  (let loop ((t t))\n    (match t\n      ((t:query  name f)      (set-subtract (f-free-vars f first-order?) (set name)))\n      ((t:quote  _)           (set))\n      ((t:var    name)        (set name))\n      ((t:prim   _)           (set))\n      ((t:app    func args)   (set-union (t-free-vars* args first-order?)\n                                         (if first-order? (set) (loop func))))\n      ((t:lambda params body) (set-subtract (loop body) (list->set params)))\n      ((t:if     c t f)       (set-union (loop c) (loop t) (loop f)))\n      ((t:let    bpairs body) (set-union (t-free-vars* (map cdr bpairs) first-order?)\n                                         (set-subtract (loop body) (list->set (map car bpairs)))))\n      ((t:letrec bpairs body) (set-subtract (set-union (t-free-vars* (map cdr bpairs) first-order?)\n                                                       (loop body))\n                                            (list->set (map car bpairs)))))))\n\n(define (t-free-vars-first-order t) (t-free-vars t #t))\n\n(define (f-free-vars f (first-order? #f))\n  (let loop ((f f))\n    (match f\n      ((f:const   _)             (set))\n      ((f:or      f1 f2)         (set-union (loop f1) (loop f2)))\n      ((f:and     f1 f2)         (set-union (loop f1) (loop f2)))\n      ((f:implies if then)       (set-union (loop if) (loop then)))\n      ((f:relate  relation args) (t-free-vars* args first-order?))\n      ((f:exist   params body)   (set-subtract (loop body) (list->set params)))\n      ((f:all     params body)   (set-subtract (loop body) (list->set params))))))\n\n(define (t-free-vars* ts (first-order? #f))\n  (foldl (lambda (t vs) (set-union vs (t-free-vars t first-order?)))\n         (set) ts))\n(define (t-free-vars-first-order* ts) (t-free-vars* ts #t))\n\n(define (f-relations f)\n  (match f\n    ((f:const   _)             (set))\n    ((f:or      f1 f2)         (set-union (f-relations f1) (f-relations f2)))\n    ((f:and     f1 f2)         (set-union (f-relations f1) (f-relations f2)))\n    ((f:implies if then)       (set-union (f-relations if) (f-relations then)))\n    ((f:relate  relation args) (set-add (t-relations* args) relation))\n    ((f:exist   params body)   (f-relations body))\n    ((f:all     params body)   (f-relations body))))\n\n(define (t-relations t)\n  (match t\n    ((t:query  _ f)         (f-relations f))\n    ((t:quote  _)           (set))\n    ((t:var    _)           (set))\n    ((t:prim   _)           (set))\n    ((t:app    func args)   (set-union (t-relations func) (t-relations* args)))\n    ((t:lambda params body) (t-relations body))\n    ((t:if     c t f)       (set-union (t-relations c) (t-relations t) (t-relations f)))\n    ((t:let    bpairs body) (set-union (t-relations* (map cdr bpairs)) (t-relations body)))\n    ((t:letrec bpairs body) (set-union (t-relations* (map cdr bpairs)) (t-relations body)))))\n\n(define (t-relations* ts)\n  (foldl (lambda (t rs) (set-union rs (t-relations t)))\n         (set) ts))\n\n(define (t-substitute t name=>name (first-order? #f))\n  (let loop ((t t))\n    (match t\n      ((t:query  name f)      (t:query name (f-substitute f (hash-remove name=>name name) first-order?)))\n      ((t:quote  _)           t)\n      ((t:var    name)        (t:var (hash-ref name=>name name name)))\n      ((t:prim   _)           t)\n      ((t:app    func args)   (t:app func (t-substitute* args name=>name first-order?)))\n      ((t:lambda params body) (t:lambda params (t-substitute body\n                                                             (hash-remove* name=>name params)\n                                                             first-order?)))\n      ((t:if     c t f)       (t:if (loop c) (loop t) (loop f)))\n      ((t:let    bpairs body) (define params (map car bpairs))\n                              (t:let (map cons params (t-substitute* (map cdr bpairs)\n                                                                     name=>name\n                                                                     first-order?))\n                                     (t-substitute body\n                                                   (hash-remove* name=>name params)\n                                                   first-order?)))\n      ((t:letrec bpairs body) (define params (map car bpairs))\n                              (define n=>n   (hash-remove* name=>name params))\n                              (t:let (map cons params (t-substitute* (map cdr bpairs)\n                                                                     n=>n\n                                                                     first-order?))\n                                     (t-substitute body\n                                                   n=>n\n                                                   first-order?))))))\n\n(define (t-substitute* ts name=>name (first-order? #f))\n  (map (lambda (t) (t-substitute t name=>name first-order?)) ts))\n\n(define (f-substitute f name=>name (first-order? #f))\n  (let loop ((f f))\n    (match f\n      ((f:const   _)             f)\n      ((f:or      f1 f2)         (f:or      (loop f1)\n                                            (loop f2)))\n      ((f:and     f1 f2)         (f:and     (loop f1)\n                                            (loop f2)))\n      ((f:implies if then)       (f:implies (loop if)\n                                            (loop then)))\n      ((f:relate  relation args) (f:relate relation (t-substitute* args name=>name first-order?)))\n      ((f:exist   params body)   (f:exist params (f-substitute body\n                                                               (hash-remove* name=>name params)\n                                                               first-order?)))\n      ((f:all     params body)   (f:all   params (f-substitute body\n                                                               (hash-remove* name=>name params)\n                                                               first-order?))))))\n\n(define (t-substitute-first-order  t  name=>name) (t-substitute  t  name=>name #t))\n(define (t-substitute-first-order* ts name=>name) (t-substitute* ts name=>name #t))\n\n;; A schema is a finite map of names to finite maps of properties to sets of\n;; values, i.e.: (=> name (=> property (set value)))\n(define schema.empty (hash))\n(define (schema:new private=>property=>value)\n  (make-immutable-hash\n    (hash-map private=>property=>value\n              (lambda (private p=>v)\n                (cons private\n                      (make-immutable-hash\n                        (hash-map p=>v (lambda (p v) (cons p (set v))))))))))\n\n(define (schema-union p=>p=>v.0 p=>p=>v.1)\n  (hash-union p=>p=>v.0 p=>p=>v.1\n              #:combine (lambda (p=>v.0 p=>v.1)\n                          (hash-union p=>v.0 p=>v.1 #:combine set-union))))\n\n(record module (terms relations assertions name=>submodule) #:prefab)\n(define module.empty (module\n                       (terms           schema.empty)\n                       (relations       schema.empty)\n                       (assertions      (set))\n                       (name=>submodule (hash))))\n\n(define (m:link     ms)        (foldl (lambda (m m.0)\n                                        (match-define (module:struct ts.0 rs.0 as.0 n=>s.0) m.0)\n                                        (match-define (module:struct ts   rs   as   n=>s)   m)\n                                        (module\n                                          (terms           (schema-union ts.0 ts))\n                                          (relations       (schema-union rs.0 rs))\n                                          (assertions      (set-union    as.0 as))\n                                          (name=>submodule (hash-union n=>s.0 n=>s #:combine\n                                                                       (lambda (s.0 s)\n                                                                         (m:link (list s.0 s)))))))\n                                      module.empty\n                                      ms))\n(define (m:named    name m)    (module:set module.empty (name=>submodule (hash       name m))))\n(define (m:term     name p=>v) (module:set module.empty (terms           (schema:new (hash name p=>v)))))\n(define (m:relation name p=>v) (module:set module.empty (relations       (schema:new (hash name p=>v)))))\n(define (m:assert   formula)   (module:set module.empty (assertions      (set        formula))))\n\n(define (module-flatten m)          (m:link (cons (module:set m (module-name=>submodule (hash)))\n                                                  (map module-flatten (hash-values (module-name=>submodule m))))))\n\n(define (module-ref     m path)     (foldl (lambda (name m)\n                                             (hash-ref (module-name=>submodule m) name module.empty))\n                                           m path))\n\n(define (module-add     m path sub) (if (null? path)\n                                      (m:link (list m sub))\n                                      (module:set m (name=>submodule\n                                                      (hash-update (module-name=>submodule m) (car path)\n                                                                   (lambda (m) (module-add m (cdr path) sub))\n                                                                   module.empty)))))\n\n(define (module-remove  m path)     (if (null? path)\n                                      module.empty\n                                      (let loop ((m m) (path path))\n                                        (module:set m (name=>submodule\n                                                        (if (null? (cdr path))\n                                                          (hash-remove (module-name=>submodule m) (car path))\n                                                          (hash-update (module-name=>submodule m) (car path)\n                                                                       (lambda (m) (loop m (cdr path)))\n                                                                       module.empty)))))))\n\n(define (module-remove* m paths)    (foldl (lambda (path m) (module-remove m path)) m paths))\n\n(define (module-wrap    m path)     (foldl (lambda (name m)\n                                             (module:set module.empty (name=>submodules (hash name m))))\n                                           m path))\n\n(define (module-unwrap  m path)     (foldl (lambda (name m)\n                                             (hash-ref (module-name=>submodule m) name module.empty))\n                                           m path))\n\n(record program (module env) #:prefab)\n(define (program:new m env) (program (module m) (env env)))\n(define program.empty (program:new module.empty env.empty))\n\n(define (program-remove* p paths) (program:set p (module (module-remove* (program-module p) paths))))\n(define (program-flatten p)       (program:set p (module (module-flatten (program-module p)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Names and parameter trees\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define fresh-name-count (make-parameter #f))\n\n(define (call-with-fresh-names thunk)\n  (if (fresh-name-count)\n    (thunk)\n    (parameterize ((fresh-name-count 0))\n      (thunk))))\n\n(define-syntax-rule (with-fresh-names body ...)\n  (call-with-fresh-names (lambda () body ...)))\n\n(define (fresh-name name)\n  (define uid.next (fresh-name-count))\n  (unless uid.next (error \"fresh name not available:\" name))\n  (fresh-name-count (+ uid.next 1))\n  (cons uid.next (if (pair? name) (cdr name) name)))\n\n(define (param-names param)\n  (match param\n    ((? symbol?)    (list param))\n    ('()            '())\n    ((cons p.a p.d) (append (param-names p.a) (param-names p.d)))\n    ((? vector?)    (param-names (vector->list param)))))\n\n(define (unique? names) (= (set-count (list->set names)) (length names)))\n\n(define (name? x) (not (or (not x) (procedure? x))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (literal? x) (or (number? x) (boolean? x) (string? x) (bytes? x)))\n(define (literal  x) (if (and (number? x) (inexact? x)) (inexact->exact x) x))\n\n(define (binding-pairs?! bps)\n  (unless (and (list? bps)\n               (andmap (lambda (bp) (and (list? bp)\n                                         (= 2 (length bp))))\n                       bps))\n    (error \"invalid binding pairs:\" bps)))\n\n(define ((simple-parser proc) stx)\n  (cond ((list? stx) (apply proc (cdr stx)))\n        (else        (error \"simple-parser expects list syntax:\" stx))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Module parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define current-env (make-parameter #f))\n\n(define (current-env-bind  vocab n  v)  (current-env (env-bind  (current-env) vocab n  v)))\n(define (current-env-bind* vocab ns vs) (current-env (env-bind* (current-env) vocab ns vs)))\n\n(define ((parse:program stx) env)\n  (unless (list? stx) (error \"invalid program syntax:\" stx))\n  (with-fresh-names\n    (parameterize ((current-env env))\n      (define resume (apply parse:module:begin stx))\n      (define env    (current-env))\n      (program:new (resume env) env))))\n\n(define (parse:module:begin . stxs)\n  (define deferred (map parse:module stxs))\n  (lambda (env) (m:link (map (lambda (d) (d env)) deferred))))\n\n(define (parse:module stx)\n  (with-fresh-names\n    (match stx\n      ((? symbol? name)\n       (define mc.b (env-ref (current-env) 'module name))\n       (cond ((procedure? mc.b) (mc.b stx))\n             (else              (error \"unknown module clause keyword:\" name mc.b))))\n      ((list operator operands ...)\n       (define mc.b (env-ref (current-env) 'module operator))\n       (cond ((procedure? mc.b) (mc.b stx))\n             (else              (error \"unknown module clause operator:\" operator mc.b))))\n      ((? procedure? self-parse) (self-parse)))))\n\n(define parse:module:module\n  (simple-match-lambda\n    ((name . body) (define resume (apply parse:module:begin body))\n                   (lambda (env) (m:named name (resume env))))))\n\n(define (quote-property property)\n  (lambda (value)\n    (lambda (env) (hash property value))))\n\n(define (parse:declare-relation:projections property msg.name)\n  (simple-match-lambda\n    (((attrs . projections))\n     (unless (unique? attrs)\n       (error (string-append msg.name \" attribute names must be unique:\") attrs))\n     (lambda (env.0)\n       (define unames (map fresh-name attrs))\n       (define env    (env-bind* env.0 'term attrs unames))\n       (hash property (cons unames (map (lambda (proj) ((parse:term* proj) env))\n                                        projections)))))))\n\n(define parse:declare-relation:indexes (parse:declare-relation:projections 'indexes \"indexes:\"))\n(define parse:declare-relation:modes   (parse:declare-relation:projections 'modes   \"modes:\"))\n\n(define (parse:module:projections property)\n  (simple-parser\n    (simple-match-lambda\n      (((relation . attrs) . projections)\n       (parse:module:relation (cons relation attrs) property (cons attrs projections))))))\n\n(define parse:declare-term:definition\n  (lambda (body)\n    (lambda (env) (hash 'definition ((parse:term body) env)))))\n\n(define (parse:declare-relation:rule type)\n  (simple-match-lambda\n    (((params . formulas))\n     (lambda (env)\n       ;; NOTE: extracting variables in first-order positions as pattern\n       ;; variables may be brittle.  It may be better to introduce a pattern\n       ;; matching vocabulary to explicitly identify pattern variables.\n       (define ts.params    (map (lambda (p) ((parse:term p) env)) params))\n       (define names.params (set->list (t-free-vars-first-order* ts.params)))\n       (define names.argument\n         (map (lambda (i) (fresh-name (string->symbol (string-append \"x.\" (number->string i)))))\n              (range (length params))))\n       (define formula\n         ((apply parse:formula:exist names.params\n                 (lambda (env)\n                   (foldl f:and\n                          (f:== (quote-literal #t) (quote-literal #t))\n                          (map (lambda (n t) (f:== (t:var n) t))\n                               names.argument\n                               (t-substitute-first-order*\n                                 ts.params\n                                 (make-immutable-hash\n                                   (map cons names.params (env-ref* env 'term names.params)))))))\n                 formulas)\n          env))\n       (hash 'rules (list (vector type names.argument formula)))))))\n\n(define (parse:module:rule type)\n  (simple-parser\n    (simple-match-lambda\n      (((relation . params) . formulas) (parse:module:relation\n                                          relation\n                                          (parse:declare-relation:rule type)\n                                          (cons params formulas))))))\n\n(define parse:module:link\n  (simple-match-lambda\n    (ms (lambda (_) (m:link ms)))))\n\n(define parse:module:parameter\n  (simple-match-lambda\n    (kvs (define kwargs (plist->alist kvs))\n         (apply parse:module:begin\n                (map (lambda (name value)\n                       (lambda () (parse:module:define name (lambda (_) (quote-literal value)))))\n                     (map car kwargs) (map cdr kwargs))))))\n\n(define (parse:module:io type)\n  (simple-match-lambda\n    (kvs (define kwargs (plist->alist kvs))\n         (apply parse:module:begin\n                (map (lambda (rsig io-device)\n                       (lambda () (parse:module:relation rsig type io-device)))\n                     (map car kwargs) (map cdr kwargs))))))\n\n(define parse:module:input  (parse:module:io (quote-property 'input)))\n(define parse:module:output (parse:module:io (quote-property 'output)))\n\n(define parse:module:define\n  (simple-match-lambda\n    (((name . params) body) (parse:module:define name (parse:term:lambda params body)))\n    ((name            body) (parse:module:term   name parse:declare-term:definition body))))\n\n(define (parse:module:declaration vocab.declare vocab.entity msg.entity m:entity)\n  (simple-match-lambda\n    ((name . kvs) (define kwargs (plist->alist kvs))\n                  (define uname  (fresh-name name))\n                  (current-env-bind vocab.entity name uname)\n                  (lambda (env)\n                    (define uname (env-ref env vocab.entity name))\n                    (unless (name? uname)\n                      (error (string-append \"invalid \" msg.entity \" renaming:\" name uname)))\n                    (m:link (map (lambda (property value)\n                                   (define p.b (if (procedure? property)\n                                                 property\n                                                 (env-ref env vocab.declare property)))\n                                   (define pmap (cond ((procedure? p.b) ((p.b value) env))\n                                                      (else             (hash (if p.b p.b property) value))))\n                                   (m:entity uname pmap))\n                                 (map car kwargs) (map cdr kwargs)))))))\n\n(define parse:module:relation\n  (simple-match-lambda\n    (((relation . attrs) . kvs) (apply parse:module:relation relation (quote-property 'attributes) attrs kvs))\n    (args                       (apply (parse:module:declaration 'declare-relation 'formula \"relation\" m:relation) args))))\n\n(define parse:module:term              (parse:module:declaration 'declare-term     'term    \"term\"     m:term))\n\n(define (parse:module:declare* parse-spec)\n  (simple-match-lambda\n    (specs (apply parse:module:begin\n                  (map (lambda (spec)\n                         (lambda () (if (list? spec)\n                                      (apply parse-spec spec)\n                                      (parse-spec       spec))))\n                       specs)))))\n\n(define parse:module:relations (parse:module:declare* parse:module:relation))\n(define parse:module:terms     (parse:module:declare* parse:module:term))\n\n(define parse:module:assert\n  (simple-match-lambda\n    ((formula) (lambda (env) (m:assert ((parse:formula formula) env))))))\n\n(define env.initial.module.declare-relation\n  (env:new\n    'declare-relation\n    '<<=     (parse:declare-relation:rule '<<=)\n    '<<+     (parse:declare-relation:rule '<<+)\n    '<<-     (parse:declare-relation:rule '<<-)\n    '<<~     (parse:declare-relation:rule '<<~)\n    'indexes parse:declare-relation:indexes\n    'modes   parse:declare-relation:modes))\n\n(define env.initial.module.declare-term\n  (env:new\n    'declare-term\n    'definition parse:declare-term:definition))\n\n(define env.initial.module.clause\n  (env:new\n    'module\n    'module          (simple-parser parse:module:module)\n    'begin           (simple-parser parse:module:begin)\n    'link            (simple-parser parse:module:link)\n    'relation        (simple-parser parse:module:relation)\n    'relations       (simple-parser parse:module:relations)\n    'term            (simple-parser parse:module:term)\n    'terms           (simple-parser parse:module:terms)\n    'indexes         (parse:module:projections parse:declare-relation:indexes)\n    'modes           (parse:module:projections parse:declare-relation:modes)\n    'parameter       (simple-parser parse:module:parameter)\n    'input           (simple-parser parse:module:input)\n    'output          (simple-parser parse:module:output)\n    'define          (simple-parser parse:module:define)\n    'assert          (simple-parser parse:module:assert)\n    '<<=             (parse:module:rule '<<=)\n    '<<+             (parse:module:rule '<<+)\n    '<<-             (parse:module:rule '<<-)\n    '<<~             (parse:module:rule '<<~)\n    ;; miniKanren style module clauses\n    'define-relation (parse:module:rule '<<=)))\n\n(define env.initial.module (env-union env.initial.module.declare-relation\n                                      env.initial.module.declare-term\n                                      env.initial.module.clause))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Formula parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define ((parse:formula stx) env)\n  (with-fresh-names\n    (match stx\n      ((? literal? data) (f:const (literal data)))\n      ((? symbol? name)\n       (define f.b (env-ref env 'formula name))\n       (cond ((procedure? f.b) ((f.b stx) env))\n             (else             (f:const (if f.b f.b name)))))\n      ((list operator operands ...)\n       (define f.b (env-ref env 'formula operator))\n       ((cond ((procedure? f.b) (f.b stx))\n              (else             (parse:formula:relate (if f.b f.b operator) operands)))\n        env))\n      ((? procedure? self-parse) (self-parse env)))))\n\n(define ((parse:formula* formulas) env)\n  (map (lambda (f) ((parse:formula f) env)) formulas))\n\n(define anonymous-vars (make-parameter #f))\n\n(define-syntax formula/anonymous-vars\n  (syntax-rules ()\n    ((_ body ...) (parameterize ((anonymous-vars '()))\n                    (define f (let () body ...))\n                    (if (null? (anonymous-vars))\n                      f\n                      (f:exist (anonymous-vars) f))))))\n\n(define ((parse:formula:relate relation operands) env)\n  (formula/anonymous-vars (f:relate relation ((parse:term* operands) env))))\n\n(define parse:formula:or\n  (simple-match-lambda\n    ((disjunct)             (parse:formula disjunct))\n    ((disjunct . disjuncts) (lambda (env) (f:or ((parse:formula disjunct)           env)\n                                                ((apply parse:formula:or disjuncts) env))))))\n\n(define parse:formula:and\n  (simple-match-lambda\n    ((conjunct)             (parse:formula conjunct))\n    ((conjunct . conjuncts) (lambda (env) (f:and ((parse:formula conjunct)            env)\n                                                 ((apply parse:formula:and conjuncts) env))))))\n\n(define parse:formula:not\n  (simple-match-lambda ((f) (lambda (env) (f:not ((parse:formula f) env))))))\n\n(define (parse:formula:quantifier f:quantifier msg.name)\n  (simple-match-lambda\n    ((names . body) (unless (unique? names)\n                      (error (string-append msg.name \" parameter names must be unique:\") names))\n                    (lambda (env)\n                      (define unames (map fresh-name names))\n                      (f:quantifier unames ((apply parse:formula:and body)\n                                            (env-bind* env 'term names unames)))))))\n\n(define parse:formula:exist (parse:formula:quantifier f:exist \"existential quantifier\"))\n(define parse:formula:all   (parse:formula:quantifier f:all   \"universal quantifier\"))\n\n(define parse:formula:implies\n  (simple-match-lambda\n    ((hypothesis conclusion) (lambda (env) (f:implies ((parse:formula hypothesis) env)\n                                                      ((parse:formula conclusion) env))))))\n\n(define parse:formula:iff\n  (simple-match-lambda\n    ((f.a f.b) (lambda (env) (f:iff ((parse:formula f.a) env)\n                                    ((parse:formula f.b) env))))))\n\n;; miniKanren style formulas\n(define parse:formula:fresh (parse:formula:quantifier f:exist \"fresh\"))\n\n(define parse:formula:conde\n  (simple-match-lambda\n    (clauses (apply parse:formula:or (map (lambda (conjuncts) (apply parse:formula:and conjuncts))\n                                          clauses)))))\n\n(define env.initial.formula\n  (env:new\n    'formula\n    'or      (simple-parser parse:formula:or)\n    'and     (simple-parser parse:formula:and)\n    'not     (simple-parser parse:formula:not)\n    'implies (simple-parser parse:formula:implies)\n    'iff     (simple-parser parse:formula:iff)\n    'exist   (simple-parser parse:formula:exist)\n    'all     (simple-parser parse:formula:all)\n    ;; miniKanren style formulas\n    'fresh   (simple-parser parse:formula:fresh)\n    'conde   (simple-parser parse:formula:conde)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Term parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (quote-literal v) (t:quote (literal v)))\n\n(define ((parse:term stx) env)\n  (with-fresh-names\n    (match stx\n      ((? literal? data) (quote-literal data))\n      ((? symbol?  name) ((parse:term:ref name) env))\n      ((list operator operands ...)\n       (define t.b (env-ref env 'term operator))\n       ((cond ((procedure? t.b) (t.b stx))\n              (else             (parse:term:app operator operands)))\n        env))\n      ((? procedure? self-parse) (self-parse env)))))\n\n(define ((parse:term* stxs) env)\n  (map (lambda (stx) ((parse:term stx) env)) stxs))\n\n(define ((parse:term:ref name) env)\n  (define t.b (env-ref env 'term name))\n  (cond ((procedure? t.b) ((t.b name) env))\n        (else             (t:var (if t.b t.b name)))))\n\n(define parse:term:query\n  (simple-match-lambda\n    ((param-pattern . body)\n     (lambda (env)\n       (cond ((symbol? param-pattern)\n              (define param (fresh-name param-pattern))\n              (t:query param ((apply parse:formula:and body)\n                              (env-bind env 'term param-pattern param))))\n             (else (define param (fresh-name 'q.0))\n                   (define names (param-names param-pattern))\n                   (define (assign-param-pattern env)\n                     (f:== param ((parse:term:simple param-pattern) env)))\n                   (t:query param ((apply parse:formula:exist names assign-param-pattern body)\n                                   env))))))))\n\n(define ((parse:term:simple pattern) env)\n  (let loop ((pattern pattern))\n    (match pattern\n      ((? symbol?)    ((parse:term:ref pattern) env))\n      ('()            (quote-literal '()))\n      ((cons p.a p.d) (t:cons (loop p.a) (loop p.d)))\n      ((? vector?)    (t:list->vector (loop (vector->list pattern)))))))\n\n(define parse:term:quote\n  (simple-match-lambda ((value) (lambda (_) (quote-literal value)))))\n\n(define parse:term:quasiquote\n  (simple-match-lambda\n    ((template)\n     (lambda (env)\n       (define ((keyword? k) n) (eq? k (env-ref env 'quasiquote n)))\n       (define (lift tag e)     (t:cons (quote-literal tag) (t:cons e (quote-literal '()))))\n       ;; NOTE: unquote-splicing support requires a safe definition of append\n       (let loop ((t template) (level 0))\n         (match t\n           ((list (? (keyword? 'unquote)    k) e) (if (= level 0)\n                                                    ((parse:term e) env)\n                                                    (lift k (loop e (- level 1)))))\n           ((list (? (keyword? 'quasiquote) k) t) (lift k (loop t (+ level 1))))\n           ((cons t.a t.d)                        (t:cons (loop t.a level) (loop t.d level)))\n           ((? vector?)                           (t:list->vector (loop (vector->list t) level)))\n           ((or (? (keyword? 'quasiquote))\n                (? (keyword? 'unquote)))          (error \"invalid quasiquote:\" t template))\n           (v                                     (quote-literal v))))))))\n\n(define parse:term:app\n  (simple-match-lambda\n    ((proc args) (lambda (env) (t:app ((parse:term proc)  env)\n                                      ((parse:term* args) env))))))\n\n(define parse:term:lambda\n  (simple-match-lambda\n    ((params body) (define names (param-names params))\n                   (unless (unique? names)\n                     (error \"lambda parameter names must be unique:\" names))\n                   (lambda (env)\n                     (define unames (map fresh-name names))\n                     (t:lambda unames ((parse:term body)\n                                       (env-bind* env 'term names unames)))))))\n\n(define parse:term:if\n  (simple-match-lambda\n    ((c t f) (lambda (env) (t:if ((parse:term c) env)\n                                 ((parse:term t) env)\n                                 ((parse:term f) env))))))\n\n(define parse:term:let\n  (simple-match-lambda\n    ((bps body) (binding-pairs?! bps)\n                (parse:term:app (parse:term:lambda (map car bps) body)\n                                (map cadr bps)))))\n\n(define parse:term:letrec\n  (simple-match-lambda\n    ((bps body) (binding-pairs?! bps)\n                (define names (param-names (map car bps)))\n                (unless (unique? names)\n                  (error \"letrec parameter names must be unique:\" names))\n                (lambda (env)\n                  (define unames (map fresh-name names))\n                  (define rhss ((parse:term* (map cadr bps)) env))\n                  (t:letrec (map cons unames rhss)\n                            ((parse:term body)\n                             (env-bind* env 'term names unames)))))))\n\n(define parse:term:and\n  (simple-match-lambda\n    (()           (lambda (_) (quote-literal #t)))\n    ((arg)        (parse:term arg))\n    ((arg . args) (parse:term:if arg\n                                 (apply parse:term:and args)\n                                 (lambda (_) (quote-literal #f))))))\n\n(define parse:term:or\n  (simple-match-lambda\n    (()           (lambda (_) (quote-literal #f)))\n    ((arg)        (parse:term arg))\n    ((arg . args) (lambda (env)\n                    ((parse:term:let (list (list 'temp arg))\n                                     (parse:term:if (parse:term:ref 'temp)\n                                                    (parse:term:ref 'temp)\n                                                    (lambda (_) ((apply parse:term:or args)\n                                                                 env))))\n                     env)))))\n\n(define parse:term:anonymous-var\n  (simple-match-lambda\n    ((stx) (lambda (_)\n             (unless (anonymous-vars) (error \"misplaced anonymous variable:\" stx))\n             (define name (fresh-name '_))\n             (anonymous-vars (cons name (anonymous-vars)))\n             (t:var name)))))\n\n(define (parse:term:prim name)\n  (simple-match-lambda\n    (((_ . args)) (lambda (env) (t:app (t:prim name) ((parse:term* args) env))))\n    ((_)          (lambda (env) (t:prim name)))))\n\n(define env.initial.term.quasiquote\n  (env:new\n    'quasiquote\n    'quasiquote 'quasiquote\n    'unquote    'unquote))\n\n(define env.initial.term.primitive\n  (apply env-union env.empty\n         (map (lambda (name) (env:new 'term name (parse:term:prim name)))\n              ;; TODO: some of these can be derived rather than primitive\n              '(apply\n                 cons car cdr\n                 list->vector vector vector-ref vector-length\n                 bytes-ref bytes-length bytes->string string->bytes\n                 symbol->string string->symbol\n                 floor + - * / =\n                 equal? not\n                 <= < >= >\n                 any<= any< any>= any>\n                 .< .<= .> .>=  ; polymorphic point-wise monotonic comparisons\n\n                 ;; TODO: can some of these be defined relationally?\n                 set set-count set-member? set-union set-intersect set-subtract\n                 dict dict-count dict-ref dict-set dict-update dict-remove dict-union dict-intersect\n\n                 min max sum length\n                 map/merge map merge filter foldl foldr))))\n\n(define env.initial.term.special\n  (env:new\n    'term\n    '_          parse:term:anonymous-var\n    'query      (simple-parser parse:term:query)\n    'quote      (simple-parser parse:term:quote)\n    'quasiquote (simple-parser parse:term:quasiquote)\n\n    'if         (simple-parser parse:term:if)\n    'lambda     (simple-parser parse:term:lambda)\n    'let        (simple-parser parse:term:let)\n    'letrec     (simple-parser parse:term:letrec)\n\n    'and        (simple-parser parse:term:and)\n    'or         (simple-parser parse:term:or)))\n\n(define env.initial.term (env-union env.initial.term.quasiquote\n                                    env.initial.term.primitive\n                                    env.initial.term.special))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Module macro expansion\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; TODO: have dbk build process values (move dbk and define-dbk out of parse.rkt)\n;; - built process will optionally inherit from one or more parent processes\n;; - if no parent is specified, automatically use an empty process with primitive environment\n;; - will no longer need dbk-environment\n;; - \"vertical\" library/language-like linking\n;;   - parent program environment(s unioned) used to initiate parsing\n;;     - as opposed to \"horizontal\" (symmetric) linking, where environments are not involved\n;;   - result will be automatically linked with parent(s)\n\n(define dbk-environment (make-parameter (env-union env.initial.term\n                                                   env.initial.formula\n                                                   env.initial.module)))\n\n(define (dbk-environment-update env->env) (dbk-environment (env->env    (dbk-environment))))\n\n(define-syntax-rule (with-dbk-environment-update env->env body ...)\n  (parameterize ((dbk-environment (env->env    (dbk-environment))))\n    body ...))\n\n;; TODO: (define-dbk name (other attributes?) (parent ...) body ...)\n(define-syntax-rule (define-dbk name body ...) (define name (dbk body ...)))\n\n;; TODO: (dbk (other attributes? such as process name) (parent ...) clauses ...) using (dbk-parse (union-of-envs-of parent ...) clauses ...)\n;; dbk-parse produces AST and residual env\n;; semantically process result of dbk-parse to produce a process value\n(define-syntax-rule (dbk clauses ...)          (dbk-parse (dbk-syntax clauses ...)))\n\n;; TODO: take initial environment as an argument\n(define-syntax-rule (dbk-parse stx)            (with-fresh-names\n                                                 ((parse:program stx) (dbk-environment))))\n\n;; TODO: implement link as a procedure\n(define-syntax link      (syntax-rules ()))\n(define-syntax parameter (syntax-rules ()))\n(define-syntax input     (syntax-rules ()))\n(define-syntax output    (syntax-rules ()))\n\n(define-syntax plist-syntax\n  (syntax-rules ()\n    ((_ key val plist ...) `(key ,val . ,(plist-syntax plist ...)))\n    ((_)                   '())))\n\n(define-syntax dbk-syntax\n  (syntax-rules (module link parameter input output)\n    ((_ (module    name cs ...) clauses ...) (cons `(module    ,name . ,(dbk-syntax cs  ...)) (dbk-syntax clauses ...)))\n    ((_ (link      modules ...) clauses ...) (cons `(link      ,modules ...)                  (dbk-syntax clauses ...)))\n    ((_ (parameter params  ...) clauses ...) (cons `(parameter . ,(plist-syntax params  ...)) (dbk-syntax clauses ...)))\n    ((_ (input     inputs  ...) clauses ...) (cons `(input     . ,(plist-syntax inputs  ...)) (dbk-syntax clauses ...)))\n    ((_ (output    outputs ...) clauses ...) (cons `(output    . ,(plist-syntax outputs ...)) (dbk-syntax clauses ...)))\n    ((_ clause                  clauses ...) (cons 'clause                                    (dbk-syntax clauses ...)))\n    ((_)                                     '())))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/old/process.rkt",
    "content": "#lang racket/base\n(provide\n  )\n(require \"abstract-syntax.rkt\" \"misc.rkt\" \"parse.rkt\"\n         racket/list racket/match racket/set)\n\n(record pstate (dbms history data program) #:prefab)\n(define (pstate:new dbms prg) (pstate (dbms                dbms)\n                                      (history             prg)\n                                      (data                'TODO)\n                                      (program             prg)))\n\n;; TODO:\n(define (pstate-query pst params formula)\n  (set))\n\n;; TODO: include stepping as a modification?\n(define-variant pmod?\n  (pmod:merge   pstates)\n  (pmod:move    path.old path.new)\n  (pmod:wrap    path)\n  (pmod:unwrap  path)\n  (pmod:rename  vocab name.old name.new))\n\n(define (pmod:remove path)       (pmod:move   path #f))\n(define (pmod:hide   vocab name) (pmod:rename vocab name #f))\n\n(define (pstate-modify pst.0 pm)\n  ;; TODO: record new pstate using dbms\n  (define pst (pstate:set pst.0 (history (cons pm (pstate-history pst.0)))))\n  (define prg (pstate-program pst))\n  (define m   (program-module prg))\n  (define env (program-env prg))\n  ;; TODO: produce renamings for public names that are shared across pstates\n  (define (public-renamings envs)\n    (hash))\n  (define (module-rename m)\n    ;; TODO: traverse (parameterized) formulas and terms\n    #f)\n  (define (data-rename d n=>n)\n    ;; TODO:\n    #f)\n  (define (data-union . ds)\n    ;; TODO:\n    #f)\n  (match pm\n    ((pmod:merge   pstates)           (define dbms (pstate-dbms pst))\n                                      (unless (andmap (lambda (s) (eqv? dbms (pstate-dbms s))) pstates)\n                                        (error \"cannot merge processes managed by a different dbms:\"\n                                               dbms (map pstate-dbms pstates)))\n                                      (with-fresh-names\n                                        (define n=>n.0 (public-renamings (map (lambda (ps) (program-env (pstate-program ps)))\n                                                                              (cons pst pstates))))\n                                        (apply (lambda (ms es ds)\n                                                 (pstate:set pst\n                                                             (program (program:set program.empty\n                                                                                   (module (m:link ms))\n                                                                                   (env    (apply env-union es))))\n                                                             (data (apply data-union ds))))\n                                               (apply map list\n                                                      (map (lambda (ps)\n                                                             (define prg                 (pstate-program ps))\n                                                             (match-define (cons m n=>n) (module-rename  (program-module prg) n=>n.0))\n                                                             (define env                 (env-rename     (program-env prg)    n=>n))\n                                                             (define data                (data-rename    (pstate-data ps)     n=>n))\n                                                             (list m env data))\n                                                           (cons pst pstates))))))\n    ((pmod:move    path.old path.new) (define m.1 (module-remove m path.old))\n                                      (define m.new (if path.new\n                                                      (module-add m.1 path.new (module-ref m path.old))\n                                                      m.1))\n                                      (pstate:set pst (program (program:set prg (module m.new)))))\n    ((pmod:wrap    path)              (pstate:set pst (program (program:set prg (module (module-wrap   m path))))))\n    ((pmod:unwrap  path)              (pstate:set pst (program (program:set prg (module (module-unwrap m path))))))\n    ((pmod:rename  vocab n.old n.new) (define env.1   (env-set env vocab n.old #f))\n                                      (define env.new (if n.new\n                                                        (env-set env.1 vocab n.new (env-ref env vocab n.old))\n                                                        env.1))\n                                      (pstate:set pst (program (program:set prg (env env.new)))))))\n\n;; TODO: return #f if quiescent\n(define (pstate-step pst)\n  #f)\n\n(define (process name state)\n  (define dbms (pstate-dbms state))\n  (method-lambda\n    ((state)           state)\n    ((branch name.new) (dbms-process-add!  dbms name.new state)\n                       (process name.new state))\n    ((move   name.new) (dbms-process-move! dbms name name.new)\n                       (set! name name.new))\n    ((modify pm)       (define state.new (pstate-modify state pm))\n                       (dbms-process-set!  dbms name state.new)\n                       (set! state state.new))\n    ((step)            (define state.new (pstate-step state))\n                       (and state.new (dbms-process-set! dbms name state.new)))\n    ((query  . args)   (apply pstate-query state args))))\n\n(define (process-query   p . args)   (apply p 'query args))\n(define (process-branch  p name.new) (p 'branch name.new))\n(define (process-move!   p name.new) (p 'move   name.new))\n(define (process-step!   p)          (p 'step))\n(define (process-modify! p pm)       (p 'modify pm))\n\n(define (process-merge! p ps)\n  (process-modify! p (pmod:merge (map (lambda (p) (p 'state)) ps))))\n\n(define (merge-processes name ps)\n  (when (null? ps) (error \"cannot merge empty list of processes:\" name))\n  (define p (process-branch (car ps) name))\n  (process-merge! p (cdr ps))\n  p)\n\n;; TODO:\n(define (dbms-process-ref     dbms name)\n  #f)\n\n(define (dbms-process-set!    dbms name pst)\n  (void))\n\n(define (dbms-process-add!    dbms name pst)\n  (void))\n\n(define (dbms-process-move!   dbms name.old name.new)\n  (void))\n\n(define (dbms-process-remove! dbms name pst.validation)\n  (void))\n\n(define (dbms-export!         dbms renamings path.out)\n  (void))\n\n(define (dbms-import!         dbms renamings path.in)\n  (void))\n\n(define (dbms-clean!          dbms)\n  (void))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/order.rkt",
    "content": "#lang racket/base\n(provide term.min term.max term.number.min term.number.max\n         term.symbol.min term.symbol.max term.string.min term.string.max\n         term.bytes.min term.bytes.max term.pair.min term.pair.max\n         term.vector.min term.vector.max\n         (struct-out bounds) bounds.any bounds-intersect\n         domain.any domain.null domain.number domain.symbol\n         domain.string domain.bytes domain.pair domain.vector domain.boolean\n         any-increment any-decrement finite-interval?\n         (struct-out interval)\n         type->compare compare-term compare-any compare-null compare-boolean\n         compare-nat compare-number\n         compare-bytes compare-string compare-symbol\n         compare-pair compare-list compare-array compare-tuple\n         compare-string/pos compare-suffix compare-suffix-string\n         compare-><=?\n         termlist x))\n                 (define xs.new (list-increment xs))\n                 (if (eq? xs xs.new) x (list->vector xs.new)))\n    (_           x)))\n\n(define (any-decrement x)\n  (define (list-decrement xs)\n    (define xs.new\n      (let loop ((xs xs))\n        (if (null? xs) '()\n          (let* ((a (car xs)) (d (cdr xs)) (d.new (loop (cdr xs))))\n            (cond ((and (pair? d.new) (eq? d d.new)) xs)\n                  ((andmap (lambda (x) (eq? x #t)) d.new)\n                   (define a.new (if (eq? a '()) #t (any-decrement a)))\n                   (if (eq? a a.new) xs (cons a.new d.new)))\n                  (else (cons a d.new)))))))\n    (cond ((eq? xs xs.new)                         xs)\n          ((andmap (lambda (x) (eq? x #t)) xs.new) (cdr xs.new))\n          (else                                    xs.new)))\n  (match x\n    (#t          #f)\n    ('#()        '(#t . #t))\n    (`(,a . ())  (define a.new (any-decrement a))\n                 (if (eq? a a.new) x `(,a.new . #t)))\n    (`(,a . ,d)  (define d.new (any-decrement d))\n                 (if (eq? d d.new) x `(,a . ,d.new)))\n    ((? vector?) (define xs (vector->list x))\n                 (define xs.new (list-decrement xs))\n                 (if (eq? xs xs.new) x (list->vector xs.new)))\n    (_           x)))\n\n(define (finite-interval? lb ub)\n  (let loop ((lb lb) (acc '()))\n    (if (equal? lb ub)\n      (reverse (cons ub acc))\n      (let ((lb.new (any-increment lb)))\n        (and (not (equal? lb lb.new))\n             (loop lb.new (cons lb acc)))))))\n\n(define ((compare-><=? compare) a b) (not (eqv? (compare a b)  1)))\n\n(define (compare-any a b) (compare/compares compares.any a b))\n(define (anyvector cs))\n  (lambda (a b)\n    (define len (vector-length compares))\n    (let loop ((i 0))\n      (if (= i len) 0\n        (let ((compare (vector-ref compares i))\n              (va (vector-ref a i)) (vb (vector-ref b i)))\n          (case (compare va vb)\n            ((-1) -1)\n            (( 1)  1)\n            (else (loop (+ i 1)))))))))\n(define ((tuplecompare type)\n  (match type\n    (#f                         compare-any)\n    ((or 'nat    `#(nat    ,_)) compare-nat)\n    ((or 'string `#(string ,_)) compare-string)\n    ((or 'symbol `#(symbol ,_)) compare-symbol)\n    ((or 'bytes  `#(bytes  ,_)) compare-bytes)\n    (`#(suffix ,source)         (compare-suffix source))\n    (`#(tuple ,@ts)             (compare-tuple (map type->compare ts)))\n    (`(,ta . ,td)               (compare-pair (type->compare ta)\n                                              (type->compare td)))\n    ('array                     (compare-array compare-any))\n    (`#(array ,_ ,t)            (compare-array (type->compare t)))\n    ('list                      (compare-list compare-any))\n    (`#(list ,_ ,t)             (compare-list (type->compare t)))\n    ('number                    compare-number)\n    ((or 'true 'false '())      compare-null)))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/semantics.rkt",
    "content": "#lang racket/base\n(provide simplify-program factor-program)\n(require racket/list racket/match racket/set)\n\n;; TODO: lift quantifiers to top of relation definition (or query) formula\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Grammar\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Program parts\n;(define (R Ns) Fs)\n;(query  Ns     Fs)\n\n;; Formulas F\n;(relate R Ts)\n;(not    F)\n;(and    Fs)\n;(or     Fs)\n;(imply  F F)\n;(iff    Fs)\n;(exist  Ns F)\n;(all    Ns F)\n\n;; Terms T\n;(quote C)\n;(var   N)\n;(app   Func Ts)\n\n(define (quote?      t) (eq? (car t) 'quote))\n(define (quote-value t) (cadr t))\n\n(define (var      n) `(var ,n))\n(define (var?     t) (eq? (car t) 'var))\n(define (var-name t) (cadr t))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Simplification\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; - classical transformations:\n;;   - `(not (not F))  ==> F`\n;;   - `(iff P Q)      ==> (or (and P Q) (and (not P) (not Q)))`\n;;   - `(imply P Q)    ==> (not (and P (not Q)))`\n;;   - `(all X F)      ==> (not (exist X (not F)))`\n\n;; - constructive/minimal transformations:\n;;   - `(not (not (not F))) ==> (not F)`\n;;   - `(not (or P Q))      ==> (and (not P) (not Q))`\n;;   - `(iff P Q)           ==> (and (imply P Q) (imply Q P))`\n;;   - `(imply P (not Q))   ==> (not (and P Q))`\n;;   - `(all X (not F))     ==> (not (exist X F))`\n\n;; - primitive transformations:\n;;   - `(not (==    A B)) ==> (=/=   A B)`\n;;   - `(not (=/=   A B)) ==> (==    A B)`\n;;   - `(not (any<= A B)) ==> (any<  B A)`\n;;   - `(not (any<  A B)) ==> (any<= B A)`\n\n(define (simplify-program full? parts)\n  (map (lambda (part)\n         (match part\n           (`(define (,r . ,params) ,f) `(define (,r . ,params) ,(simplify-formula full? f)))\n           (`(query  ,params        ,f) `(query  ,params        ,(simplify-formula full? f)))))\n       parts))\n\n(define (simplify-formula full? formula)  ; currently applying classical transformations\n  (define (loop/not f)\n    (match f\n      (`(relate      ,r ,@ts)    (let ((ts (map simplify-term ts)))\n                                   (define (k r ts) `(relate ,r . ,ts))\n                                   (match r\n                                     ('==           (k '=/=            ts))\n                                     ('=/=          (k '==             ts))\n                                     ('any<=        (k 'any<  (reverse ts)))\n                                     ('any<         (k 'any<= (reverse ts)))\n                                     (_      `(not ,(k r               ts))))))\n      (`(all         ,params ,f)      `(exist ,params ,(loop/not f)))\n      (`(exist       ,params ,f) `(not (exist ,params ,(loop     f))))\n      (`(not         ,f)         (loop f))\n      (`(and         ,@fs)       `(not (and . ,(map loop fs))))\n      (`(or          ,@fs)       `(and . ,(map loop/not fs)))\n      (`(iff         ,@fs)       (if full? ; defer iff transformation until after factoring, for efficiency\n                                   (loop/not `(or (and . ,fs)\n                                                  (and . ,(map (lambda (f) `(not ,f)) fs))))\n                                   `(not (iff . ,(map loop fs)))))\n      (`(imply       ,p ,q)      (loop/not `(not (and ,p (not ,q)))))))\n  (define (loop f)\n    (match f\n      (`(relate      ,r ,@ts)    `(relate ,r . ,(map simplify-term ts)))\n      (`(all         ,params ,f) `(not (exist ,params ,(loop/not f))))\n      (`(exist       ,params ,f)      `(exist ,params ,(loop     f)))\n      (`(not         ,f)         (loop/not f))\n      (`(and         ,@fs)       `(and . ,(map loop fs)))\n      (`(or          ,@fs)       `(or  . ,(map loop fs)))\n      (`(iff         ,@fs)       (if full? ; defer iff transformation until after factoring, for efficiency\n                                   (loop `(or (and . ,fs)\n                                              (and . ,(map (lambda (f) `(not ,f)) fs))))\n                                   `(iff . ,(map loop fs))))\n      (`(imply       ,p ,q)      (loop `(not (and ,p (not ,q)))))))\n  (loop formula))\n\n(define (simplify-term term)\n  (match term\n    (`(app ,func ,@ts)\n      (match (cons func (map simplify-term ts))\n        (`(cons         (quote ,a) (quote ,d))                                  `(quote ,(cons a d)))\n        (`(vector       . ,(? (lambda (ts) (andmap quote? ts)) ts))             `(quote ,(list->vector (map quote-value ts))))\n        (`(list->vector ,(? quote? (? (lambda (t) (list? (quote-value t))) t))) `(quote ,(list->vector (quote-value t))))\n        (`(,_           . ,ts) `(app ,func . ,ts))))\n    (_ term)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Program factoring via definition introduction\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (factor-program parts)\n  (factor-locally\n    (define factored (map (lambda (part)\n                            (match part\n                              (`(define (,r . ,params) ,f) `(define (,r . ,params) ,(factor-formula f)))\n                              (`(query  ,params        ,f) `(query  ,params                   ,(factor-formula f)))))\n                          parts))\n    (define new      (map (lambda (f&r)\n                            (match-define (cons f `(relate ,r . ,vs)) f&r)\n                            `(define (,r . ,(map (lambda (v) (match-define `(var ,name) v) name) vs)) ,f))\n                          (sort (hash->list (formula=>relate))\n                                (lambda (kv.a kv.b)\n                                  (define (kv-r kv) (cadr (caddr kv)))\n                                  (< (kv-r kv.a) (kv-r kv.b))))))\n    (append new factored)))\n\n(define (factor-formula formula)\n  (define (replace f) (rename-locally\n                        (formula-unrename-variables (formula->relate (formula-rename-variables f)))))\n  (match formula\n    (`(relate                             ,r ,@ts)    (define f.new `(relate ,r . ,ts))\n                                                      (if (foldl (lambda (t seen) (and seen (var? t) (not (set-member? seen (var-name t)))\n                                                                                       (set-add seen (var-name t))))\n                                                                 (set) ts)\n                                                        f.new\n                                                        (replace f.new)))\n    (`(,(and (or 'exist 'all) quantifier) ,params ,f) (replace `(,quantifier ,params ,(factor-formula f))))\n    (`(,connective                        ,@fs)       (replace `(,connective . ,(map factor-formula fs))))))\n\n(define-syntax-rule (factor-locally body ...) (parameterize ((formula=>relate (hash))) body ...))\n\n(define formula=>relate (make-parameter #f))\n\n(define (formula->relate f)\n  (define f=>r (formula=>relate))\n  (or (hash-ref f=>r f #f)\n      (let* ((count (hash-count f=>r))\n             (r     `(relate (new ,count) . ,(map var (remove-duplicates (formula-free-names f))))))\n        (formula=>relate (hash-set f=>r f r))\n        r)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Variable manipulation\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (term-free-names t)\n  (match t\n    (`(quote ,_)         '())\n    (`(var   ,name)      (list name))\n    (`(app   ,func ,@ts) (append* (map term-free-names ts)))))\n\n(define (formula-free-names f)\n  (match f\n    (`(relate            ,r ,@ts)    (append* (map term-free-names ts)))\n    (`(,(or 'exist 'all) ,params ,f) (define bound (list->set params))\n                                     (filter-not (lambda (n) (set-member? bound n))\n                                                 (formula-free-names f)))\n    (`(,connective       ,@fs)       (append* (map formula-free-names fs)))))\n\n(define (order-parameters params ordered-names)\n  (let loop ((ordered-names ordered-names) (params (list->set params)))\n    (match ordered-names\n      ('()                       '())\n      ((cons name ordered-names) (if (set-member? params name)\n                                   (cons name (loop ordered-names (set-remove params name)))\n                                   (loop ordered-names params))))))\n\n(define-syntax-rule (rename-locally body ...) (parameterize ((name=>renamed (hash))\n                                                             (renamed=>name (hash)))\n                                                body ...))\n\n(define name=>renamed (make-parameter #f))\n(define renamed=>name (make-parameter #f))\n\n(define (rename name)\n  (define n=>n (name=>renamed))\n  (or (hash-ref n=>n name #f)\n      (let ((count (hash-count n=>n)))\n        (name=>renamed (hash-set n=>n name count))\n        (renamed=>name (hash-set (renamed=>name) count name))\n        count)))\n\n(define (unrename name) (hash-ref (renamed=>name) name))\n\n(define (term-rename-variables term)\n  (match term\n    (`(quote ,_)       term)\n    (`(var ,name)      `(var ,(rename name)))\n    (`(app ,func ,@ts) `(app ,func . ,(map term-rename-variables ts)))))\n\n(define (term-unrename-variables term)\n  (match term\n    (`(quote ,_)       term)\n    (`(var ,name)      `(var ,(unrename name)))\n    (`(app ,func ,@ts) `(app ,func . ,(map term-unrename-variables ts)))))\n\n(define (formula-rename-variables formula)\n  (match formula\n    (`(relate                             ,r ,@ts)    `(relate      ,r . ,(map term-rename-variables ts)))\n    (`(,(and (or 'exist 'all) quantifier) ,params ,f) (define free-names (formula-free-names f))\n                                                      (for-each rename free-names)  ; allocate free names before bound names for readability\n                                                      `(,quantifier ,(map rename (order-parameters params free-names))\n                                                                    ,(formula-rename-variables f)))\n    (`(,connective                        ,@fs)       `(,connective . ,(map formula-rename-variables fs)))))\n\n(define (formula-unrename-variables formula)\n  (match formula\n    (`(relate                             ,r ,@ts)    `(relate      ,r . ,(map term-unrename-variables ts)))\n    (`(,(and (or 'exist 'all) quantifier) ,params ,f) `(,quantifier ,(map unrename params)\n                                                                    ,(formula-unrename-variables f)))\n    (`(,connective                        ,@fs)       `(,connective . ,(map formula-unrename-variables fs)))))\n\n\n;; TODO: before continuing, design data model with dataflow language for planning\n\n;; Implementation phases:\n;; - basic datalog\n;;   - only these features\n;;     - and (expressing joins)\n;;     - or  (expressing unions)\n;;     - ==, limited such that relations over == describe finite tables\n;;       - (== constant constant) can be simplified out\n;;         - could be a table with zero columns and either one or zero rows\n;;       - (== var constant) is a table with a single row and column\n;;       - no (== var1 var2) for now\n;;     - recursive relations defined by least fixed point\n;;   - no partial eval yet\n;;   - none of these yet\n;;     - not =/= < <= cons vector\n;; - TODO: describe subsequent phases in order of increasing complexity\n\n;; Compilation steps:\n;; - parse\n;; - simplify without serious inlining\n;; - introduce shared/factored definitions for remaining code\n;;   - one goal of factoring is to provide worker/wrapper separation for non-explosive inlining\n;; - simplify with more serious inlining\n;; - infer modes and [pre-]plan\n;; - generate mode/plan-specialized code\n\n;; Predictable simplification and inlining / partial eval\n;; - ideas from macro writer's bill of rights:\n;;   - the original list:\n;;     - introduce let & lambda\n;;     - ignore special cases involving constants\n;;     - ignore degenerate cases resulting in dead/useless code\n;; - local simplification\n;;   - a single-branch disjunction extends the context directly\n;;   - a multi-branch disjunction extends the context with the lattice-join of its branches\n;;   - disjunction branches that always fail in the given context should be pruned\n;;     - perform only one (left-to-right? or mode-specific?) pass to guarantee O(N) runtime\n;;       - well, it may make sense to perform two passes, where the first simplification makes it\n;;         easier to order constraints for an effective second pass\n;;       - do not compute the potentially non-linear pruning fixed point when the context is extended\n;;       - can have a separate optimization mode to compute the fixed point of such pruning\n;;   - limited inter-disjunction simplification\n;;     - fuse disjunctions when their branches can be joined at most one-to-one (i.e., no explosion)\n;;     - disjunctions should *NOT* be cross-joined/DNFed in general\n;;       - will quickly explode code size\n;;       - can have a separate optimization mode to attempt general cross-disjunction simplification\n;; - table-ification of table-like disjunctions\n;;   - table-like means a disjunction of uniform (same variable structure) conjunctions of equality constraints\n;; - inlining\n;;   - inline calls to non-recursive relations that are small enough\n;;   - inline calls to other relations based on analysis of how they are called\n;;     - inline calls with known arguments that can lead to significant simplification\n;;     - bottom-up analysis of how relation parameters are used\n;;       - knowing the shape of a parameter may eliminate many disjunction branches\n;;       - the relation may be structurally recursive on a subset of parameters\n;;       - a parameter may not be scrutinized at all, i.e., it may be invariant\n\n;; Factored relation definitions:\n;; - a simple-relate is a call to a user-defined relation where all arguments are distinct variables\n;; - a simple-cx is any of these:\n;;   - a simple-relate\n;;   - any call to a primitive constraint such as ==, =/=, <, <=\n;; - post-factoring relation definition types:\n;;   - single call to a relation with specialized arguments\n;;     - some arguments are either partially known (not variables), or use the same variable more than once\n;;   - conjunction of simple-cxs\n;;   - disjunction of simple-cxs\n;;   - negation of a simple-relate (not a simple-cx)\n;;   - quantification of a simple-relate (not a simple-cx)\n\n;; Notes and ideas on satisfiability:\n;; - a conjunction including at most one disjunction is satisfiable if one disjunct is satisfiable\n;; - for a conjunction including two or more disjunctions, satisfiability is only guaranteed via flattening into a single disjunction, where one disjunct is satisfiable\n;;   - possible to flatten by joining:\n;;     - disjunct-wise (always)\n;;     - or variable-wise (only for variables that are constrained in every disjunct in all disjunctions currently being combined)\n;;       - degenerate case: every disjunct applies the same constraint (however, possible to factor out this constraint due to being shared)\n;;   - this search for a single satisfiable flattened disjunct may be arbitrarily expensive (may be searching for a needle in a haystack)\n;;   - approaches that may be more tractable:\n;;     - two-watched disjunctions:\n;;       - each disjunction maintains two disjuncts that are locally satisfiable, along with a list of remaining disjuncts that haven't been tested yet\n;;       - if either of these watched disjuncts becomes unsatisfiable, find another from the untested list, pruning any that fail\n;;       - if only one satisfiable disjunct remains, it is promoted as an absolute part of the outer conjunction, used when filtering the other disjunctions\n;;     - learning absolute/shared constraints across all disjuncts in a disjunction:\n;;       - take the lattice join (analogous to an intersection across constraints) to find constraints that all disjuncts agree on\n;;       - e.g. `(disj (== x (cons A B)) (== x (cons C B))) ==> (conj (fresh (D) (== x (cons D B))) (disj (== x (cons A B)) (== x (cons C B))))`\n;;         - simplified: `(fresh (D) (conj (== x (cons D B)) (disj (== D A) (== D C))))`\n;;     - subsumption\n;;       - for each disjunct, starting with the smallest (least constrained), discard any other disjuncts that strictly include its constraints\n;;     - variable-wise factoring of an individual disjunction\n;;       - similar to variable-wise flattening, but without joining, instead building a new disjunction that looks like a decision tree\n;;       - for each variable (often starting with the most constrained) that is constrained by every disjunct, bisect on a constraint choice (recursively)\n;; - may unfold all relation calls except when doing so may lead to looping/redundancy\n;;   - disjunctions annotated with procedure history stack, to recognize recursive calls\n;;     - different history information granularities for different termination measures\n;;       - e.g.,\n;;         - no calls at all (least permissive, but no inlining achieved)\n;;         - or no recursive calls (least permissive while still performing some inlining)\n;;         - or no non-structural recursive calls (most permissive w/ guaranteed termination without programmer assistance)\n;;         - or no non-decreasing recursive calls according to programmer-defined measure (most permissive w/ guaranteed termination)\n;;         - any call is fine (most permissive, but no termination guarantees)\n\n;; How to handle the non-datalog subset of computation:\n\n;(struct store (var=>shape id=>cx) #:prefab)\n;; - each constraint in id=>cx is a CNF formula\n;;   - may include calls to user-defined relations that have not yet been unfolded\n;;   - its id is associated with the shape of all mentioned variables\n;; - a shape is either a t:quote, a t:cons, a t:vector, or a vcx\n;; - for implementation simplicity, avoid more complicated variable-specific indexing schemes for now\n;; - when a new constraint is inserted, apply simplification rules for any interacting variables\n;; - when a variable shape is updated, apply simplification rules for any interacting cxs\n;; - search for variable assignments that satisfy all cxs in id=>cx\n;;   - for constraints participating in satisfaction:\n;;     - run datalog sub-queries if possible\n;;     - otherwise, unfold any calls to relations\n\n;(struct vcx (lb ub cx-ids) #:prefab)\n;; each of lb and ub is an interval endpoint, and either may be open or closed\n;; cx-ids is a set of ids for the cxs that this variable interacts with\n"
  },
  {
    "path": "medikanren2/dbk/dbk/stream.rkt",
    "content": "#lang racket/base\n(provide s-next s-force s-split s-drop\n         s-take/set/steps s-take/set s-take/steps s-take\n         s-each s-foldr s-foldl s-scan\n         s-append/interleaving s-append*/interleaving\n         s-append s-append* s-map/append s-map s-filter s-group s-memo s-lazy\n         s-length s-enumerate s-dedup s-skip s-limit\n         s->list list->s)\n(require racket/function racket/match racket/set)\n\n(define (s-next  s) (if (procedure? s)          (s)  s))\n(define (s-force s) (if (procedure? s) (s-force (s)) s))\n\n;; lazy variant of s-drop\n(define (s-skip n s)\n  (cond ((= n 0)   s)\n        ((pair? s) (s-skip (- n 1) (cdr s)))\n        (else      (thunk (s-skip n (s))))))\n;; lazy variant of s-take\n(define (s-limit n s)\n  (cond ((or (= n 0) (null? s)) '())\n        ((pair? s)              (cons (car s) (s-limit (- n 1) (cdr s))))\n        (else                   (thunk (s-limit n (s))))))\n\n(define (s-split n s)\n  (match-define (cons rxs s.remaining) (s-foldl n cons '() s))\n  (cons (reverse rxs) s.remaining))\n\n(define (s-take/set/steps steps n s)\n  (if (and n (= n 0)) (set)\n    (let loop ((steps steps) (s s) (acc (set)))\n      (match s\n        ((? procedure? s) (if (and steps (= steps 0))\n                            acc\n                            (loop (and steps (- steps 1)) (s) acc)))\n        ('()              acc)\n        ((cons x s)       (define xs (set-add acc x))\n                          (if (and n (= n (set-count xs)))\n                            xs\n                            (loop steps s xs)))))))\n\n(define (s-take/steps steps n s)\n  (if (and n (= n 0)) '()\n    (match s\n      ((? procedure? s) (if (and steps (= steps 0))\n                          '()\n                          (s-take/steps (and steps (- steps 1)) n (s))))\n      ('()              '())\n      ((cons x s)       (cons x (s-take/steps steps (and n (- n 1)) s))))))\n\n(define (s-take/set n s) (s-take/set/steps #f n s))\n(define (s-take     n s) (s-take/steps #f n s))\n(define (s-drop     n s) (cdr (s-foldl n (lambda (_ acc) #t) #t s)))\n\n;; equivalent to (s-take #f s)\n(define (s->list s)\n  (cond ((null? s) '())\n        ((pair? s) (cons (car s) (s->list (cdr s))))\n        (else      (s->list (s)))))\n;; equivalent to s-lazy for a list\n(define (list->s xs)\n  (thunk (if (null? xs)\n           '()\n           (cons (car xs) (list->s (cdr xs))))))\n\n;; TODO: generalize to multiple streams\n(define (s-foldr f acc s)\n  (cond ((null? s) acc)\n        ((pair? s) (f (car s) (s-foldr f acc (cdr s))))\n        (else      (thunk (s-foldr f acc (s))))))\n\n(define (s-append*/interleaving s*) (s-foldr s-append/interleaving '() s*))\n;; TODO: generalize to multiple streams\n(define (s-append/interleaving s1 s2)\n  (cond ((null?      s1) (s2))\n        ((procedure? s1) (thunk (s-append/interleaving (s2) s1)))\n        (else (define d1  (cdr s1))\n              (define s1^ (if (procedure? d1) d1 (thunk d1)))\n              (cons (car s1) (thunk (s-append/interleaving (s2) s1^))))))\n\n(define (s-append* ss) (s-foldr s-append '() ss))\n;; TODO: generalize to multiple streams\n(define (s-append a b) (s-foldr cons b a))\n(define (s-filter ? s) (s-foldr (lambda (x acc) (if (? x) (cons x acc) acc))\n                                '() s))\n\n(define (s-map f s . ss)\n  (cond ((null? s) '())\n        ((pair? s) (let loop ((ss-pending ss) (rss '()))\n                     (if (null? ss-pending)\n                       (let ((ss (reverse rss)))\n                         (cons (apply f (car s) (map car ss))\n                               (apply s-map f (cdr s) (map cdr ss))))\n                       (let next ((ss0 (car ss-pending)))\n                         (if (procedure? ss0) (thunk (next (ss0)))\n                           (loop (cdr ss-pending) (cons ss0 rss)))))))\n        (else      (thunk (apply s-map f (s) ss)))))\n\n;; TODO: generalize to multiple streams\n(define (s-map/append f s)\n  (s-foldr (lambda (x rest) (s-append (f x) rest))\n           '() s))\n\n(define (s-each p s) (let ((s (s-force s)))\n                       (unless (null? s) (p (car s)) (s-each p (cdr s)))))\n\n(define (s-foldl n f acc s)\n  (if (and n (= n 0)) (cons acc s)\n    (let ((s (s-force s)))\n      (if (null? s) (list acc)\n        (s-foldl (and n (- n 1)) f (f (car s) acc) (cdr s))))))\n\n(define (s-scan s acc f)\n  (cons acc (cond ((null? s) '())\n                  ((pair? s) (s-scan (cdr s) (f (car s) acc) f))\n                  (else      (thunk (s-scan (s) acc f))))))\n\n(define (s-length s) (let loop ((s s) (l 0))\n                       (cond ((null? s) l)\n                             ((procedure? s) (loop (s) l))\n                             (else (loop (cdr s) (+ l 1))))))\n\n(define (s-group s ? @)\n  (let ((@ (or @ (lambda (x) x))))\n    (cond ((null? s)      '())\n          ((procedure? s) (thunk (s-group (s) ? @)))\n          (else (let next ((x (@ (car s))) (s s))\n                  (let loop ((g (list (car s))) (s (cdr s)))\n                    (cond ((null? s)      (list g))\n                          ((procedure? s) (thunk (loop g (s))))\n                          (else (let ((y (@ (car s))))\n                                  (if (? y x) (loop (cons (car s) g) (cdr s))\n                                    (cons g (next y s))))))))))))\n\n(define (s-memo s)\n  (cond ((procedure? s) (let ((v #f) (s s))\n                          (thunk (when s (set! v (s-memo (s))) (set! s #f))\n                                 v)))\n        ((null? s)      '())\n        (else           (cons (car s) (s-memo (cdr s))))))\n\n(define (s-lazy s)\n  (define (return s)\n    (cond ((null? s) '())\n          (else      (cons (car s) (s-lazy (cdr s))))))\n  (thunk (cond ((procedure? s) (let retry ((s (s)))\n                                 (cond ((procedure? s) (thunk (retry (s))))\n                                       (else           (return s)))))\n               (else           (return s)))))\n\n(define (s-enumerate i s)\n  (cond ((null? s) '())\n        ((pair? s) (cons (cons i (car s)) (s-enumerate (+ i 1) (cdr s))))\n        (else      (thunk                 (s-enumerate i           (s))))))\n\n;; NOTE: only adjacent duplicates are removed\n(define (s-dedup s)\n  (define (loop x s)\n    (cond ((null? s) (list x))\n          ((pair? s) (if (equal? x (car s)) (loop x (cdr s))\n                       (cons x (loop (car s) (cdr s)))))\n          (else      (thunk (loop x (s))))))\n  (cond ((null? s) '())\n        ((pair? s) (loop (car s) (cdr s)))\n        (else      (thunk (s-dedup (s))))))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/syntax.rkt",
    "content": "#lang racket/base\n(provide\n  (struct-out make-query)\n  (struct-out disj)\n  (struct-out conj)\n  (struct-out constrain)\n  (struct-out ==/use)\n  (struct-out var)\n  (struct-out term/vars)\n  relate\n\n  make-relation relations relations-ref relations-set! relations-set*!\n  relation letrec-relation define-relation\n  conj* disj* fresh conde :== query\n  == =/= any<=o flooro +o *o string==byteso symbol==stringo functiono\n  vector-lengtho vector-refo bytes-lengtho bytes-refo\n\n  ground? term-vars\n  make-pretty pretty)\n(require racket/match racket/set racket/vector)\n\n(struct query     (term formula)                #:prefab #:name make-query\n                                                #:constructor-name make-query)\n;; formulas\n(struct disj      (f1 f2)                       #:prefab)\n(struct conj      (f1 f2)                       #:prefab)\n(struct constrain (op terms)                    #:prefab)\n(struct ==/use    (lhs-term args rhs-proc desc) #:prefab)\n;; terms\n; term: pair or vector with embedded variables\n; vars: optional; set of variables found somewhere within term\n(struct term/vars (term vars))\n(struct var       (name))\n\n(define-syntax define-constraint\n  (syntax-rules ()\n    ((_ (op params ...)) (define (op params ...)\n                           (constrain 'op (list params ...))))))\n(define-constraint (==              t1 t2))\n(define-constraint (=/=             t1 t2))\n(define-constraint (any<=o          t1 t2))\n(define-constraint (flooro          t1 t2))\n(define-constraint (+o              t1 t2 t3))\n(define-constraint (*o              t1 t2 t3))\n(define-constraint (vector-lengtho  t l))\n(define-constraint (vector-refo     t i x))\n(define-constraint (bytes-lengtho   t l))\n(define-constraint (bytes-refo      t i x))\n(define-constraint (symbol==stringo t1 t2))\n(define-constraint (string==byteso  t1 t2))  ;; as utf-8\n(define-constraint (functiono       t1 t2))  ;; uninterpreted functional dependency\n(define (relate proc args) (constrain proc args))\n\n(define relation-registry          (make-weak-hasheq '()))\n(define (relations)                (hash->list relation-registry))\n(define (relations-ref   proc)     (hash-ref relation-registry proc))\n(define (relations-set!  proc k v) (relations-set*! proc `((,k . ,v))))\n(define (relations-set*! proc alist)\n  (hash-set! relation-registry proc\n             (foldl (lambda (kv acc) (hash-set acc (car kv) (cdr kv)))\n                    (relations-ref proc) alist)))\n(define (make-relation name attributes)\n  (define n ((make-syntax-introducer) (datum->syntax #f name)))\n  (define r (eval-syntax #`(letrec ((#,n (lambda args (relate #,n args))))\n                             #,n)))\n  (hash-set! relation-registry r (make-immutable-hash\n                                   `((name            . ,name)\n                                     (attribute-names . ,attributes))))\n  r)\n\n(define-syntax relation\n  (syntax-rules ()\n    ((_ name (param ...) f ...)\n     (let ((r (make-relation 'name '(param ...))))\n       (relations-set! r 'expand (lambda (param ...) (fresh () f ...)))\n       r))))\n(define-syntax letrec-relation\n  (syntax-rules ()\n    ((_ (((name param ...) f ...) ...) body ...)\n     (letrec ((name (relation name (param ...) f ...)) ...) body ...))))\n(define-syntax define-relation\n  (syntax-rules ()\n    ((_ (name param ...) f ...)\n     (define name (relation name (param ...) f ...)))))\n(define success (== #t #t))\n(define failure (== #f #t))\n(define (conj* . fs)\n  (if (null? fs) success\n    (foldl (lambda (f2 f1) (conj f1 f2)) (car fs) (cdr fs))))\n(define (disj* . fs)\n  (if (null? fs) failure\n    (let loop ((f (car fs)) (fs (cdr fs)))\n      (if (null? fs) f\n        (disj f (loop (car fs) (cdr fs)))))))\n(define-syntax let/fresh\n  (syntax-rules ()\n    ((_ (x ...) e ...) (let ((x (var 'x)) ...) e ...))))\n(define-syntax fresh\n  (syntax-rules ()\n    ((_ (x ...) f0 fs ...) (let/fresh (x ...) (conj* f0 fs ...)))))\n(define-syntax conde\n  (syntax-rules ()\n    ((_ (f fs ...) (h hs ...) ...)\n     (disj* (conj* f fs ...) (conj* h hs ...) ...))))\n(define-syntax :==\n  (syntax-rules ()\n    ((_ t (x ...) body ...) (==/use t (list x ...) (lambda (x ...) body ...)\n                                    `((x ...) body ...)))))\n(define-syntax query\n  (syntax-rules ()\n    ((_ (x ...) f0 fs ...)\n     (let/fresh (x ...) (make-query (list x ...) (conj* f0 fs ...))))\n    ((_ x       f0 fs ...)\n     (let/fresh (x)     (make-query x            (conj* f0 fs ...))))))\n\n(define seteq.empty (seteq))\n(define (term-vars t)\n  (cond ((var?    t) (seteq t))\n        ((pair?   t) (set-union (term-vars (car t)) (term-vars (cdr t))))\n        ((vector? t) (apply set-union seteq.empty (map term-vars (vector->list t))))\n        (else        seteq.empty)))\n(define (ground? t)\n  (cond ((var?    t) #f)\n        ((pair?   t) (and (ground? (car t)) (ground? (cdr t))))\n        ((vector? t) (andmap ground? (vector->list t)))\n        (else        #t)))\n\n(define (make-pretty)\n  (define var=>id (make-hash))\n  (define (pretty-term t)\n    (cond ((pair? t)   (cons (pretty-term (car t)) (pretty-term (cdr t))))\n          ((vector? t) (vector-map pretty-term t))\n          ((var? t)    `#s(var ,(let ((id (hash-ref   var=>id t #f))\n                                      (c  (hash-count var=>id)))\n                                  (or id (begin (hash-set! var=>id t c) c)))))\n          (else        (pretty-formula t))))\n  (define (pretty-formula f)\n    (match f\n      (`#s(disj ,f1 ,f2)         `#s(disj ,(pretty-formula f1)\n                                          ,(pretty-formula f2)))\n      (`#s(conj ,f1 ,f2)         `#s(conj ,(pretty-formula f1)\n                                          ,(pretty-formula f2)))\n      (`#s(constrain ,op ,terms) `(,op . ,(map pretty-term terms)))\n      (`#s(==/use ,lhs ,args ,rhs ,desc)\n        (define (pretty-arg t) (pretty-term t))\n        `(:== ,(pretty-term lhs)\n              #s(let ,(map list (car desc) (map pretty-arg args))\n                  ,@(cdr desc))))\n      (_ f)))\n  (lambda (x)\n    (match x\n      (`#s(query ,t ,f)\n        `#s(query ,(pretty-term t) ,(pretty-formula f)))\n      (_ (if (or (disj? x) (conj? x) (constrain? x) (==/use? x))\n           (pretty-formula x) (pretty-term x))))))\n(define (pretty x) ((make-pretty) x))\n"
  },
  {
    "path": "medikanren2/dbk/dbk/table.rkt",
    "content": "#lang racket/base\n(provide materialization value/syntax\n         (struct-out statistics) statistics-intersect\n         vector-table? encoder s-encode s-decode)\n(require \"codec.rkt\" \"config.rkt\" \"dsv.rkt\" \"misc.rkt\" \"order.rkt\" \"stream.rkt\"\n         racket/file racket/function racket/hash racket/list racket/match\n         racket/pretty racket/set racket/vector)\n\n(define (s-encode out type s) (s-each (lambda (v) (encode out type v)) s))\n(define (s-decode in type)\n  (thunk (let loop () (if (eof-object? (peek-byte in)) '()\n                        (cons (decode in type) (thunk (loop)))))))\n\n(define (encoder out type) (method-lambda ((put! v) (encode out type v))\n                                          ((close) (flush-output out))))\n\n(struct statistics (ratio cardinality) #:prefab)\n(define (statistics-intersect a b)\n  (match-define (statistics r.a c.a) a)\n  (match-define (statistics r.b c.b) b)\n  (statistics (min r.a r.b) (min c.a c.b)))\n\n;; TODO: can we simplify by virtually separating bisecting tries from random-access tries?\n;;       technically each prefix of a trie has either bisecting or random-access behavior\n;; virtualized tries can subsume each other when making progress: a kind of exclusive-or trie\n;; - exclusive-or (for grouping with subsumption)\n;; - random-access/position-key (each column value is a table position)\n;; - bisect-key                 (each column value has a unique entry)\n;; - bisect-multi               (each column value may have multiple entries)\n;(define (trie:xor ))\n;; TODO: this one is for monotone dependencies (grouping without subsumption)\n;(define (trie:or ))\n;; TODO: there could be tabular and columnar varieties of these\n;(define (trie:position-key ))\n;(define (trie:bisect-key ))\n;(define (trie:bisect-multi ))\n\n;; TODO: support multiple sorted columns using tables that share key columns\n;;       (wait until column-oriented tables are implemented for simplicity?)\n\n(define ((table ix-thunks))\n  (define ixs (map (lambda (thunk.ix) (thunk.ix)) ix-thunks))\n  (and (not (ormap not ixs))\n       (let table ((ixs         (filter (lambda (ix) (not (ix 'done?))) ixs))\n                   (col=>bounds (foldl (lambda (ix c=>b)\n                                         (hash-union c=>b (ix 'bounds)\n                                                     ;; TODO: verify no errors during testing.\n                                                     ;;       Should be able to replace this with:\n                                                     ;;       #:combine (lambda (b.0 b.1) b.0)\n                                                     #:combine/key\n                                                     (lambda (k b.0 b.1)\n                                                       (if (equal? b.0 b.1)\n                                                         b.0\n                                                         (error \"incompatible initial bounds:\" k b.0 b.1)))))\n                                       (hash) ixs)))\n         (method-lambda\n           ((done?)      (null? ixs))\n           ((bounds)     col=>bounds)\n           ((statistics) (apply hash-union (hash)\n                                (map (lambda (ix) (ix 'statistics)) ixs)\n                                #:combine statistics-intersect))\n           ((update cbs)\n            (let loop ((c=>b (foldl (lambda (cb c=>b) (hash-set c=>b (car cb) (cdr cb)))\n                                    col=>bounds cbs))\n                       (ixs.pending ixs)\n                       (ixs.updated '()))\n              (if (null? ixs.pending)\n                (table (reverse ixs.updated) c=>b)\n                (let*/and ((ix.new ((car ixs.pending) 'update c=>b))\n                           (c=>b   (hash-union c=>b (ix.new 'bounds)\n                                               #:combine (lambda (v.0 v.1) v.1))))\n                  (cond ((not (ix.new 'done?)) (loop c=>b (cdr ixs.pending) (cons ix.new ixs.updated)))\n                        ((not (ix.new 'full?)) (loop c=>b (cdr ixs.pending)              ixs.updated))\n                        (else                  (table '() c=>b)))))))))))\n\n;; TODO: reorganize to implement dicts and sets\n;; - sets can be thought of as dicts with empty value\n;; - could use same representation both for relations and for terms of these types\n;; - in terms of btrees, tries\n;; - possibly also hash tables for small cardinalities\n;; - consider manipulating low-level memory buffers via FFI\n\n;; TODO: define a finite-map that is only referenceable by key and immediately provides a single instance\n;;       of all columns (because the other columns are not sorted/deduped without the key)\n\n;; TODO: this should be called trie:row-major\n(define (tabular-trie vref key-column nonkey-columns types row-count)\n  (define (ref mask i)          (vector-ref (vref i) mask))\n  (define ((make-i<  mask v) i) (any  mask v) i) (any= mask v) i) (any<=? v (ref mask i)))\n  (define (update/pending c=>b.new cols.pending col=>bounds mask start end)\n    (define c.next    (car cols.pending))\n    (define b.current (hash-ref col=>bounds c.next bounds.any))\n    (define b         (bounds-intersect (hash-ref c=>b.new c.next bounds.any)\n                                        b.current))\n    (define (update/bounds lb lbi? ub ubi?)\n      (define start.new (bisect-next start end ((if lbi? make-i< make-i<=) mask lb)))\n      (define end.new (if (< start.new end)\n                        (bisect-prev start end ((if ubi? make-i> make-i>=) mask ub))\n                        start.new))\n      (update/trim c=>b.new cols.pending col=>bounds mask start.new end.new))\n    (cond ((equal? b b.current) (new cols.pending col=>bounds mask start end))\n          (else                 (update/bounds (bounds-lb b)\n                                               (bounds-lb-inclusive? b)\n                                               (bounds-ub b)\n                                               (bounds-ub-inclusive? b)))))\n  (define (update/trim c=>b.new cols.pending col=>bounds mask start end)\n    (if (null? cols.pending)\n      (new '() (hash-set col=>bounds key-column (bounds start #t (- end 1) #t))\n           mask start end)\n      (and (< start end)\n           (let ((c.next (car cols.pending))\n                 (lb     (ref mask start))\n                 (ub     (ref mask (- end 1))))\n             (if (equal? lb ub)\n               (update/trim c=>b.new (cdr cols.pending)\n                            (hash-set col=>bounds c.next (bounds lb #t lb #t))\n                            (+ mask 1) start end)\n               (let ((col=>bounds (hash-set (hash-set col=>bounds c.next (bounds lb #t ub #t))\n                                            key-column (if (= start (- end 1))\n                                                         start\n                                                         (bounds start #t (- end 1) #t)))))\n                 (update/pending c=>b.new cols.pending col=>bounds mask start end)))))))\n  (define (new cols.pending col=>bounds mask start end)\n    (method-lambda\n      ;; TODO: this will be incorrect if the nonkey-columns do not map to a single key, which\n      ;; can happen when the table includes the key-column as an attribute.\n      ((done?)  (null? cols.pending))\n      ;; TODO: allow full? to be #t when nonkey-columns include all attributes\n      ((full?)  (not (not key-column)))\n      ((bounds) col=>bounds)\n      ((statistics)\n       (define ratio (/ (- end start) row-count))\n       (make-immutable-hash\n         (cons (cons (car cols.pending)\n                     (statistics ratio\n                                 (let ((v.lb (ref mask start))\n                                       (v.ub (ref mask (- end 1))))\n                                   (if (equal? v.lb v.ub)\n                                     1\n                                     (+ 2 (- (bisect-prev start end (make-i>= mask v.ub))\n                                             (bisect-next start end (make-i<= mask v.lb))))))))\n               (if key-column\n                 (list (cons key-column (statistics ratio (- end start))))\n                 '()))))\n      ((update c=>b)\n       (cond (key-column\n               (define b.key.0 (hash-ref col=>bounds key-column bounds.any))\n               (define b       (hash-ref c=>b        key-column bounds.any))\n               (cond ((not (equal? b b.key.0))\n                      ;; Assume these bounds will always be numbers in c=>b\n                      (let ((lb (let ((lb.0 (bounds-lb b)))\n                                  (cond ((not (integer? lb.0))    (ceiling lb.0))\n                                        ((bounds-lb-inclusive? b)          lb.0)\n                                        (else                           (+ lb.0 1)))))\n                            (ub (let ((ub.0 (bounds-ub b)))\n                                  (cond ((not (integer? ub.0))    (floor ub.0))\n                                        ((bounds-ub-inclusive? b)        ub.0)\n                                        (else                         (- ub.0 1))))))\n                        (and (<= start lb ub) (< ub end)\n                             (update/trim c=>b cols.pending col=>bounds mask lb (+ ub 1)))))\n                     (else (update/pending c=>b cols.pending col=>bounds mask start end))))\n             (else         (update/pending c=>b cols.pending col=>bounds mask start end))))))\n  (update/trim (hash) nonkey-columns (hash) 0 0 row-count))\n\n(define (table-length t key)       (statistics-cardinality (hash-ref (t 'statistics) key)))\n(define (table-ref    t key i col) (bounds-lb (hash-ref ((t 'update (hash key (bounds i #t i #t))) 'bounds) col)))\n\n(define (table/port/offsets table.offsets key-col cols types thunk.in)\n  (define type `#(tuple ,@types))\n  (lambda ()\n    (define offsets (table.offsets))\n    (and offsets\n         (let ((in (thunk.in)))\n           (define (ref i)\n             (file-position in (table-ref offsets #t i 'offset))\n             (decode in type))\n           (tabular-trie ref key-col cols types (table-length offsets #t))))))\n\n(define (table/bytes/offsets table.offsets key-col cols types bs)\n  (define (thunk.in) (open-input-bytes bs))\n  (table/port/offsets table.offsets key-col cols types thunk.in))\n\n(define (table/port len key-col cols types thunk.in)\n  (define type `#(tuple ,@types))\n  (define width (sizeof type (void)))\n  (lambda ()\n    (define in (thunk.in))\n    (define (ref i) (file-position in (* i width)) (decode in type))\n    (tabular-trie ref key-col cols types len)))\n\n(define (table/bytes key-col cols types bs)\n  (define (thunk.in) (open-input-bytes bs))\n  (table/port (quotient (bytes-length bs) (sizeof types (void)))\n              key-col cols types thunk.in))\n\n(define ((table/vector key-col cols types v))\n  (tabular-trie (lambda (i) (vector-ref v i)) key-col cols types (vector-length v)))\n\n(define (vector-table? types v)\n  (define v< (compare->compare types)))\n  (define i (- (vector-length v) 1))\n  (or (<= i 0) (let loop ((i (- i 1)) (next (vector-ref v i)))\n                 (define current (vector-ref v i))\n                 (and (v< current next) (or (= i 0) (loop (- i 1) current))))))\n(define (vector-table-sort! types v)\n  (vector-sort! v (compare->compare `#(tuple ,@types)))))\n(define (vector-dedup v) (list->vector (s-dedup (vector->list v))))\n\n;; TODO: switch back to file->bytes once Racket IO bug is fixed\n(define (file->bytes2 file-name)\n  (define size (file-size file-name))\n  (define bs (make-bytes size))\n  (call-with-input-file\n    file-name\n    (lambda (in)\n      (let loop ((i 0))\n        (cond ((= i size) bs)\n              (else (define end (+ i (min 1073741824\n                                          (- size i))))\n                    (read-bytes! bs in i end)\n                    (loop end)))))))\n\n(define (file-stats path)\n  (and (file-exists? path)\n       `((size . ,(file-size path))\n         (time . ,(file-or-directory-modify-seconds path)))))\n\n(define (table/metadata retrieval-type directory-path info-alist)\n  (define info         (make-immutable-hash info-alist))\n  (define path-prefix  (path->string (build-path directory-path (hash-ref info 'file-prefix))))\n  (define fname.value  (value-table-file-name  path-prefix))\n  (define fname.offset (offset-table-file-name path-prefix))\n  (define offset-type  (hash-ref info 'offset-type))\n  (define fstat.value  (file-stats fname.value))\n  (define fstat.offset (and offset-type (file-stats fname.offset)))\n  (define key-name     (hash-ref info 'key-name))\n  (define column-names (hash-ref info 'column-names))\n  (define column-types (hash-ref info 'column-types))\n  (define len          (hash-ref info 'length))\n  (unless (set=? fstat.value (hash-ref info 'value-file))\n    (error \"value file stats do not match metadata:\" fname.value\n           'file: fstat.value 'metadata: (hash-ref info 'value-file)))\n  (when offset-type\n    (unless (set=? fstat.offset (hash-ref info 'offset-file))\n      (error \"offset file stats do not match metadata:\" fname.offset\n             'file: fstat.offset 'metadata: (hash-ref info 'offset-file))))\n  (case retrieval-type\n    ((disk) (define (open-input-file/memoize fname)\n              (define cell.port (make-thread-cell #f))\n              (lambda ()\n                (or (thread-cell-ref cell.port)\n                    (let ((in (open-input-file fname)))\n                      (thread-cell-set! cell.port in)\n                      in))))\n            (define thunk.in.value (open-input-file/memoize fname.value))\n            (if offset-type\n              (table/port/offsets\n                (table/port len #t '(offset) `(,offset-type)\n                            (open-input-file/memoize fname.offset))\n                key-name column-names column-types thunk.in.value)\n              (table/port len key-name column-names column-types thunk.in.value)))\n    ((bytes) (define bs.value (file->bytes2 fname.value))\n             (if offset-type\n               (table/bytes/offsets\n                 (table/bytes #t '(offset) `(,offset-type)\n                              (file->bytes2 fname.offset))\n                 key-name column-names column-types bs.value)\n               (table/bytes key-name column-names column-types bs.value)))\n    ((scm) (let/files ((in.value fname.value)) ()\n             (table/vector\n               key-name column-names column-types\n               (list->vector\n                 (s-take #f (s-decode in.value `#(tuple ,@column-types)))))))\n    (else (error \"unknown retrieval type:\" retrieval-type))))\n\n(define (bisect start end i<)\n  (let loop ((start start) (end end))\n    (if (<= end start) end\n      (let ((i (+ start (quotient (- end start) 2))))\n        (if (i< i) (loop (+ 1 i) end) (loop start i))))))\n\n(define (bisect-next start end i<)\n  (define i (- start 1))\n  (let loop ((offset 1))\n    (define next (+ i offset))\n    (cond ((and (< next end) (i< next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (next (+ i o)))\n                    (cond ((= o 0)                      (+ i 1))\n                          ((and (< next end) (i< next)) (loop next o))\n                          (else                         (loop i    o)))))))))\n\n(define (bisect-prev start end i>)\n  (define i end)\n  (let loop ((offset 1))\n    (define next (- i offset))\n    (cond ((and (>= next start) (i> next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (n (- i o)))\n                    (cond ((= o 0)                   i)\n                          ((and (>= n start) (i> n)) (loop n o))\n                          (else                      (loop i o)))))))))\n\n(define (value-table-file-name  prefix) (string-append prefix \".value.table\"))\n(define (offset-table-file-name prefix) (string-append prefix \".offset.table\"))\n(define metadata-file-name              \"metadata.scm\")\n\n(define (tabulator directory-path file-prefix\n                   column-names column-types key-name)\n  (define (unique?! as) (unless (= (length (remove-duplicates as)) (length as))\n                          (error \"duplicates:\" as)))\n  (unless (= (length column-names) (length column-types))\n    (error \"mismatching column names and types:\" column-names column-types))\n  (unique?! column-names)\n  (when (member key-name column-names)\n    (error \"key name must be distinct:\" key-name column-names))\n  (define row-type column-types)\n  (define row<     (compare->compare row-type)))\n  (define row-size (sizeof row-type (void)))\n  (define path-prefix (path->string (build-path directory-path file-prefix)))\n  (define value-file-name  (value-table-file-name path-prefix))\n  (define offset-file-name (and (not row-size)\n                                (offset-table-file-name path-prefix)))\n  (define tsorter (sorter #t value-file-name offset-file-name row-type row<))\n  (method-lambda\n    ((put! x) (tsorter 'put! x))\n    ((close) (match-define (cons offset-type item-count) (tsorter 'close))\n             `((file-prefix    . ,file-prefix)\n               (value-file     . ,(file-stats value-file-name))\n               (offset-file    . ,(and offset-file-name\n                                       (file-stats offset-file-name)))\n               (offset-type    . ,offset-type)\n               (length         . ,item-count)\n               (column-names   . ,column-names)\n               (column-types   . ,column-types)\n               (key-name       . ,key-name)))))\n\n(define (sorter dedup? value-file-name offset-file-name? type value<)\n  (define fname-sort-value  (string-append value-file-name \".value.sort\"))\n  (define fname-sort-offset (string-append value-file-name \".offset.sort\"))\n  (define out-value         (open-output-file value-file-name))\n  (define out-offset\n    (and offset-file-name?  (open-output-file offset-file-name?)))\n  (define out-sort-value    (open-output-file fname-sort-value))\n  (define out-sort-offset   (open-output-file fname-sort-offset))\n  (define ms (multi-sorter out-sort-value out-sort-offset type value<))\n  (method-lambda\n    ((put! value) (ms 'put! value))\n    ((close)\n     (match-define (vector initial-item-count chunk-count v?) (ms 'close))\n     (close-output-port out-sort-value)\n     (close-output-port out-sort-offset)\n     (define omax (if v? (sizeof `#(array ,initial-item-count ,type) v?)\n                    (file-size fname-sort-value)))\n     (define otype (and out-offset (nat-type/max omax)))\n     (define item-count\n       (cond (v? (let loop ((prev #f) (i 0) (count 0))\n                   (if (= i initial-item-count) count\n                     (let ((x (vector-ref v? i)))\n                       (cond ((not (and dedup? (< 0 i) (equal? x prev)))\n                              (when out-offset\n                                (encode out-offset otype (file-position\n                                                           out-value)))\n                              (encode out-value type x)\n                              (loop x (+ i 1) (+ count 1)))\n                             (else (loop x (+ i 1) count)))))))\n             (else (let/files ((in fname-sort-value)\n                               (in-offset fname-sort-offset)) ()\n                     (multi-merge dedup? out-value out-offset type otype value<\n                                  chunk-count in in-offset)))))\n     (delete-file fname-sort-value)\n     (delete-file fname-sort-offset)\n     (close-output-port out-value)\n     (when out-offset (close-output-port out-offset))\n     (cons otype item-count))))\n\n(define (multi-sorter out-chunk out-offset type value<)\n  (define buffer-size (current-config-ref 'buffer-size))\n  (let ((v (make-vector buffer-size)) (chunk-count 0) (item-count 0) (i 0))\n    (method-lambda\n      ((put! value) (vector-set! v i value)\n                    (set! i (+ i 1))\n                    (when (= i buffer-size)\n                      (vector-sort! v value<)\n                      (for ((x (in-vector v))) (encode out-chunk type x))\n                      (encode out-offset 'nat (file-position out-chunk))\n                      (set! item-count  (+ item-count buffer-size))\n                      (set! chunk-count (+ chunk-count 1))\n                      (set! i           0)))\n      ((close) (vector-sort! v value< 0 i)\n               (cond ((and (< 0 chunk-count) (= i 0))\n                      (vector item-count chunk-count #f))\n                     ((< 0 chunk-count)\n                      (for ((i (in-range i)))\n                        (encode out-chunk type (vector-ref v i)))\n                      (encode out-offset 'nat (file-position out-chunk))\n                      (vector (+ item-count i) (+ chunk-count 1) #f))\n                     (else (vector i 0 v)))))))\n\n(define (multi-merge\n          dedup? out out-offset type otype v< chunk-count in in-offset)\n  (define (s< sa sb) (v< (car sa) (car sb)))\n  (define (s-chunk pos end)\n    (cond ((<= end pos) '())\n          (else (file-position in pos)\n                (cons (decode in type) (let ((pos (file-position in)))\n                                         (thunk (s-chunk pos end)))))))\n  (define heap (make-vector chunk-count))\n  (let loop ((hi 0) (start 0)) (when (< hi chunk-count)\n                                 (define end (decode in-offset 'nat))\n                                 (vector-set! heap hi (s-chunk start end))\n                                 (loop (+ hi 1) end)))\n  (heap! s< heap chunk-count)\n  (let loop ((prev #f) (i 0) (hend chunk-count))\n    (if (= hend 0) i\n      (let* ((top (heap-top heap)) (x (car top)) (top (s-force (cdr top))))\n        (loop x (cond ((not (and dedup? (< 0 i) (equal? x prev)))\n                       (when out-offset (encode out-offset otype\n                                                (file-position out)))\n                       (encode out type x)\n                       (+ i 1))\n                      (else i))\n              (cond ((null? top) (heap-remove!  s< heap hend)  (- hend 1))\n                    (else        (heap-replace! s< heap hend top) hend)))))))\n\n(define (heap-top h) (vector-ref h 0))\n(define (heap! ? h end)\n  (let loop ((i (- (quotient end 2) 1)))\n    (when (<= 0 i) (heap-sink! ? h end i) (loop (- i 1)))))\n(define (heap-remove! ? h end)\n  (vector-set! h 0 (vector-ref h (- end 1))) (heap-sink! ? h (- end 1) 0))\n(define (heap-replace! ? h end top)\n  (vector-set! h 0 top)                      (heap-sink! ? h    end    0))\n(define (heap-sink! ? h end i)\n  (let loop ((i i))\n    (let ((ileft (+ i i 1)) (iright (+ i i 2)))\n      (cond ((<= end ileft))  ;; done\n            ((<= end iright)\n             (let ((p (vector-ref h i)) (l (vector-ref h ileft)))\n               (when (? l p) (vector-set! h i l) (vector-set! h ileft p))))\n            (else (let ((p (vector-ref h i))\n                        (l (vector-ref h ileft)) (r (vector-ref h iright)))\n                    (cond ((? l p) (cond ((? r l) (vector-set! h i r)\n                                                  (vector-set! h iright p)\n                                                  (loop iright))\n                                         (else (vector-set! h i l)\n                                               (vector-set! h ileft p)\n                                               (loop ileft))))\n                          ((? r p) (vector-set! h i r)\n                                   (vector-set! h iright p)\n                                   (loop iright)))))))))\n(define (heap-add! ? h end v)\n  (let loop ((i end))\n    (if (= i 0) (vector-set! h i v)\n      (let* ((iparent (- (quotient (+ i 1) 2) 1))\n             (pv      (vector-ref h iparent)))\n        (cond ((? v pv) (vector-set! h i pv) (loop iparent))\n              (else     (vector-set! h i v)))))))\n\n(define (list-arranger input-names output-names)\n  (define ss.in    (generate-temporaries input-names))\n  (define name=>ss (make-immutable-hash (map cons input-names ss.in)))\n  (define ss.out   (map (lambda (n) (hash-ref name=>ss n)) output-names))\n  (eval-syntax #`(lambda (row)\n                   (match-define (list #,@ss.in) row)\n                   (list #,@ss.out))))\n\n(define (table-materializer source-names path.dir fprefix\n                            column-names column-types key-name)\n  (define t (tabulator path.dir fprefix column-names column-types key-name))\n  (define transform (list-arranger source-names column-names))\n  (method-lambda\n    ((put! x) (t 'put! (transform x)))\n    ((close)  (t 'close))))\n\n(define (materialize-index-tables!\n          path.dir source-fprefix name->type source-names index-descriptions)\n  (cond ((null? index-descriptions) '())\n        (else\n          (define threshold (current-config-ref 'progress-logging-threshold))\n          (define index-ms\n            (map (lambda (td)\n                   (define fprefix      (alist-ref td 'file-prefix))\n                   (define column-names (alist-ref td 'column-names))\n                   (define column-types (map name->type column-names))\n                   (table-materializer source-names path.dir fprefix\n                                       column-names column-types #f))\n                 index-descriptions))\n          (logf \"Materializing ~s index table(s) from primary:\\n\"\n                (length index-ms))\n          (for-each (lambda (td) (pretty-write (alist-ref td 'column-names)))\n                    index-descriptions)\n          (let/files ((in (value-table-file-name source-fprefix))) ()\n            (define src (s-decode in (map name->type (cdr source-names))))\n            (time (s-each (lambda (x)\n                            (let ((count (car x)))\n                              (when (= 0 (remainder count threshold))\n                                (logf \"ingested ~s rows\\n\" count))\n                              (for-each (lambda (m) (m 'put! x)) index-ms)))\n                          (s-enumerate 0 src))))\n          (logf \"Processing all rows\\n\")\n          (map (lambda (m) (time (m 'close))) index-ms))))\n\n(define (valid-key-type? t)\n  (match t\n    ((or #f 'nat 'number `#(nat ,_)) #t)\n    (_                               #f)))\n\n(define (materializer path.dir source-info attribute-names attribute-types key-name\n                      table-layouts)\n  (define name=>type (make-immutable-hash (map cons attribute-names attribute-types)))\n  (define index-layouts        (cdr table-layouts))\n  (define primary-column-names (car table-layouts))\n  (define primary-source-names (cons key-name primary-column-names))\n  (define primary-column-types (map (lambda (n) (hash-ref name=>type n))\n                                    primary-column-names))\n  (make-directory* path.dir)\n  (define path.metadata (path->string (build-path path.dir metadata-file-name)))\n  (define primary-fprefix \"primary\")\n  (define primary-fname (path->string (build-path path.dir primary-fprefix)))\n  (define index-fprefixes\n    (map (lambda (i) (string-append \"index.\" (number->string i)))\n         (range (length index-layouts))))\n  (define primary-t (tabulator path.dir primary-fprefix\n                               primary-column-names primary-column-types key-name))\n  (method-lambda\n    ((put! x) (primary-t 'put! x))\n    ((close) (define primary-info (primary-t 'close))\n             (define key-type (nat-type/max (alist-ref primary-info 'length)))\n             (define name->type\n               (let ((name=>type (hash-set name=>type key-name key-type)))\n                 (lambda (n) (hash-ref name=>type n))))\n             (define index-infos\n               (materialize-index-tables!\n                 path.dir primary-fname name->type primary-source-names\n                 (map (lambda (fprefix td) `((file-prefix . ,fprefix)\n                                             (column-names . ,td)))\n                      index-fprefixes index-layouts)))\n             (write-metadata path.metadata attribute-names attribute-types\n                             primary-info index-infos source-info))))\n\n(define (write-metadata path attribute-names attribute-types primary-info index-infos source-info)\n  (let/files () ((out.metadata path))\n    (pretty-write `((metadata-format-version . ,metadata-format-version.latest)\n                    (attribute-names         . ,attribute-names)\n                    (attribute-types         . ,attribute-types)\n                    (primary-table           . ,primary-info)\n                    (index-tables            . ,index-infos)\n                    (source-info             . ,source-info))\n                  out.metadata)))\n\n(define (update-metadata path info)\n  (define path.backup (string-append path \".backup\"))\n  (when (file-exists? path.backup)\n    (error \"backup path already exists:\" path.backup))\n  (rename-file-or-directory path path.backup)\n  (apply write-metadata path\n         (map (lambda (k) (hash-ref info k))\n              '(attribute-names attribute-types primary-table index-tables source-info)))\n  (delete-file path.backup))\n\n(define (metadata/2020-12-19.0 info)\n  (define source-info (make-immutable-hash (hash-ref info 'source-info)))\n  (define source-info.new\n    (foldl (lambda (k v source-info) (hash-set source-info k v))\n           (hash-remove source-info 'transform)\n           '(map/append map filter)\n           (list (hash-ref source-info 'map/append #f)\n                 (hash-ref source-info 'map        (hash-ref source-info 'transform #f))\n                 (hash-ref source-info 'filter     #f))))\n  (foldl (lambda (k v info) (hash-set info k v))\n         info\n         '(metadata-format-version source-info)\n         `(2021-03-18.0\n           ,(if (hash-has-key? source-info.new 'path)\n              (map (lambda (k) (cons k (hash-ref source-info.new k)))\n                   '(path format header stats map/append map filter))\n              (map (lambda (k) (cons k (hash-ref source-info.new k)))\n                   '(stream map/append map filter))))))\n\n(define (metadata/2021-03-18.0 info)\n  ;; TODO: define an appropriate transformtion once this is no longer the latest version\n  info)\n\n;; TODO: when new metadata formats are introduced, update the old handlers to\n;; have them transform an instance of the old format into an instance of the\n;; newest format.  This can be done by composing handlers.\n\n;; TODO: register new metadata-format-version handlers here\n(define metadata-format-version.latest '2021-03-18.0)\n(define metadata/format-version\n  (hash '2021-03-18.0 metadata/2021-03-18.0\n        '2020-12-19.0 metadata/2020-12-19.0))\n\n(define (read-metadata path)\n  (define info.0 (let/files ((in path)) () (read in)))\n  (when (eof-object? info.0) (error \"corrupt relation metadata:\" path))\n  (define info.1 (make-immutable-hash info.0))\n  (define info ((hash-ref metadata/format-version\n                          (hash-ref info.1 'metadata-format-version '2020-12-19.0))\n                info.1))\n  (define diff\n    (foldl (lambda (k diff)\n             (cond ((not (hash-has-key? info   k)) (cons `(,k old: ,(hash-ref info.1 k)) diff))\n                   ((not (hash-has-key? info.1 k)) (cons `(,k new: ,(hash-ref info   k)) diff))\n                   (else (define v.new (hash-ref info   k))\n                         (define v.old (hash-ref info.1 k))\n                         (if (equal? v.new v.old) diff\n                           (cons `(,k old: ,v.old new: ,v.new) diff)))))\n           '()\n           (set->list (set-union (list->set (hash-keys info))\n                                 (list->set (hash-keys info.1))))))\n  (define should-update?\n    (and (not (null? diff))\n         (policy-allow?\n           (current-config-ref 'update-policy)\n           (lambda ()\n             (printf \"Current ~s is written in an old format:\\n\" path)\n             (for-each pretty-write diff))\n           \"Update ~s to the latest format?\" (list path))))\n  (when should-update? (update-metadata path info))\n  info)\n\n(define (update-materialization! path.dir info tables.added tables.removed)\n  (define path.metadata        (path->string\n                                 (build-path path.dir metadata-file-name)))\n  (define path.metadata.backup (string-append path.metadata \".backup\"))\n  (define attribute-names      (hash-ref info 'attribute-names))\n  (define attribute-types      (hash-ref info 'attribute-types))\n  (define source-info          (hash-ref info 'source-info))\n  (define primary-info         (hash-ref info 'primary-table))\n  (define index-infos          (hash-ref info 'index-tables))\n  (define primary-key-name     (alist-ref primary-info 'key-name))\n  (define primary-column-names (alist-ref primary-info 'column-names))\n  (define source-fprefix\n    (path->string (build-path path.dir (alist-ref primary-info 'file-prefix))))\n  (define source-names (cons primary-key-name primary-column-names))\n  (define key-type (nat-type/max (alist-ref primary-info 'length)))\n  (define name=>type (make-immutable-hash\n                       (cons (cons primary-key-name key-type)\n                             (map cons attribute-names attribute-types))))\n  (define (name->type n) (hash-ref name=>type n))\n  (define cols=>info\n    (make-immutable-hash\n      (map (lambda (info.it) (cons (alist-ref info.it 'column-names) info.it))\n           (hash-ref info 'index-tables))))\n  (define index-infos.current\n    (hash-values (foldl (lambda (cols c=>i) (hash-remove c=>i cols))\n                        cols=>info tables.removed)))\n  (rename-file-or-directory path.metadata path.metadata.backup)\n  (for-each\n    (lambda (cols)\n      (define info    (hash-ref cols=>info cols))\n      (define fprefix (alist-ref info 'file-prefix))\n      (define fname.v\n        (path->string (build-path path.dir (value-table-file-name  fprefix))))\n      (define fname.o\n        (path->string (build-path path.dir (offset-table-file-name fprefix))))\n      (logf \"Deleting ~s\\n\" fname.v)\n      (delete-file fname.v)\n      (when (alist-ref info 'offset-file)\n        (logf \"Deleting ~s\\n\" fname.o)\n        (delete-file fname.o)))\n    tables.removed)\n  (define index-descriptions.added\n    (let loop ((colss tables.added) (i 0))\n      (if (null? colss) '()\n        (let ((fprefix (string-append \"index.\" (number->string i))))\n          (if (file-exists?\n                (build-path path.dir (value-table-file-name fprefix)))\n            (loop colss (+ i 1))\n            (cons `((file-prefix  . ,fprefix) (column-names . ,(car colss)))\n                  (loop (cdr colss) (+ i 1))))))))\n  (define index-infos.new\n    (materialize-index-tables! path.dir source-fprefix name->type\n                               source-names index-descriptions.added))\n  (write-metadata path.metadata attribute-names attribute-types\n                  primary-info (append index-infos.current index-infos.new)\n                  source-info)\n  (delete-file path.metadata.backup))\n\n(define (materialization/vector vector.in sort? dedup? info)\n  (define key-name        (hash-ref info 'key-name))\n  (define attribute-names (hash-ref info 'attribute-names))\n  (define attribute-types (hash-ref info 'attribute-types))\n  (define table-layouts   (hash-ref info 'table-layouts))\n  (define name=>type      (hash-set (make-immutable-hash\n                                      (map cons attribute-names attribute-types))\n                                    key-name 'nat))\n  (define (name->type n) (hash-ref name=>type n))\n  (define primary-column-names (car table-layouts))\n  (define primary-column-types (map name->type primary-column-names))\n  (define primary-source-names (cons key-name primary-column-names))\n  (when sort? (vector-table-sort! primary-column-types vector.in))\n  (define primary-v (if dedup? (vector-dedup vector.in) vector.in))\n  (define primary-t (table/vector key-name primary-column-names\n                                  primary-column-types primary-v))\n  (define index-ts\n    (let* ((ss.sources (generate-temporaries primary-source-names))\n           (name=>ss   (make-immutable-hash\n                         (map cons primary-source-names ss.sources)))\n           (name->ss   (lambda (n) (hash-ref name=>ss n))))\n      (map (lambda (column-names)\n             (define column-types (map name->type column-names))\n             (define ss.columns   (map name->ss   column-names))\n             (define index-src\n               (let ((transform\n                       (eval-syntax\n                         #`(lambda (#,(car ss.sources) row)\n                             (match-define (vector #,@(cdr ss.sources)) row)\n                             (vector #,@ss.columns))))\n                     (iv (make-vector (vector-length primary-v))))\n                 (for ((i   (in-range (vector-length primary-v)))\n                       (row (in-vector primary-v)))\n                   (vector-set! iv i (transform i row)))\n                 iv))\n             (vector-table-sort! column-types index-src)\n             (table/vector #f column-names column-types\n                           (vector-dedup index-src)))\n           (cdr table-layouts))))\n  (list info (table (cons primary-t index-ts))))\n\n(define (materialization/path relation-name retrieval-type path path.dir info)\n  (unless (directory-exists? path.dir)\n    (error \"materialized relation directory does not exist:\" path.dir))\n  (define attribute-names    (hash-ref info 'attribute-names))\n  (define attribute-types    (hash-ref info 'attribute-types))\n  (define primary-info-alist (hash-ref info 'primary-table))\n  (define primary-info       (make-immutable-hash primary-info-alist))\n  (define primary-t          (table/metadata retrieval-type path.dir primary-info-alist))\n  (define key-name           (hash-ref primary-info 'key-name))\n  (define index-ts\n    (map (lambda (info) (table/metadata retrieval-type path.dir info))\n         (hash-ref info 'index-tables '())))\n  (list (foldl (lambda (k v info) (hash-set info k v)) info\n               '(    relation-name key-name retrieval-type)\n               (list relation-name key-name retrieval-type))\n        (table (cons primary-t index-ts))))\n\n(define (materialization . pargs)\n  (define kwargs          (make-immutable-hash (plist->alist pargs)))\n  (define key-name        (hash-ref kwargs 'key-name #t))\n  (define attribute-names (hash-ref kwargs 'attribute-names))\n  (define attribute-types (hash-ref kwargs 'attribute-types\n                                    (map (lambda (n)\n                                           (if (equal? n key-name) 'nat #f))\n                                         attribute-names)))\n  (define table-layouts\n    (append (hash-ref kwargs 'tables `(,(remove key-name attribute-names)))\n            (map (lambda (cols) (append cols (list key-name)))\n                 (hash-ref kwargs 'indexes '()))))\n  (unless key-name (error \"key-name cannot be #f:\" pargs))\n  (unless (= (length (remove-duplicates attribute-names))\n             (length attribute-names))\n    (error \"duplicate attribute-names:\" attribute-names))\n  (unless (= (length attribute-names) (length attribute-types))\n    (error \"mismatching attribute names and types:\"\n           attribute-names attribute-types))\n  (when (null? table-layouts)\n    (error \"empty list of table layouts for:\" attribute-names))\n  (let ((primary-column-names (car table-layouts))\n        (key-type             (alist-ref (map cons attribute-names attribute-types)\n                                         key-name 'nat)))\n    (when (member key-name primary-column-names)\n      (error \"key-name should not be a primary table column:\"\n             key-name primary-column-names))\n    (unless (set=? (set-remove attribute-names key-name) primary-column-names)\n      (error \"primary columns must include all non-key attributes:\"\n             (set->list (set-remove (list->set attribute-names) key-name))\n             (set->list (list->set primary-column-names))))\n    (unless (valid-key-type? key-type)\n      (error \"invalid key type:\" key-type key-name)))\n  (define path           (hash-ref kwargs 'path #f))\n  (define path.dir       (and path (current-config-relation-path path)))\n  (define path.metadata  (and path.dir (path->string (build-path path.dir metadata-file-name))))\n  (define (get-metadata) (and path.metadata (directory-exists? path.dir) (read-metadata path.metadata)))\n  (define metadata       (get-metadata))\n  (define src:vector.0   (hash-ref kwargs 'source-vector    #f))\n  (define src:stream     (hash-ref kwargs 'source-stream    #f))\n  (define src:path.0     (hash-ref kwargs 'source-file-path #f))\n  (define src:path       (and src:path.0 (current-config-relation-path src:path.0)))\n  (when (< 1 (length (filter-not not (list src:vector.0 src:stream src:path.0))))\n    (error \"relation cannot specify multiple data sources:\" pargs))\n  (let ((map/append-code (hash-ref kwargs 'map/append #f))\n        (map-code        (hash-ref kwargs 'map        #f))\n        (filter-code     (hash-ref kwargs 'filter     #f)))\n    (when (and map/append-code (or map-code filter-code))\n      (error \"map/append should not be used with map or filter:\"\n             `((map/append ,(code->info map/append-code))\n               (map        ,(code->info map-code))\n               (filter     ,(code->info filter-code))))))\n  (define src:format (or (hash-ref kwargs 'source-file-format #f)\n                         (and src:path.0 (path->format src:path.0))))\n  (define src:header (let ((header (hash-ref kwargs 'source-file-header '())))\n                       (if (pair? header)\n                         (map (lambda (s) (if (symbol? s) (symbol->string s) s))\n                              header)\n                         header)))\n  (define src:vector\n    (or src:vector.0\n        (and (not metadata)\n             (not src:stream)\n             (not (and src:path (file-exists? src:path)))\n             (policy-allow?\n               (current-config-ref 'allow-missing-data-policy)\n               (lambda ()\n                 (printf \"Source (~s) and processed data are both missing for ~s:\\n\"\n                         src:path.0 path))\n               \"Allow ~s to be used as an empty relation for now?\" (list path))\n             (vector))))\n  (define kwargs.1 (foldl (lambda (k v kvs) (hash-set kvs k v)) kwargs\n                          '(    path     key-name attribute-types table-layouts)\n                          (list path.dir key-name attribute-types table-layouts)))\n  (cond (src:vector\n          ;; TODO: currently only supported for vector sources\n          (define sort?  (hash-ref kwargs 'sort?  (not src:vector)))\n          (define dedup? (hash-ref kwargs 'dedup? (not src:vector)))\n          (when (and (not sort?) dedup?)\n            (error \"Cannot deduplicate without sorting:\" kwargs))\n          (materialization/vector src:vector sort? dedup?\n                                  (hash-set kwargs.1 'missing-data?\n                                            (not (hash-ref kwargs.1 'source-vector #f)))))\n        (path                       (when (or src:path.0 src:stream)\n                                      (materialize-relation! path path.dir path.metadata metadata\n                                                             src:path src:format src:header kwargs.1))\n                                    (materialization/path (hash-ref kwargs 'relation-name)\n                                                          (hash-ref kwargs 'retrieval-type 'disk)\n                                                          path path.dir (hash-set (get-metadata) 'path path.dir)))\n        ((or src:path.0 src:stream) (materialization/stream src:path src:format src:header kwargs.1))\n        (else                       (error \"missing relation path or source:\" kwargs))))\n\n(struct value+syntax (value syntax) #:prefab)\n(define-syntax-rule (value/syntax e) (value+syntax e #'e))\n(define (code->info code)\n  (cond ((procedure?    code) #t)\n        ((value+syntax? code) (syntax->datum (value+syntax-syntax code)))\n        (else                 code)))\n(define (code->value code)\n  (cond ((value+syntax? code) (value+syntax-value code))\n        (else                 code)))\n\n(define (materialization/stream path.in format header kwargs)\n  (define key-name        (hash-ref kwargs 'key-name))\n  (define attribute-names (hash-ref kwargs 'attribute-names))\n  (define attribute-types (hash-ref kwargs 'attribute-types))\n  (define table-layouts   (hash-ref kwargs 'table-layouts))\n  (define stream.in       (hash-ref kwargs 'source-stream #f))\n  (define map/append-code (hash-ref kwargs 'map/append    #f))\n  (define map-code        (hash-ref kwargs 'map           #f))\n  (define filter-code     (hash-ref kwargs 'filter        #f))\n  (define map/append?     (code->value map/append-code))\n  (define map?            (code->value map-code))\n  (define filter?         (code->value filter-code))\n  (define (materialized-stream stream)\n    (list->vector (s-take #f (s-map list->vector\n                                    (if map/append?\n                                      (s-map/append map/append? stream)\n                                      (let ((s (if map? (s-map map? stream) stream)))\n                                        (if filter? (s-filter filter? s) s)))))))\n  (materialization/vector\n    (if path.in\n      (let/files ((in path.in)) ()\n        (define stream ((format->header/port->stream format) header in))\n        (materialized-stream stream))\n      (materialized-stream (code->value stream.in)))\n    #t #t kwargs))\n\n(define (materialize-relation! path path.dir path.metadata info path.in format header kwargs)\n  (define path            (hash-ref kwargs 'path))\n  (define key-name        (hash-ref kwargs 'key-name))\n  (define attribute-names (hash-ref kwargs 'attribute-names))\n  (define attribute-types (hash-ref kwargs 'attribute-types))\n  (define table-layouts   (hash-ref kwargs 'table-layouts))\n  (define fn.in           (hash-ref kwargs 'source-file-path #f))\n  (define stream.in       (hash-ref kwargs 'source-stream    #f))\n  (define map/append-code (hash-ref kwargs 'map/append       #f))\n  (define map-code        (hash-ref kwargs 'map              #f))\n  (define filter-code     (hash-ref kwargs 'filter           #f))\n  (define threshold       (current-config-ref 'progress-logging-threshold))\n  (define path.log        (build-path path.dir \"progress.log\"))\n  (define source-info\n    (cond (path.in   `((path       . ,fn.in)\n                       (format     . ,format)\n                       (header     . ,header)\n                       (stats      . ,(or (file-stats path.in)\n                                          (and info (alist-ref (hash-ref info 'source-info '())\n                                                               'stats #f))))\n                       (map/append . ,(code->info map/append-code))\n                       (map        . ,(code->info map-code))\n                       (filter     . ,(code->info filter-code))))\n          (stream.in `((stream     . ,(code->info stream.in))\n                       (map/append . ,(code->info map/append-code))\n                       (map        . ,(code->info map-code))\n                       (filter     . ,(code->info filter-code))))\n          (else (error \"materialize-relation! missing file or stream source:\"\n                       kwargs))))\n  (define map/append? (code->value map/append-code))\n  (define map?        (code->value map-code))\n  (define filter?     (code->value filter-code))\n  (define (materialize-stream source-info stream)\n    (let ((mat (materializer path.dir source-info\n                             attribute-names attribute-types key-name\n                             table-layouts)))\n      (define count 0)\n      (time (s-each (lambda (x)\n                      (when (= 0 (remainder count threshold))\n                        (logf \"ingested ~s rows\\n\" count))\n                      (mat 'put! x)\n                      (set! count (+ count 1)))\n                    (if map/append?\n                      (s-map/append map/append? stream)\n                      (let ((s (if map? (s-map map? stream) stream)))\n                        (if filter? (s-filter filter? s) s)))))\n      (logf \"Processing ~s rows\\n\" count)\n      (time (mat 'close))\n      (logf \"Finished processing ~s rows\\n\" count)))\n  (define (materialize-source)\n    (if path.in\n      (let/files ((in path.in)) ()\n        (logf/date \"Materializing relation ~s from ~s file ~s\\n\"\n                   path format fn.in)\n        (define stream ((format->header/port->stream format) header in))\n        (materialize-stream source-info stream))\n      (begin (logf/date \"Materializing relation ~s from stream\\n\" path)\n             (materialize-stream source-info (code->value stream.in)))))\n\n  (if info\n    (let* ((source-info.old     (hash-ref info 'source-info #f))\n           (attribute-names.old (hash-ref info 'attribute-names))\n           (attribute-types.old (hash-ref info 'attribute-types))\n           (primary-table.old   (hash-ref info 'primary-table))\n           (key-name.old        (alist-ref primary-table.old 'key-name))\n           (primary-columns.old (alist-ref primary-table.old 'column-names))\n           (primary-columns.new (car table-layouts)))\n      (unless (equal? attribute-names attribute-names.old)\n        (error \"new relation attributes are incompatible with old:\" path\n               'new: attribute-names 'old: attribute-names.old))\n      (define stale-fields.0\n        (map (lambda (desc)\n               (match-define (list key new old) desc)\n               `(,key new: ,new old: ,old))\n             (filter\n               (lambda (desc)\n                 (match-define (list _ new old) desc)\n                 (not (equal? new old)))\n               `((source-info     ,source-info     ,source-info.old)\n                 (attribute-types ,attribute-types ,attribute-types.old)\n                 (key-name        ,key-name        ,key-name.old)\n                 (primary-table   ,primary-columns.new\n                                  ,primary-columns.old)))))\n      (define update-policy  (current-config-ref 'update-policy))\n      (define cleanup-policy (current-config-ref 'cleanup-policy))\n      (define stale-fields\n        (if (and (equal? '(source-info) (map car stale-fields.0))\n                 (policy-allow?\n                   update-policy\n                   (lambda ()\n                     (printf \"Existing source-info for relation ~s is stale:\\n\" path)\n                     (for-each pretty-write stale-fields.0))\n                   \"Update ~s metadata with new source-info without rematerializing?\" (list path)))\n          (begin (printf \"Updating ~s\" path.metadata)\n                 (update-metadata path.metadata (hash-set info 'source-info source-info))\n                 (printf \"Update of ~s finished\" path.metadata)\n                 '())\n          stale-fields.0))\n      (define allow-update?\n        (or (null? stale-fields)\n            (policy-allow?\n              update-policy\n              (lambda ()\n                (printf \"Existing data for relation ~s is stale:\\n\" path)\n                (for-each pretty-write stale-fields))\n              \"Update ~s?\" (list path))))\n      (cond ((and (pair? stale-fields) allow-update?)\n             (printf \"Updating ~s\\n\" path)\n             (define path.backup (string-append path.dir \".backup\"))\n             (when (directory-exists? path.backup)\n               (error \"backup path already exists:\" path.backup))\n             (rename-file-or-directory path.dir path.backup)\n             (materialize-source)\n             (printf \"Rematerialization of ~s finished\\n\" path)\n             (when (directory-exists? path.backup)\n               (if (or (equal? cleanup-policy 'always)\n                       (and (equal? cleanup-policy 'interactive)\n                            (printf \"Delete backup directory ~s? [y/n]: \"\n                                    path.backup)\n                            (case (read)\n                              ((y Y yes Yes YES) #t)\n                              (else              #f))))\n                 (begin (printf \"Deleting ~s\\n\" path.backup)\n                        (delete-directory/files path.backup #:must-exist? #f))\n                 (printf \"Not deleting ~s\\n\" path.backup))))\n            ((not allow-update?)\n             (printf \"Due to stale data, will not rematerialize ~s\\n\" path))\n            (else\n              (define colss.current\n                (map (lambda (info.it) (alist-ref info.it 'column-names))\n                     (hash-ref info 'index-tables)))\n              (define colss.new (cdr table-layouts))\n              (define (cols-current? cols) (member cols colss.current))\n              (define (cols-new?     cols) (member cols colss.new))\n              (define added   (filter-not cols-current? colss.new))\n              (define removed (filter-not cols-new?     colss.current))\n              (define add?\n                (and (pair? added)\n                     (policy-allow?\n                       update-policy\n                       (lambda ()\n                         (printf \"New index tables included for relation ~s:\\n\"\n                                 path)\n                         (for-each pretty-write added))\n                       \"Add these new index tables to ~s?\"\n                       (list path))))\n              (define remove?\n                (and (pair? removed)\n                     (policy-allow?\n                       cleanup-policy\n                       (lambda ()\n                         (printf\n                           \"Index tables no longer included for relation ~s:\\n\"\n                           path)\n                         (for-each pretty-write removed))\n                       \"Remove these old index tables from ~s?\"\n                       (list path))))\n              (when (or add? remove?)\n                (update-materialization! path.dir info\n                                         (if add?    added   '())\n                                         (if remove? removed '()))))))\n    (materialize-source)))\n"
  },
  {
    "path": "medikanren2/dbk/dbk.rkt",
    "content": "#lang racket/base\n(provide\n  (all-from-out\n    \"dbk/codec.rkt\" \"dbk/config.rkt\" \"dbk/dsv.rkt\" \"dbk/misc.rkt\" \"dbk/mk.rkt\"\n    \"dbk/order.rkt\" \"dbk/stream.rkt\" \"dbk/table.rkt\"))\n(require\n  \"dbk/codec.rkt\" \"dbk/config.rkt\" \"dbk/dsv.rkt\" \"dbk/misc.rkt\" \"dbk/mk.rkt\"\n  \"dbk/order.rkt\" \"dbk/stream.rkt\" \"dbk/table.rkt\")\n"
  },
  {
    "path": "medikanren2/dbk/test/.gitignore",
    "content": "/benchmark1\n"
  },
  {
    "path": "medikanren2/dbk/test/benchmark-sorting/radix-sort.rkt",
    "content": "#lang racket/base\n(require racket/fixnum racket/match racket/vector racket/unsafe/ops)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Enumerators\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (vector->enumerator v (start 0) (end (vector-length v)))\n  (define len (min end (vector-length v)))\n  (unsafe-vector->enumerator v (min start len) len))\n\n(define ((unsafe-vector->enumerator v (start 0) (end (unsafe-vector*-length v))) k!)\n  (let loop ((i start))\n    (when (unsafe-fx< i end)\n      (k!   (unsafe-vector*-ref v i))\n      (loop (unsafe-fx+ i 1)))))\n\n(define ((enumerator-append e.0 e.1) k!)\n  (e.0 k!)\n  (e.1 k!))\n\n(define ((enumerator-msd-radix-sort en t->key key-byte-count) k!)\n  (define size.shift           8)\n  (define mask.shift         255)\n  (define count.parts        256)\n  (define count.buffer        32)\n  (define count.initial.parts  8)\n  (define growth-factor.parts  2)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (let enumerate ((shift (unsafe-fx* 8 (unsafe-fx- key-byte-count 1))) (en en))\n    (define parts     (make-vector count.parts))\n    (define pos.parts (make-vector count.parts 0))\n    (define buf       (make-vector count.parts))\n    (define pos       (make-vector count.parts 0))\n    (let loop ((i 0))\n      (when (unsafe-fx< i count.parts)\n        (unsafe-vector*-set! parts i (make-vector count.initial.parts))\n        (unsafe-vector*-set! buf   i (make-vector count.buffer))\n        (loop (unsafe-fx+ i 1))))\n    (en (lambda (t)\n          ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n          (let* ((key     (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n                 (buf.k   (unsafe-vector*-ref buf key))\n                 (pos.k   (unsafe-vector*-ref pos key))\n                 (pos.k+1 (unsafe-fx+ pos.k 1)))\n            (unsafe-vector*-set! buf.k pos.k t)\n            (if (unsafe-fx= pos.k+1 count.buffer)\n              (begin\n                (unsafe-vector*-set! pos key 0)\n                (unsafe-vector*-set! buf key (make-vector count.buffer))\n                (let* ((parts.k       (unsafe-vector*-ref parts     key))\n                       (pos.parts.k   (unsafe-vector*-ref pos.parts key))\n                       (pos.parts.k+1 (unsafe-fx+ pos.parts.k 1))\n                       (len.parts.k   (unsafe-vector*-length parts.k)))\n                  (unsafe-vector*-set! pos.parts key pos.parts.k+1)\n                  (if (unsafe-fx= pos.parts.k+1 len.parts.k)\n                    (let ((parts.k.new (make-vector (unsafe-fx* len.parts.k growth-factor.parts))))\n                      (unsafe-vector*-set!  parts key parts.k.new)\n                      (vector-copy! parts.k.new 0 parts.k)\n                      (unsafe-vector*-set!  parts.k.new pos.parts.k buf.k))\n                    (unsafe-vector*-set! parts.k pos.parts.k buf.k))))\n              (unsafe-vector*-set! pos key pos.k+1)))))\n    (let ((k!/en (if (unsafe-fx= shift 0)\n                   (lambda (en) (en k!))\n                   (lambda (en) (enumerate (unsafe-fx- shift size.shift) en)))))\n      (let loop ((i 0))\n        (when (unsafe-fx< i count.parts)\n          (let ((parts.i     (unsafe-vector*-ref parts     i))\n                (pos.parts.i (unsafe-vector*-ref pos.parts i))\n                (buf.i       (unsafe-vector*-ref buf       i))\n                (pos.i       (unsafe-vector*-ref pos       i)))\n            (unsafe-vector*-set! parts i #f)\n            (unsafe-vector*-set! buf   i #f)\n            (k!/en (lambda (k!)\n                     ((unsafe-vector->enumerator parts.i 0 pos.parts.i)\n                      (lambda (part) ((unsafe-vector->enumerator part 0 count.buffer) k!)))\n                     ((unsafe-vector->enumerator buf.i 0 pos.i) k!)))\n            (loop (unsafe-fx+ i 1))))))))\n\n(define (vector-radix-sort! v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define len (min end (vector-length v)))\n  (unsafe-vector-radix-sort! v t->key key-byte-count (min start len) len))\n\n(define (unsafe-vector-radix-sort! v t->key key-byte-count (start 0) (end (unsafe-vector*-length v)))\n  (define size.shift               8)\n  (define mask.shift             255)\n  (define count.parts            256)\n  (define count.buffer           512)\n  (define count.initial.parts      8)\n  (define growth-factor.parts      2)\n  (define count.initial.buffers 1024)\n  (define growth-factor.buffers    2)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (define shift.final (unsafe-fx* 8 (unsafe-fx- key-byte-count 1)))\n  (define buffers     (make-vector count.initial.buffers))\n  (define pos.buffers 0)\n  (define (new-buffer)\n    (if (unsafe-fx= pos.buffers 0)\n      (make-vector count.buffer)\n      (begin (set! pos.buffers (unsafe-fx- pos.buffers 1))\n             (unsafe-vector*-ref buffers pos.buffers))))\n  (define (free-buffer b)\n    (vector-fill! b 0)\n    (when (unsafe-fx= pos.buffers (unsafe-vector*-length buffers))\n      (let ((buffers.new (make-vector (unsafe-fx* pos.buffers growth-factor.buffers))))\n        (vector-copy! buffers.new 0 buffers)\n        (set! buffers buffers.new)))\n    (unsafe-vector*-set! buffers pos.buffers b)\n    (set! pos.buffers (unsafe-fx+ pos.buffers 1)))\n  (let loop ((shift 0))\n    (define parts     (make-vector count.parts))\n    (define pos.parts (make-vector count.parts 0))\n    (define buf       (make-vector count.parts))\n    (define pos       (make-vector count.parts 0))\n    (let loop ((i 0))\n      (when (unsafe-fx< i count.parts)\n        (unsafe-vector*-set! parts i (make-vector count.initial.parts))\n        (unsafe-vector*-set! buf   i (new-buffer))\n        (loop (unsafe-fx+ i 1))))\n    (let loop ((i start))\n      (when (unsafe-fx< i end)\n        (let* ((t       (unsafe-vector*-ref v i))\n               ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n               (key     (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n               (buf.k   (unsafe-vector*-ref buf key))\n               (pos.k   (unsafe-vector*-ref pos key))\n               (pos.k+1 (unsafe-fx+ pos.k 1)))\n          (unsafe-vector*-set! buf.k pos.k t)\n          (if (unsafe-fx= pos.k+1 count.buffer)\n            (begin\n              (unsafe-vector*-set! pos key 0)\n              (unsafe-vector*-set! buf key (new-buffer))\n              (let* ((parts.k       (unsafe-vector*-ref parts     key))\n                     (pos.parts.k   (unsafe-vector*-ref pos.parts key))\n                     (pos.parts.k+1 (unsafe-fx+ pos.parts.k 1))\n                     (len.parts.k   (unsafe-vector*-length parts.k)))\n                (unsafe-vector*-set! pos.parts key pos.parts.k+1)\n                (if (unsafe-fx= pos.parts.k+1 len.parts.k)\n                  (let ((parts.k.new (make-vector (unsafe-fx* len.parts.k growth-factor.parts))))\n                    (unsafe-vector*-set!  parts key parts.k.new)\n                    (vector-copy! parts.k.new 0 parts.k)\n                    (unsafe-vector*-set!  parts.k.new pos.parts.k buf.k))\n                  (unsafe-vector*-set! parts.k pos.parts.k buf.k))))\n            (unsafe-vector*-set! pos key pos.k+1)))\n        (loop (unsafe-fx+ i 1))))\n    (let loop.all ((k 0) (j start))\n      (when (unsafe-fx< k count.parts)\n        (let ((parts.k     (unsafe-vector*-ref parts     k))\n              (pos.parts.k (unsafe-vector*-ref pos.parts k))\n              (buf.k       (unsafe-vector*-ref buf       k))\n              (pos.k       (unsafe-vector*-ref pos       k)))\n          (let loop ((i 0) (j j))\n            (if (unsafe-fx< i pos.parts.k)\n              (let ((part (unsafe-vector*-ref parts.k i)))\n                (let loop ((i 0))\n                  (when (unsafe-fx< i count.buffer)\n                    (unsafe-vector*-set! v (unsafe-fx+ j i) (unsafe-vector*-ref part i))\n                    (loop (unsafe-fx+ i 1))))\n                (free-buffer part)\n                (loop (unsafe-fx+ i 1) (unsafe-fx+ j count.buffer)))\n              (let loop ((i 0))\n                (if (unsafe-fx= i pos.k)\n                  (begin (free-buffer buf.k)\n                         (loop.all (unsafe-fx+ k 1) (unsafe-fx+ j pos.k)))\n                  (begin (unsafe-vector*-set! v (unsafe-fx+ j i) (unsafe-vector*-ref buf.k i))\n                         (loop (unsafe-fx+ i 1))))))))))\n    (when (unsafe-fx< shift shift.final)\n      (loop (unsafe-fx+ shift size.shift)))))\n\n(define (counting-radix-sort-helper v.src start.src end.src v.0 start.0 v.1 start.1 t->key key-byte-count)\n  (define size.shift    8)\n  (define mask.shift  255)\n  (define count.parts 256)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (define len         (unsafe-fx- end.src start.src))\n  (define shift.final (unsafe-fx* 8 (unsafe-fx- key-byte-count 1)))\n  (define offset      (make-vector count.parts))\n  (let loop.shift ((shift      0)\n                   (v.src      v.src) (start          start.src) (end          end.src)\n                   (v.tgt      v.0)   (start.tgt      start.0)   (end.tgt      (unsafe-fx+ start.0 len))\n                   (v.tgt.next v.1)   (start.tgt.next start.1)   (end.tgt.next (unsafe-fx+ start.1 len)))\n    (vector-fill! offset 0)\n    (let loop.count ((i start))\n      (when (unsafe-fx< i end)\n        ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n        (let ((key (unsafe-fxand mask.shift (fxrshift (t->key (unsafe-vector*-ref v.src i)) shift))))\n          (unsafe-vector*-set! offset key (unsafe-fx+ (unsafe-vector*-ref offset key) 1)))\n        (loop.count (unsafe-fx+ i 1))))\n    (let loop.offset ((k 0) (current start.tgt))\n      (when (unsafe-fx< k count.parts)\n        (let ((cardinality (unsafe-vector*-ref offset k)))\n          (unsafe-vector*-set! offset k current)\n          (loop.offset (unsafe-fx+ k 1) (unsafe-fx+ current cardinality)))))\n    (let loop.copy ((i start))\n      (when (unsafe-fx< i end)\n        ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n        (let* ((t     (unsafe-vector*-ref v.src i))\n               (key   (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n               (off.k (unsafe-vector*-ref offset key)))\n          (unsafe-vector*-set! offset key (unsafe-fx+ off.k 1))\n          (unsafe-vector*-set! v.tgt off.k t))\n        (loop.copy (unsafe-fx+ i 1))))\n    (when (unsafe-fx< shift shift.final)\n      (loop.shift (unsafe-fx+ shift size.shift)\n                  v.tgt      start.tgt      end.tgt\n                  v.tgt.next start.tgt.next end.tgt.next\n                  v.tgt      start.tgt      end.tgt))))\n\n(define (counting-radix-sort! v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define len         (- end start))\n  (define v.workspace (make-vector len))\n  (counting-radix-sort-helper v start end v.workspace 0 v start t->key key-byte-count)\n  (when (odd? key-byte-count)\n    (vector-copy! v start v.workspace 0 len)))\n\n(define (counting-radix-sort v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define len           (- end start))\n  (define v.workspace.0 (make-vector len))\n  (define v.workspace.1 (make-vector len))\n  (counting-radix-sort-helper v start end v.workspace.0 0 v.workspace.1 0 t->key key-byte-count)\n  (if (odd? key-byte-count)\n    v.workspace.0\n    v.workspace.1))\n\n(define ((enumerator-lsd-radix-sort en t->key key-byte-count) k!)\n  (define size.shift               8)\n  (define mask.shift             255)\n  (define count.parts            256)\n  (define count.buffer           512)\n  (define count.initial.parts      8)\n  (define growth-factor.parts      2)\n  (define count.initial.buffers 1024)\n  (define growth-factor.buffers    2)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (define shift.final (unsafe-fx* 8 (unsafe-fx- key-byte-count 1)))\n  (define buffers     (make-vector count.initial.buffers))\n  (define pos.buffers 0)\n  (define (new-buffer)\n    (if (unsafe-fx= pos.buffers 0)\n      (make-vector count.buffer)\n      (begin (set! pos.buffers (unsafe-fx- pos.buffers 1))\n             (unsafe-vector*-ref buffers pos.buffers))))\n  (define (free-buffer b)\n    (vector-fill! b 0)\n    (when (unsafe-fx= pos.buffers (unsafe-vector*-length buffers))\n      (let ((buffers.new (make-vector (unsafe-fx* pos.buffers growth-factor.buffers))))\n        (vector-copy! buffers.new 0 buffers)\n        (set! buffers buffers.new)))\n    (unsafe-vector*-set! buffers pos.buffers b)\n    (set! pos.buffers (unsafe-fx+ pos.buffers 1)))\n  (let enumerate ((shift 0) (en en))\n    (define parts     (make-vector count.parts))\n    (define pos.parts (make-vector count.parts 0))\n    (define buf       (make-vector count.parts))\n    (define pos       (make-vector count.parts 0))\n    (let loop ((i 0))\n      (when (unsafe-fx< i count.parts)\n        (unsafe-vector*-set! parts i (make-vector count.initial.parts))\n        (unsafe-vector*-set! buf   i (new-buffer))\n        (loop (unsafe-fx+ i 1))))\n    (en (lambda (t)\n          ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n          (let* ((key     (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n                 (buf.k   (unsafe-vector*-ref buf key))\n                 (pos.k   (unsafe-vector*-ref pos key))\n                 (pos.k+1 (unsafe-fx+ pos.k 1)))\n            (unsafe-vector*-set! buf.k pos.k t)\n            (if (unsafe-fx= pos.k+1 count.buffer)\n              (begin\n                (unsafe-vector*-set! pos key 0)\n                (unsafe-vector*-set! buf key (new-buffer))\n                (let* ((parts.k       (unsafe-vector*-ref parts     key))\n                       (pos.parts.k   (unsafe-vector*-ref pos.parts key))\n                       (pos.parts.k+1 (unsafe-fx+ pos.parts.k 1))\n                       (len.parts.k   (unsafe-vector*-length parts.k)))\n                  (unsafe-vector*-set! pos.parts key pos.parts.k+1)\n                  (if (unsafe-fx= pos.parts.k+1 len.parts.k)\n                    (let ((parts.k.new (make-vector (unsafe-fx* len.parts.k growth-factor.parts))))\n                      (unsafe-vector*-set!  parts key parts.k.new)\n                      (vector-copy! parts.k.new 0 parts.k)\n                      (unsafe-vector*-set!  parts.k.new pos.parts.k buf.k))\n                    (unsafe-vector*-set! parts.k pos.parts.k buf.k))))\n              (unsafe-vector*-set! pos key pos.k+1)))))\n    (define (en.new k!)\n      (let loop ((i 0))\n        (when (unsafe-fx< i count.parts)\n          (let ((parts.i     (unsafe-vector*-ref parts     i))\n                (pos.parts.i (unsafe-vector*-ref pos.parts i))\n                (buf.i       (unsafe-vector*-ref buf       i))\n                (pos.i       (unsafe-vector*-ref pos       i)))\n            (let loop ((i 0))\n              (if (unsafe-fx= i pos.parts.i)\n                (begin ((unsafe-vector->enumerator buf.i 0 pos.i) k!)\n                       (free-buffer buf.i))\n                (begin (let ((part (unsafe-vector*-ref parts.i i)))\n                         ((unsafe-vector->enumerator part 0 count.buffer) k!)\n                         (free-buffer part))\n                       (loop (unsafe-fx+ i 1))))))\n          (loop (unsafe-fx+ i 1)))))\n    (if (unsafe-fx= shift shift.final)\n      (en.new k!)\n      (enumerate (unsafe-fx+ shift size.shift) en.new))))\n\n(define (in-place-radix-sort! v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define threshold 268435456)\n  ;(define threshold 67108864)\n  ;(define threshold 16777216)\n  ;(define threshold  65535)\n  ;(define threshold  8192)\n  ;(define threshold  4096)\n  ;(define threshold  1024)\n  ;(define threshold  256)\n  ;(define threshold  0)\n  (define size.shift    8)\n  (define mask.shift  255)\n  (define count.parts 256)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (let loop.shift ((shift (unsafe-fx* 8 (unsafe-fx- key-byte-count 1))) (start start) (end end))\n    ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n    (define (t->byte t) (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n    (define count  (make-vector count.parts))\n    (define offset (make-vector count.parts))\n    (let loop.count ((i start))\n      (when (unsafe-fx< i end)\n        (let ((key (t->byte (unsafe-vector*-ref v i))))\n          (unsafe-vector*-set! count key (unsafe-fx+ (unsafe-vector*-ref count key) 1)))\n        (loop.count (unsafe-fx+ i 1))))\n    (let loop.offset ((k 0) (current start))\n      (when (unsafe-fx< k count.parts)\n        (let ((cardinality (unsafe-vector*-ref count k)))\n          (let loop.advance ((i current))\n            (if (and (unsafe-fx< i end) (unsafe-fx= (t->byte (unsafe-vector*-ref v i)) k))\n              (loop.advance (unsafe-fx+ i 1))\n              (let ((next (unsafe-fx+ current cardinality)))\n                (unsafe-vector*-set! offset k i)\n                (unsafe-vector*-set! count  k next)\n                (loop.offset (unsafe-fx+ k 1) next)))))))\n    (let loop.move.k ((k 0) (i.part.start start))\n      (when (unsafe-fx< k count.parts)\n        (let* ((i.start (unsafe-vector*-ref offset k))\n               (i.end   (unsafe-vector*-ref count k)))\n          (let loop.move ((i i.start))\n            (when (unsafe-fx< i i.end)\n              (let ((t (unsafe-vector*-ref v i)))\n                (let loop.swap ((t.current t)\n                                (key       (t->byte t)))\n                  (let* ((off.k (unsafe-vector*-ref offset key))\n                         (t.next (unsafe-vector*-ref v off.k)))\n                    (unsafe-vector*-set! v      off.k t.current)\n                    (unsafe-vector*-set! offset key   (unsafe-fx+ off.k 1))\n                    (let ((key (t->byte t.next)))\n                      (if (unsafe-fx= key k)\n                        (begin (unsafe-vector*-set! v i t.next)\n                               (loop.move (unsafe-fx+ i 1)))\n                        (loop.swap t.next key))))))))\n          (when (and (unsafe-fx< 0 shift) (unsafe-fx< i.part.start i.end))\n            (if (unsafe-fx<= (unsafe-fx- i.end i.part.start) threshold)\n              (counting-radix-sort! v t->key (/ shift 8) i.part.start i.end)\n              (loop.shift (unsafe-fx- shift size.shift) i.part.start i.end)))\n          (loop.move.k (unsafe-fx+ k 1) i.end))))))\n\n;; TODO: factor out enumerator-radix-partition ?\n;; simplify t->key interface to return exactly a byte, discard key-byte-count parameter\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Benchmark\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;#|\n(define key-byte-count 4)\n;(define count.node (arithmetic-shift 1 28))\n;(define count.node (arithmetic-shift 1 27))\n(define count.node (arithmetic-shift 1 25))\n;|#\n\n#|\n(define key-byte-count 3)\n;(define count.node (arithmetic-shift 1 24))\n(define count.node (arithmetic-shift 1 22))\n;|#\n\n#|\n(define key-byte-count 2)\n(define count.node (arithmetic-shift 1 16))\n;|#\n\n(define count.edge (* count.node 16))\n\n(displayln \"allocating nodes:\")\n(displayln count.node)\n(define nodes (time (make-vector count.node)))\n(displayln \"allocating edges:\")\n(displayln count.edge)\n\n;#|\n(define edges (time (make-vector count.edge)))\n(define en.edges (unsafe-vector->enumerator edges 0 count.edge))\n\n(displayln \"building edges\")\n(time (let loop ((i 0))\n        (when (< i count.edge)\n          (vector-set! edges i (random count.node))\n          ;(vector-set! edges i (cons (random count.node) (random count.node)))\n          (loop (+ i 1)))))\n;|#\n\n#|\n(define (en.edges k!)\n  (let loop ((i 0))\n    (when (< i count.edge)\n      (k! (random count.node))\n      ;(k! (cons (random count.node) (random count.node)))\n      (loop (+ i 1)))))\n;|#\n\n;(define edge->key car)\n(define (edge->key e) e)\n\n#|\n(displayln \"sorting edges\")\n(time (vector-sort!\n        edges\n        (lambda (e.0 e.1) (< (edge->key e.0) (edge->key e.1)))))\n;|#\n\n#|\n(displayln \"computing node degrees inlined\")\n(time (let loop ((i 0))\n        (when (unsafe-fx< i count.edge)\n          (let ((key (unsafe-vector*-ref edges i)))\n            (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1)))\n          (loop (unsafe-fx+ i 1)))))\n;|#\n\n#|\n(displayln \"computing node degrees\")\n(time (en.edges\n        (lambda (edge)\n         (define key (edge->key edge))\n         ;(vector-set! nodes key (+ (vector-ref nodes key) 1))\n         (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1))\n         )))\n;|#\n\n#|\n(displayln \"computing node degrees inlined after lsd-radix sorting edges in-place\")\n;(time (unsafe-vector-radix-sort! edges edge->key key-byte-count))\n;(time (counting-radix-sort! edges edge->key key-byte-count))\n(let ((v.workspace (time (make-vector count.edge))))\n  (time (collect-garbage))\n  (time (counting-radix-sort-helper edges 0 count.edge v.workspace 0 edges 0 edge->key key-byte-count))\n  (when (odd? key-byte-count)\n    (time (vector-copy! edges 0 v.workspace 0 count.edge))))\n\n(time (let loop ((i 0))\n        (when (unsafe-fx< i count.edge)\n          (let ((key (unsafe-vector*-ref edges i)))\n            (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1)))\n          (loop (unsafe-fx+ i 1)))))\n;|#\n\n#|\n(displayln \"computing node degrees inlined after in-place-msd-radix sorting edges\")\n(time (in-place-radix-sort! edges edge->key key-byte-count))\n(time (let loop ((i 0))\n        (when (unsafe-fx< i count.edge)\n          (let ((key (unsafe-vector*-ref edges i)))\n            (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1)))\n          (loop (unsafe-fx+ i 1)))))\n;|#\n\n#|\n(displayln \"computing node degrees while lsd-radix sorting edges\")\n(time ((enumerator-lsd-radix-sort en.edges edge->key key-byte-count)\n       (lambda (edge)\n         (define key (edge->key edge))\n         ;(vector-set! nodes key (+ (vector-ref nodes key) 1))\n         (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1))\n         )))\n;|#\n\n#|\n(displayln \"computing node degrees while msd-radix sorting edges\")\n(time ((enumerator-msd-radix-sort en.edges edge->key key-byte-count)\n       (lambda (edge)\n         (define key (edge->key edge))\n         ;(vector-set! nodes key (+ (vector-ref nodes key) 1))\n         (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1))\n         )))\n;|#\n\n;(displayln 'in-place-radix-sort!) (time (in-place-radix-sort! edges edge->key key-byte-count))\n(displayln 'counting-radix-sort!) (time (counting-radix-sort! edges edge->key key-byte-count))\n;(displayln 'unsafe-vector-radix-sort!) (time (unsafe-vector-radix-sort! edges edge->key key-byte-count))\n(time (let ((previous #f))\n        (en.edges\n          (lambda (edge)\n            (when (and previous (< (edge->key edge) previous))\n              (error \"not sorted!\" previous (edge->key edge)))\n            (set! previous (edge->key edge))))))\n\n#;(let ((previous #f))\n  ((enumerator-lsd-radix-sort en.edges edge->key key-byte-count)\n   (lambda (edge)\n     (when (and previous (< (edge->key edge) previous))\n       (error \"not sorted!\" previous (edge->key edge)))\n     (set! previous (edge->key edge)))))\n\n#;(let ((previous #f))\n  ((enumerator-msd-radix-sort en.edges edge->key key-byte-count)\n   (lambda (edge)\n     (when (and previous (< (edge->key edge) previous))\n       (error \"not sorted!\" previous (edge->key edge)))\n     (set! previous (edge->key edge)))))\n"
  },
  {
    "path": "medikanren2/dbk/test/benchmark-sorting/string-sort.rkt",
    "content": "#lang racket/base\n(require racket/list racket/pretty racket/unsafe/ops racket/vector)\n\n;; TODO: pre-allocate a buffer for all the threshold merge sorts to share\n;; TODO: try MSD-radix-sort with a threshold for switching to q3sort! ?\n;; TODO: try burst/trie sort?\n\n;; multi-key (aka 3-way) quicksort\n(define (q3sort! max-depth? x&depth->cmp cmp (unsafe-vector*-ref v (random start end))\n                                                 depth)\n                         (lambda (i.low i.mid)\n                           (loop.current-depth                   start i.low)\n                           (loop.current-depth                   i.mid end)\n                           (loop.next-depth (unsafe-fx+ depth 1) i.low i.mid)))))))))\n\n(define (vector-bytes-sort! v (start 0) (end (vector-length v)))\n  (define (ref x d) (unsafe-bytes-ref x d))\n  (q3sort!\n    (lambda (x depth) (unsafe-fx<= (unsafe-bytes-length x) depth))\n    (lambda (x depth) (let ((n (bytes-ref x depth)))\n                        (lambda (y)\n                          (let ((m (bytes-ref y depth)))\n                            (cond ((unsafe-fx< m n) -1)\n                                  ((unsafe-fx= m n)  0)\n                                  (else              1))))))\n    bytesstring (map (lambda (_) (integer->char (random 128))) (range (random 200)))))\n\n(define (string-sort-and-verify v)\n  (define v.expected (time (vector-sort v stringbytes (map (lambda (_) (random 128)) (range (random 300 500)))))\n\n(define (bytes-sort-and-verify v)\n  ;(define v.expected (time (vector-sort v bytesvector (map (lambda (_) (random-string)) (range test-size)))))\n(bytes-sort-and-verify (time (list->vector (map (lambda (_) (random-bytes)) (range test-size)))))\n"
  },
  {
    "path": "medikanren2/dbk/test/benchmark1.rkt",
    "content": "#lang racket/base\n(require \"../dbk.rkt\" racket/function racket/list racket/pretty)\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n\n(define-syntax-rule (test name e expected)\n  (begin (printf \"Testing ~s:\\n\" name)\n         (pretty-print 'e)\n         (let ((answer (time e)))\n           (unless (equal? answer expected)\n             (printf \"FAILED ~s:\\n\" name)\n             (printf \"  ANSWER:\\n\")\n             (pretty-print answer)\n             (printf \"  EXPECTED:\\n\")\n             (pretty-print expected)))))\n\n(for-each (lambda (key) (current-config-set! key 'always))\n          '(update-policy cleanup-policy migrate-policy))\n\n\n;; Benchmark reference: http://users.informatik.uni-halle.de/~brass/botup/\n\n(define-relation/table Q\n  'path            \"benchmark1/Q\"\n  'source-stream   (value/syntax\n                     (map (lambda (i) (list i (+ i 1))) (range 1 5001)))\n  'attribute-names '(a b)\n  'attribute-types '(nat nat)\n  ;; optionally preload into memory\n  'retrieval-type  'scm\n  )\n\n(define-relation/table R\n  'path            \"benchmark1/R\"\n  'source-stream   (value/syntax\n                     (map (lambda (i) (list i    i))    (range 1 5001)))\n  'attribute-names '(a b)\n  'attribute-types '(nat nat)\n  ;; optionally preload into memory\n  'retrieval-type  'scm\n  )\n\n(define-relation (P3.1 b y) (fresh (x) (P2.1 b x) (Q x y)))\n(define-relation (P2.1 c w) (fresh (v) (P1.1 c v) (Q v w)))\n(define-relation (P1.1 d u) (fresh (t) (P0.1 d t) (Q t u)))\n(define-relation (P0.1 e s) (R e s))\n\n;; disk: ~8000ms\n;; scm:  ~1400ms\n(test 'benchmark-1\n  (length (run* (a z) (P3.1 a z)))\n  ;; smallest: (1    4)\n  ;; largest:  (4998 5001)\n  4998)\n\n(define-relation (P3.2 x z) (fresh (y) (Q x y) (P2.2 y z)))\n(define-relation (P2.2 x z) (fresh (y) (Q x y) (P1.2 y z)))\n(define-relation (P1.2 x z) (fresh (y) (Q x y) (P0.2 y z)))\n(define-relation (P0.2 x y) (R x y))\n\n;; disk: ~8000ms\n;; scm:  ~1400ms\n(test 'benchmark-2\n  (length (run* (x z) (P3.2 x z)))\n  ;; smallest: (1    4)\n  ;; largest:  (4997 5000)\n  4997)\n\n\n;; TODO: improve performance\n\n;(define-relation/table Q.large\n;  'path            \"benchmark1/Q.large\"\n;  'source-stream   (value/syntax\n;                     (map (lambda (i) (list i (+ i 1))) (range 1 1000001)))\n;  'attribute-names '(a b)\n;  'attribute-types '(nat nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n;\n;(define-relation/table R.large\n;  'path            \"benchmark1/R.large\"\n;  'source-stream   (value/syntax\n;                     (map (lambda (i) (list i    i))    (range 1 1000001)))\n;  'attribute-names '(a b)\n;  'attribute-types '(nat nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n;\n;(define-relation (P3.2.large x z) (fresh (y) (Q.large x y) (P2.2.large y z)))\n;(define-relation (P2.2.large x z) (fresh (y) (Q.large x y) (P1.2.large y z)))\n;(define-relation (P1.2.large x z) (fresh (y) (Q.large x y) (P0.2.large y z)))\n;(define-relation (P0.2.large x y) (R.large x y))\n;\n;;; disk: ?\n;;; scm:  ?\n;(test 'benchmark-2-large\n;  (length (run* (x z) (P3.2.large x z)))\n;  '?)\n\n\n;; TODO: improve performance\n\n;(define-relation/table S\n;  'path            \"benchmark1/S\"\n;  'source-stream   (value/syntax (map list (range 1 50001)))\n;  'attribute-names '(a)\n;  'attribute-types '(nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n\n;(define-relation (P1.3 a)             (S a))\n;(define-relation (P2.3 a b)           (P1.3 a)           (membero b '(1 2)))\n;(define-relation (P3.3 a b c)         (P2.3 a b)         (membero c '(1 2)))\n;(define-relation (P4.3 a b c d)       (P3.3 a b c)       (membero d '(1 2)))\n;(define-relation (P5.3 a b c d e)     (P4.3 a b c d)     (membero e '(1 2)))\n;(define-relation (P6.3 a b c d e f)   (P5.3 a b c d e)   (membero f '(1 2)))\n;(define-relation (P7.3 a b c d e f g) (P6.3 a b c d e f) (membero g '(1 2)))\n\n;;; disk: ?\n;;; scm:  ?\n;(test 'benchmark-3\n;  (length (run* (a b c d e f g) (P7.3 a b c d e f g)))\n;  (* 50000 (expt 2 6)))\n\n\n;; TODO: fixed-point computations\n\n;(define-relation/table edge\n;  'path            \"benchmark1/edge\"\n;  'source-stream   (value/syntax\n;                     (map (lambda (i) (list i (+ i 1))) (range 1 1001)))\n;  'attribute-names '(a b)\n;  'attribute-types '(nat nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n;\n;(define-relation (path x z)\n;  (conde ((edge x z))\n;         ((fresh (y) (edge x y) (path y z)))))\n;\n;;; disk: ?\n;;; scm:  ?\n;(test 'benchmark-fixed-point\n;  (length (run* (a b) (path a b)))\n;  (/ (* 1000 (+ 1000 1)) 2))\n"
  },
  {
    "path": "medikanren2/dbk/test/test-dataflow.rkt",
    "content": "#lang racket/base\n(require\n  \"../dbk.rkt\"\n  \"../dbk/data.rkt\"\n  \"../dbk/enumerator.rkt\"\n  racket/pretty\n  racket/runtime-path\n  racket/set)\n\n(define-relation/table (cprop curie key value)   'path \"rtx2/20210204/cprop\")\n(define-relation/table (edge  id subject object) 'path \"rtx2/20210204/edge\")\n(define-relation/table (eprop id key value)      'path \"rtx2/20210204/eprop\")\n\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n(define-runtime-path path.here \".\")\n\n(define db      (database (path->string (build-path path.here \"rtx-kg2_20210204.db\"))))\n(define r.cprop (database-relation db '(rtx-kg2 cprop)))\n(define r.edge  (database-relation db '(rtx-kg2 edge)))\n(define r.eprop (database-relation db '(rtx-kg2 eprop)))\n\n(define dict.eprop.eid.value.key     (relation-index-dict r.eprop '(key value eid)))\n(define dict.edge.subject.eid.object (relation-index-dict r.edge  '(object eid subject)))\n(define dict.cprop.value.key.curie   (relation-index-dict r.cprop '(curie key value)))\n(define domain-dicts                 (relation-domain-dicts r.cprop))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define (string->id str) (dict-select dict.string=>id str))\n(define (id->string id)  (dict-select dict.id=>string id))\n\n(define (benchmark-find-treatments curie.target)\n  (define (run-query yield)\n    (define curie.nausea.id       (string->id curie.target))\n    (define ekey.predicate.id     (string->id \"predicate\"))\n    (define evalue.treats.id      (string->id \"biolink:treats\"))\n    (define ckey.category.id      (string->id \"category\"))\n    (define ckey.name.id          (string->id \"name\"))\n    (define dict.eprop.eid.value  (dict-select dict.eprop.eid.value.key     ekey.predicate.id))\n    (define dict.eprop.eid        (dict-select dict.eprop.eid.value         evalue.treats.id))\n    (define dict.edge.subject.eid (dict-select dict.edge.subject.eid.object curie.nausea.id))\n    ((merge-join dict.eprop.eid dict.edge.subject.eid)\n     (lambda (eid __ dict.edge.subject)\n       ((merge-join dict.edge.subject dict.cprop.value.key.curie)\n        (lambda (subject.id __ dict.cprop.value.key)\n          (define subject             (id->string subject.id))\n          (define dict.cprop.category (dict-select dict.cprop.value.key ckey.category.id))\n          (define dict.cprop.name     (dict-select dict.cprop.value.key ckey.name.id))\n          ((merge-join dict.cprop.category dict.id=>string)\n           (lambda (category.id __ category)\n             ((merge-join dict.cprop.name dict.id=>string)\n              (lambda (name.id __ name)\n                (yield (list subject category name)))))))))))\n  ;; Some nausea timings\n  ;; cpu time: 1485 real time: 1610 gc time: 19\n  ;; cpu time: 1539 real time: 1557 gc time: 15\n  ;; cpu time: 1538 real time: 1556 gc time: 24\n  (define results.old (time (run* (s cat name)\n                              (fresh (eid)\n                                (edge eid s curie.target)\n                                (cprop s \"category\" cat)\n                                (cprop s \"name\" name)\n                                (eprop eid \"predicate\" \"biolink:treats\")))))\n  ;; Some nausea timings\n  ;; cpu time: 27 real time: 27 gc time: 0\n  ;; cpu time: 31 real time: 31 gc time: 0\n  ;; cpu time: 30 real time: 31 gc time: 0\n  (define results.new (time (enumerator->rlist run-query)))\n  ;; 149 results\n  (pretty-write `(old:    ,(length results.old) ,results.old))\n  (pretty-write `(new:    ,(length results.new) ,results.new))\n  (pretty-write `(equal?: ,(equal? (list->set results.old) (list->set results.new)))))\n"
  },
  {
    "path": "medikanren2/dbk/test/test-ingest-example-simple.rkt",
    "content": "#lang racket/base\n(require \"../dbk/io.rkt\"\n         \"../dbk/data.rkt\"\n         \"../dbk/stream.rkt\"\n         racket/runtime-path)\n\n(define-runtime-path path.here \".\")\n\n(define db (database (build-path path.here \"example-db\")))\n\n(unless (database-relation-has? db '(example cprop))\n  (database-relation-add!\n    db '(example cprop)\n    'attributes '(curie  key    value)\n    'type       '(string string string)\n    'source     (in:file \"example/example.nodeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))))\n\n(unless (database-relation-has? db '(example edge))\n  (database-relation-add!\n    db '(example edge)\n    'attributes '(eid subject object)\n    'type       '(nat string  string)\n    'source     (s-map (lambda (row) (cons (string->number (car row)) (cdr row)))\n                       (in:file \"example/example.edge.tsv\"     'header '(\":ID\" \":START\" \":END\")))))\n\n(unless (database-relation-has? db '(example eprop))\n  (database-relation-add!\n    db '(example eprop)\n    'attributes '(eid key    value)\n    'type       '(nat string string)\n    'source     (s-map (lambda (row) (cons (string->number (car row)) (cdr row)))\n                       (in:file \"example/example.edgeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\")))))\n\n(define cprop (database-relation db '(example cprop)))\n(define edge  (database-relation db '(example edge)))\n(define eprop (database-relation db '(example eprop)))\n\n(database-compact! db)\n\n(relation-index-add! cprop\n                     '(curie key)\n                     '(key value))\n(relation-index-add! edge\n                     '(eid)\n                     '(subject object)\n                     '(subject eid)\n                     '(object  eid))\n(relation-index-add! eprop\n                     '(eid key)\n                     '(key value))\n"
  },
  {
    "path": "medikanren2/dbk/test/test-ingest-example.rkt",
    "content": "#lang racket/base\n(require \"../dbk/io.rkt\"\n         racket/match)\n\n;; TODO: require these\n(define file-checksum          #f)\n(define-syntax-rule (run* body ...) '(TODO: run* body ...))\n(define database               #f)\n(define database-relation      #f)\n(define database-update!       #f)\n(define database-checkpoint!   #f)\n(define database-index-build!  #f)\n(define database-compact!      #f)\n(define relation-database      #f)\n(define relation-name          #f)\n(define relation-insert        #f)\n(define relation-index-add!    #f)\n(define relation-index-remove! #f)\n(define relation-index-build!  #f)\n\n(define db (database \"path/to/example/db\"\n                     'immediate-checkpoint?  #f\n                     'immediate-index-build? #f\n                     'immediate-compact?     #f))\n\n(define update-history (database-relation\n                         db\n                         'name       'update-history\n                         'attributes '(relation-name update-time update-kind file-name file-size file-checksum)\n                         'type       '(#f            nat         #f          string    nat       string)))\n(database-checkpoint! db)\n\n(define cprop (database-relation\n                db '(example cprop)\n                'attributes '(curie  key    value)\n                'type       '(string string string)))\n(define eprop (database-relation\n                db '(example eprop)\n                'attributes '(eid key    value)\n                'type       '(nat string string)))\n(define edge  (database-relation\n                db '(example edge)\n                'attributes '(eid subject object)\n                'type       '(nat string  string)))\n(relation-index-add! cprop\n                     '(curie key)\n                     '(key value))\n(relation-index-add! eprop\n                     '(eid key)\n                     '(key value))\n(relation-index-add! edge\n                     '(eid)\n                     '(subject object)\n                     '(object subject))\n(database-checkpoint! db)\n\n(define (relation-ingest! R path.dir file-name file-params)\n  (define name.R              (relation-name R))\n  (define path.file           (build-path path.dir file-name))\n  (define checksum.file       (file-checksum path.file))\n  (define size.file           (file-size path.file))\n  (define file-ingest-history (run* (timestamp size checksum)\n                                (update-history name.R timestamp 'ingest file-name size checksum)))\n  (if (null? file-ingest-history)\n    (begin (database-update!\n             (relation-database R)\n             (relation-insert update-history (list (list name.R (current-milliseconds)\n                                                         'ingest file-name size.file checksum.file)))\n             (relation-insert R              (apply in:file path.file file-params)))\n           (database-checkpoint! db))\n    (unless (ormap (lambda (entry) (match entry\n                                     ((list timestamp size checksum) (and (equal? size     size.file)\n                                                                          (equal? checksum checksum.file)))\n                                     (_                              #f)))\n                   file-ingest-history)\n      (error \"inconsistent data ingestion history:\"\n             'relation-name name.R\n             'file-name     file-name\n             'file-size     size.file\n             'file-checksum checksum.file\n             'history       file-ingest-history))))\n\n(relation-ingest! cprop \"example\" \"example.nodeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))\n(relation-ingest! eprop \"example\" \"example.edgeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))\n(relation-ingest! edge  \"example\" \"example.edge.tsv\"     'header '(\":ID\" \":START\" \":END\"))\n\n(database-index-build! db)\n(database-compact!     db)\n"
  },
  {
    "path": "medikanren2/dbk/test/test-mk.rkt",
    "content": "#lang racket/base\n(require \"../dbk.rkt\" racket/function racket/list racket/pretty racket/set)\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n\n(define (sort/any xs) (sort xs anyset\n    (run* (x y z)\n      (conde ((== y 'a) (== z 'c))\n             ((== y 'a) (== z 'd))\n             ((== x '8))\n             ((== y 'b) (== x '12))\n             ((== y 'b) (== z 'f) (== x '9))\n             ((== y 'b) (== z 'g) (== x '9))\n             ((== y 'c))\n             ((== y 'd)))\n      (triple2o x y z)))\n  (list->set\n    '((4 a c)\n      (5 a c)\n      (6 a c)\n      (8 b d)\n      (9 b f)\n      (11 c a)\n      (12 c d))))\n\n(test '=/=.atom.1\n  (run* x (=/= 1 x))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) 1)))))\n(test '=/=.atom.2\n  (run* x (=/= x 2))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) 2)))))\n\n(test '=/=.atom.==.1\n  (run* x (== x 1) (=/= x 1))\n  '())\n(test '=/=.atom.==.2\n  (run* x (=/= x 2) (== x 2))\n  '())\n(test '=/=.atom.==.3\n  (run* x (=/= x 3) (== x 'not-3))\n  '(not-3))\n(test '=/=.atom.==.4\n  (run* x (== x 'not-4) (=/= x 4))\n  '(not-4))\n\n(test '=/=.var.==.1\n  (run* x\n    (fresh (y)\n      (=/= x y)\n      (== x 1)\n      (== y 1)))\n  '())\n(test '=/=.var.==.2\n  (run* x\n    (fresh (y)\n      (== x 2)\n      (== y 2)\n      (=/= x y)))\n  '())\n(test '=/=.var.==.3\n  (run* x\n    (fresh (y)\n      (== x 3)\n      (=/= x y)\n      (== y 3)))\n  '())\n(test '=/=.var.==.4\n  (run* x\n    (fresh (y z)\n      (=/= x 4)\n      (== x y)\n      (== y z)\n      (== z 4)))\n  '())\n(test '=/=.var.==.5\n  (run* x\n    (fresh (y z)\n      (=/= x 5)\n      (== y z)\n      (== x y)\n      (== z 5)))\n  '())\n(test '=/=.var.==.6\n  (run* x\n    (fresh (y)\n      (=/= x y)\n      (== x y)))\n  '())\n(test '=/=.var.==.7\n  (run* x\n    (fresh (y)\n      (=/= x y)\n      (== y x)))\n  '())\n\n(test '=/=.pair.==.1\n  (run* x\n    (=/= x '(1 . 2))\n    (==  x '(1 . 2)))\n  '())\n(test '=/=.pair.==.2\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  x `(1 . 2))\n      (==  y 2)))\n  '())\n(test '=/=.pair.==.3\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (=/= x `(1 . ,y))\n      (==  y 2)))\n  '())\n(test '=/=.pair.==.4\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (==  y 2)\n      (=/= x `(1 . ,y))))\n  '())\n(test '=/=.pair.==.5\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  y 2)\n      (==  x `(1 . 2))))\n  '())\n(test '=/=.pair.==.6\n  (run* x\n    (fresh (y)\n      (=/= `(,x .  1) `(0 . ,y))\n      (==  `(,x . ,y) '(0 .  1))))\n  '())\n(test '=/=.pair.==.7\n  (run* x\n    (fresh (y)\n      (==  `(,x . ,y) '(0 .  1))\n      (=/= `(,x .  1) `(0 . ,y))))\n  '())\n\n(test '=/=.pair.=/=.1\n  (run* x\n    (=/= x '(1 . 2))\n    (==  x '(0 . 2)))\n  '((0 . 2)))\n(test '=/=.pair.=/=.2\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  x `(1 . 2))\n      (==  y 0)))\n  '((1 . 2)))\n(test '=/=.pair.=/=.3\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (=/= x `(1 . ,y))\n      (==  y 0)))\n  '((1 . 2)))\n(test '=/=.pair.=/=.4\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (==  y 0)\n      (=/= x `(1 . ,y))))\n  '((1 . 2)))\n(test '=/=.pair.=/=.5\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  y 0)\n      (==  x `(1 . 2))))\n  '((1 . 2)))\n(test '=/=.pair.=/=.6\n  (run* x\n    (fresh (y)\n      (=/= `(,x .  1) `(0 . ,y))\n      (==  `(,x . ,y) '(0 .  2))))\n  '(0))\n(test '=/=.pair.=/=.7\n  (run* x\n    (fresh (y)\n      (==  `(,x . ,y) '(0 .  2))\n      (=/= `(,x .  1) `(0 . ,y))))\n  '(0))\n\n(test '=/=.fresh.1\n  (run* x\n    (fresh (y)\n      (=/= y 1)))\n  '(#s(cx (term: #s(var 0)) (constraints:))))\n(test '=/=.fresh.2\n  (run* x\n    (fresh (y)\n      (=/= x 0)\n      (=/= y 1)))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) 0)))))\n(test '=/=.fresh.3\n  (run* x\n    (fresh (y)\n      (=/= x 0)\n      (=/= x y)))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) #s(var 1))\n                                  (=/= #s(var 0) 0)))))\n(test '=/=.fresh.4\n  (run* (x y)\n    (fresh (z)\n      (=/= `(,x . ,y) '(0 . 2))\n      (=/= z 1)))\n  '(#s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 0) 0)))\n    #s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 1) 2)))))\n(test '=/=.fresh.5\n  (run* (x y)\n    (fresh (z)\n      (=/= `(,x ,y ,z) '(0 1 2))))\n  '(#s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 0) 0)))\n    #s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 1) 1)))\n    #s(cx (term: (#s(var 0) #s(var 1))) (constraints:))))\n\n(test 'membero.forward\n  (run* () (membero 3 '(1 2 3 4 3 5)))\n  '(()))\n(test 'membero.backward\n  (run* x (membero x '(1 2 3 4 3 5)))\n  '(1 2 3 4 5))\n(test 'not-membero.forward\n  (run* () (not-membero 0 '(1 2 3 4 5)))\n  '(()))\n(test 'not-membero.backward\n  (run* x (not-membero x '(1 2 3 4 5)) (== x 0))\n  '(0))\n(test 'uniqueo.1\n  (run* () (uniqueo '(1 2 3 4 5)))\n  '(()))\n(test 'uniqueo.2\n  (run* () (uniqueo '(1 2 3 4 2)))\n  '())\n(test 'removeo.forward\n  (run* x (removeo '3 '(1 2 3 4 5) x))\n  '((1 2 4 5)))\n(test 'removeo.backward\n  (run* x (removeo x '(1 2 3 4 5) '(1 2 4 5)))\n  '(3))\n\n\n;; More table testing\n\n(define intersected-lists\n  '(((-1 0 no)\n     (-1 1 no)\n     (-1 2 no)\n     (-1 3 no)\n     (-1 4 no)\n     (-1 5 no)\n     (-1 6 no)\n     (-1 7 no)\n     (-1 8 no)\n     (-1 9 no)\n\n     (1 1 a0)\n     (1 2 b0)\n     (1 5 c0)\n     (3 4 d0)\n     (3 8 e0)\n     (3 8 e0.1)\n     (3 8 e0.2)\n\n     (4 0 no)\n     (4 1 no)\n     (4 2 no)\n     (4 3 no)\n     (4 4 no)\n     (4 5 no)\n     (4 6 no)\n     (4 7 no)\n     (4 8 no)\n     (4 9 no)\n\n     (6 0 f0)\n     (6 3 g0)\n     (6 5 h0)\n     (7 0 i0)\n     (7 2 j0)\n     (7 4 k0)\n     (7 6 l0)\n     (7 8 m0)\n     (7 9 n0)\n     (9 1 0)\n     (9 1 o0)\n     (9 2 p0)\n     (9 5 q0))\n    ((-1 0 no)\n     (-1 1 no)\n     (-1 2 no)\n     (-1 3 no)\n     (-1 4 no)\n     (-1 5 no)\n     (-1 6 no)\n     (-1 7 no)\n     (-1 8 no)\n     (-1 9 no)\n\n     (1 1 a1)\n     (1 2 b1)\n     (2 5 c1)  ; 0\n     (2 4 d1)  ; 0\n     (3 8 e1)\n     (3 8 e1.1)\n     (6 0 f1)\n     (6 3 g1)\n     (6 5 h1)\n     (7 0 i1)\n     (7 3 j1)  ; 1\n     (7 4 k1)\n     (7 6 l1)\n     (8 8 m1)  ; 0\n     (8 9 n1)  ; 0\n     (9 1 o1)\n     (9 1 o1.1)\n     (9 4 p1)  ; 1\n     (9 5 q1))\n    (;(-1 0 no)\n     ;(-1 1 no)\n     ;(-1 2 no)\n     ;(-1 3 no)\n     ;(-1 4 no)\n     ;(-1 5 no)\n     ;(-1 6 no)\n     ;(-1 7 no)\n     ;(-1 8 no)\n     ;(-1 9 no)\n\n     (0 1 a2)  ; 0\n     (1 3 b2)  ; 1\n     (1 5 c2)  ; 1\n     (2 4 d2)\n     (3 8 e2)\n     (5 0 f2)  ; 0\n     (6 3 g2)\n     (6 5 h2)\n     (7 0 i2)\n     (7 3 j2)\n     (7 4 k2)\n     (7 4 k2.1)\n     (7 6 l2)\n     (8 8 m2)\n     (8 9 n2)\n     (9 1 o2)\n     (9 4 p2)\n     (9 5 q2)\n\n     (10 1 no)\n     (10 0 no)\n     (10 2 no)\n     (10 3 no)\n     (10 4 no)\n     (10 5 no)\n     (10 6 no)\n     (10 7 no)\n     (10 8 no)\n     (10 9 no)\n     )))\n\n(define intersected-tables\n  (map (lambda (i s)\n         (relation/table\n           'relation-name   (string->symbol (format \"intersected-table.~v\" i))\n           'attribute-names '(i n m x)\n           'key-name        'i\n           'source-stream   s))\n       (range (length intersected-lists))\n       intersected-lists))\n\n(test 'table-ref\n  (map (lambda (R) (run* (n m x) (R 0 n m x))) intersected-tables)\n  '(((-1 0 no)) ((-1 0 no)) ((0 1 a2))))\n\n(test 'table-intersection\n  (sort/any\n    (run* (n m a b c)\n      (foldl (lambda (g0 g) (fresh () g g0)) (== #t #t)\n             (map (lambda (v R) (fresh (i) (R i n m v))) (list a b c)\n                  intersected-tables))))\n  (sort/any\n    '((3 8 e0   e1   e2)\n      (3 8 e0   e1.1 e2)\n      (3 8 e0.1 e1   e2)\n      (3 8 e0.1 e1.1 e2)\n      (3 8 e0.2 e1   e2)\n      (3 8 e0.2 e1.1 e2)\n      (6 3 g0   g1   g2)\n      (6 5 h0   h1   h2)\n      (7 0 i0   i1   i2)\n      (7 4 k0   k1   k2)\n      (7 4 k0   k1   k2.1)\n      (7 6 l0   l1   l2)\n      (9 1 0    o1   o2)\n      (9 1 0    o1.1 o2)\n      (9 1 o0   o1   o2)\n      (9 1 o0   o1.1 o2)\n      (9 5 q0   q1   q2))))\n\n(test '<=.1\n  (run* n\n    (membero n '(0 1 2 3 4 5 6 7 8 9))\n    (<=o 2 n)\n    (set '((1 1)\n               (1 2)\n               (1 3)\n               (2 4)\n               (2 6)\n               (3 5)\n               (3 6)\n               (6 4)\n               (1 2)\n               (1 3)\n               (1 4)\n               (1 6)\n               (1 5)\n               (1 6)\n               (2 4)\n               (3 4)\n               (1 4)\n               (1 6)\n               (1 5)\n               (1 6)\n               (1 4)\n               (1 4)\n               (1 4)\n               (1 4))))\n(test 'path2*.set.1\n  (run*/set x (path2* x 6))\n  (list->set '(2 3 1 1 1 1)))\n(test 'path2*.set.2\n  (run*/set y (path2* 3 y))\n  (list->set '(5 6 4)))\n\n(test 'path3*.0\n  (run* (x y) (path3* x y))\n  '((1 1)\n    (1 2)\n    (1 3)\n    (2 4)\n    (2 6)\n    (3 5)\n    (3 6)\n    (6 4)\n    (1 4)\n    (1 6)\n    (1 5)\n    (1 6)\n    (2 4)\n    (3 4)\n    (1 4)\n    (1 4)))\n(test 'path3*.1\n  (run* x (path3* x 6))\n  '(2 3 1 1))\n(test 'path3*.2\n  (run* y (path3* 3 y))\n  '(5 6 4))\n\n(define-relation (edge/cycle a b)\n  (conde ((== a 5) (== b 1))\n         ((edge a b))))\n(define-relation (path/cycle* a c)\n  (conde ((edge/cycle a c))\n         ((fresh (b)\n            (=/= a b)\n            (edge/cycle a b)\n            (path/cycle* b c)))))\n(test 'path/cycle*.0\n  (run* (x y) (path/cycle* x y))\n  '((5 1)\n    (1 1)\n    (1 2)\n    (1 3)\n    (2 4)\n    (2 6)\n    (3 5)\n    (3 6)\n    (6 4)\n    (5 1)\n    (5 2)\n    (5 3)\n    (3 1)\n    (5 4)\n    (5 6)\n    (5 5)\n    (5 6)\n    (1 4)\n    (1 6)\n    (1 5)\n    (1 6)\n    (2 4)\n    (3 4)\n    (5 4)\n    (5 4)\n    (3 1)\n    (3 2)\n    (3 3)\n    (1 1)\n    (3 4)\n    (3 6)\n    (1 4)\n    (1 4)\n    (3 4)))\n(test 'path/cycle*.1\n  (run* x (path/cycle* x 6))\n  '(2 3 5 1 3))\n(test 'path/cycle*.2\n  (run* y (path/cycle* 3 y))\n  '(5 6 1 4 1 2 3 4 6 4))\n\n(test 'path/cycle*.set.0\n  (run*/set (x y) (path/cycle* x y))\n  (list->set '((5 1)\n               (1 1)\n               (1 2)\n               (1 3)\n               (2 4)\n               (2 6)\n               (3 5)\n               (3 6)\n               (6 4)\n               (5 1)\n               (5 2)\n               (5 3)\n               (3 1)\n               (5 4)\n               (5 6)\n               (5 5)\n               (5 6)\n               (1 4)\n               (1 6)\n               (1 5)\n               (1 6)\n               (2 4)\n               (3 4)\n               (5 1)\n               (5 4)\n               (5 4)\n               (1 1)\n               (5 1)\n               (5 2)\n               (5 3)\n               (3 1)\n               (3 2)\n               (3 3)\n               (1 4)\n               (1 4))))\n(test 'path/cycle*.set.1\n  (run*/set x (path/cycle* x 6))\n  (list->set '(2 3 1 5 5 3 3)))\n(test 'path/cycle*.set.2\n  (run*/set y (path/cycle* 3 y))\n  (list->set '(5 6 1 4 1 2 3 4 6 5 6 1 4 4 1 2 3 4 6 5 6 1 4 4 1 2 3)))\n\n;; Using list->set on a run result is not the same as using run/set:\n;; run/set guarantees that the result has 10 unique answers before stopping\n(test 'path/cycle*.set.n.0\n  (list->set (run 10 (x y) (path/cycle* x y)))\n  (list->set '((1 1) (1 2) (1 3) (3 6) (6 4) (2 4) (5 1) (3 5) (2 6))))\n(test 'path/cycle*.set.n.1\n  (run/set 10 (x y) (path/cycle* x y))\n  (list->set '((1 1) (1 2) (1 3) (5 2) (3 6) (6 4) (2 4) (5 1) (3 5) (2 6))))\n\n\n;; Equivalence class tests\n\n;; fast version\n(define-relation/table (uedge a b)\n  'source-stream '((0  15)\n                   (10 15)\n                   (15 20)\n                   (17 18)\n                   (17 20)\n                   (20  0)))\n\n(define-relation (node x)\n  (fresh (y)\n    (conde ((uedge x y)) ((uedge y x)))))\n\n(define-relation (equiv=/= a b)\n  (=/= a b)\n  (fresh (x)\n    (conde ((uedge a x))\n           ((uedge x a)))\n    (conde ((==       x b))\n           ((equiv=/= x b)))))\n\n(define-relation (equiv a b)\n  (node a)\n  (node b)\n  (conde ((==       a b))\n         ((equiv=/= a b))))\n\n;; cpu time: 1440 real time: 1466 gc time: 74\n(test 'equiv.0\n  (time (run*/set (x y) (equiv x y)))\n  (list->set\n    '((20 20) (10 20) (15 15) (20 10) (15 0) (0 15) (0 0) (15 17) (17 15)\n      (17 0) (15 18) (0 17) (18 15) (17 17) (0 18) (18 0) (20 15) (18 17)\n      (15 20) (17 18) (10 10) (18 18) (0 20) (20 0) (17 20) (20 17) (20 18)\n      (18 20) (10 15) (15 10) (0 10) (10 0) (10 17) (17 10) (10 18) (18 10))))\n\n;; cpu time: 298 real time: 319 gc time: 5\n(test 'equiv.1\n  (time (run*/set x (equiv 0 x)))\n  (set 0 17 18 20 10 15))\n\n;; cpu time: 459 real time: 485 gc time: 12\n(test 'equiv.2\n  (time (run*/set x (equiv x 0)))\n  (set 0 17 18 20 10 15))\n\n;; much more expensive version\n(define-relation/table (uedge.slow a b)\n  'source-stream '((0   5)\n                   (2   3)\n                   (2   5)\n                   (5   8)\n                   (5  10)\n                   (7  10)\n                   (10 13)\n                   (10 15)\n                   (12 15)\n                   (15 18)\n                   (17 18)\n                   (15 20)\n                   (17 20)\n                   (20  0)))\n\n(define-relation (node.slow x)\n  (fresh (y)\n    (conde ((uedge.slow x y)) ((uedge.slow y x)))))\n\n(define-relation (equiv=/=.slow a b)\n  (=/= a b)\n  (fresh (x)\n    (conde ((uedge.slow a x))\n           ((uedge.slow x a)))\n    (conde ((==            x b))\n           ((equiv=/=.slow x b)))))\n\n(define-relation (equiv.slow a b)\n  (node.slow a)\n  (node.slow b)\n  (conde ((==            a b))\n         ((equiv=/=.slow a b))))\n\n#|\n;; cpu time: 94756 real time: 97248 gc time: 3523\n(test 'equiv.0.slow\n  (time (run*/set (x y) (equiv.slow x y)))\n  (list->set\n    '((10 20) (12 18) (20 10) (2 12) (18 12) (7 7) (12 2) (13 17) (15 15) (17 13)\n      (10 5) (13 2) (15 0) (0 15) (3 12) (2 13) (7 8) (8 7) (12 3) (13 18) (18 13)\n      (5 10) (13 3) (12 20) (0 0) (8 8) (15 17) (17 15) (3 13) (20 12) (10 7) (15 18)\n      (0 17) (20 13) (2 15) (7 10) (12 5) (13 20) (15 2) (17 0) (18 15) (5 12) (10 8)\n      (13 5) (15 3) (17 17) (0 2) (0 18) (18 0) (5 13) (8 10) (2 0) (3 15) (12 7)\n      (17 2) (0 3) (3 0) (20 15) (2 17) (18 17) (7 12) (15 20) (17 18) (10 10) (13 7)\n      (12 8) (7 13) (8 12) (15 5) (17 3) (0 20) (20 0) (2 2) (3 17) (2 18) (18 2)\n      (18 18) (5 15) (13 8) (17 20) (0 5) (3 2) (8 13) (2 3) (3 18) (20 17) (18 3)\n      (5 0) (10 12) (12 10) (20 18) (2 20) (7 15) (15 7) (17 5) (3 3) (20 2) (18 20)\n      (5 17) (10 13) (13 10) (15 8) (0 7) (20 3) (5 18) (7 0) (8 15) (2 5) (3 20)\n      (18 5) (5 2) (12 12) (17 7) (0 8) (3 5) (20 20) (5 3) (7 17) (8 0) (10 15)\n      (13 12) (12 13) (20 5) (2 7) (18 7) (5 20) (7 2) (7 18) (8 17) (15 10) (17 8)\n      (13 13) (0 10) (3 7) (2 8) (7 3) (8 2) (8 18) (10 0) (18 8) (5 5) (10 17)\n      (12 15) (7 20) (8 3) (15 12) (17 10) (3 8) (20 7) (10 18) (15 13) (0 12)\n      (20 8) (2 10) (7 5) (8 20) (10 2) (12 0) (13 15) (18 10) (5 7) (13 0) (12 17)\n      (17 12) (0 13) (3 10) (5 8) (8 5) (10 3))))\n\n;; cpu time: 4520 real time: 4675 gc time: 123\n(test 'equiv.1.slow\n  (time (run*/set x (equiv.slow 0 x)))\n  (set 0 17 3 20 5 7 8 10 12 13 15 2 18))\n\n;; cpu time: 10254 real time: 10618 gc time: 370\n(test 'equiv.2.slow\n  (time (run*/set x (equiv.slow x 0)))\n  (set 0 17 3 20 5 7 8 10 12 13 15 2 18))\n;|#\n\n\n;; Simple relational interpreter tests\n\n(define-relation (eval-expo expr env value)\n  (conde\n    ((fresh (body)\n       (== `(lambda ,body) expr)\n       (== `(closure ,body ,env) value)))\n    ((== `(quote ,value) expr))\n    ((fresh (a*)\n       (== `(list . ,a*) expr)\n       (eval-listo a* env value)))\n    ((fresh (a d va vd)\n       (== `(cons ,a ,d) expr)\n       (== `(,va . ,vd) value)\n       (eval-expo a env va)\n       (eval-expo d env vd)))\n    ((fresh (index)\n       (== `(var ,index) expr)\n       (lookupo index env value)))\n    ((fresh (rator rand arg env^ body)\n       (== `(app ,rator ,rand) expr)\n       (eval-expo rator env `(closure ,body ,env^))\n       (eval-expo rand env arg)\n       (eval-expo body `(,arg . ,env^) value)))))\n\n(define-relation (lookupo index env value)\n  (fresh (arg e*)\n    (== `(,arg . ,e*) env)\n    (conde\n      ((== '() index) (== arg value))\n      ((fresh (i* a d)\n         (== `(s . ,i*) index)\n         (== `(,a . ,d) e*)\n         (lookupo i* e* value))))))\n\n(define-relation (eval-listo e* env value)\n  (conde\n    ((== '() e*) (== '() value))\n    ((fresh (ea ed va vd)\n       (== `(,ea . ,ed) e*)\n       (== `(,va . ,vd) value)\n       (eval-expo ea env va)\n       (eval-listo ed env vd)))))\n\n(define (evalo expr value) (eval-expo expr '() value))\n\n(test 'evalo-literal\n  (run 1 e (evalo e 5))\n  '((quote 5)))\n\n;; ~600 ms\n(test 'evalo-quine\n  (time (run 1 e (evalo e e)))\n  '((app (lambda (list (quote app) (var ())\n                       (list (quote quote) (var ()))))\n         (quote (lambda (list (quote app) (var ())\n                              (list (quote quote) (var ()))))))))\n\n;; ~5500 ms\n;(test 'evalo-twine\n;  (time (run 1 (p q) (evalo p q) (evalo q p)))\n;  '(((quote (app (lambda (list (quote quote)\n;                               (list (quote app) (var ())\n;                                     (list (quote quote) (var ())))))\n;                 (quote (lambda (list (quote quote)\n;                                      (list (quote app) (var ())\n;                                            (list (quote quote) (var ()))))))))\n;     (app (lambda (list (quote quote)\n;                        (list (quote app) (var ())\n;                              (list (quote quote) (var ())))))\n;          (quote (lambda (list (quote quote)\n;                               (list (quote app) (var ())\n;                                     (list (quote quote) (var ()))))))))))\n\n;; ~24000 ms\n;(test 'evalo-thrine\n;  (time (run 1 (p q r) (evalo p q) (evalo q r) (evalo r p)))\n;  '(((quote (quote (app (lambda (list (quote quote)\n;                                      (list (quote quote)\n;                                            (list (quote app) (var ())\n;                                                  (list (quote quote) (var ()))))))\n;                        (quote (lambda (list (quote quote)\n;                                             (list (quote quote)\n;                                                   (list (quote app) (var ())\n;                                                         (list (quote quote) (var ()))))))))))\n;     (quote (app (lambda (list (quote quote)\n;                               (list (quote quote)\n;                                     (list (quote app) (var ())\n;                                           (list (quote quote) (var ()))))))\n;                 (quote (lambda (list (quote quote)\n;                                      (list (quote quote)\n;                                            (list (quote app) (var ())\n;                                                  (list (quote quote) (var ())))))))))\n;     (app (lambda (list (quote quote)\n;                        (list (quote quote)\n;                              (list (quote app) (var ())\n;                                    (list (quote quote) (var ()))))))\n;          (quote (lambda (list (quote quote)\n;                               (list (quote quote)\n;                                     (list (quote app) (var ())\n;                                           (list (quote quote) (var ())))))))))))\n"
  },
  {
    "path": "medikanren2/dbk/toggle-git",
    "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\ncd \"$here\"\nmv .git.backup .git\n"
  },
  {
    "path": "medikanren2/dbk/toggle-git-backup",
    "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\ncd \"$here\"\nmv .git .git.backup\n"
  },
  {
    "path": "medikanren2/dbk/update",
    "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\ncd \"$here\"\n./toggle-git\n./update-snapshot\n./toggle-git-backup\n"
  },
  {
    "path": "medikanren2/dbk/update-snapshot",
    "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\ncd \"$here\"\ngit pull\ngit reset --hard master\ncommit_hash=$(git show | head -n 1 | cut -f 2 -d ' ')\nprintf \"https://github.com/gregr/dbKanren\\n$commit_hash\" > SNAPSHOT\n"
  },
  {
    "path": "medikanren2/dbk.rkt",
    "content": "#lang racket/base\n(provide (prefix-out dbk:\n                     (combine-out\n                       config.default\n                       current-config-relation-path\n                       current-config-set!/alist))\n         (except-out (all-from-out \"dbk/dbk.rkt\")\n                     config.default\n                     current-config-relation-path\n                     current-config-set!/alist))\n(require \"dbk/dbk.rkt\")\n"
  },
  {
    "path": "medikanren2/etc/config.defaults.scm",
    "content": ";; DO NOT EDIT THIS FILE!\n;; Instead, add overrides to: config.scm\n(\n (buffer-size                . 100000)\n (progress-logging-threshold . 1000000)\n ;; interactive, always, never\n (update-policy              . interactive)\n (cleanup-policy             . interactive)\n (migrate-policy             . interactive)\n (allow-missing-data-policy  . always)\n ;; biased-interleaving (default), depth-first\n (search-strategy            . #f)\n\n ;; These keys have to be in the file to let the configref.rkt library know\n ;; that the keys exist so they can be populated at runtime.\n (relation-root-path . relation-root-path-placeholder)\n (temporary-root-path . temporary-root-path-placeholder)\n\n ;; Specify installed databases as a list of symbols, e.g.:\n ;;   (databases                  . (rtx2-20210204))\n ;;\n ;; Unless more specifically configured, we assume no databases have been installed:\n (databases                  . ())\n\n ;; Disable this flag to prevent translator-web-server.rkt\n ;; and open-api/ from making downstream HTTP requests.  Useful\n ;; for functional CI tests, and for offline development.\n (trapi-enable-external-requests?  . #t)\n\n (migrated-to-new-db-versioning . #f)\n (version-for-database . (\n     (rtx-kg2 . \"20210204\")\n    ))\n\n ;; Add new configuration options as new association pairs.\n )\n"
  },
  {
    "path": "medikanren2/etc/config.stage.dev.scm",
    "content": "(\n    (migrated-to-new-db-versioning . #f)\n)\n"
  },
  {
    "path": "medikanren2/etc/config.stage.prod.scm",
    "content": "(\n    (update-policy              . never)\n    (migrated-to-new-db-versioning . #t)    \n)\n"
  },
  {
    "path": "medikanren2/ex_cohd.rkt",
    "content": "#lang racket/base\n(require \"base.rkt\"\n         (except-in racket/match ==)\n         racket/list racket/pretty)\n\n;; Command line usage: racket ex_cohd.rkt cohd-v2\n\n(define argv (current-command-line-arguments))\n(define argv-expected '#(DB_NAME))\n(when (not (= (vector-length argv-expected) (vector-length argv)))\n  (error \"command line argument mismatch:\" argv-expected argv))\n\n(define db-name  (vector-ref argv 0))\n(define (db-relative-path path) (path->string (build-path db-name path)))\n(define (db-path path) (path/data (db-relative-path path)))\n\n;; Input\n(define fnin.concepts \"concepts.txt\")\n(define fnin.edges \"paired_concept_counts_associations.txt\")\n(define header.concepts '(\"concept_id\" \"concept_name\" \"domain_id\" \"vocabulary_id\" \"concept_class_id\" \"concept_code\"))\n(define header.edges '(\"dataset_id\" \"concept_id_1\" \"concept_id_2\" \"concept_count\" \"concept_prevalence\" \"chi_square_t\" \"chi_square_p\" \"expected_count\" \"ln_ratio\" \"rel_freq_1\" \"rel_freq_2\"))\n\n(define (materialize-db-relation\n          name fnin header transform fields types indexes)\n  (materialize-relation\n    (db-relative-path name) (db-relative-path fnin) header \"\\t\"\n    dsv->stream transform fields types indexes))\n\n(materialize-db-relation\n  \"concept\" fnin.concepts header.concepts\n  (lambda (row)\n    (match-define (list id name domain vocab class code) row)\n    (list (string->number id) (string-append (string-upcase vocab) \":\" code)\n          name domain class))\n  '(id curie name domain class)\n  '(nat string string string string)\n  '((curie)\n    (name)\n    (class)\n    (domain)))\n\n(materialize-db-relation\n  \"edge\" fnin.edges header.edges\n  (lambda (row)\n    (define-values (left right) (split-at row 4))\n    (append (map string->number left) right))\n  '(dataset subject object concept_count prevalence chi_sq_t chi_sq_p expected_count ln_ratio rel_freq1 rel_freq2)\n  '(nat nat nat nat string string string string string string string)\n  '((subject)  ;; (subject object) doesn't work well currently\n    (object)))\n\n;; all indexes have implicit index made on first arg/no need to index separately\n\n(time (let ()\n        ;; ~4x faster retrieval; ~400x slower loading\n        ;(define-relation/table concept   `((path . ,(db-path \"concept\")) (retrieval-type . bytes)))\n        ;; ~10x faster retrieval; ~6000x slower loading\n        ;(define-relation/table concept   `((path . ,(db-path \"concept\")) (retrieval-type . scm)))\n        ;; baseline; including (retrieval-type . disk) is optional\n        (define-relation/table concept `((path . ,(db-path \"concept\"))))\n        (define-relation/table edge    `((path . ,(db-path \"edge\"))))\n        (time (pretty-print\n                (run 10 (id name domain class)\n                  (concept id \"RXNORM:763521\" name domain class))))\n        (newline)\n        ;; make a new relation that reflects what you want from edge\n        (define-relation (concise-edge dataset subject object chi_sq_p)\n          (fresh (concept_count prevalence chi_sq_t expected_count ln_ratio rel_freq1 rel_freq2)\n            (edge dataset subject object concept_count prevalence chi_sq_t chi_sq_p expected_count ln_ratio rel_freq1 rel_freq2)))\n        (time (pretty-print\n                (run 10 (id name dataset subject chi_sq_p)\n                  (fresh (domain class)\n                    (concept id \"SNOMED:62208003\" name domain class)\n                    (concise-edge dataset subject id chi_sq_p)))))))\n"
  },
  {
    "path": "medikanren2/gui.rkt",
    "content": "#|\n\nWEB: mediKanren 2 Explorer TODO:\n\n* Fix problem with 'Find in X's':\nwhen you enter a string in 'Find in X's' text box, and a row is hilighted,\nthe Paths and Pubmed info isn't updated, and *clicking* on the\nhilighted row doesn't update the Paths and Pubmed info.\n\n* Fix sorting by CURIE, so that DOID:26 appears before DOID:2531\n\n* fully implement concept normalization checkbox\n* fully implement lightweight reasoning checkbox\n* implement smarter copy/paste\n* make the interface faster/more responsive\n\n|#\n\n\n#lang racket\n\n(require\n \"common.rkt\"\n \"synonyms.rkt\"\n \"string-search.rkt\"\n ;; (prefix-in semmed: \"db/semmed.rkt\")\n (prefix-in rtx:    \"db/rtx2-biolink_2_1_2021_07_28.rkt\")\n (prefix-in kgx:    \"db/kgx-synonym.rkt\")\n  json\n  racket/sandbox\n  racket/gui/base\n  framework\n  racket/engine\n  racket/date\n  racket/string\n  net/sendurl\n  (except-in racket/match ==)\n  (only-in srfi/1 iota))\n\n#|\n(require \"base.rkt\"\n         (prefix-in semmed: \"db/semmed.rkt\")\n         (prefix-in rtx:    \"db/rtx2-20210204.rkt\")\n         (prefix-in kgx:    \"db/kgx-synonym.rkt\"))\n|#\n#|\n(require\n \"common.rkt\"\n \"synonyms.rkt\"\n  racket/sandbox\n  racket/gui/base\n  framework\n  racket/engine\n  racket/date\n  racket/string\n  net/sendurl\n  (except-in racket/match ==)\n  (only-in srfi/1 iota))\n|#\n\n#|\nChoice 1:\n;;; find-ids-named\n;; Consult the string index associated with rel to find the ids\n;; in rel with a (name) string matching every substr in substrs,\n;; according to options stsopt.  If the associated string index\n;; has not been previously prepared, fail.\n(define (find-ids-named rel substrs (stsopt stsopt-default))\n(edited)\n\nChoice 2:\n;; Consult the string index associated with rel to find the concepts\n;; in rel with a (name) string matching every substr in substrs,\n;; according to options stsopt.  If the associated string index\n;; has not been previously prepared, fail.\n(define (find-concepts-named rel substrs (stsopt stsopt-default))\n|#\n\n\n(provide\n  launch-gui)\n\n(define MEDIKANREN_VERSION_STRING \"mediKanren 2 Explorer 0.1.0\")\n\n(displayln \"Starting mediKanren 2 Explorer...\")\n(newline)\n(displayln \"**************************************************\")\n(displayln \"*** mediKanren 2 is for research purposes only ***\")\n(displayln \"**************************************************\")\n(newline)\n(displayln MEDIKANREN_VERSION_STRING)\n\n;;; Query save file settings\n(define WRITE_QUERY_RESULTS_TO_FILE            #f)\n(define QUERY_RESULTS_FILE_NAME                \"last.sx\")\n(define HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME \"last.txt\")\n(define SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME \"last.tsv\")\n(define QUERY_RESULTS_FILE_MODE                'replace)\n\n;;; Initial window size\n(define HORIZ-SIZE 800)\n(define VERT-SIZE 400)\n\n;;; Decreases/increases predicate names\n(define DECREASES_PREDICATE_NAMES\n  (list\n   \"biolink:ameliorates\"\n   \"biolink:approved_to_treat\"\n   \"biolink:decreases_abundance_of\"\n   \"biolink:decreases_activity_of\"\n   \"biolink:decreases_expression_of\"\n   \"biolink:decreases_synthesis_of\"\n   \"biolink:decreases_transport_of\"\n   \"biolink:decreases_uptake_of\"\n   \"biolink:disrupts\"\n   \"biolink:entity_negatively_regulates_entity\"\n   \"biolink:prevents\"\n   \"biolink:process_negatively_regulates_process\"\n   \"biolink:treats\"))\n(define INCREASES_PREDICATE_NAMES\n  (list\n   \"biolink:causes\"\n   \"biolink:causes_adverse_event\"\n   \"biolink:condition_associated_with_gene\"\n   \"biolink:contributes_to\"\n   \"biolink:decreases_degradation_of\"\n   \"biolink:enables\"\n   \"biolink:entity_positively_regulates_entity\"\n   \"biolink:exacerbates\"\n   \"biolink:gene_associated_with_condition\"\n   \"biolink:increases_abundance_of\"\n   \"biolink:increases_activity_of\"\n   \"biolink:increases_expression_of\"\n   \"biolink:increases_synthesis_of\"\n   \"biolink:increases_transport_of\"\n   \"biolink:process_positively_regulates_process\"\n   \"biolink:produces\"))\n\n\n\n\n(define (curie-string str)\n  (let ((cs (regexp-match* #px\"^[\\\\s]*(([^\\\\s]+:[^\\\\s]*)|(:[^\\\\s]+))[\\\\s]*$\" str #:match-select cadr)))\n    (if (null? cs)\n        #f\n        (car cs))))\n\n\n(define (sort-paths paths)\n  (printf \"sort-paths -- IMPLEMENT ME!\\n\")\n  paths)\n\n(define (path-confidence . args)\n  ;(printf \"path-confidence -- IMPLEMENT ME!\\n\")\n  'todo)\n\n(define (path-confidence (lambda (pr)\n          (define pubs (cdr pr))\n          (let ((pubmed-ids (if (not (string? pubs))\n                                '()\n                                (regexp-match* #rx\"PMID:([0-9]+)\" pubs #:match-select cadr))))\n            pubmed-ids))]\n    [else '()])\n  \n  ;; Old mediKanren 1 common.rkt code:\n  #;(cond\n    [(assoc \"pmids\" eprops)  ;; WEB the 'pmids' property is only used by semmed, I believe\n     => (lambda (pr) (regexp-split #rx\";\" (cdr pr)))]\n    [(assoc \"publications\" eprops)\n     => (lambda (pr)\n          (define pubs (cdr pr))\n          (if (not (string? pubs))\n            '()\n            (regexp-match* #rx\"([0-9]+)\" pubs #:match-select cadr)))]\n    [else '()])\n  )\n\n(define (python->json py)\n  (define len (string-length py))\n  (let loop ((i 0) (start 0))\n    (cond ((= i len) (if (= start 0) py (substring py start)))\n          ((eqv? (string-ref py i) #\\')\n           (string-append\n             (substring py start i) \"\\\"\"\n             (let requote ((i (+ i 1)) (start (+ i 1)))\n               (cond ((eqv? (string-ref py i) #\\')\n                      (string-append (substring py start i) \"\\\"\"\n                                     (loop (+ i 1) (+ i 1))))\n                     ((eqv? (string-ref py i) #\\\\)\n                      (if (eqv? (string-ref py (+ i 1)) #\\\")\n                        (requote (+ i 2) start)\n                        (string-append (substring py start i)\n                                       (requote (+ i 2) (+ i 1)))))\n                     ((eqv? (string-ref py i) #\\\")\n                      (string-append (substring py start i) \"\\\\\\\"\"\n                                     (requote (+ i 1) (+ i 1))))\n                     (else (requote (+ i 1) start))))))\n          ((eqv? (string-ref py i) #\\\")\n           (let skip ((i (+ i 1)) (start start))\n             (cond ((eqv? (string-ref py i) #\\\") (loop (+ i 1) start))\n                   ((eqv? (string-ref py i) #\\\\)\n                    (if (eqv? (string-ref py (+ i 1)) #\\\")\n                      (skip (+ i 2) start)\n                      (string-append (substring py start i)\n                                     (skip (+ i 2) (+ i 1)))))\n                   (else                         (skip (+ i 1) start)))))\n          (else (loop (+ i 1) start)))))\n\n(define PUBMED_URL_PREFIX \"https://www.ncbi.nlm.nih.gov/pubmed/\")\n(define (pubmed-URLs-from-edge edge)\n  (map (lambda (pubmed-id) (string-append PUBMED_URL_PREFIX (~a pubmed-id)))\n       (pubmed-ids-from-edge edge)))\n\n(define (pubmed-ids-from-edge edge)\n  (remove-duplicates\n    (match edge\n      ['path-separator '()]\n      [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n        (pubmed-ids-from-edge-props eprops)])))\n\n(define (publications-info-alist-from-edge-props eprops)\n  (cond\n    [(assoc \"publications_info\" eprops)\n     => (lambda (pr)\n          (with-handlers ([exn:fail?\n                           (lambda (v)\n                             ((error-display-handler) (exn-message v) v)\n                             '())])\n            (define pubs (cdr pr))\n            (define jason-ht (string->jsexpr (python->json pubs)))\n            (hash-map jason-ht (lambda (k v)\n                                 (cons (string-append\n                                        PUBMED_URL_PREFIX\n                                        (car (regexp-match* #rx\"([0-9]+)\" (symbol->string k) #:match-select cadr)))\n                                       (list (hash-ref v '|publication date| #f)\n                                             (hash-ref v '|subject score| #f)\n                                             (hash-ref v '|object score| #f)\n                                             (regexp-replace*\n                                              #rx\"([ ]+)\"\n                                              (hash-ref v 'sentence #f)\n                                              \" \")))))))]\n    [else '()]))\n\n(define (publications-info-alist-from-edge edge)\n  ;; ((pubmed-URL . (publication-date subject-score object-score sentence)) ...)\n  (remove-duplicates\n    (match edge\n      ['path-separator '()]\n      [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n        (publications-info-alist-from-edge-props eprops)])))\n\n\n\n(define (print-short-concept-description concepts)\n  (displayln\n   (map\n    (lambda (c)\n      (match c\n        [`(,dbname ,curie ,name . ,rest)\n         `(,curie ,name)]))\n    concepts)))\n\n(define (find-predicates/concepts subject? object? concepts)\n  ; (printf \"find-predicates/concepts subject?: ~s\\nobject?: ~s\\nconcepts: ~s\\n\\n\" subject? object? concepts)\n  (let ((ans (map\n              (lambda (c)\n                (match c\n                  [`(,dbname ,curie ,name ,cat)\n\n                   (define subject-predicates\n                       (and subject?\n                            (set->list\n                             (run*/set pred\n                               (fresh (eid o)\n                                 (edge `(,dbname . ,eid) curie o)\n                                 (eprop `(,dbname . ,eid) \"predicate\" pred))))))\n\n                   (define object-predicates\n                       (and object?\n                            (set->list\n                             (run*/set pred\n                               (fresh (eid s)\n                                 (edge `(,dbname . ,eid) s curie)\n                                 (eprop `(,dbname . ,eid) \"predicate\" pred))))))\n                   \n                   ; (printf \"subject-predicates: ~s\\n\" subject-predicates)\n                   ; (printf \"object-predicates: ~s\\n\" object-predicates)\n                   (list c subject-predicates object-predicates)]))\n              concepts)))\n    ans))\n\n;; from medikanren/common.rkt:\n;;\n#;(define (find-predicates/concepts subject? object? concepts)\n  (map (lambda (c)\n         (define subject-predicates\n           (and subject? (run* (p) (subject-predicateo c p))))\n         (define object-predicates\n           (and object? (run* (p) (object-predicateo c p))))\n         (list c subject-predicates object-predicates))\n       concepts))\n\n\n;; TODO implement or remove\n(define (find-concepts/options/curie-infer subject? object? strings)\n  '())\n\n;; from medikanren/common.rkt:\n;;\n#;(define (find-concepts/options/cui-infer subject? object? isa-count strings)\n  (define yes-cui\n    (map (lambda (s) (run* (c) (~cui*-concepto (list s) c))) strings))\n  (define no-cui (filter-not not (map (lambda (s rs) (and (null? rs) s))\n                                      strings yes-cui)))\n  (define all (append* (cons (run* (c) (~name*-concepto no-cui c)) yes-cui)))\n  (concepts/options subject? object? isa-count all))\n\n\n(define chars:ignore-typical \"-\")\n(define chars:split-typical \"\\t\\n\\v\\f\\r !\\\"#$%&'()*+,./:;<=>?@\\\\[\\\\\\\\\\\\]\\\\^_`{|}~\")\n\n(define (smart-string-matches? case-sensitive? chars:ignore chars:split str* hay)\n  (define re:ignore (and (non-empty-string? chars:ignore)\n                         (pregexp (string-append \"[\" chars:ignore \"]\"))))\n  (define re:split (and (non-empty-string? chars:split)\n                        (pregexp (string-append \"[\" chars:split \"]\"))))\n  (define (normalize s case-sensitive?)\n    (define pruned (if re:ignore (string-replace s re:ignore \"\") s))\n    (if case-sensitive? pruned (string-downcase pruned)))\n  (define (contains-upcase? s) (not (string=? s (string-downcase s))))\n  (define case-sensitive?*\n    (map (lambda (s) (or case-sensitive? (contains-upcase? s))) str*))\n  (define needles\n    (map (lambda (v case-sensitive?) (normalize v case-sensitive?))\n         str* case-sensitive?*))\n  (and hay\n       (andmap\n        (if re:split\n            (lambda (n case-sensitive?)\n              (ormap (lambda (s) (string=? s n))\n                     (string-split (normalize hay case-sensitive?) re:split)))\n            (lambda (n case-sensitive?)\n              (string-contains? (normalize hay case-sensitive?) n)))\n        needles case-sensitive?*)))\n\n\n;; from medikanren/db.rkt:\n;;\n#;(define (smart-string-matches? case-sensitive? chars:ignore chars:split str* hay)\n  (define re:ignore (and (non-empty-string? chars:ignore)\n                         (pregexp (string-append \"[\" chars:ignore \"]\"))))\n  (define re:split (and (non-empty-string? chars:split)\n                        (pregexp (string-append \"[\" chars:split \"]\"))))\n  (define (normalize s case-sensitive?)\n    (define pruned (if re:ignore (string-replace s re:ignore \"\") s))\n    (if case-sensitive? pruned (string-downcase pruned)))\n  (define (contains-upcase? s) (not (string=? s (string-downcase s))))\n  (define case-sensitive?*\n    (map (lambda (s) (or case-sensitive? (contains-upcase? s))) str*))\n  (define needles\n    (map (lambda (v case-sensitive?) (normalize v case-sensitive?))\n         str* case-sensitive?*))\n  (and hay\n       (andmap\n        (if re:split\n            (lambda (n case-sensitive?)\n              (ormap (lambda (s) (string=? s n))\n                     (string-split (normalize hay case-sensitive?) re:split)))\n            (lambda (n case-sensitive?)\n              (string-contains? (normalize hay case-sensitive?) n)))\n        needles case-sensitive?*)))\n\n\n\n\n\n\n(define (split-name-string name)\n  (string-split name #px\"\\\\s+\"))\n\n(define (empty-string? str)\n  (not (not (regexp-match #px\"^[\\\\s]*$\" str))))\n\n(define *verbose* #f)\n\n(define input-response-latency 50)\n\n(define MAX-CHAR-WIDTH 150)\n\n(define smart-column-width-list-box%\n  (class list-box%\n    (super-new)\n    (define (on-size width height)\n      (super on-size width height)\n      (set-default-column-widths this))\n    (override on-size)))\n\n(define (set-default-column-widths list-box)\n  (define label* (send list-box get-column-labels))\n  (define num-cols (length label*))\n  (define window-width (send list-box get-width))\n  (define min-width 5)\n  (define max-width 1000)\n  (define fudge-factor 4) ;; column divider width\n  (define width (min (max (- (floor (/ window-width num-cols)) fudge-factor)\n                          min-width)\n                     max-width))\n  (let loop ((col-num (sub1 num-cols)))\n    (cond\n      [(zero? col-num) (void)]\n      [else\n       (send list-box\n             set-column-width\n             col-num\n             width\n             min-width\n             max-width)\n       (loop (sub1 col-num))])))\n\n(define construct-predicate-label-string\n  (lambda (pred-string pred-name-list)\n    (~a\n     (string-append pred-string\n                   \"  (\"\n                   (foldr (lambda (str1 str2)\n                            (if (equal? \"\" str2)\n                                (string-append str1 \"\" str2)\n                                (string-append str1 \", \" str2)))\n                          \"\"\n                          pred-name-list)\n                   \")\")\n     #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")))\n\n(define DECREASES_PREDICATE_PREFIX_STRING \"decreases [synthetic]\")\n(define DECREASES_PREDICATE_STRING\n  (construct-predicate-label-string DECREASES_PREDICATE_PREFIX_STRING DECREASES_PREDICATE_NAMES))\n(define INCREASES_PREDICATE_PREFIX_STRING \"increases [synthetic]\")\n(define INCREASES_PREDICATE_STRING\n  (construct-predicate-label-string INCREASES_PREDICATE_PREFIX_STRING INCREASES_PREDICATE_NAMES))\n\n(define SYNTHETIC_PREDICATE_PREFIXES (list DECREASES_PREDICATE_PREFIX_STRING\n                                           INCREASES_PREDICATE_PREFIX_STRING\n                                           ))\n\n(define SORT_COLUMN_INCREASING 'sort-column-increasing)\n(define SORT_COLUMN_DECREASING 'sort-column-decreasing)\n\n(define *concept-1-column-sort-order*\n  (vector SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING))\n(define *last-concept-1-column-clicked-for-sorting* (box -1))\n\n(define *concept-2-column-sort-order*\n  (vector SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING))\n(define *last-concept-2-column-clicked-for-sorting* (box -1))\n\n(define *concept-X-column-sort-order*\n  (vector SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_INCREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING\n          SORT_COLUMN_DECREASING))\n(define *last-concept-X-column-clicked-for-sorting* (box -1))\n\n(define *concept-1-name-string* (box \"\"))\n(define *concept-1-node-normalization-flag* (box #t))\n(define *concept-1-lightweight-reasoning-flag* (box #f))\n(define *concept-1-choices* (box '()))\n(define *predicate-1-choices* (box '()))\n\n(define *concept-2-name-string* (box \"\"))\n(define *concept-2-node-normalization-flag* (box #t))\n(define *concept-2-lightweight-reasoning-flag* (box #f))\n(define *concept-2-choices* (box '()))\n(define *predicate-2-choices* (box '()))\n\n(define *concept-X-choices* (box '()))\n(define *full-path-choices* (box '()))\n(define *pubmed-choices* (box '()))\n\n;; saved choices used to generate\n;; paths when clicking on a concept in the X list box.\n(define *solution-concept-1-name-string* (box \"\"))\n(define *solution-concept-2-name-string* (box \"\"))\n(define *solution-concept-1-node-normalization-flag* (box #t))\n(define *solution-concept-2-node-normalization-flag* (box #t))\n(define *solution-concept-1-lightweight-reasoning-flag* (box #f))\n(define *solution-concept-2-lightweight-reasoning-flag* (box #f))\n(define *solution-concept-1-choices* (box '()))\n(define *solution-concept-2-choices* (box '()))\n(define *solution-predicate-1-choices* (box '()))\n(define *solution-predicate-2-choices* (box '()))\n\n;; ((pubmed-URL . (publication-date subject-score object-score sentence)) ...)\n(define *publications-info-alist* (box '()))\n\n(define *populate-publication-fields*\n  (lambda args\n    (error '*populate-publication-fields* \"*populate-publication-fields* function not initialized\")))\n\n(define (scheduler dependents)\n  (define mk-thread #f)\n  (define (kill-and-run p)\n    (kill-current-thread)\n    (set! mk-thread (thread p)))\n  (define (kill-current-thread)\n    (and mk-thread (begin (kill-thread mk-thread)\n                          (set! mk-thread #f)))\n    (for-each (lambda (s) (s 'kill)) dependents))\n  (lambda (op . args)\n    (case op\n      ((run)  (apply kill-and-run args))\n      ((kill) (kill-current-thread))\n      (else   (error \"invalid scheduler operation:\" op args)))))\n\n(define S (scheduler '()))\n(define S:edges S)\n(define S:X     S)\n(define S:C1P   S)\n(define S:C2P   S)\n(define S:C1    S)\n(define S:C2    S)\n\n(define handle-search-in-Xs\n  (lambda (search-in-Xs-field\n           concept-X-list-box\n           search-in-Xs-previous-button\n           search-in-Xs-next-button\n           . rest)\n    (define direction (if (and (list? rest) (= (length rest) 1)) (car rest) #f))\n    (define search-str (send search-in-Xs-field get-value))\n\n    (define current-selection (send concept-X-list-box get-selection))\n\n    (cond\n      [direction\n\n       (define count (send concept-X-list-box get-number))\n\n       (define add1/sub1 (case direction\n                           [(previous) sub1]\n                           [(next) add1]\n                           [else (error 'add1/sub1 \"unknown direction in inc/dec\")]))\n\n       (define found-selection\n         (and (> count 0)\n              (let loop ((i (add1/sub1 current-selection)))\n                (cond\n                  [(>= i count) (loop 0)]\n                  [(< i 0) (loop (- count 1))]\n                  [else\n                   (define data (send concept-X-list-box get-data i))\n                   (define name-str (list-ref data 2))\n                   (define matches?\n                     (smart-string-matches? #f\n                                            chars:ignore-typical\n                                            \"\"\n                                            (string-split search-str \" \")\n                                            name-str))\n                   (cond\n                     [matches? i]\n                     [(= i current-selection)\n                      ;; wrapped around without a match\n                      #f]\n                     [else (loop (add1/sub1 i))])]))))\n\n       (if found-selection\n           (when (not (equal? found-selection current-selection))\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))\n             (send concept-X-list-box select found-selection #t)\n             (send concept-X-list-box set-first-visible-item found-selection))\n           (begin\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))))]\n      [(empty-string? search-str)\n       (when current-selection\n         (send concept-X-list-box select current-selection #f))\n       (send search-in-Xs-previous-button enable #f)\n       (send search-in-Xs-next-button enable #f)]\n      [else\n       (define count (send concept-X-list-box get-number))\n       (define found-selection\n         (and (> count 0)\n              (let loop ((i 0))\n                (cond\n                  [(>= i count) #f]\n                  [else\n                   (define data (send concept-X-list-box get-data i))\n                   (define name-str (list-ref data 2))\n                   (define matches?\n                     (smart-string-matches? #f\n                                            chars:ignore-typical\n                                            \"\"\n                                            (string-split search-str \" \")\n                                            name-str))\n                   (if matches?\n                       i\n                       (loop (add1 i)))]))))\n\n       (if found-selection\n           (begin\n             (send search-in-Xs-previous-button enable #t)\n             (send search-in-Xs-next-button enable #t))\n           (begin\n             (send search-in-Xs-previous-button enable #f)\n             (send search-in-Xs-next-button enable #f)))\n\n       (if found-selection\n           (when (not (equal? found-selection current-selection))\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))\n             (send concept-X-list-box select found-selection #t)\n             (send concept-X-list-box set-first-visible-item found-selection))\n           (begin\n             (when current-selection\n               (send concept-X-list-box select current-selection #f))))])))\n\n(define (convert-concept-1/2-to-list-box-format concept)\n  (match concept\n    [`(,dbname ,curie ,name ,cat)\n     (list (format \"~a\" dbname)\n           (~a curie #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (format \"~a\" cat)\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\"))]))\n\n(define (convert-X-concept-to-list-box-format concept)\n  (match concept\n    [`(,dbname ,curie ,name ,cat ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-length ,confidence)\n     (list (format \"~a\" dbname)\n           (~a curie #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (~a cat #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (format \"~a\" max-pubmed-count)\n           (format \"~a\" min-pubmed-count)\n           (string-join pred-names \", \")\n           (format \"~a\" path-length)\n           (format \"~a\" confidence))]))\n\n(define (convert-concept-1/2-to-column-sorting-format concept)\n  (match concept\n    [`(,dbname ,curie ,name ,cat)\n     (list (format \"~a\" dbname)\n           (~a curie #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (~a cat #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\"))]))\n\n(define (convert-X-concept-to-column-sorting-format concept)\n  (match concept\n    [`(,dbname ,curie ,name ,cat ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-length ,confidence)\n     (list (format \"~a\" dbname)\n           (~a curie #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (~a cat #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n           max-pubmed-count\n           min-pubmed-count\n           (string-join pred-names \", \")\n           path-length\n           confidence)]))\n\n(define (make-send-concepts-to-concept-1/2-list-box concept-1/2-list-box-thunk)\n  (lambda (concepts)\n    (define concept-1/2-list-box (concept-1/2-list-box-thunk))\n    (define formatted-concepts (map convert-concept-1/2-to-list-box-format concepts))\n    (send concept-1/2-list-box\n          set\n          (map (lambda (e) (list-ref e 0)) formatted-concepts)\n          (map (lambda (e) (list-ref e 1)) formatted-concepts)\n          (map (lambda (e) (list-ref e 2)) formatted-concepts)\n          (map (lambda (e) (list-ref e 3)) formatted-concepts))))\n\n(define (make-send-concepts-to-concept-X-list-box concept-X-list-box)\n  (lambda (concepts)\n    (define formatted-concepts (map convert-X-concept-to-list-box-format concepts))\n    (send concept-X-list-box\n          set\n          (map (lambda (e) (list-ref e 0)) formatted-concepts)\n          (map (lambda (e) (list-ref e 1)) formatted-concepts)\n          (map (lambda (e) (list-ref e 2)) formatted-concepts)\n          (map (lambda (e) (list-ref e 3)) formatted-concepts)\n          (map (lambda (e) (list-ref e 4)) formatted-concepts)\n          (map (lambda (e) (list-ref e 5)) formatted-concepts)\n          (map (lambda (e) (list-ref e 6)) formatted-concepts)\n          (map (lambda (e) (list-ref e 7)) formatted-concepts)\n          (map (lambda (e) (list-ref e 8)) formatted-concepts))))\n\n(define (handle-sort-by-column-header-click event\n                                            list-box\n                                            last-column-clicked-for-sorting-box\n                                            column-sort-order-vector\n                                            choices-box\n                                            convert-values-to-column-sorting-format\n                                            send-values-to-list-box)\n\n  (printf \"handle-sort-by-column-header-click called\\n\")\n\n  ;; get previously selected choice's data, if any\n  (define current-selection (send list-box get-selection))\n  (printf \"current-selection: ~s\\n\" current-selection)\n  (define current-selection-data (and current-selection\n                                      (send list-box get-data current-selection)))\n  (printf \"current-selection-data: ~s\\n\" current-selection-data)\n\n  (when current-selection\n    (send list-box select current-selection #f))\n\n  ;; sort by column\n  (define column-clicked (send event get-column))\n  (define last-column-clicked (unbox last-column-clicked-for-sorting-box))\n\n  (define sort-order (vector-ref column-sort-order-vector column-clicked))\n\n  ;; swap sort order if user clicks on same column twice in a row\n  (when (= column-clicked last-column-clicked)\n    (set! sort-order\n          (if (eqv? sort-order SORT_COLUMN_INCREASING)\n              SORT_COLUMN_DECREASING\n              SORT_COLUMN_INCREASING))\n    (vector-set! column-sort-order-vector\n                 column-clicked\n                 sort-order))\n\n  (printf \"sorting by column ~s in ~s order\\n\" column-clicked sort-order)\n\n  (define choices (unbox choices-box))\n\n  (define sorted-choices (sort choices\n                               (lambda (c1 c2)\n                                 (let ((fc1 (convert-values-to-column-sorting-format c1))\n                                       (fc2 (convert-values-to-column-sorting-format c2)))\n                                   (let ((v1 (list-ref fc1 column-clicked))\n                                         (v2 (list-ref fc2 column-clicked)))\n                                     (let ((num-compare\n                                            (if (eqv? sort-order SORT_COLUMN_INCREASING)\n                                                <\n                                                >))\n                                           (string-compare\n                                            (if (eqv? sort-order SORT_COLUMN_INCREASING)\n                                                string?)))\n                                       (if (and (number? v1) (number? v2))\n                                           (num-compare v1 v2)\n                                           (string-compare (string-downcase v1)\n                                                           (string-downcase v2)))))))))\n\n  (set-box! last-column-clicked-for-sorting-box column-clicked)\n\n  (set-box! choices-box sorted-choices)\n\n  (send-values-to-list-box sorted-choices)\n\n  ;; add choice data to each list-box entry\n  (define len (length sorted-choices))\n  (let loop ((i 0)\n             (c* sorted-choices))\n    (cond\n      [(= len i) (void)]\n      [else\n       (send list-box set-data i (car c*))\n       (loop (add1 i)\n             (cdr c*))]))\n\n  ;; select previously selected choice in its new location, if any\n  (when (and current-selection current-selection-data)\n    (define count (send list-box get-number))\n    (printf \"count: ~s\\n\" count)\n    (define new-selection\n      (let loop ((i 0))\n        (cond\n          [(>= i count) #f]\n          [else\n           (let ((d (send list-box get-data i)))\n             (printf \"--------\\n\")\n             (printf \"d: ~s\\n\" d)\n             (printf \"(equal? d current-selection-data): ~s\\n\" (equal? d current-selection-data))\n             (if (equal? d current-selection-data)\n                 i\n                 (loop (add1 i))))])))\n    (printf \"new-selection: ~s\\n\" new-selection)\n    (when new-selection\n      (send list-box select new-selection #t)\n      (send list-box set-first-visible-item new-selection)))\n\n  (void))\n\n(define (concept-list parent\n                      parent-search/normalize/lw-panel\n                      parent-list-boxes-panel\n                      label\n                      name-string\n                      node-normalization-flag\n                      lightweight-reasoning-flag\n                      choices\n                      predicate-list-box-thunk\n                      predicate-choices\n                      edge-type\n                      last-column-clicked-for-sorting-box\n                      column-sort-order-vector\n                      choices-box\n                      convert-values-to-column-sorting-format\n                      send-values-to-list-box\n                      S:C S:CP)\n  (define name-field (new text-field%\n                          (label label)\n                          (parent parent-search/normalize/lw-panel)\n                          (init-value \"\")\n                          (callback (lambda (self event)\n                                      (define name (send self get-value))\n                                      (set-box! name-string name)\n                                      (set-box! predicate-choices '())\n                                      (send (predicate-list-box-thunk) set '())\n                                      (handle)))))\n  (define node-normalization-field (new check-box%\n                                        (parent parent-search/normalize/lw-panel)\n                                        (label \"Show concept synonyms for CURIE searches\")\n                                        (value #t)\n                                        (callback (lambda (self event) (handle)))))\n  (define lightweight-reasoning-field (new check-box%\n                                          (parent parent-search/normalize/lw-panel)\n                                          (label \"Use lightweight reasoning\")\n                                          (value #f)\n                                          ;; TODO remove the 'deleted style to show the checkbox\n                                          (style '(deleted))\n                                          (callback (lambda (self event) (handle)))))\n  (define concept-listbox (new smart-column-width-list-box%\n                               (label label)\n                               (choices '())\n                               (columns '(\"KG\" \"CURIE\" \"Category\" \"Name\"))\n                               (parent parent-list-boxes-panel)\n                               (style '(column-headers clickable-headers reorderable-headers extended))\n                               (callback (lambda (self event)\n                                           (define event-type (send event get-event-type))\n                                           (cond\n                                             [(eqv? event-type 'list-box-column)\n                                              (handle-sort-by-column-header-click\n                                                event\n                                                concept-listbox\n                                                last-column-clicked-for-sorting-box\n                                                column-sort-order-vector\n                                                choices-box\n                                                convert-values-to-column-sorting-format\n                                                send-values-to-list-box)]\n                                             [else\n                                               (define selections (send self get-selections))\n                                               (define selected-concepts\n                                                 (foldr (lambda (i l) (cons (list-ref (unbox choices) i) l)) '() selections))\n                                               (when *verbose*\n                                                 (printf \"selected concepts:\\n\")\n                                                 (print-short-concept-description selected-concepts)\n                                                 ;; Old mediKanren 1 GUI code:\n                                                 ;; (printf \"selected concepts:\\n~s\\n\" selected-concepts)\n                                                 )\n                                               (S:CP 'run\n                                                     (thunk\n                                                       (define preds-by-concept\n                                                         (time (case edge-type\n                                                                 [(in-edge)  (map caddr (find-predicates/concepts #f #t selected-concepts))]\n                                                                 [(out-edge) (map cadr (find-predicates/concepts #t #f selected-concepts))]\n                                                                 [else       (error 'concept-listbox/predicates)])))\n                                                       (define predicates\n                                                         (begin\n                                                           (printf \"preds-by-concept:\\n~s\\n\" preds-by-concept)\n                                                           (sort (remove-duplicates (apply append preds-by-concept)) string\n                   (lambda (cs)\n                     (printf \"treating '~s' as a single CURIE\\n\" cs)\n                     (printf \"performing CURIE search for: ~s\\n\" cs)\n                     (let ((synonyms (if (unbox node-normalization-flag)\n                                         (set->list\n                                          (set-union\n                                           (set cs)\n                                           (list->set\n                                            (run* x (kgx-synonym cs x)))))\n                                         (list cs))))\n                       (printf \"found synonyms:\\n~s\\n\" synonyms)\n\n                       (time (let ((result\n                                    (map (lambda (curie)\n                                           (run*/set ans\n                                             (fresh (dbname eid s o name cat)\n                                               (== `(,dbname ,curie ,name ,cat) ans)\n                                               (if subject?\n                                                   (== curie s)\n                                                   (== curie o))\n                                               (edge `(,dbname . ,eid) s o)\n                                               (cprop curie \"name\" name)\n                                               (cprop curie \"category\" cat))))\n                                         synonyms)))\n                               (if (null? result)\n                                   '()\n                                   (set->list (apply set-union result))))))))\n                  (else\n\n                   (printf \"treating '~s' as a non-CURIE search\\n\" string-parts)\n                   (printf \"performing search for: ~s\\n\" string-parts)\n\n                   (let ((string-search-curies (find-ids-named rtx:cprop string-parts)))\n\n                     (time (let ((result\n                                  (map (lambda (curie)\n                                          (run*/set ans\n                                            (fresh (dbname eid s o name cat)\n                                              (== `(,dbname ,curie ,name ,cat) ans)\n                                              (if subject?\n                                                  (== curie s)\n                                                  (== curie o))\n                                              (edge `(,dbname . ,eid) s o)\n                                              (cprop curie \"name\" name)\n                                              (cprop curie \"category\" cat))))\n                                        string-search-curies)))\n                             (if (null? result)\n                                 '()\n                                 (set->list (apply set-union result))))))\n\n                   ;; Old mediKanren 1 GUI code:\n                   ;; (time (find-concepts/options/cui-infer subject? object? isa-count string-parts))\n                   \n                   ))))\n\n      ;; (printf \"ans:\\n~s\\n\" ans)\n      \n      (set-box! choices ans)\n      (send concept-listbox\n            set\n            (map (lambda (x)\n                   (match x\n                     [`(,dbname ,curie ,name ,cat)\n                      (~a dbname #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                 ans)          \n            (map (lambda (x)\n                   (match x\n                     [`(,dbname ,curie ,name ,cat)\n                      (~a curie #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                 ans)\n            (map (lambda (x)\n                   (match x\n                     [`(,dbname ,curie ,name ,cat)\n                      (~a cat #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n                      ;; Old mediKanren 1 GUI code:\n                      ;; (~a `(,catid . ,cat) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")\n                      ]))\n                 ans)\n            (map (lambda (x)\n                   (match x\n                     [`(,dbname ,curie ,name ,cat)\n                      (~a name #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                 ans))\n\n      ;; add choice data to each list-box entry\n      (define len (length (unbox choices)))\n      (let loop ((i 0)\n                 (c* (unbox choices)))\n        (cond\n          [(= len i) (void)]\n          [else\n           (send concept-listbox set-data i (car c*))\n           (loop (add1 i)\n                 (cdr c*))]))\n\n      ;; unselect all items\n      (for ([i (length ans)])\n           (send concept-listbox select i #f))))\n\n  (define current-name \"\")\n  (define current-node-normalization #t)\n  (define current-lightweight-reasoning #f)\n  (define pending-name current-name)\n  (define timer (new timer% (notify-callback (thunk (S:C 'run mk-run)))))\n  (define (handle)\n    (define new-name (send name-field get-value))\n    (define new-node-normalization (send node-normalization-field get-value))\n    (define new-lightweight-reasoning (send lightweight-reasoning-field get-value))\n    (when (not (and (equal? current-name new-name)\n                    (equal? current-node-normalization new-node-normalization)\n                    (equal? current-lightweight-reasoning new-lightweight-reasoning)))\n      (set! current-name new-name)\n      \n      (set! current-node-normalization new-node-normalization)\n      (set-box! node-normalization-flag current-node-normalization)\n\n      (set! current-lightweight-reasoning new-lightweight-reasoning)\n      (set-box! lightweight-reasoning-flag current-lightweight-reasoning)\n      \n      (S:C 'kill)\n      (send timer stop)\n      (send timer start input-response-latency #t)))\n  concept-listbox)\n\n(define (launch-gui)\n  (launch-main-window))\n\n(define (launch-main-window)\n  (let ((frame (new frame%\n                    (label MEDIKANREN_VERSION_STRING)\n                    (width HORIZ-SIZE)\n                    (height VERT-SIZE))))\n\n    (define outer-vert-draggable-panel (new panel:vertical-dragable%\n                                            (parent frame)\n                                            (alignment '(left center))))\n\n    (define upper-pane (new panel:vertical-dragable%\n                            (parent outer-vert-draggable-panel)\n                            (alignment '(left center))))\n\n    (define lower-pane (new panel:vertical-dragable%\n                            (parent outer-vert-draggable-panel)\n                            (alignment '(left center))))\n\n    (define go-callback\n      (lambda (button event)\n\n        (printf \"go callback called...\\n\")\n        \n        (send running-status-description set-label \"Running...\")\n\n        (define concept-1-selections (send concept-1-list-box get-selections))\n        (define concept-2-selections (send concept-2-list-box get-selections))\n\n        (define concept-1-selected-concepts\n          (foldr (lambda (i l) (cons (list-ref (unbox *concept-1-choices*) i) l))\n                 '()\n                 concept-1-selections))\n        (define concept-2-selected-concepts\n          (foldr (lambda (i l) (cons (list-ref (unbox *concept-2-choices*) i) l))\n                 '()\n                 concept-2-selections))\n\n        (printf \"concept-1-selections: ~s\\n\" concept-1-selections)\n        (print-short-concept-description concept-1-selected-concepts)\n        ;; Old mediKanren 1 GUI code:\n        ;; (displayln concept-1-selected-concepts)\n        (printf \"---------------------------------\\n\")\n        (printf \"concept-2-selections: ~s\\n\" concept-2-selections)\n        (print-short-concept-description concept-2-selected-concepts)\n        ;; Old mediKanren 1 GUI code:\n        ;; (displayln concept-2-selected-concepts)\n        (printf \"---------------------------------\\n\")\n\n\n        (define predicate-1-selections (send predicate-1-list-box get-selections))\n        (define predicate-2-selections (send predicate-2-list-box get-selections))\n\n        (define predicate-1-selected-predicates\n          (foldr (lambda (i l) (cons (list-ref (unbox *predicate-1-choices*) i) l))\n                 '()\n                 predicate-1-selections))\n        (define predicate-2-selected-predicates\n          (foldr (lambda (i l) (cons (list-ref (unbox *predicate-2-choices*) i) l))\n                 '()\n                 predicate-2-selections))\n\n\n        (printf \"predicate-1-selections: ~s\\n\" predicate-1-selections)\n        (displayln predicate-1-selected-predicates)\n        (printf \"---------------------------------\\n\")\n        (printf \"predicate-2-selections: ~s\\n\" predicate-2-selections)\n        (displayln predicate-2-selected-predicates)\n        (printf \"---------------------------------\\n\")\n\n        (S:X 'run (thunk (find-X-concepts concept-1-selected-concepts\n                                          concept-2-selected-concepts\n                                          predicate-1-selected-predicates\n                                          predicate-2-selected-predicates\n                                          (unbox *predicate-1-choices*)\n                                          (unbox *predicate-2-choices*)\n                                          concept-X-list-box\n                                          running-status-description\n                                          full-path-list-box\n                                          subject-properties-list-box\n                                          edge-properties-list-box\n                                          object-properties-list-box\n                                          pubmed-list-box\n                                          search-in-Xs-field\n                                          search-in-Xs-previous-button\n                                          search-in-Xs-next-button)))))\n\n    (define concept-1-overall-pane (new vertical-pane%\n                                        (parent upper-pane)\n                                        (alignment '(left center))))\n\n    (define concept-1-search/normalize/lw-panel (new panel:horizontal-dragable%\n                                            (parent concept-1-overall-pane)\n                                            (alignment '(left center))\n                                            (stretchable-height #f)))\n    (define concept-1-list-boxes-panel (new panel:horizontal-dragable%\n                                            (parent concept-1-overall-pane)\n                                            (alignment '(left center))))\n    (define concept-1-list-box (concept-list concept-1-overall-pane\n                                             concept-1-search/normalize/lw-panel\n                                             concept-1-list-boxes-panel\n                                             \"Concept 1\"\n                                             *concept-1-name-string*\n                                             *concept-1-node-normalization-flag*\n                                             *concept-1-lightweight-reasoning-flag*\n                                             *concept-1-choices*\n                                             (lambda () predicate-1-list-box)\n                                             *predicate-1-choices*\n                                             'out-edge\n                                             *last-concept-1-column-clicked-for-sorting*\n                                             *concept-1-column-sort-order*\n                                             *concept-1-choices*\n                                             convert-concept-1/2-to-column-sorting-format\n                                             (make-send-concepts-to-concept-1/2-list-box (lambda () concept-1-list-box))\n                                             S:C1 S:C1P))\n    (define predicate-1-list-box (new list-box%\n                                      (label \"Predicate 1\")\n                                      (choices (unbox *predicate-1-choices*))\n                                      (columns '(\"Name\"))\n                                      (parent concept-1-list-boxes-panel)\n                                      (style '(extended))\n                                      (callback go-callback)))\n    (define edge-description (new message%\n                                  (parent concept-1-overall-pane)\n                                  (label \"Concept 1 -> Predicate 1 -> [X] -> Predicate 2 -> Concept 2\")))\n\n    (define concept-2-overall-pane (new vertical-pane%\n                                        (parent upper-pane)\n                                        (alignment '(left center))))\n\n    (define concept-2-search/normalize/lw-panel (new panel:horizontal-dragable%\n                                            (parent concept-2-overall-pane)\n                                            (alignment '(left center))\n                                            (stretchable-height #f)))\n    (define concept-2-list-boxes-panel (new panel:horizontal-dragable%\n                                            (parent concept-2-overall-pane)\n                                            (alignment '(left center))))\n    (define predicate-2-list-box (new list-box%\n                                      (label \"Predicate 2\")\n                                      (choices (unbox *predicate-2-choices*))\n                                      (columns '(\"Name\"))\n                                      (parent concept-2-list-boxes-panel)\n                                      (style '(extended))\n                                      (callback go-callback)))\n    (define concept-2-list-box (concept-list concept-2-overall-pane\n                                             concept-2-search/normalize/lw-panel\n                                             concept-2-list-boxes-panel\n                                             \"Concept 2\"\n                                             *concept-2-name-string*\n                                             *concept-2-node-normalization-flag*\n                                             *concept-2-lightweight-reasoning-flag*\n                                             *concept-2-choices*\n                                             (lambda () predicate-2-list-box)\n                                             *predicate-2-choices*\n                                             'in-edge\n                                             *last-concept-2-column-clicked-for-sorting*\n                                             *concept-2-column-sort-order*\n                                             *concept-2-choices*\n                                             convert-concept-1/2-to-column-sorting-format\n                                             (make-send-concepts-to-concept-1/2-list-box (lambda () concept-2-list-box))\n                                             S:C2 S:C2P))\n\n    (define running-status-description/search-in-Xs-panel\n      (new\n       horizontal-panel%\n       (parent concept-2-overall-pane)\n       (alignment '(left center))\n       (stretchable-height #f)))\n\n    (define running-status-description (new message%\n                                            (parent running-status-description/search-in-Xs-panel)\n                                            (label \"                                                                \")))\n\n    (define search-in-Xs-field (new text-field%\n                                    (label \"Find in X's\")\n                                    (parent running-status-description/search-in-Xs-panel)\n                                    (init-value \"\")\n                                    (callback (lambda (self event)\n                                                (handle-search-in-Xs self\n                                                                     concept-X-list-box\n                                                                     search-in-Xs-previous-button\n                                                                     search-in-Xs-next-button\n                                                                     )))))\n\n    (define search-in-Xs-previous-button (new button%\n                                              (parent running-status-description/search-in-Xs-panel)\n                                              (label \"Previous\")\n                                              (callback (lambda (self event)\n                                                          (handle-search-in-Xs search-in-Xs-field\n                                                                               concept-X-list-box\n                                                                               search-in-Xs-previous-button\n                                                                               search-in-Xs-next-button\n                                                                               'previous)))))\n\n    (define search-in-Xs-next-button (new button%\n                                          (parent running-status-description/search-in-Xs-panel)\n                                          (label \"Next\")\n                                          (callback (lambda (self event)\n                                                      (handle-search-in-Xs search-in-Xs-field\n                                                                           concept-X-list-box\n                                                                           search-in-Xs-previous-button\n                                                                           search-in-Xs-next-button\n                                                                           'next)))))\n\n    (define concept-X-list-box (new smart-column-width-list-box%\n                                    (label \"X\")\n                                    (choices (unbox *concept-X-choices*))\n                                    (columns '(\"KG\" \"CURIE\" \"Category\" \"Name\" \"Max PubMed #\" \"Min PubMed #\" \"Predicates\" \"Path Length\" \"Path Confidence\"))\n                                    (parent lower-pane)\n                                    (style '(column-headers clickable-headers reorderable-headers single))\n                                    (callback (lambda (self event)\n                                                (define event-type (send event get-event-type))\n                                                (S:edges 'run\n                                                         (thunk\n                                                           (cond\n                                                             [(eqv? event-type 'list-box-column)\n                                                              (handle-sort-by-column-header-click\n                                                                event\n                                                                concept-X-list-box\n                                                                *last-concept-X-column-clicked-for-sorting*\n                                                                *concept-X-column-sort-order*\n                                                                *concept-X-choices*\n                                                                convert-X-concept-to-column-sorting-format\n                                                                (make-send-concepts-to-concept-X-list-box self))]\n                                                             [(eqv? event-type 'list-box-dclick)\n                                                              (printf \"double-click!! copy name of the concept to the clipboard\\n\")\n                                                              (define time-stamp (send event get-time-stamp))\n                                                              (printf \"time stamp: ~s\\n\" time-stamp)\n                                                              (define concept-name\n                                                                (let ((sel* (send concept-X-list-box get-selections)))\n                                                                  (if (= (length sel*) 1)\n                                                                    (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n                                                                      (match selected-X\n                                                                        [`(,dbname ,curie ,name ,cat ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-count ,confidence)\n                                                                          name]\n                                                                        [else \"\"]))\n                                                                    \"\")))\n                                                              (printf \"concept name: ~s\\n\" concept-name)\n                                                              (send the-clipboard set-clipboard-string concept-name time-stamp)]\n                                                             [else\n\n                                                               ;; empty the entries in the full-path-list-box\n                                                               (send full-path-list-box set '() '() '() '() '() '() '() '())\n\n                                                               ;; empty the entries in the properties list-boxes\n                                                               (send subject-properties-list-box set '() '())\n                                                               (send edge-properties-list-box set '() '())\n                                                               (send object-properties-list-box set '() '())\n\n                                                               ;; empty the entries in the pubmed-list-box\n                                                               (send pubmed-list-box set '())\n\n                                                               (let ((sel* (send concept-X-list-box get-selections)))\n                                                                 (when (= (length sel*) 1)\n                                                                   (let ((selected-X (list-ref (unbox *concept-X-choices*) (car sel*))))\n                                                                     (let ((selected-X\n                                                                             (match selected-X\n                                                                               [`(,dbname ,curie ,name ,cat ,props ,max-pubmed-count ,min-pubmed-count ,pred-names ,path-count ,confidence)\n                                                                                 `(,dbname ,curie ,name ,cat ,props)])))\n                                                                       (printf \"selected ~s\\n\" selected-X)\n                                                                       (define concept-1* (unbox *solution-concept-1-choices*))\n                                                                       (define concept-2* (unbox *solution-concept-2-choices*))\n                                                                       (printf \"concept-1* ~s\\n\" concept-1*)\n                                                                       (printf \"concept-2* ~s\\n\" concept-2*)\n                                                                       (define predicate-1* (unbox *solution-predicate-1-choices*))\n                                                                       (define predicate-2* (unbox *solution-predicate-2-choices*))\n                                                                       (printf \"predicate-1* ~s\\n\" predicate-1*)\n                                                                       (printf \"predicate-2* ~s\\n\" predicate-2*)\n\n                                                                       (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates (unbox *predicate-1-choices*) predicate-1*))\n                                                                       (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates (unbox *predicate-2-choices*) predicate-2*))\n\n                                                                       (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n                                                                       (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n                                                                       (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n                                                                       (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n\n                                                                       (define paths '())\n\n\n                                                                       (cond\n                                                                         [(and\n                                                                            (null?\n                                                                              (split-name-string\n                                                                                (unbox *solution-concept-1-name-string*)))\n                                                                            (null?\n                                                                              (split-name-string\n                                                                                (unbox *solution-concept-2-name-string*))))\n\n                                                                          (set! paths '())]\n                                                                         [(null? (split-name-string (unbox *solution-concept-1-name-string*)))\n                                                                          (printf \"== synthetic queries 1\\n\")\n                                                                          (set! paths '())\n                                                                          ;; run synthetic queries here\n\n                                                                          (set! paths\n                                                                            (remove-duplicates\n                                                                             (append paths\n                                                                               (let ((ans\n                                                                                      (set->list\n                                                                                       (run*/set (q)\n                                                                                         (fresh (dbname eid\n                                                                                                        o-curie o-name o-cat\n                                                                                                        x-curie x-name x-cat fake-x-props\n                                                                                                        pred edge-props)\n                                                                                           (== (list `(,dbname ,eid (,x-curie ,x-name ,x-cat) (,o-curie ,o-name ,o-cat) ,pred ,edge-props)) q)\n                                                                                           (== `(,dbname ,x-curie ,x-name ,x-cat ,fake-x-props) selected-X)\n                                                                                           \n                                                                                           (membero `(,dbname ,o-curie ,o-name ,o-cat) concept-2*)\n                                                                                           (membero pred atomic-predicate-2*)\n                                                                                           (edge `(,dbname . ,eid) x-curie o-curie)\n                                                                                           (eprop `(,dbname . ,eid) \"predicate\" pred)\n                                                                                           (:== edge-props (dbname eid)\n                                                                                                (run* k/v\n                                                                                                  (fresh (k v)\n                                                                                                    (== k/v `(,k . ,v))\n                                                                                                    (eprop `(,dbname . ,eid) k v))))\n                                                                                           )))))\n                                                                                 (if (null? ans)\n                                                                                     '()\n                                                                                     (car ans))))))\n                                                                          \n                                                                          #|\n                                                                          ;; Old mediKanren 1 GUI code:\n                                                                          (set! paths\n                                                                            (remove-duplicates\n                                                                              (append paths\n                                                                                      (run* (q)\n                                                                                        (fresh (e dbname eid x o pid pred eprops)\n                                                                                          (== (list `(,dbname ,eid ,x ,o (,pid . ,pred) ,eprops)) q)\n                                                                                          (== `(,dbname . ,x) selected-X)\n                                                                                          (== `(,dbname ,eid ,x ,o (,pid . ,pred) ,eprops) e)\n                                                                                          (membero `(,dbname . ,o) concept-2*)\n                                                                                          (membero pred atomic-predicate-2*)\n                                                                                          (edgeo e))))))\n                                                                          |#\n\n                                                                          ]\n                                                                         [(null? (split-name-string (unbox *solution-concept-2-name-string*)))\n                                                                          (printf \"== synthetic queries 2\\n\")\n                                                                          (printf \"concept-1*:\\n~s\\n\" concept-1*)\n                                                                          (printf \"atomic-predicate-1*:\\n~s\\n\" atomic-predicate-1*)\n                                                                          (printf \"selected-X:\\n~s\\n\" selected-X)\n                                                                          (set! paths '())\n                                                                          ;; run synthetic queries here\n\n                                                                          (set! paths\n                                                                            (remove-duplicates\n                                                                             (append paths\n                                                                               (let ((ans\n                                                                                      (set->list\n                                                                                       (run*/set (q)\n                                                                                         (fresh (dbname eid\n                                                                                                        s-curie s-name s-cat\n                                                                                                        x-curie x-name x-cat fake-x-props\n                                                                                                        pred edge-props)\n                                                                                           (== (list `(,dbname ,eid (,s-curie ,s-name ,s-cat) (,x-curie ,x-name ,x-cat) ,pred ,edge-props)) q)\n                                                                                           (== `(,dbname ,x-curie ,x-name ,x-cat ,fake-x-props) selected-X)\n                                                                                           \n                                                                                           (membero `(,dbname ,s-curie ,s-name ,s-cat) concept-1*)\n                                                                                           (membero pred atomic-predicate-1*)\n                                                                                           (edge `(,dbname . ,eid) s-curie x-curie)\n                                                                                           (eprop `(,dbname . ,eid) \"predicate\" pred)\n                                                                                           (:== edge-props (dbname eid)\n                                                                                                (run* k/v\n                                                                                                  (fresh (k v)\n                                                                                                    (== k/v `(,k . ,v))\n                                                                                                    (eprop `(,dbname . ,eid) k v))))\n                                                                                           )))))\n                                                                                 (if (null? ans)\n                                                                                     '()\n                                                                                     (car ans))))))\n                                                                          \n                                                                          #|\n                                                                          ;; Old mediKanren 1 GUI code:\n                                                                          (set! paths\n                                                                            (remove-duplicates\n                                                                              (append paths\n                                                                                      (run* (q)\n                                                                                        (fresh (e dbname eid s x pid pred eprops)\n                                                                                          (== (list `(,dbname ,eid ,s ,x (,pid . ,pred) ,eprops)) q)\n                                                                                          (== `(,dbname . ,x) selected-X)\n                                                                                          (== `(,dbname ,eid ,s ,x (,pid . ,pred) ,eprops) e)\n                                                                                          (membero `(,dbname . ,s) concept-1*)\n                                                                                          (membero pred atomic-predicate-1*)\n                                                                                          (edgeo e))))))\n                                                                          |#\n\n                                                                          ]\n                                                                         [else\n                                                                          (printf \"== synthetic queries 3\\n\")\n                                                                           (set! paths '())\n                                                                           ;; run synthetic queries here\n\n                                                                           (printf \"selected-X:\\n~s\\n\" selected-X)\n                                                                           (printf \"concept-1*:\\n~s\\n\" concept-1*)\n                                                                           (printf \"concept-2*:\\n~s\\n\" concept-2*)\n                                                                           (printf \"atomic-predicate-1*:\\n~s\\n\" atomic-predicate-1*)\n                                                                           (printf \"atomic-predicate-2*:\\n~s\\n\" atomic-predicate-2*)\n                                                                           \n                                                                           (set! paths\n                                                                             (remove-duplicates\n                                                                              (append paths\n                                                                                (let ((ans\n                                                                                       (set->list\n                                                                                        (run*/set (q)\n                                                                                          (fresh (dbname1 dbname2\n                                                                                                  eid1 eid2\n                                                                                                  s-curie s-name s-cat\n                                                                                                  x-curie x-name x-cat fake-x-props\n                                                                                                  o-curie o-name o-cat\n                                                                                                  pred1 pred2 edge1-props edge2-props)\n                                                                                            (== (list\n                                                                                                 `(,dbname1 ,eid1 (,s-curie ,s-name ,s-cat) (,x-curie ,x-name ,x-cat) ,pred1 ,edge1-props)\n                                                                                                 `(,dbname2 ,eid2 (,x-curie ,x-name ,x-cat) (,o-curie ,o-name ,o-cat) ,pred2 ,edge2-props))\n                                                                                                q)\n                                                                                            (== `((,dbname1 ,dbname2) ,x-curie ,x-name ,x-cat ,fake-x-props) selected-X)\n                                                                                           \n                                                                                            (membero `(,dbname1 ,s-curie ,s-name ,s-cat) concept-1*)\n                                                                                            (membero `(,dbname2 ,o-curie ,o-name ,o-cat) concept-2*)\n                                                                                            (membero pred1 atomic-predicate-1*)\n                                                                                            (membero pred2 atomic-predicate-2*)\n                                                                                            (edge `(,dbname1 . ,eid1) s-curie x-curie)\n                                                                                            (edge `(,dbname2 . ,eid2) x-curie o-curie)\n                                                                                            (eprop `(,dbname1 . ,eid1) \"predicate\" pred1)\n                                                                                            (eprop `(,dbname2 . ,eid2) \"predicate\" pred2)\n                                                                                            (:== edge1-props (dbname1 eid1)\n                                                                                                 (run* k/v\n                                                                                                   (fresh (k v)\n                                                                                                     (== k/v `(,k . ,v))\n                                                                                                     (eprop `(,dbname1 . ,eid1) k v))))\n                                                                                            (:== edge2-props (dbname2 eid2)\n                                                                                                 (run* k/v\n                                                                                                   (fresh (k v)\n                                                                                                     (== k/v `(,k . ,v))\n                                                                                                     (eprop `(,dbname2 . ,eid2) k v))))\n                                                                                            )))))\n                                                                                  ;; (printf \"ans:\\n~s\\n\" ans)\n                                                                                  (if (null? ans)\n                                                                                      '()\n                                                                                      (car ans))))))\n                                                                           \n                                                                          #|\n                                                                          ;; Old mediKanren 1 GUI code:\n                                                                           (set! paths\n                                                                             (remove-duplicates\n                                                                               (append paths\n                                                                                       (run* (q)\n                                                                                         (fresh (e1 e2 dbname eid1 eid2 s x o pid1 pid2 p1 p2 eprops1 eprops2)\n                                                                                           (== `(,dbname . ,x) selected-X)\n                                                                                           (== (list\n                                                                                                 `(,dbname ,eid1 ,s ,x (,pid1 . ,p1) ,eprops1)\n                                                                                                 `(,dbname ,eid2 ,x ,o (,pid2 . ,p2) ,eprops2))\n                                                                                               q)\n                                                                                           (== `(,dbname ,eid1 ,s ,x (,pid1 . ,p1) ,eprops1) e1)\n                                                                                           (== `(,dbname ,eid2 ,x ,o (,pid2 . ,p2) ,eprops2) e2)\n                                                                                           (membero `(,dbname . ,s) concept-1*)\n                                                                                           (membero `(,dbname . ,o) concept-2*)\n                                                                                           (membero p1 atomic-predicate-1*)\n                                                                                           (membero p2 atomic-predicate-2*)\n                                                                                           (edgeo e1)\n                                                                                           (edgeo e2))))))\n                                                                           |#\n\n                                                                           ])\n\n                                                                       ;; (printf \"paths: ~s\\n\" paths)\n                                                                       (newline)\n\n                                                                       ;; This sorting affects the order of the \"Path\" list\n                                                                       ;; for the selected concept.\n                                                                       (set! paths (sort-paths paths))\n\n                                                                       (define flattened-paths\n                                                                         (let ((ls (foldr\n                                                                                     (lambda (p l)\n                                                                                       (cons\n                                                                                         'path-separator\n                                                                                         (append (reverse p) l)))\n                                                                                     '()\n                                                                                     paths)))\n                                                                           (if (null? ls)\n                                                                             ;; ls should never be null!\n                                                                             '()\n                                                                             (reverse (cdr ls)))))\n\n\n\n                                                                       (define full-path-dbname-list\n                                                                         (map (lambda (x)\n                                                                                ;(printf \"x:\\n~s\\n\" x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj ,pred ,eprops)\n                                                                                    (~a dbname)]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-eid-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj ,pred ,eprops)\n                                                                                    (~a eid)]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-subj-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid (,curie ,name ,cat) ,obj ,pred ,eprops)\n                                                                                    (~a (format \"~a (~a)\" name curie) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-pred-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj ,pred ,eprops)\n                                                                                    (~a pred #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-obj-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj (,curie ,name ,cat) ,pred ,eprops)\n                                                                                    (~a (format \"~a (~a)\" name curie) #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-subj-cat-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid (,curie ,name ,cat) ,obj ,pred ,eprops)\n                                                                                    (~a cat #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-obj-cat-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj (,curie ,name ,cat) ,pred ,eprops)\n                                                                                    (~a cat #:max-width MAX-CHAR-WIDTH #:limit-marker \"...\")]))\n                                                                              flattened-paths))\n\n                                                                       (define full-path-PubMed-count-list\n                                                                         (map (lambda (x)\n                                                                                (match x\n                                                                                  ['path-separator \"----\"]\n                                                                                  [`(,dbname ,eid ,subj ,obj ,pred ,eprops)\n                                                                                    (~a (length (pubmed-URLs-from-edge x)))]))\n                                                                              flattened-paths))\n\n                                                                       (send full-path-list-box\n                                                                             set\n                                                                             full-path-dbname-list\n                                                                             full-path-eid-list\n                                                                             full-path-subj-list\n                                                                             full-path-pred-list\n                                                                             full-path-obj-list\n                                                                             full-path-subj-cat-list\n                                                                             full-path-obj-cat-list\n                                                                             full-path-PubMed-count-list\n                                                                             )\n\n                                                                       (set-box! *full-path-choices* flattened-paths)\n\n                                                                       ;; unselect all items\n                                                                       (for ([i (length flattened-paths)])\n                                                                            (send full-path-list-box select i #f))\n\n                                                                       ;; select first item\n                                                                       (send full-path-list-box select 0 #t)\n                                                                       (populate-selected-paths))))\n                                                                 (void))])))))))\n\n    (define (populate-selected-paths)\n      (when *verbose*\n        (printf \"(unbox *full-path-choices*):\\n~s\\n\" (unbox *full-path-choices*)))\n      (define selections (send full-path-list-box get-selections))\n      (when *verbose*\n        (printf \"selection for full path:\\n~s\\n\" selections))\n      (define selected-full-paths\n        (foldr (lambda (i l) (cons (list-ref (unbox *full-path-choices*) i) l))\n               '()\n               selections))\n      (for-each\n        (lambda (x)\n          (match x\n            ['path-separator\n             (send subject-properties-list-box set '() '())\n             (send edge-properties-list-box set '() '())\n             (send object-properties-list-box set '() '())]\n            [`(,dbname ,eid\n                       (,scurie ,sname ,scat)\n                       (,ocurie ,oname ,ocat)\n                       ,pred\n                       ,eprops)\n              (define (set-properties-list-box prop-list-box props)\n                (send prop-list-box\n                      set\n                      (map\n                        (lambda (p)\n                          (~a (car p)\n                              #:max-width\n                              MAX-CHAR-WIDTH\n                              #:limit-marker\n                              \"...\"))\n                        props)\n                      (map\n                        (lambda (p)\n                          (~a (cdr p)\n                              #:max-width\n                              MAX-CHAR-WIDTH\n                              #:limit-marker\n                              \"...\"))\n                        props)))\n              (define sprops (apply append (set->list (run*/set (q) (fresh (k v) (== `(,k . ,v) q) (cprop scurie k v))))))\n              (define oprops (apply append (set->list (run*/set (q) (fresh (k v) (== `(,k . ,v) q) (cprop ocurie k v))))))\n              (printf \"eprops:\\n~s\\n\" eprops)\n              (printf \"sprops:\\n~s\\n\" sprops)\n              (printf \"oprops:\\n~s\\n\" oprops)\n              (set-properties-list-box subject-properties-list-box sprops)\n              (set-properties-list-box edge-properties-list-box eprops)\n              (set-properties-list-box object-properties-list-box oprops)]))\n        selected-full-paths)\n      (for-each\n        (lambda (edge)\n          (let ((URLs (pubmed-URLs-from-edge edge)))\n            (set-box! *pubmed-choices* URLs)\n            (send pubmed-list-box set URLs)))\n        selected-full-paths)\n      (for-each\n        (lambda (edge)\n          (let ((publications-info-alist\n                  (publications-info-alist-from-edge edge)))\n            (set-box! *publications-info-alist* publications-info-alist)))\n        selected-full-paths)\n      (when *verbose*\n        (printf \"selected full path:\\n\")\n        (for-each\n          (lambda (x)\n            (match x\n              ['path-separator\n               (printf \"-----------------------\\n\")]\n              [`(,dbname ,eid ,subj ,obj ,p ,eprops)\n                (pretty-print `(,dbname ,eid ,subj ,obj ,p ,eprops))]))\n          selected-full-paths)))\n\n    (define full-path-list-box (new smart-column-width-list-box%\n                                    (label \"Paths\")\n                                    (choices (unbox *full-path-choices*))\n                                    (columns '(\"KG\" \"EID\" \"Subject\" \"Predicate\" \"Object\" \"Subj Cat\" \"Obj Cat\" \"PubMed #\"))\n                                    (parent lower-pane)\n                                    (style '(column-headers reorderable-headers extended))\n                                    (callback (lambda (self event) (populate-selected-paths)))))\n\n    (define properties/pubmed-panel (new panel:horizontal-dragable%\n                                         (parent lower-pane)\n                                         (alignment '(left center))\n                                         (stretchable-height #t)))\n\n    (define subject-properties-list-box (new smart-column-width-list-box%\n                                             (label \"Subject\")\n                                             (choices '())\n                                             (columns '(\"Property\" \"Value\"))\n                                             (parent properties/pubmed-panel)\n                                             (style '(column-headers reorderable-headers extended))\n                                             (callback (lambda (self event)\n                                                         (void)))))\n\n    (define edge-properties-list-box (new smart-column-width-list-box%\n                                     (label \"Edge\")\n                                     (choices '())\n                                     (columns '(\"Property\" \"Value\"))\n                                     (parent properties/pubmed-panel)\n                                     (style '(column-headers reorderable-headers extended))\n                                     (callback (lambda (self event)\n                                                 (void)))))\n\n    (define object-properties-list-box (new smart-column-width-list-box%\n                                            (label \"Object\")\n                                            (choices '())\n                                            (columns '(\"Property\" \"Value\"))\n                                            (parent properties/pubmed-panel)\n                                            (style '(column-headers reorderable-headers extended))\n                                            (callback (lambda (self event)\n                                                        (void)))))\n\n    (define pubmed-list-box (new list-box%\n                                 (label \"Pubmed\")\n                                 (choices (unbox *pubmed-choices*))\n                                 (columns '(\"URL\"))\n                                 (parent properties/pubmed-panel)\n                                 (style '(column-headers reorderable-headers single))\n                                 (callback (lambda (self event)\n                                             (define event-type (send event get-event-type))\n                                             (define selections (send self get-selections))\n                                             (define selected-pubmeds\n                                               (foldr (lambda (i l) (cons (list-ref (unbox *pubmed-choices*) i) l))\n                                                      '()\n                                                      selections))\n                                             (for-each\n                                               (lambda (url)\n                                                 (printf \"url: ~s\\n\" url)\n\n                                                 (match (assoc url (unbox *publications-info-alist*))\n                                                   [`(,pubmed-URL . (,publication-date ,subject-score ,object-score ,sentence))\n                                                    (*populate-publication-fields* publication-date subject-score object-score sentence)]\n                                                   [#f (*populate-publication-fields* \"\" \"\" \"\" \"\")])\n\n                                                 (when (eqv? event-type 'list-box-dclick)\n                                                   ;; if the user double-clicked on the URL, open it in a web browser\n                                                   (send-url url)))\n                                               selected-pubmeds)))))\n\n    (define publication-info-panel (new panel:vertical-dragable%\n                                        (parent lower-pane)\n                                        (alignment '(left center))\n                                        (stretchable-height #t)))\n\n    (define publication-info-date/subject/object-panel (new horizontal-panel%\n                                                            (parent publication-info-panel)\n                                                            (alignment '(left center))\n                                                            (stretchable-height #f)))\n\n    (define publication-date (new text-field%\n                                  (label \"Publication Date\")\n                                  (parent publication-info-date/subject/object-panel)\n                                  (enabled #f)\n                                  (init-value \"\")))\n\n    (define subject-score (new text-field%\n                               (label \"Subject Score\")\n                               (parent publication-info-date/subject/object-panel)\n                               (enabled #f)\n                               (init-value \"\")))\n\n    (define object-score (new text-field%\n                              (label \"Object Score\")\n                              (parent publication-info-date/subject/object-panel)\n                              (enabled #f)\n                              (init-value \"\")))\n\n    (define publication-sentence-editor-canvas (new editor-canvas%\n                                                    (parent publication-info-panel)\n                                                    (enabled #f)\n                                                    (label \"Sentence\")))\n    (define publication-sentence-text (new text%))\n    (send publication-sentence-text insert \"\")\n    (send publication-sentence-editor-canvas set-editor publication-sentence-text)\n\n    (set! *populate-publication-fields*\n          (lambda (date subj-score obj-score sentence)\n            (send publication-date set-value date)\n            (send subject-score set-value (format \"~a\" subj-score))\n            (send object-score set-value (format \"~a\" obj-score))\n            (send publication-sentence-text erase)\n            (send publication-sentence-text insert sentence)))\n\n\n    ;; trigger reflowing of object sizes\n    (send frame reflow-container)\n\n    ;; disable previous and next buttons by default\n    (send search-in-Xs-previous-button enable #f)\n    (send search-in-Xs-next-button enable #f)\n\n    (set-default-column-widths concept-1-list-box)\n    (set-default-column-widths concept-2-list-box)\n    (set-default-column-widths concept-X-list-box)\n    (set-default-column-widths full-path-list-box)\n    (set-default-column-widths edge-properties-list-box)\n    (set-default-column-widths edge-properties-list-box)\n    (set-default-column-widths object-properties-list-box)\n\n    (send frame show #t)))\n\n(define (split-atomic/synthetic-predicates choices predicate*)\n  (define (synthetic? pred)\n    (memf (lambda (syn-prefix) (string-prefix? pred syn-prefix))\n          SYNTHETIC_PREDICATE_PREFIXES))\n\n  (define atomic-predicate* (filter-not synthetic? predicate*))\n  (define synthetic-predicate* (filter synthetic? predicate*))\n\n  (when (memf (lambda (pred) (string-prefix? pred DECREASES_PREDICATE_PREFIX_STRING))\n              synthetic-predicate*)\n    (set! atomic-predicate* (append DECREASES_PREDICATE_NAMES atomic-predicate*)))\n\n  (when (memf (lambda (pred) (string-prefix? pred INCREASES_PREDICATE_PREFIX_STRING))\n              synthetic-predicate*)\n    (set! atomic-predicate* (append INCREASES_PREDICATE_NAMES atomic-predicate*)))\n\n  (set! atomic-predicate* (set-intersect choices (remove-duplicates atomic-predicate*)))\n\n  (printf \"atomic-predicate*: ~s\\n\" atomic-predicate*)\n  (printf \"synthetic-predicate*: ~s\\n\" synthetic-predicate*)\n\n  (list atomic-predicate* synthetic-predicate*))\n\n\n(define (find-X-concepts concept-1* concept-2* predicate-1* predicate-2* predicate-1-choices predicate-2-choices concept-X-list-box running-status-description full-path-list-box subject-properties-list-box edge-properties-list-box object-properties-list-box pubmed-list-box search-in-Xs-field search-in-Xs-previous-button search-in-Xs-next-button)\n\n  (define start-time (current-milliseconds))\n  (printf \"\\nfinding concepts X for which\\n[C1] -> P1 -> [X] -> P2 -> [C2]\\n\")\n  (printf \"=============================\\n\")\n\n  (define atomic/synthetic-predicate-1* (split-atomic/synthetic-predicates predicate-1-choices predicate-1*))\n  (define atomic/synthetic-predicate-2* (split-atomic/synthetic-predicates predicate-2-choices predicate-2*))\n\n  (define atomic-predicate-1* (car atomic/synthetic-predicate-1*))\n  (define atomic-predicate-2* (car atomic/synthetic-predicate-2*))\n\n  (define synthetic-predicate-1* (cadr atomic/synthetic-predicate-1*))\n  (define synthetic-predicate-2* (cadr atomic/synthetic-predicate-2*))\n\n  (define all-X-concepts-with-edges '())\n\n  (printf \"atomic/synthetic-predicate-1*: ~s\\n\" atomic/synthetic-predicate-1*)\n  (printf \"atomic/synthetic-predicate-2*: ~s\\n\" atomic/synthetic-predicate-2*)\n  (newline)\n  (printf \"atomic-predicate-1*: ~s\\n\" atomic-predicate-1*)\n  (printf \"atomic-predicate-2*: ~s\\n\" atomic-predicate-2*)\n  (newline)\n  (printf \"synthetic-predicate-1*: ~s\\n\" synthetic-predicate-1*)\n  (printf \"synthetic-predicate-2*: ~s\\n\" synthetic-predicate-2*)\n  (newline)\n\n  (printf \"@@ entering cond\\n\")\n  \n  (cond\n    [(and\n      (null?\n       (split-name-string\n        (unbox *concept-1-name-string*)))\n      (null?\n       (split-name-string\n        (unbox *concept-2-name-string*))))\n\n     (set! all-X-concepts-with-edges '())]\n    [(null? (split-name-string (unbox *concept-1-name-string*)))\n     \n     (set! all-X-concepts-with-edges '())\n\n     ;; run synthetic queries here\n\n     (set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append* all-X-concepts-with-edges\n                     (let ((ans\n                            (apply append\n                                   (map (lambda (pred)\n                                          (apply append\n                                                 (map (lambda (concept)\n                                                        (match concept\n                                                          [`(,dbname ,o-curie ,o-name ,o-cat)\n                                                           (let ((tmp\n                                                                  (set->list\n                                                                   (run*/set (q)\n                                                                     (fresh (eid s o fake-pid edge-props e\n                                                                                 o-props\n                                                                                 s-curie s-name s-cat s-props)                        \n                                                                       (== (list dbname s (list edge-props) (list e)) q)\n                                                                       (== `(,dbname ,eid ,s ,o (,fake-pid . ,pred) ,edge-props) e)\n                                                                       (== fake-pid \"\")\n                                                                       (== `(,s-curie ,s-name ,s-cat ,s-props) s)\n                                                                       (== `(,o-curie ,o-name ,o-cat ,o-props) o)\n                                                                       ;; We get the concept properties later, when the user clicks on a path.\n                                                                       (== s-props '())\n                                                                       (== o-props '())\n                                                                       ;;\n                                                                       (edge `(,dbname . ,eid) s-curie o-curie)\n                                                                       (eprop `(,dbname . ,eid) \"predicate\" pred)\n                                                                       (cprop s-curie \"name\" s-name)\n                                                                       (cprop s-curie \"category\" s-cat)\n                                                                       ;; Only get the minimal edge properties needed to populate the X list box\n                                                                       (:== edge-props (dbname eid)\n                                                                           (run 1 k/v\n                                                                             (fresh (v)\n                                                                               (== `(\"publications\" . ,v) k/v)\n                                                                               (eprop `(,dbname . ,eid) \"publications\" v)))))))))\n                                                             tmp)]))\n                                                      concept-2*)))\n                                        atomic-predicate-2*))))\n                       ;(printf \"ans:\\n~s\\n\" ans)\n                       ans))))\n     \n     ;; Old mediKanren 1 GUI code:\n     #;(set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append all-X-concepts-with-edges\n                    (run* (q)\n                      (fresh (dbname eid s o pid pred eprops e)\n                        (== (list dbname s (list eprops) (list e)) q)\n                        (== `(,dbname ,eid ,s ,o (,pid . ,pred) ,eprops) e)\n                        (membero `(,dbname . ,o) concept-2*)\n                        (membero pred atomic-predicate-2*)\n                        (edgeo e))))))\n\n     ]\n    [(null? (split-name-string (unbox *concept-2-name-string*)))\n     (set! all-X-concepts-with-edges '())\n     \n     ;; run synthetic queries here\n     \n     (set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append* all-X-concepts-with-edges\n                    (let ((ans\n                           (apply append\n                                  (map (lambda (pred)\n                                         (apply append\n                                                (map (lambda (concept)\n                                                       (match concept\n                                                         [`(,dbname ,s-curie ,s-name ,s-cat)\n                                                          (let ((tmp\n                                                                 (set->list\n                                                                  (run*/set (q)\n                                                                    (fresh (eid s o fake-pid edge-props e\n                                                                                s-props\n                                                                                o-curie o-name o-cat o-props)                        \n                                                                      (== (list dbname o (list edge-props) (list e)) q)\n                                                                      (== `(,dbname ,eid ,s ,o (,fake-pid . ,pred) ,edge-props) e)\n                                                                      (== fake-pid \"\")\n                                                                      (== `(,s-curie ,s-name ,s-cat ,s-props) s)\n                                                                      (== `(,o-curie ,o-name ,o-cat ,o-props) o)\n                                                                      ;; We get the concept properties later, when the user clicks on a path.\n                                                                      (== s-props '())\n                                                                      (== o-props '())\n                                                                      ;;\n                                                                      (edge `(,dbname . ,eid) s-curie o-curie)\n                                                                      (eprop `(,dbname . ,eid) \"predicate\" pred)\n                                                                      (cprop o-curie \"name\" o-name)\n                                                                      (cprop o-curie \"category\" o-cat)\n                                                                      ;; Only get the minimal edge properties needed to populate the X list box\n                                                                      (:== edge-props (dbname eid)\n                                                                           (run 1 k/v\n                                                                             (fresh (v)\n                                                                               (== `(\"publications\" . ,v) k/v)\n                                                                               (eprop `(,dbname . ,eid) \"publications\" v)))))))))\n                                                            tmp)]))\n                                                     concept-1*)))\n                                       atomic-predicate-1*))))\n                      ;(printf \"ans:\\n~s\\n\" ans)\n                      ans))))\n     \n     ;; Old mediKanren 1 GUI code:\n     #;(set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append all-X-concepts-with-edges\n                    (run* (q)\n                      (fresh (dbname eid s o pid pred eprops e)\n                        (== (list dbname o (list eprops) (list e)) q)\n                        (== `(,dbname ,eid ,s ,o (,pid . ,pred) ,eprops) e)\n                        (membero `(,dbname . ,s) concept-1*)\n                        (membero pred atomic-predicate-1*)\n                        (edgeo e))))))\n\n     ]\n    [else\n     (set! all-X-concepts-with-edges '())\n\n     ;; run synthetic queries here\n\n     (set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append* all-X-concepts-with-edges\n                     (let ((ans\n                            (apply append\n                                   (map (lambda (pred1)\n                                          (apply append\n                                                 (map (lambda (pred2)\n                                                        (apply append\n                                                               (map (lambda (concept1)\n                                                                      (match concept1\n                                                                        [`(,dbname1 ,s-curie1 ,s-name1 ,s-cat1)\n                                                                         (apply append\n                                                                                (map (lambda (concept2)\n                                                                                       (match concept2\n                                                                                         [`(,dbname2 ,o-curie2 ,o-name2 ,o-cat2)\n\n                                                                                          #|\n                                                                                          (printf \"<<<<<\\n\")\n                                                                                          (printf \"concept1 ~s\\n\" concept1)\n                                                                                          (printf \"concept2 ~s\\n\" concept2)\n                                                                                          (printf \"pred1 ~s\\n\" pred1)\n                                                                                          (printf \"pred2 ~s\\n\" pred2)\n                                                                                          (printf \"s-curie1 ~s\\n\" s-curie1)\n                                                                                          (printf \"o-curie2 ~s\\n\" o-curie2)\n                                                                                          |#\n                                                                   \n                                                                                          (let ((tmp\n                                                                                                 (set->list\n                                                                                                  (run*/set (q)\n                                                                                                    (fresh (eid1 s1 fake-pid1 edge-props1 e1\n                                                                                                                 eid2 o2 fake-pid2 edge-props2 e2\n                                                                                                                 m\n                                                                                                                 m-curie m-name m-cat m-props\n                                                                                                                 s-props1\n                                                                                                                 o-props2)\n                                                                                                      (== (list (list dbname1 dbname2) m (list edge-props1 edge-props2) (list e1 e2)) q)\n                                                                                                      (== `(,dbname1 ,eid1 ,s1 ,m (,fake-pid1 . ,pred1) ,edge-props1) e1)\n                                                                                                      (== `(,dbname2 ,eid2 ,m ,o2 (,fake-pid2 . ,pred2) ,edge-props2) e2)\n                                                                                                      (== fake-pid1 \"\")\n                                                                                                      (== fake-pid2 \"\")\n                                                                                                      (== `(,m-curie ,m-name ,m-cat ,m-props) m)\n                                                                                                      (== `(,s-curie1 ,s-name1 ,s-cat1 ,s-props1) s1)\n                                                                                                      (== `(,o-curie2 ,o-name2 ,o-cat2 ,o-props2) o2)\n                                                                                                      ;; We get these concept properties later,\n                                                                                                      ;; when the user clicks on a path.\n                                                                                                      (== m-props '())\n                                                                                                      (== s-props1 '())\n                                                                                                      (== o-props2 '())\n                                                                                                      ;;\n                                                                                                      (edge `(,dbname1 . ,eid1) s-curie1 m-curie)\n                                                                                                      (edge `(,dbname2 . ,eid2) m-curie o-curie2)\n                                                                               \n                                                                                                      (eprop `(,dbname1 . ,eid1) \"predicate\" pred1)\n                                                                                                      (eprop `(,dbname2 . ,eid2) \"predicate\" pred2)\n                                                                               \n                                                                                                      (cprop m-curie \"name\" m-name)\n                                                                                                      (cprop m-curie \"category\" m-cat)\n                                                                                                      ;; Only get the minimal edge properties needed to\n                                                                                                      ;; populate the X list box.\n                                                                                                      (:== edge-props1 (dbname1 eid1)\n                                                                                                           (run 1 k/v\n                                                                                                             (fresh (v)\n                                                                                                               (== `(\"publications\" . ,v) k/v)\n                                                                                                               (eprop `(,dbname1 . ,eid1) \"publications\" v))))\n                                                                                                      (:== edge-props2 (dbname2 eid2)\n                                                                                                           (run 1 k/v\n                                                                                                             (fresh (v)\n                                                                                                               (== `(\"publications\" . ,v) k/v)\n                                                                                                               (eprop `(,dbname2 . ,eid2) \"publications\" v)))))))))\n                                                                                            tmp)]))\n                                                                                     concept-2*))]))\n                                                                    concept-1*)))\n                                                      atomic-predicate-2*)))\n                                        atomic-predicate-1*))))\n                       ;(printf \"ans:\\n~s\\n\" ans)\n                       ans))))\n     \n     ;; Old mediKanren 1 GUI code:\n     #;(set! all-X-concepts-with-edges\n           (remove-duplicates\n            (append all-X-concepts-with-edges\n                    (run* (q)\n                      (fresh (dbname eid1 eid2 s m o pid1 pid2 p1 p2 eprops1 eprops2 e1 e2)\n                        (== (list dbname m (list eprops1 eprops2) (list e1 e2)) q)\n                        (== `(,dbname ,eid1 ,s ,m (,pid1 . ,p1) ,eprops1) e1)\n                        (== `(,dbname ,eid2 ,m ,o (,pid2 . ,p2) ,eprops2) e2)\n                        (membero `(,dbname . ,s) concept-1*)\n                        (membero `(,dbname . ,o) concept-2*)\n                        (membero p1 atomic-predicate-1*)\n                        (membero p2 atomic-predicate-2*)\n                        (edgeo e1)\n                        (edgeo e2))))))\n\n     ])\n\n  (printf \"@@ exiting cond\\n\")\n\n  (define end-time (current-milliseconds))\n\n  (define elapsed-time (- end-time start-time))\n\n  (printf \"elapsed query time: ~s seconds\\n\" (/ elapsed-time 1000.0))\n  (printf \"=============================\\n\")\n\n\n  ;(printf \"all-X-concepts-with-edges:\\n\\n~s\\n\\n\" all-X-concepts-with-edges)\n  \n  ;; This sorting affects order of appearance in the \"X\" concept list\n  (set! all-X-concepts-with-edges\n    (sort\n      all-X-concepts-with-edges\n      (lambda (c1 c2)\n        (match (list c1 c2)\n          [`((,_ ,_ ,_ ,e1*) (,_ ,_ ,_ ,e2*))\n           (not (path-confidencestring (seconds->date (current-seconds)) #t))\n  (newline)\n\n\n  (define number-Xs-found (length all-X-concepts))\n  (define query-seconds (/ elapsed-time 1000.0))\n  (define query-time-format-string \"Found ~s X's after ~s seconds\")\n  (send running-status-description set-label (format query-time-format-string number-Xs-found query-seconds))\n  (printf query-time-format-string number-Xs-found query-seconds)\n  (newline)\n  (newline)\n\n\n  (set-box! *concept-X-choices* all-X-concepts)\n\n  (set-box! *solution-concept-1-name-string* (unbox *concept-1-name-string*))\n  (set-box! *solution-concept-2-name-string* (unbox *concept-2-name-string*))\n\n  (set-box! *solution-concept-1-node-normalization-flag* (unbox *concept-1-node-normalization-flag*))\n  (set-box! *solution-concept-2-node-normalization-flag* (unbox *concept-2-node-normalization-flag*))\n\n  (set-box! *solution-concept-1-lightweight-reasoning-flag* (unbox *concept-1-lightweight-reasoning-flag*))\n  (set-box! *solution-concept-2-lightweight-reasoning-flag* (unbox *concept-2-lightweight-reasoning-flag*))\n  \n  (set-box! *solution-concept-1-choices* concept-1*)\n  (set-box! *solution-concept-2-choices* concept-2*)\n  (set-box! *solution-predicate-1-choices* predicate-1*)\n  (set-box! *solution-predicate-2-choices* predicate-2*)\n\n  (printf \"*solution-concept-1-name-string*:\\n~s\\n\" (unbox *solution-concept-1-name-string*))\n  (printf \"*solution-concept-1-node-normalization-flag*:\\n~s\\n\" (unbox *solution-concept-1-node-normalization-flag*))\n  (printf \"*solution-concept-1-lightweight-reasoning-flag*:\\n~s\\n\" (unbox *solution-concept-1-lightweight-reasoning-flag*))\n  ;(printf \"*solution-concept-1-choices*:\\n\")\n  ;(pretty-print (unbox *solution-concept-1-choices*))\n  ;(printf \"*solution-predicate-1-choices*:\\n\")\n  ;(pretty-print (unbox *solution-predicate-1-choices*))\n  (newline)\n\n  (printf \"*solution-concept-2-name-string*:\\n~s\\n\" (unbox *solution-concept-2-name-string*))\n  (printf \"*solution-concept-2-node-normalization-flag*:\\n~s\\n\" (unbox *solution-concept-2-node-normalization-flag*))\n  (printf \"*solution-concept-2-lightweight-reasoning-flag*:\\n~s\\n\" (unbox *solution-concept-2-lightweight-reasoning-flag*))\n  ;(printf \"*solution-concept-2-choices*:\\n\")\n  ;(pretty-print (unbox *solution-concept-2-choices*))\n  ;(printf \"*solution-predicate-2-choices*:\\n\")\n  ;(pretty-print (unbox *solution-predicate-2-choices*))\n  (newline)\n\n  (define pretty-print-X-concepts-with-edges\n    (lambda (file-name pretty-printer print-basic-header print-low-level-query-information X-concepts-with-edges)\n      (with-output-to-file\n          file-name\n          (lambda ()\n            (when print-basic-header\n              (printf \";; mediKanren query output\\n\")\n              (printf \";; ~a\\n\" MEDIKANREN_VERSION_STRING)\n              (printf \";; \\n\")\n              (let ((local-date (seconds->date (current-seconds))))\n                (printf \";; Query run at date/time: ~s ~s ~s  ~s:~s:~s   (Year Month Day  Hour:Minute:Second)\\n\"\n                        (date-year local-date)\n                        (date-month local-date)\n                        (date-day local-date)\n                        (date-hour local-date)\n                        (date-minute local-date)\n                        (date-second local-date)))\n              (printf \";; \\n\"))\n            (when print-low-level-query-information\n              (printf \";; ===================================================\\n\")\n              (printf \";; Low-level query information from the mediKanren GUI\\n\")\n              (printf \";; ===================================================\\n\")\n              (printf \";; \\n\")\n              (printf \";; *concept-1-name-string*: ~s\\n\" (unbox *concept-1-name-string*))\n              (printf \";; *solution-concept-1-name-string*: ~s\\n\" (unbox *solution-concept-1-name-string*))\n              (printf \";; *solution-concept-1-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-concept-1-choices*))\n              (printf \"|#\\n\")\n              (printf \";; atomic/synthetic-predicate-1*: ~s\\n\" atomic/synthetic-predicate-1*)\n              (printf \";; atomic-predicate-1*: ~s\\n\" atomic-predicate-1*)\n              (printf \";; synthetic-predicate-1*: ~s\\n\" synthetic-predicate-1*)\n              (printf \";; *solution-predicate-1-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-predicate-1-choices*))\n              (printf \"|#\\n\")\n              (printf \";; \\n\")\n              (printf \";; \\n\")\n              (printf \";; \\n\")\n              (printf \";; atomic/synthetic-predicate-2*: ~s\\n\" atomic/synthetic-predicate-2*)\n              (printf \";; atomic-predicate-2*: ~s\\n\" atomic-predicate-2*)\n              (printf \";; synthetic-predicate-2*: ~s\\n\" synthetic-predicate-2*)\n              (printf \";; *solution-predicate-2-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-predicate-2-choices*))\n              (printf \"|#\\n\")\n              (printf \";; *concept-2-name-string*: ~s\\n\" (unbox *concept-2-name-string*))\n              (printf \";; *solution-concept-2-name-string*: ~s\\n\" (unbox *solution-concept-2-name-string*))\n              (printf \";; *solution-concept-2-choices*:\\n\")\n              (printf \"#|\\n\")\n              (pretty-print (unbox *solution-concept-2-choices*))\n              (printf \"|#\\n\")\n              (printf \"\\n\"))\n            (when print-basic-header\n              (printf \";; ======================================\\n\")\n              (printf \";; Query results (list of complete edges)\\n\")\n              (printf \";; ======================================\\n\"))\n            (pretty-printer X-concepts-with-edges))\n          #:mode 'text\n          #:exists QUERY_RESULTS_FILE_MODE)))\n\n  (define human-friendly-pretty-print-X-concepts-with-edges\n    (lambda (X-concepts-with-edges)\n      (for-each\n        (lambda (entry index)\n          (match entry\n            [`(,dbname\n                ,s\n                ,eprops*\n                ,edges)\n              (printf \"*** Edge group:\")\n              (for-each\n                (lambda (edge)\n                  (match edge\n                    [`(,dbname\n                       ,eid\n                       (,scurie ,sname ,scat . ,sprops)\n                       (,ocurie ,oname ,ocat . ,oprops)\n                       (,pid . ,pred) ,eprops)\n                     (let ((pubmed* (pubmed-URLs-from-edge edge)))\n                       (printf \"\\n~s\\t~s\\t~s\\t~s\\t~s\\t~s\\t~s\\t~s PubMed Entries\\n~s\\n\" index dbname sname scat pred oname ocat (length pubmed*) pubmed*))]))\n                edges)\n              (printf \"***\\n\\n\") ]))\n        X-concepts-with-edges\n        (iota (length X-concepts-with-edges) 1))))\n\n  (define spreadsheet-friendly-pretty-print-X-concepts-with-edges\n    (lambda (X-concepts-with-edges)\n      (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n              \"Subject Category\"\n              \"Subject Name\"\n\n              \"Predicate\"\n\n              \"Object Category\"\n              \"Object Name\"\n\n              \"PubMed URL\"\n\n              \"KG Name\")\n      (for-each\n        (lambda (entry index)\n          (match entry\n            [`(,dbname\n                ,s\n                ,eprops*\n                ,edges)\n              (for-each\n                (lambda (edge)\n                  (match edge\n                    [`(,dbname\n                       ,eid\n                       (,scurie ,sname ,scat . ,sprops)\n                       (,ocurie ,oname ,ocat . ,oprops)\n                       (,pid . ,pred) ,eprops)\n                     (let ((pubmed* (pubmed-URLs-from-edge edge)))\n                       (for-each\n                         (lambda (pubmed)\n                           (printf \"~a\\t~a\\t~a\\t~a\\t~a\\t~a\\t~a\\n\"\n                                   scat\n                                   sname\n\n                                   pred\n\n                                   ocat\n                                   oname\n\n                                   pubmed\n\n                                   dbname))\n                         pubmed*))]))\n                edges)]))\n        X-concepts-with-edges\n        (iota (length X-concepts-with-edges) 1))))\n\n  (when WRITE_QUERY_RESULTS_TO_FILE\n\n    (printf \"saving all-X-concepts-with-edges to '~a' file...\\n\"\n            QUERY_RESULTS_FILE_NAME)\n    (pretty-print-X-concepts-with-edges\n      QUERY_RESULTS_FILE_NAME\n      pretty-print\n      #t ;; print-basic-header flag\n      #t ;; print-low-level-query-information flag\n      all-X-concepts-with-edges)\n    (printf \"saved all-X-concepts-with-edges to '~a' file\\n\"\n            QUERY_RESULTS_FILE_NAME)\n\n    (printf \"saving human-friendly version of all-X-concepts-with-edges to '~a' file...\\n\"\n            HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n    (pretty-print-X-concepts-with-edges\n      HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME\n      human-friendly-pretty-print-X-concepts-with-edges\n      #t ;; print-basic-header flag\n      #f ;; print-low-level-query-information flag\n      all-X-concepts-with-edges)\n    (printf \"saved human-friendly version of all-X-concepts-with-edges to '~a' file\\n\"\n            HUMAN_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n\n    (printf \"saving spreadsheet-friendly version of all-X-concepts-with-edges to '~a' file...\\n\"\n            SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n    (pretty-print-X-concepts-with-edges\n      SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME\n      spreadsheet-friendly-pretty-print-X-concepts-with-edges\n      #f ;; print-basic-header flag\n      #f ;; print-low-level-query-information flag\n      all-X-concepts-with-edges)\n    (printf \"saved spreadsheet-friendly version of all-X-concepts-with-edges to '~a' file\\n\"\n            SPREADSHEET_FRIENDLY_QUERY_RESULTS_FILE_NAME)\n\n    )\n\n  (printf \"========== end query results =============\\n\")\n\n  ((make-send-concepts-to-concept-X-list-box concept-X-list-box) all-X-concepts)\n\n  ;; unselect all items\n  (for ([i (length all-X-concepts)])\n       (send concept-X-list-box select i #f))\n\n  ;; add X concept data for each list-box entry\n  (let loop ((i 0)\n             (c* all-X-concepts))\n    (cond\n      [(null? c*) (void)]\n      [else\n       (send concept-X-list-box set-data i (car c*))\n       (loop (add1 i)\n             (cdr c*))]))\n\n  ;; empty the search in X's field, and disable the previous/next buttons\n  (send search-in-Xs-field set-value \"\")\n  (send search-in-Xs-previous-button enable #f)\n  (send search-in-Xs-next-button enable #f)\n\n  ;; empty the entries in the full-path-list-box\n  (send full-path-list-box set '() '() '() '() '() '() '() '())\n\n  ;; empty the entries in the properties list-boxes\n  (send subject-properties-list-box set '() '())\n  (send edge-properties-list-box set '() '())\n  (send object-properties-list-box set '() '())\n\n  ;; empty the entries in the pubmed-list-box\n  (send pubmed-list-box set '())\n\n  )\n\n\n(displayln\n  \"Launching GUI\")\n\n(launch-gui)\n"
  },
  {
    "path": "medikanren2/ingest-pipeline-status.rkt",
    "content": "#lang racket\n(provide\n    /ingest-pipeline-status)\n(require\n  web-server/servlet\n  web-server/servlet-env\n  racket/dict\n  (prefix-in aws: aws)\n  ;(except-in aws module) ;module: identifier already required ;except-in: identifier `module' not included in nested require spec\n  aws/keys\n  aws/s3\n  json\n  net/url\n  (only-in http gmt-8601-string->seconds)\n)\n\n(define ec2-role-assumed? #f)\n\n(define (ensure-aws-credentials iam-role)\n  ;; Workaround copy paste: https://github.com/greghendershott/aws/blob/master/aws/keys.rkt\n  ;; If we just call the provided credentials-from-ec2-instance! we seem to get corrupted\n  ;; state when ec2-instance-creds-expiration gets preserved but the other parameters\n  ;; get erased for serving subsequent requests.\n\n  ;; This code avoids caching altogether.\n  (define url\n    (string->url\n    (~a \"http://169.254.169.254/latest/meta-data/iam/security-credentials/\"\n        iam-role)))\n  (match (call/input-url url get-pure-port read-json)\n    [(hash-table ['AccessKeyId     public]\n                ['SecretAccessKey private]\n                ['Token           token]\n                ['Expiration      (app gmt-8601-string->seconds exp)])\n      (public-key public)\n      (private-key private)\n      (security-token token)]))\n\n(define mime:text (string->bytes/utf-8 \"text/plain;charset=utf-8\"))\n\n(define (respond code message headers mime-type body)\n  (response/full code (string->bytes/utf-8 message)\n                 (current-seconds) mime-type headers\n                 (list body)))\n\n(define (OK req mime-type body)\n  (define headers '())\n  (define bytes.body (if (string? body) (string->bytes/utf-8 body) body))\n  (respond 200 \"OK\" headers mime-type bytes.body))\n\n(define (respond-404)\n  (respond 404 \"Not found\" '() mime:text (string->bytes/utf-8 \"\")))\n\n(define (sanitize-input-path p)\n    (define p2 (regexp-match #rx\"[a-zA-Z0-9_/\\\\.-]+\" p))\n    (define p3 (if (list? p2) (car p2) #f))\n    (if (and\n            (string? p3)\n            (or\n                (string-suffix? p3 \"completed.json\")\n                (string-suffix? p3 \"install.yaml\")))\n        p3\n        #f))\n\n;;; endpoint /ingest-pipeline-status\n;;; required parameter:\n;;;   path: an S3 URL that conforms that is a status file from kg-ingest-pipeline.\n(define (/ingest-pipeline-status req . args)\n  (define bindings (request-bindings req))\n  (ensure-aws-credentials \"transltr_eks_ci_unsecret_node_group_iam_role\")\n  (define path (sanitize-input-path (dict-ref bindings 'path \"\")))\n  (with-handlers\n    ((aws:exn:fail:aws?\n        (lambda (ex)\n            (respond-404)\n        )))\n    (if path\n        (let ((st (bytes->string/utf-8 (get/bytes path))))\n        (OK req mime:text st))\n        (respond-404)\n        )))\n\n"
  },
  {
    "path": "medikanren2/logging.rkt",
    "content": "#lang racket/base\n(provide\n  log-time log-info log-error log-once log-length)\n(require\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  json\n  memoize\n  racket/format\n  racket/date\n  )\n\n(define-syntax log-time\n  (syntax-rules ()\n    ((_ log-proc log-key label body)\n     (let-values (((result cpu real gc) (time-apply (lambda () body) '())))\n       (log-proc log-key label cpu real (car result))\n       (car result)))))\n\n(define (log-info key message)\n  (printf \"~a    ~s    ~a       ~a\\n\"\n          (date->string (seconds->date (current-seconds)) #t)\n          key\n          \"INFO\"\n          message))\n\n(define (log-error key message)\n  (printf \"~a    ~s    ~a       ~a\\n\"\n          (date->string (seconds->date (current-seconds)) #t)\n          key\n          \"ERROR\"\n          message))\n\n(define/memo* (log-once key label cpu real result)\n  (log-info key (format \"~a [cpu time: ~s real time: ~s]: ~s\" label cpu real result)))\n\n(define (log-length key label cpu real results)\n  (log-info key (format \"~a [cpu time: ~s real time: ~s]: ~s\" \n                        label cpu real (length (hash-ref  results 'results '())))))\n"
  },
  {
    "path": "medikanren2/logging2.rkt",
    "content": "#lang racket\n(provide\n  lognew-info lognew-error requestid)\n(require\n  racket/date\n  json\n)\n(define requestid (make-parameter -1))\n\n(date-display-format 'iso-8601)\n\n(define (lognew-message level msg)\n  (define t (current-seconds))\n  (define st-t (date->string (seconds->date t #f) #t))\n  (define jsexpr\n    (if (hash? msg)\n      (hash-set\n        (hash-set\n          (hash-set msg\n            'level (symbol->string level))\n          'requestid (requestid))\n        't st-t)\n      (hasheq\n        'msg msg\n        't st-t\n        'requestid (requestid)\n        'level (symbol->string level))))\n  (with-handlers ([exn:fail?\n                   (λ (e)\n                   #|\n                      Racket json is very strict about what it accepts as a jsexpr.  For example, this succeeds:\n                        (jsexpr->string (hasheq 'foo \"bar\"))\n\n                      but these both consider their input to be ill-formed and throw:\n                        (jsexpr->string (hasheq \"foo\" \"bar\"))\n\n                        (jsexpr->string (hasheq 'foo '#\"bar\"))\n                   |#\n                     (printf\n                      \"Caught exception in lognew-message when converting/printing jsexpr->string.\\nlevel:\\n~s\\nmsg:\\n~s\\njsexpr:\\n~s\\nexception:\\n~s\\n\"\n                      level\n                      msg\n                      jsexpr\n                      e))])\n    (displayln\n     (jsexpr->string jsexpr)))\n  (flush-output (current-output-port)))\n\n(define (lognew-info msg)\n  (lognew-message 'info msg))\n\n(define (lognew-error msg)\n  (lognew-message 'error msg))\n\n"
  },
  {
    "path": "medikanren2/lw-reasoning.rkt",
    "content": "#lang racket/base\n(provide (all-from-out \"synonyms.rkt\")\n         lw-reasoning?\n         inverse-of triple/inverse edge-predicate/lwr\n         subclass-of subclass-of* subclass-of+\n         is-a/subclass+ is-a/subclass*\n         is-a/lwr triple/lwr triple/inverse\n         triple/subclass triple/subclass+\n         subclasses/set\n         )\n(require\n \"common.rkt\"\n \"synonyms.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  racket/set\n  json\n  memoize\n  )\n\n\n;; Generalized transitive closure\n\n(define (transitive-closure base-relation)\n  (lambda (child parent)\n    (cond ((string? child)\n           ((transitive-closure/up base-relation) child parent))\n          ((string? parent)\n           ((transitive-closure/down base-relation) child parent))\n          (else ((transitive-closure/mid base-relation) child parent)))))\n\n;; ideally this would be the only relation, but currently the other two optimizations are needed\n(define (transitive-closure/mid base-relation)\n  (define-relation (~transitive-closure/mid child parent)\n    (conde ((base-relation child parent))\n           ((fresh (mid)\n              (base-relation child mid)\n              (base-relation mid parent)))\n           ((fresh (mid1 mid2)\n              (base-relation child mid1)\n              (~transitive-closure/mid mid1 mid2)\n              (base-relation mid2 parent)))))\n  ~transitive-closure/mid)\n\n(define (transitive-closure/down base-relation)\n  (define-relation (~transitive-closure/down child parent)\n    (fresh (mids)\n      (:== mids (parent) (run* mid (base-relation mid parent)))\n      (fresh (mid)\n        (membero mid mids)\n        (conde ((== child mid))\n               ((~transitive-closure/down child mid))))))\n  ~transitive-closure/down)\n\n;; (define (transitive-closure/down^ base-relation)\n;;   (define-relation (~transitive-closure/down^ child parent)\n;;     (conde ((base-relation child parent))\n;;            ((fresh (mid)\n;;             (base-relation mid parent)\n;;             (~transitive-closure/down^ child mid)))))\n;;   ~transitive-closure/down^)\n\n(define (transitive-closure/up base-relation)\n  (define-relation (~transitive-closure/up child parent)\n    (fresh (mids)\n      (:== mids (child) (run* mid (base-relation child mid)))\n      (fresh (mid)\n        (membero mid mids)\n        (conde ((== parent mid))\n               ((~transitive-closure/up mid parent))))))\n  ~transitive-closure/up)\n\n;; inverse predicates\n    \n(define-relation (inverse-of p p^)\n  (conde ((triple p \"biolink:inverse_of\" p^))\n         ((triple p^ \"biolink:inverse_of\" p))))\n\n(define-relation (triple/inverse s p o)\n  (conde ((triple s p o))\n         ((fresh (p^) \n            (inverse-of p p^)\n            (triple o p^ s)))))\n\n;; subclass relations\n\n(define-relation (subclass-of child parent)\n  (triple child \"biolink:subclass_of\" parent))\n\n(define subclass-of+ (transitive-closure subclass-of))\n\n(define-relation (subclass-of* child parent)\n  (conde ((== child parent))\n         ((subclass-of+ child parent))))\n\n(define-relation (edge-predicate/subclass eid p^ p)\n  (conde ((eprop eid \"predicate\" p))\n         ((subclass-of+ p^ p)\n          (eprop eid \"predicate\" p^))))\n\n(define-relation (is-a/subclass* s c^ c)\n  (is-a s c^)\n  (subclass-of* c^ c))\n\n(define-relation (is-a/subclass+ s c^ c)\n  (subclass-of+ c^ c)\n  (is-a s c^))\n\n;; for testing only; not a useful relation as far as I can see\n(define-relation (triple/subclass+ s p^ p o)\n  (subclass-of+ p^ p)\n  (triple/inverse s p^ o)) \n\n(define-relation (triple/subclass s p^ p o)\n  (conde ((triple s p o) (== p p^))\n         ((triple/subclass+ s p p^ o))))\n\n(define-relation (triple/reasoning s^ s p^ p o^ o)\n  (subclass-of* s^ s)\n  (subclass-of* p^ p)\n  (subclass-of* o^ o)\n  (triple s^ p^ o^))\n\n(define-relation (triple/reasoning+ s^ s p^ p o^ o)\n  (triple s^ p^ o^)\n  (subclass-of+ s^ s)\n  (subclass-of+ p^ p)\n  (subclass-of+ o^ o))\n\n(define lw-reasoning? (make-parameter #f))\n\n(define-relation (is-a/lwr s c)\n  (if (lw-reasoning?)\n      (fresh (c^)\n        (is-a/subclass* s c c^))\n      (is-a s c)))\n\n(define-relation (triple/lwr s p o)\n  (if (lw-reasoning?)\n      (fresh (p^) \n        (triple/subclass s p p^ o))\n      (triple s p o)))\n\n(define-relation (edge-predicate/lwr eid p)\n  (if (lw-reasoning?)\n      (fresh (p^)\n        (conde ((eprop eid \"predicate\" p))\n               ((subclass-of+ p^ p)\n                (eprop eid \"predicate\" p^))))\n      (eprop eid \"predicate\" p)))\n\n(define/memo* (subclasses/set-of curie)\n  (run* cc (subclass-of* cc curie)))\n\n(define/memo* (subclasses/set curies)\n  (set->list\n   (run*/set c (fresh (cs c^)\n                 (membero c^ curies)\n                 (:== cs (c^) (subclasses/set-of c^))\n                 (membero c cs)))))\n\n;; Attempt to do synonymization and subclasses at once \n\n(define-relation (subclass-or-synonym a b)\n  (conde ((direct-synonym a b))\n         ((direct-synonym b a))\n         ((subclass-of a b))))\n\n(define-relation (subclass-or-synonym/mid a b)\n  (conde ((subclass-or-synonym a b))\n         ((fresh (mid)\n            (subclass-or-synonym a mid)\n            (subclass-or-synonym mid b)))\n         ((fresh (mid1 mid2)\n            (subclass-or-synonym a mid1)\n            (subclass-or-synonym mid2 b)\n            (subclass-or-synonym/mid mid1 mid2)))))\n\n(define-relation (subclass-or-synonym/down a b)\n  (conde ((subclass-or-synonym a b))\n         ((fresh (mid)\n            (subclass-or-synonym mid b)\n            (subclass-or-synonym/down a mid)))))\n\n(define-relation (subclass-or-synonym/up a b)\n  (conde ((subclass-or-synonym a b))\n         ((fresh (mid)\n            (subclass-or-synonym a mid)\n            (conde ((subclass-or-synonym mid b))\n                   ((subclass-or-synonym/up mid b)))))))\n         \n\n\n         \n;; (define anxiety \"HP:0000739\")\n;; (time (display (length (set->list (synonyms/breadth anxiety 1)))))\n;; (time (display (length (set->list (synonyms/breadth anxiety 2)))))\n;; (time (display (length (set->list (synonyms/breadth anxiety 3)))))\n\n;; (time (display (length (set->list (synonyms/step anxiety 200)))))\n;; (time (display (length (set->list (synonyms/step anxiety 1000)))))\n;; (time (display (length (set->list (synonyms/step anxiety 10000)))))\n;; (define (run-test n)\n;;   (time\n;;    (display\n;;     (length\n;;      (set->list (run*/set/steps n s (subclass/synonym-of s anxiety)))))))\n;; (run-test 200)\n;; (run-test 1000)\n;; (run-test 10000)\n\n\n\n;; todo: try to make a version that terminates\n;; > (time (set-count (run*/set/steps 10000 (s path) (subclass/synonym-of s anxiety path))))\n;; cpu time: 21026 real time: 21032 gc time: 122\n;; 55\n;; >  (time (set-count (run*/set/steps 15000 (s path) (subclass/synonym-of s anxiety path))))\n;; cpu time: 32172 real time: 32184 gc time: 205\n;; 71\n;; >  (time (set-count (run*/set/steps 20000 (s path) (subclass/synonym-of s anxiety path))))\n;; cpu time: 45528 real time: 45947 gc time: 378\n;; 71\n"
  },
  {
    "path": "medikanren2/mkconfigref.rkt",
    "content": "#lang racket\n(require\n    racket/runtime-path\n)\n(provide\n    config-ref\n    load-config\n    override-config\n    override-dbkanren-defaults\n)\n(require \"configref.rkt\")\n\n(define box:verbose? (box #t))\n(define (set-verbose! b)\n  (set-box! box:verbose? b))\n\n(define (read/file path)\n  (define verbose? #t)\n  (when verbose? (printf \"loading configuration: ~a\\n\" (path->string path)))\n  (with-input-from-file  path (lambda () (read))))\n\n(define-runtime-path path:root \".\")\n(define (path/root relative-path) (build-path path:root relative-path))\n(define (path/etc relative-path) (build-path path:root \"etc\" relative-path))\n(define (path-simple path)        (path->string (simplify-path path)))\n\n(define (env-ref/utf-8 k)\n  (define v (environment-variables-ref (current-environment-variables) (string->bytes/utf-8 k)))\n  (if v\n    (bytes->string/utf-8 v)\n    #f))\n(define (path:config.user.migrated)\n    (path/etc \"config.scm\"))\n    ;; BEGIN TEMPORARY: migrated-to-new-db-versioning:\n(define (path:config.user.legacy)\n    (path/root \"config.scm\"))\n    ;; END TEMPORARY\n(define (path:config.stage.prod) (path/etc \"config.stage.prod.scm\"))\n(define (path:config.stage.dev) (path/etc \"config.stage.dev.scm\"))\n(define (path:config.installer) (path/etc \"config.installer.scm\"))\n(define (path:config.defaults) (path/etc \"config.defaults.scm\"))\n\n(define (make-rebuild-by-cbranch verbose?)\n  (define config.user\n    (let\n      ((config.tmp\n    ;; BEGIN TEMPORARY: migrated-to-new-db-versioning:\n        (if (not (file-exists? (path:config.user.migrated)))\n          (if (file-exists? (path:config.user.legacy))\n            (read/file (path:config.user.legacy))\n            '())\n    ;; END TEMPORARY\n          (if (file-exists? (path:config.user.migrated))\n            (read/file (path:config.user.migrated))\n            '()))))\n        (validate-config config.tmp)\n        config.tmp))\n  (define config.stage\n    (let* (\n        (stage (env-ref/utf-8 \"MK_STAGE\"))\n        (path1\n          (cond\n            ((equal? stage \"prod\") (path:config.stage.prod))\n            ((equal? stage \"dev\") (path:config.stage.dev))\n            ((not stage) (path:config.stage.dev))\n            (else\n              (printf \"***Warning*** unknown MK_STAGE value: ~a\" stage)\n              (path:config.stage.dev)))))\n      ;; No fallbacks for this file if missing.  Stage files should be in revision control\n      (read/file path1)))\n  (define config.installer (if (file-exists? (path:config.installer))\n                              (read/file (path:config.installer))\n                              '()))\n  (define config.defaults (read/file (path:config.defaults)))\n  (lambda (cbranch)\n    (case cbranch\n      ('user config.user)\n      ('defaults config.defaults)\n      ('installer config.installer)\n      ('stage config.stage)\n      (else (configlayer-ref cbranch '())))))\n\n(define cbranches '(defaults dbkanren-defaults installer stage user override-test override))\n\n(define (make-rebuild-flat verbose?)\n  (apply config-combine\n    (map (make-rebuild-by-cbranch verbose?) (reverse cbranches))))\n\n(define (load-config verbose?)\n  (set-verbose! verbose?)\n  (refresh-config))\n\n(set-build-thunk! (lambda () (make-rebuild-flat (unbox box:verbose?))))\n\n;; Primarily for use in the repl, secondarily for use\n;; in automated tests.  Use discouraged in applications.\n(define override-config (expose-configlayer 'override))\n;; Propagates defaults from medikanren to dbkanren.\n(define override-dbkanren-defaults (expose-configlayer 'dbkanren-defaults))\n\n(module+ test\n  ; has required package:\n  ;   raco pkg install chk\n  ;\n  ; how to run tests:\n  ;   (cd medikanren && raco test configref.rkt)\n\n  (require chk)\n\n  (chk\n      #:do (validate-config (read/file (path:config.defaults)))\n      #:t #t)\n)"
  },
  {
    "path": "medikanren2/neo/dbKanren/LICENSE",
    "content": "The MIT License (MIT)\n\nCopyright (c) 2020 Gregory Rosenblatt\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/README.md",
    "content": "# dbKanren\n\nThis implementation of Kanren supports defining, and efficiently querying,\nlarge-scale relations.\n\nTypical use:\n\n```\n(require \"PATH-TO-DBKANREN/dbk.rkt\")\n```\n\n\n## TODO\n\n- Datalog implementation\n  - Optional safety checking (we should still be able to execute unsafe programs)\n    - Total (simple) safety: no function terms or aggregation through recursion\n      - Guarantees safety regardless of evaluation strategy\n    - When total safety fails, could try to determine safety just for top-down or bottom-up evaluation\n    - More advanced checking would support recursion involving function terms and aggregation\n      - Size-based termination checking for top-down recursion using function term arguments\n      - Checking invariants that guarantee convergence for recursive aggregation\n  - Demand transformation\n    - Propagate query constants/bindings to determine needed demand signatures for each relation\n    - For each relation's demand signature, schedule its body order, informed by database statistics\n    - Generate the demand-transformed rules\n    - Adjust naive evaluation to support stratified negation/aggregation w/ demand-transformed program\n  - Semi-naive evaluation\n    - Transform a program to use delta-based rules\n    - Fixed-point calculation with 3 variants per recursive relation (old, delta, new)\n  - Lowering to relational algebra operations\n    - e.g., projecting away irrelevant variables to reduce intermediate duplication\n\n- Relation definitions and queries involving semantic extensions\n  - A relation defined with `define-relation` will raise an error if it does not support a finite mode\n    - For Racket-embedded definitions, the error cannot be issued immediately due to\n      mutually-recursive relations that may not be fully defined.  Instead, the error will be issued\n      at the earliest query or request for compilation.\n    - Use `define-search-relation` to suppress the error\n    - e.g.,\n      - Each pure relation has one finite mode: all attributes can be safely unknown, aka `#f`\n      - Terminating computational relations may have more complex modes\n        - These are recognized automatically by mode inference\n        - `(appendo xs ys xsys)` has two finite modes: `(#t #t #f)` and `(#f #f #t)`\n        - `(membero x xs)` has one finite mode: `(#f #t)`\n      - `(evalo expr env result)` has no finite modes, so it's considered a search-based relation\n        - Because exprs like `((lambda (d) (d d)) (lambda (d) (d d)))` are possible\n  - A query executed with `run` will raise an error if it cannot guarantee termination\n    - It may also provide diagnostics about worst-case behavior and execution progress\n    - Use `run-search` to suppress the error\n\n- Database improvements\n  - Maybe we don't need the augmented 0th column for relations and incomplete indexes\n    - Only index the listed columns?  Consider missing columns to have been projected away.\n  - Try switching from fxvectors to using bytes where possible, and compress fixnums otherwise\n    - `id=>id` remapping, and `col<->row` transposition with varying byte widths: annoying?\n  - Improve checkpointing storage\n    - Consolidate block files to use fewer\n      - Make use of `(file-stream-buffer-mode in 'none)` file ports\n        - `read-bytes` is as efficient as `file->bytes` if you know the `file-size` up front\n      - May need a protocol for scattered/interrupted/fragmented writes to block ids\n      - Will need a compaction protocol\n    - Should we move away from block names and just use block ids?\n  - Vectorized relational operators\n  - Consider radix burst sort for ingesting text more quickly\n    - Also consider alternatives to multi-merge for text\n\n- Data access interface for queries\n  - What form should RA-level (table-like) entities take?\n    - Include database-path and a database-local UID for recognizing identitical entities\n      - Important for using functional dependencies and other optimizations\n    - Relation type (for eliminating pointless joins/unions/differences)\n    - `index-ordering => (cons key-columns position-columns)`\n      - Once a query is planned, this info is used to build the necessary dicts\n\n- Try a simple text search strategy using a triples-containment relation\n  - Don't build this into the database, this can all be user-defined\n  - Filter name text to retain only lower-case alphanumeric (plus an empty value for 37 total values)\n  - Build the relation: `(text-contains text c0 c1 c2)` or `(text-contains text compact-c012)`\n    - Latter approach compacts c0 c1 c2 to a single 2-byte value\n      - c0 c1 c2 are treated as digits\n      - `compact-c012 = c0*37^2 + c1*37 + c2`\n      - which is `< 52059`, which is `< 2^16`\n    - Indexing `\"foobar\"` would produce these tuples:\n      ```\n      (text-contains \"foobar\" \"f\" \"o\" \"o\")\n      (text-contains \"foobar\" \"o\" \"o\" \"b\")\n      (text-contains \"foobar\" \"o\" \"b\" \"a\")\n      (text-contains \"foobar\" \"b\" \"a\" \"r\")\n      (text-contains \"foobar\" \"a\" \"r\" \"_\")\n      (text-contains \"foobar\" \"r\" \"_\" \"_\")\n      ```\n    - Searching for `\"test\"` would use this query to produce a tractable number of candidates:\n      ```\n      (run* candidate\n        (text-contains candidate \"t\" \"e\" \"s\")\n        (text-contains candidate \"e\" \"s\" \"t\"))\n      ```\n    - Candidates can then be filtered using arbitrary rules defined in Racket\n\n* a smaller extended syntax\n  * logical connectives (not, and, or)\n  * apply for relations\n  * anonymous vars\n\n* `explain` for extracting the database subset needed to reproduce a query's results\n  * with each result, run an instrumented query to record supporting facts\n  * there may be redundancy (one result could be computed in multiple ways)\n\n- analyze, simplify, and plan with query structure\n  - GOO join heuristic\n  - index-based path-finding to find candidate variable orderings\n\n* redesign states, strategies to support adaptive analysis and optimization\n  * decorate unexpanded user-defined relation constraints with the chain of\n    already-expanded parent/caller relations that led to this constraint\n    * to identify nonterminating loops\n    * to help measure progress\n  * optional bottom-up evaluation strategy\n    * safety analysis of relations referenced during query/materialization\n  * randomized variants of interleaving or depth-first search\n\n* use small tables for finite domains\n* fixed point computation\n  * binding signatures with constraints\n    * share work by generalizing signatures\n\n- improve `bounds` algebra by adding slightly-less and slightly-greater values for open interval endpoints\n  - think of these as +epsilon, -epsilon\n  - define comparison operators, min, and max, over these values\n\n* place-based concurrency/parallelism?\n* thread-safe table retrieval\n* background worker threads/places for materialization\n* documentation and examples\n  * small tsv data example for testing materialization\n  * LiveJournal, Orkut graph benchmark examples for\n    * https://github.com/frankmcsherry/blog/blob/master/posts/2019-09-06.md\n    * reachability\n    * connected components\n    * single-source shortest path\n    * http://yellowstone.cs.ucla.edu/papers/rasql.pdf\n    * http://pages.cs.wisc.edu/~aws/papers/vldb19.pdf\n* support an interactive stepping/user-choice \"strategy\"\n  * both for debugging and devising new strategies\n  * `run/interactive`\n    * same as a `run^` with `current-config` `search-strategy` set to `interactive`\n    * non-stream, first-order representation of strategy-independent states\n      * also support embedding and combining sub-states (hypothetical along a disjunct)\n        * states are just fancy representations of conjunctions, and should be\n          combinable/disolvable\n\n* relation compilation to remove interpretive overhead\n  * mode analysis\n  * represent low-level operation representation depending on mode\n    * e.g., == can act like an assignment, or a type/equality test\n      * likewise for other constraint evaluations\n  * partial evaluation\n    * e.g., unify on partially-known term structures can be unrolled\n    * constraint evaluations can be pre-simplified and reordered\n  * code generation\n\n* eventually, make sure relation metadata contains information for analysis\n  * e.g., degree constraints, fast column ordering, subsumption tag/rules\n  * descriptions used for subsumption\n    * #(,relation ,attributes-satisfied ,attributes-pending)\n    * within a relation, table constraint A subsumes B if\n      B's attributes-pending is a prefix of A's\n      AND\n      B does not have any attributes-satisfied that A does not have\n  * schema: heading, constraints, other dependencies\n    * heading: set of attributes and their types\n    * degree constraints (generalized functional dependencies)\n      * interpret degree constraints to find useful special cases\n        * functional dependency\n        * bijection (one-to-one mapping via opposing functional dependencies)\n        * uniqueness (functional dependency to full set of of attributes)\n    * maybe join and inclusion dependencies\n  * body: finite set of tuples\n\n* floating point numbers are not valid terms\n  * reordering operations endangers soundness\n  * detect float literals when doing so won't hurt performance\n\n\n### Data processing\n\n- types\n  - text suffix\n    - suffix: `(ID . start)`\n  - bigint, rational\n\n* ingestion\n  * parsing: nq (n-quads)\n  * gathering statistics\n    * reservoir sampling\n    * optional column type inference\n    * per-type statistics for polymorphic columns\n    * count, min, max, sum, min-length, max-length\n    * histogram up to distinct element threshold\n    * range bucketing\n\n\n### Database representation\n\n- intensional relation search strategy: backward or forward chaining\n  - safety-type could be inferred, or forced by parameter choice\n  - can use a begin-like macro to set the safety parameter:\n    - `(dbk-datalog-begin definitions ...)`\n    - `(dbk-total-begin   definitions ...)`\n  - forward-chaining supports stratified negation and aggregation\n\n- metadata for extensional relations (user-level)\n  - constraints:\n    - degree (subsumes uniqueness, functional dependency, cardinality)\n      - in relation R, given (A B C), how many (D E F)s are there?\n        - lower and upper bounds, i.e., 0 to 2, exactly 1, at least 5, etc.\n      - maybe support more precise constraints given specific field values\n    - monotone dependencies\n      - e.g., C is nondecreasing when sorting by (A B C D)\n      - implies sorted rows for (C A B D) appear in same order as (A B C D)\n        - one index can support either ordering\n      - generalized: (sorted-columns (A B . C) (B . D) B) means:\n        - B is already nondecreasing\n        - C becomes nondecreasing once both A and B are chosen\n        - D becomes nondecreasing once B is chosen (regardless of A)\n  - statistics (derived from table statistics)\n\n\n### Relational language for rules and queries\n\n- indicate or infer aggregation monotonicity for efficient incremental update\n\n- misc conveniences\n  - `apply` to supply a single argument/variable to an n-ary relation\n  - optional keyword argument calling convention for relations\n    - user can implement this as Racket procedures that accept plist-style keyword args\n\n* relations\n  * local relation definitions to share work (cached results) during aggregation\n    * `(let-relations (((name param ...) formula ...) ...) formula ...)`\n    * express subqueries by capturing other vars\n  * if `r` is a relation:\n    * `(r arg+ ...)` relates `arg+ ...` by `r`\n    * `(relations-ref r)` accesses a metaprogramming control structure\n      * configure persistence, representation, uniqueness and type constraints\n      * indicate evaluation preferences or hints, such as indexing\n      * dynamically disable/enable\n      * view source, statistics, configuration, preferences, other metadata\n\n* evaluation\n  * query evaluation\n    * precompute relevant persistent/cached safe relations via forward-chaining\n    * safe/finite results loop (mostly backward-chaining)\n      * prune search space top-down to shrink scale of bulk operations\n        * expand recursive relation calls while safe\n          * safety: at least one never-increasing parameter is decreasing\n            * this safety measure still allows polynomial-time computations\n            * may prefer restricting to linear-time computations\n            * or a resource budget to limit absolute cost for any complexity\n          * track call history to measure this\n          * recursive calls of exactly the same size are considered failures\n        * keep results of branching relation calls independent until join phase\n      * ~~maintain constraint satisfiability~~\n        * ~~constraint propagation loop: `state-enforce-local-consistency`~~\n          * ~~cheap first-pass via domain consistency, then arc consistency~~\n          * backjump and learn clauses when conflict is detected\n        * ~~then global satisfiability via search~~\n          * ~~choose candidate for the most-constrained variable~~\n            * ~~maybe the variable participating in largest number of constraints~~\n          * ~~interleave search candidate choice with cheap first-pass methods~~\n      * perform the (possibly multi-way) join with lowest estimated cost\n      * repeat until either all results computed or only unsafe calls remain\n    * perform unsafe interleaving until finished or safe calls reappear\n      * like typical miniKanren search\n      * if safe calls reappear, re-enter safe/finite results loop\n  * safety (and computation) categories for relations\n    * simple\n      * persistent (extensional or precomputed intensional)\n        * compute via retrieval\n      * nonrecursive\n        * compute via naive expansion\n      * \"safe\" in the datalog sense\n        * compute fixed point via semi-naive eval after top-down rewriting\n        * all relations used in the body are safe\n        * all head parameter vars mentioned in positive position in body\n          * i.e., all head parameters will be bound to ground values\n        * no constructors containing vars in \"dangerous\" positions\n          * head parameters of recursive relation\n          * arguments to recursive relations in body\n        * aggregation is stratified\n      * \"unsafe\": top-down interleaving search\n        * no safety guarantees at all\n          * refutational incompleteness\n          * unlimited answers\n          * answers with unbound variables, possibly with constraints\n    * more complex alternatives\n      * \"safe\" for forward chaining only\n        * compute fixed point via semi-naive eval\n        * generalizes \"safe\" datalog slightly\n          * constructors w/ vars allowed as args to recursive relations in body\n      * \"safe\" for backward chaining only\n        * compute via DFS\n        * may or may not guarantee all variables are bound (groundness)\n        * termination guaranteed by structural recursion argument metric\n\n* mode analysis\n  * modes as binding patterns with result cardinalities\n    * parameter binding classes from least to most constraining\n      * f: free        (no guarantees of any kind)\n      * x: constrained (if it's a variable, it at least has some constraints)\n      * c: constructed (not a variable, but not necessarily fully ground)\n      * b: bound       (fully ground)\n    * appendo: (b f f) -> (0 1) (b f b)\n      * bound first param leads to 0 or 1 result with bound third param\n  * mode-specific safety\n    * appendo termination requires (c f f) or (f f c) at every recursive call\n  * mode-specific cost\n    * different parameter bindings determine effectiveness of indices\n\n* lazy population of text/non-atomic fields\n  * equality within the same shared-id column can be done by id\n    * also possible with foreign keys\n    * analogous to pointer address equality\n  * equality within the same nonshared-id column must be done by value\n    * equal if ids are the same, but may still be equal with different ids\n  * equality between incomparable columns must be done by value\n    * address spaces are different\n  * how is this integrated with mk search and query evaluation?\n    * can do this in general for functional dependencies\n      * `(conj (relate-function x a) (relate-function x b))` implies `(== a b)`\n  * would like similar \"efficient join\" behavior for text suffix indexes\n    * given multiple text constraints, find an efficient way to filter\n      * will involve intersecting a matching suffix list for each constraint\n      * one suffix list may be tiny, another may be huge\n        * rather than finding their intersection, it's likely more efficient\n          to just throw the huge one away and run the filter directly on the\n          strings for each member of the tiny suffix set\n    * how is this integrated with mk search and query evaluation?\n      * text search can be expressed with `string-appendo` constraints\n        * `(conj (string-appendo t1 needle t2) (string-appendo t2 t3 hay))`\n      * suffix index can be searched via\n        * `(string-appendo needle t1 hay-s)`\n      * multiple needles\n        * `(conj (string-appendo n1 t1 hay-s) (string-appendo n2 t2 hay-s))`\n      * maybe best done explicitly as aggregation via `:==`\n\n\n### Aggregation ideas\n\n* finite relations may relate their tuples to an extra position parameter\n  * `(apply-relation-position R pos tuple)`\n\n* aggregation via negation\n  * can this be done efficiently?\n  * edb: `(edge x y)`\n  * ```\n    (define-relation (1-hops x targets)\n      (=/= targets '())\n      (:== targets (query y (edge x y))))\n\n    or\n\n    (define-relation (1-hops x targets)\n      (=/= targets '())\n      (query== targets y (edge x y)))\n\n    vs.\n\n    (define-relation (1-hops-rest x prev targets)\n      (conde\n        ((== targets '())\n         (not (fresh (z)\n                (any< prev z)\n                (edge x z))))\n        ((fresh (y targets.rest)\n           (== targets (cons y targets.rest))\n           (edge x y)\n           (not (fresh (z)\n                  (any< prev z)\n                  (any< z y)\n                  (edge x z)))\n           (1-hops-rest x y targets.rest)))))\n    (define-relation (1-hops x targets)\n      (fresh (y targets.rest)\n        (== targets (cons y targets.rest))\n        (edge x y)\n        (not (fresh (z)\n               (any< z y)\n               (edge x z)))\n        (1-hops-rest x y targets.rest)))\n    ```\n\n    ```\n    (define-relation (max+o threshold x xs)\n      (conde ((== xs '()) (== x threshold))\n             ((fresh (y ys)\n                (== xs (cons y ys))\n                (conde ((any<= y threshold) (max+o threshold x ys))\n                       ((any<  threshold y) (max+o y         x ys)))))))\n    (define-relation (maxo x xs)\n      (fresh (y ys)\n        (== xs (cons y ys))\n        (max+o y x ys)))\n    (define-relation (edge-largest x largest)\n      (fresh (targets)\n        (query== targets y (edge x y))\n        (maxo largest targets)))\n\n    vs.\n\n    (define-relation (edge-largest x largest)\n      (edge x largest)\n      (not (fresh (y) (any< largest y) (edge x y))))\n    ```\n\n\n### Query planning and joins\n\nWe need some low-level language for transformation (not for humans or direct interpretation).  Is this the right one?\n- is there a more operational datalog-like notation? e.g., datalog + ordering hints?\n  - (and _ ...) and (or _ ...) can be used to specify specific join/union order and nesting\n  - but these seem hard, so this idea is probably not enough:\n    - what about specifying particular kinds of joins?\n    - what about projection and filtering?\n    - what about aggregation?\n    - how about sub-computation sharing and scope?\n\nInitial sketch of relational algebra language for lower-level optimization transformations:\n```\nposition ::= \ncount    ::= \nmerge-op ::= + | * | min | max | set-union | (min-union count) | (max-union count)\nop       ::= cons | vector | list->vector | car | cdr | vector-ref | vector-length | merge-op\nexpr     ::= (quote value) | (ref position position) | (app op expr ...)\ncmp      ::= == | any<= | any< | =/=\ncx       ::= (cmp expr expr) | (and cx ...) | (or cx ...)\nrelation ::= (quote   ((value ...) ...)) ; What operator does this correspond to? Does it assume sorting/deduping? Probably no assumptions, just enumerate raw tuples.\n           | (table   rid)               ; This corresponds to a basic table scan, use a different operator for more efficient access.\n           | (rvar    name)\n           | (filter  (lambda 1 cx) relation)\n           | (project (lambda 1 (expr ...)) relation)\n           | (union   relation ...)\n           | (subtract relation relation)\n           | (cross   relation ...)      ; TODO: replace with nested [for-]loop notation.\n\n;; How do we specify n-way join shared keys?\n;; New notation for join-key specification?\n;; Operators for sorting (with direction), deduplication.\n;; Operators for skipping (dropping), and limiting (taking).\n\n           | (agg     relation (lambda 1 (expr ...)) value (lambda 1 (expr ...)) (merge-op ...))  ; rel group init map merge (map exprs and merge ops must be same length)\n           | (let     ((name relation) ...) relation)  ; Relations are materialized, nesting describes stratification.\n           | (letrec  ((name relation) ...) relation)  ; Relations computed as fixed points, relations are materialized, nesting describes stratification.\n\n;; Let-bound relations should be specific about what physical tables/indexes are formed?\n\ndirection        ::= < | >\ndirection-suffix ::= () | #f\noffset           ::= \nlimit            ::=  | #f\nquery            ::= (query offset limit (direction ... . direction-suffix) relation)  ; Do we need this? Should we embed sorting, skipping, and limiting as operators instead?\n```\n\nExample query thought experiments:\n\nMaybe bounds feedback doesn't make sense, and should be part of the plan ordering, where bounds actually come from the bottom rather than the top?\ne.g., consider variable-centric plans for:\n```\n(run* (a b d e)\n  (exist (c)\n    (and (P a b c)\n         (Q c d e)\n         (R c d e))))\n\n- c then (c d e) then c: (P ((P Q) (P R)))  ; aka semijoins\n  - (join P [2] [1 2]\n          (join (join P [2] [] Q [0] [0 1 2]) [0 1 2] [1 2]  ; this is a semijoin\n                (join P [2] [] R [0] [0 1 2]) [0 1 2] [])    ; this is also a semijoin\n          [0] [1 2])\n\n- (c d e) then c: (P (Q R))\n  - (join P [2] [1 2]\n          (join Q [0 1 2] [1 2] R [0 1 2] [])  ; no semijoining performed\n          [0] [1 2])\n\nBut neither of these gives adaptive feedback ...\nUpstream and downstream can't communicate bounds with this approach.\nIdeally we would choose an ordering like:\n- c d e\nor\n- d e c\n\nBinary joins seem too inflexible here.\n```\n\nMulti-join GOO perspective:\n```\n- (run* (a c) (exist (b) (P a b) (Q b c)))\n  - max cardinality: (* (cardinality P a) (cardinality Q c))\n- (run* (a b c) (P a b) (Q b c))\n  - max cardinality: (min (* (cardinality P a)\n                             (cardinality Q b c))\n                          (* (cardinality Q c)\n                             (cardinality P a b))\n                          (* (cardinality P a)\n                             (cardinality Q c)\n                             (min (cardinality P b)\n                                  (cardinality Q b))))\n```\n\nNaive selectivity for join cardinality estimation:\n```\n- |S join.x T| ~= (/ (* |S||T|) (max (cardinality S x) (cardinality T x)))\n- can generalize for multi-way joins:\n  - if joining k relations\n    - numerator is a product of the k relation sizes\n    - denominator is a product of the (- k 1) largest join-column cardinalities\n```\n\nNon-materializing multi-way joins may be wasteful:\n```\n- (P a b) (Q b c) (R c d) (S d e)\n- joining variables: b c d\n  - for each choice of b, we learn a set of cs and repeat some of the work of joining (R c d) (S d e) on d\n  - the repeated work has two parts:\n    - finding values of c where a satisfying (d e) exists\n    - bisection revisitation overhead in enumerating these\n  - if the result cardinality of (R c d) (S d e) is small, materializing this sub-join may be better\n- semijoins as degenerate joins\n  - (P a b) (Q b c) where P is used to reduce the size of Q based on b\n  - equivalent to (P _ b) (Q b c)\n  - Q^  = (P  _ b) (Q   b c)\n  - R^  = (Q^ _ c) (R   c d)\n  - S^  = (R^ _ d) (S   d e)\n  - R^^ = (R^ c d) (S^  d _)\n  - Q^^ = (Q^ b c) (R^^ c _)\n  - P^  = (P  a b) (Q^^ b _)\n  - arc-constrained query: (P^ a b) (Q^^ b c) (R^^ c d) (S^ d e)\n    - benefit: increased cardinality estimation accuracy\n```\n\nMulti-way joins are not wasteful when all relations share the same join attributes (assuming proper indexes):\n```\n- (P x y a) (Q x b y) (R c y x)\n- can intersect on either (x y) or (y x), and simply enumerate crosses of the non-join attributes\n```\n\nMulti-way joins may improve over binary joins whose expected result cardinality is greater than the max cardinality of either input.\n\n\n## Naming conventions\n\n```\n_    = blank\nx-y  = x  y     ; for multi-word phrases, e.g., launch-all-missiles\nx/y  = x with y\nx^y  = x superscript y\nx.y  = x subscript y   ; emphasizing grouping by x\ny:x  = x subscript y   ; emphasizing grouping by y, the subscript; e.g., a type\n                       ; y with constructors x, or implementing a common\n                       ; interface of operations x, or other situations where\n                       ; if the context is clear, the y: could be dropped from\n                       ; the name\nx@y  = x at y          ; result of projection or access using address/key y\nx->y = x to y          ; procedure mapping type x to y\nx=>y = x to y          ; finite map (e.g., hash or vector) with key type x\nx&y  = x and y         ; a pair, or sometimes a 2-element list or vector\nx*   = 0 or more xs    ; (typically homogeneous) lists, sometimes vectors\nx?   = x huh           ; x is either a boolean(-ish) value itself, or a\n                       ; predicate (procedure returning a boolean(-ish) value)\nx!   = x bang          ; x may cause important side effects, such as mutation\n                       ; or throwing an error; I/O operations often don't use\n                       ; this convention\nx?!  = assert x        ; a predicate/guard that throws an error if false\n```\n\n\n## References\n\n- [miniKanren: an embedded DSL for logic programming](http://minikanren.org)\n- [Bloom Programming Language](http://bloom-lang.net/)\n- [Dedalus: Datalog in Time and Space](http://www2.eecs.berkeley.edu/Pubs/TechRpts/2009/EECS-2009-173.pdf)\n- [Datafun Programming Language](http://www.rntz.net/datafun/)\n- [Flix Programming Language](https://flix.dev/)\n\n### Datalog and Bottom-up Evaluation Techniques\n\n- [What You Always Wanted to Know About Datalog (And Never Dared to Ask)](https://personal.utdallas.edu/~gupta/courses/acl/papers/datalog-paper.pdf)\n- [Integrating Datalog and Constraint Solving](https://biblio.ugent.be/publication/5646054/file/5646069.pdf)\n- [Compilation Of Bottom-Up Evaluation For a Pure Logic Programming Language](https://researchcommons.waikato.ac.nz/bitstream/handle/10289/12882/thesis.pdf)\n- [Bottom-Up Evaluation](http://users.informatik.uni-halle.de/~brass/lp07/c6_botup.pdf)\n- [Magic Sets](http://users.informatik.uni-halle.de/~brass/lp07/c7_magic.pdf)\n- [Automatic Reordering for Dataflow Safety of Datalog](https://doi.org/10.1145/3236950.3236954)\n- [Slides for Automatic Reordering for Dataflow Safety of Datalog](https://dodisturb.me/doc/slide/ppdp18.pdf)\n\n### Recursive Relations\n\n- [A Cost Estimation Technique for Recursive Relational Algebra](https://hal.inria.fr/hal-03004218/document)\n- [On the Optimization of Recursive Relational Queries: Application to Graph Queries](http://pierre.geneves.net/papers/mura-sigmod20.pdf)\n- [Cost-Based Optimization for Magic: Algebra and Implementation](https://dsf.berkeley.edu/papers/sigmod96-magic.pdf)\n\n### Query Plans\n\n- [How Good Are Query Optimizers, Really?](https://www.vldb.org/pvldb/vol9/p204-leis.pdf)\n- [Cardinality Estimation Done Right: Index-Based Join Sampling](http://cidrdb.org/cidr2017/papers/p9-leis-cidr17.pdf)\n- [A New Heuristic for Optimizing Large Queries](http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.31.737)\n- [Looking Ahead Makes Query Plans Robust](http://www.vldb.org/pvldb/vol10/p889-zhu.pdf)\n- [Worst-case Optimal Join Algorithms](http://pages.cs.wisc.edu/~chrisre/papers/paper49.Ngo.pdf)\n\n### Low-level Efficiency\n\n- [Sort vs. Hash joins](http://www.vldb.org/pvldb/vol7/p85-balkesen.pdf)\n- [Efficiently Compiling Efficient Query Plans for Modern Hardware](http://www.vldb.org/pvldb/vol4/p539-neumann.pdf)\n- [Push vs. Pull-Based Loop Fusion in Query Engines](https://arxiv.org/pdf/1610.09166.pdf)\n- [How to Architect a Query Compiler, Revisited](https://www.cs.purdue.edu/homes/rompf/papers/tahboub-sigmod18.pdf)\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/bcat.rkt",
    "content": "#lang racket/base\n(require \"dbk/codec.rkt\" racket/pretty racket/port)\n\n(module+ main\n  (define argv      (current-command-line-arguments))\n  (define arg-names '#(DATA-TYPE))\n  (unless (= (vector-length argv) (vector-length arg-names))\n    (error \"invalid arguments\" 'expected arg-names 'given argv))\n  (define type (with-input-from-string (vector-ref argv 0) read))\n  (define in   (current-input-port))\n  (define out  (current-output-port))\n  (with-handlers (((lambda (e)\n                     (and (exn:fail:filesystem:errno? e)\n                          (equal? (exn:fail:filesystem:errno-errno e)\n                                  '(32 . posix))))\n                   void))\n    (let loop ()\n      (unless (eof-object? (peek-byte in))\n        (pretty-write (decode in type))\n        (loop)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/csv2tsv.rkt",
    "content": "#lang racket/base\n(require \"dbk/io.rkt\")\n\n(module+ main\n  (let ((in (current-input-port)) (out (current-output-port)))\n    (with-handlers (((lambda (e)\n                       (and (exn:fail:filesystem:errno? e)\n                            (equal? (exn:fail:filesystem:errno-errno e)\n                                    '(32 . posix))))\n                     void))\n      (let loop ()\n        (let ((row (csv:read in)))\n          (unless (eof-object? row)\n            (tsv:write out row)\n            (loop)))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/abstract-syntax.rkt",
    "content": "#lang racket/base\n(provide\n  f:query f:true f:false f:relate f:imply f:iff f:or f:and f:not f:exist f:all\n  t:query t:quote t:var t:prim t:app t:lambda t:if t:let\n  scm->term)\n(require \"misc.rkt\" (except-in racket/match ==) racket/set)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Abstract syntax\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-variant formula?\n  (f:query  result param f)  ; TODO: omit this class of formula?\n  (f:true)\n  (f:false)\n  ;; TODO: local relation definitions, to express subqueries\n  ;; but this may be macro-expressible without a dedicated AST node?\n  ;(f:letrec defs)  ; defs ::= list-of (name params f)\n  (f:relate relation args)  ; finite position built-in? #f for infinite relations\n  ;; TODO:\n  ;(f:relate relation arg)  ; switch to single argument for apply-relation, where variadic version is sugar\n\n  ;(f:meta thunk)\n\n  ;; or maybe just aggregate via forall/not-exists/any<=o enumeration\n  (f:imply  if then)\n  (f:iff    f1 f2)\n  (f:or     f1 f2)\n  (f:and    f1 f2)\n  (f:not    f)\n\n  ;; TODO: single-param versions of f:exist and f:all:\n  ;(f:exist  param body)\n  ;(f:all    param body)\n\n  (f:exist  params body)\n  (f:all    params body))\n\n(define-variant term?\n  ;; TODO: simplify, removing t:query, t:lambda, t:if, t:let, t:prim, t:app\n  ;; replace t:app with t:cons and t:vector\n  (t:query  name formula)\n  (t:quote  value)\n  (t:var    name)\n  (t:prim   name)\n  (t:app    proc args)\n  (t:lambda params body)\n  (t:if     c t f)\n  (t:let    bpairs body))\n\n(define (t:cons         a d) (t:app (t:prim 'cons)          (list a d)))\n(define (t:list->vector xs)  (t:app (t:prim 'list->vector)  (list xs)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Values and term conversion\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (atom? x)\n  (or (null? x) (boolean? x) (symbol? x) (string? x) (bytes? x) (and (real? x) (exact? x)) (void? x)))\n\n(define (scm->term x)\n  (cond ((term?         x)  x)\n        ((pair?         x)  (t:cons         (scm->term (car          x))\n                                            (scm->term (cdr          x))))\n        ((vector?       x)  (t:list->vector (scm->term (vector->list x))))\n        ((atom?         x)  (t:quote        x))\n        ((and (real?    x)\n              (inexact? x)) (scm->term (inexact->exact x)))\n        (else               (error \"invalid dbk value:\" x))))\n\n(define (f-relations f)\n  (match f\n    ((f:query   _ _ f)       (f-relations f))\n    ;; TODO: no need for t-relations* if we lift all uses of t:query\n    ;((f:relate  relation args) (set-add (t-relations* args) relation))\n    ((f:relate  relation _)  (set relation))\n    ((f:imply   f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:iff     f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:or      f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:and     f1 f2)       (set-union (f-relations f1) (f-relations f2)))\n    ((f:not     f)           (f-relations f))\n    ((f:exist   _ body)      (f-relations body))\n    ((f:all     _ body)      (f-relations body))\n    ((or (f:true) (f:false)) (set))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/codec.rkt",
    "content": "#lang racket/base\n(provide encode decode sizeof nat-type/max)\n(require racket/list racket/match)\n\n(define (exact-number? x) (and (number? x) (exact? x)))\n(define (<< i s) (arithmetic-shift i s))\n(define (>> i s) (arithmetic-shift i (- s)))\n(define (& a b)  (bitwise-and a b))\n(define (\\| a b) (bitwise-ior a b))\n(define (^ a b)  (bitwise-xor a b))\n\n(match-define (list t.bytes t.string t.symbol t.array t.pair\n                    t.true t.false t.null t.number\n                    ;; TODO: support more efficient numeric representations\n                    ;; is a separate rat type (for rationals) superfluous?\n                    t.nat t.int t.rat)\n  (range (length '(t.bytes t.string t.symbol t.array t.pair\n                   t.true t.false t.null t.number\n                   t.nat t.int t.rat))))\n\n(define (nat-type/max max-nat) `#(nat ,(- (sizeof 'nat max-nat) 1)))\n\n(define (sizeof type v)\n  (match type\n    (#f                (sizeof-any          v))\n    (`#(nat    ,size)  (sizeof-nat    size  v))\n    (`#(string ,len)   (sizeof-string len   v))\n    (`#(symbol ,len)   (sizeof-symbol len   v))\n    (`#(bytes  ,len)   (sizeof-bytes  len   v))\n    (`#(array ,len ,t) (sizeof-array  len t v))\n    (`#(list  ,len ,t) (sizeof-list   len t v))\n    (`#(tuple ,@ts)    (sizeof-tuple  ts    v))\n    (`(,ta . ,td)      (sizeof-pair   ta td v))\n    ('nat              (sizeof-nat    #f    v))\n    ('string           (sizeof-string #f    v))\n    ('symbol           (sizeof-symbol #f    v))\n    ('bytes            (sizeof-bytes  #f    v))\n    ('array            (sizeof-array  #f #f v))\n    ('list             (sizeof-list   #f #f v))\n    ('number           (sizeof-number       v))\n    ((or 'true 'false '()) 0)))\n(define (sizeof-any v)\n  (define value-size\n    (cond ((vector?       v) (sizeof-array  #f #f v))\n          ((string?       v) (sizeof-string #f    v))\n          ((bytes?        v) (sizeof-bytes  #f    v))\n          ((pair?         v) (sizeof-pair   #f #f v))\n          ((exact-number? v) (sizeof-number       v))\n          ((symbol?       v) (sizeof-symbol #f    v))\n          ((or (null? v) (eqv? #t v) (not v))      0)\n          ((void? v)                              #f)\n          (else (error \"sizeof-any; invalid type:\" v))))\n  (and value-size (+ 1 value-size)))\n(define (sizeof-nat size n)\n  (cond (size      size)\n        ((void? n) #f)\n        (else (+ 1 (cond ((< n (<< 1 32)) (if (< n (<< 1 16))\n                                            (if (< n (<< 1 8))  1 2)\n                                            (if (< n (<< 1 24)) 3 4)))\n                         ((< n (<< 1 40)) 5)\n                         ((< n (<< 1 48)) 6)\n                         ((< n (<< 1 56)) 7)\n                         ((< n (<< 1 64)) 8)\n                         (else (error \"sizeof-nat; too large:\" n)))))))\n;; TODO: consider exponent representations, which may be more compact\n(define (sizeof-number v)   (sizeof-string #f (if (void? v) v\n                                                (number->string v))))\n(define (sizeof-bytes l v)  (or l (and (not (void? v))\n                                       (let ((len (bytes-length v)))\n                                         (+ len (sizeof-nat #f len))))))\n(define (sizeof-symbol l v) (or l (sizeof-string l (if (void? v) v\n                                                     (symbol->string v)))))\n(define (sizeof-string l v) (or l (sizeof-bytes l (if (void? v) v\n                                                    (string->bytes/utf-8 v)))))\n(define (sizeof-pair ta td v) (let ((za (sizeof ta (if (void? v) v (car v))))\n                                    (zd (sizeof td (if (void? v) v (cdr v)))))\n                                (and za zd (+ za zd))))\n(define (sizeof-tuple ts v) (sizeof ts (if (void? v) v (vector->list v))))\n(define (sizeof-list l t v)\n  (if l (sizeof-tuple (make-list l t) v)\n    (and (not (void? v)) (let* ((l (length v))\n                                (z (sizeof-list l t v)))\n                           (and z (+ (sizeof-nat #f l) z))))))\n(define (sizeof-array l t v)\n  (if l (sizeof-tuple (make-list l t) v)\n    (and (not (void? v)) (let ((z (sizeof-array (vector-length v) t v)))\n                           (and z (+ (sizeof-nat #f (vector-length v)) z))))))\n\n(define (encode out type v)\n  (match type\n    (#f                (encode-any    out       v))\n    (`#(nat    ,size)  (encode-nat    out size  v))\n    (`#(string ,len)   (encode-string out len   v))\n    (`#(symbol ,len)   (encode-symbol out len   v))\n    (`#(bytes  ,len)   (encode-bytes  out len   v))\n    (`#(array ,len ,t) (encode-array  out len t v))\n    (`#(list  ,len ,t) (encode-list   out len t v))\n    (`#(tuple ,@ts)    (encode-tuple  out ts    v))\n    (`(,ta . ,td)      (encode-pair   out ta td v))\n    ('nat              (encode-nat    out #f    v))\n    ('int              (encode-int    out       v))\n    ('string           (encode-string out #f    v))\n    ('symbol           (encode-symbol out #f    v))\n    ('bytes            (encode-bytes  out #f    v))\n    ('array            (encode-array  out #f #f v))\n    ('list             (encode-list   out #f #f v))\n    ('number           (encode-number out       v))\n    ((or 'true 'false '()) 0)))\n(define (encode-any out v)\n  (define (tag t) (encode-nat out 1 t))\n  (cond ((vector? v)       (tag t.array)  (encode-array  out #f #f v))\n        ((string? v)       (tag t.string) (encode-string out #f    v))\n        ((bytes?  v)       (tag t.bytes)  (encode-bytes  out #f    v))\n        ((pair?   v)       (tag t.pair)   (encode-pair   out #f #f v))\n        ((exact-number? v) (tag t.number) (encode-number out       v))\n        ((symbol? v)       (tag t.symbol) (encode-symbol out #f    v))\n        ((null?   v)       (tag t.null))\n        ((eqv? #t v)       (tag t.true))\n        ((not     v)       (tag t.false))\n        (else (error \"encode-any; invalid type:\" v))))\n(define (encode-nat out size n)\n  (define (enc/size sz) (unless (= sz 0)\n                          (write-byte (& #xFF (>> n (* 8 (- sz 1)))) out)\n                          (enc/size (- sz 1))))\n  (define (enc sz) (encode-nat out 1 sz) (enc/size sz))\n  (cond (size (enc/size size))\n        ((< n (<< 1 32)) (if (< n (<< 1 16))\n                           (if (< n (<< 1 8))  (enc 1) (enc 2))\n                           (if (< n (<< 1 24)) (enc 3) (enc 4))))\n        ((< n (<< 1 40)) (enc 5))\n        ((< n (<< 1 48)) (enc 6))\n        ((< n (<< 1 56)) (enc 7))\n        ((< n (<< 1 64)) (enc 8))\n        (else (error \"encode-nat; too large:\" n))))\n(define (encode-int out v)\n  (encode-nat out #f (+ (<< v 1) (if (< v 0) 1 0))))\n;; TODO: consider exponent representations, which may be more compact\n(define (encode-number out n) (encode-string out #f (number->string n)))\n(define (encode-bytes out len bs)\n  (unless len (encode-nat out #f (bytes-length bs)))\n  (write-bytes bs out))\n(define (encode-symbol out len s) (encode-string out len (symbol->string s)))\n(define (encode-string out len s)\n  (encode-bytes out len (string->bytes/utf-8 s)))\n(define (encode-pair   out ta td v)\n  (encode out ta (car v)) (encode out td (cdr v)))\n(define (encode-tuple out ts v) (for ((t (in-list ts)) (v (in-vector v)))\n                                     (encode out t v)))\n(define (encode-list out l t v)\n  (unless l (encode-nat out #f (length v)))\n  (for ((v (in-list v))) (encode out t v)))\n(define (encode-array out l t v)\n  (unless l (encode-nat out #f (vector-length v)))\n  (for ((v (in-vector v))) (encode out t v)))\n\n(define (decode in type)\n  (match type\n    (#f                (decode-any    in))\n    (`#(nat    ,size)  (decode-nat    in size))\n    (`#(string ,len)   (decode-string in len))\n    (`#(symbol ,len)   (decode-symbol in len))\n    (`#(bytes  ,len)   (decode-bytes  in len))\n    (`#(array ,len ,t) (decode-array  in len t))\n    (`#(list  ,len ,t) (decode-list   in len t))\n    (`#(tuple ,@ts)    (decode-tuple  in ts))\n    (`(,ta . ,td)      (decode-pair   in ta td))\n    ('nat              (decode-nat    in #f))\n    ('int              (decode-int    in))\n    ('string           (decode-string in #f))\n    ('symbol           (decode-symbol in #f))\n    ('bytes            (decode-bytes  in #f))\n    ('array            (decode-array  in #f #f))\n    ('list             (decode-list   in #f #f))\n    ('number           (decode-number in))\n    ('true             #t)\n    ('false            #f)\n    ('()               '())))\n(define (decode-any in)\n  (define tag (decode-nat in 1))\n  (define (? t) (= tag t))\n  (cond ((? t.array)  (decode-array  in #f #f))\n        ((? t.string) (decode-string in #f))\n        ((? t.bytes)  (decode-bytes  in #f))\n        ((? t.pair)   (decode-pair   in #f #f))\n        ((? t.number) (decode-number in))\n        ((? t.symbol) (decode-symbol in #f))\n        ((? t.null)   '())\n        ((? t.true)   #t)\n        ((? t.false)  #f)\n        (else (error \"decode-any; invalid tag:\" tag))))\n(define (decode-nat in size)\n  (if size (let loop ((n 0) (sz size))\n             (if (= sz 0) n\n               (loop (+ (<< n 8) (read-byte in)) (- sz 1))))\n    (let ((size (decode-nat in 1))) (decode-nat in size))))\n(define (decode-int in)\n  (define nat (decode-nat in #f))\n  (* (if (odd? nat) -1 1) (>> nat 1)))\n;; TODO: consider exponent representations, which may be more compact\n(define (decode-number in)      (string->number (decode-string in #f)))\n(define (decode-bytes in l)     (if l (read-bytes l in)\n                                  (decode-bytes in (decode-nat in #f))))\n(define (decode-symbol in l)    (string->symbol (decode-string in l)))\n(define (decode-string in l)    (bytes->string/utf-8 (decode-bytes in l)))\n(define (decode-pair  in ta td) (cons (decode in ta) (decode in td)))\n(define (decode-tuple in ts)    (list->vector (decode in ts)))\n(define (decode-list  in l t)   (if l (decode in (make-list l t))\n                                  (decode-list in (decode-nat in #f) t)))\n(define (decode-array in l t)   (if l (decode-tuple in (make-list l t))\n                                  (decode-array in (decode-nat in #f) t)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/common.rkt",
    "content": "#lang racket/base\n(provide symbolo numbero stringo byteso pairo vectoro booleano integero\n         not-symbolo not-numbero not-stringo not-byteso\n         not-pairo not-vectoro not-booleano not-integero\n         vector==listo bytes==listo <=o vector        (dbk:quasiquote/level level (q ...))))\n    ((_ level   quasiquote)                   (raise-syntax-error #f \"misplaced quasiquote\"       stx))\n    ((_ level   unquote)                      (raise-syntax-error #f \"misplaced unquote\"          stx))\n    ((_ level   unquote-splicing)             (raise-syntax-error #f \"misplaced unquote-splicing\" stx))\n    ((_ level   q)                            #'(dbk:term (quote q)))))\n\n(define-syntax-rule (dbk:quasiquote q) (dbk:quasiquote/level () q))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/concrete-syntax.rkt",
    "content": "#lang racket/base\n(provide\n  fresh-name with-fresh-names ??\n  (for-syntax current-vocabulary)\n  with-no-vocabulary with-formula-vocabulary with-term-vocabulary\n  conj disj imply iff ~ all exist fresh conde query== query\n  == =/= any<= any< flooro +o *o\n  vector-lengtho vector-refo bytes-lengtho bytes-refo symbol==stringo string==utf8-byteso\n  dbk:term dbk:app dbk:apply dbk:cons dbk:list->vector dbk:append dbk:not\n  dbk:map/merge dbk:map/append dbk:map dbk:filter dbk:filter-not\n  dbk:begin dbk:let dbk:let* dbk:lambda dbk:if dbk:when dbk:unless dbk:cond dbk:and dbk:or\n  apply-relation\n  relation-kind relation-arity relation-properties relation-properties-set!\n  relation-method relation-dirty! relation-clean!\n  define-relation define-relation/table define-relation/input\n  define-relations)\n(require \"abstract-syntax.rkt\" \"misc.rkt\" \"stream.rkt\"\n         (for-syntax racket/base) racket/list racket/struct racket/stxparam)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Names\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; TODO: this might belong in abstract-syntax.rkt\n\n(define fresh-name-count (make-parameter #f))\n\n(define (call-with-fresh-names thunk)\n  (if (fresh-name-count)\n    (thunk)\n    (parameterize ((fresh-name-count 0))\n      (thunk))))\n\n(define-syntax-rule (with-fresh-names body ...)\n  (call-with-fresh-names (lambda () body ...)))\n\n(define (fresh-name name)\n  (define uid.next (fresh-name-count))\n  (unless uid.next (error \"fresh name not available:\" name))\n  (fresh-name-count (+ uid.next 1))\n  (cons uid.next (if (pair? name) (cdr name) name)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Anonymous variables\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define anonymous-vars (make-parameter #f))\n\n(define (anonymous-var (sym '_))\n  (unless (anonymous-vars) (error \"misplaced anonymous variable\"))\n  (define name (fresh-name sym))\n  (anonymous-vars (cons name (anonymous-vars)))\n  (t:var name))\n\n(define-syntax formula/anonymous-vars\n  (syntax-rules ()\n    ((_ body ...) (parameterize ((anonymous-vars '()))\n                    (define f (let () body ...))\n                    (if (null? (anonymous-vars))\n                      f\n                      (f:exist (anonymous-vars) f))))))\n\n(define-syntax (?? stx)\n  (syntax-case stx ()\n    ((_ . args) (raise-syntax-error #f \"cannot apply anonymous variable\" stx))\n    (_          #'(anonymous-var '??))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Vocabularies\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-syntax-parameter stxparam.vocabulary #f)\n(begin-for-syntax (define-syntax-rule (current-vocabulary)\n                    (syntax-parameter-value #'stxparam.vocabulary)))\n\n(define-syntax-rule (with-no-vocabulary      body ...) (syntax-parameterize ((stxparam.vocabulary #f))       body ...))\n(define-syntax-rule (with-formula-vocabulary body ...) (syntax-parameterize ((stxparam.vocabulary 'formula)) body ...))\n(define-syntax-rule (with-term-vocabulary    body ...) (syntax-parameterize ((stxparam.vocabulary 'term))    body ...))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Relations\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (relation-apply r . args)\n  (define l.args  (length args))\n  (define l.extra (- (relation-arity r) (- l.args 1)))\n  (when (= l.args 0)\n    (error \"relation-apply requires at least one argument besides the relation:\" r args))\n  (when (< l.extra 0)\n    (error \"relation-apply number of arguments exceeds relation arity:\" r args))\n  (define rargs      (reverse args))\n  (define arg.last   (car rargs))\n  (define rargs.init (cdr rargs))\n  (define attrs      (hash-ref (relation-properties r) 'attributes (range (relation-arity r))))\n  (define names      (s-drop (- l.args 1) attrs))\n  (formula/anonymous-vars\n    (let* ((vars.last (map (lambda (n) (anonymous-var (vector 'apply n))) names))\n           (args.new  (foldl cons vars.last rargs.init)))\n      (conj (== arg.last vars.last)\n            (apply r args.new)))))\n\n(define (relation-kind            r)     (if (relation? r)\n                                           ((relation-method r) 'kind)\n                                           `(primitive ,r)))\n(define (relation-arity           r)     ((relation-method r) 'arity))\n(define (relation-properties      r)     ((relation-method r) 'properties))\n(define (relation-properties-set! r k v) ((relation-method r) 'properties-set! k v))\n(define (relation-dirty!          r)     ((relation-method r) 'dirty!))\n(define (relation-clean!          r)     ((relation-method r) 'clean!))\n\n;; TODO: maybe normalize definitions (axioms) to clausal form first, for stronger assumptions when analyzing safety\n\n;; TODO: Datalog safety check\n;; Due to mutual recursion, this will have to be run across multiple relations simultaneously, not individually.\n;(define (relation-finite? r)\n  ;(or (not (eq? 'rule (relation-kind r)))\n      ;(match-let (((f:all (f:imply f.body (f:relate _ vars.head))) ((relation-method r) 'formula)))\n        ;;; TODO:\n        ;;; all vars.head must be mentioned at least once in a positive position\n        ;;; all dependency relations must be finite (or the particular call to its args must be total)\n        ;;; all relations mentioned in subqueries must be stratified\n        ;;; all terms in recursive calls or assigned to head vars are non-function literals\n        ;;;   head vars can be function terms if this relation isn't recursive\n        ;(let loop ((f f.body) (fs.pending '()) (vars.pending (list->set vars.head)))\n          ;(match f\n            ;((f:relate r.f args.f)\n             ;;; TODO: also try totality checking\n             ;;; TODO: recognize mutual recursion\n             ;;; TODO: primitives need special handling\n             ;(and (relation-finite? r.f)\n                  ;;; TODO: what about compound/function literals?  these can violate safety\n                  ;;; TODO: look for subqueries and verify stratification\n                  ;(continue (set-subtract vars.pending (t-free-vars-positive* args.f)))))\n            ;((f:or f.1 f.2)\n             ;;; TODO: instead, reorganize finiteness checking to avoid redundant work\n             ;;; instead, we could determine what head vars are positively referenced in each of f.1 and f.2\n             ;;; taking their intersection, and subtracting that from the total\n             ;;; and if either fails to be finite locally, it can return #f to signal combined failure\n             ;(and (loop f.1 fs.pending vars.pending)\n                  ;(loop f.2 fs.pending vars.pending)))\n            ;((f:and f.1 f.2) (loop f.1 (cons f.2 fs.pending) vars.pending))\n            ;((f:not f)\n             ;;; TODO: negative polarity\n\n             ;)\n            ;((f:exist params.f body.f)\n             ;;; TODO: shadow? or is this not necessary?\n             ;(loop body.f fs.pending vars.pending))\n            ;(_ (error \"TODO: finiteness check for unhandled formula type:\" f)))))))\n\n;; TODO: should also return info about any change in arg groundness after this relation runs?\n;(define (relate-total? relation args)\n  ;)\n\n(struct relation (method)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (r) 'relation)\n             (lambda (r) (list (cons 'kind  (relation-kind       r))\n                               (cons 'arity (relation-arity      r))\n                               (relation-properties r))))))\n        #:property prop:procedure\n        (lambda (r . args)\n          (unless (= (relation-arity r) (length args))\n            (error \"relation called with invalid number of arguments\" args r))\n          (f:relate r (map scm->term args))))\n\n(define (make-relation kind arity parent->self)\n  (define properties (hash))\n  (relation\n    (parent->self\n      (method-lambda\n        ((kind)                   kind)\n        ((arity)                  arity)\n        ((properties)             properties)\n        ((properties-set!    k v) (when (eq? k 'attributes)\n                                    (unless (and (list? v) (= arity (length v)))\n                                      (error \"invalid number of attributes for arity:\" arity v)))\n                                  (set! properties (hash-set    properties k v)))\n        ((properties-remove! k)   (set! properties (hash-remove properties k)))\n        ((dirty!)                 (void))\n        ((clean!)                 (void))))))\n\n(define (relation/primitive arity name)\n  (make-relation\n    `(primitive ,name) arity\n    (lambda (parent) parent)))\n\n(define (relation/rule arity rule)\n  (define r\n    (make-relation\n      'rule arity\n      (lambda (parent)\n        (method-lambda\n          ((apply . args) (define len (length args))\n                          (unless (= len arity) (error \"invalid number of arguments:\" arity args))\n                          (apply rule args))\n          ((formula)      (define attrs  (hash-ref (relation-properties r) 'attributes (range arity)))\n                          (define params (map fresh-name attrs))\n                          (define vars   (map t:var      params))\n                          (f:all params (f:imply (apply rule vars) (apply r vars))))\n          (else           parent)))))\n  r)\n\n(define (relation/table arity path)\n  ;; TODO: if path is #f, use temporary storage\n  (make-relation\n    'table arity\n    (lambda (parent)\n      (method-lambda\n        ;; TODO:\n        ;; Define instantiation of table controllers that manage their own column constraints.\n        ;; A single query might instantiate multiple controllers for the same table, each with\n        ;; a different set of constraints/bounds.\n        ;; Controller interface provides:\n        ;; - retrieval of statistics:\n        ;;   - total tuple count\n        ;;   - per-column cardinality\n        ;;   - per-column bounds\n        ;; - update of per-column bounds\n        ;; - index descriptions\n\n        ;; TODO:\n        ;; Define an interface for updating table content.\n        ;; Maintain a log of insertions and deletions.\n        ;; Possibly support log subscriptions to allow other processes to observe changes.\n        ((path) path)\n        (else   parent)))))\n\n(define (relation/input arity produce)\n  (make-relation\n    'input arity\n    (lambda (parent)\n      (method-lambda\n        ((produce) (s-enumerate 0 (produce)))\n        (else      parent)))))\n\n(define-syntax apply-relation\n  (syntax-rules ()\n    ((_ r . args) (formula/anonymous-vars (with-term-vocabulary (relation-apply r . args))))))\n\n(define-syntax (define-relations stx)\n  (syntax-case stx ()\n    ((_ (kind (name.r param ...) body ...) ...)\n     (with-syntax (((r ...) (generate-temporaries #'(name.r ...))))\n       #'(begin (define-syntax (name.r stx)\n                  (syntax-case stx ()\n                    ((_ . args) #'(formula/anonymous-vars (with-term-vocabulary (r . args))))\n                    (_          #'r))) ...\n                (define-values (r ...)\n                  (values (defined-relation-value (kind (name.r param ...) body ...)) ...))\n                (begin (relation-properties-set! r 'name       'name.r)\n                       (relation-properties-set! r 'attributes '(param ...))) ...)))))\n\n(define-syntax defined-relation-value\n  (syntax-rules (primitive rule table input)\n    ((_ (rule      (name param ...) f ...))    (let ((r (relation/rule (length '(param ...))\n                                                                       (lambda (param ...)\n                                                                         (with-formula-vocabulary\n                                                                           (conj f ...))))))\n                                                 (relation-properties-set! r 'rule '((name param ...) :- f ...))\n                                                 r))\n    ((_ (table     (name param ...) body ...)) (relation/table     (length '(param ...)) body ...))\n    ((_ (input     (name param ...) body ...)) (relation/input     (length '(param ...)) body ...))\n    ((_ (primitive (name param ...)))          (relation/primitive (length '(param ...)) 'name))))\n\n(define-syntax-rule (define-relation           body ...) (define-relations (rule      body ...)))\n(define-syntax-rule (define-relation/table     body ...) (define-relations (table     body ...)))\n(define-syntax-rule (define-relation/input     body ...) (define-relations (input     body ...)))\n(define-syntax-rule (define-relation/primitive body ...) (define-relations (primitive body ...)))\n\n(define-syntax-rule (define-primitive-relations signature ...) (begin (define-relation/primitive signature) ...))\n\n(define-primitive-relations\n  (==                  t1 t2)\n  (=/=                 t1 t2)\n  (any<=               t1 t2)\n  (any<                t1 t2)\n  (flooro              t1 t2)\n  (+o                  t1 t2 t3)\n  (*o                  t1 t2 t3)\n  (vector-lengtho      t  l)\n  (vector-refo         t  i  x)\n  (bytes-lengtho       t  l)\n  (bytes-refo          t  i  x)\n  (symbol==stringo     t1 t2)\n  (string==utf8-byteso t1 t2))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Basic syntax for formulas and terms\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-syntax conj*\n  (syntax-rules ()\n    ((_)          f:true)\n    ((_ f)        f)\n    ((_ fs ... f) (f:and (conj* fs ...) f))))\n\n(define-syntax disj*\n  (syntax-rules ()\n    ((_)          f:false)\n    ((_ f)        f)\n    ((_ f fs ...) (f:or f (disj* fs ...)))))\n\n(define-syntax-rule (conj   fs ...)    (with-formula-vocabulary (conj*   fs ...)))\n(define-syntax-rule (disj   fs ...)    (with-formula-vocabulary (disj*   fs ...)))\n(define-syntax-rule (imply  f.h f.c)   (with-formula-vocabulary (f:imply f.h f.c)))\n(define-syntax-rule (iff    f.0 f ...) (with-formula-vocabulary (and (f:iff f.0 f) ...)))\n(define-syntax-rule (~      f)         (with-formula-vocabulary (f:not   f)))\n\n(define-syntax-rule (define-quantifier-syntax name f:quantifier)\n  (... (define-syntax (name stx)\n         (syntax-case stx ()\n           ((_ (x ...) body ...)\n            (with-syntax (((name.x ...) (generate-temporaries #'(x ...))))\n              #'(let ((name.x (fresh-name 'x)) ...)\n                  (let ((x (t:var name.x)) ...)\n                    (f:quantifier (list name.x ...) (conj body ...))))))))))\n\n(define-quantifier-syntax exist f:exist)\n(define-quantifier-syntax all   f:all)\n\n(define-syntax-rule (fresh (x ...) body ...) (exist (x ...) body ...))\n\n(define-syntax-rule (conde (f.0 fs.0 ...)\n                           (f   fs   ...) ...)\n  (disj (conj f.0 fs.0 ...)\n        (conj f   fs   ...) ...))\n\n(define-syntax query==\n  (syntax-rules ()\n    ((_ result (x ...) body ...) (query== result x.0 (exist (x ...)\n                                                       (== x.0 (list x ...))\n                                                       body ...)))\n    ((_ result x       body ...) (let* ((name.x (fresh-name 'q))\n                                        (x      (t:var      name.x)))\n                                   (f:query result name.x (conj body ...))))))\n\n;; TODO: can we auto-lift these terms via anonymous vars?\n(define-syntax query\n  (syntax-rules ()\n    ((_ (x ...) body ...) (query x.0 (exist (x ...)\n                                       (== x.0 (list x ...))\n                                       body ...)))\n    ((_ x       body ...) (with-fresh-names\n                            (let* ((name.x (fresh-name 'q))\n                                   (x      (t:var      name.x)))\n                              (t:query name.x (conj body ...)))))))\n\n(define (dbk:term         x)        (scm->term x))\n(define (dbk:app          p . args) (t:app (scm->term p) (map scm->term args)))\n(define (dbk:prim-app     p . args) (t:app (t:prim    p) (map scm->term args)))\n(define (dbk:cons         a d)      (dbk:prim-app 'cons         a d))\n(define (dbk:list->vector xs)       (dbk:prim-app 'list->vector xs))\n\n(define-syntax (dbk:apply stx)\n  (syntax-case stx ()\n    ((_ . args) #'(dbk:prim-app 'apply . args))\n    (_          #'(t:prim 'apply))))\n\n(define-syntax-rule (define-lambda (name . params) body)\n  (define-syntax (name stx)\n    (syntax-case stx ()\n      ((_ . args) #'(dbk:app (dbk:lambda params body) . args))\n      (_          #'(dbk:lambda params body)))))\n\n(define-lambda (dbk:not        x)                  (dbk:if x #f #t))\n(define-lambda (dbk:append     xs ys)              (dbk:prim-app   'append    xs ys))\n(define-lambda (dbk:map/merge  f merge default xs) (dbk:prim-app   'map/merge f merge default xs))\n(define-lambda (dbk:map/append f               xs) (dbk:map/merge  f (dbk:lambda (a b) (dbk:append a b)) '()            xs))\n(define-lambda (dbk:map        f               xs) (dbk:map/append (dbk:lambda (x) (list (dbk:app f x)))                xs))\n(define-lambda (dbk:filter     p               xs) (dbk:map/append (dbk:lambda (x) (dbk:if (dbk:app p x) (list x) '())) xs))\n(define-lambda (dbk:filter-not p               xs) (dbk:filter     (dbk:lambda (x) (dbk:not (dbk:app p x)))             xs))\n\n(define-syntax dbk:begin\n  (syntax-rules ()\n    ((_)          (dbk:term (void)))\n    ((_ e)        (dbk:term e))\n    ((_ e es ...) (dbk:let ((temp.begin (dbk:term e))) es ...))))\n\n(define-syntax dbk:let\n  (syntax-rules ()\n    ((_ ((x e) ...) body ...) (let ((name.x (fresh-name 'x)) ...)\n                                (let ((x (t:var name.x)) ...)\n                                  (with-term-vocabulary\n                                    (t:let (list (cons name.x (dbk:term e)) ...)\n                                           (dbk:begin body ...))))))))\n\n(define-syntax dbk:let*\n  (syntax-rules ()\n    ((_ ()                  body ...) (dbk:let ()                              body ...))\n    ((_ ((x e) (xs es) ...) body ...) (dbk:let ((x e)) (dbk:let* ((xs es) ...) body ...)))))\n\n(define-syntax (dbk:lambda stx)\n  (syntax-case stx ()\n    ((_ (x ...)     body ...)\n     (with-syntax (((name.x ...) (generate-temporaries #'(x ...))))\n       #'(let ((name.x (fresh-name 'x)) ...)\n           (let ((x (t:var name.x)) ...)\n             (with-term-vocabulary\n               (t:lambda (list  name.x ...)        (dbk:begin body ...)))))))\n    ((_ (x ... . y) body ...)\n     (with-syntax (((name.x ...) (generate-temporaries #'(x ...))))\n       #'(let ((name.y (fresh-name 'y)) (name.x (fresh-name 'x)) ...)\n           (let ((x (t:var name.x)) ...)\n             (with-term-vocabulary\n               (t:lambda (list* name.x ... name.y) (dbk:begin body ...)))))))))\n\n(define-syntax-rule (dbk:if     c t f)      (t:if (dbk:term c) (dbk:term t) (dbk:term f)))\n(define-syntax-rule (dbk:when   c body ...) (dbk:if c (dbk:begin body ...) (dbk:term (void))))\n(define-syntax-rule (dbk:unless c body ...) (dbk:if c (dbk:term (void))    (dbk:begin body ...)))\n\n(define-syntax (dbk:cond stx)\n  (syntax-case stx (else =>)\n    ((_)                      #'(dbk:term (void)))\n    ((_ (else e ...))         #'(dbk:begin e ...))\n    ((_ (else e ...) etc ...) (raise-syntax-error #f \"misplaced else\" stx))\n    ((_ (c => p) cs ...)      #'(dbk:let ((x c)) (dbk:if x (dbk:app   p c)   (dbk:cond cs ...))))\n    ((_ (c e ...) cs ...)     #'(                 dbk:if c (dbk:begin e ...) (dbk:cond cs ...)))\n    ((_ c cs ...)             #'(dbk:let ((x c)) (dbk:if x x                 (dbk:cond cs ...))))))\n\n(define-syntax dbk:and\n  (syntax-rules ()\n    ((_)          (dbk:term #t))\n    ((_ e)        (dbk:term e))\n    ((_ e es ...) (dbk:if e (dbk:and es ...) (dbk:term #f)))))\n\n(define-syntax dbk:or\n  (syntax-rules ()\n    ((_)          (dbk:term #f))\n    ((_ e)        (dbk:term e))\n    ((_ e es ...) (dbk:let ((temp.or e)) (dbk:if temp.or temp.or (dbk:or es ...))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/config.rkt",
    "content": "#lang racket/base\n(provide current-config config.default file->config current-config-ref\n         current-config-set current-config-set/alist\n         current-config-set! current-config-set!/alist\n         current-config-relation-path config-ref config-set config-set/alist\n         policy-allow? logf logf/date)\n(require racket/date racket/string)\n\n(define config.default\n  (make-immutable-hash\n    '((relation-root-path         . #f) ;; root path for materialized relations\n      (temporary-root-path        . #f) ;; root path for temporary caches\n      (buffer-size                . 100000)\n      (progress-logging-threshold . 100000) ;; number of rows per log message\n      ;; interactive, always, never\n      (update-policy              . interactive) ;; rebuild stale tables\n      (cleanup-policy             . interactive) ;; remove unspecified indexes\n      (migrate-policy             . interactive) ;; migrate to new data format\n      (allow-missing-data-policy  . interactive) ;; ignore missing data\n      ;; biased-interleaving (default), depth-first\n      (search-strategy            . #f))))\n\n(define (valid-config?! cfg)\n  (define (valid-policy? policy) (member policy '(always never interactive)))\n  (define (valid-path?   p)      (or (not p) (string? p) (path? p)))\n  (define-syntax validate!\n    (syntax-rules ()\n      ((_ (test ... key) ...)\n       (begin (unless (test ... (hash-ref cfg 'key))\n                (error \"invalid config:\" 'key (hash-ref cfg 'key))) ...))))\n  (validate! (valid-path?   relation-root-path)\n             (valid-path?   temporary-root-path)\n             (< 0           buffer-size)\n             (< 0           progress-logging-threshold)\n             (valid-policy? update-policy)\n             (valid-policy? cleanup-policy)\n             (valid-policy? migrate-policy))\n  cfg)\n\n(define (config-ref cfg key)       (hash-ref cfg key))\n(define (config-set cfg key value) (valid-config?! (hash-set cfg key value)))\n(define (config-set/alist cfg kvs)\n  (valid-config?! (foldl (lambda (kv cfg) (hash-set cfg (car kv) (cdr kv)))\n                         cfg kvs)))\n(define (file->config path)\n  (config-set/alist config.default (with-input-from-file path read)))\n\n(define current-config (make-parameter config.default))\n(define (current-config-ref key)       (config-ref (current-config) key))\n(define (current-config-set key value) (config-set (current-config) key value))\n(define (current-config-set/alist kvs) (config-set/alist (current-config) kvs))\n(define (current-config-set! key value)\n  (current-config (current-config-set key value)))\n(define (current-config-set!/alist kvs)\n  (current-config (current-config-set/alist kvs)))\n(define (current-config-relation-path path)\n  (cond ((and (string? path) (string-prefix? path \"/\")) path)\n        (else (define relation-root-path\n                (current-config-ref 'relation-root-path))\n              (if relation-root-path\n                (path->string (build-path relation-root-path path))\n                path))))\n\n(define (policy-allow? policy describe prompt-message prompt-args)\n  (case policy\n    ((interactive)\n     (describe)\n     (apply printf (string-append prompt-message \" [y/n]: \") prompt-args)\n     (case (read)\n       ((y Y yes Yes YES) #t)\n       (else              #f)))\n    ((always) #t)\n    (else     #f)))\n\n(define (pad2 n) (let ((s (number->string n)))\n                   (if (<= 2 (string-length s)) s\n                     (string-append \"0\" s))))\n\n(define (logf/date message . args)\n  (define msg (string-append \"[~a/~a/~a - ~a:~a:~a] \" message))\n  (define d (current-date))\n  (define stamp (list (date-month d) (date-day d)\n                      (date-hour d) (date-minute d) (date-second d)))\n  (apply eprintf msg (date-year d) (append (map pad2 stamp) args)))\n\n(define (logf message . args)\n  (define msg (string-append \"[~a:~a:~a] \" message))\n  (define d (current-date))\n  (define stamp (list (date-hour d) (date-minute d) (date-second d)))\n  (apply eprintf msg (append (map pad2 stamp) args)))\n\n;; TODO: job system\n;; single worker thread\n;; jobs w/ independent loggers (port, file, in-memory, or null)\n\n;(define (thread/wait proc)\n;  (define t (thread proc))\n;  (plumber-add-flush! (current-plumber)\n;                      (lambda (h) (thread-wait t)))\n;  t)\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/constraint.rkt",
    "content": "#lang racket/base\n(provide bis:query->stream dfs:query->stream\n         relation/table define-relation/table)\n(require \"misc.rkt\" \"order.rkt\" \"stream.rkt\" \"syntax.rkt\" \"table.rkt\"\n         (except-in racket/match ==)\n         racket/function racket/list racket/set racket/vector)\n\n#| ;; Definitions for performance diagnostics\n(require racket/pretty)\n(define (pretty-var-bindings vbs)\n  (map (lambda (vb) (cons (var-name (car vb)) (cdr vb))) vbs))\n(define (state-var-bindings st)\n  (pretty-var-bindings\n    (filter (lambda (kv) (not (vcx? (cdr kv)))) (hash->list (state-var=>cx st)))))\n;|#\n\n;; TODO:\n;; extra solvers, beyond bounds checking/limiting for domains and arcs:\n;;   +o, *o:\n;;     for generality, could use a substitute and simplify model\n;;       if a + b = c, then replace c whenever it appears\n;;       still need some functional dependencies (only forward?)\n;;          e.g., a + b = c and a + b = d implies c = d\n;;          also true that a + b = c and a + d = c implies b = d\n;;          however, substituting for c and simplifying covers this:\n;;            a + b = a + d, and simplifying shows b = d\n;;          similar for *o, but case split with 0\n;;     in special cases, can do linear programming\n;;       incremental simplex\n;;       keep in mind: flooro, X-lengtho, X-refo introduce integer constraints\n;;     in other cases: difference equations, polynomials...\n;;     calculus for optimization\n;;     etc.\n;;   (uninterpreted) functional dependencies:\n;;     == propagation forward\n;;       e.g., if (f a b = c) and (f a b = d) then (== c d)\n;;     =/= propagation in reverse\n;;       e.g., if (f a b = c) and (f a d = e) and (c =/= e) then (b =/= d)\n;;         note: this is not a bi-implication unless the function is one-to-one\n;;         (expresssed as two opposing functional dependency constraints)\n;;     also can be used to encode some forms of subsumption checking\n;;   X-refo: maintain minimum length and partial mapping\n;;   string==byteso: look for impossible utf-8 bytes (possibly partial mapping)\n\n;; TODO:\n;; satisfiability loop for a variable constraint graph:\n;;   after propagation quiessence, attempt to divide and conquer\n;;     this is attempted once each time through the satisfiability loop because\n;;       new assignments may lead to disconnection, allowing more decomposition\n;;     decompose into subproblem per subgraph of connected variables\n;;       connection comes from dependency arcs implied by shared constraints\n;;       each subgraph can be satisfied independently\n;;       subgraph solutions can be enumerated and composed\n;;\n;;   for each variable constraint subgraph:\n;;     while there are unresolved variables with possible assignments:\n;;       choose variable with lowest assignment-set cardinality\n;;       choose an assignment for the variable\n;;         may introduce/expand new constraints by stepping into a disj branch\n;;       re-enter satisfiability loop with any new constraints\n;;       if enumerating or loop fails, choose the next assignment\n;;       if no more assignments are available, fail\n;;     once no more unresolved variables, succeed\n;;   compose subgraph solutions\n;;     if any subgraph failed completely, composition also fails\n\n;;; TODO: occurs check for vector-ref\n\n(define (uid:new) (gensym))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Interval bounds for describing a (potentially-infinite) set of terms\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (term-bounds st t.0)\n  (define t (walk st t.0))\n  (cond ((pair? t)\n         (define b.a (term-bounds st (car t)))\n         (define b.d (term-bounds st (cdr t)))\n         (apply bounds\n                (append\n                  (if (bounds-lb-inclusive? b.a)\n                    (list (cons (bounds-lb b.a) (bounds-lb b.d)) (bounds-lb-inclusive? b.d))\n                    (list (cons (bounds-lb b.a) term.max)        #f))\n                  (if (bounds-ub-inclusive? b.a)\n                    (list (cons (bounds-ub b.a) (bounds-ub b.d)) (bounds-ub-inclusive? b.d))\n                    (list (cons (bounds-ub b.a) term.min)        #f)))))\n        ((vector? t)\n         (define b (term-bounds st (vector->list t)))\n         (bounds (list->vector (bounds-lb b)) (bounds-lb-inclusive? b)\n                 (list->vector (bounds-ub b)) (bounds-ub-inclusive? b)))\n        ((var? t) (vcx-bounds (state-vcx-ref st t)))\n        (else     (bounds t #t t #t))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Variable constraints\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(record vcx (bounds simple table disj use) #:transparent)\n(define vcx.empty (vcx (bounds bounds.any)\n                       (simple (seteq)) (table (seteq)) (disj (seteq)) (use (seteq))))\n\n(define (vcx-bounds-set  x b) (vcx:set x (bounds b)))\n(define (vcx-simple-add  x c) (vcx:set x (simple (set-add (vcx-simple x) c))))\n(define (vcx-table-add   x c) (vcx:set x (table  (set-add (vcx-table  x) c))))\n(define (vcx-disj-add    x c) (vcx:set x (disj   (set-add (vcx-disj   x) c))))\n(define (vcx-use-add     x c) (vcx:set x (use    (set-add (vcx-use    x) c))))\n(define (vcx-cx-clear x)      (vcx-bounds-set vcx.empty (vcx-bounds x)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Work queue with recency-based prioritization\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(struct queue (recent high low))\n(define queue.empty (queue (seteq) '() '()))\n(define (queue-empty? q) (set-empty? (queue-recent q)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Partially-satisfied state of a query's constraints\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(record state (qterm vars proc-stack log var=>cx cx pending))\n(define (state:new qterm) (state (qterm qterm) (vars (term-vars qterm)) (proc-stack '()) (log '())\n                                 (var=>cx (hash)) (cx (hash)) (pending queue.empty)))\n\n(define (state-vars-simplify st)\n  (state:set st (vars (term-vars (walk* st (set->list (state-vars st)))))))\n\n(define (state-vcx-ref st x)                          (hash-ref (state-var=>cx st) x vcx.empty))\n(define (state-vcx-set st x t) (state:set st (var=>cx (hash-set (state-var=>cx st) x t))))\n\n(define (state-proc-stack-push st proc-frame)\n  (define proc    (car proc-frame))\n  (define args    (cdr proc-frame))\n  (define parents (state-proc-stack st))\n  (let*/and ((st (c-apply st #f (c:conj (map (lambda (p)\n                                               ;(displayln `(=/= ,args ,(cdr p)))\n\n                                               (c:=/= args (cdr p)))\n                                             (filter (lambda (p) (equal? proc (car p)))\n                                                     parents))))))\n    (state:set st (proc-stack (cons proc-frame parents)))))\n(define (state-proc-stack-pop st) (state:set st (proc-stack (cdr (state-proc-stack st)))))\n\n(define (state-log-add st c)\n  (define log (state-log st))\n  (state:set st (log (and log (cons c log)))))\n\n(define (state-cx-add st vars vcx-add uid? c)\n  (if (null? vars)\n    (state-log-add st c)\n    (let ((uid (or uid? (uid:new))))\n      (foldl (lambda (x st)\n               (state-vcx-set st x (vcx-add (state-vcx-ref st x) uid)))\n             (state:set (state-log-add st c)\n                        (cx (hash-set (state-cx st) uid c)))\n             (set->list vars)))))\n\n(define (state-cx-remove* st uids)\n  (state:set st (cx (foldl (lambda (uid uid=>c) (hash-remove uid=>c uid))\n                           (state-cx st) uids))))\n\n(define (state-cx-update* st uids)\n  (define uid=>c (state-cx st))\n  (define c* (map (lambda (uid) (hash-ref uid=>c uid #f)) uids))\n  (foldl/and (lambda (uid c st) (if c (c-apply st uid c) st))\n             (state-cx-remove* st uids) uids c*))\n\n(define (state-uses-empty?! st)\n  (define uses (filter c:use? (hash-values (state-cx st))))\n  (unless (null? uses)\n    (error \":== dependencies are not ground:\"\n           (map (lambda (u)\n                  (match-define `#s(c:use ,vs ,l ,deps ,r ,desc) u)\n                  (pretty (==/use (walk* st l) (walk* st deps) r desc))\n                  (error \":== dependencies are not ground:\"\n                         (pretty (==/use (walk* st l) (walk* st deps) r desc))))\n                uses))))\n\n(define (state-solve-lte-cycles st)\n  (define cs (map (lambda (c)\n                    (match-define (c:<= lhs rhs) c)\n                    (c:<= (walk* st lhs) (walk* st rhs)))\n                  (filter c:<=? (hash-values (state-cx st)))))\n  ;; Kosaraju's algorithm for simplicity\n  (define a<=b (foldl (lambda (c a<=b)\n                        (match-define (c:<= lhs rhs) c)\n                        (hash-update a<=b lhs (lambda (rhss) (cons rhs rhss)) '()))\n                      (hash) cs))\n  (define b>=a (foldl (lambda (c b>=a)\n                        (match-define (c:<= lhs rhs) c)\n                        (hash-update b>=a rhs (lambda (lhss) (cons lhs lhss)) '()))\n                      (hash) cs))\n  (define (dfs graph pending.0 order.0 source)\n    (cond ((set-member? pending.0 source)\n           (match-define (cons pending order)\n             (foldl (lambda (target p&o)\n                      (match-define (cons p o) p&o)\n                      (dfs graph p o target))\n                    (cons (set-remove pending.0 source) order.0)\n                    (hash-ref graph source)))\n           (cons pending (cons source order)))\n          (else (cons pending.0 order.0))))\n  (define order.<=\n    (let loop ((pending (list->set (hash-keys a<=b))) (order '()))\n      (if (set-empty? pending)\n        order\n        (match-let (((cons pending order) (dfs a<=b pending order (set-first pending))))\n          (loop pending order)))))\n  (define sccs\n    (let loop ((order order.<=) (pending (list->set (hash-keys b>=a))))\n      (if (null? order)\n        '()\n        (match-let (((cons pending scc) (dfs b>=a pending '() (car order))))\n          (define rest (loop (cdr order) pending))\n          (if (null? scc) rest (cons scc rest))))))\n  (foldl/and (lambda (scc st)\n               (define t.0 (car scc))\n               (foldl/and (lambda (t st) (unify st t t.0)) st (cdr scc)))\n             st sccs))\n\n(define (state-schedule-add-var st x)\n  (define (st/q recent high low) (state:set st (pending (queue recent high low))))\n  (match-define (queue recent high low) (state-pending st))\n  (cond ((or (member x high)\n             (member x low))    st)\n        ((set-member? recent x) (st/q          recent            high (cons x low)))\n        (else                   (st/q (set-add recent x) (cons x high)        low))))\n\n(define (state-schedule-run st)\n  (define (update-and-loop st x)\n    (define t (walk st x))\n    (let*/and ((st (if (var? t) (var-update st t) st)))\n      (state-schedule-run st)))\n  (match-define (queue recent high low) (state-pending st))\n  (cond ((not (null? high)) (update-and-loop\n                              (state:set st (pending (queue recent (cdr high)     low)))\n                              (car high)))\n        ((not (null? low))  (define high.new (reverse low))\n                            (update-and-loop\n                              (state:set st (pending (queue recent (cdr high.new) '())))\n                              (car high.new)))\n        (else               (state:set st (pending queue.empty)))))\n\n(define (state-schedule-empty? st) (queue-empty? (state-pending st)))\n\n;; TODO: include a parameter to specify the degree of locality\n(define (state-enforce-local-consistency st)\n  #| ;; Performance diagnostics\n  (pretty-write `(before: term: ,(walk* st (state-qterm st))\n                          vcxs: ,(state-var-bindings st)))\n  ;|#\n  (let*/and ((st (state-schedule-run     st))\n             (st (state-solve-lte-cycles st)))\n    #| ;; Performance diagnostics\n    (pretty-write `(after: term: ,(walk* st (state-qterm st))\n                           vcxs: ,(state-var-bindings st)))\n    ;|#\n    (if (state-schedule-empty? st)\n      st\n      (state-enforce-local-consistency st))))\n\n(define (state-enforce-global-consistency st k.fail k.succeed)\n  ;; TODO: preserve progress made while finding first satisfying state (see factoring TODO below)\n  (let loop ((s (state->satisfied-states st)))\n    (match (s-next s)\n      ((? procedure? s) (thunk (loop s)))\n      ('()              (k.fail))\n      ((cons _ _)       (k.succeed st)))))\n\n;; TODO: factor out table constraint satisfaction to support pre-branch global satisfiability checking\n;;       in cases where we want to split a disjunction before committing to all table constraints\n;;       (taking the first result from a state->satisfied-states stream is not sufficient: we want to\n;;        preserve any state simplification progress made while searching for that first satisfier)\n(define (state->satisfied-states st)\n  (define (dsatisfied-states st?) '()))\n    (define st (state-cx-remove* st.0 (list uid)))\n    (s-append        (k (c-apply st #f          (car cs)))\n                     ;; TODO: negate (car cs) if possible, for better subsumption\n              (thunk (k (c-apply st uid (c:disj (cdr cs)))))))\n  (define (choose-variable st xs.observable xss)\n    (define x=>c&s\n      (foldl (lambda (x=>s x=>c&s)\n               (foldl (lambda (x&s x=>c&s)\n                        (match-define (cons x s) x&s)\n                        (match (hash-ref x=>c&s x #f)\n                          (#f (hash-set x=>c&s x (cons 1 s)))\n                          ((cons count s.0)\n                           (hash-set x=>c&s x (cons (+ count 1)\n                                                    (statistics-intersect s.0 s))))))\n                      x=>c&s (hash->list x=>s)))\n             (hash) xss))\n    ;; TODO: also consider paths provided by available table indexes, maybe via\n    ;; prioritized topological sort of SCCs.\n    (define (xcs count.a count.b)\n                            (and (= count.a count.b)\n                                 (set-member? xs.observable x.a)\n                                 (not (set-member? xs.observable x.b)))))))))\n    (define xcss   (hash->list x=>c&s))\n    (define x.best (car (foldl (lambda (xcs xcs.min) (if (xcsc&s x.best)\n                              ,(vcx-bounds (state-vcx-ref st x.best))\n                              all-choices: ,(pretty-var-bindings xcss)\n                              term: ,(walk* st (state-qterm st))\n                              vcxs: ,(state-var-bindings st)))\n    ;(read-line)\n    ;|#\n\n    (define t (bounds-lb (vcx-bounds (state-vcx-ref st x.best))))\n    (define (k st?) (if st? (state->satisfied-states st?) '()))\n    (s-append        (k (var-assign    st    x.best t))\n              (thunk (k (var-disassign st #f x.best t)))))\n  (match (state-enforce-local-consistency st)\n    (#f '())\n    (st (define cxs (hash->list (state-cx st)))\n        (match (map c:table-t (filter c:table? (map cdr cxs)))\n          ;; If there are no more table constraints, pick a disjunction to split\n          ('() (match (map (lambda (uid&c) (cons (car uid&c) (c:disj-cs (cdr uid&c))))\n                           (filter (lambda (uid&c) (c:disj? (cdr uid&c))) cxs))\n                 ;; If there are no more disjunctions either, we should be done\n                 ('() (list st))\n                 (ds  (define d.min (foldl (lambda (d d.min) (if (dc f)\n  (match f\n    (`#s(conj ,f1 ,f2) (define (f->cs f) (match (f->c f)\n                                           ((c:conj cs) cs)\n                                           (c           (list c))))\n                       (c:conj (append (f->cs f1) (f->cs f2))))\n    (`#s(disj ,f1 ,f2) (define (f->cs f) (match (f->c f)\n                                           ((c:disj cs) cs)\n                                           (c           (list c))))\n                       (c:disj (append (f->cs f1) (f->cs f2))))\n    (`#s(==/use ,lhs ,args ,proc ,desc) (c:use args lhs args proc desc))\n    (`#s(constrain =/=    (,lhs ,rhs))  (c:=/=   lhs rhs))\n    (`#s(constrain ==     (,lhs ,rhs))  (c:==    lhs rhs))\n    (`#s(constrain any<=o (,lhs ,rhs))  (c:<=    lhs rhs))\n    (`#s(constrain ,proc  ,args)        (c:proc  proc args (set)))))\n\n(define (c->f c)\n  (match c\n    ((c:==  l r)                     (==     l r))\n    ((c:=/= l r)                     (=/=    l r))\n    ((c:<=  l r)                     (any<=o l r))\n    ((c:disj cs)                     (apply disj* (map c->f cs)))\n    ((c:conj cs)                     (apply conj* (map c->f cs)))\n    ((c:table t)                     (c->f (t 'constraint)))\n    ((c:proc proc args parents)      (relate proc args))\n    ((c:use vars lhs args proc desc) (==/use lhs args proc desc))))\n\n(define (c-success? c) (and (c:conj? c) (null? (c:conj-cs c))))\n\n(define (c-simplify st.0 effort? c)\n  (let*/and ((st (c-apply (state:set st.0 (log '()) (cx (hash)))\n                          #f c))\n             (st (if effort?\n                   (let*/and ((st (foldl/and (lambda (u&c st)\n                                               (match-define (cons uid? c) u&c)\n                                               (c-apply st uid? c))\n                                             st (hash->list (state-cx st.0)))))\n                     (state-enforce-local-consistency st))\n                   st)))\n    (let ((log (state-log st)))\n      (if (and (pair? log) (null? (cdr log)))\n        (car log)\n        (c:conj log)))))\n\n(define (c-apply st uid? c)\n  (match c\n    ((c:==  l r)                     (unify        st      l r))\n    ((c:=/= l r)                     (disunify     st uid? l r))\n    ((c:<=  l r)                     (ltunify      st uid? l r))\n    ((c:disj cs)                     (disjoin      st uid? cs))\n    ((c:conj cs)                     (conjoin      st      cs))\n    ((c:table t)                     (table-update st uid? t))\n    ((c:proc proc args parents)      (proc-apply   st uid? proc args parents))\n    ((c:use vars lhs args proc desc) (use          st uid? vars lhs args proc desc))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Constraint operations\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (unify st t1 t2)\n  (let ((t1 (walk st t1)) (t2 (walk st t2)))\n    (cond ((eqv? t1 t2) st)\n          ((var?    t1) (var-assign st t1 t2))\n          ((var?    t2) (var-assign st t2 t1))\n          ((pair?   t1) (and (pair? t2)\n                             (let ((st (unify st (car t1) (car t2))))\n                               (and st (unify st (cdr t1) (cdr t2))))))\n          ((vector? t1) (and (vector? t2) (= (vector-length t1)\n                                             (vector-length t2))\n                             (unify st (vector->list t1) (vector->list t2))))\n          ((equal? t1 t2) st)\n          (else           #f))))\n\n(define (disunify st uid? t1 t2)\n  (let ((t1 (walk st t1)) (t2 (walk st t2)))\n    (cond ((eqv? t1 t2) #f)\n          ((var?    t1) (var-disassign st uid? t1 t2))\n          ((var?    t2) (var-disassign st uid? t2 t1))\n          ((pair?   t1) (cond ((not (pair? t2)) st)\n                              (else (disjoin st #f (list (c:=/= (car t1) (car t2))\n                                                         (c:=/= (cdr t1) (cdr t2)))))))\n          ((vector? t1) (cond ((not (and (vector? t2))\n                                    (= (vector-length t1) (vector-length t2))) st)\n                              (else (disjoin st #f (map c:=/=\n                                                        (vector->list t1)\n                                                        (vector->list t2))))))\n          ((equal? t1 t2) #f)\n          (else           st))))\n\n(define (ltunify st uid? t1 t2)\n  (let ((t1 (walk st t1)) (t2 (walk st t2)))\n    (cond ((or (null? t1) (eq? #t t2) (eqv? t1 t2)) st)\n          ((or (var? t1) (var? t2))\n           (match-define (bounds lb.t1 lbi.t1 ub.t1 ubi.t1) (term-bounds st t1))\n           (match-define (bounds lb.t2 lbi.t2 ub.t2 ubi.t2) (term-bounds st t2))\n           (cond ((any<=?                                ub.t1 lb.t2) st)\n                 (((if (and lbi.t1 ubi.t2) anylist (set-union vs.t1 vs.t2)))))\n                           (state-cx-add st vs vcx-simple-add uid? (c:<= t1 t2)))))))\n          ((pair? t1)\n           (cond ((pair?   t2) (let*/and ((st (ltunify st #f (car t1) (car t2))))\n                                 (disjoin st #f (list (c:=/= (car t1) (car t2))\n                                                      (c:<=  (cdr t1) (cdr t2))))))\n                 ((vector? t2)                        st)\n                 (else (and (any<=? term.pair.max t2) st))))\n          ((vector? t1)\n           (cond ((vector? t2)\n                  (define len.t1 (vector-length t1))\n                  (define len.t2 (vector-length t2))\n                  (cond ((< len.t1 len.t2) st)\n                        ((> len.t1 len.t2) #f)\n                        (else (ltunify st #f (vector->list t1) (vector->list t2)))))\n                 ((pair? t2)                            #f)\n                 (else (and (any<=? term.vector.max t2) st))))\n          (else (and (any<=? t1 t2) st)))))\n\n(define (disjoin st uid? cs)\n  (define (c-vars c)\n    (match c\n      ((c:==  l r)        (set-union (term-vars l)     (term-vars r)))\n      ((c:=/= l r)        (set-union (term-vars l)     (term-vars r)))\n      ((c:<=  l r)        (set-union (term-vars l)     (term-vars r)))\n      ((c:disj cs)        (set-union (c-vars (car cs)) (c-vars (cadr cs))))\n      ((c:conj cs)        (apply set-union (seteq) (map c-vars cs)))\n      ((c:use vs _ _ _ _) (term-vars vs))\n      ((c:table t)        (table-vars t))\n      ((c:proc  _ args _) (term-vars args))))\n  (let loop ((cs cs) (cs.new '()))\n    (if (null? cs)\n      (match cs.new\n        ('()          #f)\n        ((list c.new) (c-apply st #f c.new))\n        (_            (define cx (c:disj (reverse cs.new)))\n                      (define vs (set->list (c-vars cx)))\n                      ;; TODO: in the future when a c:proc appears in a c:disj,\n                      ;; it is possible for vs to be empty even when the disj\n                      ;; has not been satisfied (because the proc hasn't been\n                      ;; allowed to expand yet).  Figure out how to resolve\n                      ;; this, possibly by adding a queue of cxs containing\n                      ;; procs that need to be expanded.\n                      (if (null? vs)\n                        (error \"TODO: unexpanded c:proc without vars:\" cx)\n                        (state-cx-add st vs vcx-disj-add uid? cx))))\n      (match (c-simplify st #f (car cs))\n        ;; TODO: if applicable, negate (car cs) in st while simplifying (cdr cs).\n        ;; This achieves some disjoint-ness across branches, reducing redundancy\n        ;; in the search space.  (Ideally we would also do the same in reverse,\n        ;; propagating negated constraints from later branches into earlier\n        ;; branches.)\n        (#f            (loop (cdr cs) cs.new))\n        ((c:conj '())  st)\n        ((c:disj cs.d) (loop (cdr cs) (foldl cons cs.new cs.d)))\n        (c             (loop (cdr cs) (cons c cs.new)))))))\n\n(define (conjoin st cs) (foldl/and (lambda (c st) (c-apply st #f c)) st cs))\n\n(define (use st uid? t.vs lhs args proc desc)\n  (define vars.pending (set->list (term-vars (walk* st t.vs))))\n  (if (null? vars.pending)\n    (unify st lhs (apply proc (walk* st args)))\n    (state-cx-add st vars.pending vcx-use-add uid?\n                  `#s(c:use ,vars.pending ,lhs ,args ,proc ,desc))))\n\n(define (proc-apply st uid? proc args parents)\n  ;; TODO: determine whether to expand instead of adding a c:proc\n  ;; TODO: without expanding, it is possible to infinite loop when no variables\n  ;; are present in args, since in that case, state-cx-add will c-apply again.\n  ;; Figure out how to resolve this, possibly by adding a queue of cxs that\n  ;; need to be expanded.\n  (state-cx-add st (term-vars args) vcx-simple-add uid? (c:proc proc args parents)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Table interaction\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (table-update     st uid? tc) (tc 'update st uid?))\n(define (table-vars               tc) (tc 'variables))\n(define (table-statistics st      tc) (tc 'variable-statistics st))\n\n(define (relation/table . pargs)\n  (match-define (list info thunk.t.0) (apply materialization pargs))\n  (define name             (hash-ref info 'relation-name))\n  (define attribute-names  (hash-ref info 'attribute-names))\n  (define primary-key-name (hash-ref info 'key-name))\n  ;; TODO: this is a workaround to make sure key column is tracked for update.\n  (define attrs\n    (if (member primary-key-name attribute-names)\n      attribute-names\n      (cons #t attribute-names)))\n  (define (app st args.0.0)\n    ;; TODO: this introduces a phantom variable for the key column update workaround.\n    ;; Is there a better solution?\n    (define args.0\n      (if (member primary-key-name attribute-names)\n        args.0.0\n        (cons (var #t) args.0.0)))\n    (define (update-state st t)\n      (define c=>b (t 'bounds))\n      (foldl/and (lambda (c a st)\n                   (c-apply st #f (c:bounds (hash-ref c=>b c bounds.any) a)))\n                 st attrs args.0))\n    (let*/and ((t.0 (thunk.t.0))\n               (st  (update-state st t.0)))\n      (define args (walk* st args.0))\n      (define tc\n        (let controller ((t  t.0)\n                         (vs (set->list (term-vars args))))\n          (method-lambda\n            ((constraint) (c:proc r args.0.0 (set)))\n            ((variables)  vs)\n            ((variable-statistics st)\n             (define c=>stats (t 'statistics))\n             (foldl (lambda (c a x=>stats)\n                      (match (hash-ref c=>stats c #f)\n                        (#f  x=>stats)\n                        (s.x (define (merge s.0) (statistics-intersect s.0 s.x))\n                             (foldl (lambda (x x=>stats) (hash-update x=>stats x merge s.x))\n                                    x=>stats (set->list (term-vars (walk* st a)))))))\n                    (hash) attrs args))\n            ((update st uid?)\n             (let*/and ((t (t 'update (map (lambda (c a) (cons c (term-bounds st a)))\n                                           attrs args))))\n               (update-state\n                 (if (t 'done?)\n                   st\n                   ;; TODO: we only want to register with the subset of variables that are indexable\n                   (let* ((vs (set->list (term-vars (walk* st vs))))\n                          (tc (controller t vs)))\n                     (if (null? vs)\n                       (tc 'update st uid?)\n                       (state-cx-add st vs vcx-table-add uid? (c:table tc)))))\n                 t))))))\n      (c-apply st #f (c:table tc))))\n  (define r (make-relation name attribute-names))\n  (relations-set! r 'definition-info info)\n  (relations-set! r 'apply           app)\n  r)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Variable-centric constraint operations\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (var-update st x)\n  (define vcx.x (state-vcx-ref st x))\n  (foldl/and (lambda (uids st) (state-cx-update* st (set->list uids)))\n             (state-vcx-set st x (vcx-cx-clear vcx.x))\n             (list (vcx-table  vcx.x)  ;; typically the strongest constraints\n                   (vcx-simple vcx.x)\n                   (vcx-disj   vcx.x)\n                   (vcx-use    vcx.x))))\n\n(define (var-assign st x t)\n  ;; could replace occurs check with: (set-member? (term-vars (walk* st t)) x)\n  (and (not (let occurs? ((t t))\n              (cond ((pair?   t) (or (occurs? (walk st (car t)))\n                                     (occurs? (walk st (cdr t)))))\n                    ((vector? t) (let vloop ((i (- (vector-length t) 1)))\n                                   (and (<= 0 i) (or (occurs? (walk st (vector-ref t i)))\n                                                     (vloop (- i 1))))))\n                    (else        (eq? x t)))))\n       (let* ((vcx.x              (state-vcx-ref st x))\n              (vcx.t (if (var? t) (state-vcx-ref st t) vcx.empty))\n              (st    (state-log-add st (c:== x t)))\n              (st    (state-vcx-set st x t)))\n         (foldl/and (lambda (uids st) (state-cx-update* st (set->list uids)))\n                    (c-apply st #f (c:bounds (vcx-bounds vcx.x) t))\n                    (list (vcx-simple vcx.x)  ;; the least expensive constraints\n                          ;; TODO: try disjs containing only simple cxs before tables.\n                          ;; It may only make sense to try the disjs that only\n                          ;; reference this var and no others.\n                          (vcx-table  vcx.x)\n                          ;; TODO: try other disjs after tables\n                          (vcx-disj   vcx.x)\n                          (vcx-use    vcx.x))))))\n\n(define (var-disassign st uid? x t)\n  (let* ((t    (walk* st t))\n         (vs.t (term-vars t)))\n    (define (add) (state-cx-add st (set->list (set-add vs.t x))\n                                vcx-simple-add uid? (c:=/= x t)))\n    (cond ((set-member? vs.t x) st)  ;; simple occurs check\n          ((set-empty?  vs.t)\n           (match-define (bounds lb lbi ub ubi) (term-bounds st x))\n           (define (assign-bounds c b) (var-assign-bounds (state-log-add st c) x b))\n           (cond ((and lbi (equal? t lb)) (define lb.inc (any-increment lb))\n                                          (if (eq? lb lb.inc)\n                                            (assign-bounds (c:=/= lb     x) (bounds lb     #f ub ubi))\n                                            (assign-bounds (c:<=  lb.inc x) (bounds lb.inc #t ub ubi))))\n                 ((and ubi (equal? t ub)) (define ub.dec (any-decrement ub))\n                                          (if (eq? ub ub.dec)\n                                            (assign-bounds (c:=/= x ub    ) (bounds lb lbi ub     #f))\n                                            (assign-bounds (c:<=  x ub.dec) (bounds lb lbi ub.dec #t))))\n                 ((or (any<=? t lb) (any<=? ub t)) st)\n                 (else                             (add))))\n          (else (match-define (bounds lb.x lbi.x ub.x ubi.x) (term-bounds st x))\n                (match-define (bounds lb.t lbi.t ub.t ubi.t) (term-bounds st t))\n                (if (or ((if (and lbi.t ubi.x) anycx (state-var=>cx st)))\n      (let loop ((x t))\n        (define val (hash-ref v=>cx x vcx.empty))\n        (cond ((var? val) (loop val))\n              ((vcx? val) x)\n              (else       val))))\n    t))\n(define (walk* st t)\n  (let loop ((term t))\n    (define t (walk st term))\n    (cond ((pair?   t) (cons (loop (car t)) (loop (cdr t))))\n          ((vector? t) (vector-map loop t))\n          (else        t))))\n\n(define (reify st.0)\n  (define (refine-bounds x st)\n    (define (=/=? x t) (not (let*/and ((st (var-assign st x t)))\n                              (pair? (s-force (state->satisfied-states st))))))\n    (define (trim x t) (refine-bounds x (c-apply st #f (c:=/= x t))))\n    (define vcx.x (state-vcx-ref st x))\n    (match-define (bounds lb lbi? ub ubi?) (vcx-bounds vcx.x))\n    (cond ((and lbi? (=/=? x lb)) (trim x lb))\n          ((and ubi? (=/=? x ub)) (trim x ub))\n          (else                   st)))\n  (define term (walk* st.0 (state-qterm st.0)))\n  (define xs   (set->list (term-vars term)))\n  ;; Refinement should never fail after global satisfaction\n  (define st   (foldl refine-bounds st.0 xs))\n  (cond ((null? xs) (pretty term))\n        (else (define b&uids\n                (map (lambda (x)\n                       (define vcx.x (state-vcx-ref st x))\n                       (cons (vcx-bounds vcx.x) (vcx-simple vcx.x)))\n                     xs))\n              (define uids (apply set-union (seteq) (map cdr b&uids)))\n              (define cxs  (walk* st (map c->f (filter-not\n                                                 not (map (lambda (uid) (hash-ref (state-cx st) uid #f))\n                                                          (set->list uids))))))\n              (define bs\n                (append* (map (lambda (x b)\n                                (if (equal? b bounds.any)\n                                  '()\n                                  (list (list (bounds-lb b)\n                                              (if (bounds-lb-inclusive? b) '<= '<)\n                                              x\n                                              (if (bounds-ub-inclusive? b) '<= '<)\n                                              (bounds-ub b)))))\n                              xs (map car b&uids))))\n              (match-define (cons t c) (pretty (cons term (append bs cxs))))\n              `#s(cx (term: ,t) (constraints: . ,(sort c termsatisfied-states st)))\n\n(define (bis:query->stream q)\n  (match-define `#s(query ,t ,f) q)\n  (s-append* (s-map enumerate-and-reify ((bis:goal f) (state:new t)))))\n(define (bis:bind s k)\n  (cond ((null?      s) '())\n        ((procedure? s) (thunk (bis:bind (s) k)))\n        (else           (s-append/interleaving (k (car s)) (thunk (bis:bind (cdr s) k))))))\n(define ((bis:apply/expand ex args) st)\n  ((bis:goal (apply ex (walk* st args))) st))\n(define ((bis:expand ex r args) st)\n  (define frame (cons r args))\n  (thunk (bis:bind (bis:return (state-proc-stack-push st frame))\n                   (lambda (st) (bis:bind ((bis:goal (apply ex args)) st)\n                                          (lambda (st) (bis:return (state-proc-stack-pop st))))))))\n\n(define (bis:goal f)\n  (match f\n    (`#s(conj ,f1 ,f2) (let ((k1 (bis:goal f1)) (k2 (bis:goal f2)))\n                         (lambda (st) (bis:bind (k1 st) k2))))\n    (`#s(disj ,f1 ,f2) (let ((k1 (bis:goal f1)) (k2 (bis:goal f2)))\n                         (lambda (st)\n                           (state-enforce-global-consistency\n                             st\n                             (lambda ()   '())\n                             (lambda (st) (s-append/interleaving (k1 st) (thunk (k2 st))))))))\n    (`#s(constrain ,(? procedure? proc) ,args)\n      (define r (relations-ref proc))\n      (define apply/bis    (hash-ref r 'apply/bis    #f))  ; strategy-specific application\n      (define apply.r      (hash-ref r 'apply        #f))  ; strategy-agnostic application\n      (define expand       (hash-ref r 'expand       #f))  ; pure expansion\n      (cond (apply/bis    (apply/bis args))\n            (apply.r      (lambda (st) (bis:return (apply.r st args))))\n            (expand       (bis:expand expand r args))\n            (else (error \"no interpretation for:\" proc args))))\n    (_ (define c (f->c f))\n       (lambda (st) (bis:return (c-apply st #f c))))))\n(define (bis:return st)         (if st (list st) '()))\n\n(define (dfs:query->stream q)\n  ((dfs:goal (query-formula q) enumerate-and-reify)\n   (state:new (query-term q))))\n(define ((dfs:mplus k1 k2) st)\n  (state-enforce-global-consistency\n    st\n    (lambda ()   '())\n    (lambda (st) (s-append (k1 st) (thunk (k2 st))))))\n(define ((dfs:expand ex r args k) st)\n  (define frame (cons r args))\n  (dfs:return (dfs:goal (apply ex args)\n                        (lambda (st) (dfs:return k (state-proc-stack-pop st))))\n              (state-proc-stack-push st frame)))\n\n(define (dfs:goal f k)\n  (define loop dfs:goal)\n  (match f\n    (`#s(conj ,f1 ,f2) (loop f1 (loop f2 k)))\n    (`#s(disj ,f1 ,f2) (dfs:mplus (loop f1 k) (loop f2 k)))\n    (`#s(constrain ,(? procedure? proc) ,args)\n      (define r (relations-ref proc))\n      (define apply/dfs    (hash-ref r 'apply/dfs    #f))  ; strategy-specific application\n      (define apply.r      (hash-ref r 'apply        #f))  ; strategy-agnostic application\n      (define expand       (hash-ref r 'expand       #f))  ; pure expansion\n      (cond (apply/dfs    (apply/dfs k args))\n            (apply.r      (lambda (st) (dfs:return k (apply.r st args))))\n            (expand       (dfs:expand expand r args k))\n            (else (error \"no interpretation for:\" proc args))))\n    (_ (define c (f->c f))\n       (lambda (st) (dfs:return k (c-apply st #f c))))))\n(define (dfs:return k st)      (if st (k st) '()))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Syntax definitions\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-syntax define-relation/table\n  (syntax-rules ()\n    ((_ (name attr ...) pargs ...)\n     (define name (relation/table 'relation-name   'name\n                                  'attribute-names '(attr ...)\n                                  pargs ...)))\n    ((_ name pargs ...)\n     (define name (relation/table 'relation-name 'name\n                                  pargs ...)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/data.rkt",
    "content": "#lang racket/base\n(provide\n  column:const\n  column:identity\n  column:offset\n  column:vector\n  column:table\n  column:indirect\n  column:interval\n  column:bytes:nat\n  column:port\n  column:port-indirect\n  column:port-string\n  interval->dict:ordered\n  dict.empty\n  dict:integer\n  dict:ordered\n  dict:ordered:vector\n  dict:ordered:union\n  dict:ordered:subtraction\n  dict:hash\n  enumerator-project\n  enumerator-filter\n  enumerator-sort\n  enumerator-dedup\n  enumerator->dict:ordered:vector-flat\n  enumerator->dict:ordered:vector-group\n  group-fold->hash\n  group-fold\n  group-fold-ordered\n  merge-key-union\n  merge-union\n  merge-antijoin\n  merge-join\n  dict-join-unordered\n  dict-join-ordered\n  hash-join\n  dict-antijoin-unordered\n  dict-antijoin-ordered\n  hash-antijoin\n  dict-key-union-unordered\n  dict-key-union-ordered\n  dict-union-unordered\n  dict-union-ordered\n  dict-subtract-unordered\n  dict-subtract-ordered\n\n  database\n  database-path\n  database-metadata\n  database-relation\n  database-relation-names\n  database-relation-has?\n  database-relation-add!\n  database-relation-remove!\n  database-compact!\n  database-import!\n  database-export!\n\n  relation-name\n  relation-metadata\n  relation-copy!\n  relation-rename!\n  relation-delete!\n  relation-rename-attributes!\n  relation-index-add!\n  relation-index-remove!\n  relation-index-dict\n  relation-domain-dicts\n  relation-compact!\n  )\n(require \"codec.rkt\" \"enumerator.rkt\" \"heap.rkt\" \"logging.rkt\" \"misc.rkt\" \"order.rkt\" \"stream.rkt\"\n         racket/file racket/fixnum racket/list racket/match racket/pretty racket/set racket/struct\n         racket/vector racket/unsafe/ops)\n\n;; TODO:\n;bscm.rkt\n;bscm:read bscm:write ?\n;or favor a bytes-ref/bytes-set! style interface with bscm types?\n\n\n\n\n\n\n;;;;;;;;;;;;;;;;;;;;;;;\n;;; Metadata format ;;;\n;;;;;;;;;;;;;;;;;;;;;;;\n;;\n;;desc.database\n;;(hash\n;;  'relations      (hash NAME desc.relation ...)\n;;  'current        (hash PATH desc.arbitrary ...)\n;;  'pending        (list JOB ...)\n;;  )\n;;\n;;;; supports copying by sharing table and index descriptions\n;;desc.relation\n;;(hash\n;;  'attributes (list attribute-names ...)\n;;  'type       (list high-level-types ...)\n;;  'tables     (list path.table ...)\n;;  'indexes    (hash ordering (list path.table-index ...) ...)\n;;  )\n;;\n;;desc.domain\n;;(hash\n;;  'text path-to-domain-text\n;;  ...\n;;  )\n;;\n;;desc.domain-text\n;;(hash\n;;  'count         num-elements\n;;  'size.position num-bytes\n;;  'index         optional-path-to-index\n;;  )\n;;\n;;TODO:\n;;desc.domain-text-index\n;;(hash\n;;  'domain path.domain\n;;  )\n;;\n;;desc.column\n;;(hash\n;;  'type   'int|'text\n;;  'count  num-elements\n;;  'size   nat-bytes\n;;  'min    _\n;;  'max    _\n;;  'offset _\n;;  )\n;;\n;;desc.table\n;;(hash\n;;  'direction 'insert|'delete\n;;  'domain    desc.domain\n;;  'count     tuple-count\n;;  'columns   (list desc.column ...)\n;;  )\n;;\n;;desc.table-index\n;;(hash\n;;  'table            path.table\n;;  'ordering         (list 3 1 2 etc.)\n;;  'columns.value    (list desc.column ...)\n;;  'columns.indirect (list desc.column ...)  ; length is (- (length columns) 1)\n;;  )\n\n(define fnsuffix.key        \".key\")\n(define fnsuffix.indirect   \".indirect\")\n(define fnsuffix.next       \".next\")\n(define fnsuffix.initial    \".initial\")\n(define fn.metadata         \"metadata.scm\")\n(define fn.value            \"value\")\n(define fn.pos              \"position\")\n(define fn.tuple            \"tuple\")\n(define fn.col              \"column\")\n(define fn.metadata.initial (string-append fn.metadata fnsuffix.initial))\n\n(define metadata-format-version \"0\")\n\n(define (write-metadata path.metadata metadata)\n  (let/files () ((out.metadata path.metadata))\n    (pretty-write\n      (hash-set metadata 'format-version metadata-format-version)\n      out.metadata)))\n\n(define desc.database.empty\n  (hash 'relations (hash)\n        'data      (hash)))\n\n;; TODO: store redundant metadata\n;; - for optional consistency checking\n;; - also for independent file/folder exploration (e.g., analyzing trash)\n;;   - file explorer:\n;;     - display both logical and physical values\n;;     - indicate min/max\n;;     - jump to row, jump to column\n;;       - absolute or relative\n;;     - search for logical/physical value\n;;       - local (fast), or various forms of global (slow)\n;;       - optionally use full-text search indexes\n;; - \"previous\" directory supports time travel as long as most recent groups are not deleted\n\n(define (valid-attributes?! attrs)\n  (unless (list? attrs)\n    (error \"attributes must be a list\" attrs))\n  (for-each (lambda (a) (unless (symbol? a) (error \"attribute must be a symbol\" a 'in attrs)))\n            attrs)\n  (unless (= (length attrs) (set-count (list->set attrs)))\n    (error \"attributes must be unique\" attrs)))\n\n(struct wrapped-database (controller)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (db) 'database)\n             (lambda (db) (list (database-path db)\n                                (hash-ref (database-metadata db) 'relations)))))))\n\n(struct wrapped-relation (controller)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (r) 'relation)\n             (lambda (r) (list (relation-name     r)\n                               (relation-metadata r)))))))\n\n;; Racket doesn't seem to have a weak-value hash table, so we\n;; suboptimally use a weak-key hash table as a self-cleaning list.\n(define all-databases (make-weak-hash))\n(define (database path.db)\n  (let ((path.db (normalize-path path.db)))\n    (or (ormap (lambda (db) (and (equal? path.db (database-path db)) db))\n               (hash-keys all-databases))\n        (let ((db (make-database path.db)))\n          (hash-set! all-databases db (void))\n          db))))\n\n(define (make-database path.db)\n  (define (db-path   name) (path->string (build-path path.db      name)))\n  (define (data-path name) (path->string (build-path path.current name)))\n\n  (define (relations-update! f) (set! metadata (hash-update metadata 'relations f)))\n  (define (data-update!      f) (set! metadata (hash-update metadata 'data      f)))\n\n  (define (reachable (relation-names #f))\n    (define data               (hash-ref metadata 'data))\n    (define name=>relation     (hash-ref metadata 'relations))\n    (define descs.relation     (if relation-names\n                                 (map (lambda (name) (hash-ref name=>relation name)) relation-names)\n                                 (hash-values name=>relation)))\n    (define lpaths.table       (list->set (append* (map (lambda (desc.r) (hash-ref desc.r 'tables))\n                                                        descs.relation))))\n    (define lpaths.table-index (list->set (append* (map (lambda (desc.r) (append* (hash-values (hash-ref desc.r 'indexes))))\n                                                        descs.relation))))\n    (define descs.table        (set-map lpaths.table (lambda (lp) (hash-ref data lp))))\n    (define lpaths.domain-text (list->set (map (lambda (desc.t) (hash-ref (hash-ref desc.t 'domain) 'text))\n                                               descs.table)))\n    (set-union lpaths.table lpaths.table-index lpaths.domain-text))\n\n  (define (clean!)\n    (define pending-previous   (path->string (build-path path.db          \"pending-previous\")))\n    (define metadata.previous  (path->string (build-path pending-previous fn.metadata)))\n    (define lpaths.old         (if (and (directory-exists? pending-previous)\n                                        (file-exists?      metadata.previous))\n                                 (list->set (hash-keys (hash-ref (call-with-input-file metadata.previous read)\n                                                                 'data)))\n                                 (set)))\n    (define lpaths.known       (set-union lpaths.old (list->set (hash-keys (hash-ref metadata 'data)))))\n    (define lpaths.reachable   (reachable))\n    (define lpaths.all         (list->set (map path->string (directory-list path.current))))\n    (define lpaths.trash       (set->list (set-subtract lpaths.all   lpaths.known)))\n    (define lpaths.unreachable (set->list (set-subtract lpaths.known lpaths.reachable)))\n    (unless (null? lpaths.unreachable)\n      (apply pretty-log '(archiving unreachable data) lpaths.unreachable)\n      (make-directory* pending-previous)\n      (for-each (lambda (lp)\n                  (define apath (data-path lp))\n                  (when (directory-exists? apath)\n                    (rename-file-or-directory apath (build-path pending-previous lp))))\n                lpaths.unreachable))\n    (when (directory-exists? pending-previous)\n      (define upath (unique-previous-path))\n      (pretty-log `(moving ,pending-previous to ,upath))\n      (rename-file-or-directory pending-previous upath))\n    (define pending-trash (path->string (build-path path.db \"pending-trash\")))\n    (when (file-exists? path.metadata.next)\n      (pretty-log '(moving interrupted checkpoint to trash) path.metadata.next)\n      (make-directory* pending-trash)\n      (rename-file-or-directory path.metadata.next\n                                (build-path pending-trash (string-append fn.metadata fnsuffix.next))))\n    (unless (null? lpaths.trash)\n      (apply pretty-log '(moving unknown data to trash) lpaths.trash)\n      (make-directory* pending-trash)\n      (for-each (lambda (lp) (rename-file-or-directory (data-path lp) (build-path pending-trash lp)))\n                lpaths.trash))\n    (when (directory-exists? pending-trash)\n      (define upath (unique-trash-path))\n      (pretty-log `(moving ,pending-trash to ,upath))\n      (rename-file-or-directory pending-trash upath)))\n\n  (define (checkpoint!)\n    (define metadata.previous (call-with-input-file path.metadata read))\n    (when   (equal? metadata metadata.previous) (pretty-log '(no checkpoint necessary)))\n    (unless (equal? metadata metadata.previous)\n      (define lpaths.known       (list->set (hash-keys (hash-ref metadata 'data))))\n      (define lpaths.reachable   (reachable))\n      (define lpaths.unreachable (set->list (set-subtract lpaths.known lpaths.reachable)))\n      (unless (null? lpaths.unreachable)\n        (data-update! (lambda (data) (foldl (lambda (lp data) (hash-remove data lp))\n                                            data lpaths.unreachable))))\n      (call-with-output-file path.metadata.next (lambda (out) (pretty-write metadata out)))\n      (define pending-previous (build-path path.db \"pending-previous\"))\n      (make-directory* pending-previous)\n      (pretty-log `(archiving ,path.metadata))\n      (rename-file-or-directory path.metadata (build-path pending-previous fn.metadata))\n      (pretty-log '(checkpointing metadata) metadata)\n      (rename-file-or-directory path.metadata.next path.metadata)\n      (clean!)))\n\n  ;; TODO: later, consolidate subsequent inserts/deletes\n  (define (compact!)\n    (pretty-log `(compacting ,path.db))\n    (define data           (hash-ref metadata 'data))\n    (define descs.relation (hash-values (hash-ref metadata 'relations)))\n    (match-define (list paths.table descs.table paths.domain-text/duplicates)\n      (let* ((paths.table       (append* (map (lambda (desc.relation) (hash-ref desc.relation 'tables))\n                                              descs.relation)))\n             (descs.table       (map (lambda (path.table) (hash-ref data path.table)) paths.table))\n             (paths.domain-text (map (lambda (d) (hash-ref (hash-ref d 'domain) 'text))\n                                     descs.table))\n             (pdps              (map (lambda (path.table desc.table path.domain-text)\n                                       (and path.domain-text (list path.table desc.table path.domain-text)))\n                                     paths.table descs.table paths.domain-text)))\n        (apply map list (filter-not not pdps))))\n    (define paths.domain-text (set->list (list->set paths.domain-text/duplicates)))\n    (unless (< 1 (length paths.domain-text)) (pretty-log '(no compaction necessary)))\n    (when (< 1 (length paths.domain-text))\n      (define (type=>id=>id path.domain-text)\n        (hash 'text (hash-ref path.domain-text=>id=>id path.domain-text)))\n      (define path.domain-text.new     (unique-path \"domain-text\"))\n      (define descs.domain-text        (map (lambda (p) (hash-ref data p)) paths.domain-text))\n      (define compaction               (compact-text-domains\n                                         (data-path path.domain-text.new)\n                                         (map data-path paths.domain-text)\n                                         descs.domain-text))\n      (define desc.domain-text.new     (hash-ref compaction 'domain-text))\n      (define path.domain-text=>id=>id (make-immutable-hash\n                                         (map cons paths.domain-text (hash-ref compaction 'remappings))))\n      (define paths.table.new          (map (lambda (path.table desc.table path.domain-text)\n                                              (if (remap-table? desc.table (type=>id=>id path.domain-text))\n                                                (unique-path \"table\")\n                                                path.table))\n                                            paths.table descs.table paths.domain-text/duplicates))\n      (define path.t=>path.t.new       (make-immutable-hash (map cons paths.table paths.table.new)))\n      (define descs.table.new\n        (map (lambda (path.table path.table.new desc.table path.domain-text)\n               (define desc.domain.new (hash 'text path.domain-text.new))\n               (if (equal? path.table path.table.new)\n                 (begin (pretty-log '(no need to remap table) path.table)\n                        (hash-set desc.table 'domain desc.domain.new))\n                 (remap-table (data-path path.table)\n                              (data-path path.table.new)\n                              desc.table\n                              desc.domain.new\n                              (type=>id=>id path.domain-text))))\n             paths.table paths.table.new descs.table paths.domain-text/duplicates))\n      (define paths.table-index\n        (append* (map (lambda (desc.relation)\n                        (filter (lambda (path.table-index)\n                                  (define desc.table-index (hash-ref data path.table-index))\n                                  (member (hash-ref desc.table-index 'table) paths.table))\n                                (append* (hash-values (hash-ref desc.relation 'indexes)))))\n                      descs.relation)))\n      (define descs.table-index     (map (lambda (path.ti) (hash-ref data path.ti)) paths.table-index))\n      (define paths.table-index.new (map (lambda (path.ti desc.ti)\n                                           (define path.table  (hash-ref desc.ti 'table))\n                                           (define desc.domain (hash-ref (hash-ref data path.table) 'domain))\n                                           (define path.dt     (hash-ref desc.domain 'text))\n                                           (if (remap-table-index? desc.ti (type=>id=>id path.dt))\n                                             (unique-path \"table-index\")\n                                             path.ti))\n                                         paths.table-index descs.table-index))\n      (define path.ti=>path.ti.new  (make-immutable-hash (map cons paths.table-index paths.table-index.new)))\n      (define (replace-p.ti p.ti) (hash-ref path.ti=>path.ti.new p.ti p.ti))\n      (define descs.table-index.new\n        (map (lambda (path.table-index path.table-index.new desc.table-index)\n               (define path.table       (hash-ref desc.table-index   'table))\n               (define path.table.new   (hash-ref path.t=>path.t.new path.table))\n               (define path.domain-text (hash-ref (hash-ref (hash-ref data path.table) 'domain) 'text))\n               (if (equal? path.table-index path.table-index.new)\n                 (begin (pretty-log '(no need to remap table index) path.table-index)\n                        desc.table-index)\n                 (remap-table-index (data-path path.table-index)\n                                    (data-path path.table-index.new)\n                                    desc.table-index\n                                    path.table.new\n                                    (type=>id=>id path.domain-text))))\n             paths.table-index paths.table-index.new descs.table-index))\n      (pretty-log '(installing remapped data))\n      (data-update!\n        (lambda (data)\n          (apply hash-set* data\n                 path.domain-text.new desc.domain-text.new\n                 (append (append* (map list paths.table.new       descs.table.new))\n                         (append* (map list paths.table-index.new descs.table-index.new))))))\n      (pretty-log '(updating relations with remapped data))\n      (relations-update!\n        (lambda (rs)\n          (make-immutable-hash\n            (hash-map rs (lambda (name.r desc.r)\n                           (let* ((desc.r (hash-update desc.r 'tables\n                                                       (lambda (paths.table)\n                                                         (map (lambda (p) (hash-ref path.t=>path.t.new   p p))\n                                                              paths.table))))\n                                  (desc.r (hash-update desc.r 'indexes\n                                                       (lambda (ordering=>paths.table-index)\n                                                         (make-immutable-hash\n                                                           (hash-map ordering=>paths.table-index\n                                                                     (lambda (o ps.ti)\n                                                                       (cons o (map replace-p.ti ps.ti)))))))))\n                             (cons name.r desc.r)))))))\n      (checkpoint!)))\n\n  (define (unique-path str.type)\n    (define data    (hash-ref metadata 'data))\n    (define seconds (number->string (current-seconds)))\n    (let loop ((id.local 0))\n      (define candidate (string-append str.type \"-\" seconds \"-\" (number->string id.local)))\n      (cond ((hash-has-key? data candidate) (loop (+ id.local 1)))\n            (else                           (make-directory* (data-path candidate))\n                                            (data-update! (lambda (data) (hash-set data candidate #f)))\n                                            candidate))))\n  (define (unique-directory path.root str.type)\n    (define seconds (number->string (current-seconds)))\n    (let loop ((id.local 0))\n      (define candidate (string-append str.type \"-\" seconds \"-\" (number->string id.local)))\n      (define apath (path->string (build-path path.root candidate)))\n      (cond ((directory-exists? apath) (loop (+ id.local 1)))\n            (else                      apath))))\n  (define (unique-previous-path) (unique-directory path.previous \"previous\"))\n  (define (unique-trash-path)    (unique-directory path.trash    \"trash\"))\n\n  (define (new-relation?! name) (when (hash-has-key? name=>relation name)\n                                  (error \"relation already exists\" name path.db)))\n\n  (define (make-relation name)\n    (define (description)           (hash-ref (hash-ref metadata 'relations) name))\n    (define (description-update! f) (relations-update! (lambda (rs) (hash-update rs name f))))\n    (define self\n      (method-lambda\n        ((name)                     name)\n        ((metadata)                 (description))\n        ((copy!   name.new)         (pretty-log `(copying relation ,name to ,name.new))\n                                    (new-relation?! name.new)\n                                    (set! name=>relation\n                                      (hash-set name=>relation name.new (hash-ref name=>relation name)))\n                                    (relations-update! (lambda (rs) (hash-set rs name.new (hash-ref rs name))))\n                                    (checkpoint!))\n        ((rename! name.new)         (pretty-log `(renaming relation ,name to ,name.new))\n                                    (new-relation?! name.new)\n                                    (set! name=>relation (let ((r    (hash-ref    name=>relation name))\n                                                               (n=>r (hash-remove name=>relation name)))\n                                                           (hash-set n=>r name.new r)))\n                                    (relations-update! (lambda (rs) (let* ((r  (hash-ref    rs name))\n                                                                           (rs (hash-remove rs name)))\n                                                                      (hash-set rs name.new r))))\n                                    (set! name name.new)\n                                    (checkpoint!))\n        ((delete!)                  (pretty-log `(deleting relation ,name))\n                                    (set! self           #f)\n                                    (set! name=>relation (hash-remove name=>relation name))\n                                    (relations-update! (lambda (rs) (hash-remove rs name)))\n                                    (checkpoint!))\n        ((rename-attributes! attrs) (pretty-log `(renaming ,name attributes)\n                                                `(old: ,(hash-ref (description) 'attributes))\n                                                `(new: ,attrs))\n                                    (valid-attributes?! attrs)\n                                    (let ((attrs.old (hash-ref (description) 'attributes)))\n                                      (unless (= (length attrs) (length attrs.old))\n                                        (error \"cannot change the number of attributes\"\n                                               name 'new attrs 'old attrs.old)))\n                                    (relations-update! (lambda (rs) (let* ((r (hash-ref rs name))\n                                                                           (r (hash-set r 'attributes attrs)))\n                                                                      (hash-set rs name r))))\n                                    (checkpoint!))\n        ((index-add!    signatures) (apply pretty-log `(adding indexes for ,name) signatures)\n                                    (let* ((desc         (description))\n                                           (data         (hash-ref metadata 'data))\n                                           (attrs        (hash-ref desc     'attributes))\n                                           (lpaths.table (hash-ref desc     'tables))\n                                           (descs.table  (map (lambda (lp) (hash-ref data lp)) lpaths.table))\n                                           (orderings    (map (attrs->signature->ordering attrs) signatures))\n                                           (orderings    (normalize-table-index-orderings (length attrs) orderings))\n                                           (ords.current (list->set (hash-keys (hash-ref desc 'indexes))))\n                                           (ords.skipped (set->list (set-intersect (list->set orderings) ords.current)))\n                                           (ords.new     (set->list (set-subtract  (list->set orderings) ords.current))))\n                                      (define (ords->sigs ords)\n                                        (map (lambda (ordering) (map (lambda (i) (list-ref attrs i))\n                                                                     (filter-not (lambda (i) (eq? #t i))\n                                                                                 ordering)))\n                                             ords))\n                                      (apply pretty-log '(normalizing table index signatures) (ords->sigs orderings))\n                                      (unless (null? ords.skipped)\n                                        (apply pretty-log '(skipping existing table indexes)\n                                               (ords->sigs ords.skipped)))\n                                      (when   (null? ords.new) (pretty-log '(no table indexes to build)))\n                                      (unless (null? ords.new)\n                                        (define lpaths*.ti\n                                          (apply map list\n                                                 (map (lambda (lpath.table desc.table)\n                                                        (define lpaths.ti (map (lambda (_) (unique-path \"table-index\")) ords.new))\n                                                        (define descs.ti  (build-table-indexes\n                                                                            path.current lpaths.ti lpath.table desc.table ords.new))\n                                                        (data-update!\n                                                          (lambda (data) (apply hash-set* data\n                                                                                (append* (map list lpaths.ti descs.ti)))))\n                                                        lpaths.ti)\n                                                      lpaths.table descs.table)))\n                                        (description-update!\n                                          (lambda (desc) (hash-update desc 'indexes\n                                                                      (lambda (ordering=>lps)\n                                                                        (apply hash-set* ordering=>lps\n                                                                               (append* (map list ords.new lpaths*.ti)))))))\n                                        (checkpoint!))))\n        ((index-remove! signatures) (apply pretty-log `(removing indexes for ,name) signatures)\n                                    (let* ((desc         (description))\n                                           (data         (hash-ref metadata 'data))\n                                           (attrs        (hash-ref desc     'attributes))\n                                           (orderings    (map (attrs->signature->ordering attrs) signatures))\n                                           (orderings    (normalize-table-index-orderings (length attrs) orderings))\n                                           (ords.current (list->set (hash-keys (hash-ref desc 'indexes))))\n                                           (ords.missing (set->list (set-subtract  (list->set orderings) ords.current)))\n                                           (ords.found   (set->list (set-intersect (list->set orderings) ords.current))))\n                                      (define (ords->sigs ords)\n                                        (map (lambda (ordering) (map (lambda (i) (list-ref attrs i))\n                                                                     (filter-not (lambda (i) (eq? #t i))\n                                                                                 ordering)))\n                                             ords))\n                                      (apply pretty-log '(normalizing table index signatures) (ords->sigs orderings))\n                                      (unless (null? ords.missing)\n                                        (apply pretty-log '(skipping table indexes that do not exist)\n                                               (ords->sigs ords.missing)))\n                                      (when   (null? ords.found) (pretty-log '(no table indexes to remove)))\n                                      (unless (null? ords.found)\n                                        (description-update!\n                                          (lambda (desc) (hash-update desc 'indexes\n                                                                      (lambda (ordering=>lps)\n                                                                        (foldl (lambda (o o=>lps) (hash-remove o=>lps o))\n                                                                               ordering=>lps ords.found)))))\n                                        (checkpoint!))))\n        ((index-dict sig preload?)  (let* ((desc      (description))\n                                           (data      (hash-ref metadata 'data))\n                                           (attrs     (hash-ref desc     'attributes))\n                                           (ordering  ((attrs->signature->ordering attrs) sig))\n                                           (ordering  (car (normalize-table-index-orderings (length attrs) (list ordering))))\n                                           (lpaths.ti (hash-ref (hash-ref desc 'indexes) ordering\n                                                                (lambda () (error \"no relation index matches signature\"\n                                                                                  name sig)))))\n                                      (match lpaths.ti\n                                        ('() dict.empty)\n                                        ((list lpath.ti)\n                                         (define (descs->cols fnsuffix descs.col)\n                                           (map (lambda (j desc.col)\n                                                  (and desc.col\n                                                       (let ((size   (hash-ref desc.col 'size))\n                                                             (offset (hash-ref desc.col 'offset 0))) ; TODO: later, require this\n                                                         (column:offset\n                                                           (if (< 0 size)\n                                                             (let* ((fname (string-append \"column.\" (number->string j) fnsuffix))\n                                                                    (apath (build-path (data-path lpath.ti) fname)))\n                                                               (if preload?\n                                                                   (column:bytes:nat (file->bytes apath) (hash-ref desc.col 'size))\n                                                                   (column:port (open-input-file apath) `#(nat ,size))))\n                                                             column:identity)\n                                                           offset))))\n                                                (range (length descs.col)) descs.col))\n                                         (define desc.ti       (hash-ref data lpath.ti))\n                                         (define descs.col.key (hash-ref desc.ti 'columns.key))\n                                         (define cols.key      (descs->cols \".key\"      descs.col.key))\n                                         (define cols.indirect (descs->cols \".indirect\" (hash-ref desc.ti 'columns.indirect)))\n                                         (let loop ((start         0)\n                                                    (end           (hash-ref (car descs.col.key) 'count))\n                                                    (cols.key      cols.key)\n                                                    (cols.indirect cols.indirect))\n                                           (define (next start end) (loop start end (cdr cols.key) (cdr cols.indirect)))\n                                           (define i->key   (car cols.key))\n                                           (define i->value (if (null? cols.indirect)\n                                                              (column:const '())\n                                                              (let ((ci (car cols.indirect)))\n                                                                (if ci\n                                                                  (column:interval ci next)\n                                                                  (lambda (i) (next i (+ i 1)))))))\n                                           (dict:ordered i->key i->value start end)))\n                                        ;; TODO: multiple table-indexes, possibly with deletions\n                                        (_ (error \"multi-table indexes are not yet supported\" name lpaths.ti)))))\n        ;; TODO: share domain dicts when the domains are shared across relations\n        ((domain-dicts preload?)    (let* ((desc         (description))\n                                           (data         (hash-ref metadata 'data))\n                                           (lpaths.table (hash-ref desc     'tables))\n                                           (descs.table  (map (lambda (lp) (hash-ref data lp)) lpaths.table))\n                                           (descs.domain (map (lambda (desc) (hash-ref desc 'domain)) descs.table)))\n                                      (define (domain->dict-pair.text desc.domain)\n                                        (define lpath.dt     (hash-ref desc.domain 'text))\n                                        (define desc.dt      (hash-ref data        lpath.dt))\n                                        (define size.pos     (hash-ref desc.dt     'size.position))\n                                        (define count        (hash-ref desc.dt     'count))\n                                        (define apath.dt     (data-path lpath.dt))\n                                        ;; TODO: should col.pos be shared like this, or duplicated across dicts for safety?\n                                        (define col.pos      (if preload?\n                                                                 (column:bytes:nat (file->bytes (build-path apath.dt \"position\")) size.pos)\n                                                                 (column:port (open-input-file (build-path apath.dt \"position\")) `#(nat ,size.pos))))\n                                        ;; TODO: properly support all text types: bytes, string, symbol\n                                        (define id->str      (column:port-string col.pos (open-input-file (build-path apath.dt \"value\"))))\n                                        (define dict.str=>id (dict:ordered id->str (lambda (id) id) 0 count))\n                                        (define dict.id=>str (dict:integer 0       id->str          0 count))\n                                        (cons dict.str=>id dict.id=>str))\n                                      (define dict-pairs.text (map domain->dict-pair.text descs.domain))\n                                      (cons (hash 'text (map car dict-pairs.text))\n                                            (hash 'text (map cdr dict-pairs.text)))))\n        ;; TODO: only spend effort compacting this relation\n        ((compact!)                 (compact!))))\n    (wrapped-relation (lambda args\n                        (unless self (error \"cannot use deleted relation\" name))\n                        (apply self args))))\n\n  (define path.current       (db-path \"current\"))\n  (define path.previous      (db-path \"previous\"))\n  (define path.trash         (db-path \"trash\"))\n  (define path.metadata      (db-path fn.metadata))\n  (define path.metadata.next (string-append path.metadata fnsuffix.next))\n  (for-each make-directory* (list path.db path.current path.previous path.trash))\n  (define metadata\n    (cond ((file-exists? path.metadata)      (call-with-input-file path.metadata read))\n          ((file-exists? path.metadata.next) (pretty-log '(checkpointing metadata after interrupted swap))\n                                             (rename-file-or-directory path.metadata.next path.metadata)\n                                             (call-with-input-file path.metadata read))\n          (else                              (pretty-log '(creating new database) path.db)\n                                             (call-with-output-file\n                                               path.metadata\n                                               (lambda (out) (pretty-write desc.database.empty out)))\n                                             desc.database.empty)))\n  (pretty-log '(loaded metadata for) path.db metadata)\n  ;; TODO: migrate metadata if format-version is old\n  (clean!)\n\n  (define name=>relation (make-immutable-hash\n                           (hash-map (hash-ref metadata 'relations)\n                                     (lambda (name desc.relation)\n                                       (pretty-log `(loading relation ,name) desc.relation)\n                                       (cons name (make-relation name))))))\n\n  (wrapped-database\n    (method-lambda\n      ((path)                              path.db)\n      ((metadata)                          metadata)\n      ((reachable names)                   (reachable names))\n      ((relation name)                     (hash-ref name=>relation name\n                                                     (lambda () (error \"unknown relation\" name path.db))))\n      ((relation-add! name attrs type src) (apply pretty-log `(creating relation ,name)\n                                                  (map (lambda (a t) `(,a : ,t)) attrs type))\n                                           (new-relation?! name)\n                                           (valid-attributes?! attrs)\n                                           (for-each (lambda (t) (unless (member t '(nat int bytes string symbol))\n                                                                   (error \"invalid attribute type\" t 'in type)))\n                                                     type)\n                                           (unless (= (length attrs) (length type))\n                                             (error \"number of attributes must match the relation type arity\"\n                                                    name attrs type))\n                                           (define path.domain-text (unique-path \"domain-text\"))\n                                           (define path.table       (unique-path \"table\"))\n                                           (define desc.ingest      (ingest-relation-source\n                                                                      path.current path.domain-text path.table type src))\n                                           (define desc.domain-text (hash-ref (hash-ref desc.ingest 'domain) 'text))\n                                           (define desc.table       (hash-ref desc.ingest 'table))\n                                           (define desc.relation    (hash 'attributes attrs\n                                                                          'type       type\n                                                                          'tables     (list path.table)\n                                                                          'indexes    (hash)))\n                                           (data-update!      (lambda (data) (hash-set* data\n                                                                                        path.domain-text desc.domain-text\n                                                                                        path.table       desc.table)))\n                                           (relations-update! (lambda (rs)   (hash-set  rs name desc.relation)))\n                                           (checkpoint!)\n                                           (set! name=>relation (hash-set name=>relation name (make-relation name))))\n      ((import! db.in names.in)            (pretty-log `(importing relations . ,names.in) 'from: (db.in 'path) 'into: path.db)\n                                           (define path.current.in   (path->string (build-path (db.in 'path) \"current\")))\n                                           (define name=>relation.in (hash-ref (db.in 'metadata) 'relations))\n                                           (define lpath=>data.in    (hash-ref (db.in 'metadata) 'data))\n                                           (define descs.relation.in (map (lambda (name)\n                                                                            (unless (hash-has-key? name=>relation.in name)\n                                                                              (error \"cannot import non-existent relation\"\n                                                                                     name (db.in 'path)))\n                                                                            (new-relation?! name)\n                                                                            (hash-ref name=>relation.in name))\n                                                                          names.in))\n                                           (define lpaths.reachable (set->list (db.in 'reachable names.in)))\n                                           (for-each (lambda (lpath)\n                                                       (define apath.in  (path->string (build-path path.current.in lpath)))\n                                                       (define apath.out (data-path lpath))\n                                                       ;; TODO: validate that skipped data is identical\n                                                       ;; TODO: support renaming paths when non-identical data collision occurs\n                                                       (cond ((directory-exists? apath.out) (pretty-log '(skipping import copy) apath.in apath.out))\n                                                             (else                          (pretty-log '(copying for import)   apath.in apath.out)\n                                                                                            (copy-directory/files apath.in apath.out\n                                                                                                                  #:keep-modify-seconds? #t))))\n                                                     lpaths.reachable)\n                                           (data-update!      (lambda (data)\n                                                                (foldl (lambda (lpath data)\n                                                                         (hash-set data lpath (hash-ref lpath=>data.in lpath)))\n                                                                       data lpaths.reachable)))\n                                           (relations-update! (lambda (rs)\n                                                                (foldl (lambda (name desc rs) (hash-set rs name desc))\n                                                                       rs names.in descs.relation.in)))\n                                           (checkpoint!))\n      ((compact!)                          (compact!)))))\n\n(define (database-path             db)              ((wrapped-database-controller db) 'path))\n(define (database-metadata         db)              ((wrapped-database-controller db) 'metadata))\n(define (database-relation         db name)         ((wrapped-database-controller db) 'relation         name))\n(define (database-relation-names   db)              (hash-keys     (hash-ref (database-metadata db) 'relations)))\n(define (database-relation-has?    db name)         (hash-has-key? (hash-ref (database-metadata db) 'relations) name))\n(define (database-relation-add!    db name . pargs) ((wrapped-database-controller db) 'relation-add!    name\n                                                                                      (plist-ref pargs 'attributes)\n                                                                                      (plist-ref pargs 'type)\n                                                                                      (plist-ref pargs 'source)))\n(define (database-relation-remove! db name)         (relation-delete! (database-relation db name)))\n(define (database-compact!         db)              ((wrapped-database-controller db) 'compact!))\n\n(define (database-import! db db.in    . relation-names.in)\n  ((wrapped-database-controller db) 'import! (wrapped-database-controller db.in) relation-names.in))\n(define (database-export! db path.out . relation-names.out)\n  (let ((path.out (normalize-path path.out)))\n    (when (or (file-exists? path.out) (directory-exists? path.out))\n      (error \"export destination already exists\" path.out))\n    (apply database-import! (database path.out) db relation-names.out)))\n\n(define (relation-name                r)                    ((wrapped-relation-controller r) 'name))\n(define (relation-metadata            r)                    ((wrapped-relation-controller r) 'metadata))\n(define (relation-copy!               r name.new)           ((wrapped-relation-controller r) 'copy!              name.new))\n(define (relation-rename!             r name.new)           ((wrapped-relation-controller r) 'rename!            name.new))\n(define (relation-delete!             r)                    ((wrapped-relation-controller r) 'delete!))\n(define (relation-rename-attributes!  r attrs.new)          ((wrapped-relation-controller r) 'rename-attributes! attrs.new))\n(define (relation-index-add!          r . signatures)       ((wrapped-relation-controller r) 'index-add!         signatures))\n(define (relation-index-remove!       r . signatures)       ((wrapped-relation-controller r) 'index-remove!      signatures))\n(define (relation-index-dict          r signature preload?) ((wrapped-relation-controller r) 'index-dict         signature preload?))\n(define (relation-domain-dicts        r preload?)           ((wrapped-relation-controller r) 'domain-dicts       preload?))\n(define (relation-compact!            r)                    ((wrapped-relation-controller r) 'compact!))\n\n;; TODO: in-place sorting of multiple columns\n(define (int-tuplestring\n                     (build-path path.table (string-append fn.col \".\" (number->string i)))))\n       column-ids))\n\n(define (ingest-relation-source apath.root lpath.domain-text lpath.table type s.in)\n  (define bytes=>id             (make-btree))\n  (define size.bytes            0)\n  (define count.tuples.initial  0)\n  (define apath.domain.value    (path->string (build-path apath.root lpath.domain-text fn.value)))\n  (define apath.domain.pos      (path->string (build-path apath.root lpath.domain-text fn.pos)))\n  (define apath*.column         (column-paths (build-path apath.root lpath.table) (range (length type))))\n  (define apath*.column.initial (map (lambda (p.c) (string-append p.c fnsuffix.initial))\n                                     apath*.column))\n  (define (insert-bytes! b)\n    (let* ((count.0 (btree-count bytes=>id))\n           (id      (btree-ref-or-set! bytes=>id b)))\n      (unless (unsafe-fx= count.0 (btree-count bytes=>id))\n        (set! size.bytes (unsafe-fx+ size.bytes (bytes-length b))))\n      id))\n  (define row->tuple\n    (let ((col->num* (map (lambda (i t.col)\n                            (match t.col\n                              ('int    (lambda (x)\n                                         (unless (int?    x) (error \"invalid int\"    `(column: ,i) x))\n                                         x))\n                              ('nat    (lambda (x)\n                                         (unless (nat?    x) (error \"invalid nat\"    `(column: ,i) x))\n                                         x))\n                              ('bytes  (lambda (x)\n                                         (unless (bytes?  x) (error \"invalid bytes\"  `(column: ,i) x))\n                                         (insert-bytes!                                      x)))\n                              ('string (lambda (x)\n                                         (unless (string? x) (error \"invalid string\" `(column: ,i) x))\n                                         (insert-bytes! (string->bytes/utf-8                 x))))\n                              ('symbol (lambda (x)\n                                         (unless (symbol? x) (error \"invalid symbol\" `(column: ,i) x))\n                                         (insert-bytes! (string->bytes/utf-8 (symbol->string x)))))\n                              (_ (error \"(currently) unsupported type\"                `(column: ,i) t.col))))\n                          (range (length type))\n                          type)))\n      (lambda (row)\n        (set! count.tuples.initial (unsafe-fx+ count.tuples.initial 1))\n        (let loop ((col* row) (col->num* col->num*))\n          (match* (col* col->num*)\n            (((cons col col*) (cons col->num col->num*)) (cons (col->num col) (loop col* col->num*)))\n            (('()             '())                       '())\n            ((_               _)                         (error \"incorrect number of columns\" row type)))))))\n\n  (apply pretty-log '(ingesting rows and writing initial tuple columns) apath*.column.initial)\n  (call/files\n    '() apath*.column.initial\n    (lambda outs.column.initial\n      (define type.tuple (map (lambda (_) 'int) type))\n      (time/pretty-log\n        (s-each (lambda (row) (for-each encode outs.column.initial type.tuple (row->tuple row)))\n                s.in))))\n\n  (define size.pos  (min-nat-bytes size.bytes))\n  (define count.ids (btree-count bytes=>id))\n  (define id=>id    (make-fxvector count.ids))\n  (pretty-log `(ingested ,count.tuples.initial tuples))\n  (pretty-log `(enumerating ,(btree-count bytes=>id) strings -- ,size.bytes bytes total))\n  (pretty-log '(writing sorted strings to) apath.domain.value\n              '(writing positions to) apath.domain.pos)\n  (let/files () ((out.bytes.value apath.domain.value)\n                 (out.bytes.pos   apath.domain.pos))\n    (define (write-pos)\n      (write-bytes (nat->bytes size.pos (file-position out.bytes.value)) out.bytes.pos))\n    (write-pos)\n    (time/pretty-log\n      (let ((i 0))\n        (btree-enumerate\n          bytes=>id\n          (lambda (b id)\n            (write-bytes b out.bytes.value)\n            (write-pos)\n            (unsafe-fxvector-set! id=>id id i)\n            (set! i (unsafe-fx+ i 1)))))))\n  (define desc.domain-text\n    (hash 'count         count.ids\n          'size.position size.pos))\n  (write-metadata (build-path apath.root lpath.domain-text fn.metadata.initial) desc.domain-text)\n\n  (pretty-log '(remapping columns))\n  (define column-vmms\n    (map (lambda (t.col apath.in)\n           (define col->col\n             (match t.col\n               ((or 'nat 'int)              (lambda (n)  n))\n               ((or 'bytes 'string 'symbol) (lambda (id) (unsafe-fxvector-ref id=>id id)))))\n           (define (read-element in) (col->col (decode in 'int)))\n           (match-define (list vec.col min.col max.col)\n             (read-column/bounds apath.in count.tuples.initial read-element))\n           (pretty-log `(deleting ,apath.in))\n           (delete-file apath.in)\n           (list vec.col min.col max.col))\n         type apath*.column.initial))\n  (define columns (map car column-vmms))\n\n  (define tuples  (sorted-tuples count.tuples.initial columns))\n  (pretty-log '(deduplicating tuples))\n  (define (columns-set! j tuple) (for-each (lambda (vec.col value.col)\n                                             (unsafe-vector*-set! vec.col j value.col))\n                                           columns tuple))\n  (define count.tuples.unique\n    (time/pretty-log\n      (when (unsafe-fx< 0 count.tuples.initial)\n        (define t0 (unsafe-vector*-ref tuples 0))\n        (columns-set! 0 t0)\n        (let loop ((prev t0) (i 1) (j 1))\n          (if (unsafe-fx< i count.tuples.initial)\n            (let ((next (unsafe-vector*-ref tuples i)))\n              (cond ((equal? prev next) (loop prev (unsafe-fx+ i 1) j))\n                    (else (columns-set! j next)\n                          (loop next (unsafe-fx+ i 1) (unsafe-fx+ j 1)))))\n            j)))))\n\n  (define column-descriptions\n    (map (lambda (t.col vec.col min.col max.col apath.out)\n           (match-define (cons size.col offset.col)\n             (write-column apath.out count.tuples.unique vec.col min.col max.col))\n           (hash 'type   (match t.col\n                           ((or 'nat 'int)              'int)\n                           ((or 'bytes 'string 'symbol) 'text))\n                 'count  count.tuples.unique\n                 'size   size.col\n                 'offset offset.col\n                 'min    min.col\n                 'max    max.col))\n         type columns (map cadr column-vmms) (map caddr column-vmms) apath*.column))\n  (define desc.table\n    (hash 'direction 'insert\n          'domain    (hash 'text lpath.domain-text)\n          'count     count.tuples.unique\n          'columns   column-descriptions))\n  (write-metadata (build-path apath.root lpath.table fn.metadata.initial) desc.table)\n\n  (hash 'domain (hash 'text desc.domain-text)\n        'table  desc.table))\n\n(define ((multi-merge vector gens))\n  (define end (vector-length h))\n  (heap! string (build-path apath.domain-text.new fn.value)))\n  (define apath.pos    (path->string (build-path apath.domain-text.new fn.pos)))\n  (define size.bytes   (sum (map (lambda (apath.in) (file-size (build-path apath.in fn.value)))\n                                 apaths.domain-text)))\n  (define size.pos     (min-nat-bytes size.bytes))\n  (define id=>ids      (map (lambda (desc.in) (make-fxvector (hash-ref desc.in 'count)))\n                            descs.domain-text))\n  (define custodian.gs (make-custodian))\n  (define gs           (parameterize ((current-custodian custodian.gs))\n                         (map (lambda (apath.in desc.in id=>id)\n                                (define count       (hash-ref desc.in 'count))\n                                (define size.pos    (hash-ref desc.in 'size.position))\n                                (define apath.value (build-path apath.in fn.value))\n                                (define apath.pos   (build-path apath.in fn.pos))\n                                (and (unsafe-fx< 0 count)\n                                     (let ((in.value (open-input-file apath.value))\n                                           (in.pos   (open-input-file apath.pos)))\n                                       (define (read-pos) (bytes-nat-ref (read-bytes size.pos in.pos)\n                                                                         size.pos\n                                                                         0))\n                                       (let loop ((id 0) (pos.current (read-pos)))\n                                         (let ((pos.next (read-pos)))\n                                           (cons (read-bytes (unsafe-fx- pos.next pos.current) in.value)\n                                                 (lambda (i)\n                                                   (unsafe-fxvector-set! id=>id id i)\n                                                   (and (unsafe-fx< (unsafe-fx+ id 1) count)\n                                                        (loop (unsafe-fx+ id 1) pos.next)))))))))\n                              apaths.domain-text descs.domain-text id=>ids)))\n  (pretty-log '(merging domains) (map cons apaths.domain-text descs.domain-text)\n              '(writing merge-sorted strings to) apath.value\n              '(writing positions to) apath.pos)\n  (define count.ids    (let/files () ((out.value apath.value)\n                                      (out.pos   apath.pos))\n                         (define (write-pos) (write-bytes (nat->bytes size.pos\n                                                                      (file-position out.value))\n                                                          out.pos))\n                         (write-pos)\n                         (time/pretty-log\n                           ((multi-merge (lambda (g.0 g.1) (bytesid)\n                              (let loop ((i (unsafe-fx- (unsafe-fxvector-length id=>id) 1)))\n                                (and (unsafe-fx<= 0 i)\n                                     (if (unsafe-fx= i (unsafe-fxvector-ref id=>id i))\n                                       (loop (unsafe-fx- i 1))\n                                       id=>id))))\n                            id=>ids))\n  (define desc.domain-text\n    (hash 'count         count.ids\n          'size.position size.pos))\n  (write-metadata (build-path apath.domain-text.new fn.metadata.initial) desc.domain-text)\n  (hash 'domain-text desc.domain-text\n        'remappings  remappings))\n\n(define ((attrs->signature->ordering attrs) signature)\n  (map (lambda (attr) (let ((i (index-of attrs attr)))\n                        (if i i (error \"invalid signature attribute\" attr signature))))\n       signature))\n\n(define (normalize-table-index-orderings count.columns orderings)\n  (for-each (lambda (ordering) (unless (and (not (null? ordering))\n                                            (list? ordering)\n                                            (andmap (lambda (i) (and (nat? i) (<= 0 i) (< i count.columns)))\n                                                    ordering)\n                                            (= (length ordering) (set-count (list->set ordering))))\n                                 (error \"invalid index\" ordering)))\n            orderings)\n  (remove-duplicates\n    (map (lambda (ordering)\n           (define len (length ordering))\n           (cond ((= (+ len 1) count.columns) (append ordering (set-subtract (range count.columns)\n                                                                             ordering)))\n                 ((<    len    count.columns) (append ordering '(#t)))\n                 (else                                ordering)))\n         orderings)))\n\n(define (build-table-indexes apath.root lpath*.index lpath.table desc.table orderings)\n  (define apath.root.table  (path->string (build-path apath.root lpath.table)))\n  (define apath*.root.index (map (lambda (lpath.index) (path->string (build-path apath.root lpath.index)))\n                                 lpath*.index))\n  (define count.tuples      (hash-ref desc.table 'count))\n  (define desc*.column      (hash-ref desc.table 'columns))\n  (define count.columns     (length desc*.column))\n  (pretty-log '(building indexes for) apath.root.table orderings desc.table apath*.root.index)\n  (define key-used?       (ormap (lambda (ordering) (member #t ordering))\n                                 orderings))\n  (define column-ids.used (set->list (set-remove (foldl (lambda (ordering col-ids)\n                                                          (set-union col-ids (list->set ordering)))\n                                                        (set) orderings)\n                                                 #t)))\n  (define size.pos        (min-nat-bytes (- count.tuples 1)))\n  (define i=>desc.col     (make-immutable-hash\n                            (append (if key-used?\n                                      (list (cons #t (hash 'type   'int\n                                                           'count  count.tuples\n                                                           'size   size.pos\n                                                           'offset 0\n                                                           'min    0\n                                                           'max    (- count.tuples 1))))\n                                      '())\n                                    (map cons (range count.columns) desc*.column))))\n  (define i=>col          (make-immutable-hash\n                            (append (if key-used?\n                                      (list (cons #t (let ((column.key (make-vector count.tuples)))\n                                                       (let loop ((i 0))\n                                                         (when (unsafe-fx< i count.tuples)\n                                                           (unsafe-vector*-set! column.key i i)\n                                                           (loop (unsafe-fx+ i 1))))\n                                                       column.key)))\n                                      '())\n                                    (map (lambda (i.col apath.in)\n                                           (cons i.col (read-column apath.in (hash-ref i=>desc.col i.col))))\n                                         column-ids.used\n                                         (column-paths apath.root.table column-ids.used)))))\n  (map (lambda (apath.root.index ordering)\n         (pretty-log '(building index) apath.root.index '(with ordering) ordering)\n         (define columns.used        (map (lambda (i.col) (hash-ref i=>col      i.col))   ordering))\n         (define descs.used          (map (lambda (i.col) (hash-ref i=>desc.col i.col))   ordering))\n         (define s&o*.used           (map (lambda (desc) (ideal-size-and-offset (hash-ref desc 'min)\n                                                                                (hash-ref desc 'max)))\n                                          descs.used))\n         (define sizes.used          (map car s&o*.used))\n         (define offsets.used        (map cdr s&o*.used))\n         (define tuples              (sorted-tuples count.tuples columns.used))\n         (define apath*.col.key      (map (lambda (apath.col) (string-append apath.col fnsuffix.key))\n                                          (column-paths apath.root.index (range    (length ordering)))))\n         (define apath*.col.indirect (map (lambda (apath.col) (string-append apath.col fnsuffix.indirect))\n                                          (column-paths apath.root.index (range (- (length ordering) 1)))))\n         (pretty-log '(writing index columns))\n         (define counts\n           (call/files\n             '()\n             apath*.col.key\n             (lambda out*.key\n               (call/files\n                 '()\n                 apath*.col.indirect\n                 (lambda out*.indirect\n                   (time/pretty-log\n                     (when (< 0 count.tuples)\n                       (for-each (lambda (out) (write-bytes (nat->bytes size.pos 0) out))\n                                 out*.indirect)\n                       (let loop.keys ((i*.key        (range (length ordering)))\n                                       (size*.key     sizes.used)\n                                       (offset*.key   offsets.used)\n                                       (out*.key      out*.key)\n                                       (out*.indirect out*.indirect)\n                                       (pos*          (make-list (length out*.key) 0))\n                                       (start         0)\n                                       (end           count.tuples))\n                         (let ((i.key      (car i*.key))\n                               (i*.key     (cdr i*.key))\n                               (size.key   (car size*.key))\n                               (offset.key (car offset*.key)))\n                           (define (key-ref i) (unsafe-list-ref (unsafe-vector*-ref tuples i) i.key))\n                           (let ((out.key (car out*.key)))\n                             (define (write-key key) (write-bytes (nat->bytes size.key (unsafe-fx- key offset.key)) out.key))\n                             (if (null? i*.key)\n                               (let loop.final ((i start))\n                                 (cond ((unsafe-fx< i end) (write-key (key-ref i))\n                                                           (loop.final (unsafe-fx+ i 1)))\n                                       (else               (list (unsafe-fx+ (car pos*) (unsafe-fx- i start))))))\n                               (let ((out.indirect (car out*.indirect)))\n                                 (let loop.key ((pos (car pos*)) (pos* (cdr pos*)) (start start) (end end))\n                                   (if (unsafe-fx< start end)\n                                     (let ((key (key-ref start)))\n                                       (write-key key)\n                                       (let ((start.new (bisect-next start end (lambda (i) (unsafe-fx<= (key-ref i) key)))))\n                                         (let ((pos* (loop.keys i*.key\n                                                                (cdr size*.key)\n                                                                (cdr offset*.key)\n                                                                (cdr out*.key)\n                                                                (cdr out*.indirect)\n                                                                pos*\n                                                                start\n                                                                start.new)))\n                                           (write-bytes (nat->bytes size.pos (car pos*)) out.indirect)\n                                           (loop.key (unsafe-fx+ pos 1) pos* start.new end))))\n                                     (cons pos pos*)))))))))))))))\n         (define descs.column.key      (map (lambda (apath desc count size offset)\n                                              (let* ((desc (hash-set* desc 'count count 'size size 'offset offset)))\n                                                (cond ((column-consecutive? (lambda () (read-column apath desc))\n                                                                            count\n                                                                            (hash-ref desc 'min)\n                                                                            (hash-ref desc 'max))\n                                                       (delete-file apath)\n                                                       (hash-set* desc 'size 0 'offset (hash-ref desc 'min)))\n                                                      (else desc))))\n                                            apath*.col.key descs.used counts sizes.used offsets.used))\n         (define descs.column.indirect (map (lambda (apath.indirect count.current count.next)\n                                              (cond ((= count.current count.next)\n                                                     (pretty-log '(deleting identity indirection) apath.indirect)\n                                                     (delete-file apath.indirect)\n                                                     #f)\n                                                    (else (hash 'type  'int\n                                                                'count count.current\n                                                                'size  size.pos\n                                                                'min   0\n                                                                'max   count.next))))\n                                            apath*.col.indirect\n                                            (reverse (cdr (reverse counts)))\n                                            (cdr counts)))\n         (define desc.table-index      (hash 'table            lpath.table\n                                             'ordering         ordering\n                                             'columns.key      descs.column.key\n                                             'columns.indirect descs.column.indirect))\n         (write-metadata (build-path apath.root.index fn.metadata.initial) desc.table-index)\n         desc.table-index)\n       apath*.root.index orderings))\n\n(define (read-column/bounds apath.in count read-element)\n  ;; TODO: consider specialized vectors: https://docs.racket-lang.org/foreign/homogeneous-vectors.html\n  (define vec.col (make-vector count))\n  (pretty-log `(reading ,count elements and computing min/max from) apath.in)\n  (let/files ((in apath.in)) ()\n    (time/pretty-log\n      (let loop ((i 0) (min.col #f) (max.col 0))\n        (cond ((unsafe-fx< i count)\n               (define value (read-element in))\n               (unsafe-vector*-set! vec.col i value)\n               (loop (unsafe-fx+ i 1)\n                     (if min.col (unsafe-fxmin min.col value) value)\n                     (unsafe-fxmax max.col value)))\n              (else (list vec.col (or min.col 0) max.col)))))))\n\n(define (read-column apath.in desc.in)\n  (define count   (hash-ref desc.in 'count))\n  (define size    (hash-ref desc.in 'size))\n  (define offset  (hash-ref desc.in 'offset 0)) ; TODO: later, require this\n  ;; TODO: consider specialized vectors: https://docs.racket-lang.org/foreign/homogeneous-vectors.html\n  (define vec.col (make-vector count))\n  (cond ((< 0 size) (pretty-log `(reading ,count elements from) apath.in)\n                    (let/files ((in apath.in)) ()\n                      (time/pretty-log\n                        (let loop ((i 0))\n                          (cond ((unsafe-fx< i count) (define v.in (bytes-nat-ref (read-bytes size in) size 0))\n                                                      (unsafe-vector*-set! vec.col i (unsafe-fx+ offset v.in))\n                                                      (loop (unsafe-fx+ i 1)))\n                                (else                 vec.col))))))\n        (else       (pretty-log `(building ,count consecutive integers starting at ,offset)\n                                '(instead of reading from) apath.in)\n                    (let loop ((i 0))\n                      (cond ((unsafe-fx< i count) (unsafe-vector*-set! vec.col i (unsafe-fx+ offset i))\n                                                  (loop (unsafe-fx+ i 1)))\n                            (else                 vec.col))))))\n\n(define (write-column apath.out count vec.col min.col max.col)\n  (if (column-consecutive? (lambda () vec.col) count min.col max.col)\n    (begin (pretty-log '(not writing column to file because column is consecutive)\n                       `(would have written ,count elements to) apath.out\n                       `(nat-size: ,0 offset: ,min.col min: ,min.col max: ,max.col))\n           (cons 0 min.col))\n    (match-let (((cons size.col offset.col) (ideal-size-and-offset min.col max.col)))\n      (pretty-log `(writing ,count elements to) apath.out\n                  `(nat-size: ,size.col offset: ,offset.col min: ,min.col max: ,max.col))\n      (let/files () ((out apath.out))\n        (time/pretty-log\n          (let loop ((i 0))\n            (when (unsafe-fx< i count)\n              (write-bytes (nat->bytes size.col (unsafe-fx- (unsafe-vector*-ref vec.col i) offset.col)) out)\n              (loop (unsafe-fx+ i 1))))))\n      (cons size.col offset.col))))\n\n(define (ideal-size-and-offset min.col max.col)\n  (define diff.col  (- max.col min.col))\n  (define size.diff (min-nat-bytes diff.col))\n  (define size.max  (min-nat-bytes max.col))\n  (if (or (< min.col   0)\n          (< size.diff size.max))\n    (cons size.diff min.col)\n    (cons size.max  0)))\n\n(define (column-consecutive? ->vec count.col min.col max.col)\n  (and (unsafe-fx= count.col (unsafe-fx+ 1 (unsafe-fx- max.col min.col)))\n       (let ((vec.col (->vec)))\n         (let loop ((i 0) (expected min.col))\n           (or (unsafe-fx= i count.col)\n               (and (unsafe-fx= expected (unsafe-vector*-ref vec.col i))\n                    (loop (unsafe-fx+ i 1) (unsafe-fx+ expected 1))))))))\n\n(define (remap-column?      desc.col   type=>id=>id) (not (not (hash-ref type=>id=>id (hash-ref desc.col 'type) #f))))\n(define (remap-table?       desc.table type=>id=>id) (ormap (lambda (desc.col) (remap-column? desc.col type=>id=>id))\n                                                            (hash-ref desc.table 'columns)))\n(define (remap-table-index? desc.ti    type=>id=>id) (ormap (lambda (desc.col) (remap-column? desc.col type=>id=>id))\n                                                            (hash-ref desc.ti 'columns.key)))\n\n(define (remap-column apath.in apath.out desc.in type=>id=>id)\n  (pretty-log `(remapping ,apath.in to ,apath.out) desc.in)\n  (define type    (hash-ref desc.in 'type))\n  (define count   (hash-ref desc.in 'count))\n  (define size.in (hash-ref desc.in 'size))\n  (define offset  (hash-ref desc.in 'offset 0)) ; TODO: later, require this\n  (define id=>id  (hash-ref type=>id=>id type #f))\n  (cond (id=>id (match-define (list vec.col min.col max.col)\n                  (if (unsafe-fx< 0 size.in)\n                    (read-column/bounds apath.in count\n                                        (lambda (in)\n                                          (define v.in (bytes-nat-ref (read-bytes size.in in) size.in 0))\n                                          (unsafe-fxvector-ref id=>id (unsafe-fx+ offset v.in))))\n                    (let ((vec (make-fxvector count)))\n                      (let loop ((i 0))\n                        (cond ((unsafe-fx< i count) (unsafe-fxvector-set! vec i (unsafe-fxvector-ref id=>id (unsafe-fx+ offset i)))\n                                           (loop (unsafe-fx+ i 1)))\n                              (else        (list vec\n                                                 (unsafe-fxvector-ref id=>id offset)\n                                                 (unsafe-fxvector-ref id=>id (unsafe-fx+ offset (unsafe-fx- count 1))))))))))\n                (match-define (cons size.col offset.col)\n                  (write-column apath.out (vector-length vec.col) vec.col min.col max.col))\n                (hash-set* desc.in 'size size.col 'offset offset.col 'min min.col 'max max.col))\n        ((unsafe-fx= 0 size.in) (pretty-log '(identity remapping on a consecutive integer sequence: nothing to do))\n                                desc.in)\n        (else (pretty-log '(copying verbatim due to identity remapping))\n              (time/pretty-log (copy-file apath.in apath.out))\n              desc.in)))\n\n(define (remap-table apath.in apath.out desc.table.in desc.domain.new type=>id=>id)\n  (pretty-log `(remapping ,apath.in to ,apath.out) desc.table.in)\n  (define columns.in     (hash-ref desc.table.in 'columns))\n  (define columns.out    (map (lambda (apath.in.col apath.out.col desc.in.col)\n                                (remap-column apath.in.col apath.out.col desc.in.col type=>id=>id))\n                              (column-paths apath.in  (range (length columns.in)))\n                              (column-paths apath.out (range (length columns.in)))\n                              columns.in))\n  (define desc.table.out (hash 'domain  desc.domain.new\n                               'count   (hash-ref desc.table.in 'count)\n                               'columns columns.out))\n  (write-metadata (build-path apath.out fn.metadata.initial) desc.table.out)\n  desc.table.out)\n\n(define (remap-table-index apath.in apath.out desc.table-index.in lpath.table.new type=>id=>id)\n  (pretty-log `(remapping ,apath.in to ,apath.out) desc.table-index.in)\n  (define (remap fnsuffix desc*.in)\n    (map (lambda (apath.in.col apath.out.col desc.in.col)\n           (and desc.in.col (remap-column apath.in.col apath.out.col desc.in.col type=>id=>id)))\n         (map (lambda (apath.col) (string-append apath.col fnsuffix))\n              (column-paths apath.in  (range (length desc*.in))))\n         (map (lambda (apath.col) (string-append apath.col fnsuffix))\n              (column-paths apath.out (range (length desc*.in))))\n         desc*.in))\n  (define columns.key.in       (hash-ref desc.table-index.in 'columns.key))\n  (define columns.indirect.in  (hash-ref desc.table-index.in 'columns.indirect))\n  (define columns.key.out      (remap fnsuffix.key      columns.key.in))\n  (define columns.indirect.out (remap fnsuffix.indirect columns.indirect.in))\n  (define desc.table-index.out (hash-set* desc.table-index.in\n                                          'table            lpath.table.new\n                                          'columns.key      columns.key.out\n                                          'columns.indirect columns.indirect.out))\n  (write-metadata (build-path apath.out fn.metadata.initial) desc.table-index.out)\n  desc.table-index.out)\n\n;; 2-3 tree\n(define (make-btree) (vector 0 #f))\n\n(define (bytes-compare a b)\n  (let* ((len.a (unsafe-bytes-length a)) (len.b (unsafe-bytes-length b)) (end (unsafe-fxmin len.a len.b)))\n    (let loop ((i 0))\n      (if (unsafe-fx= i end)\n          (cond ((unsafe-fx< len.a len.b) -1)\n                ((unsafe-fx< len.b len.a)  1)\n                (else                      0))\n          (let ((x.a (unsafe-bytes-ref a i)) (x.b (unsafe-bytes-ref b i)))\n            (cond ((unsafe-fx< x.a x.b) -1)\n                  ((unsafe-fx< x.b x.a)  1)\n                  (else                 (loop (unsafe-fx+ i 1)))))))))\n\n(define (btree-count bt) (unsafe-vector*-ref bt 0))\n\n(define (make-btree-2 key                leaf                 l r)   (vector key                leaf                 l r))\n(define (make-btree-3 left-key right-key left-leaf right-leaf l m r) (vector left-key right-key left-leaf right-leaf l m r))\n\n(define (btree-2?      t) (unsafe-fx= (unsafe-vector*-length t) 4))\n(define (btree-2-key   t) (unsafe-vector*-ref t 0))\n(define (btree-2-leaf  t) (unsafe-vector*-ref t 1))\n(define (btree-2-left  t) (unsafe-vector*-ref t btree-2-left:i))\n(define (btree-2-right t) (unsafe-vector*-ref t btree-2-right:i))\n\n(define (btree-2-left-set!  t u) (unsafe-vector*-set! t btree-2-left:i  u))\n(define (btree-2-right-set! t u) (unsafe-vector*-set! t btree-2-right:i u))\n\n(define btree-2-left:i  2)\n(define btree-2-right:i 3)\n\n(define (btree-3-left-key   t) (unsafe-vector*-ref t 0))\n(define (btree-3-right-key  t) (unsafe-vector*-ref t 1))\n(define (btree-3-left-leaf  t) (unsafe-vector*-ref t 2))\n(define (btree-3-right-leaf t) (unsafe-vector*-ref t 3))\n(define (btree-3-left       t) (unsafe-vector*-ref t btree-3-left:i))\n(define (btree-3-middle     t) (unsafe-vector*-ref t btree-3-middle:i))\n(define (btree-3-right      t) (unsafe-vector*-ref t btree-3-right:i))\n\n(define (btree-3-left-set!   t u) (unsafe-vector*-set! t btree-3-left:i   u))\n(define (btree-3-middle-set! t u) (unsafe-vector*-set! t btree-3-middle:i u))\n(define (btree-3-right-set!  t u) (unsafe-vector*-set! t btree-3-right:i  u))\n\n(define btree-3-left:i   4)\n(define btree-3-middle:i 5)\n(define btree-3-right:i  6)\n\n(define (btree-enumerate bt yield)\n  (let loop ((t (unsafe-vector*-ref bt 1)))\n    (when t\n      (cond ((btree-2? t) (loop  (btree-2-left t))\n                          (yield (btree-2-key t) (btree-2-leaf t))\n                          (loop  (btree-2-right t)))\n            (else (loop  (btree-3-left t))\n                  (yield (btree-3-left-key t) (btree-3-left-leaf t))\n                  (loop  (btree-3-middle t))\n                  (yield (btree-3-right-key t) (btree-3-right-leaf t))\n                  (loop  (btree-3-right t)))))))\n\n;; TODO: provide an id / value that we should map x to if it's not already present\n(define (btree-ref-or-set! bt x)\n  (let loop ((t        (unsafe-vector*-ref bt 1))\n             (replace! (lambda (u)            (unsafe-vector*-set! bt 1 u)))\n             (expand!  (lambda (key leaf l r) (unsafe-vector*-set! bt 1 (vector key leaf l r)))))\n    (cond\n      ((not t) (let ((count (unsafe-vector*-ref bt 0)))\n                 (unsafe-vector*-set! bt 0 (unsafe-fx+ count 1))\n                 (expand! x count #f #f)\n                 count))\n      ((btree-2? t) (case (bytes-compare x (btree-2-key t))\n                      ((-1) (loop (btree-2-left t)\n                                  (lambda (u) (btree-2-left-set! t u))\n                                  (lambda (left-key left-leaf l m)\n                                    (replace! (make-btree-3 left-key (btree-2-key t)\n                                                            left-leaf (btree-2-leaf t)\n                                                            l m (btree-2-right t))))))\n                      (( 1) (loop (btree-2-right t)\n                                  (lambda (u) (btree-2-right-set! t u))\n                                  (lambda (right-key right-leaf m r)\n                                    (replace! (make-btree-3 (btree-2-key t) right-key\n                                                            (btree-2-leaf t) right-leaf\n                                                            (btree-2-left t) m r)))))\n                      (else (btree-2-leaf t))))\n      (else (case (bytes-compare x (btree-3-left-key t))\n              ((-1) (loop (btree-3-left t)\n                          (lambda (u) (btree-3-left-set! t u))\n                          (lambda (key leaf l r)\n                            (expand! (btree-3-left-key t)\n                                     (btree-3-left-leaf t)\n                                     (make-btree-2 key leaf l r)\n                                     (make-btree-2 (btree-3-right-key t) (btree-3-right-leaf t)\n                                                   (btree-3-middle t) (btree-3-right t))))))\n              (( 1) (case (bytes-compare x (btree-3-right-key t))\n                      ((-1) (loop (btree-3-middle t)\n                                  (lambda (u) (btree-3-middle-set! t u))\n                                  (lambda (key leaf l r)\n                                    (expand! key leaf\n                                             (make-btree-2 (btree-3-left-key t) (btree-3-left-leaf t)\n                                                           (btree-3-left t) l)\n                                             (make-btree-2 (btree-3-right-key t) (btree-3-right-leaf t)\n                                                           r (btree-3-right t))))))\n                      (( 1) (loop (btree-3-right t)\n                                  (lambda (u) (btree-3-right-set! t u))\n                                  (lambda (key leaf l r)\n                                    (expand! (btree-3-right-key t)\n                                             (btree-3-right-leaf t)\n                                             (make-btree-2 (btree-3-left-key t) (btree-3-left-leaf t)\n                                                           (btree-3-left t) (btree-3-middle t))\n                                             (make-btree-2 key leaf l r)))))\n                      (else (btree-3-right-leaf t))))\n              (else (btree-3-left-leaf t)))))))\n\n;; TODO: benchmark a design based on streams/iterators for comparison\n\n;; TODO:\n;; simple edb-relations vs. idb-relations w/ fixed-point iteration materializations (current + next-delta + now-being-produced)\n\n(define (bisect start end i<)\n  (let loop ((start start) (end end))\n    (if (<= end start) end\n      (let ((i (+ start (quotient (- end start) 2))))\n        (if (i< i) (loop (+ 1 i) end) (loop start i))))))\n\n(define (bisect-next start end i<)\n  (define i (- start 1))\n  (let loop ((offset 1))\n    (define next (+ i offset))\n    (cond ((and (< next end) (i< next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (next (+ i o)))\n                    (cond ((= o 0)                      (+ i 1))\n                          ((and (< next end) (i< next)) (loop next o))\n                          (else                         (loop i    o)))))))))\n\n(define (bisect-prev start end i>)\n  (define i end)\n  (let loop ((offset 1))\n    (define next (- i offset))\n    (cond ((and (>= next start) (i> next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (n (- i o)))\n                    (cond ((= o 0)                   i)\n                          ((and (>= n start) (i> n)) (loop n o))\n                          (else                      (loop i o)))))))))\n\n;; TODO: remove tables, or at least reduce their scope?\n(define table.empty\n  (method-lambda\n    ((length)                         0)\n    ((subtable start.sub (end.sub 0)) table.empty)\n    ((columns  start.col (end.col 0)) table.empty)\n    ((copy)                           table.empty)\n    ((dedup)                          table.empty)\n    ((dedup!)                         (void))\n    ((sort)                           table.empty)\n    ((sort!)                          (void))))\n\n(define (table columns (start 0) (end (vector-length (vector-ref columns 0))))\n  (if (= 0 (vector-length columns))\n    table.empty\n    (let loop ((start start) (end end))\n      (define (self-length)         (- end start))\n      (define (self-width)          (vector-length columns))\n      (define (self-column col)     (vector-ref    columns           col))\n      (define (self-ref  col row)   (vector-ref    (self-column col) row))\n      (define (self-set! col row v) (vector-set!   (self-column col) row v))\n      (define (self-copy)           (table (vector-map (lambda (v.col) (vector-copy v.col start end))\n                                                       columns)))\n      (define (self-dedup!)\n        (define width (self-width))\n        (let dedup ((row.prev start) (row (+ start 1)))\n          (if (= row end)\n            (when (< (+ row.prev 1) end)\n              (set! end (+ row.prev 1)))\n            (if (let duplicate? ((col 0))\n                  (or (= col width)\n                      (let ((v.col (self-column col)))\n                        (and (equal? (vector-ref v.col row.prev)\n                                     (vector-ref v.col row))\n                             (duplicate? (+ col 1))))))\n              (dedup row.prev (+ row 1))\n              (let ((row.prev (+ row.prev 1)))\n                (unless (= row.prev row)\n                  (let swap! ((col 0))\n                    (when (< col width)\n                      (let ((v.col (self-column col)))\n                        (vector-set! v.col row.prev (vector-ref v.col row))\n                        (swap! (+ col 1))))))\n                (dedup row.prev (+ row 1)))))))\n      (if (<= end start)\n        table.empty\n        (method-lambda\n          ((width)                                      (self-width))\n          ((length)                                     (self-length))\n          ((ref  col row)                               (self-ref  col row))\n          ((set! col row v)                             (self-set! col row v))\n          ((subtable start.sub (end.sub (self-length))) (loop (+ start start.sub) (+ start end.sub)))\n          ((columns  start.col (end.col (self-width)))  (table (vector-copy columns start.col end.col) start end))\n          ((copy)                                       (self-copy))\n          ((dedup)                                      (let ((t (self-copy)))\n                                                          (t 'dedup!)\n                                                          t))\n          ((dedup!)                                     (self-dedup!))\n          ;; TODO:\n          ;((sort ))\n          ;((sort! ))\n          )))))\n\n(define (table-width    t)                              (t 'width))\n(define (table-length   t)                              (t 'length))\n(define (table-ref      t col row)                      (t 'ref      col row))\n(define (table-set!     t col row v)                    (t 'set!     col row v))\n(define (table-subtable t start (end (table-length t))) (t 'subtable start end))\n(define (table-columns  t start (end (table-width  t))) (t 'columns  start end))\n(define (table-dedup    t)                              (t 'dedup))\n(define (table-dedup!   t)                              (t 'dedup!))\n(define (table-sort     t)                              (t 'sort))\n(define (table-sort!    t)                              (t 'sort!))\n\n;; TODO: support a direct-scanning operator, rather than scanning via column indices\n;; TODO: columns with methods: 'ref for what it does now, and 'enumerator for efficient scanning?\n;; TODO: more flexible/efficient method-lambda\n\n(define (column:identity                           i) i)\n(define ((column:const     c)                      _) c)\n(define ((column:offset    column offset)          i) (+ (column i) offset))\n(define ((column:vector    rows)                   i) (vector-ref rows i))\n(define ((column:table     columns)                i) (map (lambda (col) (col i)) columns))\n(define ((column:indirect  column.pos column)      i) (column (column.pos i)))\n(define ((column:interval  column.pos interval->x) i) (interval->x (column.pos i) (column.pos (+ i 1))))\n(define ((column:bytes:nat bs size)                i) (bytes-nat-ref bs size (* i size)))\n\n;; TODO: specialize to fixed-size nat\n(define (column:port                     in type) (let ((size.type (sizeof type (void))))\n                                                    (lambda (i)\n                                                      (file-position in (* i size.type))\n                                                      (decode        in type))))\n(define (column:port-indirect column.pos in type)   (lambda (i)\n                                                      (file-position in (column.pos i))\n                                                      (decode        in type)))\n;; TODO: generalize to bytes\n(define (column:port-string   column.pos in)      (column:interval\n                                                    column.pos\n                                                    (lambda (pos.0 pos.1)\n                                                      (file-position in pos.0)\n                                                      (bytes->string/utf-8 (read-bytes (- pos.1 pos.0) in)))))\n\n(define ((interval->dict:ordered i->key i->value) start end) (dict:ordered i->key i->value start end))\n\n;; TODO: not needed?\n;(define (dict:ordered:trie start end)\n  ;)\n\n\n(define dict.empty\n  (method-lambda\n    ((empty?)                  #t)\n    ((count)                   0)\n    ((=/= _)                   dict.empty)\n    ((==  _)                   dict.empty)\n    ((<=  _)                   dict.empty)\n    ((<   _)                   dict.empty)\n    ((>=  _)                   dict.empty)\n    ((>   _)                   dict.empty)\n    ((bstr-prefix   _)         dict.empty)\n    ((bstr-contains _)         dict.empty)\n    ((has-key?      _)         #f)\n    ((ref _ k.found k.missing) (k.missing))\n    ((enumerator/2)            (lambda _ (void)))\n    ((enumerator)              (lambda _ (void)))))\n\n(define (dict:integer offset.key i->value start end)\n  (let loop ((start start) (end end))\n    (define self\n      (if (<= end start)\n        dict.empty\n        (method-lambda\n          ((pop)    (loop (+ start 1) end))\n          ((empty?) (= end start))\n          ((count)  (- end start))\n          ((top)    (i->value start))\n          ((max)    (+ offset.key (- end 1)))\n          ((min)    (+ offset.key start))\n          ((>= key) (loop (max start    (- key offset.key))    end))\n          ((>  key) (loop (max start (+ (- key offset.key) 1)) end))\n          ((<= key) (loop start                                (min end (+ (- key offset.key) 1))))\n          ((<  key) (loop start                                (min end    (- key offset.key))))\n          ((== key) ((self '>= key) '<= key))\n          ((has-key? key)              (let ((self (self '>= key)))\n                                         (and (not (self 'empty?))\n                                              (equal? (self 'min) key))))\n          ((ref key k.found k.missing) (let ((self (self '>= key)))\n                                         (if (or (self 'empty?)\n                                                 (not (equal? (self 'min) key)))\n                                           (k.missing)\n                                           (k.found (self 'top)))))\n          ((enumerator/2)              (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (+ i offset.key) (i->value i))\n                                             (loop (+ i 1))))))\n          ((enumerator)                (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (+ i offset.key))\n                                             (loop (+ i 1)))))))))\n    self))\n\n(define (dict:ordered i->key i->value start end)\n  (let loop ((start start) (end end))\n    (define (after  k<) (loop (bisect-next start end (lambda (i) (k< (i->key i)))) end))\n    (define (before k>) (loop start (bisect-prev start end (lambda (i) (k> (i->key i))))))\n    (define self\n      (if (<= end start)\n        dict.empty\n        (method-lambda\n          ((pop)       (loop (+ start 1) end))\n          ((empty?)    (= end start))\n          ((count)     (- end start))\n          ((top)       (i->value start))\n          ((max)       (i->key   (- end 1)))\n          ((min)       (i->key   start))\n          ((after  k<) (after  k<))\n          ((before k>) (before k>))\n          ((>= key)    (after  (lambda (k) (any  key)    (after  (lambda (k) (any<=? k key))))\n          ((<= key)    (before (lambda (k) (any= key) '<= key))\n          ((has-key? key)              (let ((self (self '>= key)))\n                                         (and (not (self 'empty?))\n                                              (equal? (self 'min) key))))\n          ((ref key k.found k.missing) (let ((self (self '>= key)))\n                                         (if (or (self 'empty?)\n                                                 (not (equal? (self 'min) key)))\n                                           (k.missing)\n                                           (k.found (self 'top)))))\n          ((enumerator/2)              (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (i->key i) (i->value i))\n                                             (loop (+ i 1))))))\n          ((enumerator)                (lambda (yield)\n                                         (let loop ((i start))\n                                           (when (< i end)\n                                             (yield (i->key i))\n                                             (loop (+ i 1)))))))))\n    self))\n\n(define (dict:ordered:union combined-value d.left d.right)\n  (let loop ((d.left d.left) (d.right d.right))\n    (define (shared d.left d.right)\n      (method-lambda\n        ((empty?)    #f)\n        ((min)       (d.left 'min))\n        ((max)       (let ((max.left  (d.left  'max))\n                           (max.right (d.right 'max)))\n                       (if (any) (loop (d.left 'before k>) (d.right 'before k>)))\n        ((>= key)    (loop (d.left '>= key) (d.right '>= key)))\n        ((>  key)    (loop (d.left '>  key) (d.right '>  key)))\n        ((<= key)    (loop (d.left '<= key) (d.right '<= key)))\n        ((<  key)    (loop (d.left '<  key) (d.right '<  key)))\n        ((== key)    (loop (d.left '== key) (d.right '== key)))\n        ((has-key? key)              (or (d.left 'has-key? key) (d.right 'has-key? key)))\n        ((ref key k.found k.missing) (d.left 'ref key\n                                             (lambda (v.left)\n                                               (d.right 'ref key\n                                                        (lambda (v.right) (combined-value v.left v.right))\n                                                        (lambda ()        v.left)))\n                                             (lambda () (d.right 'ref key k.found k.missing))))\n\n        ((enumerator/2)              (merge-union combined-value d.left d.right))\n        ((enumerator)                (merge-key-union d.left d.right))))\n    (define (less d.left d.right)\n      (define super (shared d.left d.right))\n      (method-lambda\n        ((pop)   (loop (d.left 'pop) d.right))\n        ((top)   (d.left 'top))\n        ((count) (+ (d.left 'count) (d.right 'count)))\n        (else    super)))\n    (define (same d.left d.right)\n      (define super (shared d.left d.right))\n      (method-lambda\n        ((pop)   (loop (d.left 'pop) (d.right 'pop)))\n        ((top)   (combined-value (d.left 'top) (d.right 'top)))\n        ((count) (+ (d.left 'count) (d.right 'count) -1))\n        (else    super)))\n    (cond ((d.left  'empty?)                     d.right)\n          ((d.right 'empty?)                     d.left)\n          ((any) (loop (d.pos 'before k>) (d.neg 'before k>)))\n        ((>= key)    (loop (d.pos '>= key)    (d.neg '>= key)))\n        ((>  key)    (loop (d.pos '>  key)    (d.neg '>  key)))\n        ((<= key)    (loop (d.pos '<= key)    (d.neg '<= key)))\n        ((<  key)    (loop (d.pos '<  key)    (d.neg '<  key)))\n        ((== key)    (loop (d.pos '== key)    (d.neg '== key)))))\n    (define (less d.pos d.neg)\n      (define super (shared d.pos d.neg))\n      (method-lambda\n        ((pop) (loop (d.pos 'pop) d.neg))\n        ((top) (d.pos 'top))\n        (else  super)))\n    (define (same d.pos d.neg)\n      (if (= count.keys 1)\n        (loop (d.pos 'pop) (d.neg 'pop))\n        (let ((d.pos.top (dict:ordered:subtraction (- count.keys 1) (d.pos 'top) (d.neg 'top))))\n          (if (d.pos.top 'empty?)\n            (loop (d.pos 'pop) (d.neg 'pop))\n            (let ((super (shared d.pos d.neg)))\n              (method-lambda\n                ((pop) (loop (d.pos 'pop) (d.neg 'pop)))\n                ((top) d.pos.top)\n                (else  super)))))))\n    (define self (cond ((d.pos 'empty?) dict.empty)\n                       ((d.neg 'empty?) d.pos)\n                       (else (let ((min.pos (d.pos 'min)) (min.neg (d.neg 'min)))\n                               (cond ((any= min.pos)))\n                                     (else                    (same d.pos d.neg)))))))\n    (method-lambda\n      ((has-key? key)              (let ((self (self '>= key)))\n                                     (and (not (self 'empty?))\n                                          (equal? (self 'min) key))))\n      ((ref key k.found k.missing) (let ((self (self '>= key)))\n                                     (if (or (self 'empty?)\n                                             (not (equal? (self 'min) key)))\n                                       (k.missing)\n                                       (k.found (self 'top)))))\n      ((enumerator/2)              (lambda (yield)\n                                     (let loop ((self self))\n                                       (unless (self 'empty?)\n                                         (yield (self 'min) (self 'top))\n                                         (loop (self 'pop))))))\n      ((enumerator)                (lambda (yield)\n                                     (let loop ((self self))\n                                       (unless (self 'empty?)\n                                         (yield (self 'min))\n                                         (loop (self 'pop))))))\n      (else                        self))))\n\n(define (dict:ordered:vector rows (t->key (lambda (t) t)) (start 0) (end (vector-length rows)))\n  (define (i->value i) (vector-ref rows i))\n  (define (i->key   i) (t->key (i->value i)))\n  (dict:ordered i->key i->value start end))\n\n(define (dict:hash k=>t)\n  (let loop ((k=>t k=>t))\n    (if (= (hash-count k=>t) 0)\n      dict.empty\n      (method-lambda\n        ((empty?)                    (hash-empty? k=>t))\n        ((count)                     (hash-count  k=>t))\n        ((=/= key)                   (loop (hash-remove k=>t key)))\n        ((==  key)                   (if (hash-has-key? k=>t key)\n                                       (loop (hash key (hash-ref k=>t key)))\n                                       dict.empty))\n        ((has-key? key)              (hash-has-key? k=>t key))\n        ((ref key k.found k.missing) (if (hash-has-key? k=>t key)\n                                       (k.found (hash-ref k=>t key))\n                                       (k.missing)))\n        ((enumerator/2)              (hash->enumerator/2 k=>t))\n        ((enumerator)                (lambda (yield)\n                                       (for ((k (in-hash-keys k=>t)))\n                                         (yield k))))))))\n\n(define ((merge-join A B) yield)\n  (unless (or (A 'empty?) (B 'empty?))\n    (let loop ((A   A)\n               (k.A (A 'min))\n               (B   B)\n               (k.B (B 'min)))\n      (case (compare-any k.A k.B)\n        ((-1) (let ((A (A '>= k.B)))\n                (unless (A 'empty?)\n                  (loop A (A 'min) B k.B))))\n        (( 1) (let ((B (B '>= k.A)))\n                (unless (B 'empty?)\n                  (loop A k.A B (B 'min)))))\n        (else (let ((t.A (A 'top))\n                    (t.B (B 'top))\n                    (A   (A 'pop))\n                    (B   (B 'pop)))\n                (yield k.A t.A t.B)\n                (unless (or (A 'empty?) (B 'empty?))\n                  (loop A (A 'min) B (B 'min)))))))))\n\n(define ((merge-antijoin A B) yield)\n  ((dict-antijoin-ordered (A 'enumerator/2) B) yield))\n\n(define ((merge-key-union A B) yield)\n  ((dict-key-union-ordered (A 'enumerator) B) yield))\n\n(define ((merge-union combined-value A B) yield)\n  ((dict-union-ordered combined-value (A 'enumerator/2) B) yield))\n\n(define (group-fold->hash en v.0 f)\n  (define k=>v (hash))\n  (en (lambda (k v) (set! k=>v (hash-update k=>v k\n                                            (lambda (v.current) (f v v.current))\n                                            v.0))))\n  k=>v)\n\n(define ((group-fold en v.0 f) yield)\n  ((hash->enumerator/2 (group-fold->hash en v.0 f)) yield))\n\n(define ((group-fold-ordered en v.0 f) yield)\n  (let ((first?    #t)\n        (k.current #f)\n        (v.current v.0))\n    (en (lambda (k v)\n          (cond (first?               (set! first?    #f)\n                                      (set! k.current k)\n                                      (set! v.current (f v v.0)))\n                ((equal? k k.current) (set! v.current (f v v.current)))\n                (else                 (yield k.current v.current)\n                                      (set! k.current k)\n                                      (set! v.current (f v v.0))))))\n    (unless first?\n      (yield k.current v.current))))\n\n(define ((enumerator-dedup en) yield)\n  (define first?     #t)\n  (define t.previous #f)\n  (en (lambda (t)\n        (cond (first?                      (set! first?     #f)\n                                           (set! t.previous t)\n                                           (yield t))\n              ((not (equal? t t.previous)) (set! t.previous t)\n                                           (yield t))))))\n\n(define ((enumerator-project en f) yield)\n  (en (lambda args (apply f yield args))))\n\n(define ((enumerator-filter en ?) yield)\n  (en (lambda (t) (when (? t) (yield t)))))\n\n(define ((enumerator-sort en enumerator (sort (enumerator->rlist en) dict:ordered:vector-flat en (t->key (lambda (t) t)))\n  (dict:ordered:vector\n    (enumerator->vector (enumerator-dedup (enumerator-sort en anykey))\n\n(define (enumerator->dict:ordered:vector-group en t->key)\n  (dict:ordered:vector\n    (enumerator->vector\n      (enumerator-project\n        (group-fold-ordered\n          (enumerator-project (enumerator-dedup (enumerator-sort en anykey t) t)))\n          '() cons)\n        (lambda (yield _ ts.reversed) (yield (reverse ts.reversed)))))\n    (lambda (ts) (t->key (car ts)))))\n\n(define ((hash-join en en.hash) yield)\n  ((dict-join-unordered en (dict:hash (group-fold->hash en.hash '() cons)))\n   (lambda (k t ts.hash)\n     (for ((t.hash (in-list (reverse ts.hash))))  ; is this reversal necessary?\n       (yield k t t.hash)))))\n\n(define ((hash-antijoin en en.hash) yield)\n  ((dict-antijoin-unordered en (dict:hash (group-fold->hash en.hash (void) (lambda _ (void)))))\n   yield))\n\n(define ((dict-join-unordered en d.index) yield)\n  (unless (d.index 'empty?)\n    (en (lambda (k v) (d.index 'ref k\n                               (lambda (v.index) (yield k v v.index))\n                               (lambda ()        (void)))))))\n\n(define ((dict-join-ordered en.ordered d.index) yield)\n  (unless (d.index 'empty?)\n    (en.ordered (lambda (k v)\n                  (set! d.index (d.index '>= k))\n                  (d.index 'ref k\n                           (lambda (v.index) (yield k v v.index))\n                           (lambda ()        (void)))))))\n\n(define ((dict-antijoin-unordered en d.index) yield)\n  (en (if (d.index 'empty?)\n        yield\n        (lambda (k v) (unless (d.index 'has-key? k)\n                        (yield k v))))))\n\n(define ((dict-antijoin-ordered en.ordered d.index) yield)\n  (en.ordered (if (d.index 'empty?)\n                yield\n                (lambda (k v)\n                  (set! d.index (d.index '>= k))\n                  (unless (d.index 'has-key? k)\n                    (yield k v))))))\n\n(define ((dict-subtract-unordered en d.index) yield)\n  (en (if (d.index 'empty?)\n        yield\n        (lambda (k) (unless (d.index 'has-key? k)\n                      (yield k))))))\n\n(define ((dict-subtract-ordered en.ordered d.index) yield)\n  (en.ordered (if (d.index 'empty?)\n                yield\n                (lambda (k)\n                  (set! d.index (d.index '>= k))\n                  (unless (d.index 'has-key? k)\n                    (yield k))))))\n\n(define ((hash-key-union en en.hash) yield)\n  (define d.index (dict:hash (let ((k=> (hash)))\n                               (en.hash (lambda (k) (set! k=> (hash-set k=> k (void)))))\n                               k=>)))\n  ((dict-key-union-unordered en d.index) yield))\n\n(define ((dict-key-union-unordered en d.index) yield)\n  ((dict-subtract-unordered en d.index) yield)\n  ((d.index 'enumerator)                yield))\n\n(define ((dict-key-union-ordered en.ordered d.index) yield)\n  (en.ordered (if (d.index 'empty?)\n                yield\n                (lambda (k)\n                  (let loop ()\n                    (if (d.index 'empty?)\n                      (yield k)\n                      (let ((k.d (d.index 'min)))\n                        (case (compare-any k k.d)\n                          ((-1) (yield k))\n                          (( 1) (set! d.index (d.index 'pop))\n                                (yield k.d)\n                                (loop))\n                          (else (set! d.index (d.index 'pop))\n                                (yield k)))))))))\n  ((d.index 'enumerator) yield))\n\n(define ((dict-union-ordered combined-value en.ordered d.index) yield)\n  (en.ordered (if (d.index 'empty?)\n                yield\n                (lambda (k v)\n                  (let loop ()\n                    (if (d.index 'empty?)\n                      (yield k v)\n                      (let ((k.d (d.index 'min)))\n                        (case (compare-any k k.d)\n                          ((-1) (yield k v))\n                          (( 1) (yield k.d (d.index 'top))\n                                (set! d.index (d.index 'pop))\n                                (loop))\n                          (else (yield k (combined-value v (d.index 'top)))\n                                (set! d.index (d.index 'pop))))))))))\n  ((d.index 'enumerator/2) yield))\n\n(define ((dict-union-unordered combined-value en d.index) yield)\n  (en (if (d.index 'empty?)\n        yield\n        (lambda (k v)\n          (if (d.index 'empty?)\n            (yield k v)\n            (d.index 'ref k\n                     (lambda (v.index)\n                       (yield k (combined-value v v.index))\n                       (set! d.index (d.index '=/= k)))\n                     (lambda () (yield k v)))))))\n  ((d.index 'enumerator/2) yield))\n\n\n;; TODO: computing fixed points?\n;; - iteration: changed?\n;; - relation/variable: stable, next, to-add\n\n;; TODO: multiway-joins\n;; - extend-with\n;; - extend-anti\n;; - filter-with\n;; - filter-anti\n\n(module+ test\n  (require racket/pretty)\n\n  (define (test.0 yield.0)\n    (define (yield . args)\n      (pretty-write `(yielding: . ,args))\n      (apply yield.0 args))\n    (yield 0 1)\n    (yield 0 2)\n    (yield 0 3)\n    (yield 1 1)\n    (yield 1 2)\n    (yield 5 2)\n    (yield 5 7))\n\n  (define test.1 (enumerator->enumerator/2\n                   (vector->enumerator '#((0 . 1)\n                                          (0 . 2)\n                                          (0 . 3)\n                                          (1 . 1)\n                                          (1 . 2)\n                                          (5 . 2)\n                                          (5 . 7)))))\n\n  (displayln 'group-fold.0)\n  ((group-fold test.0 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'group-fold-ordered.0)\n  ((group-fold-ordered test.0 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'group-fold.1)\n  ((group-fold test.1 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'group-fold-ordered.1)\n  ((group-fold-ordered test.1 0 +) (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'hash-join)\n  ((hash-join\n     (enumerator->enumerator/2 (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3))))\n     (enumerator->enumerator/2 (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))))\n   (lambda (k a b) (pretty-write (list k a b))))\n\n  (displayln 'merge-join)\n  ((merge-join\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))\n       car))\n   (lambda (k a b) (pretty-write (list k a b))))\n\n  (displayln 'hash-key-union)\n  ((hash-key-union\n     (list->enumerator (map car '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3))))\n     (list->enumerator (map car '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))))\n   pretty-write)\n\n  (displayln 'merge-key-union)\n  ((merge-key-union\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))\n       car))\n   pretty-write)\n\n  (displayln 'merge-union)\n  ((merge-union\n     append\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))\n       car))\n   (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'dict:ordered:union)\n  (((dict:ordered:union\n      append\n      (enumerator->dict:ordered:vector-group\n        (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n        car)\n      (enumerator->dict:ordered:vector-group\n        (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))\n        car))\n    'enumerator/2)\n   (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'dict:ordered:subtraction)\n  (let ()\n    (define (table->dict table)\n      (if (equal? table '(()))\n        '()\n        (let* ((groups (map reverse (s-group table = car)))\n               (__ (pretty-write `(groups: ,groups)))\n               (ks (list->vector (map (lambda (rows) (car (car rows)))             groups)))\n               (vs (list->vector (map (lambda (rows) (table->dict (map cdr rows))) groups))))\n          (dict:ordered (column:vector ks) (column:vector vs) 0 (vector-length ks)))))\n    (let* ((table.example.pos '((1 1 1) (1 1 2) (1 2 0) (1 2 1) (1 2 2) (1 2 3)\n                                (2 1 1) (2 1 2) (2 2 0) (2 2 1) (2 2 2) (2 2 3) (2 3 0) (2 3 1) (2 3 2) (2 3 3)\n                                (3 1 1) (3 1 2) (3 2 0) (3 2 1) (3 2 2) (3 2 3)))\n           (table.example.neg '(        (1 1 2) (1 2 0) (1 2 1)                 (1 2 4)\n                                        (2 1 2) (2 2 0) (2 2 1)                 (2 3 0) (2 3 1)                 (2 4 0) (2 4 1)\n                                                (3 2 0) (3 2 1)         (3 2 3)))\n           (table.expected    '((1 1 1)                         (1 2 2) (1 2 3)\n                                (2 1 1)                         (2 2 2) (2 2 3)                 (2 3 2) (2 3 3)\n                                (3 1 1) (3 1 2)                 (3 2 2)        ))\n           (index.example.pos (table->dict table.example.pos))\n           (index.example.neg (table->dict table.example.neg))\n           (result.0          (filter (lambda (row) (not (member row table.example.neg)) )\n                                      table.example.pos))\n           (result.1          (enumerator->list\n                                (lambda (yield)\n                                  (((dict:ordered:subtraction\n                                      3\n                                      index.example.pos\n                                      index.example.neg)\n                                    'enumerator/2)\n                                   (lambda (k1 i2)\n                                     ((i2 'enumerator/2)\n                                      (lambda (k2 i3)\n                                        ((i3 'enumerator)\n                                         (lambda (k3)\n                                           (yield (list k1 k2 k3))))))))))))\n      (pretty-write `(via set-subtract: ,result.0))\n      (pretty-write `(via dict:ordered:subtraction ,result.1))\n      (pretty-write `(equal? ,(equal? result.0 result.1) ,(equal? table.expected result.1)))))\n\n  (displayln 'hash-antijoin)\n  ((hash-antijoin\n     (enumerator->enumerator/2 (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3))))\n     (enumerator->enumerator/2 (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))))\n   (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'merge-antijoin)\n  ((merge-antijoin\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((5 . 6) (10 . 17) (8 . 33) (1 . 5) (0 . 7) (18 . 3)))\n       car)\n     (enumerator->dict:ordered:vector-group\n       (list->enumerator '((7 . 61) (10 . 20) (18 . 33) (11 . 5) (20 . 111) (0 . 77) (8 . 3)))\n       car))\n   (lambda (k v) (pretty-write (list k v))))\n\n  (displayln 'table)\n  (let ((t (table (vector (vector  0  0  0  0  1  1  1  2  2  3  3  3  3  3  4)\n                          (vector 'a 'a 'a 'b 'a 'a 'b 'a 'a 'a 'b 'b 'c 'c 'a)\n                          (vector  0  1  1  1  0  1  1  2  2  1  1  1  1  1  7)))))\n    (for ((col (in-range (table-width t))))\n      (for ((row (in-range (table-length t))))\n        (printf \"~s \" (table-ref t col row)))\n      (newline))\n\n    (displayln 'table-dedup!)\n    (table-dedup! t)\n\n    (for ((col (in-range (table-width t))))\n      (for ((row (in-range (table-length t))))\n        (printf \"~s \" (table-ref t col row)))\n      (newline)))\n  )\n\n;; TODO:\n;join-many, need attribute order\n\n;extend-with/anti\n;filter-with/anti\n\n;;; TODO: these are analogous to operators: a set of tuples flowing through a particular program point\n;(struct idb-relation (done current new) #:prefab)\n\n;;; exponential search aka one-sided binary search\n;(define (join-tables t.0 t.1 k)\n  ;;; (k key v.0 v.1)\n;;key.0 key.1\n  ;)\n\n;;; NOTE: this semi-naive join does not correctly generalize to more than 2 relations\n;(define (join-idb-relations r.0 r.1 logic)\n  ;(append\n    ;(map (lambda (t.1)\n           ;(join-tables (idb-relation-current r.0)\n                        ;t.1\n                        ;;; TODO: no need to eta expand\n                        ;(lambda (k v.0 v.1)\n                          ;(logic k v.0 v.1))))\n         ;(idb-relation-done r.1))\n    ;(map (lambda (t.0)\n           ;(join-tables t.0\n                        ;(idb-relation-current r.1)\n                        ;(lambda (k v.0 v.1)\n                          ;(logic k v.0 v.1))))\n         ;(idb-relation-done r.0))\n    ;(join-tables (idb-relation-current r.0)\n                 ;(idb-relation-current r.1)\n                 ;(lambda (k v.0 v.1)\n                   ;(logic k v.0 v.1)))))\n\n;(define (idb-relation-step r)\n  ;(match-define (idb-relation done current new) r)\n  ;(let* ((done    (let loop ((done done) (current current))\n                    ;(match done\n                      ;('()             (list current))\n                      ;((cons top done) (if (<= (vector-length top)\n                                               ;(* 2 (vector-length current)))\n                                         ;(loop done (table-union current top))\n                                         ;(cons current (cons top done)))))))\n         ;(current (foldl (lambda (t.done next)\n                           ;(filter-not (lambda (tuple) (table-member? t.done)) next))\n                         ;(vector->list (match new\n                                         ;('()             (table '()))\n                                         ;((cons next new) (foldl table-union next new))))\n                         ;done)))\n    ;(idb-relation done current '())))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/database.rkt",
    "content": "#lang racket/base\n(provide\n  ;; TODO: move these\n  build-enumerator-relation\n  build-s-relation\n  build-tsv-relation\n\n  dict-count\n  dict-min\n  dict-min-value\n  dict-min-pop\n  dict-min-find\n  dict-max\n  dict-max-find\n  dict-empty?\n  dict->=\n  dict->\n  dict-<=\n  dict-<\n  dict-ref\n  dict-enumerator\n  dict-key-enumerator\n\n  dict:ref\n  dict.empty\n\n  merge-join\n  dict-join-ordered\n\n  database\n  database-path\n  database-commit!\n  database-revert!\n  database-trash-empty!\n  database-relation-names\n  database-relation-name?\n  database-relation\n  database-relation-builder\n  database-relation-new\n  database-relation-add!\n  relation-database\n  relation-has-name?\n  relation-name\n  relation-attributes\n  relation-type\n  relation-indexes\n  relation-delete!\n  relation-name-set!\n  relation-attributes-set!\n  relation-assign!\n  relation-index-add!\n  relation-index-remove!\n  relation-full-compact!\n  relation-incremental-compact!\n\n  relation-index-dict\n  relation-text-dicts\n\n  R.empty R+ R-\n  auto-empty-trash?\n  current-batch-size\n\n  make-btree\n  btree-count\n  btree-ref-or-set!)\n(require \"heap.rkt\" \"logging.rkt\" \"misc.rkt\" \"storage.rkt\" \"stream.rkt\"\n         \"safe-unsafe.rkt\"\n         ;racket/unsafe/ops\n         racket/file racket/fixnum racket/hash racket/list racket/match\n         racket/set racket/struct racket/vector\n         \"../../neo-utils/neo-helpers-without-db.rkt\")\n\n;(define-syntax-rule (verbose-log     description)          (void))\n;(define-syntax-rule (performance-log description body ...) (let () body ...))\n(define-syntax-rule (verbose-log     description)          (pretty-log description))\n(define-syntax-rule (performance-log description body ...) (let ()\n                                                             (pretty-log description)\n                                                             (time/pretty-log body ...)))\n\n(define (build-enumerator-relation db type.r en)\n  (let-values (((insert! finish) (database-relation-builder db type.r)))\n    (time (begin (en insert!) (time (finish))))))\n\n(define (build-s-relation db type.r s)\n  (let-values (((insert! finish) (database-relation-builder db type.r)))\n    (time (let loop ((s s))\n            (cond ((null?      s) (time (finish)))\n                  ((procedure? s) (loop (s)))\n                  (else           (insert! (car s)) (loop (cdr s))))))))\n\n(define (build-tsv-relation db type.r file-name)\n  (let-values (((insert! finish) (database-relation-builder db type.r)))\n    (call-with-input-file\n      file-name\n      (lambda (in)\n        (read-bytes-line in 'any)  ; drop header line\n        (time\n          (let tuple-loop ()\n            (let ((line (read-bytes-line in 'any)))\n              (unless (eof-object? line)\n                (insert! (map (lambda (type.field field) (if (eq? type.field 'int)\n                                                           (bytes-base10->fxnat field)\n                                                           field))\n                              type.r (unsafe-bytes-split-tab line)))\n                (tuple-loop)))))\n        (time (finish))))))\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Persistent databases ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Limitations:\n;; - A single database will not scale well to enormous numbers of relations.\n;; - This implementation will not scale well to high frequency database updates.\n;; - A single database should not be used by multiple host processes running concurrently.\n;;   Initializing the same database from concurrent processes may lead to data corruption.\n;; - Multiple threads of a single process can concurrently read from the same database, but it is\n;;   not safe for a thread to read concurrently with another thread's update to the same database.\n;; - It is not safe for multiple threads to perform concurrent updates on the same database.\n;; - While it should be possible to recover from typical process failure and interruption, sudden\n;;   host system failure and interruption may corrupt data.\n;; - Relations must contain at least one attribute.\n;; - Relation attribute types are limited to integer and text (Racket bytes).\n;;   - Integer values must fit within a Racket fixnum (-2^61 through -2^61 - 1), and the difference\n;;     between the maximum and minimum integer values must be at most 2^61 - 1.\n\n;; A database is a persistent collection of extensional relations, and is represented as a\n;; filesystem directory managed by an instance of checkpointing storage.\n\n;; An extensional relation is a uniquely named, finite set of ordered tuples.  Each tuple in the set\n;; contains the same number of fields.  For each field, every tuple assigns the same name and type\n;; to that field.  The list of field types is called the relation's type.  The field names are\n;; called the relation's attributes, and each name must be unique within the relation.\n\n;; For efficient querying, a relation can be indexed on one or more permutations of a subset of its\n;; attributes.  An index provides an efficient way to filter and enumerate a subset of the\n;; relation's tuples.  To filter the tuples, constraints are applied to a subset of the relation's\n;; attributes, eliminating tuples that do not satisfy the constraints.  The index's attribute\n;; permutation is the order in which attributes will be constrained.  Constraining attributes in\n;; this order is efficient due to the representation of the index, which is the result of sorting\n;; the relation's tuples lexicographically according to the attribute permutation.\n\n;; Databases and relations can be modified:\n;; - New relations can be added to, and existing relations can be removed from, a database.\n;; - Relations and their attributes can be renamed.\n;; - Indexes can be added to, or removed from, a relation.\n;; - Tuples can be inserted into, or deleted from, a relation.\n;; - Relations may be compacted to improve lookup efficiency.\n\n;; Modifications to a database and its relations can be used immediately, but will not persist until\n;; they are explicitly committed.  Uncommitted modifications can be reverted, restoring the most\n;; recently committed version of the database.\n\n(define version.current '2022-2-22)\n\n(define auto-empty-trash?  (make-parameter #f))\n(define current-batch-size (make-parameter (expt 2 29)))\n\n(define (database-path             db)                      ((wrapped-database-controller db) 'path))\n(define (database-commit!          db)                      ((wrapped-database-controller db) 'commit!))\n(define (database-revert!          db)                      ((wrapped-database-controller db) 'revert!))\n(define (database-trash-empty!     db)                      ((wrapped-database-controller db) 'trash-empty!))\n(define (database-relation-names   db)                      ((wrapped-database-controller db) 'relation-names))\n(define (database-relation-name?   db name)                 ((wrapped-database-controller db) 'relation-name? name))\n(define (database-relation         db name)                 ((wrapped-database-controller db) 'relation       name))\n(define (database-relation-builder db type (batch-size #f)) ((wrapped-database-controller db)\n                                                             'relation-builder type (or batch-size (current-batch-size))))\n(define (database-relation-new     db type)                 (let-values (((_ finish) (database-relation-builder db type 0)))\n                                                              (finish)))\n(define (database-relation-add!    db name attrs type)      (let ((r (database-relation-new db type)))\n                                                              (relation-name-set!       r name)\n                                                              (relation-attributes-set! r attrs)\n                                                              r))\n\n(define (relation-database        r)       ((wrapped-relation-controller r) 'database))\n(define (relation-has-name?       r)       ((wrapped-relation-controller r) 'has-name?))\n(define (relation-name            r)       ((wrapped-relation-controller r) 'name))\n(define (relation-attributes      r)       ((wrapped-relation-controller r) 'attributes))\n(define (relation-type            r)       ((wrapped-relation-controller r) 'type))\n(define (relation-indexes         r)       ((wrapped-relation-controller r) 'indexes))\n(define (relation-delete!         r)       ((wrapped-relation-controller r) 'delete!))\n(define (relation-name-set!       r name)  ((wrapped-relation-controller r) 'name-set!       name))\n(define (relation-attributes-set! r attrs) ((wrapped-relation-controller r) 'attributes-set! attrs))\n(define (relation-assign!         r expr)  ((wrapped-relation-controller r) 'assign!         expr))\n(define (relation-index-add!      r . ixs) ((wrapped-relation-controller r) 'index-add!      ixs))\n(define (relation-index-remove!   r . ixs) ((wrapped-relation-controller r) 'index-remove!   ixs))\n(define (relation-full-compact!        r)  ((wrapped-relation-controller r) 'full-compact!))\n(define (relation-incremental-compact! r)  ((wrapped-relation-controller r) 'incremental-compact!))\n\n(define (relation-index-dict r signature preload?) ((wrapped-relation-controller r) 'index-dict signature preload?))\n(define (relation-text-dicts r preload?)           ((wrapped-relation-controller r) 'text-dicts preload?))\n\n(struct wrapped-database (controller)\n        #:methods gen:custom-write\n        ((define write-proc (make-constructor-style-printer\n                              (lambda (db) 'database)\n                              (lambda (db) (list (database-path db)))))))\n\n(struct wrapped-relation (key controller)\n        #:methods gen:custom-write\n        ((define write-proc (make-constructor-style-printer\n                              (lambda (r)\n                                (if ((wrapped-relation-controller r) 'valid?)\n                                  'relation\n                                  'deleted-relation))\n                              (lambda (r)\n                                (if (and ((wrapped-relation-controller r) 'valid?)\n                                         (relation-has-name? r))\n                                  (list (relation-name r))\n                                  '()))))))\n\n(define R.empty     '())\n(define (R+ . args) (cons '+ args))\n(define (R- e0 e1)  `(- ,e0 ,e1))\n\n;;; Some rexpr rewrite rules to consider:\n\n;; easy\n;(&)                ==> #f  ; could allow this temporarily, but it is an error if it is not eliminated; maybe don't allow it here\n;(- X #f)           ==> ()\n;(- #f X)           ==> (~ X)  ; not desirable ...\n;(+ A ... #f B ...) ==> #f\n;(& A ... #f B ...) ==> (& A ... B ...)\n;(+)                ==> ()\n;(- X ())           ==> X\n;(- () X)           ==> ()\n;(+ A ... () B ...) ==> (+ A ... B ...)\n;(& A ... () B ...) ==> ()\n;;; easy\n;(+ A ... (+ B ...) C ...)                 ==> (+ A ... B ... C ...)\n;(+ X ... A Y ... A B ...)                 ==> (+ X ... A Y ... B ...)\n;(+ X ... A Y ... (- (+ A C ...) D) B ...) ==> (+ X ... A Y ... (- (+ C ...) D) B ...)\n;(& A ... (& B ...) C ...)                 ==> (& A ... B ... C ...)\n;(& X ... A Y ... A B ...)                 ==> (& X ... A Y ... B ...)\n;(& X ... A Y ... (- (& A C ...) D) B ...) ==> (& X ... A Y ... (- (& C ...) D) B ...)\n\n;;; doable\n;(& A ... X B ...    (+ C ... X D ...)    E ...) ==> (& A ... X B ... E ...)\n;(+ A ... X B ...    (& C ... X D ...)    E ...) ==> (+ A ... X B ... E ...)\n;(& A ... X B ... (- (+ C ... X D ...) Z) E ...) ==> (& A ... X B ... E ...)\n;(+ A ... X B ... (- (& C ... X D ...) Z) E ...) ==> (+ A ... X B ... E ...)\n;;; doable\n;(-    (+ A ... B C ...)    (+ D ... B E ...)) ==> (-    (+ A ... C ...)    (+ D ... B E ...))\n;(- (- (+ A ... B C ...) F) (+ D ... B E ...)) ==> (- (- (+ A ... C ...) F) (+ D ... B E ...))  ; etc.\n\n\n;(- (& A ... B C ...) (+ D ... B E ...)) ==> (- () (+ D ... B E ...))\n;;; would need us to go backwards too\n;(- A (& B ... A C ...)) ==> (- A (& B ... C ...))\n\n;;; might be expensive to recognize in general, unless we memo-map normalized subexpressions to new uids\n;(- X (- X Y)) ==> (& X Y)\n\n;;; Subsumption maps? Or not because of the differences that can't use them as easily?\n\n;;; doable\n;(+ A ... X B ...    (& C ... (+ F ... X G ...) D ...)    E ...) ==> (+ A ... X B ...    (& C ... (+ F ... G ...) D ...)    E ...)\n;(+ A ... X B ... (- (& C ... (+ F ... X G ...) D ...) Z) E ...) ==> (+ A ... X B ... (- (& C ... (+ F ... G ...) D ...) Z) E ...)\n;;; nothing correct we can do\n;(& A ... X B ...    (+ C ... (& F ... X G ...) D ...)    E ...)\n;(& A ... X B ... (- (+ C ... (& F ... X G ...) D ...) Z) E ...)\n\n\n;; TODO: support & for set intersection\n(define (rexpr-clean expr)\n  (define (loop.+ es.pending es.seen +s)\n    (if (null? es.pending)\n      (let loop ((es.seen es.seen) (es.done '()) (+s +s))\n        (if (null? es.seen)\n          (match es.done\n            ('()         '())\n            ((list expr) expr)\n            (exprs       `(+ . ,exprs)))\n          (let ((expr (car es.seen)) (es.seen (cdr es.seen)))\n            (let ((expr (match expr\n                          (`(- ,e0 ,e1) (loop.- e0 e1 +s))\n                          (_            expr))))\n              (define (loop/add e.new)\n                (if (set-member? +s e.new)\n                  (loop es.seen            es.done           +s)\n                  (loop es.seen (cons expr es.done) (set-add +s expr))))\n              (match expr\n                (`(- ,e0 ,e1) (loop/add expr))\n                ('()          (loop es.seen            es.done  +s))\n                (`(+ . ,es)   (loop es.seen (append es es.done) +s))\n                (_            (loop es.seen (cons expr es.done) +s)))))))\n      (let ((expr (car es.pending)) (es.pending (cdr es.pending)))\n        (match expr\n          ('()          '())\n          (`(+ . ,es)   (loop.+ (append es es.pending)            es.seen  +s))\n          (`(- ,e0 ,e1) (loop.+            es.pending  (cons expr es.seen) +s))\n          (_            (if (set-member? +s expr)\n                          (loop.+ es.pending            es.seen           +s)\n                          (loop.+ es.pending (cons expr es.seen) (set-add +s expr))))))))\n  (define (loop.- e0 e1 +s)\n    (let* ((e1 (loop.main e1 (set)))\n           (e0 (loop.main e0 (set-union +s (match e1\n                                             ('()        (set))\n                                             (`(+ . ,es) (list->set es))\n                                             (_          (set e1)))))))\n      (cond ((null? e0) '())\n            ((null? e1) e0)\n            (else       `(- ,e0 ,e1)))))\n  (define (loop.main expr +s)\n    (let ((expr (match expr\n                  ('()          '())\n                  (`(+ . ,es)   (loop.+ es '() +s))\n                  (`(- ,e0 ,e1) (loop.- e0 e1 +s))\n                  (_            (if (set-member? +s expr)\n                                  '()\n                                  expr)))))\n      (if (set-member? +s expr)\n        '()\n        expr)))\n  (loop.main expr (set)))\n\n(define (table-expr->table-ids texpr)\n  (let loop ((texpr texpr) (tids '()))\n    (match texpr\n      ('()          tids)\n      (`(+ . ,ts)   (foldl loop tids ts))\n      (`(- ,t0 ,t1) (loop t1 (loop t0 tids)))\n      (table-id     (cons table-id tids)))))\n\n(define (table-expr-map tid->tid texpr)\n  (let loop ((texpr texpr))\n    (match texpr\n      ('()          '())\n      (`(+ . ,ts)   `(+ . ,(map loop ts)))\n      (`(- ,t0 ,t1) `(- ,(loop t0) ,(loop t1)))\n      (table-id     (tid->tid table-id)))))\n\n(define (database path.db)\n  (define (make-relation id.self)\n    (define (invalidate!)\n      (hash-remove! id=>R (list id.self))\n      (set! self #f))\n    (define (remove-name!)\n      (when (R-has-name? id.self)\n        (stg-update! 'name=>relation-id (lambda (n=>rid) (hash-remove n=>rid (R-name id.self))))))\n    (define (index-signature->ordering ix)\n      (valid-attributes?! ix)\n      (let* ((attrs   (R-attrs id.self))\n             (a->i    (lambda (attr) (let ((i (index-of attrs attr)))\n                                       (unless i (error \"invalid index attribute\" attr ix attrs))\n                                       (+ i 1))))\n             (ord.0   (map a->i ix))\n             (missing (set-subtract (list->set attrs) (list->set ix))))\n        (cond ((set-empty? missing)      ord.0)\n              ((= (set-count missing) 1) (append ord.0 (list (a->i (car (set->list missing))))))\n              (else                      (append ord.0 '(0))))))\n    (define (update-indexes! update)\n      (stg-update! 'relation-id=>indexes (lambda (rid=>os) (hash-update rid=>os id.self update))))\n    (define self\n      (method-lambda\n        ((valid?)      #t)\n        ((database)    db)\n        ((invalidate!) (invalidate!))\n        ((has-name?)   (R-has-name? id.self))\n        ((name)        (R-name      id.self))\n        ((attributes)  (R-attrs     id.self))\n        ((type)        (R-type      id.self))\n        ((table-expr)  (R-texpr     id.self))\n        ((indexes)     (hash-keys (hash-ref (stg-ref 'relation-id=>indexes)    id.self)))\n        ((name-set! name)\n         (unless (and (R-has-name? id.self) (equal? (R-name id.self) name))\n           (new-relation?! name)\n           (remove-name!)\n           (stg-update! 'name=>relation-id (lambda (n=>rid) (hash-set n=>rid name id.self)))\n           (stg-update! 'relation-id=>name (lambda (rid=>n) (hash-set rid=>n id.self name)))))\n        ((attributes-set! attrs)\n         (valid-attributes?! attrs)\n         (let ((type (R-type id.self)))\n           (unless (= (length attrs) (length type))\n             (error \"number of attributes must match the relation type arity\"\n                    attrs type)))\n         (stg-update! 'relation-id=>attributes (lambda (rid=>as) (hash-set rid=>as id.self attrs))))\n        ((assign! expr)      (R-assign-r! id.self expr))\n        ((index-add!    ixs) (update-indexes! (lambda (os)\n                                                (foldl (lambda (ordering os) (hash-set os ordering #t))\n                                                       os\n                                                       (map index-signature->ordering ixs)))))\n        ((index-remove! ixs) (update-indexes! (lambda (os)\n                                                (foldl (lambda (ordering os) (hash-remove os ordering))\n                                                       os\n                                                       (map index-signature->ordering ixs)))))\n        ((full-compact!)        (stg-update! 'relations-to-fully-compact\n                                             (lambda (rids) (hash-set rids id.self #t))))\n        ((incremental-compact!) (stg-update! 'relations-to-incrementally-compact\n                                             (lambda (rids) (hash-set rids id.self #t))))\n        ((delete!)\n         (set-remove! rids.new id.self)\n         (remove-name!)\n         (stg-update! 'relation-id=>name       (lambda (rid=>n)  (hash-remove rid=>n  id.self)))\n         (stg-update! 'relation-id=>attributes (lambda (rid=>as) (hash-remove rid=>as id.self)))\n         (stg-update! 'relation-id=>type       (lambda (rid=>t)  (hash-remove rid=>t  id.self)))\n         (stg-update! 'relation-id=>table-expr (lambda (rid=>te) (hash-remove rid=>te id.self)))\n         (stg-update! 'relation-id=>indexes    (lambda (rid=>os) (hash-remove rid=>os id.self)))\n         (invalidate!))\n        ((index-dict signature preload-count)\n         ;; preload-count:\n         ;;   If preload-count is #f or 0, no index layers will be loaded into RAM.\n         ;;   If preload-count is #t, all index layers will be loaded into RAM.\n         ;;   Otherwise, the first preload-count index layers will be loaded into RAM.\n         ;; TODO: support complex table expressions\n         (let* ((ordering      (index-signature->ordering signature))\n                (oprefix*      (ordering->prefixes ordering))\n                (preload-count (cond ((not (boolean? preload-count)) preload-count)\n                                     (preload-count                  (length oprefix*))\n                                     (else                           0)))\n                (texpr         (R-texpr id.self)))\n           (unless (hash-ref (hash-ref (stg-ref 'relation-id=>indexes) id.self) ordering #f)\n             (error \"missing relation index\" (R-name id.self) signature))\n           (unless (number? texpr)\n             (error \"relation-index-dict with complex table expressions is not currently supported\"\n                    (R-name id.self) texpr))\n           (let ((iprefix=>cid.key (stg-ref 'index-prefix=>key-column-id))\n                 (iprefix=>cid.pos (stg-ref 'index-prefix=>position-column-id))\n                 (cid=>desc        (stg-ref 'column-id=>column))\n                 (tid              texpr))\n             (let loop ((ref.prev (lambda (_) '()))\n                        (oprefix  (car oprefix*))\n                        (oprefix* (cdr oprefix*))\n                        (level    (- (length oprefix*) 1)))\n               (let* ((iprefix    (cons tid oprefix))\n                      (desc.key   (hash-ref cid=>desc (hash-ref iprefix=>cid.key iprefix)))\n                      (mvec       (column->monovec desc.key (< level preload-count)))\n                      (ival->dict (lambda (start end) (dict:monovec mvec ref.prev start end))))\n                 (cond\n                   ((null? oprefix*) (ival->dict 0 (column-count desc.key)))\n                   (else (let* ((desc.pos (hash-ref cid=>desc (hash-ref iprefix=>cid.pos iprefix)))\n                                (ref.pos  (column->ref desc.pos (<= level preload-count))))\n                           (loop (lambda (i) (ival->dict (ref.pos i) (ref.pos (unsafe-fx+ i 1))))\n                                 (car oprefix*)\n                                 (cdr oprefix*)\n                                 (- level 1))))))))))\n        ((text-dicts preload?)\n         ;; TODO: support complex table expressions\n         (let ((texpr (R-texpr id.self)))\n           (unless (number? texpr)\n             (error \"relation-text-dict with complex table expressions is not currently supported\"\n                    (R-name id.self) texpr))\n           (let* ((tid=>cids (stg-ref 'table-id=>column-ids))\n                  (cid=>c    (stg-ref 'column-id=>column))\n                  (text-cids (list->set\n                               (filter-not not (map (lambda (cid)\n                                                      (column->text-cid (hash-ref cid=>c cid)))\n                                                    (hash-ref tid=>cids texpr))))))\n             (case (set-count text-cids)\n               ((0) (values #f #f))\n               ((1) (let ((desc.text (hash-ref cid=>c (car (set->list text-cids)))))\n                      (values (text-column->text=>id desc.text preload?)\n                              (text-column->id=>text desc.text preload?))))\n               (else (error \"relation table has multiple text columns\"\n                            (R-name id.self) texpr))))))))\n    (lambda args (apply (or self (method-lambda\n                                   ((valid?) #f)))\n                        args)))\n\n  (define (relation-builder id.R batch-size.bytes)\n    (define R (id->R id.R))\n    (define checkpoint.current (storage-checkpoint-count stg))\n    (define (valid?)\n      (and ((wrapped-relation-controller R) 'valid?)\n           (equal? (storage-checkpoint-count stg) checkpoint.current)))\n    (define (invalidate!) (set! checkpoint.current #f))\n    (cond\n      ((= 0 batch-size.bytes)\n       (values #f (lambda ()\n                    (unless (valid?) (error \"cannot use a stale relation builder\"))\n                    (invalidate!)\n                    R)))\n      ((< 0 batch-size.bytes)\n       (define (start-batch!)\n         (set! text=>id (make-btree))\n         (set! i.tuple   0)\n         (set! size.text 0))\n       (define (insert! tuple)\n         (for-each (lambda (field proj col)\n                     (fxvector-set! vec.rows (unsafe-fx+ i.tuple col) (proj field)))\n                   tuple projections cols)\n         (set! i.tuple (unsafe-fx+ i.tuple count.cols))\n         (when (or (unsafe-fx=  full-size        i.tuple)\n                   (unsafe-fx<= batch-size.bytes size.text))\n           (finish-batch!)\n           (start-batch!)))\n       (define (finish!)\n         (when (< 0 i.tuple) (finish-batch!))\n         (R-assign-t! id.R (apply R+ (reverse tables)))\n         (invalidate!)\n         R)\n       (define (finish-batch!)\n         (unless (valid?) (error \"cannot use a stale relation builder\"))\n         (define column-id.text\n           (and (ormap (lambda (type.col) (eq? type.col 'text)) column-types)\n                (let* ((width.pos        (nat-min-byte-width size.text))\n                       (count.ids        (btree-count text=>id))\n                       (id=>id           (make-fxvector count.ids))\n                       (cid.text.value   (fresh-column-id))\n                       (cid.text.pos     (fresh-column-id))\n                       (cid.text         (fresh-column-id))\n                       (bname.text.value (cons 'column cid.text.value))\n                       (bname.text.pos   (cons 'column cid.text.pos)))\n                  (define pos.final\n                    (call-with-output-file\n                      (storage-block-new! stg bname.text.value)\n                      (lambda (out.text.value)\n                        (call-with-output-file\n                          (storage-block-new! stg bname.text.pos)\n                          (lambda (out.text.pos)\n                            (define (write-pos)\n                              (write-byte-width-nat width.pos out.text.pos (file-position out.text.value)))\n                            (pretty-log `(enumerating ,(btree-count text=>id) text values))\n                            (performance-log\n                              `(writing text column: ,size.text bytes)\n                              (write-pos)\n                              (let ((i 0))\n                                (btree-enumerate\n                                  text=>id\n                                  (lambda (text id)\n                                    (write-bytes text out.text.value)\n                                    (write-pos)\n                                    (unsafe-fxvector-set! id=>id id i)\n                                    (set! i (unsafe-fx+ i 1)))))\n                              (file-position out.text.value)))))))\n                  (add-columns! cid.text.value (hash 'class     'block\n                                                     'name      bname.text.value\n                                                     'bit-width 8\n                                                     'count     size.text\n                                                     'offset    0\n                                                     'min       0\n                                                     'max       255)\n                                cid.text.pos   (hash 'class     'block\n                                                     'name      bname.text.pos\n                                                     'bit-width (* 8 width.pos)\n                                                     'count     (+ 1 count.ids)\n                                                     'offset    0\n                                                     'min       0\n                                                     'max       pos.final)\n                                cid.text       (hash 'class     'text\n                                                     'position  cid.text.pos\n                                                     'value     cid.text.value))\n                  (let* ((cols.text (filter-not not (map (lambda (type col)\n                                                           (and (eq? type 'text) col))\n                                                         column-types cols))))\n                    (let loop ((i (unsafe-fx- i.tuple count.cols)))\n                      (when (unsafe-fx<= 0 i)\n                        (for-each (lambda (col)\n                                    (unsafe-fxvector-set! vec.rows (unsafe-fx+ i col)\n                                                          (unsafe-fxvector-ref\n                                                            id=>id\n                                                            (unsafe-fxvector-ref vec.rows (unsafe-fx+ i col)))))\n                                  cols.text)\n                        (loop (unsafe-fx- i count.cols)))))\n                  cid.text)))\n         (let ((count.tuples.unique (let ((count.rows (quotient i.tuple count.cols)))\n                                      (performance-log\n                                        `(sorting ,count.rows tuples)\n                                        (row-merge-sort! vec.rows vec.cols 0 count.cols count.rows)\n                                        (unsafe-fxquotient (row-deduplicate! vec.rows 0 count.cols count.rows)\n                                                           count.cols)))))\n           (transpose-row-to-col! vec.cols vec.rows 0 count.cols count.tuples.unique)\n           (let ((table-id (build-table column-types column-id.text vec.cols count.tuples.unique)))\n             (pretty-log `(inserted batch of ,count.tuples.unique unique tuples)\n                         `(,size.text bytes for ,(btree-count text=>id) unique text values))\n             (set! tables (cons table-id tables)))))\n       (define (text->id bs)\n         (let* ((count.0 (btree-count text=>id))\n                (id      (btree-ref-or-set! text=>id bs)))\n           (unless (unsafe-fx= count.0 (btree-count text=>id))\n             (set! size.text (unsafe-fx+ size.text (bytes-length bs))))\n           id))\n       (define (identity x) x)\n       (define column-types (relation-type R))\n       (define count.cols   (length column-types))\n       (define cols         (range 0 count.cols))\n       (define column-size  (max (quotient batch-size.bytes (* (length column-types) 8)) 2))\n       (define full-size    (unsafe-fx* count.cols column-size))\n       (define tables       '())\n       (define i.tuple      0)\n       (define size.text    0)\n       (define text=>id     (make-btree))\n       (define vec.rows     (make-fxvector full-size))\n       (define vec.cols     (make-fxvector full-size))\n       (define projections  (map (lambda (ctype) (if (eq? ctype 'text)\n                                                   text->id\n                                                   identity))\n                                 column-types))\n       (start-batch!)\n       (values insert! finish!))\n      (else (error \"invalid batch size\" batch-size.bytes))))\n\n  (define (build-table column-types column-id.text vec.cols row-count)\n    (let ((count.cols      (length column-types))\n          (table-id        (fresh-table-id))\n          (cid.primary-key (fresh-column-id)))\n      (add-columns! cid.primary-key (hash 'class  'line\n                                          'count  row-count\n                                          'offset 0\n                                          'step   1))\n      (let ((cids.attrs (map (lambda (type.col col)\n                               (let ((id.col (performance-log\n                                               `(writing column: ,row-count values)\n                                               (write-fx-column vec.cols (* row-count col) row-count))))\n                                 (cond ((eq? type.col 'text)\n                                        (let ((id.remap (fresh-column-id)))\n                                          (add-columns! id.remap (hash 'class  'remap\n                                                                       'local  id.col\n                                                                       'global column-id.text))\n                                          id.remap))\n                                       (else id.col))))\n                             column-types (range count.cols))))\n        (stg-update! 'table-id=>column-ids\n                     (lambda (tid=>cids)\n                       (hash-set tid=>cids table-id (cons cid.primary-key cids.attrs)))))\n      table-id))\n\n  (define (build-table-indexes! orderings tids)\n    (for-each\n      (lambda (ordering)\n        (let ((prefixes (ordering->prefixes ordering)))\n          (for-each\n            (lambda (tid)\n              (define (has-index-prefix? prefix)\n                (hash-has-key? (stg-ref 'index-prefix=>key-column-id) (cons tid prefix)))\n              (unless (has-index-prefix? (car prefixes))\n                (define prefixes.needed  (map (lambda (p) (and (not (has-index-prefix? p)) p))\n                                              (reverse prefixes)))\n                (define cid=>desc        (stg-ref 'column-id=>column))\n                (define descs.col        (map (lambda (cid) (hash-ref cid=>desc cid))\n                                              (let ((cids (hash-ref (stg-ref 'table-id=>column-ids) tid)))\n                                                (map (lambda (pos) (list-ref cids pos))\n                                                     (car prefixes)))))\n                (define count.cols       (length descs.col))\n                (define count.rows       (column-count (car descs.col)))\n                (define vec.cols         (make-fxvector (* count.cols count.rows)))\n                (define vec.rows         (make-fxvector (* count.cols count.rows)))\n                (performance-log\n                  `(reading ,count.cols columns)\n                  (for-each (lambda (i.col desc.col)\n                              (read-fx-column/vec! desc.col vec.cols (* i.col count.rows)))\n                            (range count.cols) descs.col))\n                (clear-column-vector-cache!)\n                (transpose-col-to-row! vec.cols vec.rows 0 count.cols count.rows)\n                (performance-log\n                  `(sorting ,count.rows tuples)\n                  (row-merge-sort! vec.rows vec.cols 0 count.cols count.rows))\n                (transpose-row-to-col! vec.cols vec.rows 0 count.cols count.rows)\n                (define vs.pos (map (lambda (p) (and p (make-fxvector (+ count.rows 1))))\n                                    (cdr prefixes.needed)))\n                (for-each (lambda (v.pos) (when v.pos (unsafe-fxvector-set! v.pos 0 0))) vs.pos)\n                (define counts.key\n                  (performance-log\n                    `(grouping keys for ,count.rows tuples)\n                    (let loop.main ((base.col 0)\n                                    (vs.pos vs.pos)\n                                    (pos*   (make-list count.cols 0))\n                                    (start  0)\n                                    (end    count.rows))\n                      (if (null? vs.pos)\n                        (list end) ; final key column is already deduplicated\n                        (let ((v.pos (car vs.pos)))\n                          (let loop.key ((pos (car pos*)) (pos* (cdr pos*)) (start start) (end end))\n                            (if (unsafe-fx= start end)\n                              (cons pos pos*)\n                              (let* ((key       (unsafe-fxvector-ref vec.cols (unsafe-fx+ base.col start)))\n                                     (start.new (unsafe-fx-\n                                                  (unsafe-bisect-next\n                                                    (unsafe-fx+ base.col start)\n                                                    (unsafe-fx+ base.col end)\n                                                    (lambda (i) (unsafe-fx<= (unsafe-fxvector-ref vec.cols i) key)))\n                                                  base.col)))\n                                (unsafe-fxvector-set! vec.cols (unsafe-fx+ base.col pos) key)\n                                (let ((pos* (loop.main (unsafe-fx+ base.col count.rows)\n                                                       (cdr vs.pos) pos* start start.new))\n                                      (pos  (unsafe-fx+ pos 1)))\n                                  (when v.pos (unsafe-fxvector-set! v.pos pos (car pos*)))\n                                  (loop.key pos pos* start.new end))))))))))\n                (for-each\n                  (lambda (prefix.needed desc.key i.key v.pos count.key count.pos)\n                    (when prefix.needed\n                      (define iprefix (cons tid prefix.needed))\n                      (let* ((cid.text (column->text-cid desc.key))\n                             (cid.key  (performance-log\n                                         `(writing key column: ,count.key values)\n                                         (write-fx-column vec.cols (* i.key count.rows) count.key)))\n                             (cid.key  (if cid.text\n                                         (let ((cid.remap (fresh-column-id)))\n                                           (add-columns! cid.remap (hash 'class  'remap\n                                                                         'local  cid.key\n                                                                         'global cid.text))\n                                           cid.remap)\n                                         cid.key)))\n                        (stg-update! 'index-prefix=>key-column-id\n                                     (lambda (iprefix=>cid) (hash-set iprefix=>cid iprefix cid.key))))\n                      (when v.pos\n                        (stg-update! 'index-prefix=>position-column-id\n                                     (lambda (iprefix=>cid)\n                                       (hash-set iprefix=>cid iprefix\n                                                 (performance-log\n                                                   `(writing position column: ,count.pos values)\n                                                   (write-fx-column v.pos 0 count.pos))))))))\n                  prefixes.needed\n                  descs.col\n                  (range count.cols)\n                  (cons #f vs.pos)\n                  counts.key\n                  (cons #f (map (lambda (c) (+ c 1))\n                                (reverse (cdr (reverse counts.key))))))\n                (pretty-log `(indexed table: ,tid ordering: ,ordering))\n                (checkpoint!)))\n            tids)))\n      ;; sorting by descending-length makes it easier to share common index building work\n      (sort orderings (lambda (o1 o2) (> (length o1) (length o2))))))\n\n  (define (merge-text-columns cids.text.original)\n    (match cids.text.original\n      ('()             (values #f       (hash)))\n      ((list cid.text) (values cid.text (hash)))\n      (_ (define custodian.gs (make-custodian))\n         (define *g&count&id=>id\n           (let ((cid=>c (stg-ref 'column-id=>column)))\n             (parameterize ((current-custodian custodian.gs))\n               (map (lambda (cid)\n                      (define desc.text (hash-ref cid=>c cid))\n                      (define count     (column-count desc.text))\n                      (define s         ((column->start->s desc.text) 0))\n                      (define id=>id    (make-fxvector count))\n                      (list (and (< 0 count)\n                                 (let loop ((id 0) (s s))\n                                   (match (s) ; assume uniform stream\n                                     ((cons text s)  (cons text (lambda (i)\n                                                                  (unsafe-fxvector-set! id=>id id i)\n                                                                  (loop (unsafe-fx+ id 1) s))))\n                                     (_              #f))))\n                            count\n                            id=>id))\n                    cids.text.original))))\n         (define gs               (map car   *g&count&id=>id))\n         (define counts           (map cadr  *g&count&id=>id))\n         (define id=>ids          (map caddr *g&count&id=>id))\n         (define vec.pos          (make-fxvector (+ (foldl + 0 counts) 1)))\n         (define cid.text.value   (fresh-column-id))\n         (define cid.text         (fresh-column-id))\n         (define bname.text.value (cons 'column cid.text.value))\n         (define count.ids        (let ((i.pos 0))\n                                    (call-with-output-file\n                                      (storage-block-new! stg bname.text.value)\n                                      (lambda (out)\n                                        (define (write-pos)\n                                          (fxvector-set! vec.pos i.pos (file-position out))\n                                          (set! i.pos (unsafe-fx+ i.pos 1)))\n                                        (write-pos)\n                                        (performance-log\n                                          `(merging text columns with counts: . ,counts)\n                                          ((unsafe-multi-merge (lambda (g.0 g.1) (bytesids))))))\n\n  (define (merge-text-columns/tables tids.original)\n    (define (cid->text-cid cid) (column->text-cid (hash-ref cid=>c cid)))\n    (define tid=>cids (stg-ref 'table-id=>column-ids))\n    (define cid=>c    (stg-ref 'column-id=>column))\n    (define cids.text.original\n      (set->list\n        (list->set\n          (append*\n            (map (lambda (tid)\n                   (filter-not not (map cid->text-cid (hash-ref tid=>cids tid))))\n                 tids.original)))))\n    (define-values (cid.text.new cid.text=>id=>id) (merge-text-columns cids.text.original))\n    (define cid.text=>cid.global.new\n      (make-immutable-hash\n        (hash-map cid.text=>id=>id\n                  (lambda (cid.text id=>id)\n                    (cons cid.text\n                          (let ((cid.global.new (fresh-column-id)))\n                            (add-columns! cid.global.new\n                                          (hash 'class  'remap\n                                                'local  (write-fx-column id=>id 0 (fxvector-length id=>id))\n                                                'global cid.text.new))\n                            cid.global.new))))))\n    (make-immutable-hash\n      (map (lambda (tid)\n             (let* ((cids.original (hash-ref tid=>cids tid))\n                    (cids.new\n                      (map (lambda (cid.original)\n                             (or (let ((desc.original (hash-ref cid=>c cid.original)))\n                                   (let loop ((desc desc.original))\n                                     (case (hash-ref desc 'class)\n                                       ((remap) (let* ((cid.global  (hash-ref desc 'global))\n                                                       (desc.global (hash-ref cid=>c cid.global)))\n                                                  (let ((cid.global.new\n                                                          (case (hash-ref desc.global 'class)\n                                                            ((text) (hash-ref cid.text=>cid.global.new cid.global #f))\n                                                            (else   (loop desc.global)))))\n                                                    (and cid.global.new\n                                                         (let ((cid.new (fresh-column-id)))\n                                                           (add-columns! cid.new (hash 'class  'remap\n                                                                                       'local  (hash-ref desc 'local)\n                                                                                       'global cid.global.new))\n                                                           cid.new)))))\n                                       (else    #f))))\n                                 cid.original))\n                           cids.original)))\n               (cons tid (if (equal? cids.original cids.new)\n                           tid\n                           (let ((tid.new (fresh-table-id)))\n                             (stg-update! 'table-id=>column-ids\n                                          (lambda (tid=>cids) (hash-set tid=>cids tid.new cids.new)))\n                             tid.new)))))\n           tids.original)))\n\n  (define (merge-table-expr type.table texpr)\n    (let* ((cid=>c    (stg-ref 'column-id=>column))\n           (tid=>cids (stg-ref 'table-id=>column-ids))\n           (cid.text  ; All tables must depend on the same text value column, if any\n             (let ((i.text-col (ormap (lambda (type.col i) (and (eq? type.col 'text) i))\n                                      type.table (range 1 (+ (length type.table) 1)))))\n               (and i.text-col\n                    (let loop ((texpr texpr))\n                      (match texpr\n                        ('()          #f)\n                        (`(+ . ,ts)   (ormap loop ts))\n                        (`(- ,t0 ,t1) (or (loop t0) (loop t1)))\n                        (table-id     (column->text-cid (hash-ref cid=>c (list-ref (hash-ref tid=>cids table-id)\n                                                                                   i.text-col)))))))))\n           (count.cols (length type.table))\n           (count.rows.worst-case\n             (let-values\n               (((count.current count.max)\n                 (let loop ((texpr texpr) (count.current 0) (count.max 0))\n                   (match texpr\n                     ('()          (values count.current count.max))\n                     (`(+ . ,ts)   (match ts\n                                     ('()             (values count.current count.max))\n                                     ((cons texpr ts) (let-values (((count.current count.max)\n                                                                    (loop texpr count.current count.max)))\n                                                        (loop `(+ . ,ts) count.current count.max)))))\n                     (`(- ,t0 ,t1) (let-values (((count.current count.max) (loop t0 count.current count.max)))\n                                     (let-values (((_           count.max) (loop t1 count.current count.max)))\n                                       (values count.current count.max))))\n                     (tid          (let* ((count         (column-count (hash-ref cid=>c (car (hash-ref tid=>cids tid)))))\n                                          (count.current (+ count.current count)))\n                                     (values count.current (max count.max count.current))))))))\n               count.max))\n           (vec.cols (make-fxvector (* count.cols count.rows.worst-case)))\n           (vec.rows (make-fxvector (* count.cols count.rows.worst-case))))\n      (let ((count.rows.final\n              (unsafe-fxquotient\n                (performance-log\n                  `(merging table expr: ,texpr)\n                  (let loop ((texpr texpr) (start 0))\n                    (match texpr\n                      ('()          start)\n                      (`(+ . ,ts)   (let ((count.rows (unsafe-fxquotient (- (foldl loop start ts) start) count.cols)))\n                                      (row-merge-sort!  vec.rows vec.cols start count.cols count.rows)\n                                      (row-deduplicate! vec.rows          start count.cols count.rows)))\n                      (`(- ,t0 ,t1) (let* ((mid (loop t0 start))\n                                           (end (loop t1 mid)))\n                                      (row-subtract! vec.rows count.cols start mid end)))\n                      (tid          (let* ((cids      (cdr (hash-ref tid=>cids tid)))\n                                           (descs.col (map (lambda (cid) (hash-ref cid=>c cid)) cids))\n                                           (count     (column-count (car descs.col))))\n                                      (for-each (lambda (i.col desc.col)\n                                                  (read-fx-column/vec! desc.col vec.cols (* i.col count)))\n                                                (range count.cols) descs.col)\n                                      (clear-column-vector-cache!)\n                                      (transpose-col-to-row! vec.cols vec.rows start count.cols count)\n                                      (+ start (* count.cols count)))))))\n                count.cols)))\n        (transpose-row-to-col! vec.cols vec.rows 0 count.cols count.rows.final)\n        (if (< 0 count.rows.final)\n          (build-table type.table cid.text vec.cols count.rows.final)\n          '()))))\n\n    ;; TODO: implement these operations:\n    ;; - text value gc\n    ;;   - compute a table's reachable text ids\n    ;;     - treat each text column as a 1-column table, merge those, and enumerate the sorted/deduped ids\n    ;;   - drop ids from a text column\n    ;;     - (text-remove-ids desc.text ids)  ==>  desc.text.new\n    ;;       - id=>id remapping is implied by the set of removed ids\n\n  (define (compact-relations! rids)\n    (unless (null? rids)\n      (apply pretty-log `(fully compacting relations) (map R-name rids))\n      (let ((tid=>tid (merge-text-columns/tables\n                        (set->list\n                          (list->set\n                            (append* (map (lambda (rid) (table-expr->table-ids (R-texpr rid)))\n                                          rids)))))))\n        (for-each (lambda (rid) (R-assign-t! rid (table-expr-map (lambda (tid) (hash-ref tid=>tid tid))\n                                                                 (R-texpr rid))))\n                  rids))\n      (checkpoint!)\n      (for-each compact-relation-fully! rids)\n      ;; TODO: garbage collect unreachable shared text values\n      ;; TODO: after text value gc and applying remappings, eliminate those remappings by rewriting the affected columns\n      ))\n\n  (define (compact-relation-fully! rid)\n    (let ((texpr (R-texpr rid)))\n      (when (pair? texpr)\n        (pretty-log `(fully compacting relation: ,(R-name rid)))\n        (R-assign-t! rid (merge-table-expr (R-type rid) texpr))\n        (checkpoint!))))\n\n  (define (compact-relation-incrementally! rid)\n    (when (R-has-name? rid) (pretty-log `(incrementally compacting relation: ,(R-name rid))))\n    ;; TODO:\n    ;; - identify portion of table-expr to compact\n    ;; - consolidate relevant text columns into one shared text column\n    ;; - merge tables and update table-expr\n    (void))\n\n  (define (collect-garbage!)\n    (define (remove-unreachable! stg-key reachable)\n      (stg-update! stg-key\n                   (lambda (h)\n                     (foldl (lambda (k h) (hash-remove h k))\n                            h\n                            (set->list (set-subtract (list->set (hash-keys h)) reachable))))))\n    (let* ((cid=>c (stg-ref 'column-id=>column))\n           (table-ids.reachable\n             (list->set (append* (map table-expr->table-ids (hash-values (stg-ref 'relation-id=>table-expr))))))\n           (index-prefixes.reachable\n             (list->set (append* (hash-map (stg-ref 'relation-id=>indexes)\n                                           (lambda (rid indexes)\n                                             (let ((ordering-prefixes\n                                                     (append* (map ordering->prefixes (hash-keys indexes)))))\n                                               (append* (map (lambda (tid)\n                                                               (map (lambda (oprefix) (cons tid oprefix))\n                                                                    ordering-prefixes))\n                                                             (table-expr->table-ids (R-texpr rid))))))))))\n           (stgkey.ixp=>cid->cids\n             (lambda (stgkey)\n               (list->set (filter-not not (set-map index-prefixes.reachable\n                                                   (lambda (iprefix) (hash-ref (stg-ref stgkey) iprefix #f)))))))\n           (column-ids.reachable\n             (set-fixed-point\n               (set-union\n                 (list->set (append* (set-map table-ids.reachable\n                                              (lambda (tid) (hash-ref (stg-ref 'table-id=>column-ids) tid)))))\n                 (stgkey.ixp=>cid->cids 'index-prefix=>key-column-id)\n                 (stgkey.ixp=>cid->cids 'index-prefix=>position-column-id))\n               (lambda (cids) (apply set-union (set)\n                                     (set-map cids (lambda (cid)\n                                                     (let loop ((cid cid))\n                                                       (let ((desc (hash-ref cid=>c cid)))\n                                                         (case (hash-ref desc 'class)\n                                                           ((remap) (set-union (set cid)\n                                                                               (loop (hash-ref desc 'local))\n                                                                               (loop (hash-ref desc 'global))))\n                                                           ((text)  (set-union (set cid)\n                                                                               (loop (hash-ref desc 'position))\n                                                                               (loop (hash-ref desc 'value))))\n                                                           (else    (set cid))))))))))))\n      (apply storage-block-remove-names!\n             stg\n             (set->list (set-subtract (list->set (storage-block-names stg))\n                                      (apply set-union (set)\n                                             (set-map column-ids.reachable\n                                                      (lambda (cid)\n                                                        (let ((desc (hash-ref cid=>c cid)))\n                                                          (case (hash-ref desc 'class)\n                                                            ((block) (set (hash-ref desc 'name)))\n                                                            (else    (set))))))))))\n      (remove-unreachable! 'table-id=>column-ids             table-ids.reachable)\n      (remove-unreachable! 'index-prefix=>key-column-id      index-prefixes.reachable)\n      (remove-unreachable! 'index-prefix=>position-column-id index-prefixes.reachable)\n      (remove-unreachable! 'column-id=>column                column-ids.reachable))\n    (checkpoint!))\n\n  (define (text-column->text=>id desc preload?) (let ((count (column-count desc)))\n                                                  (dict:ref (column->ref desc preload?) bytesref (hash 'class  'line\n                                                                               'count  count\n                                                                               'offset 0\n                                                                               'step   1)\n                                                                         preload?)\n                                                            0 count)))\n  (define (text-column->id=>text desc preload?) (let ((count (column-count desc)))\n                                                  (dict:monovec\n                                                    (column->monovec (hash 'class  'line\n                                                                           'count  count\n                                                                           'offset 0\n                                                                           'step   1)\n                                                                     preload?)\n                                                    (column->ref desc preload?)\n                                                    0 count)))\n\n  (define (block-desc->path desc.col) (storage-block-path stg (hash-ref desc.col 'name)))\n  (define (open-input-block desc.col) (open-input-file (block-desc->path desc.col)))\n  (define (open-input-block/cache desc.col)\n    (let ((bpath (block-desc->path desc.col)))\n      ;; NOTE: this caching was causing a race condition when running\n      ;; two queries simultaneously.\n      ;; The caching is to prevent running out of file descriptors\n      ;; when building large knowledge graphs.\n      (or #;(hash-ref bpath=>in bpath #f)\n          (let ((in (open-input-file bpath)))\n            #;(hash-set! bpath=>in bpath in)\n            in))))\n  (define (clear-open-input-blocks!)\n    (for-each close-input-port (hash-values bpath=>in))\n    (hash-clear! bpath=>in))\n\n  (define (column-count desc.col)\n    (case (hash-ref desc.col 'class)\n      ((line block) (hash-ref desc.col 'count))\n      ((text)       (- (column-count (hash-ref (stg-ref 'column-id=>column) (hash-ref desc.col 'position))) 1))\n      ((remap)         (column-count (hash-ref (stg-ref 'column-id=>column) (hash-ref desc.col 'local))))\n      (else         (error \"column-count unimplemented for column class\" desc.col))))\n\n  (define (column-min desc.col)\n    (case (hash-ref desc.col 'class)\n      ((line)       (let ((step   (hash-ref desc.col 'step))\n                          (offset (hash-ref desc.col 'offset)))\n                      (if (<= 0 step)\n                        offset\n                        (+ (* (- (hash-ref desc.col 'count) 1) step) offset))))\n      ((block)      (hash-ref desc.col 'min))\n      ((text)       #f)\n      ((remap)      (let ((cid=>c (stg-ref 'column-id=>column)))\n                      (or (column-min (hash-ref cid=>c (hash-ref desc.col 'global)))\n                          (column-min (hash-ref cid=>c (hash-ref desc.col 'local))))))\n      (else         (error \"column-min unimplemented for column class\" desc.col))))\n\n  (define (column-max desc.col)\n    (case (hash-ref desc.col 'class)\n      ((line)       (let ((step   (hash-ref desc.col 'step))\n                          (offset (hash-ref desc.col 'offset)))\n                      (if (<= step 0)\n                        offset\n                        (+ (* (- (hash-ref desc.col 'count) 1) step) offset))))\n      ((block)      (hash-ref desc.col 'max))\n      ((text)       #f)\n      ((remap)      (let ((cid=>c (stg-ref 'column-id=>column)))\n                      (or (column-max (hash-ref cid=>c (hash-ref desc.col 'global)))\n                          (column-max (hash-ref cid=>c (hash-ref desc.col 'local))))))\n      (else         (error \"column-max unimplemented for column class\" desc.col))))\n\n  (define (column-cardinality desc.col)\n    (case (hash-ref desc.col 'class)\n      ((line)       (let ((step (hash-ref desc.col 'step)))\n                      (if (= step 0)\n                        1\n                        (hash-ref desc.col 'count))))\n      ((block)      (min (hash-ref desc.col 'count)\n                         (+ (- (hash-ref desc.col 'max) (hash-ref desc.col 'min)) 1)))\n      ((text)       (- (column-count (hash-ref (stg-ref 'column-id=>column) (hash-ref desc.col 'position))) 1))\n      ((remap)      (let ((cid=>c (stg-ref 'column-id=>column)))\n                      (min (column-cardinality (hash-ref cid=>c (hash-ref desc.col 'global)))\n                           (column-cardinality (hash-ref cid=>c (hash-ref desc.col 'local))))))\n      (else         (error \"column-count unimplemented for column class\" desc.col))))\n\n  (define ((column->start->s desc.col) start)\n    (case (hash-ref desc.col 'class)\n      ((line)  (let* ((count (max (- (hash-ref desc.col 'count) start) 0))\n                      (step  (hash-ref desc.col 'step)))\n                 (let loop ((i 0) (value (+ (hash-ref desc.col 'offset) (* step start))))\n                   (lambda ()\n                     (if (unsafe-fx< i count)\n                       (cons value (loop (unsafe-fx+ i 1) (unsafe-fx+ value step)))\n                       '())))))\n      ((block) (let* ((count.0 (hash-ref desc.col 'count))\n                      (count   (max (- count.0 start) 0))\n                      (width   (unsafe-fxrshift (hash-ref desc.col 'bit-width) 3))\n                      (offset  (hash-ref desc.col 'offset))\n                      (in      (open-input-block desc.col)))\n                 (file-position in (* width (min count.0 start)))\n                 (let loop ((i 0))\n                   (lambda ()\n                     (if (unsafe-fx< i count)\n                       (cons (unsafe-bytes-nat-ref width (read-bytes width in) 0)\n                             (loop (unsafe-fx+ i 1)))\n                       '())))))\n      ((text)  (let* ((cid=>c (stg-ref 'column-id=>column))\n                      (s.pos  ((column->start->s (hash-ref cid=>c (hash-ref desc.col 'position)))\n                               (+ start 1)))\n                      (in     (open-input-block (hash-ref cid=>c (hash-ref desc.col 'value)))))\n                 (let loop ((s.pos s.pos) (pos.current 0))\n                   (lambda ()\n                     (match (s.pos) ; assume uniform stream\n                       ((cons pos.next s.pos) (cons (read-bytes (unsafe-fx- pos.next pos.current) in)\n                                                    (loop s.pos pos.next)))\n                       (_                     '()))))))\n      ((remap) (let ((s   ((column->start->s (hash-ref (stg-ref 'column-id=>column) (hash-ref desc.col 'local)))\n                           start))\n                     (ref (column->ref (hash-ref (stg-ref 'column-id=>column) (hash-ref desc.col 'global)) #f)))\n                 (values count (s-map ref s))))\n      (else    (error \"column->start->s unimplemented for column class\" desc.col))))\n\n  (define (column->text-cid desc)\n    (case (hash-ref desc 'class)\n      ((remap)           (let* ((cid  (hash-ref desc 'global))\n                                (desc (hash-ref (stg-ref 'column-id=>column) cid)))\n                           (case (hash-ref desc 'class)\n                             ((text) cid)\n                             (else   (column->text-cid desc)))))\n      (else              #f)))\n\n  (define (column->ref desc preload?)\n    (case (hash-ref desc 'class)\n      ((text) (let* ((cid=>c     (stg-ref 'column-id=>column))\n                     (ref.pos    (column->ref (hash-ref cid=>c (hash-ref desc 'position)) preload?))\n                     (desc.value (hash-ref cid=>c (hash-ref desc 'value))))\n                (if preload?\n                    ;; TODO: cache this bytevector\n                    (let ((bs (file->bytes (block-desc->path desc.value))))\n                      (lambda (i) (let ((pos.i   (ref.pos i))\n                                        (pos.i+1 (ref.pos (unsafe-fx+ i 1))))\n                                    (subbytes bs pos.i pos.i+1))))\n                    (let ((in (open-input-block/cache desc.value)))\n                      (lambda (i) (let ((pos.i   (ref.pos i))\n                                        (pos.i+1 (ref.pos (unsafe-fx+ i 1))))\n                                    (file-position in pos.i)\n                                    (read-bytes (unsafe-fx- pos.i+1 pos.i) in)))))))\n      (else   (match-define (monovec ref fnext fprev) (column->monovec desc preload?))\n              (match (column->text-cid desc)\n                (#f       ref)\n                (cid.text (let ((ref.text (column->ref (hash-ref (stg-ref 'column-id=>column) cid.text) preload?)))\n                            (lambda (i) (ref.text (ref i)))))))))\n\n  (define (column->monovec desc preload?)\n    (define (ref->monovec ref)\n      (monovec ref (find-next:ref ref unsafe-fx<) (find-prev:ref ref unsafe-fx<)))\n    (case (hash-ref desc 'class)\n      ((line)  (let ((step   (hash-ref desc 'step))\n                     (offset (hash-ref desc 'offset)))\n                 (if (unsafe-fx= step 0)\n                     (ref->monovec (lambda (_) offset))\n                     (monovec (lambda (i) (unsafe-fx+ (unsafe-fx* step i) offset))\n                              (find-next:line offset step)\n                              (find-prev:line offset step)))))\n      ((block) (let* ((width  (unsafe-fxrshift (hash-ref desc 'bit-width) 3))\n                      (offset (hash-ref desc 'offset)))\n                 (if preload?\n                     (let ((vec (read-fx-column desc)))\n                       (ref->monovec (lambda (i) (unsafe-fxvector-ref vec i))))\n                     (let ((in (open-input-block/cache desc)))\n                       (ref->monovec (lambda (i)\n                                       (file-position in (* width i))\n                                       (unsafe-fx+ (unsafe-bytes-nat-ref width (read-bytes width in) 0) offset)))))))\n      ((text)  #f)\n      ((remap) (let* ((cid=>c      (stg-ref 'column-id=>column))\n                      (desc.global (hash-ref cid=>c (hash-ref desc 'global)))\n                      (monov.local (column->monovec (hash-ref cid=>c (hash-ref desc 'local)) preload?)))\n                 (case (hash-ref desc.global 'class)\n                   ((text) monov.local)\n                   ((line) (match-define (monovec ref.global fnext.global fprev.global) (column->monovec desc.global preload?))\n                           (match-define (monovec ref.local  fnext.local  fprev.local)  monov.local)\n                           (define (ref i) (ref.global (ref.local i)))\n                           (if (unsafe-fx= (hash-ref desc.global 'step) 0)\n                             (ref->monovec ref)\n                             (let ((end.global (hash-ref desc.global 'count)))\n                               (monovec ref\n                                        ;; We use inverse lookup for lines because it should be more efficient.\n                                        ;; TODO: test that this is worth the extra complexity.\n                                        (lambda (inclusive? i.start i.end v)\n                                          (let ((i.global (fnext.global #t 0 end.global v)))\n                                            (if (unsafe-fx< i.global end.global)\n                                              (fnext.local (or inclusive? (unsafe-fx< v (ref.global i.global)))\n                                                           i.start i.end i.global)\n                                              i.end)))\n                                        (lambda (inclusive? i.start i.end v)\n                                          (let ((i.global (fprev.global #t 0 end.global v)))\n                                            (if (unsafe-fx< 0 i.global)\n                                              (fprev.local (or inclusive? (unsafe-fx< (ref.global i.global) v))\n                                                           i.start i.end i.global)\n                                              i.start)))))))\n                   (else (let ((vec.global (read-fx-column desc.global)))\n                           (match-define (monovec ref.local fnext.local fprev.local) monov.local)\n                           (ref->monovec (lambda (i) (unsafe-fxvector-ref vec.global (ref.local i)))))))))\n      (else    (error \"column->monovec unimplemented for column class\" desc))))\n\n  (define (clear-column-vector-cache!) (hash-clear! cdesc=>v))\n\n  (define (read-fx-column desc.col)\n    (or (hash-ref cdesc=>v desc.col #f)\n        (let ((vec (make-fxvector (column-count desc.col))))\n          (read-fx-column/vec! desc.col vec 0)\n          (hash-set! cdesc=>v desc.col vec)\n          vec)))\n\n  (define (read-fx-column/vec! desc.col vec.out start.out)\n    (case (hash-ref desc.col 'class)\n      ((line)  (let* ((count (hash-ref desc.col 'count))\n                      (step  (hash-ref desc.col 'step)))\n                 (let loop ((i 0) (j start.out) (value (hash-ref desc.col 'offset)))\n                   (when (unsafe-fx< i count)\n                     (unsafe-fxvector-set! vec.out j value)\n                     (loop (unsafe-fx+ i 1) (unsafe-fx+ j 1) (unsafe-fx+ value step))))))\n      ((block) (let* ((count  (hash-ref desc.col 'count))\n                      (width  (unsafe-fxrshift (hash-ref desc.col 'bit-width) 3))\n                      (offset (hash-ref desc.col 'offset))\n                      (bs     (file->bytes (block-desc->path desc.col))))\n                 (let loop ((i 0) (j start.out) (k 0))\n                   (when (unsafe-fx< i count)\n                     (unsafe-fxvector-set! vec.out j (unsafe-fx+ (unsafe-bytes-nat-ref width bs k) offset))\n                     (loop (unsafe-fx+ i 1) (unsafe-fx+ j 1) (unsafe-fx+ k width))))))\n      ((remap) (let* ((cid=>c      (stg-ref 'column-id=>column))\n                      (desc.local  (hash-ref cid=>c (hash-ref desc.col 'local)))\n                      (desc.global (hash-ref cid=>c (hash-ref desc.col 'global)))\n                      (end         (unsafe-fx+ (column-count desc.local) start.out)))\n                 (read-fx-column/vec! desc.local vec.out start.out)\n                 ;; TODO: if global is a line, we should do something more efficient\n                 (unless (eq? (hash-ref desc.global 'class) 'text)\n                   (let ((vec.global (read-fx-column desc.global)))\n                     (let loop ((j start.out))\n                       (when (unsafe-fx< j end)\n                         (unsafe-fxvector-set! vec.out j (unsafe-fxvector-ref\n                                                           vec.global (unsafe-fxvector-ref vec.out j)))\n                         (loop (unsafe-fx+ j 1))))))))\n      (else    (error \"read-fx-column/vec! unimplemented for column class\" desc.col))))\n\n  (define (write-fx-column vec.col start count)\n    (define end (+ start count))\n    (define (write-line count offset step)\n      (verbose-log `(write-line: offset: ,offset\n                                 step:   ,step\n                                 count:  ,count))\n      (let ((id.col (fresh-column-id)))\n        (add-columns! id.col (hash 'class  'line\n                                   'count  count\n                                   'offset offset\n                                   'step   step))\n        id.col))\n    (define (write-block min.col max.col)\n      (define-values (width.col offset.col)\n        (let* ((diff.col  (- max.col min.col))\n               (size.diff (nat-min-byte-width diff.col))\n               (size.max  (nat-min-byte-width max.col)))\n          (if (or (< min.col   0)\n                  (< size.diff size.max))\n            (values size.diff min.col)\n            (values size.max  0))))\n      (verbose-log `(write-block: min:    ,min.col\n                                  max:    ,max.col\n                                  offset: ,offset.col\n                                  width:  ,width.col\n                                  count:  ,count))\n      (let* ((id.col     (fresh-column-id))\n             (name.block (cons 'column id.col))\n             (path.block (storage-block-new! stg name.block))\n             (bs.col     (make-bytes (* count width.col))))\n        (let loop ((i start) (j 0))\n          (when (unsafe-fx< i end)\n            (unsafe-bytes-nat-set! width.col bs.col j (- (unsafe-fxvector-ref vec.col i) offset.col))\n            (loop (unsafe-fx+ i 1) (unsafe-fx+ j width.col))))\n        (display-to-file bs.col path.block)\n        (add-columns! id.col (hash 'class     'block\n                                   'name      name.block\n                                   'bit-width (* 8 width.col)\n                                   'count     count\n                                   'offset    offset.col\n                                   'min       min.col\n                                   'max       max.col))\n        id.col))\n    (define (write-remapped-block min.col max.col alphabet)\n      (verbose-log `(write-remapped-block: min: ,min.col max: ,max.col))\n      (let* ((count.alphabet (set-count alphabet))\n             (alphabet       (sort (set->list alphabet) unsafe-fx<))\n             (vec.alphabet   (make-fxvector count.alphabet))\n             (n=>n           (let loop ((i        0)\n                                        (alphabet alphabet)\n                                        (n=>n     (hash)))\n                               (if (unsafe-fx< i count.alphabet)\n                                 (let ((n.next (car alphabet)))\n                                   (unsafe-fxvector-set! vec.alphabet i n.next)\n                                   (loop (unsafe-fx+ i 1)\n                                         (cdr alphabet)\n                                         (hash-set n=>n n.next i)))\n                                 n=>n)))\n             ;; TODO: using full-blown write-fx-column here is a little wasteful\n             (id.alphabet    (write-fx-column vec.alphabet 0 count.alphabet))\n             (id.remap       (fresh-column-id)))\n        (let loop ((i start))\n          (when (unsafe-fx< i end)\n            (unsafe-fxvector-set! vec.col i (hash-ref n=>n (unsafe-fxvector-ref vec.col i)))\n            (loop (unsafe-fx+ i 1))))\n        (add-columns! id.remap (hash 'class  'remap\n                                     'local  (write-block 0 (- count.alphabet 1))\n                                     'global id.alphabet))\n        id.remap))\n    (if (= count 1)\n      (write-line 1 (unsafe-fxvector-ref vec.col start) 0)\n      (let* ((n.0    (unsafe-fxvector-ref vec.col start))\n             (n.1    (unsafe-fxvector-ref vec.col (unsafe-fx+ start 1)))\n             (offset n.0)\n             (step   (unsafe-fx- n.1 n.0)))\n        (if (let loop ((i      (unsafe-fx+ start 2))\n                       (n.prev n.1))\n              (or (unsafe-fx= i end)\n                  (let ((n.next (unsafe-fxvector-ref vec.col i)))\n                    (and (unsafe-fx= (unsafe-fx- n.next n.prev) step)\n                         (loop (unsafe-fx+ i 1) n.next)))))\n          (write-line count offset step)\n          (let loop ((i       (unsafe-fx+ start 2))\n                     (min.col (min n.0 n.1))\n                     (max.col (max n.0 n.1)))\n            (if (unsafe-fx= i end)\n              (let ((count.alphabet.max (max-remap-global-count (nat-min-byte-width (- max.col min.col)) count)))\n                (let loop ((i        (unsafe-fx+ start 2))\n                           (alphabet (set n.0 n.1)))\n                  (if (unsafe-fx= i end)\n                    (write-remapped-block min.col max.col alphabet)\n                    (let ((alphabet (set-add alphabet (unsafe-fxvector-ref vec.col i))))\n                      (if (unsafe-fx< count.alphabet.max (set-count alphabet))\n                        (write-block min.col max.col)\n                        (loop (unsafe-fx+ i 1) alphabet))))))\n              (let ((n.next (unsafe-fxvector-ref vec.col i)))\n                (loop (unsafe-fx+ i 1)\n                      (min min.col n.next)\n                      (max max.col n.next)))))))))\n\n  (define (table-expr type rexpr)\n    (rexpr-clean\n      (let loop ((rexpr (rexpr-clean rexpr)))\n        (match rexpr\n          ('()                     R.empty)\n          (`(+ ,@rs)               (apply R+ (map loop rs)))\n          (`(- ,r0 ,r1)            (R- (loop r0) (loop r1)))\n          ((? wrapped-relation? R) (let* ((R    (wrapped-relation-controller R))\n                                          (path (database-path (R 'database))))\n                                     (unless (equal? path (storage-path stg))\n                                       (error \"cannot combine relations from different databases\"\n                                              path (storage-path stg)))\n                                     (unless (equal? (R 'type) type)\n                                       (error \"type mismatch\" (R 'type) type))\n                                     (R 'table-expr)))))))\n\n  (define cdesc=>v  (make-hash))\n  (define bpath=>in (make-hash))\n  (define rids.new  (mutable-set))\n  (define id=>R     (make-weak-hash))\n  (define (name->R name)\n    (id->R (hash-ref (name=>relation-id) name\n                     (lambda () (error \"unknown relation\" name (storage-path stg))))))\n  (define (id->R id.R)\n    (let* ((key.R (list id.R))\n           (R     (hash-ref id=>R key.R #f)))\n      (if R\n        (wrapped-relation (hash-ref-key id=>R key.R) R)\n        (wrapped-relation key.R                      (let ((R (make-relation id.R)))\n                                                       (hash-set! id=>R key.R R)\n                                                       R)))))\n  (define (stg-ref      key)        (storage-description-ref     stg key))\n  (define (stg-set!     key value)  (storage-description-set!    stg key value))\n  (define (stg-update!  key update) (storage-description-update! stg key update))\n  (define (R-anonymous)             (error \"anonymous relation has no name\"))\n  (define (R-valid?     id)         (hash-has-key? (stg-ref 'relation-id=>type)  id))\n  (define (R-has-name?  id)         (hash-has-key? (stg-ref 'relation-id=>name)  id))\n  (define (R-name       id)         (hash-ref (stg-ref 'relation-id=>name)       id R-anonymous))\n  (define (R-attrs      id)         (hash-ref (stg-ref 'relation-id=>attributes) id))\n  (define (R-type       id)         (hash-ref (stg-ref 'relation-id=>type)       id))\n  (define (R-texpr      id)         (hash-ref (stg-ref 'relation-id=>table-expr) id))\n  (define (R-assign-t!  id texpr)   (stg-update! 'relation-id=>table-expr\n                                                 (lambda (rid=>ts) (hash-set rid=>ts id texpr))))\n  (define (R-assign-r!  id rexpr)   (R-assign-t! id (table-expr (R-type id) rexpr)))\n  (define (name=>relation-id)       (stg-ref 'name=>relation-id))\n  (define (relation-name? name)     (hash-has-key? (name=>relation-id) name))\n  (define (new-relation?! name)     (when (relation-name? name)\n                                      (error \"relation already exists\" name (storage-path stg))))\n  (define (fresh-relation-id)       (fresh-uid))\n  (define (fresh-table-id)          (fresh-uid))\n  (define (fresh-column-id)         (fresh-uid))\n  (define (fresh-uid)               (let ((uid (stg-ref 'next-uid)))\n                                      (stg-set! 'next-uid (+ uid 1))\n                                      uid))\n  (define (add-columns! id desc . id&descs)\n    (stg-update! 'column-id=>column\n                 (lambda (cid=>desc) (apply hash-set* cid=>desc id desc id&descs))))\n  (define (checkpoint!)\n    (when (storage-checkpoint-pending? stg)\n      (storage-checkpoint! stg))\n    (when (and (auto-empty-trash?)\n               (not (storage-trash-empty? stg)))\n      (storage-trash-empty! stg)))\n  (define (revert!)\n    (for-each (lambda (rid) (let ((R (hash-ref id=>R (list rid) #f)))\n                              (when R (R 'invalidate!))))\n              (set->list rids.new))\n    (set-clear! rids.new)\n    (storage-revert! stg))\n  (define (commit!)\n    (for-each (lambda (rid)\n                (let ((R (hash-ref id=>R (list rid) #f)))\n                  (when (and R (not (R-has-name? rid)))\n                    (R 'delete!))))  ; Delete anonymous relations before checkpoint\n              (set->list rids.new))\n    (checkpoint!)\n    (set-clear! rids.new)\n    (perform-pending-jobs!))\n  (define (perform-pending-jobs!)\n    (compact-relations! (filter R-valid? (hash-keys (stg-ref 'relations-to-fully-compact))))\n    (stg-set! 'relations-to-fully-compact (hash))\n    (checkpoint!)\n    (for-each compact-relation-incrementally!\n              (filter R-valid? (hash-keys (stg-ref 'relations-to-incrementally-compact))))\n    (stg-set! 'relations-to-incrementally-compact (hash))\n    (checkpoint!)\n    (for-each\n      (lambda (rid&texpr)\n        (match-define (cons rid texpr) rid&texpr)\n        (let ((tids (set->list (list->set (table-expr->table-ids texpr)))))\n          (build-table-indexes! (hash-keys (hash-ref (stg-ref 'relation-id=>indexes) rid)) tids)))\n      (hash->list (stg-ref 'relation-id=>table-expr)))\n    (checkpoint!)\n    (collect-garbage!))\n\n  (define stg (storage:filesystem path.db))\n  (let ((version (storage-description-ref stg 'database-format-version #f)))\n    (unless (equal? version version.current)\n      (when version (error \"unknown version\" version))\n      (stg-set! 'database-format-version            version.current)\n      (stg-set! 'name=>relation-id                  (hash))\n      (stg-set! 'relation-id=>name                  (hash))\n      (stg-set! 'relation-id=>attributes            (hash))\n      (stg-set! 'relation-id=>type                  (hash))\n      ;; relation-id => table-expr\n      (stg-set! 'relation-id=>table-expr            (hash))\n      ;; relation-id => (ordering => #t)\n      (stg-set! 'relation-id=>indexes               (hash))\n      ;; table-id => (list column-id ...)\n      (stg-set! 'table-id=>column-ids               (hash))\n      ;; (cons table-id ordering-prefix) => column-id\n      (stg-set! 'index-prefix=>key-column-id        (hash))\n      ;; (cons table-id ordering-prefix) => column-id  ; for forming intervals\n      (stg-set! 'index-prefix=>position-column-id   (hash))\n      ;; desc.column:\n      ;;  (hash 'class  'line\n      ;;        'count  nat\n      ;;        'offset int\n      ;;        'step   int)\n      ;; OR\n      ;;  (hash 'class     'block\n      ;;        'name      block-name\n      ;;        'bit-width nat\n      ;;        'count     nat\n      ;;        'offset    int\n      ;;        'min       int\n      ;;        'max       int)\n      ;; OR\n      ;;  (hash 'class  'remap  ; monotonic injection from local to global namespace, possibly for compression\n      ;;        'local  column-id\n      ;;        'global column-id)\n      ;; OR\n      ;;  (hash 'class    'text\n      ;;        'position column-id\n      ;;        'value    column-id)\n      ;; column-id => desc.column\n      (stg-set! 'column-id=>column                  (hash))\n      ;; relation-id => #t\n      (stg-set! 'relations-to-fully-compact         (hash))\n      ;; relation-id => #t\n      (stg-set! 'relations-to-incrementally-compact (hash))\n      (stg-set! 'next-uid                           0)\n      (checkpoint!))\n    (perform-pending-jobs!))\n\n  (define db\n    (wrapped-database\n      (method-lambda\n        ((path)                (storage-path stg))\n        ((relation-names)      (hash-keys (name=>relation-id)))\n        ((relation-name? name) (relation-name? name))\n        ((relation       name) (name->R name))\n        ((relation-builder type batch-size)\n         (valid-relation-type?! type)\n         (define id.R (fresh-relation-id))\n         (set-add! rids.new id.R)\n         (stg-update! 'relation-id=>attributes (lambda (rid=>as) (hash-set rid=>as id.R (range (length type)))))\n         (stg-update! 'relation-id=>type       (lambda (rid=>t)  (hash-set rid=>t  id.R type)))\n         (stg-update! 'relation-id=>indexes    (lambda (rid=>is) (hash-set rid=>is id.R (hash))))\n         (R-assign-t! id.R R.empty)\n         (relation-builder id.R batch-size))\n        ((commit!)      (commit!))\n        ((revert!)      (revert!))\n        ((trash-empty!) (storage-trash-empty! stg)))))\n  db)\n\n(define (valid-attributes?! attrs)\n  (unless (list? attrs)\n    (error \"attributes must be a list\" attrs))\n  (unless (= (length attrs) (set-count (list->set attrs)))\n    (error \"attributes must be unique\" attrs)))\n\n(define (valid-relation-type?! type)\n  (unless (list? type) (error \"relation type must be a list\" type))\n  (when   (null? type) (error \"relation must include at least one attribute type\"))\n  (for-each (lambda (t) (unless (member t '(int text))\n                          (error \"invalid attribute type\" t 'in type)))\n            type))\n\n(define (ordering->prefixes ordering)\n  (let ((rcols (reverse ordering))) ; prefixes ordered from longest to shortest\n    (let loop ((c0 (car rcols)) (rcols (cdr rcols)))\n      (if (null? rcols)\n        (list (list c0))\n        (cons (reverse (cons c0 rcols))\n              (loop (car rcols) (cdr rcols)))))))\n\n(define (unsafe-fxvector-copy! vec.out out.start vec.in in.start in.end)\n  (let loop ((in in.start) (out out.start))\n    (when (unsafe-fx< in in.end)\n      (unsafe-fxvector-set! vec.out out (unsafe-fxvector-ref vec.in in))\n      (loop (unsafe-fx+ in 1) (unsafe-fx+ out 1)))))\n\n;; Performance assumption: columns are narrower than rows.  If this may be violated, perform a check\n;; and invert the looping pattern when violated, to play nicely with the CPU cache.\n(define (transpose-col-to-row! vec.cols vec.rows start.rows count.cols count.rows)\n  (let loop.row ((row        (unsafe-fx- count.rows 1))\n                 (row.scaled (unsafe-fx+ start.rows (unsafe-fx* (unsafe-fx- count.rows 1) count.cols))))\n    (when (unsafe-fx<= 0 row)\n      (let loop.col ((col        (unsafe-fx- count.cols 1))\n                     (col.scaled (unsafe-fx* (unsafe-fx- count.cols 1) count.rows)))\n        (when (unsafe-fx<= 0 col)\n          (unsafe-fxvector-set!\n            vec.rows (unsafe-fx+ row.scaled col)\n            (unsafe-fxvector-ref vec.cols (unsafe-fx+ col.scaled row)))\n          (loop.col (unsafe-fx- col 1) (unsafe-fx- col.scaled count.rows))))\n      (loop.row (unsafe-fx- row 1) (unsafe-fx- row.scaled count.cols)))))\n(define (transpose-row-to-col! vec.cols vec.rows start.rows count.cols count.rows)\n  (let loop.row ((row (unsafe-fx- count.rows 1))\n                 (row.scaled (unsafe-fx+ start.rows (unsafe-fx* (unsafe-fx- count.rows 1) count.cols))))\n    (when (unsafe-fx<= 0 row)\n      (let loop.col ((col        (unsafe-fx- count.cols 1))\n                     (col.scaled (unsafe-fx* (unsafe-fx- count.cols 1) count.rows)))\n        (when (unsafe-fx<= 0 col)\n          (unsafe-fxvector-set!\n            vec.cols (unsafe-fx+ col.scaled row)\n            (unsafe-fxvector-ref vec.rows (unsafe-fx+ row.scaled col)))\n          (loop.col (unsafe-fx- col 1) (unsafe-fx- col.scaled count.rows))))\n      (loop.row (unsafe-fx- row 1) (unsafe-fx- row.scaled count.cols)))))\n\n(define (row-merge-sort! vec.rows vec.buffer start.rows count.cols count.rows)\n  ;; Assume the same usable index range of vec.rows and vec.buffer, begnning at start.rows\n  (define (scale i) (unsafe-fx+ start.rows (unsafe-fx* count.cols i)))\n  (define (tuple)\n  (define i end)\n  (let loop ((offset 1))\n    (define next (- i offset))\n    (cond ((and (>= next start) (i> next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (n (- i o)))\n                    (cond ((= o 0)                   i)\n                          ((and (>= n start) (i> n)) (loop n o))\n                          (else                      (loop i o)))))))))\n\n(define ((unsafe-multi-merge vector gens))\n  (define end (vector-length h))\n  (heap! vector gens))\n  (define end (vector-length h))\n  (heap! id) i) (unsafe-fxvector-ref id=>id (ref i)))\n\n(define ((find-next:ref ref =        d key)             (dict-min-find d #t key))\n(define (dict->         d key)             (dict-min-find d #f key))\n(define (dict-<=        d key)             (dict-max-find d #t key))\n(define (dict-<         d key)             (dict-max-find d #f key))\n(define (dict-ref d key k.found k.missing) (let ((d (dict->= d key)))\n                                             (if (or (dict-empty? d)\n                                                     (not (equal? (dict-min d) key)))\n                                               (k.missing)\n                                               (k.found (dict-min-value d)))))\n(define ((dict-enumerator     d) yield)    (let loop ((d d))\n                                             (unless (dict-empty? d)\n                                               (yield (dict-min d) (dict-min-value d))\n                                               (loop (dict-min-pop d)))))\n(define ((dict-key-enumerator d) yield)    (let loop ((d d))\n                                             (unless (dict-empty? d)\n                                               (yield (dict-min d))\n                                               (loop (dict-min-pop d)))))\n\n(define dict.empty\n  (method-lambda\n    ((count)                   0)\n    ((min-find inclusive? key) dict.empty)\n    ((max-find inclusive? key) dict.empty)\n    ((min)                     (error \"method not supported for empty dictionary: min\"))\n    ((min-value)               (error \"method not supported for empty dictionary: min-value\"))\n    ((min-pop)                 (error \"method not supported for empty dictionary: min-pop\"))\n    ((max)                     (error \"method not supported for empty dictionary: max\"))))\n\n(define (dict:monovec monovec.key ref.value start end)\n  (match-define (monovec ref.key find-next find-prev) monovec.key)\n  (dict:basic ref.key find-next find-prev ref.value start end))\n\n(define (dict:ref ref.key = A k.B)))\n                             (unless (dict-empty? A)\n                               (loop A (dict-min A) B k.B))))\n            ((k= B k.A)))\n                             (unless (dict-empty? B)\n                               (loop A k.A B (dict-min B)))))\n            (else          (let ((t.A (dict-min-value A))\n                                 (t.B (dict-min-value B))\n                                 (A   (dict-min-pop A))\n                                 (B   (dict-min-pop B)))\n                             (yield k.A t.A t.B)\n                             (unless (or (dict-empty? A) (dict-empty? B))\n                               (loop A (dict-min A) B (dict-min B)))))))))\n\n(define ((dict-join-ordered en.ordered d.index) yield)\n  (unless (dict-empty? d.index)\n    (en.ordered (lambda (k v)\n                  (set! d.index (dict->= d.index k))\n                  (dict-ref d.index k\n                            (lambda (v.index) (yield k v v.index))\n                            (lambda ()        (void)))))))\n\n;;;;;;;;;;;;;;;;\n;;; 2-3 tree ;;;\n;;;;;;;;;;;;;;;;\n\n(define (bytes-compare a b)\n  (let* ((len.a (unsafe-bytes-length a))\n         (len.b (unsafe-bytes-length b))\n         (end   (unsafe-fxmin len.a len.b)))\n    (let loop ((i 0))\n      (if (unsafe-fx= i end)\n          (cond ((unsafe-fx< len.a len.b) -1)\n                ((unsafe-fx< len.b len.a)  1)\n                (else                      0))\n          (let ((x.a (unsafe-bytes-ref a i)) (x.b (unsafe-bytes-ref b i)))\n            (cond ((unsafe-fx< x.a x.b) -1)\n                  ((unsafe-fx< x.b x.a)  1)\n                  (else                 (loop (unsafe-fx+ i 1)))))))))\n\n;; Public\n(define (make-btree) (vector 0 #f))\n(define (btree-count bt) (unsafe-vector*-ref bt 0))\n\n;; Private\n(define (btree-count-set! bt count) (unsafe-vector*-set! bt 0 count))\n(define (btree-root       bt)       (unsafe-vector*-ref  bt 1))\n(define (btree-root-set!  bt t)     (unsafe-vector*-set! bt 1 t))\n\n(define (make-btree-2 key                leaf                 l r)   (vector key                leaf                 l r))\n(define (make-btree-3 left-key right-key left-leaf right-leaf l m r) (vector left-key right-key left-leaf right-leaf l m r))\n\n(define (btree-2?      t) (unsafe-fx= (unsafe-vector*-length t) 4))\n(define (btree-2-key   t) (unsafe-vector*-ref t 0))\n(define (btree-2-leaf  t) (unsafe-vector*-ref t 1))\n(define (btree-2-left  t) (unsafe-vector*-ref t 2))\n(define (btree-2-right t) (unsafe-vector*-ref t 3))\n\n(define (btree-2-left-set!  t u) (unsafe-vector*-set! t 2 u))\n(define (btree-2-right-set! t u) (unsafe-vector*-set! t 3 u))\n\n(define (btree-3-left-key   t) (unsafe-vector*-ref t 0))\n(define (btree-3-right-key  t) (unsafe-vector*-ref t 1))\n(define (btree-3-left-leaf  t) (unsafe-vector*-ref t 2))\n(define (btree-3-right-leaf t) (unsafe-vector*-ref t 3))\n(define (btree-3-left       t) (unsafe-vector*-ref t 4))\n(define (btree-3-middle     t) (unsafe-vector*-ref t 5))\n(define (btree-3-right      t) (unsafe-vector*-ref t 6))\n\n(define (btree-3-left-set!   t u) (unsafe-vector*-set! t 4 u))\n(define (btree-3-middle-set! t u) (unsafe-vector*-set! t 5 u))\n(define (btree-3-right-set!  t u) (unsafe-vector*-set! t 6 u))\n\n;; Public\n(define (btree-enumerate bt yield)\n  (let loop ((t (btree-root bt)))\n    (when t\n      (cond ((btree-2? t) (loop  (btree-2-left t))\n                          (yield (btree-2-key t) (btree-2-leaf t))\n                          (loop  (btree-2-right t)))\n            (else (loop  (btree-3-left t))\n                  (yield (btree-3-left-key t) (btree-3-left-leaf t))\n                  (loop  (btree-3-middle t))\n                  (yield (btree-3-right-key t) (btree-3-right-leaf t))\n                  (loop  (btree-3-right t)))))))\n\n(define (btree-ref-or-set! bt x)\n  (let loop ((t        (btree-root bt))\n             (replace! (lambda (t)            (btree-root-set! bt t)))\n             (expand!  (lambda (key leaf l r) (btree-root-set! bt (make-btree-2 key leaf l r)))))\n    (cond\n      ((not t) (let ((count (btree-count bt)))\n                 (btree-count-set! bt (unsafe-fx+ count 1))\n                 (expand! x count #f #f)\n                 count))\n      ((btree-2? t) (case (bytes-compare x (btree-2-key t))\n                      ((-1) (loop (btree-2-left t)\n                                  (lambda (u) (btree-2-left-set! t u))\n                                  ;; 2(._ key/leaf .R) ==> 3(.l left-key/left-leaf .m key/leaf .R)\n                                  (lambda (left-key left-leaf l m)\n                                    (replace! (make-btree-3 left-key (btree-2-key t)\n                                                            left-leaf (btree-2-leaf t)\n                                                            l m (btree-2-right t))))))\n                      (( 1) (loop (btree-2-right t)\n                                  (lambda (u) (btree-2-right-set! t u))\n                                  ;; 2(.L key/leaf ._) ==> 3(.L key/leaf .m right-key/right-leaf .r)\n                                  (lambda (right-key right-leaf m r)\n                                    (replace! (make-btree-3 (btree-2-key t) right-key\n                                                            (btree-2-leaf t) right-leaf\n                                                            (btree-2-left t) m r)))))\n                      (else (btree-2-leaf t))))\n      (else (case (bytes-compare x (btree-3-left-key t))\n              ((-1) (loop (btree-3-left t)\n                          (lambda (u) (btree-3-left-set! t u))\n                          ;; 3(._ left-key/left-leaf .M right-key/right-leaf .R)\n                          ;; ==>\n                          ;;           2(. left-key/left-leaf .)\n                          ;;            /                      \\\n                          ;; 2(.l key/leaf .r)        2(.M right-key/right-leaf .R)\n                          (lambda (key leaf l r)\n                            (expand! (btree-3-left-key t)\n                                     (btree-3-left-leaf t)\n                                     (make-btree-2 key leaf l r)\n                                     (make-btree-2 (btree-3-right-key t) (btree-3-right-leaf t)\n                                                   (btree-3-middle t) (btree-3-right t))))))\n              (( 1) (case (bytes-compare x (btree-3-right-key t))\n                      ((-1) (loop (btree-3-middle t)\n                                  (lambda (u) (btree-3-middle-set! t u))\n                                  ;; 3(.L left-key/left-leaf ._ right-key/right-leaf .R)\n                                  ;; ==>\n                                  ;;                       2(. key/leaf .)\n                                  ;;                        /            \\\n                                  ;; 2(.L left-key/left-leaf .l)      2(.r right-key/right-leaf .R)\n                                  (lambda (key leaf l r)\n                                    (expand!\n                                      key leaf\n                                      (make-btree-2 (btree-3-left-key t) (btree-3-left-leaf t)\n                                                    (btree-3-left t) l)\n                                      (make-btree-2 (btree-3-right-key t) (btree-3-right-leaf t)\n                                                    r (btree-3-right t))))))\n                      (( 1) (loop (btree-3-right t)\n                                  (lambda (u) (btree-3-right-set! t u))\n                                  ;; 3(.L left-key/left-leaf .M right-key/right-leaf ._)\n                                  ;; ==>\n                                  ;;                 2(. right-key/right-leaf .)\n                                  ;;                  /                        \\\n                                  ;; 2(.L left-key/left-leaf .M)        2(.l key/leaf .r)\n                                  (lambda (key leaf l r)\n                                    (expand!\n                                      (btree-3-right-key t)\n                                      (btree-3-right-leaf t)\n                                      (make-btree-2 (btree-3-left-key t) (btree-3-left-leaf t)\n                                                    (btree-3-left t) (btree-3-middle t))\n                                      (make-btree-2 key leaf l r)))))\n                      (else (btree-3-right-leaf t))))\n              (else (btree-3-left-leaf t)))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/dsv.rkt",
    "content": "#lang racket/base\n(provide tsv->stream dsv->stream csv->stream\n         path->format format->header/port->stream)\n(require racket/function racket/list racket/string)\n\n;; Informal grammar for tab-separated values (no escapes supported)\n;FIELD-SEPARATOR  ::= \\t\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= CONTENT*\n;CONTENT includes anything other than \\t, \\n, \\r\n\n(define (tsv->stream header? in)\n  (valid-header?! in header? \"\\t\")\n  (let loop () (thunk (define l (read-line in 'any))\n                      (if (eof-object? l) '()\n                        (cons (string-split l \"\\t\" #:trim? #f) (loop))))))\n\n;; Informal grammar for delimiter-separated values (escapes via double quote)\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= \\\" inner-content* \\\" | CONTENT*\n;inner-content    ::= CONTENT | \\\"\\\" | FIELD-SEPARATOR | WHITESPACE\n;CONTENT includes anything other than double-quote, field separator, whitespace\n\n(define (csv->stream header? in) (dsv->stream #\\, header? in))\n\n(define (dsv->stream field-separator header? in)\n  (define (field)\n    (define ch (peek-char in))\n    (cond ((eqv? ch field-separator) (read-char in) \"\")\n          ((or (eqv? ch #\\newline) (eqv? ch #\\return) (eof-object? ch)) \"\")\n          ((eqv? ch #\\\")\n           (read-char in)\n           (let loop ((i 0))\n             (define ch (peek-char in i))\n             (cond ((eqv? ch #\\\")\n                    (if (eqv? (peek-char in (+ i 1)) #\\\") (loop (+ i 2))\n                      (let ((qs (bytes->string/utf-8 (read-bytes i in))))\n                        (read-char in)\n                        (when (eqv? (peek-char in) field-separator)\n                          (read-char in))\n                        (string-replace qs \"\\\"\\\"\" \"\\\"\"))))\n                   (else (loop (+ i 1))))))\n          (else (let loop ((i 1))\n                  (define ch (peek-char in i))\n                  (cond ((eqv? ch field-separator)\n                         (define s (bytes->string/utf-8 (read-bytes i in)))\n                         (read-char in) s)\n                        ((or (eqv? ch #\\newline) (eqv? ch #\\return) (eof-object? ch))\n                         (bytes->string/utf-8 (read-bytes i in)))\n                        (else (loop (+ i 1))))))))\n  (define (record)\n    (cons (field)\n          (let ((ch (peek-char in)))\n            (cond ((eqv? ch #\\return) (read-char in)\n                                      (when (eqv? (peek-char in) #\\newline)\n                                        (read-char in))\n                                      '())\n                  ((eqv? ch #\\newline) (read-char in) '())\n                  ((eof-object? ch)                   '())\n                  (else                               (record))))))\n  (valid-header?! in header? (make-string 1 field-separator))\n  (let loop () (thunk (if (eof-object? (peek-char in)) '()\n                        (cons (record) (loop))))))\n\n(define (valid-header?! in header delimiter)\n  (define found    (and header (read-line in 'any)))\n  (define expected (and header (cond ((eq? header #t)  found)\n                                     ((string? header) header)\n                                     (else (string-join header delimiter)))))\n  (unless (equal? found expected)\n    (error \"invalid header:\" 'found: found 'expected: expected)))\n\n(define (path->format path)\n  (define fname (if (path? path) (path->string path) path))\n  (case (last (string-split fname \".\" #:trim? #f))\n    ((\"tsv\") 'tsv)\n    ((\"csv\") 'csv)\n    (else    #f)))\n\n(define (format->header/port->stream format)\n  (case format\n    ((tsv) tsv->stream)\n    ((csv) csv->stream)\n    (else  (error \"invalid format:\" format))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/enumerator.rkt",
    "content": "#lang racket/base\n(provide enumerator-append\n         list->enumerator enumerator->rlist enumerator->list\n         s->enumerator enumerator->s\n         vector->enumerator unsafe-vector->enumerator enumerator->rvector enumerator->vector\n         generator->enumerator\n         enumerator/2->enumerator\n         enumerator->enumerator/2\n         hash->enumerator/2)\n(require racket/control racket/unsafe/ops)\n\n(define ((enumerator-append e.0 e.1) yield)\n  (e.0 yield)\n  (e.1 yield))\n\n(define ((list->enumerator xs) yield) (for-each yield xs))\n\n(define (enumerator->rlist en)\n  (define xs '())\n  (en (lambda (x) (set! xs (cons x xs))))\n  xs)\n\n(define (enumerator->list en)\n  (reverse (enumerator->rlist en)))\n\n(define ((s->enumerator s) yield)\n  (let loop ((s s))\n    (cond ((null? s) (void))\n          ((pair? s) (yield (car s)) (loop (cdr s)))\n          (else      (loop (s))))))\n\n(define ((enumerator->s en))\n  (define tag (make-continuation-prompt-tag))\n  (reset-at tag\n            (en (lambda (x)\n                  (shift-at tag k (cons x (lambda () (k (void)))))))\n            '()))\n\n(define (enumerator->rvector en)\n  (list->vector (enumerator->rlist en)))\n\n(define (enumerator->vector en)\n  (list->vector (enumerator->list en)))\n\n(define (vector->enumerator v (start 0) (end (vector-length v)))\n  (define len (min end (vector-length v)))\n  (unsafe-vector->enumerator v (min start len) len))\n\n(define ((unsafe-vector->enumerator v (start 0) (end (unsafe-vector*-length v))) yield)\n  (let loop ((i start))\n    (when (unsafe-fx< i end)\n      (yield (unsafe-vector*-ref v i))\n      (loop (unsafe-fx+ i 1)))))\n\n(define ((generator->enumerator gen stop?) yield)\n  (let loop ()\n    (define x (gen))\n    (unless (stop? x)\n      (yield x)\n      (loop))))\n\n;; An enumerator/2 expects its iteratee to take two arguments\n(define ((enumerator/2->enumerator en) yield)\n  (en (lambda (a b) (yield (cons a b)))))\n\n(define ((enumerator->enumerator/2 en) yield)\n  (en (lambda (x&y) (yield (car x&y) (cdr x&y)))))\n\n(define ((hash->enumerator/2 kvs) yield) (hash-for-each kvs yield))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/example-concrete-syntax-extended.rkt",
    "content": "#lang racket/base\n;(provide foo bar)\n\n(require \"concrete-syntax-extended.rkt\")\n\n(define-relations\n  (rule  (foo x)      (== x 5) (bar x 1 2))\n  (table (bar id s o) \"somewhere/bar\"))\n\n((relation-method foo) 'apply 888)\nbar\n\n;(define-relation (foo x) (== x 5) (bar x 1 2))\n\n;(define-relation/table (bar id s o) \"somewhere/bar\")\n\n;(with-formula-vocabulary (foo 11))\n\n;(foo 'apply 12)\n\n;(== 1 2)\n;(with-formula-vocabulary (== 1 2))\n;==\n;;)\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/heap.rkt",
    "content": "#lang racket/base\n(provide\n  heap-top\n  heap!\n  heap-remove!\n  heap-replace!\n  heap-sink!\n  heap-add!\n  )\n\n(define (heap-top         h)         (vector-ref h 0))\n(define (heap!         format file-stats s-pop-header produce/pop-header\n         port-produce port-consume\n         out:port out:file\n         in:transform in:procedure in:port in:file\n         in:stream in:pop-header\n         jsonl:read jsonl:write json:read json:write\n         tsv:read tsv:write csv:read csv:write csv:escape)\n(require \"codec.rkt\" \"enumerator.rkt\" \"misc.rkt\" \"stream.rkt\"\n         json racket/list racket/match racket/port racket/string)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Utilities\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (path->format path.0)\n  (define path (if (path? path.0) (path->string path.0) path.0))\n  (case (last (string-split path \".\" #:trim? #f))\n    ((\"bscm\")  'bscm)\n    ((\"scm\")   'scm)\n    ((\"tsv\")   'tsv)\n    ((\"csv\")   'csv)\n    ((\"json\")  'json)\n    ((\"jsonl\") 'jsonl)\n    (else      #f)))\n\n(define (file-stats path)\n  (and (file-exists? path)\n       (hash 'size          (file-size path)\n             'time.modified (file-or-directory-modify-seconds path))))\n\n(define (s-pop-header ? expected s.0)\n  (define s (s-force s.0))\n  (unless (pair? s)   (error \"missing header:\" 'expected: expected))\n  (unless (? (car s)) (error \"invalid header:\" 'found: (car s) 'expected: expected))\n  (cdr s))\n\n(define (produce/pop-header produce header)\n  (define ((produce/pop ? h)) (s-pop-header ? h (produce)))\n  (match header\n    (#f produce)\n    (#t (produce/pop (lambda (x) #t)           #t))\n    (h  (produce/pop (lambda (x) (equal? x h)) h))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Producers and consumers\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (in:procedure  proc)           proc)\n(define (in:stream     s)              (lambda () s))\n(define (in:transform  produce f)      (cond (f    (lambda () (f (produce))))\n                                             (else produce)))\n(define (in:pop-header produce header) (produce/pop-header produce header))\n\n(define (in:port in . pargs)\n  (define kwargs (make-immutable-hash (plist->alist pargs)))\n  (define (produce) (port-produce in\n                                  (hash-ref kwargs 'close? #f)\n                                  (hash-ref kwargs 'format)\n                                  (hash-ref kwargs 'type #f)))\n  (in:transform (produce/pop-header produce (hash-ref kwargs 'header #f))\n                (hash-ref kwargs 'transform #f)))\n\n(define (in:file path.0 . pargs)\n  (define path   (if (path? path.0) (path->string path.0) path.0))\n  (define kwargs (make-immutable-hash (plist->alist pargs)))\n  (define format (hash-ref kwargs 'format (path->format path)))\n  (unless format            (error \"unknown format:\"     path))\n  (unless (file-stats path) (error \"missing input file:\" path))\n  (define (produce) (let ((in (open-input-file path)))\n                      (port-produce in (lambda () (close-input-port in))\n                                    format\n                                    (hash-ref kwargs 'type #f))))\n  (in:transform (produce/pop-header produce (hash-ref kwargs 'header #f))\n                (hash-ref kwargs 'transform #f)))\n\n(define (out:port out . pargs) (port-consume out\n                                             (plist-ref pargs 'format)\n                                             (plist-ref pargs 'type #f)))\n\n(define (out:file path.0 . pargs)\n  (define path   (if (path? path.0) (path->string path.0) path.0))\n  (define kwargs (make-immutable-hash (plist->alist pargs)))\n  (define exists (hash-ref kwargs 'exists 'error))\n  (define format (hash-ref kwargs 'format (path->format path)))\n  (unless format (error \"unknown format:\" path))\n  (let ((pargs (alist->plist (hash->list (hash-set kwargs 'format format)))))\n    (call-with-output-file path\n                           (lambda (out) (apply out:port out pargs))\n                           #:exists exists)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Port management\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (port-produce in close? format type)\n  (case format\n    ((json) (define data (vector->list (json:read in)))\n            (when close? (close?))\n            data)\n    (else   (define get\n              (case format\n                ((bscm)  (lambda () (if (eof-object? (peek-byte in)) eof (decode in type))))\n                ((scm)   (lambda () (read in)))\n                ((tsv)   (lambda () (tsv:read in)))\n                ((csv)   (lambda () (csv:read in)))\n                ((jsonl) (lambda () (jsonl:read in)))\n                (else    (error \"unsupported input format:\" format))))\n            (let loop ()\n              (lambda ()\n                (define datum (get))\n                (cond ((eof-object? datum) (when close? (close?))\n                                           '())\n                      (else                (cons datum (loop)))))))))\n\n(define (port-consume out format type)\n  (case format\n    ((json) (lambda (en) (json:write out (enumerator->list en))))\n    (else   (let ((yield (case format\n                           ((scm)   (lambda (x) (write x out) (write-char #\\newline out)))\n                           ((bscm)  (lambda (x) (encode      out type x)))\n                           ((tsv)   (lambda (x) (tsv:write   out      x)))\n                           ((csv)   (lambda (x) (csv:write   out      x)))\n                           ((jsonl) (lambda (x) (jsonl:write out      x)))\n                           (else    (error \"unsupported output format:\" format)))))\n              (lambda (en) (en yield))))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; JSON and JSONL formats\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (jsonl:read in)\n  (define s (read-line in 'any))\n  (if (eof-object? s) s (string->jsexpr s)))\n\n(define (jsonl:write out x)\n  (write-string (jsexpr->string x) out)\n  (write-char #\\newline out))\n\n(define (json:read  in)    (string->jsexpr (port->string in)))\n(define (json:write out x) (write-string (jsexpr->string x) out))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; TSV format\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Informal grammar for tab-separated values (no escapes supported)\n;FIELD-SEPARATOR  ::= \\t\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record [RECORD-SEPARATOR] EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= CONTENT*\n;CONTENT includes anything other than \\t, \\n, \\r\n\n(define (tsv:read in)\n  (define l (read-line in 'any))\n  (if (eof-object? l)\n    l\n    (let ((fields (string-split l \"\\t\" #:trim? #f)))\n      (if (null? fields)\n        '(\"\")\n        fields))))\n\n(define (tsv:write out x)\n  (write-string (string-join x \"\\t\" #:after-last \"\\n\") out))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; CSV format\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Informal grammar for delimiter-separated values (escapes via double quote)\n;RECORD-SEPARATOR ::= \\r\\n | \\n | \\r\n;record-stream    ::= EOF | record [RECORD-SEPARATOR] EOF | record RECORD-SEPARATOR record-stream\n;record           ::= field | field FIELD-SEPARATOR record\n;field            ::= \\\" inner-content* \\\" | CONTENT*\n;inner-content    ::= CONTENT | \\\"\\\" | FIELD-SEPARATOR | WHITESPACE\n;CONTENT includes anything other than double-quote, field separator, whitespace\n\n(define (csv:read in)\n  (define (field)\n    (define ch (peek-char in))\n    (cond ((eqv? ch #\\,)           (read-char in)\n                                   \"\")\n          ((or (eqv? ch #\\newline)\n               (eqv? ch #\\return)\n               (eof-object? ch))   \"\")\n\n          ((eqv? ch #\\\")           (read-char in)\n                                   (let loop ((i 0))\n                                     (define ch (peek-char in i))\n                                     (cond ((eqv? ch #\\\") (if (eqv? (peek-char in (+ i 1)) #\\\")\n                                                            (loop (+ i 2))\n                                                            (let ((qs (bytes->string/utf-8 (read-bytes i in))))\n                                                              (read-char in)\n                                                              (when (eqv? (peek-char in) #\\,)\n                                                                (read-char in))\n                                                              (string-replace qs \"\\\"\\\"\" \"\\\"\"))))\n                                           (else          (loop (+ i 1))))))\n\n          (else                    (let loop ((i 1))\n                                     (define ch (peek-char in i))\n                                     (cond ((eqv? ch #\\,)           (define s (bytes->string/utf-8 (read-bytes i in)))\n                                                                    (read-char in)\n                                                                    s)\n                                           ((or (eqv? ch #\\newline)\n                                                (eqv? ch #\\return)\n                                                (eof-object? ch))   (bytes->string/utf-8 (read-bytes i in)))\n                                           (else                    (loop (+ i 1))))))))\n  (if (eof-object? (peek-char in))\n    eof\n    (let record ()\n      (cons (field)\n            (let ((ch (peek-char in)))\n              (cond ((eqv? ch #\\return)  (read-char in)\n                                         (when (eqv? (peek-char in) #\\newline)\n                                           (read-char in))\n                                         '())\n                    ((eqv? ch #\\newline) (read-char in)\n                                         '())\n                    ((eof-object? ch)    '())\n                    (else                (record))))))))\n\n(define (csv:write out x)\n  (write-string (string-join (map csv:escape x) \",\" #:after-last \"\\n\") out))\n\n(define (csv:escape s)\n  (if (ormap (lambda (x) (string-contains? s x)) '(\",\" \"\\\"\" \"\\n\" \"\\r\"))\n    (string-append \"\\\"\" (string-replace s \"\\\"\" \"\\\"\\\"\") \"\\\"\")\n    s))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/logging.rkt",
    "content": "#lang racket/base\n(provide\n  pretty-timestamp\n  pretty-log/port\n  pretty-logf/port\n  pretty-log\n  pretty-logf\n  time/pretty-log\n  current-log-port)\n(require racket/pretty)\n\n;; TODO: eventually replace the logging in config.rkt with these definitions\n(define (pretty-timestamp)\n  (define seconds (current-seconds))\n  (define d       (seconds->date seconds #f))\n  (list seconds 'UTC\n        (date-year d) (date-month  d) (date-day    d)\n        (date-hour d) (date-minute d) (date-second d)))\n\n(define (pretty-log/port  out         . args) (pretty-write    (cons (pretty-timestamp) args) out))\n(define (pretty-logf/port out message . args) (pretty-log/port out (apply format message args)))\n\n(define current-log-port (make-parameter (current-error-port)))\n\n(define (pretty-log  . args) (apply pretty-log/port  (current-log-port) args))\n(define (pretty-logf . args) (apply pretty-logf/port (current-log-port) args))\n\n(define-syntax-rule (time/pretty-log body ...)\n  (let-values (((results time.cpu time.real time.gc) (time-apply (lambda () body ...) '())))\n    (pretty-log `(time cpu ,time.cpu real ,time.real gc ,time.gc))\n    (apply values results)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/misc.rkt",
    "content": "#lang racket/base\n(provide simple-match simple-match-lambda record\n         method-lambda method-choose method-unknown method-except method-only\n         foldl/and let*/and define-variant\n         plist->alist plist-ref alist->plist alist-ref alist-remove alist-update alist-set\n         hash-remove*\n         call/files let/files\n         map/merge map/append\n         min-bits min-bytes min-bytes-power2 int? nat?\n         bytes-nat-ref bytes-nat-set! nat->bytes bytes->nat\n         sum\n         normalize-path)\n(require (for-syntax racket/base) racket/fixnum racket/list racket/match racket/set)\n\n(define-syntax simple-match-lambda\n  (syntax-rules ()\n    ((_ (params body ...) ...) (lambda args\n                                 (simple-match args\n                                   (params body ...) ...)))))\n\n(define-syntax simple-match\n  (syntax-rules ()\n    ((_ e) (error \"no matching pattern:\" e))\n    ((_ e (pattern body ...) clauses ...)\n     (let* ((x e)\n            (k.f (lambda () (simple-match x clauses ...))))\n       (simple-match-clause (let () body ...) (k.f) x pattern)))))\n\n(define-syntax simple-match-clause\n  (syntax-rules ()\n    ((_ k.t k.f x ())          (if (null? x) k.t k.f))\n    ((_ k.t k.f x (p.a . p.d)) (if (pair? x)\n                                 (let ((x.car (car x))\n                                       (x.cdr (cdr x)))\n                                   (simple-match-clause\n                                     (simple-match-clause k.t k.f x.cdr p.d)\n                                     k.f x.car p.a))\n                                 k.f))\n    ((_ k.t k.f x #(p ...))    (if (vector? x)\n                                 (let ((x (vector->list x)))\n                                   (simple-match-clause k.t k.f x (p ...)))\n                                 k.f))\n    ((_ k.t k.f x id)          (let ((id x)) k.t))))\n\n(begin-for-syntax\n  (define (syntax/context context stx)\n    (datum->syntax context (syntax->datum stx)))\n  (define (id/suffix id str)\n    (define str.id (symbol->string (syntax->datum id)))\n    (datum->syntax id (string->symbol (string-append str.id str))))\n  (define (syntax-permute keys stx.alist blame)\n    (define kvs\n      (syntax-case stx.alist ()\n        (((key . value) ...) (map cons\n                                  (syntax->datum #'(key ...))\n                                  (syntax->list #'((key . value) ...))))))\n    (map (lambda (k) (let ((kv (assoc k kvs)))\n                       (if kv (cdr kv)\n                         (error \"missing record field:\" k blame))))\n         keys))\n  (define-syntax with-syntax*\n    (syntax-rules ()\n      ((_ ()                  body ...) (with-syntax () body ...))\n      ((_ ((p0 e0) (p e) ...) body ...) (with-syntax ((p0 e0))\n                                          (with-syntax* ((p e) ...)\n                                            body ...))))))\n\n;; (record name (field ...) extra ...)\n;; produces these definitions:\n;; * struct:         (struct name:struct (field ...) extra ...)\n;; * predicate:      name?\n;; * constructor:    (name (field expr) ...)\n;; * setter:         (name:set expr (field expr) ...)\n;; * match-expander: (name:match (field pattern) ...)\n(define-syntax (record stx)\n  (syntax-case stx ()\n    ((_ name (field-name ...) extras ...)\n     (let* ((field-names     (syntax->datum #'(field-name ...)))\n            (field-name-strs (map symbol->string field-names)))\n       (with-syntax* ((id.struct  (id/suffix #'name \":struct\"))\n                      (id.ref     (id/suffix #'name \":ref\"))\n                      (id.set     (id/suffix #'name \":set\"))\n                      (id.?       (id/suffix #'name \"?\"))\n                      (id.struct? (id/suffix #'name \":struct?\"))\n                      (id.match   (id/suffix #'name \":match\"))\n                      (ids.field-names #'(field-name ...))\n                      ((id.accessor ...)\n                       (map (lambda (f) (id/suffix #'name\n                                                   (string-append \"-\" f)))\n                            field-name-strs))\n                      ((id.struct-accessor ...)\n                       (map (lambda (f) (id/suffix #'id.struct\n                                                   (string-append \"-\" f)))\n                            field-name-strs)))\n         #`(begin\n             (struct id.struct (field-name ...) extras ...)\n             (define id.?        id.struct?)\n             (define id.accessor id.struct-accessor) ...\n             (...\n               (begin\n                 (define-syntax (name stx)\n                   (syntax-case stx ()\n                     ((_ (f e) ...)\n                      (with-syntax ((((f e) ...) (syntax-permute\n                                                   'ids.field-names\n                                                   #'((f e) ...)\n                                                   stx)))\n                        #'(let ((f e) ...) (id.struct f ...))))))\n                 (define-syntax (id.set stx)\n                   (syntax-case stx ()\n                     ((_ r (f e) ...)\n                      (let ((field-names '#,field-names))\n                        #`(let ()\n                            (match-define (id.struct #,@field-names) r)\n                            (let #,(map list\n                                        (syntax->datum #'(f ...))\n                                        (syntax->list  #'(e ...)))\n                              (id.struct #,@field-names)))))))\n                 (define-match-expander id.match\n                   (lambda (stx)\n                     (syntax-case stx ()\n                       ((_ (f p) ...)\n                        #'(struct* id.struct ((f p) ...))))))))))))))\n\n(define method-unknown\n  (case-lambda\n    (()            (case-lambda\n                     (()     '())\n                     ((name) (error \"unknown method:\" name))))\n    ((name . args) (error \"unknown method:\" name args))))\n(define (method-except m names)\n  (case-lambda\n    (()            (case-lambda\n                     (()     (set-subtract ((m)) names))\n                     ((name) (((if (member name names) method-unknown m)) name))))\n    ((name . args) (apply (if (member name names) method-unknown m) name args))))\n(define (method-only m names)\n  (case-lambda\n    (()            (case-lambda\n                     (()     (set-intersect ((m)) names))\n                     ((name) (((if (member name names) m method-unknown)) name))))\n    ((name . args) (apply (if (member name names) m method-unknown) name args))))\n\n(define-syntax method-choose\n  (syntax-rules (else)\n    ((_ ((name ...) body ...) ... (else else-body ...))\n     (case-lambda\n       (()                   (case-lambda\n                               (()            (set-union '(name ...) ... (((begin else-body ...)))))\n                               ((method-name) (case method-name\n                                                ((name ...) (let ((handler (begin body ...)))\n                                                              (lambda args (apply handler method-name args))))\n                                                ...\n                                                (else       (((begin else-body ...)) method-name))))))\n       ((method-name . args) (apply (case method-name\n                                      ((name ...) body ...) ...\n                                      (else       else-body ...))\n                                    method-name args))))\n    ((_ body ...) (method-choose body ... (else method-unknown)))))\n\n(define-syntax method-lambda\n  (syntax-rules (else)\n    ((_ ((name . param) body ...) ... (else else-body ...))\n     (method-choose ((name) (lambda (_ . param) body ...)) ... (else else-body ...)))\n    ((_ body ...) (method-lambda body ... (else method-unknown)))))\n\n(define (foldl/and f acc xs . yss)\n  (let loop ((acc acc) (xs xs) (yss yss))\n    (if (null? xs)\n      acc\n      (and acc (loop (apply f (car xs) (append (map car yss) (list acc)))\n                     (cdr xs)\n                     (map cdr yss))))))\n\n(define-syntax let*/and\n  (syntax-rules ()\n    ((_ () body ...)                   (let () body ...))\n    ((_ ((lhs rhs) rest ...) body ...) (let ((lhs rhs))\n                                         (and lhs (let*/and (rest ...)\n                                                    body ...))))))\n\n(define-syntax define-variant\n  (syntax-rules ()\n    ((_ type? (struct-name fields ...) ...)\n     (begin (define (type? x)\n              (match x\n                ((struct-name fields ...) #t) ...\n                (_                        #f)))\n            (struct struct-name (fields ...) #:prefab) ...))))\n\n(define (plist->alist plist)\n  (match plist\n    ('()                     '())\n    ((cons k (cons v plist)) (cons (cons k v) (plist->alist plist)))))\n\n(define (plist-ref plist key (default (void)))\n  (let loop ((kvs plist))\n    (match kvs\n      ('()                   (if (void? default)\n                               (error \"missing key in property list:\" key plist)\n                               default))\n      ((cons k (cons v kvs)) (if (equal? k key)\n                               v\n                               (loop kvs))))))\n\n(define (alist->plist alist)\n  (match alist\n    ('()                     '())\n    ((cons (cons k v) alist) (cons k (cons v (alist->plist alist))))))\n\n(define (alist-ref alist key (default (void)))\n  (define kv (assoc key alist))\n  (cond (kv              (cdr kv))\n        ((void? default) (error \"missing key in association list:\" key alist))\n        (else            default)))\n\n(define (alist-remove alist key)\n  (filter (lambda (kv) (not (equal? (car kv) key))) alist))\n\n(define (alist-update alist key v->v (default (void)))\n  (let loop ((kvs alist) (prev '()))\n    (cond ((null?        kvs     )\n           (when (void? default) (error \"missing key in association list:\" key alist))\n           (cons (cons key (v->v default)) alist))\n          ((equal? (caar kvs) key) (foldl cons (cons (cons key (v->v (cdar kvs))) (cdr kvs)) prev))\n          (else                    (loop (cdr kvs) (cons (car kvs) prev))))))\n\n(define (alist-set alist key value)\n  (alist-update alist key (lambda (_) value) #f))\n\n(define (hash-remove* h keys)\n  (foldl (lambda (k h) (hash-remove h k)) h keys))\n\n(define (call/files fins fouts p)\n  (let loop ((fins fins) (ins '()))\n    (if (null? fins)\n      (let loop ((fouts fouts) (outs '()))\n        (if (null? fouts)\n          (apply p (append (reverse ins) (reverse outs)))\n          (call-with-output-file\n            (car fouts) (lambda (out) (loop (cdr fouts) (cons out outs))))))\n      (call-with-input-file\n        (car fins) (lambda (in) (loop (cdr fins) (cons in ins)))))))\n\n(define-syntax-rule (let/files ((in fin) ...) ((out fout) ...) body ...)\n  (call/files (list fin ...) (list fout ...)\n              (lambda (in ... out ...) body ...)))\n\n(define (map/merge f merge default xs)\n  (define ys (reverse (cond ((list?   xs) (map f               xs))\n                            ((vector? xs) (map f (vector->list xs)))\n                            ((set?    xs) (set-map  xs f))\n                            ((hash?   xs) (hash-map xs (lambda (k v) (f (cons k v)))))\n                            (else         (error \"invalid map/merge collection:\" xs)))))\n  (if (null? ys)\n    default\n    (foldl merge (car ys) (cdr ys))))\n\n(define (map/append f xs) (append* (map f xs)))\n\n(define (min-bits n)\n  (if (< 0 n)\n    (+ 1 (min-bits (fxrshift n 1)))\n    0))\n\n(define (min-bytes n)\n  (let ((min-bits (min-bits n)))\n    (+ (quotient min-bits 8)\n       (if (= 0 (remainder min-bits 8)) 0 1))))\n\n(define (min-bytes-power2 n)\n  (define c (min-bytes n))\n  (cond ((<= c 1) 1)\n        ((<= c 2) 2)\n        ((<= c 4) 4)\n        (else     8)))\n\n(define (int? x) (and (number? x) (exact? x) (integer? x)))\n(define (nat? x) (and (int? x) (<= 0 x)))\n\n(define (bytes-nat-set! bs size offset n)\n  ;(integer->integer-bytes n size #f #t bs offset) (void)\n  (let ((end (+ offset size)))\n    (let loop ((i offset) (shift (* 8 (- size 1))))\n      (cond ((< i end) (bytes-set! bs i (bitwise-and 255 (fxrshift n shift)))\n                       (loop (+ i 1) (- shift 8)))\n            (else      bs)))))\n\n(define (bytes-nat-ref bs size offset)\n  ;(integer-bytes->integer bs #f #t offset (+ offset size))\n  (let ((end (+ offset size)))\n    (let loop ((i offset) (n 0))\n      (cond ((< i end) (loop (+ i 1) (+ (fxlshift n 8)\n                                        (bytes-ref bs i))))\n            (else      n)))))\n\n(define (nat->bytes size n)  (let ((bs (make-bytes size 0)))\n                               (bytes-nat-set! bs size 0 n)\n                               bs))\n\n(define (bytes->nat bs size) (bytes-nat-ref bs size 0))\n\n(define (sum xs) (foldl + 0 xs))\n\n(define (normalize-path path) (path->string (normal-case-path\n                                              (simplify-path\n                                                (resolve-path\n                                                  (simplify-path path))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/mk.rkt",
    "content": "#lang racket/base\n(provide (all-from-out \"common.rkt\") (all-from-out \"syntax.rkt\")\n         (all-from-out \"constraint.rkt\")\n         query->stream\n         run^ run run* run/steps run*/steps\n         run/set run*/set run/set/steps run*/set/steps)\n(require \"common.rkt\" \"config.rkt\" \"constraint.rkt\" \"stream.rkt\" \"syntax.rkt\"\n         (except-in racket/match ==))\n\n(define (query->stream q)\n  ((match (or (current-config-ref 'search-strategy) 'biased-interleaving)\n     ('biased-interleaving bis:query->stream)\n     ('depth-first         dfs:query->stream)\n     (strategy (error \"invalid search strategy:\" strategy)))\n   q))\n\n(define-syntax run^\n  (syntax-rules () ((_   body ...) (query->stream (query  body ...)))))\n(define-syntax run\n  (syntax-rules () ((_ n body ...) (s-take n      (run^   body ...)))))\n(define-syntax run*\n  (syntax-rules () ((_   body ...)                (run #f body ...))))\n(define-syntax run/steps\n  (syntax-rules () ((_ steps n body ...) (s-take/steps steps n (run^               body ...)))))\n(define-syntax run*/steps\n  (syntax-rules () ((_ steps   body ...)                       (run/steps steps #f body ...))))\n\n(define-syntax run/set\n  (syntax-rules () ((_ n body ...) (s-take/set n (run^       body ...)))))\n(define-syntax run*/set\n  (syntax-rules () ((_   body ...)               (run/set #f body ...))))\n(define-syntax run/set/steps\n  (syntax-rules () ((_ steps n body ...) (s-take/set/steps steps n (run^                   body ...)))))\n(define-syntax run*/set/steps\n  (syntax-rules () ((_ steps   body ...)                           (run/set/steps steps #f body ...))))\n\n;; TODO: special case aggregation operators that could be implemented more\n;; efficiently than post-processing `run*` results:\n;; * run/min, run/max, run/count\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/abstract-syntax.rkt",
    "content": "#lang racket/base\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; TODO\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; input and output devices are specified and created using host language\n;; - may describe data coming from arbitrary input sources:\n;;   - filesystem, network, channels, events, etc.\n;;   - all sources are assumed to be unstable across time, reflecting a dynamic system\n;;   - include metadata that will be retained in process history\n;; - modules embed input and output device specifications in appropriate temporal relation declarations\n;;   - input relations may only appear on the RHS of rules\n;;   - output relations may only appear on the LHS of indeterminate inference rules\n;;     - i.e., `<<~` (asynchronous send)\n\n;; modules\n;; - optional precomputation with indexing choices and retrieval preferences\n;; - definitions for relations\n;;   - rules for immediate inference: `define-relation` and/or `extend-relation`\n;;     - deliver new facts during current time step, until fixed point is reached\n;;     - synonym for `extend-relation`, deliver during current timestep: <<=\n;;   - rules for next-step inference\n;;     - delete at next timestep: <<-\n;;     - insert at next timestep: <<+\n;;   - rules for indeterminate inference\n;;     - deliver at arbitrary (future?) timetep: <<~\n;;     - these will write to output devices for the host system to process\n;; - assertions: queries used for property/consistency checking or other validation\n;;   - can inform data representation choices and query optimization\n;;   - can use to infer:\n;;     - uniqueness/degrees/cardinalities\n;;     - value information (types, value ranges, frequencies)\n;;     - join dependencies\n;; - module linking\n;;   - by default, a module will export all definitions\n;;   - apply visibility modifiers (such as except, only, rename, prefix) to change a module's exports\n;;     - renamings apply to a process too, so that its database relations can be targeted by new rules\n;;     - support dependency shaking\n;;       - given a root set of terms/relations, throw away everything else\n;;   - combine compatible modules to produce a new module\n;;     - same module may be linked more than once, to produce different variations (mixin-style)\n;;       - for instance, this may be used to switch io devices\n\n;; process state (like a version control system commit):\n;; - reference to the dbms that manages this process state's database\n;; - database\n;;   - schemas\n;;   - current content of all persistent temporal relations\n;;     - i.e., (indexed) tables keyed by name\n;;   - pending work (incomplete indexes)\n;; - io device temporal relation bindings and buffers\n;; - current program, describing how the process evolves each time step\n;;   - mapping of public names to internal names\n;;   - mapping of internal names to devices\n;;   - mapping of internal names to tables\n;;   - hierarchically-named subprograms w/ enabled/disabled status\n;;   - in order to run, program must not have unresolved dependencies\n;;     - terms without definitions are unresolved\n;; - residual environment (when used as a library)\n;;   - module specs inheriting from this process will be parsed using this environment\n;; - history of database transitions\n;;   - program changes\n;;   - ingestion metadata per time step\n;; - how do we check source data consistency?\n;;   - processes allow data to change, so inconsistency with original sources may be intentional\n;;   - to check consistency as in the old approach, analyze the process history for data provenance\n;;     - particularly data io device bindings and their dependencies across time steps\n;;       - input device metadata should include real world time stamps, filesystem information, transformation code, possibly content hash\n;; - main operations:\n;;   - run a query over the current database\n;;   - change current program\n;;     - enable/disable subprograms\n;;     - rename/hide public names\n;;     - hierarchy rearrangement and linking\n;;     - nontemporal relations declared to be precomputed will be precomputed before returning\n;;     - will add a program diff to the history\n;;   - step, with a step/fuel count (`#f` to run continously)\n;;     - will return unused fuel if (temporary) quiessence is detected, otherwise `#f`\n;;     - if any work was performed, this will log a new database uid in the process history\n;;     - if input was produced by devices configured for snapshot, snapshots will be included in the history\n;;       - for replay reproducibility\n;;   - synchronizable event indicating more work can be performed\n;;     - e.g., if not even temporary quiessence has been achieved yet\n;;     - e.g., if temporary quiessence had been achieved, but new input has arrived\n;;     - `#f` if permanent quiessence has been reached\n;;       - only possible if no input devices are bound\n;;       - permanence w.r.t. the current program\n;;   - save/flush (to dbms filesystem, for later reloading)\n;;     - transitions should be continuously checkpointed and saved, so this may not be necessary\n;;       - if background saving ends up being asynchronous, this operation will wait until the flush catches up\n;;     - io devices cannot be directly restored from disk\n;;       - their metadata can still be saved, however\n;;       - when restoring such a process, io device rebindings must be provided\n\n;; process (like a version control system branch):\n;; - process state\n;; - db name for stable reference in later program runs\n;; - performing operations will update the current process\n;;   - produce new process state and reassign stable name to the new state\n;; - may spawn new process sharing the current process state\n;;   - can explore diverging transitions\n;;   - can save earlier state to later revisit\n;;   - explicit garbage collection and compaction can be used to retain only data that is directly-referenced by active processes\n;;     - can optionally preserve external data ingestion snapshots to support reproducing intermediate databases\n;; - may be packaged for export to another dbms\n;;   - dbms garbage collection and process export are similar activities\n\n;; dbms (database management system):\n;; - collection of named process databases\n;; - cached relation content keyed by history dependencies, to support sharing between similar processes\n;;   - includes content of temporal relations as well as nontemporal relations declared to be cached/precomputed\n;;   - cache may include term values that were expensive to compute\n;;   - processes evolving from a common ancestor will share content unless rule extensions lead to logical divergence\n;;     - extending a precomputed relation will require precomputing a new version to be consistent\n;;       - not an error, but maybe provide a warning\n;;       - progammer decides whether multiple precomputed versions of similar rules is worth the time/space trade off\n;;         - programmer organizes modules according to this decision\n\n;; modular stratification given a partial order on relation parameters\n;; - would be convenient to define a universal <= that respected point-wise monotonicity (any<= does not)\n;; - reachability example using equivalence classes reduces materialized space usage from O(n^2) to O(n):\n;;     (define-relation/source (node n)\n;;       ;; specify graph vertex data here\n;;       )\n;;     (define-relation/source (arc a b)\n;;       ;; specify graph connection data here\n;;       )\n;;\n;;     ;; original definition of reachable before optimization\n;;     ;; materialization could take O(n^2) space\n;;     (define-relation (reachable a b)\n;;       (conde\n;;         ((node a) (== a b))\n;;         ((fresh (mid)\n;;            (reachable a mid)\n;;            (conde ((arc mid b))\n;;                   ((arc b mid)))))))\n;;\n;;     ;; new definition of reachable after optimization\n;;     (define-relation (reachable a b)\n;;       (fresh (repr)\n;;         (reachable-class repr a)\n;;         (reachable-class repr b)))\n;;\n;;     ;; materialization will take O(n) space\n;;     (define-relation (reachable-class representative x)\n;;       (string<= representative x)  ;; not required, but does this improve performance?\n;;       ;; This negated condition ensures we represent each reachability class only once, to save space.\n;;       ;; self-recursion within negation is possible due to modular stratification by string<\n;;       ;; i.e., (reachable-class r x) only depends on knowing (reachable-class p _) for all (string< p r), giving us a safe evaluation order\n;;       (not (fresh (predecessor)\n;;              (string< predecessor representative)\n;;              (reachable-class predecessor representative)))\n;;       (conde\n;;         ((node representative) (== representative x))\n;;         ((fresh (mid)\n;;            (reachable-class representative mid)\n;;            (conde ((arc mid x))\n;;                   ((arc x mid)))))))\n\n;; ACILG hierarchy for analysis and optimization\n;; - associative, commutative, idempotent, has-least-element, has-greatest-element\n;; - comprehensions: map followed by combining mapped results\n;; - an operator having all the properties in a prefix of this list may support more optimization\n;; - associative: parallelism, but may need coordination for ordering\n;; - commutative: parallelism, no ordering coordination needed\n;; - idempotent:  fixed point computation without needing stratification; may need an initial value\n;; - has-least-element: natural choice of initial value already known\n;; - has-greatest-element: some computation may be stopped early, before all data is seen, if threshold is reached\n\n;; order-by for converting sets/dicts to sequences\n\n;; compact formulas as state component?\n;; - state is a strategy-agnostic compact formula, plus a strategy-specific component (including a work scheduler)\n;; - multi-pass strategy compilation: describe this state representation in the AST for the next pass's language\n\n;; In some untyped systems, term evaluation may produce side-conditions (formulas)\n;; - e.g., (car x) may introduce the formula (pair? x)\n\n;; complex terms should be replaced with fresh variables to avoid redundant computations\n\n;; more specific variable domain constraints:\n;; - constant\n;; - non-constant data construction (cons, vector, ...)\n;;   - shape may not be fully known (vector with unspecified length)\n;; - finite domain\n;;   - could be represented as a join of constants; probably better to use a small table\n;;   - could also include a representation for semi-joined table constraints\n;; - interval domain\n;;   - possibly with gaps/subtractions (negative finite domains)\n;; - join of domain constraints\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/example/base.rkt",
    "content": "#lang racket/base\n(provide m.base)\n\n(define-dbk m.base\n  (<<= (==    u u))\n  (<<= (=/=   u v) (not (== u u)))\n  (<<= (any<= u v) (== #t (any<= u v)))\n  (<<= (any<  u v) (=/= u v) (any<= u v))\n  (<<= (any>= u v) (any<= v u))\n  (<<= (any>  u v) (any<  v u))\n\n  (relation (member x ys)\n    modes ((ys)))  ;; this mode could be inferred\n  (<<= (member x (cons x ys)))\n  (<<= (member x (cons y ys))\n    (=/= x y) (member x ys))\n  ;; member can also be defined with a single rule:\n  ;(<<= (member x ys)\n  ;  (exist (a d)\n  ;    (== ys `(,a . ,d))\n  ;    (or (== x a)\n  ;        (and (=/= x a) (member x d)))))\n\n  (relation (append xs ys xsys)\n    modes ((xs) (xsys)))  ;; these modes could be inferred\n  (<<= (append '() ys ys))\n  (<<= (append `(,x . ,xs) ys `(,x . ,xsys))\n    (append xs ys xsys))\n\n  ;; Can this theorem be proven?\n  ;(assert (all (xs ys)\n  ;          (iff (append xs ys ys)\n  ;               (== xs '()))))\n  )\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/example/counters.rkt",
    "content": "#lang racket/base\n(provide dbk.counters)\n(require \"base.rkt\"\n\n(define-dbk dbk.counters\n  (module 'foo\n    (<<+ (foo (+ n 1)) (foo n)))\n  (module 'bar\n    (<<+ (bar (+ n 1)) (bar n)))\n  (module 'initialize\n    (<<+ (foo 0))\n    (<<+ (bar 0)))\n  (module 'clean\n    (<<- (foo n) (bar n))\n    (<<- (bar n) (foo n))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/example/path.rkt",
    "content": "#lang racket/base\n(provide m.path m.edge.acyclic m.edge.cycles)\n(require \"base.rkt\")\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Define program modules\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-dbk m.path\n  (relation (edge source target)\n    indexes ((target source)))\n\n  (<<= (path s t) (edge s t))\n  (<<= (path s t) (exist (mid)\n                    (edge s mid) (path mid t))))\n\n(define-dbk m.edge.acyclic\n  (link m.base)\n  (<<+ (edge s t) (member (list s t)\n                          '((1 2)\n                            (2 4)\n                            (1 3)\n                            (3 5)\n                            (2 6)\n                            (3 6)\n                            (6 4)))))\n\n(define-dbk m.edge.cycles\n  (link m.base)\n  (<<+ (edge s t) (member (list s t)\n                          '((1 1)\n                            (5 1)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Run example\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define p (process m.path))\n\n;; edge relation is empty\n(p 'eval '(query (s t) (path s t)))\n;; ==>\n;; ()\n\n;; insert acyclic edge data\n(p 'program-set! (link m.path m.edge.acyclic))\n(p 'tick!)\n(p 'program-set! m.path)\n\n(p 'eval '(query (s t) (path s t)))\n;; ==>\n;; ? TODO\n\n;; insert extra edges that form cycles\n(p 'program-set! (link m.path m.edge.cycles))\n(p 'tick!)\n(p 'program-set! m.path)\n\n(p 'eval '(query (s t) (path s t)))\n;; ==>\n;; ? TODO\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/example/quorum.rkt",
    "content": "#lang racket/base\n(provide m.quorum-vote)\n(require \"base.rkt\")\n\n;; Based on figures 2 and 3 in: Logic and Lattices for Distributed Programming\n;; https://dsf.berkeley.edu/papers/socc12-blooml.pdf\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Define program modules\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-dbk m.quorum-vote\n  (<<+ (vote id) (vote.in id))\n\n  ;; Demonstrate intermediate term definitions\n  (define vote-count (set-count (query id (vote id))))\n  (define quorum?    (<= quorum-size count))\n  (<<~ (result.out 'success) (== #t quorum?))\n\n  ;; This is what it looks like without intermediate definitions\n  ;(<<~ (result.out 'success)\n  ;  (== #t (<= quorum-size (set-count (query id (vote id))))))\n\n  ;; And this is an alternative where <= is used as a relation instead\n  ;(<<~ (result.out 'success)\n  ;  (<= quorum-size (set-count (query id (vote id)))))\n  )\n\n(define pipe.result (dbk:pipe))\n\n(define program\n  (link m.quorum-vote\n        ;; Factored out so that m.quorum-vote is reusable\n        (dbk\n          (parameter quorum-size 3)\n          (input     (vote.in    id) _)  ; TODO: fill _ with an actual input device\n          (output    (result.out x)  (out:pipe pipe.result)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Run example\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define p (process program))\n\n;; Loop until enough votes arrive (assumes vote.in input device is populated concurrently)\n(let loop ()\n  (unless (s-member '(success) (pipe-get pipe.result))\n    (p 'tick!)\n    (loop)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/example/shortest-path.rkt",
    "content": "#lang racket/base\n(provide m.shortest-path)\n(require \"base.rkt\")\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Define program modules\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-dbk m.shortest-path\n  (link m.base)\n\n  (relation (edge source target distance)\n    indexes ((target source)))\n\n  ;; Guard against cyclic data\n  (<<= (reachable s t) (edge s t _))\n  (<<= (reachable s t) (exist (mid)\n                         (edge s mid _) (reachable mid t)))\n  (assert (not (exist (x) (reachable x x))))\n\n  ;; This relation will be infinitely large if edge describes a cyclic graph.\n  ;; To support cyclic data, we can rewrite this to stratify across time steps,\n  ;; stopping when there are no more improvements made during a single tick.\n  ;; TODO: It might be possible to avoid stratifying over time by expressing\n  ;; shortest-path directly using lattice operations for computing distance,\n  ;; allowing recursion within aggregation due to monotonicity.\n  (<<= (path s t d) (edge s t d))\n  (<<= (path s t (+ d.e d.p))\n    (exist (mid)\n      (edge s mid d.e)\n      (path mid t d.p)))\n\n  (<<= (shortest-path s t distance)\n    (=/= distance #f)\n    (== distance (merge min #f (query distance (path s t distance)))))\n\n  (<<= (edge s t distance)\n    (member (list s t distance)\n            '((a b 2)\n              (b c 5)\n              (b c 1)\n              (c d 3)\n              (c e 5)\n              (d e 1)\n              (e f 2)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Run examples\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define p (process m.shortest-path))\n\n(p 'eval '(query (s t c) (path s t c)))\n;; ==>\n;; ? TODO\n\n(p 'eval '(query (s t c) (shortest-path s t c)))\n;; ==>\n;; ? TODO\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/parse.rkt",
    "content": "#lang racket/base\n(provide\n  env.empty env:new env-ref env-ref* env-set env-set* env-remove env-remove* env-bind env-bind* env-union env-rename\n  m:named m:link m:term m:relation m:assert\n  f:const f:relate f:implies f:iff f:or f:and f:not f:exist f:all\n  f:any<= f:== f:=/=\n  t:query t:map/merge t:quote t:var t:prim t:app t:lambda t:if t:let t:letrec\n  t:apply t:cons t:car t:cdr t:vector t:list->vector t:vector-ref t:vector-length\n  t-free-vars f-free-vars t-free-vars* t-free-vars-first-order t-free-vars-first-order*\n  t-substitute f-substitute t-substitute* t-substitute-first-order t-substitute-first-order*\n  f-relations t-relations t-relations*\n  module-flatten module-ref module-add module-remove module-remove* module-wrap module-unwrap\n  program.empty program:new program:set program-module program-env program-flatten program-remove*\n  define-dbk dbk dbk-parse dbk-syntax link parameter input output\n  dbk-environment dbk-environment-update with-dbk-environment-update with-fresh-names\n  literal? literal simple-parser\n  parse:program parse:module parse:formula parse:term)\n(require \"misc.rkt\" racket/hash racket/list racket/match racket/set racket/struct)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Environments with vocabularies\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define env.empty (hash))\n\n(define (env-ref     env vocab n)     (hash-ref (hash-ref env n (hash)) vocab #f))\n(define (env-ref*    env vocab ns)    (map (lambda (n) (env-ref env vocab n)) ns))\n(define (env-set     env vocab n  v)  (let* ((vocab=>v (hash-ref env n (hash)))\n                                             (vocab=>v (if v\n                                                         (hash-set    vocab=>v vocab v)\n                                                         (hash-remove vocab=>v vocab))))\n                                        (if (hash-empty? vocab=>v)\n                                          (hash-remove env n)\n                                          (hash-set env n vocab=>v))))\n(define (env-set*    env vocab ns vs) (foldl (lambda (n v env) (env-set env vocab n v)) env ns vs))\n\n(define (env-remove  env       n)     (hash-remove env n))\n(define (env-remove* env       ns)    (foldl (lambda (n e) (env-remove env n)) env ns))\n\n(define (env-bind    env vocab n  v)  (env-set  (env-remove  env n)  vocab n  v))\n(define (env-bind*   env vocab ns vs) (env-set* (env-remove* env ns) vocab ns vs))\n\n(define (env-union   env . envs)      (foldl (lambda (e e.0)\n                                               (hash-union e.0 e #:combine\n                                                           (lambda (vocab=>v.0 vocab=>v)\n                                                             (hash-union vocab=>v.0 vocab=>v #:combine\n                                                                         (lambda (v.0 v) (if v v v.0))))))\n                                             env envs))\n\n(define (env-rename env n=>n)\n  (define (v-rename vocab v)    (cons vocab               (if (procedure? v)\n                                                            v\n                                                            (hash-ref n=>n v v))))\n  (define (n-rename n vocab=>v) (cons (hash-ref n=>n n n) (make-immutable-hash\n                                                            (hash-map vocab=>v v-rename))))\n  (make-immutable-hash (hash-map env n-rename)))\n\n(define (env:new vocab . args)\n  (define nvs (plist->alist args))\n  (env-set* env.empty vocab\n            (map car nvs)\n            (map cdr nvs)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Abstract syntax\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-variant formula?\n  (f:const   value)  ; can be thought of as a relation taking no arguments\n  (f:relate  relation args)\n  (f:implies if then)\n  (f:iff     f1 f2)\n  (f:or      f1 f2)\n  (f:and     f1 f2)\n  (f:not     f)\n  (f:exist   params body)\n  (f:all     params body))\n\n(define (f:any<= u v) (f:relate '(prim any<=) (list u v)))\n(define (f:any<  u v) (f:relate '(prim any<)  (list u v)))\n(define (f:==    u v) (f:relate '(prim ==)    (list u v)))\n(define (f:=/=   u v) (f:relate '(prim =/=)   (list u v)))\n\n;; lambda calculus extended with constants (quote), logical queries, map/merge comprehensions\n(define-variant term?\n  (t:query     name formula)\n  (t:map/merge proc.map proc.merge default xs)\n  (t:quote     value)\n  (t:var       name)\n  (t:prim      name)\n  (t:app       proc args)\n  (t:lambda    params body)\n  (t:if        c t f)\n  (t:let       bpairs body)\n  (t:letrec    bpairs body))\n\n(define (t:apply f . args)  (t:app (t:prim 'apply)         args))\n(define (t:cons a d)        (t:app (t:prim 'cons)          (list a d)))\n(define (t:car p)           (t:app (t:prim 'car)           (list p)))\n(define (t:cdr p)           (t:app (t:prim 'cdr)           (list p)))\n(define (t:vector . args)   (t:app (t:prim 'vector)        args))\n(define (t:list->vector xs) (t:app (t:prim 'list->vector)  (list xs)))\n(define (t:vector-ref v i)  (t:app (t:prim 'vector-ref)    (list v i)))\n(define (t:vector-length v) (t:app (t:prim 'vector-length) (list v)))\n\n;; TODO: use CPS yielding to efficiently support partial-answer variations\n(define (t-free-vars t (first-order? #f))\n  (let loop ((t t))\n    (match t\n      ((t:query  name f)      (set-subtract (f-free-vars f first-order?) (set name)))\n      ((t:quote  _)           (set))\n      ((t:var    name)        (set name))\n      ((t:prim   _)           (set))\n      ((t:app    func args)   (set-union (t-free-vars* args first-order?)\n                                         (if first-order? (set) (loop func))))\n      ((t:lambda params body) (set-subtract (loop body) (list->set params)))\n      ((t:if     c t f)       (set-union (loop c) (loop t) (loop f)))\n      ((t:let    bpairs body) (set-union (t-free-vars* (map cdr bpairs) first-order?)\n                                         (set-subtract (loop body) (list->set (map car bpairs)))))\n      ((t:letrec bpairs body) (set-subtract (set-union (t-free-vars* (map cdr bpairs) first-order?)\n                                                       (loop body))\n                                            (list->set (map car bpairs)))))))\n\n(define (t-free-vars-first-order t) (t-free-vars t #t))\n\n(define (f-free-vars f (first-order? #f))\n  (let loop ((f f))\n    (match f\n      ((f:const   _)             (set))\n      ((f:or      f1 f2)         (set-union (loop f1) (loop f2)))\n      ((f:and     f1 f2)         (set-union (loop f1) (loop f2)))\n      ((f:implies if then)       (set-union (loop if) (loop then)))\n      ((f:relate  relation args) (t-free-vars* args first-order?))\n      ((f:exist   params body)   (set-subtract (loop body) (list->set params)))\n      ((f:all     params body)   (set-subtract (loop body) (list->set params))))))\n\n(define (t-free-vars* ts (first-order? #f))\n  (foldl (lambda (t vs) (set-union vs (t-free-vars t first-order?)))\n         (set) ts))\n(define (t-free-vars-first-order* ts) (t-free-vars* ts #t))\n\n(define (f-relations f)\n  (match f\n    ((f:const   _)             (set))\n    ((f:or      f1 f2)         (set-union (f-relations f1) (f-relations f2)))\n    ((f:and     f1 f2)         (set-union (f-relations f1) (f-relations f2)))\n    ((f:implies if then)       (set-union (f-relations if) (f-relations then)))\n    ((f:relate  relation args) (set-add (t-relations* args) relation))\n    ((f:exist   params body)   (f-relations body))\n    ((f:all     params body)   (f-relations body))))\n\n(define (t-relations t)\n  (match t\n    ((t:query  _ f)         (f-relations f))\n    ((t:quote  _)           (set))\n    ((t:var    _)           (set))\n    ((t:prim   _)           (set))\n    ((t:app    func args)   (set-union (t-relations func) (t-relations* args)))\n    ((t:lambda params body) (t-relations body))\n    ((t:if     c t f)       (set-union (t-relations c) (t-relations t) (t-relations f)))\n    ((t:let    bpairs body) (set-union (t-relations* (map cdr bpairs)) (t-relations body)))\n    ((t:letrec bpairs body) (set-union (t-relations* (map cdr bpairs)) (t-relations body)))))\n\n(define (t-relations* ts)\n  (foldl (lambda (t rs) (set-union rs (t-relations t)))\n         (set) ts))\n\n(define (t-substitute t name=>name (first-order? #f))\n  (let loop ((t t))\n    (match t\n      ((t:query  name f)      (t:query name (f-substitute f (hash-remove name=>name name) first-order?)))\n      ((t:quote  _)           t)\n      ((t:var    name)        (t:var (hash-ref name=>name name name)))\n      ((t:prim   _)           t)\n      ((t:app    func args)   (t:app func (t-substitute* args name=>name first-order?)))\n      ((t:lambda params body) (t:lambda params (t-substitute body\n                                                             (hash-remove* name=>name params)\n                                                             first-order?)))\n      ((t:if     c t f)       (t:if (loop c) (loop t) (loop f)))\n      ((t:let    bpairs body) (define params (map car bpairs))\n                              (t:let (map cons params (t-substitute* (map cdr bpairs)\n                                                                     name=>name\n                                                                     first-order?))\n                                     (t-substitute body\n                                                   (hash-remove* name=>name params)\n                                                   first-order?)))\n      ((t:letrec bpairs body) (define params (map car bpairs))\n                              (define n=>n   (hash-remove* name=>name params))\n                              (t:let (map cons params (t-substitute* (map cdr bpairs)\n                                                                     n=>n\n                                                                     first-order?))\n                                     (t-substitute body\n                                                   n=>n\n                                                   first-order?))))))\n\n(define (t-substitute* ts name=>name (first-order? #f))\n  (map (lambda (t) (t-substitute t name=>name first-order?)) ts))\n\n(define (f-substitute f name=>name (first-order? #f))\n  (let loop ((f f))\n    (match f\n      ((f:const   _)             f)\n      ((f:or      f1 f2)         (f:or      (loop f1)\n                                            (loop f2)))\n      ((f:and     f1 f2)         (f:and     (loop f1)\n                                            (loop f2)))\n      ((f:implies if then)       (f:implies (loop if)\n                                            (loop then)))\n      ((f:relate  relation args) (f:relate relation (t-substitute* args name=>name first-order?)))\n      ((f:exist   params body)   (f:exist params (f-substitute body\n                                                               (hash-remove* name=>name params)\n                                                               first-order?)))\n      ((f:all     params body)   (f:all   params (f-substitute body\n                                                               (hash-remove* name=>name params)\n                                                               first-order?))))))\n\n(define (t-substitute-first-order  t  name=>name) (t-substitute  t  name=>name #t))\n(define (t-substitute-first-order* ts name=>name) (t-substitute* ts name=>name #t))\n\n;; A schema is a finite map of names to finite maps of properties to sets of\n;; values, i.e.: (=> name (=> property (set value)))\n(define schema.empty (hash))\n(define (schema:new private=>property=>value)\n  (make-immutable-hash\n    (hash-map private=>property=>value\n              (lambda (private p=>v)\n                (cons private\n                      (make-immutable-hash\n                        (hash-map p=>v (lambda (p v) (cons p (set v))))))))))\n\n(define (schema-union p=>p=>v.0 p=>p=>v.1)\n  (hash-union p=>p=>v.0 p=>p=>v.1\n              #:combine (lambda (p=>v.0 p=>v.1)\n                          (hash-union p=>v.0 p=>v.1 #:combine set-union))))\n\n(record module (terms relations assertions name=>submodule) #:prefab)\n(define module.empty (module\n                       (terms           schema.empty)\n                       (relations       schema.empty)\n                       (assertions      (set))\n                       (name=>submodule (hash))))\n\n(define (m:link     ms)        (foldl (lambda (m m.0)\n                                        (match-define (module:struct ts.0 rs.0 as.0 n=>s.0) m.0)\n                                        (match-define (module:struct ts   rs   as   n=>s)   m)\n                                        (module\n                                          (terms           (schema-union ts.0 ts))\n                                          (relations       (schema-union rs.0 rs))\n                                          (assertions      (set-union    as.0 as))\n                                          (name=>submodule (hash-union n=>s.0 n=>s #:combine\n                                                                       (lambda (s.0 s)\n                                                                         (m:link (list s.0 s)))))))\n                                      module.empty\n                                      ms))\n(define (m:named    name m)    (module:set module.empty (name=>submodule (hash       name m))))\n(define (m:term     name p=>v) (module:set module.empty (terms           (schema:new (hash name p=>v)))))\n(define (m:relation name p=>v) (module:set module.empty (relations       (schema:new (hash name p=>v)))))\n(define (m:assert   formula)   (module:set module.empty (assertions      (set        formula))))\n\n(define (module-flatten m)          (m:link (cons (module:set m (module-name=>submodule (hash)))\n                                                  (map module-flatten (hash-values (module-name=>submodule m))))))\n\n(define (module-ref     m path)     (foldl (lambda (name m)\n                                             (hash-ref (module-name=>submodule m) name module.empty))\n                                           m path))\n\n(define (module-add     m path sub) (if (null? path)\n                                      (m:link (list m sub))\n                                      (module:set m (name=>submodule\n                                                      (hash-update (module-name=>submodule m) (car path)\n                                                                   (lambda (m) (module-add m (cdr path) sub))\n                                                                   module.empty)))))\n\n(define (module-remove  m path)     (if (null? path)\n                                      module.empty\n                                      (let loop ((m m) (path path))\n                                        (module:set m (name=>submodule\n                                                        (if (null? (cdr path))\n                                                          (hash-remove (module-name=>submodule m) (car path))\n                                                          (hash-update (module-name=>submodule m) (car path)\n                                                                       (lambda (m) (loop m (cdr path)))\n                                                                       module.empty)))))))\n\n(define (module-remove* m paths)    (foldl (lambda (path m) (module-remove m path)) m paths))\n\n(define (module-wrap    m path)     (foldl (lambda (name m)\n                                             (module:set module.empty (name=>submodules (hash name m))))\n                                           m path))\n\n(define (module-unwrap  m path)     (foldl (lambda (name m)\n                                             (hash-ref (module-name=>submodule m) name module.empty))\n                                           m path))\n\n(record program (module env) #:prefab)\n(define (program:new m env) (program (module m) (env env)))\n(define program.empty (program:new module.empty env.empty))\n\n(define (program-remove* p paths) (program:set p (module (module-remove* (program-module p) paths))))\n(define (program-flatten p)       (program:set p (module (module-flatten (program-module p)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Names and parameter trees\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define fresh-name-count (make-parameter #f))\n\n(define (call-with-fresh-names thunk)\n  (if (fresh-name-count)\n    (thunk)\n    (parameterize ((fresh-name-count 0))\n      (thunk))))\n\n(define-syntax-rule (with-fresh-names body ...)\n  (call-with-fresh-names (lambda () body ...)))\n\n(define (fresh-name name)\n  (define uid.next (fresh-name-count))\n  (unless uid.next (error \"fresh name not available:\" name))\n  (fresh-name-count (+ uid.next 1))\n  (cons uid.next (if (pair? name) (cdr name) name)))\n\n(define (param-names param)\n  (match param\n    ((? symbol?)    (list param))\n    ('()            '())\n    ((cons p.a p.d) (append (param-names p.a) (param-names p.d)))\n    ((? vector?)    (param-names (vector->list param)))))\n\n(define (unique? names) (= (set-count (list->set names)) (length names)))\n\n(define (name? x) (not (or (not x) (procedure? x))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (literal? x) (or (number? x) (boolean? x) (string? x) (bytes? x)))\n(define (literal  x) (if (and (number? x) (inexact? x)) (inexact->exact x) x))\n\n(define (binding-pairs?! bps)\n  (unless (and (list? bps)\n               (andmap (lambda (bp) (and (list? bp)\n                                         (= 2 (length bp))))\n                       bps))\n    (error \"invalid binding pairs:\" bps)))\n\n(define ((simple-parser proc) stx)\n  (cond ((list? stx) (apply proc (cdr stx)))\n        (else        (error \"simple-parser expects list syntax:\" stx))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Module parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define current-env (make-parameter #f))\n\n(define (current-env-bind  vocab n  v)  (current-env (env-bind  (current-env) vocab n  v)))\n(define (current-env-bind* vocab ns vs) (current-env (env-bind* (current-env) vocab ns vs)))\n\n(define ((parse:program stx) env)\n  (unless (list? stx) (error \"invalid program syntax:\" stx))\n  (with-fresh-names\n    (parameterize ((current-env env))\n      (define resume (apply parse:module:begin stx))\n      (define env    (current-env))\n      (program:new (resume env) env))))\n\n(define (parse:module:begin . stxs)\n  (define deferred (map parse:module stxs))\n  (lambda (env) (m:link (map (lambda (d) (d env)) deferred))))\n\n(define (parse:module stx)\n  (with-fresh-names\n    (match stx\n      ((? symbol? name)\n       (define mc.b (env-ref (current-env) 'module name))\n       (cond ((procedure? mc.b) (mc.b stx))\n             (else              (error \"unknown module clause keyword:\" name mc.b))))\n      ((list operator operands ...)\n       (define mc.b (env-ref (current-env) 'module operator))\n       (cond ((procedure? mc.b) (mc.b stx))\n             (else              (error \"unknown module clause operator:\" operator mc.b))))\n      ((? procedure? self-parse) (self-parse)))))\n\n(define parse:module:module\n  (simple-match-lambda\n    ((name . body) (define resume (apply parse:module:begin body))\n                   (lambda (env) (m:named name (resume env))))))\n\n(define (quote-property property)\n  (lambda (value)\n    (lambda (env) (hash property value))))\n\n(define (parse:declare-relation:projections property msg.name)\n  (simple-match-lambda\n    (((attrs . projections))\n     (unless (unique? attrs)\n       (error (string-append msg.name \" attribute names must be unique:\") attrs))\n     (lambda (env.0)\n       (define unames (map fresh-name attrs))\n       (define env    (env-bind* env.0 'term attrs unames))\n       (hash property (cons unames (map (lambda (proj) ((parse:term* proj) env))\n                                        projections)))))))\n\n(define parse:declare-relation:indexes (parse:declare-relation:projections 'indexes \"indexes:\"))\n(define parse:declare-relation:modes   (parse:declare-relation:projections 'modes   \"modes:\"))\n\n(define (parse:module:projections property)\n  (simple-parser\n    (simple-match-lambda\n      (((relation . attrs) . projections)\n       (parse:module:relation (cons relation attrs) property (cons attrs projections))))))\n\n(define parse:declare-term:definition\n  (lambda (body)\n    (lambda (env) (hash 'definition ((parse:term body) env)))))\n\n(define (parse:declare-relation:rule type)\n  (simple-match-lambda\n    (((params . formulas))\n     (lambda (env)\n       ;; NOTE: extracting variables in first-order positions as pattern\n       ;; variables may be brittle.  It may be better to introduce a pattern\n       ;; matching vocabulary to explicitly identify pattern variables.\n       (define ts.params    (map (lambda (p) ((parse:term p) env)) params))\n       (define names.params (set->list (t-free-vars-first-order* ts.params)))\n       (define names.argument\n         (map (lambda (i) (fresh-name (string->symbol (string-append \"x.\" (number->string i)))))\n              (range (length params))))\n       (define formula\n         ((apply parse:formula:exist names.params\n                 (lambda (env)\n                   (foldl f:and\n                          (f:== (quote-literal #t) (quote-literal #t))\n                          (map (lambda (n t) (f:== (t:var n) t))\n                               names.argument\n                               (t-substitute-first-order*\n                                 ts.params\n                                 (make-immutable-hash\n                                   (map cons names.params (env-ref* env 'term names.params)))))))\n                 formulas)\n          env))\n       (hash 'rules (list (vector type names.argument formula)))))))\n\n(define (parse:module:rule type)\n  (simple-parser\n    (simple-match-lambda\n      (((relation . params) . formulas) (parse:module:relation\n                                          relation\n                                          (parse:declare-relation:rule type)\n                                          (cons params formulas))))))\n\n(define parse:module:link\n  (simple-match-lambda\n    (ms (lambda (_) (m:link ms)))))\n\n(define parse:module:parameter\n  (simple-match-lambda\n    (kvs (define kwargs (plist->alist kvs))\n         (apply parse:module:begin\n                (map (lambda (name value)\n                       (lambda () (parse:module:define name (lambda (_) (quote-literal value)))))\n                     (map car kwargs) (map cdr kwargs))))))\n\n(define (parse:module:io type)\n  (simple-match-lambda\n    (kvs (define kwargs (plist->alist kvs))\n         (apply parse:module:begin\n                (map (lambda (rsig io-device)\n                       (lambda () (parse:module:relation rsig type io-device)))\n                     (map car kwargs) (map cdr kwargs))))))\n\n(define parse:module:input  (parse:module:io (quote-property 'input)))\n(define parse:module:output (parse:module:io (quote-property 'output)))\n\n(define parse:module:define\n  (simple-match-lambda\n    (((name . params) body) (parse:module:define name (parse:term:lambda params body)))\n    ((name            body) (parse:module:term   name parse:declare-term:definition body))))\n\n(define (parse:module:declaration vocab.declare vocab.entity msg.entity m:entity)\n  (simple-match-lambda\n    ((name . kvs) (define kwargs (plist->alist kvs))\n                  (define uname  (fresh-name name))\n                  (current-env-bind vocab.entity name uname)\n                  (lambda (env)\n                    (define uname (env-ref env vocab.entity name))\n                    (unless (name? uname)\n                      (error (string-append \"invalid \" msg.entity \" renaming:\" name uname)))\n                    (m:link (map (lambda (property value)\n                                   (define p.b (if (procedure? property)\n                                                 property\n                                                 (env-ref env vocab.declare property)))\n                                   (define pmap (cond ((procedure? p.b) ((p.b value) env))\n                                                      (else             (hash (if p.b p.b property) value))))\n                                   (m:entity uname pmap))\n                                 (map car kwargs) (map cdr kwargs)))))))\n\n(define parse:module:relation\n  (simple-match-lambda\n    (((relation . attrs) . kvs) (apply parse:module:relation relation (quote-property 'attributes) attrs kvs))\n    (args                       (apply (parse:module:declaration 'declare-relation 'formula \"relation\" m:relation) args))))\n\n(define parse:module:term              (parse:module:declaration 'declare-term     'term    \"term\"     m:term))\n\n(define (parse:module:declare* parse-spec)\n  (simple-match-lambda\n    (specs (apply parse:module:begin\n                  (map (lambda (spec)\n                         (lambda () (if (list? spec)\n                                      (apply parse-spec spec)\n                                      (parse-spec       spec))))\n                       specs)))))\n\n(define parse:module:relations (parse:module:declare* parse:module:relation))\n(define parse:module:terms     (parse:module:declare* parse:module:term))\n\n(define parse:module:assert\n  (simple-match-lambda\n    ((formula) (lambda (env) (m:assert ((parse:formula formula) env))))))\n\n(define env.initial.module.declare-relation\n  (env:new\n    'declare-relation\n    '<<=     (parse:declare-relation:rule '<<=)\n    '<<+     (parse:declare-relation:rule '<<+)\n    '<<-     (parse:declare-relation:rule '<<-)\n    '<<~     (parse:declare-relation:rule '<<~)\n    'indexes parse:declare-relation:indexes\n    'modes   parse:declare-relation:modes))\n\n(define env.initial.module.declare-term\n  (env:new\n    'declare-term\n    'definition parse:declare-term:definition))\n\n(define env.initial.module.clause\n  (env:new\n    'module\n    'module          (simple-parser parse:module:module)\n    'begin           (simple-parser parse:module:begin)\n    'link            (simple-parser parse:module:link)\n    'relation        (simple-parser parse:module:relation)\n    'relations       (simple-parser parse:module:relations)\n    'term            (simple-parser parse:module:term)\n    'terms           (simple-parser parse:module:terms)\n    'indexes         (parse:module:projections parse:declare-relation:indexes)\n    'modes           (parse:module:projections parse:declare-relation:modes)\n    'parameter       (simple-parser parse:module:parameter)\n    'input           (simple-parser parse:module:input)\n    'output          (simple-parser parse:module:output)\n    'define          (simple-parser parse:module:define)\n    'assert          (simple-parser parse:module:assert)\n    '<<=             (parse:module:rule '<<=)\n    '<<+             (parse:module:rule '<<+)\n    '<<-             (parse:module:rule '<<-)\n    '<<~             (parse:module:rule '<<~)\n    ;; miniKanren style module clauses\n    'define-relation (parse:module:rule '<<=)))\n\n(define env.initial.module (env-union env.initial.module.declare-relation\n                                      env.initial.module.declare-term\n                                      env.initial.module.clause))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Formula parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define ((parse:formula stx) env)\n  (with-fresh-names\n    (match stx\n      ((? literal? data) (f:const (literal data)))\n      ((? symbol? name)\n       (define f.b (env-ref env 'formula name))\n       (cond ((procedure? f.b) ((f.b stx) env))\n             (else             (f:const (if f.b f.b name)))))\n      ((list operator operands ...)\n       (define f.b (env-ref env 'formula operator))\n       ((cond ((procedure? f.b) (f.b stx))\n              (else             (parse:formula:relate (if f.b f.b operator) operands)))\n        env))\n      ((? procedure? self-parse) (self-parse env)))))\n\n(define ((parse:formula* formulas) env)\n  (map (lambda (f) ((parse:formula f) env)) formulas))\n\n(define anonymous-vars (make-parameter #f))\n\n(define-syntax formula/anonymous-vars\n  (syntax-rules ()\n    ((_ body ...) (parameterize ((anonymous-vars '()))\n                    (define f (let () body ...))\n                    (if (null? (anonymous-vars))\n                      f\n                      (f:exist (anonymous-vars) f))))))\n\n(define ((parse:formula:relate relation operands) env)\n  (formula/anonymous-vars (f:relate relation ((parse:term* operands) env))))\n\n(define parse:formula:or\n  (simple-match-lambda\n    ((disjunct)             (parse:formula disjunct))\n    ((disjunct . disjuncts) (lambda (env) (f:or ((parse:formula disjunct)           env)\n                                                ((apply parse:formula:or disjuncts) env))))))\n\n(define parse:formula:and\n  (simple-match-lambda\n    ((conjunct)             (parse:formula conjunct))\n    ((conjunct . conjuncts) (lambda (env) (f:and ((parse:formula conjunct)            env)\n                                                 ((apply parse:formula:and conjuncts) env))))))\n\n(define parse:formula:not\n  (simple-match-lambda ((f) (lambda (env) (f:not ((parse:formula f) env))))))\n\n(define (parse:formula:quantifier f:quantifier msg.name)\n  (simple-match-lambda\n    ((names . body) (unless (unique? names)\n                      (error (string-append msg.name \" parameter names must be unique:\") names))\n                    (lambda (env)\n                      (define unames (map fresh-name names))\n                      (f:quantifier unames ((apply parse:formula:and body)\n                                            (env-bind* env 'term names unames)))))))\n\n(define parse:formula:exist (parse:formula:quantifier f:exist \"existential quantifier\"))\n(define parse:formula:all   (parse:formula:quantifier f:all   \"universal quantifier\"))\n\n(define parse:formula:implies\n  (simple-match-lambda\n    ((hypothesis conclusion) (lambda (env) (f:implies ((parse:formula hypothesis) env)\n                                                      ((parse:formula conclusion) env))))))\n\n(define parse:formula:iff\n  (simple-match-lambda\n    ((f.a f.b) (lambda (env) (f:iff ((parse:formula f.a) env)\n                                    ((parse:formula f.b) env))))))\n\n;; miniKanren style formulas\n(define parse:formula:fresh (parse:formula:quantifier f:exist \"fresh\"))\n\n(define parse:formula:conde\n  (simple-match-lambda\n    (clauses (apply parse:formula:or (map (lambda (conjuncts) (apply parse:formula:and conjuncts))\n                                          clauses)))))\n\n(define env.initial.formula\n  (env:new\n    'formula\n    'or      (simple-parser parse:formula:or)\n    'and     (simple-parser parse:formula:and)\n    'not     (simple-parser parse:formula:not)\n    'implies (simple-parser parse:formula:implies)\n    'iff     (simple-parser parse:formula:iff)\n    'exist   (simple-parser parse:formula:exist)\n    'all     (simple-parser parse:formula:all)\n    ;; miniKanren style formulas\n    'fresh   (simple-parser parse:formula:fresh)\n    'conde   (simple-parser parse:formula:conde)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Term parsing\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (quote-literal v) (t:quote (literal v)))\n\n(define ((parse:term stx) env)\n  (with-fresh-names\n    (match stx\n      ((? literal? data) (quote-literal data))\n      ((? symbol?  name) ((parse:term:ref name) env))\n      ((list operator operands ...)\n       (define t.b (env-ref env 'term operator))\n       ((cond ((procedure? t.b) (t.b stx))\n              (else             (parse:term:app operator operands)))\n        env))\n      ((? procedure? self-parse) (self-parse env)))))\n\n(define ((parse:term* stxs) env)\n  (map (lambda (stx) ((parse:term stx) env)) stxs))\n\n(define ((parse:term:ref name) env)\n  (define t.b (env-ref env 'term name))\n  (cond ((procedure? t.b) ((t.b name) env))\n        (else             (t:var (if t.b t.b name)))))\n\n(define parse:term:query\n  (simple-match-lambda\n    ((param-pattern . body)\n     (lambda (env)\n       (cond ((symbol? param-pattern)\n              (define param (fresh-name param-pattern))\n              (t:query param ((apply parse:formula:and body)\n                              (env-bind env 'term param-pattern param))))\n             (else (define param (fresh-name 'q.0))\n                   (define names (param-names param-pattern))\n                   (define (assign-param-pattern env)\n                     (f:== param ((parse:term:simple param-pattern) env)))\n                   (t:query param ((apply parse:formula:exist names assign-param-pattern body)\n                                   env))))))))\n\n(define ((parse:term:simple pattern) env)\n  (let loop ((pattern pattern))\n    (match pattern\n      ((? symbol?)    ((parse:term:ref pattern) env))\n      ('()            (quote-literal '()))\n      ((cons p.a p.d) (t:cons (loop p.a) (loop p.d)))\n      ((? vector?)    (t:list->vector (loop (vector->list pattern)))))))\n\n(define parse:term:quote\n  (simple-match-lambda ((value) (lambda (_) (quote-literal value)))))\n\n(define parse:term:quasiquote\n  (simple-match-lambda\n    ((template)\n     (lambda (env)\n       (define ((keyword? k) n) (eq? k (env-ref env 'quasiquote n)))\n       (define (lift tag e)     (t:cons (quote-literal tag) (t:cons e (quote-literal '()))))\n       ;; NOTE: unquote-splicing support requires a safe definition of append\n       (let loop ((t template) (level 0))\n         (match t\n           ((list (? (keyword? 'unquote)    k) e) (if (= level 0)\n                                                    ((parse:term e) env)\n                                                    (lift k (loop e (- level 1)))))\n           ((list (? (keyword? 'quasiquote) k) t) (lift k (loop t (+ level 1))))\n           ((cons t.a t.d)                        (t:cons (loop t.a level) (loop t.d level)))\n           ((? vector?)                           (t:list->vector (loop (vector->list t) level)))\n           ((or (? (keyword? 'quasiquote))\n                (? (keyword? 'unquote)))          (error \"invalid quasiquote:\" t template))\n           (v                                     (quote-literal v))))))))\n\n(define parse:term:app\n  (simple-match-lambda\n    ((proc args) (lambda (env) (t:app ((parse:term proc)  env)\n                                      ((parse:term* args) env))))))\n\n(define parse:term:lambda\n  (simple-match-lambda\n    ((params body) (define names (param-names params))\n                   (unless (unique? names)\n                     (error \"lambda parameter names must be unique:\" names))\n                   (lambda (env)\n                     (define unames (map fresh-name names))\n                     (t:lambda unames ((parse:term body)\n                                       (env-bind* env 'term names unames)))))))\n\n(define parse:term:if\n  (simple-match-lambda\n    ((c t f) (lambda (env) (t:if ((parse:term c) env)\n                                 ((parse:term t) env)\n                                 ((parse:term f) env))))))\n\n(define parse:term:let\n  (simple-match-lambda\n    ((bps body) (binding-pairs?! bps)\n                (parse:term:app (parse:term:lambda (map car bps) body)\n                                (map cadr bps)))))\n\n(define parse:term:letrec\n  (simple-match-lambda\n    ((bps body) (binding-pairs?! bps)\n                (define names (param-names (map car bps)))\n                (unless (unique? names)\n                  (error \"letrec parameter names must be unique:\" names))\n                (lambda (env)\n                  (define unames (map fresh-name names))\n                  (define rhss ((parse:term* (map cadr bps)) env))\n                  (t:letrec (map cons unames rhss)\n                            ((parse:term body)\n                             (env-bind* env 'term names unames)))))))\n\n(define parse:term:and\n  (simple-match-lambda\n    (()           (lambda (_) (quote-literal #t)))\n    ((arg)        (parse:term arg))\n    ((arg . args) (parse:term:if arg\n                                 (apply parse:term:and args)\n                                 (lambda (_) (quote-literal #f))))))\n\n(define parse:term:or\n  (simple-match-lambda\n    (()           (lambda (_) (quote-literal #f)))\n    ((arg)        (parse:term arg))\n    ((arg . args) (lambda (env)\n                    ((parse:term:let (list (list 'temp arg))\n                                     (parse:term:if (parse:term:ref 'temp)\n                                                    (parse:term:ref 'temp)\n                                                    (lambda (_) ((apply parse:term:or args)\n                                                                 env))))\n                     env)))))\n\n(define parse:term:anonymous-var\n  (simple-match-lambda\n    ((stx) (lambda (_)\n             (unless (anonymous-vars) (error \"misplaced anonymous variable:\" stx))\n             (define name (fresh-name '_))\n             (anonymous-vars (cons name (anonymous-vars)))\n             (t:var name)))))\n\n(define (parse:term:prim name)\n  (simple-match-lambda\n    (((_ . args)) (lambda (env) (t:app (t:prim name) ((parse:term* args) env))))\n    ((_)          (lambda (env) (t:prim name)))))\n\n(define env.initial.term.quasiquote\n  (env:new\n    'quasiquote\n    'quasiquote 'quasiquote\n    'unquote    'unquote))\n\n(define env.initial.term.primitive\n  (apply env-union env.empty\n         (map (lambda (name) (env:new 'term name (parse:term:prim name)))\n              ;; TODO: some of these can be derived rather than primitive\n              '(apply\n                 cons car cdr\n                 list->vector vector vector-ref vector-length\n                 bytes-ref bytes-length bytes->string string->bytes\n                 symbol->string string->symbol\n                 floor + - * / =\n                 equal? not\n                 <= < >= >\n                 any<= any< any>= any>\n                 .< .<= .> .>=  ; polymorphic point-wise monotonic comparisons\n\n                 ;; TODO: can some of these be defined relationally?\n                 set set-count set-member? set-union set-intersect set-subtract\n                 dict dict-count dict-ref dict-set dict-update dict-remove dict-union dict-intersect\n\n                 min max sum length\n                 map/merge map merge filter foldl foldr))))\n\n(define env.initial.term.special\n  (env:new\n    'term\n    '_          parse:term:anonymous-var\n    'query      (simple-parser parse:term:query)\n    'quote      (simple-parser parse:term:quote)\n    'quasiquote (simple-parser parse:term:quasiquote)\n\n    'if         (simple-parser parse:term:if)\n    'lambda     (simple-parser parse:term:lambda)\n    'let        (simple-parser parse:term:let)\n    'letrec     (simple-parser parse:term:letrec)\n\n    'and        (simple-parser parse:term:and)\n    'or         (simple-parser parse:term:or)))\n\n(define env.initial.term (env-union env.initial.term.quasiquote\n                                    env.initial.term.primitive\n                                    env.initial.term.special))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Module macro expansion\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; TODO: have dbk build process values (move dbk and define-dbk out of parse.rkt)\n;; - built process will optionally inherit from one or more parent processes\n;; - if no parent is specified, automatically use an empty process with primitive environment\n;; - will no longer need dbk-environment\n;; - \"vertical\" library/language-like linking\n;;   - parent program environment(s unioned) used to initiate parsing\n;;     - as opposed to \"horizontal\" (symmetric) linking, where environments are not involved\n;;   - result will be automatically linked with parent(s)\n\n(define dbk-environment (make-parameter (env-union env.initial.term\n                                                   env.initial.formula\n                                                   env.initial.module)))\n\n(define (dbk-environment-update env->env) (dbk-environment (env->env    (dbk-environment))))\n\n(define-syntax-rule (with-dbk-environment-update env->env body ...)\n  (parameterize ((dbk-environment (env->env    (dbk-environment))))\n    body ...))\n\n;; TODO: (define-dbk name (other attributes?) (parent ...) body ...)\n(define-syntax-rule (define-dbk name body ...) (define name (dbk body ...)))\n\n;; TODO: (dbk (other attributes? such as process name) (parent ...) clauses ...) using (dbk-parse (union-of-envs-of parent ...) clauses ...)\n;; dbk-parse produces AST and residual env\n;; semantically process result of dbk-parse to produce a process value\n(define-syntax-rule (dbk clauses ...)          (dbk-parse (dbk-syntax clauses ...)))\n\n;; TODO: take initial environment as an argument\n(define-syntax-rule (dbk-parse stx)            (with-fresh-names\n                                                 ((parse:program stx) (dbk-environment))))\n\n;; TODO: implement link as a procedure\n(define-syntax link      (syntax-rules ()))\n(define-syntax parameter (syntax-rules ()))\n(define-syntax input     (syntax-rules ()))\n(define-syntax output    (syntax-rules ()))\n\n(define-syntax plist-syntax\n  (syntax-rules ()\n    ((_ key val plist ...) `(key ,val . ,(plist-syntax plist ...)))\n    ((_)                   '())))\n\n(define-syntax dbk-syntax\n  (syntax-rules (module link parameter input output)\n    ((_ (module    name cs ...) clauses ...) (cons `(module    ,name . ,(dbk-syntax cs  ...)) (dbk-syntax clauses ...)))\n    ((_ (link      modules ...) clauses ...) (cons `(link      ,modules ...)                  (dbk-syntax clauses ...)))\n    ((_ (parameter params  ...) clauses ...) (cons `(parameter . ,(plist-syntax params  ...)) (dbk-syntax clauses ...)))\n    ((_ (input     inputs  ...) clauses ...) (cons `(input     . ,(plist-syntax inputs  ...)) (dbk-syntax clauses ...)))\n    ((_ (output    outputs ...) clauses ...) (cons `(output    . ,(plist-syntax outputs ...)) (dbk-syntax clauses ...)))\n    ((_ clause                  clauses ...) (cons 'clause                                    (dbk-syntax clauses ...)))\n    ((_)                                     '())))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/old/process.rkt",
    "content": "#lang racket/base\n(provide\n  )\n(require \"abstract-syntax.rkt\" \"misc.rkt\" \"parse.rkt\"\n         racket/list racket/match racket/set)\n\n(record pstate (dbms history data program) #:prefab)\n(define (pstate:new dbms prg) (pstate (dbms                dbms)\n                                      (history             prg)\n                                      (data                'TODO)\n                                      (program             prg)))\n\n;; TODO:\n(define (pstate-query pst params formula)\n  (set))\n\n;; TODO: include stepping as a modification?\n(define-variant pmod?\n  (pmod:merge   pstates)\n  (pmod:move    path.old path.new)\n  (pmod:wrap    path)\n  (pmod:unwrap  path)\n  (pmod:rename  vocab name.old name.new))\n\n(define (pmod:remove path)       (pmod:move   path #f))\n(define (pmod:hide   vocab name) (pmod:rename vocab name #f))\n\n(define (pstate-modify pst.0 pm)\n  ;; TODO: record new pstate using dbms\n  (define pst (pstate:set pst.0 (history (cons pm (pstate-history pst.0)))))\n  (define prg (pstate-program pst))\n  (define m   (program-module prg))\n  (define env (program-env prg))\n  ;; TODO: produce renamings for public names that are shared across pstates\n  (define (public-renamings envs)\n    (hash))\n  (define (module-rename m)\n    ;; TODO: traverse (parameterized) formulas and terms\n    #f)\n  (define (data-rename d n=>n)\n    ;; TODO:\n    #f)\n  (define (data-union . ds)\n    ;; TODO:\n    #f)\n  (match pm\n    ((pmod:merge   pstates)           (define dbms (pstate-dbms pst))\n                                      (unless (andmap (lambda (s) (eqv? dbms (pstate-dbms s))) pstates)\n                                        (error \"cannot merge processes managed by a different dbms:\"\n                                               dbms (map pstate-dbms pstates)))\n                                      (with-fresh-names\n                                        (define n=>n.0 (public-renamings (map (lambda (ps) (program-env (pstate-program ps)))\n                                                                              (cons pst pstates))))\n                                        (apply (lambda (ms es ds)\n                                                 (pstate:set pst\n                                                             (program (program:set program.empty\n                                                                                   (module (m:link ms))\n                                                                                   (env    (apply env-union es))))\n                                                             (data (apply data-union ds))))\n                                               (apply map list\n                                                      (map (lambda (ps)\n                                                             (define prg                 (pstate-program ps))\n                                                             (match-define (cons m n=>n) (module-rename  (program-module prg) n=>n.0))\n                                                             (define env                 (env-rename     (program-env prg)    n=>n))\n                                                             (define data                (data-rename    (pstate-data ps)     n=>n))\n                                                             (list m env data))\n                                                           (cons pst pstates))))))\n    ((pmod:move    path.old path.new) (define m.1 (module-remove m path.old))\n                                      (define m.new (if path.new\n                                                      (module-add m.1 path.new (module-ref m path.old))\n                                                      m.1))\n                                      (pstate:set pst (program (program:set prg (module m.new)))))\n    ((pmod:wrap    path)              (pstate:set pst (program (program:set prg (module (module-wrap   m path))))))\n    ((pmod:unwrap  path)              (pstate:set pst (program (program:set prg (module (module-unwrap m path))))))\n    ((pmod:rename  vocab n.old n.new) (define env.1   (env-set env vocab n.old #f))\n                                      (define env.new (if n.new\n                                                        (env-set env.1 vocab n.new (env-ref env vocab n.old))\n                                                        env.1))\n                                      (pstate:set pst (program (program:set prg (env env.new)))))))\n\n;; TODO: return #f if quiescent\n(define (pstate-step pst)\n  #f)\n\n(define (process name state)\n  (define dbms (pstate-dbms state))\n  (method-lambda\n    ((state)           state)\n    ((branch name.new) (dbms-process-add!  dbms name.new state)\n                       (process name.new state))\n    ((move   name.new) (dbms-process-move! dbms name name.new)\n                       (set! name name.new))\n    ((modify pm)       (define state.new (pstate-modify state pm))\n                       (dbms-process-set!  dbms name state.new)\n                       (set! state state.new))\n    ((step)            (define state.new (pstate-step state))\n                       (and state.new (dbms-process-set! dbms name state.new)))\n    ((query  . args)   (apply pstate-query state args))))\n\n(define (process-query   p . args)   (apply p 'query args))\n(define (process-branch  p name.new) (p 'branch name.new))\n(define (process-move!   p name.new) (p 'move   name.new))\n(define (process-step!   p)          (p 'step))\n(define (process-modify! p pm)       (p 'modify pm))\n\n(define (process-merge! p ps)\n  (process-modify! p (pmod:merge (map (lambda (p) (p 'state)) ps))))\n\n(define (merge-processes name ps)\n  (when (null? ps) (error \"cannot merge empty list of processes:\" name))\n  (define p (process-branch (car ps) name))\n  (process-merge! p (cdr ps))\n  p)\n\n;; TODO:\n(define (dbms-process-ref     dbms name)\n  #f)\n\n(define (dbms-process-set!    dbms name pst)\n  (void))\n\n(define (dbms-process-add!    dbms name pst)\n  (void))\n\n(define (dbms-process-move!   dbms name.old name.new)\n  (void))\n\n(define (dbms-process-remove! dbms name pst.validation)\n  (void))\n\n(define (dbms-export!         dbms renamings path.out)\n  (void))\n\n(define (dbms-import!         dbms renamings path.in)\n  (void))\n\n(define (dbms-clean!          dbms)\n  (void))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/order.rkt",
    "content": "#lang racket/base\n(provide term.min term.max term.number.min term.number.max\n         term.symbol.min term.symbol.max term.string.min term.string.max\n         term.bytes.min term.bytes.max term.pair.min term.pair.max\n         term.vector.min term.vector.max\n         (struct-out bounds) bounds.any bounds-intersect\n         domain.any domain.null domain.number domain.symbol\n         domain.string domain.bytes domain.pair domain.vector domain.boolean\n         any-increment any-decrement finite-interval?\n         (struct-out interval)\n         type->compare compare-term compare-any compare-null compare-boolean\n         compare-nat compare-number\n         compare-bytes compare-string compare-symbol\n         compare-pair compare-list compare-array compare-tuple\n         compare-string/pos compare-suffix compare-suffix-string\n         compare-><=?\n         termlist x))\n                 (define xs.new (list-increment xs))\n                 (if (eq? xs xs.new) x (list->vector xs.new)))\n    (_           x)))\n\n(define (any-decrement x)\n  (define (list-decrement xs)\n    (define xs.new\n      (let loop ((xs xs))\n        (if (null? xs) '()\n          (let* ((a (car xs)) (d (cdr xs)) (d.new (loop (cdr xs))))\n            (cond ((and (pair? d.new) (eq? d d.new)) xs)\n                  ((andmap (lambda (x) (eq? x #t)) d.new)\n                   (define a.new (if (eq? a '()) #t (any-decrement a)))\n                   (if (eq? a a.new) xs (cons a.new d.new)))\n                  (else (cons a d.new)))))))\n    (cond ((eq? xs xs.new)                         xs)\n          ((andmap (lambda (x) (eq? x #t)) xs.new) (cdr xs.new))\n          (else                                    xs.new)))\n  (match x\n    (#t          #f)\n    ('#()        '(#t . #t))\n    (`(,a . ())  (define a.new (any-decrement a))\n                 (if (eq? a a.new) x `(,a.new . #t)))\n    (`(,a . ,d)  (define d.new (any-decrement d))\n                 (if (eq? d d.new) x `(,a . ,d.new)))\n    ((? vector?) (define xs (vector->list x))\n                 (define xs.new (list-decrement xs))\n                 (if (eq? xs xs.new) x (list->vector xs.new)))\n    (_           x)))\n\n(define (finite-interval? lb ub)\n  (let loop ((lb lb) (acc '()))\n    (if (equal? lb ub)\n      (reverse (cons ub acc))\n      (let ((lb.new (any-increment lb)))\n        (and (not (equal? lb lb.new))\n             (loop lb.new (cons lb acc)))))))\n\n(define ((compare-><=? compare) a b) (not (eqv? (compare a b)  1)))\n\n(define (compare-any a b) (compare/compares compares.any a b))\n(define (anyvector cs))\n  (lambda (a b)\n    (define len (vector-length compares))\n    (let loop ((i 0))\n      (if (= i len) 0\n        (let ((compare (vector-ref compares i))\n              (va (vector-ref a i)) (vb (vector-ref b i)))\n          (case (compare va vb)\n            ((-1) -1)\n            (( 1)  1)\n            (else (loop (+ i 1)))))))))\n(define ((tuplecompare type)\n  (match type\n    (#f                         compare-any)\n    ((or 'nat    `#(nat    ,_)) compare-nat)\n    ((or 'string `#(string ,_)) compare-string)\n    ((or 'symbol `#(symbol ,_)) compare-symbol)\n    ((or 'bytes  `#(bytes  ,_)) compare-bytes)\n    (`#(suffix ,source)         (compare-suffix source))\n    (`#(tuple ,@ts)             (compare-tuple (map type->compare ts)))\n    (`(,ta . ,td)               (compare-pair (type->compare ta)\n                                              (type->compare td)))\n    ('array                     (compare-array compare-any))\n    (`#(array ,_ ,t)            (compare-array (type->compare t)))\n    ('list                      (compare-list compare-any))\n    (`#(list ,_ ,t)             (compare-list (type->compare t)))\n    ('number                    compare-number)\n    ((or 'true 'false '())      compare-null)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/safe-unsafe.rkt",
    "content": "#lang racket/base\n(provide\n  unsafe-car\n  unsafe-cdr\n  unsafe-fxmin\n  unsafe-fx=\n  unsafe-fx<=\n  unsafe-fx<\n  unsafe-fx+\n  unsafe-fx-\n  unsafe-fx*\n  unsafe-fxand\n  unsafe-fxlshift\n  unsafe-fxrshift\n  unsafe-fxquotient\n  unsafe-bytes-length\n  unsafe-bytes-ref\n  unsafe-bytes-set!\n  unsafe-vector*-length\n  unsafe-vector*-ref\n  unsafe-vector*-set!\n  unsafe-fxvector-length\n  unsafe-fxvector-ref\n  unsafe-fxvector-set!)\n(require racket/fixnum)\n\n(define unsafe-list-ref        list-ref)\n(define unsafe-car             car)\n(define unsafe-cdr             cdr)\n(define unsafe-fxmin           fxmin)\n(define unsafe-fx=             fx=)\n(define unsafe-fx<=            fx<=)\n(define unsafe-fx<             fx<)\n(define unsafe-fx+             fx+)\n(define unsafe-fx-             fx-)\n(define unsafe-fx*             fx*)\n(define unsafe-fxand           fxand)\n(define unsafe-fxlshift        fxlshift)\n(define unsafe-fxrshift        fxrshift)\n(define unsafe-fxquotient      fxquotient)\n(define unsafe-bytes-length    bytes-length)\n(define unsafe-bytes-ref       bytes-ref)\n(define unsafe-bytes-set!      bytes-set!)\n(define unsafe-vector*-length  vector-length)\n(define unsafe-vector*-ref     vector-ref)\n(define unsafe-vector*-set!    vector-set!)\n(define unsafe-fxvector-length fxvector-length)\n(define unsafe-fxvector-ref    fxvector-ref)\n(define unsafe-fxvector-set!   fxvector-set!)\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/semantics.rkt",
    "content": "#lang racket/base\n(provide simplify-program factor-program)\n(require racket/list racket/match racket/set)\n\n;; TODO: lift quantifiers to top of relation definition (or query) formula\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Grammar\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Program parts\n;(define (R Ns) Fs)\n;(query  Ns     Fs)\n\n;; Formulas F\n;(relate R Ts)\n;(not    F)\n;(and    Fs)\n;(or     Fs)\n;(imply  F F)\n;(iff    Fs)\n;(exist  Ns F)\n;(all    Ns F)\n\n;; Terms T\n;(quote C)\n;(var   N)\n;(app   Func Ts)\n\n(define (quote?      t) (eq? (car t) 'quote))\n(define (quote-value t) (cadr t))\n\n(define (var      n) `(var ,n))\n(define (var?     t) (eq? (car t) 'var))\n(define (var-name t) (cadr t))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Simplification\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; - classical transformations:\n;;   - `(not (not F))  ==> F`\n;;   - `(iff P Q)      ==> (or (and P Q) (and (not P) (not Q)))`\n;;   - `(imply P Q)    ==> (not (and P (not Q)))`\n;;   - `(all X F)      ==> (not (exist X (not F)))`\n\n;; - constructive/minimal transformations:\n;;   - `(not (not (not F))) ==> (not F)`\n;;   - `(not (or P Q))      ==> (and (not P) (not Q))`\n;;   - `(iff P Q)           ==> (and (imply P Q) (imply Q P))`\n;;   - `(imply P (not Q))   ==> (not (and P Q))`\n;;   - `(all X (not F))     ==> (not (exist X F))`\n\n;; - primitive transformations:\n;;   - `(not (==    A B)) ==> (=/=   A B)`\n;;   - `(not (=/=   A B)) ==> (==    A B)`\n;;   - `(not (any<= A B)) ==> (any<  B A)`\n;;   - `(not (any<  A B)) ==> (any<= B A)`\n\n(define (simplify-program full? parts)\n  (map (lambda (part)\n         (match part\n           (`(define (,r . ,params) ,f) `(define (,r . ,params) ,(simplify-formula full? f)))\n           (`(query  ,params        ,f) `(query  ,params        ,(simplify-formula full? f)))))\n       parts))\n\n(define (simplify-formula full? formula)  ; currently applying classical transformations\n  (define (loop/not f)\n    (match f\n      (`(relate      ,r ,@ts)    (let ((ts (map simplify-term ts)))\n                                   (define (k r ts) `(relate ,r . ,ts))\n                                   (match r\n                                     ('==           (k '=/=            ts))\n                                     ('=/=          (k '==             ts))\n                                     ('any<=        (k 'any<  (reverse ts)))\n                                     ('any<         (k 'any<= (reverse ts)))\n                                     (_      `(not ,(k r               ts))))))\n      (`(all         ,params ,f)      `(exist ,params ,(loop/not f)))\n      (`(exist       ,params ,f) `(not (exist ,params ,(loop     f))))\n      (`(not         ,f)         (loop f))\n      (`(and         ,@fs)       `(not (and . ,(map loop fs))))\n      (`(or          ,@fs)       `(and . ,(map loop/not fs)))\n      (`(iff         ,@fs)       (if full? ; defer iff transformation until after factoring, for efficiency\n                                   (loop/not `(or (and . ,fs)\n                                                  (and . ,(map (lambda (f) `(not ,f)) fs))))\n                                   `(not (iff . ,(map loop fs)))))\n      (`(imply       ,p ,q)      (loop/not `(not (and ,p (not ,q)))))))\n  (define (loop f)\n    (match f\n      (`(relate      ,r ,@ts)    `(relate ,r . ,(map simplify-term ts)))\n      (`(all         ,params ,f) `(not (exist ,params ,(loop/not f))))\n      (`(exist       ,params ,f)      `(exist ,params ,(loop     f)))\n      (`(not         ,f)         (loop/not f))\n      (`(and         ,@fs)       `(and . ,(map loop fs)))\n      (`(or          ,@fs)       `(or  . ,(map loop fs)))\n      (`(iff         ,@fs)       (if full? ; defer iff transformation until after factoring, for efficiency\n                                   (loop `(or (and . ,fs)\n                                              (and . ,(map (lambda (f) `(not ,f)) fs))))\n                                   `(iff . ,(map loop fs))))\n      (`(imply       ,p ,q)      (loop `(not (and ,p (not ,q)))))))\n  (loop formula))\n\n(define (simplify-term term)\n  (match term\n    (`(app ,func ,@ts)\n      (match (cons func (map simplify-term ts))\n        (`(cons         (quote ,a) (quote ,d))                                  `(quote ,(cons a d)))\n        (`(vector       . ,(? (lambda (ts) (andmap quote? ts)) ts))             `(quote ,(list->vector (map quote-value ts))))\n        (`(list->vector ,(? quote? (? (lambda (t) (list? (quote-value t))) t))) `(quote ,(list->vector (quote-value t))))\n        (`(,_           . ,ts) `(app ,func . ,ts))))\n    (_ term)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Program factoring via definition introduction\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (factor-program parts)\n  (factor-locally\n    (define factored (map (lambda (part)\n                            (match part\n                              (`(define (,r . ,params) ,f) `(define (,r . ,params) ,(factor-formula f)))\n                              (`(query  ,params        ,f) `(query  ,params                   ,(factor-formula f)))))\n                          parts))\n    (define new      (map (lambda (f&r)\n                            (match-define (cons f `(relate ,r . ,vs)) f&r)\n                            `(define (,r . ,(map (lambda (v) (match-define `(var ,name) v) name) vs)) ,f))\n                          (sort (hash->list (formula=>relate))\n                                (lambda (kv.a kv.b)\n                                  (define (kv-r kv) (cadr (caddr kv)))\n                                  (< (kv-r kv.a) (kv-r kv.b))))))\n    (append new factored)))\n\n(define (factor-formula formula)\n  (define (replace f) (rename-locally\n                        (formula-unrename-variables (formula->relate (formula-rename-variables f)))))\n  (match formula\n    (`(relate                             ,r ,@ts)    (define f.new `(relate ,r . ,ts))\n                                                      (if (foldl (lambda (t seen) (and seen (var? t) (not (set-member? seen (var-name t)))\n                                                                                       (set-add seen (var-name t))))\n                                                                 (set) ts)\n                                                        f.new\n                                                        (replace f.new)))\n    (`(,(and (or 'exist 'all) quantifier) ,params ,f) (replace `(,quantifier ,params ,(factor-formula f))))\n    (`(,connective                        ,@fs)       (replace `(,connective . ,(map factor-formula fs))))))\n\n(define-syntax-rule (factor-locally body ...) (parameterize ((formula=>relate (hash))) body ...))\n\n(define formula=>relate (make-parameter #f))\n\n(define (formula->relate f)\n  (define f=>r (formula=>relate))\n  (or (hash-ref f=>r f #f)\n      (let* ((count (hash-count f=>r))\n             (r     `(relate (new ,count) . ,(map var (remove-duplicates (formula-free-names f))))))\n        (formula=>relate (hash-set f=>r f r))\n        r)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Variable manipulation\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (term-free-names t)\n  (match t\n    (`(quote ,_)         '())\n    (`(var   ,name)      (list name))\n    (`(app   ,func ,@ts) (append* (map term-free-names ts)))))\n\n(define (formula-free-names f)\n  (match f\n    (`(relate            ,r ,@ts)    (append* (map term-free-names ts)))\n    (`(,(or 'exist 'all) ,params ,f) (define bound (list->set params))\n                                     (filter-not (lambda (n) (set-member? bound n))\n                                                 (formula-free-names f)))\n    (`(,connective       ,@fs)       (append* (map formula-free-names fs)))))\n\n(define (order-parameters params ordered-names)\n  (let loop ((ordered-names ordered-names) (params (list->set params)))\n    (match ordered-names\n      ('()                       '())\n      ((cons name ordered-names) (if (set-member? params name)\n                                   (cons name (loop ordered-names (set-remove params name)))\n                                   (loop ordered-names params))))))\n\n(define-syntax-rule (rename-locally body ...) (parameterize ((name=>renamed (hash))\n                                                             (renamed=>name (hash)))\n                                                body ...))\n\n(define name=>renamed (make-parameter #f))\n(define renamed=>name (make-parameter #f))\n\n(define (rename name)\n  (define n=>n (name=>renamed))\n  (or (hash-ref n=>n name #f)\n      (let ((count (hash-count n=>n)))\n        (name=>renamed (hash-set n=>n name count))\n        (renamed=>name (hash-set (renamed=>name) count name))\n        count)))\n\n(define (unrename name) (hash-ref (renamed=>name) name))\n\n(define (term-rename-variables term)\n  (match term\n    (`(quote ,_)       term)\n    (`(var ,name)      `(var ,(rename name)))\n    (`(app ,func ,@ts) `(app ,func . ,(map term-rename-variables ts)))))\n\n(define (term-unrename-variables term)\n  (match term\n    (`(quote ,_)       term)\n    (`(var ,name)      `(var ,(unrename name)))\n    (`(app ,func ,@ts) `(app ,func . ,(map term-unrename-variables ts)))))\n\n(define (formula-rename-variables formula)\n  (match formula\n    (`(relate                             ,r ,@ts)    `(relate      ,r . ,(map term-rename-variables ts)))\n    (`(,(and (or 'exist 'all) quantifier) ,params ,f) (define free-names (formula-free-names f))\n                                                      (for-each rename free-names)  ; allocate free names before bound names for readability\n                                                      `(,quantifier ,(map rename (order-parameters params free-names))\n                                                                    ,(formula-rename-variables f)))\n    (`(,connective                        ,@fs)       `(,connective . ,(map formula-rename-variables fs)))))\n\n(define (formula-unrename-variables formula)\n  (match formula\n    (`(relate                             ,r ,@ts)    `(relate      ,r . ,(map term-unrename-variables ts)))\n    (`(,(and (or 'exist 'all) quantifier) ,params ,f) `(,quantifier ,(map unrename params)\n                                                                    ,(formula-unrename-variables f)))\n    (`(,connective                        ,@fs)       `(,connective . ,(map formula-unrename-variables fs)))))\n\n\n;; TODO: before continuing, design data model with dataflow language for planning\n\n;; Implementation phases:\n;; - basic datalog\n;;   - only these features\n;;     - and (expressing joins)\n;;     - or  (expressing unions)\n;;     - ==, limited such that relations over == describe finite tables\n;;       - (== constant constant) can be simplified out\n;;         - could be a table with zero columns and either one or zero rows\n;;       - (== var constant) is a table with a single row and column\n;;       - no (== var1 var2) for now\n;;     - recursive relations defined by least fixed point\n;;   - no partial eval yet\n;;   - none of these yet\n;;     - not =/= < <= cons vector\n;; - TODO: describe subsequent phases in order of increasing complexity\n\n;; Compilation steps:\n;; - parse\n;; - simplify without serious inlining\n;; - introduce shared/factored definitions for remaining code\n;;   - one goal of factoring is to provide worker/wrapper separation for non-explosive inlining\n;; - simplify with more serious inlining\n;; - infer modes and [pre-]plan\n;; - generate mode/plan-specialized code\n\n;; Predictable simplification and inlining / partial eval\n;; - ideas from macro writer's bill of rights:\n;;   - the original list:\n;;     - introduce let & lambda\n;;     - ignore special cases involving constants\n;;     - ignore degenerate cases resulting in dead/useless code\n;; - local simplification\n;;   - a single-branch disjunction extends the context directly\n;;   - a multi-branch disjunction extends the context with the lattice-join of its branches\n;;   - disjunction branches that always fail in the given context should be pruned\n;;     - perform only one (left-to-right? or mode-specific?) pass to guarantee O(N) runtime\n;;       - well, it may make sense to perform two passes, where the first simplification makes it\n;;         easier to order constraints for an effective second pass\n;;       - do not compute the potentially non-linear pruning fixed point when the context is extended\n;;       - can have a separate optimization mode to compute the fixed point of such pruning\n;;   - limited inter-disjunction simplification\n;;     - fuse disjunctions when their branches can be joined at most one-to-one (i.e., no explosion)\n;;     - disjunctions should *NOT* be cross-joined/DNFed in general\n;;       - will quickly explode code size\n;;       - can have a separate optimization mode to attempt general cross-disjunction simplification\n;; - table-ification of table-like disjunctions\n;;   - table-like means a disjunction of uniform (same variable structure) conjunctions of equality constraints\n;; - inlining\n;;   - inline calls to non-recursive relations that are small enough\n;;   - inline calls to other relations based on analysis of how they are called\n;;     - inline calls with known arguments that can lead to significant simplification\n;;     - bottom-up analysis of how relation parameters are used\n;;       - knowing the shape of a parameter may eliminate many disjunction branches\n;;       - the relation may be structurally recursive on a subset of parameters\n;;       - a parameter may not be scrutinized at all, i.e., it may be invariant\n\n;; Factored relation definitions:\n;; - a simple-relate is a call to a user-defined relation where all arguments are distinct variables\n;; - a simple-cx is any of these:\n;;   - a simple-relate\n;;   - any call to a primitive constraint such as ==, =/=, <, <=\n;; - post-factoring relation definition types:\n;;   - single call to a relation with specialized arguments\n;;     - some arguments are either partially known (not variables), or use the same variable more than once\n;;   - conjunction of simple-cxs\n;;   - disjunction of simple-cxs\n;;   - negation of a simple-relate (not a simple-cx)\n;;   - quantification of a simple-relate (not a simple-cx)\n\n;; Notes and ideas on satisfiability:\n;; - a conjunction including at most one disjunction is satisfiable if one disjunct is satisfiable\n;; - for a conjunction including two or more disjunctions, satisfiability is only guaranteed via flattening into a single disjunction, where one disjunct is satisfiable\n;;   - possible to flatten by joining:\n;;     - disjunct-wise (always)\n;;     - or variable-wise (only for variables that are constrained in every disjunct in all disjunctions currently being combined)\n;;       - degenerate case: every disjunct applies the same constraint (however, possible to factor out this constraint due to being shared)\n;;   - this search for a single satisfiable flattened disjunct may be arbitrarily expensive (may be searching for a needle in a haystack)\n;;   - approaches that may be more tractable:\n;;     - two-watched disjunctions:\n;;       - each disjunction maintains two disjuncts that are locally satisfiable, along with a list of remaining disjuncts that haven't been tested yet\n;;       - if either of these watched disjuncts becomes unsatisfiable, find another from the untested list, pruning any that fail\n;;       - if only one satisfiable disjunct remains, it is promoted as an absolute part of the outer conjunction, used when filtering the other disjunctions\n;;     - learning absolute/shared constraints across all disjuncts in a disjunction:\n;;       - take the lattice join (analogous to an intersection across constraints) to find constraints that all disjuncts agree on\n;;       - e.g. `(disj (== x (cons A B)) (== x (cons C B))) ==> (conj (fresh (D) (== x (cons D B))) (disj (== x (cons A B)) (== x (cons C B))))`\n;;         - simplified: `(fresh (D) (conj (== x (cons D B)) (disj (== D A) (== D C))))`\n;;     - subsumption\n;;       - for each disjunct, starting with the smallest (least constrained), discard any other disjuncts that strictly include its constraints\n;;     - variable-wise factoring of an individual disjunction\n;;       - similar to variable-wise flattening, but without joining, instead building a new disjunction that looks like a decision tree\n;;       - for each variable (often starting with the most constrained) that is constrained by every disjunct, bisect on a constraint choice (recursively)\n;; - may unfold all relation calls except when doing so may lead to looping/redundancy\n;;   - disjunctions annotated with procedure history stack, to recognize recursive calls\n;;     - different history information granularities for different termination measures\n;;       - e.g.,\n;;         - no calls at all (least permissive, but no inlining achieved)\n;;         - or no recursive calls (least permissive while still performing some inlining)\n;;         - or no non-structural recursive calls (most permissive w/ guaranteed termination without programmer assistance)\n;;         - or no non-decreasing recursive calls according to programmer-defined measure (most permissive w/ guaranteed termination)\n;;         - any call is fine (most permissive, but no termination guarantees)\n\n;; How to handle the non-datalog subset of computation:\n\n;(struct store (var=>shape id=>cx) #:prefab)\n;; - each constraint in id=>cx is a CNF formula\n;;   - may include calls to user-defined relations that have not yet been unfolded\n;;   - its id is associated with the shape of all mentioned variables\n;; - a shape is either a t:quote, a t:cons, a t:vector, or a vcx\n;; - for implementation simplicity, avoid more complicated variable-specific indexing schemes for now\n;; - when a new constraint is inserted, apply simplification rules for any interacting variables\n;; - when a variable shape is updated, apply simplification rules for any interacting cxs\n;; - search for variable assignments that satisfy all cxs in id=>cx\n;;   - for constraints participating in satisfaction:\n;;     - run datalog sub-queries if possible\n;;     - otherwise, unfold any calls to relations\n\n;(struct vcx (lb ub cx-ids) #:prefab)\n;; each of lb and ub is an interval endpoint, and either may be open or closed\n;; cx-ids is a set of ids for the cxs that this variable interacts with\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/storage.rkt",
    "content": "#lang racket/base\n(provide\n  storage:filesystem\n  storage-path\n  storage-checkpoint-count\n  storage-checkpoint-pending?\n  storage-checkpoint!\n  storage-revert!\n  storage-trash-empty!\n  storage-trash-empty?\n  storage-description-keys\n  storage-description-key?\n  storage-description-ref\n  storage-description-update!\n  storage-description-set!\n  storage-description-remove!\n  storage-block-names\n  storage-block-name?\n  storage-block-path\n  storage-block-new!\n  storage-block-add-names!\n  storage-block-remove-names!\n  storage-block-rename!)\n(require \"logging.rkt\" \"misc.rkt\"\n         racket/file racket/pretty racket/set racket/struct)\n\n;; This is a simple implementation of checkpointing storage.  It includes block storage for large\n;; data, and key-value storage for small data and metadata.\n\n;; Limitations:\n;; - The default key-value store will not scale well to enormous amounts of data and/or enormous\n;;   numbers of blocks (because these require tracking metadata).\n;; - The default key-value store will not scale well to high frequency checkpoints.\n;; - A single storage location should not be used by multiple host processes running concurrently.\n;;   Initializing the same storage location from concurrent processes may lead to data corruption.\n;; - Multiple threads of a single process can read concurrently from a single storage location,\n;;   but it is not safe to read concurrently with writes or checkpoint commits to that location.\n;; - It is not safe to perform concurrent writes or checkpoint commits to a single storage location.\n;; - While it should be possible to recover from typical process failure and interruption, sudden\n;;   host system failure and interruption may corrupt data.\n\n;; Two forms of data can be stored:\n;; - Description\n;;   - \"description\" is a key-value map.\n;;   - Keys and values can be any s-expression.\n;;   - Keys can be added and removed.  A key's value can be updated.\n;; - Block\n;;   - Blocks are uninterpreted files of data.\n;;   - Blocks are referenced by names.  A name can be any s-expression.  Each name maps to at most\n;;     one block.  Multiple names can refer to the same block.\n;;   - When a new block is created, it's data can be written and modified freely until the next\n;;     checkpoint.  Once the checkpoint is committed, blocks cannot be updated.\n;;   - Block data is only expected to be read after the checkpoint that creates them.\n;;   - Blocks are not explicitly deleted.  A block is garbage collected once there are no longer\n;;     any names referring to it after a checkpoint.\n\n;; Storage system initialization and checkpoint commits will perform garbage collection of unused\n;; blocks and old state descriptions.  By default, each collection will move garbage to a new\n;; subdirectory under \"trash\", to make it possible to manually recover from mistakes.\n\n;; A storage location is a self-contained directory with the following structure:\n;;   block/\n;;     filename-for-block-id\n;;     ...\n;;   metadata/\n;;     current.scm\n;;     [next.scm]\n;;   trash/\n;;     trash-uid/\n;;       any-file ...\n;;     ...\n;;   [trash-pending/\n;;     any-file ...]\n\n;; Do not store other files anywhere within this directory structure.\n\n;; The current state of the system is stored in metadata/current.scm.  While committing a\n;; checkpoint, the next state temporarily lives in metadata/next.scm.  These states are Racket\n;; s-expressions with the following shape:\n;;   (hash\n;;     'format-version  datum\n;;     'checkpoint-time pretty-timestamp\n;;     'data            (hash\n;;                        'description (hash ,@{any-key any-value} ...)\n;;                        'block       (hash ,@{any-name block-id} ...)))\n\n(define (unique-directory path.root str.type)\n    (define seconds (number->string (current-seconds)))\n    (let loop ((id.local 0))\n      (define candidate (string-append str.type \"-\" seconds \"-\" (number->string id.local)))\n      (define apath     (path->string (build-path path.root candidate)))\n      (cond ((directory-exists? apath) (loop (+ id.local 1)))\n            (else                      apath))))\n\n(define (storage-path                s) ((wrapped-storage-controller s) 'path))\n(define (storage-checkpoint-count    s) ((wrapped-storage-controller s) 'checkpoint-count))\n(define (storage-checkpoint-pending? s) ((wrapped-storage-controller s) 'checkpoint-pending?))\n(define (storage-checkpoint!         s) ((wrapped-storage-controller s) 'checkpoint!))\n(define (storage-revert!             s) ((wrapped-storage-controller s) 'revert!))\n(define (storage-trash-empty!        s) ((wrapped-storage-controller s) 'trash-empty!))\n(define (storage-trash-empty?        s) ((wrapped-storage-controller s) 'trash-empty?))\n\n(define ((missing-key s key)) (error \"storage description key does not exist\" key (storage-path s)))\n\n(define (storage-description-keys    s)                                          (hash-keys     ((wrapped-storage-controller s) 'description)))\n(define (storage-description-key?    s key)                                      (hash-has-key? ((wrapped-storage-controller s) 'description) key))\n(define (storage-description-ref     s key        (default (missing-key s key))) (hash-ref      ((wrapped-storage-controller s) 'description) key default))\n(define (storage-description-update! s key update (default (missing-key s key))) (storage-description-set! s key (update (storage-description-ref s key default))))\n(define (storage-description-set!    s . keys-values)                            ((wrapped-storage-controller s) 'description-set*!    keys-values))\n(define (storage-description-remove! s . keys)                                   ((wrapped-storage-controller s) 'description-remove*! keys))\n\n(define (storage-block-names         s)                      ((wrapped-storage-controller s) 'block-names))\n(define (storage-block-name?         s name)                 ((wrapped-storage-controller s) 'block-name?         name))\n(define (storage-block-path          s name)                 ((wrapped-storage-controller s) 'block-path          name))\n(define (storage-block-new!          s         name . names) ((wrapped-storage-controller s) 'block-new!          (cons name names)))\n(define (storage-block-add-names!    s name.current . names) ((wrapped-storage-controller s) 'block-add-names!    name.current names))\n(define (storage-block-remove-names! s              . names) ((wrapped-storage-controller s) 'block-remove-names! names))\n(define (storage-block-rename!       s name.old name.new)\n  (storage-block-add-names!    s name.old name.new)\n  (storage-block-remove-names! s name.old))\n\n(define all-filesystem-storage-keys (weak-set))\n(define (storage:filesystem path.storage)\n  (let* ((path.storage (normalize-path path.storage))\n         (key.storage  (list path.storage)))\n    (unless (complete-path? path.storage)\n      (error \"storage path must be absolute\" path.storage))\n    (when (set-member? all-filesystem-storage-keys key.storage)\n      (error \"storage path already in use\" path.storage))\n    (set-add! all-filesystem-storage-keys key.storage)\n    (wrapped-storage key.storage (make-filesystem-storage path.storage))))\n\n(struct wrapped-storage (key controller)\n        #:methods gen:custom-write\n        ((define write-proc\n           (make-constructor-style-printer\n             (lambda (s) 'storage:filesystem)\n             (lambda (s) (list (storage-path s)))))))\n\n(define (make-state count data)\n  (hash 'format-version   version.current\n        'checkpoint-time  (pretty-timestamp)\n        'checkpoint-count count\n        'data             data))\n\n(define dir.metadata        \"metadata\")\n(define dir.block           \"block\")\n(define dir.trash           \"trash\")\n(define dir.trash-pending   \"trash-pending\")\n(define fname.state.current \"current.scm\")\n(define fname.state.next    \"next.scm\")\n(define version.current     '2021-12-31)\n(define data.empty          (hash 'description (hash)\n                                  'block       (hash)))\n\n(define (make-filesystem-storage path.storage)\n  (define (local-path relpath)  (path->string (build-path path.storage relpath)))\n  (define (desc)                (hash-ref current 'description))\n  (define (block)               (hash-ref current 'block))\n  (define (block-id? name)      (hash-ref (block) name #f))\n  (define (block-id  name)      (or (block-id? name)\n                                    (error \"storage block name does not exist\" name path.storage)))\n  (define (id->path id)         (build-path path.block (number->string id)))\n  (define (unique-block-id)     (+ (apply max\n                                          (apply max 0 (set->list ids.new))\n                                          (hash-values (hash-ref previous 'block)))\n                                   1))\n  (define (checkpoint-pending?) (not (and (set-empty? ids.new)\n                                          (equal? current previous))))\n  (define (collect-garbage!)\n    (set-clear! ids.new)\n    (define lpaths.all         (list->set (map path->string (directory-list path.block))))\n    (define lpaths.reachable   (list->set (map number->string (hash-values (block)))))\n    (define lpaths.unreachable (set->list (set-subtract lpaths.all lpaths.reachable)))\n    (when (file-exists? path.state.next)\n      (make-directory* path.trash-pending)\n      (rename-file-or-directory path.state.next (build-path path.trash-pending fname.state.next)))\n    (unless (null? lpaths.unreachable)\n      (define numbers.unreachable  (map (lambda (lp) (or (string->number lp) lp)) lpaths.unreachable))\n      (define unreachables.block   (filter number? numbers.unreachable))\n      (define unreachables.unknown (filter string? numbers.unreachable))\n      (unless (null? unreachables.unknown)\n        (error \"aborting garbage collection: found untracked files in block directory\" unreachables.unknown path.storage))\n      (pretty-log `(moving unreachable blocks to trash))\n      (make-directory* path.trash-pending)\n      (for-each (lambda (lp) (rename-file-or-directory (build-path path.block         lp)\n                                                       (build-path path.trash-pending lp)))\n                lpaths.unreachable))\n    (when (directory-exists? path.trash-pending)\n      (define upath (unique-directory path.trash \"trash\"))\n      (rename-file-or-directory path.trash-pending upath)))\n\n  (define path.metadata      (local-path dir.metadata))\n  (define path.block         (local-path dir.block))\n  (define path.trash         (local-path dir.trash))\n  (define path.trash-pending (local-path dir.trash-pending))\n  (define path.state.current (path->string (build-path path.metadata fname.state.current)))\n  (define path.state.next    (path->string (build-path path.metadata fname.state.next)))\n  (for-each make-directory* (list path.metadata path.block path.trash))\n  (define-values (checkpoint-count previous)\n    (let* ((state (cond ((file-exists? path.state.current) (call-with-input-file path.state.current read))\n                        ((file-exists? path.state.next)    (pretty-log '(finishing transition for interrupted-yet-successful checkpoint commit))\n                                                           (rename-file-or-directory path.state.next path.state.current)\n                                                           (call-with-input-file path.state.current read))\n                        (else                              (pretty-log '(creating new storage location) path.storage)\n                                                           (define state.empty (make-state 0 data.empty))\n                                                           (call-with-output-file path.state.current\n                                                                                  (lambda (out) (pretty-write state.empty out)))\n                                                           state.empty)))\n           (version (hash-ref state 'format-version)))\n      ;; TODO: attempt to migrate state to new format if version is old\n      (unless (equal? version version.current)\n        (error \"storage state format version mismatch\" `(found: ,version expected: ,version.current) path.storage))\n      (values (hash-ref state 'checkpoint-count) (hash-ref state 'data))))\n  (define current previous)\n  (define ids.new (mutable-set))\n  (pretty-log `(loaded storage state ,checkpoint-count for) path.storage)\n  (collect-garbage!)\n  (pretty-log `(collected garbage))\n\n  (method-lambda\n    ((path)                                path.storage)\n    ((checkpoint-count)                    checkpoint-count)\n    ((checkpoint-pending?)                 (checkpoint-pending?))\n    ((description)                         (hash-ref current 'description))\n    ((description-set*!    keys-values)    (set! current (hash-set current 'description\n                                                                   (apply hash-set* (desc) keys-values))))\n    ((description-remove*! keys)           (set! current (hash-set current 'description\n                                                                   (foldl (lambda (key d) (hash-remove d key)) (desc) keys))))\n    ((block-names)                         (hash-keys (block)))\n    ((block-name?                    name) (hash-has-key? (block) name))\n    ((block-path                     name) (id->path (block-id name)))\n    ((block-new!                    names) (define b (block))\n                                           (for-each (lambda (name)\n                                                       (when (hash-has-key? b name)\n                                                         (error \"cannot create new block with existing name\" name path.storage)))\n                                                     names)\n                                           (define id (unique-block-id))\n                                           (set-add! ids.new id)\n                                           (set! current (hash-set current 'block\n                                                                   (foldl (lambda (name b) (hash-set b name id)) b names)))\n                                           (id->path id))\n    ((block-add-names! name.current names) (define b  (block))\n                                           (define id (block-id name.current))\n                                           (for-each (lambda (name)\n                                                       (when (hash-has-key? b name)\n                                                         (error \"cannot add existing block name\" name path.storage)))\n                                                     names)\n                                           (set! current (hash-set current 'block\n                                                                   (foldl (lambda (name b) (hash-set b name id)) b names))))\n    ((block-remove-names!           names) (set! current (hash-set current 'block\n                                                                   (foldl (lambda (name b) (hash-remove b name)) (block) names))))\n\n    ((checkpoint!)  (cond ((checkpoint-pending?)\n                           (set! checkpoint-count (+ 1 checkpoint-count))\n                           (pretty-log `(committing checkpoint ,checkpoint-count))\n                           (define state (make-state checkpoint-count current))\n                           (call-with-output-file path.state.next (lambda (out) (pretty-write state out)))\n                           (make-directory* path.trash-pending)\n                           (rename-file-or-directory path.state.current (build-path path.trash-pending fname.state.current))\n                           (rename-file-or-directory path.state.next    path.state.current)\n                           (set! previous current)\n                           (pretty-log `(committed checkpoint ,checkpoint-count))\n                           (collect-garbage!))\n                          (else (pretty-log '(no checkpoint necessary: storage has not been modified)))))\n    ((revert!)      (cond ((checkpoint-pending?)\n                           (set! current previous)\n                           (pretty-log `(reverted to checkpoint ,checkpoint-count))\n                           (collect-garbage!))\n                          (else (pretty-log '(no revert necessary: storage has not been modified)))))\n    ((trash-empty?) (null? (directory-list path.trash #:build? #t)))\n    ((trash-empty!) (define (delete-path path)\n                      (cond ((file-exists?      path) (delete-file path))\n                            ((directory-exists? path) (for-each delete-path (directory-list path #:build? #t))\n                                                      (delete-directory path))))\n                    (define dirs.trash (directory-list path.trash #:build? #t))\n                    (cond ((null? dirs.trash) (pretty-log '(no trash to empty)))\n                          (else               (pretty-log `(deleting ,(length dirs.trash) trash subdirectories))\n                                              (for-each delete-path dirs.trash))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/stream.rkt",
    "content": "#lang racket/base\n(provide s-next s-force s-split s-drop\n         s-take/set/steps s-take/set s-take/steps s-take\n         s-each s-foldr s-foldl s-scan\n         s-append/interleaving s-append*/interleaving\n         s-append s-append* s-map/append s-map s-filter s-group s-memo s-lazy\n         s-length s-enumerate s-dedup s-skip s-limit\n         s->list list->s)\n(require racket/function racket/match racket/set)\n\n(define (s-next  s) (if (procedure? s)          (s)  s))\n(define (s-force s) (if (procedure? s) (s-force (s)) s))\n\n;; lazy variant of s-drop\n(define (s-skip n s)\n  (cond ((= n 0)   s)\n        ((pair? s) (s-skip (- n 1) (cdr s)))\n        (else      (thunk (s-skip n (s))))))\n;; lazy variant of s-take\n(define (s-limit n s)\n  (cond ((or (= n 0) (null? s)) '())\n        ((pair? s)              (cons (car s) (s-limit (- n 1) (cdr s))))\n        (else                   (thunk (s-limit n (s))))))\n\n(define (s-split n s)\n  (match-define (cons rxs s.remaining) (s-foldl n cons '() s))\n  (cons (reverse rxs) s.remaining))\n\n(define (s-take/set/steps steps n s)\n  (if (and n (= n 0)) (set)\n    (let loop ((steps steps) (s s) (acc (set)))\n      (match s\n        ((? procedure? s) (if (and steps (= steps 0))\n                            acc\n                            (loop (and steps (- steps 1)) (s) acc)))\n        ('()              acc)\n        ((cons x s)       (define xs (set-add acc x))\n                          (if (and n (= n (set-count xs)))\n                            xs\n                            (loop steps s xs)))))))\n\n(define (s-take/steps steps n s)\n  (if (and n (= n 0)) '()\n    (match s\n      ((? procedure? s) (if (and steps (= steps 0))\n                          '()\n                          (s-take/steps (and steps (- steps 1)) n (s))))\n      ('()              '())\n      ((cons x s)       (cons x (s-take/steps steps (and n (- n 1)) s))))))\n\n(define (s-take/set n s) (s-take/set/steps #f n s))\n(define (s-take     n s) (s-take/steps #f n s))\n(define (s-drop     n s) (cdr (s-foldl n (lambda (_ acc) #t) #t s)))\n\n;; equivalent to (s-take #f s)\n(define (s->list s)\n  (cond ((null? s) '())\n        ((pair? s) (cons (car s) (s->list (cdr s))))\n        (else      (s->list (s)))))\n;; equivalent to s-lazy for a list\n(define (list->s xs)\n  (thunk (if (null? xs)\n           '()\n           (cons (car xs) (list->s (cdr xs))))))\n\n;; TODO: generalize to multiple streams\n(define (s-foldr f acc s)\n  (cond ((null? s) acc)\n        ((pair? s) (f (car s) (s-foldr f acc (cdr s))))\n        (else      (thunk (s-foldr f acc (s))))))\n\n(define (s-append*/interleaving s*) (s-foldr s-append/interleaving '() s*))\n;; TODO: generalize to multiple streams\n(define (s-append/interleaving s1 s2)\n  (cond ((null?      s1) (s2))\n        ((procedure? s1) (thunk (s-append/interleaving (s2) s1)))\n        (else (define d1  (cdr s1))\n              (define s1^ (if (procedure? d1) d1 (thunk d1)))\n              (cons (car s1) (thunk (s-append/interleaving (s2) s1^))))))\n\n(define (s-append* ss) (s-foldr s-append '() ss))\n;; TODO: generalize to multiple streams\n(define (s-append a b) (s-foldr cons b a))\n(define (s-filter ? s) (s-foldr (lambda (x acc) (if (? x) (cons x acc) acc))\n                                '() s))\n\n(define (s-map f s . ss)\n  (cond ((null? s) '())\n        ((pair? s) (let loop ((ss-pending ss) (rss '()))\n                     (if (null? ss-pending)\n                       (let ((ss (reverse rss)))\n                         (cons (apply f (car s) (map car ss))\n                               (apply s-map f (cdr s) (map cdr ss))))\n                       (let next ((ss0 (car ss-pending)))\n                         (if (procedure? ss0) (thunk (next (ss0)))\n                           (loop (cdr ss-pending) (cons ss0 rss)))))))\n        (else      (thunk (apply s-map f (s) ss)))))\n\n;; TODO: generalize to multiple streams\n(define (s-map/append f s)\n  (s-foldr (lambda (x rest) (s-append (f x) rest))\n           '() s))\n\n(define (s-each p s) (let ((s (s-force s)))\n                       (unless (null? s) (p (car s)) (s-each p (cdr s)))))\n\n(define (s-foldl n f acc s)\n  (if (and n (= n 0)) (cons acc s)\n    (let ((s (s-force s)))\n      (if (null? s) (list acc)\n        (s-foldl (and n (- n 1)) f (f (car s) acc) (cdr s))))))\n\n(define (s-scan s acc f)\n  (cons acc (cond ((null? s) '())\n                  ((pair? s) (s-scan (cdr s) (f (car s) acc) f))\n                  (else      (thunk (s-scan (s) acc f))))))\n\n(define (s-length s) (let loop ((s s) (l 0))\n                       (cond ((null? s) l)\n                             ((procedure? s) (loop (s) l))\n                             (else (loop (cdr s) (+ l 1))))))\n\n(define (s-group s ? @)\n  (let ((@ (or @ (lambda (x) x))))\n    (cond ((null? s)      '())\n          ((procedure? s) (thunk (s-group (s) ? @)))\n          (else (let next ((x (@ (car s))) (s s))\n                  (let loop ((g (list (car s))) (s (cdr s)))\n                    (cond ((null? s)      (list g))\n                          ((procedure? s) (thunk (loop g (s))))\n                          (else (let ((y (@ (car s))))\n                                  (if (? y x) (loop (cons (car s) g) (cdr s))\n                                    (cons g (next y s))))))))))))\n\n(define (s-memo s)\n  (cond ((procedure? s) (let ((v #f) (s s))\n                          (thunk (when s (set! v (s-memo (s))) (set! s #f))\n                                 v)))\n        ((null? s)      '())\n        (else           (cons (car s) (s-memo (cdr s))))))\n\n(define (s-lazy s)\n  (define (return s)\n    (cond ((null? s) '())\n          (else      (cons (car s) (s-lazy (cdr s))))))\n  (thunk (cond ((procedure? s) (let retry ((s (s)))\n                                 (cond ((procedure? s) (thunk (retry (s))))\n                                       (else           (return s)))))\n               (else           (return s)))))\n\n(define (s-enumerate i s)\n  (cond ((null? s) '())\n        ((pair? s) (cons (cons i (car s)) (s-enumerate (+ i 1) (cdr s))))\n        (else      (thunk                 (s-enumerate i           (s))))))\n\n;; NOTE: only adjacent duplicates are removed\n(define (s-dedup s)\n  (define (loop x s)\n    (cond ((null? s) (list x))\n          ((pair? s) (if (equal? x (car s)) (loop x (cdr s))\n                       (cons x (loop (car s) (cdr s)))))\n          (else      (thunk (loop x (s))))))\n  (cond ((null? s) '())\n        ((pair? s) (loop (car s) (cdr s)))\n        (else      (thunk (s-dedup (s))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/syntax.rkt",
    "content": "#lang racket/base\n(provide\n  (struct-out make-query)\n  (struct-out disj)\n  (struct-out conj)\n  (struct-out constrain)\n  (struct-out ==/use)\n  (struct-out var)\n  (struct-out term/vars)\n  relate\n\n  make-relation relations relations-ref relations-set! relations-set*!\n  relation letrec-relation define-relation\n  conj* disj* fresh conde :== query\n  == =/= any<=o flooro +o *o string==byteso symbol==stringo functiono\n  vector-lengtho vector-refo bytes-lengtho bytes-refo\n\n  ground? term-vars\n  make-pretty pretty)\n(require racket/match racket/set racket/vector)\n\n(struct query     (term formula)                #:prefab #:name make-query\n                                                #:constructor-name make-query)\n;; formulas\n(struct disj      (f1 f2)                       #:prefab)\n(struct conj      (f1 f2)                       #:prefab)\n(struct constrain (op terms)                    #:prefab)\n(struct ==/use    (lhs-term args rhs-proc desc) #:prefab)\n;; terms\n; term: pair or vector with embedded variables\n; vars: optional; set of variables found somewhere within term\n(struct term/vars (term vars))\n(struct var       (name))\n\n(define-syntax define-constraint\n  (syntax-rules ()\n    ((_ (op params ...)) (define (op params ...)\n                           (constrain 'op (list params ...))))))\n(define-constraint (==              t1 t2))\n(define-constraint (=/=             t1 t2))\n(define-constraint (any<=o          t1 t2))\n(define-constraint (flooro          t1 t2))\n(define-constraint (+o              t1 t2 t3))\n(define-constraint (*o              t1 t2 t3))\n(define-constraint (vector-lengtho  t l))\n(define-constraint (vector-refo     t i x))\n(define-constraint (bytes-lengtho   t l))\n(define-constraint (bytes-refo      t i x))\n(define-constraint (symbol==stringo t1 t2))\n(define-constraint (string==byteso  t1 t2))  ;; as utf-8\n(define-constraint (functiono       t1 t2))  ;; uninterpreted functional dependency\n(define (relate proc args) (constrain proc args))\n\n(define relation-registry          (make-weak-hasheq '()))\n(define (relations)                (hash->list relation-registry))\n(define (relations-ref   proc)     (hash-ref relation-registry proc))\n(define (relations-set!  proc k v) (relations-set*! proc `((,k . ,v))))\n(define (relations-set*! proc alist)\n  (hash-set! relation-registry proc\n             (foldl (lambda (kv acc) (hash-set acc (car kv) (cdr kv)))\n                    (relations-ref proc) alist)))\n(define (make-relation name attributes)\n  (define n ((make-syntax-introducer) (datum->syntax #f name)))\n  (define r (eval-syntax #`(letrec ((#,n (lambda args (relate #,n args))))\n                             #,n)))\n  (hash-set! relation-registry r (make-immutable-hash\n                                   `((name            . ,name)\n                                     (attribute-names . ,attributes))))\n  r)\n\n(define-syntax relation\n  (syntax-rules ()\n    ((_ name (param ...) f ...)\n     (let ((r (make-relation 'name '(param ...))))\n       (relations-set! r 'expand (lambda (param ...) (fresh () f ...)))\n       r))))\n(define-syntax letrec-relation\n  (syntax-rules ()\n    ((_ (((name param ...) f ...) ...) body ...)\n     (letrec ((name (relation name (param ...) f ...)) ...) body ...))))\n(define-syntax define-relation\n  (syntax-rules ()\n    ((_ (name param ...) f ...)\n     (define name (relation name (param ...) f ...)))))\n(define success (== #t #t))\n(define failure (== #f #t))\n(define (conj* . fs)\n  (if (null? fs) success\n    (foldl (lambda (f2 f1) (conj f1 f2)) (car fs) (cdr fs))))\n(define (disj* . fs)\n  (if (null? fs) failure\n    (let loop ((f (car fs)) (fs (cdr fs)))\n      (if (null? fs) f\n        (disj f (loop (car fs) (cdr fs)))))))\n(define-syntax let/fresh\n  (syntax-rules ()\n    ((_ (x ...) e ...) (let ((x (var 'x)) ...) e ...))))\n(define-syntax fresh\n  (syntax-rules ()\n    ((_ (x ...) f0 fs ...) (let/fresh (x ...) (conj* f0 fs ...)))))\n(define-syntax conde\n  (syntax-rules ()\n    ((_ (f fs ...) (h hs ...) ...)\n     (disj* (conj* f fs ...) (conj* h hs ...) ...))))\n(define-syntax :==\n  (syntax-rules ()\n    ((_ t (x ...) body ...) (==/use t (list x ...) (lambda (x ...) body ...)\n                                    `((x ...) body ...)))))\n(define-syntax query\n  (syntax-rules ()\n    ((_ (x ...) f0 fs ...)\n     (let/fresh (x ...) (make-query (list x ...) (conj* f0 fs ...))))\n    ((_ x       f0 fs ...)\n     (let/fresh (x)     (make-query x            (conj* f0 fs ...))))))\n\n(define seteq.empty (seteq))\n(define (term-vars t)\n  (cond ((var?    t) (seteq t))\n        ((pair?   t) (set-union (term-vars (car t)) (term-vars (cdr t))))\n        ((vector? t) (apply set-union seteq.empty (map term-vars (vector->list t))))\n        (else        seteq.empty)))\n(define (ground? t)\n  (cond ((var?    t) #f)\n        ((pair?   t) (and (ground? (car t)) (ground? (cdr t))))\n        ((vector? t) (andmap ground? (vector->list t)))\n        (else        #t)))\n\n(define (make-pretty)\n  (define var=>id (make-hash))\n  (define (pretty-term t)\n    (cond ((pair? t)   (cons (pretty-term (car t)) (pretty-term (cdr t))))\n          ((vector? t) (vector-map pretty-term t))\n          ((var? t)    `#s(var ,(let ((id (hash-ref   var=>id t #f))\n                                      (c  (hash-count var=>id)))\n                                  (or id (begin (hash-set! var=>id t c) c)))))\n          (else        (pretty-formula t))))\n  (define (pretty-formula f)\n    (match f\n      (`#s(disj ,f1 ,f2)         `#s(disj ,(pretty-formula f1)\n                                          ,(pretty-formula f2)))\n      (`#s(conj ,f1 ,f2)         `#s(conj ,(pretty-formula f1)\n                                          ,(pretty-formula f2)))\n      (`#s(constrain ,op ,terms) `(,op . ,(map pretty-term terms)))\n      (`#s(==/use ,lhs ,args ,rhs ,desc)\n        (define (pretty-arg t) (pretty-term t))\n        `(:== ,(pretty-term lhs)\n              #s(let ,(map list (car desc) (map pretty-arg args))\n                  ,@(cdr desc))))\n      (_ f)))\n  (lambda (x)\n    (match x\n      (`#s(query ,t ,f)\n        `#s(query ,(pretty-term t) ,(pretty-formula f)))\n      (_ (if (or (disj? x) (conj? x) (constrain? x) (==/use? x))\n           (pretty-formula x) (pretty-term x))))))\n(define (pretty x) ((make-pretty) x))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk/table.rkt",
    "content": "#lang racket/base\n(provide materialization value/syntax\n         (struct-out statistics) statistics-intersect\n         vector-table? encoder s-encode s-decode)\n(require \"codec.rkt\" \"config.rkt\" \"dsv.rkt\" \"misc.rkt\" \"order.rkt\" \"stream.rkt\"\n         racket/file racket/function racket/hash racket/list racket/match\n         racket/pretty racket/set racket/vector)\n\n(define (s-encode out type s) (s-each (lambda (v) (encode out type v)) s))\n(define (s-decode in type)\n  (thunk (let loop () (if (eof-object? (peek-byte in)) '()\n                        (cons (decode in type) (thunk (loop)))))))\n\n(define (encoder out type) (method-lambda ((put! v) (encode out type v))\n                                          ((close) (flush-output out))))\n\n(struct statistics (ratio cardinality) #:prefab)\n(define (statistics-intersect a b)\n  (match-define (statistics r.a c.a) a)\n  (match-define (statistics r.b c.b) b)\n  (statistics (min r.a r.b) (min c.a c.b)))\n\n;; TODO: can we simplify by virtually separating bisecting tries from random-access tries?\n;;       technically each prefix of a trie has either bisecting or random-access behavior\n;; virtualized tries can subsume each other when making progress: a kind of exclusive-or trie\n;; - exclusive-or (for grouping with subsumption)\n;; - random-access/position-key (each column value is a table position)\n;; - bisect-key                 (each column value has a unique entry)\n;; - bisect-multi               (each column value may have multiple entries)\n;(define (trie:xor ))\n;; TODO: this one is for monotone dependencies (grouping without subsumption)\n;(define (trie:or ))\n;; TODO: there could be tabular and columnar varieties of these\n;(define (trie:position-key ))\n;(define (trie:bisect-key ))\n;(define (trie:bisect-multi ))\n\n;; TODO: support multiple sorted columns using tables that share key columns\n;;       (wait until column-oriented tables are implemented for simplicity?)\n\n(define ((table ix-thunks))\n  (define ixs (map (lambda (thunk.ix) (thunk.ix)) ix-thunks))\n  (and (not (ormap not ixs))\n       (let table ((ixs         (filter (lambda (ix) (not (ix 'done?))) ixs))\n                   (col=>bounds (foldl (lambda (ix c=>b)\n                                         (hash-union c=>b (ix 'bounds)\n                                                     ;; TODO: verify no errors during testing.\n                                                     ;;       Should be able to replace this with:\n                                                     ;;       #:combine (lambda (b.0 b.1) b.0)\n                                                     #:combine/key\n                                                     (lambda (k b.0 b.1)\n                                                       (if (equal? b.0 b.1)\n                                                         b.0\n                                                         (error \"incompatible initial bounds:\" k b.0 b.1)))))\n                                       (hash) ixs)))\n         (method-lambda\n           ((done?)      (null? ixs))\n           ((bounds)     col=>bounds)\n           ((statistics) (apply hash-union (hash)\n                                (map (lambda (ix) (ix 'statistics)) ixs)\n                                #:combine statistics-intersect))\n           ((update cbs)\n            (let loop ((c=>b (foldl (lambda (cb c=>b) (hash-set c=>b (car cb) (cdr cb)))\n                                    col=>bounds cbs))\n                       (ixs.pending ixs)\n                       (ixs.updated '()))\n              (if (null? ixs.pending)\n                (table (reverse ixs.updated) c=>b)\n                (let*/and ((ix.new ((car ixs.pending) 'update c=>b))\n                           (c=>b   (hash-union c=>b (ix.new 'bounds)\n                                               #:combine (lambda (v.0 v.1) v.1))))\n                  (cond ((not (ix.new 'done?)) (loop c=>b (cdr ixs.pending) (cons ix.new ixs.updated)))\n                        ((not (ix.new 'full?)) (loop c=>b (cdr ixs.pending)              ixs.updated))\n                        (else                  (table '() c=>b)))))))))))\n\n;; TODO: reorganize to implement dicts and sets\n;; - sets can be thought of as dicts with empty value\n;; - could use same representation both for relations and for terms of these types\n;; - in terms of btrees, tries\n;; - possibly also hash tables for small cardinalities\n;; - consider manipulating low-level memory buffers via FFI\n\n;; TODO: define a finite-map that is only referenceable by key and immediately provides a single instance\n;;       of all columns (because the other columns are not sorted/deduped without the key)\n\n;; TODO: this should be called trie:row-major\n(define (tabular-trie vref key-column nonkey-columns types row-count)\n  (define (ref mask i)          (vector-ref (vref i) mask))\n  (define ((make-i<  mask v) i) (any  mask v) i) (any= mask v) i) (any<=? v (ref mask i)))\n  (define (update/pending c=>b.new cols.pending col=>bounds mask start end)\n    (define c.next    (car cols.pending))\n    (define b.current (hash-ref col=>bounds c.next bounds.any))\n    (define b         (bounds-intersect (hash-ref c=>b.new c.next bounds.any)\n                                        b.current))\n    (define (update/bounds lb lbi? ub ubi?)\n      (define start.new (bisect-next start end ((if lbi? make-i< make-i<=) mask lb)))\n      (define end.new (if (< start.new end)\n                        (bisect-prev start end ((if ubi? make-i> make-i>=) mask ub))\n                        start.new))\n      (update/trim c=>b.new cols.pending col=>bounds mask start.new end.new))\n    (cond ((equal? b b.current) (new cols.pending col=>bounds mask start end))\n          (else                 (update/bounds (bounds-lb b)\n                                               (bounds-lb-inclusive? b)\n                                               (bounds-ub b)\n                                               (bounds-ub-inclusive? b)))))\n  (define (update/trim c=>b.new cols.pending col=>bounds mask start end)\n    (if (null? cols.pending)\n      (new '() (hash-set col=>bounds key-column (bounds start #t (- end 1) #t))\n           mask start end)\n      (and (< start end)\n           (let ((c.next (car cols.pending))\n                 (lb     (ref mask start))\n                 (ub     (ref mask (- end 1))))\n             (if (equal? lb ub)\n               (update/trim c=>b.new (cdr cols.pending)\n                            (hash-set col=>bounds c.next (bounds lb #t lb #t))\n                            (+ mask 1) start end)\n               (let ((col=>bounds (hash-set (hash-set col=>bounds c.next (bounds lb #t ub #t))\n                                            key-column (if (= start (- end 1))\n                                                         start\n                                                         (bounds start #t (- end 1) #t)))))\n                 (update/pending c=>b.new cols.pending col=>bounds mask start end)))))))\n  (define (new cols.pending col=>bounds mask start end)\n    (method-lambda\n      ;; TODO: this will be incorrect if the nonkey-columns do not map to a single key, which\n      ;; can happen when the table includes the key-column as an attribute.\n      ((done?)  (null? cols.pending))\n      ;; TODO: allow full? to be #t when nonkey-columns include all attributes\n      ((full?)  (not (not key-column)))\n      ((bounds) col=>bounds)\n      ((statistics)\n       (define ratio (/ (- end start) row-count))\n       (make-immutable-hash\n         (cons (cons (car cols.pending)\n                     (statistics ratio\n                                 (let ((v.lb (ref mask start))\n                                       (v.ub (ref mask (- end 1))))\n                                   (if (equal? v.lb v.ub)\n                                     1\n                                     (+ 2 (- (bisect-prev start end (make-i>= mask v.ub))\n                                             (bisect-next start end (make-i<= mask v.lb))))))))\n               (if key-column\n                 (list (cons key-column (statistics ratio (- end start))))\n                 '()))))\n      ((update c=>b)\n       (cond (key-column\n               (define b.key.0 (hash-ref col=>bounds key-column bounds.any))\n               (define b       (hash-ref c=>b        key-column bounds.any))\n               (cond ((not (equal? b b.key.0))\n                      ;; Assume these bounds will always be numbers in c=>b\n                      (let ((lb (let ((lb.0 (bounds-lb b)))\n                                  (cond ((not (integer? lb.0))    (ceiling lb.0))\n                                        ((bounds-lb-inclusive? b)          lb.0)\n                                        (else                           (+ lb.0 1)))))\n                            (ub (let ((ub.0 (bounds-ub b)))\n                                  (cond ((not (integer? ub.0))    (floor ub.0))\n                                        ((bounds-ub-inclusive? b)        ub.0)\n                                        (else                         (- ub.0 1))))))\n                        (and (<= start lb ub) (< ub end)\n                             (update/trim c=>b cols.pending col=>bounds mask lb (+ ub 1)))))\n                     (else (update/pending c=>b cols.pending col=>bounds mask start end))))\n             (else         (update/pending c=>b cols.pending col=>bounds mask start end))))))\n  (update/trim (hash) nonkey-columns (hash) 0 0 row-count))\n\n(define (table-length t key)       (statistics-cardinality (hash-ref (t 'statistics) key)))\n(define (table-ref    t key i col) (bounds-lb (hash-ref ((t 'update (hash key (bounds i #t i #t))) 'bounds) col)))\n\n(define (table/port/offsets table.offsets key-col cols types thunk.in)\n  (define type `#(tuple ,@types))\n  (lambda ()\n    (define offsets (table.offsets))\n    (and offsets\n         (let ((in (thunk.in)))\n           (define (ref i)\n             (file-position in (table-ref offsets #t i 'offset))\n             (decode in type))\n           (tabular-trie ref key-col cols types (table-length offsets #t))))))\n\n(define (table/bytes/offsets table.offsets key-col cols types bs)\n  (define (thunk.in) (open-input-bytes bs))\n  (table/port/offsets table.offsets key-col cols types thunk.in))\n\n(define (table/port len key-col cols types thunk.in)\n  (define type `#(tuple ,@types))\n  (define width (sizeof type (void)))\n  (lambda ()\n    (define in (thunk.in))\n    (define (ref i) (file-position in (* i width)) (decode in type))\n    (tabular-trie ref key-col cols types len)))\n\n(define (table/bytes key-col cols types bs)\n  (define (thunk.in) (open-input-bytes bs))\n  (table/port (quotient (bytes-length bs) (sizeof types (void)))\n              key-col cols types thunk.in))\n\n(define ((table/vector key-col cols types v))\n  (tabular-trie (lambda (i) (vector-ref v i)) key-col cols types (vector-length v)))\n\n(define (vector-table? types v)\n  (define v< (compare->compare types)))\n  (define i (- (vector-length v) 1))\n  (or (<= i 0) (let loop ((i (- i 1)) (next (vector-ref v i)))\n                 (define current (vector-ref v i))\n                 (and (v< current next) (or (= i 0) (loop (- i 1) current))))))\n(define (vector-table-sort! types v)\n  (vector-sort! v (compare->compare `#(tuple ,@types)))))\n(define (vector-dedup v) (list->vector (s-dedup (vector->list v))))\n\n;; TODO: switch back to file->bytes once Racket IO bug is fixed\n(define (file->bytes2 file-name)\n  (define size (file-size file-name))\n  (define bs (make-bytes size))\n  (call-with-input-file\n    file-name\n    (lambda (in)\n      (let loop ((i 0))\n        (cond ((= i size) bs)\n              (else (define end (+ i (min 1073741824\n                                          (- size i))))\n                    (read-bytes! bs in i end)\n                    (loop end)))))))\n\n(define (file-stats path)\n  (and (file-exists? path)\n       `((size . ,(file-size path))\n         (time . ,(file-or-directory-modify-seconds path)))))\n\n(define (table/metadata retrieval-type directory-path info-alist)\n  (define info         (make-immutable-hash info-alist))\n  (define path-prefix  (path->string (build-path directory-path (hash-ref info 'file-prefix))))\n  (define fname.value  (value-table-file-name  path-prefix))\n  (define fname.offset (offset-table-file-name path-prefix))\n  (define offset-type  (hash-ref info 'offset-type))\n  (define fstat.value  (file-stats fname.value))\n  (define fstat.offset (and offset-type (file-stats fname.offset)))\n  (define key-name     (hash-ref info 'key-name))\n  (define column-names (hash-ref info 'column-names))\n  (define column-types (hash-ref info 'column-types))\n  (define len          (hash-ref info 'length))\n  (unless (set=? fstat.value (hash-ref info 'value-file))\n    (error \"value file stats do not match metadata:\" fname.value\n           'file: fstat.value 'metadata: (hash-ref info 'value-file)))\n  (when offset-type\n    (unless (set=? fstat.offset (hash-ref info 'offset-file))\n      (error \"offset file stats do not match metadata:\" fname.offset\n             'file: fstat.offset 'metadata: (hash-ref info 'offset-file))))\n  (case retrieval-type\n    ((disk) (define (open-input-file/memoize fname)\n              (define cell.port (make-thread-cell #f))\n              (lambda ()\n                (or (thread-cell-ref cell.port)\n                    (let ((in (open-input-file fname)))\n                      (thread-cell-set! cell.port in)\n                      in))))\n            (define thunk.in.value (open-input-file/memoize fname.value))\n            (if offset-type\n              (table/port/offsets\n                (table/port len #t '(offset) `(,offset-type)\n                            (open-input-file/memoize fname.offset))\n                key-name column-names column-types thunk.in.value)\n              (table/port len key-name column-names column-types thunk.in.value)))\n    ((bytes) (define bs.value (file->bytes2 fname.value))\n             (if offset-type\n               (table/bytes/offsets\n                 (table/bytes #t '(offset) `(,offset-type)\n                              (file->bytes2 fname.offset))\n                 key-name column-names column-types bs.value)\n               (table/bytes key-name column-names column-types bs.value)))\n    ((scm) (let/files ((in.value fname.value)) ()\n             (table/vector\n               key-name column-names column-types\n               (list->vector\n                 (s-take #f (s-decode in.value `#(tuple ,@column-types)))))))\n    (else (error \"unknown retrieval type:\" retrieval-type))))\n\n(define (bisect start end i<)\n  (let loop ((start start) (end end))\n    (if (<= end start) end\n      (let ((i (+ start (quotient (- end start) 2))))\n        (if (i< i) (loop (+ 1 i) end) (loop start i))))))\n\n(define (bisect-next start end i<)\n  (define i (- start 1))\n  (let loop ((offset 1))\n    (define next (+ i offset))\n    (cond ((and (< next end) (i< next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (next (+ i o)))\n                    (cond ((= o 0)                      (+ i 1))\n                          ((and (< next end) (i< next)) (loop next o))\n                          (else                         (loop i    o)))))))))\n\n(define (bisect-prev start end i>)\n  (define i end)\n  (let loop ((offset 1))\n    (define next (- i offset))\n    (cond ((and (>= next start) (i> next)) (loop (arithmetic-shift offset 1)))\n          (else (let loop ((i i) (o offset))\n                  (let* ((o (arithmetic-shift o -1)) (n (- i o)))\n                    (cond ((= o 0)                   i)\n                          ((and (>= n start) (i> n)) (loop n o))\n                          (else                      (loop i o)))))))))\n\n(define (value-table-file-name  prefix) (string-append prefix \".value.table\"))\n(define (offset-table-file-name prefix) (string-append prefix \".offset.table\"))\n(define metadata-file-name              \"metadata.scm\")\n\n(define (tabulator directory-path file-prefix\n                   column-names column-types key-name)\n  (define (unique?! as) (unless (= (length (remove-duplicates as)) (length as))\n                          (error \"duplicates:\" as)))\n  (unless (= (length column-names) (length column-types))\n    (error \"mismatching column names and types:\" column-names column-types))\n  (unique?! column-names)\n  (when (member key-name column-names)\n    (error \"key name must be distinct:\" key-name column-names))\n  (define row-type column-types)\n  (define row<     (compare->compare row-type)))\n  (define row-size (sizeof row-type (void)))\n  (define path-prefix (path->string (build-path directory-path file-prefix)))\n  (define value-file-name  (value-table-file-name path-prefix))\n  (define offset-file-name (and (not row-size)\n                                (offset-table-file-name path-prefix)))\n  (define tsorter (sorter #t value-file-name offset-file-name row-type row<))\n  (method-lambda\n    ((put! x) (tsorter 'put! x))\n    ((close) (match-define (cons offset-type item-count) (tsorter 'close))\n             `((file-prefix    . ,file-prefix)\n               (value-file     . ,(file-stats value-file-name))\n               (offset-file    . ,(and offset-file-name\n                                       (file-stats offset-file-name)))\n               (offset-type    . ,offset-type)\n               (length         . ,item-count)\n               (column-names   . ,column-names)\n               (column-types   . ,column-types)\n               (key-name       . ,key-name)))))\n\n(define (sorter dedup? value-file-name offset-file-name? type value<)\n  (define fname-sort-value  (string-append value-file-name \".value.sort\"))\n  (define fname-sort-offset (string-append value-file-name \".offset.sort\"))\n  (define out-value         (open-output-file value-file-name))\n  (define out-offset\n    (and offset-file-name?  (open-output-file offset-file-name?)))\n  (define out-sort-value    (open-output-file fname-sort-value))\n  (define out-sort-offset   (open-output-file fname-sort-offset))\n  (define ms (multi-sorter out-sort-value out-sort-offset type value<))\n  (method-lambda\n    ((put! value) (ms 'put! value))\n    ((close)\n     (match-define (vector initial-item-count chunk-count v?) (ms 'close))\n     (close-output-port out-sort-value)\n     (close-output-port out-sort-offset)\n     (define omax (if v? (sizeof `#(array ,initial-item-count ,type) v?)\n                    (file-size fname-sort-value)))\n     (define otype (and out-offset (nat-type/max omax)))\n     (define item-count\n       (cond (v? (let loop ((prev #f) (i 0) (count 0))\n                   (if (= i initial-item-count) count\n                     (let ((x (vector-ref v? i)))\n                       (cond ((not (and dedup? (< 0 i) (equal? x prev)))\n                              (when out-offset\n                                (encode out-offset otype (file-position\n                                                           out-value)))\n                              (encode out-value type x)\n                              (loop x (+ i 1) (+ count 1)))\n                             (else (loop x (+ i 1) count)))))))\n             (else (let/files ((in fname-sort-value)\n                               (in-offset fname-sort-offset)) ()\n                     (multi-merge dedup? out-value out-offset type otype value<\n                                  chunk-count in in-offset)))))\n     (delete-file fname-sort-value)\n     (delete-file fname-sort-offset)\n     (close-output-port out-value)\n     (when out-offset (close-output-port out-offset))\n     (cons otype item-count))))\n\n(define (multi-sorter out-chunk out-offset type value<)\n  (define buffer-size (current-config-ref 'buffer-size))\n  (let ((v (make-vector buffer-size)) (chunk-count 0) (item-count 0) (i 0))\n    (method-lambda\n      ((put! value) (vector-set! v i value)\n                    (set! i (+ i 1))\n                    (when (= i buffer-size)\n                      (vector-sort! v value<)\n                      (for ((x (in-vector v))) (encode out-chunk type x))\n                      (encode out-offset 'nat (file-position out-chunk))\n                      (set! item-count  (+ item-count buffer-size))\n                      (set! chunk-count (+ chunk-count 1))\n                      (set! i           0)))\n      ((close) (vector-sort! v value< 0 i)\n               (cond ((and (< 0 chunk-count) (= i 0))\n                      (vector item-count chunk-count #f))\n                     ((< 0 chunk-count)\n                      (for ((i (in-range i)))\n                        (encode out-chunk type (vector-ref v i)))\n                      (encode out-offset 'nat (file-position out-chunk))\n                      (vector (+ item-count i) (+ chunk-count 1) #f))\n                     (else (vector i 0 v)))))))\n\n(define (multi-merge\n          dedup? out out-offset type otype v< chunk-count in in-offset)\n  (define (s< sa sb) (v< (car sa) (car sb)))\n  (define (s-chunk pos end)\n    (cond ((<= end pos) '())\n          (else (file-position in pos)\n                (cons (decode in type) (let ((pos (file-position in)))\n                                         (thunk (s-chunk pos end)))))))\n  (define heap (make-vector chunk-count))\n  (let loop ((hi 0) (start 0)) (when (< hi chunk-count)\n                                 (define end (decode in-offset 'nat))\n                                 (vector-set! heap hi (s-chunk start end))\n                                 (loop (+ hi 1) end)))\n  (heap! s< heap chunk-count)\n  (let loop ((prev #f) (i 0) (hend chunk-count))\n    (if (= hend 0) i\n      (let* ((top (heap-top heap)) (x (car top)) (top (s-force (cdr top))))\n        (loop x (cond ((not (and dedup? (< 0 i) (equal? x prev)))\n                       (when out-offset (encode out-offset otype\n                                                (file-position out)))\n                       (encode out type x)\n                       (+ i 1))\n                      (else i))\n              (cond ((null? top) (heap-remove!  s< heap hend)  (- hend 1))\n                    (else        (heap-replace! s< heap hend top) hend)))))))\n\n(define (heap-top h) (vector-ref h 0))\n(define (heap! ? h end)\n  (let loop ((i (- (quotient end 2) 1)))\n    (when (<= 0 i) (heap-sink! ? h end i) (loop (- i 1)))))\n(define (heap-remove! ? h end)\n  (vector-set! h 0 (vector-ref h (- end 1))) (heap-sink! ? h (- end 1) 0))\n(define (heap-replace! ? h end top)\n  (vector-set! h 0 top)                      (heap-sink! ? h    end    0))\n(define (heap-sink! ? h end i)\n  (let loop ((i i))\n    (let ((ileft (+ i i 1)) (iright (+ i i 2)))\n      (cond ((<= end ileft))  ;; done\n            ((<= end iright)\n             (let ((p (vector-ref h i)) (l (vector-ref h ileft)))\n               (when (? l p) (vector-set! h i l) (vector-set! h ileft p))))\n            (else (let ((p (vector-ref h i))\n                        (l (vector-ref h ileft)) (r (vector-ref h iright)))\n                    (cond ((? l p) (cond ((? r l) (vector-set! h i r)\n                                                  (vector-set! h iright p)\n                                                  (loop iright))\n                                         (else (vector-set! h i l)\n                                               (vector-set! h ileft p)\n                                               (loop ileft))))\n                          ((? r p) (vector-set! h i r)\n                                   (vector-set! h iright p)\n                                   (loop iright)))))))))\n(define (heap-add! ? h end v)\n  (let loop ((i end))\n    (if (= i 0) (vector-set! h i v)\n      (let* ((iparent (- (quotient (+ i 1) 2) 1))\n             (pv      (vector-ref h iparent)))\n        (cond ((? v pv) (vector-set! h i pv) (loop iparent))\n              (else     (vector-set! h i v)))))))\n\n(define (list-arranger input-names output-names)\n  (define ss.in    (generate-temporaries input-names))\n  (define name=>ss (make-immutable-hash (map cons input-names ss.in)))\n  (define ss.out   (map (lambda (n) (hash-ref name=>ss n)) output-names))\n  (eval-syntax #`(lambda (row)\n                   (match-define (list #,@ss.in) row)\n                   (list #,@ss.out))))\n\n(define (table-materializer source-names path.dir fprefix\n                            column-names column-types key-name)\n  (define t (tabulator path.dir fprefix column-names column-types key-name))\n  (define transform (list-arranger source-names column-names))\n  (method-lambda\n    ((put! x) (t 'put! (transform x)))\n    ((close)  (t 'close))))\n\n(define (materialize-index-tables!\n          path.dir source-fprefix name->type source-names index-descriptions)\n  (cond ((null? index-descriptions) '())\n        (else\n          (define threshold (current-config-ref 'progress-logging-threshold))\n          (define index-ms\n            (map (lambda (td)\n                   (define fprefix      (alist-ref td 'file-prefix))\n                   (define column-names (alist-ref td 'column-names))\n                   (define column-types (map name->type column-names))\n                   (table-materializer source-names path.dir fprefix\n                                       column-names column-types #f))\n                 index-descriptions))\n          (logf \"Materializing ~s index table(s) from primary:\\n\"\n                (length index-ms))\n          (for-each (lambda (td) (pretty-write (alist-ref td 'column-names)))\n                    index-descriptions)\n          (let/files ((in (value-table-file-name source-fprefix))) ()\n            (define src (s-decode in (map name->type (cdr source-names))))\n            (time (s-each (lambda (x)\n                            (let ((count (car x)))\n                              (when (= 0 (remainder count threshold))\n                                (logf \"ingested ~s rows\\n\" count))\n                              (for-each (lambda (m) (m 'put! x)) index-ms)))\n                          (s-enumerate 0 src))))\n          (logf \"Processing all rows\\n\")\n          (map (lambda (m) (time (m 'close))) index-ms))))\n\n(define (valid-key-type? t)\n  (match t\n    ((or #f 'nat 'number `#(nat ,_)) #t)\n    (_                               #f)))\n\n(define (materializer path.dir source-info attribute-names attribute-types key-name\n                      table-layouts)\n  (define name=>type (make-immutable-hash (map cons attribute-names attribute-types)))\n  (define index-layouts        (cdr table-layouts))\n  (define primary-column-names (car table-layouts))\n  (define primary-source-names (cons key-name primary-column-names))\n  (define primary-column-types (map (lambda (n) (hash-ref name=>type n))\n                                    primary-column-names))\n  (make-directory* path.dir)\n  (define path.metadata (path->string (build-path path.dir metadata-file-name)))\n  (define primary-fprefix \"primary\")\n  (define primary-fname (path->string (build-path path.dir primary-fprefix)))\n  (define index-fprefixes\n    (map (lambda (i) (string-append \"index.\" (number->string i)))\n         (range (length index-layouts))))\n  (define primary-t (tabulator path.dir primary-fprefix\n                               primary-column-names primary-column-types key-name))\n  (method-lambda\n    ((put! x) (primary-t 'put! x))\n    ((close) (define primary-info (primary-t 'close))\n             (define key-type (nat-type/max (alist-ref primary-info 'length)))\n             (define name->type\n               (let ((name=>type (hash-set name=>type key-name key-type)))\n                 (lambda (n) (hash-ref name=>type n))))\n             (define index-infos\n               (materialize-index-tables!\n                 path.dir primary-fname name->type primary-source-names\n                 (map (lambda (fprefix td) `((file-prefix . ,fprefix)\n                                             (column-names . ,td)))\n                      index-fprefixes index-layouts)))\n             (write-metadata path.metadata attribute-names attribute-types\n                             primary-info index-infos source-info))))\n\n(define (write-metadata path attribute-names attribute-types primary-info index-infos source-info)\n  (let/files () ((out.metadata path))\n    (pretty-write `((metadata-format-version . ,metadata-format-version.latest)\n                    (attribute-names         . ,attribute-names)\n                    (attribute-types         . ,attribute-types)\n                    (primary-table           . ,primary-info)\n                    (index-tables            . ,index-infos)\n                    (source-info             . ,source-info))\n                  out.metadata)))\n\n(define (update-metadata path info)\n  (define path.backup (string-append path \".backup\"))\n  (when (file-exists? path.backup)\n    (error \"backup path already exists:\" path.backup))\n  (rename-file-or-directory path path.backup)\n  (apply write-metadata path\n         (map (lambda (k) (hash-ref info k))\n              '(attribute-names attribute-types primary-table index-tables source-info)))\n  (delete-file path.backup))\n\n(define (metadata/2020-12-19.0 info)\n  (define source-info (make-immutable-hash (hash-ref info 'source-info)))\n  (define source-info.new\n    (foldl (lambda (k v source-info) (hash-set source-info k v))\n           (hash-remove source-info 'transform)\n           '(map/append map filter)\n           (list (hash-ref source-info 'map/append #f)\n                 (hash-ref source-info 'map        (hash-ref source-info 'transform #f))\n                 (hash-ref source-info 'filter     #f))))\n  (foldl (lambda (k v info) (hash-set info k v))\n         info\n         '(metadata-format-version source-info)\n         `(2021-03-18.0\n           ,(if (hash-has-key? source-info.new 'path)\n              (map (lambda (k) (cons k (hash-ref source-info.new k)))\n                   '(path format header stats map/append map filter))\n              (map (lambda (k) (cons k (hash-ref source-info.new k)))\n                   '(stream map/append map filter))))))\n\n(define (metadata/2021-03-18.0 info)\n  ;; TODO: define an appropriate transformtion once this is no longer the latest version\n  info)\n\n;; TODO: when new metadata formats are introduced, update the old handlers to\n;; have them transform an instance of the old format into an instance of the\n;; newest format.  This can be done by composing handlers.\n\n;; TODO: register new metadata-format-version handlers here\n(define metadata-format-version.latest '2021-03-18.0)\n(define metadata/format-version\n  (hash '2021-03-18.0 metadata/2021-03-18.0\n        '2020-12-19.0 metadata/2020-12-19.0))\n\n(define (read-metadata path)\n  (define info.0 (let/files ((in path)) () (read in)))\n  (when (eof-object? info.0) (error \"corrupt relation metadata:\" path))\n  (define info.1 (make-immutable-hash info.0))\n  (define info ((hash-ref metadata/format-version\n                          (hash-ref info.1 'metadata-format-version '2020-12-19.0))\n                info.1))\n  (define diff\n    (foldl (lambda (k diff)\n             (cond ((not (hash-has-key? info   k)) (cons `(,k old: ,(hash-ref info.1 k)) diff))\n                   ((not (hash-has-key? info.1 k)) (cons `(,k new: ,(hash-ref info   k)) diff))\n                   (else (define v.new (hash-ref info   k))\n                         (define v.old (hash-ref info.1 k))\n                         (if (equal? v.new v.old) diff\n                           (cons `(,k old: ,v.old new: ,v.new) diff)))))\n           '()\n           (set->list (set-union (list->set (hash-keys info))\n                                 (list->set (hash-keys info.1))))))\n  (define should-update?\n    (and (not (null? diff))\n         (policy-allow?\n           (current-config-ref 'update-policy)\n           (lambda ()\n             (printf \"Current ~s is written in an old format:\\n\" path)\n             (for-each pretty-write diff))\n           \"Update ~s to the latest format?\" (list path))))\n  (when should-update? (update-metadata path info))\n  info)\n\n(define (update-materialization! path.dir info tables.added tables.removed)\n  (define path.metadata        (path->string\n                                 (build-path path.dir metadata-file-name)))\n  (define path.metadata.backup (string-append path.metadata \".backup\"))\n  (define attribute-names      (hash-ref info 'attribute-names))\n  (define attribute-types      (hash-ref info 'attribute-types))\n  (define source-info          (hash-ref info 'source-info))\n  (define primary-info         (hash-ref info 'primary-table))\n  (define index-infos          (hash-ref info 'index-tables))\n  (define primary-key-name     (alist-ref primary-info 'key-name))\n  (define primary-column-names (alist-ref primary-info 'column-names))\n  (define source-fprefix\n    (path->string (build-path path.dir (alist-ref primary-info 'file-prefix))))\n  (define source-names (cons primary-key-name primary-column-names))\n  (define key-type (nat-type/max (alist-ref primary-info 'length)))\n  (define name=>type (make-immutable-hash\n                       (cons (cons primary-key-name key-type)\n                             (map cons attribute-names attribute-types))))\n  (define (name->type n) (hash-ref name=>type n))\n  (define cols=>info\n    (make-immutable-hash\n      (map (lambda (info.it) (cons (alist-ref info.it 'column-names) info.it))\n           (hash-ref info 'index-tables))))\n  (define index-infos.current\n    (hash-values (foldl (lambda (cols c=>i) (hash-remove c=>i cols))\n                        cols=>info tables.removed)))\n  (rename-file-or-directory path.metadata path.metadata.backup)\n  (for-each\n    (lambda (cols)\n      (define info    (hash-ref cols=>info cols))\n      (define fprefix (alist-ref info 'file-prefix))\n      (define fname.v\n        (path->string (build-path path.dir (value-table-file-name  fprefix))))\n      (define fname.o\n        (path->string (build-path path.dir (offset-table-file-name fprefix))))\n      (logf \"Deleting ~s\\n\" fname.v)\n      (delete-file fname.v)\n      (when (alist-ref info 'offset-file)\n        (logf \"Deleting ~s\\n\" fname.o)\n        (delete-file fname.o)))\n    tables.removed)\n  (define index-descriptions.added\n    (let loop ((colss tables.added) (i 0))\n      (if (null? colss) '()\n        (let ((fprefix (string-append \"index.\" (number->string i))))\n          (if (file-exists?\n                (build-path path.dir (value-table-file-name fprefix)))\n            (loop colss (+ i 1))\n            (cons `((file-prefix  . ,fprefix) (column-names . ,(car colss)))\n                  (loop (cdr colss) (+ i 1))))))))\n  (define index-infos.new\n    (materialize-index-tables! path.dir source-fprefix name->type\n                               source-names index-descriptions.added))\n  (write-metadata path.metadata attribute-names attribute-types\n                  primary-info (append index-infos.current index-infos.new)\n                  source-info)\n  (delete-file path.metadata.backup))\n\n(define (materialization/vector vector.in sort? dedup? info)\n  (define key-name        (hash-ref info 'key-name))\n  (define attribute-names (hash-ref info 'attribute-names))\n  (define attribute-types (hash-ref info 'attribute-types))\n  (define table-layouts   (hash-ref info 'table-layouts))\n  (define name=>type      (hash-set (make-immutable-hash\n                                      (map cons attribute-names attribute-types))\n                                    key-name 'nat))\n  (define (name->type n) (hash-ref name=>type n))\n  (define primary-column-names (car table-layouts))\n  (define primary-column-types (map name->type primary-column-names))\n  (define primary-source-names (cons key-name primary-column-names))\n  (when sort? (vector-table-sort! primary-column-types vector.in))\n  (define primary-v (if dedup? (vector-dedup vector.in) vector.in))\n  (define primary-t (table/vector key-name primary-column-names\n                                  primary-column-types primary-v))\n  (define index-ts\n    (let* ((ss.sources (generate-temporaries primary-source-names))\n           (name=>ss   (make-immutable-hash\n                         (map cons primary-source-names ss.sources)))\n           (name->ss   (lambda (n) (hash-ref name=>ss n))))\n      (map (lambda (column-names)\n             (define column-types (map name->type column-names))\n             (define ss.columns   (map name->ss   column-names))\n             (define index-src\n               (let ((transform\n                       (eval-syntax\n                         #`(lambda (#,(car ss.sources) row)\n                             (match-define (vector #,@(cdr ss.sources)) row)\n                             (vector #,@ss.columns))))\n                     (iv (make-vector (vector-length primary-v))))\n                 (for ((i   (in-range (vector-length primary-v)))\n                       (row (in-vector primary-v)))\n                   (vector-set! iv i (transform i row)))\n                 iv))\n             (vector-table-sort! column-types index-src)\n             (table/vector #f column-names column-types\n                           (vector-dedup index-src)))\n           (cdr table-layouts))))\n  (list info (table (cons primary-t index-ts))))\n\n(define (materialization/path relation-name retrieval-type path path.dir info)\n  (unless (directory-exists? path.dir)\n    (error \"materialized relation directory does not exist:\" path.dir))\n  (define attribute-names    (hash-ref info 'attribute-names))\n  (define attribute-types    (hash-ref info 'attribute-types))\n  (define primary-info-alist (hash-ref info 'primary-table))\n  (define primary-info       (make-immutable-hash primary-info-alist))\n  (define primary-t          (table/metadata retrieval-type path.dir primary-info-alist))\n  (define key-name           (hash-ref primary-info 'key-name))\n  (define index-ts\n    (map (lambda (info) (table/metadata retrieval-type path.dir info))\n         (hash-ref info 'index-tables '())))\n  (list (foldl (lambda (k v info) (hash-set info k v)) info\n               '(    relation-name key-name retrieval-type)\n               (list relation-name key-name retrieval-type))\n        (table (cons primary-t index-ts))))\n\n(define (materialization . pargs)\n  (define kwargs          (make-immutable-hash (plist->alist pargs)))\n  (define key-name        (hash-ref kwargs 'key-name #t))\n  (define attribute-names (hash-ref kwargs 'attribute-names))\n  (define attribute-types (hash-ref kwargs 'attribute-types\n                                    (map (lambda (n)\n                                           (if (equal? n key-name) 'nat #f))\n                                         attribute-names)))\n  (define table-layouts\n    (append (hash-ref kwargs 'tables `(,(remove key-name attribute-names)))\n            (map (lambda (cols) (append cols (list key-name)))\n                 (hash-ref kwargs 'indexes '()))))\n  (unless key-name (error \"key-name cannot be #f:\" pargs))\n  (unless (= (length (remove-duplicates attribute-names))\n             (length attribute-names))\n    (error \"duplicate attribute-names:\" attribute-names))\n  (unless (= (length attribute-names) (length attribute-types))\n    (error \"mismatching attribute names and types:\"\n           attribute-names attribute-types))\n  (when (null? table-layouts)\n    (error \"empty list of table layouts for:\" attribute-names))\n  (let ((primary-column-names (car table-layouts))\n        (key-type             (alist-ref (map cons attribute-names attribute-types)\n                                         key-name 'nat)))\n    (when (member key-name primary-column-names)\n      (error \"key-name should not be a primary table column:\"\n             key-name primary-column-names))\n    (unless (set=? (set-remove attribute-names key-name) primary-column-names)\n      (error \"primary columns must include all non-key attributes:\"\n             (set->list (set-remove (list->set attribute-names) key-name))\n             (set->list (list->set primary-column-names))))\n    (unless (valid-key-type? key-type)\n      (error \"invalid key type:\" key-type key-name)))\n  (define path           (hash-ref kwargs 'path #f))\n  (define path.dir       (and path (current-config-relation-path path)))\n  (define path.metadata  (and path.dir (path->string (build-path path.dir metadata-file-name))))\n  (define (get-metadata) (and path.metadata (directory-exists? path.dir) (read-metadata path.metadata)))\n  (define metadata       (get-metadata))\n  (define src:vector.0   (hash-ref kwargs 'source-vector    #f))\n  (define src:stream     (hash-ref kwargs 'source-stream    #f))\n  (define src:path.0     (hash-ref kwargs 'source-file-path #f))\n  (define src:path       (and src:path.0 (current-config-relation-path src:path.0)))\n  (when (< 1 (length (filter-not not (list src:vector.0 src:stream src:path.0))))\n    (error \"relation cannot specify multiple data sources:\" pargs))\n  (let ((map/append-code (hash-ref kwargs 'map/append #f))\n        (map-code        (hash-ref kwargs 'map        #f))\n        (filter-code     (hash-ref kwargs 'filter     #f)))\n    (when (and map/append-code (or map-code filter-code))\n      (error \"map/append should not be used with map or filter:\"\n             `((map/append ,(code->info map/append-code))\n               (map        ,(code->info map-code))\n               (filter     ,(code->info filter-code))))))\n  (define src:format (or (hash-ref kwargs 'source-file-format #f)\n                         (and src:path.0 (path->format src:path.0))))\n  (define src:header (let ((header (hash-ref kwargs 'source-file-header '())))\n                       (if (pair? header)\n                         (map (lambda (s) (if (symbol? s) (symbol->string s) s))\n                              header)\n                         header)))\n  (define src:vector\n    (or src:vector.0\n        (and (not metadata)\n             (not src:stream)\n             (not (and src:path (file-exists? src:path)))\n             (policy-allow?\n               (current-config-ref 'allow-missing-data-policy)\n               (lambda ()\n                 (printf \"Source (~s) and processed data are both missing for ~s:\\n\"\n                         src:path.0 path))\n               \"Allow ~s to be used as an empty relation for now?\" (list path))\n             (vector))))\n  (define kwargs.1 (foldl (lambda (k v kvs) (hash-set kvs k v)) kwargs\n                          '(    path     key-name attribute-types table-layouts)\n                          (list path.dir key-name attribute-types table-layouts)))\n  (cond (src:vector\n          ;; TODO: currently only supported for vector sources\n          (define sort?  (hash-ref kwargs 'sort?  (not src:vector)))\n          (define dedup? (hash-ref kwargs 'dedup? (not src:vector)))\n          (when (and (not sort?) dedup?)\n            (error \"Cannot deduplicate without sorting:\" kwargs))\n          (materialization/vector src:vector sort? dedup?\n                                  (hash-set kwargs.1 'missing-data?\n                                            (not (hash-ref kwargs.1 'source-vector #f)))))\n        (path                       (when (or src:path.0 src:stream)\n                                      (materialize-relation! path path.dir path.metadata metadata\n                                                             src:path src:format src:header kwargs.1))\n                                    (materialization/path (hash-ref kwargs 'relation-name)\n                                                          (hash-ref kwargs 'retrieval-type 'disk)\n                                                          path path.dir (hash-set (get-metadata) 'path path.dir)))\n        ((or src:path.0 src:stream) (materialization/stream src:path src:format src:header kwargs.1))\n        (else                       (error \"missing relation path or source:\" kwargs))))\n\n(struct value+syntax (value syntax) #:prefab)\n(define-syntax-rule (value/syntax e) (value+syntax e #'e))\n(define (code->info code)\n  (cond ((procedure?    code) #t)\n        ((value+syntax? code) (syntax->datum (value+syntax-syntax code)))\n        (else                 code)))\n(define (code->value code)\n  (cond ((value+syntax? code) (value+syntax-value code))\n        (else                 code)))\n\n(define (materialization/stream path.in format header kwargs)\n  (define key-name        (hash-ref kwargs 'key-name))\n  (define attribute-names (hash-ref kwargs 'attribute-names))\n  (define attribute-types (hash-ref kwargs 'attribute-types))\n  (define table-layouts   (hash-ref kwargs 'table-layouts))\n  (define stream.in       (hash-ref kwargs 'source-stream #f))\n  (define map/append-code (hash-ref kwargs 'map/append    #f))\n  (define map-code        (hash-ref kwargs 'map           #f))\n  (define filter-code     (hash-ref kwargs 'filter        #f))\n  (define map/append?     (code->value map/append-code))\n  (define map?            (code->value map-code))\n  (define filter?         (code->value filter-code))\n  (define (materialized-stream stream)\n    (list->vector (s-take #f (s-map list->vector\n                                    (if map/append?\n                                      (s-map/append map/append? stream)\n                                      (let ((s (if map? (s-map map? stream) stream)))\n                                        (if filter? (s-filter filter? s) s)))))))\n  (materialization/vector\n    (if path.in\n      (let/files ((in path.in)) ()\n        (define stream ((format->header/port->stream format) header in))\n        (materialized-stream stream))\n      (materialized-stream (code->value stream.in)))\n    #t #t kwargs))\n\n(define (materialize-relation! path path.dir path.metadata info path.in format header kwargs)\n  (define path            (hash-ref kwargs 'path))\n  (define key-name        (hash-ref kwargs 'key-name))\n  (define attribute-names (hash-ref kwargs 'attribute-names))\n  (define attribute-types (hash-ref kwargs 'attribute-types))\n  (define table-layouts   (hash-ref kwargs 'table-layouts))\n  (define fn.in           (hash-ref kwargs 'source-file-path #f))\n  (define stream.in       (hash-ref kwargs 'source-stream    #f))\n  (define map/append-code (hash-ref kwargs 'map/append       #f))\n  (define map-code        (hash-ref kwargs 'map              #f))\n  (define filter-code     (hash-ref kwargs 'filter           #f))\n  (define threshold       (current-config-ref 'progress-logging-threshold))\n  (define path.log        (build-path path.dir \"progress.log\"))\n  (define source-info\n    (cond (path.in   `((path       . ,fn.in)\n                       (format     . ,format)\n                       (header     . ,header)\n                       (stats      . ,(or (file-stats path.in)\n                                          (and info (alist-ref (hash-ref info 'source-info '())\n                                                               'stats #f))))\n                       (map/append . ,(code->info map/append-code))\n                       (map        . ,(code->info map-code))\n                       (filter     . ,(code->info filter-code))))\n          (stream.in `((stream     . ,(code->info stream.in))\n                       (map/append . ,(code->info map/append-code))\n                       (map        . ,(code->info map-code))\n                       (filter     . ,(code->info filter-code))))\n          (else (error \"materialize-relation! missing file or stream source:\"\n                       kwargs))))\n  (define map/append? (code->value map/append-code))\n  (define map?        (code->value map-code))\n  (define filter?     (code->value filter-code))\n  (define (materialize-stream source-info stream)\n    (let ((mat (materializer path.dir source-info\n                             attribute-names attribute-types key-name\n                             table-layouts)))\n      (define count 0)\n      (time (s-each (lambda (x)\n                      (when (= 0 (remainder count threshold))\n                        (logf \"ingested ~s rows\\n\" count))\n                      (mat 'put! x)\n                      (set! count (+ count 1)))\n                    (if map/append?\n                      (s-map/append map/append? stream)\n                      (let ((s (if map? (s-map map? stream) stream)))\n                        (if filter? (s-filter filter? s) s)))))\n      (logf \"Processing ~s rows\\n\" count)\n      (time (mat 'close))\n      (logf \"Finished processing ~s rows\\n\" count)))\n  (define (materialize-source)\n    (if path.in\n      (let/files ((in path.in)) ()\n        (logf/date \"Materializing relation ~s from ~s file ~s\\n\"\n                   path format fn.in)\n        (define stream ((format->header/port->stream format) header in))\n        (materialize-stream source-info stream))\n      (begin (logf/date \"Materializing relation ~s from stream\\n\" path)\n             (materialize-stream source-info (code->value stream.in)))))\n\n  (if info\n    (let* ((source-info.old     (hash-ref info 'source-info #f))\n           (attribute-names.old (hash-ref info 'attribute-names))\n           (attribute-types.old (hash-ref info 'attribute-types))\n           (primary-table.old   (hash-ref info 'primary-table))\n           (key-name.old        (alist-ref primary-table.old 'key-name))\n           (primary-columns.old (alist-ref primary-table.old 'column-names))\n           (primary-columns.new (car table-layouts)))\n      (unless (equal? attribute-names attribute-names.old)\n        (error \"new relation attributes are incompatible with old:\" path\n               'new: attribute-names 'old: attribute-names.old))\n      (define stale-fields.0\n        (map (lambda (desc)\n               (match-define (list key new old) desc)\n               `(,key new: ,new old: ,old))\n             (filter\n               (lambda (desc)\n                 (match-define (list _ new old) desc)\n                 (not (equal? new old)))\n               `((source-info     ,source-info     ,source-info.old)\n                 (attribute-types ,attribute-types ,attribute-types.old)\n                 (key-name        ,key-name        ,key-name.old)\n                 (primary-table   ,primary-columns.new\n                                  ,primary-columns.old)))))\n      (define update-policy  (current-config-ref 'update-policy))\n      (define cleanup-policy (current-config-ref 'cleanup-policy))\n      (define stale-fields\n        (if (and (equal? '(source-info) (map car stale-fields.0))\n                 (policy-allow?\n                   update-policy\n                   (lambda ()\n                     (printf \"Existing source-info for relation ~s is stale:\\n\" path)\n                     (for-each pretty-write stale-fields.0))\n                   \"Update ~s metadata with new source-info without rematerializing?\" (list path)))\n          (begin (printf \"Updating ~s\" path.metadata)\n                 (update-metadata path.metadata (hash-set info 'source-info source-info))\n                 (printf \"Update of ~s finished\" path.metadata)\n                 '())\n          stale-fields.0))\n      (define allow-update?\n        (or (null? stale-fields)\n            (policy-allow?\n              update-policy\n              (lambda ()\n                (printf \"Existing data for relation ~s is stale:\\n\" path)\n                (for-each pretty-write stale-fields))\n              \"Update ~s?\" (list path))))\n      (cond ((and (pair? stale-fields) allow-update?)\n             (printf \"Updating ~s\\n\" path)\n             (define path.backup (string-append path.dir \".backup\"))\n             (when (directory-exists? path.backup)\n               (error \"backup path already exists:\" path.backup))\n             (rename-file-or-directory path.dir path.backup)\n             (materialize-source)\n             (printf \"Rematerialization of ~s finished\\n\" path)\n             (when (directory-exists? path.backup)\n               (if (or (equal? cleanup-policy 'always)\n                       (and (equal? cleanup-policy 'interactive)\n                            (printf \"Delete backup directory ~s? [y/n]: \"\n                                    path.backup)\n                            (case (read)\n                              ((y Y yes Yes YES) #t)\n                              (else              #f))))\n                 (begin (printf \"Deleting ~s\\n\" path.backup)\n                        (delete-directory/files path.backup #:must-exist? #f))\n                 (printf \"Not deleting ~s\\n\" path.backup))))\n            ((not allow-update?)\n             (printf \"Due to stale data, will not rematerialize ~s\\n\" path))\n            (else\n              (define colss.current\n                (map (lambda (info.it) (alist-ref info.it 'column-names))\n                     (hash-ref info 'index-tables)))\n              (define colss.new (cdr table-layouts))\n              (define (cols-current? cols) (member cols colss.current))\n              (define (cols-new?     cols) (member cols colss.new))\n              (define added   (filter-not cols-current? colss.new))\n              (define removed (filter-not cols-new?     colss.current))\n              (define add?\n                (and (pair? added)\n                     (policy-allow?\n                       update-policy\n                       (lambda ()\n                         (printf \"New index tables included for relation ~s:\\n\"\n                                 path)\n                         (for-each pretty-write added))\n                       \"Add these new index tables to ~s?\"\n                       (list path))))\n              (define remove?\n                (and (pair? removed)\n                     (policy-allow?\n                       cleanup-policy\n                       (lambda ()\n                         (printf\n                           \"Index tables no longer included for relation ~s:\\n\"\n                           path)\n                         (for-each pretty-write removed))\n                       \"Remove these old index tables from ~s?\"\n                       (list path))))\n              (when (or add? remove?)\n                (update-materialization! path.dir info\n                                         (if add?    added   '())\n                                         (if remove? removed '()))))))\n    (materialize-source)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/dbk.rkt",
    "content": "#lang racket/base\n(provide\n  (all-from-out\n    \"dbk/codec.rkt\" \"dbk/config.rkt\" \"dbk/dsv.rkt\" \"dbk/misc.rkt\" \"dbk/mk.rkt\"\n    \"dbk/order.rkt\" \"dbk/stream.rkt\" \"dbk/table.rkt\"))\n(require\n  \"dbk/codec.rkt\" \"dbk/config.rkt\" \"dbk/dsv.rkt\" \"dbk/misc.rkt\" \"dbk/mk.rkt\"\n  \"dbk/order.rkt\" \"dbk/stream.rkt\" \"dbk/table.rkt\")\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/.gitignore",
    "content": "/benchmark1\n/example-storage\n/small\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/benchmark-sorting/radix-sort.rkt",
    "content": "#lang racket/base\n(require racket/fixnum racket/match racket/vector racket/unsafe/ops)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Enumerators\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define (vector->enumerator v (start 0) (end (vector-length v)))\n  (define len (min end (vector-length v)))\n  (unsafe-vector->enumerator v (min start len) len))\n\n(define ((unsafe-vector->enumerator v (start 0) (end (unsafe-vector*-length v))) k!)\n  (let loop ((i start))\n    (when (unsafe-fx< i end)\n      (k!   (unsafe-vector*-ref v i))\n      (loop (unsafe-fx+ i 1)))))\n\n(define ((enumerator-append e.0 e.1) k!)\n  (e.0 k!)\n  (e.1 k!))\n\n(define ((enumerator-msd-radix-sort en t->key key-byte-count) k!)\n  (define size.shift           8)\n  (define mask.shift         255)\n  (define count.parts        256)\n  (define count.buffer        32)\n  (define count.initial.parts  8)\n  (define growth-factor.parts  2)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (let enumerate ((shift (unsafe-fx* 8 (unsafe-fx- key-byte-count 1))) (en en))\n    (define parts     (make-vector count.parts))\n    (define pos.parts (make-vector count.parts 0))\n    (define buf       (make-vector count.parts))\n    (define pos       (make-vector count.parts 0))\n    (let loop ((i 0))\n      (when (unsafe-fx< i count.parts)\n        (unsafe-vector*-set! parts i (make-vector count.initial.parts))\n        (unsafe-vector*-set! buf   i (make-vector count.buffer))\n        (loop (unsafe-fx+ i 1))))\n    (en (lambda (t)\n          ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n          (let* ((key     (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n                 (buf.k   (unsafe-vector*-ref buf key))\n                 (pos.k   (unsafe-vector*-ref pos key))\n                 (pos.k+1 (unsafe-fx+ pos.k 1)))\n            (unsafe-vector*-set! buf.k pos.k t)\n            (if (unsafe-fx= pos.k+1 count.buffer)\n              (begin\n                (unsafe-vector*-set! pos key 0)\n                (unsafe-vector*-set! buf key (make-vector count.buffer))\n                (let* ((parts.k       (unsafe-vector*-ref parts     key))\n                       (pos.parts.k   (unsafe-vector*-ref pos.parts key))\n                       (pos.parts.k+1 (unsafe-fx+ pos.parts.k 1))\n                       (len.parts.k   (unsafe-vector*-length parts.k)))\n                  (unsafe-vector*-set! pos.parts key pos.parts.k+1)\n                  (if (unsafe-fx= pos.parts.k+1 len.parts.k)\n                    (let ((parts.k.new (make-vector (unsafe-fx* len.parts.k growth-factor.parts))))\n                      (unsafe-vector*-set!  parts key parts.k.new)\n                      (vector-copy! parts.k.new 0 parts.k)\n                      (unsafe-vector*-set!  parts.k.new pos.parts.k buf.k))\n                    (unsafe-vector*-set! parts.k pos.parts.k buf.k))))\n              (unsafe-vector*-set! pos key pos.k+1)))))\n    (let ((k!/en (if (unsafe-fx= shift 0)\n                   (lambda (en) (en k!))\n                   (lambda (en) (enumerate (unsafe-fx- shift size.shift) en)))))\n      (let loop ((i 0))\n        (when (unsafe-fx< i count.parts)\n          (let ((parts.i     (unsafe-vector*-ref parts     i))\n                (pos.parts.i (unsafe-vector*-ref pos.parts i))\n                (buf.i       (unsafe-vector*-ref buf       i))\n                (pos.i       (unsafe-vector*-ref pos       i)))\n            (unsafe-vector*-set! parts i #f)\n            (unsafe-vector*-set! buf   i #f)\n            (k!/en (lambda (k!)\n                     ((unsafe-vector->enumerator parts.i 0 pos.parts.i)\n                      (lambda (part) ((unsafe-vector->enumerator part 0 count.buffer) k!)))\n                     ((unsafe-vector->enumerator buf.i 0 pos.i) k!)))\n            (loop (unsafe-fx+ i 1))))))))\n\n(define (vector-radix-sort! v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define len (min end (vector-length v)))\n  (unsafe-vector-radix-sort! v t->key key-byte-count (min start len) len))\n\n(define (unsafe-vector-radix-sort! v t->key key-byte-count (start 0) (end (unsafe-vector*-length v)))\n  (define size.shift               8)\n  (define mask.shift             255)\n  (define count.parts            256)\n  (define count.buffer           512)\n  (define count.initial.parts      8)\n  (define growth-factor.parts      2)\n  (define count.initial.buffers 1024)\n  (define growth-factor.buffers    2)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (define shift.final (unsafe-fx* 8 (unsafe-fx- key-byte-count 1)))\n  (define buffers     (make-vector count.initial.buffers))\n  (define pos.buffers 0)\n  (define (new-buffer)\n    (if (unsafe-fx= pos.buffers 0)\n      (make-vector count.buffer)\n      (begin (set! pos.buffers (unsafe-fx- pos.buffers 1))\n             (unsafe-vector*-ref buffers pos.buffers))))\n  (define (free-buffer b)\n    (vector-fill! b 0)\n    (when (unsafe-fx= pos.buffers (unsafe-vector*-length buffers))\n      (let ((buffers.new (make-vector (unsafe-fx* pos.buffers growth-factor.buffers))))\n        (vector-copy! buffers.new 0 buffers)\n        (set! buffers buffers.new)))\n    (unsafe-vector*-set! buffers pos.buffers b)\n    (set! pos.buffers (unsafe-fx+ pos.buffers 1)))\n  (let loop ((shift 0))\n    (define parts     (make-vector count.parts))\n    (define pos.parts (make-vector count.parts 0))\n    (define buf       (make-vector count.parts))\n    (define pos       (make-vector count.parts 0))\n    (let loop ((i 0))\n      (when (unsafe-fx< i count.parts)\n        (unsafe-vector*-set! parts i (make-vector count.initial.parts))\n        (unsafe-vector*-set! buf   i (new-buffer))\n        (loop (unsafe-fx+ i 1))))\n    (let loop ((i start))\n      (when (unsafe-fx< i end)\n        (let* ((t       (unsafe-vector*-ref v i))\n               ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n               (key     (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n               (buf.k   (unsafe-vector*-ref buf key))\n               (pos.k   (unsafe-vector*-ref pos key))\n               (pos.k+1 (unsafe-fx+ pos.k 1)))\n          (unsafe-vector*-set! buf.k pos.k t)\n          (if (unsafe-fx= pos.k+1 count.buffer)\n            (begin\n              (unsafe-vector*-set! pos key 0)\n              (unsafe-vector*-set! buf key (new-buffer))\n              (let* ((parts.k       (unsafe-vector*-ref parts     key))\n                     (pos.parts.k   (unsafe-vector*-ref pos.parts key))\n                     (pos.parts.k+1 (unsafe-fx+ pos.parts.k 1))\n                     (len.parts.k   (unsafe-vector*-length parts.k)))\n                (unsafe-vector*-set! pos.parts key pos.parts.k+1)\n                (if (unsafe-fx= pos.parts.k+1 len.parts.k)\n                  (let ((parts.k.new (make-vector (unsafe-fx* len.parts.k growth-factor.parts))))\n                    (unsafe-vector*-set!  parts key parts.k.new)\n                    (vector-copy! parts.k.new 0 parts.k)\n                    (unsafe-vector*-set!  parts.k.new pos.parts.k buf.k))\n                  (unsafe-vector*-set! parts.k pos.parts.k buf.k))))\n            (unsafe-vector*-set! pos key pos.k+1)))\n        (loop (unsafe-fx+ i 1))))\n    (let loop.all ((k 0) (j start))\n      (when (unsafe-fx< k count.parts)\n        (let ((parts.k     (unsafe-vector*-ref parts     k))\n              (pos.parts.k (unsafe-vector*-ref pos.parts k))\n              (buf.k       (unsafe-vector*-ref buf       k))\n              (pos.k       (unsafe-vector*-ref pos       k)))\n          (let loop ((i 0) (j j))\n            (if (unsafe-fx< i pos.parts.k)\n              (let ((part (unsafe-vector*-ref parts.k i)))\n                (let loop ((i 0))\n                  (when (unsafe-fx< i count.buffer)\n                    (unsafe-vector*-set! v (unsafe-fx+ j i) (unsafe-vector*-ref part i))\n                    (loop (unsafe-fx+ i 1))))\n                (free-buffer part)\n                (loop (unsafe-fx+ i 1) (unsafe-fx+ j count.buffer)))\n              (let loop ((i 0))\n                (if (unsafe-fx= i pos.k)\n                  (begin (free-buffer buf.k)\n                         (loop.all (unsafe-fx+ k 1) (unsafe-fx+ j pos.k)))\n                  (begin (unsafe-vector*-set! v (unsafe-fx+ j i) (unsafe-vector*-ref buf.k i))\n                         (loop (unsafe-fx+ i 1))))))))))\n    (when (unsafe-fx< shift shift.final)\n      (loop (unsafe-fx+ shift size.shift)))))\n\n(define (counting-radix-sort-helper v.src start.src end.src v.0 start.0 v.1 start.1 t->key key-byte-count)\n  (define size.shift    8)\n  (define mask.shift  255)\n  (define count.parts 256)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (define len         (unsafe-fx- end.src start.src))\n  (define shift.final (unsafe-fx* 8 (unsafe-fx- key-byte-count 1)))\n  (define offset      (make-vector count.parts))\n  (let loop.shift ((shift      0)\n                   (v.src      v.src) (start          start.src) (end          end.src)\n                   (v.tgt      v.0)   (start.tgt      start.0)   (end.tgt      (unsafe-fx+ start.0 len))\n                   (v.tgt.next v.1)   (start.tgt.next start.1)   (end.tgt.next (unsafe-fx+ start.1 len)))\n    (vector-fill! offset 0)\n    (let loop.count ((i start))\n      (when (unsafe-fx< i end)\n        ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n        (let ((key (unsafe-fxand mask.shift (fxrshift (t->key (unsafe-vector*-ref v.src i)) shift))))\n          (unsafe-vector*-set! offset key (unsafe-fx+ (unsafe-vector*-ref offset key) 1)))\n        (loop.count (unsafe-fx+ i 1))))\n    (let loop.offset ((k 0) (current start.tgt))\n      (when (unsafe-fx< k count.parts)\n        (let ((cardinality (unsafe-vector*-ref offset k)))\n          (unsafe-vector*-set! offset k current)\n          (loop.offset (unsafe-fx+ k 1) (unsafe-fx+ current cardinality)))))\n    (let loop.copy ((i start))\n      (when (unsafe-fx< i end)\n        ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n        (let* ((t     (unsafe-vector*-ref v.src i))\n               (key   (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n               (off.k (unsafe-vector*-ref offset key)))\n          (unsafe-vector*-set! offset key (unsafe-fx+ off.k 1))\n          (unsafe-vector*-set! v.tgt off.k t))\n        (loop.copy (unsafe-fx+ i 1))))\n    (when (unsafe-fx< shift shift.final)\n      (loop.shift (unsafe-fx+ shift size.shift)\n                  v.tgt      start.tgt      end.tgt\n                  v.tgt.next start.tgt.next end.tgt.next\n                  v.tgt      start.tgt      end.tgt))))\n\n(define (counting-radix-sort! v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define len         (- end start))\n  (define v.workspace (make-vector len))\n  (counting-radix-sort-helper v start end v.workspace 0 v start t->key key-byte-count)\n  (when (odd? key-byte-count)\n    (vector-copy! v start v.workspace 0 len)))\n\n(define (counting-radix-sort v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define len           (- end start))\n  (define v.workspace.0 (make-vector len))\n  (define v.workspace.1 (make-vector len))\n  (counting-radix-sort-helper v start end v.workspace.0 0 v.workspace.1 0 t->key key-byte-count)\n  (if (odd? key-byte-count)\n    v.workspace.0\n    v.workspace.1))\n\n(define ((enumerator-lsd-radix-sort en t->key key-byte-count) k!)\n  (define size.shift               8)\n  (define mask.shift             255)\n  (define count.parts            256)\n  (define count.buffer           512)\n  (define count.initial.parts      8)\n  (define growth-factor.parts      2)\n  (define count.initial.buffers 1024)\n  (define growth-factor.buffers    2)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (define shift.final (unsafe-fx* 8 (unsafe-fx- key-byte-count 1)))\n  (define buffers     (make-vector count.initial.buffers))\n  (define pos.buffers 0)\n  (define (new-buffer)\n    (if (unsafe-fx= pos.buffers 0)\n      (make-vector count.buffer)\n      (begin (set! pos.buffers (unsafe-fx- pos.buffers 1))\n             (unsafe-vector*-ref buffers pos.buffers))))\n  (define (free-buffer b)\n    (vector-fill! b 0)\n    (when (unsafe-fx= pos.buffers (unsafe-vector*-length buffers))\n      (let ((buffers.new (make-vector (unsafe-fx* pos.buffers growth-factor.buffers))))\n        (vector-copy! buffers.new 0 buffers)\n        (set! buffers buffers.new)))\n    (unsafe-vector*-set! buffers pos.buffers b)\n    (set! pos.buffers (unsafe-fx+ pos.buffers 1)))\n  (let enumerate ((shift 0) (en en))\n    (define parts     (make-vector count.parts))\n    (define pos.parts (make-vector count.parts 0))\n    (define buf       (make-vector count.parts))\n    (define pos       (make-vector count.parts 0))\n    (let loop ((i 0))\n      (when (unsafe-fx< i count.parts)\n        (unsafe-vector*-set! parts i (make-vector count.initial.parts))\n        (unsafe-vector*-set! buf   i (new-buffer))\n        (loop (unsafe-fx+ i 1))))\n    (en (lambda (t)\n          ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n          (let* ((key     (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n                 (buf.k   (unsafe-vector*-ref buf key))\n                 (pos.k   (unsafe-vector*-ref pos key))\n                 (pos.k+1 (unsafe-fx+ pos.k 1)))\n            (unsafe-vector*-set! buf.k pos.k t)\n            (if (unsafe-fx= pos.k+1 count.buffer)\n              (begin\n                (unsafe-vector*-set! pos key 0)\n                (unsafe-vector*-set! buf key (new-buffer))\n                (let* ((parts.k       (unsafe-vector*-ref parts     key))\n                       (pos.parts.k   (unsafe-vector*-ref pos.parts key))\n                       (pos.parts.k+1 (unsafe-fx+ pos.parts.k 1))\n                       (len.parts.k   (unsafe-vector*-length parts.k)))\n                  (unsafe-vector*-set! pos.parts key pos.parts.k+1)\n                  (if (unsafe-fx= pos.parts.k+1 len.parts.k)\n                    (let ((parts.k.new (make-vector (unsafe-fx* len.parts.k growth-factor.parts))))\n                      (unsafe-vector*-set!  parts key parts.k.new)\n                      (vector-copy! parts.k.new 0 parts.k)\n                      (unsafe-vector*-set!  parts.k.new pos.parts.k buf.k))\n                    (unsafe-vector*-set! parts.k pos.parts.k buf.k))))\n              (unsafe-vector*-set! pos key pos.k+1)))))\n    (define (en.new k!)\n      (let loop ((i 0))\n        (when (unsafe-fx< i count.parts)\n          (let ((parts.i     (unsafe-vector*-ref parts     i))\n                (pos.parts.i (unsafe-vector*-ref pos.parts i))\n                (buf.i       (unsafe-vector*-ref buf       i))\n                (pos.i       (unsafe-vector*-ref pos       i)))\n            (let loop ((i 0))\n              (if (unsafe-fx= i pos.parts.i)\n                (begin ((unsafe-vector->enumerator buf.i 0 pos.i) k!)\n                       (free-buffer buf.i))\n                (begin (let ((part (unsafe-vector*-ref parts.i i)))\n                         ((unsafe-vector->enumerator part 0 count.buffer) k!)\n                         (free-buffer part))\n                       (loop (unsafe-fx+ i 1))))))\n          (loop (unsafe-fx+ i 1)))))\n    (if (unsafe-fx= shift shift.final)\n      (en.new k!)\n      (enumerate (unsafe-fx+ shift size.shift) en.new))))\n\n(define (in-place-radix-sort! v t->key key-byte-count (start 0) (end (vector-length v)))\n  (define threshold 268435456)\n  ;(define threshold 67108864)\n  ;(define threshold 16777216)\n  ;(define threshold  65535)\n  ;(define threshold  8192)\n  ;(define threshold  4096)\n  ;(define threshold  1024)\n  ;(define threshold  256)\n  ;(define threshold  0)\n  (define size.shift    8)\n  (define mask.shift  255)\n  (define count.parts 256)\n  (unless (fixnum? key-byte-count) (error \"key-byte-count must be a fixnum\" key-byte-count))\n  (let loop.shift ((shift (unsafe-fx* 8 (unsafe-fx- key-byte-count 1))) (start start) (end end))\n    ;; TODO: we can use unsafe-fxrshift if t->key is guaranteed to produce a fixnum\n    (define (t->byte t) (unsafe-fxand mask.shift (fxrshift (t->key t) shift)))\n    (define count  (make-vector count.parts))\n    (define offset (make-vector count.parts))\n    (let loop.count ((i start))\n      (when (unsafe-fx< i end)\n        (let ((key (t->byte (unsafe-vector*-ref v i))))\n          (unsafe-vector*-set! count key (unsafe-fx+ (unsafe-vector*-ref count key) 1)))\n        (loop.count (unsafe-fx+ i 1))))\n    (let loop.offset ((k 0) (current start))\n      (when (unsafe-fx< k count.parts)\n        (let ((cardinality (unsafe-vector*-ref count k)))\n          (let loop.advance ((i current))\n            (if (and (unsafe-fx< i end) (unsafe-fx= (t->byte (unsafe-vector*-ref v i)) k))\n              (loop.advance (unsafe-fx+ i 1))\n              (let ((next (unsafe-fx+ current cardinality)))\n                (unsafe-vector*-set! offset k i)\n                (unsafe-vector*-set! count  k next)\n                (loop.offset (unsafe-fx+ k 1) next)))))))\n    (let loop.move.k ((k 0) (i.part.start start))\n      (when (unsafe-fx< k count.parts)\n        (let* ((i.start (unsafe-vector*-ref offset k))\n               (i.end   (unsafe-vector*-ref count k)))\n          (let loop.move ((i i.start))\n            (when (unsafe-fx< i i.end)\n              (let ((t (unsafe-vector*-ref v i)))\n                (let loop.swap ((t.current t)\n                                (key       (t->byte t)))\n                  (let* ((off.k (unsafe-vector*-ref offset key))\n                         (t.next (unsafe-vector*-ref v off.k)))\n                    (unsafe-vector*-set! v      off.k t.current)\n                    (unsafe-vector*-set! offset key   (unsafe-fx+ off.k 1))\n                    (let ((key (t->byte t.next)))\n                      (if (unsafe-fx= key k)\n                        (begin (unsafe-vector*-set! v i t.next)\n                               (loop.move (unsafe-fx+ i 1)))\n                        (loop.swap t.next key))))))))\n          (when (and (unsafe-fx< 0 shift) (unsafe-fx< i.part.start i.end))\n            (if (unsafe-fx<= (unsafe-fx- i.end i.part.start) threshold)\n              (counting-radix-sort! v t->key (/ shift 8) i.part.start i.end)\n              (loop.shift (unsafe-fx- shift size.shift) i.part.start i.end)))\n          (loop.move.k (unsafe-fx+ k 1) i.end))))))\n\n;; TODO: factor out enumerator-radix-partition ?\n;; simplify t->key interface to return exactly a byte, discard key-byte-count parameter\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;; Benchmark\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;#|\n(define key-byte-count 4)\n;(define count.node (arithmetic-shift 1 28))\n;(define count.node (arithmetic-shift 1 27))\n(define count.node (arithmetic-shift 1 25))\n;|#\n\n#|\n(define key-byte-count 3)\n;(define count.node (arithmetic-shift 1 24))\n(define count.node (arithmetic-shift 1 22))\n;|#\n\n#|\n(define key-byte-count 2)\n(define count.node (arithmetic-shift 1 16))\n;|#\n\n(define count.edge (* count.node 16))\n\n(displayln \"allocating nodes:\")\n(displayln count.node)\n(define nodes (time (make-vector count.node)))\n(displayln \"allocating edges:\")\n(displayln count.edge)\n\n;#|\n(define edges (time (make-vector count.edge)))\n(define en.edges (unsafe-vector->enumerator edges 0 count.edge))\n\n(displayln \"building edges\")\n(time (let loop ((i 0))\n        (when (< i count.edge)\n          (vector-set! edges i (random count.node))\n          ;(vector-set! edges i (cons (random count.node) (random count.node)))\n          (loop (+ i 1)))))\n;|#\n\n#|\n(define (en.edges k!)\n  (let loop ((i 0))\n    (when (< i count.edge)\n      (k! (random count.node))\n      ;(k! (cons (random count.node) (random count.node)))\n      (loop (+ i 1)))))\n;|#\n\n;(define edge->key car)\n(define (edge->key e) e)\n\n#|\n(displayln \"sorting edges\")\n(time (vector-sort!\n        edges\n        (lambda (e.0 e.1) (< (edge->key e.0) (edge->key e.1)))))\n;|#\n\n#|\n(displayln \"computing node degrees inlined\")\n(time (let loop ((i 0))\n        (when (unsafe-fx< i count.edge)\n          (let ((key (unsafe-vector*-ref edges i)))\n            (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1)))\n          (loop (unsafe-fx+ i 1)))))\n;|#\n\n#|\n(displayln \"computing node degrees\")\n(time (en.edges\n        (lambda (edge)\n         (define key (edge->key edge))\n         ;(vector-set! nodes key (+ (vector-ref nodes key) 1))\n         (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1))\n         )))\n;|#\n\n#|\n(displayln \"computing node degrees inlined after lsd-radix sorting edges in-place\")\n;(time (unsafe-vector-radix-sort! edges edge->key key-byte-count))\n;(time (counting-radix-sort! edges edge->key key-byte-count))\n(let ((v.workspace (time (make-vector count.edge))))\n  (time (collect-garbage))\n  (time (counting-radix-sort-helper edges 0 count.edge v.workspace 0 edges 0 edge->key key-byte-count))\n  (when (odd? key-byte-count)\n    (time (vector-copy! edges 0 v.workspace 0 count.edge))))\n\n(time (let loop ((i 0))\n        (when (unsafe-fx< i count.edge)\n          (let ((key (unsafe-vector*-ref edges i)))\n            (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1)))\n          (loop (unsafe-fx+ i 1)))))\n;|#\n\n#|\n(displayln \"computing node degrees inlined after in-place-msd-radix sorting edges\")\n(time (in-place-radix-sort! edges edge->key key-byte-count))\n(time (let loop ((i 0))\n        (when (unsafe-fx< i count.edge)\n          (let ((key (unsafe-vector*-ref edges i)))\n            (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1)))\n          (loop (unsafe-fx+ i 1)))))\n;|#\n\n#|\n(displayln \"computing node degrees while lsd-radix sorting edges\")\n(time ((enumerator-lsd-radix-sort en.edges edge->key key-byte-count)\n       (lambda (edge)\n         (define key (edge->key edge))\n         ;(vector-set! nodes key (+ (vector-ref nodes key) 1))\n         (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1))\n         )))\n;|#\n\n#|\n(displayln \"computing node degrees while msd-radix sorting edges\")\n(time ((enumerator-msd-radix-sort en.edges edge->key key-byte-count)\n       (lambda (edge)\n         (define key (edge->key edge))\n         ;(vector-set! nodes key (+ (vector-ref nodes key) 1))\n         (unsafe-vector*-set! nodes key (unsafe-fx+ (unsafe-vector*-ref nodes key) 1))\n         )))\n;|#\n\n;(displayln 'in-place-radix-sort!) (time (in-place-radix-sort! edges edge->key key-byte-count))\n(displayln 'counting-radix-sort!) (time (counting-radix-sort! edges edge->key key-byte-count))\n;(displayln 'unsafe-vector-radix-sort!) (time (unsafe-vector-radix-sort! edges edge->key key-byte-count))\n(time (let ((previous #f))\n        (en.edges\n          (lambda (edge)\n            (when (and previous (< (edge->key edge) previous))\n              (error \"not sorted!\" previous (edge->key edge)))\n            (set! previous (edge->key edge))))))\n\n#;(let ((previous #f))\n  ((enumerator-lsd-radix-sort en.edges edge->key key-byte-count)\n   (lambda (edge)\n     (when (and previous (< (edge->key edge) previous))\n       (error \"not sorted!\" previous (edge->key edge)))\n     (set! previous (edge->key edge)))))\n\n#;(let ((previous #f))\n  ((enumerator-msd-radix-sort en.edges edge->key key-byte-count)\n   (lambda (edge)\n     (when (and previous (< (edge->key edge) previous))\n       (error \"not sorted!\" previous (edge->key edge)))\n     (set! previous (edge->key edge)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/benchmark-sorting/string-sort.rkt",
    "content": "#lang racket/base\n(require racket/list racket/pretty racket/unsafe/ops racket/vector)\n\n;; TODO: pre-allocate a buffer for all the threshold merge sorts to share\n;; TODO: try MSD-radix-sort with a threshold for switching to q3sort! ?\n;; TODO: try burst/trie sort?\n\n;; multi-key (aka 3-way) quicksort\n(define (q3sort! max-depth? x&depth->cmp cmp (unsafe-vector*-ref v (random start end))\n                                                 depth)\n                         (lambda (i.low i.mid)\n                           (loop.current-depth                   start i.low)\n                           (loop.current-depth                   i.mid end)\n                           (loop.next-depth (unsafe-fx+ depth 1) i.low i.mid)))))))))\n\n(define (vector-bytes-sort! v (start 0) (end (vector-length v)))\n  (define (ref x d) (unsafe-bytes-ref x d))\n  (q3sort!\n    (lambda (x depth) (unsafe-fx<= (unsafe-bytes-length x) depth))\n    (lambda (x depth) (let ((n (bytes-ref x depth)))\n                        (lambda (y)\n                          (let ((m (bytes-ref y depth)))\n                            (cond ((unsafe-fx< m n) -1)\n                                  ((unsafe-fx= m n)  0)\n                                  (else              1))))))\n    bytesstring (map (lambda (_) (integer->char (random 128))) (range (random 200)))))\n\n(define (string-sort-and-verify v)\n  (define v.expected (time (vector-sort v stringbytes (map (lambda (_) (random 128)) (range (random 300 500)))))\n\n(define (bytes-sort-and-verify v)\n  ;(define v.expected (time (vector-sort v bytesvector (map (lambda (_) (random-string)) (range test-size)))))\n(bytes-sort-and-verify (time (list->vector (map (lambda (_) (random-bytes)) (range test-size)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/benchmark1.rkt",
    "content": "#lang racket/base\n(require \"../dbk.rkt\" racket/function racket/list racket/pretty)\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n\n(define-syntax-rule (test name e expected)\n  (begin (printf \"Testing ~s:\\n\" name)\n         (pretty-print 'e)\n         (let ((answer (time e)))\n           (unless (equal? answer expected)\n             (printf \"FAILED ~s:\\n\" name)\n             (printf \"  ANSWER:\\n\")\n             (pretty-print answer)\n             (printf \"  EXPECTED:\\n\")\n             (pretty-print expected)))))\n\n(for-each (lambda (key) (current-config-set! key 'always))\n          '(update-policy cleanup-policy migrate-policy))\n\n\n;; Benchmark reference: http://users.informatik.uni-halle.de/~brass/botup/\n\n(define-relation/table Q\n  'path            \"benchmark1/Q\"\n  'source-stream   (value/syntax\n                     (map (lambda (i) (list i (+ i 1))) (range 1 5001)))\n  'attribute-names '(a b)\n  'attribute-types '(nat nat)\n  ;; optionally preload into memory\n  'retrieval-type  'scm\n  )\n\n(define-relation/table R\n  'path            \"benchmark1/R\"\n  'source-stream   (value/syntax\n                     (map (lambda (i) (list i    i))    (range 1 5001)))\n  'attribute-names '(a b)\n  'attribute-types '(nat nat)\n  ;; optionally preload into memory\n  'retrieval-type  'scm\n  )\n\n(define-relation (P3.1 b y) (fresh (x) (P2.1 b x) (Q x y)))\n(define-relation (P2.1 c w) (fresh (v) (P1.1 c v) (Q v w)))\n(define-relation (P1.1 d u) (fresh (t) (P0.1 d t) (Q t u)))\n(define-relation (P0.1 e s) (R e s))\n\n;; disk: ~8000ms\n;; scm:  ~1400ms\n(test 'benchmark-1\n  (length (run* (a z) (P3.1 a z)))\n  ;; smallest: (1    4)\n  ;; largest:  (4998 5001)\n  4998)\n\n(define-relation (P3.2 x z) (fresh (y) (Q x y) (P2.2 y z)))\n(define-relation (P2.2 x z) (fresh (y) (Q x y) (P1.2 y z)))\n(define-relation (P1.2 x z) (fresh (y) (Q x y) (P0.2 y z)))\n(define-relation (P0.2 x y) (R x y))\n\n;; disk: ~8000ms\n;; scm:  ~1400ms\n(test 'benchmark-2\n  (length (run* (x z) (P3.2 x z)))\n  ;; smallest: (1    4)\n  ;; largest:  (4997 5000)\n  4997)\n\n\n;; TODO: improve performance\n\n;(define-relation/table Q.large\n;  'path            \"benchmark1/Q.large\"\n;  'source-stream   (value/syntax\n;                     (map (lambda (i) (list i (+ i 1))) (range 1 1000001)))\n;  'attribute-names '(a b)\n;  'attribute-types '(nat nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n;\n;(define-relation/table R.large\n;  'path            \"benchmark1/R.large\"\n;  'source-stream   (value/syntax\n;                     (map (lambda (i) (list i    i))    (range 1 1000001)))\n;  'attribute-names '(a b)\n;  'attribute-types '(nat nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n;\n;(define-relation (P3.2.large x z) (fresh (y) (Q.large x y) (P2.2.large y z)))\n;(define-relation (P2.2.large x z) (fresh (y) (Q.large x y) (P1.2.large y z)))\n;(define-relation (P1.2.large x z) (fresh (y) (Q.large x y) (P0.2.large y z)))\n;(define-relation (P0.2.large x y) (R.large x y))\n;\n;;; disk: ?\n;;; scm:  ?\n;(test 'benchmark-2-large\n;  (length (run* (x z) (P3.2.large x z)))\n;  '?)\n\n\n;; TODO: improve performance\n\n;(define-relation/table S\n;  'path            \"benchmark1/S\"\n;  'source-stream   (value/syntax (map list (range 1 50001)))\n;  'attribute-names '(a)\n;  'attribute-types '(nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n\n;(define-relation (P1.3 a)             (S a))\n;(define-relation (P2.3 a b)           (P1.3 a)           (membero b '(1 2)))\n;(define-relation (P3.3 a b c)         (P2.3 a b)         (membero c '(1 2)))\n;(define-relation (P4.3 a b c d)       (P3.3 a b c)       (membero d '(1 2)))\n;(define-relation (P5.3 a b c d e)     (P4.3 a b c d)     (membero e '(1 2)))\n;(define-relation (P6.3 a b c d e f)   (P5.3 a b c d e)   (membero f '(1 2)))\n;(define-relation (P7.3 a b c d e f g) (P6.3 a b c d e f) (membero g '(1 2)))\n\n;;; disk: ?\n;;; scm:  ?\n;(test 'benchmark-3\n;  (length (run* (a b c d e f g) (P7.3 a b c d e f g)))\n;  (* 50000 (expt 2 6)))\n\n\n;; TODO: fixed-point computations\n\n;(define-relation/table edge\n;  'path            \"benchmark1/edge\"\n;  'source-stream   (value/syntax\n;                     (map (lambda (i) (list i (+ i 1))) (range 1 1001)))\n;  'attribute-names '(a b)\n;  'attribute-types '(nat nat)\n;  ;; optionally preload into memory\n;  'retrieval-type  'scm\n;  )\n;\n;(define-relation (path x z)\n;  (conde ((edge x z))\n;         ((fresh (y) (edge x y) (path y z)))))\n;\n;;; disk: ?\n;;; scm:  ?\n;(test 'benchmark-fixed-point\n;  (length (run* (a b) (path a b)))\n;  (/ (* 1000 (+ 1000 1)) 2))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/chinook/.gitignore",
    "content": "/Chinook_Sqlite.sql\n/Album.tsv\n/Artist.tsv\n/Customer.tsv\n/Employee.tsv\n/Genre.tsv\n/Invoice.tsv\n/InvoiceLine.tsv\n/MediaType.tsv\n/Playlist.tsv\n/PlaylistTrack.tsv\n/Track.tsv\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/chinook/README.md",
    "content": "# Chinook database testing\n\nDownload or create Chinook_Sqlite.sql.  For instructions, go here: https://github.com/lerocha/chinook-database\n\nRun `build.sh` to generate TSV files for import.\n\n## TODO\n\nBuild a database using the generated TSV files.\n\nRun test queries using the database.\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/chinook/build.sh",
    "content": "#!/bin/bash\nset -eufo pipefail\n\n# To download or create Chinook_Sqlite.sql, see: https://github.com/lerocha/chinook-database\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\ncd \"$here\"\n\ndos2unix Chinook_Sqlite.sql\nsqlite3 -init Chinook_Sqlite.sql chinook.sqlite < /dev/null\n\nfor table in Customer Employee Invoice InvoiceLine Genre Album Artist Playlist PlaylistTrack Track MediaType; do\n  printf \".mode tabs\\n.headers on\\n.output $table.tsv\\nselect * from $table;\" | sqlite3 chinook.sqlite\ndone\n\nrm chinook.sqlite\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/basic-naive.rkt",
    "content": "#lang racket/base\n(provide\n  facts\n  ==\n  fresh\n  conde\n  run*\n  define-relation)\n(require racket/list racket/match racket/set racket/struct)\n\n;; A naive Datalog implementation that can be used as a baseline\n\n;; Terms:\n;; - Constants and variables\n;; Formulas:\n;; - Existential quantification, conjunction, disjunction\n;;   - via fresh and conde\n;;   - Negation is not supported in this basic implementation\n;; - Relation calls\n;; - Equality constraints\n;; - run*\n;; Relations:\n;; - via define-relation and define-relation/facts (for convenience)\n\n;; Variables should not be nested within data structures, but this is not checked.\n;; All relations should be range restricted for safety, but this is not checked.\n\n(struct var (name) #:prefab)\n\n(define subst.empty (hash))\n(define (unpack subst names)\n  (map (lambda (n) (hash-ref subst n (lambda () (error \"unbound variable\" n)))) names))\n(define (shadow subst names)\n  (foldl (lambda (n s) (hash-remove s n)) subst names))\n(define (assign subst x t)\n  (and (not (occurs? subst x t))\n       (hash-set subst (var-name x) t)))\n(define (walk subst x)\n  (let loop ((x x))\n    (if (var? x)\n      (let ((y (hash-ref subst (var-name x) x)))\n        (if (equal? x y)\n          x\n          (loop y)))\n      x)))\n(define (occurs? subst x t)\n  (let ((x (walk subst x)) (t (walk subst t)))\n    (or (equal? x t)\n        (and (pair? t)\n             (or (occurs? subst x (car t))\n                 (occurs? subst x (cdr t))))\n        (and (vector? t)\n             (occurs? subst x (vector->list t))))))\n(define (unify subst u v)\n  (let ((u (walk subst u)) (v (walk subst v)))\n    (cond ((eqv? u v)  subst)\n          ((var? u)    (if (and (var? v) (equal? (var-name u) (var-name v)))\n                         subst\n                         (assign subst u v)))\n          ((var? v)    (assign subst v u))\n          ((pair? u)   (and (pair? v)\n                            (let ((subst (unify subst (car u) (car v))))\n                              (and subst\n                                   (unify subst (cdr u) (cdr v))))))\n          ((vector? u) (and (vector? v)\n                            (unify subst (vector->list u) (vector->list v))))\n          (else        (and (equal? u v) subst)))))\n\n(struct relation (name attrs box.current qthunk)\n        #:methods gen:custom-write\n        ((define write-proc (make-constructor-style-printer\n                              (lambda (r) 'relation)\n                              (lambda (r) (list (cons (relation-name r) (relation-attrs r)))))))\n        #:property prop:procedure\n        (lambda (r . args)\n          (unless (= (length (relation-attrs r)) (length args))\n            (error \"relation called with invalid number of arguments\" r args))\n          `(relate ,r ,args)))\n\n(define (relation-current r) (unbox (relation-box.current r)))\n(define (relation-next    r) (query-eval (relation-query  r)))\n(define (relation-query   r) ((relation-qthunk            r)))\n\n(define (query-dependencies q)\n  (let loop ((fm q) (rs (set)))\n    (match fm\n      (`(and   . ,fms) (foldl loop rs fms))\n      (`(or    . ,fms) (foldl loop rs fms))\n      (`(relate ,r ,_) (if (set-member? rs r)\n                         rs\n                         (loop (relation-query r) (set-add rs r))))\n      (`(exist ,_ ,fm) (loop fm rs))\n      (`(query ,_ ,fm) (loop fm rs))\n      (`(==    ,_ ,_)  rs))))\n\n(define (query-eval q)\n  (match q\n    (`(query ,var-names ,fm)\n      (list->set\n        (map (lambda (subst) (unpack subst var-names))\n             (let loop ((fm fm) (subst subst.empty))\n               (match fm\n                 (`(and ,fm . ,fms)  (let ((substs (loop fm subst)))\n                                       (append* (map (lambda (subst) (loop `(and . ,fms) subst))\n                                                     substs))))\n                 ('(and)             (list subst))\n                 (`(or      . ,fms)  (append* (map (lambda (fm) (loop fm subst)) fms)))\n                 (`(relate ,r ,args) (filter-not not (set-map (relation-current r)\n                                                              (lambda (tuple) (unify subst args tuple)))))\n                 (`(exist ,ns ,fm)   (map (lambda (subst) (shadow subst ns))\n                                          (loop fm (shadow subst ns))))\n                 (`(==    ,u ,v)     (let ((subst (unify subst u v)))\n                                       (if subst\n                                         (list subst)\n                                         '()))))))))))\n\n(define (query-run q)\n  (let ((r.deps (set->list (query-dependencies q))))\n    (for-each (lambda (r) (set-box! (relation-box.current r) (set))) r.deps)\n    (let loop ()\n      (when (foldl (lambda (r changed?)\n                     (let ((current (relation-current r))\n                           (next    (relation-next    r)))\n                       (if (= (set-count current) (set-count next))\n                         changed?\n                         (begin (set-box! (relation-box.current r) next)\n                                #t))))\n                   #f r.deps)\n        (loop)))\n    (query-eval q)))\n\n;;;;;;;;;;;;;;\n;;; Syntax ;;;\n;;;;;;;;;;;;;;\n\n(define (facts vars tuples)\n  `(or . ,(map (lambda (tuple) `(== ,vars ,tuple)) tuples)))\n\n(define (== u v) `(== ,u ,v))\n\n(define-syntax-rule\n  (conde (fm00 fm0* ...) (fm0 fm* ...) ...)\n  `(or (and ,fm00 ,fm0* ...) (and ,fm0 ,fm* ...) ...))\n(define-syntax-rule\n  (quantify type (x ...) fm0 fm ...)\n  (let ((x (var 'x)) ...)\n    `(type (x ...) (and ,fm0 ,fm ...))))\n(define-syntax-rule\n  (fresh          (x ...) fm0 fm ...)\n  (quantify exist (x ...) fm0 fm ...))\n(define-syntax-rule\n  (query          (x ...) fm0 fm ...)\n  (quantify query (x ...) fm0 fm ...))\n(define-syntax run*\n  (syntax-rules ()\n    ((_ (x ...) fm0 fm ...) (set->list (query-run (query (x ...) fm0 fm ...))))\n    ((_ x       fm0 fm ...) (map car (run* (x) fm0 fm ...)))))\n(define-syntax-rule\n  (define-relation (name attr ...) fm0 fm ...)\n  (define name (relation 'name '(attr ...) (box #f)\n                         (lambda () (query (attr ...) fm0 fm ...)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/compile.rkt",
    "content": "#lang racket/base\n(provide\n  current-primitive-relations\n  primitive-relations.base\n  parse-rule)\n(require racket/match racket/set)\n\n(define (relation-name            R) (cadr R))\n(define (relation-original?       R) (eq? (car R) 'orig))\n(define (relation-original     name) (list 'orig name))\n\n(define (relation-generated?      R) (eq? (car R) 'new))\n(define (relation-generated    name) (list 'new  name))\n\n(define (relation-primitive?      R) (eq? (car R) 'prim))\n(define (relation-primitive    name) (list 'prim name))\n\n(define (relation-negation?       R) (eq? (car R) 'not))\n(define (relation-negation R.target) (list 'not  R.target))\n(define (relation-negation-target R) (cadr R))\n\n(define (atom        R args) (cons R args))\n(define (atom-relation atom) (car atom))\n(define (atom-args     atom) (cdr atom))\n\n(define (var?           t) (eq? (car t) 'var))\n(define (var         name) (list 'var   name))\n(define (var-name       x) (cadr x))\n\n(define (constant?      t) (eq? (car t) 'quote))\n(define (constant   value) (list 'quote value))\n(define (constant-value c) (eq? (car c) 'quote))\n\n(define (rule head body) (cons head body))\n(define (rule-head    r) (car r))\n(define (rule-body    r) (cdr r))\n\n(define prim.==            (relation-primitive '==))\n(define prim.=/=           (relation-negation  prim.==))\n(define prim.<             (relation-primitive '<))\n(define prim.<=            (relation-primitive '<=))\n(define prim.type==        (relation-primitive 'type==))\n(define prim.cons==        (relation-primitive 'cons==))\n(define prim.+==           (relation-primitive '+==))\n(define prim.*==           (relation-primitive '*==))\n(define prim.symbol-string (relation-primitive 'symbol-string))\n(define prim.string-bytes  (relation-primitive 'string-bytes))\n(define prim.bytes-list    (relation-primitive 'bytes-list))\n(define prim.vector-list   (relation-primitive 'vector-list))\n\n(define (==            t0 t1)          (atom prim.==            (list t0 t1)))\n(define (=/=           t0 t1)          (atom prim.=/=           (list t0 t1)))\n(define (type==        t     t.result) (atom prim.type==        (list t     t.result)))\n(define (cons==        t0 t1 t.result) (atom prim.cons==        (list t0 t1 t.result)))\n(define (+==           t0 t1 t.result) (atom prim.+==           (list t0 t1 t.result)))\n(define (*==           t0 t1 t.result) (atom prim.*==           (list t0 t1 t.result)))\n(define (symbol-string t0 t1)          (atom prim.symbol-string (list t0 t1)))\n(define (string-bytes  t0 t1)          (atom prim.string-bytes  (list t0 t1)))\n(define (bytes-list    t0 t1)          (atom prim.bytes-list    (list t0 t1)))\n(define (vector-list   t0 t1)          (atom prim.vector-list   (list t0 t1)))\n\n(define primitive-relations.base\n  (hash '==           ==\n        '=/=          =/=\n        '<            (lambda (t0 t1) (atom prim.<  (list t0 t1)))\n        '<=           (lambda (t0 t1) (atom prim.<= (list t0 t1)))\n        '>            (lambda (t0 t1) (atom prim.<  (list t1 t0)))\n        '>=           (lambda (t0 t1) (atom prim.<= (list t1 t0)))))\n\n(define current-primitive-relations (make-parameter (hash)))\n\n(define (parse-fact         e) (atom (relation-original (car e)) (cdr e)))\n(define (parse-atom         e) (atom (relation-original (car e)) (map parse-term (cdr e))))\n(define (parse-negated-atom e) (let ((a (parse-atom e)))\n                                 (atom (relation-negation (atom-relation a)) (atom-args a))))\n\n(define (parse-term e)\n  (define (build-cons a d) (let ((result (fresh-var)))\n                             (implicit-atom! (cons== a d result))\n                             result))\n  (define (build-list ts)  (foldr build-cons (constant '()) ts))\n  (define (build-l2r R e)  (let ((result (fresh-var)))\n                             (implicit-atom! (R (parse-term e) result))\n                             result))\n  (define (build-r2l R e)  (let ((result (fresh-var)))\n                             (implicit-atom! (R result (parse-term e)))\n                             result))\n  (match e\n    ('_                         (fresh-var))\n    ((? symbol?)                (var e))\n    ((list 'quote      c)       (constant c))\n    ((list 'quasiquote qq)      (let parse-qq ((qq qq) (level 0))\n                                  (match qq\n                                    ((list 'unquote          e) (if (= level 0)\n                                                                  (parse-term e)\n                                                                  (build-list (constant 'unquote)\n                                                                              (parse-qq e (- level 1)))))\n                                    ((list 'quasiquote      qq) (build-list (constant 'quasiquote)\n                                                                            (parse-qq qq (+ level 1))))\n                                    ((cons 'quasiquote       _) (error \"improper quasiquote\"               qq e))\n                                    ((cons 'unquote          _) (error \"improper unquote\"                  qq e))\n                                    ((cons 'unquote-splicing _) (error \"unquote-splicing is not supported\" qq e))\n                                    ((cons qq.a qq.d)           (build-cons (parse-qq qq.a level)\n                                                                            (parse-qq qq.d level)))\n                                    ((? vector?)                (error \"quasiquoted vectors are not supported\" qq))\n                                    (_                          (constant qq)))))\n    ((cons 'quote            _) (error \"improper quote\"             e))\n    ((cons 'quasiquote       _) (error \"improper quasiquote\"        e))\n    ((cons 'unquote          _) (error \"misplaced unquote\"          e))\n    ((cons 'unquote-splicing _) (error \"misplaced unquote-splicing\" e))\n    (`(type ,e)                 (let ((result (fresh-var)))\n                                  (implicit-atom! (type== (parse-term e) result))\n                                  result))\n    (`(cons ,e.a ,e.d)          (build-cons (parse-term e.a) (parse-term e.d)))\n    (`(list ,@e*)               (build-list (map parse-term e*)))\n    (`(+ ,e.a ,e.b)             (let ((result (fresh-var)))\n                                  (implicit-atom! (+== (parse-term e.a) (parse-term e.b) result))\n                                  result))\n    (`(- ,e.a ,e.b)             (let ((result (fresh-var)))\n                                  (implicit-atom! (+== result (parse-term e.b) (parse-term e.a)))\n                                  result))\n    (`(* ,e.a ,e.b)             (let ((result (fresh-var)))\n                                  (implicit-atom! (*== (parse-term e.a) (parse-term e.b) result))\n                                  result))\n    (`(/ ,e.a ,e.b)             (let ((result (fresh-var))\n                                      (b      (parse-term e.b)))\n                                  (implicit-atom! (=/= (constant 0) b))\n                                  (implicit-atom! (*== result b (parse-term e.a)))\n                                  result))\n    (`(symbol->string ,e)       (build-l2r symbol-string e))\n    (`(string->symbol ,e)       (build-r2l symbol-string e))\n    (`(string->bytes  ,e)       (build-l2r string-bytes  e))\n    (`(bytes->string  ,e)       (build-r2l string-bytes  e))\n    (`(bytes->list    ,e)       (build-l2r bytes-list    e))\n    (`(list->bytes    ,e)       (build-r2l bytes-list    e))\n    (`(vector->list   ,e)       (build-l2r vector-list   e))\n    (`(list->vector   ,e)       (build-r2l vector-list   e))\n    ((cons _ _)                 (error \"unsupported function call\" e))\n    ((? vector?)                (error \"invalid term\" e))\n    (_                          (constant e))))\n\n(define (parse-rule e)\n  (parameterize ((current-fresh-variable 0)\n                 (current-implicit-atoms '()))\n    (let ((head (parse-atom (car e)))\n          (body (let loop ((e* (cdr e)))\n                  (match e*\n                    ('()            '())\n                    ((cons 'not e*) (map parse-negated-atom e*))\n                    ((cons e    e*) (cons (parse-atom e) (loop e*)))))))\n      (rule head (append body (current-implicit-atoms))))))\n\n(define current-fresh-relation (make-parameter #f))\n(define current-fresh-variable (make-parameter #f))\n(define current-implicit-atoms (make-parameter #f))\n\n(define (fresh-relation)\n  (let ((name.next (current-fresh-relation)))\n    (current-fresh-relation (+ name.next 1))\n    (relation-generated name.next)))\n\n(define (fresh-var)\n  (let ((name.next (current-fresh-variable)))\n    (current-fresh-variable (+ name.next 1))\n    (var name.next)))\n\n(define (implicit-atom! atom)\n  (let ((implicit-atoms (current-implicit-atoms)))\n    (unless implicit-atoms (error \"implicit-atom! called outside of a parsing context\"))\n    (current-implicit-atoms (cons atom implicit-atoms))))\n\n(define (rule-connected-components r)\n  (define (atom-vars a) (list->set (map var-name (filter var? (atom-args a)))))\n  (define (split-reachable a* vars.initial)\n    (let retry ((a* a*) (a*.reached '()) (vars.initial vars.initial))\n      (let loop ((a* a*) (a*.reached a*.reached) (a*.missed '()) (vars vars.initial))\n        (match a*\n          ('()         (if (equal? vars vars.initial)\n                         (values a*.reached a*.missed)\n                         (retry a*.missed a*.reached vars)))\n          ((cons a a*) (let ((vars.a (atom-vars a)))\n                         (if (set-empty? (set-intersect vars vars.a))\n                           (loop a* a*.reached (cons a a*.missed) vars)\n                           (loop a* (cons a a*.reached) a*.missed (set-union vars vars.a)))))))))\n  (let-values (((a*.reached a*.missed) (split-reachable (rule-body r) (atom-vars (rule-head r)))))\n    (if (null? a*.missed)\n      (list r)\n      (let ((a.factored (atom (fresh-relation) '())))\n        (cons (rule (rule-head r) (cons a.factored a*.reached))\n              (let retry ((a.head a.factored) (a* a*.missed))\n                (let ((a0 (car a*)))\n                  (let-values (((a*.reached a*.missed) (split-reachable (cdr a*) (atom-vars a0))))\n                    (if (null? a*.missed)\n                      (list (rule a.head (cons a0 a*.reached)))\n                      (let ((a.factored (atom (fresh-relation) '())))\n                        (cons (rule a.head (cons a.factored (cons a0 a*.reached)))\n                              (retry a.factored a*.missed))))))))))))\n\n(define (group x->key x->value xs)\n  (foldl (lambda (x k=>v*) (hash-update k=>v* (x->key x) (lambda (v*) (cons (x->value x) v*)) '()))\n         (hash) xs))\n\n(define (stratify rules)\n  (define (search r->r* r* seen)\n    (let loop ((r* r*) (seen seen) (finished '()))\n      (match r*\n        ('()         (values seen finished))\n        ((cons r r*) (if (set-member? seen r)\n                       (loop r* seen finished)\n                       (let-values (((seen finished) (loop (r->r* r) (set-add seen r) finished)))\n                         (loop r* seen (cons r finished))))))))\n  (define (atom-positive-relation     a) (let ((R (atom-relation a)))\n                                           (if (relation-negation? R) (relation-negation-target R) R)))\n  (define (rule-relation              r) (atom-relation (rule-head r)))\n  (define (rule-relation-dependencies r) (set->list (list->set (map atom-positive-relation (rule-body r)))))\n  (let ((R=>rule*       (group rule-relation (lambda (r) r) rules))\n        (R=>dependents* (foldl (lambda (r R=>d*)\n                                 (foldl (lambda (R R=>d*) (hash-update R=>d* R (lambda (d*) (cons r d*)) '()))\n                                        R=>d* (rule-relation-dependencies r)))\n                               (hash) rules)))\n    (define (rule-rule-dependents   r) (hash-ref R=>dependents* (rule-relation r)))\n    (define (rule-rule-dependencies r)\n      (apply append (map (lambda (R) (hash-ref R=>rule* R '())) (rule-relation-dependencies r))))\n    (let-values (((seen finished) (search rule-rule-dependencies rules (set))))\n      (let loop ((r* finished) (seen (set)) (strata '()))\n        (match r*\n          ('() strata)\n          ((cons r r*)\n           (if (set-member? seen r)\n             (loop r* seen strata)\n             (let-values (((seen scc) (search rule-rule-dependents (list r) seen)))\n               (let ((R* (list->set (map rule-relation scc))))\n                 (for-each (lambda (r)\n                             (for-each (lambda (R.neg)\n                                         (when (set-member? R* (relation-negation-target R.neg))\n                                           (error \"cyclic rule dependency through negation\"\n                                                  (map relation-name (set->list R*)))))\n                                       (filter relation-negation? (map atom-relation (rule-body r)))))\n                           scc))\n               (loop r* seen\n                     (cons (cons (if (or (pair? (cdr scc))\n                                         (member (rule-relation (car scc))\n                                                 (rule-relation-dependencies (car scc))))\n                                   'fixed-point 'once)\n                                 scc)\n                           strata))))))))))\n\n(define (hash-map-values h f) (make-immutable-hash (hash-map h (lambda (k v) (cons k (f v))))))\n\n(define R=>mode*.primitive\n  (hash-map-values\n    (hash prim.==            '((#f #t) (#t #f))\n          prim.<             '((#t #t))\n          prim.<=            '((#t #t))\n          prim.type==        '((#t #f))\n          prim.cons==        '((#t #t #f) (#f #f #t))\n          prim.+==           '((#t #t #f) (#t #f #t) (#f #t #t))\n          prim.*==           '((#t #t #f) (#t #f #t) (#f #t #t))\n          prim.symbol-string '((#f #t) (#t #f))\n          prim.string-bytes  '((#f #t) (#t #f))\n          prim.bytes-list    '((#f #t) (#t #f))\n          prim.vector-list   '((#f #t) (#t #f)))\n    list->set))\n\n(define (rule-terms r) (apply append (map atom-args (cons (rule-head r) (rule-body r)))))\n(define (rule-vars  r) (map var-name (filter var? (rule-terms r))))\n\n(define (rule-deduplicate-head-vars r)\n  (parameterize ((current-fresh-variable (+ (apply max -1 (filter integer? (rule-vars r))) 1))\n                 (current-implicit-atoms '()))\n    (let* ((head (rule-head r))\n           (args (map (let ((seen (mutable-set)))\n                        (lambda (t)\n                          (cond ((not (var? t))                  t)\n                                ((set-member? seen (var-name t)) (let ((v.new (fresh-var)))\n                                                                   (implicit-atom! (== v.new t))\n                                                                   v.new))\n                                (else                            (set-add! seen (var-name t)) t))))\n                      (atom-args head))))\n      (rule (atom (atom-relation head) args)\n            (append (current-implicit-atoms) (rule-body r))))))\n\n(define (infer-modes rules R=>mode*)\n  (let ((rules (map rule-deduplicate-head-vars rules)))\n    (let loop ((R=>mode*.initial R=>mode*))\n      (let ((R=>mode* (foldl (lambda (r R=>mode*) (rule-infer-modes r R=>mode*))\n                             R=>mode*.initial rules)))\n        (if (equal? R=>mode* R=>mode*.initial)\n          R=>mode*\n          (loop R=>mode*))))))\n\n(define (rule-infer-modes r R=>mode*)\n  (define (consistent-arity?! mode len a)\n    (unless (equal? (length mode) len)\n      (error \"relation arity mismatch\" (relation-name (atom-relation a)) (length mode) len)))\n  (let* ((head      (rule-head r))\n         (body      (rule-body r))\n         (vars.head (list->set (map var-name (filter var? (atom-args head))))))\n    (define (atom-mode* a)\n      (let ((R (atom-relation a)))\n        (let ((m* (if (relation-negation? R)\n                    (list (map (lambda (x) #t) (atom-args a)))\n                    (hash-ref R=>mode* R\n                              (lambda () (set (map (lambda (x) #f) (atom-args a)))))))\n              (l  (length (atom-args a))))\n          (for-each (lambda (m) (consistent-arity?! m l a)) (set->list m*))\n          m*)))\n    (define (atom-bound-vars a mode) (foldl (lambda (bound? t bound)\n                                              (if (and bound? (var? t))\n                                                (set-add bound (var-name t))\n                                                bound))\n                                            (set) mode (atom-args a)))\n    (define (search mode a* bound)\n      (consistent-arity?! mode (length (atom-args head)) head)\n      (let retry ((a* body) (bound.initial (set-union bound (atom-bound-vars head mode))))\n        (let loop ((a* a*) (a*.missed '()) (bound bound.initial))\n          (match a*\n            ('()\n             (cond ((not (equal? bound bound.initial)) (retry a*.missed bound))\n                   ((null? a*.missed)                  (list mode))\n                   (else (define (atom-v** a)\n                           (filter (lambda (v*) (subset? v* vars.head))\n                                   (map (lambda (m) (set-subtract (atom-bound-vars a m) bound))\n                                        (set->list (atom-mode* a)))))\n                         (define (constrain v*)\n                           (map (lambda (bound? t) (or bound? (and (var? t) (set-member? v* (var-name t)))))\n                                mode (atom-args head)))\n                         (let ((v** (foldl (lambda (v* v**.best)\n                                             (if (ormap (lambda (v*.best) (subset? v*.best v*)) v**.best)\n                                               v**.best\n                                               (cons v* v**.best)))\n                                           '() (sort (apply append (map atom-v** a*.missed))\n                                                     (lambda (a b) (< (set-count a) (set-count b)))))))\n                           (apply append (map (lambda (v*) (search (constrain v*) a*.missed bound)) v**))))))\n            ((cons a a*)\n             (let ((signature (map (lambda (t) (or (constant? t) (set-member? bound (var-name t))))\n                                   (atom-args a))))\n               (if (ormap (lambda (mode)\n                            (andmap (lambda (b?.mode b?.sig) (or b?.sig (not b?.mode))) mode signature))\n                          (set->list (atom-mode* a)))\n                 (loop a* a*.missed (set-union bound (list->set (map var-name (filter var? (atom-args a))))))\n                 (loop a* (cons a a*.missed) bound))))))))\n    (define (merge-modes mode*)\n      (define (subsumes? m0 m1) (andmap (lambda (b0? b1?) (or b1? (not b0?))) m0 m1))\n      (define (free-count m)    (length (filter not m)))\n      (foldl (lambda (m mode*) (if (ormap (lambda (m0) (subsumes? m0 m)) mode*)\n                                 mode*\n                                 (cons m mode*)))\n             '() (sort mode* (lambda (a b) (> (free-count a) (free-count b))))))\n    (let* ((vars.body   (foldl (lambda (a vars)\n                                 (foldl (lambda (t vars)\n                                          (if (var? t) (set-add vars (var-name t)) vars))\n                                        vars (atom-args a)))\n                               (set) body))\n           (vars.unused (set-subtract vars.head vars.body))\n           (m*.initial  (map (lambda (mode)\n                               (map (lambda (bound? t)\n                                      (or bound? (and (var? t) (set-member? vars.unused (var-name t)))))\n                                    mode (atom-args head)))\n                             (set->list (atom-mode* head))))\n           (m*          (merge-modes (apply append (map (lambda (m) (search m body (set))) m*.initial)))))\n      (if (null? m*)\n        (error \"relation has no finite mode\" (relation-name (atom-relation head)))\n        (hash-set R=>mode* (atom-relation head) (list->set m*))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/kanren-notation-micro.rkt",
    "content": "#lang racket/base\n(provide\n  facts fresh conde\n  define-relation\n  run*)\n(require \"micro.rkt\")  ; Basic micro core with quadratic time fact accumulation\n;(require \"micro-with-sets.rkt\")  ; A faster version of the micro core\n\n;;; Formulas are wrapped ambitions which discover their producer dependencies.\n\n(define (fm:true  seen d*) (values seen d* unit))\n(define (fm:false seen d*) (values seen d* fail))\n\n(define (fm:and fm0 fm1)\n  (lambda (seen p*)\n    (let-values (((seen p* a0) (fm0 seen p*)))\n      (let-values (((seen p* a1) (fm1 seen p*)))\n        (values seen p* (conj a0 a1))))))\n(define (fm:or fm0 fm1)\n  (lambda (seen p*)\n    (let-values (((seen p* a0) (fm0 seen p*)))\n      (let-values (((seen p* a1) (fm1 seen p*)))\n        (values seen p* (disj a0 a1))))))\n\n(define (fm:and+ fm0 fm*)\n  (if (null? fm*)\n    fm0\n    (fm:and fm0 (fm:and+ (car fm*) (cdr fm*)))))\n(define (fm:or+ fm0 fm*)\n  (if (null? fm*)\n    fm0\n    (fm:or fm0 (fm:or+ (car fm*) (cdr fm*)))))\n\n(define (fm:and* fm*)\n  (if (null? fm*)\n    fm:true\n    (fm:and+ (car fm*) (cdr fm*))))\n(define (fm:or* fm*)\n  (if (null? fm*)\n    fm:false\n    (fm:or+ (car fm*) (cdr fm*))))\n\n(define (fm:== t0 t1) (lambda (seen p*) (values seen p* (== t0 t1))))\n\n;;;;;;;;;;;;;;\n;;; Syntax ;;;\n;;;;;;;;;;;;;;\n\n;; TODO: defining facts using == leads to enormous fact production redundancy,\n;; exposing performance problems with unique-append since it is a quadratic\n;; implementation of set union.  Since we want to be able to support large\n;; relation definitions, the right way to fix this is for the core to store\n;; facts in efficient sets instead of lists.  But we could also reduce\n;; redundancy by stratifying the evaluation of relation dependencies.  This\n;; would lead to fact-oriented relations only being evaluated once, at the\n;; start of a run.\n(define (facts vars tuples)\n  (fm:or* (map (lambda (tuple) (fm:== vars tuple)) tuples)))\n\n;; TODO: rule safety checking?\n(define-syntax-rule\n  (define-relation (name attr ...) fm0 fm* ...)\n  (define (name attr ...)\n    (lambda (seen p*)\n      (let ((head   (list name (var 'attr) ...))\n            (fm     (fresh (attr ...) fm0 fm* ...))\n            (a.call (relate (list name attr ...))))\n        (if (member name seen)\n          (values seen p* a.call)\n          (let-values (((seen p* a) (fm (cons name seen) p*)))\n            (values seen (cons (realize head a) p*) a.call)))))))\n\n(define-syntax-rule\n  (fresh (x ...) fm0 fm* ...)\n  (let ((x (var 'x)) ...) (fm:and+ fm0 (list fm* ...))))\n\n(define-syntax-rule\n  (conde (fm00 fm0* ...)\n         (fm0 fm* ...) ...)\n  (fm:or+ (fm:and+ fm00 (list fm0* ...))\n          (list (fm:and+ fm0 (list fm* ...) ...) ...)))\n\n(define-syntax run*\n  (syntax-rules ()\n    ((_ (x ...) fm0 fm* ...)\n     (let ((x (var 'x)) ...)\n       (define-relation (query x ...) fm0 fm* ...)\n       (let-values (((seen p* a) ((query x ...) '() '())))\n         (let ((F* (exhaust* p* '())))\n           (map cdr (filter (lambda (F) (eq? (car F) query)) F*))))))\n    ((_ x fm0 fm* ...) (map car (run* (x) fm0 fm* ...)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/micro-plus.rkt",
    "content": "#lang racket/base\n(provide\n  (struct-out var)\n  unit fail\n  conj conj+ conj*\n  disj disj+ disj*\n  == relate reject-relate compute reject-compute\n  realize produce-once* exhaust*)\n(require racket/set)\n\n;; This version of the micro core supports fact merging for aggregation.\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Terms and substitution ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(struct var (name) #:prefab)\n(define subst.empty '())\n\n(define (subst-extend S x t)\n  (let ((name.x (var-name x)))\n    (and (not (occurs? S name.x t))\n         (cons (cons name.x t) S))))\n\n(define (walk S t)\n  (cond ((var? t) (let ((kv (assoc (var-name t) S)))\n                    (if kv (walk S (cdr kv)) t)))\n        (else     t)))\n\n(define (walk* S t)\n  (cond ((var? t)    (let ((kv (assoc (var-name t) S)))\n                       (if kv (walk* S (cdr kv)) t)))\n        ((pair? t)   (cons (walk* S (car t)) (walk* S (cdr t))))\n        ((vector? t) (list->vector (walk* S (vector->list t))))\n        (else        t)))\n\n(define (occurs? S name.x t)\n  (let ((t (walk S t)))\n    (or (and (var? t) (equal? name.x (var-name t)))\n        (and (pair? t) (or (occurs? S name.x (car t)) (occurs? S name.x (cdr t))))\n        (and (vector? t) (occurs? S name.x (vector->list t))))))\n\n(define (unify S u v)\n  (let ((u (walk S u)) (v (walk S v)))\n    (cond ((eqv? u v)  S)\n          ((var? u)    (if (and (var? v) (equal? (var-name u) (var-name v)))\n                         S\n                         (subst-extend S u v)))\n          ((var? v)    (subst-extend S v u))\n          ((pair? u)   (and (pair? v)\n                            (let ((S (unify S (car u) (car v))))\n                              (and S\n                                   (unify S (cdr u) (cdr v))))))\n          ((vector? u) (and (vector? v)\n                            (unify S (vector->list u) (vector->list v))))\n          (else        (and (equal? u v) S)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Goals, ambitions, producers ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Goal     = S -> S*\n;; Ambition = F* -> Goal\n;; Producer = F* -> F*\n\n(define (bind S* g) (if (null? S*) '() (append (g (car S*)) (bind (cdr S*) g))))\n\n(define unit         (lambda (F*) (lambda (S) (list S))))\n(define fail         (lambda (F*) (lambda (S) '())))\n(define (== t0 t1)   (lambda (F*) (lambda (S) (let ((S (unify S t0 t1)))\n                                                (if S (list S) '())))))\n;; NOTE: use =/= carefully as it currently implements negation-as-failure\n(define (=/= t0 t1)  (lambda (F*) (lambda (S) (let ((S.new (unify S t0 t1)))\n                                                (if S.new '() (list S))))))\n(define (conj a0 a1) (lambda (F*) (let ((g0 (a0 F*)) (g1 (a1 F*)))\n                                    (lambda (S) (bind (g0 S) g1)))))\n(define (disj a0 a1) (lambda (F*) (let ((g0 (a0 F*)) (g1 (a1 F*)))\n                                    (lambda (S) (append (g0 S) (g1 S))))))\n(define (conj+ a a*) (if (null? a*) a (conj a (conj+ (car a*) (cdr a*)))))\n(define (disj+ a a*) (if (null? a*) a (disj a (disj+ (car a*) (cdr a*)))))\n(define (conj* a*)   (if (null? a*) unit (conj+ (car a*) (cdr a*))))\n(define (disj* a*)   (if (null? a*) fail (disj+ (car a*) (cdr a*))))\n\n(define (relate atom)\n  (lambda (F*)  ; This staging significantly improves performance.\n    ((disj* (map (lambda (F) (== atom F))\n                 (filter (lambda (F) (unify subst.empty atom F)) F*)))\n     'ignored)))\n(define (reject-relate atom)\n  ;; NOTE: this ambition has a fully-ground mode.\n  (lambda (F*)\n    ((conj* (map (lambda (F) (=/= atom F))\n                 (filter (lambda (F) (unify subst.empty atom F)) F*)))\n     'ignored)))\n\n(define (compute proc args)\n  (lambda (F*) (lambda (S) ((apply proc (walk* S args)) S))))\n(define (reject-compute proc args)\n  ;; NOTE: this ambition has a fully-ground mode.\n  (lambda (F*) (lambda (S) (if (null? ((apply proc (walk* S args)) S))\n                             (list S)\n                             '()))))\n\n(define remember         (lambda (F*) F*))\n(define (realize atom a) (lambda (F*) (map (lambda (S) (walk* S atom))\n                                           ((a F*) subst.empty))))\n(define (combine p0 p1)  (lambda (F*) (append (p0 F*) (p1 F*))))\n(define (combine* p*)    (if (null? p*)\n                           remember\n                           (combine (car p*) (combine* (cdr p*)))))\n\n(define (aggregate predicate=>merge F*)\n  (let loop ((F*                    F*)\n             (F*.skipped            '())\n             (predicate=>key=>value (make-immutable-hash\n                                      (map (lambda (key) (cons key (hash)))\n                                           (hash-keys predicate=>merge)))))\n    (if (null? F*)\n      (apply append\n             F*.skipped\n             (map (lambda (p&k=>v)\n                    (let ((predicate (car p&k=>v)))\n                      (map (lambda (k&v)\n                             (cons predicate\n                                   (reverse (cons (cdr k&v) (car k&v)))))\n                           (hash->list (cdr p&k=>v)))))\n                  (hash->list predicate=>key=>value)))\n      (let* ((F         (car F*))\n             (predicate (car F))\n             (merge     (hash-ref predicate=>merge predicate #f)))\n        (if merge\n          (loop (cdr F*) F*.skipped\n                (hash-update\n                  predicate=>key=>value\n                  predicate\n                  (lambda (key=>value)\n                    (let* ((reversed (reverse (cdr F)))\n                           (key      (cdr reversed))\n                           (value    (car reversed)))\n                      (hash-set key=>value key\n                                (if (hash-has-key? key=>value key)\n                                  (merge (hash-ref key=>value key) value)\n                                  value))))))\n          (loop (cdr F*) (cons F F*.skipped) predicate=>key=>value))))))\n\n\n(define (produce-once p predicate=>merge F*)\n  (list->set (aggregate predicate=>merge (p (set->list F*)))))\n\n(define (produce-once* p* predicate=>merge F*)\n  (set->list (produce-once (combine* p*) predicate=>merge (list->set F*))))\n\n(define (exhaust p predicate=>merge F*)\n  (let ((F*.new (produce-once p predicate=>merge F*)))\n    (if (set=? F* F*.new)\n      F*.new\n      (exhaust p predicate=>merge F*.new))))\n\n(define (exhaust* p* predicate=>merge F*)\n  (set->list (exhaust (combine* p*) predicate=>merge (list->set F*))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/micro-with-sets.rkt",
    "content": "#lang racket/base\n(provide\n  (struct-out var)\n  unit fail\n  conj conj+ conj*\n  disj disj+ disj*\n  == relate\n  realize exhaust*)\n(require racket/set)\n\n;; This version of the micro core uses sets to accumulate facts in linear time.\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Terms and substitution ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(struct var (name) #:prefab)\n(define subst.empty '())\n\n(define (subst-extend S x t)\n  (and (not (occurs? S (walk S x) t))\n       (cons (cons (var-name x) t) S)))\n\n(define (walk S t)\n  (cond ((var? t) (let ((kv (assoc (var-name t) S)))\n                    (if kv (walk S (cdr kv)) t)))\n        (else     t)))\n\n(define (walk* S t)\n  (cond ((var? t)    (let ((kv (assoc (var-name t) S)))\n                       (if kv (walk* S (cdr kv)) t)))\n        ((pair? t)   (cons (walk* S (car t)) (walk* S (cdr t))))\n        ((vector? t) (list->vector (walk* S (vector->list t))))\n        (else        t)))\n\n(define (occurs? S x t)\n  (let ((t (walk S t)))\n    (or (equal? x t)\n        (and (pair? t) (or (occurs? S x (car t)) (occurs? S x (cdr t))))\n        (and (vector? t) (occurs? S x (vector->list t))))))\n\n(define (unify S u v)\n  (let ((u (walk S u)) (v (walk S v)))\n    (cond ((eqv? u v)  S)\n          ((var? u)    (if (and (var? v) (equal? (var-name u) (var-name v)))\n                         S\n                         (subst-extend S u v)))\n          ((var? v)    (subst-extend S v u))\n          ((pair? u)   (and (pair? v)\n                            (let ((S (unify S (car u) (car v))))\n                              (and S\n                                   (unify S (cdr u) (cdr v))))))\n          ((vector? u) (and (vector? v)\n                            (unify S (vector->list u) (vector->list v))))\n          (else        (and (equal? u v) S)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Goals, ambitions, producers ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Goal     = S -> S*\n;; Ambition = F* -> Goal\n;; Producer = F* -> F*\n\n(define (bind S* g) (if (null? S*) '() (append (g (car S*)) (bind (cdr S*) g))))\n\n(define unit         (lambda (F*) (lambda (S) (list S))))\n(define fail         (lambda (F*) (lambda (S) '())))\n(define (== t0 t1)   (lambda (F*) (lambda (S) (let ((S (unify S t0 t1)))\n                                                (if S (list S) '())))))\n(define (conj a0 a1) (lambda (F*) (let ((g0 (a0 F*)) (g1 (a1 F*)))\n                                    (lambda (S) (bind (g0 S) g1)))))\n(define (disj a0 a1) (lambda (F*) (let ((g0 (a0 F*)) (g1 (a1 F*)))\n                                    (lambda (S) (append (g0 S) (g1 S))))))\n(define (conj+ a a*) (if (null? a*) a (conj a (conj+ (car a*) (cdr a*)))))\n(define (disj+ a a*) (if (null? a*) a (disj a (disj+ (car a*) (cdr a*)))))\n(define (conj* a*)   (if (null? a*) unit (conj+ (car a*) (cdr a*))))\n(define (disj* a*)   (if (null? a*) fail (disj+ (car a*) (cdr a*))))\n\n(define (relate atom)\n  (lambda (F*)  ; This staging significantly improves performance.\n    ((disj* (map (lambda (F) (== atom F))\n                 (filter (lambda (F) (unify subst.empty atom F))\n                         (set->list F*))))\n     'ignored)))\n\n(define remember         (lambda (F*) F*))\n(define (realize atom a) (lambda (F*)\n                           (list->set (map (lambda (S) (walk* S atom))\n                                           ((a F*) subst.empty)))))\n(define (combine p0 p1)  (lambda (F*) (set-union (p0 F*) (p1 F*))))\n(define (combine* p*)    (if (null? p*)\n                           remember\n                           (combine (car p*) (combine* (cdr p*)))))\n(define (exhaust p F*)   (let ((F*.new (p F*)))\n                           (if (= (set-count F*) (set-count F*.new))\n                             F*\n                             (exhaust p F*.new))))\n(define (exhaust* p* F*) (set->list (exhaust (combine* p*) (list->set F*))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/micro.rkt",
    "content": "#lang racket/base\n(provide\n  (struct-out var)\n  unit fail\n  conj conj+ conj*\n  disj disj+ disj*\n  == relate\n  realize exhaust*)\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Terms and substitution ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(struct var (name) #:prefab)\n(define subst.empty '())\n\n(define (subst-extend S x t)\n  (let ((name.x (var-name x)))\n    (and (not (occurs? S name.x t))\n         (cons (cons name.x t) S))))\n\n(define (walk S t)\n  (cond ((var? t) (let ((kv (assoc (var-name t) S)))\n                    (if kv (walk S (cdr kv)) t)))\n        (else     t)))\n\n(define (walk* S t)\n  (cond ((var? t)    (let ((kv (assoc (var-name t) S)))\n                       (if kv (walk* S (cdr kv)) t)))\n        ((pair? t)   (cons (walk* S (car t)) (walk* S (cdr t))))\n        ((vector? t) (list->vector (walk* S (vector->list t))))\n        (else        t)))\n\n(define (occurs? S name.x t)\n  (let ((t (walk S t)))\n    (or (and (var? t) (equal? name.x (var-name t)))\n        (and (pair? t) (or (occurs? S name.x (car t)) (occurs? S name.x (cdr t))))\n        (and (vector? t) (occurs? S name.x (vector->list t))))))\n\n(define (unify S u v)\n  (let ((u (walk S u)) (v (walk S v)))\n    (cond ((eqv? u v)  S)\n          ((var? u)    (if (and (var? v) (equal? (var-name u) (var-name v)))\n                         S\n                         (subst-extend S u v)))\n          ((var? v)    (subst-extend S v u))\n          ((pair? u)   (and (pair? v)\n                            (let ((S (unify S (car u) (car v))))\n                              (and S\n                                   (unify S (cdr u) (cdr v))))))\n          ((vector? u) (and (vector? v)\n                            (unify S (vector->list u) (vector->list v))))\n          (else        (and (equal? u v) S)))))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Goals, ambitions, producers ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;\n\n;; Goal     = S -> S*\n;; Ambition = F* -> Goal\n;; Producer = F* -> F*\n\n(define (bind S* g) (if (null? S*) '() (append (g (car S*)) (bind (cdr S*) g))))\n\n(define unit         (lambda (F*) (lambda (S) (list S))))\n(define fail         (lambda (F*) (lambda (S) '())))\n(define (== t0 t1)   (lambda (F*) (lambda (S) (let ((S (unify S t0 t1)))\n                                                (if S (list S) '())))))\n(define (conj a0 a1) (lambda (F*) (let ((g0 (a0 F*)) (g1 (a1 F*)))\n                                    (lambda (S) (bind (g0 S) g1)))))\n(define (disj a0 a1) (lambda (F*) (let ((g0 (a0 F*)) (g1 (a1 F*)))\n                                    (lambda (S) (append (g0 S) (g1 S))))))\n(define (conj+ a a*) (if (null? a*) a (conj a (conj+ (car a*) (cdr a*)))))\n(define (disj+ a a*) (if (null? a*) a (disj a (disj+ (car a*) (cdr a*)))))\n(define (conj* a*)   (if (null? a*) unit (conj+ (car a*) (cdr a*))))\n(define (disj* a*)   (if (null? a*) fail (disj+ (car a*) (cdr a*))))\n\n(define (relate atom)\n  (lambda (F*)  ; This staging significantly improves performance.\n    ((disj* (map (lambda (F) (== atom F))\n                 (filter (lambda (F) (unify subst.empty atom F)) F*)))\n     'ignored)))\n\n(define (unique-cons x xs) (if (member x xs) xs (cons x xs)))\n(define (unique-append xs ys)\n  (if (null? xs)\n    ys\n    (unique-cons (car xs) (unique-append (cdr xs) ys))))\n\n(define remember         (lambda (F*) F*))\n(define (realize atom a) (lambda (F*) (map (lambda (S) (walk* S atom))\n                                           ((a F*) subst.empty))))\n(define (combine p0 p1)  (lambda (F*) (unique-append (p0 F*) (p1 F*))))\n(define (combine* p*)    (if (null? p*)\n                           remember\n                           (combine (car p*) (combine* (cdr p*)))))\n(define (exhaust p F*)   (let ((F*.new (p F*)))\n                           (if (eq? F* F*.new) F* (exhaust p F*.new))))\n(define (exhaust* p* F*) (exhaust (combine* p*) F*))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/test-basic.rkt",
    "content": "#lang racket/base\n(require \"basic-naive.rkt\" racket/list racket/pretty)\n(print-as-expression #f)\n;(pretty-print-abbreviate-read-macros #f)\n\n(define-syntax-rule\n  (pretty-results example ...)\n  (begin (begin (pretty-write 'example)\n                (pretty-write '==>)\n                (pretty-write example)\n                (newline)) ...))\n\n;;;;;;;;;;;;;;;;;;;;;;;\n;;; Graph traversal ;;;\n;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-relation (edge a b)\n  (facts (list a b)\n         '((a b)\n           (b c)\n           (d e)\n           (e f)\n           (b f)\n           (f a)  ; comment this edge for an acyclic graph\n           )))\n\n(define-relation (path a b)\n  (conde ((edge a b))\n         ((fresh (mid)\n            (edge a mid)\n            (path mid b)))))\n\n(pretty-results\n  (run* (x)   (path 'a x))\n  (run* (x)   (path x 'f))\n  (run* (x y) (path x y))\n  (run* (x y) (edge x y)))\n\n\n;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Finite arithmetic ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-relation (+o a b c)\n  (facts (list a b c)\n         (append* (map (lambda (a)\n                         (map (lambda (b) (list a b (+ a b)))\n                              (range 100)))\n                       (range 100)))))\n\n(define-relation (*o a b c)\n  (facts (list a b c)\n         (append* (map (lambda (a)\n                         (map (lambda (b) (list a b (* a b)))\n                              (range 100)))\n                       (range 100)))))\n\n(define-relation ()\n           (pretty-write result)\n           (newline)) ...))\n\n;;;;;;;;;;;;;;;;;;;;;;;\n;;; Graph traversal ;;;\n;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-relation (edge a b)\n  (facts (list a b)\n         '((a b)\n           (b c)\n           (d e)\n           (e f)\n           (b f)\n           (f a)  ; comment this edge for an acyclic graph\n           )))\n\n(define-relation (path a b)\n  (conde ((edge a b))\n         ((fresh (mid)\n            (edge a mid)\n            (path mid b)))))\n\n(pretty-results\n  (run* (x)   (path 'a x))\n  (run* (x)   (path x 'f))\n  (run* (x y) (path x y))\n  (run* (x y) (edge x y)))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Finite arithmetic ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define-relation (+o a b c)\n  (facts (list a b c)\n         (apply append (map (lambda (a)\n                              (map (lambda (b) (list a b (+ a b)))\n                                   (range 50)))\n                            (range 50)))))\n\n(define-relation (*o a b c)\n  (facts (list a b c)\n         (apply append (map (lambda (a)\n                              (map (lambda (b) (list a b (* a b)))\n                                   (range 50)))\n                            (range 50)))))\n\n(define-relation ()\n           (pretty-write result)\n           (newline)) ...))\n\n(define (run-stratified-queries\n          predicate=>compute predicate=>merge rules.query rule** facts)\n  (let ((facts (run-stratified predicate=>compute predicate=>merge\n                               (cons rules.query rule**) facts)))\n    (map (lambda (predicate.query)\n           (filter (lambda (fact) (eq? (car fact) predicate.query)) facts))\n         (map caar rules.query))))\n\n(define (run-queries rules.query rules facts)\n  (run-stratified-queries (hash) (hash) rules.query (list rules) facts))\n\n;;;;;;;;;;;;;;;;;;;;;;;\n;;; Graph traversal ;;;\n;;;;;;;;;;;;;;;;;;;;;;;\n\n(pretty-results\n  (run-queries\n    '(((q1 x)   (path 'a x))\n      ((q2 x)   (path x 'f))\n      ((q3 x y) (path x y))\n      ((q4 x y) (edge x y)))\n    '(((path x y) (edge x y))\n      ((path x z) (edge x y) (path y z)))\n    '((edge a b)\n      (edge b c)\n      (edge d e)\n      (edge e f)\n      (edge b f)\n      (edge f a)  ; comment this edge for an acyclic graph\n      )))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Finite arithmetic ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define facts.+ (apply append (map (lambda (a)\n                                     (map (lambda (b) `(+o ,a ,b ,(+ a b)))\n                                          (range 50)))\n                                   (range 50))))\n(define facts.* (apply append (map (lambda (a)\n                                     (map (lambda (b) `(*o ,a ,b ,(* a b)))\n                                          (range 50)))\n                                   (range 50))))\n(define facts.< (apply append (map (lambda (a)\n                                     (apply append (map (lambda (b) (if (< a b)\n                                                                      `(()\n           (pretty-write result)\n           (newline)) ...))\n\n(define (run-queries rules.query rules facts)\n  (let ((facts (run-datalog (append rules.query rules) facts)))\n    (map (lambda (predicate.query)\n           (filter (lambda (fact) (eq? (car fact) predicate.query)) facts))\n         (map caar rules.query))))\n\n;;;;;;;;;;;;;;;;;;;;;;;\n;;; Graph traversal ;;;\n;;;;;;;;;;;;;;;;;;;;;;;\n\n(pretty-results\n  (run-queries\n    '(((q1 x)   (path 'a x))\n      ((q2 x)   (path x 'f))\n      ((q3 x y) (path x y))\n      ((q4 x y) (edge x y)))\n    '(((path x y) (edge x y))\n      ((path x z) (edge x y) (path y z)))\n    '((edge a b)\n      (edge b c)\n      (edge d e)\n      (edge e f)\n      (edge b f)\n      (edge f a)  ; comment this edge for an acyclic graph\n      )))\n\n;;;;;;;;;;;;;;;;;;;;;;;;;\n;;; Finite arithmetic ;;;\n;;;;;;;;;;;;;;;;;;;;;;;;;\n\n(define facts.+ (apply append (map (lambda (a)\n                                     (map (lambda (b) `(+o ,a ,b ,(+ a b)))\n                                          (range 50)))\n                                   (range 50))))\n(define facts.* (apply append (map (lambda (a)\n                                     (map (lambda (b) `(*o ,a ,b ,(* a b)))\n                                          (range 50)))\n                                   (range 50))))\n(define facts.< (apply append (map (lambda (a)\n                                     (apply append (map (lambda (b) (if (< a b)\n                                                                      `((set (map var-name (filter var? atom))))\n\n(define (parse-term expr)\n  (match expr\n    ((? symbol?) (var expr))\n    (`(quote ,c) c)\n    ((cons _ _)  (error \"unsupported function call\" expr))\n    (_           expr)))\n\n(define (parse-atom expr) (cons (car expr) (map parse-term (cdr expr))))\n\n(struct rule (head body+ body-) #:prefab)\n\n(define (parse-rule expr)\n  (let ((head (parse-atom (car expr))))\n    (let loop ((e* (cdr expr)) (atoms.+ '()))\n      (define (finish atoms.-)\n        (let ((r (rule head (reverse atoms.+) atoms.-)))\n          (let ((vars.+ (apply set-union (set) (map atom-vars (rule-body+ r))))\n                (vars.- (apply set-union (set) (map atom-vars (rule-body- r)))))\n            (unless (subset? (atom-vars (rule-head r)) vars.+)\n              (error \"rule head is not range-restricted\" expr))\n            (unless (subset? vars.- vars.+)\n              (error \"rule negated body atoms are not range-restricted\" expr)))\n          r))\n      (match e*\n        ('()            (finish '()))\n        ((cons 'not e*) (finish (map parse-atom e*)))\n        ((cons e    e*) (loop e* (cons (parse-atom e) atoms.+)))))))\n\n(define (run-stratified predicate=>proc predicate=>merge e**.rules F*)\n  (define (enforce r)\n    (match-define (rule head atoms.+ atoms.-) r)\n    (define (+atom->a atom)\n      (let ((proc (hash-ref predicate=>proc (car atom) #f)))\n        (if proc\n          (compute proc (cdr atom))\n          (relate atom))))\n    (define (-atom->a atom)\n      (let ((proc (hash-ref predicate=>proc (car atom) #f)))\n        (if proc\n          (reject-compute proc (cdr atom))\n          (reject-relate atom))))\n    (realize head (conj* (append (map +atom->a atoms.+) (map -atom->a atoms.-)))))\n  (foldr (lambda (c&p* F*)\n           (match c&p*\n             (`(run-once        . ,p*) (produce-once* p* predicate=>merge F*))\n             (`(run-fixed-point . ,p*) (exhaust*      p* predicate=>merge F*))))\n         F*\n         (map (lambda (e*.rules)\n                (define (build e*) (map enforce (map parse-rule e*)))\n                (match e*.rules\n                  ((cons (and (or 'run-once 'run-fixed-point) cmd) e*.rules)\n                   (cons cmd (build e*.rules)))\n                  (_ (cons 'run-fixed-point (build e*.rules)))))\n              e**.rules)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/datalog/unmanaged-notation-micro.rkt",
    "content": "#lang racket/base\n(provide run-datalog)\n(require \"micro.rkt\" (except-in racket/match ==))\n;(require \"micro-with-sets.rkt\" (except-in racket/match ==))\n\n;; This example syntax demonstrates how to use the core concepts.  This is only\n;; one possible syntax.  For instance, you could also implement a Kanren-style\n;; syntax that uses the same core concepts.\n\n;; - Programs are made up of rules and facts:\n;;   - Atom: a predicate constant followed by zero or more terms\n;;   - Rule: a head atom followed by zero or more body atoms\n;;   - Fact: a single atom\n\n;; - Terms in rules may be variables or constants:\n;;   - An unquoted symbol is treated as a variable.\n;;   - Any quoted value is treated as a constant.\n;;   - All other non-pair values are treated as constants.\n;;   - Variables cannot appear nested in other terms.\n\n;; - Terms in facts are always unquoted constants, including symbols and pairs.\n\n;; - There are no queries.  There are only rules and facts.\n;;   - e.g., (run-datalog rules facts) ==> more-facts\n\n(define (atom-vars atom) (filter var? atom))\n\n(define (rule-safe?! rule)\n  (let ((vars.body (apply append (map atom-vars (cdr rule)))))\n    (for-each (lambda (var.head) (or (member var.head vars.body)\n                                     (error \"unsafe rule\" rule)))\n              (atom-vars (car rule)))))\n\n(define (parse-term expr)\n  (match expr\n    ((? symbol?) (var expr))\n    (`(quote ,c) c)\n    ((cons _ _)  (error \"unsupported function call\" expr))\n    (_           expr)))\n\n(define (parse-atom expr) (cons (car expr) (map parse-term (cdr expr))))\n(define (parse-rule expr) (let ((rule (map parse-atom expr)))\n                            (rule-safe?! rule)\n                            rule))\n\n(define (enforce rule) (realize (car rule) (conj* (map relate (cdr rule)))))\n\n(define (run-datalog e*.rules F*)\n  (exhaust* (map enforce (map parse-rule e*.rules)) F*))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/equivalence-database.rkt",
    "content": "#lang racket/base\n(provide build-equivalence-database)\n(require\n  racket/unsafe/ops\n  ;\"../dbk/safe-unsafe.rkt\"\n  \"../dbk/database.rkt\" racket/fixnum)\n\n(define name.equiv-edge         'equivalence-edge)\n(define name.equiv-class-member 'equivalence-class-member)\n\n;; NOTE: for best performance, the left node of each edge should be the alphabetically smaller text\n(define (build-equivalence-database path en.edge*)\n  (define db.equiv (database path))\n  (unless (or (database-relation-name? db.equiv name.equiv-edge)\n              (database-relation-name? db.equiv name.equiv-class-member))\n    (let ((r.equiv-edge (build-enumerator-relation db.equiv '(text text) en.edge*)))\n      (relation-name-set! r.equiv-edge name.equiv-edge)\n      (relation-attributes-set! r.equiv-edge '(A B))\n      (database-commit! db.equiv)))\n  (let ((r.equiv-edge (database-relation db.equiv name.equiv-edge)))\n    (relation-full-compact! r.equiv-edge)\n    (relation-index-add! r.equiv-edge '(A B))\n    (database-commit! db.equiv)\n    (unless (database-relation-name? db.equiv name.equiv-class-member)\n      (let-values (((text=>id id=>text) (relation-text-dicts r.equiv-edge #f)))\n        (let* ((A=>B=>1   (relation-index-dict r.equiv-edge '(A B) #f))\n               (count.id* (dict-count id=>text))\n               (id=>id    (make-fxvector count.id*)))\n          (define (walk i)\n            (let loop ((id.child i))\n              (let ((id.parent (unsafe-fxvector-ref id=>id id.child)))\n                (if (unsafe-fx= id.parent id.child)\n                    id.child\n                    (let ((id.top (loop id.parent)))\n                      (unless (unsafe-fx= id.top id.parent)\n                        (unsafe-fxvector-set! id=>id id.child id.top))\n                      id.top)))))\n          (range-for-each (lambda (i) (unsafe-fxvector-set! id=>id i i)) count.id*)\n          ((dict-enumerator A=>B=>1)\n           (lambda (id.A B=>1)\n             (let ((current (walk id.A)))\n               (define (unify! candidate)\n                 (let ((candidate (walk candidate)))\n                   (cond ((unsafe-fx< candidate current) (unsafe-fxvector-set! id=>id current candidate)\n                                                         (set! current candidate))\n                         (else (unsafe-fxvector-set! id=>id candidate current)))))\n               ((dict-key-enumerator B=>1) (lambda (id.B) (unify! id.B))))))\n          (range-for-each walk count.id*)  ; walk performs path compression\n          (let ((r.equiv-class-member\n                  (build-enumerator-relation\n                    db.equiv '(text text)\n                    (let ((id->text (lambda (id)\n                                      (dict-ref id=>text id (lambda (v) v)\n                                                (lambda () (error \"invalid text id\" id))))))\n                      (lambda (yield)\n                        (let loop ((i 0))\n                          (when (< i count.id*)\n                            (yield (list (id->text (unsafe-fxvector-ref id=>id i))\n                                         (id->text i)))\n                            (loop (unsafe-fx+ i 1)))))))))\n            (relation-name-set! r.equiv-class-member name.equiv-class-member)\n            (relation-attributes-set! r.equiv-class-member '(representative member))\n            (relation-delete! r.equiv-edge)\n            (database-commit! db.equiv)))))\n    (let ((r.equiv-class-member (database-relation db.equiv name.equiv-class-member)))\n      (relation-full-compact! r.equiv-class-member)\n      (relation-index-add! r.equiv-class-member '(representative member) '(member representative))\n      (database-commit! db.equiv))\n    (database-trash-empty! db.equiv)\n    db.equiv))\n\n(define (range-for-each p count)\n  (let loop ((i 0)) (when (< i count) (p i) (loop (unsafe-fx+ i 1)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/microbenchmarks/integer-bytes-throughput.rkt",
    "content": "#lang racket/base\n(require\n  racket/fixnum\n  racket/unsafe/ops\n  )\n\n(define count 32)\n;(define width 4)\n(define width 3)\n;(define width (read))\n(define total (* count width))\n(define bstr  (make-bytes total))\n(define vec   (make-vector 1))\n\n(define (bytes-nat-set! n size __ ___ bs offset)\n  ;(integer->integer-bytes n size #f #t bs offset) (void)\n  (let ((end (+ offset size)))\n    (let loop ((i offset) (shift (* 8 (- size 1))))\n      (cond ((< i end) (bytes-set! bs i (fxand 255 (fxrshift n shift)))\n                       (loop (+ i 1) (- shift 8)))\n            (else      bs)))))\n;(define (unsafe-bytes-nat-set! n size __ ___ bs offset)\n  ;(let ((end (unsafe-fx+ offset size)))\n    ;(let loop ((i offset) (shift (unsafe-fx* 8 (unsafe-fx- size 1))))\n      ;(cond ((unsafe-fx< i end) (unsafe-bytes-set! bs i (unsafe-fxand 255 (unsafe-fxrshift n shift)))\n                                ;(loop (unsafe-fx+ i 1) (unsafe-fx- shift 8)))\n            ;(else               bs)))))\n\n(define (unsafe-bytes-nat-set! n size __ ___ bs offset)\n  (let loop ((i     offset)\n             ;(shift (unsafe-fx* 8 (unsafe-fx- size 1)))\n             (shift (unsafe-fxlshift (unsafe-fx- size 1) 3))\n             )\n    (when (unsafe-fx<= 0 shift)\n      (unsafe-bytes-set! bs i (unsafe-fxand 255 (unsafe-fxrshift n shift)))\n      (loop (unsafe-fx+ i     1)\n            (unsafe-fx- shift 8)))))\n\n(define (unrolled-unsafe-bytes-nat-set!/1 n size __ ___ bs i)\n  ;; assume size=1\n  (unsafe-bytes-set! bs i n)\n  )\n\n(define (unrolled-unsafe-bytes-nat-set!/2 n size __ ___ bs i)\n  ;; assume size=2\n  (unsafe-bytes-set! bs i       (unsafe-fxand 255 (unsafe-fxrshift n 8)))\n  (unsafe-bytes-set! bs (+ i 1) (unsafe-fxand 255 n))\n  )\n\n(define (unrolled-unsafe-bytes-nat-set!/3 n size __ ___ bs i)\n  ;; assume size=3\n  (unsafe-bytes-set! bs i       (unsafe-fxand 255 (unsafe-fxrshift n 16)))\n  (unsafe-bytes-set! bs (+ i 1) (unsafe-fxand 255 (unsafe-fxrshift n 8)))\n  (unsafe-bytes-set! bs (+ i 2) (unsafe-fxand 255 n))\n  )\n\n(define (unrolled-unsafe-bytes-nat-set!/4 n size __ ___ bs i)\n  ;; assume size=4\n  (unsafe-bytes-set! bs i       (unsafe-fxand 255 (unsafe-fxrshift n 24)))\n  (unsafe-bytes-set! bs (+ i 1) (unsafe-fxand 255 (unsafe-fxrshift n 16)))\n  (unsafe-bytes-set! bs (+ i 2) (unsafe-fxand 255 (unsafe-fxrshift n 8)))\n  (unsafe-bytes-set! bs (+ i 3) (unsafe-fxand 255 n))\n  )\n\n(define (unrolled-unsafe-bytes-nat-set!/5 n size __ ___ bs i)\n  ;; assume size=5\n  (unsafe-bytes-set! bs i       (unsafe-fxand 255 (unsafe-fxrshift n 32)))\n  (unsafe-bytes-set! bs (+ i 1) (unsafe-fxand 255 (unsafe-fxrshift n 24)))\n  (unsafe-bytes-set! bs (+ i 2) (unsafe-fxand 255 (unsafe-fxrshift n 16)))\n  (unsafe-bytes-set! bs (+ i 3) (unsafe-fxand 255 (unsafe-fxrshift n 8)))\n  (unsafe-bytes-set! bs (+ i 4) (unsafe-fxand 255 n))\n  )\n\n(define (unrolled-unsafe-bytes-nat-set!/6 n size __ ___ bs i)\n  ;; assume size=6\n  (unsafe-bytes-set! bs i       (unsafe-fxand 255 (unsafe-fxrshift n 36)))\n  (unsafe-bytes-set! bs (+ i 1) (unsafe-fxand 255 (unsafe-fxrshift n 32)))\n  (unsafe-bytes-set! bs (+ i 2) (unsafe-fxand 255 (unsafe-fxrshift n 24)))\n  (unsafe-bytes-set! bs (+ i 3) (unsafe-fxand 255 (unsafe-fxrshift n 16)))\n  (unsafe-bytes-set! bs (+ i 4) (unsafe-fxand 255 (unsafe-fxrshift n 8)))\n  (unsafe-bytes-set! bs (+ i 5) (unsafe-fxand 255 n))\n  )\n\n(define (unrolled-unsafe-bytes-nat-set! n size __ ___ bs offset)\n  (case size\n    ((1) (unrolled-unsafe-bytes-nat-set!/1 n size __ ___ bs offset))\n    ((2) (unsafe-bytes-set! bs offset       (unsafe-fxand 255 (unsafe-fxrshift n 8)))\n         (unsafe-bytes-set! bs (+ offset 1) (unsafe-fxand 255 n)))\n    ((3) (unrolled-unsafe-bytes-nat-set!/3 n size __ ___ bs offset))\n    ((4) (unrolled-unsafe-bytes-nat-set!/4 n size __ ___ bs offset))\n    ((5) (unrolled-unsafe-bytes-nat-set!/5 n size __ ___ bs offset))\n    ((6) (unrolled-unsafe-bytes-nat-set!/6 n size __ ___ bs offset))\n    (else (let loop ((i     offset)\n                     ;(shift (unsafe-fx* 8 (unsafe-fx- size 1)))\n                     (shift (unsafe-fxlshift (unsafe-fx- size 1) 3))\n                     )\n            (when (unsafe-fx<= 0 shift)\n              (unsafe-bytes-set! bs i (unsafe-fxand 255 (unsafe-fxrshift n shift)))\n              (loop (unsafe-fx+ i     1)\n                    (unsafe-fx- shift 8)))))))\n\n;(define (unrolled-unsafe-bytes-nat-set! n size __ ___ bs offset)\n  ;(case size\n    ;((1) (unrolled-unsafe-bytes-nat-set!/1 n size __ ___ bs offset))\n    ;((2) (unrolled-unsafe-bytes-nat-set!/2 n size __ ___ bs offset))\n    ;((3) (unrolled-unsafe-bytes-nat-set!/3 n size __ ___ bs offset))\n    ;((4) (unrolled-unsafe-bytes-nat-set!/4 n size __ ___ bs offset))\n    ;(else (let loop ((i     offset)\n                     ;;(shift (unsafe-fx* 8 (unsafe-fx- size 1)))\n                     ;(shift (unsafe-fxlshift (unsafe-fx- size 1) 3))\n                     ;)\n            ;(when (unsafe-fx<= 0 shift)\n              ;(bytes-set! bs i (unsafe-fxand 255 (unsafe-fxrshift n shift)))\n              ;(loop (unsafe-fx+ i     1)\n                    ;(unsafe-fx- shift 8)))))))\n\n;(define i->ibs integer->integer-bytes)\n;(define i->ibs bytes-nat-set!)\n;(define i->ibs unsafe-bytes-nat-set!)\n(define i->ibs unrolled-unsafe-bytes-nat-set!)\n\n(time\n  (let repeat ((i 10000000))\n    (when (< 0 i)\n      (let loop ((i (- total width)))\n        (when (unsafe-fx<= 0 i)\n          (i->ibs i width #f #f bstr i)\n          (loop (unsafe-fx- i width))))\n      (repeat (unsafe-fx- i 1)))))\n\n#;(define (unsafe-bytes-byte-width-nat-ref bs width offset)\n  (let ((end (unsafe-fx+ offset width)))\n    (let loop ((i offset) (n 0))\n      (cond ((unsafe-fx< i end) (loop (unsafe-fx+ i 1)\n                                      (unsafe-fx+ (unsafe-fxlshift n 8)\n                                                  (unsafe-bytes-ref bs i))))\n            (else               n)))))\n\n(define (1-unrolled-unsafe-bytes-nat-ref bs i)\n  (unsafe-bytes-ref bs i))\n(define (2-unrolled-unsafe-bytes-nat-ref bs i)\n  (unsafe-fx+ (unsafe-fxlshift (unsafe-bytes-ref bs i) 8)\n              (unsafe-bytes-ref bs (unsafe-fx+ i 1))))\n(define (3-unrolled-unsafe-bytes-nat-ref bs i)\n  (unsafe-fx+ (unsafe-fxlshift (unsafe-bytes-ref bs             i)    16)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 1))  8)\n              (unsafe-bytes-ref                  bs (unsafe-fx+ i 2))))\n(define (4-unrolled-unsafe-bytes-nat-ref bs i)\n  (unsafe-fx+ (unsafe-fxlshift (unsafe-bytes-ref bs             i)    24)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 1)) 16)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 2))  8)\n              (unsafe-bytes-ref                  bs (unsafe-fx+ i 3))))\n(define (5-unrolled-unsafe-bytes-nat-ref bs i)\n  (unsafe-fx+ (unsafe-fxlshift (unsafe-bytes-ref bs             i)    32)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 1)) 24)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 2)) 16)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 3))  8)\n              (unsafe-bytes-ref                  bs (unsafe-fx+ i 4))))\n(define (6-unrolled-unsafe-bytes-nat-ref bs i)\n  (unsafe-fx+ (unsafe-fxlshift (unsafe-bytes-ref bs             i)    40)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 1)) 32)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 2)) 24)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 3)) 16)\n              (unsafe-fxlshift (unsafe-bytes-ref bs (unsafe-fx+ i 4))  8)\n              (unsafe-bytes-ref                  bs (unsafe-fx+ i 5))))\n\n(define (unsafe-bytes-byte-width-nat-ref bs width offset)\n  (case width\n    ((1) (1-unrolled-unsafe-bytes-nat-ref bs offset))\n    ((2) (2-unrolled-unsafe-bytes-nat-ref bs offset))\n    ((3) (3-unrolled-unsafe-bytes-nat-ref bs offset))\n    ((4) (4-unrolled-unsafe-bytes-nat-ref bs offset))\n    ((5) (5-unrolled-unsafe-bytes-nat-ref bs offset))\n    ((6) (6-unrolled-unsafe-bytes-nat-ref bs offset))\n    (else (let ((end (unsafe-fx+ offset width)))\n            (let loop ((i offset) (n 0))\n              (cond ((unsafe-fx< i end) (loop (unsafe-fx+ i 1)\n                                              (unsafe-fx+ (unsafe-fxlshift n 8)\n                                                          (unsafe-bytes-ref bs i))))\n                    (else               n)))))))\n\n(time\n  (let repeat ((i 10000000))\n    (when (< 0 i)\n      (let loop ((i (- total width)))\n        (when (unsafe-fx<= 0 i)\n          (unsafe-vector-set! vec 0 (unsafe-bytes-byte-width-nat-ref bstr width i))\n          (loop (unsafe-fx- i width))))\n      (repeat (unsafe-fx- i 1)))))\n\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/microbenchmarks/place1.rkt",
    "content": "#lang racket/base\n(provide place-main)\n(require \"shared.rkt\" racket/place)\n\n(define (place-main c.in)\n  (displayln \"place 1\")\n  (shared-put (+ 1 (shared-get)))\n  (place-channel-put c.in `(done: ,(shared-get))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/microbenchmarks/place2.rkt",
    "content": "#lang racket/base\n(provide place-main)\n(require racket/place)\n\n(define (place-main c.in)\n  (displayln \"place 2\")\n  (place-channel-put c.in `(done: ,(cons 'place2 (place-channel-get c.in)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/microbenchmarks/shared.rkt",
    "content": "#lang racket/base\n(provide shared-get shared-put)\n\n(define shared-value 5)\n\n(define (shared-get)\n  shared-value)\n\n(define (shared-put x)\n  (set! shared-value x))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-database-small.rkt",
    "content": "#lang racket/base\n(require \"../dbk/database.rkt\"\n         racket/list racket/pretty racket/runtime-path)\n\n(define-runtime-path path.here \".\")\n(define db (database (build-path path.here \"small\")))\n(auto-empty-trash? #t)\n\n(define (build-list-relation db type tuples)\n  (let-values (((insert! finish) (database-relation-builder db type)))\n    (time (for-each insert! tuples))\n    (time (finish))))\n\n;; (- R R) etc.\n\n(define specs `((main   . ,(map list (range 500)))\n                (lower  . ,(map list (range 200)))\n                (middle . ,(map list (range 200 300)))\n                (upper  . ,(map list (range 300 500)))))\n\n(for-each (lambda (spec)\n            (let ((name   (car spec))\n                  (tuples (cdr spec)))\n              (unless (database-relation-name? db name)\n                (let ((R (build-list-relation db '(int) tuples)))\n                  (relation-name-set! R name)\n                  (relation-attributes-set! R '(value))\n                  (database-commit! db)))))\n          specs)\n\n(unless (database-relation-name? db 'gone)\n  (let ((R.gone   (database-relation-new db '(int)))\n        (R.main   (database-relation db 'main))\n        (R.lower  (database-relation db 'lower))\n        (R.middle (database-relation db 'middle))\n        (R.upper  (database-relation db 'upper)))\n    (relation-assign! R.gone (R- R.main R.main))\n    ;(relation-assign! R.gone (R+ R.upper R.lower))\n    ;(relation-assign! R.gone (R- (R- R.main R.lower) R.upper))\n    ;(relation-assign! R.gone (R- R.main (R+ R.lower R.upper)))\n    ;(relation-assign! R.gone (R- (R- (R- R.main R.lower) R.upper) R.middle))\n    ;(relation-assign! R.gone (R- (R- R.main (R+ R.lower R.upper)) R.middle))\n    (relation-name-set! R.gone 'gone)\n    (database-commit! db)))\n\n;(relation-full-compact! (database-relation db 'gone))\n(database-commit! db)\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-dataflow.rkt",
    "content": "#lang racket/base\n(require\n  \"../dbk.rkt\"\n  \"../dbk/data.rkt\"\n  \"../dbk/enumerator.rkt\"\n  racket/pretty\n  racket/runtime-path\n  racket/set)\n\n(define-relation/table (cprop curie key value)   'path \"rtx2/20210204/cprop\")\n(define-relation/table (edge  id subject object) 'path \"rtx2/20210204/edge\")\n(define-relation/table (eprop id key value)      'path \"rtx2/20210204/eprop\")\n\n(define (dict-select d key) (d 'ref key (lambda (v) v) (lambda () (error \"dict ref failed\" key))))\n\n(define-runtime-path path.here \".\")\n\n(define db      (database (path->string (build-path path.here \"rtx-kg2_20210204.db\"))))\n(define r.cprop (database-relation db '(rtx-kg2 cprop)))\n(define r.edge  (database-relation db '(rtx-kg2 edge)))\n(define r.eprop (database-relation db '(rtx-kg2 eprop)))\n\n(define preload-index? #f)\n(define preload-text?  #f)\n\n(define dict.eprop.eid.value.key     (time (relation-index-dict r.eprop '(key value eid)      preload-index?)))\n(define dict.edge.subject.eid.object (time (relation-index-dict r.edge  '(object eid subject) preload-index?)))\n(define dict.cprop.value.key.curie   (time (relation-index-dict r.cprop '(curie key value)    preload-index?)))\n(define domain-dicts                 (time (relation-domain-dicts r.cprop preload-text?)))\n(define dict.string=>id              (car (hash-ref (car domain-dicts) 'text)))\n(define dict.id=>string              (car (hash-ref (cdr domain-dicts) 'text)))\n\n(define (string->id str) (dict-select dict.string=>id str))\n(define (id->string id)  (dict-select dict.id=>string id))\n\n(define (benchmark-find-treatments curie.target)\n  (define (run-query yield)\n    (define curie.nausea.id       (string->id curie.target))\n    (define ekey.predicate.id     (string->id \"predicate\"))\n    (define evalue.treats.id      (string->id \"biolink:treats\"))\n    (define ckey.category.id      (string->id \"category\"))\n    (define ckey.name.id          (string->id \"name\"))\n    (define dict.eprop.eid.value  (dict-select dict.eprop.eid.value.key     ekey.predicate.id))\n    (define dict.eprop.eid        (dict-select dict.eprop.eid.value         evalue.treats.id))\n    (define dict.edge.subject.eid (dict-select dict.edge.subject.eid.object curie.nausea.id))\n    ((merge-join dict.eprop.eid dict.edge.subject.eid)\n     (lambda (eid __ dict.edge.subject)\n       ((merge-join dict.edge.subject dict.cprop.value.key.curie)\n        (lambda (subject.id __ dict.cprop.value.key)\n          (define subject             (id->string subject.id))\n          (define dict.cprop.category (dict-select dict.cprop.value.key ckey.category.id))\n          (define dict.cprop.name     (dict-select dict.cprop.value.key ckey.name.id))\n          ((merge-join dict.cprop.category dict.id=>string)\n           (lambda (category.id __ category)\n             ((merge-join dict.cprop.name dict.id=>string)\n              (lambda (name.id __ name)\n                (yield (list subject category name)))))))))))\n  ;; Some nausea timings\n  ;; cpu time: 1485 real time: 1610 gc time: 19\n  ;; cpu time: 1539 real time: 1557 gc time: 15\n  ;; cpu time: 1538 real time: 1556 gc time: 24\n  (define results.old (time (run* (s cat name)\n                              (fresh (eid)\n                                (edge eid s curie.target)\n                                (cprop s \"category\" cat)\n                                (cprop s \"name\" name)\n                                (eprop eid \"predicate\" \"biolink:treats\")))))\n  ;; Some nausea timings\n  ;; cpu time: 27 real time: 27 gc time: 0\n  ;; cpu time: 31 real time: 31 gc time: 0\n  ;; cpu time: 30 real time: 31 gc time: 0\n  (define results.new (time (enumerator->rlist run-query)))\n  ;; 149 results\n  (pretty-write `(old:    ,(length results.old) ,results.old))\n  (pretty-write `(new:    ,(length results.new) ,results.new))\n  (pretty-write `(equal?: ,(equal? (list->set results.old) (list->set results.new)))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-equivalence-database.rkt",
    "content": "#lang racket/base\n(require \"equivalence-database.rkt\" \"../dbk/database.rkt\" \"../dbk/enumerator.rkt\"\n         racket/pretty racket/runtime-path)\n\n(define name.equiv-edge         'equivalence-edge)\n(define name.equiv-class-member 'equivalence-class-member)\n\n(define-runtime-path path.here \".\")\n\n(define db.equiv\n  (build-equivalence-database\n    (build-path path.here \"test-equivalence.db\")\n    (list->enumerator\n      '((#\"A\" #\"B\")\n        (#\"C\" #\"D\")\n        (#\"C\" #\"H\")\n        (#\"B\" #\"F\")\n        (#\"E\" #\"G\")\n        (#\"G\" #\"H\")\n        (#\"L\" #\"M\")\n        (#\"M\" #\"O\")\n        (#\"N\" #\"O\")\n        (#\"F\" #\"O\")))))\n\n(define r.equiv-class-member (database-relation db.equiv name.equiv-class-member))\n\n(define-values (text=>id id=>text) (relation-text-dicts r.equiv-class-member #f))\n(define (text->id text) (dict-ref text=>id text (lambda (v) v)\n                                  (lambda () (error \"invalid text\" text))))\n(define (id->text id)   (dict-ref id=>text id (lambda (v) v)\n                                  (lambda () (error \"invalid text id\" id))))\n\n(define rep=>member=>1 (relation-index-dict r.equiv-class-member '(representative member) #f))\n\n((dict-enumerator rep=>member=>1)\n (lambda (id.rep member=>1)\n   (pretty-write `(representative: ,(id->text id.rep)))\n   ((dict-key-enumerator member=>1)\n    (lambda (id.member)\n      (pretty-write `(member: ,(id->text id.member)))))\n   (newline)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-ingest-example-simple.rkt",
    "content": "#lang racket/base\n(require \"../dbk/io.rkt\"\n         \"../dbk/data.rkt\"\n         \"../dbk/stream.rkt\"\n         racket/runtime-path)\n\n(define-runtime-path path.here \".\")\n\n(define db (database (build-path path.here \"example-db\")))\n\n(unless (database-relation-has? db '(example cprop))\n  (database-relation-add!\n    db '(example cprop)\n    'attributes '(curie  key    value)\n    'type       '(string string string)\n    'source     (in:file \"example/example.nodeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))))\n\n(unless (database-relation-has? db '(example edge))\n  (database-relation-add!\n    db '(example edge)\n    'attributes '(eid subject object)\n    'type       '(nat string  string)\n    'source     (s-map (lambda (row) (cons (string->number (car row)) (cdr row)))\n                       (in:file \"example/example.edge.tsv\"     'header '(\":ID\" \":START\" \":END\")))))\n\n(unless (database-relation-has? db '(example eprop))\n  (database-relation-add!\n    db '(example eprop)\n    'attributes '(eid key    value)\n    'type       '(nat string string)\n    'source     (s-map (lambda (row) (cons (string->number (car row)) (cdr row)))\n                       (in:file \"example/example.edgeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\")))))\n\n(define cprop (database-relation db '(example cprop)))\n(define edge  (database-relation db '(example edge)))\n(define eprop (database-relation db '(example eprop)))\n\n(database-compact! db)\n\n(relation-index-add! cprop\n                     '(curie key)\n                     '(key value))\n(relation-index-add! edge\n                     '(eid)\n                     '(subject object)\n                     '(subject eid)\n                     '(object  eid))\n(relation-index-add! eprop\n                     '(eid key)\n                     '(key value))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-ingest-example.rkt",
    "content": "#lang racket/base\n(require \"../dbk/io.rkt\"\n         racket/match)\n\n;; TODO: require these\n(define file-checksum          #f)\n(define-syntax-rule (run* body ...) '(TODO: run* body ...))\n(define database               #f)\n(define database-relation      #f)\n(define database-update!       #f)\n(define database-checkpoint!   #f)\n(define database-index-build!  #f)\n(define database-compact!      #f)\n(define relation-database      #f)\n(define relation-name          #f)\n(define relation-insert        #f)\n(define relation-index-add!    #f)\n(define relation-index-remove! #f)\n(define relation-index-build!  #f)\n\n(define db (database \"path/to/example/db\"\n                     'immediate-checkpoint?  #f\n                     'immediate-index-build? #f\n                     'immediate-compact?     #f))\n\n(define update-history (database-relation\n                         db\n                         'name       'update-history\n                         'attributes '(relation-name update-time update-kind file-name file-size file-checksum)\n                         'type       '(#f            nat         #f          string    nat       string)))\n(database-checkpoint! db)\n\n(define cprop (database-relation\n                db '(example cprop)\n                'attributes '(curie  key    value)\n                'type       '(string string string)))\n(define eprop (database-relation\n                db '(example eprop)\n                'attributes '(eid key    value)\n                'type       '(nat string string)))\n(define edge  (database-relation\n                db '(example edge)\n                'attributes '(eid subject object)\n                'type       '(nat string  string)))\n(relation-index-add! cprop\n                     '(curie key)\n                     '(key value))\n(relation-index-add! eprop\n                     '(eid key)\n                     '(key value))\n(relation-index-add! edge\n                     '(eid)\n                     '(subject object)\n                     '(object subject))\n(database-checkpoint! db)\n\n(define (relation-ingest! R path.dir file-name file-params)\n  (define name.R              (relation-name R))\n  (define path.file           (build-path path.dir file-name))\n  (define checksum.file       (file-checksum path.file))\n  (define size.file           (file-size path.file))\n  (define file-ingest-history (run* (timestamp size checksum)\n                                (update-history name.R timestamp 'ingest file-name size checksum)))\n  (if (null? file-ingest-history)\n    (begin (database-update!\n             (relation-database R)\n             (relation-insert update-history (list (list name.R (current-milliseconds)\n                                                         'ingest file-name size.file checksum.file)))\n             (relation-insert R              (apply in:file path.file file-params)))\n           (database-checkpoint! db))\n    (unless (ormap (lambda (entry) (match entry\n                                     ((list timestamp size checksum) (and (equal? size     size.file)\n                                                                          (equal? checksum checksum.file)))\n                                     (_                              #f)))\n                   file-ingest-history)\n      (error \"inconsistent data ingestion history:\"\n             'relation-name name.R\n             'file-name     file-name\n             'file-size     size.file\n             'file-checksum checksum.file\n             'history       file-ingest-history))))\n\n(relation-ingest! cprop \"example\" \"example.nodeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))\n(relation-ingest! eprop \"example\" \"example.edgeprop.tsv\" 'header '(\":ID\" \"propname\" \"value\"))\n(relation-ingest! edge  \"example\" \"example.edge.tsv\"     'header '(\":ID\" \":START\" \":END\"))\n\n(database-index-build! db)\n(database-compact!     db)\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-low-level.rkt",
    "content": "#lang racket/base\n(provide\n  query:Known->Known\n  query:Known->X\n  query:X->Known\n  query:Known<-X->Known\n  query:Known->X->Known\n  query:X->Y->Known\n  query:Concept\n  concept-properties\n  concept-property-values\n  curie->properties\n  edge-properties\n  edge-property-values\n  edge-id->properties)\n(require \"../dbk/database.rkt\" \"../dbk/enumerator.rkt\" \"../dbk/stream.rkt\"\n         racket/fixnum racket/match racket/pretty racket/runtime-path racket/set)\n\n;; Control whether data is preloaded from disk and kept in-memory.\n;; NOTE: without preloading, thread-safety is not guaranteed by default.\n(define preload-index? #f)\n\n(define str.predicate \"predicate\")\n;(define str.predicate \"edge_label\")\n\n(define (dict-get d key)\n  (dict-ref d key (lambda (v) v) (lambda () (error \"dict-get failed\" key))))\n\n(define (string*->id=>1 str*) (bytes*->id=>1 (map string->bytes/utf-8 str*)))\n(define (bytes*->id=>1 text*)\n  (let* ((text* (sort (set->list (list->set text*)) bytesvector (map text->id text*))))\n    (dict:ref (lambda (i) (vector-ref id* i)) fx<\n              (lambda (_) '()) 0 (vector-length id*))))\n\n(define (string->id str) (text->id (string->bytes/utf-8 str)))\n(define (id->string id)  (bytes->string/utf-8 (id->text id)))\n(define (text->id   b)   (initialize-text!) (dict-get (thread-cell-ref tcell.text=>id) b))\n(define (id->text   id)  (initialize-text!) (dict-get (thread-cell-ref tcell.id=>text) id))\n\n(define (concept-properties)          (map id->string (enumerator->list\n                                                        (dict-key-enumerator ckey=>cvalue=>curie=>1))))\n(define (edge-properties)             (map id->string (enumerator->list\n                                                        (dict-key-enumerator ekey=>evalue=>eid=>1))))\n(define (concept-property-values key) (s-map id->string (enumerator->s\n                                                          (dict-key-enumerator\n                                                            (dict-get ckey=>cvalue=>curie=>1\n                                                                      (string->id key))))))\n(define (edge-property-values    key) (s-map id->string (enumerator->s\n                                                          (dict-key-enumerator\n                                                            (dict-get ekey=>evalue=>eid=>1\n                                                                      (string->id key))))))\n(define (curie->properties curie)\n  (enumerator->list\n    (lambda (yield)\n      ((dict-enumerator (dict-get curie=>ckey=>cvalue=>1 (string->id curie)))\n       (lambda (ckey cvalue=>1)\n         (yield (map id->string (cons ckey (enumerator->list\n                                             (dict-key-enumerator cvalue=>1))))))))))\n(define (edge-id->properties eid)\n  (enumerator->list\n    (lambda (yield)\n      ((dict-enumerator (dict-get eid=>ekey=>evalue=>1 eid))\n       (lambda (ekey evalue=>1)\n         (yield (map id->string (cons ekey (enumerator->list\n                                             (dict-key-enumerator evalue=>1))))))))))\n\n;; query:Known->X is analogous to a miniKanren-style query with this shape:\n; (run* (s sname p o oname)\n;   (fresh (id category)\n;     (edge id s o)\n;     (cprop o \"category\" category)\n;     (cprop s \"name\" sname)\n;     (cprop o \"name\" oname)\n;     (eprop id \"predicate\" p)\n;     (membero s subject-curies)\n;     (membero p predicates)\n;     (membero category object-categories)))\n\n(define (query:Known->X curie*.K predicate*.K->X category*.X)\n  (define (query. yield)\n    (let* ((ekey.predicate (string->id str.predicate))\n           (ckey.name      (string->id \"name\"))\n           (K=>1           (string*->id=>1 curie*.K)))\n      ((merge-join fx< K=>1 subject=>object=>eid=>1)\n       (lambda (id.K __ X=>eid=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< X=>eid=>1 curie=>ckey=>cvalue=>1)\n            (lambda (id.X eid=>1 ckey=>cvalue=>1)\n              (let* ((id.name.X (dict-min (dict-get ckey=>cvalue=>1 ckey.name)))\n                     (name.X    (id->string id.name.X))\n                     (X         (id->string id.X)))\n                ((dict-key-enumerator eid=>1)\n                 (lambda (eid)\n                   (let ((predicate.K->X\n                           (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                           ekey.predicate)))))\n                     (yield (list* K name.K predicate.K->X X name.X\n                                   (edge-id->properties eid))))))))))))))\n  (define (query.c yield)\n    (let* ((ekey.predicate     (string->id str.predicate))\n           (ckey.category      (string->id \"category\"))\n           (ckey.name          (string->id \"name\"))\n           (K=>1               (string*->id=>1 curie*.K))\n           (category=>1        (string*->id=>1 category*.X))\n           (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n      ((merge-join fx< K=>1 subject=>object=>eid=>1)\n       (lambda (id.K __ X=>eid=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< category=>1 category=>curie=>1)\n            (lambda (__ ___ X=>1.cprop)\n              ((merge-join fx< X=>eid=>1 X=>1.cprop)\n               (lambda (id.X eid=>1 __)\n                 (let* ((id.name.X (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.X)\n                                                       ckey.name)))\n                        (name.X    (id->string id.name.X))\n                        (X         (id->string id.X)))\n                   ((dict-key-enumerator eid=>1)\n                    (lambda (eid)\n                      (let ((predicate.K->X\n                              (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                              ekey.predicate)))))\n                        (yield (list* K name.K predicate.K->X X name.X\n                                      (edge-id->properties eid))))))))))))))))\n  (define (query.p yield)\n    (let* ((ekey.predicate     (string->id str.predicate))\n           (ckey.name          (string->id \"name\"))\n           (K=>1               (string*->id=>1 curie*.K))\n           (predicate=>1       (string*->id=>1 predicate*.K->X))\n           (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1 ekey.predicate)))\n      ((merge-join fx< K=>1 subject=>eid=>object=>1)\n       (lambda (id.K __ eid=>X=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< predicate=>1 predicate=>eid=>1)\n            (lambda (id.predicate.K->X __ eid=>1)\n              (let ((predicate.K->X (id->string id.predicate.K->X)))\n                ((merge-join fx< eid=>1 eid=>X=>1)\n                 (lambda (eid __ X=>1.edge)\n                   ((merge-join fx< X=>1.edge curie=>ckey=>cvalue=>1)\n                    (lambda (id.X __ ckey=>cvalue=>1)\n                      (let* ((id.name.X (dict-min (dict-get ckey=>cvalue=>1 ckey.name)))\n                             (name.X    (id->string id.name.X))\n                             (X         (id->string id.X)))\n                        (yield (list* K name.K predicate.K->X X name.X\n                                      (edge-id->properties eid))))))))))))))))\n  (define (query.p&c yield)\n    (let* ((ekey.predicate     (string->id str.predicate))\n           (ckey.category      (string->id \"category\"))\n           (ckey.name          (string->id \"name\"))\n           (K=>1               (string*->id=>1 curie*.K))\n           (predicate=>1       (string*->id=>1 predicate*.K->X))\n           (category=>1        (string*->id=>1 category*.X))\n           (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1   ekey.predicate))\n           (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n      ((merge-join fx< K=>1 subject=>eid=>object=>1)\n       (lambda (id.K __ eid=>X=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< predicate=>1 predicate=>eid=>1)\n            (lambda (id.predicate.K->X __ eid=>1)\n              (let ((predicate.K->X (id->string id.predicate.K->X)))\n                ((merge-join fx< eid=>1 eid=>X=>1)\n                 (lambda (eid __ X=>1.edge)\n                   ((merge-join fx< category=>1 category=>curie=>1)\n                    (lambda (__ ___ X=>1.cprop)\n                      ((dict-join-ordered\n                         (lambda (yield)\n                           ((merge-join fx< X=>1.cprop X=>1.edge)\n                            (lambda (id.X __ ___)\n                              (yield id.X '()))))\n                         curie=>ckey=>cvalue=>1)\n                       (lambda (id.X __ ckey=>cvalue=>1)\n                         (let* ((id.name.X (dict-min (dict-get ckey=>cvalue=>1 ckey.name)))\n                                (name.X    (id->string id.name.X))\n                                (X         (id->string id.X)))\n                           (yield (list* K name.K predicate.K->X X name.X\n                                         (edge-id->properties eid))))))))))))))))))\n  (time (enumerator->rlist (if predicate*.K->X\n                               (if category*.X query.p&c query.p)\n                               (if category*.X query.c   query.)))))\n\n;; query:X->Known is analogous to a miniKanren-style query with this shape:\n; (run* (s sname p o oname)\n;   (fresh (id category)\n;     (edge id s o)\n;     (cprop s \"category\" category)\n;     (cprop s \"name\" sname)\n;     (cprop o \"name\" oname)\n;     (eprop id \"predicate\" p)\n;     (membero o object-curies)\n;     (membero p predicates)\n;     (membero category subject-categories)))\n\n(define (query:X->Known category*.X predicate*.X->K curie*.K)\n  (define (query. yield)\n    (let* ((ekey.predicate (string->id str.predicate))\n           (ckey.name      (string->id \"name\"))\n           (K=>1           (string*->id=>1 curie*.K)))\n      ((merge-join fx< K=>1 object=>subject=>eid=>1)\n       (lambda (id.K __ X=>eid=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< X=>eid=>1 curie=>ckey=>cvalue=>1)\n            (lambda (id.X eid=>1 ckey=>cvalue=>1)\n              (let* ((id.name.X (dict-min (dict-get ckey=>cvalue=>1 ckey.name)))\n                     (name.X    (id->string id.name.X))\n                     (X         (id->string id.X)))\n                ((dict-key-enumerator eid=>1)\n                 (lambda (eid)\n                   (let ((predicate.X->K\n                           (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                           ekey.predicate)))))\n                     (yield (list* X name.X predicate.X->K K name.K\n                                   (edge-id->properties eid))))))))))))))\n  (define (query.c yield)\n    (let* ((ekey.predicate     (string->id str.predicate))\n           (ckey.category      (string->id \"category\"))\n           (ckey.name          (string->id \"name\"))\n           (K=>1               (string*->id=>1 curie*.K))\n           (category=>1        (string*->id=>1 category*.X))\n           (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n      ((merge-join fx< K=>1 object=>subject=>eid=>1)\n       (lambda (id.K __ X=>eid=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< category=>1 category=>curie=>1)\n            (lambda (__ ___ X=>1.cprop)\n              ((merge-join fx< X=>eid=>1 X=>1.cprop)\n               (lambda (id.X eid=>1 __)\n                 (let* ((id.name.X (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.X)\n                                                       ckey.name)))\n                        (name.X    (id->string id.name.X))\n                        (X         (id->string id.X)))\n                   ((dict-key-enumerator eid=>1)\n                    (lambda (eid)\n                      (let ((predicate.X->K\n                              (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                              ekey.predicate)))))\n                        (yield (list* X name.X predicate.X->K K name.K\n                                      (edge-id->properties eid))))))))))))))))\n  (define (query.p yield)\n    (let* ((ekey.predicate     (string->id str.predicate))\n           (ckey.name          (string->id \"name\"))\n           (K=>1               (string*->id=>1 curie*.K))\n           (predicate=>1       (string*->id=>1 predicate*.X->K))\n           (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1   ekey.predicate)))\n      ((merge-join fx< K=>1 object=>eid=>subject=>1)\n       (lambda (id.K __ eid=>X=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< predicate=>1 predicate=>eid=>1)\n            (lambda (id.predicate.X->K __ eid=>1)\n              (let ((predicate.X->K (id->string id.predicate.X->K)))\n                ((merge-join fx< eid=>1 eid=>X=>1)\n                 (lambda (eid __ X=>1.edge)\n                   ((merge-join fx< X=>1.edge curie=>ckey=>cvalue=>1)\n                    (lambda (id.X __ ckey=>cvalue=>1)\n                      (let* ((id.name.X (dict-min (dict-get ckey=>cvalue=>1 ckey.name)))\n                             (name.X    (id->string id.name.X))\n                             (X         (id->string id.X)))\n                        (yield (list* X name.X predicate.X->K K name.K\n                                      (edge-id->properties eid))))))))))))))))\n  (define (query.p&c yield)\n    (let* ((ekey.predicate     (string->id str.predicate))\n           (ckey.category      (string->id \"category\"))\n           (ckey.name          (string->id \"name\"))\n           (K=>1               (string*->id=>1 curie*.K))\n           (predicate=>1       (string*->id=>1 predicate*.X->K))\n           (category=>1        (string*->id=>1 category*.X))\n           (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1   ekey.predicate))\n           (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n      ((merge-join fx< K=>1 object=>eid=>subject=>1)\n       (lambda (id.K __ eid=>X=>1)\n         (let* ((id.name.K (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.K) ckey.name)))\n                (name.K    (id->string id.name.K))\n                (K         (id->string id.K)))\n           ((merge-join fx< predicate=>1 predicate=>eid=>1)\n            (lambda (id.predicate.X->K __ eid=>1)\n              (let ((predicate.X->K (id->string id.predicate.X->K)))\n                ((merge-join fx< eid=>1 eid=>X=>1)\n                 (lambda (eid __ X=>1.edge)\n                   ((merge-join fx< category=>1 category=>curie=>1)\n                    (lambda (__ ___ X=>1.cprop)\n                      ((dict-join-ordered\n                         (lambda (yield)\n                           ((merge-join fx< X=>1.cprop X=>1.edge)\n                            (lambda (id.X __ ___)\n                              (yield id.X '()))))\n                         curie=>ckey=>cvalue=>1)\n                       (lambda (id.X __ ckey=>cvalue=>1)\n                         (let* ((id.name.X (dict-min (dict-get ckey=>cvalue=>1 ckey.name)))\n                                (name.X    (id->string id.name.X))\n                                (X         (id->string id.X)))\n                           (yield (list* X name.X predicate.X->K K name.K\n                                         (edge-id->properties eid))))))))))))))))))\n  (time (enumerator->rlist (if predicate*.X->K\n                               (if category*.X query.p&c query.p)\n                               (if category*.X query.c   query.)))))\n\n;; query:Known<-X->Known is analogous to a miniKanren-style query with this shape:\n;(run* (K1 name.K1 predicates.K1<-X X name.X predicates.X->K1 K2 name.K2)\n;  (fresh (id1 id2 category.X)\n;    (edge id1 X K1)\n;    (edge id2 X K2)\n;    (cprop X   \"category\" category.X)\n;    (cprop X   \"name\" name.X)\n;    (cprop K1  \"name\" name.K1)\n;    (cprop K2  \"name\" name.K2)\n;    (eprop id1 \"predicate\" K1<-X)\n;    (eprop id2 \"predicate\" X->K2)\n;    (membero category.X categories.X)\n;    (membero K1         curies.K1)\n;    (membero K1<-X      predicates.K1<-X)\n;    (membero K2         curies.K2)\n;    (membero X->K2      predicates.X->K2)))\n\n(define (query:Known<-X->Known curie*.K1 predicate*.K1<-X category*.X predicate*.X->K2 curie*.K2)\n  (define (candidate*->dict candidate*)\n    (let* ((candidate* (sort candidate* (lambda (a b) (stringvector (s-group candidate* equal? car)))\n           (ref.value  (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (caar (ref.value i))) stringXK1=>1 (candidate*->dict (query:X->Known category*.X predicate*.K1<-X curie*.K1)))\n         (X=>XK2=>1 (candidate*->dict (query:X->Known category*.X predicate*.X->K2 curie*.K2))))\n    (time (enumerator->list\n            (lambda (yield)\n              ((merge-join stringXK1=>1 X=>XK2=>1)\n               (lambda (X XK1* XK2*)\n                 (for-each\n                   (lambda (XK1)\n                     (match-define (list* _ name.X predicate.X->K1 K1 name.K1 props1) XK1)\n                     (for-each\n                       (lambda (XK2)\n                         (match-define (list* _ _ X->K2 K2 name.K2 props2) XK2)\n                         (yield (append (list K1 name.K1 predicate.X->K1 X name.X X->K2 K2 name.K2)\n                                        (append props1 props2))))\n                       XK2*))\n                   XK1*))))))))\n\n(define (query:Known->X->Known curie*.K1 predicate*.K1->X category*.X predicate*.X->K2 curie*.K2)\n  (define (KX*->dict candidate*)\n    (let* ((candidate* (sort candidate* (lambda (a b) (stringvector (s-group candidate* equal? cadddr)))\n           (ref.value  (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (cadddr (car (ref.value i)))) stringdict candidate*)\n    (let* ((candidate* (sort candidate* (lambda (a b) (stringvector (s-group candidate* equal? car)))\n           (ref.value  (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (caar (ref.value i))) stringK1X* (KX*->dict (query:Known->X curie*.K1 predicate*.K1->X category*.X)))\n         (X=>XK2* (XK*->dict (query:X->Known category*.X predicate*.X->K2 curie*.K2))))\n    (time (enumerator->list\n            (lambda (yield)\n              ((merge-join stringK1X* X=>XK2*)\n               (lambda (X K1X* XK2*)\n                 (for-each\n                   (lambda (K1X)\n                     (match-define (list* K1 name.K1 predicate.X->K1 _ name.X props1) K1X)\n                     (for-each\n                       (lambda (XK2)\n                         (match-define (list* _ _ X->K2 K2 name.K2 props2) XK2)\n                         (yield (append (list K1 name.K1 predicate.X->K1 X name.X X->K2 K2 name.K2)\n                                        (append props1 props2))))\n                       XK2*))\n                   K1X*))))))))\n\n(define (query:X->Y->Known category*.X predicate*.X->Y category*.Y predicate*.Y->K curie*.K)\n  (define (result*->dict key result*)\n    (let* ((result*   (sort result* (lambda (a b) (stringvector (s-group result* equal? key)))\n           (ref.value (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (key (car (ref.value i)))) stringYK=>1 (result*->dict car    (query:X->Known category*.Y predicate*.Y->K curie*.K)))\n         (curie*.Y (enumerator->list (dict-key-enumerator Y=>YK=>1)))\n         (Y=>XY=>1 (result*->dict cadddr (query:X->Known category*.X predicate*.X->Y curie*.Y))))\n    (time (enumerator->list\n            (lambda (yield)\n              ((merge-join stringXY=>1 Y=>YK=>1)\n               (lambda (Y XY* YK*)\n                 (for-each\n                   (lambda (XY)\n                     (match-define (list* X name.X predicate.X->Y _ name.Y props.X->Y) XY)\n                     (for-each\n                       (lambda (YK)\n                         (match-define (list* _ _ Y->K K name.K props.Y->K) YK)\n                         (yield (append (list X name.X predicate.X->Y Y name.Y Y->K K name.K)\n                                        (append props.X->Y props.Y->K))))\n                       YK*))\n                   XY*))))))))\n\n(define (query:Known->Known curie*.S predicate*.S->O curie*.O)\n  (query:dict.Known->dict.Known\n    (string*->id=>1 curie*.S) predicate*.S->O (string*->id=>1 curie*.O)))\n\n(define (query:dict.Known->dict.Known curie=>1.S predicate*.S->O curie=>1.O)\n  (define (query yield)\n    (let* ((ekey.predicate    (string->id str.predicate))\n           (ckey.name         (string->id \"name\"))\n           (predicate=>1      (string*->id=>1 predicate*.S->O))\n           (predicate=>eid=>1 (dict-get ekey=>evalue=>eid=>1 ekey.predicate)))\n      ((merge-join fx< curie=>1.S subject=>eid=>object=>1)\n       (lambda (id.S __ eid=>O=>1)\n         (let* ((id.name.S (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.S) ckey.name)))\n                (name.S    (id->string id.name.S))\n                (S         (id->string id.S)))\n           ((merge-join fx< predicate=>1 predicate=>eid=>1)\n            (lambda (id.predicate.S->O __ eid=>1)\n              (let ((predicate.S->O (id->string id.predicate.S->O)))\n                ((merge-join fx< eid=>1 eid=>O=>1)\n                 (lambda (eid __ O=>1)\n                   ((merge-join fx< curie=>1.O O=>1)\n                    (lambda (id.O __ ___)\n                      (let* ((id.name.O (dict-min (dict-get (dict-get curie=>ckey=>cvalue=>1 id.O)\n                                                            ckey.name)))\n                             (name.O    (id->string id.name.O))\n                             (O         (id->string id.O)))\n                        (yield (list* S name.S predicate.S->O O name.O\n                                      (edge-id->properties eid))))))))))))))))\n  (time (enumerator->rlist query)))\n\n(define (query:Concept curie*)\n  (define (query yield)\n    (let ((curie=>1 (string*->id=>1 curie*)))\n      ((merge-join fx< curie=>1 curie=>ckey=>cvalue=>1)\n       (lambda (id.curie _ ckey=>cvalue=>1)\n         (let ((curie (id->string id.curie)))\n           ((dict-enumerator ckey=>cvalue=>1)\n            (lambda (id.key cvalue=>1)\n              (yield (list curie (id->string id.key) (id->string (dict-min cvalue=>1)))))))))))\n  (time (enumerator->list query)))\n\n(define-runtime-path path.here \".\")\n(define db (database (build-path path.here \"name-of-your-database.db\")))\n\n(define r.cprop (database-relation db 'cprop))\n(define r.edge  (database-relation db 'edge))\n(define r.eprop (database-relation db 'eprop))\n\n(define tcell.text=>id (make-thread-cell #f))\n(define tcell.id=>text (make-thread-cell #f))\n\n(define (initialize-text!)\n  (unless (thread-cell-ref tcell.text=>id)\n    (define-values (text=>id id=>text) (relation-text-dicts r.cprop #f))\n    (thread-cell-set! tcell.text=>id text=>id)\n    (thread-cell-set! tcell.id=>text id=>text)))\n\n(displayln \"Loading relation index dictionaries\")\n(define subject=>object=>eid=>1 (time (relation-index-dict r.edge  '(subject object eid) preload-index?)))\n(define object=>subject=>eid=>1 (time (relation-index-dict r.edge  '(object subject eid) preload-index?)))\n(define subject=>eid=>object=>1 (time (relation-index-dict r.edge  '(subject eid object) preload-index?)))\n(define object=>eid=>subject=>1 (time (relation-index-dict r.edge  '(object eid subject) preload-index?)))\n(define ekey=>evalue=>eid=>1    (time (relation-index-dict r.eprop '(key value eid)      preload-index?)))\n(define eid=>ekey=>evalue=>1    (time (relation-index-dict r.eprop '(eid key value)      preload-index?)))\n(define ckey=>cvalue=>curie=>1  (time (relation-index-dict r.cprop '(key value curie)    preload-index?)))\n(define curie=>ckey=>cvalue=>1  (time (relation-index-dict r.cprop '(curie key value)    preload-index?)))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-mk.rkt",
    "content": "#lang racket/base\n(require \"../dbk.rkt\" racket/function racket/list racket/pretty racket/set)\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n\n(define (sort/any xs) (sort xs anyset\n    (run* (x y z)\n      (conde ((== y 'a) (== z 'c))\n             ((== y 'a) (== z 'd))\n             ((== x '8))\n             ((== y 'b) (== x '12))\n             ((== y 'b) (== z 'f) (== x '9))\n             ((== y 'b) (== z 'g) (== x '9))\n             ((== y 'c))\n             ((== y 'd)))\n      (triple2o x y z)))\n  (list->set\n    '((4 a c)\n      (5 a c)\n      (6 a c)\n      (8 b d)\n      (9 b f)\n      (11 c a)\n      (12 c d))))\n\n(test '=/=.atom.1\n  (run* x (=/= 1 x))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) 1)))))\n(test '=/=.atom.2\n  (run* x (=/= x 2))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) 2)))))\n\n(test '=/=.atom.==.1\n  (run* x (== x 1) (=/= x 1))\n  '())\n(test '=/=.atom.==.2\n  (run* x (=/= x 2) (== x 2))\n  '())\n(test '=/=.atom.==.3\n  (run* x (=/= x 3) (== x 'not-3))\n  '(not-3))\n(test '=/=.atom.==.4\n  (run* x (== x 'not-4) (=/= x 4))\n  '(not-4))\n\n(test '=/=.var.==.1\n  (run* x\n    (fresh (y)\n      (=/= x y)\n      (== x 1)\n      (== y 1)))\n  '())\n(test '=/=.var.==.2\n  (run* x\n    (fresh (y)\n      (== x 2)\n      (== y 2)\n      (=/= x y)))\n  '())\n(test '=/=.var.==.3\n  (run* x\n    (fresh (y)\n      (== x 3)\n      (=/= x y)\n      (== y 3)))\n  '())\n(test '=/=.var.==.4\n  (run* x\n    (fresh (y z)\n      (=/= x 4)\n      (== x y)\n      (== y z)\n      (== z 4)))\n  '())\n(test '=/=.var.==.5\n  (run* x\n    (fresh (y z)\n      (=/= x 5)\n      (== y z)\n      (== x y)\n      (== z 5)))\n  '())\n(test '=/=.var.==.6\n  (run* x\n    (fresh (y)\n      (=/= x y)\n      (== x y)))\n  '())\n(test '=/=.var.==.7\n  (run* x\n    (fresh (y)\n      (=/= x y)\n      (== y x)))\n  '())\n\n(test '=/=.pair.==.1\n  (run* x\n    (=/= x '(1 . 2))\n    (==  x '(1 . 2)))\n  '())\n(test '=/=.pair.==.2\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  x `(1 . 2))\n      (==  y 2)))\n  '())\n(test '=/=.pair.==.3\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (=/= x `(1 . ,y))\n      (==  y 2)))\n  '())\n(test '=/=.pair.==.4\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (==  y 2)\n      (=/= x `(1 . ,y))))\n  '())\n(test '=/=.pair.==.5\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  y 2)\n      (==  x `(1 . 2))))\n  '())\n(test '=/=.pair.==.6\n  (run* x\n    (fresh (y)\n      (=/= `(,x .  1) `(0 . ,y))\n      (==  `(,x . ,y) '(0 .  1))))\n  '())\n(test '=/=.pair.==.7\n  (run* x\n    (fresh (y)\n      (==  `(,x . ,y) '(0 .  1))\n      (=/= `(,x .  1) `(0 . ,y))))\n  '())\n\n(test '=/=.pair.=/=.1\n  (run* x\n    (=/= x '(1 . 2))\n    (==  x '(0 . 2)))\n  '((0 . 2)))\n(test '=/=.pair.=/=.2\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  x `(1 . 2))\n      (==  y 0)))\n  '((1 . 2)))\n(test '=/=.pair.=/=.3\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (=/= x `(1 . ,y))\n      (==  y 0)))\n  '((1 . 2)))\n(test '=/=.pair.=/=.4\n  (run* x\n    (fresh (y)\n      (==  x `(1 . 2))\n      (==  y 0)\n      (=/= x `(1 . ,y))))\n  '((1 . 2)))\n(test '=/=.pair.=/=.5\n  (run* x\n    (fresh (y)\n      (=/= x `(1 . ,y))\n      (==  y 0)\n      (==  x `(1 . 2))))\n  '((1 . 2)))\n(test '=/=.pair.=/=.6\n  (run* x\n    (fresh (y)\n      (=/= `(,x .  1) `(0 . ,y))\n      (==  `(,x . ,y) '(0 .  2))))\n  '(0))\n(test '=/=.pair.=/=.7\n  (run* x\n    (fresh (y)\n      (==  `(,x . ,y) '(0 .  2))\n      (=/= `(,x .  1) `(0 . ,y))))\n  '(0))\n\n(test '=/=.fresh.1\n  (run* x\n    (fresh (y)\n      (=/= y 1)))\n  '(#s(cx (term: #s(var 0)) (constraints:))))\n(test '=/=.fresh.2\n  (run* x\n    (fresh (y)\n      (=/= x 0)\n      (=/= y 1)))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) 0)))))\n(test '=/=.fresh.3\n  (run* x\n    (fresh (y)\n      (=/= x 0)\n      (=/= x y)))\n  '(#s(cx (term: #s(var 0)) (constraints: (=/= #s(var 0) #s(var 1))\n                                  (=/= #s(var 0) 0)))))\n(test '=/=.fresh.4\n  (run* (x y)\n    (fresh (z)\n      (=/= `(,x . ,y) '(0 . 2))\n      (=/= z 1)))\n  '(#s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 0) 0)))\n    #s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 1) 2)))))\n(test '=/=.fresh.5\n  (run* (x y)\n    (fresh (z)\n      (=/= `(,x ,y ,z) '(0 1 2))))\n  '(#s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 0) 0)))\n    #s(cx (term: (#s(var 0) #s(var 1))) (constraints: (=/= #s(var 1) 1)))\n    #s(cx (term: (#s(var 0) #s(var 1))) (constraints:))))\n\n(test 'membero.forward\n  (run* () (membero 3 '(1 2 3 4 3 5)))\n  '(()))\n(test 'membero.backward\n  (run* x (membero x '(1 2 3 4 3 5)))\n  '(1 2 3 4 5))\n(test 'not-membero.forward\n  (run* () (not-membero 0 '(1 2 3 4 5)))\n  '(()))\n(test 'not-membero.backward\n  (run* x (not-membero x '(1 2 3 4 5)) (== x 0))\n  '(0))\n(test 'uniqueo.1\n  (run* () (uniqueo '(1 2 3 4 5)))\n  '(()))\n(test 'uniqueo.2\n  (run* () (uniqueo '(1 2 3 4 2)))\n  '())\n(test 'removeo.forward\n  (run* x (removeo '3 '(1 2 3 4 5) x))\n  '((1 2 4 5)))\n(test 'removeo.backward\n  (run* x (removeo x '(1 2 3 4 5) '(1 2 4 5)))\n  '(3))\n\n\n;; More table testing\n\n(define intersected-lists\n  '(((-1 0 no)\n     (-1 1 no)\n     (-1 2 no)\n     (-1 3 no)\n     (-1 4 no)\n     (-1 5 no)\n     (-1 6 no)\n     (-1 7 no)\n     (-1 8 no)\n     (-1 9 no)\n\n     (1 1 a0)\n     (1 2 b0)\n     (1 5 c0)\n     (3 4 d0)\n     (3 8 e0)\n     (3 8 e0.1)\n     (3 8 e0.2)\n\n     (4 0 no)\n     (4 1 no)\n     (4 2 no)\n     (4 3 no)\n     (4 4 no)\n     (4 5 no)\n     (4 6 no)\n     (4 7 no)\n     (4 8 no)\n     (4 9 no)\n\n     (6 0 f0)\n     (6 3 g0)\n     (6 5 h0)\n     (7 0 i0)\n     (7 2 j0)\n     (7 4 k0)\n     (7 6 l0)\n     (7 8 m0)\n     (7 9 n0)\n     (9 1 0)\n     (9 1 o0)\n     (9 2 p0)\n     (9 5 q0))\n    ((-1 0 no)\n     (-1 1 no)\n     (-1 2 no)\n     (-1 3 no)\n     (-1 4 no)\n     (-1 5 no)\n     (-1 6 no)\n     (-1 7 no)\n     (-1 8 no)\n     (-1 9 no)\n\n     (1 1 a1)\n     (1 2 b1)\n     (2 5 c1)  ; 0\n     (2 4 d1)  ; 0\n     (3 8 e1)\n     (3 8 e1.1)\n     (6 0 f1)\n     (6 3 g1)\n     (6 5 h1)\n     (7 0 i1)\n     (7 3 j1)  ; 1\n     (7 4 k1)\n     (7 6 l1)\n     (8 8 m1)  ; 0\n     (8 9 n1)  ; 0\n     (9 1 o1)\n     (9 1 o1.1)\n     (9 4 p1)  ; 1\n     (9 5 q1))\n    (;(-1 0 no)\n     ;(-1 1 no)\n     ;(-1 2 no)\n     ;(-1 3 no)\n     ;(-1 4 no)\n     ;(-1 5 no)\n     ;(-1 6 no)\n     ;(-1 7 no)\n     ;(-1 8 no)\n     ;(-1 9 no)\n\n     (0 1 a2)  ; 0\n     (1 3 b2)  ; 1\n     (1 5 c2)  ; 1\n     (2 4 d2)\n     (3 8 e2)\n     (5 0 f2)  ; 0\n     (6 3 g2)\n     (6 5 h2)\n     (7 0 i2)\n     (7 3 j2)\n     (7 4 k2)\n     (7 4 k2.1)\n     (7 6 l2)\n     (8 8 m2)\n     (8 9 n2)\n     (9 1 o2)\n     (9 4 p2)\n     (9 5 q2)\n\n     (10 1 no)\n     (10 0 no)\n     (10 2 no)\n     (10 3 no)\n     (10 4 no)\n     (10 5 no)\n     (10 6 no)\n     (10 7 no)\n     (10 8 no)\n     (10 9 no)\n     )))\n\n(define intersected-tables\n  (map (lambda (i s)\n         (relation/table\n           'relation-name   (string->symbol (format \"intersected-table.~v\" i))\n           'attribute-names '(i n m x)\n           'key-name        'i\n           'source-stream   s))\n       (range (length intersected-lists))\n       intersected-lists))\n\n(test 'table-ref\n  (map (lambda (R) (run* (n m x) (R 0 n m x))) intersected-tables)\n  '(((-1 0 no)) ((-1 0 no)) ((0 1 a2))))\n\n(test 'table-intersection\n  (sort/any\n    (run* (n m a b c)\n      (foldl (lambda (g0 g) (fresh () g g0)) (== #t #t)\n             (map (lambda (v R) (fresh (i) (R i n m v))) (list a b c)\n                  intersected-tables))))\n  (sort/any\n    '((3 8 e0   e1   e2)\n      (3 8 e0   e1.1 e2)\n      (3 8 e0.1 e1   e2)\n      (3 8 e0.1 e1.1 e2)\n      (3 8 e0.2 e1   e2)\n      (3 8 e0.2 e1.1 e2)\n      (6 3 g0   g1   g2)\n      (6 5 h0   h1   h2)\n      (7 0 i0   i1   i2)\n      (7 4 k0   k1   k2)\n      (7 4 k0   k1   k2.1)\n      (7 6 l0   l1   l2)\n      (9 1 0    o1   o2)\n      (9 1 0    o1.1 o2)\n      (9 1 o0   o1   o2)\n      (9 1 o0   o1.1 o2)\n      (9 5 q0   q1   q2))))\n\n(test '<=.1\n  (run* n\n    (membero n '(0 1 2 3 4 5 6 7 8 9))\n    (<=o 2 n)\n    (set '((1 1)\n               (1 2)\n               (1 3)\n               (2 4)\n               (2 6)\n               (3 5)\n               (3 6)\n               (6 4)\n               (1 2)\n               (1 3)\n               (1 4)\n               (1 6)\n               (1 5)\n               (1 6)\n               (2 4)\n               (3 4)\n               (1 4)\n               (1 6)\n               (1 5)\n               (1 6)\n               (1 4)\n               (1 4)\n               (1 4)\n               (1 4))))\n(test 'path2*.set.1\n  (run*/set x (path2* x 6))\n  (list->set '(2 3 1 1 1 1)))\n(test 'path2*.set.2\n  (run*/set y (path2* 3 y))\n  (list->set '(5 6 4)))\n\n(test 'path3*.0\n  (run* (x y) (path3* x y))\n  '((1 1)\n    (1 2)\n    (1 3)\n    (2 4)\n    (2 6)\n    (3 5)\n    (3 6)\n    (6 4)\n    (1 4)\n    (1 6)\n    (1 5)\n    (1 6)\n    (2 4)\n    (3 4)\n    (1 4)\n    (1 4)))\n(test 'path3*.1\n  (run* x (path3* x 6))\n  '(2 3 1 1))\n(test 'path3*.2\n  (run* y (path3* 3 y))\n  '(5 6 4))\n\n(define-relation (edge/cycle a b)\n  (conde ((== a 5) (== b 1))\n         ((edge a b))))\n(define-relation (path/cycle* a c)\n  (conde ((edge/cycle a c))\n         ((fresh (b)\n            (=/= a b)\n            (edge/cycle a b)\n            (path/cycle* b c)))))\n(test 'path/cycle*.0\n  (run* (x y) (path/cycle* x y))\n  '((5 1)\n    (1 1)\n    (1 2)\n    (1 3)\n    (2 4)\n    (2 6)\n    (3 5)\n    (3 6)\n    (6 4)\n    (5 1)\n    (5 2)\n    (5 3)\n    (3 1)\n    (5 4)\n    (5 6)\n    (5 5)\n    (5 6)\n    (1 4)\n    (1 6)\n    (1 5)\n    (1 6)\n    (2 4)\n    (3 4)\n    (5 4)\n    (5 4)\n    (3 1)\n    (3 2)\n    (3 3)\n    (1 1)\n    (3 4)\n    (3 6)\n    (1 4)\n    (1 4)\n    (3 4)))\n(test 'path/cycle*.1\n  (run* x (path/cycle* x 6))\n  '(2 3 5 1 3))\n(test 'path/cycle*.2\n  (run* y (path/cycle* 3 y))\n  '(5 6 1 4 1 2 3 4 6 4))\n\n(test 'path/cycle*.set.0\n  (run*/set (x y) (path/cycle* x y))\n  (list->set '((5 1)\n               (1 1)\n               (1 2)\n               (1 3)\n               (2 4)\n               (2 6)\n               (3 5)\n               (3 6)\n               (6 4)\n               (5 1)\n               (5 2)\n               (5 3)\n               (3 1)\n               (5 4)\n               (5 6)\n               (5 5)\n               (5 6)\n               (1 4)\n               (1 6)\n               (1 5)\n               (1 6)\n               (2 4)\n               (3 4)\n               (5 1)\n               (5 4)\n               (5 4)\n               (1 1)\n               (5 1)\n               (5 2)\n               (5 3)\n               (3 1)\n               (3 2)\n               (3 3)\n               (1 4)\n               (1 4))))\n(test 'path/cycle*.set.1\n  (run*/set x (path/cycle* x 6))\n  (list->set '(2 3 1 5 5 3 3)))\n(test 'path/cycle*.set.2\n  (run*/set y (path/cycle* 3 y))\n  (list->set '(5 6 1 4 1 2 3 4 6 5 6 1 4 4 1 2 3 4 6 5 6 1 4 4 1 2 3)))\n\n;; Using list->set on a run result is not the same as using run/set:\n;; run/set guarantees that the result has 10 unique answers before stopping\n(test 'path/cycle*.set.n.0\n  (list->set (run 10 (x y) (path/cycle* x y)))\n  (list->set '((1 1) (1 2) (1 3) (3 6) (6 4) (2 4) (5 1) (3 5) (2 6))))\n(test 'path/cycle*.set.n.1\n  (run/set 10 (x y) (path/cycle* x y))\n  (list->set '((1 1) (1 2) (1 3) (5 2) (3 6) (6 4) (2 4) (5 1) (3 5) (2 6))))\n\n\n;; Equivalence class tests\n\n;; fast version\n(define-relation/table (uedge a b)\n  'source-stream '((0  15)\n                   (10 15)\n                   (15 20)\n                   (17 18)\n                   (17 20)\n                   (20  0)))\n\n(define-relation (node x)\n  (fresh (y)\n    (conde ((uedge x y)) ((uedge y x)))))\n\n(define-relation (equiv=/= a b)\n  (=/= a b)\n  (fresh (x)\n    (conde ((uedge a x))\n           ((uedge x a)))\n    (conde ((==       x b))\n           ((equiv=/= x b)))))\n\n(define-relation (equiv a b)\n  (node a)\n  (node b)\n  (conde ((==       a b))\n         ((equiv=/= a b))))\n\n;; cpu time: 1440 real time: 1466 gc time: 74\n(test 'equiv.0\n  (time (run*/set (x y) (equiv x y)))\n  (list->set\n    '((20 20) (10 20) (15 15) (20 10) (15 0) (0 15) (0 0) (15 17) (17 15)\n      (17 0) (15 18) (0 17) (18 15) (17 17) (0 18) (18 0) (20 15) (18 17)\n      (15 20) (17 18) (10 10) (18 18) (0 20) (20 0) (17 20) (20 17) (20 18)\n      (18 20) (10 15) (15 10) (0 10) (10 0) (10 17) (17 10) (10 18) (18 10))))\n\n;; cpu time: 298 real time: 319 gc time: 5\n(test 'equiv.1\n  (time (run*/set x (equiv 0 x)))\n  (set 0 17 18 20 10 15))\n\n;; cpu time: 459 real time: 485 gc time: 12\n(test 'equiv.2\n  (time (run*/set x (equiv x 0)))\n  (set 0 17 18 20 10 15))\n\n;; much more expensive version\n(define-relation/table (uedge.slow a b)\n  'source-stream '((0   5)\n                   (2   3)\n                   (2   5)\n                   (5   8)\n                   (5  10)\n                   (7  10)\n                   (10 13)\n                   (10 15)\n                   (12 15)\n                   (15 18)\n                   (17 18)\n                   (15 20)\n                   (17 20)\n                   (20  0)))\n\n(define-relation (node.slow x)\n  (fresh (y)\n    (conde ((uedge.slow x y)) ((uedge.slow y x)))))\n\n(define-relation (equiv=/=.slow a b)\n  (=/= a b)\n  (fresh (x)\n    (conde ((uedge.slow a x))\n           ((uedge.slow x a)))\n    (conde ((==            x b))\n           ((equiv=/=.slow x b)))))\n\n(define-relation (equiv.slow a b)\n  (node.slow a)\n  (node.slow b)\n  (conde ((==            a b))\n         ((equiv=/=.slow a b))))\n\n#|\n;; cpu time: 94756 real time: 97248 gc time: 3523\n(test 'equiv.0.slow\n  (time (run*/set (x y) (equiv.slow x y)))\n  (list->set\n    '((10 20) (12 18) (20 10) (2 12) (18 12) (7 7) (12 2) (13 17) (15 15) (17 13)\n      (10 5) (13 2) (15 0) (0 15) (3 12) (2 13) (7 8) (8 7) (12 3) (13 18) (18 13)\n      (5 10) (13 3) (12 20) (0 0) (8 8) (15 17) (17 15) (3 13) (20 12) (10 7) (15 18)\n      (0 17) (20 13) (2 15) (7 10) (12 5) (13 20) (15 2) (17 0) (18 15) (5 12) (10 8)\n      (13 5) (15 3) (17 17) (0 2) (0 18) (18 0) (5 13) (8 10) (2 0) (3 15) (12 7)\n      (17 2) (0 3) (3 0) (20 15) (2 17) (18 17) (7 12) (15 20) (17 18) (10 10) (13 7)\n      (12 8) (7 13) (8 12) (15 5) (17 3) (0 20) (20 0) (2 2) (3 17) (2 18) (18 2)\n      (18 18) (5 15) (13 8) (17 20) (0 5) (3 2) (8 13) (2 3) (3 18) (20 17) (18 3)\n      (5 0) (10 12) (12 10) (20 18) (2 20) (7 15) (15 7) (17 5) (3 3) (20 2) (18 20)\n      (5 17) (10 13) (13 10) (15 8) (0 7) (20 3) (5 18) (7 0) (8 15) (2 5) (3 20)\n      (18 5) (5 2) (12 12) (17 7) (0 8) (3 5) (20 20) (5 3) (7 17) (8 0) (10 15)\n      (13 12) (12 13) (20 5) (2 7) (18 7) (5 20) (7 2) (7 18) (8 17) (15 10) (17 8)\n      (13 13) (0 10) (3 7) (2 8) (7 3) (8 2) (8 18) (10 0) (18 8) (5 5) (10 17)\n      (12 15) (7 20) (8 3) (15 12) (17 10) (3 8) (20 7) (10 18) (15 13) (0 12)\n      (20 8) (2 10) (7 5) (8 20) (10 2) (12 0) (13 15) (18 10) (5 7) (13 0) (12 17)\n      (17 12) (0 13) (3 10) (5 8) (8 5) (10 3))))\n\n;; cpu time: 4520 real time: 4675 gc time: 123\n(test 'equiv.1.slow\n  (time (run*/set x (equiv.slow 0 x)))\n  (set 0 17 3 20 5 7 8 10 12 13 15 2 18))\n\n;; cpu time: 10254 real time: 10618 gc time: 370\n(test 'equiv.2.slow\n  (time (run*/set x (equiv.slow x 0)))\n  (set 0 17 3 20 5 7 8 10 12 13 15 2 18))\n;|#\n\n\n;; Simple relational interpreter tests\n\n(define-relation (eval-expo expr env value)\n  (conde\n    ((fresh (body)\n       (== `(lambda ,body) expr)\n       (== `(closure ,body ,env) value)))\n    ((== `(quote ,value) expr))\n    ((fresh (a*)\n       (== `(list . ,a*) expr)\n       (eval-listo a* env value)))\n    ((fresh (a d va vd)\n       (== `(cons ,a ,d) expr)\n       (== `(,va . ,vd) value)\n       (eval-expo a env va)\n       (eval-expo d env vd)))\n    ((fresh (index)\n       (== `(var ,index) expr)\n       (lookupo index env value)))\n    ((fresh (rator rand arg env^ body)\n       (== `(app ,rator ,rand) expr)\n       (eval-expo rator env `(closure ,body ,env^))\n       (eval-expo rand env arg)\n       (eval-expo body `(,arg . ,env^) value)))))\n\n(define-relation (lookupo index env value)\n  (fresh (arg e*)\n    (== `(,arg . ,e*) env)\n    (conde\n      ((== '() index) (== arg value))\n      ((fresh (i* a d)\n         (== `(s . ,i*) index)\n         (== `(,a . ,d) e*)\n         (lookupo i* e* value))))))\n\n(define-relation (eval-listo e* env value)\n  (conde\n    ((== '() e*) (== '() value))\n    ((fresh (ea ed va vd)\n       (== `(,ea . ,ed) e*)\n       (== `(,va . ,vd) value)\n       (eval-expo ea env va)\n       (eval-listo ed env vd)))))\n\n(define (evalo expr value) (eval-expo expr '() value))\n\n(test 'evalo-literal\n  (run 1 e (evalo e 5))\n  '((quote 5)))\n\n;; ~600 ms\n(test 'evalo-quine\n  (time (run 1 e (evalo e e)))\n  '((app (lambda (list (quote app) (var ())\n                       (list (quote quote) (var ()))))\n         (quote (lambda (list (quote app) (var ())\n                              (list (quote quote) (var ()))))))))\n\n;; ~5500 ms\n;(test 'evalo-twine\n;  (time (run 1 (p q) (evalo p q) (evalo q p)))\n;  '(((quote (app (lambda (list (quote quote)\n;                               (list (quote app) (var ())\n;                                     (list (quote quote) (var ())))))\n;                 (quote (lambda (list (quote quote)\n;                                      (list (quote app) (var ())\n;                                            (list (quote quote) (var ()))))))))\n;     (app (lambda (list (quote quote)\n;                        (list (quote app) (var ())\n;                              (list (quote quote) (var ())))))\n;          (quote (lambda (list (quote quote)\n;                               (list (quote app) (var ())\n;                                     (list (quote quote) (var ()))))))))))\n\n;; ~24000 ms\n;(test 'evalo-thrine\n;  (time (run 1 (p q r) (evalo p q) (evalo q r) (evalo r p)))\n;  '(((quote (quote (app (lambda (list (quote quote)\n;                                      (list (quote quote)\n;                                            (list (quote app) (var ())\n;                                                  (list (quote quote) (var ()))))))\n;                        (quote (lambda (list (quote quote)\n;                                             (list (quote quote)\n;                                                   (list (quote app) (var ())\n;                                                         (list (quote quote) (var ()))))))))))\n;     (quote (app (lambda (list (quote quote)\n;                               (list (quote quote)\n;                                     (list (quote app) (var ())\n;                                           (list (quote quote) (var ()))))))\n;                 (quote (lambda (list (quote quote)\n;                                      (list (quote quote)\n;                                            (list (quote app) (var ())\n;                                                  (list (quote quote) (var ())))))))))\n;     (app (lambda (list (quote quote)\n;                        (list (quote quote)\n;                              (list (quote app) (var ())\n;                                    (list (quote quote) (var ()))))))\n;          (quote (lambda (list (quote quote)\n;                               (list (quote quote)\n;                                     (list (quote app) (var ())\n;                                           (list (quote quote) (var ())))))))))))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-semantics.rkt",
    "content": "#lang racket/base\n(require \"../dbk/semantics.rkt\" racket/pretty)\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n\n;; References:\n;; https://web.archive.org/web/20201012095657/https://sites.google.com/site/williamcushing/notes/howtoconvertfirst-orderlogicintoclausalform\n;; https://en.wikipedia.org/wiki/Drinker_paradox\n\n(define program.0 '((define (eq  a b) (relate == (var a) (var b)))\n                    (define (eq2 d c) (relate == (var c) (var d)))\n                    (query (x) (and (relate eq  (var x) (var x))\n                                    (relate eq2 (var x) (var x))))))\n(define program.1 '((query (x y) (relate == (app cons (var x) (var y)) (app cons '1 '2)))))\n\n(define program.drinking '((query ()\n                                  (all (b)\n                                    (imply (relate Bar (var b))\n                                           (exist (p)\n                                             (and (relate Person (var p))\n                                                  (relate In     (var p) (var b))\n                                                  (iff (relate Drinking (var p))\n                                                       (all (q) (imply (and (relate Person (var q))\n                                                                            (relate In     (var q) (var b)))\n                                                                       (relate Drinking (var q))))))))))))\n\n(for-each\n  (lambda (p)\n    (displayln \"ORIGINAL:\")\n    (pretty-write p)\n    (displayln \"SIMPLIFIED:\")\n    (pretty-write (simplify-program                                      #f p))\n    (displayln \"FACTORED:\")\n    (pretty-write (factor-program                                           p))\n    (displayln \"SIMPLIFIED and FACTORED:\")\n    (pretty-write (factor-program (simplify-program                      #f p)))\n    (displayln \"SIMPLIFIED and FACTORED and POST-SIMPLIFIED:\")\n    (pretty-write (simplify-program #t (factor-program (simplify-program #f p))))\n    )\n  (list\n    program.0\n    program.1\n    program.drinking\n    ))\n"
  },
  {
    "path": "medikanren2/neo/dbKanren/test/test-storage.rkt",
    "content": "#lang racket/base\n(require \"../dbk/storage.rkt\"\n         racket/pretty\n         racket/runtime-path)\n\n(define-runtime-path path.here \".\")\n\n(define stg (storage:filesystem (build-path path.here \"example-storage\")))\n;(define stg2 (storage:filesystem (build-path path.here \"example-storage\")))\n\n(storage-block-remove-names! stg '(testing 2) '(new 1) '(new 2.1) '(new 2.2))\n\n(storage-checkpoint! stg)\n\n(pretty-write (storage-description-keys stg))\n(pretty-write (storage-block-names stg))\n\n;(define (sset! . kvs) (apply storage-description-set! stg kvs))\n;(define (sref  . ks)  (map cons ks (map (lambda (k) (storage-description-ref stg k)) ks)))\n\n;(define out.1 (storage-block-new! stg '(testing 1)))\n;(pretty-write (equal? out.1 (storage-block-out stg '(testing 1))))\n\n(storage-block-new! stg '(testing 2))\n\n(call-with-output-file\n  (storage-block-new! stg '(testing 1))\n  (lambda (out) (write-string \"this is testing 1\" out)))\n(call-with-output-file\n  (storage-block-path stg '(testing 2))\n  (lambda (out) (write-string \"this is testing 2\" out)))\n\n(pretty-write (storage-block-path stg '(testing 2)))\n\n(storage-block-rename! stg '(testing 1) '(new 1))\n(storage-block-add-names! stg '(testing 2) '(new 2.1) '(new 2.2))\n\n(storage-checkpoint! stg)\n\n(pretty-write (storage-description-keys stg))\n(pretty-write (storage-block-names stg))\n(pretty-write (map (lambda (name) (storage-block-path stg name)) (storage-block-names stg)))\n\n(pretty-write `(in.1:   ,(call-with-input-file (storage-block-path stg '(new 1))     read-line)))\n(pretty-write `(in.2:   ,(call-with-input-file (storage-block-path stg '(testing 2)) read-line)))\n(pretty-write `(in.2.1: ,(call-with-input-file (storage-block-path stg '(new 2.1))   read-line)))\n(pretty-write `(in.2.2: ,(call-with-input-file (storage-block-path stg '(new 2.2))   read-line)))\n\n(storage-block-remove-names! stg '(testing 2) '(new 1) '(new 2.1) '(new 2.2))\n\n(storage-revert!     stg)\n(storage-checkpoint! stg)\n\n;(sset! 'hello 1 'world! 2)\n\n;(storage-checkpoint!  stg)\n;(storage-revert!      stg)\n;(pretty-write (storage-checkpoint-count stg))\n;(pretty-write (sref 'hello 'world!))\n\n;(sset! 'hello 1 'world! 2)\n\n;(storage-checkpoint!  stg)\n;(storage-revert!      stg)\n;(pretty-write (storage-checkpoint-count stg))\n;(pretty-write (sref 'hello 'world!))\n\n;(sset! 'hello 5 'world! 2)\n\n;(storage-revert!      stg)\n;(storage-checkpoint!  stg)\n;(pretty-write (storage-checkpoint-count stg))\n;(pretty-write (sref 'hello 'world!))\n\n;(sset! 'hello 5 'world! 2)\n\n;(storage-checkpoint!  stg)\n;(storage-revert!      stg)\n;(pretty-write (storage-checkpoint-count stg))\n;(pretty-write (sref 'hello 'world!))\n\n(storage-trash-empty! stg)\n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_2_4_8/biolink-model.yaml",
    "content": "id: https://w3id.org/biolink/biolink-model\nname: Biolink-Model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 2.4.8\n\n\n## ------------\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  alliancegenome: 'https://www.alliancegenome.org/'\n  apollo: 'https://github.com/GMOD/Apollo'\n  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='\n  biolink: 'https://w3id.org/biolink/vocab/'\n  bioschemas: 'https://bioschemas.org/'\n  linkml: 'https://w3id.org/linkml/'\n  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='\n  # Placeholder: just points to GMOD Chado wiki\n  CHADO: 'http://gmod.org/wiki/Chado/'\n  # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve\n  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='\n  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'\n  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'\n  CLINVAR: 'http://identifiers.org/clinvar'\n  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'\n  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'\n  CPT: 'https://www.ama-assn.org/practice-management/cpt/'\n  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='\n  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='\n  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='\n  CTD: 'http://ctdbase.org/'\n  DGIdb: 'https://www.dgidb.org/interaction_types'\n  dcat: 'http://www.w3.org/ns/dcat#'\n  dct: 'http://purl.org/dc/terms/'\n  dcid: 'https://datacommons.org/browser/'\n  doi: 'https://doi.org/'\n  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'\n  DrugCentral: 'http://drugcentral.org/drugcard/'\n  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'\n  EDAM-DATA: 'http://edamontology.org/data_'\n  EDAM-FORMAT: 'http://edamontology.org/format_'\n  EDAM-OPERATION: 'http://edamontology.org/operation_'\n  EDAM-TOPIC: 'http://edamontology.org/topic_'\n  EFO: 'http://www.ebi.ac.uk/efo/EFO_'\n  ExO: 'http://purl.obolibrary.org/obo/ExO_'\n  fabio: 'http://purl.org/spar/fabio/'\n  foaf: 'http://xmlns.com/foaf/0.1/'\n  foodb.food: 'http://foodb.ca/compounds/'\n  foodb.compound: 'http://foodb.ca/foods/'\n  FYECO: 'https://www.pombase.org/term/'\n  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'  # Fission Yeast Phenotype Ontology\n  GAMMA: 'http://translator.renci.org/GAMMA_'\n  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'\n  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'\n  # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)\n  GOP: 'http://purl.obolibrary.org/obo/go#'\n  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'\n  GSID: 'https://scholar.google.com/citations?user='\n  GTEx: 'https://www.gtexportal.org/home/gene/'\n  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='\n  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'\n  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'\n  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'\n  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'\n  ICD10: 'https://icd.codes/icd9cm/'\n  ICD9: 'http://translator.ncats.nih.gov/ICD9_'\n  interpro: 'https://www.ebi.ac.uk/interpro/entry/'\n  INO: 'http://purl.obolibrary.org/obo/INO_'\n  isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international\n  isni: 'https://isni.org/isni/'\n  issn: 'https://portal.issn.org/resource/ISSN/'\n  ncats.drug: 'https://drugs.ncats.io/drug/'\n  KEGG.BRITE: 'http://www.kegg.jp/entry/'\n  KEGG.DGROUP: 'http://www.kegg.jp/entry/'\n  KEGG.ENZYME: 'http://www.kegg.jp/entry/'\n  KEGG.GENE: 'http://www.kegg.jp/entry/'\n  KEGG.PATHWAY: 'https://www.kegg.jp/entry/'\n  KEGG.RCLASS: 'http://www.kegg.jp/entry/'\n  LOINC: 'http://loinc.org/rdf/'\n  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'\n  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'\n  metacyc.reaction: 'https://identifiers.org/metacyc.reaction:'\n  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'\n  MESH: 'http://id.nlm.nih.gov/mesh/'\n  MI: 'http://purl.obolibrary.org/obo/MI_'\n  mirbase: 'http://identifiers.org/mirbase'\n  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'\n  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'\n  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'\n  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'\n  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='\n  NCBIGene: 'http://identifiers.org/ncbigene/'\n  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'\n  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'\n  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='\n  OBAN: 'http://purl.org/oban/'\n  oboformat: 'http://www.geneontology.org/formats/oboInOwl#'\n  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'\n  OBOREL: 'http://purl.obolibrary.org/obo/RO_'\n  ORCID: 'https://orcid.org/'\n  ORPHA: 'http://www.orpha.net/ORDO/Orphanet_'\n  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'\n  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='\n  PathWhiz: 'http://smpdb.ca/pathways/#'  # See also https://smpdb.ca/pathwhiz/\n  pav: 'http://purl.org/pav/'\n  PHAROS: 'http://pharos.nih.gov'\n  PomBase: 'https://www.pombase.org/gene/'\n  prov: 'http://www.w3.org/ns/prov#'\n  qud: 'http://qudt.org/1.1/schema/qudt#'\n  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'\n  ResearchID: 'https://publons.com/researcher/'\n  RO: 'http://purl.obolibrary.org/obo/RO_'\n  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'\n  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='\n  schema: 'http://schema.org/'\n  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='\n  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'\n  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'\n  SIO: 'http://semanticscience.org/resource/SIO_'\n  SNOMED: 'http://www.snomedbrowser.com/Codes/Details/'\n  SNOMEDCT: 'http://www.snomedbrowser.com/Codes/Details/'\n  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'\n  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'\n  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'\n  # The UMLS Semantic types and groups namespaces don't have a directly\n  # resolvable Base URI, but we point to a pair of sensible web documents\n  STY: 'http://purl.bioontology.org/ontology/STY/'\n  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'\n  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'\n  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'\n  # The \"Variation Modelling Collaboration\" (VMC) is not (yet) a conventional namespace so we point to its Github repo\n  # See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and\n  # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/\n  VMC: 'https://github.com/ga4gh/vr-spec/'\n  WBls: 'http://purl.obolibrary.org/obo/WBBL_'\n  WBbt: 'http://purl.obolibrary.org/obo/WBBT_'\n  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'\n  WIKIDATA: 'https://www.wikidata.org/wiki/'            # Wikidata Entity\n  WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:'  # Wikidata Property - not a conventional namespace prefix\n  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'\n  XPO: 'http://purl.obolibrary.org/obo/XPO_'  # Xenopus Phenotype Ontology\n  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='\n\ndefault_prefix: biolink\ndefault_range: string\n\n# 2. The following prefix maps are retrieved from the\n#    specified contexts defined at https://prefixcommons.org/\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\n# The following 'standard' prefixes are also used.\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - OIO\n  - BIOGRID\n  - SO\n\n## ------------\n## SUBSETS\n## ------------\nenums:\n  logical_interpretation_enum:\n    permissible_values:\n      SomeSome:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as a some-some statement\n        meaning: os:SomeSomeInterpretation\n      AllSome:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as an all-some statement.\n        meaning: os:AllSomeInterpretation\n      InverseAllSome:\n\n  reaction_direction_enum:\n    permissible_values:\n      left_to_right:\n      right_to_left:\n      bidirectional:\n      neutral:\n\n  reaction_side_enum:\n    permissible_values:\n      left:\n      right:\n\n  phase_enum:\n    description: phase\n    permissible_values:\n      0:\n      1:\n      2:\n\n  strand_enum:\n    description: strand\n    permissible_values:\n      \"+\":\n        description: Positive\n      \"-\":\n        description: Negative\n      \".\":\n        description: Unstranded\n      \"?\":\n        description: Unknown\n\n  sequence_enum:\n    description: type of sequence\n    permissible_values:\n      \"NA\":\n        description: nucleic acid\n      \"AA\":\n        description: amino acid\n\n  predicate_qualifier_enum:\n    description: >-\n      constrained list of qualifying terms that soften or expand the definition of the predicate used.\n      can be used to constrain or qualify any predicate (any child of related_to).\n    permissible_values:\n      \"predicted\":\n      \"possibly\":\n      \"hypothesized\":\n      \"validated\":\n      \"supported by real-world evidence\":\n      \"supported by clinical evidence\":\n\n  druggable_gene_category_enum:\n    permissible_values:\n      \"Tclin\":\n        description: >-\n          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.\n      \"Tbio\":\n        description: >-\n          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy\n          the activity thresholds detailed below.\n      \"Tchem\":\n        description: >-\n          These targets do not have known drug or small molecule activities that satisfy the activity\n          thresholds detailed below AND satisfy one or more of the following criteria:\n          target is above the cutoff criteria for Tdark\n          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)\n          with an Experimental Evidence code\n      \"Tdark\":\n        description: >-\n          These are targets about which virtually nothing is known. They do not have known drug or small\n          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or\n          more of the following criteria:\n          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or\n          less than or equal to 50 Antibodies available according to http://antibodypedia.com.\n\n  drug_availability_enum:\n    description: >-\n    permissible_values:\n      \"over the counter\":\n        description: >-\n          chemical entity is available over the counter without a prescription.\n      \"prescription\":\n        description:\n          chemical entity is available by prescription.\n\n  drug_delivery_enum:\n    permissible_values:\n      \"inhalation\":\n      \"oral\":\n      \"absorbtion through the skin\":\n      \"intravenous injection\":\n\n  FDA_approval_status_enum:\n    description: >-\n    permissible_values:\n      \"Discovery & Development Phase\":\n        description: >-\n          Discovery & Development Phase. Discovery involves researchers finding new possibilities\n          for medication through testing molecular compounds, noting unexpected effects from existing treatments,\n          or the creation of new technology that allows novel ways of targeting medical products to sites in the body.\n          Drug development occurs after researchers identify potential compounds for experiments.\n      \"Preclinical Research Phase\":\n        description: >-\n          Preclinical Research Phase.  Once researchers have examined the possibilities a new drug may contain,\n          they must do preliminary research to determine its potential for harm (toxicity).\n          This is categorized as preclinical research and can be one of two types: in vitro or in vivo.\n      \"FDA Clinical Research Phase\":\n        description: >-\n          Clinical Research Phase. Clinical research involves trials of the drug on people,\n          and it is one of the most involved stages in the drug development and approval process.\n          Clinical trials must answer specific questions and follow a protocol determined by\n          the drug researcher or manufacturer.\n      \"FDA Review Phase 4\":\n        description: >-\n          FDA Review\n      \"FDA Post-Market Safety Monitoring\":\n        description: >-\n          FDA Post-Market Safety Monitoring.  The last phase of drug approval is an ongoing one\n          while the drug is on the marketplace. If a developer wants to change anything about the\n          drug formulation or approve it for a new use, they must apply with the FDA. The FDA also\n          frequently reviews the drug’s advertising and its manufacturing facility to make sure\n          everything involved in its creation and marketing is in compliance with regulations.\n      \"FDA Clinical Research Phase 1\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and\n          lasts several months. This phase is used to determine the safety and dosage of the drug,\n          and about 70% of these drugs move on to the next clinical research phase.\n      \"FDA Clinical Research Phase 2\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people,\n          who must have the disease or condition the drug supposes to treat. This phase can last\n          from a few months to two years, and its purpose is to monitor the efficacy of the drug,\n          as well as note side effects that may occur.\n      \"FDA Clinical Research Phase 3\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers\n          and can last up to four years. It is used to continue monitoring the efficacy of\n          the drug, as well as exploring any longer-term adverse reactions.\n      \"FDA Clinical Research Phase 4\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of\n          volunteers who have the disease or condition and continues to monitor safety and efficacy.\n          If a drug passes this phase, it goes on to FDA review.\n      \"FDA Fast Track\":\n        description: >-\n          Fast track is a process designed to facilitate the development, and expedite the\n          review of drugs to treat serious conditions and fill an unmet medical need.\n          The purpose is to get important new drugs to the patient earlier. Fast Track\n          addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track\n      \"FDA Breakthrough Therapy\":\n        description: >-\n          Breakthrough Therapy designation is a process designed to expedite the\n          development and review of drugs that are intended to treat a serious\n          condition and preliminary clinical evidence indicates that the drug may\n          demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy\n      \"FDA Accelerated Approval\":\n        description: >-\n          When studying a new drug, it can sometimes take many years to learn whether a drug actually\n          provides a real effect on how a patient survives, feels, or functions. A positive therapeutic\n          effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”.\n          Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical\n          benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs\n          for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint.\n          Using a surrogate endpoint enabled the FDA to approve these drugs faster.\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval\n      \"FDA Priority Review\":\n        description: >-\n          Prior to approval, each drug marketed in the United States must go through a detailed FDA review process.\n          In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving\n          the drug review time and created a two-tiered system of review times – Standard Review and Priority\n          Review. A Priority Review designation means FDA’s goal is to take action on an application\n          within 6 months (compared to 10 months under standard review).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review\n      \"Regular FDA Approval\":\n      \"Post-Approval Withdrawal\":\n\n\n\nsubsets:\n\n  model_organism_database:\n    description: >-\n      Subset that is relevant for a typical Model Organism Database (MOD)\n\n  translator_minimal:\n    description: >-\n      Minimum subset of translator work\n\n  samples:\n    description: >-\n      Sample/biosample datamodel\n\n  testing:\n    description: >-\n      TBD\n\n\n## ------------\n## TYPES\n## ------------\n\nimports:\n  - linkml:types\n\ntypes:\n\n  chemical formula value:\n    uri: xsd:string\n    base: str\n    description: A chemical formula\n    notes:\n      - Should be implemented as a stronger type\n\n  category type:\n    typeof: uriorcurie\n    description: >-\n      A primitive type in which the value denotes a class within the biolink model.\n      The value must be a URI or a CURIE. In a Neo4j representation, the value should\n      be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,\n      the value should be a URI such as https://w3id.org/biolink/vocab/Gene\n\n  iri type:\n    typeof: uriorcurie\n    description: >-\n      An IRI\n\n  label type:\n    typeof: string\n    description: >-\n      A string that provides a human-readable name for an entity\n\n  predicate type:\n    typeof: uriorcurie\n    description: >-\n      A CURIE from the biolink related_to hierarchy.\n      For example, biolink:related_to, biolink:causes, biolink:treats.\n\n  narrative text:\n    typeof: string\n    description: >-\n      A string that provides a human-readable description of something\n\n  symbol type:\n    typeof: string\n\n  frequency value:\n    typeof: string\n    uri: UO:0000105\n\n  percentage frequency value:\n    typeof: double\n    uri: UO:0000187\n\n  quotient:\n    aliases: ['ratio']\n    typeof: double\n    uri: UO:0010006\n\n  unit:\n    typeof: string\n    uri: UO:0000000\n    id_prefixes:\n      - UO\n    exact_mappings:\n      - qud:Unit\n\n  time type:\n    typeof: time\n\n  biological sequence:\n    typeof: string\n\n## ------------\n## SLOTS\n## ------------\n\nslots:\n\n## ---------------\n## ATTRIBUTE SLOTS\n## ---------------\n\n  has attribute:\n    description: >-\n      connects any entity to an attribute\n    domain: entity\n    range: attribute\n    multivalued: true\n    in_subset:\n      - samples\n    close_mappings:\n      # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'\n      - OBI:0001927\n    exact_mappings:\n      - SIO:000008\n    narrow_mappings:\n      # if 'has attribute' annotates a NamedThing as subject or\n      # object of an association, these OBAN mappings may apply\n      - OBAN:association_has_subject_property\n      - OBAN:association_has_object_property\n      - CPT:has_possibly_included_panel_element\n      - DRUGBANK:category\n      # RTX contributed terms. Could perhaps review for more semantically precise mappings?\n      - EFO:is_executed_in\n      - HANCESTRO:0301\n      - LOINC:has_action_guidance\n      - LOINC:has_adjustment\n      - LOINC:has_aggregation_view\n      - LOINC:has_approach_guidance\n      - LOINC:has_divisor\n      - LOINC:has_exam\n      - LOINC:has_method\n      - LOINC:has_modality_subtype\n      - LOINC:has_object_guidance\n      - LOINC:has_scale\n      - LOINC:has_suffix\n      - LOINC:has_time_aspect\n      - LOINC:has_time_modifier\n      - LOINC:has_timing_of\n      # disease is stage\n      - NCIT:R88\n      - NCIT:eo_disease_has_property_or_attribute\n      - NCIT:has_data_element\n      - NCIT:has_pharmaceutical_administration_method\n      - NCIT:has_pharmaceutical_basic_dose_form\n      - NCIT:has_pharmaceutical_intended_site\n      - NCIT:has_pharmaceutical_release_characteristics\n      - NCIT:has_pharmaceutical_state_of_matter\n      - NCIT:has_pharmaceutical_transformation\n      - NCIT:is_qualified_by\n      - NCIT:qualifier_applies_to\n      - NCIT:role_has_domain\n      - NCIT:role_has_range\n      - INO:0000154\n      - HANCESTRO:0308\n      - OMIM:has_inheritance_type\n      - ORPHA:C016\n      - ORPHA:C017\n      - RO:0000053\n      # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here\n      - RO:0000086\n      - RO:0000087\n      - SNOMED:has_access\n      - SNOMED:has_clinical_course\n      - SNOMED:has_count_of_base_of_active_ingredient\n      - SNOMED:has_dose_form_administration_method\n      - SNOMED:has_dose_form_release_characteristic\n      - SNOMED:has_dose_form_transformation\n      - SNOMED:has_finding_context\n      - SNOMED:has_finding_informer\n      - SNOMED:has_inherent_attribute\n      - SNOMED:has_intent\n      - SNOMED:has_interpretation\n      - SNOMED:has_laterality\n      - SNOMED:has_measurement_method\n      - SNOMED:has_method\n      - SNOMED:has_priority\n      - SNOMED:has_procedure_context\n      - SNOMED:has_process_duration\n      - SNOMED:has_property\n      - SNOMED:has_revision_status\n      - SNOMED:has_scale_type\n      - SNOMED:has_severity\n      - SNOMED:has_specimen\n      - SNOMED:has_state_of_matter\n      - SNOMED:has_subject_relationship_context\n      - SNOMED:has_surgical_approach\n      - SNOMED:has_technique\n      - SNOMED:has_temporal_context\n      - SNOMED:has_time_aspect\n      - SNOMED:has_units\n      - UMLS:has_structural_class\n      - UMLS:has_supported_concept_property\n      - UMLS:has_supported_concept_relationship\n      - UMLS:may_be_qualified_by\n\n  has attribute type:\n    description: >-\n      connects an attribute to a class that describes it\n    domain: attribute\n    range: ontology class\n    multivalued: false\n    required: true\n    in_subset:\n      - samples\n    narrow_mappings:\n      - LOINC:has_modality_type\n      - LOINC:has_view_type\n\n  # TRAPI Attribute schema alignment:\n  # value: NamedThing.name\n  # value_type: NamedThing.category\n  # value_type_name: quantity_value.NamedThing.name\n  has qualitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: named thing\n    multivalued: false\n    in_subset:\n      - samples\n\n  # TRAPI Attribute schema alignment:\n  # value: quantity_value.has_numeric_value[double] - may be a vector?\n  # value_type: quantity_value.has_unit.unit.uri\n  # value_type_name: quantity_value.has_unit.unit.name[string]\n  has quantitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: quantity value\n    multivalued: true\n    exact_mappings:\n      - qud:quantityValue\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_numerator_value\n      - SNOMED:has_presentation_strength_denominator_value\n      - SNOMED:has_presentation_strength_numerator_value\n    in_subset:\n      - samples\n\n  has numeric value:\n    description: >-\n      connects a quantity value to a number\n    domain: quantity value\n    range: double\n    multivalued: false\n    exact_mappings:\n      - qud:quantityValue\n    in_subset:\n      - samples\n\n  has unit:\n    description: >-\n      connects a quantity value to a unit\n    domain: quantity value\n    range: unit\n    multivalued: false\n    close_mappings:\n      # These RTX contributed terms mean \"is unit of\" which is the semantic inverse of this biolink:has_unit term\n      - EFO:0001697\n      - UO-PROPERTY:is_unit_of\n    exact_mappings:\n      - qud:unit\n      - IAO:0000039\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_denominator_unit\n      - SNOMED:has_concentration_strength_numerator_unit\n      - SNOMED:has_presentation_strength_denominator_unit\n      - SNOMED:has_presentation_strength_numerator_unit\n      - SNOMED:has_unit_of_presentation\n    in_subset:\n      - samples\n\n  base coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'one-based', 'fully-closed' ]\n    description: >-\n      A position in the base coordinate system.  Base coordinates start at position 1 instead of position 0.\n    range: integer\n\n## --------------------\n## NODE PROPERTY SLOTS\n## --------------------\n\n  node property:\n    description: >-\n      A grouping for any property that holds between a node and a value\n    domain: named thing\n\n  id:\n    identifier: true\n    description: >-\n      A unique identifier for an entity.\n      Must be either a CURIE shorthand for a URI or a complete URI\n    in_subset:\n      - translator_minimal\n    required: true\n    exact_mappings:\n      - alliancegenome:primaryId\n      - gff3:ID\n      - gpi:DB_Object_ID\n\n  iri:\n    description: >-\n      An IRI for an entity. This is determined by the id using expansion rules.\n    range: iri type\n    in_subset:\n      - translator_minimal\n      - samples\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P854\n\n  type:\n    slot_uri: rdf:type\n    exact_mappings:\n      - alliancegenome:soTermId\n      - gff3:type\n      - gpi:DB_Object_Type\n\n  category:\n    is_a: type\n    domain: entity\n    range: category type\n    designates_type: true\n    description: >-\n      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the\n      biolink entity type class.\n       * In a neo4j database this MAY correspond to the neo4j label tag.\n       * In an RDF database it should be a biolink model class URI.\n      This field is multi-valued. It should include values for ancestors of the biolink class; for example,\n      a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\n\n      In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink\n      class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`\n      may have a rdf:type assertion to a SO class such as TF_binding_site,\n      which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,\n      biolink:MolecularEntity, biolink:NamedThing}\n    is_class_field: true\n    multivalued: true\n    in_subset:\n      - translator_minimal\n\n  name:\n    aliases: [ 'label', 'display name', 'title' ]\n    description: >-\n      A human-readable name for an attribute or entity.\n    range: label type\n    in_subset:\n      - translator_minimal\n      - samples\n    #\n    # linkML doesn't like this name slot to be \"required: true\".\n    # Besides, some entity nodes/attributes may not have names?\n    # required: true\n    slot_uri: rdfs:label\n    exact_mappings:\n      - gff3:Name\n      - gpi:DB_Object_Name\n    narrow_mappings:\n      - dct:title\n      - WIKIDATA_PROPERTY:P1476\n\n  source:\n    deprecated: true\n\n  stoichiometry:\n    description: >-\n      the relationship between the relative quantities of substances taking part in a reaction or\n      forming a compound, typically a ratio of whole integers.\n    is_a: association slot\n    range: integer\n\n  reaction direction:\n    description: >-\n      the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.)\n    is_a: association slot\n    range: reaction_direction_enum\n    narrow_mappings:\n      - NCIT:C42677\n\n  reaction balanced:\n    is_a: association slot\n    range: boolean\n\n  reaction side:\n    description: >-\n      the side of a reaction being modeled (ie: left or right)\n    is_a: association slot\n    range: reaction_side_enum\n\n  symbol:\n    is_a: node property\n    domain: named thing\n    description: >-\n      Symbol for a particular thing\n    exact_mappings:\n      - alliancegenome:symbol\n      - gpi:DB_Object_Symbol\n\n  synonym:\n    is_a: node property\n    aliases: ['alias']\n    domain: named thing\n    range: label type\n    description: >-\n      Alternate human-readable names for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      # there is an interesting debate here: are these terms \"narrower\" a.k.a. more specialized instances of\n      # 'biolink:synonym' or should they be binned into their respective namesake class of mappings?\n      # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.\n      - skos:altLabel\n      - gff3:Alias\n      - alliancegenome:synonyms\n      - gpi:DB_Object_Synonyms\n      - oboInOwl:hasExactSynonym\n      - oboInOwl:hasNarrowSynonym\n      - oboInOwl:hasBroadSynonym\n      - oboInOwl:hasRelatedSynonym\n      # TODO: RTX contributed terms mapped here... May need review?\n      - HANCESTRO:0330\n      - IAO:0000136\n      - RXNORM:has_tradename\n\n  has topic:\n    aliases: ['topic', 'descriptors']\n    is_a: node property\n    range: ontology class\n    exact_mappings:\n      - foaf:topic\n    description: >-\n      Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.\n      See https://github.com/biolink/biolink-model/issues/238\n\n  xref:\n    is_a: node property\n    aliases: ['dbxref', 'Dbxref', 'DbXref']\n    domain: named thing\n    range: uriorcurie\n    description: >-\n      Alternate CURIEs for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - gff3:Dbxref\n      - gpi:DB_Xrefs\n\n  full name:\n    is_a: node property\n    domain: named thing\n    range: label type\n    description: >-\n      a long-form human readable name for a thing\n\n  description:\n    aliases: ['definition']\n    range: narrative text\n    description: >-\n      a human-readable description of an entity\n    in_subset:\n      - translator_minimal\n    slot_uri: dct:description\n    exact_mappings:\n      - IAO:0000115\n      - skos:definitions\n    narrow_mappings:\n      - gff3:Description\n\n  systematic synonym:\n    is_a: node property\n    domain: named thing\n    range: label type\n    multivalued: true\n    slot_uri: GOP:systematic_synonym\n    description: >-\n      more commonly used for gene symbols in yeast\n\n  affiliation:\n    is_a: node property\n    description: >-\n      a professional relationship between one provider (often a person) within another provider (often an organization).\n      Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.\n    domain: agent\n    range: uriorcurie\n    multivalued: true\n\n  address:\n    is_a: node property\n    description: >-\n      the particulars of the place where someone or an organization is situated.  For now, this slot is a\n      simple text \"blob\" containing all relevant details of the given location for fitness of purpose.\n      For the moment, this \"address\" can include other contact details such as email and phone number(?).\n\n  ## Space\n\n  latitude:\n    is_a: node property\n    range: float\n    description: >-\n      latitude\n    exact_mappings:\n      - wgs:lat\n\n  longitude:\n    is_a: node property\n    range: float\n    description: >-\n      longitude\n    exact_mappings:\n      - wgs:long\n\n  ## Time\n\n  timepoint:\n    aliases: ['duration']\n    range: time type\n    description: >-\n      a point in time\n\n  creation date:\n    is_a: node property\n    aliases: ['publication date']\n    range: date\n    description: >-\n      date on which an entity was created. This can be applied to nodes or edges\n    exact_mappings:\n      - dct:createdOn\n      - WIKIDATA_PROPERTY:P577\n\n  update date:\n    is_a: node property\n    range: date\n    description: >-\n      date on which an entity was updated. This can be applied to nodes or edges\n\n  ## Statistics\n\n  aggregate statistic:\n    is_a: node property\n    abstract: true\n\n  has count:\n    description: >-\n      number of things with a particular property\n    is_a: aggregate statistic\n    range: integer\n    exact_mappings:\n      - LOINC:has_count\n\n  has total:\n    description: >-\n      total number of things in a particular reference set\n    is_a: aggregate statistic\n    range: integer\n\n  has quotient:\n    is_a: aggregate statistic\n    range: double\n\n  has percentage:\n    description: >-\n      equivalent to has quotient multiplied by 100\n    is_a: aggregate statistic\n    range: double\n\n  ## Properties for Information Content Entity and Publication Nodes\n\n  has taxonomic rank:\n    is_a: node property\n    range: taxonomic rank\n    multivalued: false\n    mappings:\n      - WIKIDATA:P105\n\n  has dataset:\n    is_a: node property\n    domain: dataset version\n    range: dataset\n    slot_uri: dct:source\n\n  source web page:\n    is_a: node property\n    domain: dataset summary\n    broad_mappings:\n      - dct:source\n\n  source logo:\n    is_a: node property\n    domain: dataset summary\n    slot_uri: schema:logo\n\n  retrieved on:\n    is_a: node property\n    domain: dataset\n    range: date\n    exact_mappings:\n      - pav:retrievedOn\n\n  version of:\n    is_a: node property\n    domain: dataset version\n    range: dataset summary\n    exact_mappings:\n      - dct:isVersionOf\n\n  version:\n    is_a: node property\n    domain: dataset\n    broad_mappings:\n      - pav:version\n      - owl:versionInfo\n\n  license:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:license\n    narrow_mappings:\n      - WIKIDATA_PROPERTY:P275\n\n  rights:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:rights\n\n  format:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:format\n      - WIKIDATA_PROPERTY:P2701\n\n  created with:\n    is_a: node property\n    domain: dataset\n    exact_mappings:\n      - pav:createdWith\n\n  download url:\n    is_a: node property\n    domain: information content entity\n    slot_uri: dcat:downloadURL\n\n  dataset download url:\n    is_a: node property\n    domain: dataset\n    slot_uri: dcat:downloadURL\n\n  distribution download url:\n    is_a: node property\n    domain: dataset distribution\n    exact_mappings:\n      - dcat:downloadURL\n\n  ingest date:\n    is_a: node property\n    domain: dataset version\n    slot_uri: pav:version\n\n  has distribution:\n    is_a: node property\n    domain: dataset version\n    range: dataset distribution\n    slot_uri: dct:distribution\n\n  published in:\n    is_a: node property\n    description: >-\n      CURIE identifier of a broader publication context within which the publication may be placed,\n      e.g. a specified book or journal.\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - NLMID\n      - issn\n      - isbn\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1433\n\n  iso abbreviation:\n    is_a: node property\n    description: >-\n      Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system\n      See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,\n      then the iso abbreviation pertains to the broader publication context (the journal) within which the given\n      publication node is embedded, not the publication itself.\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1160\n\n  authors:\n    is_a: node property\n    singular_name: author\n    description: >-\n      connects an publication to the list of authors who contributed to the publication.\n      This property should be a comma-delimited list of author names. It is recommended that an author's name\n      be formatted as \"surname, firstname initial.\".   Note that this property is a node annotation expressing\n      the citation list of authorship which might typically otherwise be more completely documented in\n      biolink:PublicationToProviderAssociation defined edges which point to full details about an author\n      and possibly, some qualifiers which clarify the specific status of a given author in the publication.\n    multivalued: true\n    domain: publication\n\n  volume:\n    is_a: node property\n    description: >-\n      volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P478\n\n  chapter:\n    is_a: node property\n    description: >-\n      chapter of a book\n    domain: book chapter\n    exact_mappings:\n      - WIKIDATA:Q1980247\n\n  issue:\n    is_a: node property\n    description: >-\n      issue of a newspaper, a scientific journal or magazine for reference purpose\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P433\n\n  pages:\n    is_a: node property\n    description: >-\n      page number of source referenced for statement or publication\n    domain: publication\n    multivalued: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P304\n\n  summary:\n    is_a: node property\n    # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot,\n    # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract'\n    aliases: ['abstract']\n    description: >-\n      executive  summary of a publication\n    domain: publication\n    exact_mappings:\n      - dct:abstract\n      - WIKIDATA:Q333291\n\n  keywords:\n    is_a: node property\n    description: >-\n      keywords tagging a publication\n    domain: publication\n    multivalued: true\n\n  mesh terms:\n    is_a: node property\n    description: >-\n      mesh terms tagging a publication\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - MESH\n    multivalued: true\n    exact_mappings:\n      - dcid:MeSHTerm\n\n  ## Biology\n\n  has biological sequence:\n    is_a: node property\n    description: >-\n      connects a genomic feature to its sequence\n    range: biological sequence\n\n  has gene or gene product:\n    is_a: node property\n    description: >-\n      connects an entity with one or more gene or gene products\n    range: gene\n    multivalued: true\n\n  has gene:\n    is_a: has gene or gene product\n    description: >-\n      connects an entity associated with one or more genes\n    range: gene\n    multivalued: true\n\n  has zygosity:\n    is_a: node property\n    domain: nucleic acid entity\n    range: zygosity\n\n  ## Chemistry, drugs and food\n\n  has chemical formula:\n    is_a: node property\n    range: chemical formula value\n    description: >-\n      description of chemical compound based on element symbols\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P274\n\n  is metabolite:\n    is_a: node property\n    domain: molecular entity\n    range: boolean\n    description: >-\n      indicates whether a molecular entity is a metabolite\n    exact_mappings:\n      - CHEBI:25212\n\n  has constituent:\n    description: >-\n      one or more molecular entities within a chemical mixture\n    is_a: node property\n    range: molecular entity\n    multivalued: true\n\n  has drug:\n    is_a: node property\n    description: >-\n      connects an entity to one or more drugs\n    range: drug\n    multivalued: true\n\n  has device:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) devices\n    range: device\n    multivalued: true\n\n  has procedure:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) procedures\n    range: procedure\n    multivalued: true\n\n  ## Clinical exposures\n\n  has receptor:\n    is_a: node property\n    domain: exposure event\n    range: organismal entity\n    description: >-\n      the organism or organism part being exposed\n    exact_mappings:\n      - ExO:0000001\n\n  has stressor:\n    is_a: node property\n    domain: exposure event\n    aliases: ['has stimulus']\n    description: >-\n      the process or entity that the receptor is being exposed to\n    exact_mappings:\n      - ExO:0000000\n\n  has route:\n    is_a: node property\n    domain: exposure event\n    description: >-\n      the process that results in the stressor coming into direct contact with the receptor\n    exact_mappings:\n      - ExO:0000055\n    narrow_mappings:\n      - LOINC:has_pharmaceutical_route\n      - SNOMED:has_dose_form_intended_site\n      - SNOMED:has_route_of_administration\n\n  has population context:\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: association slot\n    range: population of individual organisms\n\n  has temporal context:\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n    is_a: association slot\n    # this resolves to the 'time' datatype, but not sure\n    # if this also represents an interval of time.\n    range: time type\n\n  is supplement:\n    description: >-\n    is_a: node property\n    range: chemical mixture\n\n  trade name:\n    description: >-\n    is_a: node property\n    range: chemical entity\n\n  available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: drug_availability_enum\n\n  is toxic:\n    description: >-\n    is_a: node property\n    multivalued: false\n    range: boolean\n\n  has chemical role:\n    is_a: node property\n    description: >-\n      \tA role is particular behaviour which a material entity may exhibit.\n    range: chemical role\n    multivalued: true\n\n  max tolerated dose:\n    description: >-\n      The highest dose of a drug or treatment that does not cause unacceptable side effects.\n      The maximum tolerated dose is determined in clinical trials by testing increasing doses\n      on different groups of people until the highest dose with acceptable side effects is\n      found. Also called MTD.\n    is_a: node property\n    multivalued: false\n    range: string\n\n  animal model available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: disease or phenotypic feature\n\n  highest FDA approval status:\n    description: >-\n      Should be the highest level of FDA approval this chemical entity or device has, regardless of which\n      disease, condition or phenotype it is currently being reviewed to treat.  For specific levels of FDA\n      approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'\n\n  drug regulatory status world wide:\n    aliases: ['max phase']\n    description: >-\n      An agglomeration of drug regulatory status worldwide. Not specific to FDA.\n    exact_mappings:\n      - NCIT:C172573\n    narrow_mappings:\n      - NCIT:R172\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n\n  routes of delivery:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    multivalued: true\n    range: drug_delivery_enum\n\n\n## --------------------\n## PREDICATES/RELATIONS\n## --------------------\n\n  related to:\n    description: >-\n      A relationship that is asserted between two named things\n    domain: named thing\n    range: named thing\n    multivalued: true\n    inherited: true\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - skos:relatedMatch\n      - UMLS:related_to\n    broad_mappings:\n      - owl:topObjectProperty\n    narrow_mappings:\n      - SEMMEDDB:compared_with\n      - SEMMEDDB:higher_than\n      - SEMMEDDB:lower_than\n      - BFO:0000054\n      - UBERON_CORE:protects\n      - GOREL:0002005\n      - GOREL:0012006\n      # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms\n      - BTO:related_to\n      - CHEBI:is_conjugate_acid_of\n      - CHEBI:is_conjugate_base_of\n      - CPT:has_add_on_code\n      - CPT:mapped_to\n      - EFO:0006351\n      - FMA:connected_to\n      - FMA:continuous_with\n      - FMA:homonym_of\n      - FMA:related_developmental_entity_of\n      - RO:0002093\n      - RO:0002092\n      - RO:0002084\n      - HCPCS:mapped_to\n      # RTX contributed terms, perhaps belong somewhere else with more precise semantics?\n      - HMDB:disease\n      - HMDB:has_protein_association\n      - IAO:0000136\n      - LOINC:has_answer\n      - LOINC:has_challenge\n      - LOINC:has_evaluation\n      - LOINC:mapped_to\n      - LOINC:mth_has_expanded_form\n      - MESH:RO\n      - MESH:has_mapping_qualifier\n      - MESH:mapped_to\n      - MONDO:disease_shares_features_of\n      - NCIT:disease_may_have_associated_disease\n      - NCIT:human_disease_maps_to_eo_disease\n      - NCIT:is_abnormal_cell_of_disease\n      - NCIT:is_related_to_endogenous_product\n      - UBERON_NONAMESPACE:connected_to\n      - UBERON_NONAMESPACE:innervated_by\n      - NBO-PROPERTY:is_about\n      - RO:0000053 # bearer_of\n      - PATO:reciprocal_of\n      - RO:0000052\n      - RO:0002001\n      - RO:0002002\n      - RO:0002003\n      - RO:0002008\n      - RO:0002134\n      - RO:0002150\n      - RO:0002159\n      - RO:0002176\n      - RO:0002177\n      - RO:0002178\n      - RO:0002179\n      - RO:0002314\n      - RO:0002322\n      # functionally related to\n      - RO:0002328\n      - RO:0002332\n      - RO:0002338\n      - RO:0002339\n      - RO:0002341\n      - RO:0002342\n      - RO:0002344\n      - RO:0002348\n      - RO:0002349\n      - RO:0002356\n      - RO:0002371\n      - RO:0002372\n      - RO:0002373\n      - RO:0002374\n      - RO:0002385\n      - RO:0002387\n      - RO:0002451\n      - RO:0002494\n      - RO:0002495\n      - RO:0002568\n      - RO:0002573\n      - RO:0004026\n      - RO:0004027\n      - RO:0009001\n      - RO:0009004\n      - RXNORM:has_form\n      - RXNORM:reformulated_to\n      - SNOMED:has_associated_morphology\n      - SNOMED:has_associated_procedure\n      - SNOMED:has_direct_morphology\n      - SNOMED:has_disposition\n      - SNOMED:has_indirect_morphology\n      - SNOMED:has_modification\n      - SNOMED:has_procedure_morphology\n      - SNOMED:has_specimen_source_morphology\n      - SNOMED:inheres_in\n      - SNOMED:is_interpreted_by\n      - SNOMED:relative_to_part_of\n      - UBERON:synapsed_by\n      - UMLS:RO\n      - UMLS:RQ\n      - UMLS:class_code_classified_by\n      - UMLS:exhibited_by\n      - UMLS:has_context_binding\n      - UMLS:has_form\n      - UMLS:has_mapping_qualifier\n      - UMLS:larger_than\n      - UMLS:mapped_to\n      - UMLS:owning_section_of\n\n  related to at concept level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between terminology components that describe the conceptual model of a domain.\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    symmetric: true\n\n  related to at instance level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between two instances of a data classes.  Much like an assertion component,\n      in an ABox, these represent facts associated with the conceptual model.\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    symmetric: true\n\n  associated with:\n    is_a: related to at instance level\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent,\n      'related to'.\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    symmetric: true\n    domain: named thing\n    range: named thing\n    exact_mappings:\n      - SEMMEDDB:associated_with\n    narrow_mappings:\n      - RO:0004029\n      - SNOMEDCT:47429007\n\n  superclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a super class of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    inverse: subclass of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q66088480\n      - CHEMBL.MECHANISM:superset_of\n      - GO:inverse_isa\n      - MESH:inverse_isa\n      - RXNORM:inverse_isa\n      - VANDF:inverse_isa\n    narrow_mappings:\n      - NCIT:cdrh_parent_of\n      - NCIT:ctcae_5_parent_of\n      - NCIT:subset_includes_concept\n      - OMIM:has_manifestation\n      - SNOMED:has_basic_dose_form\n      - UMLS:RB\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:subclass of\n\n  subclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a specialization of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:superclass of\n    close_mappings:\n      # RTX\n      - LOINC:class_of\n      - LOINC:has_class\n    exact_mappings:\n      - rdfs:subClassOf\n      - SEMMEDDB:IS_A\n      - SEMMEDDB:isa\n      - WIKIDATA_PROPERTY:P279\n      - CHEMBL.MECHANISM:subset_of\n      - GO:isa\n      - MESH:isa\n      - RXNORM:isa\n      - VANDF:isa\n    narrow_mappings:\n      - CHEBI:has_parent_hydride\n      - LOINC:has_archetype\n      - LOINC:has_parent_group\n      - LOINC:is_presence_guidance_for\n      - NCIT:gene_product_has_chemical_classification\n      # RTX mapped terms classes for biomarkers\n      - NCIT:R36\n      - NCIT:R42\n      - NCIT:A16\n      - NCIT:A11\n      - NCIT:A14\n      - NCIT:A3\n      - NDDF:has_dose_form\n      - RXNORM:has_dose_form\n      - RXNORM:has_doseformgroup\n      - SNOMED:entire_anatomy_structure_of\n      - SNOMED:has_dose_form\n      # RTX mapping\n      - rdfs:subPropertyOf\n\n  same as:\n    is_a: exact match\n    description: >-\n      holds between two entities that are considered equivalent to each other\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      # identical class extension with identical sets of individuals\n      - owl:equivalentClass\n    exact_mappings:\n      # identical individual, or identical class concept/meaning\n      - owl:sameAs\n      - skos:exactMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      # RTX suggests mapping this to proposed new \"biolink:close_match\" predicate instead\n      #- SEMMEDDB:SAME_AS\n      - WIKIDATA_PROPERTY:P2888\n      - CHEMBL.MECHANISM:equivalent_to\n      - MONDO:equivalentTo\n    narrow_mappings:\n      - DRUGBANK:external-identifier\n\n  close match:\n    is_a: related to at concept level\n    description: >-\n      a list of terms from different schemas or terminology systems that have\n      a semantically similar but not strictly equivalent, broader, or narrower\n      meaning. Such terms often describe the same general concept from\n      different ontological perspectives (e.g. drug as a type of chemical\n      entity versus drug as a type of role borne by a chemical entity).\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - skos:closeMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      - SEMMEDDB:SAME_AS\n      - SEMMEDDB:same_as\n    narrow_mappings:\n      - CHEBI:is_enantiomer_of\n      - CHEBI:is_tautomer_of\n      - MEDDRA:classified_as\n      - OIO:hasDbXref\n      - oboformat:xref\n      - RXNORM:has_quantified_form\n      - UMLS:SY\n\n  exact match:\n    is_a: close match\n    description: >-\n      holds between two entities that have strictly equivalent\n      meanings, with a high degree of confidence\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - skos:exactMatch\n      - WIKIDATA:Q39893449\n      - WIKIDATA:P2888\n\n  broad match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a broader, more general meaning. Broader terms are\n      typically shown as parents in a hierarchy or tree.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:narrow match\n    exact_mappings:\n      - skos:broadMatch\n      - WIKIDATA:Q39894595\n\n  narrow match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a narrower, more specific meaning. Narrower terms are\n      typically shown as children in a hierarchy or tree.\n    is_a: related to at concept level\n    inverse: broad match\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - skos:narrowMatch\n      - WIKIDATA:Q39893967\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:broad match\n\n  opposite of:\n    description: >-\n      x is the opposite of y if there exists some distance metric M, and there exists\n      no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002604\n    see_also:\n      - https://doi.org/10.1101/108977\n      - https://github.com/biolink/biolink-model/issues/657\n\n  has real world evidence of association with:\n    deprecated: true\n    is_a: related to at instance level\n    description: >-\n      this means that the assertion was derived by applying statistical and machine learning models to\n      clinical data such as EHR data, survey data, etc\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      tag: biolink:canonical_predicate\n      value: true\n\n  associated with likelihood of:\n    is_a: associated with\n    description: >-\n      A a relationship that holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated, wherein the state or value of one variable predicts the future state \n      or value of the other.  E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated \n      with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib \n      is associated with an increased or decreased likelihood that a patient will later exhibit MI.\n  likelihood associated with:\n    is_a: associated with\n    description: >-\n    inverse: associated with likelihood of\n\n  associated with increased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is more probable.\n  increased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with increased likelihood of\n\n  associated with decreased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is less probable.\n  decreased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with decreased likelihood of\n\n  target for:\n    is_a: related to at instance level\n    description: >-\n      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene\n      product could have a therapeutic effect\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    domain: gene\n    range: disease\n\n  has target:\n    is_a: related to at instance level\n    inverse: target for\n    domain: disease\n    range: gene\n\n  active in:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: cellular component\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002432\n\n  has active component:\n    inverse: active in\n\n\n  acts upstream of:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002263\n\n  has upstream actor:\n    is_a: related to at instance level\n    inverse: acts upstream of\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0004034\n\n  has positive upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0004035\n\n  has negative upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of negative effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002264\n\n  has upstream or within actor:\n    is_a: has upstream actor\n    inverse: acts upstream of or within\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0004032\n\n  has positive upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0004033\n\n  has negative upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within negative effect\n    domain: biological process\n    range: gene or gene product\n\n    ## Publication related predicates\n  mentions:\n    description: >-\n      refers to is a relation between one information content entity and the named thing\n      that it makes reference to.\n    is_a: related to at instance level\n    exact_mappings:\n      - IAO:0000142\n    narrow_mappings:\n      - SIO:000628\n\n  mentioned by:\n    description: >-\n      refers to is a relation between one named thing and the information content entity\n      that it makes reference to.\n    is_a: related to at instance level\n    inverse: mentions\n\n  ## Publication related predicates\n\n  contributor:\n    is_a: related to at instance level\n    domain: information content entity\n    range: agent\n    comments:\n      - This is a grouping for predicates relating entities to their associated contributors realizing them\n    abstract: true\n    exact_mappings:\n      - dct:contributor\n\n  has contributor:\n    inverse: contributor\n    is_a: related to at instance level\n    domain: agent\n    range: information content entity\n\n  provider:\n    is_a: contributor\n    description: >-\n      person, group, organization or project that provides a piece of information (e.g. a knowledge association).\n\n  has provider:\n    inverse: provider\n    is_a: has contributor\n    domain: agent\n    range: information content entity\n\n  publisher:\n    is_a: contributor\n    domain: publication\n    description: >-\n      organization or person responsible for publishing books, periodicals, podcasts, games or software.\n      Note that in the case of publications which have a containing \"published in\" node property, the publisher\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the publisher agent of the encompassing publication\n      (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).\n    exact_mappings:\n      - dct:publisher\n      - WIKIDATA_PROPERTY:P123\n\n  has publisher:\n    is_a: has contributor\n    inverse: publisher\n    domain: agent\n    range: publication\n\n  editor:\n    is_a: contributor\n    domain: publication\n    description: >-\n      editor of a compiled work such as a book or a periodical (newspaper or an academic journal).\n      Note that in the case of publications which have a containing \"published in\" node property, the editor\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the editorial agent of the encompassing publication\n      (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P98\n\n  has editor:\n    inverse: editor\n    is_a: has contributor\n    domain: agent\n    range: publication\n\n  author:\n    is_a: contributor\n    domain: publication\n    description: >-\n      an instance of one (co-)creator primarily responsible for a written work\n    exact_mappings:\n      - dct:creator\n      - WIKIDATA_PROPERTY:P50\n\n  has author:\n    inverse: author\n    is_a: has contributor\n    domain: agent\n    range: publication\n\n  ## end of Publication related predicates\n\n  assesses:\n    aliases: ['was assayed against']\n    description: >-\n      The effect of a thing on a target was interrogated in some assay.\n      A relationship between some perturbing agent (usually a chemical compound) and some target entity,\n      where the affect of the perturbing agent on the target entity was interrogated in a particular assay.\n      The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type\n      of biological entity.\n    domain: named thing\n    range: named thing\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  is assessed by:\n    inverse: assesses\n    domain: named thing\n    range: named thing\n\n  interacts with:\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between any two entities that directly or indirectly interact with each other\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002434\n      - SEMMEDDB:interacts_with\n    narrow_mappings:\n      # RO terms RTX mapped to 'biolink:related_to' but which imply a chemical interaction\n      - RO:0002103\n      - RO:0002120\n      - RO:0002130\n\n  physically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two entities that make physical contact as part of some interaction\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P129\n    close_mappings:\n      # Agents of some interaction but not the relationship of interaction\n      # These RTX mapped terms may need to be reclassified to more meaningful terms (perhaps not yet created)\n      - CHEMBL.MECHANISM:binding_agent\n      - CHEMBL.MECHANISM:chelating_agent\n      - CHEMBL.MECHANISM:cross-linking_agent\n      - CHEMBL.MECHANISM:oxidative_enzyme\n      - CHEMBL.MECHANISM:sequestering_agent\n      - CHEMBL.MECHANISM:substrate\n      - DRUGBANK:target\n    narrow_mappings:\n      # Defined more narrowly as \"substance interaction\", thus specific applies to a subclass entities?\n      - DRUGBANK:drug-interaction\n      - FMA:adheres_to\n      - NCIT:A7\n      - PR:non-covalently_bound_to\n\n  chemically interacts with:\n    is_a: physically interacts with\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    symmetric: true\n\n  molecularly interacts with:\n    is_a: physically interacts with\n    aliases: ['targets']\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      - DGIdb:antibody\n    exact_mappings:\n      - RO:0002436\n\n  genetically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two genes whose phenotypic effects are dependent on each\n      other in some way - such that their combined phenotypic effects are the\n      result of some interaction between the activity of their gene products.\n      Examples include epistasis and synthetic lethality.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    symmetric: true\n    exact_mappings:\n      - RO:0002435\n\n  affects:\n    is_a: related to at instance level\n    description: >-\n      describes an entity that has a direct affect on the state or quality\n      of another existing entity. Use of the 'affects' predicate implies that\n      the affected entity already exists, unlike predicates such as\n      'affects risk for' and 'prevents, where the outcome is something\n      that may or may not come to be.\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      # Contributed by RTX. Seems possible that a new predicate \"biolink:in_pathway\" could be justified?\n      - DRUGBANK:pathway\n    exact_mappings:\n      - SEMMEDDB:AFFECTS\n      - SEMMEDDB:affects\n      - DGIdb:affects\n    narrow_mappings:\n      - SEMMEDDB:administered_to\n      - CTD:prediction_hypothesis\n      - GOREL:0001006\n      - CTD:inferred\n      - UPHENO:0000001\n      - RO:0002263\n      - RO:0002264\n      - NCIT:R158\n      - NCIT:R160\n      - NCIT:R30\n      - NCIT:R150\n      - NCIT:R72\n      - NCIT:R146\n      - NCIT:R124\n      - NCIT:R173\n      - NCIT:R100\n      - NCIT:R102\n      - NCIT:R101\n      - NCIT:R113\n      - NCIT:R23\n      - NCIT:R25\n      - NCIT:gene_mapped_to_disease\n      - NCIT:R133\n      - RO:0002343\n      - RO:0002355\n      - RO:0002591\n      - RO:0002592\n      - RO:0012003\n      - SNOMED:has_pathological_process\n\n  affected by:\n    is_a: related to at instance level\n    description: >-\n      describes an entity of which the state or quality is affected by\n      another existing entity.\n    inverse: affects\n\n  associated with sensitivity to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of sensitivity to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    broad_mappings:\n      - PATO:0000085 # sensitivity toward\n    narrow_mappings:\n      - SNOMEDCT:418038007 # propensity to adverse reaction\n\n  sensitivity associated with:\n    is_a: associated with\n    inverse: associated with sensitivity to\n    range: named thing\n    domain: chemical entity\n\n  associated with resistance to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of resistance to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  resistance associated with:\n    is_a: associated with\n    inverse: associated with resistance to\n    range: named thing\n    domain: chemical entity\n\n  diagnoses:\n    is_a: related to at instance level\n    description: >-\n      a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      - NCIT:C15220 # diagnosis\n      - SIO:001331 # diagnosis\n    exact_mappings:\n      - DrugCentral:5271\n      - SEMMEDDB:diagnoses\n\n  is diagnosed by:\n    is_a: related to at instance level\n    inverse: diagnoses\n    range: chemical or drug or treatment\n    domain: disease or phenotypic feature\n\n  increases amount or activity of:\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that increase the amount\n      or activity of the object.\n\n  decreases amount or activity of:\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that decrease the amount\n      or activity of the object.\n\n  ## role mixins for use in tagging corresponding role predicates\n\n  chemical role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a chemical context.\n    mixin: true\n    exact_mappings:\n      - CHEBI:51086\n\n  biological role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a biological context.\n    mixin: true\n    narrow_mappings:\n      - CHEBI:24432\n\n  affects abundance of:\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one changes the amount of the\n      other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_abundance_of\n\n  abundance affected by:\n    is_a: affected by\n    inverse: affects abundance of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases abundance of:\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one increases the amount of the other within a system of interest\n    is_a: affects abundance of\n    in_subset:\n      - translator_minimal\n    mixins:\n      - increases amount or activity of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases abundance of\n    related_mappings:\n      - UBERGRAPH:is_increase_of\n\n  abundance increased by:\n    is_a: abundance affected by\n    inverse: increases abundance of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  decreases abundance of:\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one\n      decreases the amount of the other within a system of interest\n    is_a: affects abundance of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases abundance of\n\n    related_mappings:\n      - UBERGRAPH:is_decrease_of\n\n  abundance decreased by:\n    is_a: abundance affected by\n    inverse: decreases abundance of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases activity of:\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one\n      increases the activity of the other within a system of interest\n    is_a: affects activity of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    related_mappings:\n      - GAMMA:ec50\n      - GAMMA:ac50\n    narrow_mappings:\n      - GAMMA:activator\n      - GAMMA:partial_agonist\n      - GAMMA:agonist\n      - GAMMA:opener\n      - GAMMA:positive_allosteric_modulator\n      - GAMMA:positive_modulator\n      - GAMMA:inducer\n      - GAMMA:potentiator\n      - GAMMA:stimulator\n      - CHEMBL.MECHANISM:agonist\n      - CHEMBL.MECHANISM:opener\n      - CHEMBL.MECHANISM:partial_agonist\n      - CHEMBL.MECHANISM:positive_allosteric_modulator\n      - CHEMBL.MECHANISM:positive_modulator\n      - DGIdb:agonist\n      - DGIdb:partial_agonist\n      - DGIdb:inducer\n      - DGIdb:positive_allosteric_modulator\n      - DGIdb:stimulator\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases activity of\n\n  affects activity of:\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one changes the activity of the\n      other within a system of interest\n    is_a: affects\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    narrow_mappings:\n      - GAMMA:allosteric_modulator\n      - GAMMA:modulator\n      - GAMMA:regulator\n      - DGIdb:modulator\n      - DGIdb:allosteric_modulator\n\n  activity affected by:\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one is changed by the\n      activity of the other within a system of interest\n    is_a: affected by\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects activity of\n\n  activity increased by:\n    is_a: activity affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases activity of\n\n  decreases activity of:\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one decreases the\n      activity of the other within a system of interest\n    is_a: affects activity of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases activity of\n    mixins:\n      - decreases amount or activity of\n    related_mappings:\n      - GAMMA:ic50\n      - GAMMA:ki\n      - DGIdb:vaccine\n    narrow_mappings:\n      - GAMMA:allosteric_antagonist\n      - GAMMA:partial_antagonist\n      - GAMMA:antagonist\n      - GAMMA:weak_inhibitor\n      - GAMMA:inhibitor\n      - GAMMA:channel_blocker\n      - GAMMA:gating_inhibitor\n      - GAMMA:blocker\n      - GAMMA:inverse_agonist\n      - GAMMA:inactivator\n      - GAMMA:downregulator\n      - GAMMA:negative_modulator\n      - GAMMA:negative_allosteric_modulator\n      - GAMMA:inhibitory_allosteric_modulator\n      - GAMMA:aggregation_inhibitor\n      - GAMMA:conversion_inhibitor\n      - GAMMA:suppressor\n      - CHEMBL.MECHANISM:antagonist\n      - CHEMBL.MECHANISM:allosteric_antagonist\n      - CHEMBL.MECHANISM:inverse_agonist\n      - DGIdb:antagonist\n      - DGIdb:blocker\n      - DGIdb:channel_blocker\n      - DGIdb:gating_inhibitor\n      - DGIdb:inhibitor\n      - DGIdb:negative_modulator\n      - DGIdb:inhibitory_allosteric_modulator\n      - DGIdb:inverse_agonist\n\n  activity decreased by:\n    is_a: activity affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases activity of\n\n\n  affects expression of:\n    description: >-\n      holds between a named thing (most often a chemical or gene/gene product, but can also be used to link an\n      environmental affect on expression) and a nucleic acid entity where the action or effect of one changes the\n      level of expression of the other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: named thing\n    range: nucleic acid entity\n\n  expression affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: named thing\n    inverse: affects expression of\n\n  increases expression of:\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity\n      where the action or effect of one increases the level of expression of the\n      other within a system of interest\n    is_a: affects expression of\n    in_subset:\n      - translator_minimal\n    domain: named thing\n    range: nucleic acid entity\n    mixins:\n      - increases amount or activity of\n    close_mappings:\n      # Agent of the action or effect, not the relationship itself\n      - CHEMBL.MECHANISM:releasing_agent\n    exact_mappings:\n      - RO:0003003\n\n  expression increased by:\n    is_a: expression affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: named thing\n    inverse: increases expression of\n\n  decreases expression of:\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one decreases the level of expression of the\n      other within a system of interest\n    is_a: affects expression of\n    in_subset:\n      - translator_minimal\n    domain: named thing\n    range: nucleic acid entity\n    mixins:\n      - decreases amount or activity of\n    related_mappings:\n      - DGIdb:antisense\n      - DGIdb:antisense_oligonucleotide\n    exact_mappings:\n      - RO:0003002\n    narrow_mappings:\n      - CHEMBL.MECHANISM:antisense_inhibitor\n\n  expression decreased by:\n    is_a: expression affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: named thing\n    inverse: decreases expression of\n\n  affects folding of:\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one changes the rate\n      or quality of folding of the other\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_folding_of\n\n\n  folding affected by:\n    is_a: affected by\n    inverse: affects folding of\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n\n  increases folding of:\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one\n      increases the rate or quality of folding of the other\n    is_a: affects folding of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases folding of\n    exact_mappings:\n      - CTD:increases_folding_of\n\n  folding increased by:\n    is_a: folding affected by\n    inverse: increases folding of\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n\n  decreases folding of:\n    description: >-\n      holds between a chemical or gene or gene product entity and a\n      nucleic acid entity where the action or effect of one\n      decreases the rate or quality of folding of the other\n    is_a: affects folding of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases folding of\n    exact_mappings:\n      - CTD:decreases_folding_of\n\n  folding decreased by:\n    is_a: folding affected by\n    inverse: decreases folding of\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n\n  affects localization of:\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one changes the\n      localization of the other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      - GAMMA:storage\n    exact_mappings:\n      - GOREL:0002003\n\n  localization affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects localization of\n\n  increases localization of:\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one increases the proper\n      localization of the other within a system of interest\n    is_a: affects localization of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases localization of\n    exact_mappings:\n      - CTD:increases_localization_of\n\n  localization increased by:\n    is_a: localization affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases localization of\n\n  decreases localization of:\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one decreases the proper localization of the other within a system of interest\n    is_a: affects localization of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases localization of\n    exact_mappings:\n      - CTD:decreases_localization_of\n\n\n  localization decreased by:\n    is_a: localization affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases localization of\n\n  affects metabolic processing of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts the\n      metabolic processing of the other within a system of interest\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      - GAMMA:catalytic_activity\n\n  metabolic processing affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects metabolic processing of\n\n  increases metabolic processing of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one increases the rate of\n      metabolic processing of the other within a system of interest\n    is_a: affects metabolic processing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases metabolic processing of\n    exact_mappings:\n      - CTD:increases_metabolic_processing_of\n    narrow_mappings:\n      - NCIT:enzyme_metabolizes_chemical_or_drug\n\n  metabolic processing increased by:\n    is_a: metabolic processing affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases metabolic processing of\n\n  decreases metabolic processing of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one decreases the rate of\n      metabolic processing of the other within a system of interest\n    is_a: affects metabolic processing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases metabolic processing of\n    exact_mappings:\n      - CTD:decreases_metabolic_processing_of\n\n  metabolic processing decreased by:\n    is_a: metabolic processing affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases metabolic processing of\n\n  affects molecular modification of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one leads changes in the molecular\n      modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of\n      phosphoryl group, or via redox reaction that adds or subtracts electrons)\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_molecular_modification_of\n    narrow_mappings:\n      - CTD:affects_acetylation\n      - CTD:affects_acylation\n      - CTD:affects_alkylation\n      - CTD:affects_amination\n      - CTD:affects_carbamoylation\n      - CTD:affects_ethylation\n      - CTD:affects_glutathionylation\n      - CTD:affects_glycation\n      - CTD:affects_glycosylation\n      - CTD:affects_glucuronidation\n      - CTD:affects_N-linked_glycosylation\n      - CTD:affects_O-linked_glycosylation\n      - CTD:affects_hydroxylation\n      - CTD:affects_lipidation\n      - CTD:affects_farnesylation\n      - CTD:affects_geranoylation\n      - CTD:affects_myristoylation\n      - CTD:affects_palmitoylation\n      - CTD:affects_prenylation\n      - CTD:affects_methylation\n      - CTD:affects_nitrosation\n      - CTD:affects_nucleotidylation\n      - CTD:affects_phosphorylation\n      - CTD:affects_ribosylation\n      - CTD:affects_ADP-ribosylation\n      - CTD:affects_sulfation\n      - CTD:affects_sumoylation\n      - CTD:affects_ubiquitination\n      - CTD:affects_oxidation\n      - CTD:affects_reduction\n      - CTD:affects_carboxylation\n\n  molecular modification affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects molecular modification of\n\n  increases molecular modification of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one leads to\n      increased molecular modification(s) of the other (e.g. via post-translational modifications of\n      proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\n    is_a: affects molecular modification of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases molecular modification of\n    exact_mappings:\n      - CTD:increases_molecular_modification_of\n    narrow_mappings:\n      - CTD:increases_acetylation\n      - CTD:increases_acylation\n      - CTD:increases_alkylation\n      - CTD:increases_amination\n      - CTD:increases_carbamoylation\n      - CTD:increases_ethylation\n      - CTD:increases_glutathionylation\n      - CTD:increases_glycation\n      - CTD:increases_glycosylation\n      - CTD:increases_glucuronidation\n      - CTD:increases_N-linked_glycosylation\n      - CTD:increases_O-linked_glycosylation\n      - CTD:increases_hydroxylation\n      - CTD:increases_lipidation\n      - CTD:increases_farnesylation\n      - CTD:increases_geranoylation\n      - CTD:increases_myristoylation\n      - CTD:increases_palmitoylation\n      - CTD:increases_prenylation\n      - CTD:increases_methylation\n      - CTD:increases_nitrosation\n      - CTD:increases_nucleotidylation\n      - CTD:increases_phosphorylation\n      - CTD:increases_ribosylation\n      - CTD:increases_ADP-ribosylation\n      - CTD:increases_sulfation\n      - CTD:increases_sumoylation\n      - CTD:increases_ubiquitination\n      - CTD:increases_oxidation\n      - CTD:increases_reduction\n      - CTD:increases_carboxylation\n      - GAMMA:acetylation\n      - GAMMA:oxidizer\n\n  molecular modification increased by:\n    is_a: molecular modification affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases molecular modification of\n\n  decreases molecular modification of:\n    description: >-\n      holds between two chemical entities  where the action or effect of one leads to\n      decreased molecular modification(s) of the other (e.g. via post-translational modifications of\n      proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\n    is_a: affects molecular modification of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases molecular modification of\n    exact_mappings:\n      - CTD:decreases_molecular_modification_of\n    narrow_mappings:\n      - CTD:decreases_acetylation\n      - CTD:decreases_acylation\n      - CTD:decreases_alkylation\n      - CTD:decreases_amination\n      - CTD:decreases_carbamoylation\n      - CTD:decreases_ethylation\n      - CTD:decreases_glutathionylation\n      - CTD:decreases_glycation\n      - CTD:decreases_glycosylation\n      - CTD:decreases_glucuronidation\n      - CTD:decreases_N-linked_glycosylation\n      - CTD:decreases_O-linked_glycosylation\n      - CTD:decreases_hydroxylation\n      - CTD:decreases_lipidation\n      - CTD:decreases_farnesylation\n      - CTD:decreases_geranoylation\n      - CTD:decreases_myristoylation\n      - CTD:decreases_palmitoylation\n      - CTD:decreases_prenylation\n      - CTD:decreases_methylation\n      - CTD:decreases_nitrosation\n      - CTD:decreases_nucleotidylation\n      - CTD:decreases_phosphorylation\n      - CTD:decreases_ribosylation\n      - CTD:decreases_ADP-ribosylation\n      - CTD:decreases_sulfation\n      - CTD:decreases_sumoylation\n      - CTD:decreases_ubiquitination\n      - CTD:decreases_oxidation\n      - CTD:decreases_reduction\n      - CTD:decreases_carboxylation\n      - GAMMA:deoxidizer\n\n  molecular modification decreased by:\n    is_a: molecular modification affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases molecular modification of\n\n  affects synthesis of:\n    description: >-\n      holds between two chemical entities where the action or effect \n      of one impacts the rate of chemical synthesis of the other\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_synthesis_of\n\n  synthesis affected by:\n    is_a: affected by\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects synthesis of\n    in_subset:\n      - translator_minimal\n\n  increases synthesis of:\n    description: >-\n      holds between two chemical entities where the action or effect\n      of one increases the rate of chemical synthesis of the other\n    is_a: affects synthesis of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases synthesis of\n    exact_mappings:\n      - CTD:increases_synthesis_of\n\n  synthesis increased by:\n    is_a: synthesis affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases synthesis of\n\n  decreases synthesis of:\n    description: >-\n      holds between two chemical entities where the action or effect\n      of one decreases the rate of chemical synthesis of the other\n    is_a: affects synthesis of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases synthesis of\n    exact_mappings:\n      - GAMMA:inhibition_of_synthesis\n\n  synthesis decreased by:\n    is_a: synthesis affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases synthesis of\n\n  affects degradation of:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      impacts the rate of degradation of the other within a system of interest,\n      where chemical degradation is defined act or process of simplifying or breaking\n      down a molecule into smaller parts, either naturally or artificially\n      (Oxford English Dictionary, UK, 1995)\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_degradation_of\n    narrow_mappings:\n      - CTD:affects_cleavage\n      - CTD:affects_hydrolysis\n\n  degradation affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects degradation of\n\n  increases degradation of:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the rate of degradation of the other within a system of interest\n    is_a: affects degradation of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: decreases degredation of\n    related_mappings:\n      # An enzyme or reagent acts upon a substrate but that substrate may\n      # not necessarily be \"degraded\", i.e. broken into smaller parts\n      - GAMMA:substrate\n      # RTX put this under \"biolink:physically_interacts_with\" but rather we also put next to the GAMMA mapping\n      # That said, neither mapping feels like a comfortable fit here\n      - CHEMBL.MECHANISM:substrate\n    close_mappings:\n      # terms refer less to the action or effect than the agent of that action or effect\n      - CHEMBL.MECHANISM:degrader\n    narrow_mappings:\n      - CTD:increases_cleavage\n      - CTD:increases_hydrolysis\n      - GOREL:0002004\n\n  degradation increased by:\n    is_a: degradation affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases degradation of\n\n  decreases degradation of:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the rate of degradation of the other within a system of interest\n    is_a: affects degradation of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: increases degredation of\n    exact_mappings:\n      - CTD:decreases_degradation_of\n    narrow_mappings:\n      - CTD:decreases_cleavage\n      - CTD:decreases_hydrolysis\n\n  degradation decreased by:\n    is_a: degradation affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases degradation of\n\n  affects mutation rate of:\n    description: >-\n      holds between a chemical entity and a nucleic acid entity where the action or effect of the\n      chemical entity impacts the rate of mutation of the nucleic acid entity within a system of interest\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    broad_mappings:\n      # Term 'mutagenesis' generally speaks generally of the process of\n      # 'production of genetic mutations':  this term says it is affected\n      # but not specifically how\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_mutation_rate_of\n\n  mutation rate affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n    inverse: affects mutation rate of\n\n  increases mutation rate of:\n    description: >-\n      holds between a chemical entity and a nucleic acid entity where the action or effect of the\n      chemical entity increases the rate of mutation of the nucleic acid entity within a system of interest\n    is_a: affects mutation rate of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity\n    range: nucleic acid entity\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases mutation rate of\n    exact_mappings:\n      - CTD:increases_mutation_rate_of\n    broad_mappings:\n      # See 'affects mutation rate of' above\n      - CTD:increases_mutagenesis\n\n  mutation rate increased by:\n    is_a: mutation rate affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: chemical entity\n    inverse: increases mutation rate of\n\n  decreases mutation rate of:\n    description: >-\n      holds between a chemical entity and a nucleic acid entity where the action or effect of the\n      chemical entity decreases the rate of mutation of the nucleic acid entity within a system of interest\n    is_a: affects mutation rate of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity\n    range: nucleic acid entity\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases mutation rate of\n    exact_mappings:\n      - CTD:decreases_mutation_rate_of\n    broad_mappings:\n      # See 'affects mutation rate of' above\n      - CTD:decreases_mutagenesis\n\n  mutation rate decreased by:\n    is_a: mutation rate affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: chemical entity\n    inverse: decreases mutation rate of\n\n  # original definition of this predicate used molecular entity which was a\n  affects response to:\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: response affected by\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_response_to\n\n  response affected by:\n    description: >-\n      holds between two chemical entities where the susceptibility of a biological entity or system\n      (e.g. an organism, cell, cellular component, macromolecular machine mixin,\n      biological or pathological process) of one is affected by the action of the other.\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  increases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases response to\n    exact_mappings:\n      - CTD:increases_response_to\n\n\n  response increased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases response to\n\n  decreases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases response to\n    exact_mappings:\n      - CTD:decreases_response_to\n    narrow_mappings:\n      - CTD:decreases_response_to_substance\n      - GAMMA:desensitize_the_target\n\n  response decreased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases response to\n\n  affects splicing of:\n    description: >-\n      holds between a chemical entity and an mRNA where the action or effect\n      of the chemical entity impacts the splicing of the mRNA\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: transcript\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_RNA_splicing\n    broad_mappings:\n      - CTD:affects_splicing_of\n\n  splicing affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: transcript\n    range: chemical entity or gene or gene product\n    inverse: affects splicing of\n\n  increases splicing of:\n    description: >-\n      holds between a chemical entity and an mRNA where the action or effect\n      of the chemical entity increases the proper splicing of the mRNA\n    is_a: affects splicing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: transcript\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases splicing of\n    exact_mappings:\n      - CTD:increases_RNA_splicing\n    broad_mappings:\n      - CTD:increases_splicing_of\n\n  splicing increased by:\n    is_a: splicing affected by\n    in_subset:\n      - translator_minimal\n    domain: transcript\n    range: chemical entity or gene or gene product\n    inverse: increases splicing of\n\n  decreases splicing of:\n    description: >-\n      holds between a chemical entity and an mRNA where the action or\n      effect of the chemical entity decreases the proper splicing of the mRNA\n    is_a: affects splicing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: transcript\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases splicing of\n    exact_mappings:\n      - CTD:decreases_RNA_splicing\n    broad_mappings:\n      - CTD:decreases_splicing_of\n\n  splicing decreased by:\n    is_a: splicing affected by\n    in_subset:\n      - translator_minimal\n    domain: transcript\n    range: chemical entity or gene or gene product\n    inverse: decreases splicing of\n\n  affects stability of:\n    description: >-\n      holds between two entities where the action or effect of one impacts\n      the stability of the other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      - GAMMA:stabilization\n\n  stability affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects stability of\n\n  increases stability of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one\n      increases the stability of the other within a system of interest\n    is_a: affects stability of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: decreases stability of\n    close_mappings:\n      # agent of the action or effect, not the relationship\n      - CHEMBL.MECHANISM:stabiliser\n\n  stability increased by:\n    is_a: stability affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases stability of\n\n  decreases stability of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one decreases\n      the stability of the other within a system of interest\n    is_a: affects stability of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: increases stability of\n    exact_mappings:\n      - CTD:decreases_stability_of\n\n  stability decreased by:\n    is_a: stability affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases stability of\n\n  affects transport of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts\n      the rate of transport of the other across some boundary in a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_transport_of\n    narrow_mappings:\n      - RO:0002313\n      - RO:0002340\n      - RO:0002345\n\n  transport affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects transport of\n\n  increases transport of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one\n      increases the rate of transport of the other across some boundary in a system of interest\n    is_a: affects transport of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases transport of\n    close_mappings:\n      - GAMMA:carrier\n      - GAMMA:transporter\n\n  transport increased by:\n    is_a: transport affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases transport of\n\n  decreases transport of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one\n      decreases the rate of transport of the other across some boundary in a system of interest\n    is_a: affects transport of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases transport of\n    exact_mappings:\n      - CTD:decreases_transport_of\n\n  transport decreased by:\n    is_a: transport affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases transport of\n\n  affects secretion of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts the\n      rate of secretion of the other out of a cell, gland, or organ\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_secretion_of\n    broad_mappings:\n      # 'export' more general than 'secretion'\n      - CTD:affects_export\n\n  secretion affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects secretion of\n\n  increases secretion of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one increases the\n      rate of secretion of the other out of a cell, gland, or organ\n    is_a: affects secretion of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases secretion of\n    exact_mappings:\n      - CTD:increases_secretion_of\n    broad_mappings:\n      # 'export' more general than 'secretion'\n      - CTD:increases_export\n\n  secretion increased by:\n    is_a: secretion affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases secretion of\n\n  decreases secretion of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one decreases the\n      rate of secretion of the other out of a cell, gland, or organ\n    is_a: affects secretion of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases secretion of\n    exact_mappings:\n      - CTD:decreases_secretion_of\n    broad_mappings:\n      # 'export' more general than 'secretion'\n      - CTD:decreases_export\n\n  secretion decreased by:\n    is_a: secretion affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases secretion of\n\n  affects uptake of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts the rate of\n      uptake of the other into of a cell, gland, or organ\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - CTD:affects_uptake_of\n    broad_mappings:\n      # 'import' more general than 'uptake'\n      - CTD:affects_import\n\n  uptake affected by:\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects uptake of\n\n  increases uptake of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one increases the rate of\n      uptake of the other into of a cell, gland, or organ\n    is_a: affects uptake of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases uptake of\n    exact_mappings:\n      - CTD:increases_uptake_of\n    broad_mappings:\n      # 'import' more general than 'uptake'\n      - CTD:increases_import\n\n  uptake increased by:\n    is_a: uptake affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases uptake of\n\n  decreases uptake of:\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect\n      of one decreases the rate of uptake of the other into of a cell, gland, or organ\n    is_a: affects uptake of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases uptake of\n    exact_mappings:\n      - CTD:decreases_uptake_of\n    broad_mappings:\n      # 'import' more general than 'uptake'\n      - CTD:decreases_import\n\n  uptake decreased by:\n    is_a: uptake affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases uptake of\n\n  regulates:\n    # direct is_a inheritance from a non-mixin class is not allowed\n    # we defer this inheritance to the classes which this mixin in its mixins\n    # is_a: affects\n    aliases: ['regulates activity of', 'regulates expression of']\n    comments:\n      - This is a grouping for process-process and entity-entity regulation.\n    mixin: true\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      - RO:0002334\n    exact_mappings:\n      - RO:0002211\n    narrow_mappings:\n      # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology)\n      - WIKIDATA_PROPERTY:P128\n      - CHEMBL.MECHANISM:modulator\n      - RO:0002295\n      - RO:0002332\n      - RO:0002578\n  \n  regulated by:\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    mixin: true\n    inverse: regulates\n\n  positively regulates:\n    comments:\n      - This is a grouping for positive process-process and entity-entity regulation.\n    is_a: regulates\n    mixin: true\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:negatively regulates\n    close_mappings:\n      # This RTX contributed term is tagged as a inverse of this Biolink predicate\n      - RO:0002336\n    exact_mappings:\n      - RO:0002213\n    narrow_mappings:\n      - CHEMBL.MECHANISM:activator\n      - DGIdb:activator\n      - RO:0004032\n      - RO:0004034\n      - RO:0002629\n\n  positively regulated by:\n    is_a: regulated by\n    mixin: true\n    inverse: positively regulates\n\n  negatively regulates:\n    comments:\n      - This is a grouping for negative process-process and entity-entity regulation.\n    is_a: regulates\n    mixin: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      # This RTX contributed term is tagged as a inverse of this Biolink predicate\n      - RO:0002335\n    exact_mappings:\n      # Strict interpretation here is that entity A causally affects levels of B\n      - RO:0004035\n      - RO:0002212\n    broad_mappings:\n      # This term is slightly broader in that it includes that A acts within B as well\n      - RO:0004033\n    narrow_mappings:\n      - CHEMBL.MECHANISM:blocker\n      - CHEMBL.MECHANISM:inhibitor\n      - CHEMBL.MECHANISM:negative_allosteric_modulator\n      - CHEMBL.MECHANISM:negative_modulator\n      - RO:0002630\n  \n  negatively regulated by:\n    is_a: regulated by\n    mixin: true\n    inverse: negatively regulates\n\n  process regulates process:\n    is_a: affects\n    mixins:\n      - regulates\n    domain: occurrent\n    range: occurrent\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002211\n\n  process regulated by process:\n    is_a: affected by\n    domain: occurrent\n    range: occurrent\n    inverse: process regulates process\n\n  process positively regulates process:\n    is_a: process regulates process\n    mixins:\n      - positively regulates\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:process negatively regulates process\n    exact_mappings:\n      - RO:0002213\n\n  process positively regulated by process:\n    is_a: process regulated by process\n    inverse: process positively regulates process\n\n  process negatively regulates process:\n    is_a: process regulates process\n    mixins:\n      - negatively regulates\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:process positively regulates process\n    exact_mappings:\n      - RO:0002212\n\n  process negatively regulated by process:\n    is_a: process regulated by process\n    inverse: process negatively regulates process\n\n  entity regulates entity:\n    aliases: ['activity directly regulates activity of']\n    is_a: affects\n    mixins:\n      - regulates\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: entity regulated by entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    local_names:\n      translator: regulates\n      ro: activity directly regulates activity of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002448\n    narrow_mappings:\n      # Wikidata mapping copied over from 'regulates' above;\n      # considered a slightly narrower term since it applies to\n      # protein and RNA as subject regulator whereas molecular_entity\n      # may also be another class of chemical_substance?\n      - WIKIDATA_PROPERTY:P128\n\n  entity regulated by entity:\n    is_a: affected by\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: entity regulates entity\n\n  entity positively regulates entity:\n    aliases: ['activity directly positively regulates activity of', 'anatomy upregulates gene', 'disease upregulates gene']\n    is_a: entity regulates entity\n    mixins:\n      - positively regulates\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:entity negatively regulates entity\n    local_names:\n      translator: positively regulates\n      ro: activity directly positively regulates activity of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002450\n    broad_mappings:\n      # causally positive effect of A over B but not specific to nature of B\n      - RO:0004034\n    narrow_mappings:\n      # Defined more narrowly as increasing, facilitating the\n      # action or function of a \"substance interaction\", where \"substance\" is deemed a subclass of possible entity\n      - SEMMEDDB:STIMULATES\n      - SEMMEDDB:stimulates\n      - SEMMEDDB:augments\n\n  entity positively regulated by entity:\n    is_a: entity regulated by entity\n    inverse: entity positively regulates entity\n\n  entity negatively regulates entity:\n    aliases: ['activity directly negatively regulates activity of', 'anatomy downregulates gene', 'disease downregulates gene']\n    is_a: entity regulates entity\n    mixins:\n      - negatively regulates\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:entity positively regulates entity\n    local_names:\n      translator: negatively regulates\n      ro: activity directly negatively regulates activity of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002449\n    narrow_mappings:\n      # SemMedDb definition focuses on (chemical?) \"substance interactions\" which is a bit narrower?\n      - SEMMEDDB:INHIBITS\n      - SEMMEDDB:inhibits\n\n  entity negatively regulated by entity:\n    is_a: entity regulated by entity\n    inverse: entity negatively regulates entity\n\n  disrupts:\n    is_a: affects\n    aliases: ['disease causes disruption of']\n    description: >-\n      describes a relationship where one entity degrades or interferes\n      with the structure, function, or occurrence of another.\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:enables\n    exact_mappings:\n      - SEMMEDDB:DISRUPTS\n      - SEMMEDDB:disrupts\n      - CHEMBL.MECHANISM:disrupting_agent\n    narrow_mappings:\n      - RO:0004024\n      - RO:0004025\n\n  disrupted by:\n    is_a: affected by\n    description: >-\n      describes a relationship where the structure, function, or occurrence\n      of one entity is degraded or interfered with by another.\n    inverse: disrupts\n\n  gene product of:\n    is_a: related to at instance level\n    description: >-\n      definition x has gene product of y if and only if y is a gene (SO:0000704)\n      that participates in some gene expression process (GO:0010467) where the output of thatf\n      process is either y or something that is ribosomally translated from x\n    exact_mappings:\n      - RO:0002204\n    domain: gene product mixin\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    inverse: has gene product\n    in_subset:\n      - translator_minimal\n\n  has gene product:\n    is_a: related to at instance level\n    description: >-\n      holds between a gene and a transcribed and/or\n      translated product generated from it\n    domain: gene\n    range: gene product mixin\n    inverse: gene product of\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX term tagged as inverse mapping\n      - PR:has_gene_template\n    exact_mappings:\n      - RO:0002205\n      - WIKIDATA_PROPERTY:P688\n      - NCIT:gene_encodes_gene_product\n    narrow_mappings:\n      - NCIT:R178\n\n  transcribed to:\n    is_a: related to at instance level\n    domain: gene\n    range: transcript\n    description: >-\n      inverse of transcribed from\n    inverse: transcribed from\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:transcribed from\n    exact_mappings:\n      - RO:0002511\n      - SIO:010080\n\n  transcribed from:\n    is_a: related to at instance level\n    domain: transcript\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:transcribed to\n    description: >-\n      x is transcribed from y if and only if x is synthesized from template y\n    exact_mappings:\n      - RO:0002510\n      - SIO:010081\n\n  translates to:\n    is_a: related to at instance level\n    domain: transcript\n    range: protein\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:translation of\n    description: >-\n      x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome\n      reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)\n      and produces x (amino acid chain/polypeptide)\n    close_mappings:\n      - RO:0002513\n      - SIO:010082\n\n  translation of:\n    is_a: related to at instance level\n    domain: protein\n    range: transcript\n    description: >-\n      inverse of translates to\n    inverse: translates to\n    close_mappings:\n      - RO:0002512\n      - SIO:010083\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:translates to\n\n  homologous to:\n    is_a: similar to\n    aliases: ['in homology relationship with']\n    description: >-\n      holds between two biological entities that have common evolutionary origin\n    comments:\n      - typically used to describe homology relationships between genes or gene products\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:HOM0000001\n      - SIO:010302\n    narrow_mappings:\n      # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158\n      - UBERON_CORE:sexually_homologous_to\n\n  paralogous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:HOM0000011\n\n  orthologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship between entities (typically genes) that diverged after a speciation event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:HOM0000017\n      - WIKIDATA_PROPERTY:P684\n\n  xenologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:HOM0000018\n\n  coexists with:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - SEMMEDDB:COEXISTS_WITH\n      - SEMMEDDB:coexists_with\n    narrow_mappings:\n      - BSPO:0000096\n      - BSPO:0000097\n      - BSPO:0000098\n      - BSPO:0000099\n      - BSPO:0000100\n      - BSPO:0000102\n      - BSPO:0000104\n      - BSPO:0000110\n      - BSPO:0000113\n      - BSPO:0015001\n      - BSPO:0015002\n      - BSPO:0015003\n      - BSPO:0015005\n      - BSPO:0015006\n      - BSPO:0015007\n      - BSPO:0015008\n      - BSPO:0015009\n      - BSPO:0015012\n      - BSPO:0015014\n      - BSPO:parallel_to\n      - UBERON_CORE:anastomoses_with\n      - UBERON_CORE:anteriorly_connected_to\n      - UBERON_CORE:posteriorly_connected_to\n      - UBERON_CORE:channel_for\n      - UBERON_CORE:channels_from\n      - UBERON_CORE:channels_into\n      - UBERON_CORE:conduit_for\n      - UBERON_CORE:distally_connected_to\n      - UBERON_CORE:extends_fibers_into\n      - UBERON_CORE:filtered_through\n      - UBERON_CORE:indirectly_supplies\n      - UBERON_CORE:proximally_connected_to\n      - UBERON_CORE:synapsed_by\n      - UBERON_CORE:transitively_anteriorly_connected_to\n      - UBERON_CORE:transitively_connected_to\n      - UBERON_CORE:transitively_distally_connected_to\n      - UBERON_CORE:transitively_proximally_connected_to\n      # RTX contributed Environmental Ontology term meaning \"partially surrounded by\"\n      - ENVO:01001307\n      - FMA:adjacent_to\n      - FMA:afferent_to\n      - FMA:anterior_to\n      - FMA:anteroinferior_to\n      - FMA:anterolateral_to\n      - FMA:anteromedial_to\n      - FMA:anterosuperior_to\n      # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics?\n      # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink\n      - FMA:arterial_supply_of\n      - FMA:has_arterial_supply\n      - FMA:articulates_with\n      - FMA:attaches_to\n      - FMA:bounded_by\n      - FMA:bounds\n      - FMA:branch_of\n      - FMA:connection_type_of\n      - FMA:continuation_branch_of\n      - FMA:continuous_distally_with\n      - FMA:continuous_proximally_with\n      - FMA:corresponds_to\n      - FMA:development_type_of\n      - FMA:developmental_stage_of\n      - FMA:direct_cell_shape_of\n      - FMA:direct_left_of\n      - FMA:direct_right_of\n      - FMA:distal_to\n      - FMA:drains_into\n      - FMA:efferent_to\n      - FMA:external_to\n      - FMA:formed_by\n      - FMA:forms\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:full_grown_phenotype_of\n      - FMA:has_full_grown_phenotype\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:fuses_with\n      - FMA:fusion_of\n      - FMA:has_fusion\n      - FMA:germ_origin_of\n      - FMA:has_germ_origin\n      - FMA:has_adherent\n      - FMA:has_branch\n      - FMA:has_connection_type\n      - FMA:has_continuation_branch\n      - FMA:has_development_type\n      - FMA:has_developmental_stage\n      - FMA:has_direct_cell_shape\n      - FMA:has_inherent_3d_shape\n      - FMA:has_insertion\n      - FMA:has_lymphatic_drainage\n      - FMA:has_nerve_supply\n      - FMA:has_observed_anatomical_entity\n      - FMA:has_origin\n      - FMA:has_primary_segmental_supply\n      - FMA:has_projection\n      - FMA:has_regional_part\n      - FMA:has_related_developmental_entity\n      - FMA:has_secondary_segmental_supply\n      - FMA:has_segmental_composition\n      - FMA:has_segmental_supply\n      - FMA:has_tributary\n      - FMA:has_venous_drainage\n      - FMA:inferior_to\n      - FMA:inferolateral_to\n      - FMA:inferomedial_to\n      - FMA:inherent_3d_shape_of\n      - FMA:insertion_of\n      - FMA:internal_to\n      - FMA:lateral_to\n      - FMA:left_lateral_to\n      - FMA:left_medial_to\n      - FMA:lymphatic_drainage_of\n      - FMA:matures_from\n      - FMA:matures_into\n      - FMA:medial_to\n      - FMA:merges_with\n      - FMA:nerve_supply_of\n      - FMA:origin_of\n      - FMA:posterior_to\n      - FMA:posteroinferior_to\n      - FMA:posterolateral_to\n      - FMA:posteromedial_to\n      - FMA:posterosuperior_to\n      - FMA:primary_segmental_supply_of\n      - FMA:projects_from\n      - FMA:projects_to\n      - FMA:proximal_to\n      - FMA:receives_attachment_from\n      - FMA:receives_drainage_from\n      - FMA:receives_input_from\n      - FMA:receives_projection\n      - FMA:related_part\n      - FMA:right_lateral_to\n      - FMA:right_medial_to\n      - FMA:secondary_segmental_supply_of\n      - FMA:segmental_composition_of\n      - FMA:segmental_supply_of\n      - FMA:sends_output_to\n      - FMA:superior_to\n      - FMA:superolateral_to\n      - FMA:superomedial_to\n      - FMA:surrounded_by\n      - FMA:surrounds\n      - FMA:tributary_of\n      - FMA:venous_drainage_of\n      # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute'\n      # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now\n      - LOINC:has_lateral_anatomic_location\n      - LOINC:has_lateral_location_presence\n      - UBERON_NONAMESPACE:distally_connected_to\n      - UBERON_NONAMESPACE:subdivision_of\n      # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to'\n      - RO:0002219\n      - RO:0002220\n      - RO:0002221\n      - SO:has_origin\n      # RTX mapped these UBERON terms all here\n      - UBERON:anastomoses_with\n      - UBERON:anteriorly_connected_to\n      - UBERON:channel_for\n      - UBERON:channels_from\n      - UBERON:channels_into\n      - UBERON:conduit_for\n      - UBERON:distally_connected_to\n      - UBERON:existence_starts_and_ends_during\n      - UBERON:extends_fibers_into\n      - UBERON:filtered_through\n      - UBERON:in_central_side_of\n      - UBERON:in_innermost_side_of\n      - UBERON:in_outermost_side_of\n      - UBERON:indirectly_supplies\n      - UBERON:posteriorly_connected_to\n      - UBERON:protects\n      - UBERON:proximally_connected_to\n      - UBERON:sexually_homologous_to\n\n  in pathway with:\n    description: >-\n      holds between two genes or gene products that are part of in the same biological pathway\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      # generally pertains to membership of a (subject) component - gene,\n      # metabolite, etc? - in an (object) metabolic pathway\n      - SIO:010532\n\n  in complex with:\n    description: >-\n      holds between two genes or gene products that are part of (or code for\n      products that are part of) in the same macromolecular complex mixin\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though)\n      - SIO:010497\n    broad_mappings:\n      # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes)\n      - SIO:010285\n\n  in cell population with:\n    description: >-\n      holds between two genes or gene products that are expressed in the same cell type or population\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  colocalizes with:\n    description: >-\n      holds between two entities that are observed to be located in the same place.\n    is_a: coexists with\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:00002325\n\n  # Despite the name, note that this particular entity is\n  # NOT a biolink:Association but rather, a biolink:predicate\n  genetic association:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    description: >-\n      Co-occurrence of a certain allele of a genetic marker and the phenotype\n      of interest in the same individuals at above-chance level\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2293\n\n  gene associated with condition:\n    is_a: genetic association\n    description: >-\n      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,\n      contribute to, or correlate with\n    domain: gene\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - GENO:0000840 # broader than a single gene: 'genotype' pathogenic for condition\n      - GENO:0000841\n    narrow_mappings:\n      # narrower: just diseases, not phenotypic features as well\n      - NCIT:R38\n      - NCIT:R175\n      - NCIT:R48\n\n  condition associated with gene:\n    is_a: genetic association\n    aliases: ['disease associated with gene']\n    description: >-\n      holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products\n    domain: disease or phenotypic feature\n    range: gene\n    in_subset:\n      - translator_minimal\n    inverse: gene associated with condition\n    narrow_mappings:\n      # narrower since just diseases, not phenotypic features as well\n      - NCIT:R176\n\n  affects risk for:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where exposure to one entity alters the chance of developing the other\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n\n  risk affected by:\n    is_a: related to at instance level\n    inverse: affects risk for\n\n  predisposes:\n    is_a: affects risk for\n    description: >-\n      holds between two entities where exposure to one entity increases the chance of developing the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:prevents\n    exact_mappings:\n      - SEMMEDDB:predisposes\n\n  has predisposing factor:\n    inverse: predisposes\n    in_subset:\n      - translator_minimal\n\n  # TODO: inverse of predisposes\n\n  contributes to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes or contributes to the\n      occurrence or generation of the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      # RTX contributed mapping tagged as 'inverse' of this Biolink predicate\n      - IDO:0000664\n    exact_mappings:\n      - RO:0002326\n    narrow_mappings:\n      - CTD:marker_mechanism\n      - MONDO:predisposes_towards\n      # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002255\n      # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here\n      - RO:0003304\n\n  contribution from:\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    inverse: contributes to\n\n  causes:\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes the occurrence\n      or generation of the other\n    is_a: contributes to\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:prevents\n    exact_mappings:\n      - SEMMEDDB:CAUSES\n      - SEMMEDDB:causes\n      - WIKIDATA_PROPERTY:P1542\n      - SNOMED:cause_of\n      - RO:0003303\n    broad_mappings:\n      - RO:0002410\n      - RO:0002506\n    narrow_mappings:\n      - MONDO:disease_triggers\n      - GOREL:0000040\n      - MONDO:disease_causes_feature\n      - MONDO:disease_triggers\n      - NCIT:allele_has_abnormality\n      - NCIT:biological_process_has_result_biological_process\n      - NCIT:chemical_or_drug_has_physiologic_effect\n      # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'?\n      - NCIT:chemical_or_drug_initiates_biological_process\n      - NCIT:process_initiates_biological_process\n      - NCIT:chromosome_mapped_to_disease\n      - NCIT:disease_has_normal_tissue_origin\n      - NBO-PROPERTY:in_response_to\n      - ORPHA:317343\n      - ORPHA:317344\n      - ORPHA:317346\n      - ORPHA:410295\n      - ORPHA:410296\n      # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002256\n      - RO:0002315\n      - RO:0002507\n      - RO:0002509\n      - RO:0004001\n      - SNOMED:causative_agent_of\n      - SNOMED:has_realization\n      - UMLS:has_physiologic_effect\n\n  caused by:\n    description: >-\n      holds between two entities where the occurrence, existence,\n      or activity of one is caused by the occurrence or generation of the other\n    is_a: related to at instance level\n    aliases: ['disease caused by disruption of', 'disease has basis in dysfunction of', 'realized in response to', 'realized in response to stimulus']\n    in_subset:\n      - translator_minimal\n    inverse: causes\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P828\n    narrow_mappings:\n      - RO:0001022\n      - RO:0002608\n      - RO:0004019\n      - RO:0004020\n      - RO:0004028\n      - RO:0009501\n\n  # TODO: ameliorates and exacerbates inverses.\n  ameliorates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a genotype,\n      genetic variation, chemical, or environmental exposure)\n      and a condition (a phenotype or disease), where the\n      presence of the entity reduces or eliminates some or\n      all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:exacerbates\n    exact_mappings:\n      - RO:0003307\n\n  is ameliorated by:\n    inverse: ameliorates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n\n  exacerbates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a chemical,\n      environmental exposure, or some form of genetic variation)\n      and a condition (a phenotype or disease), where the presence\n      of the entity worsens some or all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0003309\n    broad_mappings:\n      - SEMMEDDB:complicates\n\n  is exacerbated by:\n    inverse: exacerbates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n    in_subset:\n      - translator_minimal\n\n  treats:\n    aliases: ['is substance that treats', 'indicated for']\n    is_a: ameliorates\n    description: >-\n      holds between a therapeutic procedure or chemical entity\n      and a disease or phenotypic feature that it is used to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:contraindicated for\n    in_subset:\n      - translator_minimal\n    related_mappings:\n      - MONDO:disease_responds_to\n    exact_mappings:\n      - DRUGBANK:treats\n      - SEMMEDDB:TREATS\n      - SEMMEDDB:treats\n      - WIKIDATA_PROPERTY:P2175\n    narrow_mappings:\n      # \"is substance that treats\" constrains statements to\n      # a subset of the universe of all possible treatments\n      - RO:0002606\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n      - SNOMED:plays_role\n\n  treated by:\n    is_a: related to at instance level\n    description: >-\n      holds between a disease or phenotypic feature and a therapeutic\n      process or chemical entity that is used to treat the condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    # range: chemical or drug or treatement\n    in_subset:\n      - translator_minimal\n    inverse: treats\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2176\n      # RTX contributed term tagged as inverse of 'biolink:treats'\n      - MONDO:disease_responds_to\n    narrow_mappings:\n      # \"is treated by substance\" constrains statements to\n      # subset of the universe of all possible treatments\n      - RO:0002302\n\n  approved to treat:\n    deprecated: true\n    description: >-\n      holds between a therapeutic procedure or chemical entity\n      and a disease or phenotypic feature for which it is approved\n      for treatment to some level of clinical trial. Note that in\n      terms of REPODB narrow mappings, terms containing 'suspended',\n      'terminated' or 'withdrawn' should be mapped onto associations\n      using this term for which 'negated: true' is asserted.\n    is_a: treats\n    domain: chemical or drug or treatment\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  approved for treatment by:\n    description: >-\n      holds between a disease or phenotypic feature and a therapeutic process\n      or chemical entity that is approved for treatment of the condition\n      (or not, if negated) to some level of clinical trial\n    is_a: treated by\n    range: chemical or drug or treatment\n    inverse: approved to treat\n\n  prevents:\n    is_a: affects risk for\n    description: >-\n      holds between an entity whose application or use reduces\n      the likelihood of a potential outcome. Typically used to associate\n      a chemical entity, exposure, activity, or medical intervention\n      that can prevent the onset a disease or phenotypic feature.\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:predisposes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:PREVENTS\n      - SEMMEDDB:prevents\n    narrow_mappings:\n      # more restricted case of a material entity mitigating a pathological process\n      - RO:0002599\n  \n  prevented by:\n    is_a: risk affected by\n    description: >-\n      holds between a potential outcome of which the likelihood\n      was reduced by the application or use of an entity.\n    inverse: prevents\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:enabled by\n\n  correlated with:\n    is_a: associated with\n    description: >-\n      holds between any two named thing entities. For example, correlated_with\n      holds between a disease or phenotypic feature and a measurable molecular\n      entity that is used as an indicator of the presence or state of the disease or feature.\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002610\n      - PATO:correlates_with\n\n  # proposed positive and negative semantic extensions to the general \"correlated with\" predicate\n\n  positively correlated with:\n    is_a: correlated with\n    description: >-\n      holds between any two named thing entities \"correlated with\" one another in a positive manner.\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:negatively correlated with\n    exact_mappings:\n      - CTD:positive_correlation\n\n  negatively correlated with:\n    is_a: correlated with\n    description: >-\n      holds between any two named thing entities \"correlated with\" one another in a negative manner.\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:positively correlated with\n    exact_mappings:\n      - CTD:negative_correlation\n\n  occurs together in literature with:\n    is_a: correlated with\n    description: >-\n      holds between two entities where their co-occurrence is correlated by counts of publications\n      in which both occur, using some threshold of occurrence as defined by the edge provider.\n    domain: named thing\n    range: named thing\n    in_subset: translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  coexpressed with:\n    is_a: correlated with\n    description: >-\n      holds between any two genes or gene products, in which both are\n      generally expressed within a single defined experimental context.\n    domain: gene or gene product\n    range: gene or gene product\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  has biomarker:\n    is_a: correlated with\n    description: >-\n      holds between a disease or phenotypic feature and a measurable\n      chemical entity that is used as an indicator of the presence\n      or state of the disease or feature.\n      # metabolite\n    domain: disease or phenotypic feature\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    inverse: biomarker for\n    narrow_mappings:\n      # some RTX terms contributed as inverses of 'biolink:biomarker_for'\n      - NCIT:disease_has_molecular_abnormality\n      - NCIT:disease_is_marked_by_gene\n\n  biomarker for:\n    is_a: correlated with\n    description: >-\n      holds between a measurable chemical entity and a disease\n      or phenotypic feature, where the entity is used as an indicator\n      of the presence or state of the disease or feature.\n    domain: chemical entity or gene or gene product\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - NCIT:R39\n    broad_mappings:\n      # Generic marker definition not specific to biomarkers per say\n      - RO:0002607\n    narrow_mappings:\n      - NCIT:R47\n      # RTX term was tagged as 'biolink:actively_involved_in' but maps better here?\n      - NCIT:genetic_biomarker_related_to\n      - NCIT:is_molecular_abnormality_of_disease\n      - ORPHA:465410\n\n  # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in'\n  # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates\n  # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others\n  expressed in:\n    is_a: located in\n    description: >-\n      holds between a gene or gene product and an anatomical entity in which it is expressed\n    domain: gene or gene product\n    range: anatomical entity\n    multivalued: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002206\n    narrow_mappings:\n      - NCIT:R49\n      - NCIT:R46\n\n  expresses:\n    is_a: location of\n    aliases: ['anatomy expresses gene']\n    description: >-\n      holds between an anatomical entity and gene or gene product that is expressed there\n    domain: anatomical entity\n    range: gene or gene product\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    inverse: expressed in\n    exact_mappings:\n      - RO:0002292\n\n  has phenotype:\n    is_a: related to at instance level\n    aliases: ['disease presents symptom']\n    description: >-\n      holds between a biological entity and a phenotype, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should\n      translate into this predicate.\n    domain: biological entity\n    range: phenotypic feature\n    multivalued: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    notes:\n      - check the range\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002200\n    broad_mappings:\n      - NCIT:R115\n      - NCIT:R108\n    narrow_mappings:\n      - NCIT:R89\n      - DOID-PROPERTY:has_symptom\n      - RO:0004022\n\n  phenotype of:\n    is_a: related to at instance level\n    description: >-\n      holds between a phenotype and a biological entity, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature).\n    domain: phenotypic feature\n    range: biological entity\n    multivalued: true\n    inverse: has phenotype\n    notes:\n      - check the domain\n    in_subset:\n      - translator_minimal\n\n  # TODO: predicate inverse for occurs in\n  occurs in:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a material entity or site within which the process occurs\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      # These RTX mapped terms tagged as the inverse of \"biolink:occurs_in\", i.e. Entity/Site contains Process\"\n      - BFO:0000067\n      - SNOMED:has_occurrence\n      - UBERON:site_of\n    exact_mappings:\n      - BFO:0000066\n      - PathWhiz:has_location\n      - SNOMED:occurs_in\n    narrow_mappings:\n      # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population\n      - SEMMEDDB:OCCURS_IN\n      - SEMMEDDB:occurs_in\n      # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity\n      - SEMMEDDB:PROCESS_OF\n      - SEMMEDDB:process_of\n      # Uberon term constrained to a 'site' as object concept\n      - UBERON_CORE:site_of\n      - LOINC:has_imaged_location\n      - PathWhiz:in_species\n      - RO:0002231\n      - RO:0002232\n      - SNOMED:has_direct_procedure_site\n      - SNOMED:has_direct_site\n      - SNOMED:has_procedure_site\n\n  contains process:\n    is_a: related to at instance level\n    inverse: occurs in\n\n  located in:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a material entity or site\n      within which it is located (but of which it is not considered a part)\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0001025\n      - FMA:has_location\n    narrow_mappings:\n      - GOREL:0001004\n      - BSPO:0000107\n      - BSPO:0000108\n      - BSPO:0000120\n      - BSPO:0000121\n      - BSPO:0000122\n      - BSPO:0000123\n      - BSPO:0000124\n      - BSPO:0000125\n      - BSPO:0000126\n      - BSPO:0001100\n      - BSPO:0001101\n      - BSPO:0001107\n      - BSPO:0015101\n      - BSPO:0015102\n      - BSPO:0015202\n      - UBERON_CORE:in_central_side_of\n      - UBERON_CORE:in_innermost_side_of\n      - UBERON_CORE:in_outermost_side_of\n      - NCIT:R100\n      - EFO:0000784\n      - FMA:has_location\n      - HMDB:at_cellular_location\n      - HMDB:at_tissue\n      - HMDB:in_biospecimen\n      - LOINC:has_imaging_focus\n      - NCIT:R156\n      - NCIT:R155\n      - NCIT:R145\n      - NCIT:R40\n      - NCIT:R171\n      - NCIT:R167\n      - NCIT:R165\n      - NCIT:R169\n      - NCIT:R170\n      - NCIT:R166\n      - NCIT:R168\n      - RO:0002303\n      - SNOMED:has_finding_site\n      - SNOMED:has_indirect_procedure_site\n      - SNOMED:has_inherent_location\n    domain: named thing\n    range: named thing\n\n  location of:\n    is_a: related to at instance level\n    aliases: ['site of']\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between material entity or site and a material entity\n      that is located within it (but not considered a part of it)\n    in_subset:\n      - translator_minimal\n    inverse: located in\n    exact_mappings:\n      - RO:0001015\n      - SEMMEDDB:LOCATION_OF\n      - SEMMEDDB:location_of\n      - WIKIDATA_PROPERTY:P276\n      # RTX tagged this as an inverse of biolink:located_in\n      - FMA:location_of\n    narrow_mappings:\n      - SNOMED:inherent_location_of\n      - NCIT:Anatomic_Structure_Has_Location_Role\n\n  disease has location:\n    description: >-\n      A relationship between a disease and an anatomical entity where the\n      disease has one or more features that are located in that entity.\n    is_a: related to\n    exact_mappings:\n      - RO:0004026\n      - MONDO:disease_has_location\n\n  similar to:\n      is_a: related to at instance level\n      description: >-\n        holds between an entity and some other entity with similar features.\n      in_subset:\n        - translator_minimal\n      symmetric: true\n      annotations:\n        biolink:canonical_predicate:\n          tag: biolink:canonical_predicate\n          value: true\n      exact_mappings:\n        - RO:HOM0000000               #I don't understand this identifier, but I think it's equivalent\n        - SO:similar_to               #equivalent\n\n  chemically similar to:\n    is_a: similar to\n    description: >-\n      holds between one small molecule entity and another that it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    narrow_mappings:\n      - CHEBI:has_parent_hydride    #subproperty\n      - CHEBI:has_functional_parent #subproperty\n      - CHEBI:is_conjugate_acid_of  #subproperty\n      - CHEBI:is_conjugate_base_of  #subproperty\n      - CHEBI:is_enantiomer_of      #subproperty\n      - CHEBI:is_tautomer_of        #subproperty\n      - NCIT:has_salt_form\n\n  has sequence location:\n    is_a: related to at instance level\n    description: >-\n      holds between two nucleic acid entities when the subject can be localized\n      in sequence coordinates on the object. For example, between\n      an exon and a chromosome/contig.\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - faldo:location\n\n  sequence location of:\n    is_a: related to at instance level\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    inverse: has sequence location\n\n  model of:\n    is_a: related to at instance level\n    description: >-\n      holds between a thing and some other thing it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0003301\n    narrow_mappings:\n      - FOODON:00001301\n\n  models:\n    is_a: related to at instance level\n    inverse: model of\n\n  overlaps:\n    is_a: related to at instance level\n    description: >-\n      holds between entities that overlap in their extents (materials or processes)\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - RO:0002131\n    narrow_mappings:\n      - BSPO:0005001\n      - CHEMBL.MECHANISM:overlaps_with\n      - RO:0002100\n      - RO:0002102\n      - RO:0002433\n\n  has part:\n    is_a: overlaps\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:lacks part\n    description: >-\n      holds between wholes and their parts (material entities or processes)\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000051\n      # term name seems to be 'realizes' but RTX maps this term here\n      - BFO:0000055\n      - WIKIDATA_PROPERTY:P527\n      - RO:0001019\n      - RXNORM:consists_of\n      - RXNORM:has_part\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'; slightly broader?\n      - RO:0001019\n      - FMA:contains\n      - RXNORM:contains\n    narrow_mappings:\n      - BFO:0000117\n      # RTX term originally mapped to 'biolink:coexists_with'?\n      - FMA:has_constitutional_part\n      - FMA:has_part\n      # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'?\n      - FMA:has_member\n      - FOODON:00001563\n      - FOODON:00002420\n      - LOINC:has_component\n      - LOINC:has_member\n      - MEDDRA:has_member\n      - MONDO:disease_has_major_feature\n      - NCIT:complex_has_physical_part\n      - NDDF:has_ingredient\n      - PathWhiz:has_element_in_bound\n      # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature\n      - NCIT:R50\n      - PathWhiz:has_protein_in_complex\n      - RO:0002104\n      - RO:0002180\n      - RO:0002351\n      - RO:0002473\n      - RO:0002524\n      - RO:0002551\n      - RXNORM:has_ingredient\n      - SNOMED:has_component\n      - UMLS:has_component\n\n  has plasma membrane part:\n    is_a: has part\n    description: >-\n      Holds between a cell c and a protein complex or protein p if\n      and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.\n    exact_mappings:\n      - RO:0002104\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n\n  composed primarily of:\n    is_a: related to\n    description: >-\n      x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.\n    exact_mappings:\n      - RO:0002473\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n\n  plasma membrane part of:\n    is_a: part of\n    inverse: has plasma membrane part\n\n  part of:\n    is_a: overlaps\n    description: >-\n      holds between parts and wholes (material entities or processes)\n    in_subset:\n      - translator_minimal\n    inverse: has part\n    exact_mappings:\n      - BFO:0000050\n      - SEMMEDDB:PART_OF\n      - SEMMEDDB:part_of\n      - WIKIDATA_PROPERTY:P361\n      - FMA:part_of\n      - RXNORM:constitutes\n      - RXNORM:part_of\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'\n      - RO:0001018\n      - FMA:contained_in\n      - RXNORM:contained_in\n    narrow_mappings:\n      - BSPO:0001106\n      - BSPO:0001108\n      - BSPO:0001113\n      - BSPO:0001115\n      - UBERON_CORE:layer_part_of\n      - UBERON_CORE:subdivision_of\n      - UBERON_CORE:trunk_part_of\n      - CHEBI:is_substituent_group_from\n      - CPT:panel_element_of\n      - CPT:panel_element_of_possibly_included\n      - DRUGBANK:component_of\n      - FMA:constitutional_part_of\n      - FMA:member_of\n      - FMA:regional_part_of\n      - FMA:related_developmental_entity_of\n      - LOINC:component_of\n      - LOINC:has_supersystem\n      - LOINC:member_of\n      - LOINC:multipart_of\n      - MEDDRA:member_of\n      - MONDO:part_of_progression_of_disease\n      - NCIT:R82\n      - NCIT:R27\n      - NCIT:is_component_of_chemotherapy_regimen\n      - NDDF:ingredient_of\n      - RO:0002007\n      - RO:0002350\n      - RO:0002376\n      - RO:0002380\n      - RO:0002571\n      - RO:0002572\n      - RO:0002576\n      - RXNORM:ingredient_of\n      - RXNORM:ingredients_of\n      - RXNORM:precise_ingredient_of\n      - SNOMED:active_ingredient_of\n      - SNOMED:basis_of_strength_substance_of\n      - SNOMED:component_of\n      - SNOMED:direct_substance_of\n      - SNOMED:during\n      - SNOMED:focus_of\n      - SNOMED:has_dependent\n      - SNOMED:part_anatomy_structure_of\n      - SNOMED:precise_active_ingredient_of\n      - UBERON:subdivision_of\n      - UMLS:component_of\n      - UMLS:has_owning_affiliate\n      - UMLS:owning_subsection_of\n      - VANDF:ingredient_of\n\n  has input:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an input into the process\n    domain: occurrent\n    range: biological process or activity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has output\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX inverse mapping to to 'biolink:has_input'\n      - RO:0002352\n    exact_mappings:\n      - RO:0002233\n      - SEMMEDDB:USES\n      - SEMMEDDB:uses\n    narrow_mappings:\n      - LOINC:has_fragments_for_synonyms\n      - LOINC:has_system\n      - PathWhiz:has_left_element\n      - RO:0002590\n      - RO:0004009\n      - SNOMED:has_finding_method\n      - SNOMED:has_precondition\n      - SNOMED:has_specimen_source_identity\n      - SNOMED:has_specimen_substance\n      - SNOMED:uses_access_device\n      - SNOMED:uses_device\n      - SNOMED:uses_energy\n      - SNOMED:uses_substance\n\n  is input of:\n    is_a: participates in\n    domain: biological process or activity\n    range: occurrent\n    inverse: has input\n    in_subset:\n      - translator_minimal\n\n  has output:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an output of the process\n    domain: occurrent\n    range: biological process or activity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has input\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - RO:0002353\n      - RO:0002354\n    exact_mappings:\n      - RO:0002234\n    narrow_mappings:\n      - NCIT:R31\n      - OBI:0000299\n      - PathWhiz:has_right_element\n      - RO:0002296\n      - RO:0002297\n      - RO:0002298\n      - RO:0002299\n      - RO:0002588\n      - RO:0004008\n\n  is output of:\n    is_a: participates in\n    range: occurrent\n    domain: biological process or activity\n    inverse: has output\n    in_subset:\n      - translator_minimal\n\n  has participant:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a continuant, where the continuant is somehow involved in the process\n    domain: occurrent\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - WIKIDATA_PROPERTY:P2283\n    exact_mappings:\n      - RO:0000057\n      - RO:has_participant\n    narrow_mappings:\n      - BFO:0000167\n      # Several of the following RTX terms tagged as inverse to 'biolink:participates_in'\n      - LOINC:has_subject\n      - NCIT:process_involves_gene\n      - NBO-PROPERTY:has_participant\n      - PathWhiz:has_bound\n      - PathWhiz:has_compound\n      - PathWhiz:has_element_collection\n      - PathWhiz:has_enzyme\n      - OBI:0000293\n      - PathWhiz:has_nucleic_acid\n      - PathWhiz:has_protein\n      - PathWhiz:has_reaction\n      - RO:0004007\n      - RO:0004020\n      - RO:0004021\n      - SNOMED:has_indirect_device\n      - SNOMED:has_procedure_device\n      - SNOMED:has_recipient_category\n\n  catalyzes:\n    is_a: participates in\n    # domain: nucleic acid entity\n    # range: molecular activity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  has catalyst:\n    is_a: has participant\n    inverse: catalyzes\n\n  has substrate:\n    is_a: has participant\n    # domain: molecular activity\n    # range: chemical entity or gene or gene product\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  is substrate of:\n    is_a: participates in\n    inverse: has substrate\n\n  participates in:\n    is_a: related to at instance level\n    description: >-\n      holds between a continuant and a process, where the continuant is somehow involved\n      in the process\n    range: occurrent\n    inverse: has participant\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0000056\n      - BFO:0000056\n    narrow_mappings:\n      - DRUGBANK:pathway\n      - HMDB:in_pathway\n      - LOINC:is_given_pharmaceutical_substance_for\n      - NCIT:R130\n      - NCIT:R37\n      - NCIT:R131\n      - NCIT:R51\n      - NCIT:R53\n      - OBI:0000295\n      - RO:0002216\n      - RO:0002505\n      - RO:0002565\n      - SNOMED:has_direct_device\n\n  actively involved in:\n    is_a: participates in\n    aliases: ['involved in']\n    description: >-\n      holds between a continuant and a process or function, where\n      the continuant actively contributes to part or all of\n      the process or function it realizes\n    domain: molecular activity\n    range: occurrent\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002331\n      - RO:0002432\n    narrow_mappings:\n      - NBO-PROPERTY:by_means\n      - ORPHA:317348\n      - ORPHA:317349\n      - ORPHA:327767\n      - RO:0002503\n\n  actively involves:\n    is_a: has participant\n    domain: occurrent\n    range: molecular activity\n    inverse: actively involved in\n    exact_mappings:\n      - RO:0002331\n    in_subset:\n      - translator_minimal\n\n  capable of:\n    is_a: actively involved in\n    description: >-\n      holds between a physical entity and process or function, where the\n      continuant alone has the ability to carry out the process or function.\n    range: occurrent\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002215\n    narrow_mappings:\n      - NCIT:R52\n      - RO:0002500\n\n  has capability:\n    is_a: actively involves\n    inverse: capable of\n\n  enables:\n    is_a: participates in\n    description: >-\n      holds between a physical entity and a process, where the physical entity executes the process\n    domain: physical entity\n    range: biological process or activity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:prevents\n    in_subset:\n      - translator_minimal\n    inverse: enabled by\n    exact_mappings:\n      - RO:0002327\n\n  enabled by:\n    is_a: has participant\n    description: >-\n      holds between a process and a physical entity, where the physical entity executes the process\n    domain: biological process or activity\n    range: physical entity\n    in_subset:\n      - translator_minimal\n    inverse: enables\n    exact_mappings:\n      - RO:0002333\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:prevented by\n\n  derives into:\n    is_a: related to at instance level\n    aliases: ['is normal cell origin of disease','may be normal cell origin of disease']\n    description: >-\n      holds between two distinct material entities, the old entity and\n      the new entity, in which the new entity begins to exist when\n      the old entity ceases to exist, and the new entity inherits\n      the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n    inverse: derives from\n    # TODO: fix this according to WG notes. Example of both opposite and inverse\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:subclass of\n    exact_mappings:\n      - RO:0001001\n      - SEMMEDDB:CONVERTS_TO\n      - SEMMEDDB:converts_to\n      # RTX posted terms as inverse of 'biolink:derives_from'\n      - FMA:derives\n\n  derives from:\n    is_a: related to at instance level\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    description: >-\n      holds between two distinct material entities, the new entity\n      and the old entity, in which the new entity begins to exist\n      when the old entity ceases to exist, and the new entity\n      inherits the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n      - samples\n    inverse: derives into\n    exact_mappings:\n      - RO:0001000\n      - FMA:derives_from\n      - DOID-PROPERTY:derives_from\n    narrow_mappings:\n      - CHEBI:has_functional_parent\n      - SNOMED:has_specimen_source_topography\n\n  is metabolite of:\n    is_a: derives from\n    description: >-\n      holds between two molecular entities in which the first one is derived\n      from the second one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    inverse: has metabolite\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  has metabolite:\n    is_a: derives into\n    description: >-\n      holds between two molecular entities in which the second one is derived from the first\n      one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  food component of:\n    is_a: part of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has food component\n    #mappings:\n    #  -\n\n  has food component:\n    is_a: has part\n    description: >-\n      holds between food and one or more chemical entities composing it,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n\n  nutrient of:\n    is_a: food component of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has nutrient\n    #exact_mappings:\n    #  -\n\n  has nutrient:\n    is_a: has food component\n    description: >-\n      one or more nutrients which are growth factors for a living organism\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q181394\n\n  is active ingredient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug, in which the former\n      is a part of the latter, and is a biologically active component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has active ingredient\n    mappings:\n      - RO:0002249\n\n  has active ingredient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entity in which the latter\n      is a part of the former, and is a biologically active component\n    domain: drug\n    range: molecular entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:is excipient of\n    in_subset:\n      - translator_minimal\n    inverse: is active ingredient of\n    mappings:\n      - RO:0002248\n\n  is excipient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug in which the former is\n      a part of the latter, and is a biologically inactive component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has excipient\n    mappings:\n      - WIKIDATA:Q902638\n\n  has excipient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entities in which the latter\n      is a part of the former, and is a biologically inactive component\n    domain: drug\n    range: molecular entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    mappings:\n      - WIKIDATA:Q902638\n\n  manifestation of:\n    is_a: related to at instance level\n    description: >-\n      that part of a phenomenon which is directly observable or\n      visibly expressed, or which gives evidence to the underlying\n      process; used in SemMedDB for linking things like dysfunctions\n      and processes to some disease or syndrome\n    range: disease\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:MANIFESTATION_OF\n      - SEMMEDDB:manifestation_of\n      - OMIM:manifestation_of\n    broad_mappings:\n      # Wikidata definition slightly broader: \"inherent and characteristic embodiment of a given concept\"\n      - WIKIDATA_PROPERTY:P1557\n    narrow_mappings:\n      - SNOMED:has_definitional_manifestation\n\n  has manifestation:\n    is_a: related to at instance level\n    domain: disease\n    inverse: manifestation of\n\n  produces:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a product that is generated\n      through the intentional actions or functioning of the material entity\n    in_subset:\n      - translator_minimal\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      - GOREL:0001010\n    exact_mappings:\n      - RO:0003000\n      - WIKIDATA_PROPERTY:P1056\n      - SEMMEDDB:PRODUCES\n      - SEMMEDDB:produces\n    narrow_mappings:\n      - NCIT:R29\n      - SNOMED:has_process_output\n      - SNOMED:specimen_procedure_of\n\n  produced by:\n    is_a: related to at instance level\n    inverse: produces\n    exact_mappings:\n      - RO:0003001\n\n  consumes:\n    is_a: has input\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    narrow_mappings:\n      - RO:0004009\n\n  consumed by:\n    is_a: is input of\n    inverse: consumes\n\n  temporally related to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities with a temporal relationship\n    domain: occurrent\n    range: occurrent\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - SNOMED:temporally_related_to\n    narrow_mappings:\n      # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here\n      - RO:0002082\n      - RO:0002083\n      - RO:0002092\n      - RO:0002093\n      - RO:0002223\n      - RO:0002224\n      - RO:0002229\n      - RO:0002230\n      - RO:0002488\n      - RO:0002489\n      - RO:0002492\n      - RO:0002493\n      - RO:0002496\n      - RO:0002497\n\n  precedes:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where one completes before the other begins\n    domain: occurrent\n    range: occurrent\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:preceded by\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # the subject of these terms is a material entity, not a process,\n      # but affects a process which causes a second process to occur\n      - RO:0002263\n      - RO:0002264\n    exact_mappings:\n      - BFO:0000063\n      - SEMMEDDB:PRECEDES\n      - SEMMEDDB:precedes\n      - SNOMED:occurs_before\n    broad_mappings:\n      # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature\n      - WIKIDATA_PROPERTY:P156\n    narrow_mappings:\n      - FMA:transforms_into\n      - RO:0002090\n      - RO:0002411\n      - RO:0002412\n\n  preceded by:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where the other is completed before the one begins\n    domain: occurrent\n    range: occurrent\n    inverse: precedes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000062\n    broad_mappings:\n      # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'?\n      - GENEPIO:0001739\n    narrow_mappings:\n      # RTX contributed mapping was given as the inverse of 'biolink:precedes'\n      - FMA:transforms_from\n      - RO:0002087\n      - RO:0002285\n\n  directly interacts with:\n    is_a: interacts with\n    description: Holds between chemical entities that physically and directly interact\n      with each other\n    domain: chemical entity\n    range: chemical entity or gene or gene product\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    related_mappings:\n      - GAMMA:kd\n      - GAMMA:kb\n      - GAMMA:potency\n    exact_mappings:\n      - GAMMA:interacts_with\n    broad_mappings:\n      # Definition of this term is more generic than direct physical molecular interactions:\n      # A is connected to B iff there exists a fiat, material or temporal path between A and B.\n      - SIO:000203\n    narrow_mappings:\n      - PHAROS:drug_targets\n      - DRUGBANK:chelator\n      - GAMMA:antibody_binding\n      - GAMMA:pharmacological_chaperone\n      - GAMMA:releasing_agent\n      - GAMMA:pharmacological_chaperone\n      - GAMMA:releasing_agent\n      - GAMMA:binder\n      - GAMMA:binding\n      - GAMMA:ligand\n      - GAMMA:cofactor\n      - GAMMA:multitarget\n      - GAMMA:chaperone\n      - GAMMA:component\n      - GAMMA:adduct\n      - GAMMA:antibody\n      - CTD:affects_binding\n      - DGIdb:binder\n      - DGIdb:cofactor\n\n  affects expression in:\n    is_a: affects\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    description: Holds between a variant and an anatomical entity where the expression of the variant\n       is located in.\n    exact_mappings:\n      - GTEx:affects_expression_in\n\n  has variant part:\n    is_a: has part\n    description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - GENO:0000382\n\n  variant part of:\n    is_a: part of\n    inverse: has variant part\n\n  related condition:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - GENO:0000790\n\n  ## Predicates relating variants to genes\n\n  is sequence variant of:\n    is_a: related to at instance level\n    aliases: ['gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product']\n    description: holds between a sequence variant and a nucleic acid entity\n    domain: sequence variant\n    range: nucleic acid entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    narrow_mappings:\n      - WIKIDATA:P3433\n\n  has sequence variant:\n    is_a: related to at instance level\n    inverse: is sequence variant of\n    domain: nucleic acid entity\n    range: sequence variant\n\n  is missense variant of:\n    is_a: is sequence variant of\n    description: holds between a gene  and a sequence variant, such the sequence variant\n      results in a different amino acid sequence but where the length is preserved.\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - SO:0001583\n\n  has missense variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is missense variant of\n\n  is synonymous variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the coding sequence of the gene, but results in the same amino acid sequence\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - SO:0001819\n\n  has synonymous variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is synonymous variant of\n    aliases: ['stop gained']\n\n  is nonsense variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      results in a premature stop codon\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    broad_mappings:\n      # Term definition broader than nonsense codon: A sequence variant whereby\n      # the gene product has diminished or abolished function.\n      - SO:0002054\n\n  has nonsense variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is nonsense variant of\n\n  is frameshift variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      causes a disruption of the translational reading frame, because the number of\n      nucleotides inserted or deleted is not a multiple of three.\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - SO:0001589\n    aliases: ['frameshift variant', 'start lost', 'stop lost']\n\n  has frameshift variant:\n    is_a: has sequence variant\n    inverse: is frameshift variant of\n    domain: gene\n    range: sequence variant\n    aliases: ['splice region variant', 'splice acceptor variant', 'splice donor variant']\n\n  is splice site variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the canonical splice site of one of the gene's exons.\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - SO:0001629\n\n\n  has splice site variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is splice site variant of\n    aliases: ['downstream gene variant', 'upstream gene variant']\n\n  is nearby variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene sequence that the variant\n      is genomically close to.\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - GAMMA:0000102\n\n  has nearby variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is nearby variant of\n    aliases: ['intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant']\n\n  is non coding variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, where the variant does\n      not affect the coding sequence\n    domain: sequence variant\n    range: gene\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - GAMMA:0000103\n\n  has non coding variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is non coding variant of\n\n  # relating disease to process\n\n  disease has basis in:\n    description: A relation that holds between a disease and an entity where the state\n      of the entity has contribution to the disease.\n    is_a: related to at instance level\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    narrow_mappings:\n      # These two MONDO terms seem more particular than the predicate\n      - MONDO:disease_has_basis_in_development_of\n      - MONDO:disease_has_basis_in_accumulation_of\n\n  occurs in disease:\n    is_a: related to at instance level\n    inverse: disease has basis in\n\n  # These may be pushable to causal relationships, but seem important for clarity\n  # Also because causes adverse event tends to be very noisy and it's useful to be able\n  # to distinguish it.  maybe not the best way to do that though.\n\n  causes adverse event:\n    is_a: causes\n    description: holds between a drug and a disease or phenotype that can be caused\n      by the drug\n    domain: drug\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    narrow_mappings:\n      - NCIT:C2861 # side effect\n\n  adverse event caused by:\n    is_a: causes\n    domain: disease or phenotypic feature\n    range: drug\n    inverse: causes adverse event\n\n  contraindicated for:\n    is_a: related to at instance level\n    description: Holds between a drug and a disease or phenotype, such that a person\n      with that disease should not be treated with the drug.\n    domain: drug\n    range: disease or phenotypic feature\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:treats\n    exact_mappings:\n      - NCIT:C37933\n\n  has contraindication:\n    is_a: related to at instance level\n    domain: disease or phenotypic feature\n    range: drug\n    inverse: contraindicated for\n\n  # The remaining new slots are here because we ran across them somewhere and\n  # they didn't seem to map well to anything else.\n\n  has not completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of,\n      but has not completed\n    exact_mappings:\n      - CL:has_not_completed\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has completed\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n\n  not completed by:\n    is_a: related to at instance level\n    inverse: has not completed\n\n  has completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of\n      and has completed\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has not completed\n    exact_mappings:\n      - CL:has_completed\n\n  completed by:\n    is_a: related to at instance level\n    inverse: has completed\n\n  decreases molecular interaction:\n    is_a: molecularly interacts with\n    description: indicates that the source decreases the molecular interaction between\n      the target and some other chemical entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:increases molecular interaction\n    exact_mappings:\n      - CTD:decreases_molecular_interaction_with\n    mixins:\n      - decreases amount or activity of\n\n\n  molecular interaction decreased by:\n    is_a: molecularly interacts with\n    inverse: decreases molecular interaction\n\n  increases molecular interaction:\n    is_a: molecularly interacts with\n    description: indicates that the source increases the molecular interaction between\n      the target and some other chemical entity\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:decreases molecular interaction\n    exact_mappings:\n      - CTD:increases_molecular_interaction_with\n    mixins:\n      - increases amount or activity of\n\n  molecular interaction increased by:\n    is_a: molecularly interacts with\n    inverse: increases molecular interaction\n\n  in linkage disequilibrium with:\n    is_a: related to at instance level\n    description: holds between two sequence variants, the presence of which are correlated\n      in a population\n    symmetric: true\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    exact_mappings:\n      - NCIT:C16798\n\n  has increased amount:\n    is_a: related to at instance level\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has decreased amount\n    narrow_mappings:\n      - CL:has_high_plasma_membrane_amount\n\n  increased amount of:\n    is_a: related to at instance level\n    inverse: has increased amount\n\n  has decreased amount:\n    is_a: related to at instance level\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has increased amount\n    narrow_mappings:\n      - CL:has_low_plasma_membrane_amount\n\n  decreased amount in:\n    is_a: related to at instance level\n    inverse: has decreased amount\n\n  lacks part:\n    is_a: related to at instance level\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:has part\n    exact_mappings:\n      - CL:lacks_part\n      - PR:lacks_part\n    narrow_mappings:\n      - CL:lacks_plasma_membrane_part\n\n\n  missing from:\n    is_a: related to at instance level\n    inverse: lacks part\n\n  develops from:\n    is_a: related to at instance level\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    close_mappings:\n      # RTX mapping seems to be inverse of 'biolink:develops_from'\n      - RO:0002203\n      - FMA:develops_into\n    exact_mappings:\n      - BTO:develops_from\n      - DDANAT:develops_from\n      - FMA:develops_from\n      - RO:0002202\n    narrow_mappings:\n      - RO:0002207\n      - RO:0002225 # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y\n      - RO:0002226 # x develops_in y if x is located in y whilst x is developing\n\n  develops into:\n     is_a: related to at instance level\n     inverse: develops from\n\n  in taxon:\n    aliases: ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism',' gene product has organism source']\n    is_a: related to at instance level\n    domain: thing with taxon\n    range: organism taxon\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    description: >-\n      connects an entity to its taxonomic classification. Only certain kinds\n      of entities can be taxonomically classified; see 'thing with taxon'\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002162\n      - WIKIDATA_PROPERTY:P703\n    narrow_mappings:\n      - RO:0002160\n\n  taxon of:\n    is_a: related to at instance level\n    inverse: in taxon\n    domain: organism taxon\n    range: thing with taxon\n\n  has molecular consequence:\n    is_a: related to at instance level\n    aliases: ['allele has activity']\n    description: >-\n      connects a sequence variant to a class describing the molecular\n      consequence. E.g.  SO:0001583\n    range: ontology class\n    annotations:\n      biolink:canonical_predicate:\n        tag: biolink:canonical_predicate\n        value: true\n    narrow_mappings:\n      - NCIT:allele_has_activity\n\n  is molecular consequence of:\n    is_a: related to at instance level\n    domain: ontology class\n    inverse: has molecular consequence\n\n## --------------------\n## ASSOCIATION SLOTS\n## --------------------\n\n  association slot:\n    abstract: true\n    domain: association\n    aliases: ['edge property','statement property']\n    description: >-\n      any slot that relates an association to another entity\n\n  original subject:\n    is_a: association slot\n    description: >-\n      used to hold the original subject of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original object:\n    is_a: association slot\n    description: >-\n      used to hold the original object of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original predicate:\n    aliases: ['original relation', 'relation']\n    is_a: association slot\n    description: >-\n      used to hold the original relation/predicate that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n    id_prefixes:\n      - RO\n      - BSPO\n      - SIO\n    domain: association\n    range: uriorcurie\n\n  subject:\n    is_a: association slot\n    local_names:\n      ga4gh: annotation subject\n      neo4j: node with outgoing relationship\n    description: >-\n      connects an association to the subject of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    slot_uri: rdf:subject\n    exact_mappings:\n      - owl:annotatedSource\n      - OBAN:association_has_subject\n\n  object:\n    is_a: association slot\n    description: >-\n      connects an association to the object of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    local_names:\n      ga4gh: descriptor\n      neo4j: node with incoming relationship\n    slot_uri: rdf:object\n    exact_mappings:\n      - owl:annotatedTarget\n      - OBAN:association_has_object\n\n  predicate:\n    is_a: association slot\n    description: >-\n      A high-level grouping for the relationship type. AKA minimal predicate.\n      This is analogous to category for nodes.\n    domain: association\n    notes: >-\n      Has a value from the Biolink related_to hierarchy. In RDF,  this\n      corresponds to rdf:predicate and in Neo4j this corresponds to the\n      relationship type. The convention is for an edge label in snake_case\n      form. For example, biolink:related_to, biolink:causes, biolink:treats\n    range: predicate type\n    required: true\n    local_names:\n      ga4gh: annotation predicate\n      translator: predicate\n    slot_uri: rdf:predicate\n    exact_mappings:\n      - owl:annotatedProperty\n      - OBAN:association_has_predicate\n\n  logical interpretation:\n    is_a: association slot\n    required: false\n    domain: association\n    range: logical_interpretation_enum\n    exact_mappings:\n      - os:LogicalInterpretation\n\n  relation:\n    deprecated: true\n\n  negated:\n    is_a: association slot\n    range: boolean\n    description: >-\n      if set to true, then the association is negated i.e. is not true\n\n  has confidence level:\n    is_a: association slot\n    range: confidence level\n    description: >-\n      connects an association to a qualitative term denoting the level of confidence\n\n  has evidence:\n    is_a: association slot\n    range: evidence type\n    description: >-\n      connects an association to an instance of supporting evidence\n    exact_mappings:\n      - RO:0002558\n    multivalued: true\n\n  mechanism of action:\n    is_a: association slot\n    range: boolean\n    description: >-\n      a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes\n      the mechanism of action for a result.\n    exact_mappings:\n      - NCIT:C54680\n      - MI:2044\n      - LOINC:MTHU019741\n\n  knowledge source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which the knowledge expressed in an Association was\n      retrieved, directly or indirectly. This can be any resource through which the\n      knowledge passed on its way to its currently serialized form. In practice,\n      implementers should use one of the more specific subtypes of this generic property.\n    range: information resource\n    close_mappings:\n      - pav:providedBy\n\n  provided by:\n    is_a: node property\n    description: >-\n      The value in this node property represents the knowledge provider that created or assembled the\n      node and all of its attributes.  Used internally to represent how a particular node made its way into a\n      knowledge provider or graph.\n    multivalued: true\n\n  primary knowledge source:\n     is_a: knowledge source\n     description: >-\n       The most upstream source of the knowledge expressed in an Association that an\n       implementer can identify (may or may not be the 'original' source).\n     range: information resource\n     multivalued: false\n\n  original knowledge source:\n    deprecated: true\n\n  aggregator knowledge source:\n    is_a: knowledge source\n    description: >-\n      An intermediate aggregator resource from which knowledge expressed in an Association was\n      retrieved downstream of the original source, on its path to its current serialized form.\n    range: information resource\n    multivalued: true\n\n  supporting data source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which data was retrieved and subsequently used as\n      evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n\n  association type:\n    is_a: association slot\n    range: category type\n    deprecated: >-\n      This slot is deprecated in favor of 'category' slot.\n    deprecated_element_has_exact_replacement: category\n    description: >-\n      connects an association to the category of association (e.g. gene to phenotype)\n\n  chi squared statistic:\n    is_a: association slot\n    range: float\n    description: >-\n      represents the chi-squared statistic computed from observations\n    exact_mappings:\n      - STATO:0000030\n\n  p value:\n    is_a: association slot\n    range: float\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    exact_mappings:\n      - OBI:0000175\n      - NCIT:C44185\n      - EDAM-DATA:1669\n\n  interacting molecules category:\n    is_a: association slot\n    range: ontology class\n    exact_mappings:\n      - MI:1046\n    values_from:\n      - MI\n    examples:\n      - value: MI:1048\n        description: smallmolecule-protein\n\n  quantifier qualifier:\n    is_a: association slot\n    range: ontology class\n    description: >-\n      A measurable quantity for the object of the association\n    narrow_mappings:\n      # TODO: RTX contributed terms mapped here... May need review?\n      - LOINC:analyzes\n      - LOINC:measured_by\n      - LOINC:property_of\n      - SEMMEDDB:measures\n      - UMLS:measures\n\n  catalyst qualifier:\n    is_a: association slot\n    multivalued: true\n    range: macromolecular machine mixin\n    description: >-\n      a qualifier that connects an association between two causally connected\n      entities (for example, two chemical entities, or a chemical entity in\n      that changes location) and the gene product, gene, or complex that\n      enables or catalyzes the change.\n\n  expression site:\n    description: >-\n      location in which gene or protein expression takes place.\n      May be cell, tissue, or organ.\n    is_a: association slot\n    range: anatomical entity\n    examples:\n      - value: UBERON:0002037\n        description: cerebellum\n\n  stage qualifier:\n    description: >-\n      stage during which gene or protein expression of takes place.\n    is_a: association slot\n    range: life stage\n    # path: \"object/during\"\n    examples:\n      - value: UBERON:0000069\n        description: larval stage\n\n  phenotypic state:\n    description: >-\n      in experiments (e.g. gene expression) assaying diseased or unhealthy\n      tissue, the phenotypic state can be put here, e.g. MONDO ID.\n      For healthy tissues, use XXX.\n    is_a: association slot\n    range: disease or phenotypic feature\n\n  qualifiers:\n    singular_name: qualifier\n    description: >-\n      connects an association to qualifiers that modify or\n      qualify the meaning of that association\n    local_names:\n      ga4gh: annotation qualifier\n    is_a: association slot\n    multivalued: true\n    range: ontology class\n\n  frequency qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\n    is_a: association slot\n    range: frequency value\n\n  severity qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      how severe the phenotype is in the subject\n    is_a: association slot\n    range: severity value\n\n  sex qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state whether\n      the association is specific to a particular sex.\n    is_a: association slot\n    range: biological sex\n\n  onset qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      when the phenotype appears is in the subject\n    is_a: association slot\n    range: onset\n\n  clinical modifier qualifier:\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the Phenotypic abnormality subontology,\n      with respect to severity, laterality, age of onset, and other aspects\n    is_a: association slot\n    range: clinical modifier\n\n  sequence variant qualifier:\n    description: >-\n      a qualifier used in an association with the variant\n    is_a: association slot\n    range: sequence variant\n\n  publications:\n    singular_name: publication\n    description: >-\n      connects an association to publications supporting the association\n    is_a: association slot\n    multivalued: true\n    range: publication\n\n  associated environmental context:\n    is_a: association slot\n    description: >-\n      An attribute that can be applied to an association where the association holds between two entities\n      located or occurring in a particular environment. For example, two microbial taxa may interact in the context of\n      a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure.\n  # TODO: add examples of values for this property.\n      \n  sequence localization attribute:\n    is_a: association slot\n    domain: genomic sequence localization\n    description: >-\n      An attribute that can be applied to a genome sequence localization edge. These edges\n      connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used\n      to ascribe specific positional information and other metadata to the localization. In pragmatic terms\n      this can be thought of as columns in a GFF3 line.\n\n  interbase coordinate:\n    is_a: sequence localization attribute\n    aliases: ['zero-based', 'half-open', 'space-based']\n    description: >-\n      A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1.\n      This is applied to a sequence localization edge.\n    range: integer\n\n  start interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 0).\n    close_mappings:\n      - faldo:begin\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:end interbase coordinate\n\n  end interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity ends\n      on the chromosome or other entity to which it is located on.\n    close_mappings:\n      - faldo:end\n    annotations:\n      biolink:opposite_of:\n        tag: biolink:opposite_of\n        value: biolink:start interbase coordinate\n\n  start coordinate:\n    is_a: base coordinate\n    aliases: ['start']\n    description: >-\n      The position at which the subject genomic entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 1).\n    exact_mappings:\n      - gff3:start\n    close_mappings:\n      - faldo:begin\n\n  end coordinate:\n    is_a: base coordinate\n    aliases: ['end']\n    description: >-\n      The position at which the subject genomic entity ends\n      on the chromosome or other entity to which it is located on.\n    exact_mappings:\n      - gff3:end\n    close_mappings:\n      - faldo:end\n\n  genome build:\n    is_a: sequence localization attribute\n    description: >-\n      The version of the genome on which a feature is located.\n      For example, GRCh38 for Homo sapiens.\n    range: strand_enum\n    exact_mappings:\n      - gff3:strand\n\n  strand:\n    is_a: sequence localization attribute\n    description: >-\n      The strand on which a feature is located. Has a value of '+'\n      (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).\n    range: strand_enum\n    exact_mappings:\n      - gff3:strand\n\n  phase:\n    is_a: sequence localization attribute\n    domain: coding sequence\n    description: >-\n      The phase for a coding sequence entity. For example, phase of a\n      CDS as represented in a GFF3 with a value of 0, 1 or 2.\n    range: phase_enum\n    exact_mappings:\n      - gff3:phase\n\n  FDA approval status:\n    is_a: association slot\n    description: >-\n    range: FDA_approval_status_enum\n\n  supporting study metadata:\n    is_a: association slot\n    description: >-\n      Information about a study used to generate information used as evidence to support the knowledge expressed in an \n      Association. In practice, data creators should use one of the more specific subtypes of this property.\n    abstract: true\n\n  supporting study method type:\n    is_a: supporting study metadata\n    description: >- \n      A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of \n      experimental assay, or statistical calculation, or computational analysis).\n    range: uriorcurie\n\n  supporting study method description:\n    is_a: supporting study metadata\n    description: >-\n      A uri or curie pointing to information about the methodology used to generate data supporting an Association.\n    range: uriorcurie\n\n  supporting study size:\n    is_a: supporting study metadata\n    description: >- \n      The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a \n      clinical study).\n    range: integer\n\n  supporting study cohort:\n    is_a: supporting study metadata\n    description: >-\n      A description of a study population/cohort that was interrogated to provide evidence for the association \n      (e.g. the inclusion and exclusion criteria).\n    range: string\n\n  supporting study date range:\n    is_a: supporting study metadata\n    description: >- \n      The date range over which data was collected in a study that provided evidence for an Association.\n    range: string\n\n  supporting study context:\n    is_a: supporting study metadata\n    description: >-\n      A term or terms describing the experimental setting/context in which evidence supporting the Association was \n      generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue \n      type, disease, etc.).\n    range: string\n\n\nclasses:\n\n  ## ----------\n  ## ATTRIBUTES\n  ## ----------\n\n  ## Ontology Classes\n\n  ontology class:\n    mixin: true\n    slots:\n      - id\n    description: >-\n      a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in\n      a biolink compatible KG can be considered both instances of biolink classes, and\n      OWL classes in their own right. In general you should not need to use this class directly.\n      Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897),\n      use bl:BiologicalProcess as the type.\n    exact_mappings:\n      - owl:Class\n      - schema:Class\n    comments:\n      - >-\n         This is modeled as a mixin. 'ontology class' should not be the primary type of a\n         node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity\n         (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\n      - >-\n         Note that formally this is a metaclass. Instances of this class are instances in the graph,\n         but can be the object of 'type' edges. For example, if we had a node in the graph representing\n         a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample,\n         and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\n    see_also:\n      - https://github.com/biolink/biolink-model/issues/486\n    examples:\n      - value: UBERON:0000955\n        description: >-\n          the class 'brain' from the Uberon anatomy ontology\n    id_prefixes:\n      - MESH\n      - UMLS\n      - KEGG.BRITE ## br/ko number\n  \n  annotation:\n    description: >-\n      Biolink Model root class for entity annotations.\n    abstract: true\n\n  quantity value:\n    is_a: annotation\n    description: >-\n      A value of an attribute that is quantitative and measurable,\n      expressed as a combination of a unit and a numeric value\n    slots:\n      - has unit\n      - has numeric value\n\n  # Alignment attempted of the biolink:Attribute model\n  # to the proposed TRAPI Release 1.1 Attribute schema, i.e.\n  #\n  # attribute_name: \"assertionAuthoredBy\",\n  # attribute_type: SEPIO:0000130,\n  # value: \"ORCID:12345\",\n  # value_type: \"wd:Q51044\",\n  # value_type_name: \"ORCID ID\"\n  # url: https://orcid.org/12345\n  # source: ORCID\n\n  attribute:\n    is_a: named thing\n    mixins:\n      - ontology class\n    description: >-\n      A property or characteristic of an entity.\n      For example, an apple may have properties such as color, shape, age, crispiness.\n      An environmental sample may have attributes such as depth, lat, long, material.\n    slots:\n      - name                   # 'attribute_name'\n      - has attribute type     # 'attribute_type'\n      # 'value', 'value_type', 'value_type_name'\n      # extracted from either of the next two slots\n      - has quantitative value\n      - has qualitative value\n      - iri                    # 'url'\n      - source                 # 'source'\n    slot_usage:\n      name:\n        description: >-\n          The human-readable 'attribute name' can be set to a string which reflects its context of\n          interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default\n          to the name associated with the 'has attribute type' slot ontology term.\n    id_prefixes:\n      - EDAM-DATA\n      - EDAM-FORMAT\n      - EDAM-OPERATION\n      - EDAM-TOPIC\n    exact_mappings:\n      - SIO:000614\n    in_subset:\n      - samples\n\n  chemical role:\n    is_a: attribute\n\n  biological sex:\n    is_a: attribute\n    exact_mappings:\n     - PATO:0000047\n\n  phenotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the phenotypic sex of the individual,\n      based upon the reproductive organs present.\n    exact_mappings:\n     - PATO:0001894\n\n  genotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the genotypic sex of the individual,\n      based upon genotypic composition of sex chromosomes.\n    exact_mappings:\n     - PATO:0020000\n\n  severity value:\n    is_a: attribute\n    description: >-\n      describes the severity of a phenotypic feature or disease\n\n  relationship quantifier:\n    mixin: true\n\n  sensitivity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  specificity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  pathognomonicity quantifier:\n    is_a: specificity quantifier\n    description: >-\n      A relationship quantifier between a variant or symptom and a disease, which is\n      high when the presence of the feature implies the existence of the disease\n    mixin: true\n\n  frequency quantifier:\n    is_a: relationship quantifier\n    mixin: true\n    slots:\n      - has count\n      - has total\n      - has quotient\n      - has percentage\n\n  chemical or drug or treatment:\n    mixin: true\n\n  ## ------\n  ## THINGS\n  ## ------\n\n  entity:\n    description: >-\n      Root Biolink Model class for all things and informational relationships, real or imagined.\n    abstract: true\n    slots:\n      - id\n      - iri\n      - category\n      - type   # rdf:type\n      - name\n      - description\n      - source\n      - has attribute\n      # evidence code(s)?\n\n  named thing:\n    is_a: entity\n    description: \"a databased entity or concept/class\"\n    slots:\n      - provided by\n      - xref\n    slot_usage:\n      category:\n        required: true\n        pattern: '^biolink:\\d+$'\n    exact_mappings:\n      - BFO:0000001\n      - WIKIDATA:Q35120\n      # UMLS Semantic Group \"Objects\"\n      - UMLSSG:OBJC\n      # Entity\n      - STY:T071\n      - dcid:Thing\n\n  relationship type:\n    is_a: ontology class\n    description: >-\n      An OWL property used as an edge label\n\n  gene ontology class:\n    deprecated: true\n\n  unclassified ontology class:\n    deprecated: true\n\n  taxonomic rank:\n    description: >-\n      A descriptor for the rank within a taxonomic classification.\n      Example instance: TAXRANK:0000017 (kingdom)\n    is_a: ontology class\n    id_prefixes:\n      - TAXRANK\n    mappings:\n      - WIKIDATA:Q427626\n\n  organism taxon:\n    aliases: ['taxon', 'taxonomic classification']\n    description: >-\n      A classification of a set of organisms. Example instances:\n      NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria).\n      Can also be used to represent strains or subspecies.\n    is_a: named thing\n    slot_usage:\n      has taxonomic rank:\n        range: taxonomic rank\n        multivalued: false\n        mappings:\n          - WIKIDATA:P105\n    values_from:\n      - NCBITaxon\n    exact_mappings:\n      - WIKIDATA:Q16521\n      - STY:T001\n      - bioschemas:Taxon\n    narrow_mappings:\n      - dcid:BiologicalSpecies\n    id_prefixes:\n      - NCBITaxon\n      - MESH\n    in_subset:\n      - model_organism_database\n  \n  ## Temporal Entities\n  \n  event:\n    is_a: named thing\n    description: >-\n      Something that happens at a given place and time.\n    exact_mappings:\n      - NCIT:C25499\n      # UMLS \"Event\"\n      - STY:T051\n\n  ## Administrative Entities\n\n  administrative entity:\n    is_a: named thing\n    abstract: true\n\n  agent:\n    is_a: administrative entity\n    aliases: ['group']\n    description: >-\n      person, group, organization or project that provides\n      a piece of information (i.e. a knowledge association)\n    slots:\n      - affiliation\n      - address\n    exact_mappings:\n      - prov:Agent\n      - dct:Agent\n    narrow_mappings:\n      # Organization\n      - UMLSSG:ORGA\n      - STY:T092\n      # Health Care Related Organization\n      - STY:T093\n      # Professional Society\n      - STY:T094\n      # Self-help or Relief Organization\n      - STY:T095\n      # Group\n      - STY:T096\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Different classes of agents have distinct preferred identifiers.\n          For publishers, use the ISBN publisher code.\n          See https://grp.isbn-international.org/ for publisher code lookups.\n          For editors, authors and  individual providers, use the individual's\n          ORCID if available; Otherwise, a ScopusID, ResearchID or\n          Google Scholar ID ('GSID') may be used if the author ORCID is unknown.\n          Institutional agents could be identified by an\n          International Standard Name Identifier ('ISNI') code.\n        values_from:\n          # CURIE space for publishers\n          - isbn\n          # CURIE space for authors\n          - ORCID\n          - ScopusID\n          - ResearchID\n          - GSID\n          # Institutional agents\n          - isni\n      name:\n        description: >-\n          it is recommended that an author's 'name' property\n          be formatted as \"surname, firstname initial.\"\n    id_prefixes:\n      - isbn\n      - ORCID\n      - ScopusID\n      - ResearchID\n      - GSID\n      - isni\n\n  ## General Information Entities\n\n  information content entity:\n    aliases: ['information', 'information artefact', 'information entity']\n    abstract: true\n    is_a: named thing\n    description: >-\n      a piece of information that typically describes\n      some topic of discourse or is used as support.\n    slots:\n      - license\n      - rights\n      - format\n      - creation date\n    id_prefixes:\n      - doi\n    exact_mappings:\n      - IAO:0000030\n    narrow_mappings:\n      # UMLS Semantic Group \"Concepts & Ideas\"\n      - UMLSSG:CONC\n      # Conceptual Entity\n      - STY:T077\n      # Idea or Concept\n      - STY:T078\n      # Temporal Concept\n      - STY:T079\n      # Qualitative Concept\n      - STY:T080\n      # Quantitative Concept\n      - STY:T081\n      # Spatial Concept\n      - STY:T082\n      # Regulation or Law\n      - STY:T089\n      # Group Attribute\n      - STY:T102\n      # Functional Concept\n      - STY:T169\n      # Language\n      - STY:T171\n      # Classification\n      - STY:T185\n\n  dataset:\n    description: >-\n      an item that refers to a collection of data from a data source.\n    is_a: information content entity\n    exact_mappings:\n      - IAO:0000100\n      - dctypes:Dataset\n      - schema:dataset\n      - dcid:Dataset\n\n  dataset distribution:\n    is_a: information content entity\n    description: >-\n      an item that holds distribution level information about a dataset.\n    slots:\n      - distribution download url\n    exact_mappings:\n      - dcat:Distribution\n\n  dataset version:\n    description: >-\n      an item that holds version level information about a dataset.\n    is_a: information content entity\n    slots:\n      - has dataset\n      - ingest date\n      - has distribution\n\n  dataset summary:\n    description: >-\n      an item that holds summary level information about a dataset.\n    is_a: information content entity\n    slots:\n      - source web page\n      - source logo\n\n  confidence level:\n    is_a: information content entity\n    description: >-\n      Level of confidence in a statement\n    values_from:\n      - cio\n    exact_mappings:\n      - CIO:0000028\n      # statement confidence\n      - SEPIO:0000187\n    close_mappings:\n      # assertion confidence levels\n      - SEPIO:0000167\n\n  evidence type:\n    is_a: information content entity\n    aliases: ['evidence code']\n    description: >-\n      Class of evidence that supports an association\n    values_from:\n      - eco\n    exact_mappings:\n      - ECO:0000000\n\n  information resource:\n    is_a: information content entity\n    aliases: ['knowledgebase']\n    description: >-\n      A database or knowledgebase and its supporting ecosystem of interfaces \n      and services that deliver content to consumers (e.g. web portals, APIs, \n      query endpoints, streaming services, data downloads, etc.).\n      A single Information Resource by this definition may span many different datasets or\n      databases, and include many access endpoints and user\n      interfaces. Information Resources include project-specific resources\n      such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.\n    in_subset:\n        - translator_minimal      \n\n\n  ## Publications\n\n  # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies\n  publication:\n    is_a: information content entity\n    description: >-\n      Any published piece of information. Can refer to a whole publication,\n      its encompassing publication (i.e. journal or book) or to a part of a\n      publication, if of significant knowledge scope (e.g. a figure, figure\n      legend, or section highlighted by NLP). The scope is intended to be\n      general and include information published on the web, as well as printed\n      materials, either directly or in one of the Publication Biolink\n      category subclasses.\n    slots:\n      - authors\n      - pages\n      - summary\n      - keywords\n      - mesh terms\n      - xref\n    # In addition to embedded slots, instances of 'contributor association'\n    # may be used to more extensively document publisher, editor and author details\n    slot_usage:\n      id:\n        description: >-\n          Different kinds of publication subtypes will have different preferred\n          identifiers (curies when feasible). Precedence of identifiers for\n          scientific articles is as follows: PMID if available; DOI if not; actual\n          alternate CURIE otherwise. Enclosing publications (i.e. referenced by\n          'published in' node property) such as books and journals, should have\n          industry-standard identifier such as from ISBN and ISSN.\n      name:\n        description: >-\n          the 'title' of the publication is generally recorded in the 'name'\n          property (inherited from NamedThing). The field name 'title' is now also\n          tagged as an acceptable alias for the node property 'name' (just in case).\n      type:\n        slot_uri: dct:type\n        required: true\n        description: >-\n          Ontology term for publication type may be drawn from\n          Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),\n          FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),\n          the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),\n          the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres\n          (http://vocabularies.coar-repositories.org/documentation/resource_types/),\n          Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or\n          equivalent publication type ontology. When a given publication type ontology term\n          is used within a given knowledge graph, then the CURIE identified term must be\n          documented in the graph as a concept node of biolink:category biolink:OntologyClass.\n        values_from:  # Not sure which takes precedence, if any...\n          - dctypes\n          - fabio\n          - MESH_PUB\n          - COAR_RESOURCE\n          - WIKIDATA\n      pages:\n        multivalued: true\n        description: >-\n          When a 2-tuple of page numbers are provided, they represent\n          the start and end page of the publication within its parent publication context.\n          For books, this may be set to the total number of pages of the book.\n    exact_mappings:\n      - IAO:0000311\n    narrow_mappings:\n      - IAO:0000013\n      # UMLS Semantic Type \"Intellectual Product\"\n      - STY:T170\n    id_prefixes:\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book:\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Books should have industry-standard identifier such as from ISBN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'book'.\n    id_prefixes:\n      - isbn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book chapter:\n    is_a: publication\n    slots:\n      - published in\n      - volume\n      - chapter\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent book containing the chapter\n          should have industry-standard identifier from ISBN.\n    in_subset:\n      - model_organism_database\n\n  serial:\n    aliases: ['journal']\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slots:\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Serials (journals) should have industry-standard identifier such as from ISSN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'serial' or 'journal'.\n    id_prefixes:\n      - issn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  article:\n    is_a: publication\n    slots:\n      - published in\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent serial containing the article should\n          have industry-standard identifier from ISSN.\n      iso abbreviation:\n        description: >-\n          Optional value, if used locally as a convenience, is set\n          to the iso abbreviation of the 'published in' parent.\n    id_prefixes:\n      # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces\n      - PMID\n    in_subset:\n      - model_organism_database\n\n  ## Top Level Abstractions of Material & Process Entities\n\n  physical essence or occurrent:\n    description: >-\n      Either a physical or processual entity.\n    mixin: true\n\n\n  physical essence:\n    description: >-\n      Semantic mixin concept.  Pertains to entities that have\n      physical properties such as mass, volume, or charge.\n    is_a: physical essence or occurrent\n    mixin: true\n\n  physical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n    description: >-\n      An entity that has material reality (a.k.a. physical essence).\n    exact_mappings:\n      # Physical Object\n      - STY:T072\n    narrow_mappings:\n      # Manufactured Object\n      - STY:T073\n\n  occurrent:\n    description: >-\n      A processual entity.\n    # biolink:Occurrent is most consistently used as a mixin thus it should\n    # be declared as such and cannot inherit from the non-mixin biolink:NamedThing\n    is_a: physical essence or occurrent\n    mixin: true\n    exact_mappings:\n      - BFO:0000003\n\n  activity and behavior:\n    is_a: occurrent\n    mixin: true\n    description: >-\n      Activity or behavior of any independent integral living,\n      organization or mechanical actor in the world\n    exact_mappings:\n      # Activities & Behaviors\n      - UMLSSG:ACTI\n\n  activity:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      An activity is something that occurs over a period of time and acts upon\n      or with entities; it may include consuming, processing, transforming,\n      modifying, relocating, using, or generating entities.\n    exact_mappings:\n      - prov:Activity\n      - NCIT:C43431\n      # Activity\n      - STY:T052\n    narrow_mappings:\n      # Daily or Recreational Activity\n      - STY:T056\n      # Occupational Activity\n      - STY:T057\n      # Governmental or Regulatory Activity\n      - STY:T064\n      # Machine Activity\n      - STY:T066\n      # Research Activity\n      - STY:T062\n      # Educational Activity\n      - STY:T065\n      # Health Care Activity\n      - STY:T058\n\n  procedure:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      A series of actions conducted in a certain order or manner\n    exact_mappings:\n      # Procedures\n      - UMLSSG:PROC\n      - dcid:MedicalProcedure\n    narrow_mappings:\n      # Laboratory Procedure\n      - STY:T059\n      # Diagnostic Procedure\n      - STY:T060\n      # Therapeutic or Preventive Procedure\n      - STY:T061\n      # Molecular Biology Research Technique\n      - STY:T063\n    id_prefixes:\n      - CPT\n      \n  phenomenon:\n    is_a: named thing\n    mixins:\n      - occurrent\n    description: >-\n      a fact or situation that is observed to exist or happen,\n      especially one whose cause or explanation is in question\n    broad_mappings:\n      # the inclusion of 'process' in the definition of these\n      # terms broadens them, relative to 'phenomenon'\n      # Phenomenon or Process\n      - STY:T067\n      # Human-caused Phenomenon or Process\n      - STY:T068\n      # Natural Phenomenon or Process\n      - STY:T070\n    exact_mappings:\n      # Phenomena\n      - UMLSSG:PHEN\n    narrow_mappings:\n      # Laboratory or Test Result\n      - STY:T034\n      # Biologic Function\n      - STY:T038\n      # Environmental Effect of Humans\n      - STY:T069\n\n  device:\n    is_a: named thing\n    description: >-\n      A thing made or adapted for a particular purpose, especially\n      a piece of mechanical or electronic equipment\n    narrow_mappings:\n      # Devices\n      - UMLSSG:DEVI\n      # Medical Device\n      - STY:T074\n      # Research Device\n      - STY:T075\n      # Drug Delivery Device\n      - STY:T203\n      # Biomedical or Dental Material\n      - STY:T122\n\n  ## Scientific Studies\n\n  study population:\n    is_a: population of individual organisms\n    description: >-\n      A group of people banded together or treated as a group as participants in a research study.\n    close_mappings:\n      - WIKIDATA:Q7229825\n\n  subject of investigation:\n    mixin: true\n    description: >-\n      An entity that has the role of being studied in an investigation, study, or experiment\n\n  material sample:\n    aliases: ['biospecimen', 'sample', 'biosample', 'physical sample']\n    is_a: physical entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A sample is a limited quantity of something (e.g. an individual or set of individuals\n      from a population, or a portion of a substance) to be used for testing, analysis,\n      inspection, investigation, demonstration, or trial use. [SIO]\n    exact_mappings:\n      - OBI:0000747\n      - SIO:001050\n    id_prefixes:\n      - BIOSAMPLE\n      - GOLD.META\n\n  ## Earth Sciences\n\n  planetary entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists at the level of the whole planet\n\n  environmental process:\n    is_a: planetary entity\n    mixins:\n      - occurrent\n    exact_mappings:\n      - ENVO:02500000\n\n  environmental feature:\n    is_a: planetary entity\n    exact_mappings:\n      - ENVO:01000254\n\n  geographic location:\n    is_a: planetary entity\n    description: >-\n      a location that can be described in lat/long coordinates\n    slots:\n      - latitude\n      - longitude\n    exact_mappings:\n      # Geographic Areas\n      - UMLSSG:GEOG\n      # Geographic Area\n      - STY:T083\n\n  geographic location at time:\n    is_a: geographic location\n    description: >-\n      a location that can be described in lat/long coordinates, for a particular time\n    slots:\n      - timepoint\n\n  ## Biological Sciences\n\n  thing with taxon:\n    mixin: true\n    description: >-\n      A mixin that can be used on any entity that can be taxonomically classified.\n      This includes individual organisms; genes, their products and other molecular\n      entities; body parts; biological processes\n    slots:\n      - in taxon\n\n  biological entity:\n    is_a: named thing\n    aliases: ['bioentity']\n    abstract: true\n    mixins:\n      - thing with taxon\n    narrow_mappings:\n      - WIKIDATA:Q28845870\n      # UMLS Semantic Type \"Experimental Model of Disease\"\n      - STY:T050\n      # SIO term is 'biological entity' but less inclusive than the Biolink scope\n      - SIO:010046\n\n  genomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - STY:T028   # Gene or Genome\n      - GENO:0000897  # Genomic Entity\n\n  molecular entity:\n    is_a: chemical entity\n    description: >-\n      A molecular entity is a chemical entity composed of individual or\n      covalently bonded atoms.\n    slots:\n      - is metabolite\n    narrow_mappings:\n      - STY:T088 # Carbohydrate\n      - STY:T085 # Molecular Sequence\n      - CHEBI:23367 # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical,\n                    # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.\n      - bioschemas:MolecularEntity\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  chemical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n      - chemical or drug or treatment # issue 701\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    description: >-\n      A chemical entity is a physical entity that pertains to chemistry or\n      biochemistry.\n    slots:\n      - trade name\n      - available from\n      - max tolerated dose\n      - is toxic\n      - has chemical role\n    exact_mappings:\n      - CHEBI:24431\n      - SIO:010004 # Chemical entity\n      - WIKIDATA:Q79529 # Chemical substance\n      - STY:T103 # Chemical\n    narrow_mappings:\n      - WIKIDATA:Q43460564\n      - STY:T129 # (imft, full name: Immunologic Factor\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - UNII\n      - MESH\n      - CAS #CAS numbers are given for things like plant extracts as well.\n      - UMLS\n      - ncats.drug\n\n  chemical substance:\n    deprecated: >-\n      This class is deprecated in favor of 'small molecule.'\n\n  small molecule:\n    is_a: molecular entity\n    aliases: [ 'chemical substance']\n    description: >-\n        A small molecule entity is a molecular entity characterized by availability\n        in small-molecule databases of SMILES, InChI, IUPAC, or other\n        unambiguous representation of its precise chemical structure; for\n        convenience of representation, any valid chemical representation is\n        included, even if it is not strictly molecular (e.g., sodium ion).\n    narrow_mappings:\n      - STY:T196 # Element, Ion, or Isotope\n      - CHEBI:59999\n      - bioschemas:ChemicalSubstance\n      - STY:T123 #(bacs, full name: Biologically Active Substance)\n      - STY:T131 #(hops, full name: Hazardous or Poisonous Substance)\n      - STY:T125 #(horm, full name: Hormone)\n      - STY:T197 #(inch, full name: Inorganic Chemical)\n      - STY:T109 #(orch, full name: Organic Chemical)\n      - STY:T118 #(carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files)\n      - STY:T111 #(eico, full name: Eicosanoid) - same note as above\n      - STY:T119 #(lipd, full name: Lipid) - same note as above\n      - STY:T124 #(nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above\n      - STY:T115 #(opco, full name: Organophosphorus Compound) - same note as above\n      - STY:T110 #(strd, full name: Steroid) - same note as above\n      - STY:T127 # vitamin\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - BIGG.METABOLITE\n      - UMLS\n      - foodb.compound\n    slot_usage:\n      id:\n        examples:\n          - value: CHEBI:29101\n            description: sodium ion\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n\n  chemical mixture:\n    is_a: chemical entity\n    description: >-\n      A chemical mixture is a chemical entity composed of two or more\n      molecular entities.\n    slots:\n      - is supplement\n      - highest FDA approval status\n      - drug regulatory status world wide\n      - routes of delivery\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n    close_mappings:\n      - dcid:ChemicalCompound\n    narrow_mappings:\n      - NCIT:C20401 # monoclonal antibody\n      - SNOMEDCT:49616005 # monoclonal antibody (substance)\n\n  nucleic acid entity:\n    is_a: molecular entity\n    description: >-\n      A nucleic acid entity is a molecular entity characterized by\n      availability in gene databases of nucleotide-based sequence\n      representations of its precise sequence; for convenience of\n      representation, partial sequences of various kinds are included.\n    aliases: [ 'sequence feature', 'genomic entity' ]\n    mixins:\n      - genomic entity\n      - thing with taxon\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000110\n    narrow_mappings:\n      - STY:T086   # Nucleotide Sequence\n      - STY:T114   # Nucleic Acid, Nucleoside, or Nucleotide\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  # G number\n      - KEGG.ENVIRON # E number\n\n  molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A molecular mixture is a chemical mixture composed of two or more\n      molecular entities with known concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n      - ncats.drug\n\n  complex molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A complex molecular mixture is a chemical mixture composed of two or\n      more molecular entities with unknown concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  biological process or activity:\n    description: >-\n      Either an individual molecular activity, or a collection of\n      causally connected molecular activities in a biological system.\n    is_a: biological entity\n    mixins:\n      - occurrent\n      - ontology class\n    id_prefixes:\n      - GO\n      - REACT\n    slots:\n      - has input\n      - has output\n      - enabled by\n\n  molecular activity:\n    description: >-\n      An execution of a molecular function carried out by a\n      gene product or macromolecular complex.\n    is_a: biological process or activity\n    aliases: ['molecular function', 'molecular event', 'reaction']\n    mixins:\n      - occurrent\n      - ontology class\n    slot_usage:\n      has input:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the input for the reaction\n      has output:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the output for the reaction\n      enabled by:\n        range: macromolecular machine mixin\n        description: >-\n          The gene product, gene, or complex that catalyzes the reaction\n    exact_mappings:\n      - GO:0003674\n      # UMLS Semantic Type \"Molecular Function\"\n      - STY:T044\n    id_prefixes:\n      - GO\n      - REACT\n      - RHEA\n      - metacyc.reaction\n      - EC\n      - TCDB\n      - KEGG.REACTION  ## R number\n      - KEGG.RCLASS    ## RC number\n      - KEGG.ENZYME    ## EC number\n      - KEGG.ORTHOLOGY ## in particular for gut microbiome use case in issue #888\n      - UMLS\n      - BIGG.REACTION\n      - SEED.REACTION\n      - METANETX.REACTION\n\n  biological process:\n    is_a: biological process or activity\n    mixins:\n      - occurrent\n      - ontology class\n    description: >-\n      One or more causally connected executions of molecular functions\n    exact_mappings:\n      - GO:0008150\n      - SIO:000006\n      - WIKIDATA:Q2996394\n    broad_mappings:\n      - WIKIDATA:P682\n    id_prefixes:\n      - GO\n      - REACT\n      - metacyc.reaction\n      - KEGG.MODULE ## M number\n\n  pathway:\n    is_a: biological process\n    mixins:\n      - ontology class\n    exact_mappings:\n      - PW:0000001\n      - WIKIDATA:Q4915012\n    narrow_mappings:\n      - SIO:010526\n      - GO:0007165\n    id_prefixes:\n      - GO\n      - REACT\n      - KEGG\n      - SMPDB\n      - MSigDB\n      - PHARMGKB.PATHWAYS\n      - WIKIPATHWAYS\n      - FB  # FlyBase FBgg*\n      - PANTHER.PATHWAY\n      - KEGG.PATHWAY\n      - ncats.bioplanet\n\n  physiological process:\n    aliases: ['physiology']\n    is_a: biological process\n    mixins:\n      - ontology class\n    close_mappings:\n    exact_mappings:\n      # Physiologic Function\n      - STY:T039\n      - WIKIDATA:Q30892994\n    narrow_mappings:\n      # Organism Function\n      - STY:T040\n      # Organ or Tissue Function\n      - STY:T042\n      # Cell Function\n      - STY:T043\n      # Genetic Function\n      - STY:T045\n    id_prefixes:\n      - GO\n      - REACT\n\n  behavior:\n    is_a: biological process\n    mixins:\n      - ontology class\n      - activity and behavior\n    exact_mappings:\n      - GO:0007610\n      # Behavior\n      - STY:T053\n    narrow_mappings:\n      # Mental Process\n      - STY:T041\n      # Social Behavior\n      - STY:T054\n      # Individual Behavior\n      - STY:T055\n\n  ## (Bio)chemistry\n\n  processed material:\n    is_a: chemical mixture\n    description: >-\n      A chemical entity (often a mixture) processed\n      for consumption for nutritional, medical or technical use.\n      Is a material entity that is created or changed during material processing.\n    exact_mappings:\n      - OBI:0000047\n    id_prefixes:\n      - UMLS\n\n  drug:\n    is_a: molecular mixture\n    mixins:\n      - chemical or drug or treatment\n      - ontology class\n    description: >-\n      A substance intended for use in the diagnosis, cure,\n      mitigation, treatment, or prevention of disease\n    comments:\n      - The CHEBI ID represents a role rather than a substance\n    broad_mappings:\n      # Pharmacologic Substance: Any natural, endogenously-derived,\n      # synthetic or semi-synthetic compound with pharmacologic activity.\n      - STY:T121\n    exact_mappings:\n      - WIKIDATA:Q12140\n      - CHEBI:23888\n      # UMLS Semantic Type \"Clinical Drug\"\n      - STY:T200\n      - dcid:Drug\n    narrow_mappings:\n      # Antibiotic\n      - STY:T195\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n\n  ## Food\n\n  environmental food contaminant:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:78299\n\n  food additive:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:64047\n\n  nutrient:\n    deprecated: true\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:33284\n\n  macronutrient:\n    deprecated: true\n    is_a: nutrient\n    related_mappings:\n      # substance role\n      - CHEBI:33937\n\n  micronutrient:\n    deprecated: true\n    is_a: nutrient\n    related_mappings:\n      # substance role\n      - CHEBI:27027\n\n  vitamin:\n    deprecated: true\n    is_a: micronutrient\n    related_mappings:\n      # substance role\n      - CHEBI:33229\n      # Vitamin\n      - STY:T127\n\n  food:\n    is_a: chemical mixture\n    description: >-\n      A substance consumed by a living organism as a source of nutrition\n    id_prefixes:\n      - foodb.food\n      - FOODON\n      - UMLS\n      - NCIT\n    exact_mappings:\n      # Food\n      - STY:T168\n\n  ## Biology and Biomedical Sciences\n\n  ## Biological Attributes\n\n  organism attribute:\n    is_a: attribute\n    description: >-\n      describes a characteristic of an organismal entity.\n    exact_mappings:\n      # Organism Attribute\n      - STY:T032\n\n  phenotypic quality:\n    aliases: ['phenotypic properties']\n    is_a: organism attribute\n    description: >-\n      A property of a phenotype\n    examples:\n      - value: weight\n\n    mappings:\n      - PATO:0000001\n\n  inheritance:\n    is_a: organism attribute\n    description: >-\n      The pattern or 'mode' in which a particular genetic trait or disorder is passed from one\n      generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\n    exact_mappings:\n      - HP:0000005\n      - GENO:0000141\n      - NCIT:C45827\n\n  ## Biological Entities\n\n  organismal entity:\n    description: >-\n      A named entity that is either a part of an organism, a whole organism,\n      population or clade of organisms, excluding chemical entities\n    abstract: true\n    is_a: biological entity\n    slot_usage:\n      has attribute:\n        description: >-\n          may often be an organism attribute\n    exact_mappings:\n      - WIKIDATA:Q7239\n      # UMLS Semantic Group \"Living Beings\"\n      # Several of the associated semantic types here are probably not\n      # that relevant to the Biolink world but we keep them here for now.\n      - UMLSSG:LIVB\n\n  life stage:\n    is_a: organismal entity\n    description: >-\n      A stage of development or growth of an organism,\n      including post-natal adult stages\n    exact_mappings:\n      - UBERON:0000105\n    narrow_mappings:\n      # constrained to human life cycles\n      - HsapDv:0000000\n    in_subset:\n      - model_organism_database\n    id_prefixes:\n      - HsapDv\n      - MmusDv\n      - ZFS\n      - FBdv\n      - WBls\n      - UBERON\n\n  individual organism:\n    aliases: ['organism']\n    description: >-\n      An instance of an organism. For example, Richard Nixon,\n      Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576\n    is_a: organismal entity\n    exact_mappings:\n      - SIO:010000\n      # Organism\n      - STY:T001\n    narrow_mappings:\n      # Wikidata considers its definition of 'individual' to be constrained to human persons?\n      - WIKIDATA:Q795052\n      - foaf:Person\n    id_prefixes:\n      - ORCID\n\n  population of individual organisms:\n    description: >-\n      A collection of individuals from the same taxonomic class\n      distinguished by one or more characteristics.  Characteristics can\n      include, but are not limited to, shared geographic location, genetics,\n      phenotypes.\n    local_names:\n      ga4gh: population\n    is_a: organismal entity\n    exact_mappings:\n      - PCO:0000001\n      - SIO:001061\n      # UMLS Semantic Type \"Population Group\"\n      - STY:T098\n      - OBI:0000181\n    id_prefixes:\n      - HANCESTRO\n    in_subset:\n      - model_organism_database\n\n  disease or phenotypic feature:\n    aliases: ['phenome']\n    is_a: biological entity\n    description: >-\n      Either one of a disease or an individual phenotypic feature.\n      Some knowledge resources such as Monarch treat these as\n      distinct, others such as MESH conflate.\n    union_of:\n      - disease\n      - phenotypic feature\n    narrow_mappings:\n      # UMLS Semantic Type \"Finding\" - more specialized use of 'disease or phenotypic feature'\n      - STY:T033\n\n  disease:\n    aliases: ['condition', 'disorder', 'medical condition']\n    is_a: disease or phenotypic feature\n    exact_mappings:\n      - MONDO:0000001\n      - DOID:4\n      - NCIT:C2991\n      - WIKIDATA:Q12136\n      - SIO:010299\n      # UMLS Semantic Group \"Disorders\"\n      - UMLSSG:DISO\n      # Disease or Syndrome\n      - STY:T047\n      - dcid:Disease\n    narrow_mappings:\n      # Congenital Abnormality\n      - STY:T019\n      # Acquired Abnormality\n      - STY:T020\n      # Mental or Behavioral Dysfunction\n      - STY:T048\n      # Cell or Molecular Dysfunction\n      - STY:T049\n      # Anatomical Abnormality\n      - STY:T190\n      # Neoplastic Process\n      - STY:T191\n      # disease susceptibility\n      - MONDO:0042489\n    id_prefixes:\n      - MONDO\n      - DOID\n      - OMIM\n      - OMIM.PS\n      - ORPHANET\n      - EFO\n      - UMLS\n      - MESH\n      - MEDDRA\n      - NCIT\n      - SNOMEDCT\n      - medgen\n      - ICD10\n      - ICD9\n      - KEGG.DISEASE ## H number\n      - HP\n      - MP\n    in_subset:\n      - model_organism_database\n\n  phenotypic feature:\n    aliases: ['sign', 'symptom', 'phenotype', 'trait', 'endophenotype']\n    is_a: disease or phenotypic feature\n    description: >-\n      A combination of entity and quality that makes up a phenotyping statement.\n    examples:\n      - value: MP:0001262\n        description: decreased body weight\n    exact_mappings:\n      - UPHENO:0001001\n      - SIO:010056\n      - WIKIDATA:Q104053\n    narrow_mappings:\n      # Sign or Symptom\n      - STY:T184\n      - WIKIDATA:Q169872\n      # presentation of a disease in clinical medicine\n      - WIKIDATA:Q25203551\n    id_prefixes:\n      - HP\n      - EFO\n      - NCIT\n      - UMLS\n      - MEDDRA\n      - MP\n      - ZP\n      - UPHENO\n      - APO\n      - FBcv\n      - WBPhenotype\n      - SNOMEDCT\n      - MESH\n      - XPO\n      - FYPO\n      - TO\n    in_subset:\n      - model_organism_database\n\n  behavioral feature:\n    description: >-\n      A phenotypic feature which is behavioral in nature.\n    is_a: phenotypic feature\n    exact_mappings:\n      - NBO:0000243\n\n  anatomical entity:\n    is_a: organismal entity\n    mixins:\n      - physical essence\n    description: >-\n      A subcellular location, cell type or gross anatomical part\n    exact_mappings:\n      - UBERON:0001062\n      - WIKIDATA:Q4936952\n      # UMLS Semantic Group \"Anatomy\"\n      - UMLSSG:ANAT\n      # UMLS Semantic Type \"Anatomical Structure\"\n      - STY:T017\n    id_prefixes:\n      - UBERON\n      - GO\n      - CL\n      - UMLS\n      - MESH\n      - NCIT\n      - EMAPA\n      - ZFA\n      - FBbt\n      - WBbt\n    in_subset:\n      - model_organism_database\n\n  cellular component:\n    aliases: ['cell component','cell part']\n    is_a: anatomical entity\n    description: >-\n      A location in or around a cell\n    exact_mappings:\n      - GO:0005575\n      - SIO:001400\n      - WIKIDATA:Q5058355\n      # Cell Component\n      - STY:T026\n    broad_mappings:\n      - WIKIDATA:P681\n    id_prefixes:\n      - GO\n      - MESH\n      - UMLS\n      - NCIT\n      - SNOMEDCT\n      - CL\n      - UBERON\n\n  cell:\n    is_a: anatomical entity\n    exact_mappings:\n      - GO:0005623\n      - CL:0000000\n      - SIO:010001\n      - WIKIDATA:Q7868\n      # UMLS Semantic Type \"Cell\"\n      - STY:T025\n    id_prefixes:\n      - CL\n      - PO\n      - UMLS\n      - NCIT\n      - MESH\n      - UBERON\n      - SNOMEDCT\n\n  cell line:\n    is_a: organismal entity\n    exact_mappings:\n      - CLO:0000031\n    id_prefixes:\n      - CLO\n\n  gross anatomical structure:\n    aliases: ['tissue', 'organ']\n    is_a: anatomical entity\n    exact_mappings:\n      - UBERON:0010000\n      - WIKIDATA:Q4936952\n    narrow_mappings:\n      # UMLS Semantic Type \"Body Part, Organ, or Organ Component\"\n      - STY:T023\n      # UMLS Semantic Type \"Tissue\"\n      - STY:T024\n      # Embryonic Structure\n      - STY:T018\n    id_prefixes:\n      - UBERON\n      - UMLS\n      - MESH\n      - NCIT\n      - PO\n      - FAO\n      \n\n  ## entity mixins\n\n  chemical entity or gene or gene product:\n    description: >-\n      A union of chemical entities and children, and gene or gene product.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  chemical entity or protein or polypeptide:\n    description: >-\n      A union of chemical entities and children, and protein and polypeptide.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  macromolecular machine mixin:\n    description: >-\n      A union of gene locus, gene product, and macromolecular complex mixin. These are\n      the basic units of function in a cell. They either carry out individual\n      biological activities, or they encode molecules which do this.\n    mixin: true\n    slots:\n      - name\n    slot_usage:\n      name:\n        range: symbol type\n        description: >-\n          genes are typically designated by a short symbol and a full name.\n          We map the symbol to the default display name\n          and use an additional slot for full name\n\n  gene or gene product:\n    description: >-\n      A union of gene loci or gene products.\n      Frequently an identifier for one will be used as proxy for another\n    is_a: macromolecular machine mixin\n    mixin: true\n    id_prefixes:\n      - CHEMBL.TARGET\n      - IUPHAR.FAMILY\n\n  gene:\n    description: >-\n      A region (or regions) that includes all of the sequence elements\n      necessary to encode a functional transcript. A gene locus may include\n      regulatory regions, transcribed regions and/or other\n      functional sequence regions.\n    is_a: biological entity\n    mixins:\n      - gene or gene product\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    slots:\n      - symbol\n      - synonym\n      - xref\n    narrow_mappings:\n      - bioschemas:gene\n    broad_mappings:\n      - NCIT:C45822\n    exact_mappings:\n      - SO:0000704\n      - SIO:010035\n      - WIKIDATA:Q7187\n      - dcid:Gene\n    id_prefixes:\n      - NCBIGene\n      - ENSEMBL\n      - HGNC\n      - MGI\n      - ZFIN\n      - dictyBase\n      - WB\n      - WormBase # we have two prefixes here as wormbase supports WormBase:WBGene00000898\n                 # and alliancegenome.org and identifiers.org supports WB:WBGene00000898.\n      - FB  # FlyBase FBgn*\n      - RGD\n      - SGD\n      - PomBase\n      - OMIM\n      - KEGG.GENE ## org:gene\n      - UMLS\n      - Xenbase\n      - AspGD\n      # - IUPHAR\n    in_subset:\n      - model_organism_database\n\n  gene product mixin:\n    description: >-\n      The functional molecular product of a single gene locus.\n      Gene products are either proteins or functional RNA molecules.\n    is_a: gene or gene product\n    mixin: true\n    slots:\n      - synonym\n      - xref\n    exact_mappings:\n      - WIKIDATA:Q424689\n      - GENO:0000907\n      - NCIT:C26548\n    id_prefixes:\n      - UniProtKB\n      - gtpo\n      - PR\n\n  gene product isoform mixin:\n    description: >-\n      This is an abstract class that can be mixed in with different kinds of\n      gene products to indicate that the gene product is intended to represent\n      a specific isoform rather than a canonical or reference or generic\n      product. The designation of canonical or reference may be arbitrary,\n      or it may represent the superclass of all isoforms.\n    is_a: gene product mixin\n    mixin: true\n\n  macromolecular complex mixin:\n    description: >-\n      A stable assembly of two or more macromolecules, i.e. proteins,\n      nucleic acids, carbohydrates or lipids, in which at least one\n      component is a protein and the constituent parts function together.\n    is_a: macromolecular machine mixin\n    mixin: true\n    exact_mappings:\n      - GO:0032991\n      - WIKIDATA:Q22325163\n    id_prefixes:\n      - INTACT\n      - GO\n      - PR\n      - REACT\n    in_subset:\n      - model_organism_database\n\n  ## Genomic Classes\n\n  genome:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A genome is the sum of genetic material within a cell or virion.\n    exact_mappings:\n      - SO:0001026\n      - SIO:000984\n      - WIKIDATA:Q7020\n    close_mappings:\n      - dcid:GenomeAssemblyUnit\n    in_subset:\n      - model_organism_database\n\n  exon:\n    is_a: nucleic acid entity\n    description: >-\n      A region of the transcript sequence within a gene which is not\n      removed from the primary RNA transcript by RNA splicing.\n    exact_mappings:\n      - SO:0000147\n      - SIO:010445\n      - WIKIDATA:Q373027\n\n  transcript:\n    is_a: nucleic acid entity\n    description: >-\n      An RNA synthesized on a DNA or RNA template by an RNA polymerase.\n    exact_mappings:\n      - SO:0000673\n      - SIO:010450\n      - WIKIDATA:Q7243183\n      - dcid:RNATranscript\n    id_prefixes:\n      - ENSEMBL # ENSEMBL:ENST for human\n      - FB      # FlyBase:FBtr\n    in_subset:\n      - model_organism_database\n\n  coding sequence:\n    is_a: nucleic acid entity\n    exact_mappings:\n      - SO:0000316\n      - SIO:001390\n\n  polypeptide:\n    aliases: [ 'amino acid entity' ]\n    is_a: biological entity\n    description: >-\n      A polypeptide is a molecular entity characterized by availability\n      in protein databases of amino-acid-based sequence representations\n      of its precise primary structure; for convenience of representation,\n      partial sequences of various kinds are included, even if they do not\n      represent a physical molecule.\n    mixins:\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n    in_subset:\n      - model_organism_database\n    narrow_mappings:\n      - SO:0000104 # polypeptide definde in SO conflates protein and polypeptide\n      # Amino Acid, Peptide, or Protein\n      - STY:T116\n      # Amino Acid Sequence\n      - STY:T087\n\n  protein:\n    description: >-\n      A gene product that is composed of a chain of amino acid sequences\n      and is produced by ribosome-mediated translation of mRNA\n    is_a: polypeptide\n    mixins:\n      - gene product mixin\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n      - MESH\n      - ncats.drug\n    broad_mappings:\n      - bioschemas:Protein\n    exact_mappings:\n      - PR:000000001\n      - SIO:010043\n      - WIKIDATA:Q8054\n    narrow_mappings:\n      # Enzyme\n      - STY:T126\n      # Receptor\n      - STY:T192\n\n  protein isoform:\n    aliases: ['proteoform']\n    is_a: protein\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or\n      reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - UniProtKB # UniProtKB:([A-Z0-9]+-\\d+)\n      - UNIPROT.ISOFORM \n      - PR\n      - ENSEMBL\n\n  protein domain:\n    is_a: biological entity\n    description: >-\n      A conserved part of protein sequence and (tertiary) structure that can evolve,\n      function, and exist independently of the rest of the protein chain.\n      Protein domains maintain their structure and function independently of the proteins in which they are found.\n      e.g. an SH3 domain.\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    exact_mappings:\n      - NCIT:C13379\n      - SIO:001379\n      - UMLS:C1514562\n\n  protein family:\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n\n  nucleic acid sequence motif:\n    aliases: ['consensus sequence']\n    is_a: biological entity\n    description: >-\n      A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have,\n      a biological significance. e.g. the TATA box promoter motif, transcription factor binding\n      consensus sequences.\n\n  RNA product:\n    is_a: transcript\n    mixins:\n      - gene product mixin\n    exact_mappings:\n      - CHEBI:33697\n      # This SIO term here also mapped to 'biolink:Transcript'; however,\n      # since this 'biolink:RNAProduct' relates more to the biochemical\n      # essence of RNA, then map the SIO term instead to 'biolink:Transcript'\n      # - SIO:010450\n      - WIKIDATA:Q11053\n    id_prefixes:\n      - RNACENTRAL\n\n  RNA product isoform:\n    is_a: RNA product\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or reference RNA\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - RNACENTRAL\n\n  noncoding RNA product:\n    is_a: RNA product\n    id_prefixes:\n      - RNACENTRAL\n      - NCBIGene\n      - ENSEMBL\n    exact_mappings:\n      - SO:0000655\n      - SIO:001235\n\n  microRNA:\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000276\n      - SIO:001397\n      - WIKIDATA:Q310899\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  siRNA:\n    aliases: ['small interfering RNA', 'RNAi']\n    description: >-\n      A small RNA molecule that is the product of a longer exogenous or\n      endogenous dsRNA, which is either a bimolecular duplex or very long\n      hairpin, processed (via the Dicer pathway) such that numerous siRNAs\n      accumulate from both strands of the dsRNA. SRNAs trigger the cleavage\n      of their target molecules.\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000646\n      - WIKIDATA:Q203221\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  gene grouping mixin:\n    description: >-\n      any grouping of multiple genes or gene products\n    mixin: true\n    slots:\n      - has gene or gene product\n\n  gene family:\n    aliases: ['orthogroup','protein family']\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      # These term definitions focus only on proteins;\n      # the 'biolink:GeneFamily' term would be more inclusive\n      # to describe gene loci, non-coding RNA, etc.\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    description: >-\n      any grouping of multiple genes or gene products related by common descent\n    id_prefixes:\n      - PANTHER.FAMILY\n      - HGNC.FAMILY\n      - FB       # FlyBase FBgg*\n      - interpro # note: may be better to introduce a protein domain/family\n      - CATH\n      - CDD\n      - HAMAP\n      - PFAM\n      - PIRSF\n      - PRINTS\n      - PRODOM\n      - PROSITE\n      - SMART\n      - SUPFAM\n      - TIGRFAM\n      - CATH.SUPERFAMILY\n      - RFAM ## RNAs only\n      - KEGG.ORTHOLOGY ## aka KEGG.KO: K number\n      - EGGNOG\n      - COG\n    in_subset:\n      - model_organism_database\n\n  zygosity:\n    is_a: attribute\n    exact_mappings:\n      - GENO:0000133\n\n  genotype:\n    is_a: biological entity\n    mixins:\n      - physical essence\n      - genomic entity\n      - ontology class\n    description: >-\n      An information content entity that describes a genome by specifying the\n      total variation in genomic sequence and/or gene expression, relative to\n      some established background\n    comments:\n      - Consider renaming as genotypic entity\n    slots:\n      - has zygosity\n    exact_mappings:\n      - GENO:0000536\n      - SIO:001079\n    id_prefixes:\n      - ZFIN\n      - FB   # FlyBase FBba*\n    in_subset:\n      - model_organism_database\n\n  haplotype:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A set of zero or more Alleles on a single instance of a Sequence[VMC]\n#    slots:\n#      - completeness\n    exact_mappings:\n      - GENO:0000871\n      - SO:0001024\n      - VMC:Haplotype\n\n  sequence variant:\n    aliases: ['allele']\n    local_names:\n      agr: allele\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      An allele that varies in its sequence from what is considered\n      the reference allele at that locus.\n    comments:\n      - This class is for modeling the specific state at a locus.\n        A single DBSNP rs ID could correspond to more than one sequence variants\n        (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\n    broad_mappings:\n      # slightly broader semantics than SO:0001059 - 'sequence alteration'\n      # describes a sequence feature that may have 1..* sequence alterations\n      - SO:0001060\n    exact_mappings:\n      - GENO:0000002\n      - WIKIDATA:Q15304597\n      - SIO:010277\n      - VMC:Allele\n      - SO:0001059\n    close_mappings:\n      - dcid:Allele\n    id_prefixes:\n      - CAID # ClinGen Allele Registry\n      - CLINVAR\n      - ClinVarVariant\n      - WIKIDATA\n      # - CIViC needs IRI mapping\n      - DBSNP\n      # - MYVARIANT_HG19 needs IRI mapping\n      # - MYVARIANT_HG38 needs IRI mapping\n      # - HGVS needs IRI mapping\n      - MGI\n      - ZFIN # ZFIN:ZDB-ALT-*\n      - FB   # FlyBase FBal*\n      - WB\n      - WormBase ## WormBase:WBVar*\n    alt_descriptions:\n      AGR: >-\n        An entity that describes a single affected, endogenous allele.\n        These can be of any type that matches that definition\n      VMC: >-\n        A contiguous change at a Location\n    slots:\n      - has gene\n    slot_usage:\n      has gene:\n        multivalued: true\n        description: Each allele can be associated with any number of genes\n      has biological sequence:\n        description: >-\n          The state of the sequence w.r.t a reference sequence\n      id:\n        examples:\n          - value: ZFIN:ZDB-ALT-980203-1091\n            description: ti282a allele from ZFIN\n          - value: ClinVarVariant:17681\n            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\n    in_subset:\n      - model_organism_database\n\n  snv:\n    aliases: ['single nucleotide variant','single nucleotide polymorphism', 'snp']\n    is_a: sequence variant\n    description: >-\n      SNVs are single nucleotide positions in genomic DNA at\n      which different sequence alternatives exist\n    exact_mappings:\n      - SO:0001483\n\n  reagent targeted gene:\n    aliases: ['sequence targeting reagent']\n    is_a: biological entity\n    description: >-\n      A gene altered in its expression level in the context of some\n      experiment as a result of being targeted by gene-knockdown\n      reagent(s) such as a morpholino or RNAi.\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - GENO:0000504\n    in_subset:\n      - model_organism_database\n\n  ## --------------------\n  ## Clinical\n  ## Attributes, Cohort,\n  ## Exposures & Outcomes\n  ## --------------------\n\n  ## Clinical Attributes\n\n  clinical attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a clinical manifestation\n    exact_mappings:\n      # Clinical Attribute\n      - STY:T201\n\n  clinical measurement:\n    is_a: clinical attribute\n    description: >-\n      A clinical measurement is a special kind of attribute which results\n      from a laboratory observation from a subject individual or sample.\n      Measurements can be connected to their subject by the 'has attribute' slot.\n    slot_usage:\n      has attribute type:\n        required: true\n        multivalued: false\n        values_from:\n          - EFO\n          - LOINC\n    exact_mappings:\n      - EFO:0001444\n\n  clinical modifier:\n    is_a: clinical attribute\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the phenotypic abnormality sub-ontology, with respect\n      to severity, laterality, and other aspects\n    exact_mappings:\n      - HP:0012823\n\n  clinical course:\n    is_a: clinical attribute\n    description: >-\n      The course a disease typically takes from its onset, progression in time, and\n      eventual resolution or death of the affected individual\n    exact_mappings:\n      - HP:0031797\n\n  onset:\n    is_a: clinical course\n    description: >-\n      The age group in which (disease) symptom manifestations appear\n    exact_mappings:\n      - HP:0003674\n\n  clinical entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists in the clinical domain and outside the\n      biological realm. Diseases are placed under biological entities\n\n  clinical trial:\n    is_a: clinical entity\n\n  clinical intervention:\n    is_a: clinical entity\n\n  clinical finding:\n    is_a: phenotypic feature\n    description: >-\n      this category is currently considered broad enough to tag clinical lab\n      measurements and other biological attributes taken as 'clinical traits'\n      with some statistical score, for example, a p value in genetic associations.\n    slot_usage:\n      has attribute:\n        range: clinical attribute\n    id_prefixes:\n      - LOINC\n      - NCIT\n      - EFO\n\n  hospitalization:\n    is_a: clinical intervention\n    exact_mappings:\n      - SNOMEDCT:32485007\n      - WIKIDATA:Q3140971\n\n  socioeconomic attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a socioeconomic manifestation\n    #slot_usage:\n    # need a suitable qualifying socioeconomic ontology target here?\n    # Perhaps some subset of ECTO: https://github.com/EnvironmentOntology/environmental-exposure-ontology\n    #  has attribute type:\n    #     range: socioeconomic ontology\n    # exact_mappings:\n    #  - ??\n\n  ## Cohorts\n\n  case:\n    aliases: ['patient', 'proband']\n    is_a: individual organism\n    description: >-\n      An individual (human) organism that has a patient role in some clinical context.\n\n  cohort:\n    is_a: study population\n    description: >-\n      A group of people banded together or treated as a group who share common characteristics.\n      A cohort 'study' is a particular form of longitudinal study that samples a cohort,\n      performing a cross-section at intervals through time.\n    #\n    # As of this moment (Nov. 22), the jury is still out on what metadata of a cohort\n    # will be common to all cohort descriptions versus cohort-specific annotation.\n    # The former should be embedded as explicit slots in the cohort category. The latter\n    # ought to be documented as (ontology term constrained) extended node attributes.\n    #\n    #slots:\n    #  - general disease focus,\n    #  - specific inclusion/exclusion criteria,\n    #  - year(s) of cohort creation,\n    #  - institution.\n    exact_mappings:\n      - WIKIDATA:Q1303415\n    narrow_mappings:\n      # Professional or Occupational Group\n      - STY:T097\n      # Family Group\n      - STY:T099\n      # Age Group\n      - STY:T100\n      # Patient or Disabled Group\n      - STY:T101\n\n  ## Exposures\n\n  exposure event:\n    is_a: named thing\n    aliases: ['exposure', 'experimental condition']\n    mixin: true\n    slots:\n      - timepoint\n    description: >-\n      A (possibly time bounded) incidence of a feature of the environment of an organism that\n      influences one or more phenotypic features of that organism, potentially mediated by genes\n    exact_mappings:\n      - XCO:0000000\n    in_subset:\n      - model_organism_database\n\n  # TODO - confirm that genomic backgrounds are exposures\n  genomic background exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - gene grouping mixin\n      - physical essence\n      - genomic entity\n      - thing with taxon\n      - ontology class\n    description: >-\n      A genomic background exposure is where an individual's specific genomic background\n      of genes, sequence variants or other pre-existing genomic conditions constitute\n      a kind of 'exposure' to the organism, leading to or influencing an outcome.\n\n  pathological entity mixin:\n    description: >-\n      A pathological (abnormal) structure or process.\n    mixin: true\n    exact_mappings:\n      - MPATH:0\n    narrow_mappings:\n      - HP:0000118\n\n  pathological process:\n    description: >-\n      A biologic function or a process having an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: biological process\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - OBI:1110122\n      - NCIT:C16956\n    narrow_mappings:\n      # metastasis\n      - NCIT:C19151\n      - EFO:0009708\n      - STY:T046\n      - STY:T037\n\n  pathological process exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A pathological process, when viewed as an exposure, representing\n      a precondition, leading to or influencing an outcome,\n      e.g. autoimmunity leading to disease.\n\n  pathological anatomical structure:\n    description: >-\n      An anatomical structure with the potential of have an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: anatomical entity\n    mixins:\n      - pathological entity mixin\n\n  pathological anatomical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      An abnormal anatomical structure, when viewed as an exposure,\n      representing an precondition, leading to or influencing an outcome,\n      e.g. thrombosis leading to an ischemic disease outcome.\n\n  disease or phenotypic feature exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - pathological entity mixin\n    description: >-\n      A disease or phenotypic feature state, when viewed as an exposure,\n      represents an precondition, leading to or influencing an outcome,\n      e.g. HIV predisposing an individual to infections; a relative deficiency\n      of skin pigmentation predisposing an individual to skin cancer.\n\n  chemical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    slots:\n      - has quantitative value\n    description: >-\n      A chemical exposure is an intake of a particular\n      chemical entity.\n    exact_mappings:\n      # this ECTO term is not visibly defined but\n      # the 9000000-series identifiers seems to be the\n      # numeric space of chemical exposure definitions\n      - ECTO:9000000\n      - SIO:001399\n\n  complex chemical exposure:\n    is_a: attribute\n    description: >-\n      A complex chemical exposure is an intake of a chemical\n      mixture (e.g. gasoline), other than a drug.\n\n  drug exposure:\n    is_a: chemical exposure\n    aliases: ['drug intake', 'drug dose', 'medication intake']\n    description: >-\n      A drug exposure is an intake of a particular drug.\n    mixins:\n      - exposure event\n    broad_mappings:\n      # slightly broader than just drug effects on a biological system\n      - SIO:001005\n    exact_mappings:\n      - ECTO:0000509\n\n  # TODO: deprecate?\n  drug to gene interaction exposure:\n    description: >-\n      drug to gene interaction exposure is a drug exposure is where the\n      interactions of the drug with specific genes are known to constitute\n      an 'exposure' to the organism, leading to or influencing an outcome.\n    is_a: drug exposure\n    mixins:\n      - gene grouping mixin\n\n  treatment:\n    aliases: ['medical action', 'medical intervention']\n    # 'named thing' seems too generic here but not sure what applies better here\n    is_a: named thing\n    mixins:\n      - exposure event\n      - chemical or drug or treatment\n    description: >-\n      A treatment is targeted at a disease or phenotype and may involve\n      multiple drug 'exposures', medical devices and/or procedures\n    slots:\n      - has drug\n      - has device\n      - has procedure\n    exact_mappings:\n      - OGMS:0000090\n      - SIO:001398\n    broad_mappings:\n      - MAXO:0000058\n\n  biotic exposure:\n    is_a: attribute\n    aliases: ['viral exposure','bacterial exposure']\n    mixins:\n      - exposure event\n    description: >-\n      An external biotic exposure is an intake of (sometimes pathological)\n      biological organisms (including viruses).\n\n  geographic exposure:\n    is_a: environmental exposure\n    mixins:\n      - exposure event\n    description: >-\n      A geographic exposure is a factor relating to geographic\n      proximity to some impactful entity.\n    close_mappings:\n      - dcid:GeologicalEvent\n    narrow_mappings:\n      - dcid:IceStoremEvent\n      - dcid:LakeEffectSnowEvent\n      - dcid:LandslideEvent\n      - dcid:MarineDenseFogEvent\n      - dcid:MarineLighteningEvent\n      - dcid:MarineStrongWindEvent\n      - dcid:MarineThunderstormWindEvent\n      - dcid:StormEvent\n      - dcid:StormSurgeTideEvent\n      - dcid:StrongWindEvent\n      - dcid:ThunderstormWindEvent\n      - dcid:TornadoEvent\n      - dcid:TropicalDepressionEvent\n      - dcid:WinterStoremEvent\n\n  environmental exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A environmental exposure is a factor relating to abiotic processes\n      in the environment including sunlight (UV-B), atmospheric (heat,\n      cold, general pollution) and water-born contaminants.\n\n  behavioral exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A behavioral exposure is a factor relating to behavior impacting an individual.\n\n  socioeconomic exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A socioeconomic exposure is a factor relating to social and\n      financial status of an affected individual (e.g. poverty).\n    slot_usage:\n      has attribute:\n        range: socioeconomic attribute\n        required: true\n\n  ## Outcomes\n\n  outcome:\n    mixin: true\n    description: >-\n      An entity that has the role of being the consequence of an exposure event.\n      This is an abstract mixin grouping of various categories of possible\n      biological or non-biological (e.g. clinical) outcomes.\n\n  pathological process outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of a pathological process.\n\n  pathological anatomical outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of an abnormal anatomical structure.\n\n  disease or phenotypic feature outcome:\n    mixins:\n      - outcome\n    description: >-\n      Physiological outcomes resulting from an exposure event which\n      is the manifestation of a disease or other characteristic phenotype.\n\n  behavioral outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the manifestation of human behavior.\n\n  hospitalization outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the increased manifestation of acute (e.g. emergency\n      room visit) or chronic (inpatient) hospitalization.\n\n  mortality outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome of death from resulting from an exposure event.\n\n  epidemiological outcome:\n    mixins:\n      - outcome\n    description: >-\n      An epidemiological outcome, such as societal disease\n      burden, resulting from an exposure event.\n    related_mappings:\n      - NCIT:C19291\n\n  socioeconomic outcome:\n    mixins:\n      - outcome\n    description: >-\n      An general social or economic outcome, such as\n      healthcare costs, utilization, etc., resulting from an exposure event\n\n  ## ------------\n  ## ASSOCIATIONS\n  ## ------------\n\n  association:\n    is_a: entity\n    description: >-\n      A typed association between two entities, supported by evidence\n    comments:\n      - This is roughly the model used by biolink and ontobio at the moment\n    slots:\n      - subject\n      - predicate\n      - object\n      - negated\n      - qualifiers\n      - publications\n      - has evidence\n      - knowledge source\n      - original knowledge source\n      - primary knowledge source\n      - aggregator knowledge source\n      - timepoint\n    slot_usage:\n      type:\n        description: rdf:type of biolink:Association should be fixed at rdf:Statement\n      category:\n        range: category type\n        required: false\n    exact_mappings:\n      - OBAN:association\n      - rdf:Statement\n      - owl:Axiom\n\n  chemical entity assesses named thing association:\n    is_a: association\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: assesses\n\n\n  contributor association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      Any association between an entity (such as a publication)\n      and various agents that contribute to its realisation\n    slot_usage:\n      subject:\n        range: information content entity\n        description: >-\n          information content entity which an agent has helped realise\n      predicate:\n        subproperty_of: contributor\n        description: >-\n          generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\n      object:\n        range: agent\n        description: >-\n          agent helping to realise the given entity (e.g. such as a publication)\n      qualifiers:\n        description: >-\n          this field can be used to annotate special characteristics of an\n          agent relationship, such as the fact that a given author agent of\n          a publication is the 'corresponding author'\n\n  genotype to genotype part association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a genotypic entity that is a sub-component of it\n    slot_usage:\n      predicate:\n        subproperty_of: has variant part\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: genotype\n        description: >-\n          child genotype\n\n  genotype to gene association:\n    description: >-\n      Any association between a genotype and a gene.\n      The genotype have have multiple variants in that gene or a single one.\n      There is no assumption of cardinality\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: gene\n        description: >-\n          gene implicated in genotype\n\n  genotype to variant association:\n    description: >-\n      Any association between a genotype and a sequence variant.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: sequence variant\n        description: >-\n          gene implicated in genotype\n\n  gene to gene association:\n    aliases: ['molecular or genetic interaction']\n    description: >-\n      abstract parent class for different kinds of gene-gene or gene product\n      to gene product relationships. Includes homology and interaction.\n    abstract: true\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          the subject gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n      object:\n        range: gene or gene product\n        description: >-\n          the object gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n\n  gene to gene homology association:\n    description: >-\n      A homology association between two genes. May be orthology (in which\n      case the species of subject and object should differ) or paralogy\n      (in which case the species may be the same)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n      predicate:\n        subproperty_of: homologous to\n        symmetric: true\n        description: >-\n          homology relationship type\n      object:\n        range: gene or gene product\n\n  gene expression mixin:\n    description: >-\n      Observed gene expression intensity, context (site, stage) and\n      associated phenotypic status within which the expression occurs.\n    mixin: true\n    slots:\n      - quantifier qualifier\n      - expression site\n      - stage qualifier\n      - phenotypic state\n    slot_usage:\n      quantifier qualifier:\n        description: >-\n          Optional quantitative value indicating degree of expression.\n\n  gene to gene coexpression association:\n    description: >-\n      Indicates that two genes are co-expressed,\n      generally under the same conditions.\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: coexpressed with\n        symmetric: true\n\n  pairwise gene to gene interaction:\n    description: >-\n      An interaction between two genes or two gene products.\n      May be physical (e.g. protein binding) or genetic (between genes).\n      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      predicate:\n        subproperty_of: interacts with\n        symmetric: true\n        description: \"interaction relationship type\"\n    narrow_mappings:\n      - dcid:ProteinProteinInteraction\n\n  pairwise molecular interaction:\n    description: >-\n      An interaction at the molecular level between two physical entities\n    is_a: pairwise gene to gene interaction\n    slots:\n      # need to declare a slot before it is used,\n      # then list it in 'slots', not just a slot_usage\n      - interacting molecules category\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: molecular entity\n      id:\n        description: >-\n          identifier for the interaction. This may come from an interaction database such as IMEX.\n        examples:\n          - value: WB:WBInteraction000538741\n        values_from:\n          - IMEX\n          - BioGRID\n      predicate:\n        subproperty_of: molecularly interacts with\n        description: \"interaction relationship type\"\n        examples:\n          - value: RO:0002447\n            description: the subject molecular phosphorylates the object molecule\n      object:\n        range: molecular entity\n\n  cell line to entity association mixin:\n    description: >-\n      An relationship between a cell line and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: cell line\n\n  # TODO: figure out what gives with subject range\n  cell line to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - cell line to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    description: >-\n      An relationship between a cell line and a disease or a phenotype, where\n      the cell line is derived from an individual with that disease or phenotype.\n    slot_usage:\n      subject:\n#        - range: cell line\n#        - range: disease or phenotypic feature\n        range: disease or phenotypic feature\n\n  chemical entity to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity that is an interactor\"\n\n  drug to entity association mixin:\n    description: >-\n      An interaction between a drug and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: drug\n        description: \"the drug that is an interactor\"\n\n  chemical to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity or entity that is an interactor\"\n\n  case to entity association mixin:\n    description: >-\n      An abstract association for use where the case is the subject\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: case\n        description: \"the case (e.g. patient) that has the property\"\n\n  chemical to chemical association:\n    description: >-\n      A relationship between two chemical entities. This can encompass actual\n      interactions as well as temporal causal edges, e.g. one chemical converted to another.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: chemical entity\n        description: \"the chemical element that is the target of the statement\"\n\n  reaction to participant association:\n    description:\n    is_a: chemical to chemical association\n    slots:\n      - stoichiometry\n      - reaction direction\n      - reaction side\n    slot_usage:\n      subject:\n        range: molecular entity\n    defining_slots:\n      - subject\n      - predicate\n      - object\n\n  reaction to catalyst association:\n    description:\n    is_a: reaction to participant association\n    slot_usage:\n      object:\n        range: gene or gene product\n\n  chemical to chemical derivation association:\n    description: >-\n      A causal relationship between two chemical entities, where the subject\n      represents the upstream entity and the object represents the downstream.\n      For any such association there is an implicit reaction:\n        IF\n        R has-input C1 AND\n        R has-output C2 AND\n        R enabled-by P AND\n        R type Reaction\n        THEN\n        C1 derives-into C2 <>\n    is_a: chemical to chemical association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - catalyst qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: >-\n          the upstream chemical entity\n      object:\n        range: chemical entity\n        description: >-\n          the downstream chemical entity\n      predicate:\n        subproperty_of: derives into\n      catalyst qualifier:\n        description: >-\n          this connects the derivation edge to the chemical entity that\n          catalyzes the reaction that causes the subject chemical to\n          transform into the object chemical.\n\n  chemical to disease or phenotypic feature association:\n    description: >-\n      An interaction between a chemical entity and a phenotype or disease,\n      where the presence of the chemical gives rise to or exacerbates the phenotype.\n    is_a: association\n    narrow_mappings:\n      - SIO:000993\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"the disease or phenotype that is affected by the chemical\"\n\n  gene to pathway association:\n    description: >-\n      An interaction between a gene or gene product and a biological process or pathway.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"the gene or gene product entity that participates or influences the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that includes or is affected by the gene or gene product\"\n\n  molecular activity to pathway association:\n    description: >-\n      Association that holds the relationship between a reaction and the pathway it participates in.\n    is_a: association\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: pathway\n      predicate:\n        subproperty_of: part of\n\n  chemical to pathway association:\n    description: >-\n      An interaction between a chemical entity and a biological process or pathway.\n    is_a: association\n    exact_mappings:\n      - SIO:001250\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: \"the chemical entity that is affecting the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that is affected by the chemical\"\n\n  chemical to gene association:\n    description: >-\n      An interaction between a chemical entity and a gene or gene product.\n    is_a: association\n    exact_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: >-\n          the gene or gene product that is affected by the chemical.\n\n  drug to gene association:\n    description: >-\n      An interaction between a drug and a gene or gene product.\n    is_a: association\n    related_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - drug to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: \"the gene or gene product that is affected by the drug\"\n\n  material sample to entity association mixin:\n    description: >-\n      An association between a material sample and something.\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n\n  material sample derivation association:\n    description: >-\n      An association between a material sample and\n      the material entity from which it is derived.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n      object:\n        description: >-\n          the material entity the sample was derived from. This may be another\n          material sample, or any other material entity, including for example\n          an organism, a geographic feature, or some environmental material.\n      predicate:\n        description: >-\n          derivation relationship\n        subproperty_of: derives from\n\n  material sample to disease or phenotypic feature association:\n    description: >-\n      An association between a material sample and a disease or phenotype.\n    is_a: association\n    mixins:\n      - material sample to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    defining_slots:\n      - subject\n      - object\n\n  disease to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease\n        description: \"disease class\"\n        values_from: ['mondo', 'omim', 'orphanet', 'ncit', 'doid']\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n\n  entity to exposure event association mixin:\n    description: >-\n      An association between some entity and an exposure event.\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: exposure event\n\n  disease to exposure event association:\n    description: >-\n      An association between an exposure event and a disease.\n    is_a: association\n    mixins:\n      - disease to entity association mixin\n      - entity to exposure event association mixin\n    defining_slots:\n      - subject\n      - object\n\n  exposure event to entity association mixin:\n    deprecated: true\n\n  entity to outcome association mixin:\n    description: >-\n      An association between some entity and an outcome\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: outcome\n\n  exposure event to outcome association:\n    description: >-\n      An association between an exposure event and an outcome.\n    is_a: association\n    mixins:\n      - exposure event to entity association mixin\n      - entity to outcome association mixin\n    slots:\n      - has population context\n      - has temporal context\n    defining_slots:\n      - subject\n      - object\n\n  frequency qualifier mixin:\n    mixin: true\n    description: >-\n      Qualifier for frequency type associations\n    slots:\n      - frequency qualifier\n\n  entity to feature or disease qualifiers mixin:\n    description: >-\n      Qualifiers for entity to disease or phenotype associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - severity qualifier\n      - onset qualifier\n\n  entity to phenotypic feature association mixin:\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: phenotypic feature\n        values_from: ['upheno', 'hp', 'mp', 'wbphenotype']\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n    slots:\n      - sex qualifier\n\n  information content entity to named thing association:\n    description: >-\n      association between a named thing and a information content entity where the specific context\n      of the relationship between that named thing and the publication is unknown. For\n      example, model organisms databases often capture the knowledge that a gene is found in a\n      journal article, but not specifically the context in which that gene was documented in the article.\n      In these cases, this association with the accompanying predicate 'mentions' could be used.\n      Conversely, for more specific associations (like 'gene to disease association', the publication should\n      be captured as an edge property).\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        domain: publication\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: mentions\n    in_subset:\n      - model_organism_database\n\n  entity to disease association mixin:\n    description: >-\n      mixin class for any association whose object (target node) is a disease\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease\n        description: \"disease\"\n        examples:\n          - value: MONDO:0020066\n            description: \"Ehlers-Danlos syndrome\"\n\n  disease or phenotypic feature to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  disease or phenotypic feature to location association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      an anatomical entity, where the disease/feature manifests in that site.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      object:\n        range: anatomical entity\n        description: >-\n          anatomical entity in which the disease or feature is found.\n        examples:\n          - value: UBERON:0002048\n            description: \"lung\"\n\n  entity to disease or phenotypic feature association mixin:\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  genotype to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: genotype\n        description: \"genotype that is the subject of the association\"\n\n  genotype to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a phenotypic feature, where having\n      the genotype confers the phenotype, either in isolation or through environment\n    mixins:\n      - entity to phenotypic feature association mixin\n      - genotype to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has phenotype\n      subject:\n        range: genotype\n        description: >-\n          genotype that is associated with the phenotypic feature\n\n  # ie: smoke exposure to coughing phenotype? is this a denormalization?\n  exposure event to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between an environment and a phenotypic feature,\n      where being in the environment influences the phenotype.\n    mixins:\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: exposure event\n\n  disease to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      An association between a disease and a phenotypic feature in which the\n      phenotypic feature is associated with the disease in some way.\n    mixins:\n      - entity to phenotypic feature association mixin\n      - disease to entity association mixin\n    close_mappings:\n      - dcid:DiseaseSymptomAssociation\n    slot_usage:\n      subject:\n        range: disease\n      object:\n        range: phenotypic feature\n\n  case to phenotypic feature association:\n    description: >-\n      An association between a case (e.g. individual patient) and a phenotypic\n      feature in which the individual has or has had the phenotype.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - case to entity association mixin\n\n  behavior to behavioral feature association:\n    description: >-\n      An association between an mixture behavior and\n      a behavioral feature manifested by\n      the individual exhibited or has exhibited the behavior.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: behavior\n        description: >-\n          behavior that is the subject of the association\n      object:\n        range: behavioral feature\n        description: >-\n          behavioral feature that is the object of the association\n    mixins:\n      - entity to phenotypic feature association mixin\n\n  gene to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene that is the subject of the association\n\n  variant to entity association mixin:\n    local_names:\n      ga4gh: variant annotation\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is associated with some other entity\n        examples:\n          - value: ClinVar:38077\n            description: \"ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n          - value: ClinGen:CA024716\n            description: \"chr13:g.32921033G>C (hg19) in ClinGen\"\n\n  gene to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n      - WBVocab:Gene-Phenotype-Association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      object:\n        range: phenotypic feature\n\n  gene to disease association:\n    is_a: association\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n    exact_mappings:\n      - SIO:000983\n    close_mappings:\n      - dcid:DiseaseGeneAssociation\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease,\n          may be protective or causative or associative, or as a model\n      object:\n        range: disease\n\n  druggable gene to disease association:\n    is_a: gene to disease association\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease\n          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and\n          this leads to a protective or improving disease state.\n      predicate:\n        subproperty_of: target for\n      has evidence:\n        range: druggable_gene_category_enum\n    defining_slots:\n      - subject\n      - object\n      - predicate\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n\n  variant to gene association:\n    description: >-\n      An association between a variant and a gene, where the variant has\n      a genetic association with the gene (i.e. is in linkage disequilibrium)\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - variant to entity association mixin\n    slot_usage:\n      object:\n        range: gene\n      predicate:\n        subproperty_of: genetic association\n\n  variant to gene expression association:\n    description: >-\n      An association between a variant and expression of a gene (i.e. e-QTL)\n    is_a: variant to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: affects expression of\n\n  variant to population association:\n    description: >-\n      An association between a variant and a population, where the variant has\n      particular frequency in the population\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - frequency quantifier\n      - frequency qualifier mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          an allele that has a certain frequency in a given population\n        examples:\n          - value: \"NC_000017.11:g.43051071A>T\"\n            description: >-\n              17:41203088 A/C in gnomad\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that is observed to have the frequency\n        examples:\n          - value: HANCESTRO:0010\n            description: African\n      has quotient:\n        description: >-\n          frequency of allele in population, expressed as a number with allele\n          divided by number in reference population, aka allele frequency\n        examples:\n          - value: \"0.0001666\"\n      has count:\n        description: >-\n          number in object population that carry a particular allele, aka allele count\n        examples:\n          - value: \"4\"\n            description: 4 individuals in gnomad set\n      has total:\n        description: >-\n          number all populations that carry a particular allele, aka allele number\n        examples:\n          - value: \"24014\"\n            description: 24014 individuals in gnomad set\n\n  population to population association:\n    description: >-\n      An association between a two populations\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: population of individual organisms\n        description: >-\n          the population that form the subject of the association\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that form the object of the association\n      predicate:\n        # subproperty_of: ???\n        description: >-\n          A relationship type that holds between the subject and object\n          populations. Standard mereological relations can be used.\n          E.g. subject part-of object, subject overlaps object.\n          Derivation relationships can also be used\n\n  variant to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is\n          associated in some way with the phenotype state\n\n  variant to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a sequence variant in which the allele state\n          is associated in some way with the disease state\n        examples:\n          - value: ClinVar:52241\n            description: \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that variant\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  genotype to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - genotype to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a genotype that is associated in some way with a disease state\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that genotype\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  model to disease association mixin:\n    description: >-\n      This mixin is used for any association class for which the subject\n      (source node) plays the role of a 'model', in that it recapitulates some\n      features of the disease in a way that is useful for studying the disease\n      outside a patient carrying the disease\n    mixin: true\n    slot_usage:\n      subject:\n        description: >-\n          The entity that serves as the model of the disease. This may be\n          an organism, a strain of organism, a genotype or variant that exhibits\n          similar features, or a gene that when mutated exhibits features of the disease\n      predicate:\n        subproperty_of: model of\n        description: >-\n          The relationship to the disease\n\n  gene as a model of disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be a model\n          organism ortholog of a known disease gene, or it may be a gene whose\n          mutants recapitulate core features of the disease.\n\n  variant as a model of disease association:\n    is_a: variant to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          A variant that has a role in modeling the disease.\n\n  genotype as a model of disease association:\n    is_a: genotype to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: genotype\n        description: >-\n          A genotype that has a role in modeling the disease.\n\n  cell line as a model of disease association:\n    is_a: cell line to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: cell line\n        description: >-\n          A cell line derived from an organismal entity with a disease state that is used\n          as a model of that disease.\n\n  organismal entity as a model of disease association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: organismal entity\n        description: >-\n          A organismal entity (strain, breed) with a predisposition to a disease, or bred/created\n          specifically to model a disease.\n\n  organism to organism association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: individual organism\n      object:\n        range: individual organism\n        description: >-\n          An association between two individual organisms.\n\n  taxon to taxon association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n        description: >-\n          An association between individuals of different taxa.\n\n  gene has variant that contributes to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - sequence variant qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be\n          a model organism ortholog of a known disease gene, or it may be\n          a gene whose mutants recapitulate core features of the disease.\n\n  gene to expression site association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      An association between a gene and a gene expression site,\n      possibly qualified by stage/timing info.\n    notes:\n      - \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n    see_also: \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n    slots:\n      - stage qualifier\n      - quantifier qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          Gene or gene product positively within the specified\n          anatomical entity (or subclass, i.e. cellular component) location.\n      object:\n        range: anatomical entity\n        description: \"location in which the gene is expressed\"\n        examples:\n          - value: UBERON:0002037\n            description: cerebellum\n      predicate:\n        description: \"expression relationship\"\n        subproperty_of: expressed in\n      stage qualifier:\n        range: life stage\n        description: \"stage at which the gene is expressed in the site\"\n        examples:\n          - value: UBERON:0000069\n            description: larval stage\n      quantifier qualifier:\n        description: >-\n          can be used to indicate magnitude, or also ranking\n\n  sequence variant modulates treatment association:\n    is_a: association\n    description: >-\n      An association between a sequence variant and a treatment or health intervention.\n      The treatment object itself encompasses both the disease and the drug used.\n    comments:\n      - An alternate way to model the same information could be via a qualifier\n    defining_slots:\n      - subject\n      - object\n    abstract: true\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: \"variant that modulates the treatment of some disease\"\n      object:\n        range: treatment\n        description: \"treatment whose efficacy is modulated by the subject variant\"\n\n  functional association:\n    is_a: association\n    description: >-\n      An association between a macromolecular machine mixin (gene, gene product or\n      complex of gene products) and either a molecular activity, a biological\n      process or a cellular location in which a function is executed.\n    slot_usage:\n      subject:\n        range: macromolecular machine mixin\n        description: >-\n          gene, product or macromolecular complex mixin that\n          has the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: gene ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n          - value: GO:0045211\n            description: postsynaptic membrane\n\n  macromolecular machine to entity association mixin:\n    description: >-\n      an association which has a macromolecular machine mixin as a subject\n    mixin: true\n    slot_usage:\n      subject:\n        domain: macromolecular machine mixin\n\n  macromolecular machine to molecular activity association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a molecular activity (as represented\n      in the GO molecular function branch), where the entity\n      carries out the activity, or contributes to its execution.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: molecular activity\n\n  macromolecular machine to biological process association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a biological process or pathway\n      (as represented in the GO biological process branch), where the entity\n      carries out some part of the process, regulates it, or acts upstream of it.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: biological process\n\n  macromolecular machine to cellular component association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a cellular component (as represented\n      in the GO cellular component branch), where the entity\n      carries out its function in the cellular component.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: cellular component\n\n  molecular activity to chemical entity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: chemical entity\n\n  molecular activity to molecular activity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: molecular activity\n\n\n  gene to go term association:\n    aliases: ['functional association']\n    is_a: functional association\n    exact_mappings:\n      - WBVocab:Gene-GO-Association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene\n        description: >-\n          gene, product or macromolecular complex that has\n          the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: gene ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n\n  entity to disease association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  entity to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  ## -----------------\n  ## SEQUENCE FEATURES\n  ## -----------------\n\n  sequence association:\n    is_a: association\n    description: >-\n      An association between a sequence feature and a nucleic acid entity it is localized to.\n\n  genomic sequence localization:\n    is_a: sequence association\n    description: >-\n      A relationship between a sequence feature and a nucleic acid entity\n      it is localized to. The reference entity may be a chromosome,\n      chromosome region or information entity such as a contig.\n    slot_usage:\n      subject:\n        aliases: ['sequence feature']\n        range: nucleic acid entity\n      object:\n        aliases: ['reference']\n        range: nucleic acid entity # typically a chromosome use monochrom\n      predicate:\n        subproperty_of: has sequence location\n    slots:\n      - start interbase coordinate\n      - end interbase coordinate\n      - genome build\n      - strand\n      - phase\n    broad_mappings:\n      - dcid:Chromosome\n    exact_mappings:\n      - dcid:GenomeAnnotation\n\n  sequence feature relationship:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      For example, a particular exon is part of a particular transcript or gene\n    slot_usage:\n      subject:\n        range: nucleic acid entity\n      object:\n        range: nucleic acid entity # typically a chromosome\n    exact_mappings:\n      - CHADO:feature_relationship\n\n  transcript to gene relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is a collection of transcripts\n    slot_usage:\n      subject:\n        range: transcript\n      object:\n        range: gene\n\n  gene to gene product relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is transcribed and potentially translated to a gene product\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene product mixin\n      predicate:\n        subproperty_of: has gene product\n\n  exon to transcript relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A transcript is formed from multiple exons\n    slot_usage:\n      subject:\n        range: exon\n      object:\n        range: transcript\n\n  gene regulatory relationship:\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n      subject:\n        range: gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n\n  anatomical entity to anatomical entity association: # schema: gocam\n    is_a: association\n    abstract: true\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: anatomical entity\n      object:\n        range: anatomical entity\n\n  anatomical entity to anatomical entity part of association:\n#      schema: gocam\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is mereological, i.e the two entities are related by parthood. This\n      includes relationships between cellular components and cells, between\n      cells and tissues, tissues and whole organisms\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the part\n      object:\n        range: anatomical entity\n        description: >-\n          the whole\n      predicate:\n        subproperty_of: part of\n\n  anatomical entity to anatomical entity ontogenic association:\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is ontogenic, i.e. the two entities are related by development. A number\n      of different relationship types can be used to specify the precise\n      nature of the relationship.\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the structure at a later time\n      object:\n        range: anatomical entity\n        description: >-\n          the structure at an earlier time\n      predicate:\n         subproperty_of: develops from\n\n  organism taxon to entity association:\n    mixin: true\n    description: >-\n      An association between an organism taxon and another entity\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: organism taxon\n        description: >-\n          organism taxon that is the subject of the association\n      \n  organism taxon to organism taxon association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    description: >-\n      A relationship between two organism taxon nodes\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n\n  organism taxon to organism taxon specialization:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      A child-parent relationship between two taxa.\n      For example: Homo sapiens subclass_of Homo\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: child taxon\n        description: >-\n          the more specific taxon\n      object:\n        range: organism taxon\n        role: parent taxon\n        description: >-\n          the more general taxon\n      predicate:\n         subproperty_of: subclass of\n\n  organism taxon to organism taxon interaction:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      An interaction relationship between two taxa. This may be a symbiotic\n      relationship (encompassing mutualism and parasitism), or it may be non-symbiotic.\n      Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens\n    defining_slots:\n      - predicate\n    slots:\n      - associated environmental context\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        range: organism taxon\n        role: interactee taxon\n        description: >-\n          the taxon that is the subject of the association\n      predicate:\n         subproperty_of: interacts with\n      associated environmental context:\n         description: >-\n           the environment in which the two taxa interact\n\n  organism taxon to environment association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        role: environmental context\n        description: >-\n          the environment in which the organism occurs\n      predicate:\n        description: >-\n          predicate describing the relationship between the taxon and the environment\n           \n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_3_0_3/biolink-model.yaml",
    "content": "id: https://w3id.org/biolink/biolink-model\nname: Biolink-Model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 3.0.3\n\n\n\n## ------------\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  AGRKB: 'https://www.alliancegenome.org/'\n  apollo: 'https://github.com/GMOD/Apollo'\n  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='\n  biolink: 'https://w3id.org/biolink/vocab/'\n  bioschemas: 'https://bioschemas.org/'\n  linkml: 'https://w3id.org/linkml/'\n  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='\n  # Placeholder: just points to GMOD Chado wiki\n  CHADO: 'http://gmod.org/wiki/Chado/'\n  # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve\n  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='\n  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'\n  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'\n  CLINVAR: 'http://identifiers.org/clinvar'\n  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'\n  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'\n  CPT: 'https://www.ama-assn.org/practice-management/cpt/'\n  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='\n  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='\n  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='\n  CTD: 'http://ctdbase.org/'\n  DGIdb: 'https://www.dgidb.org/interaction_types'\n  dcat: 'http://www.w3.org/ns/dcat#'\n  dct: 'http://purl.org/dc/terms/'\n  dcid: 'https://datacommons.org/browser/'\n  doi: 'https://doi.org/'\n  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'\n  DrugCentral: 'http://drugcentral.org/drugcard/'\n  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'\n  EDAM-DATA: 'http://edamontology.org/data_'\n  EDAM-FORMAT: 'http://edamontology.org/format_'\n  EDAM-OPERATION: 'http://edamontology.org/operation_'\n  EDAM-TOPIC: 'http://edamontology.org/topic_'\n  EFO: 'http://www.ebi.ac.uk/efo/EFO_'\n  ExO: 'http://purl.obolibrary.org/obo/ExO_'\n  fabio: 'http://purl.org/spar/fabio/'\n  foaf: 'http://xmlns.com/foaf/0.1/'\n  foodb.food: 'http://foodb.ca/compounds/'\n  foodb.compound: 'http://foodb.ca/foods/'\n  FYECO: 'https://www.pombase.org/term/'\n  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'  # Fission Yeast Phenotype Ontology\n  GAMMA: 'http://translator.renci.org/GAMMA_'\n  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'\n  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'\n  # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)\n  GOP: 'http://purl.obolibrary.org/obo/go#'\n  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'\n  GSID: 'https://scholar.google.com/citations?user='\n  GTEx: 'https://www.gtexportal.org/home/gene/'\n  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='\n  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'\n  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'\n  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'\n  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'\n  ICD10: 'https://icd.codes/icd9cm/'\n  ICD9: 'http://translator.ncats.nih.gov/ICD9_'\n  interpro: 'https://www.ebi.ac.uk/interpro/entry/'\n  INO: 'http://purl.obolibrary.org/obo/INO_'\n  isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international\n  isni: 'https://isni.org/isni/'\n  issn: 'https://portal.issn.org/resource/ISSN/'\n  ncats.drug: 'https://drugs.ncats.io/drug/'\n  KEGG.BRITE: 'http://www.kegg.jp/entry/'\n  KEGG.DGROUP: 'http://www.kegg.jp/entry/'\n  KEGG.ENZYME: 'http://www.kegg.jp/entry/'\n  KEGG.GENE: 'http://www.kegg.jp/entry/'\n  KEGG.PATHWAY: 'https://www.kegg.jp/entry/'\n  KEGG.RCLASS: 'http://www.kegg.jp/entry/'\n  LOINC: 'http://loinc.org/rdf/'\n  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'\n  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'\n  metacyc.reaction: 'https://identifiers.org/metacyc.reaction:'\n  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'\n  MESH: 'http://id.nlm.nih.gov/mesh/'\n  MI: 'http://purl.obolibrary.org/obo/MI_'\n  mirbase: 'http://identifiers.org/mirbase'\n  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'\n  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'\n  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'\n  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'\n  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='\n  NCBIGene: 'http://identifiers.org/ncbigene/'\n  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'\n  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'\n  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='\n  OBAN: 'http://purl.org/oban/'\n  oboformat: 'http://www.geneontology.org/formats/oboInOwl#'\n  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'\n  OBOREL: 'http://purl.obolibrary.org/obo/RO_'\n  ORCID: 'https://orcid.org/'\n  ORPHA: 'http://www.orpha.net/ORDO/Orphanet_'\n  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'\n  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='\n  PathWhiz: 'http://smpdb.ca/pathways/#'  # See also https://smpdb.ca/pathwhiz/\n  pav: 'http://purl.org/pav/'\n  PHAROS: 'http://pharos.nih.gov'\n  PomBase: 'https://www.pombase.org/gene/'\n  prov: 'http://www.w3.org/ns/prov#'\n  qud: 'http://qudt.org/1.1/schema/qudt#'\n  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'\n  ResearchID: 'https://publons.com/researcher/'\n  RO: 'http://purl.obolibrary.org/obo/RO_'\n  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'\n  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='\n  schema: 'http://schema.org/'\n  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='\n  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'\n  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'\n  SIO: 'http://semanticscience.org/resource/SIO_'\n  SNOMED: 'http://www.snomedbrowser.com/Codes/Details/'\n  SNOMEDCT: 'http://www.snomedbrowser.com/Codes/Details/'\n  SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'\n  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'\n  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'\n  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'\n  # The UMLS Semantic types and groups namespaces don't have a directly\n  # resolvable Base URI, but we point to a pair of sensible web documents\n  STY: 'http://purl.bioontology.org/ontology/STY/'\n  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'\n  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'\n  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'\n  # The \"Variation Modelling Collaboration\" (VMC) is not (yet) a conventional namespace so we point to its Github repo\n  # See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and\n  # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/\n  VMC: 'https://github.com/ga4gh/vr-spec/'\n  WBls: 'http://purl.obolibrary.org/obo/WBBL_'\n  WBbt: 'http://purl.obolibrary.org/obo/WBBT_'\n  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'\n  WIKIDATA: 'https://www.wikidata.org/wiki/'            # Wikidata Entity\n  WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:'  # Wikidata Property - not a conventional namespace prefix\n  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'\n  XPO: 'http://purl.obolibrary.org/obo/XPO_'  # Xenopus Phenotype Ontology\n  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='\n\ndefault_prefix: biolink\ndefault_range: string\n\n# 2. The following prefix maps are retrieved from the\n#    specified contexts defined at https://prefixcommons.org/\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\n# The following 'standard' prefixes are also used.\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - OIO\n  - BIOGRID\n  - SO\n\n## ------------\n## SUBSETS\n## ------------\n\n\nsubsets:\n\n  model_organism_database:\n    description: >-\n      Subset that is relevant for a typical Model Organism Database (MOD)\n\n  translator_minimal:\n    description: >-\n      Minimum subset of translator work\n\n  samples:\n    description: >-\n      Sample/biosample datamodel\n\n  testing:\n    description: >-\n      TBD\n\n\n## ------------\n## TYPES\n## ------------\n\nimports:\n  - linkml:types\n\ntypes:\n\n  chemical formula value:\n    uri: xsd:string\n    base: str\n    description: A chemical formula\n    notes:\n      - Should be implemented as a stronger type\n\n  category type:\n    typeof: uriorcurie\n    description: >-\n      A primitive type in which the value denotes a class within the biolink model.\n      The value must be a URI or a CURIE. In a Neo4j representation, the value should\n      be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,\n      the value should be a URI such as https://w3id.org/biolink/vocab/Gene\n\n  iri type:\n    typeof: uriorcurie\n    description: >-\n      An IRI\n\n  label type:\n    typeof: string\n    description: >-\n      A string that provides a human-readable name for an entity\n\n  predicate type:\n    typeof: uriorcurie\n    description: >-\n      A CURIE from the biolink related_to hierarchy.\n      For example, biolink:related_to, biolink:causes, biolink:treats.\n\n  narrative text:\n    typeof: string\n    description: >-\n      A string that provides a human-readable description of something\n\n  symbol type:\n    typeof: string\n\n  frequency value:\n    typeof: string\n    uri: UO:0000105\n\n  percentage frequency value:\n    typeof: double\n    uri: UO:0000187\n\n  quotient:\n    aliases: [ 'ratio' ]\n    typeof: double\n    uri: UO:0010006\n\n  unit:\n    typeof: string\n    uri: UO:0000000\n    id_prefixes:\n      - UO\n    exact_mappings:\n      - qud:Unit\n\n  time type:\n    typeof: time\n\n  biological sequence:\n    typeof: string\n\n## ------------\n## SLOTS\n## ------------\n\nslots:\n\n  ## ---------------\n  ## ATTRIBUTE SLOTS\n  ## ---------------\n\n  has attribute:\n    description: >-\n      connects any entity to an attribute\n    domain: entity\n    range: attribute\n    multivalued: true\n    in_subset:\n      - samples\n    close_mappings:\n      # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'\n      - OBI:0001927\n    exact_mappings:\n      - SIO:000008\n    narrow_mappings:\n      # if 'has attribute' annotates a NamedThing as subject or\n      # object of an association, these OBAN mappings may apply\n      - OBAN:association_has_subject_property\n      - OBAN:association_has_object_property\n      - CPT:has_possibly_included_panel_element\n      - DRUGBANK:category\n      # RTX contributed terms. Could perhaps review for more semantically precise mappings?\n      - EFO:is_executed_in\n      - HANCESTRO:0301\n      - LOINC:has_action_guidance\n      - LOINC:has_adjustment\n      - LOINC:has_aggregation_view\n      - LOINC:has_approach_guidance\n      - LOINC:has_divisor\n      - LOINC:has_exam\n      - LOINC:has_method\n      - LOINC:has_modality_subtype\n      - LOINC:has_object_guidance\n      - LOINC:has_scale\n      - LOINC:has_suffix\n      - LOINC:has_time_aspect\n      - LOINC:has_time_modifier\n      - LOINC:has_timing_of\n      # disease is stage\n      - NCIT:R88\n      - NCIT:eo_disease_has_property_or_attribute\n      - NCIT:has_data_element\n      - NCIT:has_pharmaceutical_administration_method\n      - NCIT:has_pharmaceutical_basic_dose_form\n      - NCIT:has_pharmaceutical_intended_site\n      - NCIT:has_pharmaceutical_release_characteristics\n      - NCIT:has_pharmaceutical_state_of_matter\n      - NCIT:has_pharmaceutical_transformation\n      - NCIT:is_qualified_by\n      - NCIT:qualifier_applies_to\n      - NCIT:role_has_domain\n      - NCIT:role_has_range\n      - INO:0000154\n      - HANCESTRO:0308\n      - OMIM:has_inheritance_type\n      - ORPHA:C016\n      - ORPHA:C017\n      - RO:0000053\n      # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here\n      - RO:0000086\n      - RO:0000087\n      - SNOMED:has_access\n      - SNOMED:has_clinical_course\n      - SNOMED:has_count_of_base_of_active_ingredient\n      - SNOMED:has_dose_form_administration_method\n      - SNOMED:has_dose_form_release_characteristic\n      - SNOMED:has_dose_form_transformation\n      - SNOMED:has_finding_context\n      - SNOMED:has_finding_informer\n      - SNOMED:has_inherent_attribute\n      - SNOMED:has_intent\n      - SNOMED:has_interpretation\n      - SNOMED:has_laterality\n      - SNOMED:has_measurement_method\n      - SNOMED:has_method\n      - SNOMED:has_priority\n      - SNOMED:has_procedure_context\n      - SNOMED:has_process_duration\n      - SNOMED:has_property\n      - SNOMED:has_revision_status\n      - SNOMED:has_scale_type\n      - SNOMED:has_severity\n      - SNOMED:has_specimen\n      - SNOMED:has_state_of_matter\n      - SNOMED:has_subject_relationship_context\n      - SNOMED:has_surgical_approach\n      - SNOMED:has_technique\n      - SNOMED:has_temporal_context\n      - SNOMED:has_time_aspect\n      - SNOMED:has_units\n      - UMLS:has_structural_class\n      - UMLS:has_supported_concept_property\n      - UMLS:has_supported_concept_relationship\n      - UMLS:may_be_qualified_by\n\n  has attribute type:\n    description: >-\n      connects an attribute to a class that describes it\n    domain: attribute\n    range: ontology class\n    multivalued: false\n    required: true\n    in_subset:\n      - samples\n    narrow_mappings:\n      - LOINC:has_modality_type\n      - LOINC:has_view_type\n\n  # TRAPI Attribute schema alignment:\n  # value: NamedThing.name\n  # value_type: NamedThing.category\n  # value_type_name: quantity_value.NamedThing.name\n  has qualitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: named thing\n    multivalued: false\n    in_subset:\n      - samples\n\n  # TRAPI Attribute schema alignment:\n  # value: quantity_value.has_numeric_value[double] - may be a vector?\n  # value_type: quantity_value.has_unit.unit.uri\n  # value_type_name: quantity_value.has_unit.unit.name[string]\n  has quantitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: quantity value\n    multivalued: true\n    exact_mappings:\n      - qud:quantityValue\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_numerator_value\n      - SNOMED:has_presentation_strength_denominator_value\n      - SNOMED:has_presentation_strength_numerator_value\n    in_subset:\n      - samples\n\n  has numeric value:\n    description: >-\n      connects a quantity value to a number\n    domain: quantity value\n    range: double\n    multivalued: false\n    exact_mappings:\n      - qud:quantityValue\n    in_subset:\n      - samples\n\n  has unit:\n    description: >-\n      connects a quantity value to a unit\n    domain: quantity value\n    range: unit\n    multivalued: false\n    close_mappings:\n      # These RTX contributed terms mean \"is unit of\" which is the semantic inverse of this biolink:has_unit term\n      - EFO:0001697\n      - UO-PROPERTY:is_unit_of\n    exact_mappings:\n      - qud:unit\n      - IAO:0000039\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_denominator_unit\n      - SNOMED:has_concentration_strength_numerator_unit\n      - SNOMED:has_presentation_strength_denominator_unit\n      - SNOMED:has_presentation_strength_numerator_unit\n      - SNOMED:has_unit_of_presentation\n    in_subset:\n      - samples\n\n  base coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'one-based', 'fully-closed' ]\n    description: >-\n      A position in the base coordinate system.  Base coordinates start at position 1 instead of position 0.\n    range: integer\n\n  ## --------------------\n  ## NODE PROPERTY SLOTS\n  ## --------------------\n\n  node property:\n    description: >-\n      A grouping for any property that holds between a node and a value\n    domain: named thing\n\n  id:\n    identifier: true\n    description: >-\n      A unique identifier for an entity.\n      Must be either a CURIE shorthand for a URI or a complete URI\n    in_subset:\n      - translator_minimal\n    required: true\n    exact_mappings:\n      - agrkb:primaryId\n      - gff3:ID\n      - gpi:DB_Object_ID\n\n  iri:\n    description: >-\n      An IRI for an entity. This is determined by the id using expansion rules.\n    range: iri type\n    in_subset:\n      - translator_minimal\n      - samples\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P854\n\n  type:\n    slot_uri: rdf:type\n    exact_mappings:\n      - agrkb:soTermId\n      - gff3:type\n      - gpi:DB_Object_Type\n\n  category:\n    is_a: type\n    domain: entity\n    range: category type\n    designates_type: true\n    description: >-\n      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the\n      biolink entity type class.\n       * In a neo4j database this MAY correspond to the neo4j label tag.\n       * In an RDF database it should be a biolink model class URI.\n      This field is multi-valued. It should include values for ancestors of the biolink class; for example,\n      a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\n\n      In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink\n      class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`\n      may have a rdf:type assertion to a SO class such as TF_binding_site,\n      which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,\n      biolink:MolecularEntity, biolink:NamedThing}\n    is_class_field: true\n    multivalued: true\n    in_subset:\n      - translator_minimal\n\n  name:\n    aliases: [ 'label', 'display name', 'title' ]\n    description: >-\n      A human-readable name for an attribute or entity.\n    range: label type\n    in_subset:\n      - translator_minimal\n      - samples\n    #\n    # linkML doesn't like this name slot to be \"required: true\".\n    # Besides, some entity nodes/attributes may not have names?\n    # required: true\n    slot_uri: rdfs:label\n    exact_mappings:\n      - gff3:Name\n      - gpi:DB_Object_Name\n    narrow_mappings:\n      - dct:title\n      - WIKIDATA_PROPERTY:P1476\n\n  stoichiometry:\n    description: >-\n      the relationship between the relative quantities of substances taking part in a reaction or\n      forming a compound, typically a ratio of whole integers.\n    is_a: association slot\n    range: integer\n\n  reaction direction:\n    description: >-\n      the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.)\n    is_a: association slot\n    range: reaction_direction_enum\n    narrow_mappings:\n      - NCIT:C42677\n\n  reaction balanced:\n    is_a: association slot\n    range: boolean\n\n  reaction side:\n    description: >-\n      the side of a reaction being modeled (ie: left or right)\n    is_a: association slot\n    range: reaction_side_enum\n\n  symbol:\n    is_a: node property\n    domain: named thing\n    description: >-\n      Symbol for a particular thing\n    exact_mappings:\n      - agrkb:symbol\n      - gpi:DB_Object_Symbol\n\n  synonym:\n    is_a: node property\n    aliases: [ 'alias' ]\n    domain: named thing\n    range: label type\n    description: >-\n      Alternate human-readable names for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      # there is an interesting debate here: are these terms \"narrower\" a.k.a. more specialized instances of\n      # 'biolink:synonym' or should they be binned into their respective namesake class of mappings?\n      # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.\n      - skos:altLabel\n      - gff3:Alias\n      - agrkb:synonyms\n      - gpi:DB_Object_Synonyms\n      # TODO: RTX contributed terms mapped here... May need review?\n      - HANCESTRO:0330\n      - IAO:0000136\n      - RXNORM:has_tradename\n\n  exact_synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasExactSynonym\n\n  broad_synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasBroadSynonym\n\n  narrow_synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasNarrowSynonym\n\n  related_synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasRelatedSynonym\n\n  has topic:\n    aliases: [ 'topic', 'descriptors' ]\n    is_a: node property\n    range: ontology class\n    exact_mappings:\n      - foaf:topic\n    description: >-\n      Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.\n      See https://github.com/biolink/biolink-model/issues/238\n\n  xref:\n    is_a: node property\n    aliases: [ 'dbxref', 'Dbxref', 'DbXref' ]\n    domain: named thing\n    range: uriorcurie\n    description: >-\n      Alternate CURIEs for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - gff3:Dbxref\n      - gpi:DB_Xrefs\n\n  full name:\n    is_a: node property\n    domain: named thing\n    range: label type\n    description: >-\n      a long-form human readable name for a thing\n\n  description:\n    aliases: [ 'definition' ]\n    range: narrative text\n    description: >-\n      a human-readable description of an entity\n    in_subset:\n      - translator_minimal\n    slot_uri: dct:description\n    exact_mappings:\n      - IAO:0000115\n      - skos:definitions\n    narrow_mappings:\n      - gff3:Description\n\n  systematic synonym:\n    is_a: node property\n    domain: named thing\n    range: label type\n    multivalued: true\n    slot_uri: GOP:systematic_synonym\n    description: >-\n      more commonly used for gene symbols in yeast\n\n  affiliation:\n    is_a: node property\n    description: >-\n      a professional relationship between one provider (often a person) within another provider (often an organization).\n      Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.\n    domain: agent\n    range: uriorcurie\n    multivalued: true\n\n  address:\n    is_a: node property\n    description: >-\n      the particulars of the place where someone or an organization is situated.  For now, this slot is a\n      simple text \"blob\" containing all relevant details of the given location for fitness of purpose.\n      For the moment, this \"address\" can include other contact details such as email and phone number(?).\n\n  ## Space\n\n  latitude:\n    is_a: node property\n    range: float\n    description: >-\n      latitude\n    exact_mappings:\n      - wgs:lat\n\n  longitude:\n    is_a: node property\n    range: float\n    description: >-\n      longitude\n    exact_mappings:\n      - wgs:long\n\n  ## Time\n\n  timepoint:\n    aliases: [ 'duration' ]\n    range: time type\n    description: >-\n      a point in time\n\n  creation date:\n    is_a: node property\n    aliases: [ 'publication date' ]\n    range: date\n    description: >-\n      date on which an entity was created. This can be applied to nodes or edges\n    exact_mappings:\n      - dct:createdOn\n      - WIKIDATA_PROPERTY:P577\n\n  update date:\n    is_a: node property\n    range: date\n    description: >-\n      date on which an entity was updated. This can be applied to nodes or edges\n\n  ## Statistics\n\n  aggregate statistic:\n    is_a: node property\n    abstract: true\n\n  has count:\n    description: >-\n      number of things with a particular property\n    is_a: aggregate statistic\n    range: integer\n    exact_mappings:\n      - LOINC:has_count\n\n  has total:\n    description: >-\n      total number of things in a particular reference set\n    is_a: aggregate statistic\n    range: integer\n\n  has quotient:\n    is_a: aggregate statistic\n    range: double\n\n  has percentage:\n    description: >-\n      equivalent to has quotient multiplied by 100\n    is_a: aggregate statistic\n    range: double\n\n  ## Properties for Information Content Entity and Publication Nodes\n\n  has taxonomic rank:\n    is_a: node property\n    range: taxonomic rank\n    multivalued: false\n    mappings:\n      - WIKIDATA:P105\n\n  has dataset:\n    is_a: node property\n    domain: dataset version\n    range: dataset\n    slot_uri: dct:source\n\n  source web page:\n    is_a: node property\n    domain: dataset summary\n    broad_mappings:\n      - dct:source\n\n  source logo:\n    is_a: node property\n    domain: dataset summary\n    slot_uri: schema:logo\n\n  retrieved on:\n    is_a: node property\n    domain: dataset\n    range: date\n    exact_mappings:\n      - pav:retrievedOn\n\n  version of:\n    is_a: node property\n    domain: dataset version\n    range: dataset summary\n    exact_mappings:\n      - dct:isVersionOf\n\n  version:\n    is_a: node property\n    domain: dataset\n    broad_mappings:\n      - pav:version\n      - owl:versionInfo\n\n  license:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:license\n    narrow_mappings:\n      - WIKIDATA_PROPERTY:P275\n\n  rights:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:rights\n\n  format:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:format\n      - WIKIDATA_PROPERTY:P2701\n\n  created with:\n    is_a: node property\n    domain: dataset\n    exact_mappings:\n      - pav:createdWith\n\n  download url:\n    is_a: node property\n    domain: information content entity\n    slot_uri: dcat:downloadURL\n\n  dataset download url:\n    is_a: node property\n    domain: dataset\n    slot_uri: dcat:downloadURL\n\n  distribution download url:\n    is_a: node property\n    domain: dataset distribution\n    exact_mappings:\n      - dcat:downloadURL\n\n  ingest date:\n    is_a: node property\n    domain: dataset version\n    slot_uri: pav:version\n\n  has distribution:\n    is_a: node property\n    domain: dataset version\n    range: dataset distribution\n    slot_uri: dct:distribution\n\n  published in:\n    is_a: node property\n    description: >-\n      CURIE identifier of a broader publication context within which the publication may be placed,\n      e.g. a specified book or journal.\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - NLMID\n      - issn\n      - isbn\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1433\n\n  iso abbreviation:\n    is_a: node property\n    description: >-\n      Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system\n      See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,\n      then the iso abbreviation pertains to the broader publication context (the journal) within which the given\n      publication node is embedded, not the publication itself.\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1160\n\n  authors:\n    is_a: node property\n    singular_name: author\n    description: >-\n      connects an publication to the list of authors who contributed to the publication.\n      This property should be a comma-delimited list of author names. It is recommended that an author's name\n      be formatted as \"surname, firstname initial.\".   Note that this property is a node annotation expressing\n      the citation list of authorship which might typically otherwise be more completely documented in\n      biolink:PublicationToProviderAssociation defined edges which point to full details about an author\n      and possibly, some qualifiers which clarify the specific status of a given author in the publication.\n    multivalued: true\n    domain: publication\n\n  volume:\n    is_a: node property\n    description: >-\n      volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P478\n\n  chapter:\n    is_a: node property\n    description: >-\n      chapter of a book\n    domain: book chapter\n    exact_mappings:\n      - WIKIDATA:Q1980247\n\n  issue:\n    is_a: node property\n    description: >-\n      issue of a newspaper, a scientific journal or magazine for reference purpose\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P433\n\n  pages:\n    is_a: node property\n    description: >-\n      page number of source referenced for statement or publication\n    domain: publication\n    multivalued: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P304\n\n  summary:\n    is_a: node property\n    # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot,\n    # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract'\n    aliases: [ 'abstract' ]\n    description: >-\n      executive  summary of a publication\n    domain: publication\n    exact_mappings:\n      - dct:abstract\n      - WIKIDATA:Q333291\n\n  keywords:\n    is_a: node property\n    description: >-\n      keywords tagging a publication\n    domain: publication\n    multivalued: true\n\n  mesh terms:\n    is_a: node property\n    description: >-\n      mesh terms tagging a publication\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - MESH\n    multivalued: true\n    exact_mappings:\n      - dcid:MeSHTerm\n\n  ## Biology\n\n  has biological sequence:\n    is_a: node property\n    description: >-\n      connects a genomic feature to its sequence\n    range: biological sequence\n\n  has gene or gene product:\n    is_a: node property\n    description: >-\n      connects an entity with one or more gene or gene products\n    range: gene\n    multivalued: true\n\n  has gene:\n    is_a: has gene or gene product\n    description: >-\n      connects an entity associated with one or more genes\n    range: gene\n    multivalued: true\n\n  has zygosity:\n    is_a: node property\n    domain: nucleic acid entity\n    range: zygosity\n\n  ## Chemistry, drugs and food\n\n  has chemical formula:\n    is_a: node property\n    range: chemical formula value\n    description: >-\n      description of chemical compound based on element symbols\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P274\n\n  is metabolite:\n    is_a: node property\n    domain: molecular entity\n    range: boolean\n    description: >-\n      indicates whether a molecular entity is a metabolite\n    exact_mappings:\n      - CHEBI:25212\n\n  has constituent:\n    description: >-\n      one or more molecular entities within a chemical mixture\n    is_a: node property\n    range: molecular entity\n    multivalued: true\n\n  has drug:\n    is_a: node property\n    description: >-\n      connects an entity to one or more drugs\n    range: drug\n    multivalued: true\n\n  has device:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) devices\n    range: device\n    multivalued: true\n\n  has procedure:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) procedures\n    range: procedure\n    multivalued: true\n\n  ## Clinical exposures\n\n  has receptor:\n    is_a: node property\n    domain: exposure event\n    range: organismal entity\n    description: >-\n      the organism or organism part being exposed\n    exact_mappings:\n      - ExO:0000001\n\n  has stressor:\n    is_a: node property\n    domain: exposure event\n    aliases: [ 'has stimulus' ]\n    description: >-\n      the process or entity that the receptor is being exposed to\n    exact_mappings:\n      - ExO:0000000\n\n  has route:\n    is_a: node property\n    domain: exposure event\n    description: >-\n      the process that results in the stressor coming into direct contact with the receptor\n    exact_mappings:\n      - ExO:0000055\n    narrow_mappings:\n      - LOINC:has_pharmaceutical_route\n      - SNOMED:has_dose_form_intended_site\n      - SNOMED:has_route_of_administration\n\n  has population context:\n    deprecated: true\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: association slot\n    range: population of individual organisms\n\n  population context qualifier:\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: association slot\n    range: population of individual organisms\n\n  has temporal context:\n    deprecated: true\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n    is_a: association slot\n    range: time type\n\n  temporal context qualifier:\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n      for time intervales, use temporal interval qualifier.\n    is_a: association slot\n    range: time type\n\n  temporal interval qualifier:\n    is_a: temporal context qualifier\n    description: >-\n      a constraint of a time interval placed upon the truth value of an\n      association.\n\n  is supplement:\n    description: >-\n    is_a: node property\n    range: chemical mixture\n\n  trade name:\n    description: >-\n    is_a: node property\n    range: chemical entity\n\n  available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: drug_availability_enum\n\n  is toxic:\n    description: >-\n    is_a: node property\n    multivalued: false\n    range: boolean\n\n  has chemical role:\n    is_a: node property\n    description: >-\n      A role is particular behaviour which a material entity may exhibit.\n    range: chemical role\n    multivalued: true\n\n  max tolerated dose:\n    description: >-\n      The highest dose of a drug or treatment that does not cause unacceptable side effects.\n      The maximum tolerated dose is determined in clinical trials by testing increasing doses\n      on different groups of people until the highest dose with acceptable side effects is\n      found. Also called MTD.\n    is_a: node property\n    multivalued: false\n    range: string\n\n  animal model available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: disease or phenotypic feature\n\n  FDA adverse event level:\n    description: >-\n    is_a: association slot\n    range: FDA_IDA_adverse_event_enum\n\n  highest FDA approval status:\n    description: >-\n      Should be the highest level of FDA approval this chemical entity or device has, regardless of which\n      disease, condition or phenotype it is currently being reviewed to treat.  For specific levels of FDA\n      approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'\n\n  drug regulatory status world wide:\n    aliases: [ 'max phase' ]\n    description: >-\n      An agglomeration of drug regulatory status worldwide. Not specific to FDA.\n    exact_mappings:\n      - NCIT:C172573\n    narrow_mappings:\n      - NCIT:R172\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n\n  routes of delivery:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    multivalued: true\n    range: drug_delivery_enum\n\n  ## -------------------\n  ## QUALIFIERS\n  ## -------------------\n\n  form or variant qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.\n    examples:\n      - value: mutation\n    notes: >-\n      please see the chemical_or_gene_or_gene_product_form_enum (below) for examples of 'form or variant qualifier'\n      terms in the gene->chemical association space. \n\n  aspect qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    notes: >-\n      for good examples of aspects in the gene-> chemical space, please see the \n      gene_or_gene_product_or_chemical_entity_aspect_enum (below) which lists many aspects that can be used to qualify \n      the gene making the full subject a different ontological type.  \n\n  derivative qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.\n    examples:\n      - value: metabolite\n\n  part qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).\n    examples:\n      - value: polyA tail\n      - value: upstream control region\n\n  context qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.\n    examples:\n      - value: cohort x\n      - value: blood\n      - value: gut microbiome\n\n  direction qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n\n  subject aspect qualifier:\n    is_a: aspect qualifier\n\n  subject form or variant qualifier:\n    is_a: form or variant qualifier\n\n  subject part qualifier:\n    is_a: part qualifier\n\n  subject derivative qualifier:\n    is_a: derivative qualifier\n\n  subject context qualifier:\n    is_a: context qualifier\n\n  subject direction qualifier:\n    is_a: direction qualifier\n\n  object aspect qualifier:\n    is_a: aspect qualifier\n\n  object form or variant qualifier:\n    is_a: form or variant qualifier\n\n  object part qualifier:\n    is_a: part qualifier\n\n  object derivative qualifier:\n    is_a: derivative qualifier\n\n  object context qualifier:\n    is_a: context qualifier\n\n  object direction qualifier:\n    is_a: direction qualifier\n    range: direction_qualifier_enum\n\n  qualified predicate:\n    is_a: association slot\n    description: >-\n      predicate to be used in an association when subject and object qualifiers are present and the full\n      reading of the statement requires a qualification to the predicate in use in order to refine or \n      increase the specificity of the full statement reading\n\n  statement qualifier:\n    is_a: association slot\n    description: >-\n\n  causal mechanism qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a type of molecular control mechanism through which an\n      effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition',\n      'allosteric modulation', 'channel blocker')\n\n  anatomical context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing an anatomical location where an relationship expressed in an\n      association took place (can be a tissue, cell type, or subcellular location).\n    range: anatomical_context_qualifier_enum\n    notes: >-\n      Anatomical context values can be any term from UBERON. See anatomical_context_qualifier_enum for more\n      details.\n\n  species context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a taxonomic category of species in which a relationship\n      expressed in an association took place.\n    range: organism taxon\n\n  qualifiers:\n    singular_name: qualifier\n    description: >-\n      connects an association to qualifiers that modify or\n      qualify the meaning of that association\n    local_names:\n      ga4gh: annotation qualifier\n    is_a: association slot\n    multivalued: true\n    range: ontology class\n\n  frequency qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\n    is_a: association slot\n    range: frequency value\n\n  severity qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      how severe the phenotype is in the subject\n    is_a: association slot\n    range: severity value\n\n  sex qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state whether\n      the association is specific to a particular sex.\n    is_a: association slot\n    range: biological sex\n\n  onset qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      when the phenotype appears is in the subject\n    is_a: association slot\n    range: onset\n\n  clinical modifier qualifier:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    is_a: association slot\n    range: clinical modifier\n\n  sequence variant qualifier:\n    description: >-\n      a qualifier used in an association with the variant\n    is_a: association slot\n    range: sequence variant\n\n  quantifier qualifier:\n    is_a: association slot\n    range: ontology class\n    description: >-\n      A measurable quantity for the object of the association\n    narrow_mappings:\n      # TODO: RTX contributed terms mapped here... May need review?\n      - LOINC:analyzes\n      - LOINC:measured_by\n      - LOINC:property_of\n      - SEMMEDDB:measures\n      - UMLS:measures\n\n  catalyst qualifier:\n    is_a: association slot\n    multivalued: true\n    range: macromolecular machine mixin\n    description: >-\n      a qualifier that connects an association between two causally connected\n      entities (for example, two chemical entities, or a chemical entity in\n      that changes location) and the gene product, gene, or complex that\n      enables or catalyzes the change.\n\n  stage qualifier:\n    description: >-\n      stage during which gene or protein expression of takes place.\n    is_a: association slot\n    range: life stage\n    # path: \"object/during\"\n    examples:\n      - value: UBERON:0000069\n        description: larval stage\n\n  ## --------------------\n  ## PREDICATES/RELATIONS\n  ## --------------------\n\n  related to:\n    description: >-\n      A relationship that is asserted between two named things\n    domain: named thing\n    range: named thing\n    multivalued: true\n    inherited: true\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:relatedMatch\n      - UMLS:related_to\n    broad_mappings:\n      - owl:topObjectProperty\n    narrow_mappings:\n      - SEMMEDDB:compared_with\n      - SEMMEDDB:higher_than\n      - SEMMEDDB:lower_than\n      - BFO:0000054\n      - UBERON_CORE:protects\n      - GOREL:0002005\n      - GOREL:0012006\n      # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms\n      - BTO:related_to\n      - CHEBI:is_conjugate_acid_of\n      - CHEBI:is_conjugate_base_of\n      - CPT:has_add_on_code\n      - CPT:mapped_to\n      - EFO:0006351\n      - FMA:connected_to\n      - FMA:continuous_with\n      - FMA:homonym_of\n      - FMA:related_developmental_entity_of\n      - RO:0002093\n      - RO:0002092\n      - RO:0002084\n      - HCPCS:mapped_to\n      # RTX contributed terms, perhaps belong somewhere else with more precise semantics?\n      - HMDB:disease\n      - HMDB:has_protein_association\n      - IAO:0000136\n      - LOINC:has_answer\n      - LOINC:has_challenge\n      - LOINC:has_evaluation\n      - LOINC:mapped_to\n      - LOINC:mth_has_expanded_form\n      - MESH:RO\n      - MESH:has_mapping_qualifier\n      - MESH:mapped_to\n      - MONDO:disease_shares_features_of\n      - NCIT:disease_may_have_associated_disease\n      - NCIT:human_disease_maps_to_eo_disease\n      - NCIT:is_abnormal_cell_of_disease\n      - NCIT:is_related_to_endogenous_product\n      - UBERON_NONAMESPACE:connected_to\n      - UBERON_NONAMESPACE:innervated_by\n      - NBO-PROPERTY:is_about\n      - RO:0000053 # bearer_of\n      - PATO:reciprocal_of\n      - RO:0000052\n      - RO:0002001\n      - RO:0002002\n      - RO:0002003\n      - RO:0002008\n      - RO:0002134\n      - RO:0002150\n      - RO:0002159\n      - RO:0002176\n      - RO:0002177\n      - RO:0002178\n      - RO:0002179\n      - RO:0002314\n      - RO:0002322\n      # functionally related to\n      - RO:0002328\n      - RO:0002332\n      - RO:0002338\n      - RO:0002339\n      - RO:0002341\n      - RO:0002342\n      - RO:0002344\n      - RO:0002348\n      - RO:0002349\n      - RO:0002356\n      - RO:0002371\n      - RO:0002372\n      - RO:0002373\n      - RO:0002374\n      - RO:0002385\n      - RO:0002387\n      - RO:0002451\n      - RO:0002494\n      - RO:0002495\n      - RO:0002568\n      - RO:0002573\n      - RO:0004026\n      - RO:0004027\n      - RO:0009001\n      - RO:0009004\n      - RXNORM:has_form\n      - RXNORM:reformulated_to\n      - SNOMED:has_associated_morphology\n      - SNOMED:has_associated_procedure\n      - SNOMED:has_direct_morphology\n      - SNOMED:has_disposition\n      - SNOMED:has_indirect_morphology\n      - SNOMED:has_modification\n      - SNOMED:has_procedure_morphology\n      - SNOMED:has_specimen_source_morphology\n      - SNOMED:inheres_in\n      - SNOMED:is_interpreted_by\n      - SNOMED:relative_to_part_of\n      - UBERON:synapsed_by\n      - UMLS:RO\n      - UMLS:RQ\n      - UMLS:class_code_classified_by\n      - UMLS:exhibited_by\n      - UMLS:has_context_binding\n      - UMLS:has_form\n      - UMLS:has_mapping_qualifier\n      - UMLS:larger_than\n      - UMLS:mapped_to\n      - UMLS:owning_section_of\n\n  related to at concept level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between terminology components that describe the conceptual model of a domain.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  related to at instance level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between two instances of a data classes.  Much like an assertion component,\n      in an ABox, these represent facts associated with the conceptual model.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  associated with:\n    is_a: related to at instance level\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent,\n      'related to'. This relationship holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated.  E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial \n      Infarction (MI)” asserts that having Afib is not statistically independent from whether a patient \n      will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to \n      the statistical variables, or represent related entities for which the variables serve as proxies in an \n      Association (e.g. diseases, chemical entities or processes).\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    domain: named thing\n    range: named thing\n    exact_mappings:\n      - SEMMEDDB:associated_with\n    narrow_mappings:\n      - RO:0004029\n      - SNOMEDCT:47429007\n\n  superclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a super class of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    inverse: subclass of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q66088480\n      - CHEMBL.MECHANISM:superset_of\n      - GO:inverse_isa\n      - MESH:inverse_isa\n      - RXNORM:inverse_isa\n      - VANDF:inverse_isa\n    narrow_mappings:\n      - NCIT:cdrh_parent_of\n      - NCIT:ctcae_5_parent_of\n      - NCIT:subset_includes_concept\n      - OMIM:has_manifestation\n      - SNOMED:has_basic_dose_form\n      - UMLS:RB\n    annotations:\n      opposite_of: subclass of\n\n  subclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a specialization of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: superclass of\n    close_mappings:\n      # RTX\n      - LOINC:class_of\n      - LOINC:has_class\n    exact_mappings:\n      - rdfs:subClassOf\n      - SEMMEDDB:IS_A\n      - SEMMEDDB:isa\n      - WIKIDATA_PROPERTY:P279\n      - CHEMBL.MECHANISM:subset_of\n      - GO:isa\n      - MESH:isa\n      - RXNORM:isa\n      - VANDF:isa\n    narrow_mappings:\n      - CHEBI:has_parent_hydride\n      - LOINC:has_archetype\n      - LOINC:has_parent_group\n      - LOINC:is_presence_guidance_for\n      - NCIT:gene_product_has_chemical_classification\n      # RTX mapped terms classes for biomarkers\n      - NCIT:R36\n      - NCIT:R42\n      - NCIT:A16\n      - NCIT:A11\n      - NCIT:A14\n      - NCIT:A3\n      - NDDF:has_dose_form\n      - RXNORM:has_dose_form\n      - RXNORM:has_doseformgroup\n      - SNOMED:entire_anatomy_structure_of\n      - SNOMED:has_dose_form\n      # RTX mapping\n      - rdfs:subPropertyOf\n\n  same as:\n    is_a: exact match\n    description: >-\n      holds between two entities that are considered equivalent to each other\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # identical class extension with identical sets of individuals\n      - owl:equivalentClass\n    exact_mappings:\n      # identical individual, or identical class concept/meaning\n      - owl:sameAs\n      - skos:exactMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      # RTX suggests mapping this to proposed new \"biolink:close_match\" predicate instead\n      #- SEMMEDDB:SAME_AS\n      - WIKIDATA_PROPERTY:P2888\n      - CHEMBL.MECHANISM:equivalent_to\n      - MONDO:equivalentTo\n    narrow_mappings:\n      - DRUGBANK:external-identifier\n\n  close match:\n    is_a: related to at concept level\n    description: >-\n      a list of terms from different schemas or terminology systems that have\n      a semantically similar but not strictly equivalent, broader, or narrower\n      meaning. Such terms often describe the same general concept from\n      different ontological perspectives (e.g. drug as a type of chemical\n      entity versus drug as a type of role borne by a chemical entity).\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:closeMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      - SEMMEDDB:SAME_AS\n      - SEMMEDDB:same_as\n    narrow_mappings:\n      - CHEBI:is_enantiomer_of\n      - CHEBI:is_tautomer_of\n      - MEDDRA:classified_as\n      - OIO:hasDbXref\n      - oboformat:xref\n      - RXNORM:has_quantified_form\n      - UMLS:SY\n\n  exact match:\n    is_a: close match\n    description: >-\n      holds between two entities that have strictly equivalent\n      meanings, with a high degree of confidence\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:exactMatch\n      - WIKIDATA:Q39893449\n      - WIKIDATA:P2888\n\n  broad match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a broader, more general meaning. Broader terms are\n      typically shown as parents in a hierarchy or tree.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: narrow match\n    exact_mappings:\n      - skos:broadMatch\n      - WIKIDATA:Q39894595\n\n  narrow match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a narrower, more specific meaning. Narrower terms are\n      typically shown as children in a hierarchy or tree.\n    is_a: related to at concept level\n    inverse: broad match\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - skos:narrowMatch\n      - WIKIDATA:Q39893967\n    annotations:\n      opposite_of: broad match\n\n  opposite of:\n    description: >-\n      x is the opposite of y if there exists some distance metric M, and there exists\n      no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002604\n    see_also:\n      - https://doi.org/10.1101/108977\n      - https://github.com/biolink/biolink-model/issues/657\n\n  has real world evidence of association with:\n    deprecated: true\n\n  associated with likelihood of:\n    is_a: associated with\n    description: >-\n      A a relationship that holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated, wherein the state or value of one variable predicts the future state \n      or value of the other.  E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated \n      with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib \n      is associated with an increased or decreased likelihood that a patient will later exhibit MI. \n\n  likelihood associated with:\n    is_a: associated with\n    description: >-\n    inverse: associated with likelihood of\n\n  associated with increased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is more probable. \n\n  increased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with increased likelihood of\n\n  associated with decreased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is less probable. \n\n  decreased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with decreased likelihood of\n\n  target for:\n    is_a: related to at instance level\n    description: >-\n      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene\n      product could have a therapeutic effect\n    annotations:\n      canonical_predicate: true\n    domain: gene\n    range: disease\n\n  has target:\n    is_a: related to at instance level\n    inverse: target for\n    domain: disease\n    range: gene\n\n  active in:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: cellular component\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002432\n\n  has active component:\n    inverse: active in\n\n  acts upstream of:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002263\n\n  has upstream actor:\n    is_a: related to at instance level\n    inverse: acts upstream of\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004034\n\n  has positive upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004035\n\n  has negative upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of negative effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002264\n\n  has upstream or within actor:\n    is_a: has upstream actor\n    inverse: acts upstream of or within\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004032\n\n  has positive upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004033\n\n  has negative upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within negative effect\n    domain: biological process\n    range: gene or gene product\n\n    ## Publication related predicates\n  mentions:\n    description: >-\n      refers to is a relation between one information content entity and the named thing\n      that it makes reference to.\n    is_a: related to at instance level\n    exact_mappings:\n      - IAO:0000142\n    narrow_mappings:\n      - SIO:000628\n\n  mentioned by:\n    description: >-\n      refers to is a relation between one named thing and the information content entity\n      that it makes reference to.\n    is_a: related to at instance level\n    inverse: mentions\n\n  ## Publication related predicates\n\n  contributor:\n    is_a: related to at instance level\n    domain: information content entity\n    range: agent\n    comments:\n      - This is a grouping for predicates relating entities to their associated contributors realizing them\n    abstract: true\n    exact_mappings:\n      - dct:contributor\n\n  has contributor:\n    inverse: contributor\n    is_a: related to at instance level\n    domain: agent\n    range: information content entity\n\n  provider:\n    is_a: contributor\n    description: >-\n      person, group, organization or project that provides a piece of information (e.g. a knowledge association).\n\n  has provider:\n    inverse: provider\n    is_a: has contributor\n    domain: agent\n    range: information content entity\n\n  publisher:\n    is_a: contributor\n    domain: publication\n    description: >-\n      organization or person responsible for publishing books, periodicals, podcasts, games or software.\n      Note that in the case of publications which have a containing \"published in\" node property, the publisher\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the publisher agent of the encompassing publication\n      (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).\n    exact_mappings:\n      - dct:publisher\n      - WIKIDATA_PROPERTY:P123\n\n  has publisher:\n    is_a: has contributor\n    inverse: publisher\n    domain: agent\n    range: publication\n\n  editor:\n    is_a: contributor\n    domain: publication\n    description: >-\n      editor of a compiled work such as a book or a periodical (newspaper or an academic journal).\n      Note that in the case of publications which have a containing \"published in\" node property, the editor\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the editorial agent of the encompassing publication\n      (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P98\n\n  has editor:\n    inverse: editor\n    is_a: has contributor\n    domain: agent\n    range: publication\n\n  author:\n    is_a: contributor\n    domain: publication\n    description: >-\n      an instance of one (co-)creator primarily responsible for a written work\n    exact_mappings:\n      - dct:creator\n      - WIKIDATA_PROPERTY:P50\n\n  has author:\n    inverse: author\n    is_a: has contributor\n    domain: agent\n    range: publication\n\n  ## end of Publication related predicates\n\n  assesses:\n    aliases: [ 'was assayed against' ]\n    description: >-\n      The effect of a thing on a target was interrogated in some assay.\n      A relationship between some perturbing agent (usually a chemical compound) and some target entity,\n      where the affect of the perturbing agent on the target entity was interrogated in a particular assay.\n      The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type\n      of biological entity.\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n\n  is assessed by:\n    inverse: assesses\n    domain: named thing\n    range: named thing\n\n  interacts with:\n    abstract: true\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between any two entities that directly or indirectly interact with each other\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002434\n      - SEMMEDDB:interacts_with\n    narrow_mappings:\n      # RO terms RTX mapped to 'biolink:related_to' but which imply a chemical interaction\n      - RO:0002103\n      - RO:0002120\n      - RO:0002130\n    notes: >-\n      please use a more specific child predicate of interacts with, either physically interacts with\n      or genetically interacts with. \n\n  physically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two entities that make physical contact as part of some interaction. \n      does not imply a causal relationship.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P129\n    close_mappings:\n      - CHEMBL.MECHANISM:binding_agent\n      - CHEMBL.MECHANISM:chelating_agent\n      - CHEMBL.MECHANISM:cross-linking_agent\n      - CHEMBL.MECHANISM:oxidative_enzyme\n      - CHEMBL.MECHANISM:sequestering_agent\n      - CHEMBL.MECHANISM:substrate\n      - DRUGBANK:target\n    narrow_mappings:\n      # Defined more narrowly as \"substance interaction\", thus specific applies to a subclass entities\n      - DRUGBANK:drug-interaction\n      - FMA:adheres_to\n      - NCIT:A7\n      - PR:non-covalently_bound_to\n\n  directly physically interacts with:\n    is_a: physically interacts with\n    description: >-\n      A causal mechanism mediated by a direct contact between the effector and target entities (this contact may \n      be weak or strong, transient or stable).\n    symmetric: true\n\n  binds:\n    is_a: directly physically interacts with\n    description: >-\n      A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, \n      which form a stable physical interaction.\n    symmetric: true\n\n  indirectly physically interacts with:\n    is_a: physically interacts with\n    symmetric: true\n\n  chemically interacts with:\n    deprecated: true\n    is_a: physically interacts with\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    symmetric: true\n\n  molecularly interacts with:\n    deprecated: true\n    is_a: physically interacts with\n    aliases: [ 'targets' ]\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - DGIdb:antibody\n    exact_mappings:\n      - RO:0002436\n\n  genetically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two genes whose phenotypic effects are dependent on each\n      other in some way - such that their combined phenotypic effects are the\n      result of some interaction between the activity of their gene products.\n      Examples include epistasis and synthetic lethality.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    exact_mappings:\n      - RO:0002435\n\n  affects:\n    is_a: related to at instance level\n    description: >-\n      describes an entity that has a direct affect on the state or quality\n      of another existing entity. Use of the 'affects' predicate implies that\n      the affected entity already exists, unlike predicates such as\n      'affects risk for' and 'prevents, where the outcome is something\n      that may or may not come to be.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # Contributed by RTX. Seems possible that a new predicate \"biolink:in_pathway\" could be justified?\n      - DRUGBANK:pathway\n    exact_mappings:\n      - SEMMEDDB:AFFECTS\n      - SEMMEDDB:affects\n      - DGIdb:affects\n    narrow_mappings:\n      - SEMMEDDB:administered_to\n      - CTD:prediction_hypothesis\n      - GOREL:0001006\n      - CTD:inferred\n      - UPHENO:0000001\n      - RO:0002263\n      - RO:0002264\n      - NCIT:R158\n      - NCIT:R160\n      - NCIT:R30\n      - NCIT:R150\n      - NCIT:R72\n      - NCIT:R146\n      - NCIT:R124\n      - NCIT:R173\n      - NCIT:R100\n      - NCIT:R102\n      - NCIT:R101\n      - NCIT:R113\n      - NCIT:R23\n      - NCIT:R25\n      - NCIT:gene_mapped_to_disease\n      - NCIT:R133\n      - RO:0002343\n      - RO:0002355\n      - RO:0002591\n      - RO:0002592\n      - RO:0012003\n      - SNOMED:has_pathological_process\n\n  affected by:\n    is_a: related to at instance level\n    description: >-\n      describes an entity of which the state or quality is affected by\n      another existing entity.\n    inverse: affects\n\n  associated with sensitivity to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of sensitivity to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - PATO:0000085 # sensitivity toward\n    narrow_mappings:\n      - SNOMEDCT:418038007 # propensity to adverse reaction\n\n  sensitivity associated with:\n    is_a: associated with\n    inverse: associated with sensitivity to\n    range: named thing\n    domain: chemical entity\n\n  associated with resistance to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of resistance to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n\n  resistance associated with:\n    is_a: associated with\n    inverse: associated with resistance to\n    range: named thing\n    domain: chemical entity\n\n  diagnoses:\n    is_a: related to at instance level\n    description: >-\n      a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - NCIT:C15220 # diagnosis\n      - SIO:001331 # diagnosis\n    exact_mappings:\n      - DrugCentral:5271\n      - SEMMEDDB:diagnoses\n\n  is diagnosed by:\n    is_a: related to at instance level\n    inverse: diagnoses\n    range: chemical or drug or treatment\n    domain: disease or phenotypic feature\n\n  increases amount or activity of:\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that increase the amount\n      or activity of the object.\n\n  amount or activity increased by:\n    is_a: related to at instance level\n    inverse: increases amount or activity of\n\n  decreases amount or activity of:\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that decrease the amount\n      or activity of the object.\n\n  amount or activity decreased by:\n    is_a: related to at instance level\n    inverse: decreases amount or activity of\n\n  ## role mixins for use in tagging corresponding role predicates\n\n  chemical role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a chemical context.\n    mixin: true\n    exact_mappings:\n      - CHEBI:51086\n\n  biological role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a biological context.\n    mixin: true\n    narrow_mappings:\n      - CHEBI:24432\n\n  affects abundance of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one changes the amount of the\n      other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_abundance_of\n\n  abundance affected by:\n    deprecated: true\n    is_a: affected by\n    inverse: affects abundance of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases abundance of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one increases the \n      amount of the other within a system of interest\n    is_a: affects abundance of\n    in_subset:\n      - translator_minimal\n    mixins:\n      - increases amount or activity of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases abundance of\n    related_mappings:\n      - UBERGRAPH:is_increase_of\n\n  abundance increased by:\n    deprecated: true\n    is_a: abundance affected by\n    inverse: increases abundance of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  decreases abundance of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one\n      decreases the amount of the other within a system of interest\n    is_a: affects abundance of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases abundance of\n\n    related_mappings:\n      - UBERGRAPH:is_decrease_of\n\n  abundance decreased by:\n    deprecated: true\n    is_a: abundance affected by\n    inverse: decreases abundance of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases activity of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one\n      increases the activity of the other within a system of interest\n    is_a: affects activity of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    related_mappings:\n      - GAMMA:ec50\n      - GAMMA:ac50\n    narrow_mappings:\n      - GAMMA:activator\n      - GAMMA:partial_agonist\n      - GAMMA:agonist\n      - GAMMA:opener\n      - GAMMA:positive_allosteric_modulator\n      - GAMMA:positive_modulator\n      - GAMMA:inducer\n      - GAMMA:potentiator\n      - GAMMA:stimulator\n      - CHEMBL.MECHANISM:agonist\n      - CHEMBL.MECHANISM:opener\n      - CHEMBL.MECHANISM:partial_agonist\n      - CHEMBL.MECHANISM:positive_allosteric_modulator\n      - CHEMBL.MECHANISM:positive_modulator\n      - DGIdb:agonist\n      - DGIdb:partial_agonist\n      - DGIdb:inducer\n      - DGIdb:positive_allosteric_modulator\n      - DGIdb:stimulator\n    annotations:\n      opposite_of: decreases activity of\n\n  affects activity of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one changes the activity of the\n      other within a system of interest\n    is_a: affects\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    narrow_mappings:\n      - GAMMA:allosteric_modulator\n      - GAMMA:modulator\n      - GAMMA:regulator\n      - DGIdb:modulator\n      - DGIdb:allosteric_modulator\n\n  activity affected by:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one is changed by the\n      activity of the other within a system of interest\n    is_a: affected by\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects activity of\n\n  activity increased by:\n    deprecated: true\n    is_a: activity affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases activity of\n\n  decreases activity of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product where the action or effect of one decreases the\n      activity of the other within a system of interest\n    is_a: affects activity of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases activity of\n    mixins:\n      - decreases amount or activity of\n    related_mappings:\n      - GAMMA:ic50\n      - GAMMA:ki\n      - DGIdb:vaccine\n    narrow_mappings:\n      - GAMMA:allosteric_antagonist\n      - GAMMA:partial_antagonist\n      - GAMMA:antagonist\n      - GAMMA:weak_inhibitor\n      - GAMMA:inhibitor\n      - GAMMA:channel_blocker\n      - GAMMA:gating_inhibitor\n      - GAMMA:blocker\n      - GAMMA:inverse_agonist\n      - GAMMA:inactivator\n      - GAMMA:downregulator\n      - GAMMA:negative_modulator\n      - GAMMA:negative_allosteric_modulator\n      - GAMMA:inhibitory_allosteric_modulator\n      - GAMMA:aggregation_inhibitor\n      - GAMMA:conversion_inhibitor\n      - GAMMA:suppressor\n      - CHEMBL.MECHANISM:antagonist\n      - CHEMBL.MECHANISM:allosteric_antagonist\n      - CHEMBL.MECHANISM:inverse_agonist\n      - DGIdb:antagonist\n      - DGIdb:blocker\n      - DGIdb:channel_blocker\n      - DGIdb:gating_inhibitor\n      - DGIdb:inhibitor\n      - DGIdb:negative_modulator\n      - DGIdb:inhibitory_allosteric_modulator\n      - DGIdb:inverse_agonist\n\n  activity decreased by:\n    deprecated: true\n    is_a: activity affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases activity of\n\n\n  affects expression of:\n    deprecated: true\n    description: >-\n      holds between a named thing (most often a chemical or gene/gene product, but can also be used to link an\n      environmental affect on expression) and a nucleic acid entity where the action or effect of one changes the\n      level of expression of the other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: named thing\n    range: nucleic acid entity\n\n  expression affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: named thing\n    inverse: affects expression of\n\n  increases expression of:\n    deprecated: true\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity\n      where the action or effect of one increases the level of expression of the\n      other within a system of interest\n    is_a: affects expression of\n    in_subset:\n      - translator_minimal\n    domain: named thing\n    range: nucleic acid entity\n    mixins:\n      - increases amount or activity of\n    close_mappings:\n      # Agent of the action or effect, not the relationship itself\n      - CHEMBL.MECHANISM:releasing_agent\n    exact_mappings:\n      - RO:0003003\n\n  expression increased by:\n    deprecated: true\n    is_a: expression affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: named thing\n    inverse: increases expression of\n\n  decreases expression of:\n    deprecated: true\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one decreases the level of expression of the\n      other within a system of interest\n    is_a: affects expression of\n    in_subset:\n      - translator_minimal\n    domain: named thing\n    range: nucleic acid entity\n    mixins:\n      - decreases amount or activity of\n    related_mappings:\n      - DGIdb:antisense\n      - DGIdb:antisense_oligonucleotide\n    exact_mappings:\n      - RO:0003002\n    narrow_mappings:\n      - CHEMBL.MECHANISM:antisense_inhibitor\n\n  expression decreased by:\n    deprecated: true\n    is_a: expression affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: named thing\n    inverse: decreases expression of\n\n  affects folding of:\n    deprecated: true\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one changes the rate\n      or quality of folding of the other\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_folding_of\n\n\n  folding affected by:\n    deprecated: true\n    is_a: affected by\n    inverse: affects folding of\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n\n  increases folding of:\n    deprecated: true\n    description: >-\n      holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one\n      increases the rate or quality of folding of the other\n    is_a: affects folding of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases folding of\n    exact_mappings:\n      - CTD:increases_folding_of\n\n  folding increased by:\n    deprecated: true\n    is_a: folding affected by\n    inverse: increases folding of\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n\n  decreases folding of:\n    deprecated: true\n    description: >-\n      holds between a chemical or gene or gene product entity and a\n      nucleic acid entity where the action or effect of one\n      decreases the rate or quality of folding of the other\n    is_a: affects folding of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases folding of\n    exact_mappings:\n      - CTD:decreases_folding_of\n\n  folding decreased by:\n    deprecated: true\n    is_a: folding affected by\n    inverse: decreases folding of\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n\n  affects localization of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one changes the\n      localization of the other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GAMMA:storage\n    exact_mappings:\n      - GOREL:0002003\n\n  localization affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects localization of\n\n  increases localization of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one increases the proper\n      localization of the other within a system of interest\n    is_a: affects localization of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases localization of\n    exact_mappings:\n      - CTD:increases_localization_of\n\n  localization increased by:\n    deprecated: true\n    is_a: localization affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases localization of\n\n  decreases localization of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities where the action or effect of one decreases the proper localization of the other within a system of interest\n    is_a: affects localization of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases localization of\n    exact_mappings:\n      - CTD:decreases_localization_of\n\n\n  localization decreased by:\n    deprecated: true\n    is_a: localization affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases localization of\n\n  affects metabolic processing of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts the\n      metabolic processing of the other within a system of interest\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GAMMA:catalytic_activity\n\n  metabolic processing affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects metabolic processing of\n\n  increases metabolic processing of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one increases the rate of\n      metabolic processing of the other within a system of interest\n    is_a: affects metabolic processing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases metabolic processing of\n    exact_mappings:\n      - CTD:increases_metabolic_processing_of\n    narrow_mappings:\n      - NCIT:enzyme_metabolizes_chemical_or_drug\n\n  metabolic processing increased by:\n    deprecated: true\n    is_a: metabolic processing affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases metabolic processing of\n\n  decreases metabolic processing of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one decreases the rate of\n      metabolic processing of the other within a system of interest\n    is_a: affects metabolic processing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases metabolic processing of\n    exact_mappings:\n      - CTD:decreases_metabolic_processing_of\n\n  metabolic processing decreased by:\n    deprecated: true\n    is_a: metabolic processing affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases metabolic processing of\n\n  affects molecular modification of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one leads changes in the molecular\n      modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of\n      phosphoryl group, or via redox reaction that adds or subtracts electrons)\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_molecular_modification_of\n    narrow_mappings:\n      - CTD:affects_acetylation\n      - CTD:affects_acylation\n      - CTD:affects_alkylation\n      - CTD:affects_amination\n      - CTD:affects_carbamoylation\n      - CTD:affects_ethylation\n      - CTD:affects_glutathionylation\n      - CTD:affects_glycation\n      - CTD:affects_glycosylation\n      - CTD:affects_glucuronidation\n      - CTD:affects_N-linked_glycosylation\n      - CTD:affects_O-linked_glycosylation\n      - CTD:affects_hydroxylation\n      - CTD:affects_lipidation\n      - CTD:affects_farnesylation\n      - CTD:affects_geranoylation\n      - CTD:affects_myristoylation\n      - CTD:affects_palmitoylation\n      - CTD:affects_prenylation\n      - CTD:affects_methylation\n      - CTD:affects_nitrosation\n      - CTD:affects_nucleotidylation\n      - CTD:affects_phosphorylation\n      - CTD:affects_ribosylation\n      - CTD:affects_ADP-ribosylation\n      - CTD:affects_sulfation\n      - CTD:affects_sumoylation\n      - CTD:affects_ubiquitination\n      - CTD:affects_oxidation\n      - CTD:affects_reduction\n      - CTD:affects_carboxylation\n\n  molecular modification affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects molecular modification of\n\n  increases molecular modification of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one leads to\n      increased molecular modification(s) of the other (e.g. via post-translational modifications of\n      proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\n    is_a: affects molecular modification of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases molecular modification of\n    exact_mappings:\n      - CTD:increases_molecular_modification_of\n    narrow_mappings:\n      - CTD:increases_acetylation\n      - CTD:increases_acylation\n      - CTD:increases_alkylation\n      - CTD:increases_amination\n      - CTD:increases_carbamoylation\n      - CTD:increases_ethylation\n      - CTD:increases_glutathionylation\n      - CTD:increases_glycation\n      - CTD:increases_glycosylation\n      - CTD:increases_glucuronidation\n      - CTD:increases_N-linked_glycosylation\n      - CTD:increases_O-linked_glycosylation\n      - CTD:increases_hydroxylation\n      - CTD:increases_lipidation\n      - CTD:increases_farnesylation\n      - CTD:increases_geranoylation\n      - CTD:increases_myristoylation\n      - CTD:increases_palmitoylation\n      - CTD:increases_prenylation\n      - CTD:increases_methylation\n      - CTD:increases_nitrosation\n      - CTD:increases_nucleotidylation\n      - CTD:increases_phosphorylation\n      - CTD:increases_ribosylation\n      - CTD:increases_ADP-ribosylation\n      - CTD:increases_sulfation\n      - CTD:increases_sumoylation\n      - CTD:increases_ubiquitination\n      - CTD:increases_oxidation\n      - CTD:increases_reduction\n      - CTD:increases_carboxylation\n      - GAMMA:acetylation\n      - GAMMA:oxidizer\n\n  molecular modification increased by:\n    deprecated: true\n    is_a: molecular modification affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases molecular modification of\n\n  decreases molecular modification of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities  where the action or effect of one leads to\n      decreased molecular modification(s) of the other (e.g. via post-translational modifications of\n      proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)\n    is_a: affects molecular modification of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases molecular modification of\n    exact_mappings:\n      - CTD:decreases_molecular_modification_of\n    narrow_mappings:\n      - CTD:decreases_acetylation\n      - CTD:decreases_acylation\n      - CTD:decreases_alkylation\n      - CTD:decreases_amination\n      - CTD:decreases_carbamoylation\n      - CTD:decreases_ethylation\n      - CTD:decreases_glutathionylation\n      - CTD:decreases_glycation\n      - CTD:decreases_glycosylation\n      - CTD:decreases_glucuronidation\n      - CTD:decreases_N-linked_glycosylation\n      - CTD:decreases_O-linked_glycosylation\n      - CTD:decreases_hydroxylation\n      - CTD:decreases_lipidation\n      - CTD:decreases_farnesylation\n      - CTD:decreases_geranoylation\n      - CTD:decreases_myristoylation\n      - CTD:decreases_palmitoylation\n      - CTD:decreases_prenylation\n      - CTD:decreases_methylation\n      - CTD:decreases_nitrosation\n      - CTD:decreases_nucleotidylation\n      - CTD:decreases_phosphorylation\n      - CTD:decreases_ribosylation\n      - CTD:decreases_ADP-ribosylation\n      - CTD:decreases_sulfation\n      - CTD:decreases_sumoylation\n      - CTD:decreases_ubiquitination\n      - CTD:decreases_oxidation\n      - CTD:decreases_reduction\n      - CTD:decreases_carboxylation\n      - GAMMA:deoxidizer\n\n  molecular modification decreased by:\n    deprecated: true\n    is_a: molecular modification affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases molecular modification of\n\n  affects synthesis of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities where the action or effect \n      of one impacts the rate of chemical synthesis of the other\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_synthesis_of\n\n  synthesis affected by:\n    deprecated: true\n    is_a: affected by\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects synthesis of\n    in_subset:\n      - translator_minimal\n\n  increases synthesis of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities where the action or effect\n      of one increases the rate of chemical synthesis of the other\n    is_a: affects synthesis of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases synthesis of\n    exact_mappings:\n      - CTD:increases_synthesis_of\n\n  synthesis increased by:\n    deprecated: true\n    is_a: synthesis affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases synthesis of\n\n  decreases synthesis of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities where the action or effect\n      of one decreases the rate of chemical synthesis of the other\n    is_a: affects synthesis of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases synthesis of\n    exact_mappings:\n      - GAMMA:inhibition_of_synthesis\n\n  synthesis decreased by:\n    deprecated: true\n    is_a: synthesis affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases synthesis of\n\n  affects degradation of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      impacts the rate of degradation of the other within a system of interest,\n      where chemical degradation is defined act or process of simplifying or breaking\n      down a molecule into smaller parts, either naturally or artificially\n      (Oxford English Dictionary, UK, 1995)\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_degradation_of\n    narrow_mappings:\n      - CTD:affects_cleavage\n      - CTD:affects_hydrolysis\n\n  degradation affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects degradation of\n\n  increases degradation of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the rate of degradation of the other within a system of interest\n    is_a: affects degradation of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases degredation of\n    related_mappings:\n      # An enzyme or reagent acts upon a substrate but that substrate may\n      # not necessarily be \"degraded\", i.e. broken into smaller parts\n      - GAMMA:substrate\n      # RTX put this under \"biolink:physically_interacts_with\" but rather we also put next to the GAMMA mapping\n      # That said, neither mapping feels like a comfortable fit here\n      - CHEMBL.MECHANISM:substrate\n    close_mappings:\n      # terms refer less to the action or effect than the agent of that action or effect\n      - CHEMBL.MECHANISM:degrader\n    narrow_mappings:\n      - CTD:increases_cleavage\n      - CTD:increases_hydrolysis\n      - GOREL:0002004\n\n  degradation increased by:\n    deprecated: true\n    is_a: degradation affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases degradation of\n\n  decreases degradation of:\n    deprecated: true\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the rate of degradation of the other within a system of interest\n    is_a: affects degradation of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases degredation of\n    exact_mappings:\n      - CTD:decreases_degradation_of\n    narrow_mappings:\n      - CTD:decreases_cleavage\n      - CTD:decreases_hydrolysis\n\n  degradation decreased by:\n    deprecated: true\n    is_a: degradation affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases degradation of\n\n  affects mutation rate of:\n    deprecated: true\n    description: >-\n      holds between a chemical entity and a nucleic acid entity where the action or effect of the\n      chemical entity impacts the rate of mutation of the nucleic acid entity within a system of interest\n    is_a: affects\n    domain: chemical entity or gene or gene product\n    range: nucleic acid entity\n    broad_mappings:\n    # Term 'mutagenesis' generally speaks generally of the process of\n    # 'production of genetic mutations':  this term says it is affected\n    # but not specifically how\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_mutation_rate_of\n\n  mutation rate affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: chemical entity or gene or gene product\n    inverse: affects mutation rate of\n\n  increases mutation rate of:\n    deprecated: true\n    description: >-\n      holds between a chemical entity and a nucleic acid entity where the action or effect of the\n      chemical entity increases the rate of mutation of the nucleic acid entity within a system of interest\n    is_a: affects mutation rate of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity\n    range: nucleic acid entity\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases mutation rate of\n    exact_mappings:\n      - CTD:increases_mutation_rate_of\n    broad_mappings:\n      # See 'affects mutation rate of' above\n      - CTD:increases_mutagenesis\n\n  mutation rate increased by:\n    deprecated: true\n    is_a: mutation rate affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: chemical entity\n    inverse: increases mutation rate of\n\n  decreases mutation rate of:\n    deprecated: true\n    description: >-\n      holds between a chemical entity and a nucleic acid entity where the action or effect of the\n      chemical entity decreases the rate of mutation of the nucleic acid entity within a system of interest\n    is_a: affects mutation rate of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity\n    range: nucleic acid entity\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases mutation rate of\n    exact_mappings:\n      - CTD:decreases_mutation_rate_of\n    broad_mappings:\n      # See 'affects mutation rate of' above\n      - CTD:decreases_mutagenesis\n\n  mutation rate decreased by:\n    deprecated: true\n    is_a: mutation rate affected by\n    in_subset:\n      - translator_minimal\n    domain: nucleic acid entity\n    range: chemical entity\n    inverse: decreases mutation rate of\n\n  affects response to:\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: response affected by\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_response_to\n\n  response affected by:\n    description: >-\n      holds between two chemical entities where the susceptibility of a biological entity or system\n      (e.g. an organism, cell, cellular component, macromolecular machine mixin,\n      biological or pathological process) of one is affected by the action of the other.\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n\n  increases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases response to\n    exact_mappings:\n      - CTD:increases_response_to\n\n  response increased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases response to\n\n  decreases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases response to\n    exact_mappings:\n      - CTD:decreases_response_to\n    narrow_mappings:\n      - CTD:decreases_response_to_substance\n      - GAMMA:desensitize_the_target\n\n  response decreased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases response to\n\n  affects splicing of:\n    deprecated: true\n    description: >-\n      holds between a chemical entity and an mRNA where the action or effect\n      of the chemical entity impacts the splicing of the mRNA\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: transcript\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_RNA_splicing\n    broad_mappings:\n      - CTD:affects_splicing_of\n\n  splicing affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: transcript\n    range: chemical entity or gene or gene product\n    inverse: affects splicing of\n\n  increases splicing of:\n    deprecated: true\n    description: >-\n      holds between a chemical entity and an mRNA where the action or effect\n      of the chemical entity increases the proper splicing of the mRNA\n    is_a: affects splicing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: transcript\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases splicing of\n    exact_mappings:\n      - CTD:increases_RNA_splicing\n    broad_mappings:\n      - CTD:increases_splicing_of\n\n  splicing increased by:\n    deprecated: true\n    is_a: splicing affected by\n    in_subset:\n      - translator_minimal\n    domain: transcript\n    range: chemical entity or gene or gene product\n    inverse: increases splicing of\n\n  decreases splicing of:\n    deprecated: true\n    description: >-\n      holds between a chemical entity and an mRNA where the action or\n      effect of the chemical entity decreases the proper splicing of the mRNA\n    is_a: affects splicing of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: transcript\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases splicing of\n    exact_mappings:\n      - CTD:decreases_RNA_splicing\n    broad_mappings:\n      - CTD:decreases_splicing_of\n\n  splicing decreased by:\n    deprecated: true\n    is_a: splicing affected by\n    in_subset:\n      - translator_minimal\n    domain: transcript\n    range: chemical entity or gene or gene product\n    inverse: decreases splicing of\n\n  affects stability of:\n    deprecated: true\n    description: >-\n      holds between two entities where the action or effect of one impacts\n      the stability of the other within a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - GAMMA:stabilization\n\n  stability affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects stability of\n\n  increases stability of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one\n      increases the stability of the other within a system of interest\n    is_a: affects stability of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases stability of\n    close_mappings:\n      # agent of the action or effect, not the relationship\n      - CHEMBL.MECHANISM:stabiliser\n\n  stability increased by:\n    deprecated: true\n    is_a: stability affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases stability of\n\n  decreases stability of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one decreases\n      the stability of the other within a system of interest\n    is_a: affects stability of\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases stability of\n    exact_mappings:\n      - CTD:decreases_stability_of\n\n  stability decreased by:\n    deprecated: true\n    is_a: stability affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases stability of\n\n  affects transport of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts\n      the rate of transport of the other across some boundary in a system of interest\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_transport_of\n    narrow_mappings:\n      - RO:0002313\n      - RO:0002340\n      - RO:0002345\n\n  transport affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects transport of\n\n  increases transport of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one\n      increases the rate of transport of the other across some boundary in a system of interest\n    is_a: affects transport of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases transport of\n    close_mappings:\n      - GAMMA:carrier\n      - GAMMA:transporter\n\n  transport increased by:\n    deprecated: true\n    is_a: transport affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases transport of\n\n  decreases transport of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one\n      decreases the rate of transport of the other across some boundary in a system of interest\n    is_a: affects transport of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases transport of\n    exact_mappings:\n      - CTD:decreases_transport_of\n\n  transport decreased by:\n    deprecated: true\n    is_a: transport affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases transport of\n\n  affects secretion of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts the\n      rate of secretion of the other out of a cell, gland, or organ\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_secretion_of\n    broad_mappings:\n      # 'export' more general than 'secretion'\n      - CTD:affects_export\n\n  secretion affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects secretion of\n\n  increases secretion of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one increases the\n      rate of secretion of the other out of a cell, gland, or organ\n    is_a: affects secretion of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases secretion of\n    exact_mappings:\n      - CTD:increases_secretion_of\n    broad_mappings:\n      # 'export' more general than 'secretion'\n      - CTD:increases_export\n\n  secretion increased by:\n    deprecated: true\n    is_a: secretion affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases secretion of\n\n  decreases secretion of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one decreases the\n      rate of secretion of the other out of a cell, gland, or organ\n    is_a: affects secretion of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases secretion of\n    exact_mappings:\n      - CTD:decreases_secretion_of\n    broad_mappings:\n      # 'export' more general than 'secretion'\n      - CTD:decreases_export\n\n  secretion decreased by:\n    deprecated: true\n    is_a: secretion affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases secretion of\n\n  affects uptake of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one impacts the rate of\n      uptake of the other into of a cell, gland, or organ\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_uptake_of\n    broad_mappings:\n      # 'import' more general than 'uptake'\n      - CTD:affects_import\n\n  uptake affected by:\n    deprecated: true\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: affects uptake of\n\n  increases uptake of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect of one increases the rate of\n      uptake of the other into of a cell, gland, or organ\n    is_a: affects uptake of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - increases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases uptake of\n    exact_mappings:\n      - CTD:increases_uptake_of\n    broad_mappings:\n      # 'import' more general than 'uptake'\n      - CTD:increases_import\n\n  uptake increased by:\n    deprecated: true\n    is_a: uptake affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases uptake of\n\n  decreases uptake of:\n    deprecated: true\n    description: >-\n      holds between two chemical or gene/gene product entities  where the action or effect\n      of one decreases the rate of uptake of the other into of a cell, gland, or organ\n    is_a: affects uptake of\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    mixins:\n      - decreases amount or activity of\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases uptake of\n    exact_mappings:\n      - CTD:decreases_uptake_of\n    broad_mappings:\n      # 'import' more general than 'uptake'\n      - CTD:decreases_import\n\n  uptake decreased by:\n    deprecated: true\n    is_a: uptake affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases uptake of\n\n  regulates:\n    is_a: affects\n    description: >-\n      A more specific form of affects, that implies the effect results from a biologically evolved control mechanism.\n      Gene-affects-gene relationships will (almost) always involve regulation.  Chemical-affects-gene relationships \n      may in some cases be considered regulation (if the chemical is some endogenously produced signaling molecule \n      created to execute a certain function/activity), but exogenous/environmental chemical-affects-gene relationships \n      are usually not cases of regulation.\n    mixin: true\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - RO:0002334\n    exact_mappings:\n      - RO:0002211\n    narrow_mappings:\n      # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology)\n      - WIKIDATA_PROPERTY:P128\n      - CHEMBL.MECHANISM:modulator\n      - RO:0002295\n      - RO:0002332\n      - RO:0002578\n\n  regulated by:\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    mixin: true\n    inverse: regulates\n\n  positively regulates:\n    deprecated: true\n    comments:\n      - This is a grouping for positive process-process and entity-entity regulation.\n    is_a: regulates\n    mixin: true\n    annotations:\n      opposite_of: negatively regulates\n    close_mappings:\n      # This RTX contributed term is tagged as a inverse of this Biolink predicate\n      - RO:0002336\n    exact_mappings:\n      - RO:0002213\n    narrow_mappings:\n      - CHEMBL.MECHANISM:activator\n      - DGIdb:activator\n      - RO:0004032\n      - RO:0004034\n      - RO:0002629\n\n  positively regulated by:\n    deprecated: true\n    is_a: regulated by\n    mixin: true\n    inverse: positively regulates\n\n  negatively regulates:\n    deprecated: true\n    comments:\n      - This is a grouping for negative process-process and entity-entity regulation.\n    is_a: regulates\n    mixin: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # This RTX contributed term is tagged as a inverse of this Biolink predicate\n      - RO:0002335\n    exact_mappings:\n      # Strict interpretation here is that entity A causally affects levels of B\n      - RO:0004035\n      - RO:0002212\n    broad_mappings:\n      # This term is slightly broader in that it includes that A acts within B as well\n      - RO:0004033\n    narrow_mappings:\n      - CHEMBL.MECHANISM:blocker\n      - CHEMBL.MECHANISM:inhibitor\n      - CHEMBL.MECHANISM:negative_allosteric_modulator\n      - CHEMBL.MECHANISM:negative_modulator\n      - RO:0002630\n\n  negatively regulated by:\n    deprecated: true\n    is_a: regulated by\n    mixin: true\n    inverse: negatively regulates\n\n  process regulates process:\n    deprecated: true\n    is_a: affects\n    mixins:\n      - regulates\n    domain: occurrent\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002211\n\n  process regulated by process:\n    deprecated: true\n    is_a: affected by\n    domain: occurrent\n    range: occurrent\n    inverse: process regulates process\n\n  process positively regulates process:\n    deprecated: true\n    is_a: process regulates process\n    mixins:\n      - positively regulates\n    annotations:\n      canonical_predicate: true\n      opposite_of: process negatively regulates process\n    exact_mappings:\n      - RO:0002213\n\n  process positively regulated by process:\n    deprecated: true\n    is_a: process regulated by process\n    inverse: process positively regulates process\n\n  process negatively regulates process:\n    deprecated: true\n    is_a: process regulates process\n    mixins:\n      - negatively regulates\n    annotations:\n      canonical_predicate: true\n      opposite_of: process positively regulates process\n    exact_mappings:\n      - RO:0002212\n\n  process negatively regulated by process:\n    deprecated: true\n    is_a: process regulated by process\n    inverse: process negatively regulates process\n\n  entity regulates entity:\n    deprecated: true\n    aliases: [ 'activity directly regulates activity of' ]\n    is_a: affects\n    mixins:\n      - regulates\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: entity regulated by entity\n    annotations:\n      canonical_predicate: true\n    local_names:\n      translator: regulates\n      ro: activity directly regulates activity of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002448\n    narrow_mappings:\n      # Wikidata mapping copied over from 'regulates' above;\n      # considered a slightly narrower term since it applies to\n      # protein and RNA as subject regulator whereas molecular_entity\n      # may also be another class of chemical_substance?\n      - WIKIDATA_PROPERTY:P128\n\n  entity regulated by entity:\n    deprecated: true\n    is_a: affected by\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: entity regulates entity\n\n  entity positively regulates entity:\n    deprecated: true\n    aliases: [ 'activity directly positively regulates activity of', 'anatomy upregulates gene', 'disease upregulates gene' ]\n    is_a: entity regulates entity\n    mixins:\n      - positively regulates\n    annotations:\n      canonical_predicate: true\n      opposite_of: entity negatively regulates entity\n    local_names:\n      translator: positively regulates\n      ro: activity directly positively regulates activity of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002450\n    broad_mappings:\n      # causally positive effect of A over B but not specific to nature of B\n      - RO:0004034\n    narrow_mappings:\n      # Defined more narrowly as increasing, facilitating the\n      # action or function of a \"substance interaction\", where \"substance\" is deemed a subclass of possible entity\n      - SEMMEDDB:STIMULATES\n      - SEMMEDDB:stimulates\n      - SEMMEDDB:augments\n\n  entity positively regulated by entity:\n    deprecated: true\n    is_a: entity regulated by entity\n    inverse: entity positively regulates entity\n\n  entity negatively regulates entity:\n    deprecated: true\n    aliases: [ 'activity directly negatively regulates activity of', 'anatomy downregulates gene', 'disease downregulates gene' ]\n    is_a: entity regulates entity\n    mixins:\n      - negatively regulates\n    annotations:\n      canonical_predicate: true\n      opposite_of: entity positively regulates entity\n    local_names:\n      translator: negatively regulates\n      ro: activity directly negatively regulates activity of\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002449\n    narrow_mappings:\n      # SemMedDb definition focuses on (chemical?) \"substance interactions\" which is a bit narrower?\n      - SEMMEDDB:INHIBITS\n      - SEMMEDDB:inhibits\n\n  entity negatively regulated by entity:\n    deprecated: true\n    is_a: entity regulated by entity\n    inverse: entity negatively regulates entity\n\n  disrupts:\n    is_a: affects\n    aliases: [ 'disease causes disruption of' ]\n    description: >-\n      describes a relationship where one entity degrades or interferes\n      with the structure, function, or occurrence of another.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: enables\n    exact_mappings:\n      - SEMMEDDB:DISRUPTS\n      - SEMMEDDB:disrupts\n      - CHEMBL.MECHANISM:disrupting_agent\n    narrow_mappings:\n      - RO:0004024\n      - RO:0004025\n\n  disrupted by:\n    is_a: affected by\n    description: >-\n      describes a relationship where the structure, function, or occurrence\n      of one entity is degraded or interfered with by another.\n    inverse: disrupts\n\n  gene product of:\n    is_a: related to at instance level\n    description: >-\n      definition x has gene product of y if and only if y is a gene (SO:0000704)\n      that participates in some gene expression process (GO:0010467) where the output of thatf\n      process is either y or something that is ribosomally translated from x\n    exact_mappings:\n      - RO:0002204\n    domain: gene product mixin\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: has gene product\n    in_subset:\n      - translator_minimal\n\n  has gene product:\n    is_a: related to at instance level\n    description: >-\n      holds between a gene and a transcribed and/or\n      translated product generated from it\n    domain: gene\n    range: gene product mixin\n    inverse: gene product of\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX term tagged as inverse mapping\n      - PR:has_gene_template\n    exact_mappings:\n      - RO:0002205\n      - WIKIDATA_PROPERTY:P688\n      - NCIT:gene_encodes_gene_product\n    narrow_mappings:\n      - NCIT:R178\n\n  transcribed to:\n    is_a: related to at instance level\n    domain: gene\n    range: transcript\n    description: >-\n      inverse of transcribed from\n    inverse: transcribed from\n    annotations:\n      opposite_of: transcribed from\n    exact_mappings:\n      - RO:0002511\n      - SIO:010080\n\n  transcribed from:\n    is_a: related to at instance level\n    domain: transcript\n    range: gene\n    annotations:\n      canonical_predicate: true\n      opposite_of: transcribed to\n    description: >-\n      x is transcribed from y if and only if x is synthesized from template y\n    exact_mappings:\n      - RO:0002510\n      - SIO:010081\n\n  translates to:\n    is_a: related to at instance level\n    domain: transcript\n    range: protein\n    annotations:\n      canonical_predicate: true\n      opposite_of: translation of\n    description: >-\n      x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome\n      reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)\n      and produces x (amino acid chain/polypeptide)\n    close_mappings:\n      - RO:0002513\n      - SIO:010082\n\n  translation of:\n    is_a: related to at instance level\n    domain: protein\n    range: transcript\n    description: >-\n      inverse of translates to\n    inverse: translates to\n    close_mappings:\n      - RO:0002512\n      - SIO:010083\n    annotations:\n      opposite_of: translates to\n\n  homologous to:\n    is_a: similar to\n    aliases: [ 'in homology relationship with' ]\n    description: >-\n      holds between two biological entities that have common evolutionary origin\n    comments:\n      - typically used to describe homology relationships between genes or gene products\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000001\n      - SIO:010302\n    narrow_mappings:\n      # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158\n      - UBERON_CORE:sexually_homologous_to\n\n  paralogous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000011\n\n  orthologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship between entities (typically genes) that diverged after a speciation event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000017\n      - WIKIDATA_PROPERTY:P684\n\n  xenologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000018\n\n  coexists with:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SEMMEDDB:COEXISTS_WITH\n      - SEMMEDDB:coexists_with\n    narrow_mappings:\n      - BSPO:0000096\n      - BSPO:0000097\n      - BSPO:0000098\n      - BSPO:0000099\n      - BSPO:0000100\n      - BSPO:0000102\n      - BSPO:0000104\n      - BSPO:0000110\n      - BSPO:0000113\n      - BSPO:0015001\n      - BSPO:0015002\n      - BSPO:0015003\n      - BSPO:0015005\n      - BSPO:0015006\n      - BSPO:0015007\n      - BSPO:0015008\n      - BSPO:0015009\n      - BSPO:0015012\n      - BSPO:0015014\n      - BSPO:parallel_to\n      - UBERON_CORE:anastomoses_with\n      - UBERON_CORE:anteriorly_connected_to\n      - UBERON_CORE:posteriorly_connected_to\n      - UBERON_CORE:channel_for\n      - UBERON_CORE:channels_from\n      - UBERON_CORE:channels_into\n      - UBERON_CORE:conduit_for\n      - UBERON_CORE:distally_connected_to\n      - UBERON_CORE:extends_fibers_into\n      - UBERON_CORE:filtered_through\n      - UBERON_CORE:indirectly_supplies\n      - UBERON_CORE:proximally_connected_to\n      - UBERON_CORE:synapsed_by\n      - UBERON_CORE:transitively_anteriorly_connected_to\n      - UBERON_CORE:transitively_connected_to\n      - UBERON_CORE:transitively_distally_connected_to\n      - UBERON_CORE:transitively_proximally_connected_to\n      # RTX contributed Environmental Ontology term meaning \"partially surrounded by\"\n      - ENVO:01001307\n      - FMA:adjacent_to\n      - FMA:afferent_to\n      - FMA:anterior_to\n      - FMA:anteroinferior_to\n      - FMA:anterolateral_to\n      - FMA:anteromedial_to\n      - FMA:anterosuperior_to\n      # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics?\n      # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink\n      - FMA:arterial_supply_of\n      - FMA:has_arterial_supply\n      - FMA:articulates_with\n      - FMA:attaches_to\n      - FMA:bounded_by\n      - FMA:bounds\n      - FMA:branch_of\n      - FMA:connection_type_of\n      - FMA:continuation_branch_of\n      - FMA:continuous_distally_with\n      - FMA:continuous_proximally_with\n      - FMA:corresponds_to\n      - FMA:development_type_of\n      - FMA:developmental_stage_of\n      - FMA:direct_cell_shape_of\n      - FMA:direct_left_of\n      - FMA:direct_right_of\n      - FMA:distal_to\n      - FMA:drains_into\n      - FMA:efferent_to\n      - FMA:external_to\n      - FMA:formed_by\n      - FMA:forms\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:full_grown_phenotype_of\n      - FMA:has_full_grown_phenotype\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:fuses_with\n      - FMA:fusion_of\n      - FMA:has_fusion\n      - FMA:germ_origin_of\n      - FMA:has_germ_origin\n      - FMA:has_adherent\n      - FMA:has_branch\n      - FMA:has_connection_type\n      - FMA:has_continuation_branch\n      - FMA:has_development_type\n      - FMA:has_developmental_stage\n      - FMA:has_direct_cell_shape\n      - FMA:has_inherent_3d_shape\n      - FMA:has_insertion\n      - FMA:has_lymphatic_drainage\n      - FMA:has_nerve_supply\n      - FMA:has_observed_anatomical_entity\n      - FMA:has_origin\n      - FMA:has_primary_segmental_supply\n      - FMA:has_projection\n      - FMA:has_regional_part\n      - FMA:has_related_developmental_entity\n      - FMA:has_secondary_segmental_supply\n      - FMA:has_segmental_composition\n      - FMA:has_segmental_supply\n      - FMA:has_tributary\n      - FMA:has_venous_drainage\n      - FMA:inferior_to\n      - FMA:inferolateral_to\n      - FMA:inferomedial_to\n      - FMA:inherent_3d_shape_of\n      - FMA:insertion_of\n      - FMA:internal_to\n      - FMA:lateral_to\n      - FMA:left_lateral_to\n      - FMA:left_medial_to\n      - FMA:lymphatic_drainage_of\n      - FMA:matures_from\n      - FMA:matures_into\n      - FMA:medial_to\n      - FMA:merges_with\n      - FMA:nerve_supply_of\n      - FMA:origin_of\n      - FMA:posterior_to\n      - FMA:posteroinferior_to\n      - FMA:posterolateral_to\n      - FMA:posteromedial_to\n      - FMA:posterosuperior_to\n      - FMA:primary_segmental_supply_of\n      - FMA:projects_from\n      - FMA:projects_to\n      - FMA:proximal_to\n      - FMA:receives_attachment_from\n      - FMA:receives_drainage_from\n      - FMA:receives_input_from\n      - FMA:receives_projection\n      - FMA:related_part\n      - FMA:right_lateral_to\n      - FMA:right_medial_to\n      - FMA:secondary_segmental_supply_of\n      - FMA:segmental_composition_of\n      - FMA:segmental_supply_of\n      - FMA:sends_output_to\n      - FMA:superior_to\n      - FMA:superolateral_to\n      - FMA:superomedial_to\n      - FMA:surrounded_by\n      - FMA:surrounds\n      - FMA:tributary_of\n      - FMA:venous_drainage_of\n      # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute'\n      # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now\n      - LOINC:has_lateral_anatomic_location\n      - LOINC:has_lateral_location_presence\n      - UBERON_NONAMESPACE:distally_connected_to\n      - UBERON_NONAMESPACE:subdivision_of\n      # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to'\n      - RO:0002219\n      - RO:0002220\n      - RO:0002221\n      - SO:has_origin\n      # RTX mapped these UBERON terms all here\n      - UBERON:anastomoses_with\n      - UBERON:anteriorly_connected_to\n      - UBERON:channel_for\n      - UBERON:channels_from\n      - UBERON:channels_into\n      - UBERON:conduit_for\n      - UBERON:distally_connected_to\n      - UBERON:existence_starts_and_ends_during\n      - UBERON:extends_fibers_into\n      - UBERON:filtered_through\n      - UBERON:in_central_side_of\n      - UBERON:in_innermost_side_of\n      - UBERON:in_outermost_side_of\n      - UBERON:indirectly_supplies\n      - UBERON:posteriorly_connected_to\n      - UBERON:protects\n      - UBERON:proximally_connected_to\n      - UBERON:sexually_homologous_to\n\n  in pathway with:\n    description: >-\n      holds between two genes or gene products that are part of in the same biological pathway\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # generally pertains to membership of a (subject) component - gene,\n      # metabolite, etc? - in an (object) metabolic pathway\n      - SIO:010532\n\n  in complex with:\n    description: >-\n      holds between two genes or gene products that are part of (or code for\n      products that are part of) in the same macromolecular complex mixin\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though)\n      - SIO:010497\n    broad_mappings:\n      # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes)\n      - SIO:010285\n\n  in cell population with:\n    description: >-\n      holds between two genes or gene products that are expressed in the same cell type or population\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  colocalizes with:\n    description: >-\n      holds between two entities that are observed to be located in the same place.\n    is_a: coexists with\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:00002325\n\n  # Despite the name, note that this particular entity is\n  # NOT a biolink:Association but rather, a biolink:predicate\n  genetic association:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    description: >-\n      Co-occurrence of a certain allele of a genetic marker and the phenotype\n      of interest in the same individuals at above-chance level\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2293\n\n  gene associated with condition:\n    is_a: genetic association\n    description: >-\n      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,\n      contribute to, or correlate with\n    domain: gene\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - GENO:0000840 # broader than a single gene: 'genotype' pathogenic for condition\n      - GENO:0000841\n    narrow_mappings:\n      # narrower: just diseases, not phenotypic features as well\n      - NCIT:R38\n      - NCIT:R175\n      - NCIT:R48\n\n  condition associated with gene:\n    is_a: genetic association\n    aliases: [ 'disease associated with gene' ]\n    description: >-\n      holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products\n    domain: disease or phenotypic feature\n    range: gene\n    in_subset:\n      - translator_minimal\n    inverse: gene associated with condition\n    narrow_mappings:\n      # narrower since just diseases, not phenotypic features as well\n      - NCIT:R176\n\n  affects risk for:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where exposure to one entity alters the chance of developing the other\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  risk affected by:\n    is_a: related to at instance level\n    inverse: affects risk for\n\n  predisposes:\n    is_a: affects risk for\n    description: >-\n      holds between two entities where exposure to one entity increases the chance of developing the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:predisposes\n\n  has predisposing factor:\n    inverse: predisposes\n    in_subset:\n      - translator_minimal\n\n  # TODO: inverse of predisposes\n\n  contributes to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes or contributes to the\n      occurrence or generation of the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX contributed mapping tagged as 'inverse' of this Biolink predicate\n      - IDO:0000664\n    exact_mappings:\n      - RO:0002326\n    narrow_mappings:\n      - CTD:marker_mechanism\n      - MONDO:predisposes_towards\n      # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002255\n      # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here\n      - RO:0003304\n\n  contribution from:\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    inverse: contributes to\n\n  causes:\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes the occurrence\n      or generation of the other\n    is_a: contributes to\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:CAUSES\n      - SEMMEDDB:causes\n      - WIKIDATA_PROPERTY:P1542\n      - SNOMED:cause_of\n      - RO:0003303\n    broad_mappings:\n      - RO:0002410\n      - RO:0002506\n    narrow_mappings:\n      - MONDO:disease_triggers\n      - GOREL:0000040\n      - MONDO:disease_causes_feature\n      - MONDO:disease_triggers\n      - NCIT:allele_has_abnormality\n      - NCIT:biological_process_has_result_biological_process\n      - NCIT:chemical_or_drug_has_physiologic_effect\n      # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'?\n      - NCIT:chemical_or_drug_initiates_biological_process\n      - NCIT:process_initiates_biological_process\n      - NCIT:chromosome_mapped_to_disease\n      - NCIT:disease_has_normal_tissue_origin\n      - NBO-PROPERTY:in_response_to\n      - ORPHA:317343\n      - ORPHA:317344\n      - ORPHA:317346\n      - ORPHA:410295\n      - ORPHA:410296\n      # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002256\n      - RO:0002315\n      - RO:0002507\n      - RO:0002509\n      - RO:0004001\n      - SNOMED:causative_agent_of\n      - SNOMED:has_realization\n      - UMLS:has_physiologic_effect\n\n  caused by:\n    description: >-\n      holds between two entities where the occurrence, existence,\n      or activity of one is caused by the occurrence or generation of the other\n    is_a: related to at instance level\n    aliases: [ 'disease caused by disruption of', 'disease has basis in dysfunction of',\n               'realized in response to', 'realized in response to stimulus' ]\n    in_subset:\n      - translator_minimal\n    inverse: causes\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P828\n    narrow_mappings:\n      - RO:0001022\n      - RO:0002608\n      - RO:0004019\n      - RO:0004020\n      - RO:0004028\n      - RO:0009501\n\n  # TODO: ameliorates and exacerbates inverses.\n  ameliorates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a genotype,\n      genetic variation, chemical, or environmental exposure)\n      and a condition (a phenotype or disease), where the\n      presence of the entity reduces or eliminates some or\n      all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: exacerbates\n    exact_mappings:\n      - RO:0003307\n\n  is ameliorated by:\n    inverse: ameliorates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n\n  exacerbates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a chemical,\n      environmental exposure, or some form of genetic variation)\n      and a condition (a phenotype or disease), where the presence\n      of the entity worsens some or all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0003309\n    broad_mappings:\n      - SEMMEDDB:complicates\n\n  is exacerbated by:\n    inverse: exacerbates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n    in_subset:\n      - translator_minimal\n\n  treats:\n    aliases: [ 'is substance that treats', 'indicated for' ]\n    is_a: ameliorates\n    description: >-\n      holds between a therapeutic procedure or chemical entity\n      and a disease or phenotypic feature that it is used to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: contraindicated for\n    in_subset:\n      - translator_minimal\n    related_mappings:\n      - MONDO:disease_responds_to\n    exact_mappings:\n      - DRUGBANK:treats\n      - SEMMEDDB:TREATS\n      - SEMMEDDB:treats\n      - WIKIDATA_PROPERTY:P2175\n    narrow_mappings:\n      # \"is substance that treats\" constrains statements to\n      # a subset of the universe of all possible treatments\n      - RO:0002606\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n      - SNOMED:plays_role\n\n  treated by:\n    is_a: is ameliorated by\n    description: >-\n      holds between a disease or phenotypic feature and a therapeutic\n      process or chemical entity that is used to treat the condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    # range: chemical or drug or treatement\n    in_subset:\n      - translator_minimal\n    inverse: treats\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2176\n      # RTX contributed term tagged as inverse of 'biolink:treats'\n      - MONDO:disease_responds_to\n    narrow_mappings:\n      # \"is treated by substance\" constrains statements to\n      # subset of the universe of all possible treatments\n      - RO:0002302\n\n  prevents:\n    is_a: affects risk for\n    description: >-\n      holds between an entity whose application or use reduces\n      the likelihood of a potential outcome. Typically used to associate\n      a chemical entity, exposure, activity, or medical intervention\n      that can prevent the onset a disease or phenotypic feature.\n    annotations:\n      canonical_predicate: true\n      opposite_of: predisposes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:PREVENTS\n      - SEMMEDDB:prevents\n    narrow_mappings:\n      # more restricted case of a material entity mitigating a pathological process\n      - RO:0002599\n\n  prevented by:\n    is_a: risk affected by\n    description: >-\n      holds between a potential outcome of which the likelihood\n      was reduced by the application or use of an entity.\n    inverse: prevents\n    annotations:\n      opposite_of: enabled by\n\n  correlated with:\n    is_a: associated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical dependence is \n      demonstrated using a correlation analysis method.\n    notes: >-\n      These concepts may map exactly to the statistical variables, or represent related entities for which the \n      variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002610\n      - PATO:correlates_with\n\n  # proposed positive and negative semantic extensions to the general \"correlated with\" predicate\n\n  positively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or \n      presence of one correlates with an increase or presence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: negatively correlated with\n    exact_mappings:\n      - CTD:positive_correlation\n\n  negatively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of \n      one correlates with a decrease or absence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: positively correlated with\n    exact_mappings:\n      - CTD:negative_correlation\n\n  occurs together in literature with:\n    is_a: correlated with\n    description: >-\n      holds between two entities where their co-occurrence is correlated by counts of publications\n      in which both occur, using some threshold of occurrence as defined by the edge provider.\n    domain: named thing\n    range: named thing\n    in_subset: translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  coexpressed with:\n    is_a: correlated with\n    description: >-\n      holds between any two genes or gene products, in which both are\n      generally expressed within a single defined experimental context.\n    domain: gene or gene product\n    range: gene or gene product\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  has biomarker:\n    is_a: correlated with\n    description: >-\n      holds between a disease or phenotypic feature and a measurable\n      chemical entity that is used as an indicator of the presence\n      or state of the disease or feature.\n      # metabolite\n    domain: disease or phenotypic feature\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    inverse: biomarker for\n    narrow_mappings:\n      # some RTX terms contributed as inverses of 'biolink:biomarker_for'\n      - NCIT:disease_has_molecular_abnormality\n      - NCIT:disease_is_marked_by_gene\n\n  biomarker for:\n    is_a: correlated with\n    description: >-\n      holds between a measurable chemical entity and a disease\n      or phenotypic feature, where the entity is used as an indicator\n      of the presence or state of the disease or feature.\n    domain: chemical entity or gene or gene product\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - NCIT:R39\n    broad_mappings:\n      # Generic marker definition not specific to biomarkers per say\n      - RO:0002607\n    narrow_mappings:\n      - NCIT:R47\n      # RTX term was tagged as 'biolink:actively_involved_in' but maps better here?\n      - NCIT:genetic_biomarker_related_to\n      - NCIT:is_molecular_abnormality_of_disease\n      - ORPHA:465410\n\n  # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in'\n  # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates\n  # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others\n  expressed in:\n    is_a: located in\n    description: >-\n      holds between a gene or gene product and an anatomical entity in which it is expressed\n    domain: gene or gene product\n    range: anatomical entity\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002206\n    narrow_mappings:\n      - NCIT:R49\n      - NCIT:R46\n\n  expresses:\n    is_a: location of\n    aliases: [ 'anatomy expresses gene' ]\n    description: >-\n      holds between an anatomical entity and gene or gene product that is expressed there\n    domain: anatomical entity\n    range: gene or gene product\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    inverse: expressed in\n    exact_mappings:\n      - RO:0002292\n\n  has phenotype:\n    is_a: related to at instance level\n    aliases: [ 'disease presents symptom' ]\n    description: >-\n      holds between a biological entity and a phenotype, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should\n      translate into this predicate.\n    domain: biological entity\n    range: phenotypic feature\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    notes:\n      - check the range\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002200\n    broad_mappings:\n      - NCIT:R115\n      - NCIT:R108\n    narrow_mappings:\n      - NCIT:R89\n      - DOID-PROPERTY:has_symptom\n      - RO:0004022\n\n  phenotype of:\n    is_a: related to at instance level\n    description: >-\n      holds between a phenotype and a biological entity, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature).\n    domain: phenotypic feature\n    range: biological entity\n    multivalued: true\n    inverse: has phenotype\n    notes:\n      - check the domain\n    in_subset:\n      - translator_minimal\n\n  # TODO: predicate inverse for occurs in\n  occurs in:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a material entity or site within which the process occurs\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # These RTX mapped terms tagged as the inverse of \"biolink:occurs_in\", i.e. Entity/Site contains Process\"\n      - BFO:0000067\n      - SNOMED:has_occurrence\n      - UBERON:site_of\n    exact_mappings:\n      - BFO:0000066\n      - PathWhiz:has_location\n      - SNOMED:occurs_in\n    narrow_mappings:\n      # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population\n      - SEMMEDDB:OCCURS_IN\n      - SEMMEDDB:occurs_in\n      # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity\n      - SEMMEDDB:PROCESS_OF\n      - SEMMEDDB:process_of\n      # Uberon term constrained to a 'site' as object concept\n      - UBERON_CORE:site_of\n      - LOINC:has_imaged_location\n      - PathWhiz:in_species\n      - RO:0002231\n      - RO:0002232\n      - SNOMED:has_direct_procedure_site\n      - SNOMED:has_direct_site\n      - SNOMED:has_procedure_site\n\n  contains process:\n    is_a: related to at instance level\n    inverse: occurs in\n\n  located in:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a material entity or site\n      within which it is located (but of which it is not considered a part)\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0001025\n      - FMA:has_location\n    narrow_mappings:\n      - GOREL:0001004\n      - BSPO:0000107\n      - BSPO:0000108\n      - BSPO:0000120\n      - BSPO:0000121\n      - BSPO:0000122\n      - BSPO:0000123\n      - BSPO:0000124\n      - BSPO:0000125\n      - BSPO:0000126\n      - BSPO:0001100\n      - BSPO:0001101\n      - BSPO:0001107\n      - BSPO:0015101\n      - BSPO:0015102\n      - BSPO:0015202\n      - UBERON_CORE:in_central_side_of\n      - UBERON_CORE:in_innermost_side_of\n      - UBERON_CORE:in_outermost_side_of\n      - NCIT:R100\n      - EFO:0000784\n      - FMA:has_location\n      - HMDB:at_cellular_location\n      - HMDB:at_tissue\n      - HMDB:in_biospecimen\n      - LOINC:has_imaging_focus\n      - NCIT:R156\n      - NCIT:R155\n      - NCIT:R145\n      - NCIT:R40\n      - NCIT:R171\n      - NCIT:R167\n      - NCIT:R165\n      - NCIT:R169\n      - NCIT:R170\n      - NCIT:R166\n      - NCIT:R168\n      - RO:0002303\n      - SNOMED:has_finding_site\n      - SNOMED:has_indirect_procedure_site\n      - SNOMED:has_inherent_location\n    domain: named thing\n    range: named thing\n\n  location of:\n    is_a: related to at instance level\n    aliases: [ 'site of' ]\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between material entity or site and a material entity\n      that is located within it (but not considered a part of it)\n    in_subset:\n      - translator_minimal\n    inverse: located in\n    exact_mappings:\n      - RO:0001015\n      - SEMMEDDB:LOCATION_OF\n      - SEMMEDDB:location_of\n      - WIKIDATA_PROPERTY:P276\n      # RTX tagged this as an inverse of biolink:located_in\n      - FMA:location_of\n    narrow_mappings:\n      - SNOMED:inherent_location_of\n      - NCIT:Anatomic_Structure_Has_Location_Role\n\n  disease has location:\n    description: >-\n      A relationship between a disease and an anatomical entity where the\n      disease has one or more features that are located in that entity.\n    is_a: related to\n    exact_mappings:\n      - RO:0004026\n      - MONDO:disease_has_location\n\n  location of disease:\n    is_a: related to\n    inverse: disease has location\n\n  similar to:\n    is_a: related to at instance level\n    description: >-\n      holds between an entity and some other entity with similar features.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000000               #I don't understand this identifier, but I think it's equivalent\n      - SO:similar_to               #equivalent\n\n  chemically similar to:\n    is_a: similar to\n    description: >-\n      holds between one small molecule entity and another that it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - CHEBI:has_parent_hydride    #subproperty\n      - CHEBI:has_functional_parent #subproperty\n      - CHEBI:is_conjugate_acid_of  #subproperty\n      - CHEBI:is_conjugate_base_of  #subproperty\n      - CHEBI:is_enantiomer_of      #subproperty\n      - CHEBI:is_tautomer_of        #subproperty\n      - NCIT:has_salt_form\n\n  has sequence location:\n    is_a: related to at instance level\n    description: >-\n      holds between two nucleic acid entities when the subject can be localized\n      in sequence coordinates on the object. For example, between\n      an exon and a chromosome/contig.\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - faldo:location\n\n  sequence location of:\n    is_a: related to at instance level\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    inverse: has sequence location\n\n  model of:\n    is_a: related to at instance level\n    description: >-\n      holds between a thing and some other thing it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0003301\n    narrow_mappings:\n      - FOODON:00001301\n\n  models:\n    is_a: related to at instance level\n    inverse: model of\n\n  overlaps:\n    is_a: related to at instance level\n    description: >-\n      holds between entities that overlap in their extents (materials or processes)\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002131\n    narrow_mappings:\n      - BSPO:0005001\n      - CHEMBL.MECHANISM:overlaps_with\n      - RO:0002100\n      - RO:0002102\n      - RO:0002433\n\n  has part:\n    is_a: overlaps\n    annotations:\n      canonical_predicate: true\n      opposite_of: lacks part\n    description: >-\n      holds between wholes and their parts (material entities or processes)\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000051\n      # term name seems to be 'realizes' but RTX maps this term here\n      - BFO:0000055\n      - WIKIDATA_PROPERTY:P527\n      - RO:0001019\n      - RXNORM:consists_of\n      - RXNORM:has_part\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'; slightly broader?\n      - RO:0001019\n      - FMA:contains\n      - RXNORM:contains\n    narrow_mappings:\n      - BFO:0000117\n      # RTX term originally mapped to 'biolink:coexists_with'?\n      - FMA:has_constitutional_part\n      - FMA:has_part\n      # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'?\n      - FMA:has_member\n      - FOODON:00001563\n      - FOODON:00002420\n      - LOINC:has_component\n      - LOINC:has_member\n      - MEDDRA:has_member\n      - MONDO:disease_has_major_feature\n      - NCIT:complex_has_physical_part\n      - NDDF:has_ingredient\n      - PathWhiz:has_element_in_bound\n      # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature\n      - NCIT:R50\n      - PathWhiz:has_protein_in_complex\n      - RO:0002104\n      - RO:0002180\n      - RO:0002351\n      - RO:0002473\n      - RO:0002524\n      - RO:0002551\n      - RXNORM:has_ingredient\n      - SNOMED:has_component\n      - UMLS:has_component\n\n  has plasma membrane part:\n    is_a: has part\n    description: >-\n      Holds between a cell c and a protein complex or protein p if\n      and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.\n    exact_mappings:\n      - RO:0002104\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  composed primarily of:\n    is_a: related to\n    description: >-\n      x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.\n    exact_mappings:\n      - RO:0002473\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  primarily composed of:\n    inverse: composed primarily of\n    is_a: related to\n\n  plasma membrane part of:\n    is_a: part of\n    inverse: has plasma membrane part\n\n  part of:\n    is_a: overlaps\n    description: >-\n      holds between parts and wholes (material entities or processes)\n    in_subset:\n      - translator_minimal\n    inverse: has part\n    exact_mappings:\n      - BFO:0000050\n      - SEMMEDDB:PART_OF\n      - SEMMEDDB:part_of\n      - WIKIDATA_PROPERTY:P361\n      - FMA:part_of\n      - RXNORM:constitutes\n      - RXNORM:part_of\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'\n      - RO:0001018\n      - FMA:contained_in\n      - RXNORM:contained_in\n    narrow_mappings:\n      - BSPO:0001106\n      - BSPO:0001108\n      - BSPO:0001113\n      - BSPO:0001115\n      - UBERON_CORE:layer_part_of\n      - UBERON_CORE:subdivision_of\n      - UBERON_CORE:trunk_part_of\n      - CHEBI:is_substituent_group_from\n      - CPT:panel_element_of\n      - CPT:panel_element_of_possibly_included\n      - DRUGBANK:component_of\n      - FMA:constitutional_part_of\n      - FMA:member_of\n      - FMA:regional_part_of\n      - FMA:related_developmental_entity_of\n      - LOINC:component_of\n      - LOINC:has_supersystem\n      - LOINC:member_of\n      - LOINC:multipart_of\n      - MEDDRA:member_of\n      - MONDO:part_of_progression_of_disease\n      - NCIT:R82\n      - NCIT:R27\n      - NCIT:is_component_of_chemotherapy_regimen\n      - NDDF:ingredient_of\n      - RO:0002007\n      - RO:0002350\n      - RO:0002376\n      - RO:0002380\n      - RO:0002571\n      - RO:0002572\n      - RO:0002576\n      - RXNORM:ingredient_of\n      - RXNORM:ingredients_of\n      - RXNORM:precise_ingredient_of\n      - SNOMED:active_ingredient_of\n      - SNOMED:basis_of_strength_substance_of\n      - SNOMED:component_of\n      - SNOMED:direct_substance_of\n      - SNOMED:during\n      - SNOMED:focus_of\n      - SNOMED:has_dependent\n      - SNOMED:part_anatomy_structure_of\n      - SNOMED:precise_active_ingredient_of\n      - UBERON:subdivision_of\n      - UMLS:component_of\n      - UMLS:has_owning_affiliate\n      - UMLS:owning_subsection_of\n      - VANDF:ingredient_of\n\n  has input:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an input into the process\n    domain: occurrent\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n      opposite_of: has output\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX inverse mapping to to 'biolink:has_input'\n      - RO:0002352\n    exact_mappings:\n      - RO:0002233\n      - SEMMEDDB:USES\n      - SEMMEDDB:uses\n    narrow_mappings:\n      - LOINC:has_fragments_for_synonyms\n      - LOINC:has_system\n      - PathWhiz:has_left_element\n      - RO:0002590\n      - RO:0004009\n      - SNOMED:has_finding_method\n      - SNOMED:has_precondition\n      - SNOMED:has_specimen_source_identity\n      - SNOMED:has_specimen_substance\n      - SNOMED:uses_access_device\n      - SNOMED:uses_device\n      - SNOMED:uses_energy\n      - SNOMED:uses_substance\n\n  is input of:\n    is_a: participates in\n    domain: biological process or activity\n    range: occurrent\n    inverse: has input\n    in_subset:\n      - translator_minimal\n\n  has output:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an output of the process\n    domain: occurrent\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n      opposite_of: has input\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - RO:0002353\n      - RO:0002354\n    exact_mappings:\n      - RO:0002234\n    narrow_mappings:\n      - NCIT:R31\n      - OBI:0000299\n      - PathWhiz:has_right_element\n      - RO:0002296\n      - RO:0002297\n      - RO:0002298\n      - RO:0002299\n      - RO:0002588\n      - RO:0004008\n\n  is output of:\n    is_a: participates in\n    range: occurrent\n    domain: biological process or activity\n    inverse: has output\n    in_subset:\n      - translator_minimal\n\n  has participant:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a continuant, where the continuant is somehow involved in the process\n    domain: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - WIKIDATA_PROPERTY:P2283\n    exact_mappings:\n      - RO:0000057\n      - RO:has_participant\n    narrow_mappings:\n      - BFO:0000167\n      # Several of the following RTX terms tagged as inverse to 'biolink:participates_in'\n      - LOINC:has_subject\n      - NCIT:process_involves_gene\n      - NBO-PROPERTY:has_participant\n      - PathWhiz:has_bound\n      - PathWhiz:has_compound\n      - PathWhiz:has_element_collection\n      - PathWhiz:has_enzyme\n      - OBI:0000293\n      - PathWhiz:has_nucleic_acid\n      - PathWhiz:has_protein\n      - PathWhiz:has_reaction\n      - RO:0004007\n      - RO:0004020\n      - RO:0004021\n      - SNOMED:has_indirect_device\n      - SNOMED:has_procedure_device\n      - SNOMED:has_recipient_category\n\n  catalyzes:\n    is_a: participates in\n    # domain: nucleic acid entity\n    # range: molecular activity\n    annotations:\n      canonical_predicate: true\n\n  has catalyst:\n    is_a: has participant\n    inverse: catalyzes\n\n  has substrate:\n    is_a: has participant\n    # domain: molecular activity\n    # range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n\n  is substrate of:\n    is_a: participates in\n    inverse: has substrate\n\n  participates in:\n    is_a: related to at instance level\n    description: >-\n      holds between a continuant and a process, where the continuant is somehow involved\n      in the process\n    range: occurrent\n    inverse: has participant\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0000056\n      - BFO:0000056\n    narrow_mappings:\n      - DRUGBANK:pathway\n      - HMDB:in_pathway\n      - LOINC:is_given_pharmaceutical_substance_for\n      - NCIT:R130\n      - NCIT:R37\n      - NCIT:R131\n      - NCIT:R51\n      - NCIT:R53\n      - OBI:0000295\n      - RO:0002216\n      - RO:0002505\n      - RO:0002565\n      - SNOMED:has_direct_device\n\n  actively involved in:\n    is_a: participates in\n    aliases: [ 'involved in' ]\n    description: >-\n      holds between a continuant and a process or function, where\n      the continuant actively contributes to part or all of\n      the process or function it realizes\n    domain: molecular activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002331\n      - RO:0002432\n    narrow_mappings:\n      - NBO-PROPERTY:by_means\n      - ORPHA:317348\n      - ORPHA:317349\n      - ORPHA:327767\n      - RO:0002503\n\n  actively involves:\n    is_a: has participant\n    domain: occurrent\n    range: molecular activity\n    inverse: actively involved in\n    exact_mappings:\n      - RO:0002331\n    in_subset:\n      - translator_minimal\n\n  capable of:\n    is_a: actively involved in\n    description: >-\n      holds between a physical entity and process or function, where the\n      continuant alone has the ability to carry out the process or function.\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002215\n    narrow_mappings:\n      - NCIT:R52\n      - RO:0002500\n\n  has capability:\n    is_a: actively involves\n    inverse: capable of\n\n  enables:\n    is_a: participates in\n    description: >-\n      holds between a physical entity and a process, where the physical entity executes the process\n    domain: physical entity\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    in_subset:\n      - translator_minimal\n    inverse: enabled by\n    exact_mappings:\n      - RO:0002327\n\n  enabled by:\n    is_a: has participant\n    description: >-\n      holds between a process and a physical entity, where the physical entity executes the process\n    domain: biological process or activity\n    range: physical entity\n    in_subset:\n      - translator_minimal\n    inverse: enables\n    exact_mappings:\n      - RO:0002333\n    annotations:\n      opposite_of: prevented by\n\n  derives into:\n    is_a: related to at instance level\n    aliases: [ 'is normal cell origin of disease','may be normal cell origin of disease' ]\n    description: >-\n      holds between two distinct material entities, the old entity and\n      the new entity, in which the new entity begins to exist when\n      the old entity ceases to exist, and the new entity inherits\n      the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n    inverse: derives from\n    # TODO: fix this according to WG notes. Example of both opposite and inverse\n    annotations:\n      opposite_of: subclass of\n    exact_mappings:\n      - RO:0001001\n      - SEMMEDDB:CONVERTS_TO\n      - SEMMEDDB:converts_to\n      # RTX posted terms as inverse of 'biolink:derives_from'\n      - FMA:derives\n\n  derives from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    description: >-\n      holds between two distinct material entities, the new entity\n      and the old entity, in which the new entity begins to exist\n      when the old entity ceases to exist, and the new entity\n      inherits the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n      - samples\n    inverse: derives into\n    exact_mappings:\n      - RO:0001000\n      - FMA:derives_from\n      - DOID-PROPERTY:derives_from\n    narrow_mappings:\n      - CHEBI:has_functional_parent\n      - SNOMED:has_specimen_source_topography\n\n  is metabolite of:\n    is_a: derives from\n    description: >-\n      holds between two molecular entities in which the first one is derived\n      from the second one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    inverse: has metabolite\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  has metabolite:\n    is_a: derives into\n    description: >-\n      holds between two molecular entities in which the second one is derived from the first\n      one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  food component of:\n    is_a: part of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has food component\n    #mappings:\n    #  -\n\n  has food component:\n    is_a: has part\n    description: >-\n      holds between food and one or more chemical entities composing it,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  nutrient of:\n    is_a: food component of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has nutrient\n    #exact_mappings:\n    #  -\n\n  has nutrient:\n    is_a: has food component\n    description: >-\n      one or more nutrients which are growth factors for a living organism\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q181394\n\n  is active ingredient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug, in which the former\n      is a part of the latter, and is a biologically active component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has active ingredient\n    mappings:\n      - RO:0002249\n\n  has active ingredient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entity in which the latter\n      is a part of the former, and is a biologically active component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: is excipient of\n    in_subset:\n      - translator_minimal\n    inverse: is active ingredient of\n    mappings:\n      - RO:0002248\n\n  is excipient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug in which the former is\n      a part of the latter, and is a biologically inactive component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has excipient\n    mappings:\n      - WIKIDATA:Q902638\n\n  has excipient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entities in which the latter\n      is a part of the former, and is a biologically inactive component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    mappings:\n      - WIKIDATA:Q902638\n\n  manifestation of:\n    is_a: related to at instance level\n    description: >-\n      that part of a phenomenon which is directly observable or\n      visibly expressed, or which gives evidence to the underlying\n      process; used in SemMedDB for linking things like dysfunctions\n      and processes to some disease or syndrome\n    range: disease\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:MANIFESTATION_OF\n      - SEMMEDDB:manifestation_of\n      - OMIM:manifestation_of\n    broad_mappings:\n      # Wikidata definition slightly broader: \"inherent and characteristic embodiment of a given concept\"\n      - WIKIDATA_PROPERTY:P1557\n    narrow_mappings:\n      - SNOMED:has_definitional_manifestation\n\n  has manifestation:\n    is_a: related to at instance level\n    domain: disease\n    inverse: manifestation of\n\n  mode of inheritance of:\n    is_a: manifestation of\n    domain: genetic inheritance\n    range: disease or phenotypic feature\n    inverse: has mode of inheritance\n\n  has mode of inheritance:\n    is_a: has manifestation\n    description: >-\n      Relates a disease or phenotypic feature to its observed genetic segregation and assumed\n      associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).\n    domain: disease or phenotypic feature\n    range: genetic inheritance\n    annotations:\n      # This canonical order reverses that of its parent 'has manifestation' class\n      # but seems a more natural direction in the pertinent edge relationships.\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  produces:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a product that is generated\n      through the intentional actions or functioning of the material entity\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GOREL:0001010\n    exact_mappings:\n      - RO:0003000\n      - WIKIDATA_PROPERTY:P1056\n      - SEMMEDDB:PRODUCES\n      - SEMMEDDB:produces\n    narrow_mappings:\n      - NCIT:R29\n      - SNOMED:has_process_output\n      - SNOMED:specimen_procedure_of\n\n  produced by:\n    is_a: related to at instance level\n    inverse: produces\n    exact_mappings:\n      - RO:0003001\n\n  consumes:\n    is_a: has input\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - RO:0004009\n\n  consumed by:\n    is_a: is input of\n    inverse: consumes\n\n  temporally related to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities with a temporal relationship\n    domain: occurrent\n    range: occurrent\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SNOMED:temporally_related_to\n    narrow_mappings:\n      # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here\n      - RO:0002082\n      - RO:0002083\n      - RO:0002092\n      - RO:0002093\n      - RO:0002223\n      - RO:0002224\n      - RO:0002229\n      - RO:0002230\n      - RO:0002488\n      - RO:0002489\n      - RO:0002492\n      - RO:0002493\n      - RO:0002496\n      - RO:0002497\n\n  precedes:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where one completes before the other begins\n    domain: occurrent\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n      opposite_of: preceded by\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # the subject of these terms is a material entity, not a process,\n      # but affects a process which causes a second process to occur\n      - RO:0002263\n      - RO:0002264\n    exact_mappings:\n      - BFO:0000063\n      - SEMMEDDB:PRECEDES\n      - SEMMEDDB:precedes\n      - SNOMED:occurs_before\n    broad_mappings:\n      # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature\n      - WIKIDATA_PROPERTY:P156\n    narrow_mappings:\n      - FMA:transforms_into\n      - RO:0002090\n      - RO:0002411\n      - RO:0002412\n\n  preceded by:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where the other is completed before the one begins\n    domain: occurrent\n    range: occurrent\n    inverse: precedes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000062\n    broad_mappings:\n      # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'?\n      - GENEPIO:0001739\n    narrow_mappings:\n      # RTX contributed mapping was given as the inverse of 'biolink:precedes'\n      - FMA:transforms_from\n      - RO:0002087\n      - RO:0002285\n\n  directly interacts with:\n    deprecated: true\n    is_a: interacts with\n    description: Holds between chemical entities that physically and directly interact\n      with each other\n    domain: chemical entity\n    range: chemical entity or gene or gene product\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GAMMA:kd\n      - GAMMA:kb\n      - GAMMA:potency\n    exact_mappings:\n      - GAMMA:interacts_with\n    broad_mappings:\n      # Definition of this term is more generic than direct physical molecular interactions:\n      # A is connected to B iff there exists a fiat, material or temporal path between A and B.\n      - SIO:000203\n    narrow_mappings:\n      - PHAROS:drug_targets\n      - DRUGBANK:chelator\n      - GAMMA:antibody_binding\n      - GAMMA:pharmacological_chaperone\n      - GAMMA:releasing_agent\n      - GAMMA:pharmacological_chaperone\n      - GAMMA:releasing_agent\n      - GAMMA:binder\n      - GAMMA:binding\n      - GAMMA:ligand\n      - GAMMA:cofactor\n      - GAMMA:multitarget\n      - GAMMA:chaperone\n      - GAMMA:component\n      - GAMMA:adduct\n      - GAMMA:antibody\n      - CTD:affects_binding\n      - DGIdb:binder\n      - DGIdb:cofactor\n\n  affects expression in:\n    deprecated: true\n    is_a: affects\n    annotations:\n      canonical_predicate: true\n    description: Holds between a variant and an anatomical entity where the expression of the variant\n      is located in.\n    exact_mappings:\n      - GTEx:affects_expression_in\n\n  has variant part:\n    is_a: has part\n    description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000382\n\n  variant part of:\n    is_a: part of\n    inverse: has variant part\n\n  related condition:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000790\n\n  ## Predicates relating variants to genes\n\n  is sequence variant of:\n    is_a: related to at instance level\n    aliases: [ 'gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product' ]\n    description: holds between a sequence variant and a nucleic acid entity\n    domain: sequence variant\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - WIKIDATA:P3433\n\n  has sequence variant:\n    is_a: related to at instance level\n    inverse: is sequence variant of\n    domain: nucleic acid entity\n    range: sequence variant\n\n  is missense variant of:\n    is_a: is sequence variant of\n    description: holds between a gene  and a sequence variant, such the sequence variant\n      results in a different amino acid sequence but where the length is preserved.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001583\n\n  has missense variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is missense variant of\n\n  is synonymous variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the coding sequence of the gene, but results in the same amino acid sequence\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001819\n\n  has synonymous variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is synonymous variant of\n    aliases: [ 'stop gained' ]\n\n  is nonsense variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      results in a premature stop codon\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      # Term definition broader than nonsense codon: A sequence variant whereby\n      # the gene product has diminished or abolished function.\n      - SO:0002054\n\n  has nonsense variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is nonsense variant of\n\n  is frameshift variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      causes a disruption of the translational reading frame, because the number of\n      nucleotides inserted or deleted is not a multiple of three.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001589\n    aliases: [ 'frameshift variant', 'start lost', 'stop lost' ]\n\n  has frameshift variant:\n    is_a: has sequence variant\n    inverse: is frameshift variant of\n    domain: gene\n    range: sequence variant\n    aliases: [ 'splice region variant', 'splice acceptor variant', 'splice donor variant' ]\n\n  is splice site variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the canonical splice site of one of the gene's exons.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001629\n\n\n  has splice site variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is splice site variant of\n    aliases: [ 'downstream gene variant', 'upstream gene variant' ]\n\n  is nearby variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene sequence that the variant\n      is genomically close to.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GAMMA:0000102\n\n  has nearby variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is nearby variant of\n    aliases: [ 'intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant' ]\n\n  is non coding variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, where the variant does\n      not affect the coding sequence\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GAMMA:0000103\n\n  has non coding variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is non coding variant of\n\n  # relating disease to process\n\n  disease has basis in:\n    description: A relation that holds between a disease and an entity where the state\n      of the entity has contribution to the disease.\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      # These two MONDO terms seem more particular than the predicate\n      - MONDO:disease_has_basis_in_development_of\n      - MONDO:disease_has_basis_in_accumulation_of\n\n  occurs in disease:\n    is_a: related to at instance level\n    inverse: disease has basis in\n\n\n  has adverse event:\n    is_a: affects\n    aliases: [ 'adverse effect']\n    description: >-\n      An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment \n      with a therapeutic agent. Adverse events may be caused by something \n      other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or \n      diseases temporally associated with the treatment, whether or not considered related to the treatment. \n      Adverse events are unintended effects that occur when a medication is administered correctly.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n\n  adverse event of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has adverse event\n\n  has side effect:\n    aliases: [ 'adverse drug reaction']\n    is_a: affects\n    description: >-\n      An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment.\n      Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of \n      the medication.\n    notes: >-\n      Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative.\n      Aeolus, Sider are both resources that provide side effects.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C2861 # side effect\n\n  is side effect of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  contraindicated for:\n    is_a: related to at instance level\n    description: Holds between a drug and a disease or phenotype, such that a person\n      with that disease should not be treated with the drug.\n    domain: drug\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: treats\n    exact_mappings:\n      - NCIT:C37933\n\n  has contraindication:\n    is_a: related to at instance level\n    domain: disease or phenotypic feature\n    range: drug\n    inverse: contraindicated for\n\n  # The remaining new slots are here because we ran across them somewhere and\n  # they didn't seem to map well to anything else.\n\n  has not completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of,\n      but has not completed\n    exact_mappings:\n      - CL:has_not_completed\n    annotations:\n      opposite_of: has completed\n      canonical_predicate: true\n\n  not completed by:\n    is_a: related to at instance level\n    inverse: has not completed\n\n  has completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of\n      and has completed\n    annotations:\n      canonical_predicate: true\n      opposite_of: has not completed\n    exact_mappings:\n      - CL:has_completed\n\n  completed by:\n    is_a: related to at instance level\n    inverse: has completed\n\n  decreases molecular interaction:\n    deprecated: true\n    is_a: molecularly interacts with\n    description: indicates that the source decreases the molecular interaction between\n      the target and some other chemical entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases molecular interaction\n    exact_mappings:\n      - CTD:decreases_molecular_interaction_with\n    mixins:\n      - decreases amount or activity of\n\n  molecular interaction decreased by:\n    deprecated: true\n    is_a: molecularly interacts with\n    inverse: decreases molecular interaction\n\n  increases molecular interaction:\n    deprecated: true\n    is_a: molecularly interacts with\n    description: indicates that the source increases the molecular interaction between\n      the target and some other chemical entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases molecular interaction\n    exact_mappings:\n      - CTD:increases_molecular_interaction_with\n    mixins:\n      - increases amount or activity of\n\n  molecular interaction increased by:\n    deprecated: true\n    is_a: molecularly interacts with\n    inverse: increases molecular interaction\n\n  in linkage disequilibrium with:\n    is_a: related to at instance level\n    description: holds between two sequence variants, the presence of which are correlated\n      in a population\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C16798\n\n  has increased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has decreased amount\n    narrow_mappings:\n      - CL:has_high_plasma_membrane_amount\n\n  increased amount of:\n    is_a: related to at instance level\n    inverse: has increased amount\n\n  has decreased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has increased amount\n    narrow_mappings:\n      - CL:has_low_plasma_membrane_amount\n\n  decreased amount in:\n    is_a: related to at instance level\n    inverse: has decreased amount\n\n  lacks part:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has part\n    exact_mappings:\n      - CL:lacks_part\n      - PR:lacks_part\n    narrow_mappings:\n      - CL:lacks_plasma_membrane_part\n\n  missing from:\n    is_a: related to at instance level\n    inverse: lacks part\n\n  develops from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX mapping seems to be inverse of 'biolink:develops_from'\n      - RO:0002203\n      - FMA:develops_into\n    exact_mappings:\n      - BTO:develops_from\n      - DDANAT:develops_from\n      - FMA:develops_from\n      - RO:0002202\n    narrow_mappings:\n      - RO:0002207\n      - RO:0002225 # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y\n      - RO:0002226 # x develops_in y if x is located in y whilst x is developing\n\n  develops into:\n    is_a: related to at instance level\n    inverse: develops from\n\n  in taxon:\n    aliases: [ 'instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism',' gene product has organism source' ]\n    is_a: related to at instance level\n    domain: thing with taxon\n    range: organism taxon\n    annotations:\n      canonical_predicate: true\n    description: >-\n      connects an entity to its taxonomic classification. Only certain kinds\n      of entities can be taxonomically classified; see 'thing with taxon'\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002162\n      - WIKIDATA_PROPERTY:P703\n    narrow_mappings:\n      - RO:0002160\n\n  taxon of:\n    is_a: related to at instance level\n    inverse: in taxon\n    domain: organism taxon\n    range: thing with taxon\n\n  has molecular consequence:\n    is_a: related to at instance level\n    aliases: [ 'allele has activity' ]\n    description: >-\n      connects a sequence variant to a class describing the molecular\n      consequence. E.g.  SO:0001583\n    range: ontology class\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - NCIT:allele_has_activity\n\n  is molecular consequence of:\n    is_a: related to at instance level\n    domain: ontology class\n    inverse: has molecular consequence\n\n  ## --------------------\n  ## ASSOCIATION SLOTS\n  ## --------------------\n\n  association slot:\n    abstract: true\n    domain: association\n    aliases: [ 'edge property','statement property','node qualifier','edge qualifier','statement qualifier' ]\n    description: >-\n      any slot that relates an association to another entity\n\n  original subject:\n    is_a: association slot\n    description: >-\n      used to hold the original subject of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original object:\n    is_a: association slot\n    description: >-\n      used to hold the original object of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original predicate:\n    aliases: [ 'original relation', 'relation' ]\n    is_a: association slot\n    description: >-\n      used to hold the original relation/predicate that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n    id_prefixes:\n      - RO\n      - BSPO\n      - SIO\n    domain: association\n    range: uriorcurie\n\n  subject:\n    is_a: association slot\n    local_names:\n      ga4gh: annotation subject\n      neo4j: node with outgoing relationship\n    description: >-\n      connects an association to the subject of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    slot_uri: rdf:subject\n    exact_mappings:\n      - owl:annotatedSource\n      - OBAN:association_has_subject\n\n  object:\n    is_a: association slot\n    description: >-\n      connects an association to the object of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    local_names:\n      ga4gh: descriptor\n      neo4j: node with incoming relationship\n    slot_uri: rdf:object\n    exact_mappings:\n      - owl:annotatedTarget\n      - OBAN:association_has_object\n\n  predicate:\n    is_a: association slot\n    description: >-\n      A high-level grouping for the relationship type. AKA minimal predicate.\n      This is analogous to category for nodes.\n    domain: association\n    notes: >-\n      Has a value from the Biolink related_to hierarchy. In RDF,  this\n      corresponds to rdf:predicate and in Neo4j this corresponds to the\n      relationship type. The convention is for an edge label in snake_case\n      form. For example, biolink:related_to, biolink:causes, biolink:treats\n    range: predicate type\n    required: true\n    local_names:\n      ga4gh: annotation predicate\n      translator: predicate\n    slot_uri: rdf:predicate\n    exact_mappings:\n      - owl:annotatedProperty\n      - OBAN:association_has_predicate\n\n  logical interpretation:\n    is_a: association slot\n    required: false\n    domain: association\n    range: logical_interpretation_enum\n    exact_mappings:\n      - os:LogicalInterpretation\n\n  relation:\n    deprecated: true\n\n  negated:\n    is_a: association slot\n    range: boolean\n    description: >-\n      if set to true, then the association is negated i.e. is not true\n\n  has confidence level:\n    is_a: association slot\n    range: confidence level\n    description: >-\n      connects an association to a qualitative term denoting the level of confidence\n\n  has evidence:\n    is_a: association slot\n    range: evidence type\n    description: >-\n      connects an association to an instance of supporting evidence\n    exact_mappings:\n      - RO:0002558\n    multivalued: true\n\n  has supporting study result:\n    is_a: related to at instance level\n    description: >-\n      connects an association to an instance of supporting study result\n\n  mechanism of action:\n    is_a: association slot\n    range: boolean\n    description: >-\n      a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes\n      the mechanism of action for a result.\n    exact_mappings:\n      - NCIT:C54680\n      - MI:2044\n      - LOINC:MTHU019741\n\n  knowledge source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which the knowledge expressed in an Association was\n      retrieved, directly or indirectly. This can be any resource through which the\n      knowledge passed on its way to its currently serialized form. In practice,\n      implementers should use one of the more specific subtypes of this generic property.\n    range: information resource\n    close_mappings:\n      - pav:providedBy\n\n  source:\n    deprecated: true\n\n  provided by:\n    is_a: node property\n    description: >-\n      The value in this node property represents the knowledge provider that created or assembled the\n      node and all of its attributes.  Used internally to represent how a particular node made its way into a\n      knowledge provider or graph.\n    multivalued: true\n\n  primary knowledge source:\n    is_a: knowledge source\n    description: >-\n      The most upstream source of the knowledge expressed in an Association that an\n      implementer can identify.  Performing a rigorous analysis of upstream data providers is expected; every effort\n      is made to catalog the most upstream source of data in this property.  Only one data source should be declared\n      primary in any association.  \"aggregator knowledge source\" can be used to caputre non-primary sources.\n    range: information resource\n    notes: >-\n      For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then \n      incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to \n      the NCATS ARS. The retrieval path for this Edge is as follows: \n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   MolePro  --retrieved_from--> ChEMBL --retrieved_from-->  ClinicalTrials.gov\n      The \"primary knowledge source\" for this edge is \"infores:clinical-trials-gov\".  \"infores:chembl\" and \"infores:molecular_data_provider\"\n      are listed in the \"aggregator knowledge source\" property.\n    multivalued: false\n\n  original knowledge source:\n    deprecated: true\n\n  aggregator knowledge source:\n    is_a: knowledge source\n    description: >-\n      An intermediate aggregator resource from which knowledge expressed in an Association was\n      retrieved downstream of the original source, on its path to its current serialized form.\n    range: information resource\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which data was retrieved and subsequently used as\n      evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data set:\n    is_a: association slot\n    description: >-\n      A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n\n  association type:\n    is_a: association slot\n    range: category type\n    deprecated: >-\n      This slot is deprecated in favor of 'category' slot.\n    deprecated_element_has_exact_replacement: category\n    description: >-\n      connects an association to the category of association (e.g. gene to phenotype)\n\n  chi squared statistic:\n    is_a: association slot\n    range: float\n    description: >-\n      represents the chi-squared statistic computed from observations\n    exact_mappings:\n      - STATO:0000030\n\n  p value:\n    aliases: ['unadjusted p value']\n    is_a: association slot\n    range: float\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    exact_mappings:\n      - OBI:0000175\n      - NCIT:C44185\n      - EDAM-DATA:1669\n\n  evidence count:\n    is_a: association slot\n    description: >-\n      The number of evidence instances that are connected to an association.\n    range: integer\n\n  concept count subject:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the subject slot of an association.\n    range: integer\n    examples:\n      - value: 489\n\n  concept count object:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the object slot of an association.\n    range: integer\n\n  concept pair count:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      both the subject and object concept of an association.\n    range: integer\n    examples:\n      - value: 1731\n\n  expected count:\n    is_a: association slot\n    description: >-\n      The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and \n      object concept of an association if the subject and object concepts are independent.\n\n  relative frequency subject:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the subject\n      concept appears in these same records.\n    range: float\n    examples:\n      - value: 0.01840490798\n\n  relative frequency object:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the object\n      concept appears in these same records.\n    range: string\n\n  relative frequency subject confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_subject calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  relative frequency object confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_object calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  adjusted p value:\n    is_a: p value\n    description: >-\n      The adjusted p-value is the probability of obtaining test results\n      at least as extreme as the results actually observed, under the assumption that\n      the null hypothesis is correct, adjusted for multiple comparisons.  \n      P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) \n      rather than expressing a statement of inequality (P<. 05), unless P<.\n    range: float\n\n  bonferonni adjusted p value:\n    is_a: adjusted p value\n    description: >-\n      The Bonferroni correction is an adjustment made to P values when several dependent or independent \n      statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni \n      correction, divide the critical P value (α) by the number of comparisons being made.  P is always italicized and \n      capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality \n      (P<. 05), unless P<.\n    range: float\n    examples:\n      - value: 0.018\n\n  supporting text:\n    is_a: association slot\n    description: The segment of text from a document that supports the mined assertion.\n    range: string\n    examples:\n      - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer.\n\n  supporting document:\n    is_a: association slot\n    description: >-\n      A publication or other document that reports the statement expressed in an Association, or \n      provides information used as evidence supporting this statement.\n    range: uriorcurie\n    examples:\n      - value: PMID:12345678\n\n  subject location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the subject concept of the extracted assertion.\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  object location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the object concept of the extracted assertion\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  extraction confidence score:\n    is_a: association slot\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    range: integer\n    examples:\n        - value: 15\n\n  supporting document type:\n    is_a: association slot\n    description: >-\n      The document type (e.g., Journal Article, Case Study, Preprint) for\n      the supporting document used in a Text Mining Result.\n    range: string\n    examples:\n      - value: Journal Article\n\n  supporting document year:\n    is_a: association slot\n    description: >-\n      The document year (typically the publication year) for the supporting\n      document used in a Text Mining Result.\n    range: integer\n    examples:\n      - value: 1999\n\n  supporting text section type:\n    is_a: association slot\n    description: >-\n      The section of the supporting text of a Text Mining Result within\n      the supporting document. This is in the form of the name of the document section\n      (e.g., Abstract, Introduction) that contains the supporting text.\n    range: string\n    examples:\n      - value: Introduction\n\n  ln ratio:\n    is_a: association slot\n    description: the natural log of the ratio of co-occurrence to expected\n    range: float\n    examples:\n      - value: 2.922827136\n\n  ln ratio confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the ln_ratio calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: float\n    examples:\n      - value: 2.922827136\n\n  interacting molecules category:\n    is_a: association slot\n    range: ontology class\n    exact_mappings:\n      - MI:1046\n    values_from:\n      - MI\n    examples:\n      - value: MI:1048\n        description: smallmolecule-protein\n\n  expression site:\n    description: >-\n      location in which gene or protein expression takes place.\n      May be cell, tissue, or organ.\n    is_a: association slot\n    range: anatomical entity\n    examples:\n      - value: UBERON:0002037\n        description: cerebellum\n\n  phenotypic state:\n    description: >-\n      in experiments (e.g. gene expression) assaying diseased or unhealthy\n      tissue, the phenotypic state can be put here, e.g. MONDO ID.\n      For healthy tissues, use XXX.\n    is_a: association slot\n    range: disease or phenotypic feature\n\n  publications:\n    singular_name: publication\n    description: >-\n      connects an association to publications supporting the association\n    is_a: association slot\n    multivalued: true\n    range: publication\n\n  associated environmental context:\n    is_a: association slot\n    description: >-\n      An attribute that can be applied to an association where the association holds between two entities\n      located or occurring in a particular environment. For example, two microbial taxa may interact in the context of\n      a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure.\n      # TODO: add examples of values for this property.\n\n  sequence localization attribute:\n    is_a: association slot\n    domain: genomic sequence localization\n    description: >-\n      An attribute that can be applied to a genome sequence localization edge. These edges\n      connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used\n      to ascribe specific positional information and other metadata to the localization. In pragmatic terms\n      this can be thought of as columns in a GFF3 line.\n\n  interbase coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'zero-based', 'half-open', 'space-based' ]\n    description: >-\n      A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1.\n      This is applied to a sequence localization edge.\n    range: integer\n\n  start interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 0).\n    close_mappings:\n      - faldo:begin\n    annotations:\n      opposite_of: end interbase coordinate\n\n  end interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity ends\n      on the chromosome or other entity to which it is located on.\n    close_mappings:\n      - faldo:end\n    annotations:\n      opposite_of: start interbase coordinate\n\n  start coordinate:\n    is_a: base coordinate\n    aliases: [ 'start' ]\n    description: >-\n      The position at which the subject genomic entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 1).\n    exact_mappings:\n      - gff3:start\n    close_mappings:\n      - faldo:begin\n\n  end coordinate:\n    is_a: base coordinate\n    aliases: [ 'end' ]\n    description: >-\n      The position at which the subject genomic entity ends\n      on the chromosome or other entity to which it is located on.\n    exact_mappings:\n      - gff3:end\n    close_mappings:\n      - faldo:end\n\n  genome build:\n    is_a: sequence localization attribute\n    description: >-\n      The version of the genome on which a feature is located.\n      For example, GRCh38 for Homo sapiens.\n    range: strand_enum\n    exact_mappings:\n      - gff3:strand\n\n  strand:\n    is_a: sequence localization attribute\n    description: >-\n      The strand on which a feature is located. Has a value of '+'\n      (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).\n    range: strand_enum\n    exact_mappings:\n      - gff3:strand\n\n  phase:\n    is_a: sequence localization attribute\n    domain: coding sequence\n    description: >-\n      The phase for a coding sequence entity. For example, phase of a\n      CDS as represented in a GFF3 with a value of 0, 1 or 2.\n    range: phase_enum\n    exact_mappings:\n      - gff3:phase\n\n  FDA approval status:\n    is_a: association slot\n    description: >-\n    range: FDA_approval_status_enum\n\n\n\n  supporting study metadata:\n    is_a: association slot\n    description: >-\n      Information about a study used to generate information used as evidence to support the knowledge expressed in an \n      Association. In practice, data creators should use one of the more specific subtypes of this property.\n    abstract: true\n\n  supporting study method type:\n    is_a: supporting study metadata\n    description: >-\n      A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of \n      experimental assay, or statistical calculation, or computational analysis).\n    range: uriorcurie\n\n  supporting study method description:\n    is_a: supporting study metadata\n    description: >-\n      A uri or curie pointing to information about the methodology used to generate data supporting an Association.\n    range: uriorcurie\n\n  supporting study size:\n    is_a: supporting study metadata\n    description: >-\n      The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a \n      clinical study).\n    range: integer\n\n  supporting study cohort:\n    is_a: supporting study metadata\n    description: >-\n      A description of a study population/cohort that was interrogated to provide evidence for the association \n      (e.g. the inclusion and exclusion criteria).\n    range: string\n\n  supporting study date range:\n    is_a: supporting study metadata\n    description: >-\n      The date range over which data was collected in a study that provided evidence for an Association.\n    range: string\n\n  supporting study context:\n    is_a: supporting study metadata\n    description: >-\n      A term or terms describing the experimental setting/context in which evidence supporting the Association was \n      generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue \n      type, disease, etc.).\n    range: string\n\nclasses:\n\n  ## ----------\n  ## ATTRIBUTES\n  ## ----------\n\n  ## Ontology Classes\n\n  ontology class:\n    mixin: true\n    slots:\n      - id\n    description: >-\n      a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in\n      a biolink compatible KG can be considered both instances of biolink classes, and\n      OWL classes in their own right. In general you should not need to use this class directly.\n      Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897),\n      use bl:BiologicalProcess as the type.\n    exact_mappings:\n      - owl:Class\n      - schema:Class\n    comments:\n      - >-\n        This is modeled as a mixin. 'ontology class' should not be the primary type of a\n        node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity\n        (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\n      - >-\n        Note that formally this is a metaclass. Instances of this class are instances in the graph,\n        but can be the object of 'type' edges. For example, if we had a node in the graph representing\n        a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample,\n        and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\n    see_also:\n      - https://github.com/biolink/biolink-model/issues/486\n    examples:\n      - value: UBERON:0000955\n        description: >-\n          the class 'brain' from the Uberon anatomy ontology\n    id_prefixes:\n      - MESH\n      - UMLS\n      - KEGG.BRITE ## br/ko number\n  \n  annotation:\n    description: >-\n      Biolink Model root class for entity annotations.\n    abstract: true\n\n  quantity value:\n    is_a: annotation\n    description: >-\n      A value of an attribute that is quantitative and measurable,\n      expressed as a combination of a unit and a numeric value\n    slots:\n      - has unit\n      - has numeric value\n\n  # Alignment attempted of the biolink:Attribute model\n  # to the proposed TRAPI Release 1.1 Attribute schema, i.e.\n  #\n  # attribute_name: \"assertionAuthoredBy\",\n  # attribute_type: SEPIO:0000130,\n  # value: \"ORCID:12345\",\n  # value_type: \"wd:Q51044\",\n  # value_type_name: \"ORCID ID\"\n  # url: https://orcid.org/12345\n  # source: ORCID\n\n  attribute:\n    is_a: named thing\n    mixins:\n      - ontology class\n    description: >-\n      A property or characteristic of an entity.\n      For example, an apple may have properties such as color, shape, age, crispiness.\n      An environmental sample may have attributes such as depth, lat, long, material.\n    slots:\n      - name                   # 'attribute_name'\n      - has attribute type     # 'attribute_type'\n      # 'value', 'value_type', 'value_type_name'\n      # extracted from either of the next two slots\n      - has quantitative value\n      - has qualitative value\n      - iri                    # 'url'\n      - source                 # 'source'\n    slot_usage:\n      name:\n        description: >-\n          The human-readable 'attribute name' can be set to a string which reflects its context of\n          interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default\n          to the name associated with the 'has attribute type' slot ontology term.\n    id_prefixes:\n      - EDAM-DATA\n      - EDAM-FORMAT\n      - EDAM-OPERATION\n      - EDAM-TOPIC\n    exact_mappings:\n      - SIO:000614\n    in_subset:\n      - samples\n\n  chemical role:\n    is_a: attribute\n\n  biological sex:\n    is_a: attribute\n    exact_mappings:\n      - PATO:0000047\n\n  phenotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the phenotypic sex of the individual,\n      based upon the reproductive organs present.\n    exact_mappings:\n      - PATO:0001894\n\n  genotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the genotypic sex of the individual,\n      based upon genotypic composition of sex chromosomes.\n    exact_mappings:\n      - PATO:0020000\n\n  severity value:\n    is_a: attribute\n    description: >-\n      describes the severity of a phenotypic feature or disease\n\n  relationship quantifier:\n    mixin: true\n\n  sensitivity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  specificity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  pathognomonicity quantifier:\n    is_a: specificity quantifier\n    description: >-\n      A relationship quantifier between a variant or symptom and a disease, which is\n      high when the presence of the feature implies the existence of the disease\n    mixin: true\n\n  frequency quantifier:\n    is_a: relationship quantifier\n    mixin: true\n    slots:\n      - has count\n      - has total\n      - has quotient\n      - has percentage\n\n  chemical or drug or treatment:\n    mixin: true\n\n  ## ------\n  ## THINGS\n  ## ------\n\n  entity:\n    description: >-\n      Root Biolink Model class for all things and informational relationships, real or imagined.\n    abstract: true\n    slots:\n      - id\n      - iri\n      - category\n      - type   # rdf:type\n      - name\n      - description\n      - source\n      - has attribute\n      # evidence code(s)?\n\n  named thing:\n    is_a: entity\n    description: \"a databased entity or concept/class\"\n    slots:\n      - provided by\n      - xref\n    slot_usage:\n      category:\n        required: true\n        pattern: '^biolink:\\d+$'\n    exact_mappings:\n      - BFO:0000001\n      - WIKIDATA:Q35120\n      # UMLS Semantic Group \"Objects\"\n      - UMLSSG:OBJC\n      # Entity\n      - STY:T071\n      - dcid:Thing\n\n  relationship type:\n    is_a: ontology class\n    description: >-\n      An OWL property used as an edge label\n\n  gene ontology class:\n    deprecated: true\n\n  unclassified ontology class:\n    deprecated: true\n\n  taxonomic rank:\n    description: >-\n      A descriptor for the rank within a taxonomic classification.\n      Example instance: TAXRANK:0000017 (kingdom)\n    is_a: ontology class\n    id_prefixes:\n      - TAXRANK\n    mappings:\n      - WIKIDATA:Q427626\n\n  organism taxon:\n    aliases: [ 'taxon', 'taxonomic classification' ]\n    description: >-\n      A classification of a set of organisms. Example instances:\n      NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria).\n      Can also be used to represent strains or subspecies.\n    is_a: named thing\n    slot_usage:\n      has taxonomic rank:\n        range: taxonomic rank\n        multivalued: false\n        mappings:\n          - WIKIDATA:P105\n    values_from:\n      - NCBITaxon\n    exact_mappings:\n      - WIKIDATA:Q16521\n      - STY:T001\n      - bioschemas:Taxon\n    narrow_mappings:\n      - dcid:BiologicalSpecies\n    id_prefixes:\n      - NCBITaxon\n      - MESH\n      - UMLS\n    in_subset:\n      - model_organism_database\n  \n  ## Temporal Entities\n  \n  event:\n    is_a: named thing\n    description: >-\n      Something that happens at a given place and time.\n    exact_mappings:\n      - NCIT:C25499\n      # UMLS \"Event\"\n      - STY:T051\n\n  ## Administrative Entities\n\n  administrative entity:\n    is_a: named thing\n    abstract: true\n\n  study result:\n    abstract: true\n    description: >- \n      A collection of data items from a study that are about a particular study subject or experimental unit (the \n      'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation\n      of this data as evidence.\n    notes:\n      The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, \n      that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific \n      focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any \n      scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational \n      analyses, or a larger scale clinical trial or experimental research investigation.\n    is_a: information content entity\n\n  ## epc result sets\n  concept count analysis result:\n    is_a: study result\n    description: >-\n      A result of a concept count analysis.\n\n  observed expected frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a observed expected frequency analysis.\n\n  relative frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a relative frequency analysis.\n\n  text mining result:\n    is_a: study result\n    description: >-\n      A result of text mining.\n\n  chi squared analysis result:\n    is_a: study result\n    description: >-\n      A result of a chi squared analysis.\n\n  agent:\n    is_a: administrative entity\n    aliases: [ 'group' ]\n    description: >-\n      person, group, organization or project that provides\n      a piece of information (i.e. a knowledge association)\n    slots:\n      - affiliation\n      - address\n    exact_mappings:\n      - prov:Agent\n      - dct:Agent\n    narrow_mappings:\n      # Organization\n      - UMLSSG:ORGA\n      - STY:T092\n      # Health Care Related Organization\n      - STY:T093\n      # Professional Society\n      - STY:T094\n      # Self-help or Relief Organization\n      - STY:T095\n      # Group\n      - STY:T096\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Different classes of agents have distinct preferred identifiers.\n          For publishers, use the ISBN publisher code.\n          See https://grp.isbn-international.org/ for publisher code lookups.\n          For editors, authors and  individual providers, use the individual's\n          ORCID if available; Otherwise, a ScopusID, ResearchID or\n          Google Scholar ID ('GSID') may be used if the author ORCID is unknown.\n          Institutional agents could be identified by an\n          International Standard Name Identifier ('ISNI') code.\n        values_from:\n          # CURIE space for publishers\n          - isbn\n          # CURIE space for authors\n          - ORCID\n          - ScopusID\n          - ResearchID\n          - GSID\n          # Institutional agents\n          - isni\n      name:\n        description: >-\n          it is recommended that an author's 'name' property\n          be formatted as \"surname, firstname initial.\"\n    id_prefixes:\n      - isbn\n      - ORCID\n      - ScopusID\n      - ResearchID\n      - GSID\n      - isni\n\n  ## General Information Entities\n\n  information content entity:\n    aliases: [ 'information', 'information artefact', 'information entity' ]\n    abstract: true\n    is_a: named thing\n    description: >-\n      a piece of information that typically describes\n      some topic of discourse or is used as support.\n    slots:\n      - license\n      - rights\n      - format\n      - creation date\n    id_prefixes:\n      - doi\n    exact_mappings:\n      - IAO:0000030\n    narrow_mappings:\n      # UMLS Semantic Group \"Concepts & Ideas\"\n      - UMLSSG:CONC\n      # Conceptual Entity\n      - STY:T077\n      # Idea or Concept\n      - STY:T078\n      # Temporal Concept\n      - STY:T079\n      # Qualitative Concept\n      - STY:T080\n      # Quantitative Concept\n      - STY:T081\n      # Spatial Concept\n      - STY:T082\n      # Regulation or Law\n      - STY:T089\n      # Group Attribute\n      - STY:T102\n      # Functional Concept\n      - STY:T169\n      # Language\n      - STY:T171\n      # Classification\n      - STY:T185\n\n  dataset:\n    description: >-\n      an item that refers to a collection of data from a data source.\n    is_a: information content entity\n    exact_mappings:\n      - IAO:0000100\n      - dctypes:Dataset\n      - schema:dataset\n      - dcid:Dataset\n\n  dataset distribution:\n    is_a: information content entity\n    description: >-\n      an item that holds distribution level information about a dataset.\n    slots:\n      - distribution download url\n    exact_mappings:\n      - dcat:Distribution\n\n  dataset version:\n    description: >-\n      an item that holds version level information about a dataset.\n    is_a: information content entity\n    slots:\n      - has dataset\n      - ingest date\n      - has distribution\n\n  dataset summary:\n    description: >-\n      an item that holds summary level information about a dataset.\n    is_a: information content entity\n    slots:\n      - source web page\n      - source logo\n\n  confidence level:\n    is_a: information content entity\n    description: >-\n      Level of confidence in a statement\n    values_from:\n      - cio\n    exact_mappings:\n      - CIO:0000028\n      # statement confidence\n      - SEPIO:0000187\n    close_mappings:\n      # assertion confidence levels\n      - SEPIO:0000167\n\n  evidence type:\n    is_a: information content entity\n    aliases: [ 'evidence code' ]\n    description: >-\n      Class of evidence that supports an association\n    values_from:\n      - eco\n    exact_mappings:\n      - ECO:0000000\n\n  information resource:\n    is_a: information content entity\n    aliases: [ 'knowledgebase' ]\n    description: >-\n      A database or knowledgebase and its supporting ecosystem of interfaces \n      and services that deliver content to consumers (e.g. web portals, APIs, \n      query endpoints, streaming services, data downloads, etc.).\n      A single Information Resource by this definition may span many different datasets or\n      databases, and include many access endpoints and user\n      interfaces. Information Resources include project-specific resources\n      such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.\n    in_subset:\n      - translator_minimal\n\n\n  ## Publications\n\n  # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies\n  publication:\n    is_a: information content entity\n    description: >-\n      Any published piece of information. Can refer to a whole publication,\n      its encompassing publication (i.e. journal or book) or to a part of a\n      publication, if of significant knowledge scope (e.g. a figure, figure\n      legend, or section highlighted by NLP). The scope is intended to be\n      general and include information published on the web, as well as printed\n      materials, either directly or in one of the Publication Biolink\n      category subclasses.\n    slots:\n      - authors\n      - pages\n      - summary\n      - keywords\n      - mesh terms\n      - xref\n    # In addition to embedded slots, instances of 'contributor association'\n    # may be used to more extensively document publisher, editor and author details\n    slot_usage:\n      id:\n        description: >-\n          Different kinds of publication subtypes will have different preferred\n          identifiers (curies when feasible). Precedence of identifiers for\n          scientific articles is as follows: PMID if available; DOI if not; actual\n          alternate CURIE otherwise. Enclosing publications (i.e. referenced by\n          'published in' node property) such as books and journals, should have\n          industry-standard identifier such as from ISBN and ISSN.\n      name:\n        description: >-\n          the 'title' of the publication is generally recorded in the 'name'\n          property (inherited from NamedThing). The field name 'title' is now also\n          tagged as an acceptable alias for the node property 'name' (just in case).\n      type:\n        slot_uri: dct:type\n        required: true\n        description: >-\n          Ontology term for publication type may be drawn from\n          Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),\n          FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),\n          the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),\n          the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres\n          (http://vocabularies.coar-repositories.org/documentation/resource_types/),\n          Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or\n          equivalent publication type ontology. When a given publication type ontology term\n          is used within a given knowledge graph, then the CURIE identified term must be\n          documented in the graph as a concept node of biolink:category biolink:OntologyClass.\n        values_from: # Not sure which takes precedence, if any...\n          - dctypes\n          - fabio\n          - MESH_PUB\n          - COAR_RESOURCE\n          - WIKIDATA\n      pages:\n        multivalued: true\n        description: >-\n          When a 2-tuple of page numbers are provided, they represent\n          the start and end page of the publication within its parent publication context.\n          For books, this may be set to the total number of pages of the book.\n    exact_mappings:\n      - IAO:0000311\n    narrow_mappings:\n      - IAO:0000013\n      # UMLS Semantic Type \"Intellectual Product\"\n      - STY:T170\n    id_prefixes:\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book:\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Books should have industry-standard identifier such as from ISBN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'book'.\n    id_prefixes:\n      - isbn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book chapter:\n    is_a: publication\n    slots:\n      - published in\n      - volume\n      - chapter\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent book containing the chapter\n          should have industry-standard identifier from ISBN.\n    in_subset:\n      - model_organism_database\n\n  serial:\n    aliases: [ 'journal' ]\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slots:\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Serials (journals) should have industry-standard identifier such as from ISSN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'serial' or 'journal'.\n    id_prefixes:\n      - issn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  article:\n    is_a: publication\n    slots:\n      - published in\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent serial containing the article should\n          have industry-standard identifier from ISSN.\n      iso abbreviation:\n        description: >-\n          Optional value, if used locally as a convenience, is set\n          to the iso abbreviation of the 'published in' parent.\n    id_prefixes:\n      # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces\n      - PMID\n    in_subset:\n      - model_organism_database\n\n  ## Top Level Abstractions of Material & Process Entities\n\n  physical essence or occurrent:\n    description: >-\n      Either a physical or processual entity.\n    mixin: true\n\n\n  physical essence:\n    description: >-\n      Semantic mixin concept.  Pertains to entities that have\n      physical properties such as mass, volume, or charge.\n    is_a: physical essence or occurrent\n    mixin: true\n\n  physical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n    description: >-\n      An entity that has material reality (a.k.a. physical essence).\n    exact_mappings:\n      # Physical Object\n      - STY:T072\n    narrow_mappings:\n      # Manufactured Object\n      - STY:T073\n\n  occurrent:\n    description: >-\n      A processual entity.\n    # biolink:Occurrent is most consistently used as a mixin thus it should\n    # be declared as such and cannot inherit from the non-mixin biolink:NamedThing\n    is_a: physical essence or occurrent\n    mixin: true\n    exact_mappings:\n      - BFO:0000003\n\n  activity and behavior:\n    is_a: occurrent\n    mixin: true\n    description: >-\n      Activity or behavior of any independent integral living,\n      organization or mechanical actor in the world\n    exact_mappings:\n      # Activities & Behaviors\n      - UMLSSG:ACTI\n\n  activity:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      An activity is something that occurs over a period of time and acts upon\n      or with entities; it may include consuming, processing, transforming,\n      modifying, relocating, using, or generating entities.\n    exact_mappings:\n      - prov:Activity\n      - NCIT:C43431\n      # Activity\n      - STY:T052\n    narrow_mappings:\n      # Daily or Recreational Activity\n      - STY:T056\n      # Occupational Activity\n      - STY:T057\n      # Governmental or Regulatory Activity\n      - STY:T064\n      # Machine Activity\n      - STY:T066\n      # Research Activity\n      - STY:T062\n      # Educational Activity\n      - STY:T065\n      # Health Care Activity\n      - STY:T058\n\n  procedure:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      A series of actions conducted in a certain order or manner\n    exact_mappings:\n      # Procedures\n      - UMLSSG:PROC\n      - dcid:MedicalProcedure\n    narrow_mappings:\n      # Laboratory Procedure\n      - STY:T059\n      # Diagnostic Procedure\n      - STY:T060\n      # Therapeutic or Preventive Procedure\n      - STY:T061\n      # Molecular Biology Research Technique\n      - STY:T063\n    id_prefixes:\n      - CPT\n\n  phenomenon:\n    is_a: named thing\n    mixins:\n      - occurrent\n    description: >-\n      a fact or situation that is observed to exist or happen,\n      especially one whose cause or explanation is in question\n    broad_mappings:\n      # the inclusion of 'process' in the definition of these\n      # terms broadens them, relative to 'phenomenon'\n      # Phenomenon or Process\n      - STY:T067\n      # Human-caused Phenomenon or Process\n      - STY:T068\n      # Natural Phenomenon or Process\n      - STY:T070\n    exact_mappings:\n      # Phenomena\n      - UMLSSG:PHEN\n    narrow_mappings:\n      # Laboratory or Test Result\n      - STY:T034\n      # Biologic Function\n      - STY:T038\n      # Environmental Effect of Humans\n      - STY:T069\n\n  device:\n    is_a: named thing\n    description: >-\n      A thing made or adapted for a particular purpose, especially\n      a piece of mechanical or electronic equipment\n    narrow_mappings:\n      # Devices\n      - UMLSSG:DEVI\n      # Medical Device\n      - STY:T074\n      # Research Device\n      - STY:T075\n      # Drug Delivery Device\n      - STY:T203\n      # Biomedical or Dental Material\n      - STY:T122\n\n  ## Scientific Studies\n\n  study population:\n    is_a: population of individual organisms\n    description: >-\n      A group of people banded together or treated as a group as participants in a research study.\n    close_mappings:\n      - WIKIDATA:Q7229825\n\n  subject of investigation:\n    mixin: true\n    description: >-\n      An entity that has the role of being studied in an investigation, study, or experiment\n\n  material sample:\n    aliases: [ 'biospecimen', 'sample', 'biosample', 'physical sample' ]\n    is_a: physical entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A sample is a limited quantity of something (e.g. an individual or set of individuals\n      from a population, or a portion of a substance) to be used for testing, analysis,\n      inspection, investigation, demonstration, or trial use. [SIO]\n    exact_mappings:\n      - OBI:0000747\n      - SIO:001050\n    id_prefixes:\n      - BIOSAMPLE\n      - GOLD.META\n\n  ## Earth Sciences\n\n  planetary entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists at the level of the whole planet\n\n  environmental process:\n    is_a: planetary entity\n    mixins:\n      - occurrent\n    exact_mappings:\n      - ENVO:02500000\n\n  environmental feature:\n    is_a: planetary entity\n    exact_mappings:\n      - ENVO:01000254\n\n  geographic location:\n    is_a: planetary entity\n    description: >-\n      a location that can be described in lat/long coordinates\n    slots:\n      - latitude\n      - longitude\n    exact_mappings:\n      # Geographic Areas\n      - UMLSSG:GEOG\n      # Geographic Area\n      - STY:T083\n\n  geographic location at time:\n    is_a: geographic location\n    description: >-\n      a location that can be described in lat/long coordinates, for a particular time\n    slots:\n      - timepoint\n\n  ## Biological Sciences\n\n  thing with taxon:\n    mixin: true\n    description: >-\n      A mixin that can be used on any entity that can be taxonomically classified.\n      This includes individual organisms; genes, their products and other molecular\n      entities; body parts; biological processes\n    slots:\n      - in taxon\n\n  biological entity:\n    is_a: named thing\n    aliases: [ 'bioentity' ]\n    abstract: true\n    mixins:\n      - thing with taxon\n    narrow_mappings:\n      - WIKIDATA:Q28845870\n      # UMLS Semantic Type \"Experimental Model of Disease\"\n      - STY:T050\n      # SIO term is 'biological entity' but less inclusive than the Biolink scope\n      - SIO:010046\n\n  genomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - STY:T028   # Gene or Genome\n      - GENO:0000897  # Genomic Entity\n\n  molecular entity:\n    is_a: chemical entity\n    description: >-\n      A molecular entity is a chemical entity composed of individual or\n      covalently bonded atoms.\n    slots:\n      - is metabolite\n    narrow_mappings:\n      - STY:T088 # Carbohydrate\n      - STY:T085 # Molecular Sequence\n      - CHEBI:23367 # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical,\n      # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.\n      - bioschemas:MolecularEntity\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  chemical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n      - chemical or drug or treatment # issue 701\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    description: >-\n      A chemical entity is a physical entity that pertains to chemistry or\n      biochemistry.\n    slots:\n      - trade name\n      - available from\n      - max tolerated dose\n      - is toxic\n      - has chemical role\n    exact_mappings:\n      - CHEBI:24431\n      - SIO:010004 # Chemical entity\n      - WIKIDATA:Q79529 # Chemical substance\n      - STY:T103 # Chemical\n    narrow_mappings:\n      - WIKIDATA:Q43460564\n      - STY:T129 # (imft, full name: Immunologic Factor\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - UNII\n      - MESH\n      - CAS #CAS numbers are given for things like plant extracts as well.\n      - UMLS\n      - ncats.drug\n\n  small molecule:\n    is_a: molecular entity\n    aliases: [ 'chemical substance' ]\n    description: >-\n      A small molecule entity is a molecular entity characterized by availability\n      in small-molecule databases of SMILES, InChI, IUPAC, or other\n      unambiguous representation of its precise chemical structure; for\n      convenience of representation, any valid chemical representation is\n      included, even if it is not strictly molecular (e.g., sodium ion).\n    narrow_mappings:\n      - STY:T196 # Element, Ion, or Isotope\n      - CHEBI:59999\n      - bioschemas:ChemicalSubstance\n      - STY:T123 #(bacs, full name: Biologically Active Substance)\n      - STY:T131 #(hops, full name: Hazardous or Poisonous Substance)\n      - STY:T125 #(horm, full name: Hormone)\n      - STY:T197 #(inch, full name: Inorganic Chemical)\n      - STY:T109 #(orch, full name: Organic Chemical)\n      - STY:T118 #(carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files)\n      - STY:T111 #(eico, full name: Eicosanoid) - same note as above\n      - STY:T119 #(lipd, full name: Lipid) - same note as above\n      - STY:T124 #(nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above\n      - STY:T115 #(opco, full name: Organophosphorus Compound) - same note as above\n      - STY:T110 #(strd, full name: Steroid) - same note as above\n      - STY:T127 # vitamin\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - BIGG.METABOLITE\n      - UMLS\n      - foodb.compound\n    slot_usage:\n      id:\n        examples:\n          - value: CHEBI:29101\n            description: sodium ion\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n\n  chemical mixture:\n    is_a: chemical entity\n    description: >-\n      A chemical mixture is a chemical entity composed of two or more\n      molecular entities.\n    slots:\n      - is supplement\n      - highest FDA approval status\n      - drug regulatory status world wide\n      - routes of delivery\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n    close_mappings:\n      - dcid:ChemicalCompound\n    narrow_mappings:\n      - NCIT:C20401 # monoclonal antibody\n      - SNOMEDCT:49616005 # monoclonal antibody (substance)\n\n  nucleic acid entity:\n    is_a: molecular entity\n    description: >-\n      A nucleic acid entity is a molecular entity characterized by\n      availability in gene databases of nucleotide-based sequence\n      representations of its precise sequence; for convenience of\n      representation, partial sequences of various kinds are included.\n    aliases: [ 'sequence feature', 'genomic entity' ]\n    mixins:\n      - genomic entity\n      - thing with taxon\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000110\n    narrow_mappings:\n      - STY:T086   # Nucleotide Sequence\n      - STY:T114   # Nucleic Acid, Nucleoside, or Nucleotide\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  # G number\n      - KEGG.ENVIRON # E number\n\n  molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A molecular mixture is a chemical mixture composed of two or more\n      molecular entities with known concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n      - ncats.drug\n\n  complex molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A complex molecular mixture is a chemical mixture composed of two or\n      more molecular entities with unknown concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  biological process or activity:\n    description: >-\n      Either an individual molecular activity, or a collection of\n      causally connected molecular activities in a biological system.\n    is_a: biological entity\n    mixins:\n      - occurrent\n      - ontology class\n    id_prefixes:\n      - GO\n      - REACT\n    slots:\n      - has input\n      - has output\n      - enabled by\n\n  molecular activity:\n    description: >-\n      An execution of a molecular function carried out by a\n      gene product or macromolecular complex.\n    is_a: biological process or activity\n    aliases: [ 'molecular function', 'molecular event', 'reaction' ]\n    mixins:\n      - occurrent\n      - ontology class\n    slot_usage:\n      has input:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the input for the reaction\n      has output:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the output for the reaction\n      enabled by:\n        range: macromolecular machine mixin\n        description: >-\n          The gene product, gene, or complex that catalyzes the reaction\n    exact_mappings:\n      - GO:0003674\n      # UMLS Semantic Type \"Molecular Function\"\n      - STY:T044\n    id_prefixes:\n      - GO\n      - REACT\n      - RHEA\n      - metacyc.reaction\n      - EC\n      - TCDB\n      - KEGG.REACTION  ## R number\n      - KEGG.RCLASS    ## RC number\n      - KEGG.ENZYME    ## EC number\n      - KEGG.ORTHOLOGY ## in particular for gut microbiome use case in issue #888\n      - UMLS\n      - BIGG.REACTION\n      - SEED.REACTION\n      - METANETX.REACTION\n\n  biological process:\n    is_a: biological process or activity\n    mixins:\n      - occurrent\n      - ontology class\n    description: >-\n      One or more causally connected executions of molecular functions\n    exact_mappings:\n      - GO:0008150\n      - SIO:000006\n      - WIKIDATA:Q2996394\n    broad_mappings:\n      - WIKIDATA:P682\n    id_prefixes:\n      - GO\n      - REACT\n      - metacyc.reaction\n      - KEGG.MODULE ## M number\n\n  pathway:\n    is_a: biological process\n    mixins:\n      - ontology class\n    exact_mappings:\n      - PW:0000001\n      - WIKIDATA:Q4915012\n    narrow_mappings:\n      - SIO:010526\n      - GO:0007165\n    id_prefixes:\n      - GO\n      - REACT\n      - KEGG\n      - SMPDB\n      - MSigDB\n      - PHARMGKB.PATHWAYS\n      - WIKIPATHWAYS\n      - FB  # FlyBase FBgg*\n      - PANTHER.PATHWAY\n      - KEGG.PATHWAY\n      - ncats.bioplanet\n\n  physiological process:\n    aliases: [ 'physiology' ]\n    is_a: biological process\n    mixins:\n      - ontology class\n    close_mappings:\n    exact_mappings:\n      # Physiologic Function\n      - STY:T039\n      - WIKIDATA:Q30892994\n    narrow_mappings:\n      # Organism Function\n      - STY:T040\n      # Organ or Tissue Function\n      - STY:T042\n      # Cell Function\n      - STY:T043\n      # Genetic Function\n      - STY:T045\n    id_prefixes:\n      - GO\n      - REACT\n\n  behavior:\n    is_a: biological process\n    mixins:\n      - ontology class\n      - activity and behavior\n    exact_mappings:\n      - GO:0007610\n      # Behavior\n      - STY:T053\n    narrow_mappings:\n      # Mental Process\n      - STY:T041\n      # Social Behavior\n      - STY:T054\n      # Individual Behavior\n      - STY:T055\n\n  ## (Bio)chemistry\n\n  processed material:\n    is_a: chemical mixture\n    description: >-\n      A chemical entity (often a mixture) processed\n      for consumption for nutritional, medical or technical use.\n      Is a material entity that is created or changed during material processing.\n    exact_mappings:\n      - OBI:0000047\n    id_prefixes:\n      - UMLS\n\n  drug:\n    is_a: molecular mixture\n    mixins:\n      - chemical or drug or treatment\n      - ontology class\n    description: >-\n      A substance intended for use in the diagnosis, cure,\n      mitigation, treatment, or prevention of disease\n    comments:\n      - The CHEBI ID represents a role rather than a substance\n    broad_mappings:\n      # Pharmacologic Substance: Any natural, endogenously-derived,\n      # synthetic or semi-synthetic compound with pharmacologic activity.\n      - STY:T121\n    exact_mappings:\n      - WIKIDATA:Q12140\n      - CHEBI:23888\n      # UMLS Semantic Type \"Clinical Drug\"\n      - STY:T200\n      - dcid:Drug\n    narrow_mappings:\n      # Antibiotic\n      - STY:T195\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n\n  ## Food\n\n  environmental food contaminant:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:78299\n\n  food additive:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:64047\n\n  nutrient:\n    deprecated: true\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:33284\n\n  macronutrient:\n    deprecated: true\n    is_a: nutrient\n    related_mappings:\n      # substance role\n      - CHEBI:33937\n\n  micronutrient:\n    deprecated: true\n    is_a: nutrient\n    related_mappings:\n      # substance role\n      - CHEBI:27027\n\n  vitamin:\n    deprecated: true\n    is_a: micronutrient\n    related_mappings:\n      # substance role\n      - CHEBI:33229\n      # Vitamin\n      - STY:T127\n\n  food:\n    is_a: chemical mixture\n    description: >-\n      A substance consumed by a living organism as a source of nutrition\n    id_prefixes:\n      - foodb.food\n      - FOODON\n      - UMLS\n      - NCIT\n    exact_mappings:\n      # Food\n      - STY:T168\n\n  ## Biology and Biomedical Sciences\n\n  ## Biological Attributes\n\n  organism attribute:\n    is_a: attribute\n    description: >-\n      describes a characteristic of an organismal entity.\n    exact_mappings:\n      # Organism Attribute\n      - STY:T032\n\n  phenotypic quality:\n    aliases: [ 'phenotypic properties' ]\n    is_a: organism attribute\n    description: >-\n      A property of a phenotype\n    examples:\n      - value: weight\n\n    mappings:\n      - PATO:0000001\n\n  inheritance:\n    deprecated: true\n    is_a: organism attribute\n    description: >-\n      The name of this attribute and its inheritance from organism attribute, indeed,\n      its designation as an attribute is problematic. First, the isolated word 'inheritance'\n      is too ambiguous (especially when embedded inside an ontology with inheritance!).\n      'Genetic inheritance' would be more precise. Second, in terms of the scientific usage here,\n      genetic inheritance would not be a direct property at the topmost organism level, but rather\n      (as hinted in the definition) is more a commentary on the nature of phenotype (including \n      genetic disease as a characteristic set of associated phenotypes) against the (hidden)\n      context of (meiotic/somatic/mitochondrial) DNA segregation and expression.  Third, placing \n      the term in the attribute, rather than named thing category concept hierarchy, is perhaps\n      less flexible in terms of its usage as a first class concept for semantic queries.\n      Thus, we deprecate this term, moving it to the 'new' category of 'genetic inheritance', \n      as a child of 'biological entity' (to emphasize its biological conceptual nature).\n\n  genetic inheritance:\n    aliases: [ 'inheritance' ]\n    is_a: biological entity\n    description: >-\n      The pattern or 'mode' in which a particular genetic trait or disorder is passed from one\n      generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\n    exact_mappings:\n      - HP:0000005\n      - GENO:0000141\n      - NCIT:C45827\n    close_mappings:\n      - STY:T045\n    id_prefixes:\n      - HP\n      - GENO\n      - NCIT\n\n  ## Biological Entities\n\n  organismal entity:\n    description: >-\n      A named entity that is either a part of an organism, a whole organism,\n      population or clade of organisms, excluding chemical entities\n    abstract: true\n    is_a: biological entity\n    slot_usage:\n      has attribute:\n        description: >-\n          may often be an organism attribute\n    exact_mappings:\n      - WIKIDATA:Q7239\n      # UMLS Semantic Group \"Living Beings\"\n      # Several of the associated semantic types here are probably not\n      # that relevant to the Biolink world but we keep them here for now.\n      - UMLSSG:LIVB\n      - CARO:0001010\n\n  virus:\n    is_a: organismal entity\n    description: >-\n      A virus is a microorganism that replicates itself as a microRNA\n      and infects the host cell.\n    exact_mappings:\n      - NCBITaxon:10239\n\n  cellular organism:\n    is_a: organismal entity\n    description: >-\n    exact_mappings:\n      - NCBITaxon:131567\n\n  life stage:\n    is_a: organismal entity\n    description: >-\n      A stage of development or growth of an organism,\n      including post-natal adult stages\n    exact_mappings:\n      - UBERON:0000105\n    narrow_mappings:\n      # constrained to human life cycles\n      - HsapDv:0000000\n    in_subset:\n      - model_organism_database\n    id_prefixes:\n      - HsapDv\n      - MmusDv\n      - ZFS\n      - FBdv\n      - WBls\n      - UBERON\n\n  individual organism:\n    aliases: [ 'organism' ]\n    description: >-\n      An instance of an organism. For example, Richard Nixon,\n      Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576\n    is_a: organismal entity\n    exact_mappings:\n      - SIO:010000\n      # Organism\n      - STY:T001\n    narrow_mappings:\n      # Wikidata considers its definition of 'individual' to be constrained to human persons?\n      - WIKIDATA:Q795052\n      - foaf:Person\n    id_prefixes:\n      - ORCID\n\n  population of individual organisms:\n    description: >-\n      A collection of individuals from the same taxonomic class\n      distinguished by one or more characteristics.  Characteristics can\n      include, but are not limited to, shared geographic location, genetics,\n      phenotypes.\n    local_names:\n      ga4gh: population\n    is_a: organismal entity\n    exact_mappings:\n      - PCO:0000001\n      - SIO:001061\n      # UMLS Semantic Type \"Population Group\"\n      - STY:T098\n      - OBI:0000181\n    id_prefixes:\n      - HANCESTRO\n    in_subset:\n      - model_organism_database\n\n  disease or phenotypic feature:\n    aliases: [ 'phenome' ]\n    is_a: biological entity\n    description: >-\n      Either one of a disease or an individual phenotypic feature.\n      Some knowledge resources such as Monarch treat these as\n      distinct, others such as MESH conflate.  Please see definitions of phenotypic feature and disease in this model\n      for their independent descriptions.  This class is helpful to enforce domains and ranges  \n      that may involve either a disease or a phenotypic feature.\n    union_of:\n      - disease\n      - phenotypic feature\n    narrow_mappings:\n      # UMLS Semantic Type \"Finding\" - more specialized use of 'disease or phenotypic feature'\n      - STY:T033\n\n  disease:\n    aliases: [ 'condition', 'disorder', 'medical condition' ]\n    description: >-\n      A disorder of structure or function, especially one that produces specific \n      signs, phenotypes or symptoms or that affects a specific location and is not simply a \n      direct result of physical injury.  A disposition to undergo pathological processes that exists in an \n      organism because of one or more disorders in that organism.\n    is_a: disease or phenotypic feature\n    exact_mappings:\n      - MONDO:0000001\n      - DOID:4\n      - NCIT:C2991\n      - WIKIDATA:Q12136\n      - SIO:010299\n      # UMLS Semantic Group \"Disorders\"\n      - UMLSSG:DISO\n      # Disease or Syndrome\n      - STY:T047\n      - dcid:Disease\n    narrow_mappings:\n      # Congenital Abnormality\n      - STY:T019\n      # Acquired Abnormality\n      - STY:T020\n      # Mental or Behavioral Dysfunction\n      - STY:T048\n      # Cell or Molecular Dysfunction\n      - STY:T049\n      # Anatomical Abnormality\n      - STY:T190\n      # Neoplastic Process\n      - STY:T191\n      # disease susceptibility\n      - MONDO:0042489\n    id_prefixes:\n      - MONDO\n      - DOID\n      - OMIM\n      - OMIM.PS\n      - ORPHANET\n      - EFO\n      - UMLS\n      - MESH\n      - MEDDRA\n      - NCIT\n      - SNOMEDCT\n      - medgen\n      - ICD10\n      - ICD9\n      - KEGG.DISEASE ## H number\n      - HP\n      - MP\n    in_subset:\n      - model_organism_database\n\n  phenotypic feature:\n    aliases: [ 'sign', 'symptom', 'phenotype', 'trait', 'endophenotype' ]\n    is_a: disease or phenotypic feature\n    description: >-\n      A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an \n      individual resulting from the interaction of its genotype with its molecular and physical environment.\n    examples:\n      - value: MP:0001262\n        description: decreased body weight\n    exact_mappings:\n      - UPHENO:0001001\n      - SIO:010056\n      - WIKIDATA:Q104053\n      - UMLS:C4021819\n      - NCIT:C16977\n      - SNOMEDCT:8116006 # documented as phenotypic finding and phenotype, also referred to as \"SCTID:8116006\" at SNOMEDCT\n      - MESH:D010641 # phenotype\n    narrow_mappings:\n      - STY:T184 # Sign or Symptom\n      - WIKIDATA:Q169872 # Sign or Symptom\n      # presentation of a disease in clinical medicine\n      - WIKIDATA:Q25203551\n      - ZP:00000000 # zebrafish phenotype\n      - FBcv:0001347 # fly phenotype\n      - HP:0000118 # human phenotype\n      - MP:0000001 # mouse phenotype\n      - WBPhenotype:0000886 # worm phenotype\n      - XPO:00000000 # frog phenotype\n      - FYPO:0000001 # fission yeast phenotype\n      - APO:0000017 # phenotype\n      - TO:0000387 # more narrowly defined here for plants; our definition conflates trait and phenotype.\n    broad_mappings:\n      - BFO:0000019 # quality\n      - PATO:0000001 # quality\n    id_prefixes:\n      - HP\n      - EFO # covered by BFO quality mapping\n      - NCIT\n      - UMLS\n      - MEDDRA # can not find a mapping\n      - MP\n      - ZP\n      - UPHENO\n      - APO\n      - FBcv\n      - WBPhenotype\n      - SNOMEDCT\n      - MESH\n      - XPO\n      - FYPO\n      - TO\n    in_subset:\n      - model_organism_database\n\n  behavioral feature:\n    description: >-\n      A phenotypic feature which is behavioral in nature.\n    is_a: phenotypic feature\n    exact_mappings:\n      - NBO:0000243\n\n  anatomical entity:\n    is_a: organismal entity\n    mixins:\n      - physical essence\n    description: >-\n      A subcellular location, cell type or gross anatomical part\n    exact_mappings:\n      - UBERON:0001062\n      - WIKIDATA:Q4936952\n      # UMLS Semantic Group \"Anatomy\"\n      - UMLSSG:ANAT\n      # UMLS Semantic Type \"Anatomical Structure\"\n      - STY:T017\n      - FMA:62955 # anatomical entity\n      - CARO:0000000  # anatomical entity\n      - SIO:001262 # anatomical entity\n    narrow_mappings:\n      - ZFA:0100000 # zebrafish anatomical entity\n      - FBbt:10000000 # fly anatomical entity\n      - EMAPA:0 # mouse anatomical entity\n      - MA:0000001 # mouse anatomical entity\n      - XAO:0000000 # frog anatomical entity\n      - WBbt:0000100 # c. elegans anatomical entity\n      - NCIT:C12219 # human anatomical entity\n      - GO:0110165 # cellular anatomical entity, also used directly in CL\n    related_mappings:\n      - SNOMEDCT:123037004 # body structure\n    id_prefixes:\n      - UBERON\n      - GO\n      - CL\n      - UMLS\n      - MESH\n      - NCIT\n      - EMAPA\n      - ZFA\n      - FBbt\n      - WBbt\n    in_subset:\n      - model_organism_database\n\n  cellular component:\n    aliases: [ 'cell component','cell part' ]\n    is_a: anatomical entity\n    description: >-\n      A location in or around a cell\n    exact_mappings:\n      - GO:0005575\n      - SIO:001400\n      - WIKIDATA:Q5058355\n      # Cell Component\n      - STY:T026\n    broad_mappings:\n      - WIKIDATA:P681\n    id_prefixes:\n      - GO\n      - MESH\n      - UMLS\n      - NCIT\n      - SNOMEDCT\n      - CL\n      - UBERON\n\n  cell:\n    is_a: anatomical entity\n    exact_mappings:\n      - GO:0005623\n      - CL:0000000\n      - SIO:010001\n      - WIKIDATA:Q7868\n      # UMLS Semantic Type \"Cell\"\n      - STY:T025\n      - MESH:D002477 # cells\n    id_prefixes:\n      - CL\n      - PO\n      - UMLS\n      - NCIT\n      - MESH\n      - UBERON\n      - SNOMEDCT\n      - MESH\n\n  cell line:\n    is_a: organismal entity\n    exact_mappings:\n      - CLO:0000031\n    id_prefixes:\n      - CLO\n\n  gross anatomical structure:\n    aliases: [ 'tissue', 'organ' ]\n    is_a: anatomical entity\n    exact_mappings:\n      - UBERON:0010000\n      - WIKIDATA:Q4936952\n    narrow_mappings:\n      # UMLS Semantic Type \"Body Part, Organ, or Organ Component\"\n      - STY:T023\n      # UMLS Semantic Type \"Tissue\"\n      - STY:T024\n      # Embryonic Structure\n      - STY:T018\n    id_prefixes:\n      - UBERON\n      - UMLS\n      - MESH\n      - NCIT\n      - PO\n      - FAO\n\n\n  ## entity mixins\n\n  chemical entity or gene or gene product:\n    description: >-\n      A union of chemical entities and children, and gene or gene product.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  chemical entity or protein or polypeptide:\n    description: >-\n      A union of chemical entities and children, and protein and polypeptide.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  macromolecular machine mixin:\n    description: >-\n      A union of gene locus, gene product, and macromolecular complex mixin. These are\n      the basic units of function in a cell. They either carry out individual\n      biological activities, or they encode molecules which do this.\n    mixin: true\n    slots:\n      - name\n    slot_usage:\n      name:\n        range: symbol type\n        description: >-\n          genes are typically designated by a short symbol and a full name.\n          We map the symbol to the default display name\n          and use an additional slot for full name\n\n  gene or gene product:\n    description: >-\n      A union of gene loci or gene products.\n      Frequently an identifier for one will be used as proxy for another\n    is_a: macromolecular machine mixin\n    mixin: true\n    id_prefixes:\n      - CHEMBL.TARGET\n      - IUPHAR.FAMILY\n\n  gene:\n    description: >-\n      A region (or regions) that includes all of the sequence elements\n      necessary to encode a functional transcript. A gene locus may include\n      regulatory regions, transcribed regions and/or other\n      functional sequence regions.\n    is_a: biological entity\n    mixins:\n      - gene or gene product\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    slots:\n      - symbol\n      - synonym\n      - xref\n    narrow_mappings:\n      - bioschemas:gene\n    broad_mappings:\n      - NCIT:C45822\n    exact_mappings:\n      - SO:0000704\n      - SIO:010035\n      - WIKIDATA:Q7187\n      - dcid:Gene\n    id_prefixes:\n      - NCBIGene\n      - ENSEMBL\n      - HGNC\n      - MGI\n      - ZFIN\n      - dictyBase\n      - WB\n      - WormBase # we have two prefixes here as wormbase supports WormBase:WBGene00000898\n      # and alliancegenome.org and identifiers.org supports WB:WBGene00000898.\n      - FB\n      - RGD\n      - SGD\n      - PomBase\n      - OMIM\n      - KEGG.GENE ## org:gene\n      - UMLS\n      - Xenbase\n      - AspGD\n    in_subset:\n      - model_organism_database\n\n  gene product mixin:\n    description: >-\n      The functional molecular product of a single gene locus.\n      Gene products are either proteins or functional RNA molecules.\n    is_a: gene or gene product\n    mixin: true\n    slots:\n      - synonym\n      - xref\n    exact_mappings:\n      - WIKIDATA:Q424689\n      - GENO:0000907\n      - NCIT:C26548\n    id_prefixes:\n      - UniProtKB\n      - gtpo\n      - PR\n\n  gene product isoform mixin:\n    description: >-\n      This is an abstract class that can be mixed in with different kinds of\n      gene products to indicate that the gene product is intended to represent\n      a specific isoform rather than a canonical or reference or generic\n      product. The designation of canonical or reference may be arbitrary,\n      or it may represent the superclass of all isoforms.\n    is_a: gene product mixin\n    mixin: true\n\n  macromolecular complex mixin:\n    description: >-\n      A stable assembly of two or more macromolecules, i.e. proteins,\n      nucleic acids, carbohydrates or lipids, in which at least one\n      component is a protein and the constituent parts function together.\n    is_a: macromolecular machine mixin\n    mixin: true\n    exact_mappings:\n      - GO:0032991\n      - WIKIDATA:Q22325163\n    id_prefixes:\n      - INTACT\n      - GO\n      - PR\n      - REACT\n    in_subset:\n      - model_organism_database\n\n  ## Genomic Classes\n\n  genome:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A genome is the sum of genetic material within a cell or virion.\n    exact_mappings:\n      - SO:0001026\n      - SIO:000984\n      - WIKIDATA:Q7020\n    close_mappings:\n      - dcid:GenomeAssemblyUnit\n    in_subset:\n      - model_organism_database\n\n  exon:\n    is_a: nucleic acid entity\n    description: >-\n      A region of the transcript sequence within a gene which is not\n      removed from the primary RNA transcript by RNA splicing.\n    exact_mappings:\n      - SO:0000147\n      - SIO:010445\n      - WIKIDATA:Q373027\n\n  transcript:\n    is_a: nucleic acid entity\n    description: >-\n      An RNA synthesized on a DNA or RNA template by an RNA polymerase.\n    exact_mappings:\n      - SO:0000673\n      - SIO:010450\n      - WIKIDATA:Q7243183\n      - dcid:RNATranscript\n    id_prefixes:\n      - ENSEMBL # ENSEMBL:ENST for human\n      - FB      # FlyBase:FBtr\n    in_subset:\n      - model_organism_database\n\n  coding sequence:\n    is_a: nucleic acid entity\n    exact_mappings:\n      - SO:0000316\n      - SIO:001390\n\n  polypeptide:\n    aliases: [ 'amino acid entity' ]\n    is_a: biological entity\n    description: >-\n      A polypeptide is a molecular entity characterized by availability\n      in protein databases of amino-acid-based sequence representations\n      of its precise primary structure; for convenience of representation,\n      partial sequences of various kinds are included, even if they do not\n      represent a physical molecule.\n    mixins:\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n    in_subset:\n      - model_organism_database\n    narrow_mappings:\n      - SO:0000104 # polypeptide definde in SO conflates protein and polypeptide\n      # Amino Acid, Peptide, or Protein\n      - STY:T116\n      # Amino Acid Sequence\n      - STY:T087\n\n  protein:\n    description: >-\n      A gene product that is composed of a chain of amino acid sequences\n      and is produced by ribosome-mediated translation of mRNA\n    is_a: polypeptide\n    mixins:\n      - gene product mixin\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n      - MESH\n      - ncats.drug\n    broad_mappings:\n      - bioschemas:Protein\n    exact_mappings:\n      - PR:000000001\n      - SIO:010043\n      - WIKIDATA:Q8054\n    narrow_mappings:\n      # Enzyme\n      - STY:T126\n      # Receptor\n      - STY:T192\n\n  protein isoform:\n    aliases: [ 'proteoform' ]\n    is_a: protein\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or\n      reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - UniProtKB # UniProtKB:([A-Z0-9]+-\\d+)\n      - UNIPROT.ISOFORM\n      - PR\n      - ENSEMBL\n\n  protein domain:\n    is_a: biological entity\n    description: >-\n      A conserved part of protein sequence and (tertiary) structure that can evolve,\n      function, and exist independently of the rest of the protein chain.\n      Protein domains maintain their structure and function independently of the proteins in which they are found.\n      e.g. an SH3 domain.\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    exact_mappings:\n      - NCIT:C13379\n      - SIO:001379\n      - UMLS:C1514562\n\n  protein family:\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n\n  nucleic acid sequence motif:\n    aliases: [ 'consensus sequence' ]\n    is_a: biological entity\n    description: >-\n      A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have,\n      a biological significance. e.g. the TATA box promoter motif, transcription factor binding\n      consensus sequences.\n\n  RNA product:\n    is_a: transcript\n    mixins:\n      - gene product mixin\n    exact_mappings:\n      - CHEBI:33697\n      # This SIO term here also mapped to 'biolink:Transcript'; however,\n      # since this 'biolink:RNAProduct' relates more to the biochemical\n      # essence of RNA, then map the SIO term instead to 'biolink:Transcript'\n      # - SIO:010450\n      - WIKIDATA:Q11053\n    id_prefixes:\n      - RNACENTRAL\n\n  RNA product isoform:\n    is_a: RNA product\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or reference RNA\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - RNACENTRAL\n\n  noncoding RNA product:\n    is_a: RNA product\n    id_prefixes:\n      - RNACENTRAL\n      - NCBIGene\n      - ENSEMBL\n    exact_mappings:\n      - SO:0000655\n      - SIO:001235\n\n  microRNA:\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000276\n      - SIO:001397\n      - WIKIDATA:Q310899\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  siRNA:\n    aliases: [ 'small interfering RNA', 'RNAi' ]\n    description: >-\n      A small RNA molecule that is the product of a longer exogenous or\n      endogenous dsRNA, which is either a bimolecular duplex or very long\n      hairpin, processed (via the Dicer pathway) such that numerous siRNAs\n      accumulate from both strands of the dsRNA. SRNAs trigger the cleavage\n      of their target molecules.\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000646\n      - WIKIDATA:Q203221\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  gene grouping mixin:\n    description: >-\n      any grouping of multiple genes or gene products\n    mixin: true\n    slots:\n      - has gene or gene product\n\n  gene family:\n    aliases: [ 'orthogroup','protein family' ]\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      # These term definitions focus only on proteins;\n      # the 'biolink:GeneFamily' term would be more inclusive\n      # to describe gene loci, non-coding RNA, etc.\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    description: >-\n      any grouping of multiple genes or gene products related by common descent\n    id_prefixes:\n      - PANTHER.FAMILY\n      - HGNC.FAMILY\n      - FB       # FlyBase FBgg*\n      - interpro # note: may be better to introduce a protein domain/family\n      - CATH\n      - CDD\n      - HAMAP\n      - PFAM\n      - PIRSF\n      - PRINTS\n      - PRODOM\n      - PROSITE\n      - SMART\n      - SUPFAM\n      - TIGRFAM\n      - CATH.SUPERFAMILY\n      - RFAM ## RNAs only\n      - KEGG.ORTHOLOGY ## aka KEGG.KO: K number\n      - EGGNOG\n      - COG\n    in_subset:\n      - model_organism_database\n\n  zygosity:\n    is_a: attribute\n    exact_mappings:\n      - GENO:0000133\n\n  genotype:\n    is_a: biological entity\n    mixins:\n      - physical essence\n      - genomic entity\n      - ontology class\n    description: >-\n      An information content entity that describes a genome by specifying the\n      total variation in genomic sequence and/or gene expression, relative to\n      some established background\n    comments:\n      - Consider renaming as genotypic entity\n    slots:\n      - has zygosity\n    exact_mappings:\n      - GENO:0000536\n      - SIO:001079\n    id_prefixes:\n      - ZFIN\n      - FB   # FlyBase FBba*\n    in_subset:\n      - model_organism_database\n\n  haplotype:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A set of zero or more Alleles on a single instance of a Sequence[VMC]\n    #    slots:\n    #      - completeness\n    exact_mappings:\n      - GENO:0000871\n      - SO:0001024\n      - VMC:Haplotype\n\n  sequence variant:\n    aliases: [ 'allele' ]\n    local_names:\n      agr: allele\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      An allele that varies in its sequence from what is considered\n      the reference allele at that locus.\n    comments:\n      - This class is for modeling the specific state at a locus.\n        A single DBSNP rs ID could correspond to more than one sequence variants\n        (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\n    broad_mappings:\n      # slightly broader semantics than SO:0001059 - 'sequence alteration'\n      # describes a sequence feature that may have 1..* sequence alterations\n      - SO:0001060\n    exact_mappings:\n      - GENO:0000002\n      - WIKIDATA:Q15304597\n      - SIO:010277\n      - VMC:Allele\n      - SO:0001059\n    close_mappings:\n      - dcid:Allele\n    id_prefixes:\n      - CAID # ClinGen Allele Registry\n      - CLINVAR\n      - ClinVarVariant\n      - WIKIDATA\n      # - CIViC needs IRI mapping\n      - DBSNP\n      - MGI\n      - ZFIN\n      - FB\n      - RGD\n      - AGRKB\n      - SPDI\n      - WB\n      - WormBase\n    alt_descriptions:\n      AGR: >-\n        An entity that describes a single affected, endogenous allele.\n        These can be of any type that matches that definition\n      VMC: >-\n        A contiguous change at a Location\n    slots:\n      - has gene\n    slot_usage:\n      has gene:\n        multivalued: true\n        description: Each allele can be associated with any number of genes\n      has biological sequence:\n        description: >-\n          The state of the sequence w.r.t a reference sequence\n      id:\n        examples:\n          - value: ZFIN:ZDB-ALT-980203-1091\n            description: ti282a allele from ZFIN\n          - value: ClinVarVariant:17681\n            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\n    in_subset:\n      - model_organism_database\n\n  snv:\n    aliases: [ 'single nucleotide variant','single nucleotide polymorphism', 'snp' ]\n    is_a: sequence variant\n    description: >-\n      SNVs are single nucleotide positions in genomic DNA at\n      which different sequence alternatives exist\n    exact_mappings:\n      - SO:0001483\n\n  reagent targeted gene:\n    aliases: [ 'sequence targeting reagent' ]\n    is_a: biological entity\n    description: >-\n      A gene altered in its expression level in the context of some\n      experiment as a result of being targeted by gene-knockdown\n      reagent(s) such as a morpholino or RNAi.\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - GENO:0000504\n    in_subset:\n      - model_organism_database\n\n  ## --------------------\n  ## Clinical\n  ## Attributes, Cohort,\n  ## Exposures & Outcomes\n  ## --------------------\n\n  ## Clinical Attributes\n\n  clinical attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a clinical manifestation\n    exact_mappings:\n      # Clinical Attribute\n      - STY:T201\n\n  clinical measurement:\n    is_a: clinical attribute\n    description: >-\n      A clinical measurement is a special kind of attribute which results\n      from a laboratory observation from a subject individual or sample.\n      Measurements can be connected to their subject by the 'has attribute' slot.\n    slot_usage:\n      has attribute type:\n        required: true\n        multivalued: false\n        values_from:\n          - EFO\n          - LOINC\n    exact_mappings:\n      - EFO:0001444\n\n  clinical modifier:\n    is_a: clinical attribute\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the phenotypic abnormality sub-ontology, with respect\n      to severity, laterality, and other aspects\n    exact_mappings:\n      - HP:0012823\n\n  clinical course:\n    is_a: clinical attribute\n    description: >-\n      The course a disease typically takes from its onset, progression in time, and\n      eventual resolution or death of the affected individual\n    exact_mappings:\n      - HP:0031797\n\n  onset:\n    is_a: clinical course\n    description: >-\n      The age group in which (disease) symptom manifestations appear\n    exact_mappings:\n      - HP:0003674\n\n  clinical entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists in the clinical domain and outside the\n      biological realm. Diseases are placed under biological entities\n\n  clinical trial:\n    is_a: clinical entity\n\n  clinical intervention:\n    is_a: clinical entity\n\n  clinical finding:\n    is_a: phenotypic feature\n    description: >-\n      this category is currently considered broad enough to tag clinical lab\n      measurements and other biological attributes taken as 'clinical traits'\n      with some statistical score, for example, a p value in genetic associations.\n    slot_usage:\n      has attribute:\n        range: clinical attribute\n    id_prefixes:\n      - LOINC\n      - NCIT\n      - EFO\n\n  hospitalization:\n    is_a: clinical intervention\n    exact_mappings:\n      - SNOMEDCT:32485007\n      - WIKIDATA:Q3140971\n\n  socioeconomic attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a socioeconomic manifestation\n    #slot_usage:\n    # need a suitable qualifying socioeconomic ontology target here?\n    # Perhaps some subset of ECTO: https://github.com/EnvironmentOntology/environmental-exposure-ontology\n    #  has attribute type:\n    #     range: socioeconomic ontology\n    # exact_mappings:\n    #  - ??\n\n  ## Cohorts\n\n  case:\n    aliases: [ 'patient', 'proband' ]\n    is_a: individual organism\n    description: >-\n      An individual (human) organism that has a patient role in some clinical context.\n\n  cohort:\n    is_a: study population\n    description: >-\n      A group of people banded together or treated as a group who share common characteristics.\n      A cohort 'study' is a particular form of longitudinal study that samples a cohort,\n      performing a cross-section at intervals through time.\n    exact_mappings:\n      - WIKIDATA:Q1303415\n    narrow_mappings:\n      # Professional or Occupational Group\n      - STY:T097\n      # Family Group\n      - STY:T099\n      # Age Group\n      - STY:T100\n      # Patient or Disabled Group\n      - STY:T101\n\n  ## Exposures\n\n  exposure event:\n    is_a: named thing\n    aliases: [ 'exposure', 'experimental condition' ]\n    mixin: true\n    slots:\n      - timepoint\n    description: >-\n      A (possibly time bounded) incidence of a feature of the environment of an organism that\n      influences one or more phenotypic features of that organism, potentially mediated by genes\n    exact_mappings:\n      - XCO:0000000\n    in_subset:\n      - model_organism_database\n\n  # TODO - confirm that genomic backgrounds are exposures\n  genomic background exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - gene grouping mixin\n      - physical essence\n      - genomic entity\n      - thing with taxon\n      - ontology class\n    description: >-\n      A genomic background exposure is where an individual's specific genomic background\n      of genes, sequence variants or other pre-existing genomic conditions constitute\n      a kind of 'exposure' to the organism, leading to or influencing an outcome.\n\n  pathological entity mixin:\n    description: >-\n      A pathological (abnormal) structure or process.\n    mixin: true\n    exact_mappings:\n      - MPATH:0\n    narrow_mappings:\n      - HP:0000118\n\n  pathological process:\n    description: >-\n      A biologic function or a process having an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: biological process\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - OBI:1110122\n      - NCIT:C16956\n    narrow_mappings:\n      # metastasis\n      - NCIT:C19151\n      - EFO:0009708\n      - STY:T046\n      - STY:T037\n\n  pathological process exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A pathological process, when viewed as an exposure, representing\n      a precondition, leading to or influencing an outcome,\n      e.g. autoimmunity leading to disease.\n\n  pathological anatomical structure:\n    description: >-\n      An anatomical structure with the potential of have an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: anatomical entity\n    mixins:\n      - pathological entity mixin\n\n  pathological anatomical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      An abnormal anatomical structure, when viewed as an exposure,\n      representing an precondition, leading to or influencing an outcome,\n      e.g. thrombosis leading to an ischemic disease outcome.\n\n  disease or phenotypic feature exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - pathological entity mixin\n    description: >-\n      A disease or phenotypic feature state, when viewed as an exposure,\n      represents an precondition, leading to or influencing an outcome,\n      e.g. HIV predisposing an individual to infections; a relative deficiency\n      of skin pigmentation predisposing an individual to skin cancer.\n\n  chemical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    slots:\n      - has quantitative value\n    description: >-\n      A chemical exposure is an intake of a particular\n      chemical entity.\n    exact_mappings:\n      # this ECTO term is not visibly defined but\n      # the 9000000-series identifiers seems to be the\n      # numeric space of chemical exposure definitions\n      - ECTO:9000000\n      - SIO:001399\n\n  complex chemical exposure:\n    is_a: attribute\n    description: >-\n      A complex chemical exposure is an intake of a chemical\n      mixture (e.g. gasoline), other than a drug.\n\n  drug exposure:\n    is_a: chemical exposure\n    aliases: [ 'drug intake', 'drug dose', 'medication intake' ]\n    description: >-\n      A drug exposure is an intake of a particular drug.\n    mixins:\n      - exposure event\n    broad_mappings:\n      # slightly broader than just drug effects on a biological system\n      - SIO:001005\n    exact_mappings:\n      - ECTO:0000509\n\n  # TODO: deprecate?\n  drug to gene interaction exposure:\n    description: >-\n      drug to gene interaction exposure is a drug exposure is where the\n      interactions of the drug with specific genes are known to constitute\n      an 'exposure' to the organism, leading to or influencing an outcome.\n    is_a: drug exposure\n    mixins:\n      - gene grouping mixin\n\n  treatment:\n    aliases: [ 'medical action', 'medical intervention' ]\n    # 'named thing' seems too generic here but not sure what applies better here\n    is_a: named thing\n    mixins:\n      - exposure event\n      - chemical or drug or treatment\n    description: >-\n      A treatment is targeted at a disease or phenotype and may involve\n      multiple drug 'exposures', medical devices and/or procedures\n    slots:\n      - has drug\n      - has device\n      - has procedure\n    exact_mappings:\n      - OGMS:0000090\n      - SIO:001398\n    broad_mappings:\n      - MAXO:0000058\n\n  biotic exposure:\n    is_a: attribute\n    aliases: [ 'viral exposure','bacterial exposure' ]\n    mixins:\n      - exposure event\n    description: >-\n      An external biotic exposure is an intake of (sometimes pathological)\n      biological organisms (including viruses).\n\n  geographic exposure:\n    is_a: environmental exposure\n    mixins:\n      - exposure event\n    description: >-\n      A geographic exposure is a factor relating to geographic\n      proximity to some impactful entity.\n    close_mappings:\n      - dcid:GeologicalEvent\n    narrow_mappings:\n      - dcid:IceStoremEvent\n      - dcid:LakeEffectSnowEvent\n      - dcid:LandslideEvent\n      - dcid:MarineDenseFogEvent\n      - dcid:MarineLighteningEvent\n      - dcid:MarineStrongWindEvent\n      - dcid:MarineThunderstormWindEvent\n      - dcid:StormEvent\n      - dcid:StormSurgeTideEvent\n      - dcid:StrongWindEvent\n      - dcid:ThunderstormWindEvent\n      - dcid:TornadoEvent\n      - dcid:TropicalDepressionEvent\n      - dcid:WinterStoremEvent\n\n  environmental exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A environmental exposure is a factor relating to abiotic processes\n      in the environment including sunlight (UV-B), atmospheric (heat,\n      cold, general pollution) and water-born contaminants.\n\n  behavioral exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A behavioral exposure is a factor relating to behavior impacting an individual.\n\n  socioeconomic exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A socioeconomic exposure is a factor relating to social and\n      financial status of an affected individual (e.g. poverty).\n    slot_usage:\n      has attribute:\n        range: socioeconomic attribute\n        required: true\n\n  ## Outcomes\n\n  outcome:\n    mixin: true\n    description: >-\n      An entity that has the role of being the consequence of an exposure event.\n      This is an abstract mixin grouping of various categories of possible\n      biological or non-biological (e.g. clinical) outcomes.\n\n  pathological process outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of a pathological process.\n\n  pathological anatomical outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of an abnormal anatomical structure.\n\n  disease or phenotypic feature outcome:\n    mixins:\n      - outcome\n    description: >-\n      Physiological outcomes resulting from an exposure event which\n      is the manifestation of a disease or other characteristic phenotype.\n\n  behavioral outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the manifestation of human behavior.\n\n  hospitalization outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the increased manifestation of acute (e.g. emergency\n      room visit) or chronic (inpatient) hospitalization.\n\n  mortality outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome of death from resulting from an exposure event.\n\n  epidemiological outcome:\n    mixins:\n      - outcome\n    description: >-\n      An epidemiological outcome, such as societal disease\n      burden, resulting from an exposure event.\n    related_mappings:\n      - NCIT:C19291\n\n  socioeconomic outcome:\n    mixins:\n      - outcome\n    description: >-\n      An general social or economic outcome, such as\n      healthcare costs, utilization, etc., resulting from an exposure event\n\n  ## ------------\n  ## ASSOCIATIONS\n  ## ------------\n\n  association:\n    is_a: entity\n    description: >-\n      A typed association between two entities, supported by evidence\n    comments:\n      - This is roughly the model used by biolink and ontobio at the moment\n    slots:\n      - subject\n      - predicate\n      - object\n      - negated\n      - qualifiers\n      - publications\n      - has evidence\n      - knowledge source\n      - original knowledge source\n      - primary knowledge source\n      - aggregator knowledge source\n      - timepoint\n    slot_usage:\n      type:\n        description: rdf:type of biolink:Association should be fixed at rdf:Statement\n      category:\n        range: category type\n        required: false\n    exact_mappings:\n      - OBAN:association\n      - rdf:Statement\n      - owl:Axiom\n\n\n  chemical entity assesses named thing association:\n    is_a: association\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: assesses\n\n\n  contributor association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      Any association between an entity (such as a publication)\n      and various agents that contribute to its realisation\n    slot_usage:\n      subject:\n        range: information content entity\n        description: >-\n          information content entity which an agent has helped realise\n      predicate:\n        subproperty_of: contributor\n        description: >-\n          generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\n      object:\n        range: agent\n        description: >-\n          agent helping to realise the given entity (e.g. such as a publication)\n      qualifiers:\n        description: >-\n          this field can be used to annotate special characteristics of an\n          agent relationship, such as the fact that a given author agent of\n          a publication is the 'corresponding author'\n\n  genotype to genotype part association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a genotypic entity that is a sub-component of it\n    slot_usage:\n      predicate:\n        subproperty_of: has variant part\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: genotype\n        description: >-\n          child genotype\n\n  genotype to gene association:\n    description: >-\n      Any association between a genotype and a gene.\n      The genotype have have multiple variants in that gene or a single one.\n      There is no assumption of cardinality\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: gene\n        description: >-\n          gene implicated in genotype\n\n  genotype to variant association:\n    description: >-\n      Any association between a genotype and a sequence variant.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: sequence variant\n        description: >-\n          gene implicated in genotype\n\n  gene to gene association:\n    aliases: [ 'molecular or genetic interaction' ]\n    description: >-\n      abstract parent class for different kinds of gene-gene or gene product\n      to gene product relationships. Includes homology and interaction.\n    abstract: true\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          the subject gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n      object:\n        range: gene or gene product\n        description: >-\n          the object gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n\n  gene to gene homology association:\n    description: >-\n      A homology association between two genes. May be orthology (in which\n      case the species of subject and object should differ) or paralogy\n      (in which case the species may be the same)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n      predicate:\n        subproperty_of: homologous to\n        symmetric: true\n        description: >-\n          homology relationship type\n      object:\n        range: gene or gene product\n\n  gene expression mixin:\n    description: >-\n      Observed gene expression intensity, context (site, stage) and\n      associated phenotypic status within which the expression occurs.\n    mixin: true\n    slots:\n      - quantifier qualifier\n      - expression site\n      - stage qualifier\n      - phenotypic state\n    slot_usage:\n      quantifier qualifier:\n        description: >-\n          Optional quantitative value indicating degree of expression.\n\n  gene to gene coexpression association:\n    description: >-\n      Indicates that two genes are co-expressed,\n      generally under the same conditions.\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: coexpressed with\n        symmetric: true\n\n  pairwise gene to gene interaction:\n    description: >-\n      An interaction between two genes or two gene products.\n      May be physical (e.g. protein binding) or genetic (between genes).\n      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      predicate:\n        subproperty_of: interacts with\n        symmetric: true\n        description: \"interaction relationship type\"\n    narrow_mappings:\n      - dcid:ProteinProteinInteraction\n\n  pairwise molecular interaction:\n    description: >-\n      An interaction at the molecular level between two physical entities\n    is_a: pairwise gene to gene interaction\n    slots:\n      - interacting molecules category\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: molecular entity\n      id:\n        description: >-\n          identifier for the interaction. This may come from an interaction database such as IMEX.\n        examples:\n          - value: WB:WBInteraction000538741\n        values_from:\n          - IMEX\n          - BioGRID\n      predicate:\n        subproperty_of: interacts with\n        description: \"interaction relationship type\"\n        examples:\n          - value: RO:0002447\n            description: the subject molecular phosphorylates the object molecule\n      object:\n        range: molecular entity\n\n  cell line to entity association mixin:\n    description: >-\n      An relationship between a cell line and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: cell line\n\n  # TODO: figure out what gives with subject range\n  cell line to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - cell line to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    description: >-\n      An relationship between a cell line and a disease or a phenotype, where\n      the cell line is derived from an individual with that disease or phenotype.\n    slot_usage:\n      subject:\n        #        - range: cell line\n        #        - range: disease or phenotypic feature\n        range: disease or phenotypic feature\n\n  chemical entity to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity that is an interactor\"\n\n  drug to entity association mixin:\n    description: >-\n      An interaction between a drug and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: drug\n        description: \"the drug that is an interactor\"\n\n  chemical to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity or entity that is an interactor\"\n\n  case to entity association mixin:\n    description: >-\n      An abstract association for use where the case is the subject\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: case\n        description: \"the case (e.g. patient) that has the property\"\n\n  chemical to chemical association:\n    description: >-\n      A relationship between two chemical entities. This can encompass actual\n      interactions as well as temporal causal edges, e.g. one chemical converted to another.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: chemical entity\n        description: \"the chemical element that is the target of the statement\"\n\n  reaction to participant association:\n    description:\n    is_a: chemical to chemical association\n    slots:\n      - stoichiometry\n      - reaction direction\n      - reaction side\n    slot_usage:\n      subject:\n        range: molecular entity\n    defining_slots:\n      - subject\n      - predicate\n      - object\n\n  reaction to catalyst association:\n    description:\n    is_a: reaction to participant association\n    slot_usage:\n      object:\n        range: gene or gene product\n\n  chemical to chemical derivation association:\n    description: >-\n      A causal relationship between two chemical entities, where the subject\n      represents the upstream entity and the object represents the downstream.\n      For any such association there is an implicit reaction:\n        IF\n        R has-input C1 AND\n        R has-output C2 AND\n        R enabled-by P AND\n        R type Reaction\n        THEN\n        C1 derives-into C2 <>\n    is_a: chemical to chemical association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - catalyst qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: >-\n          the upstream chemical entity\n      object:\n        range: chemical entity\n        description: >-\n          the downstream chemical entity\n      predicate:\n        subproperty_of: derives into\n      catalyst qualifier:\n        description: >-\n          this connects the derivation edge to the chemical entity that\n          catalyzes the reaction that causes the subject chemical to\n          transform into the object chemical.\n\n  chemical to disease or phenotypic feature association:\n    description: >-\n      An interaction between a chemical entity and a phenotype or disease,\n      where the presence of the chemical gives rise to or exacerbates the phenotype.\n    is_a: association\n    narrow_mappings:\n      - SIO:000993\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"the disease or phenotype that is affected by the chemical\"\n\n  chemical or drug or treatment to disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary undesirable effect.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slots:\n      - FDA adverse event level\n    slot_usage:\n      predicate:\n        subproperty_of: has adverse event\n\n  chemical or drug or treatment side effect disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.\n    is_a: chemical or drug or treatment to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has side effect\n\n  gene to pathway association:\n    description: >-\n      An interaction between a gene or gene product and a biological process or pathway.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"the gene or gene product entity that participates or influences the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that includes or is affected by the gene or gene product\"\n\n  molecular activity to pathway association:\n    description: >-\n      Association that holds the relationship between a reaction and the pathway it participates in.\n    is_a: association\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: pathway\n      predicate:\n        subproperty_of: part of\n\n  chemical to pathway association:\n    description: >-\n      An interaction between a chemical entity and a biological process or pathway.\n    is_a: association\n    exact_mappings:\n      - SIO:001250\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: \"the chemical entity that is affecting the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that is affected by the chemical\"\n\n  named thing associated with likelihood of named thing association:\n    # TODO: better name\n    description: >-\n    is_a: association\n    defining_slots:\n      - subject\n      - subject aspect qualifier\n      - subject context qualifier\n      - predicate\n      - object\n      - object aspect qualifier\n      - object context qualifier\n      - population context qualifier\n    slot_usage:\n      predicate:\n        subproperty_of: associated with\n      subject aspect qualifier:\n      # TODO: range\n      subject context qualifier:\n        range: ontology class\n      object aspect qualifier:\n      # TODO: range\n      object context qualifier:\n        range: ontology class\n\n  chemical to gene association:\n    deprecated: true\n    description: >-\n      An interaction between a chemical entity and a gene or gene product.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: >-\n          the gene or gene product that is affected by the chemical.\n\n  chemical gene interaction association:\n    description: >-\n      describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical\n      effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type\n      (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)\n    is_a: association\n    exact_mappings:\n      - SIO:001257\n    mixins:\n      - chemical to entity association mixin\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object context qualifier\n      - anatomical context qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: gene or gene product\n      predicate:\n        subproperty_of: physically interacts with\n      subject form or variant qualifier:\n        range: chemical_or_gene_or_gene_product_form_enum\n      subject part qualifier:\n        range: gene_or_gene_product_or_chemical_part_qualifier_enum\n      subject derivative qualifier:\n        range: chemical_entity_derivative_enum\n      subject context qualifier:\n        range: anatomical entity\n      object form or variant qualifier:\n        range: chemical_or_gene_or_gene_product_form_enum\n      object part qualifier:\n        range: gene_or_gene_product_or_chemical_part_qualifier_enum\n      object context qualifier:\n        range: anatomical entity\n      anatomical context qualifier:\n        range: anatomical entity\n\n  chemical affects gene association:\n    description: >-\n      Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,\n      localization, processing, expression, etc.)\n    is_a: association\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject aspect qualifier\n      - subject context qualifier\n      - subject direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object aspect qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - qualified predicate\n    slot_usage:\n      subject:\n        range: chemical entity\n      subject form or variant qualifier:\n        range: chemical_or_gene_or_gene_product_form_enum\n      subject part qualifier:\n        range: gene_or_gene_product_or_chemical_part_qualifier_enum\n      subject derivative qualifier:\n        range: chemical_entity_derivative_enum\n      subject aspect qualifier:\n        range: gene_or_gene_product_or_chemical_entity_aspect_enum\n      subject context qualifier:\n        range: anatomical entity\n      subject direction qualifier:\n        range: direction_qualifier_enum\n      predicate:\n        subproperty_of: affects\n      qualified predicate:\n        subproperty_of: causes\n      object:\n        range: gene or gene product\n      object form or variant qualifier:\n        range: chemical_or_gene_or_gene_product_form_enum\n      object part qualifier:\n        range: gene_or_gene_product_or_chemical_part_qualifier_enum\n      object aspect qualifier:\n        range: gene_or_gene_product_or_chemical_entity_aspect_enum\n      object context qualifier:\n        range: anatomical entity\n      object direction qualifier:\n        range: direction_qualifier_enum\n      causal mechanism qualifier:\n        range: causal_mechanism_qualifier_enum\n      anatomical context qualifier:\n        range: anatomical entity\n      species context qualifier:\n        range: organism taxon\n\n  drug to gene association:\n    description: >-\n      An interaction between a drug and a gene or gene product.\n    is_a: association\n    related_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - drug to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: \"the gene or gene product that is affected by the drug\"\n\n  material sample to entity association mixin:\n    description: >-\n      An association between a material sample and something.\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n\n  material sample derivation association:\n    description: >-\n      An association between a material sample and\n      the material entity from which it is derived.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n      object:\n        description: >-\n          the material entity the sample was derived from. This may be another\n          material sample, or any other material entity, including for example\n          an organism, a geographic feature, or some environmental material.\n      predicate:\n        description: >-\n          derivation relationship\n        subproperty_of: derives from\n\n  material sample to disease or phenotypic feature association:\n    description: >-\n      An association between a material sample and a disease or phenotype.\n    is_a: association\n    mixins:\n      - material sample to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    defining_slots:\n      - subject\n      - object\n\n  disease to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease\n        description: \"disease class\"\n        values_from: [ 'mondo', 'omim', 'orphanet', 'ncit', 'doid' ]\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n\n  entity to exposure event association mixin:\n    description: >-\n      An association between some entity and an exposure event.\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: exposure event\n\n  disease to exposure event association:\n    description: >-\n      An association between an exposure event and a disease.\n    is_a: association\n    mixins:\n      - disease to entity association mixin\n      - entity to exposure event association mixin\n    defining_slots:\n      - subject\n      - object\n\n  exposure event to entity association mixin:\n    deprecated: true\n\n  entity to outcome association mixin:\n    description: >-\n      An association between some entity and an outcome\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: outcome\n\n  exposure event to outcome association:\n    description: >-\n      An association between an exposure event and an outcome.\n    is_a: association\n    mixins:\n      - exposure event to entity association mixin\n      - entity to outcome association mixin\n    slots:\n      - has population context\n      - has temporal context\n    defining_slots:\n      - subject\n      - object\n\n  frequency qualifier mixin:\n    mixin: true\n    description: >-\n      Qualifier for frequency type associations\n    slots:\n      - frequency qualifier\n\n  entity to feature or disease qualifiers mixin:\n    description: >-\n      Qualifiers for entity to disease or phenotype associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - severity qualifier\n      - onset qualifier\n\n  entity to phenotypic feature association mixin:\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: phenotypic feature\n        values_from: [ 'upheno', 'hp', 'mp', 'wbphenotype' ]\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n    slots:\n      - sex qualifier\n\n  information content entity to named thing association:\n    description: >-\n      association between a named thing and a information content entity where the specific context\n      of the relationship between that named thing and the publication is unknown. For\n      example, model organisms databases often capture the knowledge that a gene is found in a\n      journal article, but not specifically the context in which that gene was documented in the article.\n      In these cases, this association with the accompanying predicate 'mentions' could be used.\n      Conversely, for more specific associations (like 'gene to disease association', the publication should\n      be captured as an edge property).\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        domain: publication\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: mentions\n    in_subset:\n      - model_organism_database\n\n  entity to disease association mixin:\n    description: >-\n      mixin class for any association whose object (target node) is a disease\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease\n        description: \"disease\"\n        examples:\n          - value: MONDO:0020066\n            description: \"Ehlers-Danlos syndrome\"\n\n  disease or phenotypic feature to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  disease or phenotypic feature to location association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      an anatomical entity, where the disease/feature manifests in that site.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      object:\n        range: anatomical entity\n        description: >-\n          anatomical entity in which the disease or feature is found.\n        examples:\n          - value: UBERON:0002048\n            description: \"lung\"\n\n  disease or phenotypic feature to genetic inheritance association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      its mode of (genetic) inheritance.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has mode of inheritance\n      object:\n        range: genetic inheritance\n        description: >-\n          genetic inheritance associated with the specified disease or phenotypic feature.\n        examples:\n          - value: HP:0001417\n            description: \"X-linked inheritance\"\n\n  entity to disease or phenotypic feature association mixin:\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  genotype to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: genotype\n        description: \"genotype that is the subject of the association\"\n\n  genotype to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a phenotypic feature, where having\n      the genotype confers the phenotype, either in isolation or through environment\n    mixins:\n      - entity to phenotypic feature association mixin\n      - genotype to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has phenotype\n      subject:\n        range: genotype\n        description: >-\n          genotype that is associated with the phenotypic feature\n\n  # ie: smoke exposure to coughing phenotype? is this a denormalization?\n  exposure event to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between an environment and a phenotypic feature,\n      where being in the environment influences the phenotype.\n    mixins:\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: exposure event\n\n  disease to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      An association between a disease and a phenotypic feature in which the\n      phenotypic feature is associated with the disease in some way.\n    mixins:\n      - entity to phenotypic feature association mixin\n      - disease to entity association mixin\n    close_mappings:\n      - dcid:DiseaseSymptomAssociation\n    slot_usage:\n      subject:\n        range: disease\n      object:\n        range: phenotypic feature\n\n  case to phenotypic feature association:\n    description: >-\n      An association between a case (e.g. individual patient) and a phenotypic\n      feature in which the individual has or has had the phenotype.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - case to entity association mixin\n\n  behavior to behavioral feature association:\n    description: >-\n      An association between an mixture behavior and\n      a behavioral feature manifested by\n      the individual exhibited or has exhibited the behavior.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: behavior\n        description: >-\n          behavior that is the subject of the association\n      object:\n        range: behavioral feature\n        description: >-\n          behavioral feature that is the object of the association\n    mixins:\n      - entity to phenotypic feature association mixin\n\n  gene to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene that is the subject of the association\n\n  variant to entity association mixin:\n    local_names:\n      ga4gh: variant annotation\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is associated with some other entity\n        examples:\n          - value: ClinVar:38077\n            description: \"ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n          - value: ClinGen:CA024716\n            description: \"chr13:g.32921033G>C (hg19) in ClinGen\"\n\n  gene to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n      - WBVocab:Gene-Phenotype-Association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      object:\n        range: phenotypic feature\n\n  gene to disease association:\n    is_a: association\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n    exact_mappings:\n      - SIO:000983\n    close_mappings:\n      - dcid:DiseaseGeneAssociation\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease,\n          may be protective or causative or associative, or as a model\n      object:\n        range: disease\n\n  druggable gene to disease association:\n    is_a: gene to disease association\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease\n          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and\n          this leads to a protective or improving disease state.\n      predicate:\n        subproperty_of: target for\n      has evidence:\n        range: druggable_gene_category_enum\n    defining_slots:\n      - subject\n      - object\n      - predicate\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n\n  variant to gene association:\n    description: >-\n      An association between a variant and a gene, where the variant has\n      a genetic association with the gene (i.e. is in linkage disequilibrium)\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - variant to entity association mixin\n    slot_usage:\n      object:\n        range: gene\n      predicate:\n        subproperty_of: genetic association\n\n  variant to gene expression association:\n    description: >-\n      An association between a variant and expression of a gene (i.e. e-QTL)\n    is_a: variant to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: affects expression of\n\n  variant to population association:\n    description: >-\n      An association between a variant and a population, where the variant has\n      particular frequency in the population\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - frequency quantifier\n      - frequency qualifier mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          an allele that has a certain frequency in a given population\n        examples:\n          - value: \"NC_000017.11:g.43051071A>T\"\n            description: >-\n              17:41203088 A/C in gnomad\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that is observed to have the frequency\n        examples:\n          - value: HANCESTRO:0010\n            description: African\n      has quotient:\n        description: >-\n          frequency of allele in population, expressed as a number with allele\n          divided by number in reference population, aka allele frequency\n        examples:\n          - value: \"0.0001666\"\n      has count:\n        description: >-\n          number in object population that carry a particular allele, aka allele count\n        examples:\n          - value: \"4\"\n            description: 4 individuals in gnomad set\n      has total:\n        description: >-\n          number all populations that carry a particular allele, aka allele number\n        examples:\n          - value: \"24014\"\n            description: 24014 individuals in gnomad set\n\n  population to population association:\n    description: >-\n      An association between a two populations\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: population of individual organisms\n        description: >-\n          the population that form the subject of the association\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that form the object of the association\n      predicate:\n        # subproperty_of: ???\n        description: >-\n          A relationship type that holds between the subject and object\n          populations. Standard mereological relations can be used.\n          E.g. subject part-of object, subject overlaps object.\n          Derivation relationships can also be used\n\n  variant to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is\n          associated in some way with the phenotype state\n\n  variant to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a sequence variant in which the allele state\n          is associated in some way with the disease state\n        examples:\n          - value: ClinVar:52241\n            description: \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that variant\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  genotype to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - genotype to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a genotype that is associated in some way with a disease state\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that genotype\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  model to disease association mixin:\n    description: >-\n      This mixin is used for any association class for which the subject\n      (source node) plays the role of a 'model', in that it recapitulates some\n      features of the disease in a way that is useful for studying the disease\n      outside a patient carrying the disease\n    mixin: true\n    slot_usage:\n      subject:\n        description: >-\n          The entity that serves as the model of the disease. This may be\n          an organism, a strain of organism, a genotype or variant that exhibits\n          similar features, or a gene that when mutated exhibits features of the disease\n      predicate:\n        subproperty_of: model of\n        description: >-\n          The relationship to the disease\n\n  gene as a model of disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be a model\n          organism ortholog of a known disease gene, or it may be a gene whose\n          mutants recapitulate core features of the disease.\n\n  variant as a model of disease association:\n    is_a: variant to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          A variant that has a role in modeling the disease.\n\n  genotype as a model of disease association:\n    is_a: genotype to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: genotype\n        description: >-\n          A genotype that has a role in modeling the disease.\n\n  cell line as a model of disease association:\n    is_a: cell line to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: cell line\n        description: >-\n          A cell line derived from an organismal entity with a disease state that is used\n          as a model of that disease.\n\n  organismal entity as a model of disease association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: organismal entity\n        description: >-\n          A organismal entity (strain, breed) with a predisposition to a disease, or bred/created\n          specifically to model a disease.\n\n  organism to organism association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: individual organism\n      object:\n        range: individual organism\n        description: >-\n          An association between two individual organisms.\n\n  taxon to taxon association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n        description: >-\n          An association between individuals of different taxa.\n\n  gene has variant that contributes to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - sequence variant qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be\n          a model organism ortholog of a known disease gene, or it may be\n          a gene whose mutants recapitulate core features of the disease.\n\n  gene to expression site association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      An association between a gene and a gene expression site,\n      possibly qualified by stage/timing info.\n    notes:\n      - \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n    see_also: \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n    slots:\n      - stage qualifier\n      - quantifier qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          Gene or gene product positively within the specified\n          anatomical entity (or subclass, i.e. cellular component) location.\n      object:\n        range: anatomical entity\n        description: \"location in which the gene is expressed\"\n        examples:\n          - value: UBERON:0002037\n            description: cerebellum\n      predicate:\n        description: \"expression relationship\"\n        subproperty_of: expressed in\n      stage qualifier:\n        range: life stage\n        description: \"stage at which the gene is expressed in the site\"\n        examples:\n          - value: UBERON:0000069\n            description: larval stage\n      quantifier qualifier:\n        description: >-\n          can be used to indicate magnitude, or also ranking\n\n  sequence variant modulates treatment association:\n    is_a: association\n    description: >-\n      An association between a sequence variant and a treatment or health intervention.\n      The treatment object itself encompasses both the disease and the drug used.\n    comments:\n      - An alternate way to model the same information could be via a qualifier\n    defining_slots:\n      - subject\n      - object\n    abstract: true\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: \"variant that modulates the treatment of some disease\"\n      object:\n        range: treatment\n        description: \"treatment whose efficacy is modulated by the subject variant\"\n\n  functional association:\n    is_a: association\n    description: >-\n      An association between a macromolecular machine mixin (gene, gene product or\n      complex of gene products) and either a molecular activity, a biological\n      process or a cellular location in which a function is executed.\n    slot_usage:\n      subject:\n        range: macromolecular machine mixin\n        description: >-\n          gene, product or macromolecular complex mixin that\n          has the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: gene ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n          - value: GO:0045211\n            description: postsynaptic membrane\n\n  macromolecular machine to entity association mixin:\n    description: >-\n      an association which has a macromolecular machine mixin as a subject\n    mixin: true\n    slot_usage:\n      subject:\n        domain: macromolecular machine mixin\n\n  macromolecular machine to molecular activity association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a molecular activity (as represented\n      in the GO molecular function branch), where the entity\n      carries out the activity, or contributes to its execution.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: molecular activity\n\n  macromolecular machine to biological process association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a biological process or pathway\n      (as represented in the GO biological process branch), where the entity\n      carries out some part of the process, regulates it, or acts upstream of it.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: biological process\n\n  macromolecular machine to cellular component association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a cellular component (as represented\n      in the GO cellular component branch), where the entity\n      carries out its function in the cellular component.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: cellular component\n\n  molecular activity to chemical entity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: chemical entity\n\n  molecular activity to molecular activity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: molecular activity\n\n\n  gene to go term association:\n    aliases: [ 'functional association' ]\n    is_a: functional association\n    exact_mappings:\n      - WBVocab:Gene-GO-Association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene\n        description: >-\n          gene, product or macromolecular complex that has\n          the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: gene ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n\n  entity to disease association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  entity to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  ## -----------------\n  ## SEQUENCE FEATURES\n  ## -----------------\n\n  sequence association:\n    is_a: association\n    description: >-\n      An association between a sequence feature and a nucleic acid entity it is localized to.\n\n  genomic sequence localization:\n    is_a: sequence association\n    description: >-\n      A relationship between a sequence feature and a nucleic acid entity\n      it is localized to. The reference entity may be a chromosome,\n      chromosome region or information entity such as a contig.\n    slot_usage:\n      subject:\n        aliases: [ 'sequence feature' ]\n        range: nucleic acid entity\n      object:\n        aliases: [ 'reference' ]\n        range: nucleic acid entity # typically a chromosome use monochrom\n      predicate:\n        subproperty_of: has sequence location\n    slots:\n      - start interbase coordinate\n      - end interbase coordinate\n      - genome build\n      - strand\n      - phase\n    broad_mappings:\n      - dcid:Chromosome\n    exact_mappings:\n      - dcid:GenomeAnnotation\n\n  sequence feature relationship:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      For example, a particular exon is part of a particular transcript or gene\n    slot_usage:\n      subject:\n        range: nucleic acid entity\n      object:\n        range: nucleic acid entity # typically a chromosome\n    exact_mappings:\n      - CHADO:feature_relationship\n\n  transcript to gene relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is a collection of transcripts\n    slot_usage:\n      subject:\n        range: transcript\n      object:\n        range: gene\n\n  gene to gene product relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is transcribed and potentially translated to a gene product\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene product mixin\n      predicate:\n        subproperty_of: has gene product\n\n  exon to transcript relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A transcript is formed from multiple exons\n    slot_usage:\n      subject:\n        range: exon\n      object:\n        range: transcript\n\n  gene regulatory relationship:\n    deprecated: true\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n      subject:\n        range: gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n\n  chemical entity or gene or gene product regulates gene association:\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slots:\n      - object direction qualifier\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n        subproperty_of: regulates\n      subject:\n        range: chemical entity or gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n      object direction qualifier:\n        range: direction_qualifier_enum\n\n  anatomical entity to anatomical entity association: # schema: gocam\n    is_a: association\n    abstract: true\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: anatomical entity\n      object:\n        range: anatomical entity\n\n  anatomical entity to anatomical entity part of association:\n    #      schema: gocam\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is mereological, i.e the two entities are related by parthood. This\n      includes relationships between cellular components and cells, between\n      cells and tissues, tissues and whole organisms\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the part\n      object:\n        range: anatomical entity\n        description: >-\n          the whole\n      predicate:\n        subproperty_of: part of\n\n  anatomical entity to anatomical entity ontogenic association:\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is ontogenic, i.e. the two entities are related by development. A number\n      of different relationship types can be used to specify the precise\n      nature of the relationship.\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the structure at a later time\n      object:\n        range: anatomical entity\n        description: >-\n          the structure at an earlier time\n      predicate:\n        subproperty_of: develops from\n\n  organism taxon to entity association:\n    mixin: true\n    description: >-\n      An association between an organism taxon and another entity\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: organism taxon\n        description: >-\n          organism taxon that is the subject of the association\n\n  organism taxon to organism taxon association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    description: >-\n      A relationship between two organism taxon nodes\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n\n  organism taxon to organism taxon specialization:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      A child-parent relationship between two taxa.\n      For example: Homo sapiens subclass_of Homo\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: child taxon\n        description: >-\n          the more specific taxon\n      object:\n        range: organism taxon\n        role: parent taxon\n        description: >-\n          the more general taxon\n      predicate:\n        subproperty_of: subclass of\n\n  organism taxon to organism taxon interaction:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      An interaction relationship between two taxa. This may be a symbiotic\n      relationship (encompassing mutualism and parasitism), or it may be non-symbiotic.\n      Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens\n    defining_slots:\n      - predicate\n    slots:\n      - associated environmental context\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        range: organism taxon\n        role: interactee taxon\n        description: >-\n          the taxon that is the subject of the association\n      predicate:\n        subproperty_of: interacts with\n      associated environmental context:\n        description: >-\n          the environment in which the two taxa interact\n\n  organism taxon to environment association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        role: environmental context\n        description: >-\n          the environment in which the organism occurs\n      predicate:\n        description: >-\n          predicate describing the relationship between the taxon and the environment\n\nenums:\n\n  anatomical_context_qualifier_enum:\n    reachable_from:\n      source_ontology: bioregistry:uberon\n      source_nodes:\n        - UBERON:0001062\n      is_direct: false\n      relationship_types:\n        - rdfs:subClassOf\n\n  direction_qualifier_enum:\n    permissible_values:\n      increased:\n      upregulated:\n        is_a: increased\n      decreased:\n      downregulated:\n        is_a: decreased\n\n  chemical_entity_derivative_enum:\n    permissible_values:\n      metabolite:\n\n  chemical_or_gene_or_gene_product_form_enum:\n    permissible_values:\n      modified form:\n      mutant form:\n      polymorphism:\n      SNP:\n      analog:\n\n  gene_or_gene_product_or_chemical_part_qualifier_enum:\n    permissible_values:\n      3' UTR:\n      5' UTR:\n      polyA tail:\n      promoter:\n      enhancer:\n      exon:\n      intron:\n\n  gene_or_gene_product_or_chemical_entity_aspect_enum:\n    permissible_values:\n      activity or abundance:\n        description: >- \n          Used in cases where the specificity of the relationship can not be determined to be either activity \n          or abundance.  In general, a more specific value from this enumeration should be used.\n      abundance:\n        is_a: activity or abundance\n      activity:\n        is_a: activity or abundance\n      expression:\n        is_a: abundance\n      synthesis:\n        is_a: abundance\n      degradation:\n        is_a: abundance # negate the direction qualifier necessary.\n      cleavage:\n        is_a: degradation\n      hydrolysis:\n        is_a: degradation\n      metabolic processing:\n      mutation rate:\n      stability:\n      localization:\n      transport:\n      secretion:\n        is_a: transport\n      uptake:\n        is_a: transport\n      molecular modification:\n      acetylation:\n        is_a: molecular modification\n      acylation:\n        is_a: molecular modification\n      alkylation:\n        is_a: molecular modification\n      amination:\n        is_a: molecular modification\n      carbamoylation:\n        is_a: molecular modification\n      ethylation:\n        is_a: molecular modification\n      glutathionylation:\n        is_a: molecular modification\n      glycation:\n        is_a: molecular modification\n      glycosylation:\n        is_a: molecular modification\n      glucuronidation:\n        is_a: molecular modification\n      N-linked glycosylation:\n        is_a: molecular modification\n      O-linked glycosylation:\n        is_a: molecular modification\n      hydroxylation:\n        is_a: molecular modification\n      lipidation:\n        is_a: molecular modification\n      farnesylation:\n        is_a: molecular modification\n      geranoylation:\n        is_a: molecular modification\n      myristoylation:\n        is_a: molecular modification\n      palmitoylation:\n        is_a: molecular modification\n      prenylation:\n        is_a: molecular modification\n      methylation:\n        is_a: molecular modification\n      nitrosation:\n        is_a: molecular modification\n      nucleotidylation:\n        is_a: molecular modification\n      phosphorylation:\n        is_a: molecular modification\n      ribosylation:\n        is_a: molecular modification\n      ADP-ribosylation:\n        is_a: molecular modification\n      sulfation:\n        is_a: molecular modification\n      sumoylation:\n        is_a: molecular modification\n      ubiquitination:\n        is_a: molecular modification\n      oxidation:\n        is_a: molecular modification\n      reduction:\n        is_a: molecular modification\n      carboxylation:\n        is_a: molecular modification\n\n  causal_mechanism_qualifier_enum:\n    permissible_values:\n      binding:\n        description: >-\n          A causal mechanism mediated by the direct contact between effector and target chemical or \n          biomolecular entity, which form a stable physical interaction.\n      inhibition:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to the target and negatively effects its normal function, \n          e.g. prevention of enzymatic reaction or activation of downstream pathway.\n      antibody inhibition:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which an antibody specifically binds to and interferes with the target.\n      antagonism:\n        is_a: inhibition\n        description: >-\n          A causal mecahnism in which the effector binds to a receptor and prevents activation by an agonist \n          through competing for the binding site.\n      molecular channel blockage:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and prevents or reduces \n          transport of ions through it.\n      inverse agonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes\n          its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.\n      negative allosteric modulation:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a \n          receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n      agonism:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an \n          endogenous ligand.\n      molecular channel opening:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and facilitates transport of \n          ions through it.\n      positive allosteric modulation:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by \n          binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n      potentiation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector  binds to and enhances or intensifies the effect of some \n          other chemical or drug on its target.\n      activation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.\n      inducer:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that \n          processes drugs in the body.\n      transcriptional regulation:\n        description: >-\n          A causal mechanism mediated by through the control of target gene transcription\n      signaling-mediated control:\n        description: >-\n          A causal mechanism mediated by the activation or control of signaling events that influence the some aspect \n          of the target entity (e.g. its activity, processing, transport, etc)\n\n  logical_interpretation_enum:\n    permissible_values:\n      SomeSome:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as a some-some statement\n        meaning: os:SomeSomeInterpretation\n      AllSome:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as an all-some statement.\n        meaning: os:AllSomeInterpretation\n      InverseAllSome:\n\n  reaction_direction_enum:\n    permissible_values:\n      left_to_right:\n      right_to_left:\n      bidirectional:\n      neutral:\n\n  reaction_side_enum:\n    permissible_values:\n      left:\n      right:\n\n  phase_enum:\n    description: phase\n    permissible_values:\n      0:\n      1:\n      2:\n\n  strand_enum:\n    description: strand\n    permissible_values:\n      \"+\":\n        description: Positive\n      \"-\":\n        description: Negative\n      \".\":\n        description: Unstranded\n      \"?\":\n        description: Unknown\n\n  sequence_enum:\n    description: type of sequence\n    permissible_values:\n      \"NA\":\n        description: nucleic acid\n      \"AA\":\n        description: amino acid\n\n  druggable_gene_category_enum:\n    permissible_values:\n      \"Tclin\":\n        description: >-\n          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.\n      \"Tbio\":\n        description: >-\n          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy\n          the activity thresholds detailed below.\n      \"Tchem\":\n        description: >-\n          These targets do not have known drug or small molecule activities that satisfy the activity\n          thresholds detailed below AND satisfy one or more of the following criteria:\n          target is above the cutoff criteria for Tdark\n          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)\n          with an Experimental Evidence code\n      \"Tdark\":\n        description: >-\n          These are targets about which virtually nothing is known. They do not have known drug or small\n          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or\n          more of the following criteria:\n          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or\n          less than or equal to 50 Antibodies available according to http://antibodypedia.com.\n\n  drug_availability_enum:\n    description: >-\n    permissible_values:\n      \"over the counter\":\n        description: >-\n          chemical entity is available over the counter without a prescription.\n      \"prescription\":\n        description:\n          chemical entity is available by prescription.\n\n  drug_delivery_enum:\n    permissible_values:\n      \"inhalation\":\n      \"oral\":\n      \"absorbtion through the skin\":\n      \"intravenous injection\":\n\n  FDA_approval_status_enum:\n    description: >-\n    permissible_values:\n      \"Discovery & Development Phase\":\n        description: >-\n          Discovery & Development Phase. Discovery involves researchers finding new possibilities\n          for medication through testing molecular compounds, noting unexpected effects from existing treatments,\n          or the creation of new technology that allows novel ways of targeting medical products to sites in the body.\n          Drug development occurs after researchers identify potential compounds for experiments.\n      \"Preclinical Research Phase\":\n        description: >-\n          Preclinical Research Phase.  Once researchers have examined the possibilities a new drug may contain,\n          they must do preliminary research to determine its potential for harm (toxicity).\n          This is categorized as preclinical research and can be one of two types: in vitro or in vivo.\n      \"FDA Clinical Research Phase\":\n        description: >-\n          Clinical Research Phase. Clinical research involves trials of the drug on people,\n          and it is one of the most involved stages in the drug development and approval process.\n          Clinical trials must answer specific questions and follow a protocol determined by\n          the drug researcher or manufacturer.\n      \"FDA Review Phase 4\":\n        description: >-\n          FDA Review\n      \"FDA Post-Market Safety Monitoring\":\n        description: >-\n          FDA Post-Market Safety Monitoring.  The last phase of drug approval is an ongoing one\n          while the drug is on the marketplace. If a developer wants to change anything about the\n          drug formulation or approve it for a new use, they must apply with the FDA. The FDA also\n          frequently reviews the drug’s advertising and its manufacturing facility to make sure\n          everything involved in its creation and marketing is in compliance with regulations.\n      \"FDA Clinical Research Phase 1\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and\n          lasts several months. This phase is used to determine the safety and dosage of the drug,\n          and about 70% of these drugs move on to the next clinical research phase.\n      \"FDA Clinical Research Phase 2\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people,\n          who must have the disease or condition the drug supposes to treat. This phase can last\n          from a few months to two years, and its purpose is to monitor the efficacy of the drug,\n          as well as note side effects that may occur.\n      \"FDA Clinical Research Phase 3\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers\n          and can last up to four years. It is used to continue monitoring the efficacy of\n          the drug, as well as exploring any longer-term adverse reactions.\n      \"FDA Clinical Research Phase 4\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of\n          volunteers who have the disease or condition and continues to monitor safety and efficacy.\n          If a drug passes this phase, it goes on to FDA review.\n      \"FDA Fast Track\":\n        description: >-\n          Fast track is a process designed to facilitate the development, and expedite the\n          review of drugs to treat serious conditions and fill an unmet medical need.\n          The purpose is to get important new drugs to the patient earlier. Fast Track\n          addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track\n      \"FDA Breakthrough Therapy\":\n        description: >-\n          Breakthrough Therapy designation is a process designed to expedite the\n          development and review of drugs that are intended to treat a serious\n          condition and preliminary clinical evidence indicates that the drug may\n          demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy\n      \"FDA Accelerated Approval\":\n        description: >-\n          When studying a new drug, it can sometimes take many years to learn whether a drug actually\n          provides a real effect on how a patient survives, feels, or functions. A positive therapeutic\n          effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”.\n          Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical\n          benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs\n          for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint.\n          Using a surrogate endpoint enabled the FDA to approve these drugs faster.\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval\n      \"FDA Priority Review\":\n        description: >-\n          Prior to approval, each drug marketed in the United States must go through a detailed FDA review process.\n          In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving\n          the drug review time and created a two-tiered system of review times – Standard Review and Priority\n          Review. A Priority Review designation means FDA’s goal is to take action on an application\n          within 6 months (compared to 10 months under standard review).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review\n      \"Regular FDA Approval\":\n      \"Post-Approval Withdrawal\":\n\n  FDA_IDA_adverse_event_enum:\n    description: >-\n      please consult with the FDA guidelines as proposed in this document:\n      https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32\n    permissible_values:\n      \"Life-threatening adverse event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either \n          the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. \n          It does not include an adverse event or suspected adverse reaction that, had it occurred in a more \n          severe form, might have caused death.\n      \"Serious adverse event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the \n          investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event,\n          inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity \n          or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth \n          defect. Important medical events that may not result in death, be life-threatening, or require hospitalization\n          may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or \n          subject and may require medical or surgical intervention to prevent one of the outcomes listed in this \n          definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment \n          in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient \n          hospitalization, or the development of drug dependency or drug abuse.\n      \"Suspected adverse reaction\":\n         description: >-\n           means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. \n           For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a \n           causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser \n           degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.\n      \"Unexpected adverse event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the \n          investigator brochure or is not listed at the specificity or severity that has been observed; or, if an \n          investigator brochure is not required or available, is not consistent with the risk information described \n          in the general investigational plan or elsewhere in the current application, as amended. For example, \n          under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the \n          investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral \n          thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the \n          investigator brochure listed only cerebral vascular accidents. 'Unexpected,' as used in this definition, \n          also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure\n          as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but \n          are not specifically mentioned as occurring with the particular drug under investigation.\n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_3_1_1/biolink-model.yaml",
    "content": "id: https://w3id.org/biolink/biolink-model\nname: Biolink-Model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 3.1.1\n\n\n## ------------\n##\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  AGRKB: 'https://www.alliancegenome.org/'\n  apollo: 'https://github.com/GMOD/Apollo'\n  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='\n  biolink: 'https://w3id.org/biolink/vocab/'\n  bioschemas: 'https://bioschemas.org/'\n  linkml: 'https://w3id.org/linkml/'\n  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='\n  # Placeholder: just points to GMOD Chado wiki\n  CHADO: 'http://gmod.org/wiki/Chado/'\n  # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve\n  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='\n  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'\n  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'\n  CLINVAR: 'http://identifiers.org/clinvar'\n  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'\n  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'\n  ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'\n  CPT: 'https://www.ama-assn.org/practice-management/cpt/'\n  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='\n  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='\n  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='\n  CTD: 'http://ctdbase.org/'\n  DGIdb: 'https://www.dgidb.org/interaction_types'\n  dcat: 'http://www.w3.org/ns/dcat#'\n  dct: 'http://purl.org/dc/terms/'\n  dcid: 'https://datacommons.org/browser/'\n  doi: 'https://doi.org/'\n  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'\n  DrugCentral: 'http://drugcentral.org/drugcard/'\n  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'\n  EDAM-DATA: 'http://edamontology.org/data_'\n  EDAM-FORMAT: 'http://edamontology.org/format_'\n  EDAM-OPERATION: 'http://edamontology.org/operation_'\n  EDAM-TOPIC: 'http://edamontology.org/topic_'\n  EFO: 'http://www.ebi.ac.uk/efo/EFO_'\n  ExO: 'http://purl.obolibrary.org/obo/ExO_'\n  fabio: 'http://purl.org/spar/fabio/'\n  foaf: 'http://xmlns.com/foaf/0.1/'\n  foodb.food: 'http://foodb.ca/compounds/'\n  foodb.compound: 'http://foodb.ca/foods/'\n  FYECO: 'https://www.pombase.org/term/'\n  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'  # Fission Yeast Phenotype Ontology\n  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'\n  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'\n  # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)\n  GOP: 'http://purl.obolibrary.org/obo/go#'\n  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'\n  GSID: 'https://scholar.google.com/citations?user='\n  GTEx: 'https://www.gtexportal.org/home/gene/'\n  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='\n  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'\n  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'\n  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'\n  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'\n  ICD10: 'https://icd.codes/icd9cm/'\n  ICD9: 'http://translator.ncats.nih.gov/ICD9_'\n  interpro: 'https://www.ebi.ac.uk/interpro/entry/'\n  INO: 'http://purl.obolibrary.org/obo/INO_'\n  isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international\n  isni: 'https://isni.org/isni/'\n  issn: 'https://portal.issn.org/resource/ISSN/'\n  ncats.drug: 'https://drugs.ncats.io/drug/'\n  KEGG.BRITE: 'http://www.kegg.jp/entry/'\n  KEGG.DGROUP: 'http://www.kegg.jp/entry/'\n  KEGG.ENZYME: 'http://www.kegg.jp/entry/'\n  KEGG.GENE: 'http://www.kegg.jp/entry/'\n  KEGG.PATHWAY: 'https://www.kegg.jp/entry/'\n  KEGG.RCLASS: 'http://www.kegg.jp/entry/'\n  LOINC: 'http://loinc.org/rdf/'\n  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'\n  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'\n  metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'\n  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'\n  MESH: 'http://id.nlm.nih.gov/mesh/'\n  MI: 'http://purl.obolibrary.org/obo/MI_'\n  mirbase: 'http://identifiers.org/mirbase'\n  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'\n  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'\n  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'\n  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'\n  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='\n  NCBIGene: 'http://identifiers.org/ncbigene/'\n  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'\n  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'\n  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='\n  OBAN: 'http://purl.org/oban/'\n  oboformat: 'http://www.geneontology.org/formats/oboInOwl#'\n  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'\n  ORCID: 'https://orcid.org/'\n  orphanet: 'http://www.orpha.net/ORDO/Orphanet_'\n  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'\n  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='\n  PathWhiz: 'http://smpdb.ca/pathways/#'  # See also https://smpdb.ca/pathwhiz/\n  pav: 'http://purl.org/pav/'\n  PHAROS: 'http://pharos.nih.gov'\n  PomBase: 'https://www.pombase.org/gene/'\n  prov: 'http://www.w3.org/ns/prov#'\n  qud: 'http://qudt.org/1.1/schema/qudt#'\n  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'\n  ResearchID: 'https://publons.com/researcher/'\n  RO: 'http://purl.obolibrary.org/obo/RO_'\n  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'\n  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='\n  schema: 'http://schema.org/'\n  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='\n  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'\n  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'\n  SIO: 'http://semanticscience.org/resource/SIO_'\n  SNOMEDCT: 'http://snomed.info/id/'\n  SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'\n  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'\n  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'\n  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'\n  # The UMLS Semantic types and groups namespaces don't have a directly\n  # resolvable Base URI, but we point to a pair of sensible web documents\n  STY: 'http://purl.bioontology.org/ontology/STY/'\n  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'\n  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'\n  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'\n  # The \"Variation Modelling Collaboration\" (VMC) is not (yet) a conventional namespace so we point to its Github repo\n  # See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and\n  # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/\n  VMC: 'https://github.com/ga4gh/vr-spec/'\n  WBls: 'http://purl.obolibrary.org/obo/WBBL_'\n  WBbt: 'http://purl.obolibrary.org/obo/WBBT_'\n  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'\n  WIKIDATA: 'https://www.wikidata.org/wiki/'            # Wikidata Entity\n  WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:'  # Wikidata Property - not a conventional namespace prefix\n  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'\n  XPO: 'http://purl.obolibrary.org/obo/XPO_'  # Xenopus Phenotype Ontology\n  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='\n\ndefault_prefix: biolink\ndefault_range: string\n\n# 2. The following prefix maps are retrieved from the\n#    specified contexts defined at https://prefixcommons.org/\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\n# The following 'standard' prefixes are also used.\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - OIO\n  - BIOGRID\n  - SO\n\n## ------------\n## SUBSETS\n## ------------\n\n\nsubsets:\n\n  model_organism_database:\n    description: >-\n      Subset that is relevant for a typical Model Organism Database (MOD)\n\n  translator_minimal:\n    description: >-\n      Minimum subset of translator work\n\n  samples:\n    description: >-\n      Sample/biosample datamodel\n\n  testing:\n    description: >-\n      TBD\n\n\n## ------------\n## TYPES\n## ------------\n\nimports:\n  - linkml:types\n\ntypes:\n\n  chemical formula value:\n    uri: xsd:string\n    base: str\n    description: A chemical formula\n    notes:\n      - Should be implemented as a stronger type\n\n  category type:\n    typeof: uriorcurie\n    description: >-\n      A primitive type in which the value denotes a class within the biolink model.\n      The value must be a URI or a CURIE. In a Neo4j representation, the value should\n      be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,\n      the value should be a URI such as https://w3id.org/biolink/vocab/Gene\n\n  iri type:\n    typeof: uriorcurie\n    description: >-\n      An IRI\n\n  label type:\n    typeof: string\n    description: >-\n      A string that provides a human-readable name for an entity\n\n  predicate type:\n    typeof: uriorcurie\n    description: >-\n      A CURIE from the biolink related_to hierarchy.\n      For example, biolink:related_to, biolink:causes, biolink:treats.\n\n  narrative text:\n    typeof: string\n    description: >-\n      A string that provides a human-readable description of something\n\n  symbol type:\n    typeof: string\n\n  frequency value:\n    typeof: string\n    uri: UO:0000105\n\n  percentage frequency value:\n    typeof: double\n    uri: UO:0000187\n\n  quotient:\n    aliases: [ 'ratio' ]\n    typeof: double\n    uri: UO:0010006\n\n  unit:\n    typeof: string\n    uri: UO:0000000\n    id_prefixes:\n      - UO\n    exact_mappings:\n      - qud:Unit\n\n  time type:\n    typeof: time\n\n  biological sequence:\n    typeof: string\n\n## ------------\n## SLOTS\n## ------------\n\nslots:\n\n  ## ---------------\n  ## ATTRIBUTE SLOTS\n  ## ---------------\n\n  has attribute:\n    description: >-\n      connects any entity to an attribute\n    domain: entity\n    range: attribute\n    multivalued: true\n    in_subset:\n      - samples\n    close_mappings:\n      # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'\n      - OBI:0001927\n    exact_mappings:\n      - SIO:000008\n    narrow_mappings:\n      # if 'has attribute' annotates a NamedThing as subject or\n      # object of an association, these OBAN mappings may apply\n      - OBAN:association_has_subject_property\n      - OBAN:association_has_object_property\n      - CPT:has_possibly_included_panel_element\n      - DRUGBANK:category\n      # RTX contributed terms. Could perhaps review for more semantically precise mappings?\n      - EFO:is_executed_in\n      - HANCESTRO:0301\n      - LOINC:has_action_guidance\n      - LOINC:has_adjustment\n      - LOINC:has_aggregation_view\n      - LOINC:has_approach_guidance\n      - LOINC:has_divisor\n      - LOINC:has_exam\n      - LOINC:has_method\n      - LOINC:has_modality_subtype\n      - LOINC:has_object_guidance\n      - LOINC:has_scale\n      - LOINC:has_suffix\n      - LOINC:has_time_aspect\n      - LOINC:has_time_modifier\n      - LOINC:has_timing_of\n      # disease is stage\n      - NCIT:R88\n      - NCIT:eo_disease_has_property_or_attribute\n      - NCIT:has_data_element\n      - NCIT:has_pharmaceutical_administration_method\n      - NCIT:has_pharmaceutical_basic_dose_form\n      - NCIT:has_pharmaceutical_intended_site\n      - NCIT:has_pharmaceutical_release_characteristics\n      - NCIT:has_pharmaceutical_state_of_matter\n      - NCIT:has_pharmaceutical_transformation\n      - NCIT:is_qualified_by\n      - NCIT:qualifier_applies_to\n      - NCIT:role_has_domain\n      - NCIT:role_has_range\n      - INO:0000154\n      - HANCESTRO:0308\n      - OMIM:has_inheritance_type\n      - orphanet:C016\n      - orphanet:C017\n      - RO:0000053\n      # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here\n      - RO:0000086\n      - RO:0000087\n      - SNOMED:has_access\n      - SNOMED:has_clinical_course\n      - SNOMED:has_count_of_base_of_active_ingredient\n      - SNOMED:has_dose_form_administration_method\n      - SNOMED:has_dose_form_release_characteristic\n      - SNOMED:has_dose_form_transformation\n      - SNOMED:has_finding_context\n      - SNOMED:has_finding_informer\n      - SNOMED:has_inherent_attribute\n      - SNOMED:has_intent\n      - SNOMED:has_interpretation\n      - SNOMED:has_laterality\n      - SNOMED:has_measurement_method\n      - SNOMED:has_method\n      - SNOMED:has_priority\n      - SNOMED:has_procedure_context\n      - SNOMED:has_process_duration\n      - SNOMED:has_property\n      - SNOMED:has_revision_status\n      - SNOMED:has_scale_type\n      - SNOMED:has_severity\n      - SNOMED:has_specimen\n      - SNOMED:has_state_of_matter\n      - SNOMED:has_subject_relationship_context\n      - SNOMED:has_surgical_approach\n      - SNOMED:has_technique\n      - SNOMED:has_temporal_context\n      - SNOMED:has_time_aspect\n      - SNOMED:has_units\n      - UMLS:has_structural_class\n      - UMLS:has_supported_concept_property\n      - UMLS:has_supported_concept_relationship\n      - UMLS:may_be_qualified_by\n\n  has attribute type:\n    description: >-\n      connects an attribute to a class that describes it\n    domain: attribute\n    range: ontology class\n    multivalued: false\n    required: true\n    in_subset:\n      - samples\n    narrow_mappings:\n      - LOINC:has_modality_type\n      - LOINC:has_view_type\n\n  # TRAPI Attribute schema alignment:\n  # value: NamedThing.name\n  # value_type: NamedThing.category\n  # value_type_name: quantity_value.NamedThing.name\n  has qualitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: named thing\n    multivalued: false\n    in_subset:\n      - samples\n\n  # TRAPI Attribute schema alignment:\n  # value: quantity_value.has_numeric_value[double] - may be a vector?\n  # value_type: quantity_value.has_unit.unit.uri\n  # value_type_name: quantity_value.has_unit.unit.name[string]\n  has quantitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: quantity value\n    multivalued: true\n    exact_mappings:\n      - qud:quantityValue\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_numerator_value\n      - SNOMED:has_presentation_strength_denominator_value\n      - SNOMED:has_presentation_strength_numerator_value\n    in_subset:\n      - samples\n\n  has numeric value:\n    description: >-\n      connects a quantity value to a number\n    domain: quantity value\n    range: double\n    multivalued: false\n    exact_mappings:\n      - qud:quantityValue\n    in_subset:\n      - samples\n\n  has unit:\n    description: >-\n      connects a quantity value to a unit\n    domain: quantity value\n    range: unit\n    multivalued: false\n    close_mappings:\n      # These RTX contributed terms mean \"is unit of\" which is the semantic inverse of this biolink:has_unit term\n      - EFO:0001697\n      - UO-PROPERTY:is_unit_of\n    exact_mappings:\n      - qud:unit\n      - IAO:0000039\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_denominator_unit\n      - SNOMED:has_concentration_strength_numerator_unit\n      - SNOMED:has_presentation_strength_denominator_unit\n      - SNOMED:has_presentation_strength_numerator_unit\n      - SNOMED:has_unit_of_presentation\n    in_subset:\n      - samples\n\n  base coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'one-based', 'fully-closed' ]\n    description: >-\n      A position in the base coordinate system.  Base coordinates start at position 1 instead of position 0.\n    range: integer\n\n  ## --------------------\n  ## NODE PROPERTY SLOTS\n  ## --------------------\n\n  node property:\n    description: >-\n      A grouping for any property that holds between a node and a value\n    domain: named thing\n\n  id:\n    identifier: true\n    description: >-\n      A unique identifier for an entity.\n      Must be either a CURIE shorthand for a URI or a complete URI\n    in_subset:\n      - translator_minimal\n    required: true\n    exact_mappings:\n      - AGRKB:primaryId\n      - gff3:ID\n      - gpi:DB_Object_ID\n\n  iri:\n    description: >-\n      An IRI for an entity. This is determined by the id using expansion rules.\n    range: iri type\n    in_subset:\n      - translator_minimal\n      - samples\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P854\n\n  type:\n    slot_uri: rdf:type\n    exact_mappings:\n      - AGRKB:soTermId\n      - gff3:type\n      - gpi:DB_Object_Type\n\n  category:\n    is_a: type\n    domain: entity\n    range: category type\n    designates_type: true\n    description: >-\n      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the\n      biolink entity type class.\n       * In a neo4j database this MAY correspond to the neo4j label tag.\n       * In an RDF database it should be a biolink model class URI.\n      This field is multi-valued. It should include values for ancestors of the biolink class; for example,\n      a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\n\n      In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink\n      class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`\n      may have a rdf:type assertion to a SO class such as TF_binding_site,\n      which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,\n      biolink:MolecularEntity, biolink:NamedThing}\n    is_class_field: true\n    multivalued: true\n    in_subset:\n      - translator_minimal\n\n  name:\n    aliases: [ 'label', 'display name', 'title' ]\n    description: >-\n      A human-readable name for an attribute or entity.\n    range: label type\n    in_subset:\n      - translator_minimal\n      - samples\n    #\n    # linkML doesn't like this name slot to be \"required: true\".\n    # Besides, some entity nodes/attributes may not have names?\n    # required: true\n    slot_uri: rdfs:label\n    exact_mappings:\n      - gff3:Name\n      - gpi:DB_Object_Name\n    narrow_mappings:\n      - dct:title\n      - WIKIDATA_PROPERTY:P1476\n\n  stoichiometry:\n    description: >-\n      the relationship between the relative quantities of substances taking part in a reaction or\n      forming a compound, typically a ratio of whole integers.\n    is_a: association slot\n    range: integer\n\n  reaction direction:\n    description: >-\n      the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)\n    is_a: association slot\n    range: ReactionDirectionEnum\n    narrow_mappings:\n      - NCIT:C42677\n\n  reaction balanced:\n    is_a: association slot\n    range: boolean\n\n  reaction side:\n    description: >-\n      the side of a reaction being modeled (ie: left or right)\n    is_a: association slot\n    range: ReactionSideEnum\n\n  symbol:\n    is_a: node property\n    domain: named thing\n    description: >-\n      Symbol for a particular thing\n    exact_mappings:\n      - AGRKB:symbol\n      - gpi:DB_Object_Symbol\n\n  synonym:\n    is_a: node property\n    aliases: [ 'alias' ]\n    domain: named thing\n    range: label type\n    description: >-\n      Alternate human-readable names for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      # there is an interesting debate here: are these terms \"narrower\" a.k.a. more specialized instances of\n      # 'biolink:synonym' or should they be binned into their respective namesake class of mappings?\n      # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.\n      - skos:altLabel\n      - gff3:Alias\n      - AGRKB:synonyms\n      - gpi:DB_Object_Synonyms\n      # TODO: RTX contributed terms mapped here... May need review?\n      - HANCESTRO:0330\n      - IAO:0000136\n      - RXNORM:has_tradename\n\n  exact synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasExactSynonym\n\n  broad synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasBroadSynonym\n\n  narrow synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasNarrowSynonym\n\n  related synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasRelatedSynonym\n\n  has topic:\n    aliases: [ 'topic', 'descriptors' ]\n    is_a: node property\n    range: ontology class\n    exact_mappings:\n      - foaf:topic\n    description: >-\n      Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.\n      See https://github.com/biolink/biolink-model/issues/238\n\n  xref:\n    is_a: node property\n    aliases: [ 'dbxref', 'Dbxref', 'DbXref' ]\n    domain: named thing\n    range: uriorcurie\n    description: >-\n      Alternate CURIEs for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - gff3:Dbxref\n      - gpi:DB_Xrefs\n\n  full name:\n    is_a: node property\n    domain: named thing\n    range: label type\n    description: >-\n      a long-form human readable name for a thing\n\n  description:\n    aliases: [ 'definition' ]\n    range: narrative text\n    description: >-\n      a human-readable description of an entity\n    in_subset:\n      - translator_minimal\n    slot_uri: dct:description\n    exact_mappings:\n      - IAO:0000115\n      - skos:definitions\n    narrow_mappings:\n      - gff3:Description\n\n  systematic synonym:\n    is_a: node property\n    domain: named thing\n    range: label type\n    multivalued: true\n    slot_uri: GOP:systematic_synonym\n    description: >-\n      more commonly used for gene symbols in yeast\n\n  affiliation:\n    is_a: node property\n    description: >-\n      a professional relationship between one provider (often a person) within another provider (often an organization).\n      Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.\n    domain: agent\n    range: uriorcurie\n    multivalued: true\n\n  address:\n    is_a: node property\n    description: >-\n      the particulars of the place where someone or an organization is situated.  For now, this slot is a\n      simple text \"blob\" containing all relevant details of the given location for fitness of purpose.\n      For the moment, this \"address\" can include other contact details such as email and phone number(?).\n\n  ## Space\n\n  latitude:\n    is_a: node property\n    range: float\n    description: >-\n      latitude\n    exact_mappings:\n      - wgs:lat\n\n  longitude:\n    is_a: node property\n    range: float\n    description: >-\n      longitude\n    exact_mappings:\n      - wgs:long\n\n  ## Time\n\n  timepoint:\n    aliases: [ 'duration' ]\n    range: time type\n    description: >-\n      a point in time\n\n  creation date:\n    is_a: node property\n    aliases: [ 'publication date' ]\n    range: date\n    description: >-\n      date on which an entity was created. This can be applied to nodes or edges\n    exact_mappings:\n      - dct:createdOn\n      - WIKIDATA_PROPERTY:P577\n\n  update date:\n    is_a: node property\n    range: date\n    description: >-\n      date on which an entity was updated. This can be applied to nodes or edges\n\n  ## Statistics\n\n  aggregate statistic:\n    is_a: node property\n    abstract: true\n\n  has count:\n    description: >-\n      number of things with a particular property\n    is_a: aggregate statistic\n    range: integer\n    exact_mappings:\n      - LOINC:has_count\n\n  has total:\n    description: >-\n      total number of things in a particular reference set\n    is_a: aggregate statistic\n    range: integer\n\n  has quotient:\n    is_a: aggregate statistic\n    range: double\n\n  has percentage:\n    description: >-\n      equivalent to has quotient multiplied by 100\n    is_a: aggregate statistic\n    range: double\n\n  ## Properties for Information Content Entity and Publication Nodes\n\n  has taxonomic rank:\n    is_a: node property\n    range: taxonomic rank\n    multivalued: false\n    mappings:\n      - WIKIDATA:P105\n\n  has dataset:\n    is_a: node property\n    domain: dataset version\n    range: dataset\n    slot_uri: dct:source\n\n  source web page:\n    is_a: node property\n    domain: dataset summary\n    broad_mappings:\n      - dct:source\n\n  source logo:\n    is_a: node property\n    domain: dataset summary\n    slot_uri: schema:logo\n\n  retrieved on:\n    is_a: node property\n    domain: dataset\n    range: date\n    exact_mappings:\n      - pav:retrievedOn\n\n  version of:\n    is_a: node property\n    domain: dataset version\n    range: dataset summary\n    exact_mappings:\n      - dct:isVersionOf\n\n  version:\n    is_a: node property\n    domain: dataset\n    broad_mappings:\n      - pav:version\n      - owl:versionInfo\n\n  license:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:license\n    narrow_mappings:\n      - WIKIDATA_PROPERTY:P275\n\n  rights:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:rights\n\n  format:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:format\n      - WIKIDATA_PROPERTY:P2701\n\n  created with:\n    is_a: node property\n    domain: dataset\n    exact_mappings:\n      - pav:createdWith\n\n  download url:\n    is_a: node property\n    domain: information content entity\n    slot_uri: dcat:downloadURL\n\n  dataset download url:\n    is_a: node property\n    domain: dataset\n    slot_uri: dcat:downloadURL\n\n  distribution download url:\n    is_a: node property\n    domain: dataset distribution\n    exact_mappings:\n      - dcat:downloadURL\n\n  ingest date:\n    is_a: node property\n    domain: dataset version\n    slot_uri: pav:version\n\n  has distribution:\n    is_a: node property\n    domain: dataset version\n    range: dataset distribution\n    slot_uri: dct:distribution\n\n  published in:\n    is_a: node property\n    description: >-\n      CURIE identifier of a broader publication context within which the publication may be placed,\n      e.g. a specified book or journal.\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - NLMID\n      - issn\n      - isbn\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1433\n\n  iso abbreviation:\n    is_a: node property\n    description: >-\n      Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system\n      See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,\n      then the iso abbreviation pertains to the broader publication context (the journal) within which the given\n      publication node is embedded, not the publication itself.\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1160\n\n  authors:\n    is_a: node property\n    singular_name: author\n    description: >-\n      connects an publication to the list of authors who contributed to the publication.\n      This property should be a comma-delimited list of author names. It is recommended that an author's name\n      be formatted as \"surname, firstname initial.\".   Note that this property is a node annotation expressing\n      the citation list of authorship which might typically otherwise be more completely documented in\n      biolink:PublicationToProviderAssociation defined edges which point to full details about an author\n      and possibly, some qualifiers which clarify the specific status of a given author in the publication.\n    multivalued: true\n    domain: publication\n\n  volume:\n    is_a: node property\n    description: >-\n      volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P478\n\n  chapter:\n    is_a: node property\n    description: >-\n      chapter of a book\n    domain: book chapter\n    exact_mappings:\n      - WIKIDATA:Q1980247\n\n  issue:\n    is_a: node property\n    description: >-\n      issue of a newspaper, a scientific journal or magazine for reference purpose\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P433\n\n  pages:\n    is_a: node property\n    description: >-\n      page number of source referenced for statement or publication\n    domain: publication\n    multivalued: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P304\n\n  summary:\n    is_a: node property\n    # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot,\n    # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract'\n    aliases: [ 'abstract' ]\n    description: >-\n      executive  summary of a publication\n    domain: publication\n    exact_mappings:\n      - dct:abstract\n      - WIKIDATA:Q333291\n\n  keywords:\n    is_a: node property\n    description: >-\n      keywords tagging a publication\n    domain: publication\n    multivalued: true\n\n  mesh terms:\n    is_a: node property\n    description: >-\n      mesh terms tagging a publication\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - MESH\n    multivalued: true\n    exact_mappings:\n      - dcid:MeSHTerm\n\n  ## Biology\n\n  has biological sequence:\n    is_a: node property\n    description: >-\n      connects a genomic feature to its sequence\n    range: biological sequence\n\n  has gene or gene product:\n    is_a: node property\n    description: >-\n      connects an entity with one or more gene or gene products\n    range: gene\n    multivalued: true\n\n  has gene:\n    is_a: has gene or gene product\n    description: >-\n      connects an entity associated with one or more genes\n    range: gene\n    multivalued: true\n\n  has zygosity:\n    is_a: node property\n    domain: nucleic acid entity\n    range: zygosity\n\n  ## Chemistry, drugs and food\n\n  has chemical formula:\n    is_a: node property\n    range: chemical formula value\n    description: >-\n      description of chemical compound based on element symbols\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P274\n\n  is metabolite:\n    is_a: node property\n    domain: molecular entity\n    range: boolean\n    description: >-\n      indicates whether a molecular entity is a metabolite\n    exact_mappings:\n      - CHEBI:25212\n\n  has constituent:\n    description: >-\n      one or more molecular entities within a chemical mixture\n    is_a: node property\n    range: molecular entity\n    multivalued: true\n\n  has drug:\n    is_a: node property\n    description: >-\n      connects an entity to one or more drugs\n    range: drug\n    multivalued: true\n\n  has device:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) devices\n    range: device\n    multivalued: true\n\n  has procedure:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) procedures\n    range: procedure\n    multivalued: true\n\n  ## Clinical exposures\n\n  has receptor:\n    is_a: node property\n    domain: exposure event\n    range: organismal entity\n    description: >-\n      the organism or organism part being exposed\n    exact_mappings:\n      - ExO:0000001\n\n  has stressor:\n    is_a: node property\n    domain: exposure event\n    aliases: [ 'has stimulus' ]\n    description: >-\n      the process or entity that the receptor is being exposed to\n    exact_mappings:\n      - ExO:0000000\n\n  has route:\n    is_a: node property\n    domain: exposure event\n    description: >-\n      the process that results in the stressor coming into direct contact with the receptor\n    exact_mappings:\n      - ExO:0000055\n    narrow_mappings:\n      - LOINC:has_pharmaceutical_route\n      - SNOMED:has_dose_form_intended_site\n      - SNOMED:has_route_of_administration\n\n\n  population context qualifier:\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: association slot\n    range: population of individual organisms\n\n  temporal context qualifier:\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n      for time intervales, use temporal interval qualifier.\n    is_a: association slot\n    range: time type\n\n  temporal interval qualifier:\n    is_a: temporal context qualifier\n    description: >-\n      a constraint of a time interval placed upon the truth value of an\n      association.\n\n  is supplement:\n    description: >-\n    is_a: node property\n    range: chemical mixture\n\n  trade name:\n    description: >-\n    is_a: node property\n    range: chemical entity\n\n  available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: DrugAvailabilityEnum\n\n  is toxic:\n    description: >-\n    is_a: node property\n    multivalued: false\n    range: boolean\n\n  has chemical role:\n    is_a: node property\n    description: >-\n      A role is particular behaviour which a chemical entity may exhibit.\n    range: chemical role\n    multivalued: true\n\n  max tolerated dose:\n    description: >-\n      The highest dose of a drug or treatment that does not cause unacceptable side effects.\n      The maximum tolerated dose is determined in clinical trials by testing increasing doses\n      on different groups of people until the highest dose with acceptable side effects is\n      found. Also called MTD.\n    is_a: node property\n    multivalued: false\n    range: string\n\n  animal model available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: disease or phenotypic feature\n\n  FDA adverse event level:\n    description: >-\n    is_a: association slot\n    range: FDAIDAAdverseEventEnum\n\n  highest FDA approval status:\n    description: >-\n      Should be the highest level of FDA approval this chemical entity or device has, regardless of which\n      disease, condition or phenotype it is currently being reviewed to treat.  For specific levels of FDA\n      approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'\n\n  drug regulatory status world wide:\n    aliases: [ 'max phase' ]\n    description: >-\n      An agglomeration of drug regulatory status worldwide. Not specific to FDA.\n    exact_mappings:\n      - NCIT:C172573\n    narrow_mappings:\n      - NCIT:R172\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n\n  routes of delivery:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    multivalued: true\n    range: DrugDeliveryEnum\n\n  ## -------------------\n  ## QUALIFIERS\n  ## -------------------\n\n  form or variant qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.\n    examples:\n      - value: mutation\n      - value: late stage\n      - value: severe\n      - value: transplant\n      - value: chemical analong\n    notes: >-\n      please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier'\n      terms in the gene->chemical association space. \n      the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’.\n      the qualifier ‘Late Stage’ combines with a core concept of ‘Disease X’ to express the  more specific concept ‘Late Stage forms of Disease X’\n      the qualifier ‘Severe’ combines with a core concept of ‘Bleeding’ to express the  more specific concept ‘Severe forms of Bleeding’\n      the qualifier ‘Liver’ combines with a core concept of ‘Surgical Transplant’ to express the composed concept ‘Liver Transplant’\n      the qualifier ‘Recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’\n      the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’\n\n\n  aspect qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.  The purpose of the aspect slot is to indicate what aspect is being affected in an \n      'affects' association.\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    notes: >-\n      for good examples of aspects in the gene-> chemical space, please see the \n      GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify \n      the gene making the full subject a different ontological type.  \n      the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process)\n      the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process)\n      the qualifier ‘Activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity)\n      the qualifier ‘Emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event)\n      the qualifier ‘Infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process)\n      the qualifier ‘Severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality)\n      the qualifier ‘Abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)\n\n  derivative qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.\n    examples:\n      - value: metabolite\n\n  part qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).\n    examples:\n      - value: polyA tail\n      - value: upstream control region\n\n  context qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.\n    examples:\n      - value: cohort x\n      - value: blood\n      - value: gut microbiome\n    notes: >-\n      the context qualifier ‘hippocampus’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in \n      the hippocampus’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity\n\n\n  direction qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n    notes: >-\n      the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’   \n      the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’\n\n  mapped predicate:\n    description: >-\n      The predicate that is being replaced by the fully qualified representation of predicate + subject and object \n      qualifiers.  Only to be used in test data and mapping data to help with the transition to the fully qualified\n      predicate model. Not to be used in knowledge graphs.\n\n  predicate mappings:\n    description: >- \n      A collection of relationships that are not used in biolink, but have biolink patterns that can \n      be used to replace them.  This is a temporary slot to help with the transition to the fully qualified predicate\n      model in Biolink3.\n    multivalued: true\n    range: predicate mapping\n    inlined_as_list: true\n\n  exact matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      an identical meaning. Such terms often describe the same concept from\n      different ontological perspectives.\n    multivalued: true\n\n  narrow matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a narrower meaning. Such terms often describe a more specific concept\n      from different ontological perspectives.\n    multivalued: true\n\n  broad matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a broader meaning. Such terms often describe a more general concept\n      from different ontological perspectives.\n    multivalued: true\n\n  subject aspect qualifier:\n    is_a: aspect qualifier\n\n  subject form or variant qualifier:\n    is_a: form or variant qualifier\n\n  subject part qualifier:\n    is_a: part qualifier\n\n  subject derivative qualifier:\n    is_a: derivative qualifier\n\n  subject context qualifier:\n    is_a: context qualifier\n\n  subject direction qualifier:\n    is_a: direction qualifier\n\n  object aspect qualifier:\n    is_a: aspect qualifier\n\n  object form or variant qualifier:\n    is_a: form or variant qualifier\n\n  object part qualifier:\n    is_a: part qualifier\n\n  object derivative qualifier:\n    is_a: derivative qualifier\n\n  object context qualifier:\n    is_a: context qualifier\n\n  object direction qualifier:\n    is_a: direction qualifier\n    range: DirectionQualifierEnum\n\n  qualified predicate:\n    is_a: association slot\n    description: >-\n      Predicate to be used in an association when subject and object qualifiers are present and the full\n      reading of the statement requires a qualification to the predicate in use in order to refine or \n      increase the specificity of the full statement reading.  This qualifier holds a relationship to be used instead of that \n      expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based \n      semantics are included.  This is necessary only in cases where the primary predicate does not work in a \n      full statement reading.\n    notes: >-\n      to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read \n      using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using \n      the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, \n      object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but doesnt make \n      sense in the full statement reading  (because “Chemical X affects increased expression of Gene Y'' is not \n      what we mean to say here: it causes increased expression of Gene Y)\n\n\n  statement qualifier:\n    is_a: association slot\n    description: >-\n\n  causal mechanism qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a type of molecular control mechanism through which an\n      effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition',\n      'allosteric modulation', 'channel blocker')\n\n  anatomical context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing an anatomical location where an relationship expressed in an\n      association took place (can be a tissue, cell type, or subcellular location).\n    range: AnatomicalContextQualifierEnum\n    notes: >-\n      Anatomical context values can be any term from UBERON. See AnatomicalContextQualifierEnum for more\n      details.\n\n  species context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a taxonomic category of species in which a relationship\n      expressed in an association took place.\n    range: organism taxon\n\n  qualifiers:\n    singular_name: qualifier\n    description: >-\n      connects an association to qualifiers that modify or\n      qualify the meaning of that association\n    local_names:\n      ga4gh: annotation qualifier\n    is_a: association slot\n    multivalued: true\n    range: ontology class\n\n  frequency qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\n    is_a: association slot\n    range: frequency value\n\n  severity qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      how severe the phenotype is in the subject\n    is_a: association slot\n    range: severity value\n\n  sex qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state whether\n      the association is specific to a particular sex.\n    is_a: association slot\n    range: biological sex\n\n  onset qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      when the phenotype appears is in the subject\n    is_a: association slot\n    range: onset\n\n  clinical modifier qualifier:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    is_a: association slot\n    range: clinical modifier\n\n  sequence variant qualifier:\n    description: >-\n      a qualifier used in an association with the variant\n    is_a: association slot\n    range: sequence variant\n\n  quantifier qualifier:\n    is_a: association slot\n    range: ontology class\n    description: >-\n      A measurable quantity for the object of the association\n    narrow_mappings:\n      # TODO: RTX contributed terms mapped here... May need review?\n      - LOINC:analyzes\n      - LOINC:measured_by\n      - LOINC:property_of\n      - SEMMEDDB:MEASURES\n      - UMLS:measures\n\n  catalyst qualifier:\n    is_a: association slot\n    multivalued: true\n    range: macromolecular machine mixin\n    description: >-\n      a qualifier that connects an association between two causally connected\n      entities (for example, two chemical entities, or a chemical entity in\n      that changes location) and the gene product, gene, or complex that\n      enables or catalyzes the change.\n\n  stage qualifier:\n    description: >-\n      stage during which gene or protein expression of takes place.\n    is_a: association slot\n    range: life stage\n    # path: \"object/during\"\n    examples:\n      - value: UBERON:0000069\n        description: larval stage\n\n  ## --------------------\n  ## PREDICATES/RELATIONS\n  ## --------------------\n\n  related to:\n    description: >-\n      A relationship that is asserted between two named things\n    domain: named thing\n    range: named thing\n    multivalued: true\n    inherited: true\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:relatedMatch\n      - UMLS:related_to\n    broad_mappings:\n      - owl:topObjectProperty\n    narrow_mappings:\n      - SEMMEDDB:ASSOCIATED_WITH\n      - SEMMEDDB:compared_with\n      - SEMMEDDB:higher_than\n      - SEMMEDDB:lower_than\n      - BFO:0000054\n      - UBERON_CORE:protects\n      - GOREL:0002005\n      - GOREL:0012006\n      # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms\n      - BTO:related_to\n      - CHEBI:is_conjugate_acid_of\n      - CHEBI:is_conjugate_base_of\n      - CPT:has_add_on_code\n      - CPT:mapped_to\n      - EFO:0006351\n      - FMA:connected_to\n      - FMA:continuous_with\n      - FMA:homonym_of\n      - FMA:related_developmental_entity_of\n      - RO:0002093\n      - RO:0002092\n      - RO:0002084\n      - HCPCS:mapped_to\n      # RTX contributed terms, perhaps belong somewhere else with more precise semantics?\n      - HMDB:disease\n      - HMDB:has_protein_association\n      - IAO:0000136\n      - LOINC:has_answer\n      - LOINC:has_challenge\n      - LOINC:has_evaluation\n      - LOINC:mapped_to\n      - LOINC:mth_has_expanded_form\n      - MESH:RO\n      - MESH:has_mapping_qualifier\n      - MESH:mapped_to\n      - MONDO:disease_shares_features_of\n      - NCIT:disease_may_have_associated_disease\n      - NCIT:human_disease_maps_to_eo_disease\n      - NCIT:is_abnormal_cell_of_disease\n      - NCIT:is_related_to_endogenous_product\n      - UBERON_NONAMESPACE:connected_to\n      - UBERON_NONAMESPACE:innervated_by\n      - NBO-PROPERTY:is_about\n      - RO:0000053 # bearer_of\n      - PATO:reciprocal_of\n      - RO:0000052\n      - RO:0002001\n      - RO:0002002\n      - RO:0002003\n      - RO:0002008\n      - RO:0002134\n      - RO:0002150\n      - RO:0002159\n      - RO:0002176\n      - RO:0002177\n      - RO:0002178\n      - RO:0002179\n      - RO:0002314\n      - RO:0002322\n      # functionally related to\n      - RO:0002328\n      - RO:0002332\n      - RO:0002338\n      - RO:0002339\n      - RO:0002341\n      - RO:0002342\n      - RO:0002344\n      - RO:0002348\n      - RO:0002349\n      - RO:0002356\n      - RO:0002371\n      - RO:0002372\n      - RO:0002373\n      - RO:0002374\n      - RO:0002385\n      - RO:0002387\n      - RO:0002451\n      - RO:0002494\n      - RO:0002495\n      - RO:0002568\n      - RO:0002573\n      - RO:0004026\n      - RO:0004027\n      - RO:0009001\n      - RO:0009004\n      - RXNORM:has_form\n      - RXNORM:reformulated_to\n      - SNOMED:has_associated_morphology\n      - SNOMED:has_associated_procedure\n      - SNOMED:has_direct_morphology\n      - SNOMED:has_disposition\n      - SNOMED:has_indirect_morphology\n      - SNOMED:has_modification\n      - SNOMED:has_procedure_morphology\n      - SNOMED:has_specimen_source_morphology\n      - SNOMED:inheres_in\n      - SNOMED:is_interpreted_by\n      - SNOMED:relative_to_part_of\n      - UBERON:synapsed_by\n      - UMLS:RO\n      - UMLS:RQ\n      - UMLS:class_code_classified_by\n      - UMLS:exhibited_by\n      - UMLS:has_context_binding\n      - UMLS:has_form\n      - UMLS:has_mapping_qualifier\n      - UMLS:larger_than\n      - UMLS:mapped_to\n      - UMLS:owning_section_of\n\n  related to at concept level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between terminology components that describe the conceptual model of a domain.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  related to at instance level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between two instances of a data classes.  Much like an assertion component,\n      in an ABox, these represent facts associated with the conceptual model.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  associated with:\n    is_a: related to at instance level\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent,\n      'related to'. This relationship holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated.  E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial \n      Infarction (MI)” asserts that having Afib is not statistically independent from whether a patient \n      will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to \n      the statistical variables, or represent related entities for which the variables serve as proxies in an \n      Association (e.g. diseases, chemical entities or processes).\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    domain: named thing\n    range: named thing\n    narrow_mappings:\n      - RO:0004029\n      - SNOMEDCT:47429007\n\n  superclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a super class of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q66088480\n      - CHEMBL.MECHANISM:superset_of\n      - GO:inverse_isa\n      - MESH:inverse_isa\n      - RXNORM:inverse_isa\n      - VANDF:inverse_isa\n    narrow_mappings:\n      - NCIT:cdrh_parent_of\n      - NCIT:ctcae_5_parent_of\n      - NCIT:subset_includes_concept\n      - OMIM:has_manifestation\n      - SNOMED:has_basic_dose_form\n      - UMLS:RB\n\n  subclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a specialization of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX\n      - LOINC:class_of\n      - LOINC:has_class\n    exact_mappings:\n      - rdfs:subClassOf\n      - SEMMEDDB:ISA\n      - WIKIDATA_PROPERTY:P279\n      - CHEMBL.MECHANISM:subset_of\n      - GO:isa\n      - MESH:isa\n      - RXNORM:isa\n      - VANDF:isa\n    narrow_mappings:\n      - CHEBI:has_parent_hydride\n      - LOINC:has_archetype\n      - LOINC:has_parent_group\n      - LOINC:is_presence_guidance_for\n      - NCIT:gene_product_has_chemical_classification\n      # RTX mapped terms classes for biomarkers\n      - NCIT:R36\n      - NCIT:R42\n      - NCIT:A16\n      - NCIT:A11\n      - NCIT:A14\n      - NCIT:A3\n      - NDDF:has_dose_form\n      - RXNORM:has_dose_form\n      - RXNORM:has_doseformgroup\n      - SNOMED:entire_anatomy_structure_of\n      - SNOMED:has_dose_form\n      # RTX mapping\n      - rdfs:subPropertyOf\n\n  same as:\n    is_a: exact match\n    description: >-\n      holds between two entities that are considered equivalent to each other\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # identical class extension with identical sets of individuals\n      - owl:equivalentClass\n    exact_mappings:\n      # identical individual, or identical class concept/meaning\n      - owl:sameAs\n      - skos:exactMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      # RTX suggests mapping this to proposed new \"biolink:close_match\" predicate instead\n      #- SEMMEDDB:same_as\n      - WIKIDATA_PROPERTY:P2888\n      - CHEMBL.MECHANISM:equivalent_to\n      - MONDO:equivalentTo\n    narrow_mappings:\n      - DRUGBANK:external-identifier\n\n  close match:\n    is_a: related to at concept level\n    description: >-\n      a list of terms from different schemas or terminology systems that have\n      a semantically similar but not strictly equivalent, broader, or narrower\n      meaning. Such terms often describe the same general concept from\n      different ontological perspectives (e.g. drug as a type of chemical\n      entity versus drug as a type of role borne by a chemical entity).\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:closeMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      - SEMMEDDB:same_as\n    narrow_mappings:\n      - CHEBI:is_enantiomer_of\n      - CHEBI:is_tautomer_of\n      - MEDDRA:classified_as\n      - OIO:hasDbXref\n      - oboformat:xref\n      - RXNORM:has_quantified_form\n      - UMLS:SY\n\n  exact match:\n    is_a: close match\n    description: >-\n      holds between two entities that have strictly equivalent\n      meanings, with a high degree of confidence\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:exactMatch\n      - WIKIDATA:Q39893449\n      - WIKIDATA:P2888\n\n  broad match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a broader, more general meaning. Broader terms are\n      typically shown as parents in a hierarchy or tree.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: narrow match\n    exact_mappings:\n      - skos:broadMatch\n      - WIKIDATA:Q39894595\n\n  narrow match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a narrower, more specific meaning. Narrower terms are\n      typically shown as children in a hierarchy or tree.\n    is_a: related to at concept level\n    inverse: broad match\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - skos:narrowMatch\n      - WIKIDATA:Q39893967\n    annotations:\n      opposite_of: broad match\n\n  member of:\n    description: >-\n      Defines a mereological relation between a item and a collection.\n    is_a: related to at concept level\n    inverse: has member\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002350\n    close_mappings:\n      - skos:member\n\n  has member:\n    description: >-\n      Defines a mereological relation between a collection and an item.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002351\n      - skos:member\n\n  opposite of:\n    description: >-\n      x is the opposite of y if there exists some distance metric M, and there exists\n      no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002604\n    see_also:\n      - https://doi.org/10.1101/108977\n      - https://github.com/biolink/biolink-model/issues/657\n\n\n  associated with likelihood of:\n    is_a: associated with\n    description: >-\n      A a relationship that holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated, wherein the state or value of one variable predicts the future state \n      or value of the other.  E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated \n      with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib \n      is associated with an increased or decreased likelihood that a patient will later exhibit MI.\n    annotations:\n      canonical_predicate: true\n\n  likelihood associated with:\n    is_a: associated with\n    description: >-\n    inverse: associated with likelihood of\n\n  associated with increased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is more probable.\n    annotations:\n      canonical_predicate: true\n\n  increased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with increased likelihood of\n\n  associated with decreased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is less probable.\n    annotations:\n      canonical_predicate: true\n\n  decreased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with decreased likelihood of\n\n  target for:\n    is_a: related to at instance level\n    description: >-\n      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene\n      product could have a therapeutic effect\n    annotations:\n      canonical_predicate: true\n    domain: gene\n    range: disease\n\n  has target:\n    is_a: related to at instance level\n    inverse: target for\n    domain: disease\n    range: gene\n\n  active in:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: cellular component\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002432\n\n  has active component:\n    is_a: related to at instance level\n    inverse: active in\n    domain: cellular component\n    range: gene or gene product\n\n  acts upstream of:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002263\n\n  has upstream actor:\n    is_a: related to at instance level\n    inverse: acts upstream of\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004034\n\n  has positive upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004035\n\n  has negative upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of negative effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002264\n\n  has upstream or within actor:\n    is_a: has upstream actor\n    inverse: acts upstream of or within\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004032\n\n  has positive upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004033\n\n  has negative upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within negative effect\n    domain: biological process\n    range: gene or gene product\n\n    ## Publication related predicates\n  mentions:\n    description: >-\n      refers to is a relation between one information content entity and the named thing\n      that it makes reference to.\n    is_a: related to at instance level\n    exact_mappings:\n      - IAO:0000142\n    narrow_mappings:\n      - SIO:000628\n\n  mentioned by:\n    description: >-\n      refers to is a relation between one named thing and the information content entity\n      that it makes reference to.\n    is_a: related to at instance level\n    inverse: mentions\n\n  ## Publication related predicates\n\n  contributor:\n    is_a: related to at instance level\n    domain: agent\n    range: information content entity\n    comments:\n      - This is a grouping for predicates relating entities to their associated contributors realizing them\n    abstract: true\n    exact_mappings:\n      - dct:contributor\n\n  has contributor:\n    inverse: contributor\n    is_a: related to at instance level\n    domain: information content entity\n    range: agent\n\n  provider:\n    is_a: contributor\n    description: >-\n      person, group, organization or project that provides a piece of information (e.g. a knowledge association).\n\n  has provider:\n    inverse: provider\n    is_a: has contributor\n    domain: information content entity\n    range: agent\n\n  publisher:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      organization or person responsible for publishing books, periodicals, podcasts, games or software.\n      Note that in the case of publications which have a containing \"published in\" node property, the publisher\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the publisher agent of the encompassing publication\n      (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).\n    exact_mappings:\n      - dct:publisher\n      - WIKIDATA_PROPERTY:P123\n\n  has publisher:\n    is_a: has contributor\n    inverse: publisher\n    domain: publication\n    range: agent\n\n  editor:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      editor of a compiled work such as a book or a periodical (newspaper or an academic journal).\n      Note that in the case of publications which have a containing \"published in\" node property, the editor\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the editorial agent of the encompassing publication\n      (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P98\n\n  has editor:\n    inverse: editor\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n  author:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      an instance of one (co-)creator primarily responsible for a written work\n    exact_mappings:\n      - dct:creator\n      - WIKIDATA_PROPERTY:P50\n\n  has author:\n    inverse: author\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n  ## end of Publication related predicates\n\n  assesses:\n    is_a: related to at instance level\n    aliases: [ 'was assayed against' ]\n    description: >-\n      The effect of a thing on a target was interrogated in some assay.\n      A relationship between some perturbing agent (usually a chemical compound) and some target entity,\n      where the affect of the perturbing agent on the target entity was interrogated in a particular assay.\n      The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type\n      of biological entity.\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n\n  is assessed by:\n    is_a: related to at instance level\n    inverse: assesses\n    domain: named thing\n    range: named thing\n\n  interacts with:\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between any two entities that directly or indirectly interact with each other\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002434\n      - SEMMEDDB:INTERACTS_WITH\n    narrow_mappings:\n      # RO terms RTX mapped to 'biolink:related_to' but which imply a chemical interaction\n      - RO:0002103\n      - RO:0002120\n      - RO:0002130\n    notes: >-\n      please use a more specific child predicate of interacts with, either physically interacts with\n      or genetically interacts with. \n\n  physically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two entities that make physical contact as part of some interaction. \n      does not imply a causal relationship.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P129\n    close_mappings:\n      - CHEMBL.MECHANISM:binding_agent\n      - CHEMBL.MECHANISM:chelating_agent\n      - CHEMBL.MECHANISM:cross-linking_agent\n      - CHEMBL.MECHANISM:oxidative_enzyme\n      - CHEMBL.MECHANISM:sequestering_agent\n      - CHEMBL.MECHANISM:substrate\n      - DRUGBANK:target\n\n    narrow_mappings:\n      # Defined more narrowly as \"substance interaction\", thus specific applies to a subclass entities\n      - DRUGBANK:drug-interaction\n      - FMA:adheres_to\n      - NCIT:A7\n      - PR:non-covalently_bound_to\n\n  directly physically interacts with:\n    is_a: physically interacts with\n    description: >-\n      A causal mechanism mediated by a direct contact between the effector and target entities (this contact may \n      be weak or strong, transient or stable).\n    symmetric: true\n    exact_mappings:\n      - RO:0002436\n    broad_mappings:\n      # Definition of this term is more generic than direct physical molecular interactions:\n      # A is connected to B iff there exists a fiat, material or temporal path between A and B.\n      - SIO:000203\n      - RO:0002578\n    narrow_mappings:\n      - PHAROS:drug_targets\n      - DRUGBANK:chelator\n      - CTD:affects_binding\n      - DGIdb:cofactor\n    annotations:\n      canonical_predicate: true\n\n  binds:\n    is_a: directly physically interacts with\n    description: >-\n      A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, \n      which form a stable physical interaction.\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - DGIdb:binder\n\n  indirectly physically interacts with:\n    is_a: physically interacts with\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  genetically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two genes whose phenotypic effects are dependent on each\n      other in some way - such that their combined phenotypic effects are the\n      result of some interaction between the activity of their gene products.\n      Examples include epistasis and synthetic lethality.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    exact_mappings:\n      - RO:0002435\n\n  affects:\n    is_a: related to at instance level\n    description: >-\n      describes an entity that has a direct affect on the state or quality\n      of another existing entity. Use of the 'affects' predicate implies that\n      the affected entity already exists, unlike predicates such as\n      'affects risk for' and 'prevents, where the outcome is something\n      that may or may not come to be.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # Contributed by RTX. Seems possible that a new predicate \"biolink:in_pathway\" could be justified?\n      - DRUGBANK:pathway\n    exact_mappings:\n      - SEMMEDDB:AFFECTS\n      - DGIdb:affects\n    narrow_mappings:\n      - SEMMEDDB:ADMINISTERED_TO\n      - CTD:prediction_hypothesis\n      - GOREL:0001006\n      - CTD:inferred\n      - UPHENO:0000001\n      - RO:0002263\n      - RO:0002264\n      - NCIT:R158\n      - NCIT:R160\n      - NCIT:R30\n      - NCIT:R150\n      - NCIT:R72\n      - NCIT:R146\n      - NCIT:R124\n      - NCIT:R173\n      - NCIT:R100\n      - NCIT:R102\n      - NCIT:R101\n      - NCIT:R113\n      - NCIT:R23\n      - NCIT:R25\n      - NCIT:gene_mapped_to_disease\n      - NCIT:R133\n      - RO:0002343\n      - RO:0002355\n      - RO:0002591\n      - RO:0002592\n      - RO:0012003\n      - SNOMED:has_pathological_process\n      - UBERGRAPH:is_increase_of # talked to Jim Balhoff, this is a valid mapping\n      - UBERGRAPH:is_decrease_of # talked to Jim Balhoff, this is a valid mapping\n\n  affected by:\n    is_a: related to at instance level\n    description: >-\n      describes an entity of which the state or quality is affected by\n      another existing entity.\n    inverse: affects\n\n  associated with sensitivity to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of sensitivity to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - PATO:0000085 # sensitivity toward\n    narrow_mappings:\n      - SNOMEDCT:418038007 # propensity to adverse reaction\n\n  sensitivity associated with:\n    is_a: associated with\n    inverse: associated with sensitivity to\n    range: named thing\n    domain: chemical entity\n\n  associated with resistance to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of resistance to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n\n  resistance associated with:\n    is_a: associated with\n    inverse: associated with resistance to\n    range: named thing\n    domain: chemical entity\n\n  diagnoses:\n    is_a: related to at instance level\n    description: >-\n      a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - NCIT:C15220 # diagnosis\n      - SIO:001331 # diagnosis\n    exact_mappings:\n      - DrugCentral:5271\n      - SEMMEDDB:DIAGNOSES\n\n  is diagnosed by:\n    is_a: related to at instance level\n    inverse: diagnoses\n    range: chemical or drug or treatment\n    domain: disease or phenotypic feature\n\n  increases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that increase the amount\n      or activity of the object.\n\n  amount or activity increased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: increases amount or activity of\n\n  decreases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that decrease the amount\n      or activity of the object.\n\n  amount or activity decreased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: decreases amount or activity of\n\n  ## role mixins for use in tagging corresponding role predicates\n\n  chemical role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a chemical context.\n    mixin: true\n    exact_mappings:\n      - CHEBI:51086\n\n  biological role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a biological context.\n    mixin: true\n    narrow_mappings:\n      - CHEBI:24432\n\n  affects response to:\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: response affected by\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_response_to\n\n  response affected by:\n    description: >-\n      holds between two chemical entities where the susceptibility of a biological entity or system\n      (e.g. an organism, cell, cellular component, macromolecular machine mixin,\n      biological or pathological process) of one is affected by the action of the other.\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases response to\n    exact_mappings:\n      - CTD:increases_response_to\n\n  response increased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases response to\n\n  decreases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases response to\n    exact_mappings:\n      - CTD:decreases_response_to\n    narrow_mappings:\n      - CTD:decreases_response_to_substance\n\n  response decreased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases response to\n\n  regulates:\n    is_a: affects\n    description: >-\n      A more specific form of affects, that implies the effect results from a biologically evolved control mechanism.\n      Gene-affects-gene relationships will (almost) always involve regulation.  Chemical-affects-gene relationships \n      may in some cases be considered regulation (if the chemical is some endogenously produced signaling molecule \n      created to execute a certain function/activity), but exogenous/environmental chemical-affects-gene relationships \n      are usually not cases of regulation.\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - RO:0002334\n    exact_mappings:\n      - RO:0002211\n    narrow_mappings:\n      # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology)\n      - WIKIDATA_PROPERTY:P128\n      - CHEMBL.MECHANISM:modulator\n      - RO:0002295\n      - RO:0002332\n      - RO:0002211\n      - RO:0002448\n      - WIKIDATA_PROPERTY:P128\n\n  regulated by:\n    is_a: affected by\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    inverse: regulates\n\n  disrupts:\n    is_a: affects\n    aliases: [ 'disease causes disruption of' ]\n    description: >-\n      describes a relationship where one entity degrades or interferes\n      with the structure, function, or occurrence of another.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: enables\n    exact_mappings:\n      - SEMMEDDB:DISRUPTS\n      - CHEMBL.MECHANISM:disrupting_agent\n    narrow_mappings:\n      - RO:0004024\n      - RO:0004025\n\n  disrupted by:\n    is_a: affected by\n    description: >-\n      describes a relationship where the structure, function, or occurrence\n      of one entity is degraded or interfered with by another.\n    inverse: disrupts\n\n  gene product of:\n    is_a: related to at instance level\n    description: >-\n      definition x has gene product of y if and only if y is a gene (SO:0000704)\n      that participates in some gene expression process (GO:0010467) where the output of thatf\n      process is either y or something that is ribosomally translated from x\n    exact_mappings:\n      - RO:0002204\n    domain: gene product mixin\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: has gene product\n    in_subset:\n      - translator_minimal\n\n  has gene product:\n    is_a: related to at instance level\n    description: >-\n      holds between a gene and a transcribed and/or\n      translated product generated from it\n    domain: gene\n    range: gene product mixin\n    inverse: gene product of\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX term tagged as inverse mapping\n      - PR:has_gene_template\n    exact_mappings:\n      - RO:0002205\n      - WIKIDATA_PROPERTY:P688\n      - NCIT:gene_encodes_gene_product\n    narrow_mappings:\n      - NCIT:R178\n\n  transcribed to:\n    is_a: related to at instance level\n    domain: gene\n    range: transcript\n    description: >-\n      inverse of transcribed from\n    inverse: transcribed from\n    exact_mappings:\n      - RO:0002511\n      - SIO:010080\n\n  transcribed from:\n    is_a: related to at instance level\n    domain: transcript\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: transcribed to\n    description: >-\n      x is transcribed from y if and only if x is synthesized from template y\n    exact_mappings:\n      - RO:0002510\n      - SIO:010081\n\n  translates to:\n    is_a: related to at instance level\n    domain: transcript\n    range: protein\n    annotations:\n      canonical_predicate: true\n    inverse: translation of\n    description: >-\n      x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome\n      reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)\n      and produces x (amino acid chain/polypeptide)\n    close_mappings:\n      - RO:0002513\n      - SIO:010082\n\n  translation of:\n    is_a: related to at instance level\n    domain: protein\n    range: transcript\n    description: >-\n      inverse of translates to\n    inverse: translates to\n    close_mappings:\n      - RO:0002512\n      - SIO:010083\n\n  homologous to:\n    is_a: similar to\n    aliases: [ 'in homology relationship with' ]\n    description: >-\n      holds between two biological entities that have common evolutionary origin\n    comments:\n      - typically used to describe homology relationships between genes or gene products\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000001\n      - SIO:010302\n    narrow_mappings:\n      # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158\n      - UBERON_CORE:sexually_homologous_to\n\n  paralogous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000011\n\n  orthologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship between entities (typically genes) that diverged after a speciation event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000017\n      - WIKIDATA_PROPERTY:P684\n\n  xenologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000018\n\n  coexists with:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SEMMEDDB:COEXISTS_WITH\n    narrow_mappings:\n      - BSPO:0000096\n      - BSPO:0000097\n      - BSPO:0000098\n      - BSPO:0000099\n      - BSPO:0000100\n      - BSPO:0000102\n      - BSPO:0000104\n      - BSPO:0000110\n      - BSPO:0000113\n      - BSPO:0015001\n      - BSPO:0015002\n      - BSPO:0015003\n      - BSPO:0015005\n      - BSPO:0015006\n      - BSPO:0015007\n      - BSPO:0015008\n      - BSPO:0015009\n      - BSPO:0015012\n      - BSPO:0015014\n      - BSPO:parallel_to\n      - UBERON_CORE:anastomoses_with\n      - UBERON_CORE:anteriorly_connected_to\n      - UBERON_CORE:posteriorly_connected_to\n      - UBERON_CORE:channel_for\n      - UBERON_CORE:channels_from\n      - UBERON_CORE:channels_into\n      - UBERON_CORE:conduit_for\n      - UBERON_CORE:distally_connected_to\n      - UBERON_CORE:extends_fibers_into\n      - UBERON_CORE:filtered_through\n      - UBERON_CORE:indirectly_supplies\n      - UBERON_CORE:proximally_connected_to\n      - UBERON_CORE:synapsed_by\n      - UBERON_CORE:transitively_anteriorly_connected_to\n      - UBERON_CORE:transitively_connected_to\n      - UBERON_CORE:transitively_distally_connected_to\n      - UBERON_CORE:transitively_proximally_connected_to\n      # RTX contributed Environmental Ontology term meaning \"partially surrounded by\"\n      - ENVO:01001307\n      - FMA:adjacent_to\n      - FMA:afferent_to\n      - FMA:anterior_to\n      - FMA:anteroinferior_to\n      - FMA:anterolateral_to\n      - FMA:anteromedial_to\n      - FMA:anterosuperior_to\n      # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics?\n      # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink\n      - FMA:arterial_supply_of\n      - FMA:has_arterial_supply\n      - FMA:articulates_with\n      - FMA:attaches_to\n      - FMA:bounded_by\n      - FMA:bounds\n      - FMA:branch_of\n      - FMA:connection_type_of\n      - FMA:continuation_branch_of\n      - FMA:continuous_distally_with\n      - FMA:continuous_proximally_with\n      - FMA:corresponds_to\n      - FMA:development_type_of\n      - FMA:developmental_stage_of\n      - FMA:direct_cell_shape_of\n      - FMA:direct_left_of\n      - FMA:direct_right_of\n      - FMA:distal_to\n      - FMA:drains_into\n      - FMA:efferent_to\n      - FMA:external_to\n      - FMA:formed_by\n      - FMA:forms\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:full_grown_phenotype_of\n      - FMA:has_full_grown_phenotype\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:fuses_with\n      - FMA:fusion_of\n      - FMA:has_fusion\n      - FMA:germ_origin_of\n      - FMA:has_germ_origin\n      - FMA:has_adherent\n      - FMA:has_branch\n      - FMA:has_connection_type\n      - FMA:has_continuation_branch\n      - FMA:has_development_type\n      - FMA:has_developmental_stage\n      - FMA:has_direct_cell_shape\n      - FMA:has_inherent_3d_shape\n      - FMA:has_insertion\n      - FMA:has_lymphatic_drainage\n      - FMA:has_nerve_supply\n      - FMA:has_observed_anatomical_entity\n      - FMA:has_origin\n      - FMA:has_primary_segmental_supply\n      - FMA:has_projection\n      - FMA:has_regional_part\n      - FMA:has_related_developmental_entity\n      - FMA:has_secondary_segmental_supply\n      - FMA:has_segmental_composition\n      - FMA:has_segmental_supply\n      - FMA:has_tributary\n      - FMA:has_venous_drainage\n      - FMA:inferior_to\n      - FMA:inferolateral_to\n      - FMA:inferomedial_to\n      - FMA:inherent_3d_shape_of\n      - FMA:insertion_of\n      - FMA:internal_to\n      - FMA:lateral_to\n      - FMA:left_lateral_to\n      - FMA:left_medial_to\n      - FMA:lymphatic_drainage_of\n      - FMA:matures_from\n      - FMA:matures_into\n      - FMA:medial_to\n      - FMA:merges_with\n      - FMA:nerve_supply_of\n      - FMA:origin_of\n      - FMA:posterior_to\n      - FMA:posteroinferior_to\n      - FMA:posterolateral_to\n      - FMA:posteromedial_to\n      - FMA:posterosuperior_to\n      - FMA:primary_segmental_supply_of\n      - FMA:projects_from\n      - FMA:projects_to\n      - FMA:proximal_to\n      - FMA:receives_attachment_from\n      - FMA:receives_drainage_from\n      - FMA:receives_input_from\n      - FMA:receives_projection\n      - FMA:related_part\n      - FMA:right_lateral_to\n      - FMA:right_medial_to\n      - FMA:secondary_segmental_supply_of\n      - FMA:segmental_composition_of\n      - FMA:segmental_supply_of\n      - FMA:sends_output_to\n      - FMA:superior_to\n      - FMA:superolateral_to\n      - FMA:superomedial_to\n      - FMA:surrounded_by\n      - FMA:surrounds\n      - FMA:tributary_of\n      - FMA:venous_drainage_of\n      # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute'\n      # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now\n      - LOINC:has_lateral_anatomic_location\n      - LOINC:has_lateral_location_presence\n      - UBERON_NONAMESPACE:distally_connected_to\n      - UBERON_NONAMESPACE:subdivision_of\n      # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to'\n      - RO:0002219\n      - RO:0002220\n      - RO:0002221\n      - SO:has_origin\n      # RTX mapped these UBERON terms all here\n      - UBERON:anastomoses_with\n      - UBERON:anteriorly_connected_to\n      - UBERON:channel_for\n      - UBERON:channels_from\n      - UBERON:channels_into\n      - UBERON:conduit_for\n      - UBERON:distally_connected_to\n      - UBERON:existence_starts_and_ends_during\n      - UBERON:extends_fibers_into\n      - UBERON:filtered_through\n      - UBERON:in_central_side_of\n      - UBERON:in_innermost_side_of\n      - UBERON:in_outermost_side_of\n      - UBERON:indirectly_supplies\n      - UBERON:posteriorly_connected_to\n      - UBERON:protects\n      - UBERON:proximally_connected_to\n      - UBERON:sexually_homologous_to\n\n  in pathway with:\n    description: >-\n      holds between two genes or gene products that are part of in the same biological pathway\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # generally pertains to membership of a (subject) component - gene,\n      # metabolite, etc? - in an (object) metabolic pathway\n      - SIO:010532\n\n  in complex with:\n    description: >-\n      holds between two genes or gene products that are part of (or code for\n      products that are part of) in the same macromolecular complex\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though)\n      - SIO:010497\n    broad_mappings:\n      # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes)\n      - SIO:010285\n\n  in cell population with:\n    description: >-\n      holds between two genes or gene products that are expressed in the same cell type or population\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  colocalizes with:\n    description: >-\n      holds between two entities that are observed to be located in the same place.\n    is_a: coexists with\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:00002325\n\n  # Despite the name, note that this particular entity is\n  # NOT a biolink:Association but rather, a biolink:predicate\n  genetic association:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    description: >-\n      Co-occurrence of a certain allele of a genetic marker and the phenotype\n      of interest in the same individuals at above-chance level\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2293\n\n  gene associated with condition:\n    is_a: genetic association\n    description: >-\n      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,\n      contribute to, or correlate with\n    domain: disease or phenotypic feature\n    range: gene\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - GENO:0000840 # broader than a single gene: 'genotype' pathogenic for condition\n      - GENO:0000841\n    narrow_mappings:\n      # narrower: just diseases, not phenotypic features as well\n      - NCIT:R38\n      - NCIT:R175\n      - NCIT:R48\n\n  condition associated with gene:\n    is_a: genetic association\n    aliases: [ 'disease associated with gene' ]\n    description: >-\n      holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products\n    domain: gene\n    range: disease or phenotypic feature\n    in_subset:\n      - translator_minimal\n    inverse: gene associated with condition\n    narrow_mappings:\n      # narrower since just diseases, not phenotypic features as well\n      - NCIT:R176\n\n  affects risk for:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where exposure to one entity alters the chance of developing the other\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  risk affected by:\n    is_a: related to at instance level\n    inverse: affects risk for\n\n  predisposes:\n    is_a: affects risk for\n    description: >-\n      holds between two entities where exposure to one entity increases the chance of developing the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:PREDISPOSES\n\n  has predisposing factor:\n    is_a: risk affected by\n    inverse: predisposes\n    in_subset:\n      - translator_minimal\n\n  contributes to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes or contributes to the\n      occurrence or generation of the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX contributed mapping tagged as 'inverse' of this Biolink predicate\n      - IDO:0000664\n    exact_mappings:\n      - RO:0002326\n    narrow_mappings:\n      - CTD:marker_mechanism\n      - MONDO:predisposes_towards\n      # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002255\n      # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here\n      - RO:0003304\n\n  contribution from:\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    inverse: contributes to\n\n  causes:\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes the occurrence\n      or generation of the other\n    is_a: contributes to\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:CAUSES\n      - WIKIDATA_PROPERTY:P1542\n      - SNOMED:cause_of\n      - RO:0003303\n    broad_mappings:\n      - RO:0002410\n      - RO:0002506\n    narrow_mappings:\n      - MONDO:disease_triggers\n      - GOREL:0000040\n      - MONDO:disease_causes_feature\n      - MONDO:disease_triggers\n      - NCIT:allele_has_abnormality\n      - NCIT:biological_process_has_result_biological_process\n      - NCIT:chemical_or_drug_has_physiologic_effect\n      # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'?\n      - NCIT:chemical_or_drug_initiates_biological_process\n      - NCIT:process_initiates_biological_process\n      - NCIT:chromosome_mapped_to_disease\n      - NCIT:disease_has_normal_tissue_origin\n      - NBO-PROPERTY:in_response_to\n      - orphanet:317343\n      - orphanet:317344\n      - orphanet:317346\n      - orphanet:410295\n      - orphanet:410296\n      # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002256\n      - RO:0002315\n      - RO:0002507\n      - RO:0002509\n      - RO:0004001\n      - SNOMED:causative_agent_of\n      - SNOMED:has_realization\n      - UMLS:has_physiologic_effect\n\n  caused by:\n    description: >-\n      holds between two entities where the occurrence, existence,\n      or activity of one is caused by the occurrence or generation of the other\n    is_a: related to at instance level\n    aliases: [ 'disease caused by disruption of', 'disease has basis in dysfunction of',\n               'realized in response to', 'realized in response to stimulus' ]\n    in_subset:\n      - translator_minimal\n    inverse: causes\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P828\n    narrow_mappings:\n      - RO:0001022\n      - RO:0002608\n      - RO:0004019\n      - RO:0004020\n      - RO:0004028\n      - RO:0009501\n\n  # TODO: ameliorates and exacerbates inverses.\n  ameliorates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a genotype,\n      genetic variation, chemical, or environmental exposure, clinical intervention)\n      and a condition (a phenotype or disease), where the\n      presence of the entity reduces or eliminates some or\n      all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: named thing\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: exacerbates\n    exact_mappings:\n      - RO:0003307\n\n  is ameliorated by:\n    inverse: ameliorates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: named thing\n\n  exacerbates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a chemical,\n      environmental exposure, or some form of genetic variation)\n      and a condition (a phenotype or disease), where the presence\n      of the entity worsens some or all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0003309\n    broad_mappings:\n      - SEMMEDDB:COMPLICATES\n\n  is exacerbated by:\n    inverse: exacerbates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n    in_subset:\n      - translator_minimal\n\n  treats:\n    aliases: [ 'is substance that treats', 'indicated for' ]\n    is_a: ameliorates\n    description: >-\n      holds between a therapeutic procedure or chemical entity\n      and a disease or phenotypic feature that it is used to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: contraindicated for\n    in_subset:\n      - translator_minimal\n    related_mappings:\n      - MONDO:disease_responds_to\n    exact_mappings:\n      - DRUGBANK:treats\n      - SEMMEDDB:TREATS\n      - WIKIDATA_PROPERTY:P2175\n    narrow_mappings:\n      # \"is substance that treats\" constrains statements to\n      # a subset of the universe of all possible treatments\n      - RO:0002606\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n      - SNOMED:plays_role\n\n  treated by:\n    is_a: is ameliorated by\n    description: >-\n      holds between a disease or phenotypic feature and a therapeutic\n      process or chemical entity that is used to treat the condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    # range: chemical or drug or treatement\n    in_subset:\n      - translator_minimal\n    inverse: treats\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2176\n      # RTX contributed term tagged as inverse of 'biolink:treats'\n      - MONDO:disease_responds_to\n    narrow_mappings:\n      # \"is treated by substance\" constrains statements to\n      # subset of the universe of all possible treatments\n      - RO:0002302\n\n  prevents:\n    is_a: affects risk for\n    description: >-\n      holds between an entity whose application or use reduces\n      the likelihood of a potential outcome. Typically used to associate\n      a chemical entity, exposure, activity, or medical intervention\n      that can prevent the onset a disease or phenotypic feature.\n    annotations:\n      canonical_predicate: true\n      opposite_of: predisposes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:PREVENTS\n    narrow_mappings:\n      # more restricted case of a material entity mitigating a pathological process\n      - RO:0002599\n\n  prevented by:\n    is_a: risk affected by\n    description: >-\n      holds between a potential outcome of which the likelihood\n      was reduced by the application or use of an entity.\n    inverse: prevents\n    annotations:\n      opposite_of: enabled by\n\n  correlated with:\n    is_a: associated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical dependence is \n      demonstrated using a correlation analysis method.\n    notes: >-\n      These concepts may map exactly to the statistical variables, or represent related entities for which the \n      variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002610\n      - PATO:correlates_with\n\n  # proposed positive and negative semantic extensions to the general \"correlated with\" predicate\n\n  positively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or \n      presence of one correlates with an increase or presence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: negatively correlated with\n    exact_mappings:\n      - CTD:positive_correlation\n\n  negatively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of \n      one correlates with a decrease or absence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: positively correlated with\n    exact_mappings:\n      - CTD:negative_correlation\n\n  occurs together in literature with:\n    is_a: correlated with\n    description: >-\n      holds between two entities where their co-occurrence is correlated by counts of publications\n      in which both occur, using some threshold of occurrence as defined by the edge provider.\n    domain: named thing\n    range: named thing\n    in_subset: translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  coexpressed with:\n    is_a: correlated with\n    description: >-\n      holds between any two genes or gene products, in which both are\n      generally expressed within a single defined experimental context.\n    domain: gene or gene product\n    range: gene or gene product\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  has biomarker:\n    is_a: correlated with\n    description: >-\n      holds between a disease or phenotypic feature and a measurable\n      chemical entity that is used as an indicator of the presence\n      or state of the disease or feature.\n      # metabolite\n    domain: disease or phenotypic feature\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    inverse: biomarker for\n    narrow_mappings:\n      # some RTX terms contributed as inverses of 'biolink:biomarker_for'\n      - NCIT:disease_has_molecular_abnormality\n      - NCIT:disease_is_marked_by_gene\n\n  biomarker for:\n    is_a: correlated with\n    description: >-\n      holds between a measurable chemical entity and a disease\n      or phenotypic feature, where the entity is used as an indicator\n      of the presence or state of the disease or feature.\n    domain: chemical entity or gene or gene product\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - NCIT:R39\n    broad_mappings:\n      # Generic marker definition not specific to biomarkers per say\n      - RO:0002607\n    narrow_mappings:\n      - NCIT:R47\n      # RTX term was tagged as 'biolink:actively_involved_in' but maps better here?\n      - NCIT:genetic_biomarker_related_to\n      - NCIT:is_molecular_abnormality_of_disease\n      - orphanet:465410\n\n  # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in'\n  # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates\n  # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others\n  expressed in:\n    is_a: located in\n    description: >-\n      holds between a gene or gene product and an anatomical entity in which it is expressed\n    domain: gene or gene product\n    range: anatomical entity\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002206\n    narrow_mappings:\n      - NCIT:R49\n      - NCIT:R46\n\n  expresses:\n    is_a: location of\n    aliases: [ 'anatomy expresses gene' ]\n    description: >-\n      holds between an anatomical entity and gene or gene product that is expressed there\n    domain: anatomical entity\n    range: gene or gene product\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    inverse: expressed in\n    exact_mappings:\n      - RO:0002292\n\n  has phenotype:\n    is_a: related to at instance level\n    aliases: [ 'disease presents symptom' ]\n    description: >-\n      holds between a biological entity and a phenotype, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should\n      translate into this predicate.\n    domain: biological entity\n    range: phenotypic feature\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    notes:\n      - check the range\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002200\n    broad_mappings:\n      - NCIT:R115\n      - NCIT:R108\n    narrow_mappings:\n      - NCIT:R89\n      - DOID-PROPERTY:has_symptom\n      - RO:0004022\n\n  phenotype of:\n    is_a: related to at instance level\n    domain: phenotypic feature\n    range: biological entity\n    multivalued: true\n    inverse: has phenotype\n\n  # TODO: predicate inverse for occurs in\n  occurs in:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a material entity or site within which the process occurs\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # These RTX mapped terms tagged as the inverse of \"biolink:occurs_in\", i.e. Entity/Site contains Process\n      - BFO:0000067\n      - SNOMED:has_occurrence\n      - UBERON:site_of\n    exact_mappings:\n      - BFO:0000066\n      - PathWhiz:has_location\n      - SNOMED:occurs_in\n    narrow_mappings:\n      # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population\n      - SEMMEDDB:OCCURS_IN\n      # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity\n      - SEMMEDDB:PROCESS_OF\n      # Uberon term constrained to a 'site' as object concept\n      - UBERON_CORE:site_of\n      - LOINC:has_imaged_location\n      - PathWhiz:in_species\n      - RO:0002231\n      - RO:0002232\n      - SNOMED:has_direct_procedure_site\n      - SNOMED:has_direct_site\n      - SNOMED:has_procedure_site\n\n  contains process:\n    is_a: related to at instance level\n    inverse: occurs in\n\n  located in:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a material entity or site\n      within which it is located (but of which it is not considered a part)\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0001025\n      - FMA:has_location\n    narrow_mappings:\n      - GOREL:0001004\n      - BSPO:0000107\n      - BSPO:0000108\n      - BSPO:0000120\n      - BSPO:0000121\n      - BSPO:0000122\n      - BSPO:0000123\n      - BSPO:0000124\n      - BSPO:0000125\n      - BSPO:0000126\n      - BSPO:0001100\n      - BSPO:0001101\n      - BSPO:0001107\n      - BSPO:0015101\n      - BSPO:0015102\n      - BSPO:0015202\n      - UBERON_CORE:in_central_side_of\n      - UBERON_CORE:in_innermost_side_of\n      - UBERON_CORE:in_outermost_side_of\n      - NCIT:R100\n      - EFO:0000784\n      - FMA:has_location\n      - HMDB:at_cellular_location\n      - HMDB:at_tissue\n      - HMDB:in_biospecimen\n      - LOINC:has_imaging_focus\n      - NCIT:R156\n      - NCIT:R155\n      - NCIT:R145\n      - NCIT:R40\n      - NCIT:R171\n      - NCIT:R167\n      - NCIT:R165\n      - NCIT:R169\n      - NCIT:R170\n      - NCIT:R166\n      - NCIT:R168\n      - RO:0002303\n      - SNOMED:has_finding_site\n      - SNOMED:has_indirect_procedure_site\n      - SNOMED:has_inherent_location\n    domain: named thing\n    range: named thing\n\n  location of:\n    is_a: related to at instance level\n    aliases: [ 'site of' ]\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between material entity or site and a material entity\n      that is located within it (but not considered a part of it)\n    in_subset:\n      - translator_minimal\n    inverse: located in\n    exact_mappings:\n      - RO:0001015\n      - SEMMEDDB:LOCATION_OF\n      - WIKIDATA_PROPERTY:P276\n      # RTX tagged this as an inverse of biolink:located_in\n      - FMA:location_of\n    narrow_mappings:\n      - SNOMED:inherent_location_of\n      - NCIT:Anatomic_Structure_Has_Location_Role\n\n  disease has location:\n    description: >-\n      A relationship between a disease and an anatomical entity where the\n      disease has one or more features that are located in that entity.\n    is_a: related to\n    exact_mappings:\n      - RO:0004026\n      - MONDO:disease_has_location\n\n  location of disease:\n    is_a: related to\n    inverse: disease has location\n\n  similar to:\n    is_a: related to at instance level\n    description: >-\n      holds between an entity and some other entity with similar features.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000000               #I don't understand this identifier, but I think it's equivalent\n      - SO:similar_to               #equivalent\n\n  chemically similar to:\n    is_a: similar to\n    description: >-\n      holds between one small molecule entity and another that it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - CHEBI:has_parent_hydride    #subproperty\n      - CHEBI:has_functional_parent #subproperty\n      - CHEBI:is_conjugate_acid_of  #subproperty\n      - CHEBI:is_conjugate_base_of  #subproperty\n      - CHEBI:is_enantiomer_of      #subproperty\n      - CHEBI:is_tautomer_of        #subproperty\n      - NCIT:has_salt_form\n\n  has sequence location:\n    is_a: related to at instance level\n    description: >-\n      holds between two nucleic acid entities when the subject can be localized\n      in sequence coordinates on the object. For example, between\n      an exon and a chromosome/contig.\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - faldo:location\n\n  sequence location of:\n    is_a: related to at instance level\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    inverse: has sequence location\n\n  model of:\n    is_a: related to at instance level\n    description: >-\n      holds between a thing and some other thing it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0003301\n    narrow_mappings:\n      - FOODON:00001301\n\n  models:\n    is_a: related to at instance level\n    inverse: model of\n\n  overlaps:\n    is_a: related to at instance level\n    description: >-\n      holds between entities that overlap in their extents (materials or processes)\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002131\n    narrow_mappings:\n      - BSPO:0005001\n      - CHEMBL.MECHANISM:overlaps_with\n      - RO:0002100\n      - RO:0002102\n      - RO:0002433\n\n  has part:\n    is_a: overlaps\n    annotations:\n      canonical_predicate: true\n      opposite_of: lacks part\n    description: >-\n      holds between wholes and their parts (material entities or processes)\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000051\n      # term name seems to be 'realizes' but RTX maps this term here\n      - BFO:0000055\n      - WIKIDATA_PROPERTY:P527\n      - RO:0001019\n      - RXNORM:consists_of\n      - RXNORM:has_part\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'; slightly broader?\n      - RO:0001019\n      - FMA:contains\n      - RXNORM:contains\n    narrow_mappings:\n      - BFO:0000117\n      # RTX term originally mapped to 'biolink:coexists_with'?\n      - FMA:has_constitutional_part\n      - FMA:has_part\n      # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'?\n      - FMA:has_member\n      - FOODON:00001563\n      - FOODON:00002420\n      - LOINC:has_component\n      - LOINC:has_member\n      - MEDDRA:has_member\n      - MONDO:disease_has_major_feature\n      - NCIT:complex_has_physical_part\n      - NDDF:has_ingredient\n      - PathWhiz:has_element_in_bound\n      # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature\n      - NCIT:R50\n      - PathWhiz:has_protein_in_complex\n      - RO:0002104\n      - RO:0002180\n      - RO:0002351\n      - RO:0002473\n      - RO:0002524\n      - RO:0002551\n      - RXNORM:has_ingredient\n      - SNOMED:has_component\n      - UMLS:has_component\n\n  has plasma membrane part:\n    is_a: has part\n    description: >-\n      Holds between a cell c and a protein complex or protein p if\n      and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.\n    exact_mappings:\n      - RO:0002104\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  composed primarily of:\n    is_a: related to\n    description: >-\n      x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.\n    exact_mappings:\n      - RO:0002473\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  primarily composed of:\n    inverse: composed primarily of\n    is_a: related to\n\n  plasma membrane part of:\n    is_a: part of\n    inverse: has plasma membrane part\n\n  part of:\n    is_a: overlaps\n    description: >-\n      holds between parts and wholes (material entities or processes)\n    in_subset:\n      - translator_minimal\n    inverse: has part\n    exact_mappings:\n      - BFO:0000050\n      - SEMMEDDB:PART_OF\n      - WIKIDATA_PROPERTY:P361\n      - FMA:part_of\n      - RXNORM:constitutes\n      - RXNORM:part_of\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'\n      - RO:0001018\n      - FMA:contained_in\n      - RXNORM:contained_in\n    narrow_mappings:\n      - BSPO:0001106\n      - BSPO:0001108\n      - BSPO:0001113\n      - BSPO:0001115\n      - UBERON_CORE:layer_part_of\n      - UBERON_CORE:subdivision_of\n      - UBERON_CORE:trunk_part_of\n      - CHEBI:is_substituent_group_from\n      - CPT:panel_element_of\n      - CPT:panel_element_of_possibly_included\n      - DRUGBANK:component_of\n      - FMA:constitutional_part_of\n      - FMA:member_of\n      - FMA:regional_part_of\n      - FMA:related_developmental_entity_of\n      - LOINC:component_of\n      - LOINC:has_supersystem\n      - LOINC:member_of\n      - LOINC:multipart_of\n      - MEDDRA:member_of\n      - MONDO:part_of_progression_of_disease\n      - NCIT:R82\n      - NCIT:R27\n      - NCIT:is_component_of_chemotherapy_regimen\n      - NDDF:ingredient_of\n      - RO:0002007\n      - RO:0002350\n      - RO:0002376\n      - RO:0002380\n      - RO:0002571\n      - RO:0002572\n      - RO:0002576\n      - RXNORM:ingredient_of\n      - RXNORM:ingredients_of\n      - RXNORM:precise_ingredient_of\n      - SNOMED:active_ingredient_of\n      - SNOMED:basis_of_strength_substance_of\n      - SNOMED:component_of\n      - SNOMED:direct_substance_of\n      - SNOMED:during\n      - SNOMED:focus_of\n      - SNOMED:has_dependent\n      - SNOMED:part_anatomy_structure_of\n      - SNOMED:precise_active_ingredient_of\n      - UBERON:subdivision_of\n      - UMLS:component_of\n      - UMLS:has_owning_affiliate\n      - UMLS:owning_subsection_of\n      - VANDF:ingredient_of\n\n  has input:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an input into the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n      opposite_of: has output\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX inverse mapping to 'biolink:has_input'\n      - RO:0002352\n    exact_mappings:\n      - RO:0002233\n      - SEMMEDDB:USES\n    narrow_mappings:\n      - LOINC:has_fragments_for_synonyms\n      - LOINC:has_system\n      - PathWhiz:has_left_element\n      - RO:0002590\n      - RO:0004009\n      - SNOMED:has_finding_method\n      - SNOMED:has_precondition\n      - SNOMED:has_specimen_source_identity\n      - SNOMED:has_specimen_substance\n      - SNOMED:uses_access_device\n      - SNOMED:uses_device\n      - SNOMED:uses_energy\n      - SNOMED:uses_substance\n\n  is input of:\n    is_a: participates in\n    domain: occurrent\n    range: biological process or activity\n    inverse: has input\n    in_subset:\n      - translator_minimal\n\n  has output:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an output of the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n      opposite_of: has input\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - RO:0002353\n      - RO:0002354\n    exact_mappings:\n      - RO:0002234\n    narrow_mappings:\n      - NCIT:R31\n      - OBI:0000299\n      - PathWhiz:has_right_element\n      - RO:0002296\n      - RO:0002297\n      - RO:0002298\n      - RO:0002299\n      - RO:0002588\n      - RO:0004008\n\n  is output of:\n    is_a: participates in\n    domain: occurrent\n    range: biological process or activity\n    inverse: has output\n    in_subset:\n      - translator_minimal\n\n  has participant:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a continuant, where the continuant is somehow involved in the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - WIKIDATA_PROPERTY:P2283\n    exact_mappings:\n      - RO:0000057\n      - RO:has_participant\n    narrow_mappings:\n      - BFO:0000167\n      # Several of the following RTX terms tagged as inverse to 'biolink:participates_in'\n      - LOINC:has_subject\n      - NCIT:process_involves_gene\n      - NBO-PROPERTY:has_participant\n      - PathWhiz:has_bound\n      - PathWhiz:has_compound\n      - PathWhiz:has_element_collection\n      - PathWhiz:has_enzyme\n      - OBI:0000293\n      - PathWhiz:has_nucleic_acid\n      - PathWhiz:has_protein\n      - PathWhiz:has_reaction\n      - RO:0004007\n      - RO:0004020\n      - RO:0004021\n      - SNOMED:has_indirect_device\n      - SNOMED:has_procedure_device\n      - SNOMED:has_recipient_category\n\n  catalyzes:\n    is_a: participates in\n    domain: nucleic acid entity\n    range: molecular activity\n    annotations:\n      canonical_predicate: true\n\n  has catalyst:\n    is_a: has participant\n    inverse: catalyzes\n    domain: molecular activity\n    range: nucleic acid entity\n\n  has substrate:\n    is_a: has participant\n    domain: molecular activity\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n\n  is substrate of:\n    is_a: participates in\n    inverse: has substrate\n    domain: chemical entity or gene or gene product\n    range: molecular activity\n\n  participates in:\n    is_a: related to at instance level\n    description: >-\n      holds between a continuant and a process, where the continuant is somehow involved\n      in the process\n    range: biological process or activity\n    domain: occurrent\n    inverse: has participant\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0000056\n      - BFO:0000056\n    narrow_mappings:\n      - DRUGBANK:pathway\n      - HMDB:in_pathway\n      - LOINC:is_given_pharmaceutical_substance_for\n      - NCIT:R130\n      - NCIT:R37\n      - NCIT:R131\n      - NCIT:R51\n      - NCIT:R53\n      - OBI:0000295\n      - RO:0002216\n      - RO:0002505\n      - RO:0002565\n      - SNOMED:has_direct_device\n\n  actively involved in:\n    is_a: participates in\n    aliases: [ 'involved in' ]\n    description: >-\n      holds between a continuant and a process or function, where\n      the continuant actively contributes to part or all of\n      the process or function it realizes\n    domain: occurrent\n    range: molecular activity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002331\n      - RO:0002432\n    narrow_mappings:\n      - NBO-PROPERTY:by_means\n      - orphanet:317348\n      - orphanet:317349\n      - orphanet:327767\n      - RO:0002503\n\n  actively involves:\n    is_a: has participant\n    domain: molecular activity\n    range: occurrent\n    inverse: actively involved in\n    exact_mappings:\n      - RO:0002331\n    in_subset:\n      - translator_minimal\n\n  capable of:\n    is_a: actively involved in\n    description: >-\n      holds between a physical entity and process or function, where the\n      continuant alone has the ability to carry out the process or function.\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002215\n    narrow_mappings:\n      - NCIT:R52\n      - RO:0002500\n\n  has capability:\n    is_a: actively involves\n    inverse: capable of\n    domain: occurrent\n\n  enables:\n    is_a: participates in\n    description: >-\n      holds between a physical entity and a process, where the physical entity executes the process\n    domain: physical entity\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    in_subset:\n      - translator_minimal\n    inverse: enabled by\n    exact_mappings:\n      - RO:0002327\n\n  enabled by:\n    is_a: has participant\n    description: >-\n      holds between a process and a physical entity, where the physical entity executes the process\n    domain: biological process or activity\n    range: physical entity\n    in_subset:\n      - translator_minimal\n    inverse: enables\n    exact_mappings:\n      - RO:0002333\n    annotations:\n      opposite_of: prevented by\n\n  derives into:\n    is_a: related to at instance level\n    aliases: [ 'is normal cell origin of disease', 'may be normal cell origin of disease' ]\n    description: >-\n      holds between two distinct material entities, the old entity and\n      the new entity, in which the new entity begins to exist when\n      the old entity ceases to exist, and the new entity inherits\n      the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n    inverse: derives from\n    # TODO: fix this according to WG notes. Example of both opposite and inverse\n    # Commenting as it feels very wrong. A good example with both opposite and inverse is `has active ingredient`\n    # annotations:\n    #   opposite_of: subclass of\n    exact_mappings:\n      - RO:0001001\n      - SEMMEDDB:CONVERTS_TO\n      # RTX posted terms as inverse of 'biolink:derives_from'\n      - FMA:derives\n\n  derives from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    description: >-\n      holds between two distinct material entities, the new entity\n      and the old entity, in which the new entity begins to exist\n      when the old entity ceases to exist, and the new entity\n      inherits the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n      - samples\n    inverse: derives into\n    exact_mappings:\n      - RO:0001000\n      - FMA:derives_from\n      - DOID-PROPERTY:derives_from\n    narrow_mappings:\n      - CHEBI:has_functional_parent\n      - SNOMED:has_specimen_source_topography\n\n  is metabolite of:\n    is_a: derives from\n    description: >-\n      holds between two molecular entities in which the first one is derived\n      from the second one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    inverse: has metabolite\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  has metabolite:\n    is_a: derives into\n    description: >-\n      holds between two molecular entities in which the second one is derived from the first\n      one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  food component of:\n    is_a: part of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has food component\n    #mappings:\n    #  -\n\n  has food component:\n    is_a: has part\n    description: >-\n      holds between food and one or more chemical entities composing it,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  nutrient of:\n    is_a: food component of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has nutrient\n    #exact_mappings:\n    #  -\n\n  has nutrient:\n    is_a: has food component\n    description: >-\n      one or more nutrients which are growth factors for a living organism\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q181394\n\n  is active ingredient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug, in which the former\n      is a part of the latter, and is a biologically active component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has active ingredient\n    mappings:\n      - RO:0002249\n\n  has active ingredient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entity in which the latter\n      is a part of the former, and is a biologically active component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: is excipient of\n    in_subset:\n      - translator_minimal\n    inverse: is active ingredient of\n    mappings:\n      - RO:0002248\n\n  is excipient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug in which the former is\n      a part of the latter, and is a biologically inactive component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has excipient\n    mappings:\n      - WIKIDATA:Q902638\n\n  has excipient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entities in which the latter\n      is a part of the former, and is a biologically inactive component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    mappings:\n      - WIKIDATA:Q902638\n\n  manifestation of:\n    is_a: related to at instance level\n    description: >-\n      that part of a phenomenon which is directly observable or\n      visibly expressed, or which gives evidence to the underlying\n      process; used in SemMedDB for linking things like dysfunctions\n      and processes to some disease or syndrome\n    range: disease\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:MANIFESTATION_OF\n      - OMIM:manifestation_of\n    broad_mappings:\n      # Wikidata's definition is slightly broader: \"inherent and characteristic embodiment of a given concept\"\n      - WIKIDATA_PROPERTY:P1557\n    narrow_mappings:\n      - SNOMED:has_definitional_manifestation\n\n  has manifestation:\n    is_a: related to at instance level\n    domain: disease\n    inverse: manifestation of\n\n  mode of inheritance of:\n    is_a: manifestation of\n    domain: genetic inheritance\n    range: disease or phenotypic feature\n    inverse: has mode of inheritance\n\n  has mode of inheritance:\n    is_a: has manifestation\n    description: >-\n      Relates a disease or phenotypic feature to its observed genetic segregation and assumed\n      associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).\n    domain: disease or phenotypic feature\n    range: genetic inheritance\n    annotations:\n      # This canonical order reverses that of its parent 'has manifestation' class\n      # but seems a more natural direction in the pertinent edge relationships.\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  produces:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a product that is generated\n      through the intentional actions or functioning of the material entity\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GOREL:0001010\n    exact_mappings:\n      - RO:0003000\n      - WIKIDATA_PROPERTY:P1056\n      - SEMMEDDB:PRODUCES\n    narrow_mappings:\n      - NCIT:R29\n      - SNOMED:has_process_output\n      - SNOMED:specimen_procedure_of\n\n  produced by:\n    is_a: related to at instance level\n    inverse: produces\n    exact_mappings:\n      - RO:0003001\n\n  consumes:\n    is_a: has input\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - RO:0004009\n\n  consumed by:\n    is_a: is input of\n    inverse: consumes\n\n  temporally related to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities with a temporal relationship\n    domain: occurrent\n    range: occurrent\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SNOMED:temporally_related_to\n    narrow_mappings:\n      # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here\n      - RO:0002082\n      - RO:0002083\n      - RO:0002092\n      - RO:0002093\n      - RO:0002223\n      - RO:0002224\n      - RO:0002229\n      - RO:0002230\n      - RO:0002488\n      - RO:0002489\n      - RO:0002492\n      - RO:0002493\n      - RO:0002496\n      - RO:0002497\n\n  precedes:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where one completes before the other begins\n    domain: occurrent\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    inverse: preceded by\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # the subject of these terms is a material entity, not a process,\n      # but affects a process which causes a second process to occur\n      - RO:0002263\n      - RO:0002264\n    exact_mappings:\n      - BFO:0000063\n      - SEMMEDDB:PRECEDES\n      - SNOMED:occurs_before\n    broad_mappings:\n      # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature\n      - WIKIDATA_PROPERTY:P156\n    narrow_mappings:\n      - FMA:transforms_into\n      - RO:0002090\n      - RO:0002411\n      - RO:0002412\n\n  preceded by:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where the other is completed before the one begins\n    domain: occurrent\n    range: occurrent\n    inverse: precedes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000062\n    broad_mappings:\n      # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'?\n      - GENEPIO:0001739\n    narrow_mappings:\n      # RTX contributed mapping was given as the inverse of 'biolink:precedes'\n      - FMA:transforms_from\n      - RO:0002087\n      - RO:0002285\n\n  has variant part:\n    is_a: has part\n    description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000382\n\n  variant part of:\n    is_a: part of\n    inverse: has variant part\n\n  related condition:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000790\n\n  ## Predicates relating variants to genes\n\n  is sequence variant of:\n    is_a: related to at instance level\n    aliases: [ 'gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product' ]\n    description: holds between a sequence variant and a nucleic acid entity\n    domain: sequence variant\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - WIKIDATA:P3433\n\n  has sequence variant:\n    is_a: related to at instance level\n    inverse: is sequence variant of\n    domain: nucleic acid entity\n    range: sequence variant\n\n  is missense variant of:\n    is_a: is sequence variant of\n    description: holds between a gene  and a sequence variant, such the sequence variant\n      results in a different amino acid sequence but where the length is preserved.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001583\n\n  has missense variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is missense variant of\n\n  is synonymous variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the coding sequence of the gene, but results in the same amino acid sequence\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001819\n\n  has synonymous variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is synonymous variant of\n    aliases: [ 'stop gained' ]\n\n  is nonsense variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      results in a premature stop codon\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      # Term definition broader than nonsense codon: A sequence variant whereby\n      # the gene product has diminished or abolished function.\n      - SO:0002054\n\n  has nonsense variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is nonsense variant of\n\n  is frameshift variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      causes a disruption of the translational reading frame, because the number of\n      nucleotides inserted or deleted is not a multiple of three.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001589\n    aliases: [ 'frameshift variant', 'start lost', 'stop lost' ]\n\n  has frameshift variant:\n    is_a: has sequence variant\n    inverse: is frameshift variant of\n    domain: gene\n    range: sequence variant\n    aliases: [ 'splice region variant', 'splice acceptor variant', 'splice donor variant' ]\n\n  is splice site variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the canonical splice site of one of the gene's exons.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001629\n\n\n  has splice site variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is splice site variant of\n    aliases: [ 'downstream gene variant', 'upstream gene variant' ]\n\n  is nearby variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene sequence that the variant\n      is genomically close to.\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n\n  has nearby variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is nearby variant of\n    aliases: [ 'intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant' ]\n\n  is non coding variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, where the variant does\n      not affect the coding sequence\n    domain: sequence variant\n    range: gene\n    annotations:\n      canonical_predicate: true\n\n  has non coding variant:\n    is_a: has sequence variant\n    domain: gene\n    range: sequence variant\n    inverse: is non coding variant of\n\n  # relating disease to process\n\n  disease has basis in:\n    description: A relation that holds between a disease and an entity where the state\n      of the entity has contribution to the disease.\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      # These two MONDO terms seem more particular than the predicate\n      - MONDO:disease_has_basis_in_development_of\n      - MONDO:disease_has_basis_in_accumulation_of\n\n  occurs in disease:\n    is_a: related to at instance level\n    inverse: disease has basis in\n\n\n  has adverse event:\n    is_a: affects\n    aliases: [ 'adverse effect']\n    description: >-\n      An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment \n      with a therapeutic agent. Adverse events may be caused by something \n      other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or \n      diseases temporally associated with the treatment, whether or not considered related to the treatment. \n      Adverse events are unintended effects that occur when a medication is administered correctly.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n\n  adverse event of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has adverse event\n\n  has side effect:\n    aliases: [ 'adverse drug reaction']\n    is_a: affects\n    description: >-\n      An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment.\n      Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of \n      the medication.\n    notes: >-\n      Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative.\n      Aeolus, Sider are both resources that provide side effects.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C2861 # side effect\n\n  is side effect of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has side effect\n\n  contraindicated for:\n    is_a: related to at instance level\n    description: Holds between a drug and a disease or phenotype, such that a person\n      with that disease should not be treated with the drug.\n    domain: drug\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: treats\n    exact_mappings:\n      - NCIT:C37933\n\n  has contraindication:\n    is_a: related to at instance level\n    domain: disease or phenotypic feature\n    range: drug\n    inverse: contraindicated for\n\n  # The remaining new slots are here because we ran across them somewhere and\n  # they didn't seem to map well to anything else.\n\n  has not completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of,\n      but has not completed\n    exact_mappings:\n      - CL:has_not_completed\n    annotations:\n      opposite_of: has completed\n      canonical_predicate: true\n\n  not completed by:\n    is_a: related to at instance level\n    inverse: has not completed\n\n  has completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of\n      and has completed\n    annotations:\n      canonical_predicate: true\n      opposite_of: has not completed\n    exact_mappings:\n      - CL:has_completed\n\n  completed by:\n    is_a: related to at instance level\n    inverse: has completed\n\n\n  in linkage disequilibrium with:\n    is_a: related to at instance level\n    description: holds between two sequence variants, the presence of which are correlated\n      in a population\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C16798\n\n  has increased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has decreased amount\n    narrow_mappings:\n      - CL:has_high_plasma_membrane_amount\n\n  increased amount of:\n    is_a: related to at instance level\n    inverse: has increased amount\n\n  has decreased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has increased amount\n    narrow_mappings:\n      - CL:has_low_plasma_membrane_amount\n\n  decreased amount in:\n    is_a: related to at instance level\n    inverse: has decreased amount\n\n  lacks part:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has part\n    exact_mappings:\n      - CL:lacks_part\n      - PR:lacks_part\n    narrow_mappings:\n      - CL:lacks_plasma_membrane_part\n\n  missing from:\n    is_a: related to at instance level\n    inverse: lacks part\n\n  develops from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX mapping seems to be inverse of 'biolink:develops_from'\n      - RO:0002203\n      - FMA:develops_into\n    exact_mappings:\n      - BTO:develops_from\n      - DDANAT:develops_from\n      - FMA:develops_from\n      - RO:0002202\n    narrow_mappings:\n      - RO:0002207\n      - RO:0002225 # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y\n      - RO:0002226 # x develops_in y if x is located in y whilst x is developing\n\n  develops into:\n    is_a: related to at instance level\n    inverse: develops from\n\n  in taxon:\n    aliases: [ 'instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source' ]\n    is_a: related to at instance level\n    domain: thing with taxon\n    range: organism taxon\n    annotations:\n      canonical_predicate: true\n    description: >-\n      connects an entity to its taxonomic classification. Only certain kinds\n      of entities can be taxonomically classified; see 'thing with taxon'\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002162\n      - WIKIDATA_PROPERTY:P703\n    narrow_mappings:\n      - RO:0002160\n\n  taxon of:\n    is_a: related to at instance level\n    inverse: in taxon\n    domain: organism taxon\n    range: thing with taxon\n\n  has molecular consequence:\n    is_a: related to at instance level\n    aliases: [ 'allele has activity' ]\n    description: >-\n      connects a sequence variant to a class describing the molecular\n      consequence. E.g.  SO:0001583\n    range: ontology class\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - NCIT:allele_has_activity\n\n  is molecular consequence of:\n    is_a: related to at instance level\n    domain: ontology class\n    inverse: has molecular consequence\n\n  ## --------------------\n  ## ASSOCIATION SLOTS\n  ## --------------------\n\n  association slot:\n    abstract: true\n    domain: association\n    aliases: [ 'edge property', 'statement property', 'node qualifier', 'edge qualifier', 'statement qualifier' ]\n    description: >-\n      any slot that relates an association to another entity\n\n  original subject:\n    is_a: association slot\n    description: >-\n      used to hold the original subject of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original object:\n    is_a: association slot\n    description: >-\n      used to hold the original object of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original predicate:\n    aliases: [ 'original relation', 'relation' ]\n    is_a: association slot\n    description: >-\n      used to hold the original relation/predicate that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n    id_prefixes:\n      - RO\n      - BSPO\n      - SIO\n    domain: association\n    range: uriorcurie\n\n  subject:\n    is_a: association slot\n    local_names:\n      ga4gh: annotation subject\n      neo4j: node with outgoing relationship\n    description: >-\n      connects an association to the subject of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    slot_uri: rdf:subject\n    exact_mappings:\n      - owl:annotatedSource\n      - OBAN:association_has_subject\n\n  object:\n    is_a: association slot\n    description: >-\n      connects an association to the object of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    local_names:\n      ga4gh: descriptor\n      neo4j: node with incoming relationship\n    slot_uri: rdf:object\n    exact_mappings:\n      - owl:annotatedTarget\n      - OBAN:association_has_object\n\n  predicate:\n    is_a: association slot\n    description: >-\n      A high-level grouping for the relationship type. AKA minimal predicate.\n      This is analogous to category for nodes.\n    domain: association\n    notes: >-\n      Has a value from the Biolink related_to hierarchy. In RDF,  this\n      corresponds to rdf:predicate and in Neo4j this corresponds to the\n      relationship type. The convention is for an edge label in snake_case\n      form. For example, biolink:related_to, biolink:causes, biolink:treats\n    range: predicate type\n    required: true\n    local_names:\n      ga4gh: annotation predicate\n      translator: predicate\n    slot_uri: rdf:predicate\n    exact_mappings:\n      - owl:annotatedProperty\n      - OBAN:association_has_predicate\n\n  logical interpretation:\n    is_a: association slot\n    required: false\n    domain: association\n    range: LogicalInterpretationEnum\n    exact_mappings:\n      - os:LogicalInterpretation\n\n  relation:\n    deprecated: true\n\n  negated:\n    is_a: association slot\n    range: boolean\n    description: >-\n      if set to true, then the association is negated i.e. is not true\n\n  has confidence level:\n    is_a: association slot\n    range: confidence level\n    description: >-\n      connects an association to a qualitative term denoting the level of confidence\n\n  has evidence:\n    is_a: association slot\n    range: evidence type\n    description: >-\n      connects an association to an instance of supporting evidence\n    exact_mappings:\n      - RO:0002558\n    multivalued: true\n\n  has supporting study result:\n    is_a: association slot\n    description: >-\n      connects an association to an instance of supporting study result\n    \n  mechanism of action:\n    is_a: association slot\n    range: boolean\n    description: >-\n      a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes\n      the mechanism of action for a result.\n    exact_mappings:\n      - NCIT:C54680\n      - MI:2044\n      - LOINC:MTHU019741\n\n  knowledge source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which the knowledge expressed in an Association was\n      retrieved, directly or indirectly. This can be any resource through which the\n      knowledge passed on its way to its currently serialized form. In practice,\n      implementers should use one of the more specific subtypes of this generic property.\n    range: information resource\n    close_mappings:\n      - pav:providedBy\n\n  provided by:\n    is_a: node property\n    description: >-\n      The value in this node property represents the knowledge provider that created or assembled the\n      node and all of its attributes.  Used internally to represent how a particular node made its way into a\n      knowledge provider or graph.\n    multivalued: true\n\n  primary knowledge source:\n    is_a: knowledge source\n    description: >-\n      The most upstream source of the knowledge expressed in an Association that an\n      implementer can identify.  Performing a rigorous analysis of upstream data providers is expected; every effort\n      is made to catalog the most upstream source of data in this property.  Only one data source should be declared\n      primary in any association.  \"aggregator knowledge source\" can be used to caputre non-primary sources.\n    range: information resource\n    notes: >-\n      For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then \n      incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to \n      the NCATS ARS. The retrieval path for this Edge is as follows: \n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   MolePro  --retrieved_from--> ChEMBL --retrieved_from-->  ClinicalTrials.gov\n      The \"primary knowledge source\" for this edge is \"infores:clinical-trials-gov\".  \"infores:chembl\" and \"infores:molecular_data_provider\"\n      are listed in the \"aggregator knowledge source\" property.\n    multivalued: false\n\n  aggregator knowledge source:\n    is_a: knowledge source\n    description: >-\n      An intermediate aggregator resource from which knowledge expressed in an Association was\n      retrieved downstream of the original source, on its path to its current serialized form.\n    range: information resource\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which data was retrieved and subsequently used as\n      evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data set:\n    is_a: association slot\n    description: >-\n      A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n\n  chi squared statistic:\n    is_a: association slot\n    range: float\n    description: >-\n      represents the chi-squared statistic computed from observations\n    exact_mappings:\n      - STATO:0000030\n\n  p value:\n    aliases: ['unadjusted p value']\n    is_a: association slot\n    range: float\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    exact_mappings:\n      - OBI:0000175\n      - NCIT:C44185\n      - EDAM-DATA:1669\n\n  evidence count:\n    is_a: association slot\n    description: >-\n      The number of evidence instances that are connected to an association.\n    range: integer\n\n  concept count subject:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the subject slot of an association.\n    range: integer\n    examples:\n      - value: 489\n\n  concept count object:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the object slot of an association.\n    range: integer\n\n  concept pair count:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      both the subject and object concept of an association.\n    range: integer\n    examples:\n      - value: 1731\n\n  expected count:\n    is_a: association slot\n    description: >-\n      The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and \n      object concept of an association if the subject and object concepts are independent.\n\n  relative frequency subject:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the subject\n      concept appears in these same records.\n    range: float\n    examples:\n      - value: 0.01840490798\n\n  relative frequency object:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the object\n      concept appears in these same records.\n    range: string\n\n  relative frequency subject confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_subject calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  relative frequency object confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_object calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  adjusted p value:\n    is_a: p value\n    description: >-\n      The adjusted p-value is the probability of obtaining test results\n      at least as extreme as the results actually observed, under the assumption that\n      the null hypothesis is correct, adjusted for multiple comparisons.  \n      P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) \n      rather than expressing a statement of inequality (P<. 05), unless P<.\n    range: float\n\n  bonferonni adjusted p value:\n    is_a: adjusted p value\n    description: >-\n      The Bonferroni correction is an adjustment made to P values when several dependent or independent \n      statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni \n      correction, divide the critical P value (α) by the number of comparisons being made.  P is always italicized and \n      capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality \n      (P<. 05), unless P<.\n    range: float\n    examples:\n      - value: 0.018\n\n  supporting text:\n    is_a: association slot\n    description: The segment of text from a document that supports the mined assertion.\n    multivalued: true\n    range: string\n    examples:\n      - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer.\n\n  supporting documents:\n    is_a: association slot\n    description: >-\n      One or more referencable documents that report the statement expressed in an Association, or provide \n      information used as evidence supporting this statement.\n    range: uriorcurie\n    multivalued: true\n    examples:\n      - value: PMID:12345678\n\n  subject location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the subject concept of the extracted assertion.\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  object location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the object concept of the extracted assertion\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  extraction confidence score:\n    is_a: association slot\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    range: integer\n    examples:\n        - value: 15\n\n  supporting document type:\n    is_a: association slot\n    description: >-\n      The document type (e.g., Journal Article, Case Study, Preprint) for\n      the supporting document used in a Text Mining Result.\n    range: string\n    examples:\n      - value: Journal Article\n\n  supporting document year:\n    is_a: association slot\n    description: >-\n      The document year (typically the publication year) for the supporting\n      document used in a Text Mining Result.\n    range: integer\n    examples:\n      - value: 1999\n\n  supporting text section type:\n    is_a: association slot\n    description: >-\n      The section of the supporting text of a Text Mining Result within\n      the supporting document. This is in the form of the name of the document section\n      (e.g., Abstract, Introduction) that contains the supporting text.\n    range: string\n    examples:\n      - value: Introduction\n\n  ln ratio:\n    is_a: association slot\n    description: the natural log of the ratio of co-occurrence to expected\n    range: float\n    examples:\n      - value: 2.922827136\n\n  ln ratio confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the ln_ratio calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: float\n    examples:\n      - value: 2.922827136\n\n  interacting molecules category:\n    is_a: association slot\n    range: ontology class\n    exact_mappings:\n      - MI:1046\n    values_from:\n      - MI\n    examples:\n      - value: MI:1048\n        description: smallmolecule-protein\n\n  expression site:\n    description: >-\n      location in which gene or protein expression takes place.\n      May be cell, tissue, or organ.\n    is_a: association slot\n    range: anatomical entity\n    examples:\n      - value: UBERON:0002037\n        description: cerebellum\n\n  phenotypic state:\n    description: >-\n      in experiments (e.g. gene expression) assaying diseased or unhealthy\n      tissue, the phenotypic state can be put here, e.g. MONDO ID.\n      For healthy tissues, use XXX.\n    is_a: association slot\n    range: disease or phenotypic feature\n\n  publications:\n    aliases: [\"supporting publications\"]\n    singular_name: publication\n    description: >-\n      One or more publications that report the statement expressed in an Association, or provide information used as \n      evidence supporting this statement.\n    is_a: supporting documents\n    multivalued: true\n    range: publication\n\n  associated environmental context:\n    is_a: association slot\n    description: >-\n      An attribute that can be applied to an association where the association holds between two entities\n      located or occurring in a particular environment. For example, two microbial taxa may interact in the context of\n      a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure.\n      # TODO: add examples of values for this property.\n\n  sequence localization attribute:\n    is_a: association slot\n    domain: genomic sequence localization\n    description: >-\n      An attribute that can be applied to a genome sequence localization edge. These edges\n      connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used\n      to ascribe specific positional information and other metadata to the localization. In pragmatic terms\n      this can be thought of as columns in a GFF3 line.\n\n  interbase coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'zero-based', 'half-open', 'space-based' ]\n    description: >-\n      A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1.\n      This is applied to a sequence localization edge.\n    range: integer\n\n  start interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 0).\n    close_mappings:\n      - faldo:begin\n    annotations:\n      opposite_of: end interbase coordinate\n\n  end interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity ends\n      on the chromosome or other entity to which it is located on.\n    close_mappings:\n      - faldo:end\n    annotations:\n      opposite_of: start interbase coordinate\n\n  start coordinate:\n    is_a: base coordinate\n    aliases: [ 'start' ]\n    description: >-\n      The position at which the subject genomic entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 1).\n    exact_mappings:\n      - gff3:start\n    close_mappings:\n      - faldo:begin\n\n  end coordinate:\n    is_a: base coordinate\n    aliases: [ 'end' ]\n    description: >-\n      The position at which the subject genomic entity ends\n      on the chromosome or other entity to which it is located on.\n    exact_mappings:\n      - gff3:end\n    close_mappings:\n      - faldo:end\n\n  genome build:\n    is_a: sequence localization attribute\n    description: >-\n      The version of the genome on which a feature is located.\n      For example, GRCh38 for Homo sapiens.\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  strand:\n    is_a: sequence localization attribute\n    description: >-\n      The strand on which a feature is located. Has a value of '+'\n      (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  phase:\n    is_a: sequence localization attribute\n    domain: coding sequence\n    description: >-\n      The phase for a coding sequence entity. For example, phase of a\n      CDS as represented in a GFF3 with a value of 0, 1 or 2.\n    range: PhaseEnum\n    exact_mappings:\n      - gff3:phase\n\n  FDA approval status:\n    is_a: association slot\n    description: >-\n    range: FDAApprovalStatusEnum\n\n  supporting study metadata:\n    is_a: association slot\n    description: >-\n      Information about a study used to generate information used as evidence to support the knowledge expressed in an \n      Association. In practice, data creators should use one of the more specific subtypes of this property.\n    abstract: true\n\n  supporting study method type:\n    is_a: supporting study metadata\n    description: >-\n      A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of \n      experimental assay, or statistical calculation, or computational analysis).\n    range: uriorcurie\n\n  supporting study method description:\n    is_a: supporting study metadata\n    description: >-\n      A uri or curie pointing to information about the methodology used to generate data supporting an Association.\n    range: uriorcurie\n\n  supporting study size:\n    is_a: supporting study metadata\n    description: >-\n      The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a \n      clinical study).\n    range: integer\n\n  supporting study cohort:\n    is_a: supporting study metadata\n    description: >-\n      A description of a study population/cohort that was interrogated to provide evidence for the association \n      (e.g. the inclusion and exclusion criteria).\n    range: string\n\n  supporting study date range:\n    is_a: supporting study metadata\n    description: >-\n      The date range over which data was collected in a study that provided evidence for an Association.\n    range: string\n\n  supporting study context:\n    is_a: supporting study metadata\n    description: >-\n      A term or terms describing the experimental setting/context in which evidence supporting the Association was \n      generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue \n      type, disease, etc.).\n    range: string\nclasses:\n\n  mapping collection:\n    description: >-\n      A collection of deprecated mappings.\n    abstract: true\n    slots:\n      - predicate mappings\n    tree_root: true\n\n  predicate mapping:\n    description: >-\n      A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should\n      be done to use a qualified statement in its place.\n    slots:\n      - mapped predicate\n      - subject aspect qualifier\n      - subject direction qualifier\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - predicate\n      - qualified predicate\n      - object aspect qualifier\n      - object direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object derivative qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - species context qualifier\n      - exact match\n      - narrow match\n      - broad match\n\n\n  ## ----------\n  ## ATTRIBUTES\n  ## ----------\n\n  ## Ontology Classes\n\n  ontology class:\n    mixin: true\n    slots:\n      - id\n    description: >-\n      a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in\n      a biolink compatible KG can be considered both instances of biolink classes, and\n      OWL classes in their own right. In general you should not need to use this class directly.\n      Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897),\n      use bl:BiologicalProcess as the type.\n    exact_mappings:\n      - owl:Class\n      - schema:Class\n    comments:\n      - >-\n        This is modeled as a mixin. 'ontology class' should not be the primary type of a\n        node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity\n        (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\n      - >-\n        Note that formally this is a metaclass. Instances of this class are instances in the graph,\n        but can be the object of 'type' edges. For example, if we had a node in the graph representing\n        a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample,\n        and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\n    see_also:\n      - https://github.com/biolink/biolink-model/issues/486\n    examples:\n      - value: UBERON:0000955\n        description: >-\n          the class 'brain' from the Uberon anatomy ontology\n    id_prefixes:\n      - MESH\n      - UMLS\n      - KEGG.BRITE ## br/ko number\n  \n  annotation:\n    description: >-\n      Biolink Model root class for entity annotations.\n    abstract: true\n\n  quantity value:\n    is_a: annotation\n    description: >-\n      A value of an attribute that is quantitative and measurable,\n      expressed as a combination of a unit and a numeric value\n    slots:\n      - has unit\n      - has numeric value\n\n  # Alignment attempted of the biolink:Attribute model\n  # to the proposed TRAPI Release 1.1 Attribute schema, i.e.\n  #\n  # attribute_name: \"assertionAuthoredBy\",\n  # attribute_type: SEPIO:0000130,\n  # value: \"ORCID:12345\",\n  # value_type: \"wd:Q51044\",\n  # value_type_name: \"ORCID ID\"\n  # url: https://orcid.org/12345\n  # source: ORCID\n\n  attribute:\n    is_a: named thing\n    mixins:\n      - ontology class\n    description: >-\n      A property or characteristic of an entity.\n      For example, an apple may have properties such as color, shape, age, crispiness.\n      An environmental sample may have attributes such as depth, lat, long, material.\n    slots:\n      - name                   # 'attribute_name'\n      - has attribute type     # 'attribute_type'\n      # 'value', 'value_type', 'value_type_name'\n      # extracted from either of the next two slots\n      - has quantitative value\n      - has qualitative value\n      - iri                    # 'url'\n    slot_usage:\n      name:\n        description: >-\n          The human-readable 'attribute name' can be set to a string which reflects its context of\n          interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default\n          to the name associated with the 'has attribute type' slot ontology term.\n    id_prefixes:\n      - EDAM-DATA\n      - EDAM-FORMAT\n      - EDAM-OPERATION\n      - EDAM-TOPIC\n    exact_mappings:\n      - SIO:000614\n    in_subset:\n      - samples\n\n  chemical role:\n    is_a: attribute\n    description: >-\n      \tA role played by the molecular entity or part thereof within a chemical context.\n    id_prefixes:\n      - CHEBI\n    exact_mappings:\n      - CHEBI:51086\n    examples:\n      - value: CHEBI:35469 # antidepressant role\n\n  biological sex:\n    is_a: attribute\n    exact_mappings:\n      - PATO:0000047\n\n  phenotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the phenotypic sex of the individual,\n      based upon the reproductive organs present.\n    exact_mappings:\n      - PATO:0001894\n\n  genotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the genotypic sex of the individual,\n      based upon genotypic composition of sex chromosomes.\n    exact_mappings:\n      - PATO:0020000\n\n  severity value:\n    is_a: attribute\n    description: >-\n      describes the severity of a phenotypic feature or disease\n\n  relationship quantifier:\n    mixin: true\n\n  sensitivity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  specificity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  pathognomonicity quantifier:\n    is_a: specificity quantifier\n    description: >-\n      A relationship quantifier between a variant or symptom and a disease, which is\n      high when the presence of the feature implies the existence of the disease\n    mixin: true\n\n  frequency quantifier:\n    is_a: relationship quantifier\n    mixin: true\n    slots:\n      - has count\n      - has total\n      - has quotient\n      - has percentage\n\n  chemical or drug or treatment:\n    mixin: true\n\n  ## ------\n  ## THINGS\n  ## ------\n\n  entity:\n    description: >-\n      Root Biolink Model class for all things and informational relationships, real or imagined.\n    abstract: true\n    slots:\n      - id\n      - iri\n      - category\n      - type   # rdf:type\n      - name\n      - description\n      - has attribute\n      # evidence code(s)?\n\n  named thing:\n    is_a: entity\n    description: \"a databased entity or concept/class\"\n    slots:\n      - provided by\n      - xref\n    slot_usage:\n      category:\n        required: true\n        pattern: '^biolink:\\d+$'\n    exact_mappings:\n      - BFO:0000001\n      - WIKIDATA:Q35120\n      # UMLS Semantic Group \"Objects\"\n      - UMLSSG:OBJC\n      # Entity\n      - STY:T071\n      - dcid:Thing\n\n  relationship type:\n    is_a: ontology class\n    description: >-\n      An OWL property used as an edge label\n\n  taxonomic rank:\n    description: >-\n      A descriptor for the rank within a taxonomic classification.\n      Example instance: TAXRANK:0000017 (kingdom)\n    is_a: ontology class\n    id_prefixes:\n      - TAXRANK\n    mappings:\n      - WIKIDATA:Q427626\n\n  organism taxon:\n    aliases: [ 'taxon', 'taxonomic classification' ]\n    description: >-\n      A classification of a set of organisms. Example instances:\n      NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria).\n      Can also be used to represent strains or subspecies.\n    is_a: named thing\n    slot_usage:\n      has taxonomic rank:\n        range: taxonomic rank\n        multivalued: false\n        mappings:\n          - WIKIDATA:P105\n    values_from:\n      - NCBITaxon\n    exact_mappings:\n      - WIKIDATA:Q16521\n      - STY:T001\n      - bioschemas:Taxon\n    narrow_mappings:\n      - dcid:BiologicalSpecies\n    id_prefixes:\n      - NCBITaxon\n      - MESH\n      - UMLS\n    in_subset:\n      - model_organism_database\n  \n  ## Temporal Entities\n  \n  event:\n    is_a: named thing\n    description: >-\n      Something that happens at a given place and time.\n    exact_mappings:\n      - NCIT:C25499\n      # UMLS \"Event\"\n      - STY:T051\n\n  ## Administrative Entities\n\n  administrative entity:\n    is_a: named thing\n    abstract: true\n\n  study result:\n    abstract: true\n    description: >- \n      A collection of data items from a study that are about a particular study subject or experimental unit (the \n      'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation\n      of this data as evidence.\n    notes:\n      The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, \n      that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific \n      focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any \n      scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational \n      analyses, or a larger scale clinical trial or experimental research investigation.\n    is_a: information content entity\n\n  study:\n    description: a detailed investigation and/or analysis\n    is_a: information content entity\n    exact_mappings:\n      - NCIT:C63536\n    close_mappings:\n      - SIO:001066\n      - SEPIO:0000004\n    narrow_mappings:\n      - SIO:000994\n\n  study variable:\n    is_a: information content entity\n    description: a variable that is used as a measure in the investigation of a study\n    narrow_mappings:\n      - NCIT:C142192 # specifies clinical study\n    close_mappings:\n      - STATO:0000258\n      - SIO:000367\n\n  common data element:\n    is_a: information content entity\n    description: >- \n      A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable \n      responses, used systematically across different sites, studies, or clinical trials to ensure consistent \n      data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. \n      (https://cde.nlm.nih.gov/home)\n    close_mappings:\n      - NCIT:C19984\n\n  ## epc result sets\n  concept count analysis result:\n    is_a: study result\n    description: >-\n      A result of a concept count analysis.\n\n  observed expected frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a observed expected frequency analysis.\n\n  relative frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a relative frequency analysis.\n\n  text mining result:\n    is_a: study result\n    description: >-\n      A result of text mining.\n\n  chi squared analysis result:\n    is_a: study result\n    description: >-\n      A result of a chi squared analysis.\n\n  agent:\n    is_a: administrative entity\n    aliases: [ 'group' ]\n    description: >-\n      person, group, organization or project that provides\n      a piece of information (i.e. a knowledge association)\n    slots:\n      - affiliation\n      - address\n    exact_mappings:\n      - prov:Agent\n      - dct:Agent\n    narrow_mappings:\n      # Organization\n      - UMLSSG:ORGA\n      - STY:T092\n      # Health Care Related Organization\n      - STY:T093\n      # Professional Society\n      - STY:T094\n      # Self-help or Relief Organization\n      - STY:T095\n      # Group\n      - STY:T096\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Different classes of agents have distinct preferred identifiers.\n          For publishers, use the ISBN publisher code.\n          See https://grp.isbn-international.org/ for publisher code lookups.\n          For editors, authors and  individual providers, use the individual's\n          ORCID if available; Otherwise, a ScopusID, ResearchID or\n          Google Scholar ID ('GSID') may be used if the author ORCID is unknown.\n          Institutional agents could be identified by an\n          International Standard Name Identifier ('ISNI') code.\n        values_from:\n          # CURIE space for publishers\n          - isbn\n          # CURIE space for authors\n          - ORCID\n          - ScopusID\n          - ResearchID\n          - GSID\n          # Institutional agents\n          - isni\n      name:\n        description: >-\n          it is recommended that an author's 'name' property\n          be formatted as \"surname, firstname initial.\"\n    id_prefixes:\n      - isbn\n      - ORCID\n      - ScopusID\n      - ResearchID\n      - GSID\n      - isni\n\n  ## General Information Entities\n\n  information content entity:\n    aliases: [ 'information', 'information artefact', 'information entity' ]\n    abstract: true\n    is_a: named thing\n    description: >-\n      a piece of information that typically describes\n      some topic of discourse or is used as support.\n    slots:\n      - license\n      - rights\n      - format\n      - creation date\n    id_prefixes:\n      - doi\n    exact_mappings:\n      - IAO:0000030\n    narrow_mappings:\n      # UMLS Semantic Group \"Concepts & Ideas\"\n      - UMLSSG:CONC\n      # Conceptual Entity\n      - STY:T077\n      # Idea or Concept\n      - STY:T078\n      # Temporal Concept\n      - STY:T079\n      # Qualitative Concept\n      - STY:T080\n      # Quantitative Concept\n      - STY:T081\n      # Spatial Concept\n      - STY:T082\n      # Regulation or Law\n      - STY:T089\n      # Group Attribute\n      - STY:T102\n      # Functional Concept\n      - STY:T169\n      # Language\n      - STY:T171\n      # Classification\n      - STY:T185\n\n  dataset:\n    description: >-\n      an item that refers to a collection of data from a data source.\n    is_a: information content entity\n    exact_mappings:\n      - IAO:0000100\n      - dctypes:Dataset\n      - schema:dataset\n      - dcid:Dataset\n\n  dataset distribution:\n    is_a: information content entity\n    description: >-\n      an item that holds distribution level information about a dataset.\n    slots:\n      - distribution download url\n    exact_mappings:\n      - dcat:Distribution\n\n  dataset version:\n    description: >-\n      an item that holds version level information about a dataset.\n    is_a: information content entity\n    slots:\n      - has dataset\n      - ingest date\n      - has distribution\n\n  dataset summary:\n    description: >-\n      an item that holds summary level information about a dataset.\n    is_a: information content entity\n    slots:\n      - source web page\n      - source logo\n\n  confidence level:\n    is_a: information content entity\n    description: >-\n      Level of confidence in a statement\n    values_from:\n      - cio\n    exact_mappings:\n      - CIO:0000028\n      # statement confidence\n      - SEPIO:0000187\n    close_mappings:\n      # assertion confidence levels\n      - SEPIO:0000167\n\n  evidence type:\n    is_a: information content entity\n    aliases: [ 'evidence code' ]\n    description: >-\n      Class of evidence that supports an association\n    values_from:\n      - eco\n    exact_mappings:\n      - ECO:0000000\n\n  information resource:\n    is_a: information content entity\n    aliases: [ 'knowledgebase' ]\n    description: >-\n      A database or knowledgebase and its supporting ecosystem of interfaces \n      and services that deliver content to consumers (e.g. web portals, APIs, \n      query endpoints, streaming services, data downloads, etc.).\n      A single Information Resource by this definition may span many different datasets or\n      databases, and include many access endpoints and user\n      interfaces. Information Resources include project-specific resources\n      such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.\n    in_subset:\n      - translator_minimal\n\n\n  ## Publications\n\n  # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies\n  publication:\n    is_a: information content entity\n    description: >-\n      Any published piece of information. Can refer to a whole publication,\n      its encompassing publication (i.e. journal or book) or to a part of a\n      publication, if of significant knowledge scope (e.g. a figure, figure\n      legend, or section highlighted by NLP). The scope is intended to be\n      general and include information published on the web, as well as printed\n      materials, either directly or in one of the Publication Biolink\n      category subclasses.\n    slots:\n      - authors\n      - pages\n      - summary\n      - keywords\n      - mesh terms\n      - xref\n    # In addition to embedded slots, instances of 'contributor association'\n    # may be used to more extensively document publisher, editor and author details\n    slot_usage:\n      id:\n        description: >-\n          Different kinds of publication subtypes will have different preferred\n          identifiers (curies when feasible). Precedence of identifiers for\n          scientific articles is as follows: PMID if available; DOI if not; actual\n          alternate CURIE otherwise. Enclosing publications (i.e. referenced by\n          'published in' node property) such as books and journals, should have\n          industry-standard identifier such as from ISBN and ISSN.\n      name:\n        description: >-\n          the 'title' of the publication is generally recorded in the 'name'\n          property (inherited from NamedThing). The field name 'title' is now also\n          tagged as an acceptable alias for the node property 'name' (just in case).\n      type:\n        slot_uri: dct:type\n        required: true\n        description: >-\n          Ontology term for publication type may be drawn from\n          Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),\n          FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),\n          the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),\n          the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres\n          (http://vocabularies.coar-repositories.org/documentation/resource_types/),\n          Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or\n          equivalent publication type ontology. When a given publication type ontology term\n          is used within a given knowledge graph, then the CURIE identified term must be\n          documented in the graph as a concept node of biolink:category biolink:OntologyClass.\n        values_from: # Not sure which takes precedence, if any...\n          - dctypes\n          - fabio\n          - MESH_PUB\n          - COAR_RESOURCE\n          - WIKIDATA\n      pages:\n        multivalued: true\n        description: >-\n          When a 2-tuple of page numbers are provided, they represent\n          the start and end page of the publication within its parent publication context.\n          For books, this may be set to the total number of pages of the book.\n    exact_mappings:\n      - IAO:0000311\n    narrow_mappings:\n      - IAO:0000013\n      # UMLS Semantic Type \"Intellectual Product\"\n      - STY:T170\n    id_prefixes:\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book:\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Books should have industry-standard identifier such as from ISBN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'book'.\n    id_prefixes:\n      - isbn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book chapter:\n    is_a: publication\n    slots:\n      - published in\n      - volume\n      - chapter\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent book containing the chapter\n          should have industry-standard identifier from ISBN.\n    in_subset:\n      - model_organism_database\n\n  serial:\n    aliases: [ 'journal' ]\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slots:\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Serials (journals) should have industry-standard identifier such as from ISSN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'serial' or 'journal'.\n    id_prefixes:\n      - issn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  article:\n    is_a: publication\n    slots:\n      - published in\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent serial containing the article should\n          have industry-standard identifier from ISSN.\n      iso abbreviation:\n        description: >-\n          Optional value, if used locally as a convenience, is set\n          to the iso abbreviation of the 'published in' parent.\n    id_prefixes:\n      # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces\n      - PMID\n    in_subset:\n      - model_organism_database\n\n  ## Top Level Abstractions of Material & Process Entities\n\n  physical essence or occurrent:\n    description: >-\n      Either a physical or processual entity.\n    mixin: true\n\n\n  physical essence:\n    description: >-\n      Semantic mixin concept.  Pertains to entities that have\n      physical properties such as mass, volume, or charge.\n    is_a: physical essence or occurrent\n    mixin: true\n\n  physical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n    description: >-\n      An entity that has material reality (a.k.a. physical essence).\n    exact_mappings:\n      # Physical Object\n      - STY:T072\n    narrow_mappings:\n      # Manufactured Object\n      - STY:T073\n\n  occurrent:\n    description: >-\n      A processual entity.\n    # biolink:Occurrent is most consistently used as a mixin thus it should\n    # be declared as such and cannot inherit from the non-mixin biolink:NamedThing\n    is_a: physical essence or occurrent\n    mixin: true\n    exact_mappings:\n      - BFO:0000003\n\n  activity and behavior:\n    is_a: occurrent\n    mixin: true\n    description: >-\n      Activity or behavior of any independent integral living,\n      organization or mechanical actor in the world\n    exact_mappings:\n      # Activities & Behaviors\n      - UMLSSG:ACTI\n\n  activity:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      An activity is something that occurs over a period of time and acts upon\n      or with entities; it may include consuming, processing, transforming,\n      modifying, relocating, using, or generating entities.\n    exact_mappings:\n      - prov:Activity\n      - NCIT:C43431\n      # Activity\n      - STY:T052\n    narrow_mappings:\n      # Daily or Recreational Activity\n      - STY:T056\n      # Occupational Activity\n      - STY:T057\n      # Governmental or Regulatory Activity\n      - STY:T064\n      # Machine Activity\n      - STY:T066\n      # Research Activity\n      - STY:T062\n      # Educational Activity\n      - STY:T065\n      # Health Care Activity\n      - STY:T058\n\n  procedure:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      A series of actions conducted in a certain order or manner\n    exact_mappings:\n      # Procedures\n      - UMLSSG:PROC\n      - dcid:MedicalProcedure\n    narrow_mappings:\n      # Laboratory Procedure\n      - STY:T059\n      # Diagnostic Procedure\n      - STY:T060\n      # Therapeutic or Preventive Procedure\n      - STY:T061\n      # Molecular Biology Research Technique\n      - STY:T063\n    id_prefixes:\n      - CPT\n\n  phenomenon:\n    is_a: named thing\n    mixins:\n      - occurrent\n    description: >-\n      a fact or situation that is observed to exist or happen,\n      especially one whose cause or explanation is in question\n    broad_mappings:\n      # the inclusion of 'process' in the definition of these\n      # terms broadens them, relative to 'phenomenon'\n      # Phenomenon or Process\n      - STY:T067\n      # Human-caused Phenomenon or Process\n      - STY:T068\n      # Natural Phenomenon or Process\n      - STY:T070\n    exact_mappings:\n      # Phenomena\n      - UMLSSG:PHEN\n    narrow_mappings:\n      # Laboratory or Test Result\n      - STY:T034\n      # Biologic Function\n      - STY:T038\n      # Environmental Effect of Humans\n      - STY:T069\n\n  device:\n    is_a: named thing\n    description: >-\n      A thing made or adapted for a particular purpose, especially\n      a piece of mechanical or electronic equipment\n    narrow_mappings:\n      # Devices\n      - UMLSSG:DEVI\n      # Medical Device\n      - STY:T074\n      # Research Device\n      - STY:T075\n      # Drug Delivery Device\n      - STY:T203\n      # Biomedical or Dental Material\n      - STY:T122\n\n  ## Scientific Studies\n\n  study population:\n    is_a: population of individual organisms\n    description: >-\n      A group of people banded together or treated as a group as participants in a research study.\n    close_mappings:\n      - WIKIDATA:Q7229825\n\n  subject of investigation:\n    mixin: true\n    description: >-\n      An entity that has the role of being studied in an investigation, study, or experiment\n\n  material sample:\n    aliases: [ 'biospecimen', 'sample', 'biosample', 'physical sample' ]\n    is_a: physical entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A sample is a limited quantity of something (e.g. an individual or set of individuals\n      from a population, or a portion of a substance) to be used for testing, analysis,\n      inspection, investigation, demonstration, or trial use. [SIO]\n    exact_mappings:\n      - OBI:0000747\n      - SIO:001050\n    id_prefixes:\n      - BIOSAMPLE\n      - GOLD.META\n\n  ## Earth Sciences\n\n  planetary entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists at the level of the whole planet\n\n  environmental process:\n    is_a: planetary entity\n    mixins:\n      - occurrent\n    exact_mappings:\n      - ENVO:02500000\n\n  environmental feature:\n    is_a: planetary entity\n    exact_mappings:\n      - ENVO:01000254\n\n  geographic location:\n    is_a: planetary entity\n    description: >-\n      a location that can be described in lat/long coordinates\n    slots:\n      - latitude\n      - longitude\n    exact_mappings:\n      # Geographic Areas\n      - UMLSSG:GEOG\n      # Geographic Area\n      - STY:T083\n\n  geographic location at time:\n    is_a: geographic location\n    description: >-\n      a location that can be described in lat/long coordinates, for a particular time\n    slots:\n      - timepoint\n\n  ## Biological Sciences\n\n  thing with taxon:\n    mixin: true\n    description: >-\n      A mixin that can be used on any entity that can be taxonomically classified.\n      This includes individual organisms; genes, their products and other molecular\n      entities; body parts; biological processes\n    slots:\n      - in taxon\n\n  biological entity:\n    is_a: named thing\n    aliases: [ 'bioentity' ]\n    abstract: true\n    mixins:\n      - thing with taxon\n    narrow_mappings:\n      - WIKIDATA:Q28845870\n      # UMLS Semantic Type \"Experimental Model of Disease\"\n      - STY:T050\n      # SIO term is 'biological entity' but less inclusive than the Biolink scope\n      - SIO:010046\n\n  genomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - STY:T028   # Gene or Genome\n      - GENO:0000897  # Genomic Entity\n\n  epigenomic entity:\n      mixin: true\n      slots:\n        - has biological sequence\n      in_subset:\n        - translator_minimal\n      narrow_mappings:\n\n  molecular entity:\n    is_a: chemical entity\n    description: >-\n      A molecular entity is a chemical entity composed of individual or\n      covalently bonded atoms.\n    slots:\n      - is metabolite\n    narrow_mappings:\n      - STY:T088 # Carbohydrate\n      - STY:T085 # Molecular Sequence\n      - CHEBI:23367 # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical,\n      # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.\n      - bioschemas:MolecularEntity\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  chemical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n      - chemical or drug or treatment # issue 701\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    description: >-\n      A chemical entity is a physical entity that pertains to chemistry or\n      biochemistry.\n    slots:\n      - trade name\n      - available from\n      - max tolerated dose\n      - is toxic\n      - has chemical role\n    exact_mappings:\n      - CHEBI:24431\n      - SIO:010004 # Chemical entity\n      - WIKIDATA:Q79529 # Chemical substance\n      - STY:T103 # Chemical\n    narrow_mappings:\n      - WIKIDATA:Q43460564\n      - STY:T129 # (imft, full name: Immunologic Factor\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS #CAS numbers are given for things like plant extracts as well.\n      - UMLS\n      - ncats.drug\n\n  small molecule:\n    is_a: molecular entity\n    aliases: [ 'chemical substance' ]\n    description: >-\n      A small molecule entity is a molecular entity characterized by availability\n      in small-molecule databases of SMILES, InChI, IUPAC, or other\n      unambiguous representation of its precise chemical structure; for\n      convenience of representation, any valid chemical representation is\n      included, even if it is not strictly molecular (e.g., sodium ion).\n    narrow_mappings:\n      - STY:T196 # Element, Ion, or Isotope\n      - CHEBI:59999\n      - bioschemas:ChemicalSubstance\n      - STY:T123 #(bacs, full name: Biologically Active Substance)\n      - STY:T131 #(hops, full name: Hazardous or Poisonous Substance)\n      - STY:T125 #(horm, full name: Hormone)\n      - STY:T197 #(inch, full name: Inorganic Chemical)\n      - STY:T109 #(orch, full name: Organic Chemical)\n      - STY:T118 #(carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files)\n      - STY:T111 #(eico, full name: Eicosanoid) - same note as above\n      - STY:T119 #(lipd, full name: Lipid) - same note as above\n      - STY:T124 #(nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above\n      - STY:T115 #(opco, full name: Organophosphorus Compound) - same note as above\n      - STY:T110 #(strd, full name: Steroid) - same note as above\n      - STY:T127 # vitamin\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - BIGG.METABOLITE\n      - UMLS\n      - foodb.compound\n    slot_usage:\n      id:\n        examples:\n          - value: CHEBI:29101\n            description: sodium ion\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n\n  chemical mixture:\n    is_a: chemical entity\n    description: >-\n      A chemical mixture is a chemical entity composed of two or more\n      molecular entities.\n    slots:\n      - is supplement\n      - highest FDA approval status\n      - drug regulatory status world wide\n      - routes of delivery\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n    close_mappings:\n      - dcid:ChemicalCompound\n    narrow_mappings:\n      - NCIT:C20401 # monoclonal antibody\n      - SNOMEDCT:49616005 # monoclonal antibody (substance)\n\n  nucleic acid entity:\n    is_a: molecular entity\n    description: >-\n      A nucleic acid entity is a molecular entity characterized by\n      availability in gene databases of nucleotide-based sequence\n      representations of its precise sequence; for convenience of\n      representation, partial sequences of various kinds are included.\n    aliases: [ 'sequence feature', 'genomic entity' ]\n    mixins:\n      - genomic entity\n      - thing with taxon\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000110\n    narrow_mappings:\n      - STY:T086   # Nucleotide Sequence\n      - STY:T114   # Nucleic Acid, Nucleoside, or Nucleotide\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  # G number\n      - KEGG.ENVIRON # E number\n\n  molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A molecular mixture is a chemical mixture composed of two or more\n      molecular entities with known concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n      - ncats.drug\n\n  complex molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A complex molecular mixture is a chemical mixture composed of two or\n      more molecular entities with unknown concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  biological process or activity:\n    description: >-\n      Either an individual molecular activity, or a collection of\n      causally connected molecular activities in a biological system.\n    is_a: biological entity\n    mixins:\n      - occurrent\n      - ontology class\n    id_prefixes:\n      - GO\n      - REACT\n    slots:\n      - has input\n      - has output\n      - enabled by\n\n  molecular activity:\n    description: >-\n      An execution of a molecular function carried out by a\n      gene product or macromolecular complex.\n    is_a: biological process or activity\n    aliases: [ 'molecular function', 'molecular event', 'reaction' ]\n    mixins:\n      - occurrent\n      - ontology class\n    slot_usage:\n      has input:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the input for the reaction\n      has output:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the output for the reaction\n      enabled by:\n        range: macromolecular machine mixin\n        description: >-\n          The gene product, gene, or complex that catalyzes the reaction\n    exact_mappings:\n      - GO:0003674\n      # UMLS Semantic Type \"Molecular Function\"\n      - STY:T044\n    id_prefixes:\n      - GO\n      - REACT\n      - RHEA\n      - metacyc.reaction\n      - EC\n      - TCDB\n      - KEGG.REACTION  ## R number\n      - KEGG.RCLASS    ## RC number\n      - KEGG.ENZYME    ## EC number\n      - KEGG.ORTHOLOGY ## in particular for gut microbiome use case in issue #888\n      - UMLS\n      - BIGG.REACTION\n      - SEED.REACTION\n      - METANETX.REACTION\n\n  biological process:\n    is_a: biological process or activity\n    mixins:\n      - occurrent\n      - ontology class\n    description: >-\n      One or more causally connected executions of molecular functions\n    exact_mappings:\n      - GO:0008150\n      - SIO:000006\n      - WIKIDATA:Q2996394\n    broad_mappings:\n      - WIKIDATA:P682\n    id_prefixes:\n      - GO\n      - REACT\n      - metacyc.reaction\n      - KEGG.MODULE ## M number\n\n  pathway:\n    is_a: biological process\n    mixins:\n      - ontology class\n    exact_mappings:\n      - PW:0000001\n      - WIKIDATA:Q4915012\n    narrow_mappings:\n      - SIO:010526\n      - GO:0007165\n    id_prefixes:\n      - GO\n      - REACT\n      - KEGG\n      - SMPDB\n      - MSigDB\n      - PHARMGKB.PATHWAYS\n      - WIKIPATHWAYS\n      - FB  # FlyBase FBgg*\n      - PANTHER.PATHWAY\n      - KEGG.PATHWAY\n      - ncats.bioplanet\n\n  physiological process:\n    aliases: [ 'physiology' ]\n    is_a: biological process\n    mixins:\n      - ontology class\n    close_mappings:\n    exact_mappings:\n      # Physiologic Function\n      - STY:T039\n      - WIKIDATA:Q30892994\n    narrow_mappings:\n      # Organism Function\n      - STY:T040\n      # Organ or Tissue Function\n      - STY:T042\n      # Cell Function\n      - STY:T043\n      # Genetic Function\n      - STY:T045\n    id_prefixes:\n      - GO\n      - REACT\n\n  behavior:\n    is_a: biological process\n    mixins:\n      - ontology class\n      - activity and behavior\n    exact_mappings:\n      - GO:0007610\n      # Behavior\n      - STY:T053\n    narrow_mappings:\n      # Mental Process\n      - STY:T041\n      # Social Behavior\n      - STY:T054\n      # Individual Behavior\n      - STY:T055\n\n  ## (Bio)chemistry\n\n  processed material:\n    is_a: chemical mixture\n    description: >-\n      A chemical entity (often a mixture) processed\n      for consumption for nutritional, medical or technical use.\n      Is a material entity that is created or changed during material processing.\n    exact_mappings:\n      - OBI:0000047\n    id_prefixes:\n      - UMLS\n\n  drug:\n    is_a: molecular mixture\n    mixins:\n      - chemical or drug or treatment\n      - ontology class\n    description: >-\n      A substance intended for use in the diagnosis, cure,\n      mitigation, treatment, or prevention of disease\n    comments:\n      - The CHEBI ID represents a role rather than a substance\n    broad_mappings:\n      # Pharmacologic Substance: Any natural, endogenously-derived,\n      # synthetic or semi synthetic compound with pharmacologic activity.\n      - STY:T121\n    exact_mappings:\n      - WIKIDATA:Q12140\n      - CHEBI:23888\n      # UMLS Semantic Type \"Clinical Drug\"\n      - STY:T200\n      - dcid:Drug\n    narrow_mappings:\n      # Antibiotic\n      - STY:T195\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n\n  ## Food\n\n  environmental food contaminant:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:78299\n\n  food additive:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:64047\n\n  food:\n    is_a: chemical mixture\n    description: >-\n      A substance consumed by a living organism as a source of nutrition\n    id_prefixes:\n      - foodb.food\n      - FOODON\n      - UMLS\n      - NCIT\n    exact_mappings:\n      # Food\n      - STY:T168\n\n  ## Biology and Biomedical Sciences\n\n  ## Biological Attributes\n\n  organism attribute:\n    is_a: attribute\n    description: >-\n      describes a characteristic of an organismal entity.\n    exact_mappings:\n      # Organism Attribute\n      - STY:T032\n\n  phenotypic quality:\n    aliases: [ 'phenotypic properties' ]\n    is_a: organism attribute\n    description: >-\n      A property of a phenotype\n    examples:\n      - value: weight\n\n    mappings:\n      - PATO:0000001\n\n  genetic inheritance:\n    aliases: [ 'inheritance' ]\n    is_a: biological entity\n    description: >-\n      The pattern or 'mode' in which a particular genetic trait or disorder is passed from one\n      generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\n    exact_mappings:\n      - HP:0000005\n      - GENO:0000141\n      - NCIT:C45827\n    close_mappings:\n      - STY:T045\n    id_prefixes:\n      - HP\n      - GENO\n      - NCIT\n\n  ## Biological Entities\n\n  organismal entity:\n    description: >-\n      A named entity that is either a part of an organism, a whole organism,\n      population or clade of organisms, excluding chemical entities\n    abstract: true\n    is_a: biological entity\n    mixins:\n      - subject of investigation\n    slot_usage:\n      has attribute:\n        description: >-\n          may often be an organism attribute\n    exact_mappings:\n      - WIKIDATA:Q7239\n      # UMLS Semantic Group \"Living Beings\"\n      # Several of the associated semantic types here are probably not\n      # that relevant to the Biolink world, but we keep them here for now.\n      - UMLSSG:LIVB\n      - CARO:0001010\n\n  virus:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A virus is a microorganism that replicates itself as a microRNA\n      and infects the host cell.\n    exact_mappings:\n      - NCBITaxon:10239\n\n  cellular organism:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n    exact_mappings:\n      - NCBITaxon:131567\n\n  life stage:\n    is_a: organismal entity\n    description: >-\n      A stage of development or growth of an organism,\n      including post-natal adult stages\n    exact_mappings:\n      - UBERON:0000105\n    narrow_mappings:\n      # constrained to human life cycles\n      - HsapDv:0000000\n    in_subset:\n      - model_organism_database\n    id_prefixes:\n      - HsapDv\n      - MmusDv\n      - ZFS\n      - FBdv\n      - WBls\n      - UBERON\n\n  individual organism:\n    aliases: [ 'organism' ]\n    description: >-\n      An instance of an organism. For example, Richard Nixon,\n      Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - SIO:010000\n      # Organism\n      - STY:T001\n    narrow_mappings:\n      # Wikidata considers its definition of 'individual' to be constrained to human persons?\n      - WIKIDATA:Q795052\n      - foaf:Person\n    id_prefixes:\n      - ORCID\n\n  population of individual organisms:\n    description: >-\n      A collection of individuals from the same taxonomic class\n      distinguished by one or more characteristics.  Characteristics can\n      include, but are not limited to, shared geographic location, genetics,\n      phenotypes.\n    local_names:\n      ga4gh: population\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - PCO:0000001\n      - SIO:001061\n      # UMLS Semantic Type \"Population Group\"\n      - STY:T098\n      - OBI:0000181\n    id_prefixes:\n      - HANCESTRO\n    in_subset:\n      - model_organism_database\n\n  disease or phenotypic feature:\n    aliases: [ 'phenome' ]\n    is_a: biological entity\n    description: >-\n      Either one of a disease or an individual phenotypic feature.\n      Some knowledge resources such as Monarch treat these as\n      distinct, others such as MESH conflate.  Please see definitions of phenotypic feature and disease in this model\n      for their independent descriptions.  This class is helpful to enforce domains and ranges  \n      that may involve either a disease or a phenotypic feature.\n    union_of:\n      - disease\n      - phenotypic feature\n    narrow_mappings:\n      # UMLS Semantic Type \"Finding\" - more specialized use of 'disease or phenotypic feature'\n      - STY:T033\n\n  disease:\n    aliases: [ 'condition', 'disorder', 'medical condition' ]\n    description: >-\n      A disorder of structure or function, especially one that produces specific \n      signs, phenotypes or symptoms or that affects a specific location and is not simply a \n      direct result of physical injury.  A disposition to undergo pathological processes that exists in an \n      organism because of one or more disorders in that organism.\n    is_a: disease or phenotypic feature\n    exact_mappings:\n      - MONDO:0000001\n      - DOID:4\n      - NCIT:C2991\n      - WIKIDATA:Q12136\n      - SIO:010299\n      # UMLS Semantic Group \"Disorders\"\n      - UMLSSG:DISO\n      # Disease or Syndrome\n      - STY:T047\n      - dcid:Disease\n    narrow_mappings:\n      # Congenital Abnormality\n      - STY:T019\n      # Acquired Abnormality\n      - STY:T020\n      # Mental or Behavioral Dysfunction\n      - STY:T048\n      # Cell or Molecular Dysfunction\n      - STY:T049\n      # Anatomical Abnormality\n      - STY:T190\n      # Neoplastic Process\n      - STY:T191\n      # disease susceptibility\n      - MONDO:0042489\n    id_prefixes:\n      - MONDO\n      - DOID\n      - OMIM\n      - OMIM.PS\n      - orphanet\n      - EFO\n      - UMLS\n      - MESH\n      - MEDDRA\n      - NCIT\n      - SNOMEDCT\n      - medgen\n      - ICD10\n      - ICD9\n      - KEGG.DISEASE ## H number\n      - HP\n      - MP\n    in_subset:\n      - model_organism_database\n\n  phenotypic feature:\n    aliases: [ 'sign', 'symptom', 'phenotype', 'trait', 'endophenotype' ]\n    is_a: disease or phenotypic feature\n    description: >-\n      A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an \n      individual resulting from the interaction of its genotype with its molecular and physical environment.\n    examples:\n      - value: MP:0001262\n        description: decreased body weight\n    exact_mappings:\n      - UPHENO:0001001\n      - SIO:010056\n      - WIKIDATA:Q104053\n      - UMLS:C4021819\n      - NCIT:C16977\n      - SNOMEDCT:8116006 # documented as phenotypic finding and phenotype, also referred to as \"SCTID:8116006\" at SNOMEDCT\n      - MESH:D010641 # phenotype\n    narrow_mappings:\n      - STY:T184 # Sign or Symptom\n      - WIKIDATA:Q169872 # Sign or Symptom\n      # presentation of a disease in clinical medicine\n      - WIKIDATA:Q25203551\n      - ZP:00000000 # zebrafish phenotype\n      - FBcv:0001347 # fly phenotype\n      - HP:0000118 # human phenotype\n      - MP:0000001 # mouse phenotype\n      - WBPhenotype:0000886 # worm phenotype\n      - XPO:00000000 # frog phenotype\n      - FYPO:0000001 # fission yeast phenotype\n      - APO:0000017 # phenotype\n      - TO:0000387 # more narrowly defined here for plants; our definition conflates trait and phenotype.\n    broad_mappings:\n      - BFO:0000019 # quality\n      - PATO:0000001 # quality\n    id_prefixes:\n      - HP\n      - EFO # covered by BFO quality mapping\n      - NCIT\n      - UMLS\n      - MEDDRA # can not find a mapping\n      - MP\n      - ZP\n      - UPHENO\n      - APO\n      - FBcv\n      - WBPhenotype\n      - SNOMEDCT\n      - MESH\n      - XPO\n      - FYPO\n      - TO\n    in_subset:\n      - model_organism_database\n\n  behavioral feature:\n    description: >-\n      A phenotypic feature which is behavioral in nature.\n    is_a: phenotypic feature\n    exact_mappings:\n      - NBO:0000243\n\n  anatomical entity:\n    is_a: organismal entity\n    mixins:\n      - physical essence\n    description: >-\n      A subcellular location, cell type or gross anatomical part\n    exact_mappings:\n      - UBERON:0001062\n      - WIKIDATA:Q4936952\n      # UMLS Semantic Group \"Anatomy\"\n      - UMLSSG:ANAT\n      # UMLS Semantic Type \"Anatomical Structure\"\n      - STY:T017\n      - FMA:62955 # anatomical entity\n      - CARO:0000000  # anatomical entity\n      - SIO:001262 # anatomical entity\n    narrow_mappings:\n      - ZFA:0100000 # zebrafish anatomical entity\n      - FBbt:10000000 # fly anatomical entity\n      - EMAPA:0 # mouse anatomical entity\n      - MA:0000001 # mouse anatomical entity\n      - XAO:0000000 # frog anatomical entity\n      - WBbt:0000100 # c. elegans anatomical entity\n      - NCIT:C12219 # human anatomical entity\n      - GO:0110165 # cellular anatomical entity, also used directly in CL\n    related_mappings:\n      - SNOMEDCT:123037004 # body structure\n    id_prefixes:\n      - UBERON\n      - GO\n      - CL\n      - UMLS\n      - MESH\n      - NCIT\n      - EMAPA\n      - ZFA\n      - FBbt\n      - WBbt\n    in_subset:\n      - model_organism_database\n\n  cellular component:\n    aliases: [ 'cell component', 'cell part' ]\n    is_a: anatomical entity\n    description: >-\n      A location in or around a cell\n    exact_mappings:\n      - GO:0005575\n      - SIO:001400\n      - WIKIDATA:Q5058355\n      # Cell Component\n      - STY:T026\n    broad_mappings:\n      - WIKIDATA:P681\n    id_prefixes:\n      - GO\n      - MESH\n      - UMLS\n      - NCIT\n      - SNOMEDCT\n      - CL\n      - UBERON\n\n  cell:\n    is_a: anatomical entity\n    exact_mappings:\n      - GO:0005623\n      - CL:0000000\n      - SIO:010001\n      - WIKIDATA:Q7868\n      # UMLS Semantic Type \"Cell\"\n      - STY:T025\n      - MESH:D002477 # cells\n    id_prefixes:\n      - CL\n      - PO\n      - UMLS\n      - NCIT\n      - MESH\n      - UBERON\n      - SNOMEDCT\n      - MESH\n\n  cell line:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - CLO:0000031\n    id_prefixes:\n      - CLO\n\n  gross anatomical structure:\n    aliases: [ 'tissue', 'organ' ]\n    is_a: anatomical entity\n    exact_mappings:\n      - UBERON:0010000\n      - WIKIDATA:Q4936952\n    narrow_mappings:\n      # UMLS Semantic Type \"Body Part, Organ, or Organ Component\"\n      - STY:T023\n      # UMLS Semantic Type \"Tissue\"\n      - STY:T024\n      # Embryonic Structure\n      - STY:T018\n    id_prefixes:\n      - UBERON\n      - UMLS\n      - MESH\n      - NCIT\n      - PO\n      - FAO\n\n\n  ## entity mixins\n\n  chemical entity or gene or gene product:\n    description: >-\n      A union of chemical entities and children, and gene or gene product.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  chemical entity or protein or polypeptide:\n    description: >-\n      A union of chemical entities and children, and protein and polypeptide.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  macromolecular machine mixin:\n    description: >-\n      A union of gene locus, gene product, and macromolecular complex. These are\n      the basic units of function in a cell. They either carry out individual\n      biological activities, or they encode molecules which do this.\n    mixin: true\n    slots:\n      - name\n    slot_usage:\n      name:\n        range: symbol type\n        description: >-\n          genes are typically designated by a short symbol and a full name.\n          We map the symbol to the default display name\n          and use an additional slot for full name\n\n  gene or gene product:\n    description: >-\n      A union of gene loci or gene products.\n      Frequently an identifier for one will be used as proxy for another\n    is_a: macromolecular machine mixin\n    mixin: true\n    id_prefixes:\n      - CHEMBL.TARGET\n      - IUPHAR.FAMILY\n\n  gene:\n    description: >-\n      A region (or regions) that includes all of the sequence elements\n      necessary to encode a functional transcript. A gene locus may include\n      regulatory regions, transcribed regions and/or other\n      functional sequence regions.\n    is_a: biological entity\n    mixins:\n      - gene or gene product\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    slots:\n      - symbol\n      - synonym\n      - xref\n    narrow_mappings:\n      - bioschemas:gene\n    broad_mappings:\n      - NCIT:C45822\n    exact_mappings:\n      - SO:0000704\n      - SIO:010035\n      - WIKIDATA:Q7187\n      - dcid:Gene\n    id_prefixes:\n      - NCBIGene\n      - ENSEMBL\n      - HGNC\n      - MGI\n      - ZFIN\n      - dictyBase\n      - WB\n      - WormBase # we have two prefixes here as wormbase supports WormBase:WBGene00000898\n      # and alliancegenome.org and identifiers.org supports WB:WBGene00000898.\n      - FB\n      - RGD\n      - SGD\n      - PomBase\n      - OMIM\n      - KEGG.GENE ## org:gene\n      - UMLS\n      - Xenbase\n      - AspGD\n    in_subset:\n      - model_organism_database\n\n  gene product mixin:\n    description: >-\n      The functional molecular product of a single gene locus.\n      Gene products are either proteins or functional RNA molecules.\n    is_a: gene or gene product\n    mixin: true\n    slots:\n      - synonym\n      - xref\n    exact_mappings:\n      - WIKIDATA:Q424689\n      - GENO:0000907\n      - NCIT:C26548\n    id_prefixes:\n      - UniProtKB\n      - gtpo\n      - PR\n\n  gene product isoform mixin:\n    description: >-\n      This is an abstract class that can be mixed in with different kinds of\n      gene products to indicate that the gene product is intended to represent\n      a specific isoform rather than a canonical or reference or generic\n      product. The designation of canonical or reference may be arbitrary,\n      or it may represent the superclass of all isoforms.\n    is_a: gene product mixin\n    mixin: true\n\n  macromolecular complex:\n    description: >-\n      A stable assembly of two or more macromolecules, i.e. proteins,\n      nucleic acids, carbohydrates or lipids, in which at least one\n      component is a protein and the constituent parts function together.\n    is_a: biological entity\n    mixins:\n      - macromolecular machine mixin\n    exact_mappings:\n      - GO:0032991\n      - WIKIDATA:Q22325163\n    id_prefixes:\n      - INTACT\n      - GO\n      - PR\n      - REACT\n      - ComplexPortal\n    in_subset:\n      - model_organism_database\n\n  ## Genomic Classes\n  nucleosome modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform.\n      e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.\n    mixins:\n      - gene product isoform mixin\n      - genomic entity\n      - epigenomic entity\n\n  genome:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A genome is the sum of genetic material within a cell or virion.\n    exact_mappings:\n      - SO:0001026\n      - SIO:000984\n      - WIKIDATA:Q7020\n    close_mappings:\n      - dcid:GenomeAssemblyUnit\n    in_subset:\n      - model_organism_database\n\n  exon:\n    is_a: nucleic acid entity\n    description: >-\n      A region of the transcript sequence within a gene which is not\n      removed from the primary RNA transcript by RNA splicing.\n    exact_mappings:\n      - SO:0000147\n      - SIO:010445\n      - WIKIDATA:Q373027\n\n  transcript:\n    is_a: nucleic acid entity\n    description: >-\n      An RNA synthesized on a DNA or RNA template by an RNA polymerase.\n    exact_mappings:\n      - SO:0000673\n      - SIO:010450\n      - WIKIDATA:Q7243183\n      - dcid:RNATranscript\n    id_prefixes:\n      - ENSEMBL # ENSEMBL:ENST for human\n      - FB      # FlyBase:FBtr\n    in_subset:\n      - model_organism_database\n\n  coding sequence:\n    is_a: nucleic acid entity\n    exact_mappings:\n      - SO:0000316\n      - SIO:001390\n\n  polypeptide:\n    aliases: [ 'amino acid entity' ]\n    is_a: biological entity\n    description: >-\n      A polypeptide is a molecular entity characterized by availability\n      in protein databases of amino-acid-based sequence representations\n      of its precise primary structure; for convenience of representation,\n      partial sequences of various kinds are included, even if they do not\n      represent a physical molecule.\n    mixins:\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n    in_subset:\n      - model_organism_database\n    narrow_mappings:\n      - SO:0000104 # polypeptide definde in SO conflates protein and polypeptide\n      # Amino Acid, Peptide, or Protein\n      - STY:T116\n      # Amino Acid Sequence\n      - STY:T087\n\n  protein:\n    description: >-\n      A gene product that is composed of a chain of amino acid sequences\n      and is produced by ribosome-mediated translation of mRNA\n    is_a: polypeptide\n    mixins:\n      - gene product mixin\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n      - MESH\n      - ncats.drug\n    broad_mappings:\n      - bioschemas:Protein\n    exact_mappings:\n      - PR:000000001\n      - SIO:010043\n      - WIKIDATA:Q8054\n    narrow_mappings:\n      # Enzyme\n      - STY:T126\n      # Receptor\n      - STY:T192\n\n  protein isoform:\n    aliases: [ 'proteoform' ]\n    is_a: protein\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or\n      reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - UniProtKB # UniProtKB:([A-Z0-9]+-\\d+)\n      - UNIPROT.ISOFORM\n      - PR\n      - ENSEMBL\n\n  protein domain:\n    is_a: biological entity\n    description: >-\n      A conserved part of protein sequence and (tertiary) structure that can evolve,\n      function, and exist independently of the rest of the protein chain.\n      Protein domains maintain their structure and function independently of the proteins in which they are found.\n      e.g. an SH3 domain.\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    exact_mappings:\n      - NCIT:C13379\n      - SIO:001379\n      - UMLS:C1514562\n  \n  posttranslational modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a polypeptide or protein that occurs after translation. \n      e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, \n      protein ubiquitination.\n    mixins:\n      - gene product isoform mixin\n  \n  protein family:\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n\n  nucleic acid sequence motif:\n    aliases: [ 'consensus sequence' ]\n    is_a: biological entity\n    description: >-\n      A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have,\n      a biological significance. e.g. the TATA box promoter motif, transcription factor binding\n      consensus sequences.\n\n  RNA product:\n    is_a: transcript\n    mixins:\n      - gene product mixin\n    exact_mappings:\n      - CHEBI:33697\n      # This SIO term here also mapped to 'biolink:Transcript'; however,\n      # since this 'biolink:RNAProduct' relates more to the biochemical\n      # essence of RNA, then map the SIO term instead to 'biolink:Transcript'\n      # - SIO:010450\n      - WIKIDATA:Q11053\n    id_prefixes:\n      - RNACENTRAL\n\n  RNA product isoform:\n    is_a: RNA product\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or reference RNA\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - RNACENTRAL\n\n  noncoding RNA product:\n    is_a: RNA product\n    id_prefixes:\n      - RNACENTRAL\n      - NCBIGene\n      - ENSEMBL\n    exact_mappings:\n      - SO:0000655\n      - SIO:001235\n\n  microRNA:\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000276\n      - SIO:001397\n      - WIKIDATA:Q310899\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  siRNA:\n    aliases: [ 'small interfering RNA', 'RNAi' ]\n    description: >-\n      A small RNA molecule that is the product of a longer exogenous or\n      endogenous dsRNA, which is either a bimolecular duplex or very long\n      hairpin, processed (via the Dicer pathway) such that numerous siRNAs\n      accumulate from both strands of the dsRNA. SRNAs trigger the cleavage\n      of their target molecules.\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000646\n      - WIKIDATA:Q203221\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  gene grouping mixin:\n    description: >-\n      any grouping of multiple genes or gene products\n    mixin: true\n    slots:\n      - has gene or gene product\n\n  gene family:\n    aliases: [ 'orthogroup', 'protein family' ]\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      # These term definitions focus only on proteins;\n      # the 'biolink:GeneFamily' term would be more inclusive\n      # to describe gene loci, non-coding RNA, etc.\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    description: >-\n      any grouping of multiple genes or gene products related by common descent\n    id_prefixes:\n      - PANTHER.FAMILY\n      - HGNC.FAMILY\n      - FB       # FlyBase FBgg*\n      - interpro # note: may be better to introduce a protein domain/family\n      - CATH\n      - CDD\n      - HAMAP\n      - PFAM\n      - PIRSF\n      - PRINTS\n      - PRODOM\n      - PROSITE\n      - SMART\n      - SUPFAM\n      - TIGRFAM\n      - CATH.SUPERFAMILY\n      - RFAM ## RNAs only\n      - KEGG.ORTHOLOGY ## aka KEGG.KO: K number\n      - EGGNOG\n      - COG\n    in_subset:\n      - model_organism_database\n\n  zygosity:\n    is_a: attribute\n    exact_mappings:\n      - GENO:0000133\n\n  genotype:\n    is_a: biological entity\n    mixins:\n      - physical essence\n      - genomic entity\n      - ontology class\n    description: >-\n      An information content entity that describes a genome by specifying the\n      total variation in genomic sequence and/or gene expression, relative to\n      some established background\n    comments:\n      - Consider renaming as genotypic entity\n    slots:\n      - has zygosity\n    exact_mappings:\n      - GENO:0000536\n      - SIO:001079\n    id_prefixes:\n      - ZFIN\n      - FB   # FlyBase FBba*\n    in_subset:\n      - model_organism_database\n\n  haplotype:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A set of zero or more Alleles on a single instance of a Sequence[VMC]\n    #    slots:\n    #      - completeness\n    exact_mappings:\n      - GENO:0000871\n      - SO:0001024\n      - VMC:Haplotype\n\n  sequence variant:\n    aliases: [ 'allele' ]\n    local_names:\n      agr: allele\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.\n    comments:\n      - This class is for modeling the specific state at a locus.\n        A single DBSNP rs ID could correspond to more than one sequence variants\n        (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\n    exact_mappings:\n      # slightly broader semantics than SO:0001059 - 'sequence alteration'\n      # describes a sequence feature that may have 1..* sequence alterations\n      - WIKIDATA:Q15304597\n    close_mappings:\n      - dcid:Allele\n      - SO:0001060\n      - VMC:Allele\n      - GENO:0000002\n      - SIO:010277\n      - SO:0001060\n    id_prefixes:\n      - CAID # ClinGen Allele Registry\n      - CLINVAR\n      - WIKIDATA\n      # - CIViC needs IRI mapping\n      - DBSNP\n      - MGI\n      - ZFIN\n      - FB\n      - RGD\n      - AGRKB\n      - SPDI\n      - WB\n      - WormBase\n    alt_descriptions:\n      AGR: >-\n        An entity that describes a single affected, endogenous allele.\n        These can be of any type that matches that definition\n      VMC: >-\n        A contiguous change at a Location\n    slots:\n      - has gene\n    slot_usage:\n      has gene:\n        multivalued: true\n        description: Each allele can be associated with any number of genes\n      has biological sequence:\n        description: >-\n          The state of the sequence w.r.t a reference sequence\n      id:\n        examples:\n          - value: ZFIN:ZDB-ALT-980203-1091\n            description: ti282a allele from ZFIN\n          - value: CLINVAR:17681\n            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\n    in_subset:\n      - model_organism_database\n\n  snv:\n    aliases: [ 'single nucleotide variant', 'single nucleotide polymorphism', 'snp' ]\n    is_a: sequence variant\n    description: >-\n      SNVs are single nucleotide positions in genomic DNA at\n      which different sequence alternatives exist\n    exact_mappings:\n      - SO:0001483\n\n  reagent targeted gene:\n    aliases: [ 'sequence targeting reagent' ]\n    is_a: biological entity\n    description: >-\n      A gene altered in its expression level in the context of some\n      experiment as a result of being targeted by gene-knockdown\n      reagent(s) such as a morpholino or RNAi.\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - GENO:0000504\n    in_subset:\n      - model_organism_database\n\n  ## --------------------\n  ## Clinical\n  ## Attributes, Cohort,\n  ## Exposures & Outcomes\n  ## --------------------\n\n  ## Clinical Attributes\n\n  clinical attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a clinical manifestation\n    exact_mappings:\n      # Clinical Attribute\n      - STY:T201\n\n  clinical measurement:\n    is_a: clinical attribute\n    description: >-\n      A clinical measurement is a special kind of attribute which results\n      from a laboratory observation from a subject individual or sample.\n      Measurements can be connected to their subject by the 'has attribute' slot.\n    slot_usage:\n      has attribute type:\n        required: true\n        multivalued: false\n        values_from:\n          - EFO\n          - LOINC\n    exact_mappings:\n      - EFO:0001444\n\n  clinical modifier:\n    is_a: clinical attribute\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the phenotypic abnormality sub-ontology, with respect\n      to severity, laterality, and other aspects\n    exact_mappings:\n\n\n  clinical course:\n    is_a: clinical attribute\n    description: >-\n      The course a disease typically takes from its onset, progression in time, and\n      eventual resolution or death of the affected individual\n    exact_mappings:\n      - HP:0031797\n\n  onset:\n    is_a: clinical course\n    description: >-\n      The age group in which (disease) symptom manifestations appear\n    exact_mappings:\n      - HP:0003674\n\n  clinical entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists in the clinical domain and outside the\n      biological realm. Diseases are placed under biological entities\n\n  clinical trial:\n    is_a: clinical entity\n\n  clinical intervention:\n    is_a: clinical entity\n\n  clinical finding:\n    is_a: phenotypic feature\n    description: >-\n      this category is currently considered broad enough to tag clinical lab\n      measurements and other biological attributes taken as 'clinical traits'\n      with some statistical score, for example, a p value in genetic associations.\n    slot_usage:\n      has attribute:\n        range: clinical attribute\n    id_prefixes:\n      - LOINC\n      - NCIT\n      - EFO\n\n  hospitalization:\n    is_a: clinical intervention\n    exact_mappings:\n      - SNOMEDCT:32485007\n      - WIKIDATA:Q3140971\n\n  socioeconomic attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a socioeconomic manifestation\n    #slot_usage:\n    # need a suitable qualifying socioeconomic ontology target here?\n    # Perhaps some subset of ECTO: https://github.com/EnvironmentOntology/environmental-exposure-ontology\n    #  has attribute type:\n    #     range: socioeconomic ontology\n    # exact_mappings:\n    #  - ??\n\n  ## Cohorts\n\n  case:\n    aliases: [ 'patient', 'proband' ]\n    is_a: individual organism\n    description: >-\n      An individual (human) organism that has a patient role in some clinical context.\n    mixins:\n      - subject of investigation\n\n  cohort:\n    is_a: study population\n    description: >-\n      A group of people banded together or treated as a group who share common characteristics.\n      A cohort 'study' is a particular form of longitudinal study that samples a cohort,\n      performing a cross-section at intervals through time.\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - WIKIDATA:Q1303415\n    narrow_mappings:\n      # Professional or Occupational Group\n      - STY:T097\n      # Family Group\n      - STY:T099\n      # Age Group\n      - STY:T100\n      # Patient or Disabled Group\n      - STY:T101\n\n  ## Exposures\n\n  exposure event:\n    is_a: ontology class\n    aliases: [ 'exposure', 'experimental condition' ]\n    mixin: true\n    slots:\n      - timepoint\n    description: >-\n      A (possibly time bounded) incidence of a feature of the environment of an organism that\n      influences one or more phenotypic features of that organism, potentially mediated by genes\n    exact_mappings:\n      - XCO:0000000\n    in_subset:\n      - model_organism_database\n\n  # TODO - confirm that genomic backgrounds are exposures\n  genomic background exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - gene grouping mixin\n      - physical essence\n      - genomic entity\n      - thing with taxon\n      - ontology class\n    description: >-\n      A genomic background exposure is where an individual's specific genomic background\n      of genes, sequence variants or other pre-existing genomic conditions constitute\n      a kind of 'exposure' to the organism, leading to or influencing an outcome.\n\n  pathological entity mixin:\n    description: >-\n      A pathological (abnormal) structure or process.\n    mixin: true\n    exact_mappings:\n      - MPATH:0\n    narrow_mappings:\n      - HP:0000118\n\n  pathological process:\n    description: >-\n      A biologic function or a process having an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: biological process\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - OBI:1110122\n      - NCIT:C16956\n    narrow_mappings:\n      # metastasis\n      - NCIT:C19151\n      - EFO:0009708\n      - STY:T046\n      - STY:T037\n\n  pathological process exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A pathological process, when viewed as an exposure, representing\n      a precondition, leading to or influencing an outcome,\n      e.g. autoimmunity leading to disease.\n\n  pathological anatomical structure:\n    description: >-\n      An anatomical structure with the potential of have an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: anatomical entity\n    mixins:\n      - pathological entity mixin\n\n  pathological anatomical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      An abnormal anatomical structure, when viewed as an exposure,\n      representing an precondition, leading to or influencing an outcome,\n      e.g. thrombosis leading to an ischemic disease outcome.\n\n  disease or phenotypic feature exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - pathological entity mixin\n    description: >-\n      A disease or phenotypic feature state, when viewed as an exposure,\n      represents an precondition, leading to or influencing an outcome,\n      e.g. HIV predisposing an individual to infections; a relative deficiency\n      of skin pigmentation predisposing an individual to skin cancer.\n\n  chemical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    slots:\n      - has quantitative value\n    description: >-\n      A chemical exposure is an intake of a particular\n      chemical entity.\n    exact_mappings:\n      # this ECTO term is not visibly defined but\n      # the 9000000-series identifiers seems to be the\n      # numeric space of chemical exposure definitions\n      - ECTO:9000000\n      - SIO:001399\n\n  complex chemical exposure:\n    is_a: attribute\n    description: >-\n      A complex chemical exposure is an intake of a chemical\n      mixture (e.g. gasoline), other than a drug.\n\n  drug exposure:\n    is_a: chemical exposure\n    aliases: [ 'drug intake', 'drug dose', 'medication intake' ]\n    description: >-\n      A drug exposure is an intake of a particular drug.\n    mixins:\n      - exposure event\n    broad_mappings:\n      # slightly broader than just drug effects on a biological system\n      - SIO:001005\n    exact_mappings:\n      - ECTO:0000509\n\n  # TODO: deprecate?\n  drug to gene interaction exposure:\n    description: >-\n      drug to gene interaction exposure is a drug exposure is where the\n      interactions of the drug with specific genes are known to constitute\n      an 'exposure' to the organism, leading to or influencing an outcome.\n    is_a: drug exposure\n    mixins:\n      - gene grouping mixin\n\n  treatment:\n    aliases: [ 'medical action', 'medical intervention' ]\n    # 'named thing' seems too generic here but not sure what applies better here\n    is_a: named thing\n    mixins:\n      - exposure event\n      - chemical or drug or treatment\n    description: >-\n      A treatment is targeted at a disease or phenotype and may involve\n      multiple drug 'exposures', medical devices and/or procedures\n    slots:\n      - has drug\n      - has device\n      - has procedure\n    exact_mappings:\n      - OGMS:0000090\n      - SIO:001398\n    broad_mappings:\n      - MAXO:0000058\n\n  biotic exposure:\n    is_a: attribute\n    aliases: [ 'viral exposure', 'bacterial exposure' ]\n    mixins:\n      - exposure event\n    description: >-\n      An external biotic exposure is an intake of (sometimes pathological)\n      biological organisms (including viruses).\n\n  geographic exposure:\n    is_a: environmental exposure\n    mixins:\n      - exposure event\n    description: >-\n      A geographic exposure is a factor relating to geographic\n      proximity to some impactful entity.\n    close_mappings:\n      - dcid:GeologicalEvent\n    narrow_mappings:\n      - dcid:IceStoremEvent\n      - dcid:LakeEffectSnowEvent\n      - dcid:LandslideEvent\n      - dcid:MarineDenseFogEvent\n      - dcid:MarineLighteningEvent\n      - dcid:MarineStrongWindEvent\n      - dcid:MarineThunderstormWindEvent\n      - dcid:StormEvent\n      - dcid:StormSurgeTideEvent\n      - dcid:StrongWindEvent\n      - dcid:ThunderstormWindEvent\n      - dcid:TornadoEvent\n      - dcid:TropicalDepressionEvent\n      - dcid:WinterStoremEvent\n\n  environmental exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A environmental exposure is a factor relating to abiotic processes\n      in the environment including sunlight (UV-B), atmospheric (heat,\n      cold, general pollution) and water-born contaminants.\n\n  behavioral exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A behavioral exposure is a factor relating to behavior impacting an individual.\n\n  socioeconomic exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A socioeconomic exposure is a factor relating to social and\n      financial status of an affected individual (e.g. poverty).\n    slot_usage:\n      has attribute:\n        range: socioeconomic attribute\n        required: true\n\n  ## Outcomes\n\n  outcome:\n    mixin: true\n    description: >-\n      An entity that has the role of being the consequence of an exposure event.\n      This is an abstract mixin grouping of various categories of possible\n      biological or non-biological (e.g. clinical) outcomes.\n\n  pathological process outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of a pathological process.\n\n  pathological anatomical outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of an abnormal anatomical structure.\n\n  disease or phenotypic feature outcome:\n    mixins:\n      - outcome\n    description: >-\n      Physiological outcomes resulting from an exposure event which\n      is the manifestation of a disease or other characteristic phenotype.\n\n  behavioral outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the manifestation of human behavior.\n\n  hospitalization outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the increased manifestation of acute (e.g. emergency\n      room visit) or chronic (inpatient) hospitalization.\n\n  mortality outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome of death from resulting from an exposure event.\n\n  epidemiological outcome:\n    mixins:\n      - outcome\n    description: >-\n      An epidemiological outcome, such as societal disease\n      burden, resulting from an exposure event.\n    related_mappings:\n      - NCIT:C19291\n\n  socioeconomic outcome:\n    mixins:\n      - outcome\n    description: >-\n      An general social or economic outcome, such as\n      healthcare costs, utilization, etc., resulting from an exposure event\n\n  ## ------------\n  ## ASSOCIATIONS\n  ## ------------\n\n  association:\n    is_a: entity\n    description: >-\n      A typed association between two entities, supported by evidence\n    comments:\n      - This is roughly the model used by biolink and ontobio at the moment\n    slots:\n      - subject\n      - predicate\n      - object\n      - negated\n      - qualifiers\n      - publications\n      - has evidence\n      - knowledge source\n      - primary knowledge source\n      - aggregator knowledge source\n      - timepoint\n      - original subject\n      - original predicate\n      - original object\n    slot_usage:\n      type:\n        description: rdf:type of biolink:Association should be fixed at rdf:Statement\n      category:\n        range: category type\n        required: false\n    exact_mappings:\n      - OBAN:association\n      - rdf:Statement\n      - owl:Axiom\n\n\n  chemical entity assesses named thing association:\n    is_a: association\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: assesses\n\n\n  contributor association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      Any association between an entity (such as a publication)\n      and various agents that contribute to its realisation\n    slot_usage:\n      subject:\n        range: information content entity\n        description: >-\n          information content entity which an agent has helped realise\n      predicate:\n        subproperty_of: contributor\n        description: >-\n          generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\n      object:\n        range: agent\n        description: >-\n          agent helping to realise the given entity (e.g. such as a publication)\n      qualifiers:\n        description: >-\n          this field can be used to annotate special characteristics of an\n          agent relationship, such as the fact that a given author agent of\n          a publication is the 'corresponding author'\n\n  genotype to genotype part association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a genotypic entity that is a sub-component of it\n    slot_usage:\n      predicate:\n        subproperty_of: has variant part\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: genotype\n        description: >-\n          child genotype\n\n  genotype to gene association:\n    description: >-\n      Any association between a genotype and a gene.\n      The genotype have have multiple variants in that gene or a single one.\n      There is no assumption of cardinality\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: gene\n        description: >-\n          gene implicated in genotype\n\n  genotype to variant association:\n    description: >-\n      Any association between a genotype and a sequence variant.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: sequence variant\n        description: >-\n          gene implicated in genotype\n\n  gene to gene association:\n    aliases: [ 'molecular or genetic interaction' ]\n    description: >-\n      abstract parent class for different kinds of gene-gene or gene product\n      to gene product relationships. Includes homology and interaction.\n    abstract: true\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          the subject gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n      object:\n        range: gene or gene product\n        description: >-\n          the object gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n\n  gene to gene homology association:\n    description: >-\n      A homology association between two genes. May be orthology (in which\n      case the species of subject and object should differ) or paralogy\n      (in which case the species may be the same)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n      predicate:\n        subproperty_of: homologous to\n        symmetric: true\n        description: >-\n          homology relationship type\n      object:\n        range: gene or gene product\n\n  gene to gene family association:\n    description: >-\n      Set membership of a gene in a family of genes related by common\n      evolutionary ancestry usually inferred by sequence comparisons.\n      The genes in a given family generally share common sequence motifs which\n      generally map onto shared gene product structure-function relationships.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene family\n      predicate:\n        subproperty_of: member of\n        symmetric: false\n        description: >-\n          membership of the gene in the given gene family.\n\n  gene expression mixin:\n    description: >-\n      Observed gene expression intensity, context (site, stage) and\n      associated phenotypic status within which the expression occurs.\n    mixin: true\n    slots:\n      - quantifier qualifier\n      - expression site\n      - stage qualifier\n      - phenotypic state\n    slot_usage:\n      quantifier qualifier:\n        description: >-\n          Optional quantitative value indicating degree of expression.\n\n  gene to gene coexpression association:\n    description: >-\n      Indicates that two genes are co-expressed,\n      generally under the same conditions.\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: coexpressed with\n        symmetric: true\n\n  pairwise gene to gene interaction:\n    description: >-\n      An interaction between two genes or two gene products.\n      May be physical (e.g. protein binding) or genetic (between genes).\n      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      predicate:\n        subproperty_of: interacts with\n        symmetric: true\n        description: \"interaction relationship type\"\n    narrow_mappings:\n      - dcid:ProteinProteinInteraction\n\n  pairwise molecular interaction:\n    description: >-\n      An interaction at the molecular level between two physical entities\n    is_a: pairwise gene to gene interaction\n    slots:\n      - interacting molecules category\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: molecular entity\n      id:\n        description: >-\n          identifier for the interaction. This may come from an interaction database such as IMEX.\n        examples:\n          - value: WB:WBInteraction000538741\n        values_from:\n          - IMEX\n          - BioGRID\n      predicate:\n        subproperty_of: interacts with\n        description: \"interaction relationship type\"\n        examples:\n          - value: RO:0002447\n            description: the subject molecular phosphorylates the object molecule\n      object:\n        range: molecular entity\n\n  cell line to entity association mixin:\n    description: >-\n      An relationship between a cell line and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: cell line\n\n  # TODO: figure out what gives with subject range\n  cell line to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - cell line to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    description: >-\n      An relationship between a cell line and a disease or a phenotype, where\n      the cell line is derived from an individual with that disease or phenotype.\n    slot_usage:\n      subject:\n        #        - range: cell line\n        #        - range: disease or phenotypic feature\n        range: disease or phenotypic feature\n\n  chemical entity to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity that is an interactor\"\n\n  drug to entity association mixin:\n    description: >-\n      An interaction between a drug and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: drug\n        description: \"the drug that is an interactor\"\n\n  chemical to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity or entity that is an interactor\"\n\n  case to entity association mixin:\n    description: >-\n      An abstract association for use where the case is the subject\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: case\n        description: \"the case (e.g. patient) that has the property\"\n\n  chemical to chemical association:\n    description: >-\n      A relationship between two chemical entities. This can encompass actual\n      interactions as well as temporal causal edges, e.g. one chemical converted to another.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: chemical entity\n        description: \"the chemical element that is the target of the statement\"\n\n  reaction to participant association:\n    description:\n    is_a: chemical to chemical association\n    slots:\n      - stoichiometry\n      - reaction direction\n      - reaction side\n    slot_usage:\n      subject:\n        range: molecular entity\n    defining_slots:\n      - subject\n      - predicate\n      - object\n\n  reaction to catalyst association:\n    description:\n    is_a: reaction to participant association\n    slot_usage:\n      object:\n        range: gene or gene product\n\n  chemical to chemical derivation association:\n    description: >-\n      A causal relationship between two chemical entities, where the subject\n      represents the upstream entity and the object represents the downstream.\n      For any such association there is an implicit reaction:\n        IF\n        R has-input C1 AND\n        R has-output C2 AND\n        R enabled-by P AND\n        R type Reaction\n        THEN\n        C1 derives-into C2 <>\n    is_a: chemical to chemical association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - catalyst qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: >-\n          the upstream chemical entity\n      object:\n        range: chemical entity\n        description: >-\n          the downstream chemical entity\n      predicate:\n        subproperty_of: derives into\n      catalyst qualifier:\n        description: >-\n          this connects the derivation edge to the chemical entity that\n          catalyzes the reaction that causes the subject chemical to\n          transform into the object chemical.\n\n  chemical to disease or phenotypic feature association:\n    description: >-\n      An interaction between a chemical entity and a phenotype or disease,\n      where the presence of the chemical gives rise to or exacerbates the phenotype.\n    is_a: association\n    narrow_mappings:\n      - SIO:000993\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"the disease or phenotype that is affected by the chemical\"\n\n  chemical or drug or treatment to disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary undesirable effect.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slots:\n      - FDA adverse event level\n    slot_usage:\n      predicate:\n        subproperty_of: has adverse event\n\n  chemical or drug or treatment side effect disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.\n    is_a: chemical or drug or treatment to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has side effect\n\n  gene to pathway association:\n    description: >-\n      An interaction between a gene or gene product and a biological process or pathway.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"the gene or gene product entity that participates or influences the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that includes or is affected by the gene or gene product\"\n\n  molecular activity to pathway association:\n    description: >-\n      Association that holds the relationship between a reaction and the pathway it participates in.\n    is_a: association\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: pathway\n      predicate:\n        subproperty_of: part of\n\n  chemical to pathway association:\n    description: >-\n      An interaction between a chemical entity and a biological process or pathway.\n    is_a: association\n    exact_mappings:\n      - SIO:001250\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: \"the chemical entity that is affecting the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that is affected by the chemical\"\n\n  named thing associated with likelihood of named thing association:\n    # TODO: better name\n    description: >-\n    is_a: association\n    defining_slots:\n      - subject\n      - subject aspect qualifier\n      - subject context qualifier\n      - predicate\n      - object\n      - object aspect qualifier\n      - object context qualifier\n      - population context qualifier\n    slot_usage:\n      predicate:\n        subproperty_of: associated with\n      subject aspect qualifier:\n      # TODO: range\n      subject context qualifier:\n        range: ontology class\n      object aspect qualifier:\n      # TODO: range\n      object context qualifier:\n        range: ontology class\n\n  chemical gene interaction association:\n    description: >-\n      describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical\n      effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type\n      (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)\n    is_a: association\n    exact_mappings:\n      - SIO:001257\n    mixins:\n      - chemical to entity association mixin\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object context qualifier\n      - anatomical context qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: gene or gene product\n      predicate:\n        subproperty_of: physically interacts with\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject context qualifier:\n        range: anatomical entity\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object context qualifier:\n        range: anatomical entity\n      anatomical context qualifier:\n        range: anatomical entity\n\n  chemical affects gene association:\n    description: >-\n      Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,\n      localization, processing, expression, etc.)\n    is_a: association\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject aspect qualifier\n      - subject context qualifier\n      - subject direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object aspect qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - qualified predicate\n    slot_usage:\n      subject:\n        range: chemical entity\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject context qualifier:\n        range: anatomical entity\n      subject direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n      qualified predicate:\n        subproperty_of: causes\n      object:\n        range: gene or gene product\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object aspect qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object context qualifier:\n        range: anatomical entity\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      causal mechanism qualifier:\n        range: CausalMechanismQualifierEnum\n      anatomical context qualifier:\n        range: anatomical entity\n      species context qualifier:\n        range: organism taxon\n\n  drug to gene association:\n    description: >-\n      An interaction between a drug and a gene or gene product.\n    is_a: association\n    related_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - drug to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: \"the gene or gene product that is affected by the drug\"\n\n  material sample to entity association mixin:\n    description: >-\n      An association between a material sample and something.\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n\n  material sample derivation association:\n    description: >-\n      An association between a material sample and\n      the material entity from which it is derived.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n      object:\n        description: >-\n          the material entity the sample was derived from. This may be another\n          material sample, or any other material entity, including for example\n          an organism, a geographic feature, or some environmental material.\n      predicate:\n        description: >-\n          derivation relationship\n        subproperty_of: derives from\n\n  material sample to disease or phenotypic feature association:\n    description: >-\n      An association between a material sample and a disease or phenotype.\n    is_a: association\n    mixins:\n      - material sample to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    defining_slots:\n      - subject\n      - object\n\n  disease to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease\n        description: \"disease class\"\n        values_from: [ 'mondo', 'omim', 'orphanet', 'ncit', 'doid' ]\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n\n  entity to exposure event association mixin:\n    description: >-\n      An association between some entity and an exposure event.\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: exposure event\n\n  disease to exposure event association:\n    description: >-\n      An association between an exposure event and a disease.\n    is_a: association\n    mixins:\n      - disease to entity association mixin\n      - entity to exposure event association mixin\n    defining_slots:\n      - subject\n      - object\n\n\n  entity to outcome association mixin:\n    description: >-\n      An association between some entity and an outcome\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: outcome\n\n  exposure event to outcome association:\n    description: >-\n      An association between an exposure event and an outcome.\n    is_a: association\n    mixins:\n      - entity to outcome association mixin\n    slots:\n      - population context qualifier\n      - temporal context qualifier\n    defining_slots:\n      - subject\n      - object\n\n  frequency qualifier mixin:\n    mixin: true\n    description: >-\n      Qualifier for frequency type associations\n    slots:\n      - frequency qualifier\n\n  entity to feature or disease qualifiers mixin:\n    description: >-\n      Qualifiers for entity to disease or phenotype associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - severity qualifier\n      - onset qualifier\n\n  entity to phenotypic feature association mixin:\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    mixins:\n      - frequency quantifier\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: phenotypic feature\n        values_from: [ 'upheno', 'hp', 'mp', 'wbphenotype' ]\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n    slots:\n      - sex qualifier\n\n  information content entity to named thing association:\n    description: >-\n      association between a named thing and a information content entity where the specific context\n      of the relationship between that named thing and the publication is unknown. For\n      example, model organisms databases often capture the knowledge that a gene is found in a\n      journal article, but not specifically the context in which that gene was documented in the article.\n      In these cases, this association with the accompanying predicate 'mentions' could be used.\n      Conversely, for more specific associations (like 'gene to disease association', the publication should\n      be captured as an edge property).\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        domain: publication\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: mentions\n    in_subset:\n      - model_organism_database\n\n  entity to disease association mixin:\n    description: >-\n      mixin class for any association whose object (target node) is a disease\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease\n        description: \"disease\"\n        examples:\n          - value: MONDO:0020066\n            description: \"Ehlers-Danlos syndrome\"\n\n  disease or phenotypic feature to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  disease or phenotypic feature to location association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      an anatomical entity, where the disease/feature manifests in that site.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      object:\n        range: anatomical entity\n        description: >-\n          anatomical entity in which the disease or feature is found.\n        examples:\n          - value: UBERON:0002048\n            description: \"lung\"\n\n  disease or phenotypic feature to genetic inheritance association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      its mode of (genetic) inheritance.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has mode of inheritance\n      object:\n        range: genetic inheritance\n        description: >-\n          genetic inheritance associated with the specified disease or phenotypic feature.\n        examples:\n          - value: HP:0001417\n            description: \"X-linked inheritance\"\n\n  entity to disease or phenotypic feature association mixin:\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  genotype to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: genotype\n        description: \"genotype that is the subject of the association\"\n\n  genotype to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a phenotypic feature, where having\n      the genotype confers the phenotype, either in isolation or through environment\n    mixins:\n      - entity to phenotypic feature association mixin\n      - genotype to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has phenotype\n      subject:\n        range: genotype\n        description: >-\n          genotype that is associated with the phenotypic feature\n\n  # ie: smoke exposure to coughing phenotype? is this a denormalization?\n  exposure event to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between an environment and a phenotypic feature,\n      where being in the environment influences the phenotype.\n    mixins:\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: exposure event\n\n  disease to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      An association between a disease and a phenotypic feature in which the\n      phenotypic feature is associated with the disease in some way.\n    mixins:\n      - entity to phenotypic feature association mixin\n      - disease to entity association mixin\n    close_mappings:\n      - dcid:DiseaseSymptomAssociation\n    slot_usage:\n      subject:\n        range: disease\n      object:\n        range: phenotypic feature\n\n  case to phenotypic feature association:\n    description: >-\n      An association between a case (e.g. individual patient) and a phenotypic\n      feature in which the individual has or has had the phenotype.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - case to entity association mixin\n\n  behavior to behavioral feature association:\n    description: >-\n      An association between an mixture behavior and\n      a behavioral feature manifested by\n      the individual exhibited or has exhibited the behavior.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: behavior\n        description: >-\n          behavior that is the subject of the association\n      object:\n        range: behavioral feature\n        description: >-\n          behavioral feature that is the object of the association\n    mixins:\n      - entity to phenotypic feature association mixin\n\n  gene to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene that is the subject of the association\n\n  variant to entity association mixin:\n    local_names:\n      ga4gh: variant annotation\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is associated with some other entity\n        examples:\n          - value: CLINVAR:38077\n            description: \"CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n          - value: ClinGen:CA024716\n            description: \"chr13:g.32921033G>C (hg19) in ClinGen\"\n\n  gene to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n      - WBVocab:Gene-Phenotype-Association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      object:\n        range: phenotypic feature\n\n  gene to disease association:\n    is_a: association\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n    exact_mappings:\n      - SIO:000983\n    close_mappings:\n      - dcid:DiseaseGeneAssociation\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease,\n          may be protective or causative or associative, or as a model\n      object:\n        range: disease\n\n  druggable gene to disease association:\n    is_a: gene to disease association\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease\n          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and\n          this leads to a protective or improving disease state.\n      predicate:\n        subproperty_of: target for\n      has evidence:\n        range: DruggableGeneCategoryEnum\n    defining_slots:\n      - subject\n      - object\n      - predicate\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n\n  variant to gene association:\n    description: >-\n      An association between a variant and a gene, where the variant has\n      a genetic association with the gene (i.e. is in linkage disequilibrium)\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - variant to entity association mixin\n    slot_usage:\n      object:\n        range: gene\n      predicate:\n        subproperty_of: genetic association\n\n  variant to gene expression association:\n    description: >-\n      An association between a variant and expression of a gene (i.e. e-QTL)\n    is_a: variant to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: affects\n\n  variant to population association:\n    description: >-\n      An association between a variant and a population, where the variant has\n      particular frequency in the population\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - frequency quantifier\n      - frequency qualifier mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          an allele that has a certain frequency in a given population\n        examples:\n          - value: \"NC_000017.11:g.43051071A>T\"\n            description: >-\n              17:41203088 A/C in gnomad\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that is observed to have the frequency\n        examples:\n          - value: HANCESTRO:0010\n            description: African\n      has quotient:\n        description: >-\n          frequency of allele in population, expressed as a number with allele\n          divided by number in reference population, aka allele frequency\n        examples:\n          - value: \"0.0001666\"\n      has count:\n        description: >-\n          number in object population that carry a particular allele, aka allele count\n        examples:\n          - value: \"4\"\n            description: 4 individuals in gnomad set\n      has total:\n        description: >-\n          number all populations that carry a particular allele, aka allele number\n        examples:\n          - value: \"24014\"\n            description: 24014 individuals in gnomad set\n\n  population to population association:\n    description: >-\n      An association between a two populations\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: population of individual organisms\n        description: >-\n          the population that form the subject of the association\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that form the object of the association\n      predicate:\n        # subproperty_of: ???\n        description: >-\n          A relationship type that holds between the subject and object\n          populations. Standard mereological relations can be used.\n          E.g. subject part-of object, subject overlaps object.\n          Derivation relationships can also be used\n\n  variant to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is\n          associated in some way with the phenotype state\n\n  variant to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a sequence variant in which the allele state\n          is associated in some way with the disease state\n        examples:\n          - value: CLINVAR:52241\n            description: \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that variant\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  genotype to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - genotype to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a genotype that is associated in some way with a disease state\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that genotype\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  model to disease association mixin:\n    description: >-\n      This mixin is used for any association class for which the subject\n      (source node) plays the role of a 'model', in that it recapitulates some\n      features of the disease in a way that is useful for studying the disease\n      outside a patient carrying the disease\n    mixin: true\n    slot_usage:\n      subject:\n        description: >-\n          The entity that serves as the model of the disease. This may be\n          an organism, a strain of organism, a genotype or variant that exhibits\n          similar features, or a gene that when mutated exhibits features of the disease\n      predicate:\n        subproperty_of: model of\n        description: >-\n          The relationship to the disease\n\n  gene as a model of disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be a model\n          organism ortholog of a known disease gene, or it may be a gene whose\n          mutants recapitulate core features of the disease.\n\n  variant as a model of disease association:\n    is_a: variant to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          A variant that has a role in modeling the disease.\n\n  genotype as a model of disease association:\n    is_a: genotype to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: genotype\n        description: >-\n          A genotype that has a role in modeling the disease.\n\n  cell line as a model of disease association:\n    is_a: cell line to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: cell line\n        description: >-\n          A cell line derived from an organismal entity with a disease state that is used\n          as a model of that disease.\n\n  organismal entity as a model of disease association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: organismal entity\n        description: >-\n          A organismal entity (strain, breed) with a predisposition to a disease, or bred/created\n          specifically to model a disease.\n\n  organism to organism association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: individual organism\n      object:\n        range: individual organism\n        description: >-\n          An association between two individual organisms.\n\n  taxon to taxon association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n        description: >-\n          An association between individuals of different taxa.\n\n  gene has variant that contributes to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - sequence variant qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be\n          a model organism ortholog of a known disease gene, or it may be\n          a gene whose mutants recapitulate core features of the disease.\n\n  gene to expression site association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      An association between a gene and a gene expression site,\n      possibly qualified by stage/timing info.\n    notes:\n      - \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n    see_also: \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n    slots:\n      - stage qualifier\n      - quantifier qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          Gene or gene product positively within the specified\n          anatomical entity (or subclass, i.e. cellular component) location.\n      object:\n        range: anatomical entity\n        description: \"location in which the gene is expressed\"\n        examples:\n          - value: UBERON:0002037\n            description: cerebellum\n      predicate:\n        description: \"expression relationship\"\n        subproperty_of: expressed in\n      stage qualifier:\n        range: life stage\n        description: \"stage at which the gene is expressed in the site\"\n        examples:\n          - value: UBERON:0000069\n            description: larval stage\n      quantifier qualifier:\n        description: >-\n          can be used to indicate magnitude, or also ranking\n\n  sequence variant modulates treatment association:\n    is_a: association\n    description: >-\n      An association between a sequence variant and a treatment or health intervention.\n      The treatment object itself encompasses both the disease and the drug used.\n    comments:\n      - An alternate way to model the same information could be via a qualifier\n    defining_slots:\n      - subject\n      - object\n    abstract: true\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: \"variant that modulates the treatment of some disease\"\n      object:\n        range: treatment\n        description: \"treatment whose efficacy is modulated by the subject variant\"\n\n  functional association:\n    is_a: association\n    description: >-\n      An association between a macromolecular machine mixin (gene, gene product or\n      complex of gene products) and either a molecular activity, a biological\n      process or a cellular location in which a function is executed.\n    slot_usage:\n      subject:\n        range: macromolecular machine mixin\n        description: >-\n          gene, product or macromolecular complex that\n          has the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n          - value: GO:0045211\n            description: postsynaptic membrane\n\n  macromolecular machine to entity association mixin:\n    description: >-\n      an association which has a macromolecular machine mixin as a subject\n    mixin: true\n    slot_usage:\n      subject:\n        domain: macromolecular machine mixin\n\n  macromolecular machine to molecular activity association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a molecular activity (as represented\n      in the GO molecular function branch), where the entity\n      carries out the activity, or contributes to its execution.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: molecular activity\n\n  macromolecular machine to biological process association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a biological process or pathway\n      (as represented in the GO biological process branch), where the entity\n      carries out some part of the process, regulates it, or acts upstream of it.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: biological process\n\n  macromolecular machine to cellular component association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a cellular component (as represented\n      in the GO cellular component branch), where the entity\n      carries out its function in the cellular component.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: cellular component\n\n  molecular activity to chemical entity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: chemical entity\n\n  molecular activity to molecular activity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: molecular activity\n\n\n  gene to go term association:\n    aliases: [ 'functional association' ]\n    is_a: functional association\n    exact_mappings:\n      - WBVocab:Gene-GO-Association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene\n        description: >-\n          gene, product or macromolecular complex that has\n          the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n\n  entity to disease association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  entity to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  ## -----------------\n  ## SEQUENCE FEATURES\n  ## -----------------\n\n  sequence association:\n    is_a: association\n    description: >-\n      An association between a sequence feature and a nucleic acid entity it is localized to.\n\n  genomic sequence localization:\n    is_a: sequence association\n    description: >-\n      A relationship between a sequence feature and a nucleic acid entity\n      it is localized to. The reference entity may be a chromosome,\n      chromosome region or information entity such as a contig.\n    slot_usage:\n      subject:\n        aliases: [ 'sequence feature' ]\n        range: nucleic acid entity\n      object:\n        aliases: [ 'reference' ]\n        range: nucleic acid entity # typically a chromosome use monochrom\n      predicate:\n        subproperty_of: has sequence location\n    slots:\n      - start interbase coordinate\n      - end interbase coordinate\n      - genome build\n      - strand\n      - phase\n    broad_mappings:\n      - dcid:Chromosome\n    exact_mappings:\n      - dcid:GenomeAnnotation\n\n  sequence feature relationship:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      For example, a particular exon is part of a particular transcript or gene\n    slot_usage:\n      subject:\n        range: nucleic acid entity\n      object:\n        range: nucleic acid entity # typically a chromosome\n    exact_mappings:\n      - CHADO:feature_relationship\n\n  transcript to gene relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is a collection of transcripts\n    slot_usage:\n      subject:\n        range: transcript\n      object:\n        range: gene\n\n  gene to gene product relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is transcribed and potentially translated to a gene product\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene product mixin\n      predicate:\n        subproperty_of: has gene product\n\n  exon to transcript relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A transcript is formed from multiple exons\n    slot_usage:\n      subject:\n        range: exon\n      object:\n        range: transcript\n\n  chemical entity or gene or gene product regulates gene association:\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slots:\n      - object direction qualifier\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n        subproperty_of: regulates\n      subject:\n        range: chemical entity or gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n      object direction qualifier:\n        range: DirectionQualifierEnum\n\n  anatomical entity to anatomical entity association: # schema: gocam\n    is_a: association\n    abstract: true\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: anatomical entity\n      object:\n        range: anatomical entity\n\n  anatomical entity to anatomical entity part of association:\n    #      schema: gocam\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is mereological, i.e the two entities are related by parthood. This\n      includes relationships between cellular components and cells, between\n      cells and tissues, tissues and whole organisms\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the part\n      object:\n        range: anatomical entity\n        description: >-\n          the whole\n      predicate:\n        subproperty_of: part of\n\n  anatomical entity to anatomical entity ontogenic association:\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is ontogenic, i.e. the two entities are related by development. A number\n      of different relationship types can be used to specify the precise\n      nature of the relationship.\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the structure at a later time\n      object:\n        range: anatomical entity\n        description: >-\n          the structure at an earlier time\n      predicate:\n        subproperty_of: develops from\n\n  organism taxon to entity association:\n    mixin: true\n    description: >-\n      An association between an organism taxon and another entity\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: organism taxon\n        description: >-\n          organism taxon that is the subject of the association\n\n  organism taxon to organism taxon association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    description: >-\n      A relationship between two organism taxon nodes\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n\n  organism taxon to organism taxon specialization:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      A child-parent relationship between two taxa.\n      For example: Homo sapiens subclass_of Homo\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: child taxon\n        description: >-\n          the more specific taxon\n      object:\n        range: organism taxon\n        role: parent taxon\n        description: >-\n          the more general taxon\n      predicate:\n        subproperty_of: subclass of\n\n  organism taxon to organism taxon interaction:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      An interaction relationship between two taxa. This may be a symbiotic\n      relationship (encompassing mutualism and parasitism), or it may be non-symbiotic.\n      Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens\n    defining_slots:\n      - predicate\n    slots:\n      - associated environmental context\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        range: organism taxon\n        role: interactee taxon\n        description: >-\n          the taxon that is the subject of the association\n      predicate:\n        subproperty_of: interacts with\n      associated environmental context:\n        description: >-\n          the environment in which the two taxa interact\n\n  organism taxon to environment association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        role: environmental context\n        description: >-\n          the environment in which the organism occurs\n      predicate:\n        description: >-\n          predicate describing the relationship between the taxon and the environment\n\nenums:\n\n  AnatomicalContextQualifierEnum:\n    reachable_from:\n      source_ontology: bioregistry:uberon\n      source_nodes:\n        - UBERON:0001062\n      is_direct: false\n      relationship_types:\n        - rdfs:subClassOf\n\n  DirectionQualifierEnum:\n    permissible_values:\n      increased:\n      upregulated:\n        is_a: increased\n        close_mappings:\n          - RO:0002336\n        exact_mappings:\n          - RO:0002213\n        narrow_mappings:\n          - RO:0004032\n          - RO:0004034\n          - RO:0002629\n      decreased:\n      downregulated:\n        is_a: decreased\n        exact_mappings:\n          - RO:0004035\n          - RO:0002212\n        close_mappings:\n          # This RTX contributed term is tagged as an inverse of this Biolink predicate\n          - RO:0002335\n        broad_mappings:\n          # This term is slightly broader in that it includes that A acts within B as well\n          - RO:0004033\n\n  ChemicalEntityDerivativeEnum:\n    permissible_values:\n      metabolite:\n\n  ChemicalOrGeneOrGeneProductFormOrVariantEnum:\n    permissible_values:\n      genetic_variant_form:\n        is_a: modified form\n      mutant_form:\n        is_a: genetic variant form\n      polymorphic_form:\n        is_a: mutant form\n      snp_form:\n        is_a: polymorphic form\n      analog_form:\n\n  GeneOrGeneProductOrChemicalPartQualifierEnum:\n    permissible_values:\n      3_prime_utr:\n      5_prime_utr:\n      polya_tail:\n      promoter:\n      enhancer:\n      exon:\n      intron:\n\n  GeneOrGeneProductOrChemicalEntityAspectEnum:\n    permissible_values:\n      activity_or_abundance:\n        description: >- \n          Used in cases where the specificity of the relationship can not be determined to be either activity \n          or abundance.  In general, a more specific value from this enumeration should be used.\n      abundance:\n        is_a: activity_or_abundance\n      activity:\n        is_a: activity_or_abundance\n      expression:\n        is_a: abundance\n      synthesis:\n        is_a: abundance\n      degradation:\n        is_a: abundance # negate the direction qualifier necessary.\n      cleavage:\n        is_a: degradation\n      hydrolysis:\n        is_a: degradation\n      metabolic_processing:\n      mutation_rate:\n      stability:\n      folding:\n      localization:\n      transport:\n      secretion:\n        is_a: transport\n      uptake:\n        is_a: transport\n      molecular_modification:\n      acetylation:\n        is_a: molecular_modification\n      acylation:\n        is_a: molecular_modification\n      alkylation:\n        is_a: molecular_modification\n      amination:\n        is_a: molecular_modification\n      carbamoylation:\n        is_a: molecular_modification\n      ethylation:\n        is_a: molecular_modification\n      glutathionylation:\n        is_a: molecular_modification\n      glycation:\n        is_a: molecular_modification\n      glycosylation:\n        is_a: molecular_modification\n      glucuronidation:\n        is_a: molecular_modification\n      n_linked_glycosylation:\n        is_a: molecular_modification\n      o_linked_glycosylation:\n        is_a: molecular_modification\n      hydroxylation:\n        is_a: molecular_modification\n      lipidation:\n        is_a: molecular_modification\n      farnesylation:\n        is_a: molecular_modification\n      geranoylation:\n        is_a: molecular_modification\n      myristoylation:\n        is_a: molecular_modification\n      palmitoylation:\n        is_a: molecular_modification\n      prenylation:\n        is_a: molecular_modification\n      methylation:\n        is_a: molecular_modification\n      nitrosation:\n        is_a: molecular_modification\n      nucleotidylation:\n        is_a: molecular_modification\n      phosphorylation:\n        is_a: molecular_modification\n      ribosylation:\n        is_a: molecular_modification\n      ADP-ribosylation:\n        is_a: molecular_modification\n      sulfation:\n        is_a: molecular_modification\n      sumoylation:\n        is_a: molecular_modification\n      ubiquitination:\n        is_a: molecular_modification\n      oxidation:\n        is_a: molecular_modification\n      reduction:\n        is_a: molecular_modification\n      carboxylation:\n        is_a: molecular_modification\n\n  CausalMechanismQualifierEnum:\n    permissible_values:\n      binding:\n        description: >-\n          A causal mechanism mediated by the direct contact between effector and target chemical or \n          biomolecular entity, which form a stable physical interaction.\n      inhibition:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to the target and negatively effects its normal function, \n          e.g. prevention of enzymatic reaction or activation of downstream pathway.\n        close_mappings:\n          - DGIdb:inhibitor\n          - SEMMEDDB:INHIBITS\n        narrow_mappings:\n          - DGIdb:blocker\n          - DGIdb:channel_blocker\n          - DGIdb:gating_inhibitor\n          - CHEMBL.MECHANISM:antisense_inhibitor\n          - CHEMBL.MECHANISM:blocker\n          - CHEMBL.MECHANISM:inhibitor\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - CHEMBL.MECHANISM:negative_modulator\n          - DGIdb:negative_modulator\n      antibody_inhibition:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which an antibody specifically binds to and interferes with the target.\n      antagonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist \n          through competing for the binding site.\n        close_mappings:\n          - DGIdb:antagonist\n          - CHEMBL.MECHANISM:antagonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:allosteric_antagonist\n      molecular_channel_blockage:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and prevents or reduces \n          transport of ions through it.\n      inverse_agonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes\n          its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.\n        close_mappings:\n          - CHEMBL.MECHANISM:inverse_agonist\n          - DGIdb:inverse_agonist\n      negative_allosteric_modulation:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a \n          receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - DGIdb:inhibitory_allosteric_modulator\n        narrow_mappings:\n          - DGIdb:negative_modulator\n      agonism:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an \n          endogenous ligand.\n        close_mappings:\n          - CHEMBL.MECHANISM:agonist\n          - DGIdb:agonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:partial_agonist\n          - DGIdb:partial_agonist\n      molecular_channel_opening:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and facilitates transport of \n          ions through it.\n        close_mappings:\n          - CHEMBL.MECHANISM:opener\n      positive_allosteric_modulation:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by \n          binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:positive_allosteric_modulator\n          - CHEMBL.MECHANISM:positive_modulator\n          - DGIdb:positive_allosteric_modulator\n        broad_mappings:\n          - DGIdb:modulator\n          - DGIdb:allosteric_modulator\n      potentiation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector  binds to and enhances or intensifies the effect of some \n          other chemical or drug on its target.\n        close_mappings:\n      activation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.\n        close_mappings:\n          - CHEMBL.MECHANISM:activator\n          - DGIdb:activator\n      inducer:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that \n          processes drugs in the body.\n        close_mappings:\n          - DGIdb:inducer\n      transcriptional_regulation:\n        description: >-\n          A causal mechanism mediated by through the control of target gene transcription\n      signaling_mediated_control:\n        description: >-\n          A causal mechanism mediated by the activation or control of signaling events that influence the some aspect \n          of the target entity (e.g. its activity, processing, transport, etc)\n      stabilization:\n        is_a: activation\n        close_mappings:\n          - CHEMBL.MECHANISM:stabiliser\n      stimulation:\n        is_a: activation\n        close_mappings:\n          - DGIdb:stimulator\n          - SEMMEDDB:STIMULATES\n          - DGIdb:stimulator\n      releasing_activity:\n        is_a: activation\n        close_mappings:\n          - CHEMBL:MECHANISM:releasing_agent\n\n  LogicalInterpretationEnum:\n    permissible_values:\n      some_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as a some-some statement\n        meaning: os:SomeSomeInterpretation\n      all_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as an all-some statement.\n        meaning: os:AllSomeInterpretation\n      inverse_all_some:\n\n  ReactionDirectionEnum:\n    permissible_values:\n      left_to_right:\n      right_to_left:\n      bidirectional:\n      neutral:\n\n  ReactionSideEnum:\n    permissible_values:\n      left:\n      right:\n\n  PhaseEnum:\n    description: phase\n    permissible_values:\n      0:\n      1:\n      2:\n\n  StrandEnum:\n    description: strand\n    permissible_values:\n      \"+\":\n        description: Positive\n      \"-\":\n        description: Negative\n      \".\":\n        description: Unstranded\n      \"?\":\n        description: Unknown\n\n  SequenceEnum:\n    description: type of sequence\n    permissible_values:\n      \"na\":\n        description: nucleic acid\n      \"aa\":\n        description: amino acid\n\n  DruggableGeneCategoryEnum:\n    permissible_values:\n      \"tclin\":\n        description: >-\n          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.\n      \"tbio\":\n        description: >-\n          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy\n          the activity thresholds detailed below.\n      \"tchem\":\n        description: >-\n          These targets do not have known drug or small molecule activities that satisfy the activity\n          thresholds detailed below AND satisfy one or more of the following criteria:\n          target is above the cutoff criteria for Tdark\n          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)\n          with an Experimental Evidence code\n      \"tdark\":\n        description: >-\n          These are targets about which virtually nothing is known. They do not have known drug or small\n          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or\n          more of the following criteria:\n          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or\n          less than or equal to 50 Antibodies available according to http://antibodypedia.com.\n\n  DrugAvailabilityEnum:\n    description: >-\n    permissible_values:\n      \"over_the_counter\":\n        description: >-\n          chemical entity is available over the counter without a prescription.\n      \"prescription\":\n        description:\n          chemical entity is available by prescription.\n\n  DrugDeliveryEnum:\n    permissible_values:\n      \"inhalation\":\n      \"oral\":\n      \"absorbtion_through_the_skin\":\n      \"intravenous_injection\":\n\n  FDAApprovalStatusEnum:\n    description: >-\n    permissible_values:\n      \"discovery_and_development_phase\":\n        description: >-\n          Discovery & Development Phase. Discovery involves researchers finding new possibilities\n          for medication through testing molecular compounds, noting unexpected effects from existing treatments,\n          or the creation of new technology that allows novel ways of targeting medical products to sites in the body.\n          Drug development occurs after researchers identify potential compounds for experiments.\n      \"preclinical_research_phase\":\n        description: >-\n          Preclinical Research Phase.  Once researchers have examined the possibilities a new drug may contain,\n          they must do preliminary research to determine its potential for harm (toxicity).\n          This is categorized as preclinical research and can be one of two types: in vitro or in vivo.\n      \"fda_clinical_research_phase\":\n        description: >-\n          Clinical Research Phase. Clinical research involves trials of the drug on people,\n          and it is one of the most involved stages in the drug development and approval process.\n          Clinical trials must answer specific questions and follow a protocol determined by\n          the drug researcher or manufacturer.\n      \"fda_review_phase_4\":\n        description: >-\n          FDA Review\n      \"fda_post_market_safety_review\":\n        description: >-\n          FDA Post-Market Safety Monitoring.  The last phase of drug approval is an ongoing one\n          while the drug is on the marketplace. If a developer wants to change anything about the\n          drug formulation or approve it for a new use, they must apply with the FDA. The FDA also\n          frequently reviews the drug’s advertising and its manufacturing facility to make sure\n          everything involved in its creation and marketing is in compliance with regulations.\n      \"fda_clinical_research_phase_1\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and\n          lasts several months. This phase is used to determine the safety and dosage of the drug,\n          and about 70% of these drugs move on to the next clinical research phase.\n      \"fda_clinical_research_phase_2\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people,\n          who must have the disease or condition the drug supposes to treat. This phase can last\n          from a few months to two years, and its purpose is to monitor the efficacy of the drug,\n          as well as note side effects that may occur.\n      \"fda_clinical_research_phase_3\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers\n          and can last up to four years. It is used to continue monitoring the efficacy of\n          the drug, as well as exploring any longer-term adverse reactions.\n      \"fda_clinical_research_phase_4\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of\n          volunteers who have the disease or condition and continues to monitor safety and efficacy.\n          If a drug passes this phase, it goes on to FDA review.\n      \"fda_fast_track\":\n        description: >-\n          Fast track is a process designed to facilitate the development, and expedite the\n          review of drugs to treat serious conditions and fill an unmet medical need.\n          The purpose is to get important new drugs to the patient earlier. Fast Track\n          addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track\n      \"fda_breakthrough_therapy\":\n        description: >-\n          Breakthrough Therapy designation is a process designed to expedite the\n          development and review of drugs that are intended to treat a serious\n          condition and preliminary clinical evidence indicates that the drug may\n          demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy\n      \"fda_accelerated_approval\":\n        description: >-\n          When studying a new drug, it can sometimes take many years to learn whether a drug actually\n          provides a real effect on how a patient survives, feels, or functions. A positive therapeutic\n          effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”.\n          Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical\n          benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs\n          for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint.\n          Using a surrogate endpoint enabled the FDA to approve these drugs faster.\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval\n      \"fda_priority_review\":\n        description: >-\n          Prior to approval, each drug marketed in the United States must go through a detailed FDA review process.\n          In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving\n          the drug review time and created a two-tiered system of review times – Standard Review and Priority\n          Review. A Priority Review designation means FDA’s goal is to take action on an application\n          within 6 months (compared to 10 months under standard review).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review\n      \"regular_fda_approval\":\n        description: >-\n          Regular FDA Approval.  The last phase of drug approval is an ongoing one while the drug is on the marketplace.\n          If a developer wants to change anything about the drug formulation or approve it for a new use,\n          they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its\n          manufacturing facility to make sure everything involved in its creation and marketing is in compliance\n          with regulations.\n      \"post_approval_withdrawal\":\n\n  FDAIDAAdverseEventEnum:\n    description: >-\n      please consult with the FDA guidelines as proposed in this document:\n      https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32\n    permissible_values:\n      \"life_threatening_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either \n          the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. \n          It does not include an adverse event or suspected adverse reaction that, had it occurred in a more \n          severe form, might have caused death.\n      \"serious_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the \n          investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event,\n          inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity \n          or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth \n          defect. Important medical events that may not result in death, be life-threatening, or require hospitalization\n          may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or \n          subject and may require medical or surgical intervention to prevent one of the outcomes listed in this \n          definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment \n          in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient \n          hospitalization, or the development of drug dependency or drug abuse.\n      \"suspected_adverse_reaction\":\n         description: >-\n           means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. \n           For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a \n           causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser \n           degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.\n      \"unexpected_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the \n          investigator brochure or is not listed at the specificity or severity that has been observed; or, if an \n          investigator brochure is not required or available, is not consistent with the risk information described \n          in the general investigational plan or elsewhere in the current application, as amended. For example, \n          under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the \n          investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral \n          thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the \n          investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, \n          also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure\n          as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but \n          are not specifically mentioned as occurring with the particular drug under investigation.\n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_3_1_2/biolink-model.yaml",
    "content": "id: https://w3id.org/biolink/biolink-model\nname: Biolink-Model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 3.1.2\n\n\n## ------------\n##\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  AGRKB: 'https://www.alliancegenome.org/'\n  apollo: 'https://github.com/GMOD/Apollo'\n  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='\n  biolink: 'https://w3id.org/biolink/vocab/'\n  bioschemas: 'https://bioschemas.org/'\n  linkml: 'https://w3id.org/linkml/'\n  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='\n  # Placeholder: just points to GMOD Chado wiki\n  CHADO: 'http://gmod.org/wiki/Chado/'\n  # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve\n  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='\n  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'\n  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'\n  CLINVAR: 'http://identifiers.org/clinvar'\n  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'\n  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'\n  ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'\n  CPT: 'https://www.ama-assn.org/practice-management/cpt/'\n  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='\n  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='\n  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='\n  CTD: 'http://ctdbase.org/'\n  DGIdb: 'https://www.dgidb.org/interaction_types'\n  dcat: 'http://www.w3.org/ns/dcat#'\n  dct: 'http://purl.org/dc/terms/'\n  dcid: 'https://datacommons.org/browser/'\n  doi: 'https://doi.org/'\n  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'\n  DrugCentral: 'http://drugcentral.org/drugcard/'\n  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'\n  EDAM-DATA: 'http://edamontology.org/data_'\n  EDAM-FORMAT: 'http://edamontology.org/format_'\n  EDAM-OPERATION: 'http://edamontology.org/operation_'\n  EDAM-TOPIC: 'http://edamontology.org/topic_'\n  EFO: 'http://www.ebi.ac.uk/efo/EFO_'\n  ExO: 'http://purl.obolibrary.org/obo/ExO_'\n  fabio: 'http://purl.org/spar/fabio/'\n  foaf: 'http://xmlns.com/foaf/0.1/'\n  foodb.food: 'http://foodb.ca/compounds/'\n  foodb.compound: 'http://foodb.ca/foods/'\n  FYECO: 'https://www.pombase.org/term/'\n  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'  # Fission Yeast Phenotype Ontology\n  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'\n  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'\n  # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)\n  GOP: 'http://purl.obolibrary.org/obo/go#'\n  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'\n  GSID: 'https://scholar.google.com/citations?user='\n  GTEx: 'https://www.gtexportal.org/home/gene/'\n  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='\n  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'\n  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'\n  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'\n  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'\n  ICD10: 'https://icd.codes/icd9cm/'\n  ICD9: 'http://translator.ncats.nih.gov/ICD9_'\n  interpro: 'https://www.ebi.ac.uk/interpro/entry/'\n  INO: 'http://purl.obolibrary.org/obo/INO_'\n  isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international\n  isni: 'https://isni.org/isni/'\n  issn: 'https://portal.issn.org/resource/ISSN/'\n  ncats.drug: 'https://drugs.ncats.io/drug/'\n  KEGG.BRITE: 'http://www.kegg.jp/entry/'\n  KEGG.DGROUP: 'http://www.kegg.jp/entry/'\n  KEGG.ENZYME: 'http://www.kegg.jp/entry/'\n  KEGG.GENE: 'http://www.kegg.jp/entry/'\n  KEGG.PATHWAY: 'https://www.kegg.jp/entry/'\n  KEGG.RCLASS: 'http://www.kegg.jp/entry/'\n  LOINC: 'http://loinc.org/rdf/'\n  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'\n  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'\n  metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'\n  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'\n  MESH: 'http://id.nlm.nih.gov/mesh/'\n  MI: 'http://purl.obolibrary.org/obo/MI_'\n  mirbase: 'http://identifiers.org/mirbase'\n  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'\n  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'\n  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'\n  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'\n  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='\n  NCBIGene: 'http://identifiers.org/ncbigene/'\n  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'\n  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'\n  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='\n  OBAN: 'http://purl.org/oban/'\n  oboformat: 'http://www.geneontology.org/formats/oboInOwl#'\n  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'\n  ORCID: 'https://orcid.org/'\n  orphanet: 'http://www.orpha.net/ORDO/Orphanet_'\n  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'\n  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='\n  PathWhiz: 'http://smpdb.ca/pathways/#'  # See also https://smpdb.ca/pathwhiz/\n  pav: 'http://purl.org/pav/'\n  PHAROS: 'http://pharos.nih.gov'\n  PomBase: 'https://www.pombase.org/gene/'\n  prov: 'http://www.w3.org/ns/prov#'\n  qud: 'http://qudt.org/1.1/schema/qudt#'\n  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'\n  ResearchID: 'https://publons.com/researcher/'\n  RO: 'http://purl.obolibrary.org/obo/RO_'\n  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'\n  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='\n  schema: 'http://schema.org/'\n  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='\n  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'\n  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'\n  SIO: 'http://semanticscience.org/resource/SIO_'\n  SNOMEDCT: 'http://snomed.info/id/'\n  SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'\n  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'\n  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'\n  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'\n  # The UMLS Semantic types and groups namespaces don't have a directly\n  # resolvable Base URI, but we point to a pair of sensible web documents\n  STY: 'http://purl.bioontology.org/ontology/STY/'\n  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'\n  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'\n  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'\n  # The \"Variation Modelling Collaboration\" (VMC) is not (yet) a conventional namespace so we point to its Github repo\n  # See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and\n  # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/\n  VMC: 'https://github.com/ga4gh/vr-spec/'\n  WBls: 'http://purl.obolibrary.org/obo/WBBL_'\n  WBbt: 'http://purl.obolibrary.org/obo/WBBT_'\n  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'\n  WIKIDATA: 'https://www.wikidata.org/wiki/'            # Wikidata Entity\n  WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:'  # Wikidata Property - not a conventional namespace prefix\n  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'\n  XPO: 'http://purl.obolibrary.org/obo/XPO_'  # Xenopus Phenotype Ontology\n  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='\n\ndefault_prefix: biolink\ndefault_range: string\n\n# 2. The following prefix maps are retrieved from the\n#    specified contexts defined at https://prefixcommons.org/\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\n# The following 'standard' prefixes are also used.\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - OIO\n  - BIOGRID\n  - SO\n\n## ------------\n## SUBSETS\n## ------------\n\n\nsubsets:\n\n  model_organism_database:\n    description: >-\n      Subset that is relevant for a typical Model Organism Database (MOD)\n\n  translator_minimal:\n    description: >-\n      Minimum subset of translator work\n\n  samples:\n    description: >-\n      Sample/biosample datamodel\n\n  testing:\n    description: >-\n      TBD\n\n\n## ------------\n## TYPES\n## ------------\n\nimports:\n  - linkml:types\n\ntypes:\n\n  chemical formula value:\n    uri: xsd:string\n    base: str\n    description: A chemical formula\n    notes:\n      - Should be implemented as a stronger type\n\n  category type:\n    typeof: uriorcurie\n    description: >-\n      A primitive type in which the value denotes a class within the biolink model.\n      The value must be a URI or a CURIE. In a Neo4j representation, the value should\n      be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,\n      the value should be a URI such as https://w3id.org/biolink/vocab/Gene\n\n  iri type:\n    typeof: uriorcurie\n    description: >-\n      An IRI\n\n  label type:\n    typeof: string\n    description: >-\n      A string that provides a human-readable name for an entity\n\n  predicate type:\n    typeof: uriorcurie\n    description: >-\n      A CURIE from the biolink related_to hierarchy.\n      For example, biolink:related_to, biolink:causes, biolink:treats.\n\n  narrative text:\n    typeof: string\n    description: >-\n      A string that provides a human-readable description of something\n\n  symbol type:\n    typeof: string\n\n  frequency value:\n    typeof: string\n    uri: UO:0000105\n\n  percentage frequency value:\n    typeof: double\n    uri: UO:0000187\n\n  quotient:\n    aliases: [ 'ratio' ]\n    typeof: double\n    uri: UO:0010006\n\n  unit:\n    typeof: string\n    uri: UO:0000000\n    id_prefixes:\n      - UO\n    exact_mappings:\n      - qud:Unit\n\n  time type:\n    typeof: time\n\n  biological sequence:\n    typeof: string\n\n## ------------\n## SLOTS\n## ------------\n\nslots:\n\n  ## ---------------\n  ## ATTRIBUTE SLOTS\n  ## ---------------\n\n  has attribute:\n    description: >-\n      connects any entity to an attribute\n    domain: entity\n    range: attribute\n    multivalued: true\n    in_subset:\n      - samples\n    close_mappings:\n      # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'\n      - OBI:0001927\n    exact_mappings:\n      - SIO:000008\n    narrow_mappings:\n      # if 'has attribute' annotates a NamedThing as subject or\n      # object of an association, these OBAN mappings may apply\n      - OBAN:association_has_subject_property\n      - OBAN:association_has_object_property\n      - CPT:has_possibly_included_panel_element\n      - DRUGBANK:category\n      # RTX contributed terms. Could perhaps review for more semantically precise mappings?\n      - EFO:is_executed_in\n      - HANCESTRO:0301\n      - LOINC:has_action_guidance\n      - LOINC:has_adjustment\n      - LOINC:has_aggregation_view\n      - LOINC:has_approach_guidance\n      - LOINC:has_divisor\n      - LOINC:has_exam\n      - LOINC:has_method\n      - LOINC:has_modality_subtype\n      - LOINC:has_object_guidance\n      - LOINC:has_scale\n      - LOINC:has_suffix\n      - LOINC:has_time_aspect\n      - LOINC:has_time_modifier\n      - LOINC:has_timing_of\n      # disease is stage\n      - NCIT:R88\n      - NCIT:eo_disease_has_property_or_attribute\n      - NCIT:has_data_element\n      - NCIT:has_pharmaceutical_administration_method\n      - NCIT:has_pharmaceutical_basic_dose_form\n      - NCIT:has_pharmaceutical_intended_site\n      - NCIT:has_pharmaceutical_release_characteristics\n      - NCIT:has_pharmaceutical_state_of_matter\n      - NCIT:has_pharmaceutical_transformation\n      - NCIT:is_qualified_by\n      - NCIT:qualifier_applies_to\n      - NCIT:role_has_domain\n      - NCIT:role_has_range\n      - INO:0000154\n      - HANCESTRO:0308\n      - OMIM:has_inheritance_type\n      - orphanet:C016\n      - orphanet:C017\n      - RO:0000053\n      # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here\n      - RO:0000086\n      - RO:0000087\n      - SNOMED:has_access\n      - SNOMED:has_clinical_course\n      - SNOMED:has_count_of_base_of_active_ingredient\n      - SNOMED:has_dose_form_administration_method\n      - SNOMED:has_dose_form_release_characteristic\n      - SNOMED:has_dose_form_transformation\n      - SNOMED:has_finding_context\n      - SNOMED:has_finding_informer\n      - SNOMED:has_inherent_attribute\n      - SNOMED:has_intent\n      - SNOMED:has_interpretation\n      - SNOMED:has_laterality\n      - SNOMED:has_measurement_method\n      - SNOMED:has_method\n      - SNOMED:has_priority\n      - SNOMED:has_procedure_context\n      - SNOMED:has_process_duration\n      - SNOMED:has_property\n      - SNOMED:has_revision_status\n      - SNOMED:has_scale_type\n      - SNOMED:has_severity\n      - SNOMED:has_specimen\n      - SNOMED:has_state_of_matter\n      - SNOMED:has_subject_relationship_context\n      - SNOMED:has_surgical_approach\n      - SNOMED:has_technique\n      - SNOMED:has_temporal_context\n      - SNOMED:has_time_aspect\n      - SNOMED:has_units\n      - UMLS:has_structural_class\n      - UMLS:has_supported_concept_property\n      - UMLS:has_supported_concept_relationship\n      - UMLS:may_be_qualified_by\n\n  has attribute type:\n    description: >-\n      connects an attribute to a class that describes it\n    domain: attribute\n    range: ontology class\n    multivalued: false\n    required: true\n    in_subset:\n      - samples\n    narrow_mappings:\n      - LOINC:has_modality_type\n      - LOINC:has_view_type\n\n  # TRAPI Attribute schema alignment:\n  # value: NamedThing.name\n  # value_type: NamedThing.category\n  # value_type_name: quantity_value.NamedThing.name\n  has qualitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: named thing\n    multivalued: false\n    in_subset:\n      - samples\n\n  # TRAPI Attribute schema alignment:\n  # value: quantity_value.has_numeric_value[double] - may be a vector?\n  # value_type: quantity_value.has_unit.unit.uri\n  # value_type_name: quantity_value.has_unit.unit.name[string]\n  has quantitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: quantity value\n    multivalued: true\n    exact_mappings:\n      - qud:quantityValue\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_numerator_value\n      - SNOMED:has_presentation_strength_denominator_value\n      - SNOMED:has_presentation_strength_numerator_value\n    in_subset:\n      - samples\n\n  has numeric value:\n    description: >-\n      connects a quantity value to a number\n    domain: quantity value\n    range: double\n    multivalued: false\n    exact_mappings:\n      - qud:quantityValue\n    in_subset:\n      - samples\n\n  has unit:\n    description: >-\n      connects a quantity value to a unit\n    domain: quantity value\n    range: unit\n    multivalued: false\n    close_mappings:\n      # These RTX contributed terms mean \"is unit of\" which is the semantic inverse of this biolink:has_unit term\n      - EFO:0001697\n      - UO-PROPERTY:is_unit_of\n    exact_mappings:\n      - qud:unit\n      - IAO:0000039\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_denominator_unit\n      - SNOMED:has_concentration_strength_numerator_unit\n      - SNOMED:has_presentation_strength_denominator_unit\n      - SNOMED:has_presentation_strength_numerator_unit\n      - SNOMED:has_unit_of_presentation\n    in_subset:\n      - samples\n\n  base coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'one-based', 'fully-closed' ]\n    description: >-\n      A position in the base coordinate system.  Base coordinates start at position 1 instead of position 0.\n    range: integer\n\n  ## --------------------\n  ## NODE PROPERTY SLOTS\n  ## --------------------\n\n  node property:\n    description: >-\n      A grouping for any property that holds between a node and a value\n    domain: named thing\n\n  id:\n    identifier: true\n    description: >-\n      A unique identifier for an entity.\n      Must be either a CURIE shorthand for a URI or a complete URI\n    in_subset:\n      - translator_minimal\n    required: true\n    exact_mappings:\n      - AGRKB:primaryId\n      - gff3:ID\n      - gpi:DB_Object_ID\n\n  iri:\n    description: >-\n      An IRI for an entity. This is determined by the id using expansion rules.\n    range: iri type\n    in_subset:\n      - translator_minimal\n      - samples\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P854\n\n  type:\n    slot_uri: rdf:type\n    exact_mappings:\n      - AGRKB:soTermId\n      - gff3:type\n      - gpi:DB_Object_Type\n\n  category:\n    is_a: type\n    domain: entity\n    range: category type\n    designates_type: true\n    description: >-\n      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the\n      biolink entity type class.\n       * In a neo4j database this MAY correspond to the neo4j label tag.\n       * In an RDF database it should be a biolink model class URI.\n      This field is multi-valued. It should include values for ancestors of the biolink class; for example,\n      a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\n\n      In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink\n      class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`\n      may have a rdf:type assertion to a SO class such as TF_binding_site,\n      which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,\n      biolink:MolecularEntity, biolink:NamedThing}\n    is_class_field: true\n    multivalued: true\n    in_subset:\n      - translator_minimal\n\n  name:\n    aliases: [ 'label', 'display name', 'title' ]\n    description: >-\n      A human-readable name for an attribute or entity.\n    range: label type\n    in_subset:\n      - translator_minimal\n      - samples\n    #\n    # linkML doesn't like this name slot to be \"required: true\".\n    # Besides, some entity nodes/attributes may not have names?\n    # required: true\n    slot_uri: rdfs:label\n    exact_mappings:\n      - gff3:Name\n      - gpi:DB_Object_Name\n    narrow_mappings:\n      - dct:title\n      - WIKIDATA_PROPERTY:P1476\n\n  stoichiometry:\n    description: >-\n      the relationship between the relative quantities of substances taking part in a reaction or\n      forming a compound, typically a ratio of whole integers.\n    is_a: association slot\n    range: integer\n\n  reaction direction:\n    description: >-\n      the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)\n    is_a: association slot\n    range: ReactionDirectionEnum\n    narrow_mappings:\n      - NCIT:C42677\n\n  reaction balanced:\n    is_a: association slot\n    range: boolean\n\n  reaction side:\n    description: >-\n      the side of a reaction being modeled (ie: left or right)\n    is_a: association slot\n    range: ReactionSideEnum\n\n  symbol:\n    is_a: node property\n    domain: named thing\n    description: >-\n      Symbol for a particular thing\n    exact_mappings:\n      - AGRKB:symbol\n      - gpi:DB_Object_Symbol\n\n  synonym:\n    is_a: node property\n    aliases: [ 'alias' ]\n    domain: named thing\n    range: label type\n    description: >-\n      Alternate human-readable names for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      # there is an interesting debate here: are these terms \"narrower\" a.k.a. more specialized instances of\n      # 'biolink:synonym' or should they be binned into their respective namesake class of mappings?\n      # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.\n      - skos:altLabel\n      - gff3:Alias\n      - AGRKB:synonyms\n      - gpi:DB_Object_Synonyms\n      # TODO: RTX contributed terms mapped here... May need review?\n      - HANCESTRO:0330\n      - IAO:0000136\n      - RXNORM:has_tradename\n\n  exact synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasExactSynonym\n\n  broad synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasBroadSynonym\n\n  narrow synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasNarrowSynonym\n\n  related synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasRelatedSynonym\n\n  has topic:\n    aliases: [ 'topic', 'descriptors' ]\n    is_a: node property\n    range: ontology class\n    exact_mappings:\n      - foaf:topic\n    description: >-\n      Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.\n      See https://github.com/biolink/biolink-model/issues/238\n\n  xref:\n    is_a: node property\n    aliases: [ 'dbxref', 'Dbxref', 'DbXref' ]\n    domain: named thing\n    range: uriorcurie\n    description: >-\n      Alternate CURIEs for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - gff3:Dbxref\n      - gpi:DB_Xrefs\n\n  full name:\n    is_a: node property\n    domain: named thing\n    range: label type\n    description: >-\n      a long-form human readable name for a thing\n\n  description:\n    aliases: [ 'definition' ]\n    range: narrative text\n    description: >-\n      a human-readable description of an entity\n    in_subset:\n      - translator_minimal\n    slot_uri: dct:description\n    exact_mappings:\n      - IAO:0000115\n      - skos:definitions\n    narrow_mappings:\n      - gff3:Description\n\n  systematic synonym:\n    is_a: node property\n    domain: named thing\n    range: label type\n    multivalued: true\n    slot_uri: GOP:systematic_synonym\n    description: >-\n      more commonly used for gene symbols in yeast\n\n  affiliation:\n    is_a: node property\n    description: >-\n      a professional relationship between one provider (often a person) within another provider (often an organization).\n      Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.\n    domain: agent\n    range: uriorcurie\n    multivalued: true\n\n  address:\n    is_a: node property\n    description: >-\n      the particulars of the place where someone or an organization is situated.  For now, this slot is a\n      simple text \"blob\" containing all relevant details of the given location for fitness of purpose.\n      For the moment, this \"address\" can include other contact details such as email and phone number(?).\n\n  ## Space\n\n  latitude:\n    is_a: node property\n    range: float\n    description: >-\n      latitude\n    exact_mappings:\n      - wgs:lat\n\n  longitude:\n    is_a: node property\n    range: float\n    description: >-\n      longitude\n    exact_mappings:\n      - wgs:long\n\n  ## Time\n\n  timepoint:\n    aliases: [ 'duration' ]\n    range: time type\n    description: >-\n      a point in time\n\n  creation date:\n    is_a: node property\n    aliases: [ 'publication date' ]\n    range: date\n    description: >-\n      date on which an entity was created. This can be applied to nodes or edges\n    exact_mappings:\n      - dct:createdOn\n      - WIKIDATA_PROPERTY:P577\n\n  update date:\n    is_a: node property\n    range: date\n    description: >-\n      date on which an entity was updated. This can be applied to nodes or edges\n\n  ## Statistics\n\n  aggregate statistic:\n    is_a: node property\n    abstract: true\n\n  has count:\n    description: >-\n      number of things with a particular property\n    is_a: aggregate statistic\n    range: integer\n    exact_mappings:\n      - LOINC:has_count\n\n  has total:\n    description: >-\n      total number of things in a particular reference set\n    is_a: aggregate statistic\n    range: integer\n\n  has quotient:\n    is_a: aggregate statistic\n    range: double\n\n  has percentage:\n    description: >-\n      equivalent to has quotient multiplied by 100\n    is_a: aggregate statistic\n    range: double\n\n  ## Properties for Information Content Entity and Publication Nodes\n\n  has taxonomic rank:\n    is_a: node property\n    range: taxonomic rank\n    multivalued: false\n    mappings:\n      - WIKIDATA:P105\n\n  has dataset:\n    is_a: node property\n    domain: dataset version\n    range: dataset\n    slot_uri: dct:source\n\n  source web page:\n    is_a: node property\n    domain: dataset summary\n    broad_mappings:\n      - dct:source\n\n  source logo:\n    is_a: node property\n    domain: dataset summary\n    slot_uri: schema:logo\n\n  retrieved on:\n    is_a: node property\n    domain: dataset\n    range: date\n    exact_mappings:\n      - pav:retrievedOn\n\n  version of:\n    is_a: node property\n    domain: dataset version\n    range: dataset summary\n    exact_mappings:\n      - dct:isVersionOf\n\n  version:\n    is_a: node property\n    domain: dataset\n    broad_mappings:\n      - pav:version\n      - owl:versionInfo\n\n  license:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:license\n    narrow_mappings:\n      - WIKIDATA_PROPERTY:P275\n\n  rights:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:rights\n\n  format:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:format\n      - WIKIDATA_PROPERTY:P2701\n\n  created with:\n    is_a: node property\n    domain: dataset\n    exact_mappings:\n      - pav:createdWith\n\n  download url:\n    is_a: node property\n    domain: information content entity\n    slot_uri: dcat:downloadURL\n\n  dataset download url:\n    is_a: node property\n    domain: dataset\n    slot_uri: dcat:downloadURL\n\n  distribution download url:\n    is_a: node property\n    domain: dataset distribution\n    exact_mappings:\n      - dcat:downloadURL\n\n  ingest date:\n    is_a: node property\n    domain: dataset version\n    slot_uri: pav:version\n\n  has distribution:\n    is_a: node property\n    domain: dataset version\n    range: dataset distribution\n    slot_uri: dct:distribution\n\n  published in:\n    is_a: node property\n    description: >-\n      CURIE identifier of a broader publication context within which the publication may be placed,\n      e.g. a specified book or journal.\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - NLMID\n      - issn\n      - isbn\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1433\n\n  iso abbreviation:\n    is_a: node property\n    description: >-\n      Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system\n      See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,\n      then the iso abbreviation pertains to the broader publication context (the journal) within which the given\n      publication node is embedded, not the publication itself.\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1160\n\n  authors:\n    is_a: node property\n    singular_name: author\n    description: >-\n      connects an publication to the list of authors who contributed to the publication.\n      This property should be a comma-delimited list of author names. It is recommended that an author's name\n      be formatted as \"surname, firstname initial.\".   Note that this property is a node annotation expressing\n      the citation list of authorship which might typically otherwise be more completely documented in\n      biolink:PublicationToProviderAssociation defined edges which point to full details about an author\n      and possibly, some qualifiers which clarify the specific status of a given author in the publication.\n    multivalued: true\n    domain: publication\n\n  volume:\n    is_a: node property\n    description: >-\n      volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P478\n\n  chapter:\n    is_a: node property\n    description: >-\n      chapter of a book\n    domain: book chapter\n    exact_mappings:\n      - WIKIDATA:Q1980247\n\n  issue:\n    is_a: node property\n    description: >-\n      issue of a newspaper, a scientific journal or magazine for reference purpose\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P433\n\n  pages:\n    is_a: node property\n    description: >-\n      page number of source referenced for statement or publication\n    domain: publication\n    multivalued: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P304\n\n  summary:\n    is_a: node property\n    # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot,\n    # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract'\n    aliases: [ 'abstract' ]\n    description: >-\n      executive  summary of a publication\n    domain: publication\n    exact_mappings:\n      - dct:abstract\n      - WIKIDATA:Q333291\n\n  keywords:\n    is_a: node property\n    description: >-\n      keywords tagging a publication\n    domain: publication\n    multivalued: true\n\n  mesh terms:\n    is_a: node property\n    description: >-\n      mesh terms tagging a publication\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - MESH\n    multivalued: true\n    exact_mappings:\n      - dcid:MeSHTerm\n\n  ## Biology\n\n  has biological sequence:\n    is_a: node property\n    description: >-\n      connects a genomic feature to its sequence\n    range: biological sequence\n\n  has gene or gene product:\n    is_a: node property\n    description: >-\n      connects an entity with one or more gene or gene products\n    range: gene\n    multivalued: true\n\n  has gene:\n    is_a: has gene or gene product\n    description: >-\n      connects an entity associated with one or more genes\n    range: gene\n    multivalued: true\n\n  has zygosity:\n    is_a: node property\n    domain: nucleic acid entity\n    range: zygosity\n\n  ## Chemistry, drugs and food\n\n  has chemical formula:\n    is_a: node property\n    range: chemical formula value\n    description: >-\n      description of chemical compound based on element symbols\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P274\n\n  is metabolite:\n    is_a: node property\n    domain: molecular entity\n    range: boolean\n    description: >-\n      indicates whether a molecular entity is a metabolite\n    exact_mappings:\n      - CHEBI:25212\n\n  has constituent:\n    description: >-\n      one or more molecular entities within a chemical mixture\n    is_a: node property\n    range: molecular entity\n    multivalued: true\n\n  has drug:\n    is_a: node property\n    description: >-\n      connects an entity to one or more drugs\n    range: drug\n    multivalued: true\n\n  has device:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) devices\n    range: device\n    multivalued: true\n\n  has procedure:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) procedures\n    range: procedure\n    multivalued: true\n\n  ## Clinical exposures\n\n  has receptor:\n    is_a: node property\n    domain: exposure event\n    range: organismal entity\n    description: >-\n      the organism or organism part being exposed\n    exact_mappings:\n      - ExO:0000001\n\n  has stressor:\n    is_a: node property\n    domain: exposure event\n    aliases: [ 'has stimulus' ]\n    description: >-\n      the process or entity that the receptor is being exposed to\n    exact_mappings:\n      - ExO:0000000\n\n  has route:\n    is_a: node property\n    domain: exposure event\n    description: >-\n      the process that results in the stressor coming into direct contact with the receptor\n    exact_mappings:\n      - ExO:0000055\n    narrow_mappings:\n      - LOINC:has_pharmaceutical_route\n      - SNOMED:has_dose_form_intended_site\n      - SNOMED:has_route_of_administration\n\n\n  population context qualifier:\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: association slot\n    range: population of individual organisms\n\n  temporal context qualifier:\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n      for time intervales, use temporal interval qualifier.\n    is_a: association slot\n    range: time type\n\n  temporal interval qualifier:\n    is_a: temporal context qualifier\n    description: >-\n      a constraint of a time interval placed upon the truth value of an\n      association.\n\n  is supplement:\n    description: >-\n    is_a: node property\n    range: chemical mixture\n\n  trade name:\n    description: >-\n    is_a: node property\n    range: chemical entity\n\n  available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: DrugAvailabilityEnum\n\n  is toxic:\n    description: >-\n    is_a: node property\n    multivalued: false\n    range: boolean\n\n  has chemical role:\n    is_a: related to at concept level\n    description: >-\n      A role is particular behaviour which a chemical entity may exhibit.\n    range: chemical role\n    multivalued: true\n\n  max tolerated dose:\n    description: >-\n      The highest dose of a drug or treatment that does not cause unacceptable side effects.\n      The maximum tolerated dose is determined in clinical trials by testing increasing doses\n      on different groups of people until the highest dose with acceptable side effects is\n      found. Also called MTD.\n    is_a: node property\n    multivalued: false\n    range: string\n\n  animal model available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: disease or phenotypic feature\n\n  FDA adverse event level:\n    description: >-\n    is_a: association slot\n    range: FDAIDAAdverseEventEnum\n\n  highest FDA approval status:\n    description: >-\n      Should be the highest level of FDA approval this chemical entity or device has, regardless of which\n      disease, condition or phenotype it is currently being reviewed to treat.  For specific levels of FDA\n      approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'\n\n  drug regulatory status world wide:\n    aliases: [ 'max phase' ]\n    description: >-\n      An agglomeration of drug regulatory status worldwide. Not specific to FDA.\n    exact_mappings:\n      - NCIT:C172573\n    narrow_mappings:\n      - NCIT:R172\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n\n  routes of delivery:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    multivalued: true\n    range: DrugDeliveryEnum\n\n  ## -------------------\n  ## QUALIFIERS\n  ## -------------------\n\n  form or variant qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.\n    examples:\n      - value: mutation\n      - value: late stage\n      - value: severe\n      - value: transplant\n      - value: chemical analog\n    notes: >-\n      please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier'\n      terms in the gene->chemical association space. \n      the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’.\n      the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the  more specific concept ‘Late Stage forms of Disease X’\n      the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’\n      the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’\n\n\n  aspect qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.  The purpose of the aspect slot is to indicate what aspect is being affected in an \n      'affects' association.\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    notes: >-\n      for good examples of aspects in the gene-> chemical space, please see the \n      GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify \n      the gene making the full subject a different ontological type.  \n      the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process)\n      the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process)\n      the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity)\n      the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event)\n      the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process)\n      the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality)\n      the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)\n\n  derivative qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.\n    examples:\n      - value: metabolite\n\n  part qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).\n    examples:\n      - value: polyA tail\n      - value: upstream control region\n\n  context qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.\n    examples:\n      - value: cohort x (e.g. a specific population, referenced by an identifier)\n      - value: gut microbiome # OHMI:0000020\n\n  direction qualifier:\n    is_a: association slot\n    abstract: true\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n    notes: >-\n      the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’   \n      the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’\n\n  mapped predicate:\n    description: >-\n      The predicate that is being replaced by the fully qualified representation of predicate + subject and object \n      qualifiers.  Only to be used in test data and mapping data to help with the transition to the fully qualified\n      predicate model. Not to be used in knowledge graphs.\n\n  predicate mappings:\n    description: >- \n      A collection of relationships that are not used in biolink, but have biolink patterns that can \n      be used to replace them.  This is a temporary slot to help with the transition to the fully qualified predicate\n      model in Biolink3.\n    multivalued: true\n    range: predicate mapping\n    inlined_as_list: true\n\n  exact matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      an identical meaning. Such terms often describe the same concept from\n      different ontological perspectives.\n    multivalued: true\n\n  narrow matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a narrower meaning. Such terms often describe a more specific concept\n      from different ontological perspectives.\n    multivalued: true\n\n  broad matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a broader meaning. Such terms often describe a more general concept\n      from different ontological perspectives.\n    multivalued: true\n\n  subject aspect qualifier:\n    is_a: aspect qualifier\n\n  subject form or variant qualifier:\n    is_a: form or variant qualifier\n\n  subject part qualifier:\n    is_a: part qualifier\n\n  subject derivative qualifier:\n    is_a: derivative qualifier\n\n  subject context qualifier:\n    is_a: context qualifier\n\n  subject direction qualifier:\n    is_a: direction qualifier\n\n  object aspect qualifier:\n    is_a: aspect qualifier\n\n  object form or variant qualifier:\n    is_a: form or variant qualifier\n\n  object part qualifier:\n    is_a: part qualifier\n\n  object derivative qualifier:\n    is_a: derivative qualifier\n\n  object context qualifier:\n    is_a: context qualifier\n\n  object direction qualifier:\n    is_a: direction qualifier\n    range: DirectionQualifierEnum\n\n  qualified predicate:\n    is_a: association slot\n    description: >-\n      Predicate to be used in an association when subject and object qualifiers are present and the full\n      reading of the statement requires a qualification to the predicate in use in order to refine or \n      increase the specificity of the full statement reading.  This qualifier holds a relationship to be used instead of that \n      expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based \n      semantics are included.  This is necessary only in cases where the primary predicate does not work in a \n      full statement reading.\n    notes: >-\n      to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read \n      using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using \n      the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, \n      object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but doesnt make \n      sense in the full statement reading  (because “Chemical X affects increased expression of Gene Y'' is not \n      what we mean to say here: it causes increased expression of Gene Y)\n\n\n  statement qualifier:\n    is_a: association slot\n    description: >-\n\n  causal mechanism qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a type of molecular control mechanism through which an\n      effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition',\n      'allosteric modulation', 'channel blocker')\n\n  anatomical context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing an anatomical location where an relationship expressed in an\n      association took place (can be a tissue, cell type, or sub-cellular location).\n    range: AnatomicalContextQualifierEnum\n    notes: >-\n      Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ \n      combines with a core concept of ‘neuron’ \n      to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies \n      taxonomic context, e.g. species-specific molecular activity.  Ontology CURIEs are expected as values \n      here, the examples below are intended to help clarify the content of the CURIEs.\n    examples:\n      - value: blood # UBERON:0000178\n      - value: cerebral cortext # UBERON:0000956\n\n  species context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a taxonomic category of species in which a relationship\n      expressed in an association took place.\n    range: organism taxon\n    examples:\n      - value: zebrafish # NCBITaxon:7955\n      - value: human # NCBITaxon:9606\n    notes: >- \n      Ontology CURIEs are expected as values\n      here, the examples below are intended to help clarify the content of the CURIEs.\n\n  qualifiers:\n    singular_name: qualifier\n    description: >-\n      connects an association to qualifiers that modify or\n      qualify the meaning of that association\n    local_names:\n      ga4gh: annotation qualifier\n    is_a: association slot\n    multivalued: true\n    range: ontology class\n\n  frequency qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\n    is_a: association slot\n    range: frequency value\n\n  severity qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      how severe the phenotype is in the subject\n    is_a: association slot\n    range: severity value\n\n  sex qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state whether\n      the association is specific to a particular sex.\n    is_a: association slot\n    range: biological sex\n\n  onset qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      when the phenotype appears is in the subject\n    is_a: association slot\n    range: onset\n\n  clinical modifier qualifier:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    is_a: association slot\n    range: clinical modifier\n\n  sequence variant qualifier:\n    description: >-\n      a qualifier used in an association with the variant\n    is_a: association slot\n    range: sequence variant\n\n  quantifier qualifier:\n    is_a: association slot\n    range: ontology class\n    description: >-\n      A measurable quantity for the object of the association\n    narrow_mappings:\n      # TODO: RTX contributed terms mapped here... May need review?\n      - LOINC:analyzes\n      - LOINC:measured_by\n      - LOINC:property_of\n      - SEMMEDDB:MEASURES\n      - UMLS:measures\n\n  catalyst qualifier:\n    is_a: association slot\n    multivalued: true\n    range: macromolecular machine mixin\n    description: >-\n      a qualifier that connects an association between two causally connected\n      entities (for example, two chemical entities, or a chemical entity in\n      that changes location) and the gene product, gene, or complex that\n      enables or catalyzes the change.\n\n  stage qualifier:\n    description: >-\n      stage during which gene or protein expression of takes place.\n    is_a: association slot\n    range: life stage\n    # path: \"object/during\"\n    examples:\n      - value: UBERON:0000069\n        description: larval stage\n\n  ## --------------------\n  ## PREDICATES/RELATIONS\n  ## --------------------\n\n  related to:\n    description: >-\n      A relationship that is asserted between two named things\n    domain: named thing\n    range: named thing\n    multivalued: true\n    inherited: true\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:relatedMatch\n      - UMLS:related_to\n    broad_mappings:\n      - owl:topObjectProperty\n    narrow_mappings:\n      - SEMMEDDB:ASSOCIATED_WITH\n      - SEMMEDDB:compared_with\n      - SEMMEDDB:higher_than\n      - SEMMEDDB:lower_than\n      - BFO:0000054\n      - UBERON_CORE:protects\n      - GOREL:0002005\n      - GOREL:0012006\n      # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms\n      - BTO:related_to\n      - CHEBI:is_conjugate_acid_of\n      - CHEBI:is_conjugate_base_of\n      - CPT:has_add_on_code\n      - CPT:mapped_to\n      - EFO:0006351\n      - FMA:connected_to\n      - FMA:continuous_with\n      - FMA:homonym_of\n      - FMA:related_developmental_entity_of\n      - RO:0002093\n      - RO:0002092\n      - RO:0002084\n      - HCPCS:mapped_to\n      # RTX contributed terms, perhaps belong somewhere else with more precise semantics?\n      - HMDB:disease\n      - HMDB:has_protein_association\n      - IAO:0000136\n      - LOINC:has_answer\n      - LOINC:has_challenge\n      - LOINC:has_evaluation\n      - LOINC:mapped_to\n      - LOINC:mth_has_expanded_form\n      - MESH:RO\n      - MESH:has_mapping_qualifier\n      - MESH:mapped_to\n      - MONDO:disease_shares_features_of\n      - NCIT:disease_may_have_associated_disease\n      - NCIT:human_disease_maps_to_eo_disease\n      - NCIT:is_abnormal_cell_of_disease\n      - NCIT:is_related_to_endogenous_product\n      - UBERON_NONAMESPACE:connected_to\n      - UBERON_NONAMESPACE:innervated_by\n      - NBO-PROPERTY:is_about\n      - RO:0000053 # bearer_of\n      - PATO:reciprocal_of\n      - RO:0000052\n      - RO:0002001\n      - RO:0002002\n      - RO:0002003\n      - RO:0002008\n      - RO:0002134\n      - RO:0002150\n      - RO:0002159\n      - RO:0002176\n      - RO:0002177\n      - RO:0002178\n      - RO:0002179\n      - RO:0002314\n      - RO:0002322\n      # functionally related to\n      - RO:0002328\n      - RO:0002332\n      - RO:0002338\n      - RO:0002339\n      - RO:0002341\n      - RO:0002342\n      - RO:0002344\n      - RO:0002348\n      - RO:0002349\n      - RO:0002356\n      - RO:0002371\n      - RO:0002372\n      - RO:0002373\n      - RO:0002374\n      - RO:0002385\n      - RO:0002387\n      - RO:0002451\n      - RO:0002494\n      - RO:0002495\n      - RO:0002568\n      - RO:0002573\n      - RO:0004026\n      - RO:0004027\n      - RO:0009001\n      - RO:0009004\n      - RXNORM:has_form\n      - RXNORM:reformulated_to\n      - SNOMED:has_associated_morphology\n      - SNOMED:has_associated_procedure\n      - SNOMED:has_direct_morphology\n      - SNOMED:has_disposition\n      - SNOMED:has_indirect_morphology\n      - SNOMED:has_modification\n      - SNOMED:has_procedure_morphology\n      - SNOMED:has_specimen_source_morphology\n      - SNOMED:inheres_in\n      - SNOMED:is_interpreted_by\n      - SNOMED:relative_to_part_of\n      - UBERON:synapsed_by\n      - UMLS:RO\n      - UMLS:RQ\n      - UMLS:class_code_classified_by\n      - UMLS:exhibited_by\n      - UMLS:has_context_binding\n      - UMLS:has_form\n      - UMLS:has_mapping_qualifier\n      - UMLS:larger_than\n      - UMLS:mapped_to\n      - UMLS:owning_section_of\n\n  related to at concept level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between terminology components that describe the conceptual model of a domain.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  related to at instance level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between two instances of a data classes.  Much like an assertion component,\n      in an ABox, these represent facts associated with the conceptual model.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  associated with:\n    is_a: related to at instance level\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent,\n      'related to'. This relationship holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated.  E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial \n      Infarction (MI)” asserts that having Afib is not statistically independent from whether a patient \n      will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to \n      the statistical variables, or represent related entities for which the variables serve as proxies in an \n      Association (e.g. diseases, chemical entities or processes).\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    domain: named thing\n    range: named thing\n    narrow_mappings:\n      - RO:0004029\n      - SNOMEDCT:47429007\n\n  superclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a super class of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q66088480\n      - CHEMBL.MECHANISM:superset_of\n      - GO:inverse_isa\n      - MESH:inverse_isa\n      - RXNORM:inverse_isa\n      - VANDF:inverse_isa\n    narrow_mappings:\n      - NCIT:cdrh_parent_of\n      - NCIT:ctcae_5_parent_of\n      - NCIT:subset_includes_concept\n      - OMIM:has_manifestation\n      - SNOMED:has_basic_dose_form\n      - UMLS:RB\n\n  subclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a specialization of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: True\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX\n      - LOINC:class_of\n      - LOINC:has_class\n    exact_mappings:\n      - rdfs:subClassOf\n      - SEMMEDDB:ISA\n      - WIKIDATA_PROPERTY:P279\n      - CHEMBL.MECHANISM:subset_of\n      - GO:isa\n      - MESH:isa\n      - RXNORM:isa\n      - VANDF:isa\n    narrow_mappings:\n      - CHEBI:has_parent_hydride\n      - LOINC:has_archetype\n      - LOINC:has_parent_group\n      - LOINC:is_presence_guidance_for\n      - NCIT:gene_product_has_chemical_classification\n      # RTX mapped terms classes for biomarkers\n      - NCIT:R36\n      - NCIT:R42\n      - NCIT:A16\n      - NCIT:A11\n      - NCIT:A14\n      - NCIT:A3\n      - NDDF:has_dose_form\n      - RXNORM:has_dose_form\n      - RXNORM:has_doseformgroup\n      - SNOMED:entire_anatomy_structure_of\n      - SNOMED:has_dose_form\n      # RTX mapping\n      - rdfs:subPropertyOf\n\n  same as:\n    is_a: exact match\n    description: >-\n      holds between two entities that are considered equivalent to each other\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # identical class extension with identical sets of individuals\n      - owl:equivalentClass\n    exact_mappings:\n      # identical individual, or identical class concept/meaning\n      - owl:sameAs\n      - skos:exactMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      # RTX suggests mapping this to proposed new \"biolink:close_match\" predicate instead\n      #- SEMMEDDB:same_as\n      - WIKIDATA_PROPERTY:P2888\n      - CHEMBL.MECHANISM:equivalent_to\n      - MONDO:equivalentTo\n    narrow_mappings:\n      - DRUGBANK:external-identifier\n\n  close match:\n    is_a: related to at concept level\n    description: >-\n      a list of terms from different schemas or terminology systems that have\n      a semantically similar but not strictly equivalent, broader, or narrower\n      meaning. Such terms often describe the same general concept from\n      different ontological perspectives (e.g. drug as a type of chemical\n      entity versus drug as a type of role borne by a chemical entity).\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:closeMatch\n      # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      - SEMMEDDB:same_as\n    narrow_mappings:\n      - CHEBI:is_enantiomer_of\n      - CHEBI:is_tautomer_of\n      - MEDDRA:classified_as\n      - OIO:hasDbXref\n      - oboformat:xref\n      - RXNORM:has_quantified_form\n      - UMLS:SY\n\n  exact match:\n    is_a: close match\n    description: >-\n      holds between two entities that have strictly equivalent\n      meanings, with a high degree of confidence\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:exactMatch\n      - WIKIDATA:Q39893449\n      - WIKIDATA:P2888\n\n  broad match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a broader, more general meaning. Broader terms are\n      typically shown as parents in a hierarchy or tree.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: narrow match\n    exact_mappings:\n      - skos:broadMatch\n      - WIKIDATA:Q39894595\n\n  narrow match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a narrower, more specific meaning. Narrower terms are\n      typically shown as children in a hierarchy or tree.\n    is_a: related to at concept level\n    inverse: broad match\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - skos:narrowMatch\n      - WIKIDATA:Q39893967\n    annotations:\n      opposite_of: broad match\n\n  member of:\n    description: >-\n      Defines a mereological relation between a item and a collection.\n    is_a: related to at concept level\n    inverse: has member\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002350\n    close_mappings:\n      - skos:member\n\n  has member:\n    description: >-\n      Defines a mereological relation between a collection and an item.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002351\n      - skos:member\n\n  opposite of:\n    description: >-\n      x is the opposite of y if there exists some distance metric M, and there exists\n      no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002604\n    see_also:\n      - https://doi.org/10.1101/108977\n      - https://github.com/biolink/biolink-model/issues/657\n\n\n  associated with likelihood of:\n    is_a: associated with\n    description: >-\n      A a relationship that holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated, wherein the state or value of one variable predicts the future state \n      or value of the other.  E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated \n      with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib \n      is associated with an increased or decreased likelihood that a patient will later exhibit MI.\n    annotations:\n      canonical_predicate: true\n\n  likelihood associated with:\n    is_a: associated with\n    description: >-\n    inverse: associated with likelihood of\n\n  associated with increased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is more probable.\n    annotations:\n      canonical_predicate: true\n\n  increased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with increased likelihood of\n\n  associated with decreased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is less probable.\n    annotations:\n      canonical_predicate: true\n\n  decreased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with decreased likelihood of\n\n  target for:\n    is_a: related to at instance level\n    description: >-\n      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene\n      product could have a therapeutic effect\n    annotations:\n      canonical_predicate: true\n    domain: gene\n    range: disease\n\n  has target:\n    is_a: related to at instance level\n    inverse: target for\n    domain: disease\n    range: gene\n\n  active in:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: cellular component\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002432\n\n  has active component:\n    is_a: related to at instance level\n    inverse: active in\n    domain: cellular component\n    range: gene or gene product\n\n  acts upstream of:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002263\n\n  has upstream actor:\n    is_a: related to at instance level\n    inverse: acts upstream of\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004034\n\n  has positive upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004035\n\n  has negative upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of negative effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002264\n\n  has upstream or within actor:\n    is_a: has upstream actor\n    inverse: acts upstream of or within\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within positive effect:\n    is_a: acts upstream of or within\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004032\n\n  has positive upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within negative effect:\n    is_a: acts upstream of or within\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004033\n\n  has negative upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within negative effect\n    domain: biological process\n    range: gene or gene product\n\n    ## Publication related predicates\n  mentions:\n    description: >-\n      refers to is a relation between one information content entity and the named thing\n      that it makes reference to.\n    is_a: related to at instance level\n    exact_mappings:\n      - IAO:0000142\n    narrow_mappings:\n      - SIO:000628\n\n  mentioned by:\n    description: >-\n      refers to is a relation between one named thing and the information content entity\n      that it makes reference to.\n    is_a: related to at instance level\n    inverse: mentions\n\n  ## Publication related predicates\n\n  contributor:\n    is_a: related to at instance level\n    domain: agent\n    range: information content entity\n    comments:\n      - This is a grouping for predicates relating entities to their associated contributors realizing them\n    abstract: true\n    exact_mappings:\n      - dct:contributor\n\n  has contributor:\n    inverse: contributor\n    is_a: related to at instance level\n    domain: information content entity\n    range: agent\n\n  provider:\n    is_a: contributor\n    description: >-\n      person, group, organization or project that provides a piece of information (e.g. a knowledge association).\n\n  has provider:\n    inverse: provider\n    is_a: has contributor\n    domain: information content entity\n    range: agent\n\n  publisher:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      organization or person responsible for publishing books, periodicals, podcasts, games or software.\n      Note that in the case of publications which have a containing \"published in\" node property, the publisher\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the publisher agent of the encompassing publication\n      (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).\n    exact_mappings:\n      - dct:publisher\n      - WIKIDATA_PROPERTY:P123\n\n  has publisher:\n    is_a: has contributor\n    inverse: publisher\n    domain: publication\n    range: agent\n\n  editor:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      editor of a compiled work such as a book or a periodical (newspaper or an academic journal).\n      Note that in the case of publications which have a containing \"published in\" node property, the editor\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the editorial agent of the encompassing publication\n      (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P98\n\n  has editor:\n    inverse: editor\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n  author:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      an instance of one (co-)creator primarily responsible for a written work\n    exact_mappings:\n      - dct:creator\n      - WIKIDATA_PROPERTY:P50\n\n  has author:\n    inverse: author\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n  ## end of Publication related predicates\n\n  assesses:\n    is_a: related to at instance level\n    aliases: [ 'was assayed against' ]\n    description: >-\n      The effect of a thing on a target was interrogated in some assay.\n      A relationship between some perturbing agent (usually a chemical compound) and some target entity,\n      where the affect of the perturbing agent on the target entity was interrogated in a particular assay.\n      The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type\n      of biological entity.\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n\n  is assessed by:\n    is_a: related to at instance level\n    inverse: assesses\n    domain: named thing\n    range: named thing\n\n  interacts with:\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between any two entities that directly or indirectly interact with each other\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    mixin: true\n    exact_mappings:\n      - SEMMEDDB:INTERACTS_WITH\n    notes: >-\n      please use a more specific child predicate of interacts with, either physically interacts with\n      or genetically interacts with. \n\n  physically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two entities that make physical contact as part of some interaction. \n      does not imply a causal relationship.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - WIKIDATA_PROPERTY:P129\n    close_mappings:\n      - CHEMBL.MECHANISM:binding_agent\n      - CHEMBL.MECHANISM:chelating_agent\n      - CHEMBL.MECHANISM:cross-linking_agent\n      - CHEMBL.MECHANISM:oxidative_enzyme\n      - CHEMBL.MECHANISM:sequestering_agent\n      - CHEMBL.MECHANISM:substrate\n      - DRUGBANK:target\n    narrow_mappings:\n      # Defined more narrowly as \"substance interaction\", thus specific applies to a subclass entities\n      - DRUGBANK:drug-interaction\n      - FMA:adheres_to\n      - NCIT:A7\n      - PR:non-covalently_bound_to\n    mixins:\n      - interacts with\n\n  directly physically interacts with:\n    is_a: physically interacts with\n    description: >-\n      A causal mechanism mediated by a direct contact between the effector and target entities (this contact may \n      be weak or strong, transient or stable).\n    symmetric: true\n    exact_mappings:\n      - RO:0002436\n    broad_mappings:\n      # Definition of this term is more generic than direct physical molecular interactions:\n      # A is connected to B iff there exists a fiat, material or temporal path between A and B.\n      - SIO:000203\n      - RO:0002578\n    narrow_mappings:\n      - PHAROS:drug_targets\n      - DRUGBANK:chelator\n      - CTD:affects_binding\n      - DGIdb:cofactor\n    annotations:\n      canonical_predicate: true\n\n  binds:\n    deprecated: true\n    is_a: directly physically interacts with\n    description: >-\n      A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, \n      which form a stable physical interaction.\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - DGIdb:binder\n\n  indirectly physically interacts with:\n    is_a: physically interacts with\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  genetically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two genes whose phenotypic effects are dependent on each\n      other in some way - such that their combined phenotypic effects are the\n      result of some interaction between the activity of their gene products.\n      Examples include epistasis and synthetic lethality.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    exact_mappings:\n      - RO:0002435\n\n  affects:\n    is_a: related to at instance level\n    description: >-\n      describes an entity that has a direct affect on the state or quality\n      of another existing entity. Use of the 'affects' predicate implies that\n      the affected entity already exists, unlike predicates such as\n      'affects risk for' and 'prevents, where the outcome is something\n      that may or may not come to be.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # Contributed by RTX. Seems possible that a new predicate \"biolink:in_pathway\" could be justified?\n      - DRUGBANK:pathway\n    exact_mappings:\n      - SEMMEDDB:AFFECTS\n      - DGIdb:affects\n    narrow_mappings:\n      - SEMMEDDB:ADMINISTERED_TO\n      - CTD:prediction_hypothesis\n      - GOREL:0001006\n      - CTD:inferred\n      - UPHENO:0000001\n      - RO:0002263\n      - RO:0002264\n      - NCIT:R158\n      - NCIT:R160\n      - NCIT:R30\n      - NCIT:R150\n      - NCIT:R72\n      - NCIT:R146\n      - NCIT:R124\n      - NCIT:R173\n      - NCIT:R100\n      - NCIT:R102\n      - NCIT:R101\n      - NCIT:R113\n      - NCIT:R23\n      - NCIT:R25\n      - NCIT:gene_mapped_to_disease\n      - NCIT:R133\n      - RO:0002343\n      - RO:0002355\n      - RO:0002591\n      - RO:0002592\n      - RO:0012003\n      - SNOMED:has_pathological_process\n      - UBERGRAPH:is_increase_of # talked to Jim Balhoff, this is a valid mapping\n      - UBERGRAPH:is_decrease_of # talked to Jim Balhoff, this is a valid mapping\n\n  affected by:\n    is_a: related to at instance level\n    description: >-\n      describes an entity of which the state or quality is affected by\n      another existing entity.\n    inverse: affects\n\n  associated with sensitivity to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of sensitivity to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - PATO:0000085 # sensitivity toward\n    narrow_mappings:\n      - SNOMEDCT:418038007 # propensity to adverse reaction\n\n  sensitivity associated with:\n    is_a: associated with\n    inverse: associated with sensitivity to\n    range: named thing\n    domain: chemical entity\n\n  associated with resistance to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of resistance to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n\n  resistance associated with:\n    is_a: associated with\n    inverse: associated with resistance to\n    range: named thing\n    domain: chemical entity\n\n  diagnoses:\n    is_a: related to at instance level\n    description: >-\n      a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - NCIT:C15220 # diagnosis\n      - SIO:001331 # diagnosis\n    exact_mappings:\n      - DrugCentral:5271\n      - SEMMEDDB:DIAGNOSES\n\n  is diagnosed by:\n    is_a: related to at instance level\n    inverse: diagnoses\n    range: chemical or drug or treatment\n    domain: disease or phenotypic feature\n\n  increases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that increase the amount\n      or activity of the object.\n\n  amount or activity increased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: increases amount or activity of\n\n  decreases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that decrease the amount\n      or activity of the object.\n\n  amount or activity decreased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: decreases amount or activity of\n\n  ## role mixins for use in tagging corresponding role predicates\n\n  chemical role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a chemical context.\n    mixin: true\n    exact_mappings:\n      - CHEBI:51086\n\n  biological role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a biological context.\n    mixin: true\n    narrow_mappings:\n      - CHEBI:24432\n\n  affects response to:\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: response affected by\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_response_to\n\n  response affected by:\n    description: >-\n      holds between two chemical entities where the susceptibility of a biological entity or system\n      (e.g. an organism, cell, cellular component, macromolecular machine mixin,\n      biological or pathological process) of one is affected by the action of the other.\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases response to\n    exact_mappings:\n      - CTD:increases_response_to\n\n  response increased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases response to\n\n  decreases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases response to\n    exact_mappings:\n      - CTD:decreases_response_to\n    narrow_mappings:\n      - CTD:decreases_response_to_substance\n\n  response decreased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases response to\n\n  regulates:\n    is_a: affects\n    description: >-\n      A more specific form of affects, that implies the effect results from a biologically evolved control mechanism.\n      Gene-affects-gene relationships will (almost) always involve regulation.  Exogenous/environmental chemical-affects-gene relationships \n      are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or\n      possibly one of the 'interacts with' predicates depending on the nature of the interaction.\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002448\n    broad_mappings:\n      # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology)\n      - WIKIDATA_PROPERTY:P128\n      - CHEMBL.MECHANISM:modulator\n      - RO:0002295\n      - RO:0002332\n      - RO:0002448\n    notes: >-\n      The RO definition of 'directly regulates the activity of' is an exact_mapping here because \n      it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to\n      \"RO:0002211\" which describes process to process regulation.\n    mixins:\n      - interacts with\n\n  regulated by:\n    is_a: affected by\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    inverse: regulates\n\n  disrupts:\n    is_a: affects\n    aliases: [ 'disease causes disruption of' ]\n    description: >-\n      describes a relationship where one entity degrades or interferes\n      with the structure, function, or occurrence of another.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: enables\n    exact_mappings:\n      - SEMMEDDB:DISRUPTS\n      - CHEMBL.MECHANISM:disrupting_agent\n    narrow_mappings:\n      - RO:0004024\n      - RO:0004025\n\n  disrupted by:\n    is_a: affected by\n    description: >-\n      describes a relationship where the structure, function, or occurrence\n      of one entity is degraded or interfered with by another.\n    inverse: disrupts\n\n  gene product of:\n    is_a: related to at instance level\n    description: >-\n      definition x has gene product of y if and only if y is a gene (SO:0000704)\n      that participates in some gene expression process (GO:0010467) where the output of thatf\n      process is either y or something that is ribosomally translated from x\n    exact_mappings:\n      - RO:0002204\n    domain: gene product mixin\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: has gene product\n    in_subset:\n      - translator_minimal\n\n  has gene product:\n    is_a: related to at instance level\n    description: >-\n      holds between a gene and a transcribed and/or\n      translated product generated from it\n    domain: gene\n    range: gene product mixin\n    inverse: gene product of\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX term tagged as inverse mapping\n      - PR:has_gene_template\n    exact_mappings:\n      - RO:0002205\n      - WIKIDATA_PROPERTY:P688\n      - NCIT:gene_encodes_gene_product\n    narrow_mappings:\n      - NCIT:R178\n\n  transcribed to:\n    is_a: related to at instance level\n    domain: gene\n    range: transcript\n    description: >-\n      inverse of transcribed from\n    inverse: transcribed from\n    exact_mappings:\n      - RO:0002511\n      - SIO:010080\n\n  transcribed from:\n    is_a: related to at instance level\n    domain: transcript\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: transcribed to\n    description: >-\n      x is transcribed from y if and only if x is synthesized from template y\n    exact_mappings:\n      - RO:0002510\n      - SIO:010081\n\n  translates to:\n    is_a: related to at instance level\n    domain: transcript\n    range: protein\n    annotations:\n      canonical_predicate: true\n    inverse: translation of\n    description: >-\n      x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome\n      reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)\n      and produces x (amino acid chain/polypeptide)\n    close_mappings:\n      - RO:0002513\n      - SIO:010082\n\n  translation of:\n    is_a: related to at instance level\n    domain: protein\n    range: transcript\n    description: >-\n      inverse of translates to\n    inverse: translates to\n    close_mappings:\n      - RO:0002512\n      - SIO:010083\n\n  homologous to:\n    is_a: similar to\n    aliases: [ 'in homology relationship with' ]\n    description: >-\n      holds between two biological entities that have common evolutionary origin\n    comments:\n      - typically used to describe homology relationships between genes or gene products\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000001\n      - SIO:010302\n    narrow_mappings:\n      # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158\n      - UBERON_CORE:sexually_homologous_to\n\n  paralogous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000011\n\n  orthologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship between entities (typically genes) that diverged after a speciation event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000017\n      - WIKIDATA_PROPERTY:P684\n\n  xenologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000018\n\n  coexists with:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SEMMEDDB:COEXISTS_WITH\n    narrow_mappings:\n      - BSPO:0000096\n      - BSPO:0000097\n      - BSPO:0000098\n      - BSPO:0000099\n      - BSPO:0000100\n      - BSPO:0000102\n      - BSPO:0000104\n      - BSPO:0000110\n      - BSPO:0000113\n      - BSPO:0015001\n      - BSPO:0015002\n      - BSPO:0015003\n      - BSPO:0015005\n      - BSPO:0015006\n      - BSPO:0015007\n      - BSPO:0015008\n      - BSPO:0015009\n      - BSPO:0015012\n      - BSPO:0015014\n      - BSPO:parallel_to\n      - UBERON_CORE:anastomoses_with\n      - UBERON_CORE:anteriorly_connected_to\n      - UBERON_CORE:posteriorly_connected_to\n      - UBERON_CORE:channel_for\n      - UBERON_CORE:channels_from\n      - UBERON_CORE:channels_into\n      - UBERON_CORE:conduit_for\n      - UBERON_CORE:distally_connected_to\n      - UBERON_CORE:extends_fibers_into\n      - UBERON_CORE:filtered_through\n      - UBERON_CORE:indirectly_supplies\n      - UBERON_CORE:proximally_connected_to\n      - UBERON_CORE:synapsed_by\n      - UBERON_CORE:transitively_anteriorly_connected_to\n      - UBERON_CORE:transitively_connected_to\n      - UBERON_CORE:transitively_distally_connected_to\n      - UBERON_CORE:transitively_proximally_connected_to\n      # RTX contributed Environmental Ontology term meaning \"partially surrounded by\"\n      - ENVO:01001307\n      - FMA:adjacent_to\n      - FMA:afferent_to\n      - FMA:anterior_to\n      - FMA:anteroinferior_to\n      - FMA:anterolateral_to\n      - FMA:anteromedial_to\n      - FMA:anterosuperior_to\n      # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics?\n      # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink\n      - FMA:arterial_supply_of\n      - FMA:has_arterial_supply\n      - FMA:articulates_with\n      - FMA:attaches_to\n      - FMA:bounded_by\n      - FMA:bounds\n      - FMA:branch_of\n      - FMA:connection_type_of\n      - FMA:continuation_branch_of\n      - FMA:continuous_distally_with\n      - FMA:continuous_proximally_with\n      - FMA:corresponds_to\n      - FMA:development_type_of\n      - FMA:developmental_stage_of\n      - FMA:direct_cell_shape_of\n      - FMA:direct_left_of\n      - FMA:direct_right_of\n      - FMA:distal_to\n      - FMA:drains_into\n      - FMA:efferent_to\n      - FMA:external_to\n      - FMA:formed_by\n      - FMA:forms\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:full_grown_phenotype_of\n      - FMA:has_full_grown_phenotype\n      # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:fuses_with\n      - FMA:fusion_of\n      - FMA:has_fusion\n      - FMA:germ_origin_of\n      - FMA:has_germ_origin\n      - FMA:has_adherent\n      - FMA:has_branch\n      - FMA:has_connection_type\n      - FMA:has_continuation_branch\n      - FMA:has_development_type\n      - FMA:has_developmental_stage\n      - FMA:has_direct_cell_shape\n      - FMA:has_inherent_3d_shape\n      - FMA:has_insertion\n      - FMA:has_lymphatic_drainage\n      - FMA:has_nerve_supply\n      - FMA:has_observed_anatomical_entity\n      - FMA:has_origin\n      - FMA:has_primary_segmental_supply\n      - FMA:has_projection\n      - FMA:has_regional_part\n      - FMA:has_related_developmental_entity\n      - FMA:has_secondary_segmental_supply\n      - FMA:has_segmental_composition\n      - FMA:has_segmental_supply\n      - FMA:has_tributary\n      - FMA:has_venous_drainage\n      - FMA:inferior_to\n      - FMA:inferolateral_to\n      - FMA:inferomedial_to\n      - FMA:inherent_3d_shape_of\n      - FMA:insertion_of\n      - FMA:internal_to\n      - FMA:lateral_to\n      - FMA:left_lateral_to\n      - FMA:left_medial_to\n      - FMA:lymphatic_drainage_of\n      - FMA:matures_from\n      - FMA:matures_into\n      - FMA:medial_to\n      - FMA:merges_with\n      - FMA:nerve_supply_of\n      - FMA:origin_of\n      - FMA:posterior_to\n      - FMA:posteroinferior_to\n      - FMA:posterolateral_to\n      - FMA:posteromedial_to\n      - FMA:posterosuperior_to\n      - FMA:primary_segmental_supply_of\n      - FMA:projects_from\n      - FMA:projects_to\n      - FMA:proximal_to\n      - FMA:receives_attachment_from\n      - FMA:receives_drainage_from\n      - FMA:receives_input_from\n      - FMA:receives_projection\n      - FMA:related_part\n      - FMA:right_lateral_to\n      - FMA:right_medial_to\n      - FMA:secondary_segmental_supply_of\n      - FMA:segmental_composition_of\n      - FMA:segmental_supply_of\n      - FMA:sends_output_to\n      - FMA:superior_to\n      - FMA:superolateral_to\n      - FMA:superomedial_to\n      - FMA:surrounded_by\n      - FMA:surrounds\n      - FMA:tributary_of\n      - FMA:venous_drainage_of\n      # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute'\n      # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now\n      - LOINC:has_lateral_anatomic_location\n      - LOINC:has_lateral_location_presence\n      - UBERON_NONAMESPACE:distally_connected_to\n      - UBERON_NONAMESPACE:subdivision_of\n      # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to'\n      - RO:0002219\n      - RO:0002220\n      - RO:0002221\n      - SO:has_origin\n      # RTX mapped these UBERON terms all here\n      - UBERON:anastomoses_with\n      - UBERON:anteriorly_connected_to\n      - UBERON:channel_for\n      - UBERON:channels_from\n      - UBERON:channels_into\n      - UBERON:conduit_for\n      - UBERON:distally_connected_to\n      - UBERON:existence_starts_and_ends_during\n      - UBERON:extends_fibers_into\n      - UBERON:filtered_through\n      - UBERON:in_central_side_of\n      - UBERON:in_innermost_side_of\n      - UBERON:in_outermost_side_of\n      - UBERON:indirectly_supplies\n      - UBERON:posteriorly_connected_to\n      - UBERON:protects\n      - UBERON:proximally_connected_to\n      - UBERON:sexually_homologous_to\n\n  in pathway with:\n    description: >-\n      holds between two genes or gene products that are part of in the same biological pathway\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # generally pertains to membership of a (subject) component - gene,\n      # metabolite, etc? - in an (object) metabolic pathway\n      - SIO:010532\n\n  in complex with:\n    description: >-\n      holds between two genes or gene products that are part of (or code for\n      products that are part of) in the same macromolecular complex\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though)\n      - SIO:010497\n    broad_mappings:\n      # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes)\n      - SIO:010285\n\n  in cell population with:\n    description: >-\n      holds between two genes or gene products that are expressed in the same cell type or population\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  colocalizes with:\n    description: >-\n      holds between two entities that are observed to be located in the same place.\n    is_a: coexists with\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:00002325\n\n  # Despite the name, note that this particular entity is\n  # NOT a biolink:Association but rather, a biolink:predicate\n  genetic association:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    description: >-\n      Co-occurrence of a certain allele of a genetic marker and the phenotype\n      of interest in the same individuals at above-chance level\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2293\n\n  gene associated with condition:\n    is_a: genetic association\n    description: >-\n      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,\n      contribute to, or correlate with\n    domain: disease or phenotypic feature\n    range: gene\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - GENO:0000840 # broader than a single gene: 'genotype' pathogenic for condition\n      - GENO:0000841\n    narrow_mappings:\n      # narrower: just diseases, not phenotypic features as well\n      - NCIT:R38\n      - NCIT:R175\n      - NCIT:R48\n\n  condition associated with gene:\n    is_a: genetic association\n    aliases: [ 'disease associated with gene' ]\n    description: >-\n      holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products\n    domain: gene\n    range: disease or phenotypic feature\n    in_subset:\n      - translator_minimal\n    inverse: gene associated with condition\n    narrow_mappings:\n      # narrower since just diseases, not phenotypic features as well\n      - NCIT:R176\n\n  affects risk for:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where exposure to one entity alters the chance of developing the other\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  risk affected by:\n    is_a: related to at instance level\n    inverse: affects risk for\n\n  predisposes:\n    is_a: affects risk for\n    description: >-\n      holds between two entities where exposure to one entity increases the chance of developing the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:PREDISPOSES\n\n  has predisposing factor:\n    is_a: risk affected by\n    inverse: predisposes\n    in_subset:\n      - translator_minimal\n\n  contributes to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes or contributes to the\n      occurrence or generation of the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX contributed mapping tagged as 'inverse' of this Biolink predicate\n      - IDO:0000664\n    exact_mappings:\n      - RO:0002326\n    narrow_mappings:\n      - CTD:marker_mechanism\n      - MONDO:predisposes_towards\n      # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002255\n      # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here\n      - RO:0003304\n\n  contribution from:\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    inverse: contributes to\n\n  causes:\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes the occurrence\n      or generation of the other\n    is_a: contributes to\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:CAUSES\n      - WIKIDATA_PROPERTY:P1542\n      - SNOMED:cause_of\n      - RO:0003303\n    broad_mappings:\n      - RO:0002410\n      - RO:0002506\n    narrow_mappings:\n      - MONDO:disease_triggers\n      - GOREL:0000040\n      - MONDO:disease_causes_feature\n      - MONDO:disease_triggers\n      - NCIT:allele_has_abnormality\n      - NCIT:biological_process_has_result_biological_process\n      - NCIT:chemical_or_drug_has_physiologic_effect\n      # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'?\n      - NCIT:chemical_or_drug_initiates_biological_process\n      - NCIT:process_initiates_biological_process\n      - NCIT:chromosome_mapped_to_disease\n      - NCIT:disease_has_normal_tissue_origin\n      - NBO-PROPERTY:in_response_to\n      - orphanet:317343\n      - orphanet:317344\n      - orphanet:317346\n      - orphanet:410295\n      - orphanet:410296\n      # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002256\n      - RO:0002315\n      - RO:0002507\n      - RO:0002509\n      - RO:0004001\n      - SNOMED:causative_agent_of\n      - SNOMED:has_realization\n      - UMLS:has_physiologic_effect\n\n  caused by:\n    description: >-\n      holds between two entities where the occurrence, existence,\n      or activity of one is caused by the occurrence or generation of the other\n    is_a: contribution from\n    aliases: [ 'disease caused by disruption of', 'disease has basis in dysfunction of',\n               'realized in response to', 'realized in response to stimulus' ]\n    in_subset:\n      - translator_minimal\n    inverse: causes\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P828\n    narrow_mappings:\n      - RO:0001022\n      - RO:0002608\n      - RO:0004019\n      - RO:0004020\n      - RO:0004028\n      - RO:0009501\n\n  # TODO: ameliorates and exacerbates inverses.\n  ameliorates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a genotype,\n      genetic variation, chemical, or environmental exposure, clinical intervention)\n      and a condition (a phenotype or disease), where the\n      presence of the entity reduces or eliminates some or\n      all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: named thing\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: exacerbates\n    exact_mappings:\n      - RO:0003307\n\n  is ameliorated by:\n    inverse: ameliorates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: named thing\n\n  exacerbates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a chemical,\n      environmental exposure, or some form of genetic variation)\n      and a condition (a phenotype or disease), where the presence\n      of the entity worsens some or all aspects of the condition.\n    # 'biological entity' currently includes 'exposure event' which covers alot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0003309\n    broad_mappings:\n      - SEMMEDDB:COMPLICATES\n\n  is exacerbated by:\n    inverse: exacerbates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n    in_subset:\n      - translator_minimal\n\n  treats:\n    aliases: [ 'is substance that treats', 'indicated for' ]\n    is_a: ameliorates\n    description: >-\n      holds between a therapeutic procedure or chemical entity\n      and a disease or phenotypic feature that it is used to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: contraindicated for\n    in_subset:\n      - translator_minimal\n    related_mappings:\n      - MONDO:disease_responds_to\n    exact_mappings:\n      - DRUGBANK:treats\n      - SEMMEDDB:TREATS\n      - WIKIDATA_PROPERTY:P2175\n    narrow_mappings:\n      # \"is substance that treats\" constrains statements to\n      # a subset of the universe of all possible treatments\n      - RO:0002606\n      - NCIT:regimen_has_accepted_use_for_disease\n      # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n      - SNOMED:plays_role\n\n  treated by:\n    is_a: is ameliorated by\n    description: >-\n      holds between a disease or phenotypic feature and a therapeutic\n      process or chemical entity that is used to treat the condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    # range: chemical or drug or treatement\n    in_subset:\n      - translator_minimal\n    inverse: treats\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2176\n      # RTX contributed term tagged as inverse of 'biolink:treats'\n      - MONDO:disease_responds_to\n    narrow_mappings:\n      # \"is treated by substance\" constrains statements to\n      # subset of the universe of all possible treatments\n      - RO:0002302\n\n  prevents:\n    is_a: affects risk for\n    description: >-\n      holds between an entity whose application or use reduces\n      the likelihood of a potential outcome. Typically used to associate\n      a chemical entity, exposure, activity, or medical intervention\n      that can prevent the onset a disease or phenotypic feature.\n    annotations:\n      canonical_predicate: true\n      opposite_of: predisposes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:PREVENTS\n    narrow_mappings:\n      # more restricted case of a material entity mitigating a pathological process\n      - RO:0002599\n\n  prevented by:\n    is_a: risk affected by\n    description: >-\n      holds between a potential outcome of which the likelihood\n      was reduced by the application or use of an entity.\n    inverse: prevents\n    annotations:\n      opposite_of: enabled by\n\n  correlated with:\n    is_a: associated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical dependence is \n      demonstrated using a correlation analysis method.\n    notes: >-\n      These concepts may map exactly to the statistical variables, or represent related entities for which the \n      variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002610\n      - PATO:correlates_with\n\n  # proposed positive and negative semantic extensions to the general \"correlated with\" predicate\n\n  positively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or \n      presence of one correlates with an increase or presence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: negatively correlated with\n    exact_mappings:\n      - CTD:positive_correlation\n\n  negatively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of \n      one correlates with a decrease or absence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: positively correlated with\n    exact_mappings:\n      - CTD:negative_correlation\n\n  occurs together in literature with:\n    is_a: correlated with\n    description: >-\n      holds between two entities where their co-occurrence is correlated by counts of publications\n      in which both occur, using some threshold of occurrence as defined by the edge provider.\n    domain: named thing\n    range: named thing\n    in_subset: translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  coexpressed with:\n    is_a: correlated with\n    description: >-\n      holds between any two genes or gene products, in which both are\n      generally expressed within a single defined experimental context.\n    domain: gene or gene product\n    range: gene or gene product\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  has biomarker:\n    is_a: correlated with\n    description: >-\n      holds between a disease or phenotypic feature and a measurable\n      chemical entity that is used as an indicator of the presence\n      or state of the disease or feature.\n      # metabolite\n    domain: disease or phenotypic feature\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    inverse: biomarker for\n    narrow_mappings:\n      # some RTX terms contributed as inverses of 'biolink:biomarker_for'\n      - NCIT:disease_has_molecular_abnormality\n      - NCIT:disease_is_marked_by_gene\n\n  biomarker for:\n    is_a: correlated with\n    description: >-\n      holds between a measurable chemical entity and a disease\n      or phenotypic feature, where the entity is used as an indicator\n      of the presence or state of the disease or feature.\n    domain: chemical entity or gene or gene product\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - NCIT:R39\n    broad_mappings:\n      # Generic marker definition not specific to biomarkers per say\n      - RO:0002607\n    narrow_mappings:\n      - NCIT:R47\n      # RTX term was tagged as 'biolink:actively_involved_in' but maps better here?\n      - NCIT:genetic_biomarker_related_to\n      - NCIT:is_molecular_abnormality_of_disease\n      - orphanet:465410\n\n  # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in'\n  # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates\n  # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others\n  expressed in:\n    is_a: located in\n    description: >-\n      holds between a gene or gene product and an anatomical entity in which it is expressed\n    domain: gene or gene product\n    range: anatomical entity\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002206\n    narrow_mappings:\n      - NCIT:R49\n      - NCIT:R46\n\n  expresses:\n    is_a: location of\n    aliases: [ 'anatomy expresses gene' ]\n    description: >-\n      holds between an anatomical entity and gene or gene product that is expressed there\n    domain: anatomical entity\n    range: gene or gene product\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    inverse: expressed in\n    exact_mappings:\n      - RO:0002292\n\n  has phenotype:\n    is_a: related to at instance level\n    aliases: [ 'disease presents symptom' ]\n    description: >-\n      holds between a biological entity and a phenotype, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should\n      translate into this predicate.\n    domain: biological entity\n    range: phenotypic feature\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    notes:\n      - check the range\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002200\n    broad_mappings:\n      - NCIT:R115\n      - NCIT:R108\n    narrow_mappings:\n      - NCIT:R89\n      - DOID-PROPERTY:has_symptom\n      - RO:0004022\n\n  phenotype of:\n    is_a: related to at instance level\n    domain: phenotypic feature\n    range: biological entity\n    multivalued: true\n    inverse: has phenotype\n\n  # TODO: predicate inverse for occurs in\n  occurs in:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a material entity or site within which the process occurs\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # These RTX mapped terms tagged as the inverse of \"biolink:occurs_in\", i.e. Entity/Site contains Process\n      - BFO:0000067\n      - SNOMED:has_occurrence\n      - UBERON:site_of\n    exact_mappings:\n      - BFO:0000066\n      - PathWhiz:has_location\n      - SNOMED:occurs_in\n    narrow_mappings:\n      # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population\n      - SEMMEDDB:OCCURS_IN\n      # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity\n      - SEMMEDDB:PROCESS_OF\n      # Uberon term constrained to a 'site' as object concept\n      - UBERON_CORE:site_of\n      - LOINC:has_imaged_location\n      - PathWhiz:in_species\n      - RO:0002231\n      - RO:0002232\n      - SNOMED:has_direct_procedure_site\n      - SNOMED:has_direct_site\n      - SNOMED:has_procedure_site\n\n  contains process:\n    is_a: related to at instance level\n    inverse: occurs in\n\n  located in:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a material entity or site\n      within which it is located (but of which it is not considered a part)\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0001025\n      - FMA:has_location\n    narrow_mappings:\n      - GOREL:0001004\n      - BSPO:0000107\n      - BSPO:0000108\n      - BSPO:0000120\n      - BSPO:0000121\n      - BSPO:0000122\n      - BSPO:0000123\n      - BSPO:0000124\n      - BSPO:0000125\n      - BSPO:0000126\n      - BSPO:0001100\n      - BSPO:0001101\n      - BSPO:0001107\n      - BSPO:0015101\n      - BSPO:0015102\n      - BSPO:0015202\n      - UBERON_CORE:in_central_side_of\n      - UBERON_CORE:in_innermost_side_of\n      - UBERON_CORE:in_outermost_side_of\n      - NCIT:R100\n      - EFO:0000784\n      - FMA:has_location\n      - HMDB:at_cellular_location\n      - HMDB:at_tissue\n      - HMDB:in_biospecimen\n      - LOINC:has_imaging_focus\n      - NCIT:R156\n      - NCIT:R155\n      - NCIT:R145\n      - NCIT:R40\n      - NCIT:R171\n      - NCIT:R167\n      - NCIT:R165\n      - NCIT:R169\n      - NCIT:R170\n      - NCIT:R166\n      - NCIT:R168\n      - RO:0002303\n      - SNOMED:has_finding_site\n      - SNOMED:has_indirect_procedure_site\n      - SNOMED:has_inherent_location\n    domain: named thing\n    range: named thing\n\n  location of:\n    is_a: related to at instance level\n    aliases: [ 'site of' ]\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between material entity or site and a material entity\n      that is located within it (but not considered a part of it)\n    in_subset:\n      - translator_minimal\n    inverse: located in\n    exact_mappings:\n      - RO:0001015\n      - SEMMEDDB:LOCATION_OF\n      - WIKIDATA_PROPERTY:P276\n      # RTX tagged this as an inverse of biolink:located_in\n      - FMA:location_of\n    narrow_mappings:\n      - SNOMED:inherent_location_of\n      - NCIT:Anatomic_Structure_Has_Location_Role\n\n  disease has location:\n    description: >-\n      A relationship between a disease and an anatomical entity where the\n      disease has one or more features that are located in that entity.\n    is_a: related to\n    exact_mappings:\n      - RO:0004026\n      - MONDO:disease_has_location\n\n  location of disease:\n    is_a: related to\n    inverse: disease has location\n\n  similar to:\n    is_a: related to at instance level\n    description: >-\n      holds between an entity and some other entity with similar features.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000000               #I don't understand this identifier, but I think it's equivalent\n      - SO:similar_to               #equivalent\n\n  chemically similar to:\n    is_a: similar to\n    description: >-\n      holds between one small molecule entity and another that it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - CHEBI:has_parent_hydride    #subproperty\n      - CHEBI:has_functional_parent #subproperty\n      - CHEBI:is_conjugate_acid_of  #subproperty\n      - CHEBI:is_conjugate_base_of  #subproperty\n      - CHEBI:is_enantiomer_of      #subproperty\n      - CHEBI:is_tautomer_of        #subproperty\n      - NCIT:has_salt_form\n\n  has sequence location:\n    is_a: related to at instance level\n    description: >-\n      holds between two nucleic acid entities when the subject can be localized\n      in sequence coordinates on the object. For example, between\n      an exon and a chromosome/contig.\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - faldo:location\n\n  sequence location of:\n    is_a: related to at instance level\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    inverse: has sequence location\n\n  model of:\n    is_a: related to at instance level\n    description: >-\n      holds between a thing and some other thing it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0003301\n    narrow_mappings:\n      - FOODON:00001301\n\n  models:\n    is_a: related to at instance level\n    inverse: model of\n\n  overlaps:\n    is_a: related to at instance level\n    description: >-\n      holds between entities that overlap in their extents (materials or processes)\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002131\n    narrow_mappings:\n      - BSPO:0005001\n      - CHEMBL.MECHANISM:overlaps_with\n      - RO:0002100\n      - RO:0002102\n      - RO:0002433\n\n  has part:\n    is_a: overlaps\n    annotations:\n      canonical_predicate: true\n      opposite_of: lacks part\n    description: >-\n      holds between wholes and their parts (material entities or processes)\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000051\n      # term name seems to be 'realizes' but RTX maps this term here\n      - BFO:0000055\n      - WIKIDATA_PROPERTY:P527\n      - RO:0001019\n      - RXNORM:consists_of\n      - RXNORM:has_part\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'; slightly broader?\n      - RO:0001019\n      - FMA:contains\n      - RXNORM:contains\n    narrow_mappings:\n      - BFO:0000117\n      # RTX term originally mapped to 'biolink:coexists_with'?\n      - FMA:has_constitutional_part\n      - FMA:has_part\n      # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'?\n      - FMA:has_member\n      - FOODON:00001563\n      - FOODON:00002420\n      - LOINC:has_component\n      - LOINC:has_member\n      - MEDDRA:has_member\n      - MONDO:disease_has_major_feature\n      - NCIT:complex_has_physical_part\n      - NDDF:has_ingredient\n      - PathWhiz:has_element_in_bound\n      # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature\n      - NCIT:R50\n      - PathWhiz:has_protein_in_complex\n      - RO:0002104\n      - RO:0002180\n      - RO:0002351\n      - RO:0002473\n      - RO:0002524\n      - RO:0002551\n      - RXNORM:has_ingredient\n      - SNOMED:has_component\n      - UMLS:has_component\n\n  has plasma membrane part:\n    is_a: has part\n    description: >-\n      Holds between a cell c and a protein complex or protein p if\n      and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.\n    exact_mappings:\n      - RO:0002104\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  composed primarily of:\n    is_a: related to\n    description: >-\n      x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.\n    exact_mappings:\n      - RO:0002473\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  primarily composed of:\n    inverse: composed primarily of\n    is_a: related to\n\n  plasma membrane part of:\n    is_a: part of\n    inverse: has plasma membrane part\n\n  part of:\n    is_a: overlaps\n    description: >-\n      holds between parts and wholes (material entities or processes)\n    in_subset:\n      - translator_minimal\n    inverse: has part\n    exact_mappings:\n      - BFO:0000050\n      - SEMMEDDB:PART_OF\n      - WIKIDATA_PROPERTY:P361\n      - FMA:part_of\n      - RXNORM:constitutes\n      - RXNORM:part_of\n    broad_mappings:\n      # To 'contain' is 'to have something inside or include something as a part'\n      - RO:0001018\n      - FMA:contained_in\n      - RXNORM:contained_in\n    narrow_mappings:\n      - BSPO:0001106\n      - BSPO:0001108\n      - BSPO:0001113\n      - BSPO:0001115\n      - UBERON_CORE:layer_part_of\n      - UBERON_CORE:subdivision_of\n      - UBERON_CORE:trunk_part_of\n      - CHEBI:is_substituent_group_from\n      - CPT:panel_element_of\n      - CPT:panel_element_of_possibly_included\n      - DRUGBANK:component_of\n      - FMA:constitutional_part_of\n      - FMA:member_of\n      - FMA:regional_part_of\n      - FMA:related_developmental_entity_of\n      - LOINC:component_of\n      - LOINC:has_supersystem\n      - LOINC:member_of\n      - LOINC:multipart_of\n      - MEDDRA:member_of\n      - MONDO:part_of_progression_of_disease\n      - NCIT:R82\n      - NCIT:R27\n      - NCIT:is_component_of_chemotherapy_regimen\n      - NDDF:ingredient_of\n      - RO:0002007\n      - RO:0002350\n      - RO:0002376\n      - RO:0002380\n      - RO:0002571\n      - RO:0002572\n      - RO:0002576\n      - RXNORM:ingredient_of\n      - RXNORM:ingredients_of\n      - RXNORM:precise_ingredient_of\n      - SNOMED:active_ingredient_of\n      - SNOMED:basis_of_strength_substance_of\n      - SNOMED:component_of\n      - SNOMED:direct_substance_of\n      - SNOMED:during\n      - SNOMED:focus_of\n      - SNOMED:has_dependent\n      - SNOMED:part_anatomy_structure_of\n      - SNOMED:precise_active_ingredient_of\n      - UBERON:subdivision_of\n      - UMLS:component_of\n      - UMLS:has_owning_affiliate\n      - UMLS:owning_subsection_of\n      - VANDF:ingredient_of\n\n  has input:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an input into the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n      opposite_of: has output\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # RTX inverse mapping to 'biolink:has_input'\n      - RO:0002352\n    exact_mappings:\n      - RO:0002233\n      - SEMMEDDB:USES\n    narrow_mappings:\n      - LOINC:has_fragments_for_synonyms\n      - LOINC:has_system\n      - PathWhiz:has_left_element\n      - RO:0002590\n      - RO:0004009\n      - SNOMED:has_finding_method\n      - SNOMED:has_precondition\n      - SNOMED:has_specimen_source_identity\n      - SNOMED:has_specimen_substance\n      - SNOMED:uses_access_device\n      - SNOMED:uses_device\n      - SNOMED:uses_energy\n      - SNOMED:uses_substance\n\n  is input of:\n    is_a: participates in\n    domain: occurrent\n    range: biological process or activity\n    inverse: has input\n    in_subset:\n      - translator_minimal\n\n  has output:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an output of the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n      opposite_of: has input\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - RO:0002353\n      - RO:0002354\n    exact_mappings:\n      - RO:0002234\n    narrow_mappings:\n      - NCIT:R31\n      - OBI:0000299\n      - PathWhiz:has_right_element\n      - RO:0002296\n      - RO:0002297\n      - RO:0002298\n      - RO:0002299\n      - RO:0002588\n      - RO:0004008\n\n  is output of:\n    is_a: participates in\n    domain: occurrent\n    range: biological process or activity\n    inverse: has output\n    in_subset:\n      - translator_minimal\n\n  has participant:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a continuant, where the continuant is somehow involved in the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - WIKIDATA_PROPERTY:P2283\n    exact_mappings:\n      - RO:0000057\n      - RO:has_participant\n    narrow_mappings:\n      - BFO:0000167\n      # Several of the following RTX terms tagged as inverse to 'biolink:participates_in'\n      - LOINC:has_subject\n      - NCIT:process_involves_gene\n      - NBO-PROPERTY:has_participant\n      - PathWhiz:has_bound\n      - PathWhiz:has_compound\n      - PathWhiz:has_element_collection\n      - PathWhiz:has_enzyme\n      - OBI:0000293\n      - PathWhiz:has_nucleic_acid\n      - PathWhiz:has_protein\n      - PathWhiz:has_reaction\n      - RO:0004007\n      - RO:0004020\n      - RO:0004021\n      - SNOMED:has_indirect_device\n      - SNOMED:has_procedure_device\n      - SNOMED:has_recipient_category\n\n  catalyzes:\n    is_a: participates in\n    domain: nucleic acid entity\n    range: molecular activity\n    annotations:\n      canonical_predicate: true\n\n  has catalyst:\n    is_a: has participant\n    inverse: catalyzes\n    domain: molecular activity\n    range: nucleic acid entity\n\n  has substrate:\n    is_a: has participant\n    domain: molecular activity\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n\n  is substrate of:\n    is_a: participates in\n    inverse: has substrate\n    domain: chemical entity or gene or gene product\n    range: molecular activity\n\n  participates in:\n    is_a: related to at instance level\n    description: >-\n      holds between a continuant and a process, where the continuant is somehow involved\n      in the process\n    range: biological process or activity\n    domain: occurrent\n    inverse: has participant\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0000056\n      - BFO:0000056\n    narrow_mappings:\n      - DRUGBANK:pathway\n      - HMDB:in_pathway\n      - LOINC:is_given_pharmaceutical_substance_for\n      - NCIT:R130\n      - NCIT:R37\n      - NCIT:R131\n      - NCIT:R51\n      - NCIT:R53\n      - OBI:0000295\n      - RO:0002216\n      - RO:0002505\n      - RO:0002565\n      - SNOMED:has_direct_device\n\n  actively involved in:\n    is_a: participates in\n    aliases: [ 'involved in' ]\n    description: >-\n      holds between a continuant and a process or function, where\n      the continuant actively contributes to part or all of\n      the process or function it realizes\n    domain: occurrent\n    range: molecular activity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002331\n      - RO:0002432\n    narrow_mappings:\n      - NBO-PROPERTY:by_means\n      - orphanet:317348\n      - orphanet:317349\n      - orphanet:327767\n      - RO:0002503\n\n  actively involves:\n    is_a: has participant\n    domain: molecular activity\n    range: occurrent\n    inverse: actively involved in\n    exact_mappings:\n      - RO:0002331\n    in_subset:\n      - translator_minimal\n\n  capable of:\n    is_a: actively involved in\n    description: >-\n      holds between a physical entity and process or function, where the\n      continuant alone has the ability to carry out the process or function.\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002215\n    narrow_mappings:\n      - NCIT:R52\n      - RO:0002500\n\n  can be carried out by:\n    is_a: actively involves\n    inverse: capable of\n    domain: occurrent\n\n  enables:\n    is_a: participates in\n    description: >-\n      holds between a physical entity and a process, where the physical entity executes the process\n    domain: physical entity\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    in_subset:\n      - translator_minimal\n    inverse: enabled by\n    exact_mappings:\n      - RO:0002327\n\n  enabled by:\n    is_a: has participant\n    description: >-\n      holds between a process and a physical entity, where the physical entity executes the process\n    domain: biological process or activity\n    range: physical entity\n    in_subset:\n      - translator_minimal\n    inverse: enables\n    exact_mappings:\n      - RO:0002333\n    annotations:\n      opposite_of: prevented by\n\n  derives into:\n    is_a: related to at instance level\n    aliases: [ 'is normal cell origin of disease', 'may be normal cell origin of disease' ]\n    description: >-\n      holds between two distinct material entities, the old entity and\n      the new entity, in which the new entity begins to exist when\n      the old entity ceases to exist, and the new entity inherits\n      the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n    inverse: derives from\n    # TODO: fix this according to WG notes. Example of both opposite and inverse\n    # Commenting as it feels very wrong. A good example with both opposite and inverse is `has active ingredient`\n    # annotations:\n    #   opposite_of: subclass of\n    exact_mappings:\n      - RO:0001001\n      - SEMMEDDB:CONVERTS_TO\n      # RTX posted terms as inverse of 'biolink:derives_from'\n      - FMA:derives\n\n  derives from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    description: >-\n      holds between two distinct material entities, the new entity\n      and the old entity, in which the new entity begins to exist\n      when the old entity ceases to exist, and the new entity\n      inherits the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n      - samples\n    inverse: derives into\n    exact_mappings:\n      - RO:0001000\n      - FMA:derives_from\n      - DOID-PROPERTY:derives_from\n    narrow_mappings:\n      - CHEBI:has_functional_parent\n      - SNOMED:has_specimen_source_topography\n\n  is metabolite of:\n    is_a: derives from\n    description: >-\n      holds between two molecular entities in which the first one is derived\n      from the second one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    inverse: has metabolite\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  has metabolite:\n    is_a: derives into\n    description: >-\n      holds between two molecular entities in which the second one is derived from the first\n      one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  food component of:\n    is_a: part of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has food component\n    #mappings:\n    #  -\n\n  has food component:\n    is_a: has part\n    description: >-\n      holds between food and one or more chemical entities composing it,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  nutrient of:\n    is_a: food component of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has nutrient\n    #exact_mappings:\n    #  -\n\n  has nutrient:\n    is_a: has food component\n    description: >-\n      one or more nutrients which are growth factors for a living organism\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q181394\n\n  is active ingredient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug, in which the former\n      is a part of the latter, and is a biologically active component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has active ingredient\n    mappings:\n      - RO:0002249\n\n  has active ingredient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entity in which the latter\n      is a part of the former, and is a biologically active component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: is excipient of\n    in_subset:\n      - translator_minimal\n    inverse: is active ingredient of\n    mappings:\n      - RO:0002248\n\n  is excipient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug in which the former is\n      a part of the latter, and is a biologically inactive component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has excipient\n    mappings:\n      - WIKIDATA:Q902638\n\n  has excipient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entities in which the latter\n      is a part of the former, and is a biologically inactive component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    mappings:\n      - WIKIDATA:Q902638\n\n  manifestation of:\n    is_a: related to at instance level\n    description: >-\n      that part of a phenomenon which is directly observable or\n      visibly expressed, or which gives evidence to the underlying\n      process; used in SemMedDB for linking things like dysfunctions\n      and processes to some disease or syndrome\n    range: disease\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:MANIFESTATION_OF\n      - OMIM:manifestation_of\n    broad_mappings:\n      # Wikidata's definition is slightly broader: \"inherent and characteristic embodiment of a given concept\"\n      - WIKIDATA_PROPERTY:P1557\n    narrow_mappings:\n      - SNOMED:has_definitional_manifestation\n\n  has manifestation:\n    is_a: related to at instance level\n    domain: disease\n    inverse: manifestation of\n\n  mode of inheritance of:\n    is_a: manifestation of\n    domain: genetic inheritance\n    range: disease or phenotypic feature\n    inverse: has mode of inheritance\n\n  has mode of inheritance:\n    is_a: has manifestation\n    description: >-\n      Relates a disease or phenotypic feature to its observed genetic segregation and assumed\n      associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).\n    domain: disease or phenotypic feature\n    range: genetic inheritance\n    annotations:\n      # This canonical order reverses that of its parent 'has manifestation' class\n      # but seems a more natural direction in the pertinent edge relationships.\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  produces:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a product that is generated\n      through the intentional actions or functioning of the material entity\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GOREL:0001010\n    exact_mappings:\n      - RO:0003000\n      - WIKIDATA_PROPERTY:P1056\n      - SEMMEDDB:PRODUCES\n    narrow_mappings:\n      - NCIT:R29\n      - SNOMED:has_process_output\n      - SNOMED:specimen_procedure_of\n\n  produced by:\n    is_a: related to at instance level\n    inverse: produces\n    exact_mappings:\n      - RO:0003001\n\n  consumes:\n    is_a: has input\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - RO:0004009\n\n  consumed by:\n    is_a: is input of\n    inverse: consumes\n\n  temporally related to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities with a temporal relationship\n    domain: occurrent\n    range: occurrent\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SNOMED:temporally_related_to\n    narrow_mappings:\n      # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here\n      - RO:0002082\n      - RO:0002083\n      - RO:0002092\n      - RO:0002093\n      - RO:0002223\n      - RO:0002224\n      - RO:0002229\n      - RO:0002230\n      - RO:0002488\n      - RO:0002489\n      - RO:0002492\n      - RO:0002493\n      - RO:0002496\n      - RO:0002497\n\n  precedes:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where one completes before the other begins\n    domain: occurrent\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    inverse: preceded by\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      # the subject of these terms is a material entity, not a process,\n      # but affects a process which causes a second process to occur\n      - RO:0002263\n      - RO:0002264\n    exact_mappings:\n      - BFO:0000063\n      - SEMMEDDB:PRECEDES\n      - SNOMED:occurs_before\n    broad_mappings:\n      # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature\n      - WIKIDATA_PROPERTY:P156\n    narrow_mappings:\n      - FMA:transforms_into\n      - RO:0002090\n      - RO:0002411\n      - RO:0002412\n\n  preceded by:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where the other is completed before the one begins\n    domain: occurrent\n    range: occurrent\n    inverse: precedes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000062\n    broad_mappings:\n      # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'?\n      - GENEPIO:0001739\n    narrow_mappings:\n      # RTX contributed mapping was given as the inverse of 'biolink:precedes'\n      - FMA:transforms_from\n      - RO:0002087\n      - RO:0002285\n\n  has variant part:\n    is_a: has part\n    description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000382\n\n  variant part of:\n    is_a: part of\n    inverse: has variant part\n\n  related condition:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000790\n\n  ## Predicates relating variants to genes\n\n  is sequence variant of:\n    is_a: related to at instance level\n    aliases: [ 'gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product' ]\n    description: holds between a sequence variant and a nucleic acid entity\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - WIKIDATA:P3433\n\n  has sequence variant:\n    is_a: related to at instance level\n    inverse: is sequence variant of\n    domain: genomic entity\n    range: sequence variant\n\n  is missense variant of:\n    is_a: is sequence variant of\n    description: holds between a gene  and a sequence variant, such the sequence variant\n      results in a different amino acid sequence but where the length is preserved.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001583\n\n  has missense variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is missense variant of\n\n  is synonymous variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the coding sequence of the gene, but results in the same amino acid sequence\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001819\n\n  has synonymous variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is synonymous variant of\n    aliases: [ 'stop gained' ]\n\n  is nonsense variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      results in a premature stop codon\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      # Term definition broader than nonsense codon: A sequence variant whereby\n      # the gene product has diminished or abolished function.\n      - SO:0002054\n\n  has nonsense variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is nonsense variant of\n\n  is frameshift variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      causes a disruption of the translational reading frame, because the number of\n      nucleotides inserted or deleted is not a multiple of three.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001589\n    aliases: [ 'frameshift variant', 'start lost', 'stop lost' ]\n\n  has frameshift variant:\n    is_a: has sequence variant\n    inverse: is frameshift variant of\n    domain: genomic entity\n    range: sequence variant\n    aliases: [ 'splice region variant', 'splice acceptor variant', 'splice donor variant' ]\n\n  is splice site variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the canonical splice site of one of the gene's exons.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001629\n\n\n  has splice site variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is splice site variant of\n    aliases: [ 'downstream gene variant', 'upstream gene variant' ]\n\n  is nearby variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene sequence that the variant\n      is genomically close to.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n\n  has nearby variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is nearby variant of\n    aliases: [ 'intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant' ]\n\n  is non coding variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, where the variant does\n      not affect the coding sequence\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n\n  has non coding variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is non coding variant of\n\n  # relating disease to process\n\n  disease has basis in:\n    description: A relation that holds between a disease and an entity where the state\n      of the entity has contribution to the disease.\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      # These two MONDO terms seem more particular than the predicate\n      - MONDO:disease_has_basis_in_development_of\n      - MONDO:disease_has_basis_in_accumulation_of\n\n  occurs in disease:\n    is_a: related to at instance level\n    inverse: disease has basis in\n\n\n  has adverse event:\n    is_a: affects\n    aliases: [ 'adverse effect']\n    description: >-\n      An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment \n      with a therapeutic agent. Adverse events may be caused by something \n      other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or \n      diseases temporally associated with the treatment, whether or not considered related to the treatment. \n      Adverse events are unintended effects that occur when a medication is administered correctly.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n\n  adverse event of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has adverse event\n\n  has side effect:\n    aliases: [ 'adverse drug reaction']\n    is_a: affects\n    description: >-\n      An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment.\n      Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of \n      the medication.\n    notes: >-\n      Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative.\n      Aeolus, Sider are both resources that provide side effects.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C2861 # side effect\n\n  is side effect of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has side effect\n\n  contraindicated for:\n    is_a: related to at instance level\n    description: Holds between a drug and a disease or phenotype, such that a person\n      with that disease should not be treated with the drug.\n    domain: drug\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: treats\n    exact_mappings:\n      - NCIT:C37933\n\n  has contraindication:\n    is_a: related to at instance level\n    domain: disease or phenotypic feature\n    range: drug\n    inverse: contraindicated for\n\n  # The remaining new slots are here because we ran across them somewhere and\n  # they didn't seem to map well to anything else.\n\n  has not completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of,\n      but has not completed\n    exact_mappings:\n      - CL:has_not_completed\n    annotations:\n      opposite_of: has completed\n      canonical_predicate: true\n\n  not completed by:\n    is_a: related to at instance level\n    inverse: has not completed\n\n  has completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of\n      and has completed\n    annotations:\n      canonical_predicate: true\n      opposite_of: has not completed\n    exact_mappings:\n      - CL:has_completed\n\n  completed by:\n    is_a: related to at instance level\n    inverse: has completed\n\n\n  in linkage disequilibrium with:\n    is_a: related to at instance level\n    description: holds between two sequence variants, the presence of which are correlated\n      in a population\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C16798\n\n  has increased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has decreased amount\n    narrow_mappings:\n      - CL:has_high_plasma_membrane_amount\n\n  increased amount of:\n    is_a: related to at instance level\n    inverse: has increased amount\n\n  has decreased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has increased amount\n    narrow_mappings:\n      - CL:has_low_plasma_membrane_amount\n\n  decreased amount in:\n    is_a: related to at instance level\n    inverse: has decreased amount\n\n  lacks part:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has part\n    exact_mappings:\n      - CL:lacks_part\n      - PR:lacks_part\n    narrow_mappings:\n      - CL:lacks_plasma_membrane_part\n\n  missing from:\n    is_a: related to at instance level\n    inverse: lacks part\n\n  develops from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      # RTX mapping seems to be inverse of 'biolink:develops_from'\n      - RO:0002203\n      - FMA:develops_into\n    exact_mappings:\n      - BTO:develops_from\n      - DDANAT:develops_from\n      - FMA:develops_from\n      - RO:0002202\n    narrow_mappings:\n      - RO:0002207\n      - RO:0002225 # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y\n      - RO:0002226 # x develops_in y if x is located in y whilst x is developing\n\n  develops into:\n    is_a: related to at instance level\n    inverse: develops from\n\n  in taxon:\n    aliases: [ 'instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source' ]\n    is_a: related to at instance level\n    domain: thing with taxon\n    range: organism taxon\n    annotations:\n      canonical_predicate: true\n    description: >-\n      connects an entity to its taxonomic classification. Only certain kinds\n      of entities can be taxonomically classified; see 'thing with taxon'\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002162\n      - WIKIDATA_PROPERTY:P703\n    narrow_mappings:\n      - RO:0002160\n\n  taxon of:\n    is_a: related to at instance level\n    inverse: in taxon\n    domain: organism taxon\n    range: thing with taxon\n\n  has molecular consequence:\n    is_a: related to at instance level\n    aliases: [ 'allele has activity' ]\n    description: >-\n      connects a sequence variant to a class describing the molecular\n      consequence. E.g.  SO:0001583\n    range: ontology class\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - NCIT:allele_has_activity\n\n  is molecular consequence of:\n    is_a: related to at instance level\n    domain: ontology class\n    inverse: has molecular consequence\n\n  ## --------------------\n  ## ASSOCIATION SLOTS\n  ## --------------------\n\n  association slot:\n    abstract: true\n    domain: association\n    aliases: [ 'edge property', 'statement property', 'node qualifier', 'edge qualifier', 'statement qualifier' ]\n    description: >-\n      any slot that relates an association to another entity\n\n  original subject:\n    is_a: association slot\n    description: >-\n      used to hold the original subject of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original object:\n    is_a: association slot\n    description: >-\n      used to hold the original object of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original predicate:\n    aliases: [ 'original relation', 'relation' ]\n    is_a: association slot\n    description: >-\n      used to hold the original relation/predicate that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n    id_prefixes:\n      - RO\n      - BSPO\n      - SIO\n    domain: association\n    range: uriorcurie\n\n  subject:\n    is_a: association slot\n    local_names:\n      ga4gh: annotation subject\n      neo4j: node with outgoing relationship\n    description: >-\n      connects an association to the subject of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    slot_uri: rdf:subject\n    exact_mappings:\n      - owl:annotatedSource\n      - OBAN:association_has_subject\n\n  object:\n    is_a: association slot\n    description: >-\n      connects an association to the object of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    range: named thing\n    local_names:\n      ga4gh: descriptor\n      neo4j: node with incoming relationship\n    slot_uri: rdf:object\n    exact_mappings:\n      - owl:annotatedTarget\n      - OBAN:association_has_object\n\n  predicate:\n    is_a: association slot\n    description: >-\n      A high-level grouping for the relationship type. AKA minimal predicate.\n      This is analogous to category for nodes.\n    domain: association\n    notes: >-\n      Has a value from the Biolink related_to hierarchy. In RDF,  this\n      corresponds to rdf:predicate and in Neo4j this corresponds to the\n      relationship type. The convention is for an edge label in snake_case\n      form. For example, biolink:related_to, biolink:causes, biolink:treats\n    range: predicate type\n    required: true\n    local_names:\n      ga4gh: annotation predicate\n      translator: predicate\n    slot_uri: rdf:predicate\n    exact_mappings:\n      - owl:annotatedProperty\n      - OBAN:association_has_predicate\n\n  logical interpretation:\n    is_a: association slot\n    required: false\n    domain: association\n    range: LogicalInterpretationEnum\n    exact_mappings:\n      - os:LogicalInterpretation\n\n  relation:\n    deprecated: true\n\n  negated:\n    is_a: association slot\n    range: boolean\n    description: >-\n      if set to true, then the association is negated i.e. is not true\n\n  has confidence level:\n    is_a: association slot\n    range: confidence level\n    description: >-\n      connects an association to a qualitative term denoting the level of confidence\n\n  has evidence:\n    is_a: association slot\n    range: evidence type\n    description: >-\n      connects an association to an instance of supporting evidence\n    exact_mappings:\n      - RO:0002558\n    multivalued: true\n\n  has supporting study result:\n    is_a: association slot\n    description: >-\n      connects an association to an instance of supporting study result\n    \n  mechanism of action:\n    is_a: association slot\n    range: boolean\n    description: >-\n      a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes\n      the mechanism of action for a result.\n    exact_mappings:\n      - NCIT:C54680\n      - MI:2044\n      - LOINC:MTHU019741\n\n  knowledge source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which the knowledge expressed in an Association was\n      retrieved, directly or indirectly. This can be any resource through which the\n      knowledge passed on its way to its currently serialized form. In practice,\n      implementers should use one of the more specific subtypes of this generic property.\n    range: information resource\n    close_mappings:\n      - pav:providedBy\n\n  provided by:\n    is_a: node property\n    description: >-\n      The value in this node property represents the knowledge provider that created or assembled the\n      node and all of its attributes.  Used internally to represent how a particular node made its way into a\n      knowledge provider or graph.\n    multivalued: true\n\n  primary knowledge source:\n    is_a: knowledge source\n    description: >-\n      The most upstream source of the knowledge expressed in an Association that an\n      implementer can identify.  Performing a rigorous analysis of upstream data providers is expected; every effort\n      is made to catalog the most upstream source of data in this property.  Only one data source should be declared\n      primary in any association.  \"aggregator knowledge source\" can be used to caputre non-primary sources.\n    range: information resource\n    notes: >-\n      For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then \n      incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to \n      the NCATS ARS. The retrieval path for this Edge is as follows: \n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   MolePro  --retrieved_from--> ChEMBL --retrieved_from-->  ClinicalTrials.gov\n      The \"primary knowledge source\" for this edge is \"infores:clinical-trials-gov\".  \"infores:chembl\" and \"infores:molecular_data_provider\"\n      are listed in the \"aggregator knowledge source\" property.\n    multivalued: false\n\n  aggregator knowledge source:\n    is_a: knowledge source\n    description: >-\n      An intermediate aggregator resource from which knowledge expressed in an Association was\n      retrieved downstream of the original source, on its path to its current serialized form.\n    range: information resource\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which data was retrieved and subsequently used as\n      evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data set:\n    is_a: association slot\n    description: >-\n      A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    range: information resource\n    multivalued: true\n\n  chi squared statistic:\n    is_a: association slot\n    range: float\n    description: >-\n      represents the chi-squared statistic computed from observations\n    exact_mappings:\n      - STATO:0000030\n\n  p value:\n    aliases: ['unadjusted p value']\n    is_a: association slot\n    range: float\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    exact_mappings:\n      - OBI:0000175\n      - NCIT:C44185\n      - EDAM-DATA:1669\n\n  evidence count:\n    is_a: association slot\n    description: >-\n      The number of evidence instances that are connected to an association.\n    range: integer\n\n  concept count subject:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the subject slot of an association.\n    range: integer\n    examples:\n      - value: 489\n\n  concept count object:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the object slot of an association.\n    range: integer\n\n  concept pair count:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      both the subject and object concept of an association.\n    range: integer\n    examples:\n      - value: 1731\n\n  expected count:\n    is_a: association slot\n    description: >-\n      The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and \n      object concept of an association if the subject and object concepts are independent.\n\n  relative frequency subject:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the subject\n      concept appears in these same records.\n    range: float\n    examples:\n      - value: 0.01840490798\n\n  relative frequency object:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the object\n      concept appears in these same records.\n    range: string\n\n  relative frequency subject confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_subject calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  relative frequency object confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_object calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  adjusted p value:\n    is_a: p value\n    description: >-\n      The adjusted p-value is the probability of obtaining test results\n      at least as extreme as the results actually observed, under the assumption that\n      the null hypothesis is correct, adjusted for multiple comparisons.  \n      P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) \n      rather than expressing a statement of inequality (P<. 05), unless P<.\n    range: float\n\n  bonferonni adjusted p value:\n    is_a: adjusted p value\n    description: >-\n      The Bonferroni correction is an adjustment made to P values when several dependent or independent \n      statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni \n      correction, divide the critical P value (α) by the number of comparisons being made.  P is always italicized and \n      capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality \n      (P<. 05), unless P<.\n    range: float\n    examples:\n      - value: 0.018\n\n  supporting text:\n    is_a: association slot\n    description: The segment of text from a document that supports the mined assertion.\n    multivalued: true\n    range: string\n    examples:\n      - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer.\n\n  supporting documents:\n    is_a: association slot\n    description: >-\n      One or more referencable documents that report the statement expressed in an Association, or provide \n      information used as evidence supporting this statement.\n    range: uriorcurie\n    multivalued: true\n    examples:\n      - value: PMID:12345678\n\n  subject location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the subject concept of the extracted assertion.\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  object location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the object concept of the extracted assertion\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  extraction confidence score:\n    is_a: association slot\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    range: integer\n    examples:\n        - value: 15\n\n  supporting document type:\n    is_a: association slot\n    description: >-\n      The document type (e.g., Journal Article, Case Study, Preprint) for\n      the supporting document used in a Text Mining Result.\n    range: string\n    examples:\n      - value: Journal Article\n\n  supporting document year:\n    is_a: association slot\n    description: >-\n      The document year (typically the publication year) for the supporting\n      document used in a Text Mining Result.\n    range: integer\n    examples:\n      - value: 1999\n\n  supporting text section type:\n    is_a: association slot\n    description: >-\n      The section of the supporting text of a Text Mining Result within\n      the supporting document. This is in the form of the name of the document section\n      (e.g., Abstract, Introduction) that contains the supporting text.\n    range: string\n    examples:\n      - value: Introduction\n\n  ln ratio:\n    is_a: association slot\n    description: the natural log of the ratio of co-occurrence to expected\n    range: float\n    examples:\n      - value: 2.922827136\n\n  ln ratio confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the ln_ratio calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: float\n    examples:\n      - value: 2.922827136\n\n  interacting molecules category:\n    is_a: association slot\n    range: ontology class\n    exact_mappings:\n      - MI:1046\n    values_from:\n      - MI\n    examples:\n      - value: MI:1048\n        description: smallmolecule-protein\n\n  expression site:\n    description: >-\n      location in which gene or protein expression takes place.\n      May be cell, tissue, or organ.\n    is_a: association slot\n    range: anatomical entity\n    examples:\n      - value: UBERON:0002037\n        description: cerebellum\n\n  phenotypic state:\n    description: >-\n      in experiments (e.g. gene expression) assaying diseased or unhealthy\n      tissue, the phenotypic state can be put here, e.g. MONDO ID.\n      For healthy tissues, use XXX.\n    is_a: association slot\n    range: disease or phenotypic feature\n\n  publications:\n    aliases: [\"supporting publications\"]\n    singular_name: publication\n    description: >-\n      One or more publications that report the statement expressed in an Association, or provide information used as \n      evidence supporting this statement.\n    is_a: supporting documents\n    multivalued: true\n    range: publication\n\n  associated environmental context:\n    is_a: association slot\n    description: >-\n      An attribute that can be applied to an association where the association holds between two entities\n      located or occurring in a particular environment. For example, two microbial taxa may interact in the context of\n      a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure.\n      # TODO: add examples of values for this property.\n\n  sequence localization attribute:\n    is_a: association slot\n    domain: genomic sequence localization\n    description: >-\n      An attribute that can be applied to a genome sequence localization edge. These edges\n      connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used\n      to ascribe specific positional information and other metadata to the localization. In pragmatic terms\n      this can be thought of as columns in a GFF3 line.\n\n  interbase coordinate:\n    is_a: sequence localization attribute\n    aliases: [ 'zero-based', 'half-open', 'space-based' ]\n    description: >-\n      A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1.\n      This is applied to a sequence localization edge.\n    range: integer\n\n  start interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 0).\n    close_mappings:\n      - faldo:begin\n    annotations:\n      opposite_of: end interbase coordinate\n\n  end interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity ends\n      on the chromosome or other entity to which it is located on.\n    close_mappings:\n      - faldo:end\n    annotations:\n      opposite_of: start interbase coordinate\n\n  start coordinate:\n    is_a: base coordinate\n    aliases: [ 'start' ]\n    description: >-\n      The position at which the subject genomic entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 1).\n    exact_mappings:\n      - gff3:start\n    close_mappings:\n      - faldo:begin\n\n  end coordinate:\n    is_a: base coordinate\n    aliases: [ 'end' ]\n    description: >-\n      The position at which the subject genomic entity ends\n      on the chromosome or other entity to which it is located on.\n    exact_mappings:\n      - gff3:end\n    close_mappings:\n      - faldo:end\n\n  genome build:\n    is_a: sequence localization attribute\n    description: >-\n      The version of the genome on which a feature is located.\n      For example, GRCh38 for Homo sapiens.\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  strand:\n    is_a: sequence localization attribute\n    description: >-\n      The strand on which a feature is located. Has a value of '+'\n      (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  phase:\n    is_a: sequence localization attribute\n    domain: coding sequence\n    description: >-\n      The phase for a coding sequence entity. For example, phase of a\n      CDS as represented in a GFF3 with a value of 0, 1 or 2.\n    range: PhaseEnum\n    exact_mappings:\n      - gff3:phase\n\n  FDA approval status:\n    is_a: association slot\n    description: >-\n    range: FDAApprovalStatusEnum\n\n  supporting study metadata:\n    is_a: association slot\n    description: >-\n      Information about a study used to generate information used as evidence to support the knowledge expressed in an \n      Association. In practice, data creators should use one of the more specific subtypes of this property.\n    abstract: true\n\n  supporting study method type:\n    is_a: supporting study metadata\n    description: >-\n      A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of \n      experimental assay, or statistical calculation, or computational analysis).\n    range: uriorcurie\n\n  supporting study method description:\n    is_a: supporting study metadata\n    description: >-\n      A uri or curie pointing to information about the methodology used to generate data supporting an Association.\n    range: uriorcurie\n\n  supporting study size:\n    is_a: supporting study metadata\n    description: >-\n      The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a \n      clinical study).\n    range: integer\n\n  supporting study cohort:\n    is_a: supporting study metadata\n    description: >-\n      A description of a study population/cohort that was interrogated to provide evidence for the association \n      (e.g. the inclusion and exclusion criteria).\n    range: string\n\n  supporting study date range:\n    is_a: supporting study metadata\n    description: >-\n      The date range over which data was collected in a study that provided evidence for an Association.\n    range: string\n\n  supporting study context:\n    is_a: supporting study metadata\n    description: >-\n      A term or terms describing the experimental setting/context in which evidence supporting the Association was \n      generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue \n      type, disease, etc.).\n    range: string\nclasses:\n\n  mapping collection:\n    description: >-\n      A collection of deprecated mappings.\n    abstract: true\n    slots:\n      - predicate mappings\n    tree_root: true\n\n  predicate mapping:\n    description: >-\n      A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should\n      be done to use a qualified statement in its place.\n    slots:\n      - mapped predicate\n      - subject aspect qualifier\n      - subject direction qualifier\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - predicate\n      - qualified predicate\n      - object aspect qualifier\n      - object direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object derivative qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - species context qualifier\n      - exact match\n      - narrow match\n      - broad match\n\n\n  ## ----------\n  ## ATTRIBUTES\n  ## ----------\n\n  ## Ontology Classes\n\n  ontology class:\n    mixin: true\n    slots:\n      - id\n    description: >-\n      a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in\n      a biolink compatible KG can be considered both instances of biolink classes, and\n      OWL classes in their own right. In general you should not need to use this class directly.\n      Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897),\n      use bl:BiologicalProcess as the type.\n    exact_mappings:\n      - owl:Class\n      - schema:Class\n    comments:\n      - >-\n        This is modeled as a mixin. 'ontology class' should not be the primary type of a\n        node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity\n        (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\n      - >-\n        Note that formally this is a metaclass. Instances of this class are instances in the graph,\n        but can be the object of 'type' edges. For example, if we had a node in the graph representing\n        a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample,\n        and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\n    see_also:\n      - https://github.com/biolink/biolink-model/issues/486\n    examples:\n      - value: UBERON:0000955\n        description: >-\n          the class 'brain' from the Uberon anatomy ontology\n    id_prefixes:\n      - MESH\n      - UMLS\n      - KEGG.BRITE ## br/ko number\n  \n  annotation:\n    description: >-\n      Biolink Model root class for entity annotations.\n    abstract: true\n\n  quantity value:\n    is_a: annotation\n    description: >-\n      A value of an attribute that is quantitative and measurable,\n      expressed as a combination of a unit and a numeric value\n    slots:\n      - has unit\n      - has numeric value\n\n  # Alignment attempted of the biolink:Attribute model\n  # to the proposed TRAPI Release 1.1 Attribute schema, i.e.\n  #\n  # attribute_name: \"assertionAuthoredBy\",\n  # attribute_type: SEPIO:0000130,\n  # value: \"ORCID:12345\",\n  # value_type: \"wd:Q51044\",\n  # value_type_name: \"ORCID ID\"\n  # url: https://orcid.org/12345\n  # source: ORCID\n\n  attribute:\n    is_a: named thing\n    mixins:\n      - ontology class\n    description: >-\n      A property or characteristic of an entity.\n      For example, an apple may have properties such as color, shape, age, crispiness.\n      An environmental sample may have attributes such as depth, lat, long, material.\n    slots:\n      - name                   # 'attribute_name'\n      - has attribute type     # 'attribute_type'\n      # 'value', 'value_type', 'value_type_name'\n      # extracted from either of the next two slots\n      - has quantitative value\n      - has qualitative value\n      - iri                    # 'url'\n    slot_usage:\n      name:\n        description: >-\n          The human-readable 'attribute name' can be set to a string which reflects its context of\n          interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default\n          to the name associated with the 'has attribute type' slot ontology term.\n    id_prefixes:\n      - EDAM-DATA\n      - EDAM-FORMAT\n      - EDAM-OPERATION\n      - EDAM-TOPIC\n    exact_mappings:\n      - SIO:000614\n    in_subset:\n      - samples\n\n  chemical role:\n    is_a: attribute\n    description: >-\n      \tA role played by the molecular entity or part thereof within a chemical context.\n    id_prefixes:\n      - CHEBI\n    exact_mappings:\n      - CHEBI:51086\n    examples:\n      - value: CHEBI:35469 # antidepressant role\n\n  biological sex:\n    is_a: attribute\n    exact_mappings:\n      - PATO:0000047\n\n  phenotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the phenotypic sex of the individual,\n      based upon the reproductive organs present.\n    exact_mappings:\n      - PATO:0001894\n\n  genotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the genotypic sex of the individual,\n      based upon genotypic composition of sex chromosomes.\n    exact_mappings:\n      - PATO:0020000\n\n  severity value:\n    is_a: attribute\n    description: >-\n      describes the severity of a phenotypic feature or disease\n\n  relationship quantifier:\n    mixin: true\n\n  sensitivity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  specificity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  pathognomonicity quantifier:\n    is_a: specificity quantifier\n    description: >-\n      A relationship quantifier between a variant or symptom and a disease, which is\n      high when the presence of the feature implies the existence of the disease\n    mixin: true\n\n  frequency quantifier:\n    is_a: relationship quantifier\n    mixin: true\n    slots:\n      - has count\n      - has total\n      - has quotient\n      - has percentage\n\n  chemical or drug or treatment:\n    mixin: true\n\n  ## ------\n  ## THINGS\n  ## ------\n\n  entity:\n    description: >-\n      Root Biolink Model class for all things and informational relationships, real or imagined.\n    abstract: true\n    slots:\n      - id\n      - iri\n      - category\n      - type   # rdf:type\n      - name\n      - description\n      - has attribute\n      # evidence code(s)?\n\n  named thing:\n    is_a: entity\n    description: \"a databased entity or concept/class\"\n    slots:\n      - provided by\n      - xref\n    slot_usage:\n      category:\n        required: true\n        pattern: '^biolink:\\d+$'\n    exact_mappings:\n      - BFO:0000001\n      - WIKIDATA:Q35120\n      # UMLS Semantic Group \"Objects\"\n      - UMLSSG:OBJC\n      # Entity\n      - STY:T071\n      - dcid:Thing\n\n  relationship type:\n    is_a: ontology class\n    description: >-\n      An OWL property used as an edge label\n\n  taxonomic rank:\n    description: >-\n      A descriptor for the rank within a taxonomic classification.\n      Example instance: TAXRANK:0000017 (kingdom)\n    is_a: ontology class\n    id_prefixes:\n      - TAXRANK\n    mappings:\n      - WIKIDATA:Q427626\n\n  organism taxon:\n    aliases: [ 'taxon', 'taxonomic classification' ]\n    description: >-\n      A classification of a set of organisms. Example instances:\n      NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria).\n      Can also be used to represent strains or subspecies.\n    is_a: named thing\n    slot_usage:\n      has taxonomic rank:\n        range: taxonomic rank\n        multivalued: false\n        mappings:\n          - WIKIDATA:P105\n    values_from:\n      - NCBITaxon\n    exact_mappings:\n      - WIKIDATA:Q16521\n      - STY:T001\n      - bioschemas:Taxon\n    narrow_mappings:\n      - dcid:BiologicalSpecies\n    id_prefixes:\n      - NCBITaxon\n      - MESH\n      - UMLS\n    in_subset:\n      - model_organism_database\n  \n  ## Temporal Entities\n  \n  event:\n    is_a: named thing\n    description: >-\n      Something that happens at a given place and time.\n    exact_mappings:\n      - NCIT:C25499\n      # UMLS \"Event\"\n      - STY:T051\n\n  ## Administrative Entities\n\n  administrative entity:\n    is_a: named thing\n    abstract: true\n\n  study result:\n    abstract: true\n    description: >- \n      A collection of data items from a study that are about a particular study subject or experimental unit (the \n      'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation\n      of this data as evidence.\n    notes:\n      The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, \n      that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific \n      focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any \n      scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational \n      analyses, or a larger scale clinical trial or experimental research investigation.\n    is_a: information content entity\n\n  study:\n    description: a detailed investigation and/or analysis\n    is_a: information content entity\n    exact_mappings:\n      - NCIT:C63536\n    close_mappings:\n      - SIO:001066\n      - SEPIO:0000004\n    narrow_mappings:\n      - SIO:000994\n\n  study variable:\n    is_a: information content entity\n    description: a variable that is used as a measure in the investigation of a study\n    narrow_mappings:\n      - NCIT:C142192 # specifies clinical study\n    close_mappings:\n      - STATO:0000258\n      - SIO:000367\n\n  common data element:\n    is_a: information content entity\n    description: >- \n      A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable \n      responses, used systematically across different sites, studies, or clinical trials to ensure consistent \n      data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. \n      (https://cde.nlm.nih.gov/home)\n    close_mappings:\n      - NCIT:C19984\n\n  ## epc result sets\n  concept count analysis result:\n    is_a: study result\n    description: >-\n      A result of a concept count analysis.\n\n  observed expected frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a observed expected frequency analysis.\n\n  relative frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a relative frequency analysis.\n\n  text mining result:\n    is_a: study result\n    description: >-\n      A result of text mining.\n\n  chi squared analysis result:\n    is_a: study result\n    description: >-\n      A result of a chi squared analysis.\n\n  agent:\n    is_a: administrative entity\n    aliases: [ 'group' ]\n    description: >-\n      person, group, organization or project that provides\n      a piece of information (i.e. a knowledge association)\n    slots:\n      - affiliation\n      - address\n    exact_mappings:\n      - prov:Agent\n      - dct:Agent\n    narrow_mappings:\n      # Organization\n      - UMLSSG:ORGA\n      - STY:T092\n      # Health Care Related Organization\n      - STY:T093\n      # Professional Society\n      - STY:T094\n      # Self-help or Relief Organization\n      - STY:T095\n      # Group\n      - STY:T096\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Different classes of agents have distinct preferred identifiers.\n          For publishers, use the ISBN publisher code.\n          See https://grp.isbn-international.org/ for publisher code lookups.\n          For editors, authors and  individual providers, use the individual's\n          ORCID if available; Otherwise, a ScopusID, ResearchID or\n          Google Scholar ID ('GSID') may be used if the author ORCID is unknown.\n          Institutional agents could be identified by an\n          International Standard Name Identifier ('ISNI') code.\n        values_from:\n          # CURIE space for publishers\n          - isbn\n          # CURIE space for authors\n          - ORCID\n          - ScopusID\n          - ResearchID\n          - GSID\n          # Institutional agents\n          - isni\n      name:\n        description: >-\n          it is recommended that an author's 'name' property\n          be formatted as \"surname, firstname initial.\"\n    id_prefixes:\n      - isbn\n      - ORCID\n      - ScopusID\n      - ResearchID\n      - GSID\n      - isni\n\n  ## General Information Entities\n\n  information content entity:\n    aliases: [ 'information', 'information artefact', 'information entity' ]\n    abstract: true\n    is_a: named thing\n    description: >-\n      a piece of information that typically describes\n      some topic of discourse or is used as support.\n    slots:\n      - license\n      - rights\n      - format\n      - creation date\n    id_prefixes:\n      - doi\n    exact_mappings:\n      - IAO:0000030\n    narrow_mappings:\n      # UMLS Semantic Group \"Concepts & Ideas\"\n      - UMLSSG:CONC\n      # Conceptual Entity\n      - STY:T077\n      # Idea or Concept\n      - STY:T078\n      # Temporal Concept\n      - STY:T079\n      # Qualitative Concept\n      - STY:T080\n      # Quantitative Concept\n      - STY:T081\n      # Spatial Concept\n      - STY:T082\n      # Regulation or Law\n      - STY:T089\n      # Group Attribute\n      - STY:T102\n      # Functional Concept\n      - STY:T169\n      # Language\n      - STY:T171\n      # Classification\n      - STY:T185\n\n  dataset:\n    description: >-\n      an item that refers to a collection of data from a data source.\n    is_a: information content entity\n    exact_mappings:\n      - IAO:0000100\n      - dctypes:Dataset\n      - schema:dataset\n      - dcid:Dataset\n\n  dataset distribution:\n    is_a: information content entity\n    description: >-\n      an item that holds distribution level information about a dataset.\n    slots:\n      - distribution download url\n    exact_mappings:\n      - dcat:Distribution\n\n  dataset version:\n    description: >-\n      an item that holds version level information about a dataset.\n    is_a: information content entity\n    slots:\n      - has dataset\n      - ingest date\n      - has distribution\n\n  dataset summary:\n    description: >-\n      an item that holds summary level information about a dataset.\n    is_a: information content entity\n    slots:\n      - source web page\n      - source logo\n\n  confidence level:\n    is_a: information content entity\n    description: >-\n      Level of confidence in a statement\n    values_from:\n      - cio\n    exact_mappings:\n      - CIO:0000028\n      # statement confidence\n      - SEPIO:0000187\n    close_mappings:\n      # assertion confidence levels\n      - SEPIO:0000167\n\n  evidence type:\n    is_a: information content entity\n    aliases: [ 'evidence code' ]\n    description: >-\n      Class of evidence that supports an association\n    values_from:\n      - eco\n    exact_mappings:\n      - ECO:0000000\n\n  information resource:\n    is_a: information content entity\n    aliases: [ 'knowledgebase' ]\n    description: >-\n      A database or knowledgebase and its supporting ecosystem of interfaces \n      and services that deliver content to consumers (e.g. web portals, APIs, \n      query endpoints, streaming services, data downloads, etc.).\n      A single Information Resource by this definition may span many different datasets or\n      databases, and include many access endpoints and user\n      interfaces. Information Resources include project-specific resources\n      such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.\n    in_subset:\n      - translator_minimal\n\n\n  ## Publications\n\n  # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies\n  publication:\n    is_a: information content entity\n    description: >-\n      Any published piece of information. Can refer to a whole publication,\n      its encompassing publication (i.e. journal or book) or to a part of a\n      publication, if of significant knowledge scope (e.g. a figure, figure\n      legend, or section highlighted by NLP). The scope is intended to be\n      general and include information published on the web, as well as printed\n      materials, either directly or in one of the Publication Biolink\n      category subclasses.\n    slots:\n      - authors\n      - pages\n      - summary\n      - keywords\n      - mesh terms\n      - xref\n    # In addition to embedded slots, instances of 'contributor association'\n    # may be used to more extensively document publisher, editor and author details\n    slot_usage:\n      id:\n        description: >-\n          Different kinds of publication subtypes will have different preferred\n          identifiers (curies when feasible). Precedence of identifiers for\n          scientific articles is as follows: PMID if available; DOI if not; actual\n          alternate CURIE otherwise. Enclosing publications (i.e. referenced by\n          'published in' node property) such as books and journals, should have\n          industry-standard identifier such as from ISBN and ISSN.\n      name:\n        description: >-\n          the 'title' of the publication is generally recorded in the 'name'\n          property (inherited from NamedThing). The field name 'title' is now also\n          tagged as an acceptable alias for the node property 'name' (just in case).\n      type:\n        slot_uri: dct:type\n        required: true\n        description: >-\n          Ontology term for publication type may be drawn from\n          Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),\n          FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),\n          the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),\n          the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres\n          (http://vocabularies.coar-repositories.org/documentation/resource_types/),\n          Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or\n          equivalent publication type ontology. When a given publication type ontology term\n          is used within a given knowledge graph, then the CURIE identified term must be\n          documented in the graph as a concept node of biolink:category biolink:OntologyClass.\n        values_from: # Not sure which takes precedence, if any...\n          - dctypes\n          - fabio\n          - MESH_PUB\n          - COAR_RESOURCE\n          - WIKIDATA\n      pages:\n        multivalued: true\n        description: >-\n          When a 2-tuple of page numbers are provided, they represent\n          the start and end page of the publication within its parent publication context.\n          For books, this may be set to the total number of pages of the book.\n    exact_mappings:\n      - IAO:0000311\n    narrow_mappings:\n      - IAO:0000013\n      # UMLS Semantic Type \"Intellectual Product\"\n      - STY:T170\n    id_prefixes:\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book:\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Books should have industry-standard identifier such as from ISBN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'book'.\n    id_prefixes:\n      - isbn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book chapter:\n    is_a: publication\n    slots:\n      - published in\n      - volume\n      - chapter\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent book containing the chapter\n          should have industry-standard identifier from ISBN.\n    in_subset:\n      - model_organism_database\n\n  serial:\n    aliases: [ 'journal' ]\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slots:\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Serials (journals) should have industry-standard identifier such as from ISSN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'serial' or 'journal'.\n    id_prefixes:\n      - issn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  article:\n    is_a: publication\n    slots:\n      - published in\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent serial containing the article should\n          have industry-standard identifier from ISSN.\n      iso abbreviation:\n        description: >-\n          Optional value, if used locally as a convenience, is set\n          to the iso abbreviation of the 'published in' parent.\n    id_prefixes:\n      # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces\n      - PMID\n    in_subset:\n      - model_organism_database\n\n  ## Top Level Abstractions of Material & Process Entities\n\n  physical essence or occurrent:\n    description: >-\n      Either a physical or processual entity.\n    mixin: true\n\n\n  physical essence:\n    description: >-\n      Semantic mixin concept.  Pertains to entities that have\n      physical properties such as mass, volume, or charge.\n    is_a: physical essence or occurrent\n    mixin: true\n\n  physical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n    description: >-\n      An entity that has material reality (a.k.a. physical essence).\n    exact_mappings:\n      # Physical Object\n      - STY:T072\n    narrow_mappings:\n      # Manufactured Object\n      - STY:T073\n\n  occurrent:\n    description: >-\n      A processual entity.\n    # biolink:Occurrent is most consistently used as a mixin thus it should\n    # be declared as such and cannot inherit from the non-mixin biolink:NamedThing\n    is_a: physical essence or occurrent\n    mixin: true\n    exact_mappings:\n      - BFO:0000003\n\n  activity and behavior:\n    is_a: occurrent\n    mixin: true\n    description: >-\n      Activity or behavior of any independent integral living,\n      organization or mechanical actor in the world\n    exact_mappings:\n      # Activities & Behaviors\n      - UMLSSG:ACTI\n\n  activity:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      An activity is something that occurs over a period of time and acts upon\n      or with entities; it may include consuming, processing, transforming,\n      modifying, relocating, using, or generating entities.\n    exact_mappings:\n      - prov:Activity\n      - NCIT:C43431\n      # Activity\n      - STY:T052\n    narrow_mappings:\n      # Daily or Recreational Activity\n      - STY:T056\n      # Occupational Activity\n      - STY:T057\n      # Governmental or Regulatory Activity\n      - STY:T064\n      # Machine Activity\n      - STY:T066\n      # Research Activity\n      - STY:T062\n      # Educational Activity\n      - STY:T065\n      # Health Care Activity\n      - STY:T058\n\n  procedure:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      A series of actions conducted in a certain order or manner\n    exact_mappings:\n      # Procedures\n      - UMLSSG:PROC\n      - dcid:MedicalProcedure\n    narrow_mappings:\n      # Laboratory Procedure\n      - STY:T059\n      # Diagnostic Procedure\n      - STY:T060\n      # Therapeutic or Preventive Procedure\n      - STY:T061\n      # Molecular Biology Research Technique\n      - STY:T063\n    id_prefixes:\n      - CPT\n\n  phenomenon:\n    is_a: named thing\n    mixins:\n      - occurrent\n    description: >-\n      a fact or situation that is observed to exist or happen,\n      especially one whose cause or explanation is in question\n    broad_mappings:\n      # the inclusion of 'process' in the definition of these\n      # terms broadens them, relative to 'phenomenon'\n      # Phenomenon or Process\n      - STY:T067\n      # Human-caused Phenomenon or Process\n      - STY:T068\n      # Natural Phenomenon or Process\n      - STY:T070\n    exact_mappings:\n      # Phenomena\n      - UMLSSG:PHEN\n    narrow_mappings:\n      # Laboratory or Test Result\n      - STY:T034\n      # Biologic Function\n      - STY:T038\n      # Environmental Effect of Humans\n      - STY:T069\n\n  device:\n    is_a: named thing\n    description: >-\n      A thing made or adapted for a particular purpose, especially\n      a piece of mechanical or electronic equipment\n    narrow_mappings:\n      # Devices\n      - UMLSSG:DEVI\n      # Medical Device\n      - STY:T074\n      # Research Device\n      - STY:T075\n      # Drug Delivery Device\n      - STY:T203\n      # Biomedical or Dental Material\n      - STY:T122\n\n  ## Scientific Studies\n\n  study population:\n    is_a: population of individual organisms\n    description: >-\n      A group of people banded together or treated as a group as participants in a research study.\n    close_mappings:\n      - WIKIDATA:Q7229825\n\n  subject of investigation:\n    mixin: true\n    description: >-\n      An entity that has the role of being studied in an investigation, study, or experiment\n\n  material sample:\n    aliases: [ 'biospecimen', 'sample', 'biosample', 'physical sample' ]\n    is_a: physical entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A sample is a limited quantity of something (e.g. an individual or set of individuals\n      from a population, or a portion of a substance) to be used for testing, analysis,\n      inspection, investigation, demonstration, or trial use. [SIO]\n    exact_mappings:\n      - OBI:0000747\n      - SIO:001050\n    id_prefixes:\n      - BIOSAMPLE\n      - GOLD.META\n\n  ## Earth Sciences\n\n  planetary entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists at the level of the whole planet\n\n  environmental process:\n    is_a: planetary entity\n    mixins:\n      - occurrent\n    exact_mappings:\n      - ENVO:02500000\n\n  environmental feature:\n    is_a: planetary entity\n    exact_mappings:\n      - ENVO:01000254\n\n  geographic location:\n    is_a: planetary entity\n    description: >-\n      a location that can be described in lat/long coordinates\n    slots:\n      - latitude\n      - longitude\n    exact_mappings:\n      # Geographic Areas\n      - UMLSSG:GEOG\n      # Geographic Area\n      - STY:T083\n\n  geographic location at time:\n    is_a: geographic location\n    description: >-\n      a location that can be described in lat/long coordinates, for a particular time\n    slots:\n      - timepoint\n\n  ## Biological Sciences\n\n  thing with taxon:\n    mixin: true\n    description: >-\n      A mixin that can be used on any entity that can be taxonomically classified.\n      This includes individual organisms; genes, their products and other molecular\n      entities; body parts; biological processes\n    slots:\n      - in taxon\n\n  biological entity:\n    is_a: named thing\n    aliases: [ 'bioentity' ]\n    abstract: true\n    mixins:\n      - thing with taxon\n    narrow_mappings:\n      - WIKIDATA:Q28845870\n      # UMLS Semantic Type \"Experimental Model of Disease\"\n      - STY:T050\n      # SIO term is 'biological entity' but less inclusive than the Biolink scope\n      - SIO:010046\n\n  genomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - STY:T028   # Gene or Genome\n      - GENO:0000897  # Genomic Entity\n\n  epigenomic entity:\n      mixin: true\n      slots:\n        - has biological sequence\n      in_subset:\n        - translator_minimal\n      narrow_mappings:\n\n  molecular entity:\n    is_a: chemical entity\n    description: >-\n      A molecular entity is a chemical entity composed of individual or\n      covalently bonded atoms.\n    slots:\n      - is metabolite\n    narrow_mappings:\n      - STY:T088 # Carbohydrate\n      - STY:T085 # Molecular Sequence\n      - CHEBI:23367 # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical,\n      # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.\n      - bioschemas:MolecularEntity\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  chemical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n      - chemical or drug or treatment # issue 701\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    description: >-\n      A chemical entity is a physical entity that pertains to chemistry or\n      biochemistry.\n    slots:\n      - trade name\n      - available from\n      - max tolerated dose\n      - is toxic\n      - has chemical role\n    exact_mappings:\n      - CHEBI:24431\n      - SIO:010004 # Chemical entity\n      - WIKIDATA:Q79529 # Chemical substance\n      - STY:T103 # Chemical\n    narrow_mappings:\n      - WIKIDATA:Q43460564\n      - STY:T129 # (imft, full name: Immunologic Factor\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS #CAS numbers are given for things like plant extracts as well.\n      - UMLS\n      - ncats.drug\n\n  small molecule:\n    is_a: molecular entity\n    aliases: [ 'chemical substance' ]\n    description: >-\n      A small molecule entity is a molecular entity characterized by availability\n      in small-molecule databases of SMILES, InChI, IUPAC, or other\n      unambiguous representation of its precise chemical structure; for\n      convenience of representation, any valid chemical representation is\n      included, even if it is not strictly molecular (e.g., sodium ion).\n    narrow_mappings:\n      - STY:T196 # Element, Ion, or Isotope\n      - CHEBI:59999\n      - bioschemas:ChemicalSubstance\n      - STY:T123 #(bacs, full name: Biologically Active Substance)\n      - STY:T131 #(hops, full name: Hazardous or Poisonous Substance)\n      - STY:T125 #(horm, full name: Hormone)\n      - STY:T197 #(inch, full name: Inorganic Chemical)\n      - STY:T109 #(orch, full name: Organic Chemical)\n      - STY:T118 #(carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files)\n      - STY:T111 #(eico, full name: Eicosanoid) - same note as above\n      - STY:T119 #(lipd, full name: Lipid) - same note as above\n      - STY:T124 #(nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above\n      - STY:T115 #(opco, full name: Organophosphorus Compound) - same note as above\n      - STY:T110 #(strd, full name: Steroid) - same note as above\n      - STY:T127 # vitamin\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - BIGG.METABOLITE\n      - UMLS\n      - foodb.compound\n    slot_usage:\n      id:\n        examples:\n          - value: CHEBI:29101\n            description: sodium ion\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n\n  chemical mixture:\n    is_a: chemical entity\n    description: >-\n      A chemical mixture is a chemical entity composed of two or more\n      molecular entities.\n    slots:\n      - is supplement\n      - highest FDA approval status\n      - drug regulatory status world wide\n      - routes of delivery\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n    close_mappings:\n      - dcid:ChemicalCompound\n    narrow_mappings:\n      - NCIT:C20401 # monoclonal antibody\n      - SNOMEDCT:49616005 # monoclonal antibody (substance)\n\n  nucleic acid entity:\n    is_a: molecular entity\n    description: >-\n      A nucleic acid entity is a molecular entity characterized by\n      availability in gene databases of nucleotide-based sequence\n      representations of its precise sequence; for convenience of\n      representation, partial sequences of various kinds are included.\n    aliases: [ 'sequence feature', 'genomic entity' ]\n    mixins:\n      - genomic entity\n      - thing with taxon\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000110\n    narrow_mappings:\n      - STY:T086   # Nucleotide Sequence\n      - STY:T114   # Nucleic Acid, Nucleoside, or Nucleotide\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  # G number\n      - KEGG.ENVIRON # E number\n\n  molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A molecular mixture is a chemical mixture composed of two or more\n      molecular entities with known concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n      - ncats.drug\n\n  complex molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A complex molecular mixture is a chemical mixture composed of two or\n      more molecular entities with unknown concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES  # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN  ## G number\n      - KEGG.DRUG    ## D number\n      - KEGG.DGROUP  ## DG number\n      - KEGG.ENVIRON ## E number\n      - UMLS\n\n  biological process or activity:\n    description: >-\n      Either an individual molecular activity, or a collection of\n      causally connected molecular activities in a biological system.\n    is_a: biological entity\n    mixins:\n      - occurrent\n      - ontology class\n    id_prefixes:\n      - GO\n      - REACT\n    slots:\n      - has input\n      - has output\n      - enabled by\n\n  molecular activity:\n    description: >-\n      An execution of a molecular function carried out by a\n      gene product or macromolecular complex.\n    is_a: biological process or activity\n    aliases: [ 'molecular function', 'molecular event', 'reaction' ]\n    mixins:\n      - occurrent\n      - ontology class\n    slot_usage:\n      has input:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the input for the reaction\n      has output:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the output for the reaction\n      enabled by:\n        range: macromolecular machine mixin\n        description: >-\n          The gene product, gene, or complex that catalyzes the reaction\n    exact_mappings:\n      - GO:0003674\n      # UMLS Semantic Type \"Molecular Function\"\n      - STY:T044\n    id_prefixes:\n      - GO\n      - REACT\n      - RHEA\n      - metacyc.reaction\n      - EC\n      - TCDB\n      - KEGG.REACTION  ## R number\n      - KEGG.RCLASS    ## RC number\n      - KEGG.ENZYME    ## EC number\n      - KEGG.ORTHOLOGY ## in particular for gut microbiome use case in issue #888\n      - UMLS\n      - BIGG.REACTION\n      - SEED.REACTION\n      - METANETX.REACTION\n\n  biological process:\n    is_a: biological process or activity\n    mixins:\n      - occurrent\n      - ontology class\n    description: >-\n      One or more causally connected executions of molecular functions\n    exact_mappings:\n      - GO:0008150\n      - SIO:000006\n      - WIKIDATA:Q2996394\n    broad_mappings:\n      - WIKIDATA:P682\n    id_prefixes:\n      - GO\n      - REACT\n      - metacyc.reaction\n      - KEGG.MODULE ## M number\n\n  pathway:\n    is_a: biological process\n    mixins:\n      - ontology class\n    exact_mappings:\n      - PW:0000001\n      - WIKIDATA:Q4915012\n    narrow_mappings:\n      - SIO:010526\n      - GO:0007165\n    id_prefixes:\n      - GO\n      - REACT\n      - KEGG\n      - SMPDB\n      - MSigDB\n      - PHARMGKB.PATHWAYS\n      - WIKIPATHWAYS\n      - FB  # FlyBase FBgg*\n      - PANTHER.PATHWAY\n      - KEGG.PATHWAY\n      - ncats.bioplanet\n\n  physiological process:\n    aliases: [ 'physiology' ]\n    is_a: biological process\n    mixins:\n      - ontology class\n    close_mappings:\n    exact_mappings:\n      # Physiologic Function\n      - STY:T039\n      - WIKIDATA:Q30892994\n    narrow_mappings:\n      # Organism Function\n      - STY:T040\n      # Organ or Tissue Function\n      - STY:T042\n      # Cell Function\n      - STY:T043\n      # Genetic Function\n      - STY:T045\n    id_prefixes:\n      - GO\n      - REACT\n\n  behavior:\n    is_a: biological process\n    mixins:\n      - ontology class\n      - activity and behavior\n    exact_mappings:\n      - GO:0007610\n      # Behavior\n      - STY:T053\n    narrow_mappings:\n      # Mental Process\n      - STY:T041\n      # Social Behavior\n      - STY:T054\n      # Individual Behavior\n      - STY:T055\n\n  ## (Bio)chemistry\n\n  processed material:\n    is_a: chemical mixture\n    description: >-\n      A chemical entity (often a mixture) processed\n      for consumption for nutritional, medical or technical use.\n      Is a material entity that is created or changed during material processing.\n    exact_mappings:\n      - OBI:0000047\n    id_prefixes:\n      - UMLS\n\n  drug:\n    is_a: molecular mixture\n    mixins:\n      - chemical or drug or treatment\n      - ontology class\n    description: >-\n      A substance intended for use in the diagnosis, cure,\n      mitigation, treatment, or prevention of disease\n    comments:\n      - The CHEBI ID represents a role rather than a substance\n    broad_mappings:\n      # Pharmacologic Substance: Any natural, endogenously-derived,\n      # synthetic or semi synthetic compound with pharmacologic activity.\n      - STY:T121\n    exact_mappings:\n      - WIKIDATA:Q12140\n      - CHEBI:23888\n      # UMLS Semantic Type \"Clinical Drug\"\n      - STY:T200\n      - dcid:Drug\n    narrow_mappings:\n      # Antibiotic\n      - STY:T195\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n\n  ## Food\n\n  environmental food contaminant:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:78299\n\n  food additive:\n    is_a: chemical entity\n    related_mappings:\n      # substance role\n      - CHEBI:64047\n\n  food:\n    is_a: chemical mixture\n    description: >-\n      A substance consumed by a living organism as a source of nutrition\n    id_prefixes:\n      - foodb.food\n      - FOODON\n      - UMLS\n      - NCIT\n    exact_mappings:\n      # Food\n      - STY:T168\n\n  ## Biology and Biomedical Sciences\n\n  ## Biological Attributes\n\n  organism attribute:\n    is_a: attribute\n    description: >-\n      describes a characteristic of an organismal entity.\n    exact_mappings:\n      # Organism Attribute\n      - STY:T032\n\n  phenotypic quality:\n    aliases: [ 'phenotypic properties' ]\n    is_a: organism attribute\n    description: >-\n      A property of a phenotype\n    examples:\n      - value: weight\n\n    mappings:\n      - PATO:0000001\n\n  genetic inheritance:\n    aliases: [ 'inheritance' ]\n    is_a: biological entity\n    description: >-\n      The pattern or 'mode' in which a particular genetic trait or disorder is passed from one\n      generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\n    exact_mappings:\n      - HP:0000005\n      - GENO:0000141\n      - NCIT:C45827\n    close_mappings:\n      - STY:T045\n    id_prefixes:\n      - HP\n      - GENO\n      - NCIT\n\n  ## Biological Entities\n\n  organismal entity:\n    description: >-\n      A named entity that is either a part of an organism, a whole organism,\n      population or clade of organisms, excluding chemical entities\n    abstract: true\n    is_a: biological entity\n    mixins:\n      - subject of investigation\n    slot_usage:\n      has attribute:\n        description: >-\n          may often be an organism attribute\n    exact_mappings:\n      - WIKIDATA:Q7239\n      # UMLS Semantic Group \"Living Beings\"\n      # Several of the associated semantic types here are probably not\n      # that relevant to the Biolink world, but we keep them here for now.\n      - UMLSSG:LIVB\n      - CARO:0001010\n\n  virus:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A virus is a microorganism that replicates itself as a microRNA\n      and infects the host cell.\n    exact_mappings:\n      - NCBITaxon:10239\n\n  cellular organism:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n    exact_mappings:\n      - NCBITaxon:131567\n\n  life stage:\n    is_a: organismal entity\n    description: >-\n      A stage of development or growth of an organism,\n      including post-natal adult stages\n    exact_mappings:\n      - UBERON:0000105\n    narrow_mappings:\n      # constrained to human life cycles\n      - HsapDv:0000000\n    in_subset:\n      - model_organism_database\n    id_prefixes:\n      - HsapDv\n      - MmusDv\n      - ZFS\n      - FBdv\n      - WBls\n      - UBERON\n\n  individual organism:\n    aliases: [ 'organism' ]\n    description: >-\n      An instance of an organism. For example, Richard Nixon,\n      Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - SIO:010000\n      # Organism\n      - STY:T001\n    narrow_mappings:\n      # Wikidata considers its definition of 'individual' to be constrained to human persons?\n      - WIKIDATA:Q795052\n      - foaf:Person\n    id_prefixes:\n      - ORCID\n\n  population of individual organisms:\n    description: >-\n      A collection of individuals from the same taxonomic class\n      distinguished by one or more characteristics.  Characteristics can\n      include, but are not limited to, shared geographic location, genetics,\n      phenotypes.\n    local_names:\n      ga4gh: population\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - PCO:0000001\n      - SIO:001061\n      # UMLS Semantic Type \"Population Group\"\n      - STY:T098\n      - OBI:0000181\n    id_prefixes:\n      - HANCESTRO\n    in_subset:\n      - model_organism_database\n\n  disease or phenotypic feature:\n    aliases: [ 'phenome' ]\n    is_a: biological entity\n    description: >-\n      Either one of a disease or an individual phenotypic feature.\n      Some knowledge resources such as Monarch treat these as\n      distinct, others such as MESH conflate.  Please see definitions of phenotypic feature and disease in this model\n      for their independent descriptions.  This class is helpful to enforce domains and ranges  \n      that may involve either a disease or a phenotypic feature.\n    union_of:\n      - disease\n      - phenotypic feature\n    narrow_mappings:\n      # UMLS Semantic Type \"Finding\" - more specialized use of 'disease or phenotypic feature'\n      - STY:T033\n\n  disease:\n    aliases: [ 'condition', 'disorder', 'medical condition' ]\n    description: >-\n      A disorder of structure or function, especially one that produces specific \n      signs, phenotypes or symptoms or that affects a specific location and is not simply a \n      direct result of physical injury.  A disposition to undergo pathological processes that exists in an \n      organism because of one or more disorders in that organism.\n    is_a: disease or phenotypic feature\n    exact_mappings:\n      - MONDO:0000001\n      - DOID:4\n      - NCIT:C2991\n      - WIKIDATA:Q12136\n      - SIO:010299\n      # UMLS Semantic Group \"Disorders\"\n      - UMLSSG:DISO\n      # Disease or Syndrome\n      - STY:T047\n      - dcid:Disease\n    narrow_mappings:\n      # Congenital Abnormality\n      - STY:T019\n      # Acquired Abnormality\n      - STY:T020\n      # Mental or Behavioral Dysfunction\n      - STY:T048\n      # Cell or Molecular Dysfunction\n      - STY:T049\n      # Anatomical Abnormality\n      - STY:T190\n      # Neoplastic Process\n      - STY:T191\n      # disease susceptibility\n      - MONDO:0042489\n    id_prefixes:\n      - MONDO\n      - DOID\n      - OMIM\n      - OMIM.PS\n      - orphanet\n      - EFO\n      - UMLS\n      - MESH\n      - MEDDRA\n      - NCIT\n      - SNOMEDCT\n      - medgen\n      - ICD10\n      - ICD9\n      - KEGG.DISEASE ## H number\n      - HP\n      - MP\n    in_subset:\n      - model_organism_database\n\n  phenotypic feature:\n    aliases: [ 'sign', 'symptom', 'phenotype', 'trait', 'endophenotype' ]\n    is_a: disease or phenotypic feature\n    description: >-\n      A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an \n      individual resulting from the interaction of its genotype with its molecular and physical environment.\n    examples:\n      - value: MP:0001262\n        description: decreased body weight\n    exact_mappings:\n      - UPHENO:0001001\n      - SIO:010056\n      - WIKIDATA:Q104053\n      - UMLS:C4021819\n      - NCIT:C16977\n      - SNOMEDCT:8116006 # documented as phenotypic finding and phenotype, also referred to as \"SCTID:8116006\" at SNOMEDCT\n      - MESH:D010641 # phenotype\n    narrow_mappings:\n      - STY:T184 # Sign or Symptom\n      - WIKIDATA:Q169872 # Sign or Symptom\n      # presentation of a disease in clinical medicine\n      - WIKIDATA:Q25203551\n      - ZP:00000000 # zebrafish phenotype\n      - FBcv:0001347 # fly phenotype\n      - HP:0000118 # human phenotype\n      - MP:0000001 # mouse phenotype\n      - WBPhenotype:0000886 # worm phenotype\n      - XPO:00000000 # frog phenotype\n      - FYPO:0000001 # fission yeast phenotype\n      - APO:0000017 # phenotype\n      - TO:0000387 # more narrowly defined here for plants; our definition conflates trait and phenotype.\n    broad_mappings:\n      - BFO:0000019 # quality\n      - PATO:0000001 # quality\n    id_prefixes:\n      - HP\n      - EFO # covered by BFO quality mapping\n      - NCIT\n      - UMLS\n      - MEDDRA # can not find a mapping\n      - MP\n      - ZP\n      - UPHENO\n      - APO\n      - FBcv\n      - WBPhenotype\n      - SNOMEDCT\n      - MESH\n      - XPO\n      - FYPO\n      - TO\n    in_subset:\n      - model_organism_database\n\n  behavioral feature:\n    description: >-\n      A phenotypic feature which is behavioral in nature.\n    is_a: phenotypic feature\n    exact_mappings:\n      - NBO:0000243\n\n  anatomical entity:\n    is_a: organismal entity\n    mixins:\n      - physical essence\n    description: >-\n      A subcellular location, cell type or gross anatomical part\n    exact_mappings:\n      - UBERON:0001062\n      - WIKIDATA:Q4936952\n      # UMLS Semantic Group \"Anatomy\"\n      - UMLSSG:ANAT\n      # UMLS Semantic Type \"Anatomical Structure\"\n      - STY:T017\n      - FMA:62955 # anatomical entity\n      - CARO:0000000  # anatomical entity\n      - SIO:001262 # anatomical entity\n    narrow_mappings:\n      - ZFA:0100000 # zebrafish anatomical entity\n      - FBbt:10000000 # fly anatomical entity\n      - EMAPA:0 # mouse anatomical entity\n      - MA:0000001 # mouse anatomical entity\n      - XAO:0000000 # frog anatomical entity\n      - WBbt:0000100 # c. elegans anatomical entity\n      - NCIT:C12219 # human anatomical entity\n      - GO:0110165 # cellular anatomical entity, also used directly in CL\n    related_mappings:\n      - SNOMEDCT:123037004 # body structure\n    id_prefixes:\n      - UBERON\n      - GO\n      - CL\n      - UMLS\n      - MESH\n      - NCIT\n      - EMAPA\n      - ZFA\n      - FBbt\n      - WBbt\n    in_subset:\n      - model_organism_database\n\n  cellular component:\n    aliases: [ 'cell component', 'cell part' ]\n    is_a: anatomical entity\n    description: >-\n      A location in or around a cell\n    exact_mappings:\n      - GO:0005575\n      - SIO:001400\n      - WIKIDATA:Q5058355\n      # Cell Component\n      - STY:T026\n    broad_mappings:\n      - WIKIDATA:P681\n    id_prefixes:\n      - GO\n      - MESH\n      - UMLS\n      - NCIT\n      - SNOMEDCT\n      - CL\n      - UBERON\n\n  cell:\n    is_a: anatomical entity\n    exact_mappings:\n      - GO:0005623\n      - CL:0000000\n      - SIO:010001\n      - WIKIDATA:Q7868\n      # UMLS Semantic Type \"Cell\"\n      - STY:T025\n      - MESH:D002477 # cells\n    id_prefixes:\n      - CL\n      - PO\n      - UMLS\n      - NCIT\n      - MESH\n      - UBERON\n      - SNOMEDCT\n      - MESH\n\n  cell line:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - CLO:0000031\n    id_prefixes:\n      - CLO\n\n  gross anatomical structure:\n    aliases: [ 'tissue', 'organ' ]\n    is_a: anatomical entity\n    exact_mappings:\n      - UBERON:0010000\n      - WIKIDATA:Q4936952\n    narrow_mappings:\n      # UMLS Semantic Type \"Body Part, Organ, or Organ Component\"\n      - STY:T023\n      # UMLS Semantic Type \"Tissue\"\n      - STY:T024\n      # Embryonic Structure\n      - STY:T018\n    id_prefixes:\n      - UBERON\n      - UMLS\n      - MESH\n      - NCIT\n      - PO\n      - FAO\n\n\n  ## entity mixins\n\n  chemical entity or gene or gene product:\n    description: >-\n      A union of chemical entities and children, and gene or gene product.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  chemical entity or protein or polypeptide:\n    description: >-\n      A union of chemical entities and children, and protein and polypeptide.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  macromolecular machine mixin:\n    description: >-\n      A union of gene locus, gene product, and macromolecular complex. These are\n      the basic units of function in a cell. They either carry out individual\n      biological activities, or they encode molecules which do this.\n    mixin: true\n    slots:\n      - name\n    slot_usage:\n      name:\n        range: symbol type\n        description: >-\n          genes are typically designated by a short symbol and a full name.\n          We map the symbol to the default display name\n          and use an additional slot for full name\n\n  gene or gene product:\n    description: >-\n      A union of gene loci or gene products.\n      Frequently an identifier for one will be used as proxy for another\n    is_a: macromolecular machine mixin\n    mixin: true\n    id_prefixes:\n      - CHEMBL.TARGET\n      - IUPHAR.FAMILY\n\n  gene:\n    description: >-\n      A region (or regions) that includes all of the sequence elements\n      necessary to encode a functional transcript. A gene locus may include\n      regulatory regions, transcribed regions and/or other\n      functional sequence regions.\n    is_a: biological entity\n    mixins:\n      - gene or gene product\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    slots:\n      - symbol\n      - synonym\n      - xref\n    exact_mappings:\n      - SO:0000704\n      - SIO:010035\n      - WIKIDATA:Q7187\n      - dcid:Gene\n    id_prefixes:\n      - NCBIGene\n      - ENSEMBL\n      - HGNC\n      - MGI\n      - ZFIN\n      - dictyBase\n      - WB\n      - WormBase # we have two prefixes here as wormbase supports WormBase:WBGene00000898\n      # and alliancegenome.org and identifiers.org supports WB:WBGene00000898.\n      - FB\n      - RGD\n      - SGD\n      - PomBase\n      - OMIM\n      - KEGG.GENE ## org:gene\n      - UMLS\n      - Xenbase\n      - AspGD\n    in_subset:\n      - translator_minimal\n      - model_organism_database\n    narrow_mappings:\n      - bioschemas:gene\n    broad_mappings:\n      - NCIT:C45822\n\n\n  gene product mixin:\n    description: >-\n      The functional molecular product of a single gene locus.\n      Gene products are either proteins or functional RNA molecules.\n    is_a: gene or gene product\n    mixin: true\n    slots:\n      - synonym\n      - xref\n    exact_mappings:\n      - WIKIDATA:Q424689\n      - GENO:0000907\n      - NCIT:C26548\n    id_prefixes:\n      - UniProtKB\n      - gtpo\n      - PR\n\n  gene product isoform mixin:\n    description: >-\n      This is an abstract class that can be mixed in with different kinds of\n      gene products to indicate that the gene product is intended to represent\n      a specific isoform rather than a canonical or reference or generic\n      product. The designation of canonical or reference may be arbitrary,\n      or it may represent the superclass of all isoforms.\n    is_a: gene product mixin\n    mixin: true\n\n  macromolecular complex:\n    description: >-\n      A stable assembly of two or more macromolecules, i.e. proteins,\n      nucleic acids, carbohydrates or lipids, in which at least one\n      component is a protein and the constituent parts function together.\n    is_a: biological entity\n    mixins:\n      - macromolecular machine mixin\n    exact_mappings:\n      - GO:0032991\n      - WIKIDATA:Q22325163\n    id_prefixes:\n      - INTACT\n      - GO\n      - PR\n      - REACT\n      - ComplexPortal\n    in_subset:\n      - model_organism_database\n\n  ## Genomic Classes\n  nucleosome modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform.\n      e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.\n    mixins:\n      - gene product isoform mixin\n      - genomic entity\n      - epigenomic entity\n\n  genome:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A genome is the sum of genetic material within a cell or virion.\n    exact_mappings:\n      - SO:0001026\n      - SIO:000984\n      - WIKIDATA:Q7020\n    close_mappings:\n      - dcid:GenomeAssemblyUnit\n    in_subset:\n      - model_organism_database\n\n  exon:\n    is_a: nucleic acid entity\n    description: >-\n      A region of the transcript sequence within a gene which is not\n      removed from the primary RNA transcript by RNA splicing.\n    exact_mappings:\n      - SO:0000147\n      - SIO:010445\n      - WIKIDATA:Q373027\n\n  transcript:\n    is_a: nucleic acid entity\n    description: >-\n      An RNA synthesized on a DNA or RNA template by an RNA polymerase.\n    exact_mappings:\n      - SO:0000673\n      - SIO:010450\n      - WIKIDATA:Q7243183\n      - dcid:RNATranscript\n    id_prefixes:\n      - ENSEMBL # ENSEMBL:ENST for human\n      - FB      # FlyBase:FBtr\n    in_subset:\n      - model_organism_database\n\n  coding sequence:\n    is_a: nucleic acid entity\n    exact_mappings:\n      - SO:0000316\n      - SIO:001390\n\n  polypeptide:\n    aliases: [ 'amino acid entity' ]\n    is_a: biological entity\n    description: >-\n      A polypeptide is a molecular entity characterized by availability\n      in protein databases of amino-acid-based sequence representations\n      of its precise primary structure; for convenience of representation,\n      partial sequences of various kinds are included, even if they do not\n      represent a physical molecule.\n    mixins:\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n    in_subset:\n      - model_organism_database\n    narrow_mappings:\n      - SO:0000104 # polypeptide definde in SO conflates protein and polypeptide\n      # Amino Acid, Peptide, or Protein\n      - STY:T116\n      # Amino Acid Sequence\n      - STY:T087\n\n  protein:\n    description: >-\n      A gene product that is composed of a chain of amino acid sequences\n      and is produced by ribosome-mediated translation of mRNA\n    is_a: polypeptide\n    mixins:\n      - gene product mixin\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL # ENSEMBL:ENSP*\n      - FB      # FlyBase FBpp*\n      - UMLS\n      - MESH\n      - ncats.drug\n    broad_mappings:\n      - bioschemas:Protein\n    exact_mappings:\n      - PR:000000001\n      - SIO:010043\n      - WIKIDATA:Q8054\n    narrow_mappings:\n      # Enzyme\n      - STY:T126\n      # Receptor\n      - STY:T192\n\n  protein isoform:\n    aliases: [ 'proteoform' ]\n    is_a: protein\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or\n      reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - UniProtKB # UniProtKB:([A-Z0-9]+-\\d+)\n      - UNIPROT.ISOFORM\n      - PR\n      - ENSEMBL\n\n  protein domain:\n    is_a: biological entity\n    description: >-\n      A conserved part of protein sequence and (tertiary) structure that can evolve,\n      function, and exist independently of the rest of the protein chain.\n      Protein domains maintain their structure and function independently of the proteins in which they are found.\n      e.g. an SH3 domain.\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    exact_mappings:\n      - NCIT:C13379\n      - SIO:001379\n      - UMLS:C1514562\n  \n  posttranslational modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a polypeptide or protein that occurs after translation. \n      e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, \n      protein ubiquitination.\n    mixins:\n      - gene product isoform mixin\n  \n  protein family:\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n\n  nucleic acid sequence motif:\n    aliases: [ 'consensus sequence' ]\n    is_a: biological entity\n    description: >-\n      A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have,\n      a biological significance. e.g. the TATA box promoter motif, transcription factor binding\n      consensus sequences.\n\n  RNA product:\n    is_a: transcript\n    mixins:\n      - gene product mixin\n    exact_mappings:\n      - CHEBI:33697\n      # This SIO term here also mapped to 'biolink:Transcript'; however,\n      # since this 'biolink:RNAProduct' relates more to the biochemical\n      # essence of RNA, then map the SIO term instead to 'biolink:Transcript'\n      # - SIO:010450\n      - WIKIDATA:Q11053\n    id_prefixes:\n      - RNACENTRAL\n\n  RNA product isoform:\n    is_a: RNA product\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or reference RNA\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - RNACENTRAL\n\n  noncoding RNA product:\n    is_a: RNA product\n    id_prefixes:\n      - RNACENTRAL\n      - NCBIGene\n      - ENSEMBL\n    exact_mappings:\n      - SO:0000655\n      - SIO:001235\n\n  microRNA:\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000276\n      - SIO:001397\n      - WIKIDATA:Q310899\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  siRNA:\n    aliases: [ 'small interfering RNA', 'RNAi' ]\n    description: >-\n      A small RNA molecule that is the product of a longer exogenous or\n      endogenous dsRNA, which is either a bimolecular duplex or very long\n      hairpin, processed (via the Dicer pathway) such that numerous siRNAs\n      accumulate from both strands of the dsRNA. SRNAs trigger the cleavage\n      of their target molecules.\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000646\n      - WIKIDATA:Q203221\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  gene grouping mixin:\n    description: >-\n      any grouping of multiple genes or gene products\n    mixin: true\n    slots:\n      - has gene or gene product\n\n  gene family:\n    aliases: [ 'orthogroup', 'protein family' ]\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      # These term definitions focus only on proteins;\n      # the 'biolink:GeneFamily' term would be more inclusive\n      # to describe gene loci, non-coding RNA, etc.\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    description: >-\n      any grouping of multiple genes or gene products related by common descent\n    id_prefixes:\n      - PANTHER.FAMILY\n      - HGNC.FAMILY\n      - FB       # FlyBase FBgg*\n      - interpro # note: may be better to introduce a protein domain/family\n      - CATH\n      - CDD\n      - HAMAP\n      - PFAM\n      - PIRSF\n      - PRINTS\n      - PRODOM\n      - PROSITE\n      - SMART\n      - SUPFAM\n      - TIGRFAM\n      - CATH.SUPERFAMILY\n      - RFAM ## RNAs only\n      - KEGG.ORTHOLOGY ## aka KEGG.KO: K number\n      - EGGNOG\n      - COG\n    in_subset:\n      - model_organism_database\n\n  zygosity:\n    is_a: attribute\n    exact_mappings:\n      - GENO:0000133\n\n  genotype:\n    is_a: biological entity\n    mixins:\n      - physical essence\n      - genomic entity\n      - ontology class\n    description: >-\n      An information content entity that describes a genome by specifying the\n      total variation in genomic sequence and/or gene expression, relative to\n      some established background\n    comments:\n      - Consider renaming as genotypic entity\n    slots:\n      - has zygosity\n    exact_mappings:\n      - GENO:0000536\n      - SIO:001079\n    id_prefixes:\n      - ZFIN\n      - FB   # FlyBase FBba*\n    in_subset:\n      - model_organism_database\n\n  haplotype:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A set of zero or more Alleles on a single instance of a Sequence[VMC]\n    #    slots:\n    #      - completeness\n    exact_mappings:\n      - GENO:0000871\n      - SO:0001024\n      - VMC:Haplotype\n\n  sequence variant:\n    aliases: [ 'allele' ]\n    local_names:\n      agr: allele\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.\n    comments:\n      - This class is for modeling the specific state at a locus.\n        A single DBSNP rs ID could correspond to more than one sequence variants\n        (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\n    exact_mappings:\n      # slightly broader semantics than SO:0001059 - 'sequence alteration'\n      # describes a sequence feature that may have 1..* sequence alterations\n      - WIKIDATA:Q15304597\n    close_mappings:\n      - dcid:Allele\n      - SO:0001060\n      - VMC:Allele\n      - GENO:0000002\n      - SIO:010277\n      - SO:0001060\n    id_prefixes:\n      - CAID # ClinGen Allele Registry\n      - CLINVAR\n      - WIKIDATA\n      # - CIViC needs IRI mapping\n      - DBSNP\n      - MGI\n      - ZFIN\n      - FB\n      - RGD\n      - AGRKB\n      - SPDI\n      - WB\n      - WormBase\n    alt_descriptions:\n      AGR: >-\n        An entity that describes a single affected, endogenous allele.\n        These can be of any type that matches that definition\n      VMC: >-\n        A contiguous change at a Location\n    slots:\n      - has gene\n    slot_usage:\n      has gene:\n        multivalued: true\n        description: Each allele can be associated with any number of genes\n      has biological sequence:\n        description: >-\n          The state of the sequence w.r.t a reference sequence\n      id:\n        examples:\n          - value: ZFIN:ZDB-ALT-980203-1091\n            description: ti282a allele from ZFIN\n          - value: CLINVAR:17681\n            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\n    in_subset:\n      - model_organism_database\n\n  snv:\n    aliases: [ 'single nucleotide variant', 'single nucleotide polymorphism', 'snp' ]\n    is_a: sequence variant\n    description: >-\n      SNVs are single nucleotide positions in genomic DNA at\n      which different sequence alternatives exist\n    exact_mappings:\n      - SO:0001483\n\n  reagent targeted gene:\n    aliases: [ 'sequence targeting reagent' ]\n    is_a: biological entity\n    description: >-\n      A gene altered in its expression level in the context of some\n      experiment as a result of being targeted by gene-knockdown\n      reagent(s) such as a morpholino or RNAi.\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - GENO:0000504\n    in_subset:\n      - model_organism_database\n\n  ## --------------------\n  ## Clinical\n  ## Attributes, Cohort,\n  ## Exposures & Outcomes\n  ## --------------------\n\n  ## Clinical Attributes\n\n  clinical attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a clinical manifestation\n    exact_mappings:\n      # Clinical Attribute\n      - STY:T201\n\n  clinical measurement:\n    is_a: clinical attribute\n    description: >-\n      A clinical measurement is a special kind of attribute which results\n      from a laboratory observation from a subject individual or sample.\n      Measurements can be connected to their subject by the 'has attribute' slot.\n    slot_usage:\n      has attribute type:\n        required: true\n        multivalued: false\n        values_from:\n          - EFO\n          - LOINC\n    exact_mappings:\n      - EFO:0001444\n\n  clinical modifier:\n    is_a: clinical attribute\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the phenotypic abnormality sub-ontology, with respect\n      to severity, laterality, and other aspects\n    exact_mappings:\n\n\n  clinical course:\n    is_a: clinical attribute\n    description: >-\n      The course a disease typically takes from its onset, progression in time, and\n      eventual resolution or death of the affected individual\n    exact_mappings:\n      - HP:0031797\n\n  onset:\n    is_a: clinical course\n    description: >-\n      The age group in which (disease) symptom manifestations appear\n    exact_mappings:\n      - HP:0003674\n\n  clinical entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists in the clinical domain and outside the\n      biological realm. Diseases are placed under biological entities\n\n  clinical trial:\n    is_a: clinical entity\n\n  clinical intervention:\n    is_a: clinical entity\n\n  clinical finding:\n    is_a: phenotypic feature\n    description: >-\n      this category is currently considered broad enough to tag clinical lab\n      measurements and other biological attributes taken as 'clinical traits'\n      with some statistical score, for example, a p value in genetic associations.\n    slot_usage:\n      has attribute:\n        range: clinical attribute\n    id_prefixes:\n      - LOINC\n      - NCIT\n      - EFO\n\n  hospitalization:\n    is_a: clinical intervention\n    exact_mappings:\n      - SNOMEDCT:32485007\n      - WIKIDATA:Q3140971\n\n  socioeconomic attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a socioeconomic manifestation\n    #slot_usage:\n    # need a suitable qualifying socioeconomic ontology target here?\n    # Perhaps some subset of ECTO: https://github.com/EnvironmentOntology/environmental-exposure-ontology\n    #  has attribute type:\n    #     range: socioeconomic ontology\n    # exact_mappings:\n    #  - ??\n\n  ## Cohorts\n\n  case:\n    aliases: [ 'patient', 'proband' ]\n    is_a: individual organism\n    description: >-\n      An individual (human) organism that has a patient role in some clinical context.\n    mixins:\n      - subject of investigation\n\n  cohort:\n    is_a: study population\n    description: >-\n      A group of people banded together or treated as a group who share common characteristics.\n      A cohort 'study' is a particular form of longitudinal study that samples a cohort,\n      performing a cross-section at intervals through time.\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - WIKIDATA:Q1303415\n    narrow_mappings:\n      # Professional or Occupational Group\n      - STY:T097\n      # Family Group\n      - STY:T099\n      # Age Group\n      - STY:T100\n      # Patient or Disabled Group\n      - STY:T101\n\n  ## Exposures\n\n  exposure event:\n    is_a: ontology class\n    aliases: [ 'exposure', 'experimental condition' ]\n    mixin: true\n    slots:\n      - timepoint\n    description: >-\n      A (possibly time bounded) incidence of a feature of the environment of an organism that\n      influences one or more phenotypic features of that organism, potentially mediated by genes\n    exact_mappings:\n      - XCO:0000000\n    in_subset:\n      - model_organism_database\n\n  # TODO - confirm that genomic backgrounds are exposures\n  genomic background exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - gene grouping mixin\n      - physical essence\n      - genomic entity\n      - thing with taxon\n      - ontology class\n    description: >-\n      A genomic background exposure is where an individual's specific genomic background\n      of genes, sequence variants or other pre-existing genomic conditions constitute\n      a kind of 'exposure' to the organism, leading to or influencing an outcome.\n\n  pathological entity mixin:\n    description: >-\n      A pathological (abnormal) structure or process.\n    mixin: true\n    exact_mappings:\n      - MPATH:0\n    narrow_mappings:\n      - HP:0000118\n\n  pathological process:\n    description: >-\n      A biologic function or a process having an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: biological process\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - OBI:1110122\n      - NCIT:C16956\n    narrow_mappings:\n      # metastasis\n      - NCIT:C19151\n      - EFO:0009708\n      - STY:T046\n      - STY:T037\n\n  pathological process exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A pathological process, when viewed as an exposure, representing\n      a precondition, leading to or influencing an outcome,\n      e.g. autoimmunity leading to disease.\n\n  pathological anatomical structure:\n    description: >-\n      An anatomical structure with the potential of have an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: anatomical entity\n    mixins:\n      - pathological entity mixin\n\n  pathological anatomical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      An abnormal anatomical structure, when viewed as an exposure,\n      representing an precondition, leading to or influencing an outcome,\n      e.g. thrombosis leading to an ischemic disease outcome.\n\n  disease or phenotypic feature exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - pathological entity mixin\n    description: >-\n      A disease or phenotypic feature state, when viewed as an exposure,\n      represents an precondition, leading to or influencing an outcome,\n      e.g. HIV predisposing an individual to infections; a relative deficiency\n      of skin pigmentation predisposing an individual to skin cancer.\n\n  chemical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    slots:\n      - has quantitative value\n    description: >-\n      A chemical exposure is an intake of a particular\n      chemical entity.\n    exact_mappings:\n      # this ECTO term is not visibly defined but\n      # the 9000000-series identifiers seems to be the\n      # numeric space of chemical exposure definitions\n      - ECTO:9000000\n      - SIO:001399\n\n  complex chemical exposure:\n    is_a: attribute\n    description: >-\n      A complex chemical exposure is an intake of a chemical\n      mixture (e.g. gasoline), other than a drug.\n\n  drug exposure:\n    is_a: chemical exposure\n    aliases: [ 'drug intake', 'drug dose', 'medication intake' ]\n    description: >-\n      A drug exposure is an intake of a particular drug.\n    mixins:\n      - exposure event\n    broad_mappings:\n      # slightly broader than just drug effects on a biological system\n      - SIO:001005\n    exact_mappings:\n      - ECTO:0000509\n\n  # TODO: deprecate?\n  drug to gene interaction exposure:\n    description: >-\n      drug to gene interaction exposure is a drug exposure is where the\n      interactions of the drug with specific genes are known to constitute\n      an 'exposure' to the organism, leading to or influencing an outcome.\n    is_a: drug exposure\n    mixins:\n      - gene grouping mixin\n\n  treatment:\n    aliases: [ 'medical action', 'medical intervention' ]\n    # 'named thing' seems too generic here but not sure what applies better here\n    is_a: named thing\n    mixins:\n      - exposure event\n      - chemical or drug or treatment\n    description: >-\n      A treatment is targeted at a disease or phenotype and may involve\n      multiple drug 'exposures', medical devices and/or procedures\n    slots:\n      - has drug\n      - has device\n      - has procedure\n    exact_mappings:\n      - OGMS:0000090\n      - SIO:001398\n    broad_mappings:\n      - MAXO:0000058\n\n  biotic exposure:\n    is_a: attribute\n    aliases: [ 'viral exposure', 'bacterial exposure' ]\n    mixins:\n      - exposure event\n    description: >-\n      An external biotic exposure is an intake of (sometimes pathological)\n      biological organisms (including viruses).\n\n  geographic exposure:\n    is_a: environmental exposure\n    mixins:\n      - exposure event\n    description: >-\n      A geographic exposure is a factor relating to geographic\n      proximity to some impactful entity.\n    close_mappings:\n      - dcid:GeologicalEvent\n    narrow_mappings:\n      - dcid:IceStoremEvent\n      - dcid:LakeEffectSnowEvent\n      - dcid:LandslideEvent\n      - dcid:MarineDenseFogEvent\n      - dcid:MarineLighteningEvent\n      - dcid:MarineStrongWindEvent\n      - dcid:MarineThunderstormWindEvent\n      - dcid:StormEvent\n      - dcid:StormSurgeTideEvent\n      - dcid:StrongWindEvent\n      - dcid:ThunderstormWindEvent\n      - dcid:TornadoEvent\n      - dcid:TropicalDepressionEvent\n      - dcid:WinterStoremEvent\n\n  environmental exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A environmental exposure is a factor relating to abiotic processes\n      in the environment including sunlight (UV-B), atmospheric (heat,\n      cold, general pollution) and water-born contaminants.\n\n  behavioral exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A behavioral exposure is a factor relating to behavior impacting an individual.\n\n  socioeconomic exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A socioeconomic exposure is a factor relating to social and\n      financial status of an affected individual (e.g. poverty).\n    slot_usage:\n      has attribute:\n        range: socioeconomic attribute\n        required: true\n\n  ## Outcomes\n\n  outcome:\n    mixin: true\n    description: >-\n      An entity that has the role of being the consequence of an exposure event.\n      This is an abstract mixin grouping of various categories of possible\n      biological or non-biological (e.g. clinical) outcomes.\n\n  pathological process outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of a pathological process.\n\n  pathological anatomical outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of an abnormal anatomical structure.\n\n  disease or phenotypic feature outcome:\n    mixins:\n      - outcome\n    description: >-\n      Physiological outcomes resulting from an exposure event which\n      is the manifestation of a disease or other characteristic phenotype.\n\n  behavioral outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the manifestation of human behavior.\n\n  hospitalization outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the increased manifestation of acute (e.g. emergency\n      room visit) or chronic (inpatient) hospitalization.\n\n  mortality outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome of death from resulting from an exposure event.\n\n  epidemiological outcome:\n    mixins:\n      - outcome\n    description: >-\n      An epidemiological outcome, such as societal disease\n      burden, resulting from an exposure event.\n    related_mappings:\n      - NCIT:C19291\n\n  socioeconomic outcome:\n    mixins:\n      - outcome\n    description: >-\n      An general social or economic outcome, such as\n      healthcare costs, utilization, etc., resulting from an exposure event\n\n  ## ------------\n  ## ASSOCIATIONS\n  ## ------------\n\n  association:\n    is_a: entity\n    description: >-\n      A typed association between two entities, supported by evidence\n    comments:\n      - This is roughly the model used by biolink and ontobio at the moment\n    slots:\n      - subject\n      - predicate\n      - object\n      - negated\n      - qualifiers\n      - publications\n      - has evidence\n      - knowledge source\n      - primary knowledge source\n      - aggregator knowledge source\n      - timepoint\n      - original subject\n      - original predicate\n      - original object\n    slot_usage:\n      type:\n        description: rdf:type of biolink:Association should be fixed at rdf:Statement\n      category:\n        range: category type\n        required: false\n    exact_mappings:\n      - OBAN:association\n      - rdf:Statement\n      - owl:Axiom\n\n\n  chemical entity assesses named thing association:\n    is_a: association\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: assesses\n\n\n  contributor association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      Any association between an entity (such as a publication)\n      and various agents that contribute to its realisation\n    slot_usage:\n      subject:\n        range: information content entity\n        description: >-\n          information content entity which an agent has helped realise\n      predicate:\n        subproperty_of: contributor\n        description: >-\n          generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\n      object:\n        range: agent\n        description: >-\n          agent helping to realise the given entity (e.g. such as a publication)\n      qualifiers:\n        description: >-\n          this field can be used to annotate special characteristics of an\n          agent relationship, such as the fact that a given author agent of\n          a publication is the 'corresponding author'\n\n  genotype to genotype part association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a genotypic entity that is a sub-component of it\n    slot_usage:\n      predicate:\n        subproperty_of: has variant part\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: genotype\n        description: >-\n          child genotype\n\n  genotype to gene association:\n    description: >-\n      Any association between a genotype and a gene.\n      The genotype have have multiple variants in that gene or a single one.\n      There is no assumption of cardinality\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: gene\n        description: >-\n          gene implicated in genotype\n\n  genotype to variant association:\n    description: >-\n      Any association between a genotype and a sequence variant.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: sequence variant\n        description: >-\n          gene implicated in genotype\n\n  gene to gene association:\n    aliases: [ 'molecular or genetic interaction' ]\n    description: >-\n      abstract parent class for different kinds of gene-gene or gene product\n      to gene product relationships. Includes homology and interaction.\n    abstract: true\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          the subject gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n      object:\n        range: gene or gene product\n        description: >-\n          the object gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n\n  gene to gene homology association:\n    description: >-\n      A homology association between two genes. May be orthology (in which\n      case the species of subject and object should differ) or paralogy\n      (in which case the species may be the same)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n      predicate:\n        subproperty_of: homologous to\n        symmetric: true\n        description: >-\n          homology relationship type\n      object:\n        range: gene or gene product\n\n  gene to gene family association:\n    description: >-\n      Set membership of a gene in a family of genes related by common\n      evolutionary ancestry usually inferred by sequence comparisons.\n      The genes in a given family generally share common sequence motifs which\n      generally map onto shared gene product structure-function relationships.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene family\n      predicate:\n        subproperty_of: member of\n        symmetric: false\n        description: >-\n          membership of the gene in the given gene family.\n\n  gene expression mixin:\n    description: >-\n      Observed gene expression intensity, context (site, stage) and\n      associated phenotypic status within which the expression occurs.\n    mixin: true\n    slots:\n      - quantifier qualifier\n      - expression site\n      - stage qualifier\n      - phenotypic state\n    slot_usage:\n      quantifier qualifier:\n        description: >-\n          Optional quantitative value indicating degree of expression.\n\n  gene to gene coexpression association:\n    description: >-\n      Indicates that two genes are co-expressed,\n      generally under the same conditions.\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: coexpressed with\n        symmetric: true\n\n  pairwise gene to gene interaction:\n    description: >-\n      An interaction between two genes or two gene products.\n      May be physical (e.g. protein binding) or genetic (between genes).\n      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      predicate:\n        subproperty_of: interacts with\n        symmetric: true\n        description: \"interaction relationship type\"\n    narrow_mappings:\n      - dcid:ProteinProteinInteraction\n\n  pairwise molecular interaction:\n    description: >-\n      An interaction at the molecular level between two physical entities\n    is_a: pairwise gene to gene interaction\n    slots:\n      - interacting molecules category\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: molecular entity\n      id:\n        description: >-\n          identifier for the interaction. This may come from an interaction database such as IMEX.\n        examples:\n          - value: WB:WBInteraction000538741\n        values_from:\n          - IMEX\n          - BioGRID\n      predicate:\n        subproperty_of: interacts with\n        description: \"interaction relationship type\"\n        examples:\n          - value: RO:0002447\n            description: the subject molecular phosphorylates the object molecule\n      object:\n        range: molecular entity\n\n  cell line to entity association mixin:\n    description: >-\n      An relationship between a cell line and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: cell line\n\n  # TODO: figure out what gives with subject range\n  cell line to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - cell line to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    description: >-\n      An relationship between a cell line and a disease or a phenotype, where\n      the cell line is derived from an individual with that disease or phenotype.\n    slot_usage:\n      subject:\n        #        - range: cell line\n        #        - range: disease or phenotypic feature\n        range: disease or phenotypic feature\n\n  chemical entity to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity that is an interactor\"\n\n  drug to entity association mixin:\n    description: >-\n      An interaction between a drug and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: drug\n        description: \"the drug that is an interactor\"\n\n  chemical to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity or entity that is an interactor\"\n\n  case to entity association mixin:\n    description: >-\n      An abstract association for use where the case is the subject\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: case\n        description: \"the case (e.g. patient) that has the property\"\n\n  chemical to chemical association:\n    description: >-\n      A relationship between two chemical entities. This can encompass actual\n      interactions as well as temporal causal edges, e.g. one chemical converted to another.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: chemical entity\n        description: \"the chemical element that is the target of the statement\"\n\n  reaction to participant association:\n    description:\n    is_a: chemical to chemical association\n    slots:\n      - stoichiometry\n      - reaction direction\n      - reaction side\n    slot_usage:\n      subject:\n        range: molecular entity\n    defining_slots:\n      - subject\n      - predicate\n      - object\n\n  reaction to catalyst association:\n    description:\n    is_a: reaction to participant association\n    slot_usage:\n      object:\n        range: gene or gene product\n\n  chemical to chemical derivation association:\n    description: >-\n      A causal relationship between two chemical entities, where the subject\n      represents the upstream entity and the object represents the downstream.\n      For any such association there is an implicit reaction:\n        IF\n        R has-input C1 AND\n        R has-output C2 AND\n        R enabled-by P AND\n        R type Reaction\n        THEN\n        C1 derives-into C2 <>\n    is_a: chemical to chemical association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - catalyst qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: >-\n          the upstream chemical entity\n      object:\n        range: chemical entity\n        description: >-\n          the downstream chemical entity\n      predicate:\n        subproperty_of: derives into\n      catalyst qualifier:\n        description: >-\n          this connects the derivation edge to the chemical entity that\n          catalyzes the reaction that causes the subject chemical to\n          transform into the object chemical.\n\n  chemical to disease or phenotypic feature association:\n    description: >-\n      An interaction between a chemical entity and a phenotype or disease,\n      where the presence of the chemical gives rise to or exacerbates the phenotype.\n    is_a: association\n    narrow_mappings:\n      - SIO:000993\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"the disease or phenotype that is affected by the chemical\"\n\n  chemical or drug or treatment to disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary undesirable effect.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slots:\n      - FDA adverse event level\n    slot_usage:\n      predicate:\n        subproperty_of: has adverse event\n\n  chemical or drug or treatment side effect disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.\n    is_a: chemical or drug or treatment to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has side effect\n\n  gene to pathway association:\n    description: >-\n      An interaction between a gene or gene product and a biological process or pathway.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"the gene or gene product entity that participates or influences the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that includes or is affected by the gene or gene product\"\n\n  molecular activity to pathway association:\n    description: >-\n      Association that holds the relationship between a reaction and the pathway it participates in.\n    is_a: association\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: pathway\n      predicate:\n        subproperty_of: part of\n\n  chemical to pathway association:\n    description: >-\n      An interaction between a chemical entity and a biological process or pathway.\n    is_a: association\n    exact_mappings:\n      - SIO:001250\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: \"the chemical entity that is affecting the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that is affected by the chemical\"\n\n  named thing associated with likelihood of named thing association:\n    # TODO: better name\n    description: >-\n    is_a: association\n    defining_slots:\n      - subject\n      - subject aspect qualifier\n      - subject context qualifier\n      - predicate\n      - object\n      - object aspect qualifier\n      - object context qualifier\n      - population context qualifier\n    slot_usage:\n      predicate:\n        subproperty_of: associated with\n      subject aspect qualifier:\n      # TODO: range\n      subject context qualifier:\n        range: ontology class\n      object aspect qualifier:\n      # TODO: range\n      object context qualifier:\n        range: ontology class\n\n  chemical gene interaction association:\n    description: >-\n      describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical\n      effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type\n      (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)\n    is_a: association\n    exact_mappings:\n      - SIO:001257\n    mixins:\n      - chemical to entity association mixin\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object context qualifier\n      - anatomical context qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: gene or gene product\n      predicate:\n        subproperty_of: physically interacts with\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject context qualifier:\n        range: anatomical entity\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object context qualifier:\n        range: anatomical entity\n      anatomical context qualifier:\n        range: anatomical entity\n\n  chemical affects gene association:\n    description: >-\n      Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,\n      localization, processing, expression, etc.)\n    is_a: association\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject aspect qualifier\n      - subject context qualifier\n      - subject direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object aspect qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - qualified predicate\n    slot_usage:\n      subject:\n        range: chemical entity\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject context qualifier:\n        range: anatomical entity\n      subject direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n      qualified predicate:\n        subproperty_of: causes\n      object:\n        range: gene or gene product\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object aspect qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object context qualifier:\n        range: anatomical entity\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      causal mechanism qualifier:\n        range: CausalMechanismQualifierEnum\n      anatomical context qualifier:\n        range: anatomical entity\n      species context qualifier:\n        range: organism taxon\n\n  drug to gene association:\n    description: >-\n      An interaction between a drug and a gene or gene product.\n    is_a: association\n    related_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - drug to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: \"the gene or gene product that is affected by the drug\"\n\n  material sample to entity association mixin:\n    description: >-\n      An association between a material sample and something.\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n\n  material sample derivation association:\n    description: >-\n      An association between a material sample and\n      the material entity from which it is derived.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n      object:\n        description: >-\n          the material entity the sample was derived from. This may be another\n          material sample, or any other material entity, including for example\n          an organism, a geographic feature, or some environmental material.\n      predicate:\n        description: >-\n          derivation relationship\n        subproperty_of: derives from\n\n  material sample to disease or phenotypic feature association:\n    description: >-\n      An association between a material sample and a disease or phenotype.\n    is_a: association\n    mixins:\n      - material sample to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    defining_slots:\n      - subject\n      - object\n\n  disease to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease\n        description: \"disease class\"\n        values_from: [ 'mondo', 'omim', 'orphanet', 'ncit', 'doid' ]\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n\n  entity to exposure event association mixin:\n    description: >-\n      An association between some entity and an exposure event.\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: exposure event\n\n  disease to exposure event association:\n    description: >-\n      An association between an exposure event and a disease.\n    is_a: association\n    mixins:\n      - disease to entity association mixin\n      - entity to exposure event association mixin\n    defining_slots:\n      - subject\n      - object\n\n\n  entity to outcome association mixin:\n    description: >-\n      An association between some entity and an outcome\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: outcome\n\n  exposure event to outcome association:\n    description: >-\n      An association between an exposure event and an outcome.\n    is_a: association\n    mixins:\n      - entity to outcome association mixin\n    slots:\n      - population context qualifier\n      - temporal context qualifier\n    defining_slots:\n      - subject\n      - object\n\n  frequency qualifier mixin:\n    mixin: true\n    description: >-\n      Qualifier for frequency type associations\n    slots:\n      - frequency qualifier\n\n  entity to feature or disease qualifiers mixin:\n    description: >-\n      Qualifiers for entity to disease or phenotype associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - severity qualifier\n      - onset qualifier\n\n  entity to phenotypic feature association mixin:\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    mixins:\n      - frequency quantifier\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: phenotypic feature\n        values_from: [ 'upheno', 'hp', 'mp', 'wbphenotype' ]\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n    slots:\n      - sex qualifier\n\n  information content entity to named thing association:\n    description: >-\n      association between a named thing and a information content entity where the specific context\n      of the relationship between that named thing and the publication is unknown. For\n      example, model organisms databases often capture the knowledge that a gene is found in a\n      journal article, but not specifically the context in which that gene was documented in the article.\n      In these cases, this association with the accompanying predicate 'mentions' could be used.\n      Conversely, for more specific associations (like 'gene to disease association', the publication should\n      be captured as an edge property).\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        domain: publication\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: mentions\n    in_subset:\n      - model_organism_database\n\n  entity to disease association mixin:\n    description: >-\n      mixin class for any association whose object (target node) is a disease\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease\n        description: \"disease\"\n        examples:\n          - value: MONDO:0020066\n            description: \"Ehlers-Danlos syndrome\"\n\n  disease or phenotypic feature to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  disease or phenotypic feature to location association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      an anatomical entity, where the disease/feature manifests in that site.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      object:\n        range: anatomical entity\n        description: >-\n          anatomical entity in which the disease or feature is found.\n        examples:\n          - value: UBERON:0002048\n            description: \"lung\"\n\n  disease or phenotypic feature to genetic inheritance association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      its mode of (genetic) inheritance.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has mode of inheritance\n      object:\n        range: genetic inheritance\n        description: >-\n          genetic inheritance associated with the specified disease or phenotypic feature.\n        examples:\n          - value: HP:0001417\n            description: \"X-linked inheritance\"\n\n  entity to disease or phenotypic feature association mixin:\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  genotype to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: genotype\n        description: \"genotype that is the subject of the association\"\n\n  genotype to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a phenotypic feature, where having\n      the genotype confers the phenotype, either in isolation or through environment\n    mixins:\n      - entity to phenotypic feature association mixin\n      - genotype to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has phenotype\n      subject:\n        range: genotype\n        description: >-\n          genotype that is associated with the phenotypic feature\n\n  # ie: smoke exposure to coughing phenotype? is this a denormalization?\n  exposure event to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between an environment and a phenotypic feature,\n      where being in the environment influences the phenotype.\n    mixins:\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: exposure event\n\n  disease to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      An association between a disease and a phenotypic feature in which the\n      phenotypic feature is associated with the disease in some way.\n    mixins:\n      - entity to phenotypic feature association mixin\n      - disease to entity association mixin\n    close_mappings:\n      - dcid:DiseaseSymptomAssociation\n    slot_usage:\n      subject:\n        range: disease\n      object:\n        range: phenotypic feature\n\n  case to phenotypic feature association:\n    description: >-\n      An association between a case (e.g. individual patient) and a phenotypic\n      feature in which the individual has or has had the phenotype.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - case to entity association mixin\n\n  behavior to behavioral feature association:\n    description: >-\n      An association between an mixture behavior and\n      a behavioral feature manifested by\n      the individual exhibited or has exhibited the behavior.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: behavior\n        description: >-\n          behavior that is the subject of the association\n      object:\n        range: behavioral feature\n        description: >-\n          behavioral feature that is the object of the association\n    mixins:\n      - entity to phenotypic feature association mixin\n\n  gene to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene that is the subject of the association\n\n  variant to entity association mixin:\n    local_names:\n      ga4gh: variant annotation\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is associated with some other entity\n        examples:\n          - value: CLINVAR:38077\n            description: \"CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n          - value: ClinGen:CA024716\n            description: \"chr13:g.32921033G>C (hg19) in ClinGen\"\n\n  gene to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n      - WBVocab:Gene-Phenotype-Association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      object:\n        range: phenotypic feature\n\n  gene to disease association:\n    is_a: association\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n    exact_mappings:\n      - SIO:000983\n    close_mappings:\n      - dcid:DiseaseGeneAssociation\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease,\n          may be protective or causative or associative, or as a model\n      object:\n        range: disease\n\n  druggable gene to disease association:\n    is_a: gene to disease association\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease\n          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and\n          this leads to a protective or improving disease state.\n      predicate:\n        subproperty_of: target for\n      has evidence:\n        range: DruggableGeneCategoryEnum\n    defining_slots:\n      - subject\n      - object\n      - predicate\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n\n  variant to gene association:\n    description: >-\n      An association between a variant and a gene, where the variant has\n      a genetic association with the gene (i.e. is in linkage disequilibrium)\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - variant to entity association mixin\n    slot_usage:\n      object:\n        range: gene\n      predicate:\n        subproperty_of: genetic association\n\n  variant to gene expression association:\n    description: >-\n      An association between a variant and expression of a gene (i.e. e-QTL)\n    is_a: variant to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: affects\n\n  variant to population association:\n    description: >-\n      An association between a variant and a population, where the variant has\n      particular frequency in the population\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - frequency quantifier\n      - frequency qualifier mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          an allele that has a certain frequency in a given population\n        examples:\n          - value: \"NC_000017.11:g.43051071A>T\"\n            description: >-\n              17:41203088 A/C in gnomad\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that is observed to have the frequency\n        examples:\n          - value: HANCESTRO:0010\n            description: African\n      has quotient:\n        description: >-\n          frequency of allele in population, expressed as a number with allele\n          divided by number in reference population, aka allele frequency\n        examples:\n          - value: \"0.0001666\"\n      has count:\n        description: >-\n          number in object population that carry a particular allele, aka allele count\n        examples:\n          - value: \"4\"\n            description: 4 individuals in gnomad set\n      has total:\n        description: >-\n          number all populations that carry a particular allele, aka allele number\n        examples:\n          - value: \"24014\"\n            description: 24014 individuals in gnomad set\n\n  population to population association:\n    description: >-\n      An association between a two populations\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: population of individual organisms\n        description: >-\n          the population that form the subject of the association\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that form the object of the association\n      predicate:\n        # subproperty_of: ???\n        description: >-\n          A relationship type that holds between the subject and object\n          populations. Standard mereological relations can be used.\n          E.g. subject part-of object, subject overlaps object.\n          Derivation relationships can also be used\n\n  variant to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is\n          associated in some way with the phenotype state\n\n  variant to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a sequence variant in which the allele state\n          is associated in some way with the disease state\n        examples:\n          - value: CLINVAR:52241\n            description: \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that variant\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  genotype to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - genotype to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a genotype that is associated in some way with a disease state\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that genotype\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  model to disease association mixin:\n    description: >-\n      This mixin is used for any association class for which the subject\n      (source node) plays the role of a 'model', in that it recapitulates some\n      features of the disease in a way that is useful for studying the disease\n      outside a patient carrying the disease\n    mixin: true\n    slot_usage:\n      subject:\n        description: >-\n          The entity that serves as the model of the disease. This may be\n          an organism, a strain of organism, a genotype or variant that exhibits\n          similar features, or a gene that when mutated exhibits features of the disease\n      predicate:\n        subproperty_of: model of\n        description: >-\n          The relationship to the disease\n\n  gene as a model of disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be a model\n          organism ortholog of a known disease gene, or it may be a gene whose\n          mutants recapitulate core features of the disease.\n\n  variant as a model of disease association:\n    is_a: variant to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          A variant that has a role in modeling the disease.\n\n  genotype as a model of disease association:\n    is_a: genotype to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: genotype\n        description: >-\n          A genotype that has a role in modeling the disease.\n\n  cell line as a model of disease association:\n    is_a: cell line to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: cell line\n        description: >-\n          A cell line derived from an organismal entity with a disease state that is used\n          as a model of that disease.\n\n  organismal entity as a model of disease association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: organismal entity\n        description: >-\n          A organismal entity (strain, breed) with a predisposition to a disease, or bred/created\n          specifically to model a disease.\n\n  organism to organism association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: individual organism\n      object:\n        range: individual organism\n        description: >-\n          An association between two individual organisms.\n\n  taxon to taxon association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n        description: >-\n          An association between individuals of different taxa.\n\n  gene has variant that contributes to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - subject form or variant qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be\n          a model organism ortholog of a known disease gene, or it may be\n          a gene whose mutants recapitulate core features of the disease.\n      object:\n        range: disease\n      predicate:\n        subproperty_of: contributes to\n\n  gene to expression site association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      An association between a gene and a gene expression site,\n      possibly qualified by stage/timing info.\n    notes:\n      - \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n    see_also: \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n    slots:\n      - stage qualifier\n      - quantifier qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          Gene or gene product positively within the specified\n          anatomical entity (or subclass, i.e. cellular component) location.\n      object:\n        range: anatomical entity\n        description: \"location in which the gene is expressed\"\n        examples:\n          - value: UBERON:0002037\n            description: cerebellum\n      predicate:\n        description: \"expression relationship\"\n        subproperty_of: expressed in\n      stage qualifier:\n        range: life stage\n        description: \"stage at which the gene is expressed in the site\"\n        examples:\n          - value: UBERON:0000069\n            description: larval stage\n      quantifier qualifier:\n        description: >-\n          can be used to indicate magnitude, or also ranking\n\n  sequence variant modulates treatment association:\n    is_a: association\n    description: >-\n      An association between a sequence variant and a treatment or health intervention.\n      The treatment object itself encompasses both the disease and the drug used.\n    comments:\n      - An alternate way to model the same information could be via a qualifier\n    defining_slots:\n      - subject\n      - object\n    abstract: true\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: \"variant that modulates the treatment of some disease\"\n      object:\n        range: treatment\n        description: \"treatment whose efficacy is modulated by the subject variant\"\n\n  functional association:\n    is_a: association\n    description: >-\n      An association between a macromolecular machine mixin (gene, gene product or\n      complex of gene products) and either a molecular activity, a biological\n      process or a cellular location in which a function is executed.\n    slot_usage:\n      subject:\n        range: macromolecular machine mixin\n        description: >-\n          gene, product or macromolecular complex that\n          has the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n          - value: GO:0045211\n            description: postsynaptic membrane\n\n  macromolecular machine to entity association mixin:\n    description: >-\n      an association which has a macromolecular machine mixin as a subject\n    mixin: true\n    slot_usage:\n      subject:\n        domain: macromolecular machine mixin\n\n  macromolecular machine to molecular activity association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a molecular activity (as represented\n      in the GO molecular function branch), where the entity\n      carries out the activity, or contributes to its execution.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: molecular activity\n\n  macromolecular machine to biological process association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a biological process or pathway\n      (as represented in the GO biological process branch), where the entity\n      carries out some part of the process, regulates it, or acts upstream of it.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: biological process\n\n  macromolecular machine to cellular component association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a cellular component (as represented\n      in the GO cellular component branch), where the entity\n      carries out its function in the cellular component.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: cellular component\n\n  molecular activity to chemical entity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: chemical entity\n\n  molecular activity to molecular activity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: molecular activity\n\n\n  gene to go term association:\n    aliases: [ 'functional association' ]\n    is_a: functional association\n    exact_mappings:\n      - WBVocab:Gene-GO-Association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene\n        description: >-\n          gene, product or macromolecular complex that has\n          the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n\n  entity to disease association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  entity to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  ## -----------------\n  ## SEQUENCE FEATURES\n  ## -----------------\n\n  sequence association:\n    is_a: association\n    description: >-\n      An association between a sequence feature and a nucleic acid entity it is localized to.\n\n  genomic sequence localization:\n    is_a: sequence association\n    description: >-\n      A relationship between a sequence feature and a nucleic acid entity\n      it is localized to. The reference entity may be a chromosome,\n      chromosome region or information entity such as a contig.\n    slot_usage:\n      subject:\n        aliases: [ 'sequence feature' ]\n        range: nucleic acid entity\n      object:\n        aliases: [ 'reference' ]\n        range: nucleic acid entity # typically a chromosome use monochrom\n      predicate:\n        subproperty_of: has sequence location\n    slots:\n      - start interbase coordinate\n      - end interbase coordinate\n      - genome build\n      - strand\n      - phase\n    broad_mappings:\n      - dcid:Chromosome\n    exact_mappings:\n      - dcid:GenomeAnnotation\n\n  sequence feature relationship:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      For example, a particular exon is part of a particular transcript or gene\n    slot_usage:\n      subject:\n        range: nucleic acid entity\n      object:\n        range: nucleic acid entity # typically a chromosome\n    exact_mappings:\n      - CHADO:feature_relationship\n\n  transcript to gene relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is a collection of transcripts\n    slot_usage:\n      subject:\n        range: transcript\n      object:\n        range: gene\n\n  gene to gene product relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is transcribed and potentially translated to a gene product\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene product mixin\n      predicate:\n        subproperty_of: has gene product\n\n  exon to transcript relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A transcript is formed from multiple exons\n    slot_usage:\n      subject:\n        range: exon\n      object:\n        range: transcript\n\n  chemical entity or gene or gene product regulates gene association:\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slots:\n      - object direction qualifier\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n        subproperty_of: regulates\n      subject:\n        range: chemical entity or gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n      object direction qualifier:\n        range: DirectionQualifierEnum\n\n  anatomical entity to anatomical entity association: # schema: gocam\n    is_a: association\n    abstract: true\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: anatomical entity\n      object:\n        range: anatomical entity\n\n  anatomical entity to anatomical entity part of association:\n    #      schema: gocam\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is mereological, i.e the two entities are related by parthood. This\n      includes relationships between cellular components and cells, between\n      cells and tissues, tissues and whole organisms\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the part\n      object:\n        range: anatomical entity\n        description: >-\n          the whole\n      predicate:\n        subproperty_of: part of\n\n  anatomical entity to anatomical entity ontogenic association:\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is ontogenic, i.e. the two entities are related by development. A number\n      of different relationship types can be used to specify the precise\n      nature of the relationship.\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the structure at a later time\n      object:\n        range: anatomical entity\n        description: >-\n          the structure at an earlier time\n      predicate:\n        subproperty_of: develops from\n\n  organism taxon to entity association:\n    mixin: true\n    description: >-\n      An association between an organism taxon and another entity\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: organism taxon\n        description: >-\n          organism taxon that is the subject of the association\n\n  organism taxon to organism taxon association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    description: >-\n      A relationship between two organism taxon nodes\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n\n  organism taxon to organism taxon specialization:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      A child-parent relationship between two taxa.\n      For example: Homo sapiens subclass_of Homo\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: child taxon\n        description: >-\n          the more specific taxon\n      object:\n        range: organism taxon\n        role: parent taxon\n        description: >-\n          the more general taxon\n      predicate:\n        subproperty_of: subclass of\n\n  organism taxon to organism taxon interaction:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      An interaction relationship between two taxa. This may be a symbiotic\n      relationship (encompassing mutualism and parasitism), or it may be non-symbiotic.\n      Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens\n    defining_slots:\n      - predicate\n    slots:\n      - associated environmental context\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        range: organism taxon\n        role: interactee taxon\n        description: >-\n          the taxon that is the subject of the association\n      predicate:\n        subproperty_of: interacts with\n      associated environmental context:\n        description: >-\n          the environment in which the two taxa interact\n\n  organism taxon to environment association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        role: environmental context\n        description: >-\n          the environment in which the organism occurs\n      predicate:\n        description: >-\n          predicate describing the relationship between the taxon and the environment\n\nenums:\n\n  AnatomicalContextQualifierEnum:\n    reachable_from:\n      source_ontology: bioregistry:uberon\n      source_nodes:\n        - UBERON:0001062\n      is_direct: false\n      relationship_types:\n        - rdfs:subClassOf\n\n  DirectionQualifierEnum:\n    permissible_values:\n      increased:\n      upregulated:\n        is_a: increased\n        close_mappings:\n          - RO:0002336\n        exact_mappings:\n          - RO:0002213\n        narrow_mappings:\n          - RO:0004032\n          - RO:0004034\n          - RO:0002629\n      decreased:\n      downregulated:\n        is_a: decreased\n        exact_mappings:\n          - RO:0004035\n          - RO:0002212\n        close_mappings:\n          # This RTX contributed term is tagged as an inverse of this Biolink predicate\n          - RO:0002335\n        broad_mappings:\n          # This term is slightly broader in that it includes that A acts within B as well\n          - RO:0004033\n\n  ChemicalEntityDerivativeEnum:\n    permissible_values:\n      metabolite:\n\n  ChemicalOrGeneOrGeneProductFormOrVariantEnum:\n    permissible_values:\n      genetic_variant_form:\n        is_a: modified_form\n      modified_form:\n        is_a: genetic_variant_form\n      loss_of_function_variant_form:\n        is_a: genetic_variant_form\n      gain_of_function_variant_form:\n        is_a: genetic_variant_form\n      polymorphic_form:\n        is_a: genetic_variant_form\n      snp_form:\n        is_a: polymorphic_form\n      analog_form:\n        is_a: modified_form\n\n  GeneOrGeneProductOrChemicalPartQualifierEnum:\n    permissible_values:\n      3_prime_utr:\n      5_prime_utr:\n      polya_tail:\n      promoter:\n      enhancer:\n      exon:\n      intron:\n\n  GeneOrGeneProductOrChemicalEntityAspectEnum:\n    permissible_values:\n      activity_or_abundance:\n        description: >- \n          Used in cases where the specificity of the relationship can not be determined to be either activity \n          or abundance.  In general, a more specific value from this enumeration should be used.\n      abundance:\n        is_a: activity_or_abundance\n      activity:\n        is_a: activity_or_abundance\n      expression:\n        is_a: abundance\n      synthesis:\n        is_a: abundance\n      degradation:\n        is_a: abundance # negate the direction qualifier necessary.\n      cleavage:\n        is_a: degradation\n      hydrolysis:\n        is_a: degradation\n      metabolic_processing:\n      mutation_rate:\n      stability:\n      folding:\n      localization:\n      transport:\n      secretion:\n        is_a: transport\n      uptake:\n        is_a: transport\n      molecular_modification:\n      acetylation:\n        is_a: molecular_modification\n      acylation:\n        is_a: molecular_modification\n      alkylation:\n        is_a: molecular_modification\n      amination:\n        is_a: molecular_modification\n      carbamoylation:\n        is_a: molecular_modification\n      ethylation:\n        is_a: molecular_modification\n      glutathionylation:\n        is_a: molecular_modification\n      glycation:\n        is_a: molecular_modification\n      glycosylation:\n        is_a: molecular_modification\n      glucuronidation:\n        is_a: molecular_modification\n      n_linked_glycosylation:\n        is_a: molecular_modification\n      o_linked_glycosylation:\n        is_a: molecular_modification\n      hydroxylation:\n        is_a: molecular_modification\n      lipidation:\n        is_a: molecular_modification\n      farnesylation:\n        is_a: molecular_modification\n      geranoylation:\n        is_a: molecular_modification\n      myristoylation:\n        is_a: molecular_modification\n      palmitoylation:\n        is_a: molecular_modification\n      prenylation:\n        is_a: molecular_modification\n      methylation:\n        is_a: molecular_modification\n      nitrosation:\n        is_a: molecular_modification\n      nucleotidylation:\n        is_a: molecular_modification\n      phosphorylation:\n        is_a: molecular_modification\n      ribosylation:\n        is_a: molecular_modification\n      ADP-ribosylation:\n        is_a: molecular_modification\n      sulfation:\n        is_a: molecular_modification\n      sumoylation:\n        is_a: molecular_modification\n      ubiquitination:\n        is_a: molecular_modification\n      oxidation:\n        is_a: molecular_modification\n      reduction:\n        is_a: molecular_modification\n      carboxylation:\n        is_a: molecular_modification\n\n  CausalMechanismQualifierEnum:\n    permissible_values:\n      binding:\n        description: >-\n          A causal mechanism mediated by the direct contact between effector and target chemical or \n          biomolecular entity, which form a stable physical interaction.\n      inhibition:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to the target and negatively effects its normal function, \n          e.g. prevention of enzymatic reaction or activation of downstream pathway.\n        close_mappings:\n          - DGIdb:inhibitor\n          - SEMMEDDB:INHIBITS\n        narrow_mappings:\n          - DGIdb:blocker\n          - DGIdb:channel_blocker\n          - DGIdb:gating_inhibitor\n          - CHEMBL.MECHANISM:antisense_inhibitor\n          - CHEMBL.MECHANISM:blocker\n          - CHEMBL.MECHANISM:inhibitor\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - CHEMBL.MECHANISM:negative_modulator\n          - DGIdb:negative_modulator\n      antibody_inhibition:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which an antibody specifically binds to and interferes with the target.\n      antagonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist \n          through competing for the binding site.\n        close_mappings:\n          - DGIdb:antagonist\n          - CHEMBL.MECHANISM:antagonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:allosteric_antagonist\n      molecular_channel_blockage:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and prevents or reduces \n          transport of ions through it.\n      inverse_agonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes\n          its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.\n        close_mappings:\n          - CHEMBL.MECHANISM:inverse_agonist\n          - DGIdb:inverse_agonist\n      negative_allosteric_modulation:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a \n          receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - DGIdb:inhibitory_allosteric_modulator\n        narrow_mappings:\n          - DGIdb:negative_modulator\n      agonism:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an \n          endogenous ligand.\n        close_mappings:\n          - CHEMBL.MECHANISM:agonist\n          - DGIdb:agonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:partial_agonist\n          - DGIdb:partial_agonist\n      molecular_channel_opening:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and facilitates transport of \n          ions through it.\n        close_mappings:\n          - CHEMBL.MECHANISM:opener\n      positive_allosteric_modulation:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by \n          binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:positive_allosteric_modulator\n          - CHEMBL.MECHANISM:positive_modulator\n          - DGIdb:positive_allosteric_modulator\n        broad_mappings:\n          - DGIdb:modulator\n          - DGIdb:allosteric_modulator\n      potentiation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector  binds to and enhances or intensifies the effect of some \n          other chemical or drug on its target.\n        close_mappings:\n      activation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.\n        close_mappings:\n          - CHEMBL.MECHANISM:activator\n          - DGIdb:activator\n      inducer:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that \n          processes drugs in the body.\n        close_mappings:\n          - DGIdb:inducer\n      transcriptional_regulation:\n        description: >-\n          A causal mechanism mediated by through the control of target gene transcription\n      signaling_mediated_control:\n        description: >-\n          A causal mechanism mediated by the activation or control of signaling events that influence the some aspect \n          of the target entity (e.g. its activity, processing, transport, etc)\n      stabilization:\n        is_a: activation\n        close_mappings:\n          - CHEMBL.MECHANISM:stabiliser\n      stimulation:\n        is_a: activation\n        close_mappings:\n          - DGIdb:stimulator\n          - SEMMEDDB:STIMULATES\n          - DGIdb:stimulator\n      releasing_activity:\n        is_a: activation\n        close_mappings:\n          - CHEMBL:MECHANISM:releasing_agent\n\n  LogicalInterpretationEnum:\n    permissible_values:\n      some_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as a some-some statement\n        meaning: os:SomeSomeInterpretation\n      all_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as an all-some statement.\n        meaning: os:AllSomeInterpretation\n      inverse_all_some:\n\n  ReactionDirectionEnum:\n    permissible_values:\n      left_to_right:\n      right_to_left:\n      bidirectional:\n      neutral:\n\n  ReactionSideEnum:\n    permissible_values:\n      left:\n      right:\n\n  PhaseEnum:\n    description: phase\n    permissible_values:\n      0:\n      1:\n      2:\n\n  StrandEnum:\n    description: strand\n    permissible_values:\n      \"+\":\n        description: Positive\n      \"-\":\n        description: Negative\n      \".\":\n        description: Unstranded\n      \"?\":\n        description: Unknown\n\n  SequenceEnum:\n    description: type of sequence\n    permissible_values:\n      \"na\":\n        description: nucleic acid\n      \"aa\":\n        description: amino acid\n\n  DruggableGeneCategoryEnum:\n    permissible_values:\n      \"tclin\":\n        description: >-\n          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.\n      \"tbio\":\n        description: >-\n          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy\n          the activity thresholds detailed below.\n      \"tchem\":\n        description: >-\n          These targets do not have known drug or small molecule activities that satisfy the activity\n          thresholds detailed below AND satisfy one or more of the following criteria:\n          target is above the cutoff criteria for Tdark\n          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)\n          with an Experimental Evidence code\n      \"tdark\":\n        description: >-\n          These are targets about which virtually nothing is known. They do not have known drug or small\n          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or\n          more of the following criteria:\n          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or\n          less than or equal to 50 Antibodies available according to http://antibodypedia.com.\n\n  DrugAvailabilityEnum:\n    description: >-\n    permissible_values:\n      \"over_the_counter\":\n        description: >-\n          chemical entity is available over the counter without a prescription.\n      \"prescription\":\n        description:\n          chemical entity is available by prescription.\n\n  DrugDeliveryEnum:\n    permissible_values:\n      \"inhalation\":\n      \"oral\":\n      \"absorption_through_the_skin\":\n      \"intravenous_injection\":\n\n  FDAApprovalStatusEnum:\n    description: >-\n    permissible_values:\n      \"discovery_and_development_phase\":\n        description: >-\n          Discovery & Development Phase. Discovery involves researchers finding new possibilities\n          for medication through testing molecular compounds, noting unexpected effects from existing treatments,\n          or the creation of new technology that allows novel ways of targeting medical products to sites in the body.\n          Drug development occurs after researchers identify potential compounds for experiments.\n      \"preclinical_research_phase\":\n        description: >-\n          Preclinical Research Phase.  Once researchers have examined the possibilities a new drug may contain,\n          they must do preliminary research to determine its potential for harm (toxicity).\n          This is categorized as preclinical research and can be one of two types: in vitro or in vivo.\n      \"fda_clinical_research_phase\":\n        description: >-\n          Clinical Research Phase. Clinical research involves trials of the drug on people,\n          and it is one of the most involved stages in the drug development and approval process.\n          Clinical trials must answer specific questions and follow a protocol determined by\n          the drug researcher or manufacturer.\n      \"fda_review_phase_4\":\n        description: >-\n          FDA Review\n      \"fda_post_market_safety_review\":\n        description: >-\n          FDA Post-Market Safety Monitoring.  The last phase of drug approval is an ongoing one\n          while the drug is on the marketplace. If a developer wants to change anything about the\n          drug formulation or approve it for a new use, they must apply with the FDA. The FDA also\n          frequently reviews the drug’s advertising and its manufacturing facility to make sure\n          everything involved in its creation and marketing is in compliance with regulations.\n      \"fda_clinical_research_phase_1\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and\n          lasts several months. This phase is used to determine the safety and dosage of the drug,\n          and about 70% of these drugs move on to the next clinical research phase.\n      \"fda_clinical_research_phase_2\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people,\n          who must have the disease or condition the drug supposes to treat. This phase can last\n          from a few months to two years, and its purpose is to monitor the efficacy of the drug,\n          as well as note side effects that may occur.\n      \"fda_clinical_research_phase_3\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers\n          and can last up to four years. It is used to continue monitoring the efficacy of\n          the drug, as well as exploring any longer-term adverse reactions.\n      \"fda_clinical_research_phase_4\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of\n          volunteers who have the disease or condition and continues to monitor safety and efficacy.\n          If a drug passes this phase, it goes on to FDA review.\n      \"fda_fast_track\":\n        description: >-\n          Fast track is a process designed to facilitate the development, and expedite the\n          review of drugs to treat serious conditions and fill an unmet medical need.\n          The purpose is to get important new drugs to the patient earlier. Fast Track\n          addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track\n      \"fda_breakthrough_therapy\":\n        description: >-\n          Breakthrough Therapy designation is a process designed to expedite the\n          development and review of drugs that are intended to treat a serious\n          condition and preliminary clinical evidence indicates that the drug may\n          demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy\n      \"fda_accelerated_approval\":\n        description: >-\n          When studying a new drug, it can sometimes take many years to learn whether a drug actually\n          provides a real effect on how a patient survives, feels, or functions. A positive therapeutic\n          effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”.\n          Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical\n          benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs\n          for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint.\n          Using a surrogate endpoint enabled the FDA to approve these drugs faster.\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval\n      \"fda_priority_review\":\n        description: >-\n          Prior to approval, each drug marketed in the United States must go through a detailed FDA review process.\n          In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving\n          the drug review time and created a two-tiered system of review times – Standard Review and Priority\n          Review. A Priority Review designation means FDA’s goal is to take action on an application\n          within 6 months (compared to 10 months under standard review).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review\n      \"regular_fda_approval\":\n        description: >-\n          Regular FDA Approval.  The last phase of drug approval is an ongoing one while the drug is on the marketplace.\n          If a developer wants to change anything about the drug formulation or approve it for a new use,\n          they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its\n          manufacturing facility to make sure everything involved in its creation and marketing is in compliance\n          with regulations.\n      \"post_approval_withdrawal\":\n\n  FDAIDAAdverseEventEnum:\n    description: >-\n      please consult with the FDA guidelines as proposed in this document:\n      https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32\n    permissible_values:\n      \"life_threatening_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either \n          the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. \n          It does not include an adverse event or suspected adverse reaction that, had it occurred in a more \n          severe form, might have caused death.\n      \"serious_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the \n          investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event,\n          inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity \n          or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth \n          defect. Important medical events that may not result in death, be life-threatening, or require hospitalization\n          may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or \n          subject and may require medical or surgical intervention to prevent one of the outcomes listed in this \n          definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment \n          in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient \n          hospitalization, or the development of drug dependency or drug abuse.\n      \"suspected_adverse_reaction\":\n         description: >-\n           means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. \n           For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a \n           causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser \n           degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.\n      \"unexpected_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the \n          investigator brochure or is not listed at the specificity or severity that has been observed; or, if an \n          investigator brochure is not required or available, is not consistent with the risk information described \n          in the general investigational plan or elsewhere in the current application, as amended. For example, \n          under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the \n          investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral \n          thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the \n          investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, \n          also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure\n          as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but \n          are not specifically mentioned as occurring with the particular drug under investigation.\n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_3_5_2/biolink-model.yaml",
    "content": "---\nid: https://w3id.org/biolink/biolink-model\nname: Biolink-Model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 3.5.2\n\n\n## ------------\n##\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  AGRKB: 'https://www.alliancegenome.org/'\n  apollo: 'https://github.com/GMOD/Apollo'\n  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='\n  biolink: 'https://w3id.org/biolink/vocab/'\n  bioschemas: 'https://bioschemas.org/'\n  linkml: 'https://w3id.org/linkml/'\n  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='\n   # Placeholder: just points to GMOD Chado wiki\n  CHADO: 'http://gmod.org/wiki/Chado/'\n   # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve\n  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='\n  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'\n  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'\n  CLINVAR: 'http://identifiers.org/clinvar'\n  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'\n  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'\n  ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'\n  CPT: 'https://www.ama-assn.org/practice-management/cpt/'\n  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='\n  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='\n  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='\n  CTD: 'http://ctdbase.org/'\n  DGIdb: 'https://www.dgidb.org/interaction_types'\n  dcat: 'http://www.w3.org/ns/dcat#'\n  dct: 'http://purl.org/dc/terms/'\n  dcid: 'https://datacommons.org/browser/'\n  doi: 'https://doi.org/'\n  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'\n  DrugCentral: 'http://drugcentral.org/drugcard/'\n  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'\n  EDAM-DATA: 'http://edamontology.org/data_'\n  EDAM-FORMAT: 'http://edamontology.org/format_'\n  EDAM-OPERATION: 'http://edamontology.org/operation_'\n  EDAM-TOPIC: 'http://edamontology.org/topic_'\n  EFO: 'http://www.ebi.ac.uk/efo/EFO_'\n  ExO: 'http://purl.obolibrary.org/obo/ExO_'\n  fabio: 'http://purl.org/spar/fabio/'\n  foaf: 'http://xmlns.com/foaf/0.1/'\n  foodb.food: 'http://foodb.ca/compounds/'\n  foodb.compound: 'http://foodb.ca/foods/'\n  FYECO: 'https://www.pombase.org/term/'\n  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'   # Fission Yeast Phenotype Ontology\n  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'\n  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'\n   # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)\n  GOP: 'http://purl.obolibrary.org/obo/go#'\n  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'\n  GSID: 'https://scholar.google.com/citations?user='\n  GTEx: 'https://www.gtexportal.org/home/gene/'\n  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='\n  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'\n  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'\n  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'\n  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'\n  ICD10: 'https://icd.codes/icd9cm/'\n  ICD9: 'http://translator.ncats.nih.gov/ICD9_'\n  interpro: 'https://www.ebi.ac.uk/interpro/entry/'\n  INO: 'http://purl.obolibrary.org/obo/INO_'\n  isbn: 'https://www.isbn-international.org/identifier/'  # note: a resolvable base URI not available from isbn-international\n  isni: 'https://isni.org/isni/'\n  issn: 'https://portal.issn.org/resource/ISSN/'\n  ncats.drug: 'https://drugs.ncats.io/drug/'\n  KEGG.BRITE: 'https://bioregistry.io/kegg.brite:'\n  KEGG: 'http://www.kegg.jp/entry/'\n  KEGG.GENES: 'https://bioregistry.io/kegg.genes:bsu:'\n  KEGG.PATHWAY: 'https://bioregistry.io/kegg.pathway:'\n  KEGG.RCLASS: 'https://www.genome.jp/dbget-bin/www_bget?rc:'\n  LOINC: 'http://loinc.org/rdf/'\n  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'\n  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'\n  metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'\n  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'\n  MESH: 'http://id.nlm.nih.gov/mesh/'\n  MI: 'http://purl.obolibrary.org/obo/MI_'\n  mirbase: 'http://identifiers.org/mirbase'\n  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'\n  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'\n  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'\n  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'\n  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='\n  NCBIGene: 'http://identifiers.org/ncbigene/'\n  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'\n  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'\n  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='\n  OBAN: 'http://purl.org/oban/'\n  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'\n  ORCID: 'https://orcid.org/'\n  orphanet: 'http://www.orpha.net/ORDO/Orphanet_'\n  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'\n  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='\n  PathWhiz: 'http://smpdb.ca/pathways/#'   #  See also https://smpdb.ca/pathwhiz/\n  pav: 'http://purl.org/pav/'\n  PHARMGKB.CHEMICAL: 'https://www.pharmgkb.org/chemical/'\n  PHARMGKB.DISEASE: 'https://www.pharmgkb.org/disease/'\n  PHARMGKB.GENE: 'https://www.pharmgkb.org/gene/'\n  PHARMGKB.PATHWAYS: 'https://www.pharmgkb.org/pathway/'\n  PHARMGKB.VARIANT: 'https://www.pharmgkb.org/variant/'\n  PHAROS: 'http://pharos.nih.gov'\n  PomBase: 'https://www.pombase.org/gene/'\n  prov: 'http://www.w3.org/ns/prov#'\n  qud: 'http://qudt.org/1.1/schema/qudt#'\n  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'\n  ResearchID: 'https://publons.com/researcher/'\n  RO: 'http://purl.obolibrary.org/obo/RO_'\n  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'\n  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='\n  schema: 'http://schema.org/'\n  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='\n  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'\n  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'\n  SIO: 'http://semanticscience.org/resource/SIO_'\n  SNOMEDCT: 'http://snomed.info/id/'\n  SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'\n  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'\n  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'\n  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'\n  STY: 'http://purl.bioontology.org/ontology/STY/'\n  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'\n  UniProtKB: 'http://purl.uniprot.org/uniprot/'\n  UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/'\n  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'\n  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'\n  VMC: 'https://github.com/ga4gh/vr-spec/'\n  WBls: 'http://purl.obolibrary.org/obo/WBls_'\n  WBbt: 'http://purl.obolibrary.org/obo/WBbt_'\n  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'\n  WIKIDATA: 'https://www.wikidata.org/entity/'             #  Wikidata Entity\n  WIKIDATA_PROPERTY: 'https://www.wikidata.org/prop/'\n  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'\n  XPO: 'http://purl.obolibrary.org/obo/XPO_'   #  Xenopus Phenotype Ontology\n  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='\n  PMC: 'http://europepmc.org/articles/PMC'\n\ndefault_prefix: biolink\ndefault_range: string\n\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - oboInOwl\n  - BIOGRID\n  - SO\n\n## ------------\n## SUBSETS\n## ------------\n\n\nsubsets:\n\n  model_organism_database:\n    description: >-\n      Subset that is relevant for a typical Model Organism Database (MOD)\n\n  translator_minimal:\n    description: >-\n      Minimum subset of translator work\n\n  samples:\n    description: >-\n      Sample/biosample datamodel\n\n  testing:\n    description: >-\n      TBD\n\n\n## ------------\n## TYPES\n## ------------\n\nimports:\n  - linkml:types\n\ntypes:\n\n  chemical formula value:\n    uri: xsd:string\n    base: str\n    description: A chemical formula\n    notes:\n      - Should be implemented as a stronger type\n\n  category type:\n    typeof: uriorcurie\n    description: >-\n      A primitive type in which the value denotes a class within the biolink model.\n      The value must be a URI or a CURIE. In a Neo4j representation, the value should\n      be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,\n      the value should be a URI such as https://w3id.org/biolink/vocab/Gene\n\n  iri type:\n    typeof: uriorcurie\n    description: >-\n      An IRI\n\n  label type:\n    typeof: string\n    description: >-\n      A string that provides a human-readable name for an entity\n\n  predicate type:\n    typeof: uriorcurie\n    description: >-\n      A CURIE from the biolink related_to hierarchy.\n      For example, biolink:related_to, biolink:causes, biolink:treats.\n\n  narrative text:\n    typeof: string\n    description: >-\n      A string that provides a human-readable description of something\n\n  symbol type:\n    typeof: string\n\n  frequency value:\n    typeof: string\n    uri: UO:0000105\n\n  percentage frequency value:\n    typeof: double\n    uri: UO:0000187\n\n  quotient:\n    aliases: ['ratio']\n    typeof: double\n    uri: UO:0010006\n\n  unit:\n    typeof: string\n    uri: UO:0000000\n    id_prefixes:\n      - UO\n    exact_mappings:\n      - qud:Unit\n\n  time type:\n    typeof: time\n\n  biological sequence:\n    typeof: string\n\n## ------------\n## SLOTS\n## ------------\n\nslots:\n\n  has attribute:\n    description: >-\n      connects any entity to an attribute\n    domain: entity\n    range: attribute\n    multivalued: true\n    in_subset:\n      - samples\n    close_mappings:\n       # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'\n      - OBI:0001927\n    exact_mappings:\n      - SIO:000008\n    narrow_mappings:\n       # if 'has attribute' annotates a NamedThing as subject or\n       # object of an association, these OBAN mappings may apply\n      - OBAN:association_has_subject_property\n      - OBAN:association_has_object_property\n      - CPT:has_possibly_included_panel_element\n      - DRUGBANK:category\n       # RTX contributed terms. Could perhaps review for more semantically precise mappings?\n      - EFO:is_executed_in\n      - HANCESTRO:0301\n      - LOINC:has_action_guidance\n      - LOINC:has_adjustment\n      - LOINC:has_aggregation_view\n      - LOINC:has_approach_guidance\n      - LOINC:has_divisor\n      - LOINC:has_exam\n      - LOINC:has_method\n      - LOINC:has_modality_subtype\n      - LOINC:has_object_guidance\n      - LOINC:has_scale\n      - LOINC:has_suffix\n      - LOINC:has_time_aspect\n      - LOINC:has_time_modifier\n      - LOINC:has_timing_of\n       # disease is stage\n      - NCIT:R88\n      - NCIT:eo_disease_has_property_or_attribute\n      - NCIT:has_data_element\n      - NCIT:has_pharmaceutical_administration_method\n      - NCIT:has_pharmaceutical_basic_dose_form\n      - NCIT:has_pharmaceutical_intended_site\n      - NCIT:has_pharmaceutical_release_characteristics\n      - NCIT:has_pharmaceutical_state_of_matter\n      - NCIT:has_pharmaceutical_transformation\n      - NCIT:is_qualified_by\n      - NCIT:qualifier_applies_to\n      - NCIT:role_has_domain\n      - NCIT:role_has_range\n      - INO:0000154\n      - HANCESTRO:0308\n      - OMIM:has_inheritance_type\n      - orphanet:C016\n      - orphanet:C017\n      - RO:0000053\n       # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here\n      - RO:0000086\n      - RO:0000087\n      - SNOMED:has_access\n      - SNOMED:has_clinical_course\n      - SNOMED:has_count_of_base_of_active_ingredient\n      - SNOMED:has_dose_form_administration_method\n      - SNOMED:has_dose_form_release_characteristic\n      - SNOMED:has_dose_form_transformation\n      - SNOMED:has_finding_context\n      - SNOMED:has_finding_informer\n      - SNOMED:has_inherent_attribute\n      - SNOMED:has_intent\n      - SNOMED:has_interpretation\n      - SNOMED:has_laterality\n      - SNOMED:has_measurement_method\n      - SNOMED:has_method\n      - SNOMED:has_priority\n      - SNOMED:has_procedure_context\n      - SNOMED:has_process_duration\n      - SNOMED:has_property\n      - SNOMED:has_revision_status\n      - SNOMED:has_scale_type\n      - SNOMED:has_severity\n      - SNOMED:has_specimen\n      - SNOMED:has_state_of_matter\n      - SNOMED:has_subject_relationship_context\n      - SNOMED:has_surgical_approach\n      - SNOMED:has_technique\n      - SNOMED:has_temporal_context\n      - SNOMED:has_time_aspect\n      - SNOMED:has_units\n      - UMLS:has_structural_class\n      - UMLS:has_supported_concept_property\n      - UMLS:has_supported_concept_relationship\n      - UMLS:may_be_qualified_by\n\n  has attribute type:\n    description: >-\n      connects an attribute to a class that describes it\n    domain: attribute\n    range: ontology class\n    multivalued: false\n    required: true\n    in_subset:\n      - samples\n    narrow_mappings:\n      - LOINC:has_modality_type\n      - LOINC:has_view_type\n\n   # TRAPI Attribute schema alignment:\n   # value: NamedThing.name\n   # value_type: NamedThing.category\n   # value_type_name: quantity_value.NamedThing.name\n  has qualitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: named thing\n    multivalued: false\n    in_subset:\n      - samples\n\n   # TRAPI Attribute schema alignment:\n   # value: quantity_value.has_numeric_value[double] - may be a vector?\n   # value_type: quantity_value.has_unit.unit.uri\n   # value_type_name: quantity_value.has_unit.unit.name[string]\n  has quantitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: quantity value\n    multivalued: true\n    exact_mappings:\n      - qud:quantityValue\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_numerator_value\n      - SNOMED:has_presentation_strength_denominator_value\n      - SNOMED:has_presentation_strength_numerator_value\n    in_subset:\n      - samples\n\n  has numeric value:\n    description: >-\n      connects a quantity value to a number\n    domain: quantity value\n    range: double\n    multivalued: false\n    exact_mappings:\n      - qud:quantityValue\n    in_subset:\n      - samples\n\n  has unit:\n    description: >-\n      connects a quantity value to a unit\n    domain: quantity value\n    range: unit\n    multivalued: false\n    close_mappings:\n       # These RTX contributed terms mean \"is unit of\" which is the semantic inverse of this biolink:has_unit term\n      - EFO:0001697\n      - UO-PROPERTY:is_unit_of\n    exact_mappings:\n      - qud:unit\n      - IAO:0000039\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_denominator_unit\n      - SNOMED:has_concentration_strength_numerator_unit\n      - SNOMED:has_presentation_strength_denominator_unit\n      - SNOMED:has_presentation_strength_numerator_unit\n      - SNOMED:has_unit_of_presentation\n    in_subset:\n      - samples\n\n  base coordinate:\n    is_a: sequence localization attribute\n    aliases: ['one-based', 'fully-closed']\n    description: >-\n      A position in the base coordinate system.  Base coordinates start at position 1 instead of position 0.\n    range: integer\n\n   ## --------------------\n   ## NODE PROPERTY SLOTS\n   ## --------------------\n\n  node property:\n    description: >-\n      A grouping for any property that holds between a node and a value\n    domain: named thing\n\n  id:\n    identifier: true\n    domain: entity\n    description: >-\n      A unique identifier for an entity.\n      Must be either a CURIE shorthand for a URI or a complete URI\n    in_subset:\n      - translator_minimal\n    required: true\n    exact_mappings:\n      - AGRKB:primaryId\n      - gff3:ID\n      - gpi:DB_Object_ID\n\n  iri:\n    description: >-\n      An IRI for an entity. This is determined by the id using expansion rules.\n    range: iri type\n    in_subset:\n      - translator_minimal\n      - samples\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P854\n\n  type:\n    slot_uri: rdf:type\n    domain: entity\n    exact_mappings:\n      - AGRKB:soTermId\n      - gff3:type\n      - gpi:DB_Object_Type\n    multivalued: true\n\n  category:\n    is_a: type\n    domain: entity\n    range: category type\n    designates_type: true\n    description: >-\n      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the\n      biolink entity type class.\n       * In a neo4j database this MAY correspond to the neo4j label tag.\n       * In an RDF database it should be a biolink model class URI.\n      This field is multi-valued. It should include values for ancestors of the biolink class; for example,\n      a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\n\n      In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink\n      class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`\n      may have a rdf:type assertion to a SO class such as TF_binding_site,\n      which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,\n      biolink:MolecularEntity, biolink:NamedThing}\n    is_class_field: true\n    multivalued: true\n    in_subset:\n      - translator_minimal\n\n  publication type:\n    slot_uri: dct:type\n    description: >-\n      Ontology term for publication type may be drawn from\n      Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),\n      FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),\n      the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),\n      the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres\n      (http://vocabularies.coar-repositories.org/documentation/resource_types/),\n      Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or\n      equivalent publication type ontology. When a given publication type ontology term\n      is used within a given knowledge graph, then the CURIE identified term must be\n      documented in the graph as a concept node of biolink:category biolink:OntologyClass.\n    values_from:  # Not sure which takes precedence, if any...\n      - dctypes\n      - fabio\n      - MESH_PUB\n      - COAR_RESOURCE\n      - WIKIDATA\n    multivalued: true\n\n  name:\n    aliases: ['label', 'display name', 'title']\n    description: >-\n      A human-readable name for an attribute or entity.\n    domain: entity\n    range: label type\n    in_subset:\n      - translator_minimal\n      - samples\n    slot_uri: rdfs:label\n    exact_mappings:\n      - gff3:Name\n      - gpi:DB_Object_Name\n    narrow_mappings:\n      - dct:title\n      - WIKIDATA_PROPERTY:P1476\n\n  stoichiometry:\n    description: >-\n      the relationship between the relative quantities of substances taking part in a reaction or\n      forming a compound, typically a ratio of whole integers.\n    is_a: association slot\n    range: integer\n\n  reaction direction:\n    description: >-\n      the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)\n    is_a: association slot\n    range: ReactionDirectionEnum\n    narrow_mappings:\n      - NCIT:C42677\n\n  reaction balanced:\n    is_a: association slot\n    range: boolean\n\n  reaction side:\n    description: >-\n      the side of a reaction being modeled (ie: left or right)\n    is_a: association slot\n    range: ReactionSideEnum\n\n  symbol:\n    is_a: node property\n    domain: named thing\n    description: >-\n      Symbol for a particular thing\n    exact_mappings:\n      - AGRKB:symbol\n      - gpi:DB_Object_Symbol\n\n  synonym:\n    is_a: node property\n    aliases: ['alias']\n    domain: named thing\n    range: label type\n    description: >-\n      Alternate human-readable names for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n       # there is an interesting debate here: are these terms \"narrower\" a.k.a. more specialized instances of\n       # 'biolink:synonym' or should they be binned into their respective namesake class of mappings?\n       # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.\n      - skos:altLabel\n      - gff3:Alias\n      - AGRKB:synonyms\n      - gpi:DB_Object_Synonyms\n       # TODO: RTX contributed terms mapped here... May need review?\n      - HANCESTRO:0330\n      - IAO:0000136\n      - RXNORM:has_tradename\n\n  exact synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasExactSynonym\n\n  broad synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasBroadSynonym\n\n  narrow synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasNarrowSynonym\n\n  related synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasRelatedSynonym\n\n  has topic:\n    aliases: ['topic', 'descriptors']\n    is_a: node property\n    range: ontology class\n    exact_mappings:\n      - foaf:topic\n    description: >-\n      Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.\n      See https://github.com/biolink/biolink-model/issues/238\n\n  xref:\n    aliases: ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls']\n    domain: named thing\n    range: uriorcurie\n    description: >-\n      A database cross reference or alternative identifier for a NamedThing or edge between two \n      NamedThings.  This property should point to a database record or webpage that supports the existence of the edge, or \n      gives more detail about the edge. This property can be used on a node or edge to provide multiple\n      URIs or CURIE cross references.\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - gff3:Dbxref\n      - gpi:DB_Xrefs\n\n  support graphs:\n    description: >-\n      A list of knowledge graphs that support the existence of this node.\n    multivalued: true\n    in_subset:\n      - translator_minimal\n  \n  resource id:\n    is_a: node property\n    description: >-\n      The CURIE for an Information Resource that served as a source\n      of knowledge expressed in an Edge, or a source of data used to\n      generate this knowledge.\n    domain: retrieval source\n    range: uriorcurie\n    in_subset:\n      - translator_minimal\n  \n  resource role:\n    is_a: node property\n    description: >-\n      The role played by the InformationResource in serving as a\n      source for an Edge. Note that a given Edge should have one\n      and only one 'primary' source, and may have any number of\n      'aggregator' or 'supporting data' sources.\n    domain: retrieval source\n    range: ResourceRoleEnum\n    in_subset:\n      - translator_minimal\n\n  retrieval source ids:\n    description: >-\n        A list of retrieval sources that served as a source of knowledge\n        expressed in an Edge, or a source of data used to generate this\n        knowledge.\n    multivalued: true\n    range: retrieval source\n    in_subset:\n      - translator_minimal\n\n  full name:\n    is_a: node property\n    domain: named thing\n    range: label type\n    description: >-\n      a long-form human readable name for a thing\n\n  upstream resource ids:\n    is_a: node property\n    description: >-\n      An upstream InformationResource from which the resource\n      being described directly retrieved a record of the knowledge\n      expressed in the Edge, or data used to generate this knowledge.\n      This is an array because there are cases where a merged Edge\n      holds knowledge that was retrieved from multiple sources. e.g.\n      an Edge provided by the ARAGORN ARA can expressing knowledge it\n      retrieved from both the automat-mychem-info and molepro KPs,\n      which both provided it with records of this single fact.\n    domain: retrieval source\n    range: uriorcurie\n\n  description:\n    aliases: ['definition']\n    range: narrative text\n    description: >-\n      a human-readable description of an entity\n    in_subset:\n      - translator_minimal\n    slot_uri: dct:description\n    exact_mappings:\n      - IAO:0000115\n      - skos:definitions\n    narrow_mappings:\n      - gff3:Description\n\n  systematic synonym:\n    is_a: node property\n    domain: named thing\n    range: label type\n    multivalued: true\n    slot_uri: GOP:systematic_synonym\n    description: >-\n      more commonly used for gene symbols in yeast\n\n  affiliation:\n    is_a: node property\n    description: >-\n      a professional relationship between one provider (often a person) within another provider (often an organization).\n      Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.\n    domain: agent\n    range: uriorcurie\n    multivalued: true\n\n  address:\n    is_a: node property\n    description: >-\n      the particulars of the place where someone or an organization is situated.  For now, this slot is a\n      simple text \"blob\" containing all relevant details of the given location for fitness of purpose.\n      For the moment, this \"address\" can include other contact details such as email and phone number(?).\n\n   ## Space\n\n  latitude:\n    is_a: node property\n    range: float\n    description: >-\n      latitude\n    exact_mappings:\n      - wgs:lat\n\n  longitude:\n    is_a: node property\n    range: float\n    description: >-\n      longitude\n    exact_mappings:\n      - wgs:long\n\n   ## Time\n\n  timepoint:\n    aliases: ['duration']\n    range: time type\n    description: >-\n      a point in time\n\n  creation date:\n    is_a: node property\n    aliases: ['publication date']\n    range: date\n    description: >-\n      date on which an entity was created. This can be applied to nodes or edges\n    exact_mappings:\n      - dct:createdOn\n      - WIKIDATA_PROPERTY:P577\n\n  update date:\n    is_a: node property\n    range: date\n    description: >-\n      date on which an entity was updated. This can be applied to nodes or edges\n\n   ## Statistics\n\n  aggregate statistic:\n    is_a: node property\n    abstract: true\n\n  has count:\n    description: >-\n      number of things with a particular property\n    is_a: aggregate statistic\n    range: integer\n    exact_mappings:\n      - LOINC:has_count\n\n  has total:\n    description: >-\n      total number of things in a particular reference set\n    is_a: aggregate statistic\n    range: integer\n\n  has quotient:\n    is_a: aggregate statistic\n    range: double\n\n  has percentage:\n    description: >-\n      equivalent to has quotient multiplied by 100\n    is_a: aggregate statistic\n    range: double\n\n   ## Properties for Information Content Entity and Publication Nodes\n\n  has taxonomic rank:\n    is_a: node property\n    range: taxonomic rank\n    multivalued: false\n    mappings:\n      - WIKIDATA:P105\n\n  has dataset:\n    is_a: node property\n    domain: dataset version\n    range: dataset\n    broad_mappings:\n      - dct:source\n\n  source web page:\n    is_a: node property\n    domain: dataset summary\n    broad_mappings:\n      - dct:source\n\n  source logo:\n    is_a: node property\n    domain: dataset summary\n    slot_uri: schema:logo\n\n  retrieved on:\n    is_a: node property\n    domain: dataset\n    range: date\n    exact_mappings:\n      - pav:retrievedOn\n\n  version of:\n    is_a: node property\n    domain: dataset version\n    range: dataset summary\n    exact_mappings:\n      - dct:isVersionOf\n\n  version:\n    is_a: node property\n    domain: dataset\n    broad_mappings:\n      - pav:version\n      - owl:versionInfo\n\n  license:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:license\n    narrow_mappings:\n      - WIKIDATA_PROPERTY:P275\n\n  rights:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:rights\n\n  format:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:format\n      - WIKIDATA_PROPERTY:P2701\n\n  created with:\n    is_a: node property\n    domain: dataset\n    exact_mappings:\n      - pav:createdWith\n\n  download url:\n    is_a: node property\n    domain: information content entity\n    slot_uri: dcat:downloadURL\n\n  dataset download url:\n    is_a: node property\n    domain: dataset\n    slot_uri: dcat:downloadURL\n\n  distribution download url:\n    is_a: node property\n    domain: dataset distribution\n    exact_mappings:\n      - dcat:downloadURL\n\n  ingest date:\n    is_a: node property\n    domain: dataset version\n    broad_mappings:\n      - dct:issued\n\n  has distribution:\n    is_a: node property\n    domain: dataset version\n    range: dataset distribution\n    slot_uri: dct:distribution\n\n  published in:\n    is_a: node property\n    description: >-\n      CURIE identifier of a broader publication context within which the publication may be placed,\n      e.g. a specified book or journal.\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - NLMID\n      - issn\n      - isbn\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1433\n\n  iso abbreviation:\n    is_a: node property\n    description: >-\n      Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system\n      See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,\n      then the iso abbreviation pertains to the broader publication context (the journal) within which the given\n      publication node is embedded, not the publication itself.\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1160\n\n  authors:\n    is_a: node property\n    description: >-\n      connects an publication to the list of authors who contributed to the publication.\n      This property should be a comma-delimited list of author names. It is recommended that an author's name\n      be formatted as \"surname, firstname initial.\".   Note that this property is a node annotation expressing\n      the citation list of authorship which might typically otherwise be more completely documented in\n      biolink:PublicationToProviderAssociation defined edges which point to full details about an author\n      and possibly, some qualifiers which clarify the specific status of a given author in the publication.\n    multivalued: true\n    domain: publication\n    range: agent\n\n  volume:\n    is_a: node property\n    description: >-\n      volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P478\n\n  chapter:\n    is_a: node property\n    description: >-\n      chapter of a book\n    domain: book chapter\n    exact_mappings:\n      - WIKIDATA:Q1980247\n\n  issue:\n    is_a: node property\n    description: >-\n      issue of a newspaper, a scientific journal or magazine for reference purpose\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P433\n\n  pages:\n    is_a: node property\n    description: >-\n      page number of source referenced for statement or publication\n    domain: publication\n    multivalued: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P304\n\n  summary:\n    is_a: node property\n     # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot,\n     # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract'\n    aliases: ['abstract']\n    description: >-\n      executive  summary of a publication\n    domain: publication\n    exact_mappings:\n      - dct:abstract\n      - WIKIDATA:Q333291\n\n  keywords:\n    is_a: node property\n    description: >-\n      keywords tagging a publication\n    domain: publication\n    multivalued: true\n\n  mesh terms:\n    is_a: node property\n    description: >-\n      mesh terms tagging a publication\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - MESH\n    multivalued: true\n    exact_mappings:\n      - dcid:MeSHTerm\n\n   ## Biology\n\n  has biological sequence:\n    is_a: node property\n    description: >-\n      connects a genomic feature to its sequence\n    range: biological sequence\n\n  has gene or gene product:\n    is_a: node property\n    description: >-\n      connects an entity with one or more gene or gene products\n    range: gene\n    multivalued: true\n\n  has gene:\n    is_a: has gene or gene product\n    description: >-\n      connects an entity associated with one or more genes\n    range: gene\n    multivalued: true\n\n  has zygosity:\n    is_a: node property\n    domain: nucleic acid entity\n    range: zygosity\n\n   ## Chemistry, drugs and food\n\n  has chemical formula:\n    is_a: node property\n    range: chemical formula value\n    description: >-\n      description of chemical compound based on element symbols\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P274\n\n  is metabolite:\n    is_a: node property\n    domain: molecular entity\n    range: boolean\n    description: >-\n      indicates whether a molecular entity is a metabolite\n    exact_mappings:\n      - CHEBI:25212\n\n  has constituent:\n    description: >-\n      one or more molecular entities within a chemical mixture\n    is_a: node property\n    range: molecular entity\n    multivalued: true\n\n  has drug:\n    is_a: node property\n    description: >-\n      connects an entity to one or more drugs\n    range: drug\n    multivalued: true\n\n  has device:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) devices\n    range: device\n    multivalued: true\n\n  has procedure:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) procedures\n    range: procedure\n    multivalued: true\n\n   ## Clinical exposures\n\n  has receptor:\n    is_a: node property\n    domain: exposure event\n    range: organismal entity\n    description: >-\n      the organism or organism part being exposed\n    exact_mappings:\n      - ExO:0000001\n\n  has stressor:\n    is_a: node property\n    domain: exposure event\n    aliases: ['has stimulus']\n    description: >-\n      the process or entity that the receptor is being exposed to\n    exact_mappings:\n      - ExO:0000000\n\n  has route:\n    is_a: node property\n    domain: exposure event\n    description: >-\n      the process that results in the stressor coming into direct contact with the receptor\n    exact_mappings:\n      - ExO:0000055\n    narrow_mappings:\n      - LOINC:has_pharmaceutical_route\n      - SNOMED:has_dose_form_intended_site\n      - SNOMED:has_route_of_administration\n\n\n  population context qualifier:\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: qualifier\n    range: population of individual organisms\n\n  temporal context qualifier:\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n      for time intervales, use temporal interval qualifier.\n    is_a: qualifier\n    range: time type\n\n  temporal interval qualifier:\n    is_a: temporal context qualifier\n    description: >-\n      a constraint of a time interval placed upon the truth value of an\n      association.\n\n  is supplement:\n    description: >-\n    is_a: node property\n    range: chemical mixture\n\n  trade name:\n    description: >-\n    is_a: node property\n    range: chemical entity\n\n  available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: DrugAvailabilityEnum\n\n  is toxic:\n    description: >-\n    is_a: node property\n    multivalued: false\n    range: boolean\n\n  has chemical role:\n    is_a: related to at concept level\n    description: >-\n      A role is particular behaviour which a chemical entity may exhibit.\n    range: chemical role\n    multivalued: true\n    id_prefixes:\n      - CHEBI\n    comments: >-\n      We expect primarily to use CHEBI chemical roles here; however, we are looking for a mapping between\n      CHEBI And ATC codes to support this slot.\n\n  max tolerated dose:\n    description: >-\n      The highest dose of a drug or treatment that does not cause unacceptable side effects.\n      The maximum tolerated dose is determined in clinical trials by testing increasing doses\n      on different groups of people until the highest dose with acceptable side effects is\n      found. Also called MTD.\n    is_a: node property\n    multivalued: false\n    range: string\n\n  animal model available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: disease or phenotypic feature\n\n  FDA adverse event level:\n    description: >-\n    is_a: association slot\n    range: FDAIDAAdverseEventEnum\n\n  highest FDA approval status:\n    description: >-\n      Should be the highest level of FDA approval this chemical entity or device has, regardless of which\n      disease, condition or phenotype it is currently being reviewed to treat.  For specific levels of FDA\n      approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'\n\n  drug regulatory status world wide:\n    aliases: ['max phase']\n    description: >-\n      An agglomeration of drug regulatory status worldwide. Not specific to FDA.\n    exact_mappings:\n      - NCIT:C172573\n    narrow_mappings:\n      - NCIT:R172\n      - NCIT:regimen_has_accepted_use_for_disease\n       # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n\n  routes of delivery:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    multivalued: true\n    range: DrugDeliveryEnum\n\n   ## -------------------\n   ## QUALIFIERS\n   ## -------------------\n\n  form or variant qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.\n    examples:\n      - value: mutation\n      - value: late stage\n      - value: severe\n      - value: transplant\n      - value: chemical analog\n    notes: >-\n      please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier'\n      terms in the gene->chemical association space. \n      the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’.\n      the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the  more specific concept ‘Late Stage forms of Disease X’\n      the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’\n      the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’\n    in_subset:\n      - translator_minimal\n\n  aspect qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.  The purpose of the aspect slot is to indicate what aspect is being affected in an \n      'affects' association.\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    notes: >-\n      for good examples of aspects in the gene-> chemical space, please see the \n      GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify \n      the gene making the full subject a different ontological type.  \n      the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process)\n      the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process)\n      the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity)\n      the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event)\n      the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process)\n      the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality)\n      the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)\n    in_subset:\n      - translator_minimal\n\n  derivative qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.\n    examples:\n      - value: metabolite\n    in_subset:\n      - translator_minimal\n\n  part qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).\n    examples:\n      - value: polyA tail\n      - value: upstream control region\n    in_subset:\n      - translator_minimal\n\n  context qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.\n    examples:\n      - value: cohort x (e.g. a specific population, referenced by an identifier)\n      - value: gut microbiome  # OHMI:0000020\n    in_subset:\n      - translator_minimal\n\n  direction qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n    notes: >-\n      the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’   \n      the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’\n    in_subset:\n      - translator_minimal\n\n  mapped predicate:\n    description: >-\n      The predicate that is being replaced by the fully qualified representation of predicate + subject and object \n      qualifiers.  Only to be used in test data and mapping data to help with the transition to the fully qualified\n      predicate model. Not to be used in knowledge graphs.\n\n  predicate mappings:\n    description: >- \n      A collection of relationships that are not used in biolink, but have biolink patterns that can \n      be used to replace them.  This is a temporary slot to help with the transition to the fully qualified predicate\n      model in Biolink3.\n    multivalued: true\n    range: predicate mapping\n    inlined_as_list: true\n\n  exact matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      an identical meaning. Such terms often describe the same concept from\n      different ontological perspectives.\n    multivalued: true\n\n  narrow matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a narrower meaning. Such terms often describe a more specific concept\n      from different ontological perspectives.\n    multivalued: true\n\n  broad matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a broader meaning. Such terms often describe a more general concept\n      from different ontological perspectives.\n    multivalued: true\n\n  subject aspect qualifier:\n    is_a: aspect qualifier\n    in_subset:\n      - translator_minimal\n\n  subject form or variant qualifier:\n    is_a: form or variant qualifier\n    in_subset:\n      - translator_minimal\n\n  subject part qualifier:\n    is_a: part qualifier\n    in_subset:\n      - translator_minimal\n\n  subject derivative qualifier:\n    is_a: derivative qualifier\n    in_subset:\n      - translator_minimal\n\n  subject context qualifier:\n    is_a: context qualifier\n    in_subset:\n      - translator_minimal\n\n  subject direction qualifier:\n    is_a: direction qualifier\n    range: DirectionQualifierEnum\n    in_subset:\n      - translator_minimal\n\n  object aspect qualifier:\n    is_a: aspect qualifier\n    in_subset:\n      - translator_minimal\n\n  object form or variant qualifier:\n    is_a: form or variant qualifier\n    in_subset:\n      - translator_minimal\n\n  object part qualifier:\n    is_a: part qualifier\n    in_subset:\n      - translator_minimal\n\n  object derivative qualifier:\n    is_a: derivative qualifier\n    in_subset:\n      - translator_minimal\n\n  object context qualifier:\n    is_a: context qualifier\n    in_subset:\n      - translator_minimal\n\n  object direction qualifier:\n    is_a: direction qualifier\n    range: DirectionQualifierEnum\n    in_subset:\n      - translator_minimal\n\n  qualified predicate:\n    is_a: qualifier\n    description: >-\n      Predicate to be used in an association when subject and object qualifiers are present and the full\n      reading of the statement requires a qualification to the predicate in use in order to refine or \n      increase the specificity of the full statement reading.  This qualifier holds a relationship to be used instead of that \n      expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based \n      semantics are included.  This is necessary only in cases where the primary predicate does not work in a \n      full statement reading.\n    notes: >-\n      to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read \n      using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using \n      the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, \n      object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make \n      sense in the full statement reading  (because “Chemical X affects increased expression of Gene Y'' is not \n      what we mean to say here: it causes increased expression of Gene Y)\n\n  qualifier:\n    is_a: association slot\n    description: >- \n      grouping slot for all qualifiers on an edge.  useful for testing compliance with association classes\n    in_subset:\n      - translator_minimal\n\n  statement qualifier:\n    is_a: qualifier\n    description: >-\n    in_subset:\n      - translator_minimal\n\n  causal mechanism qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a type of molecular control mechanism through which an\n      effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition',\n      'allosteric modulation', 'channel blocker')\n    range: CausalMechanismQualifierEnum\n    in_subset:\n      - translator_minimal\n\n  anatomical context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing an anatomical location where an relationship expressed in an\n      association took place (can be a tissue, cell type, or sub-cellular location).\n    notes: >-\n      Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ \n      combines with a core concept of ‘neuron’ \n      to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies \n      taxonomic context, e.g. species-specific molecular activity.  Ontology CURIEs are expected as values \n      here, the examples below are intended to help clarify the content of the CURIEs.\n    examples:\n      - value: blood  # UBERON:0000178\n      - value: cerebral cortext  # UBERON:0000956\n    in_subset:\n      - translator_minimal\n\n  species context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a taxonomic category of species in which a relationship\n      expressed in an association took place.\n    range: organism taxon\n    examples:\n      - value: zebrafish  # NCBITaxon:7955\n      - value: human  # NCBITaxon:9606\n    notes: >- \n      Ontology CURIEs are expected as values\n      here, the examples below are intended to help clarify the content of the CURIEs.\n    in_subset:\n      - translator_minimal\n\n  qualifiers:\n    deprecated: true\n    description: >-\n      connects an association to qualifiers that modify or\n      qualify the meaning of that association\n    local_names:\n      ga4gh: annotation qualifier\n    is_a: association slot\n    multivalued: true\n    range: ontology class\n\n  frequency qualifier:\n    is_a: qualifier\n    description: >-\n      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\n    range: frequency value\n    in_subset:\n      - translator_minimal\n\n  severity qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      how severe the phenotype is in the subject\n    is_a: qualifier\n    range: severity value\n    in_subset:\n      - translator_minimal\n\n  sex qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state whether\n      the association is specific to a particular sex.\n    is_a: qualifier\n    range: biological sex\n    in_subset:\n      - translator_minimal\n\n  onset qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      when the phenotype appears is in the subject\n    is_a: qualifier\n    range: onset\n    in_subset:\n      - translator_minimal\n\n  clinical modifier qualifier:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    is_a: association slot\n    range: clinical modifier\n\n  sequence variant qualifier:\n    description: >-\n      a qualifier used in an association with the variant\n    is_a: association slot\n    range: sequence variant\n\n  quantifier qualifier:\n    is_a: association slot\n    range: ontology class\n    description: >-\n      A measurable quantity for the object of the association\n    narrow_mappings:\n       # TODO: RTX contributed terms mapped here... May need review?\n      - LOINC:analyzes\n      - LOINC:measured_by\n      - LOINC:property_of\n      - SEMMEDDB:MEASURES\n      - UMLS:measures\n\n  catalyst qualifier:\n    is_a: association slot\n    multivalued: true\n    range: macromolecular machine mixin\n    description: >-\n      a qualifier that connects an association between two causally connected\n      entities (for example, two chemical entities, or a chemical entity in\n      that changes location) and the gene product, gene, or complex that\n      enables or catalyzes the change.\n\n  stage qualifier:\n    description: >-\n      stage during which gene or protein expression of takes place.\n    is_a: association slot\n    range: life stage\n     # path: \"object/during\"\n    examples:\n      - value: UBERON:0000069\n        description: larval stage\n    in_subset:\n      - translator_minimal\n\n   ## --------------------\n   ## PREDICATES/RELATIONS\n   ## --------------------\n\n  related to:\n    description: >-\n      A relationship that is asserted between two named things\n    domain: named thing\n    range: named thing\n    multivalued: true\n    inherited: true\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:relatedMatch\n      - UMLS:related_to\n      - SEMMEDDB:ASSOCIATED_WITH\n      - SEMMEDDB:ADMINISTERED_TO\n    broad_mappings:\n      - owl:topObjectProperty\n    narrow_mappings:\n      - SEMMEDDB:compared_with\n      - SEMMEDDB:higher_than\n      - SEMMEDDB:lower_than\n      - BFO:0000054\n      - UBERON_CORE:protects\n      - GOREL:0002005\n      - GOREL:0012006\n       # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms\n      - BTO:related_to\n      - CHEBI:is_conjugate_acid_of\n      - CHEBI:is_conjugate_base_of\n      - CPT:has_add_on_code\n      - CPT:mapped_to\n      - EFO:0006351\n      - FMA:connected_to\n      - FMA:continuous_with\n      - FMA:homonym_of\n      - FMA:related_developmental_entity_of\n      - RO:0002093\n      - RO:0002092\n      - RO:0002084\n      - HCPCS:mapped_to\n       # RTX contributed terms, perhaps belong somewhere else with more precise semantics?\n      - HMDB:disease\n      - HMDB:has_protein_association\n      - IAO:0000136\n      - LOINC:has_answer\n      - LOINC:has_challenge\n      - LOINC:has_evaluation\n      - LOINC:mapped_to\n      - LOINC:mth_has_expanded_form\n      - MESH:RO\n      - MESH:has_mapping_qualifier\n      - MESH:mapped_to\n      - MONDO:disease_shares_features_of\n      - NCIT:disease_may_have_associated_disease\n      - NCIT:human_disease_maps_to_eo_disease\n      - NCIT:is_abnormal_cell_of_disease\n      - NCIT:is_related_to_endogenous_product\n      - UBERON_NONAMESPACE:connected_to\n      - UBERON_NONAMESPACE:innervated_by\n      - NBO-PROPERTY:is_about\n      - RO:0000053  # bearer_of\n      - PATO:reciprocal_of\n      - RO:0000052\n      - RO:0002001\n      - RO:0002002\n      - RO:0002003\n      - RO:0002008\n      - RO:0002134\n      - RO:0002150\n      - RO:0002159\n      - RO:0002176\n      - RO:0002177\n      - RO:0002178\n      - RO:0002179\n      - RO:0002314\n      - RO:0002322\n       # functionally related to\n      - RO:0002328\n      - RO:0002332\n      - RO:0002338\n      - RO:0002339\n      - RO:0002341\n      - RO:0002342\n      - RO:0002344\n      - RO:0002348\n      - RO:0002349\n      - RO:0002356\n      - RO:0002371\n      - RO:0002372\n      - RO:0002373\n      - RO:0002374\n      - RO:0002385\n      - RO:0002387\n      - RO:0002451\n      - RO:0002494\n      - RO:0002495\n      - RO:0002568\n      - RO:0002573\n      - RO:0004026\n      - RO:0004027\n      - RO:0009001\n      - RO:0009004\n      - RXNORM:has_form\n      - RXNORM:reformulated_to\n      - SNOMED:has_associated_morphology\n      - SNOMED:has_associated_procedure\n      - SNOMED:has_direct_morphology\n      - SNOMED:has_disposition\n      - SNOMED:has_indirect_morphology\n      - SNOMED:has_modification\n      - SNOMED:has_procedure_morphology\n      - SNOMED:has_specimen_source_morphology\n      - SNOMED:inheres_in\n      - SNOMED:is_interpreted_by\n      - SNOMED:relative_to_part_of\n      - UBERON:synapsed_by\n      - UMLS:RO\n      - UMLS:RQ\n      - UMLS:class_code_classified_by\n      - UMLS:exhibited_by\n      - UMLS:has_context_binding\n      - UMLS:has_form\n      - UMLS:has_mapping_qualifier\n      - UMLS:larger_than\n      - UMLS:mapped_to\n      - UMLS:owning_section_of\n\n  related to at concept level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between terminology components that describe the conceptual model of a domain.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  related to at instance level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between two instances of a data classes.  Much like an assertion component,\n      in an ABox, these represent facts associated with the conceptual model.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  associated with:\n    is_a: related to at instance level\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent,\n      'related to'. This relationship holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated.  E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial \n      Infraction (MI)” asserts that having Afib is not statistically independent from whether a patient \n      will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to \n      the statistical variables, or represent related entities for which the variables serve as proxies in an \n      Association (e.g. diseases, chemical entities or processes).\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    domain: named thing\n    range: named thing\n    narrow_mappings:\n      - RO:0004029\n      - SNOMEDCT:47429007\n\n  superclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a super class of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q66088480\n      - CHEMBL.MECHANISM:superset_of\n      - GO:inverse_isa\n      - RXNORM:inverse_isa\n      - MESH:inverse_isa\n      - VANDF:inverse_isa\n    narrow_mappings:\n      - NCIT:cdrh_parent_of\n      - NCIT:ctcae_5_parent_of\n      - NCIT:subset_includes_concept\n      - OMIM:has_manifestation\n      - SNOMED:has_basic_dose_form\n      - UMLS:RB\n\n  subclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a specialization of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # RTX\n      - LOINC:class_of\n      - LOINC:has_class\n    exact_mappings:\n      - rdfs:subClassOf\n      - SEMMEDDB:ISA\n      - WIKIDATA_PROPERTY:P279\n      - CHEMBL.MECHANISM:subset_of\n      - GO:isa\n      - MESH:isa\n      - RXNORM:isa\n      - VANDF:isa\n    narrow_mappings:\n      - CHEBI:has_parent_hydride\n      - LOINC:has_archetype\n      - LOINC:has_parent_group\n      - LOINC:is_presence_guidance_for\n      - NCIT:gene_product_has_chemical_classification\n       # RTX mapped terms classes for biomarkers\n      - NCIT:R36\n      - NCIT:R42\n      - NCIT:A16\n      - NCIT:A11\n      - NCIT:A14\n      - NCIT:A3\n      - NDDF:has_dose_form\n      - RXNORM:has_dose_form\n      - RXNORM:has_doseformgroup\n      - SNOMED:entire_anatomy_structure_of\n      - SNOMED:has_dose_form\n       # RTX mapping\n      - rdfs:subPropertyOf\n\n  same as:\n    is_a: exact match\n    description: >-\n      holds between two entities that are considered equivalent to each other\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # identical class extension with identical sets of individuals\n      - owl:equivalentClass\n    exact_mappings:\n       # identical individual, or identical class concept/meaning\n      - owl:sameAs\n      - skos:exactMatch\n       # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n       # RTX suggests mapping this to proposed new \"biolink:close_match\" predicate instead\n       # - SEMMEDDB:same_as\n      - WIKIDATA_PROPERTY:P2888\n      - CHEMBL.MECHANISM:equivalent_to\n      - MONDO:equivalentTo\n    narrow_mappings:\n      - DRUGBANK:external-identifier\n\n  close match:\n    is_a: related to at concept level\n    description: >-\n      a list of terms from different schemas or terminology systems that have\n      a semantically similar but not strictly equivalent, broader, or narrower\n      meaning. Such terms often describe the same general concept from\n      different ontological perspectives (e.g. drug as a type of chemical\n      entity versus drug as a type of role borne by a chemical entity).\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:closeMatch\n       # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      - SEMMEDDB:same_as\n    narrow_mappings:\n      - CHEBI:is_enantiomer_of\n      - CHEBI:is_tautomer_of\n      - MEDDRA:classified_as\n      - oboInOwl:hasDbXref\n      - RXNORM:has_quantified_form\n      - UMLS:SY\n\n  exact match:\n    is_a: close match\n    description: >-\n      holds between two entities that have strictly equivalent\n      meanings, with a high degree of confidence\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:exactMatch\n      - WIKIDATA:Q39893449\n      - WIKIDATA:P2888\n\n  broad match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a broader, more general meaning. Broader terms are\n      typically shown as parents in a hierarchy or tree.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: narrow match\n    exact_mappings:\n      - skos:broadMatch\n      - WIKIDATA:Q39894595\n\n  narrow match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a narrower, more specific meaning. Narrower terms are\n      typically shown as children in a hierarchy or tree.\n    is_a: related to at concept level\n    inverse: broad match\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - skos:narrowMatch\n      - WIKIDATA:Q39893967\n    annotations:\n      opposite_of: broad match\n\n  member of:\n    description: >-\n      Defines a mereological relation between a item and a collection.\n    is_a: related to at concept level\n    inverse: has member\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002350\n    close_mappings:\n      - skos:member\n\n  has member:\n    description: >-\n      Defines a mereological relation between a collection and an item.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002351\n      - skos:member\n\n  opposite of:\n    description: >-\n      x is the opposite of y if there exists some distance metric M, and there exists\n      no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002604\n    see_also:\n      - https://doi.org/10.1101/108977\n      - https://github.com/biolink/biolink-model/issues/657\n\n\n  associated with likelihood of:\n    is_a: associated with\n    description: >-\n      A a relationship that holds between two concepts represented by variables for which a statistical \n      dependence is demonstrated, wherein the state or value of one variable predicts the future state \n      or value of the other.  E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated \n      with likelihood of a Myocardial Infraction (MI) diagnosis” asserts that the state of having Afib \n      is associated with an increased or decreased likelihood that a patient will later exhibit MI.\n    annotations:\n      canonical_predicate: true\n\n  likelihood associated with:\n    is_a: associated with\n    description: >-\n    inverse: associated with likelihood of\n\n  associated with increased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is more probable.\n    annotations:\n      canonical_predicate: true\n\n  increased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with increased likelihood of\n\n  associated with decreased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is less probable.\n    annotations:\n      canonical_predicate: true\n\n  decreased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with decreased likelihood of\n\n  target for:\n    is_a: related to at instance level\n    description: >-\n      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene\n      product could have a therapeutic effect\n    annotations:\n      canonical_predicate: true\n    domain: gene\n    range: disease\n\n  has target:\n    is_a: related to at instance level\n    inverse: target for\n    domain: disease\n    range: gene\n\n  active in:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: cellular component\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002432\n\n  has active component:\n    is_a: related to at instance level\n    inverse: active in\n    domain: cellular component\n    range: gene or gene product\n\n  acts upstream of:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002263\n\n  has upstream actor:\n    is_a: related to at instance level\n    inverse: acts upstream of\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004034\n\n  has positive upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004035\n\n  has negative upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of negative effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002264\n\n  has upstream or within actor:\n    is_a: has upstream actor\n    inverse: acts upstream of or within\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within positive effect:\n    is_a: acts upstream of or within\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004032\n\n  has positive upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within negative effect:\n    is_a: acts upstream of or within\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004033\n\n  has negative upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within negative effect\n    domain: biological process\n    range: gene or gene product\n\n     ## Publication related predicates\n  mentions:\n    description: >-\n      refers to is a relation between one information content entity and the named thing\n      that it makes reference to.\n    is_a: related to at instance level\n    exact_mappings:\n      - IAO:0000142\n    narrow_mappings:\n      - SIO:000628\n\n  mentioned by:\n    description: >-\n      refers to is a relation between one named thing and the information content entity\n      that it makes reference to.\n    is_a: related to at instance level\n    inverse: mentions\n\n   ## Publication related predicates\n\n  contributor:\n    is_a: related to at instance level\n    domain: agent\n    range: information content entity\n    comments:\n      - This is a grouping for predicates relating entities to their associated contributors realizing them\n    abstract: true\n    exact_mappings:\n      - dct:contributor\n\n  has contributor:\n    inverse: contributor\n    is_a: related to at instance level\n    domain: information content entity\n    range: agent\n\n  provider:\n    is_a: contributor\n    description: >-\n      person, group, organization or project that provides a piece of information (e.g. a knowledge association).\n\n  has provider:\n    inverse: provider\n    is_a: has contributor\n    domain: information content entity\n    range: agent\n\n  publisher:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      organization or person responsible for publishing books, periodicals, podcasts, games or software.\n      Note that in the case of publications which have a containing \"published in\" node property, the publisher\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the publisher agent of the encompassing publication\n      (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).\n    exact_mappings:\n      - dct:publisher\n      - WIKIDATA_PROPERTY:P123\n\n  has publisher:\n    is_a: has contributor\n    inverse: publisher\n    domain: publication\n    range: agent\n\n  editor:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      editor of a compiled work such as a book or a periodical (newspaper or an academic journal).\n      Note that in the case of publications which have a containing \"published in\" node property, the editor\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the editorial agent of the encompassing publication\n      (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P98\n\n  has editor:\n    inverse: editor\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n  author:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      an instance of one (co-)creator primarily responsible for a written work\n    exact_mappings:\n      - dct:creator\n      - WIKIDATA_PROPERTY:P50\n\n  has author:\n    inverse: author\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n   ## end of Publication related predicates\n\n  assesses:\n    is_a: related to at instance level\n    aliases: ['was assayed against']\n    description: >-\n      The effect of a thing on a target was interrogated in some assay.\n      A relationship between some perturbing agent (usually a chemical compound) and some target entity,\n      where the affect of the perturbing agent on the target entity was interrogated in a particular assay.\n      The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type\n      of biological entity.\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n\n  is assessed by:\n    is_a: related to at instance level\n    inverse: assesses\n    domain: named thing\n    range: named thing\n\n  interacts with:\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between any two entities that directly or indirectly interact with each other\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    mixin: true\n    exact_mappings:\n      - SEMMEDDB:INTERACTS_WITH\n    notes: >-\n      please use a more specific child predicate of interacts with, either physically interacts with\n      or genetically interacts with. \n\n  physically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two entities that make physical contact as part of some interaction. \n      does not imply a causal relationship.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - WIKIDATA_PROPERTY:P129\n    close_mappings:\n      - CHEMBL.MECHANISM:binding_agent\n      - CHEMBL.MECHANISM:chelating_agent\n      - CHEMBL.MECHANISM:cross-linking_agent\n      - CHEMBL.MECHANISM:oxidative_enzyme\n      - CHEMBL.MECHANISM:sequestering_agent\n      - CHEMBL.MECHANISM:substrate\n      - DRUGBANK:target\n    narrow_mappings:\n       # Defined more narrowly as \"substance interaction\", thus specific applies to a subclass entities\n      - DRUGBANK:drug-interaction\n      - FMA:adheres_to\n      - NCIT:A7\n      - PR:non-covalently_bound_to\n    mixins:\n      - interacts with\n\n  directly physically interacts with:\n    is_a: physically interacts with\n    description: >-\n      A causal mechanism mediated by a direct contact between the effector and target entities (this contact may \n      be weak or strong, transient or stable).\n    symmetric: true\n    exact_mappings:\n      - RO:0002436\n    broad_mappings:\n       # Definition of this term is more generic than direct physical molecular interactions:\n       # A is connected to B iff there exists a fiat, material or temporal path between A and B.\n      - SIO:000203\n      - RO:0002578\n    narrow_mappings:\n      - PHAROS:drug_targets\n      - DRUGBANK:chelator\n      - CTD:affects_binding\n      - DGIdb:cofactor\n    annotations:\n      canonical_predicate: true\n\n  binds:\n    deprecated: true\n    is_a: directly physically interacts with\n    description: >-\n      A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, \n      which form a stable physical interaction.\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - DGIdb:binder\n\n  indirectly physically interacts with:\n    is_a: physically interacts with\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  genetically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two genes whose phenotypic effects are dependent on each\n      other in some way - such that their combined phenotypic effects are the\n      result of some interaction between the activity of their gene products.\n      Examples include epistasis and synthetic lethality.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    exact_mappings:\n      - RO:0002435\n      \n  gene_fusion_with:\n    is_a: genetically interacts with\n    description: >-\n      holds between two independent genes that have fused through \n      translocation, interstitial deletion, or chromosomal inversion to \n      form a new, hybrid gene. Fusion genes are often implicated in various neoplasms\n      and cancers.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    \n  genetic_neighborhood_of:\n    is_a: genetically interacts with\n    description: >-\n      holds between two genes located nearby one another on a chromosome. \n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  affects:\n    is_a: related to at instance level\n    description: >-\n      describes an entity that has a direct affect on the state or quality\n      of another existing entity. Use of the 'affects' predicate implies that\n      the affected entity already exists, unlike predicates such as\n      'affects risk for' and 'prevents, where the outcome is something\n      that may or may not come to be.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n       # Contributed by RTX. Seems possible that a new predicate \"biolink:in_pathway\" could be justified?\n      - DRUGBANK:pathway\n    exact_mappings:\n      - SEMMEDDB:AFFECTS\n      - DGIdb:affects\n    narrow_mappings:\n      - CTD:prediction_hypothesis\n      - GOREL:0001006\n      - CTD:inferred\n      - UPHENO:0000001\n      - RO:0002263\n      - RO:0002264\n      - NCIT:R158\n      - NCIT:R160\n      - NCIT:R30\n      - NCIT:R150\n      - NCIT:R72\n      - NCIT:R146\n      - NCIT:R124\n      - NCIT:R173\n      - NCIT:R100\n      - NCIT:R102\n      - NCIT:R101\n      - NCIT:R113\n      - NCIT:R23\n      - NCIT:R25\n      - NCIT:gene_mapped_to_disease\n      - NCIT:R133\n      - RO:0002343\n      - RO:0002355\n      - RO:0002591\n      - RO:0002592\n      - RO:0012003\n      - SNOMED:has_pathological_process\n      - UBERGRAPH:is_increase_of  # talked to Jim Balhoff, this is a valid mapping\n      - UBERGRAPH:is_decrease_of  # talked to Jim Balhoff, this is a valid mapping\n\n  affected by:\n    is_a: related to at instance level\n    description: >-\n      describes an entity of which the state or quality is affected by\n      another existing entity.\n    inverse: affects\n\n  associated with sensitivity to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of sensitivity to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - PATO:0000085  # sensitivity toward\n    narrow_mappings:\n      - SNOMEDCT:418038007  # propensity to adverse reaction\n\n  sensitivity associated with:\n    is_a: associated with\n    inverse: associated with sensitivity to\n    range: named thing\n    domain: chemical entity\n\n  associated with resistance to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of resistance to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n\n  resistance associated with:\n    is_a: associated with\n    inverse: associated with resistance to\n    range: named thing\n    domain: chemical entity\n\n  diagnoses:\n    is_a: related to at instance level\n    description: >-\n      a relationship that identifies the nature of (an illness or other problem) by examination \n      of the symptoms.\n    domain: diagnostic aid\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - NCIT:C15220  # diagnosis\n      - SIO:001331  # diagnosis\n    exact_mappings:\n      - DrugCentral:5271\n      - SEMMEDDB:DIAGNOSES\n\n  is diagnosed by:\n    is_a: related to at instance level\n    inverse: diagnoses\n    domain: disease or phenotypic feature\n    range: diagnostic aid\n\n  increases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that increase the amount\n      or activity of the object.\n\n  amount or activity increased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: increases amount or activity of\n\n  decreases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that decrease the amount\n      or activity of the object.\n\n  amount or activity decreased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: decreases amount or activity of\n\n   ## role mixins for use in tagging corresponding role predicates\n\n  chemical role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a chemical context.\n    mixin: true\n    exact_mappings:\n      - CHEBI:51086\n\n  biological role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a biological context.\n    mixin: true\n    narrow_mappings:\n      - CHEBI:24432\n\n  affects response to:\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: response affected by\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_response_to\n\n  response affected by:\n    description: >-\n      holds between two chemical entities where the susceptibility of a biological entity or system\n      (e.g. an organism, cell, cellular component, macromolecular machine mixin,\n      biological or pathological process) of one is affected by the action of the other.\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases response to\n    exact_mappings:\n      - CTD:increases_response_to\n\n  response increased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases response to\n\n  decreases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases response to\n    exact_mappings:\n      - CTD:decreases_response_to\n    narrow_mappings:\n      - CTD:decreases_response_to_substance\n\n  response decreased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases response to\n\n  regulates:\n    is_a: affects\n    description: >-\n      A more specific form of affects, that implies the effect results from a biologically evolved control mechanism.\n      Gene-affects-gene relationships will (almost) always involve regulation.  Exogenous/environmental chemical-affects-gene relationships \n      are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or\n      possibly one of the 'interacts with' predicates depending on the nature of the interaction.\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002448\n    broad_mappings:\n       # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology)\n      - WIKIDATA_PROPERTY:P128\n      - CHEMBL.MECHANISM:modulator\n      - RO:0002295\n      - RO:0002332\n      - RO:0002448\n    notes: >-\n      The RO definition of 'directly regulates the activity of' is an exact_mapping here because \n      it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to\n      \"RO:0002211\" which describes process to process regulation.\n    mixins:\n      - interacts with\n\n  regulated by:\n    is_a: affected by\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    inverse: regulates\n\n  disrupts:\n    is_a: affects\n    aliases: ['disease causes disruption of']\n    description: >-\n      describes a relationship where one entity degrades or interferes\n      with the structure, function, or occurrence of another.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: enables\n    exact_mappings:\n      - SEMMEDDB:DISRUPTS\n      - CHEMBL.MECHANISM:disrupting_agent\n    narrow_mappings:\n      - RO:0004024\n      - RO:0004025\n\n  disrupted by:\n    is_a: affected by\n    description: >-\n      describes a relationship where the structure, function, or occurrence\n      of one entity is degraded or interfered with by another.\n    inverse: disrupts\n\n  gene product of:\n    is_a: related to at instance level\n    description: >-\n      definition x has gene product of y if and only if y is a gene (SO:0000704)\n      that participates in some gene expression process (GO:0010467) where the output of thatf\n      process is either y or something that is ribosomally translated from x\n    exact_mappings:\n      - RO:0002204\n    domain: gene product mixin\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: has gene product\n    in_subset:\n      - translator_minimal\n\n  has gene product:\n    is_a: related to at instance level\n    description: >-\n      holds between a gene and a transcribed and/or\n      translated product generated from it\n    domain: gene\n    range: gene product mixin\n    inverse: gene product of\n    in_subset:\n      - translator_minimal\n    close_mappings:\n       # RTX term tagged as inverse mapping\n      - PR:has_gene_template\n    exact_mappings:\n      - RO:0002205\n      - WIKIDATA_PROPERTY:P688\n      - NCIT:gene_encodes_gene_product\n    narrow_mappings:\n      - NCIT:R178\n\n  transcribed to:\n    is_a: related to at instance level\n    domain: gene\n    range: transcript\n    description: >-\n      inverse of transcribed from\n    inverse: transcribed from\n    exact_mappings:\n      - RO:0002511\n      - SIO:010080\n\n  transcribed from:\n    is_a: related to at instance level\n    domain: transcript\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: transcribed to\n    description: >-\n      x is transcribed from y if and only if x is synthesized from template y\n    exact_mappings:\n      - RO:0002510\n      - SIO:010081\n\n  translates to:\n    is_a: related to at instance level\n    domain: transcript\n    range: protein\n    annotations:\n      canonical_predicate: true\n    inverse: translation of\n    description: >-\n      x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome\n      reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)\n      and produces x (amino acid chain/polypeptide)\n    close_mappings:\n      - RO:0002513\n      - SIO:010082\n\n  translation of:\n    is_a: related to at instance level\n    domain: protein\n    range: transcript\n    description: >-\n      inverse of translates to\n    inverse: translates to\n    close_mappings:\n      - RO:0002512\n      - SIO:010083\n\n  homologous to:\n    is_a: similar to\n    aliases: ['in homology relationship with']\n    description: >-\n      holds between two biological entities that have common evolutionary origin\n    comments:\n      - typically used to describe homology relationships between genes or gene products\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000001\n      - SIO:010302\n    narrow_mappings:\n       # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158\n      - UBERON_CORE:sexually_homologous_to\n\n  paralogous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000011\n\n  orthologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship between entities (typically genes) that diverged after a speciation event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000017\n      - WIKIDATA_PROPERTY:P684\n\n  xenologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000018\n\n  coexists with:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - SEMMEDDB:COEXISTS_WITH\n    narrow_mappings:\n      - BSPO:0000096\n      - BSPO:0000097\n      - BSPO:0000098\n      - BSPO:0000099\n      - BSPO:0000100\n      - BSPO:0000102\n      - BSPO:0000104\n      - BSPO:0000110\n      - BSPO:0000113\n      - BSPO:0015001\n      - BSPO:0015002\n      - BSPO:0015003\n      - BSPO:0015005\n      - BSPO:0015006\n      - BSPO:0015007\n      - BSPO:0015008\n      - BSPO:0015009\n      - BSPO:0015012\n      - BSPO:0015014\n      - BSPO:parallel_to\n      - UBERON_CORE:anastomoses_with\n      - UBERON_CORE:anteriorly_connected_to\n      - UBERON_CORE:posteriorly_connected_to\n      - UBERON_CORE:channel_for\n      - UBERON_CORE:channels_from\n      - UBERON_CORE:channels_into\n      - UBERON_CORE:conduit_for\n      - UBERON_CORE:distally_connected_to\n      - UBERON_CORE:extends_fibers_into\n      - UBERON_CORE:filtered_through\n      - UBERON_CORE:indirectly_supplies\n      - UBERON_CORE:proximally_connected_to\n      - UBERON_CORE:synapsed_by\n      - UBERON_CORE:transitively_anteriorly_connected_to\n      - UBERON_CORE:transitively_connected_to\n      - UBERON_CORE:transitively_distally_connected_to\n      - UBERON_CORE:transitively_proximally_connected_to\n       # RTX contributed Environmental Ontology term meaning \"partially surrounded by\"\n      - ENVO:01001307\n      - FMA:adjacent_to\n      - FMA:afferent_to\n      - FMA:anterior_to\n      - FMA:anteroinferior_to\n      - FMA:anterolateral_to\n      - FMA:anteromedial_to\n      - FMA:anterosuperior_to\n       # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics?\n       # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink\n      - FMA:arterial_supply_of\n      - FMA:has_arterial_supply\n      - FMA:articulates_with\n      - FMA:attaches_to\n      - FMA:bounded_by\n      - FMA:bounds\n      - FMA:branch_of\n      - FMA:connection_type_of\n      - FMA:continuation_branch_of\n      - FMA:continuous_distally_with\n      - FMA:continuous_proximally_with\n      - FMA:corresponds_to\n      - FMA:development_type_of\n      - FMA:developmental_stage_of\n      - FMA:direct_cell_shape_of\n      - FMA:direct_left_of\n      - FMA:direct_right_of\n      - FMA:distal_to\n      - FMA:drains_into\n      - FMA:efferent_to\n      - FMA:external_to\n      - FMA:formed_by\n      - FMA:forms\n       # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:full_grown_phenotype_of\n      - FMA:has_full_grown_phenotype\n       # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:fuses_with\n      - FMA:fusion_of\n      - FMA:has_fusion\n      - FMA:germ_origin_of\n      - FMA:has_germ_origin\n      - FMA:has_adherent\n      - FMA:has_branch\n      - FMA:has_connection_type\n      - FMA:has_continuation_branch\n      - FMA:has_development_type\n      - FMA:has_developmental_stage\n      - FMA:has_direct_cell_shape\n      - FMA:has_inherent_3d_shape\n      - FMA:has_insertion\n      - FMA:has_lymphatic_drainage\n      - FMA:has_nerve_supply\n      - FMA:has_observed_anatomical_entity\n      - FMA:has_origin\n      - FMA:has_primary_segmental_supply\n      - FMA:has_projection\n      - FMA:has_regional_part\n      - FMA:has_related_developmental_entity\n      - FMA:has_secondary_segmental_supply\n      - FMA:has_segmental_composition\n      - FMA:has_segmental_supply\n      - FMA:has_tributary\n      - FMA:has_venous_drainage\n      - FMA:inferior_to\n      - FMA:inferolateral_to\n      - FMA:inferomedial_to\n      - FMA:inherent_3d_shape_of\n      - FMA:insertion_of\n      - FMA:internal_to\n      - FMA:lateral_to\n      - FMA:left_lateral_to\n      - FMA:left_medial_to\n      - FMA:lymphatic_drainage_of\n      - FMA:matures_from\n      - FMA:matures_into\n      - FMA:medial_to\n      - FMA:merges_with\n      - FMA:nerve_supply_of\n      - FMA:origin_of\n      - FMA:posterior_to\n      - FMA:posteroinferior_to\n      - FMA:posterolateral_to\n      - FMA:posteromedial_to\n      - FMA:posterosuperior_to\n      - FMA:primary_segmental_supply_of\n      - FMA:projects_from\n      - FMA:projects_to\n      - FMA:proximal_to\n      - FMA:receives_attachment_from\n      - FMA:receives_drainage_from\n      - FMA:receives_input_from\n      - FMA:receives_projection\n      - FMA:related_part\n      - FMA:right_lateral_to\n      - FMA:right_medial_to\n      - FMA:secondary_segmental_supply_of\n      - FMA:segmental_composition_of\n      - FMA:segmental_supply_of\n      - FMA:sends_output_to\n      - FMA:superior_to\n      - FMA:superolateral_to\n      - FMA:superomedial_to\n      - FMA:surrounded_by\n      - FMA:surrounds\n      - FMA:tributary_of\n      - FMA:venous_drainage_of\n       # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute'\n       # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now\n      - LOINC:has_lateral_anatomic_location\n      - LOINC:has_lateral_location_presence\n      - UBERON_NONAMESPACE:distally_connected_to\n      - UBERON_NONAMESPACE:subdivision_of\n       # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to'\n      - RO:0002219\n      - RO:0002220\n      - RO:0002221\n      - SO:has_origin\n       # RTX mapped these UBERON terms all here\n      - UBERON:anastomoses_with\n      - UBERON:anteriorly_connected_to\n      - UBERON:channel_for\n      - UBERON:channels_from\n      - UBERON:channels_into\n      - UBERON:conduit_for\n      - UBERON:distally_connected_to\n      - UBERON:existence_starts_and_ends_during\n      - UBERON:extends_fibers_into\n      - UBERON:filtered_through\n      - UBERON:in_central_side_of\n      - UBERON:in_innermost_side_of\n      - UBERON:in_outermost_side_of\n      - UBERON:indirectly_supplies\n      - UBERON:posteriorly_connected_to\n      - UBERON:protects\n      - UBERON:proximally_connected_to\n      - UBERON:sexually_homologous_to\n\n  in pathway with:\n    description: >-\n      holds between two genes or gene products that are part of in the same biological pathway\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n       # generally pertains to membership of a (subject) component - gene,\n       # metabolite, etc? - in an (object) metabolic pathway\n      - SIO:010532\n\n  in complex with:\n    description: >-\n      holds between two genes or gene products that are part of (or code for\n      products that are part of) in the same macromolecular complex\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n       # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though)\n      - SIO:010497\n    broad_mappings:\n       # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes)\n      - SIO:010285\n\n  in cell population with:\n    description: >-\n      holds between two genes or gene products that are expressed in the same cell type or population\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  colocalizes with:\n    description: >-\n      holds between two entities that are observed to be located in the same place.\n    is_a: coexists with\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002325\n\n   # Despite the name, note that this particular entity is\n   # NOT a biolink:Association but rather, a biolink:predicate\n  genetic association:\n    deprecated: true\n    deprecated_element_has_exact_replacement: biolink:genetically_associated_with\n    is_a: associated with\n    symmetric: true\n\n  genetically associated with:\n    is_a: associated with\n    description: >-\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      description: >-\n        Co-occurrence of a certain allele of a genetic marker and the phenotype\n        of interest in the same individuals at above-chance level\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2293\n    in_subset:\n      - translator_minimal\n\n  gene associated with condition:\n    is_a: genetically associated with\n    description: >-\n      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,\n      contribute to, or correlate with\n    domain: disease or phenotypic feature\n    range: gene\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - GENO:0000840  # broader than a single gene: 'genotype' pathogenic for condition\n      - GENO:0000841\n    narrow_mappings:\n       # narrower: just diseases, not phenotypic features as well\n      - NCIT:R38\n      - NCIT:R175\n      - NCIT:R48\n\n  condition associated with gene:\n    is_a: genetically associated with\n    aliases: ['disease associated with gene']\n    description: >-\n      holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products\n    domain: gene\n    range: disease or phenotypic feature\n    in_subset:\n      - translator_minimal\n    inverse: gene associated with condition\n    narrow_mappings:\n       # narrower since just diseases, not phenotypic features as well\n      - NCIT:R176\n\n  affects risk for:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where exposure to one entity alters the chance of developing the other\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  risk affected by:\n    is_a: related to at instance level\n    inverse: affects risk for\n\n  predisposes:\n    is_a: affects risk for\n    description: >-\n      holds between two entities where exposure to one entity increases the chance of developing the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:PREDISPOSES\n\n  has predisposing factor:\n    is_a: risk affected by\n    inverse: predisposes\n    in_subset:\n      - translator_minimal\n\n  contributes to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one contributes to the\n      occurrence or generation of the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # RTX contributed mapping tagged as 'inverse' of this Biolink predicate\n      - IDO:0000664\n    exact_mappings:\n      - RO:0002326\n    narrow_mappings:\n      - CTD:marker_mechanism\n      - MONDO:predisposes_towards\n       # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002255\n       # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here\n      - RO:0003304\n\n  contribution from:\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    inverse: contributes to\n\n  causes:\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes the occurrence\n      or generation of the other\n    is_a: contributes to\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    exact_mappings:\n      - SEMMEDDB:CAUSES\n      - WIKIDATA_PROPERTY:P1542\n      - SNOMED:cause_of\n      - RO:0003303\n    broad_mappings:\n      - RO:0002410\n      - RO:0002506\n    narrow_mappings:\n      - MONDO:disease_triggers\n      - GOREL:0000040\n      - MONDO:disease_causes_feature\n      - MONDO:disease_triggers\n      - NCIT:allele_has_abnormality\n      - NCIT:biological_process_has_result_biological_process\n      - NCIT:chemical_or_drug_has_physiologic_effect\n       # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'?\n      - NCIT:chemical_or_drug_initiates_biological_process\n      - NCIT:process_initiates_biological_process\n      - NCIT:chromosome_mapped_to_disease\n      - NCIT:disease_has_normal_tissue_origin\n      - NBO-PROPERTY:in_response_to\n      - orphanet:317343\n      - orphanet:317344\n      - orphanet:317346\n      - orphanet:410295\n      - orphanet:410296\n       # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002256\n      - RO:0002315\n      - RO:0002507\n      - RO:0002509\n      - RO:0004001\n      - SNOMED:causative_agent_of\n      - SNOMED:has_realization\n      - UMLS:has_physiologic_effect\n\n  caused by:\n    description: >-\n      holds between two entities where the occurrence, existence,\n      or activity of one is caused by the occurrence or generation of the other\n    is_a: contribution from\n    aliases: ['disease caused by disruption of', 'disease has basis in dysfunction of',\n              'realized in response to', 'realized in response to stimulus']\n    in_subset:\n      - translator_minimal\n    inverse: causes\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P828\n    narrow_mappings:\n      - RO:0001022\n      - RO:0002608\n      - RO:0004019\n      - RO:0004020\n      - RO:0004028\n      - RO:0009501\n\n   # TODO: ameliorates and exacerbates inverses.\n  ameliorates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a genotype,\n      genetic variation, chemical, or environmental exposure, clinical intervention)\n      and a condition (a phenotype or disease), where the\n      presence of the entity reduces or eliminates some or\n      all aspects of the condition.\n     # 'biological entity' currently includes 'exposure event' which covers a lot of related ground\n    domain: named thing\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: exacerbates\n    exact_mappings:\n      - RO:0003307\n\n  is ameliorated by:\n    inverse: ameliorates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: named thing\n\n  exacerbates:\n    is_a: affects\n    description: >-\n      A relationship between an entity (e.g. a chemical,\n      environmental exposure, or some form of genetic variation)\n      and a condition (a phenotype or disease), where the presence\n      of the entity worsens some or all aspects of the condition.\n     # 'biological entity' currently includes 'exposure event' which covers a lot of related ground\n    domain: biological entity\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0003309\n    broad_mappings:\n      - SEMMEDDB:COMPLICATES\n\n  is exacerbated by:\n    inverse: exacerbates\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: biological entity\n    in_subset:\n      - translator_minimal\n\n  treats:\n    aliases: ['is substance that treats', 'indicated for']\n    is_a: ameliorates\n    description: >-\n      holds between a therapeutic procedure or chemical entity\n      and a disease or phenotypic feature that it is used to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: contraindicated for\n    in_subset:\n      - translator_minimal\n    related_mappings:\n      - MONDO:disease_responds_to\n    exact_mappings:\n      - DRUGBANK:treats\n      - SEMMEDDB:TREATS\n      - WIKIDATA_PROPERTY:P2175\n    narrow_mappings:\n       # \"is substance that treats\" constrains statements to\n       # a subset of the universe of all possible treatments\n      - RO:0002606\n      - NCIT:regimen_has_accepted_use_for_disease\n       # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n      - SNOMED:plays_role\n\n  treated by:\n    is_a: is ameliorated by\n    description: >-\n      holds between a disease or phenotypic feature and a therapeutic\n      process or chemical entity that is used to treat the condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n     # range: chemical or drug or treatment\n    in_subset:\n      - translator_minimal\n    inverse: treats\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2176\n       # RTX contributed term tagged as inverse of 'biolink:treats'\n      - MONDO:disease_responds_to\n    narrow_mappings:\n       # \"is treated by substance\" constrains statements to\n       # subset of the universe of all possible treatments\n      - RO:0002302\n\n  prevents:\n    is_a: affects risk for\n    description: >-\n      holds between an entity whose application or use reduces\n      the likelihood of a potential outcome. Typically used to associate\n      a chemical entity, exposure, activity, or medical intervention\n      that can prevent the onset a disease or phenotypic feature.\n    annotations:\n      canonical_predicate: true\n      opposite_of: predisposes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:PREVENTS\n    narrow_mappings:\n       # more restricted case of a material entity mitigating a pathological process\n      - RO:0002599\n\n  prevented by:\n    is_a: risk affected by\n    description: >-\n      holds between a potential outcome of which the likelihood\n      was reduced by the application or use of an entity.\n    inverse: prevents\n    annotations:\n      opposite_of: enabled by\n\n  correlated with:\n    is_a: associated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical dependence is \n      demonstrated using a correlation analysis method.\n    notes: >-\n      These concepts may map exactly to the statistical variables, or represent related entities for which the \n      variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002610\n      - PATO:correlates_with\n\n   # proposed positive and negative semantic extensions to the general \"correlated with\" predicate\n\n  positively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or \n      presence of one correlates with an increase or presence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: negatively correlated with\n    exact_mappings:\n      - CTD:positive_correlation\n\n  negatively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation \n      is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of \n      one correlates with a decrease or absence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: positively correlated with\n    exact_mappings:\n      - CTD:negative_correlation\n\n  occurs together in literature with:\n    is_a: correlated with\n    description: >-\n      holds between two entities where their co-occurrence is correlated by counts of publications\n      in which both occur, using some threshold of occurrence as defined by the edge provider.\n    domain: named thing\n    range: named thing\n    in_subset: translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  coexpressed with:\n    is_a: correlated with\n    description: >-\n      holds between any two genes or gene products, in which both are\n      generally expressed within a single defined experimental context.\n    domain: gene or gene product\n    range: gene or gene product\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  has biomarker:\n    is_a: correlated with\n    description: >-\n      holds between a disease or phenotypic feature and a measurable\n      chemical entity that is used as an indicator of the presence\n      or state of the disease or feature.\n       # metabolite\n    domain: disease or phenotypic feature\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    inverse: biomarker for\n    narrow_mappings:\n       # some RTX terms contributed as inverses of 'biolink:biomarker_for'\n      - NCIT:disease_has_molecular_abnormality\n      - NCIT:disease_is_marked_by_gene\n\n  biomarker for:\n    is_a: correlated with\n    description: >-\n      holds between a measurable chemical entity and a disease\n      or phenotypic feature, where the entity is used as an indicator\n      of the presence or state of the disease or feature.\n    domain: chemical entity or gene or gene product\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - NCIT:R39\n    broad_mappings:\n       # Generic marker definition not specific to biomarkers per say\n      - RO:0002607\n    narrow_mappings:\n      - NCIT:R47\n       # RTX term was tagged as 'biolink:actively_involved_in' but maps better here?\n      - NCIT:genetic_biomarker_related_to\n      - NCIT:is_molecular_abnormality_of_disease\n      - orphanet:465410\n\n   # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in'\n   # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates\n   # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others\n  expressed in:\n    is_a: located in\n    description: >-\n      holds between a gene or gene product and an anatomical entity in which it is expressed\n    domain: gene or gene product\n    range: anatomical entity\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002206\n    narrow_mappings:\n      - NCIT:R49\n      - NCIT:R46\n\n  expresses:\n    is_a: location of\n    aliases: ['anatomy expresses gene']\n    description: >-\n      holds between an anatomical entity and gene or gene product that is expressed there\n    domain: anatomical entity\n    range: gene or gene product\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    inverse: expressed in\n    exact_mappings:\n      - RO:0002292\n\n  has phenotype:\n    is_a: related to at instance level\n    aliases: ['disease presents symptom']\n    description: >-\n      holds between a biological entity and a phenotype, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should\n      translate into this predicate.\n    domain: biological entity\n    range: phenotypic feature\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    notes:\n      - check the range\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002200\n    broad_mappings:\n      - NCIT:R115\n      - NCIT:R108\n    narrow_mappings:\n      - NCIT:R89\n      - DOID-PROPERTY:has_symptom\n      - RO:0004022\n\n  phenotype of:\n    is_a: related to at instance level\n    domain: phenotypic feature\n    range: biological entity\n    multivalued: true\n    inverse: has phenotype\n\n   # TODO: predicate inverse for occurs in\n  occurs in:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a material entity or site within which the process occurs\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # These RTX mapped terms tagged as the inverse of \"biolink:occurs_in\", i.e. Entity/Site contains Process\n      - BFO:0000067\n      - SNOMED:has_occurrence\n      - UBERON:site_of\n    exact_mappings:\n      - BFO:0000066\n      - PathWhiz:has_location\n      - SNOMED:occurs_in\n    narrow_mappings:\n       # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population\n      - SEMMEDDB:OCCURS_IN\n       # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity\n      - SEMMEDDB:PROCESS_OF\n       # Uberon term constrained to a 'site' as object concept\n      - UBERON_CORE:site_of\n      - LOINC:has_imaged_location\n      - PathWhiz:in_species\n      - RO:0002231\n      - RO:0002232\n      - SNOMED:has_direct_procedure_site\n      - SNOMED:has_direct_site\n      - SNOMED:has_procedure_site\n\n  contains process:\n    is_a: related to at instance level\n    inverse: occurs in\n\n  located in:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a material entity or site\n      within which it is located (but of which it is not considered a part)\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0001025\n      - FMA:has_location\n    narrow_mappings:\n      - GOREL:0001004\n      - BSPO:0000107\n      - BSPO:0000108\n      - BSPO:0000120\n      - BSPO:0000121\n      - BSPO:0000122\n      - BSPO:0000123\n      - BSPO:0000124\n      - BSPO:0000125\n      - BSPO:0000126\n      - BSPO:0001100\n      - BSPO:0001101\n      - BSPO:0001107\n      - BSPO:0015101\n      - BSPO:0015102\n      - BSPO:0015202\n      - UBERON_CORE:in_central_side_of\n      - UBERON_CORE:in_innermost_side_of\n      - UBERON_CORE:in_outermost_side_of\n      - NCIT:R100\n      - EFO:0000784\n      - FMA:has_location\n      - HMDB:at_cellular_location\n      - HMDB:at_tissue\n      - HMDB:in_biospecimen\n      - LOINC:has_imaging_focus\n      - NCIT:R156\n      - NCIT:R155\n      - NCIT:R145\n      - NCIT:R40\n      - NCIT:R171\n      - NCIT:R167\n      - NCIT:R165\n      - NCIT:R169\n      - NCIT:R170\n      - NCIT:R166\n      - NCIT:R168\n      - RO:0002303\n      - SNOMED:has_finding_site\n      - SNOMED:has_indirect_procedure_site\n      - SNOMED:has_inherent_location\n    domain: named thing\n    range: named thing\n\n  location of:\n    is_a: related to at instance level\n    aliases: ['site of']\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between material entity or site and a material entity\n      that is located within it (but not considered a part of it)\n    in_subset:\n      - translator_minimal\n    inverse: located in\n    exact_mappings:\n      - RO:0001015\n      - SEMMEDDB:LOCATION_OF\n      - WIKIDATA_PROPERTY:P276\n       # RTX tagged this as an inverse of biolink:located_in\n      - FMA:location_of\n    narrow_mappings:\n      - SNOMED:inherent_location_of\n      - NCIT:Anatomic_Structure_Has_Location_Role\n\n  disease has location:\n    description: >-\n      A relationship between a disease and an anatomical entity where the\n      disease has one or more features that are located in that entity.\n    is_a: related to\n    exact_mappings:\n      - RO:0004026\n      - MONDO:disease_has_location\n\n  location of disease:\n    is_a: related to\n    inverse: disease has location\n\n  similar to:\n    is_a: related to at instance level\n    description: >-\n      holds between an entity and some other entity with similar features.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000000\n      - SO:similar_to\n\n  chemically similar to:\n    is_a: similar to\n    description: >-\n      holds between one small molecule entity and another that it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - CHEBI:has_parent_hydride     # subproperty\n      - CHEBI:has_functional_parent  # subproperty\n      - CHEBI:is_conjugate_acid_of   # subproperty\n      - CHEBI:is_conjugate_base_of   # subproperty\n      - CHEBI:is_enantiomer_of       # subproperty\n      - CHEBI:is_tautomer_of         # subproperty\n      - NCIT:has_salt_form\n\n  has sequence location:\n    is_a: related to at instance level\n    description: >-\n      holds between two nucleic acid entities when the subject can be localized\n      in sequence coordinates on the object. For example, between\n      an exon and a chromosome/contig.\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - faldo:location\n\n  sequence location of:\n    is_a: related to at instance level\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    inverse: has sequence location\n\n  model of:\n    is_a: related to at instance level\n    description: >-\n      holds between a thing and some other thing it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0003301\n    narrow_mappings:\n      - FOODON:00001301\n\n  models:\n    is_a: related to at instance level\n    inverse: model of\n\n  overlaps:\n    is_a: related to at instance level\n    description: >-\n      holds between entities that overlap in their extents (materials or processes)\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002131\n    narrow_mappings:\n      - BSPO:0005001\n      - CHEMBL.MECHANISM:overlaps_with\n      - RO:0002100\n      - RO:0002102\n      - RO:0002433\n\n  has part:\n    is_a: overlaps\n    annotations:\n      canonical_predicate: true\n      opposite_of: lacks part\n    description: >-\n      holds between wholes and their parts (material entities or processes)\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000051\n       # term name seems to be 'realizes' but RTX maps this term here\n      - BFO:0000055\n      - WIKIDATA_PROPERTY:P527\n      - RO:0001019\n      - RXNORM:consists_of\n      - RXNORM:has_part\n    broad_mappings:\n       # To 'contain' is 'to have something inside or include something as a part'; slightly broader?\n      - RO:0001019\n      - FMA:contains\n      - RXNORM:contains\n    narrow_mappings:\n      - BFO:0000117\n       # RTX term originally mapped to 'biolink:coexists_with'?\n      - FMA:has_constitutional_part\n      - FMA:has_part\n       # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'?\n      - FMA:has_member\n      - FOODON:00001563\n      - FOODON:00002420\n      - LOINC:has_component\n      - LOINC:has_member\n      - MEDDRA:has_member\n      - MONDO:disease_has_major_feature\n      - NCIT:complex_has_physical_part\n      - NDDF:has_ingredient\n      - PathWhiz:has_element_in_bound\n       # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature\n      - NCIT:R50\n      - PathWhiz:has_protein_in_complex\n      - RO:0002104\n      - RO:0002180\n      - RO:0002351\n      - RO:0002473\n      - RO:0002524\n      - RO:0002551\n      - RXNORM:has_ingredient\n      - SNOMED:has_component\n      - UMLS:has_component\n\n  has plasma membrane part:\n    is_a: has part\n    description: >-\n      Holds between a cell c and a protein complex or protein p if\n      and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.\n    exact_mappings:\n      - RO:0002104\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  composed primarily of:\n    is_a: related to\n    description: >-\n      x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.\n    exact_mappings:\n      - RO:0002473\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  primarily composed of:\n    inverse: composed primarily of\n    is_a: related to\n\n  plasma membrane part of:\n    is_a: part of\n    inverse: has plasma membrane part\n\n  part of:\n    is_a: overlaps\n    description: >-\n      holds between parts and wholes (material entities or processes)\n    in_subset:\n      - translator_minimal\n    inverse: has part\n    exact_mappings:\n      - BFO:0000050\n      - SEMMEDDB:PART_OF\n      - WIKIDATA_PROPERTY:P361\n      - FMA:part_of\n      - RXNORM:constitutes\n      - RXNORM:part_of\n    broad_mappings:\n       # To 'contain' is 'to have something inside or include something as a part'\n      - RO:0001018\n      - FMA:contained_in\n      - RXNORM:contained_in\n    narrow_mappings:\n      - BSPO:0001106\n      - BSPO:0001108\n      - BSPO:0001113\n      - BSPO:0001115\n      - UBERON_CORE:layer_part_of\n      - UBERON_CORE:subdivision_of\n      - UBERON_CORE:trunk_part_of\n      - CHEBI:is_substituent_group_from\n      - CPT:panel_element_of\n      - CPT:panel_element_of_possibly_included\n      - DRUGBANK:component_of\n      - FMA:constitutional_part_of\n      - FMA:member_of\n      - FMA:regional_part_of\n      - FMA:related_developmental_entity_of\n      - LOINC:component_of\n      - LOINC:has_supersystem\n      - LOINC:member_of\n      - LOINC:multipart_of\n      - MEDDRA:member_of\n      - MONDO:part_of_progression_of_disease\n      - NCIT:R82\n      - NCIT:R27\n      - NCIT:is_component_of_chemotherapy_regimen\n      - NDDF:ingredient_of\n      - RO:0002007\n      - RO:0002350\n      - RO:0002376\n      - RO:0002380\n      - RO:0002571\n      - RO:0002572\n      - RO:0002576\n      - RXNORM:ingredient_of\n      - RXNORM:ingredients_of\n      - RXNORM:precise_ingredient_of\n      - SNOMED:active_ingredient_of\n      - SNOMED:basis_of_strength_substance_of\n      - SNOMED:component_of\n      - SNOMED:direct_substance_of\n      - SNOMED:during\n      - SNOMED:focus_of\n      - SNOMED:has_dependent\n      - SNOMED:part_anatomy_structure_of\n      - SNOMED:precise_active_ingredient_of\n      - UBERON:subdivision_of\n      - UMLS:component_of\n      - UMLS:has_owning_affiliate\n      - UMLS:owning_subsection_of\n      - VANDF:ingredient_of\n\n  has input:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an input into the process\n    domain: biological process or activity\n    range: named thing\n    annotations:\n      canonical_predicate: true\n      opposite_of: has output\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002233\n      - SEMMEDDB:USES\n    narrow_mappings:\n      - LOINC:has_fragments_for_synonyms\n      - LOINC:has_system\n      - PathWhiz:has_left_element\n      - RO:0002590\n      - RO:0004009\n      - SNOMED:has_finding_method\n      - SNOMED:has_precondition\n      - SNOMED:has_specimen_source_identity\n      - SNOMED:has_specimen_substance\n      - SNOMED:uses_access_device\n      - SNOMED:uses_device\n      - SNOMED:uses_energy\n      - SNOMED:uses_substance\n\n  is input of:\n    is_a: participates in\n    domain: named thing\n    range: biological process or activity\n    inverse: has input\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002352\n\n  has output:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an output of the process\n    domain: biological process or activity\n    range: named thing\n    annotations:\n      canonical_predicate: true\n      opposite_of: has input\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002234\n    narrow_mappings:\n      - NCIT:R31\n      - OBI:0000299\n      - PathWhiz:has_right_element\n      - RO:0002296\n      - RO:0002297\n      - RO:0002298\n      - RO:0002299\n      - RO:0002588\n      - RO:0004008\n\n  is output of:\n    is_a: participates in\n    domain: named thing\n    range: biological process or activity\n    inverse: has output\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002353\n    narrow_mappings:\n      - RO:0002354\n\n  has participant:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a continuant, where the continuant is somehow involved in the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - WIKIDATA_PROPERTY:P2283\n    exact_mappings:\n      - RO:0000057\n      - RO:has_participant\n    narrow_mappings:\n      - BFO:0000167\n       # Several of the following RTX terms tagged as inverse to 'biolink:participates_in'\n      - LOINC:has_subject\n      - NCIT:process_involves_gene\n      - NBO-PROPERTY:has_participant\n      - PathWhiz:has_bound\n      - PathWhiz:has_compound\n      - PathWhiz:has_element_collection\n      - PathWhiz:has_enzyme\n      - OBI:0000293\n      - PathWhiz:has_nucleic_acid\n      - PathWhiz:has_protein\n      - PathWhiz:has_reaction\n      - RO:0002565\n      - RO:0004007\n      - RO:0004020\n      - RO:0004021\n      - SNOMED:has_indirect_device\n      - SNOMED:has_procedure_device\n      - SNOMED:has_recipient_category\n\n  catalyzes:\n    is_a: participates in\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002327\n\n  has catalyst:\n    is_a: has participant\n    inverse: catalyzes\n\n  has substrate:\n    is_a: has participant\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n\n  is substrate of:\n    is_a: participates in\n    inverse: has substrate\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  participates in:\n    is_a: related to at instance level\n    description: >-\n      holds between a continuant and a process, where the continuant is somehow involved\n      in the process\n    range: biological process or activity\n    domain: occurrent\n    inverse: has participant\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0000056\n      - BFO:0000056\n    narrow_mappings:\n      - DRUGBANK:pathway\n      - HMDB:in_pathway\n      - LOINC:is_given_pharmaceutical_substance_for\n      - NCIT:R130\n      - NCIT:R37\n      - NCIT:R131\n      - NCIT:R51\n      - NCIT:R53\n      - OBI:0000295\n      - RO:0002216\n      - RO:0002505\n      - SNOMED:has_direct_device\n\n  actively involved in:\n    is_a: participates in\n    aliases: ['involved in']\n    description: >-\n      holds between a continuant and a process or function, where\n      the continuant actively contributes to part or all of\n      the process or function it realizes\n    domain: named thing\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002331\n    narrow_mappings:\n      - NBO-PROPERTY:by_means\n      - orphanet:317348\n      - orphanet:317349\n      - orphanet:327767\n      - RO:0002503\n\n  actively involves:\n    is_a: has participant\n    domain: biological process or activity\n    range: named thing\n    inverse: actively involved in\n    in_subset:\n      - translator_minimal\n\n  capable of:\n    is_a: actively involved in\n    description: >-\n      holds between a physical entity and process or function, where the\n      continuant alone has the ability to carry out the process or function.\n    domain: named thing\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002215\n    narrow_mappings:\n      - NCIT:R52\n      - RO:0002500\n\n  can be carried out by:\n    is_a: actively involves\n    inverse: capable of\n    domain: occurrent\n    range: named thing\n\n  enables:\n    is_a: participates in\n    description: >-\n      holds between a physical entity and a process, where the physical entity executes the process\n    domain: physical entity\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n      opposite_of: prevents\n    in_subset:\n      - translator_minimal\n    inverse: enabled by\n    exact_mappings:\n      - RO:0002327\n\n  enabled by:\n    is_a: has participant\n    description: >-\n      holds between a process and a physical entity, where the physical entity executes the process\n    domain: biological process or activity\n    range: physical entity\n    in_subset:\n      - translator_minimal\n    inverse: enables\n    exact_mappings:\n      - RO:0002333\n    annotations:\n      opposite_of: prevented by\n\n  derives into:\n    is_a: related to at instance level\n    aliases: ['is normal cell origin of disease', 'may be normal cell origin of disease']\n    description: >-\n      holds between two distinct material entities, the old entity and\n      the new entity, in which the new entity begins to exist when\n      the old entity ceases to exist, and the new entity inherits\n      the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n    inverse: derives from\n     # TODO: fix this according to WG notes. Example of both opposite and inverse\n     # Commenting as it feels very wrong. A good example with both opposite and inverse is `has active ingredient`\n     # annotations:\n     #   opposite_of: subclass of\n    exact_mappings:\n      - RO:0001001\n      - SEMMEDDB:CONVERTS_TO\n       # RTX posted terms as inverse of 'biolink:derives_from'\n      - FMA:derives\n\n  derives from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    description: >-\n      holds between two distinct material entities, the new entity\n      and the old entity, in which the new entity begins to exist\n      when the old entity ceases to exist, and the new entity\n      inherits the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n      - samples\n    inverse: derives into\n    exact_mappings:\n      - RO:0001000\n      - FMA:derives_from\n      - DOID-PROPERTY:derives_from\n    narrow_mappings:\n      - CHEBI:has_functional_parent\n      - SNOMED:has_specimen_source_topography\n\n  is metabolite of:\n    is_a: derives from\n    description: >-\n      holds between two molecular entities in which the first one is derived\n      from the second one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    inverse: has metabolite\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  has metabolite:\n    is_a: derives into\n    description: >-\n      holds between two molecular entities in which the second one is derived from the first\n      one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  food component of:\n    is_a: part of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has food component\n\n  has food component:\n    is_a: has part\n    description: >-\n      holds between food and one or more chemical entities composing it,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  nutrient of:\n    is_a: food component of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has nutrient\n\n  has nutrient:\n    is_a: has food component\n    description: >-\n      one or more nutrients which are growth factors for a living organism\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q181394\n\n  is active ingredient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug, in which the former\n      is a part of the latter, and is a biologically active component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has active ingredient\n    mappings:\n      - RO:0002249\n\n  has active ingredient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entity in which the latter\n      is a part of the former, and is a biologically active component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: is excipient of\n    in_subset:\n      - translator_minimal\n    inverse: is active ingredient of\n    mappings:\n      - RO:0002248\n\n  is excipient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug in which the former is\n      a part of the latter, and is a biologically inactive component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has excipient\n    mappings:\n      - WIKIDATA:Q902638\n\n  has excipient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entities in which the latter\n      is a part of the former, and is a biologically inactive component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    mappings:\n      - WIKIDATA:Q902638\n\n  manifestation of:\n    is_a: related to at instance level\n    description: >-\n      that part of a phenomenon which is directly observable or\n      visibly expressed, or which gives evidence to the underlying\n      process; used in SemMedDB for linking things like dysfunctions\n      and processes to some disease or syndrome\n    range: disease\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:MANIFESTATION_OF\n      - OMIM:manifestation_of\n    broad_mappings:\n       # Wikidata's definition is slightly broader: \"inherent and characteristic embodiment of a given concept\"\n      - WIKIDATA_PROPERTY:P1557\n    narrow_mappings:\n      - SNOMED:has_definitional_manifestation\n\n  has manifestation:\n    is_a: related to at instance level\n    domain: disease\n    inverse: manifestation of\n\n  mode of inheritance of:\n    is_a: manifestation of\n    domain: genetic inheritance\n    range: disease or phenotypic feature\n    inverse: has mode of inheritance\n\n  has mode of inheritance:\n    is_a: has manifestation\n    description: >-\n      Relates a disease or phenotypic feature to its observed genetic segregation and assumed\n      associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).\n    domain: disease or phenotypic feature\n    range: genetic inheritance\n    annotations:\n       # This canonical order reverses that of its parent 'has manifestation' class\n       # but seems a more natural direction in the pertinent edge relationships.\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  produces:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a product that is generated\n      through the intentional actions or functioning of the material entity\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GOREL:0001010\n    exact_mappings:\n      - RO:0003000\n      - WIKIDATA_PROPERTY:P1056\n      - SEMMEDDB:PRODUCES\n    narrow_mappings:\n      - NCIT:R29\n      - SNOMED:has_process_output\n      - SNOMED:specimen_procedure_of\n\n  produced by:\n    is_a: related to at instance level\n    inverse: produces\n    exact_mappings:\n      - RO:0003001\n\n  consumes:\n    is_a: has input\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - RO:0004009\n\n  consumed by:\n    is_a: is input of\n    inverse: consumes\n    domain: named thing\n    range: named thing\n\n  temporally related to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities with a temporal relationship\n    domain: occurrent\n    range: occurrent\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SNOMED:temporally_related_to\n    narrow_mappings:\n       # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here\n      - RO:0002082\n      - RO:0002083\n      - RO:0002092\n      - RO:0002093\n      - RO:0002223\n      - RO:0002224\n      - RO:0002229\n      - RO:0002230\n      - RO:0002488\n      - RO:0002489\n      - RO:0002492\n      - RO:0002493\n      - RO:0002496\n      - RO:0002497\n\n  precedes:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where one completes before the other begins\n    domain: occurrent\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    inverse: preceded by\n    in_subset:\n      - translator_minimal\n    close_mappings:\n       # the subject of these terms is a material entity, not a process,\n       # but affects a process which causes a second process to occur\n      - RO:0002263\n      - RO:0002264\n    exact_mappings:\n      - BFO:0000063\n      - SEMMEDDB:PRECEDES\n      - SNOMED:occurs_before\n    broad_mappings:\n       # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature\n      - WIKIDATA_PROPERTY:P156\n    narrow_mappings:\n      - FMA:transforms_into\n      - RO:0002090\n      - RO:0002411\n      - RO:0002412\n\n  preceded by:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where the other is completed before the one begins\n    domain: occurrent\n    range: occurrent\n    inverse: precedes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000062\n    broad_mappings:\n       # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'?\n      - GENEPIO:0001739\n    narrow_mappings:\n       # RTX contributed mapping was given as the inverse of 'biolink:precedes'\n      - FMA:transforms_from\n      - RO:0002087\n      - RO:0002285\n\n  has variant part:\n    is_a: has part\n    description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000382\n\n  variant part of:\n    is_a: part of\n    inverse: has variant part\n\n  related condition:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000790\n\n   ## Predicates relating variants to genes\n\n  is sequence variant of:\n    is_a: related to at instance level\n    aliases: ['gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product']\n    description: holds between a sequence variant and a nucleic acid entity\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - WIKIDATA:P3433\n\n  has sequence variant:\n    is_a: related to at instance level\n    inverse: is sequence variant of\n    domain: genomic entity\n    range: sequence variant\n\n  is missense variant of:\n    is_a: is sequence variant of\n    description: holds between a gene  and a sequence variant, such the sequence variant\n      results in a different amino acid sequence but where the length is preserved.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001583\n\n  has missense variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is missense variant of\n\n  is synonymous variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the coding sequence of the gene, but results in the same amino acid sequence\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001819\n\n  has synonymous variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is synonymous variant of\n    aliases: ['stop gained']\n\n  is nonsense variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      results in a premature stop codon\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n       # Term definition broader than nonsense codon: A sequence variant whereby\n       # the gene product has diminished or abolished function.\n      - SO:0002054\n\n  has nonsense variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is nonsense variant of\n\n  is frameshift variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      causes a disruption of the translational reading frame, because the number of\n      nucleotides inserted or deleted is not a multiple of three.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001589\n    aliases: ['frameshift variant', 'start lost', 'stop lost']\n\n  has frameshift variant:\n    is_a: has sequence variant\n    inverse: is frameshift variant of\n    domain: genomic entity\n    range: sequence variant\n    aliases: ['splice region variant', 'splice acceptor variant', 'splice donor variant']\n\n  is splice site variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the canonical splice site of one of the gene's exons.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001629\n\n\n  has splice site variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is splice site variant of\n    aliases: ['downstream gene variant', 'upstream gene variant']\n\n  is nearby variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene sequence that the variant\n      is genomically close to.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n\n  has nearby variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is nearby variant of\n    aliases: ['intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant']\n\n  is non coding variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, where the variant does\n      not affect the coding sequence\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n\n  has non coding variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is non coding variant of\n\n   # relating disease to process\n\n  disease has basis in:\n    description: A relation that holds between a disease and an entity where the state\n      of the entity has contribution to the disease.\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n       # These two MONDO terms seem more particular than the predicate\n      - MONDO:disease_has_basis_in_development_of\n      - MONDO:disease_has_basis_in_accumulation_of\n\n  occurs in disease:\n    is_a: related to at instance level\n    inverse: disease has basis in\n\n\n  has adverse event:\n    is_a: affects\n    aliases: ['adverse effect']\n    description: >-\n      An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment \n      with a therapeutic agent. Adverse events may be caused by something \n      other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or \n      diseases temporally associated with the treatment, whether or not considered related to the treatment. \n      Adverse events are unintended effects that occur when a medication is administered correctly.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n\n  adverse event of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has adverse event\n\n  has side effect:\n    aliases: ['adverse drug reaction']\n    is_a: affects\n    description: >-\n      An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment.\n      Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of \n      the medication.\n    notes: >-\n      Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative.\n      Aeolus, Sider are both resources that provide side effects.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C2861  # side effect\n\n  is side effect of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has side effect\n\n  contraindicated for:\n    is_a: related to at instance level\n    description: Holds between a drug and a disease or phenotype, such that a person\n      with that disease should not be treated with the drug.\n    domain: drug\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: treats\n    exact_mappings:\n      - NCIT:C37933\n\n  has contraindication:\n    is_a: related to at instance level\n    domain: disease or phenotypic feature\n    range: drug\n    inverse: contraindicated for\n\n   # The remaining new slots are here because we ran across them somewhere and\n   # they didn't seem to map well to anything else.\n\n  has not completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of,\n      but has not completed\n    exact_mappings:\n      - CL:has_not_completed\n    annotations:\n      opposite_of: has completed\n      canonical_predicate: true\n\n  not completed by:\n    is_a: related to at instance level\n    inverse: has not completed\n\n  has completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of\n      and has completed\n    annotations:\n      canonical_predicate: true\n      opposite_of: has not completed\n    exact_mappings:\n      - CL:has_completed\n\n  completed by:\n    is_a: related to at instance level\n    inverse: has completed\n\n\n  in linkage disequilibrium with:\n    is_a: related to at instance level\n    description: holds between two sequence variants, the presence of which are correlated\n      in a population\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C16798\n\n  has increased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has decreased amount\n    narrow_mappings:\n      - CL:has_high_plasma_membrane_amount\n\n  increased amount of:\n    is_a: related to at instance level\n    inverse: has increased amount\n\n  has decreased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has increased amount\n    narrow_mappings:\n      - CL:has_low_plasma_membrane_amount\n\n  decreased amount in:\n    is_a: related to at instance level\n    inverse: has decreased amount\n\n  lacks part:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has part\n    exact_mappings:\n      - CL:lacks_part\n      - PR:lacks_part\n    narrow_mappings:\n      - CL:lacks_plasma_membrane_part\n\n  missing from:\n    is_a: related to at instance level\n    inverse: lacks part\n\n  develops from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # RTX mapping seems to be inverse of 'biolink:develops_from'\n      - RO:0002203\n      - FMA:develops_into\n    exact_mappings:\n      - BTO:develops_from\n      - DDANAT:develops_from\n      - FMA:develops_from\n      - RO:0002202\n    narrow_mappings:\n      - RO:0002207\n      - RO:0002225  # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y\n      - RO:0002226  # x develops_in y if x is located in y whilst x is developing\n\n  develops into:\n    is_a: related to at instance level\n    inverse: develops from\n\n  in taxon:\n    aliases: ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source']\n    is_a: related to at instance level\n    domain: thing with taxon\n    range: organism taxon\n    annotations:\n      canonical_predicate: true\n    description: >-\n      connects an entity to its taxonomic classification. Only certain kinds\n      of entities can be taxonomically classified; see 'thing with taxon'\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002162\n      - WIKIDATA_PROPERTY:P703\n    narrow_mappings:\n      - RO:0002160\n\n  in taxon label:\n    is_a: node property\n    domain: thing with taxon\n    range: label type\n    description: >-\n      The human readable scientific name for the taxon of the entity.\n    in_subset:\n      - translator_minimal\n    slot_uri: rdfs:label\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P225\n    annotations:\n      denormalized: true\n\n  taxon of:\n    is_a: related to at instance level\n    inverse: in taxon\n    domain: organism taxon\n    range: thing with taxon\n\n  has molecular consequence:\n    is_a: related to at instance level\n    aliases: ['allele has activity']\n    description: >-\n      connects a sequence variant to a class describing the molecular\n      consequence. E.g.  SO:0001583\n    range: ontology class\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - NCIT:allele_has_activity\n\n  is molecular consequence of:\n    is_a: related to at instance level\n    domain: ontology class\n    inverse: has molecular consequence\n\n   ## --------------------\n   ## ASSOCIATION SLOTS\n   ## --------------------\n\n  association slot:\n    abstract: true\n    domain: association\n    aliases: ['edge property', 'statement property', 'node qualifier', 'edge qualifier', 'statement qualifier']\n    description: >-\n      any slot that relates an association to another entity\n\n  original subject:\n    is_a: association slot\n    description: >-\n      used to hold the original subject of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original object:\n    is_a: association slot\n    description: >-\n      used to hold the original object of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original predicate:\n    aliases: ['original relation', 'relation']\n    is_a: association slot\n    description: >-\n      used to hold the original relation/predicate that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n    id_prefixes:\n      - RO\n      - BSPO\n      - SIO\n    domain: association\n    range: uriorcurie\n\n  subject closure:\n    is_a: association slot\n    description: >-\n      Used to hold the subject closure of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    annotations:\n      denormalized: true\n     \n  object closure:\n    is_a: association slot\n    description: >-\n      Used to hold the object closure of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    examples:\n      - value: [\"MONDO:0000167\", \"MONDO:0005395\"]\n        description: >-\n          The object closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          diseases that are ancestors of 'breast cancer' in the\n          MONDO ontology.  Note: typically the \"subclass of\" and \"part of\" \n          relations are used to construct the closure, but other relations\n          may be used as well.\n    annotations:\n      denormalized: true\n\n  subject category:\n    is_a: association slot\n    description: >-\n      Used to hold the biolink class/category of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: ontology class\n    examples:\n      - value: \"biolink:Gene\"\n        description: >-\n          The subject category of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is 'biolink:Gene'.\n    annotations:\n      denormalized: true\n\n  object category:\n    is_a: association slot\n    description: >-\n      Used to hold the biolink class/category of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: ontology class\n    examples:\n      - value: \"biolink:Disease\"\n        description: >-\n            The object category of the association between the gene\n            'BRCA1' and the disease 'breast cancer' is 'biolink:Disease'.\n    annotations:\n      denormalized: true\n\n  subject category closure:\n    is_a: association slot\n    description: >-\n      Used to hold the subject category closure of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: ontology class\n    examples:\n      - value: ['biolink:Gene\", \"biolink:NamedThing']\n        description: >-\n          The subject category closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          biolink classes that are ancestors of 'biolink:Gene' in the\n          biolink model.  Note: typically the \"subclass of\" and \"part of\" \n          relations are used to construct the closure, but other relations\n          may be used as well.\n    annotations:\n      denormalized: true\n\n  object category closure:\n    is_a: association slot\n    description: >-\n      Used to hold the object category closure of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: ontology class\n    examples:\n      - value: ['biolink:Disease\", \"biolink:NamedThing']\n        description: >-\n          The object category closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          biolink classes that are ancestors of 'biolink:Disease' in the\n          biolink model.  Note: typically the \"subclass of\" and \"part of\" \n          relations are used to construct the closure, but other relations\n          may be used as well.\n    annotations:\n      denormalized: true\n\n  subject label closure:\n    is_a: association slot\n    description: >-\n      Used to hold the subject label closure of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: string\n    examples:\n      - value: [\"BRACA1\"]\n        description: >-\n          The subject label closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          labels that are ancestors of 'BRCA1' in the\n          biolink model.\n    annotations:\n      denormalized: true\n\n  object label closure:\n    is_a: association slot\n    description: >-\n      Used to hold the object label closure of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: string\n    examples:\n      - value: [\"breast cancer\", \"cancer\"]\n        description: >-\n          The object label closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          labels that are ancestors of 'breast cancer' in the\n          biolink model.\n    annotations:\n      denormalized: true\n\n  subject namespace:\n    aliases: [\"subject prefix\"]\n    is_a: association slot\n    description: >-\n      Used to hold the subject namespace of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: string\n    examples:\n      - value: \"NCBIGene\"\n        description: >-\n          The subject namespace of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is 'NCBIGene'.\n    annotations:\n      denormalized: true\n\n  object namespace:\n    aliases: [\"object prefix\"]\n    is_a: association slot\n    description: >-\n      Used to hold the object namespace of an association. This is a denormalized \n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: string\n    examples:\n      - value: \"MONDO\"\n        description: >-\n          The object namespace of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is 'MONDO'.\n    annotations:\n      denormalized: true\n\n  subject:\n    is_a: association slot\n    local_names:\n      ga4gh: annotation subject\n      neo4j: node with outgoing relationship\n    description: >-\n      connects an association to the subject of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    domain: association\n    range: named thing\n    slot_uri: rdf:subject\n    exact_mappings:\n      - owl:annotatedSource\n      - OBAN:association_has_subject\n\n  object:\n    is_a: association slot\n    description: >-\n      connects an association to the object of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    domain: association\n    range: named thing\n    local_names:\n      ga4gh: descriptor\n      neo4j: node with incoming relationship\n    slot_uri: rdf:object\n    exact_mappings:\n      - owl:annotatedTarget\n      - OBAN:association_has_object\n\n  predicate:\n    is_a: association slot\n    description: >-\n      A high-level grouping for the relationship type. AKA minimal predicate.\n      This is analogous to category for nodes.\n    domain: association\n    notes: >-\n      Has a value from the Biolink related_to hierarchy. In RDF,  this\n      corresponds to rdf:predicate and in Neo4j this corresponds to the\n      relationship type. The convention is for an edge label in snake_case\n      form. For example, biolink:related_to, biolink:causes, biolink:treats\n    range: predicate type\n    required: true\n    local_names:\n      ga4gh: annotation predicate\n      translator: predicate\n    slot_uri: rdf:predicate\n    exact_mappings:\n      - owl:annotatedProperty\n      - OBAN:association_has_predicate\n\n  logical interpretation:\n    is_a: association slot\n    required: false\n    domain: association\n    range: LogicalInterpretationEnum\n    exact_mappings:\n      - os:LogicalInterpretation\n\n  relation:\n    deprecated: true\n\n  negated:\n    is_a: association slot\n    range: boolean\n    description: >-\n      if set to true, then the association is negated i.e. is not true\n\n  has confidence level:\n    is_a: association slot\n    range: confidence level\n    description: >-\n      connects an association to a qualitative term denoting the level of confidence\n\n  has evidence:\n    is_a: association slot\n    range: evidence type\n    description: >-\n      connects an association to an instance of supporting evidence\n    exact_mappings:\n      - RO:0002558\n    multivalued: true\n\n  has supporting study result:\n    is_a: association slot\n    description: >-\n      connects an association to an instance of supporting study result\n\n  log odds ratio:\n    is_a: association slot\n    description: >-\n      The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the \n      odds of event Y occurring in a non-exposed group.\n    range: float\n\n  log odds ratio 95 ci:\n    is_a: association slot\n    description: >-\n      The ninety-five percent confidence range in which the true log odds ratio for the sample population falls.\n    range: float\n\n  total sample size:\n    is_a: dataset count\n    description: >-\n      The total number of patients or participants within a sample population.\n    range: integer\n\n\n  mechanism of action:\n    is_a: association slot\n    range: boolean\n    description: >-\n      a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes\n      the mechanism of action for a result.\n    exact_mappings:\n      - NCIT:C54680\n      - MI:2044\n      - LOINC:MTHU019741\n\n  knowledge source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which the knowledge expressed in an Association was\n      retrieved, directly or indirectly. This can be any resource through which the\n      knowledge passed on its way to its currently serialized form. In practice,\n      implementers should use one of the more specific subtypes of this generic property.\n    close_mappings:\n      - pav:providedBy\n\n  provided by:\n    is_a: node property\n    description: >-\n      The value in this node property represents the knowledge provider that created or assembled the\n      node and all of its attributes.  Used internally to represent how a particular node made its way into a\n      knowledge provider or graph.\n    multivalued: true\n\n  primary knowledge source:\n    is_a: knowledge source\n    description: >-\n      The most upstream source of the knowledge expressed in an Association that an\n      implementer can identify.  Performing a rigorous analysis of upstream data providers is expected; every effort\n      is made to catalog the most upstream source of data in this property.  Only one data source should be declared\n      primary in any association.  \"aggregator knowledge source\" can be used to capture non-primary sources.\n    notes: >-\n      For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then \n      incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to \n      the NCATS ARS. The retrieval path for this Edge is as follows: \n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   MolePro  --retrieved_from--> ChEMBL --retrieved_from-->  ClinicalTrials.gov\n      The \"primary knowledge source\" for this edge is \"infores:clinical-trials-gov\".  \"infores:chembl\" and \"infores:molecular_data_provider\"\n      are listed in the \"aggregator knowledge source\" property.\n    multivalued: false\n\n  aggregator knowledge source:\n    is_a: knowledge source\n    description: >-\n      An intermediate aggregator resource from which knowledge expressed in an Association was\n      retrieved downstream of the original source, on its path to its current serialized form.\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which data was retrieved and subsequently used as\n      evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, \n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, \n      the Edge is passed to the Ranking Agent’s ARAGORN ARA, \n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of \n      data from which the knowledge was derived.   \n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data set:\n    is_a: association slot\n    description: >-\n      A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    multivalued: true\n\n  chi squared statistic:\n    is_a: association slot\n    range: float\n    description: >-\n      represents the chi-squared statistic computed from observations\n    exact_mappings:\n      - STATO:0000030\n\n  p value:\n    aliases: ['unadjusted p value']\n    is_a: association slot\n    range: float\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    exact_mappings:\n      - OBI:0000175\n      - NCIT:C44185\n      - EDAM-DATA:1669\n\n  evidence count:\n    is_a: association slot\n    description: >-\n      The number of evidence instances that are connected to an association.\n    range: integer\n\n  dataset count:\n    is_a: association slot\n    description: >-\n      The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort.\n    range: integer\n    examples:\n      - value: 100000\n\n  concept count subject:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the subject slot of an association.\n    range: integer\n    examples:\n      - value: 489\n\n  concept count object:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the object slot of an association.\n    range: integer\n\n  concept pair count:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      both the subject and object concept of an association.\n    range: integer\n    examples:\n      - value: 1731\n\n  expected count:\n    is_a: association slot\n    description: >-\n      The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and \n      object concept of an association if the subject and object concepts are independent.\n\n  relative frequency subject:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the subject\n      concept appears in these same records.\n    range: float\n    examples:\n      - value: 0.01840490798\n\n  relative frequency object:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in \n      records within a dataset/cohort, relative to the frequency at which the object\n      concept appears in these same records.\n    range: string\n\n  relative frequency subject confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_subject calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  relative frequency object confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_object calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  adjusted p value:\n    is_a: p value\n    description: >-\n      The adjusted p-value is the probability of obtaining test results\n      at least as extreme as the results actually observed, under the assumption that\n      the null hypothesis is correct, adjusted for multiple comparisons.  \n      P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) \n      rather than expressing a statement of inequality (P<. 05), unless P<.\n    range: float\n\n  bonferonni adjusted p value:\n    is_a: adjusted p value\n    description: >-\n      The Bonferroni correction is an adjustment made to P values when several dependent or independent \n      statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni \n      correction, divide the critical P value (α) by the number of comparisons being made.  P is always italicized and \n      capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality \n      (P<. 05), unless P<.\n    range: float\n    examples:\n      - value: 0.018\n\n  supporting text:\n    is_a: association slot\n    description: The segment of text from a document that supports the mined assertion.\n    multivalued: true\n    range: string\n    examples:\n      - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer.\n\n  supporting documents:\n    deprecated: true\n    is_a: association slot\n    description: >-\n      One or more referenceable documents that report the statement expressed in an Association, or provide \n      information used as evidence supporting this statement.\n    range: uriorcurie\n    multivalued: true\n    examples:\n      - value: PMID:12345678\n\n  subject location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the subject concept of the extracted assertion.\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  object location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the object concept of the extracted assertion\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  extraction confidence score:\n    is_a: association slot\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    range: integer\n    examples:\n      - value: 15\n\n  supporting document type:\n    is_a: association slot\n    description: >-\n      The document type (e.g., Journal Article, Case Study, Preprint) for\n      the supporting document used in a Text Mining Result.\n    range: string\n    examples:\n      - value: Journal Article\n\n  supporting document year:\n    is_a: association slot\n    description: >-\n      The document year (typically the publication year) for the supporting\n      document used in a Text Mining Result.\n    range: integer\n    examples:\n      - value: 1999\n\n  supporting text section type:\n    is_a: association slot\n    description: >-\n      The section of the supporting text of a Text Mining Result within\n      the supporting document. This is in the form of the name of the document section\n      (e.g., Abstract, Introduction) that contains the supporting text.\n    range: string\n    examples:\n      - value: Introduction\n\n  ln ratio:\n    is_a: association slot\n    description: the natural log of the ratio of co-occurrence to expected\n    range: float\n    examples:\n      - value: 2.922827136\n\n  ln ratio confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the ln_ratio calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: float\n    examples:\n      - value: 2.922827136\n\n  interacting molecules category:\n    is_a: association slot\n    range: ontology class\n    exact_mappings:\n      - MI:1046\n    values_from:\n      - MI\n    examples:\n      - value: MI:1048\n        description: smallmolecule-protein\n\n  expression site:\n    description: >-\n      location in which gene or protein expression takes place.\n      May be cell, tissue, or organ.\n    is_a: association slot\n    range: anatomical entity\n    examples:\n      - value: UBERON:0002037\n        description: cerebellum\n\n  phenotypic state:\n    description: >-\n      in experiments (e.g. gene expression) assaying diseased or unhealthy\n      tissue, the phenotypic state can be put here, e.g. MONDO ID.\n      For healthy tissues, use XXX.\n    is_a: association slot\n    range: disease or phenotypic feature\n\n\n  publications:\n    aliases: ['supporting publications', 'supporting documents']\n    description: >-\n      One or more publications that report the statement expressed in an \n      Association, or provide information used as evidence supporting this statement.\n    comments: >-\n        The notion of a ‘Publication’ is considered broadly to include any \n        document made available for public consumption. It covers journal issues, \n        individual articles, and books - and also things like article pre-prints, \n        white papers, patents, drug labels, web pages, protocol documents, etc. \n    is_a: association slot\n    multivalued: true\n    range: publication\n\n  associated environmental context:\n    is_a: association slot\n    description: >-\n      An attribute that can be applied to an association where the association holds between two entities\n      located or occurring in a particular environment. For example, two microbial taxa may interact in the context of\n      a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure.\n       # TODO: add examples of values for this property.\n\n  sequence localization attribute:\n    is_a: association slot\n    domain: genomic sequence localization\n    description: >-\n      An attribute that can be applied to a genome sequence localization edge. These edges\n      connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used\n      to ascribe specific positional information and other metadata to the localization. In pragmatic terms\n      this can be thought of as columns in a GFF3 line.\n\n  interbase coordinate:\n    is_a: sequence localization attribute\n    aliases: ['zero-based', 'half-open', 'space-based']\n    description: >-\n      A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1.\n      This is applied to a sequence localization edge.\n    range: integer\n\n  start interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 0).\n    close_mappings:\n      - faldo:begin\n    annotations:\n      opposite_of: end interbase coordinate\n\n  end interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity ends\n      on the chromosome or other entity to which it is located on.\n    close_mappings:\n      - faldo:end\n    annotations:\n      opposite_of: start interbase coordinate\n\n  start coordinate:\n    is_a: base coordinate\n    aliases: ['start']\n    description: >-\n      The position at which the subject genomic entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 1).\n    exact_mappings:\n      - gff3:start\n    close_mappings:\n      - faldo:begin\n\n  end coordinate:\n    is_a: base coordinate\n    aliases: ['end']\n    description: >-\n      The position at which the subject genomic entity ends\n      on the chromosome or other entity to which it is located on.\n    exact_mappings:\n      - gff3:end\n    close_mappings:\n      - faldo:end\n\n  genome build:\n    is_a: sequence localization attribute\n    description: >-\n      The version of the genome on which a feature is located.\n      For example, GRCh38 for Homo sapiens.\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  strand:\n    is_a: sequence localization attribute\n    description: >-\n      The strand on which a feature is located. Has a value of '+'\n      (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  phase:\n    is_a: sequence localization attribute\n    domain: coding sequence\n    description: >-\n      The phase for a coding sequence entity. For example, phase of a\n      CDS as represented in a GFF3 with a value of 0, 1 or 2.\n    range: PhaseEnum\n    exact_mappings:\n      - gff3:phase\n\n  FDA approval status:\n    is_a: association slot\n    description: >-\n    range: FDAApprovalStatusEnum\n\n  supporting study metadata:\n    is_a: association slot\n    description: >-\n      Information about a study used to generate information used as evidence to support the knowledge expressed in an \n      Association. In practice, data creators should use one of the more specific subtypes of this property.\n    abstract: true\n\n  supporting study method type:\n    is_a: supporting study metadata\n    description: >-\n      A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of \n      experimental assay, or statistical calculation, or computational analysis).\n    range: uriorcurie\n\n  supporting study method description:\n    is_a: supporting study metadata\n    description: >-\n      A uri or curie pointing to information about the methodology used to generate data supporting an Association.\n    range: uriorcurie\n\n  supporting study size:\n    is_a: supporting study metadata\n    description: >-\n      The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a \n      clinical study).\n    range: integer\n\n  supporting study cohort:\n    is_a: supporting study metadata\n    description: >-\n      A description of a study population/cohort that was interrogated to provide evidence for the association \n      (e.g. the inclusion and exclusion criteria).\n    range: string\n\n  supporting study date range:\n    is_a: supporting study metadata\n    description: >-\n      The date range over which data was collected in a study that provided evidence for an Association.\n    range: string\n\n  supporting study context:\n    is_a: supporting study metadata\n    description: >-\n      A term or terms describing the experimental setting/context in which evidence supporting the Association was \n      generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue \n      type, disease, etc.).\n    range: string\n\nclasses:\n\n  mapping collection:\n    description: >-\n      A collection of deprecated mappings.\n    abstract: true\n    slots:\n      - predicate mappings\n    tree_root: true\n\n  predicate mapping:\n    description: >-\n      A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should\n      be done to use a qualified statement in its place.\n    slots:\n      - mapped predicate\n      - subject aspect qualifier\n      - subject direction qualifier\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - predicate\n      - qualified predicate\n      - object aspect qualifier\n      - object direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object derivative qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - species context qualifier\n      - exact match\n      - narrow match\n      - broad match\n\n\n   ## ----------\n   ## ATTRIBUTES\n   ## ----------\n\n   ## Ontology Classes\n\n  ontology class:\n    mixin: true\n    slots:\n      - id\n    description: >-\n      a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in\n      a biolink compatible KG can be considered both instances of biolink classes, and\n      OWL classes in their own right. In general you should not need to use this class directly.\n      Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897),\n      use bl:BiologicalProcess as the type.\n    exact_mappings:\n      - owl:Class\n      - schema:Class\n    comments:\n      - >-\n        This is modeled as a mixin. 'ontology class' should not be the primary type of a\n        node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity\n        (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\n      - >-\n        Note that formally this is a metaclass. Instances of this class are instances in the graph,\n        but can be the object of 'type' edges. For example, if we had a node in the graph representing\n        a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample,\n        and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\n    see_also:\n      - https://github.com/biolink/biolink-model/issues/486\n    examples:\n      - value: UBERON:0000955\n        description: >-\n          the class 'brain' from the Uberon anatomy ontology\n    id_prefixes:\n      - MESH\n      - UMLS\n      - KEGG.BRITE  ## br/ko number\n  \n  annotation:\n    description: >-\n      Biolink Model root class for entity annotations.\n    abstract: true\n\n  quantity value:\n    is_a: annotation\n    description: >-\n      A value of an attribute that is quantitative and measurable,\n      expressed as a combination of a unit and a numeric value\n    slots:\n      - has unit\n      - has numeric value\n\n   # Alignment attempted of the biolink:Attribute model\n   # to the proposed TRAPI Release 1.1 Attribute schema, i.e.\n   #\n   # attribute_name: \"assertionAuthoredBy\",\n   # attribute_type: SEPIO:0000130,\n   # value: \"ORCID:12345\",\n   # value_type: \"wd:Q51044\",\n   # value_type_name: \"ORCID ID\"\n   # url: https://orcid.org/12345\n   # source: ORCID\n\n  attribute:\n    is_a: named thing\n    mixins:\n      - ontology class\n    description: >-\n      A property or characteristic of an entity.\n      For example, an apple may have properties such as color, shape, age, crispiness.\n      An environmental sample may have attributes such as depth, lat, long, material.\n    slots:\n      - name                    # 'attribute_name'\n      - has attribute type      # 'attribute_type'\n       # 'value', 'value_type', 'value_type_name'\n       # extracted from either of the next two slots\n      - has quantitative value\n      - has qualitative value\n      - iri                     # 'url'\n    slot_usage:\n      name:\n        description: >-\n          The human-readable 'attribute name' can be set to a string which reflects its context of\n          interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default\n          to the name associated with the 'has attribute type' slot ontology term.\n    id_prefixes:\n      - EDAM-DATA\n      - EDAM-FORMAT\n      - EDAM-OPERATION\n      - EDAM-TOPIC\n    exact_mappings:\n      - SIO:000614\n    in_subset:\n      - samples\n\n  chemical role:\n    is_a: attribute\n    description: >-\n      \tA role played by the molecular entity or part thereof within a chemical context.\n    id_prefixes:\n      - CHEBI\n    exact_mappings:\n      - CHEBI:51086\n    examples:\n      - value: CHEBI:35469  # antidepressant role\n\n  biological sex:\n    is_a: attribute\n    exact_mappings:\n      - PATO:0000047\n\n  phenotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the phenotypic sex of the individual,\n      based upon the reproductive organs present.\n    exact_mappings:\n      - PATO:0001894\n\n  genotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the genotypic sex of the individual,\n      based upon genotypic composition of sex chromosomes.\n    exact_mappings:\n      - PATO:0020000\n\n  severity value:\n    is_a: attribute\n    description: >-\n      describes the severity of a phenotypic feature or disease\n\n  relationship quantifier:\n    mixin: true\n\n  sensitivity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  specificity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  pathognomonicity quantifier:\n    is_a: specificity quantifier\n    description: >-\n      A relationship quantifier between a variant or symptom and a disease, which is\n      high when the presence of the feature implies the existence of the disease\n    mixin: true\n\n  frequency quantifier:\n    is_a: relationship quantifier\n    mixin: true\n    slots:\n      - has count\n      - has total\n      - has quotient\n      - has percentage\n\n  chemical or drug or treatment:\n    mixin: true\n\n   ## ------\n   ## THINGS\n   ## ------\n\n  entity:\n    description: >-\n      Root Biolink Model class for all things and informational relationships, real or imagined.\n    abstract: true\n    slots:\n      - id\n      - iri\n      - category\n      - type    # rdf:type\n      - name\n      - description\n      - has attribute\n       # evidence code(s)?\n\n  named thing:\n    is_a: entity\n    description: \"a databased entity or concept/class\"\n    slots:\n      - provided by\n      - xref\n      - full name\n    slot_usage:\n      category:\n        required: true\n        pattern: '^biolink:[A-Z][A-Za-z]+$'\n    exact_mappings:\n      - BFO:0000001\n      - WIKIDATA:Q35120\n       # UMLS Semantic Group \"Objects\"\n      - UMLSSG:OBJC\n       # Entity\n      - STY:T071\n      - dcid:Thing\n\n  relationship type:\n    is_a: ontology class\n    description: >-\n      An OWL property used as an edge label\n\n  taxonomic rank:\n    description: >-\n      A descriptor for the rank within a taxonomic classification.\n      Example instance: TAXRANK:0000017 (kingdom)\n    is_a: ontology class\n    id_prefixes:\n      - TAXRANK\n    mappings:\n      - WIKIDATA:Q427626\n\n  organism taxon:\n    aliases: ['taxon', 'taxonomic classification']\n    description: >-\n      A classification of a set of organisms. Example instances:\n      NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria).\n      Can also be used to represent strains or subspecies.\n    is_a: named thing\n    slot_usage:\n      has taxonomic rank:\n        range: taxonomic rank\n        multivalued: false\n        mappings:\n          - WIKIDATA:P105\n    values_from:\n      - NCBITaxon\n    exact_mappings:\n      - WIKIDATA:Q16521\n      - STY:T001\n      - bioschemas:Taxon\n    narrow_mappings:\n      - dcid:BiologicalSpecies\n    id_prefixes:\n      - NCBITaxon\n      - MESH\n      - UMLS\n    in_subset:\n      - model_organism_database\n  \n   ## Temporal Entities\n  \n  event:\n    is_a: named thing\n    description: >-\n      Something that happens at a given place and time.\n    exact_mappings:\n      - NCIT:C25499\n       # UMLS \"Event\"\n      - STY:T051\n\n   ## Administrative Entities\n\n  administrative entity:\n    is_a: named thing\n    abstract: true\n\n  study result:\n    abstract: true\n    description: >- \n      A collection of data items from a study that are about a particular study subject or experimental unit (the \n      'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation\n      of this data as evidence.\n    notes:\n      The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, \n      that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific \n      focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any \n      scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational \n      analyses, or a larger scale clinical trial or experimental research investigation.\n    is_a: information content entity\n\n  study:\n    description: a detailed investigation and/or analysis\n    is_a: activity\n    exact_mappings:\n      - NCIT:C63536\n    close_mappings:\n      - SIO:001066\n      - SEPIO:0000004\n    narrow_mappings:\n      - SIO:000994\n\n  study variable:\n    is_a: information content entity\n    description: a variable that is used as a measure in the investigation of a study\n    narrow_mappings:\n      - NCIT:C142192  # specifies clinical study\n    close_mappings:\n      - STATO:0000258\n      - SIO:000367\n\n  common data element:\n    is_a: information content entity\n    description: >- \n      A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable \n      responses, used systematically across different sites, studies, or clinical trials to ensure consistent \n      data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. \n      (https://cde.nlm.nih.gov/home)\n    close_mappings:\n      - NCIT:C19984\n\n   ## epc result sets\n  concept count analysis result:\n    is_a: study result\n    description: >-\n      A result of a concept count analysis.\n\n  observed expected frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a observed expected frequency analysis.\n\n  relative frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a relative frequency analysis.\n\n  text mining result:\n    is_a: study result\n    description: >-\n      A result of text mining.\n\n  chi squared analysis result:\n    is_a: study result\n    description: >-\n      A result of a chi squared analysis.\n\n  log odds analysis result:\n    is_a: study result\n    description: >-\n      A result of a log odds ratio analysis.\n\n  agent:\n    is_a: administrative entity\n    aliases: ['group']\n    description: >-\n      person, group, organization or project that provides\n      a piece of information (i.e. a knowledge association)\n    slots:\n      - affiliation\n      - address\n    exact_mappings:\n      - prov:Agent\n      - dct:Agent\n    narrow_mappings:\n       # Organization\n      - UMLSSG:ORGA\n      - STY:T092\n       # Health Care Related Organization\n      - STY:T093\n       # Professional Society\n      - STY:T094\n       # Self-help or Relief Organization\n      - STY:T095\n       # Group\n      - STY:T096\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Different classes of agents have distinct preferred identifiers.\n          For publishers, use the ISBN publisher code.\n          See https://grp.isbn-international.org/ for publisher code lookups.\n          For editors, authors and  individual providers, use the individual's\n          ORCID if available; Otherwise, a ScopusID, ResearchID or\n          Google Scholar ID ('GSID') may be used if the author ORCID is unknown.\n          Institutional agents could be identified by an\n          International Standard Name Identifier ('ISNI') code.\n        values_from:\n           # CURIE space for publishers\n          - isbn\n           # CURIE space for authors\n          - ORCID\n          - ScopusID\n          - ResearchID\n          - GSID\n           # Institutional agents\n          - isni\n      name:\n        description: >-\n          it is recommended that an author's 'name' property\n          be formatted as \"surname, firstname initial.\"\n    id_prefixes:\n      - isbn\n      - ORCID\n      - ScopusID\n      - ResearchID\n      - GSID\n      - isni\n\n   ## General Information Entities\n\n  information content entity:\n    aliases: ['information', 'information artefact', 'information entity']\n    abstract: true\n    is_a: named thing\n    description: >-\n      a piece of information that typically describes\n      some topic of discourse or is used as support.\n    slots:\n      - license\n      - rights\n      - format\n      - creation date\n    id_prefixes:\n      - doi\n    exact_mappings:\n      - IAO:0000030\n    narrow_mappings:\n       # UMLS Semantic Group \"Concepts & Ideas\"\n      - UMLSSG:CONC\n       # Conceptual Entity\n      - STY:T077\n       # Idea or Concept\n      - STY:T078\n       # Temporal Concept\n      - STY:T079\n       # Qualitative Concept\n      - STY:T080\n       # Quantitative Concept\n      - STY:T081\n       # Spatial Concept\n      - STY:T082\n       # Regulation or Law\n      - STY:T089\n       # Group Attribute\n      - STY:T102\n       # Functional Concept\n      - STY:T169\n       # Language\n      - STY:T171\n       # Classification\n      - STY:T185\n\n  dataset:\n    description: >-\n      an item that refers to a collection of data from a data source.\n    is_a: information content entity\n    exact_mappings:\n      - IAO:0000100\n      - dctypes:Dataset\n      - schema:dataset\n      - dcid:Dataset\n\n  dataset distribution:\n    is_a: information content entity\n    description: >-\n      an item that holds distribution level information about a dataset.\n    slots:\n      - distribution download url\n    exact_mappings:\n      - dcat:Distribution\n\n  dataset version:\n    description: >-\n      an item that holds version level information about a dataset.\n    is_a: information content entity\n    slots:\n      - has dataset\n      - ingest date\n      - has distribution\n\n  dataset summary:\n    description: >-\n      an item that holds summary level information about a dataset.\n    is_a: information content entity\n    slots:\n      - source web page\n      - source logo\n\n  confidence level:\n    is_a: information content entity\n    description: >-\n      Level of confidence in a statement\n    values_from:\n      - cio\n    exact_mappings:\n      - CIO:0000028\n       # statement confidence\n      - SEPIO:0000187\n    close_mappings:\n       # assertion confidence levels\n      - SEPIO:0000167\n\n  evidence type:\n    is_a: information content entity\n    aliases: ['evidence code']\n    description: >-\n      Class of evidence that supports an association\n    values_from:\n      - eco\n    exact_mappings:\n      - ECO:0000000\n\n   ## Publications\n\n   # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies\n  publication:\n    is_a: information content entity\n    description: >-\n      Any ‘published’ piece of information. Publications are considered broadly \n      to include any document or document part made available in print or on the \n      web - which may include scientific journal issues, individual articles, and \n      books - as well as things like pre-prints, white papers, patents, drug \n      labels, web pages, protocol documents,  and even a part of a publication if \n      of significant knowledge scope (e.g. a figure, figure legend, or section \n      highlighted by NLP). \n    slots:\n      - authors\n      - pages\n      - summary\n      - keywords\n      - mesh terms\n      - xref\n     # In addition to embedded slots, instances of 'contributor association'\n     # may be used to more extensively document publisher, editor and author details\n    slot_usage:\n      id:\n        description: >-\n          Different kinds of publication subtypes will have different preferred\n          identifiers (curies when feasible). Precedence of identifiers for\n          scientific articles is as follows: PMID if available; DOI if not; actual\n          alternate CURIE otherwise. Enclosing publications (i.e. referenced by\n          'published in' node property) such as books and journals, should have\n          industry-standard identifier such as from ISBN and ISSN.\n      name:\n        description: >-\n          the 'title' of the publication is generally recorded in the 'name'\n          property (inherited from NamedThing). The field name 'title' is now also\n          tagged as an acceptable alias for the node property 'name' (just in case).\n      publication type:\n        required: true\n      pages:\n        multivalued: true\n        description: >-\n          When a 2-tuple of page numbers are provided, they represent\n          the start and end page of the publication within its parent publication context.\n          For books, this may be set to the total number of pages of the book.\n    exact_mappings:\n      - IAO:0000311\n    narrow_mappings:\n      - IAO:0000013\n       # UMLS Semantic Type \"Intellectual Product\"\n      - STY:T170\n    id_prefixes:\n      - PMID\n      - PMC\n      - doi\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book:\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Books should have industry-standard identifier such as from ISBN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'book'.\n    id_prefixes:\n      - isbn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book chapter:\n    is_a: publication\n    slots:\n      - published in\n      - volume\n      - chapter\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent book containing the chapter\n          should have industry-standard identifier from ISBN.\n    in_subset:\n      - model_organism_database\n\n  serial:\n    aliases: ['journal']\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slots:\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Serials (journals) should have industry-standard identifier such as from ISSN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'serial' or 'journal'.\n    id_prefixes:\n      - issn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  article:\n    is_a: publication\n    description: >-\n      a piece of writing on a particular topic presented as a stand-alone \n      section of a larger publication\t  \n    slots:\n      - published in\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent serial containing the article should\n          have industry-standard identifier from ISSN.\n      iso abbreviation:\n        description: >-\n          Optional value, if used locally as a convenience, is set\n          to the iso abbreviation of the 'published in' parent.\n    exact_mappings:\n      - SIO:000154\n      - fabio:article\n    id_prefixes:\n       # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces\n      - PMID\n    in_subset:\n      - model_organism_database\n\n  journal article:\n    is_a: article\n    description: >-\n      an article, typically presenting results of research, that is published \n      in an issue of a scientific journal.\n    exact_mappings:\n      - IAO:0000013\n      - fabio:JournalArticle\n    id_prefixes:\n      - PMID\n      - PMCID\n      - doi\n     \n  patent:\n    is_a: publication\n    description: >-\n      a legal document granted by a patent issuing authority which confers upon \n      the patenter the sole right to make, use and sell an invention for a set\n      period of time. \n    exact_mappings:\n      - SIO:000153\n      - IAO:0000313\n      - fabio:Patent\n\n  web page:\n    is_a: publication\n    description: >-\n      a document that is published according to World Wide Web standards, which \n      may incorporate text, graphics, sound, and/or other features.\n    exact_mappings:\n      - SIO:000302\n      - NCIT-OBO:C142749\n      - fabio:WebPage\n      \n  preprint publication:\n    is_a: publication\n    description: >-\n      a document reresenting an early version of an author's original scholarly work, \n      such as a research paper or a review, prior to formal peer review and publication \n      in a peer-reviewed scholarly or scientific journal.\n    exact_mappings:\n      - EFO:0010558\n      - fabio:Preprint\n\n  drug label:\n    is_a: publication\n    description: >-\n      a document accompanying a drug or its container that provides written, printed or\n      graphic information about the drug, including drug contents, specific instructions \n      or warnings for administration, storage and disposal instructions, etc. \n    broad_mappings:\n      - NCIT-OBO:C41203\n\n  retrieval source:\n    is_a: information content entity\n    description: >-\n      Provides information about how a particular InformationResource\n      served as a source from which knowledge expressed in an Edge, or\n      data used to generate this knowledge, was retrieved.\n    slots:\n      - resource id\n      - resource role\n      - upstream resource ids\n      - xref\n    slot_usage:\n      resource id:\n        required: true\n        description: >-\n          The InformationResource that served as a source for the\n          knowledge expressed in an Edge, or data used to generate this knowledge.\n      resource role:\n        required: true\n        description: >-\n            The role of the InformationResource in the retrieval of the\n            knowledge expressed in an Edge, or data used to generate this knowledge.\n      upstream resource ids:\n        description: >-\n          The InformationResources that served as a source for the\n          InformationResource that served as a source for the knowledge\n          expressed in an Edge, or data used to generate this knowledge.\n\n   ## Top Level Abstractions of Material & Process Entities\n\n  physical essence or occurrent:\n    description: >-\n      Either a physical or processual entity.\n    mixin: true\n\n  physical essence:\n    description: >-\n      Semantic mixin concept.  Pertains to entities that have\n      physical properties such as mass, volume, or charge.\n    is_a: physical essence or occurrent\n    mixin: true\n\n  physical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n    description: >-\n      An entity that has material reality (a.k.a. physical essence).\n    exact_mappings:\n       # Physical Object\n      - STY:T072\n    narrow_mappings:\n       # Manufactured Object\n      - STY:T073\n\n  occurrent:\n    description: >-\n      A processual entity.\n     # biolink:Occurrent is most consistently used as a mixin thus it should\n     # be declared as such and cannot inherit from the non-mixin biolink:NamedThing\n    is_a: physical essence or occurrent\n    mixin: true\n    exact_mappings:\n      - BFO:0000003\n\n  activity and behavior:\n    is_a: occurrent\n    mixin: true\n    description: >-\n      Activity or behavior of any independent integral living,\n      organization or mechanical actor in the world\n    exact_mappings:\n       # Activities & Behaviors\n      - UMLSSG:ACTI\n\n  activity:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      An activity is something that occurs over a period of time and acts upon\n      or with entities; it may include consuming, processing, transforming,\n      modifying, relocating, using, or generating entities.\n    exact_mappings:\n      - prov:Activity\n      - NCIT:C43431\n       # Activity\n      - STY:T052\n    narrow_mappings:\n       # Daily or Recreational Activity\n      - STY:T056\n       # Occupational Activity\n      - STY:T057\n       # Governmental or Regulatory Activity\n      - STY:T064\n       # Machine Activity\n      - STY:T066\n       # Research Activity\n      - STY:T062\n       # Educational Activity\n      - STY:T065\n       # Health Care Activity\n      - STY:T058\n\n  procedure:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      A series of actions conducted in a certain order or manner\n    exact_mappings:\n       # Procedures\n      - UMLSSG:PROC\n      - dcid:MedicalProcedure\n    narrow_mappings:\n       # Laboratory Procedure\n      - STY:T059\n       # Diagnostic Procedure\n      - STY:T060\n       # Therapeutic or Preventive Procedure\n      - STY:T061\n       # Molecular Biology Research Technique\n      - STY:T063\n    id_prefixes:\n      - CPT\n\n  phenomenon:\n    is_a: named thing\n    mixins:\n      - occurrent\n    description: >-\n      a fact or situation that is observed to exist or happen,\n      especially one whose cause or explanation is in question\n    broad_mappings:\n       # the inclusion of 'process' in the definition of these\n       # terms broadens them, relative to 'phenomenon'\n       # Phenomenon or Process\n      - STY:T067\n       # Human-caused Phenomenon or Process\n      - STY:T068\n       # Natural Phenomenon or Process\n      - STY:T070\n    exact_mappings:\n       # Phenomena\n      - UMLSSG:PHEN\n    narrow_mappings:\n       # Laboratory or Test Result\n      - STY:T034\n       # Biologic Function\n      - STY:T038\n       # Environmental Effect of Humans\n      - STY:T069\n\n  device:\n    is_a: named thing\n    description: >-\n      A thing made or adapted for a particular purpose, especially\n      a piece of mechanical or electronic equipment\n    narrow_mappings:\n      # Devices\n      - UMLSSG:DEVI\n      # Medical Device\n      - STY:T074\n      # Research Device\n      - STY:T075\n      # Drug Delivery Device\n      - STY:T203\n      # Biomedical or Dental Material\n      - STY:T122\n\n  diagnostic aid:\n    is_a: named thing\n    description: >-\n      A device or substance used to help diagnose disease or injury\n    exact_mappings:\n      - STY:T130  # Diagnostic Aid\n      - SNOMED:2949005  # Diagnostic aid\n\n   ## Scientific Studies\n\n  study population:\n    is_a: population of individual organisms\n    description: >-\n      A group of people banded together or treated as a group as participants in a research study.\n    close_mappings:\n      - WIKIDATA:Q7229825\n\n  subject of investigation:\n    mixin: true\n    description: >-\n      An entity that has the role of being studied in an investigation, study, or experiment\n\n  material sample:\n    aliases: ['biospecimen', 'sample', 'biosample', 'physical sample']\n    is_a: physical entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A sample is a limited quantity of something (e.g. an individual or set of individuals\n      from a population, or a portion of a substance) to be used for testing, analysis,\n      inspection, investigation, demonstration, or trial use. [SIO]\n    exact_mappings:\n      - OBI:0000747\n      - SIO:001050\n    id_prefixes:\n      - BIOSAMPLE\n      - GOLD.META\n\n   ## Earth Sciences\n\n  planetary entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists at the level of the whole planet\n\n  environmental process:\n    is_a: planetary entity\n    mixins:\n      - occurrent\n    exact_mappings:\n      - ENVO:02500000\n\n  environmental feature:\n    is_a: planetary entity\n    exact_mappings:\n      - ENVO:01000254\n\n  geographic location:\n    is_a: planetary entity\n    description: >-\n      a location that can be described in lat/long coordinates\n    slots:\n      - latitude\n      - longitude\n    exact_mappings:\n       # Geographic Areas\n      - UMLSSG:GEOG\n       # Geographic Area\n      - STY:T083\n\n  geographic location at time:\n    is_a: geographic location\n    description: >-\n      a location that can be described in lat/long coordinates, for a particular time\n    slots:\n      - timepoint\n\n   ## Biological Sciences\n\n  thing with taxon:\n    mixin: true\n    description: >-\n      A mixin that can be used on any entity that can be taxonomically classified.\n      This includes individual organisms; genes, their products and other molecular\n      entities; body parts; biological processes\n    slots:\n      - in taxon\n      - in taxon label\n\n  biological entity:\n    is_a: named thing\n    aliases: ['bioentity']\n    abstract: true\n    mixins:\n      - thing with taxon\n    narrow_mappings:\n      - WIKIDATA:Q28845870\n       # UMLS Semantic Type \"Experimental Model of Disease\"\n      - STY:T050\n       # SIO term is 'biological entity' but less inclusive than the Biolink scope\n      - SIO:010046\n      - STY:T129  # (imft, full name: Immunologic Factor\n\n  genomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - STY:T028    # Gene or Genome\n      - GENO:0000897   # Genomic Entity\n\n  epigenomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n\n  molecular entity:\n    is_a: chemical entity\n    description: >-\n      A molecular entity is a chemical entity composed of individual or\n      covalently bonded atoms.\n    slots:\n      - is metabolite\n    narrow_mappings:\n      - STY:T088  # Carbohydrate\n      - STY:T085  # Molecular Sequence\n      - CHEBI:23367  # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical,\n       # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.\n      - bioschemas:MolecularEntity\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.DRUG     # D number\n      - KEGG.ENVIRON  # E number\n      - KEGG\n      - UMLS\n\n  chemical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n      - chemical or drug or treatment  # issue 701\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    description: >-\n      A chemical entity is a physical entity that pertains to chemistry or\n      biochemistry.\n    slots:\n      - trade name\n      - available from\n      - max tolerated dose\n      - is toxic\n      - has chemical role\n    exact_mappings:\n      - CHEBI:24431\n      - SIO:010004  # Chemical entity\n      - WIKIDATA:Q79529  # Chemical substance\n      - STY:T103  # Chemical\n    narrow_mappings:\n      - WIKIDATA:Q43460564\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS  # CAS numbers are given for things like plant extracts as well.\n      - UMLS\n      - ncats.drug\n      - PHARMGKB.CHEMICAL\n\n  small molecule:\n    is_a: molecular entity\n    aliases: ['chemical substance']\n    description: >-\n      A small molecule entity is a molecular entity characterized by availability\n      in small-molecule databases of SMILES, InChI, IUPAC, or other\n      unambiguous representation of its precise chemical structure; for\n      convenience of representation, any valid chemical representation is\n      included, even if it is not strictly molecular (e.g., sodium ion).\n    narrow_mappings:\n      - STY:T196  # Element, Ion, or Isotope\n      - CHEBI:59999\n      - bioschemas:ChemicalSubstance\n      - STY:T123  # (bacs, full name: Biologically Active Substance)\n      - STY:T131  # (hops, full name: Hazardous or Poisonous Substance)\n      - STY:T125  # (horm, full name: Hormone)\n      - STY:T197  # (inch, full name: Inorganic Chemical)\n      - STY:T109  # (orch, full name: Organic Chemical)\n      - STY:T118  # (carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files)\n      - STY:T111  # (eico, full name: Eicosanoid) - same note as above\n      - STY:T119  # (lipd, full name: Lipid) - same note as above\n      - STY:T124  # (nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above\n      - STY:T115  # (opco, full name: Organophosphorus Compound) - same note as above\n      - STY:T110  # (strd, full name: Steroid) - same note as above\n      - STY:T127  # vitamin\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG.ENVIRON  ## E number\n      - KEGG\n      - BIGG.METABOLITE\n      - UMLS\n      - foodb.compound\n    slot_usage:\n      id:\n        examples:\n          - value: CHEBI:29101\n            description: sodium ion\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n\n  chemical mixture:\n    is_a: chemical entity\n    description: >-\n      A chemical mixture is a chemical entity composed of two or more\n      molecular entities.\n    slots:\n      - is supplement\n      - highest FDA approval status\n      - drug regulatory status world wide\n      - routes of delivery\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG\n      - KEGG.ENVIRON  ## E number\n      - UMLS\n    close_mappings:\n      - dcid:ChemicalCompound\n    narrow_mappings:\n      - NCIT:C20401  # monoclonal antibody\n      - SNOMEDCT:49616005  # monoclonal antibody (substance)\n\n  nucleic acid entity:\n    is_a: molecular entity\n    description: >-\n      A nucleic acid entity is a molecular entity characterized by\n      availability in gene databases of nucleotide-based sequence\n      representations of its precise sequence; for convenience of\n      representation, partial sequences of various kinds are included.\n    aliases: ['sequence feature', 'genomic entity']\n    mixins:\n      - genomic entity\n      - thing with taxon\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000110\n    narrow_mappings:\n      - STY:T086    # Nucleotide Sequence\n      - STY:T114    # Nucleic Acid, Nucleoside, or Nucleotide\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n\n  regulatory region:\n    aliases: ['regulatory element']\n    description: >-\n      A region (or regions) of the genome that contains known or putative regulatory elements\n      that act in cis- or trans- to affect the transcription of gene\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0005836\n      - SIO:001225\n      - WIKIDATA:Q3238407\n\n  accessible dna region:\n    aliases: ['dnase-seq accessible region', 'atac-seq accessible region']\n    description: >-\n      A region (or regions) of a chromatinized genome that has been measured to be more\n      accessible to an enzyme such as DNase-I or Tn5 Transpose\n    is_a: regulatory region\n    mixins:\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0002231\n\n  transcription factor binding site:\n    aliases: ['tf binding site', 'binding site']\n    description: >-\n      A region (or regions) of the genome that contains a region of DNA known or predicted\n      to bind a protein that modulates gene transcription\n    is_a: regulatory region\n    mixins:\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000235\n\n  molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A molecular mixture is a chemical mixture composed of two or more\n      molecular entities with known concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG\n      - KEGG.ENVIRON  ## E number\n      - UMLS\n      - ncats.drug\n\n  complex molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A complex molecular mixture is a chemical mixture composed of two or\n      more molecular entities with unknown concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG\n      - KEGG.ENVIRON  ## E number\n      - UMLS\n\n  biological process or activity:\n    description: >-\n      Either an individual molecular activity, or a collection of\n      causally connected molecular activities in a biological system.\n    is_a: biological entity\n    mixins:\n      - occurrent\n      - ontology class\n    id_prefixes:\n      - GO\n      - REACT\n    slots:\n      - has input\n      - has output\n      - enabled by\n\n  molecular activity:\n    description: >-\n      An execution of a molecular function carried out by a\n      gene product or macromolecular complex.\n    is_a: biological process or activity\n    aliases: ['molecular function', 'molecular event', 'reaction']\n    mixins:\n      - occurrent\n      - ontology class\n    slot_usage:\n      has input:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the input for the reaction\n      has output:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the output for the reaction\n      enabled by:\n        range: macromolecular machine mixin\n        description: >-\n          The gene product, gene, or complex that catalyzes the reaction\n    exact_mappings:\n      - GO:0003674\n      # UMLS Semantic Type \"Molecular Function\"\n      - STY:T044\n    broad_mappings:\n      - STY:T045  # Genetic Function\n    id_prefixes:\n      - GO\n      - REACT\n      - RHEA\n      - metacyc.reaction\n      - EC\n      - TCDB\n      - KEGG.REACTION   ## R number\n      - KEGG\n      - KEGG.ORTHOLOGY  ## in particular for gut microbiome use case in issue  #888\n      - UMLS\n      - BIGG.REACTION\n      - SEED.REACTION\n      - METANETX.REACTION\n\n  biological process:\n    is_a: biological process or activity\n    mixins:\n      - occurrent\n      - ontology class\n    description: >-\n      One or more causally connected executions of molecular functions\n    exact_mappings:\n      - GO:0008150\n      - SIO:000006\n      - WIKIDATA:Q2996394\n    broad_mappings:\n      - WIKIDATA:P682\n    id_prefixes:\n      - GO\n      - REACT\n      - metacyc.reaction\n      - KEGG.MODULE  ## M number\n      - KEGG\n\n  pathway:\n    is_a: biological process\n    mixins:\n      - ontology class\n    exact_mappings:\n      - PW:0000001\n      - WIKIDATA:Q4915012\n    narrow_mappings:\n      - SIO:010526\n      - GO:0007165\n    id_prefixes:\n      - GO\n      - REACT\n      - KEGG\n      - SMPDB\n      - MSigDB\n      - PHARMGKB.PATHWAYS\n      - WIKIPATHWAYS\n      - FB   # FlyBase FBgg*\n      - PANTHER.PATHWAY\n      - KEGG.PATHWAY\n      - ncats.bioplanet\n\n  physiological process:\n    aliases: ['physiology']\n    is_a: biological process\n    mixins:\n      - ontology class\n    close_mappings:\n    exact_mappings:\n       # Physiologic Function\n      - STY:T039\n      - WIKIDATA:Q30892994\n    narrow_mappings:\n       # Organism Function\n      - STY:T040\n       # Organ or Tissue Function\n      - STY:T042\n       # Cell Function\n      - STY:T043\n       # Genetic Function\n      - STY:T045\n    id_prefixes:\n      - GO\n      - REACT\n\n  behavior:\n    is_a: biological process\n    mixins:\n      - ontology class\n      - activity and behavior\n    exact_mappings:\n      - GO:0007610\n       # Behavior\n      - STY:T053\n    narrow_mappings:\n       # Mental Process\n      - STY:T041\n       # Social Behavior\n      - STY:T054\n       # Individual Behavior\n      - STY:T055\n\n   ## (Bio)chemistry\n\n  processed material:\n    is_a: chemical mixture\n    description: >-\n      A chemical entity (often a mixture) processed\n      for consumption for nutritional, medical or technical use.\n      Is a material entity that is created or changed during material processing.\n    exact_mappings:\n      - OBI:0000047\n    id_prefixes:\n      - UMLS\n\n  drug:\n    is_a: molecular mixture\n    mixins:\n      - chemical or drug or treatment\n      - ontology class\n    description: >-\n      A substance intended for use in the diagnosis, cure,\n      mitigation, treatment, or prevention of disease\n    comments:\n      - The CHEBI ID represents a role rather than a substance\n    broad_mappings:\n       # Pharmacologic Substance: Any natural, endogenously-derived,\n       # synthetic or semi synthetic compound with pharmacologic activity.\n      - STY:T121\n    exact_mappings:\n      - WIKIDATA:Q12140\n      - CHEBI:23888\n       # UMLS Semantic Type \"Clinical Drug\"\n      - STY:T200\n      - dcid:Drug\n    narrow_mappings:\n       # Antibiotic\n      - STY:T195\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n\n   ## Food\n\n  environmental food contaminant:\n    is_a: chemical entity\n    related_mappings:\n       # substance role\n      - CHEBI:78299\n\n  food additive:\n    is_a: chemical entity\n    related_mappings:\n       # substance role\n      - CHEBI:64047\n\n  food:\n    is_a: chemical mixture\n    description: >-\n      A substance consumed by a living organism as a source of nutrition\n    id_prefixes:\n      - foodb.food\n      - FOODON\n      - UMLS\n      - NCIT\n    exact_mappings:\n       # Food\n      - STY:T168\n\n   ## Biology and Biomedical Sciences\n\n   ## Biological Attributes\n\n  organism attribute:\n    is_a: attribute\n    description: >-\n      describes a characteristic of an organismal entity.\n    exact_mappings:\n       # Organism Attribute\n      - STY:T032\n\n  phenotypic quality:\n    aliases: ['phenotypic properties']\n    is_a: organism attribute\n    description: >-\n      A property of a phenotype\n    examples:\n      - value: weight\n\n    mappings:\n      - PATO:0000001\n\n  genetic inheritance:\n    aliases: ['inheritance']\n    is_a: biological entity\n    description: >-\n      The pattern or 'mode' in which a particular genetic trait or disorder is passed from one\n      generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\n    exact_mappings:\n      - HP:0000005\n      - GENO:0000141\n      - NCIT:C45827\n    close_mappings:\n      - STY:T045\n    id_prefixes:\n      - HP\n      - GENO\n      - NCIT\n\n    ## Biological Entities\n\n  organismal entity:\n    description: >-\n      A named entity that is either a part of an organism, a whole organism,\n      population or clade of organisms, excluding chemical entities\n    abstract: true\n    is_a: biological entity\n    mixins:\n      - subject of investigation\n    slot_usage:\n      has attribute:\n        description: >-\n          may often be an organism attribute\n    exact_mappings:\n      - WIKIDATA:Q7239\n        # UMLS Semantic Group \"Living Beings\"\n        # Several of the associated semantic types here are probably not\n      # that relevant to the Biolink world, but we keep them here for now.\n      - UMLSSG:LIVB\n      - CARO:0001010\n    narrow_mappings:\n      - STY:T008  # animal\n\n  bacterium:\n    is_a: organismal entity\n    description: >-\n      A member of a group of unicellular microorganisms lacking a nuclear membrane,\n      that reproduce by binary fission and are often motile.\n    exact_mappings:\n      - NCBITaxon:1869227\n      - STY:T007  # Bacterium\n\n  virus:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A virus is a microorganism that replicates itself as a microRNA\n      and infects the host cell.\n    exact_mappings:\n      - NCBITaxon:10239\n      - STY:T005  # Virus\n\n  cellular organism:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n    exact_mappings:\n      - NCBITaxon:131567\n\n  mammal:\n    is_a: cellular organism\n    mixins:\n      - subject of investigation\n    description: >-\n      A member of the class Mammalia, a clade of endothermic amniotes\n      distinguished from reptiles and birds by the possession of hair,\n      three middle ear bones, mammary glands, and a neocortex\n    exact_mappings:\n      - NCBITaxon:40674  # mammal\n      - STY:T015  # mammal\n      - NCIT:C14234  # Mamalia\n      - FOODON:03411134  # mammal\n\n  human:\n    is_a: mammal\n    mixins:\n      - subject of investigation\n    description: >-\n      A member of the the species Homo sapiens.\n    exact_mappings:\n      - STY:T016\n      - NCBITaxon:9606\n      - SIO:000485\n      - NCIT:C14225\n\n  plant:\n    is_a: cellular organism\n    description: >-\n    exact_mappings:\n      - NCIT:C14258  # plant\n      - STY:T002  # plant\n      - PO:0000003  # whole plant\n      - NCIT:C79659  # plant, whole\n\n  invertebrate:\n    is_a: cellular organism\n    description: >-\n      An animal lacking a vertebral column. This group consists of 98% of all animal species.\n    exact_mappings:\n      - NCIT:C14228  # invertebrate\n      - OMIT:0008565  # invertebrates\n      - FOODON:00002452  # invertebrate animals\n      - STY:T011\n    related_mappings:\n      - NCBITaxon:1767184  # unidentified invertebrate\n\n  vertebrate:\n    is_a: cellular organism\n    description: >-\n      A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.\n    exact_mappings:\n      - STY:T010\n      - NCBITaxon:7742  # vertebrata\n      - OMIT:0015545  # vertebrates\n    related_mappings:\n      - NCBITaxon:2662825  # unclassified vertebrata (in:vertebrates)\n\n  fungus:\n    is_a: cellular organism\n    description: >-\n      A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, \n      including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or\n      asexually, and have life cycles that range from simple to complex. Filamentous \n      fungi refer to those that grow as multicellular colonies (mushrooms and molds).\n    exact_mappings:\n      - STY:T004\n      - NCIT:C14209\n      - FOODON:03411261\n    narrow_mappings:\n      - FOODON:03315605  # fungus (edible)\n      - NCBITaxon:1670606  # fungus metagenome\n\n  life stage:\n    is_a: organismal entity\n    description: >-\n      A stage of development or growth of an organism,\n      including post-natal adult stages\n    exact_mappings:\n      - UBERON:0000105\n    narrow_mappings:\n      # constrained to human life cycles\n      - HsapDv:0000000\n    in_subset:\n      - model_organism_database\n    id_prefixes:\n      - HsapDv\n      - MmusDv\n      - ZFS\n      - FBdv\n      - WBls\n      - UBERON\n\n  individual organism:\n    aliases: ['organism']\n    description: >-\n      An instance of an organism. For example, Richard Nixon,\n      Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - SIO:010000\n      # Organism\n      - STY:T001\n    narrow_mappings:\n      # Wikidata considers its definition of 'individual' to be constrained to human persons?\n      - WIKIDATA:Q795052\n      - foaf:Person\n    id_prefixes:\n      - ORCID\n\n  population of individual organisms:\n    description: >-\n      A collection of individuals from the same taxonomic class\n      distinguished by one or more characteristics.  Characteristics can\n      include, but are not limited to, shared geographic location, genetics,\n      phenotypes.\n    local_names:\n      ga4gh: population\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - PCO:0000001\n      - SIO:001061\n      # UMLS Semantic Type \"Population Group\"\n      - STY:T098\n      - OBI:0000181\n    id_prefixes:\n      - HANCESTRO\n    in_subset:\n      - model_organism_database\n\n  disease or phenotypic feature:\n    aliases: ['phenome']\n    is_a: biological entity\n    description: >-\n      Either one of a disease or an individual phenotypic feature.\n      Some knowledge resources such as Monarch treat these as\n      distinct, others such as MESH conflate.  Please see definitions of phenotypic feature and disease in this model\n      for their independent descriptions.  This class is helpful to enforce domains and ranges  \n      that may involve either a disease or a phenotypic feature.\n    union_of:\n      - disease\n      - phenotypic feature\n    narrow_mappings:\n      # UMLS Semantic Type \"Finding\" - more specialized use of 'disease or phenotypic feature'\n      - STY:T033\n\n  disease:\n    aliases: ['condition', 'disorder', 'medical condition']\n    description: >-\n      A disorder of structure or function, especially one that produces specific \n      signs, phenotypes or symptoms or that affects a specific location and is not simply a \n      direct result of physical injury.  A disposition to undergo pathological processes that exists in an \n      organism because of one or more disorders in that organism.\n    is_a: disease or phenotypic feature\n    exact_mappings:\n      - MONDO:0000001\n      - DOID:4\n      - NCIT:C2991\n      - WIKIDATA:Q12136\n      - SIO:010299\n       # UMLS Semantic Group \"Disorders\"\n      - UMLSSG:DISO\n       # Disease or Syndrome\n      - STY:T047\n      - dcid:Disease\n    narrow_mappings:\n       # Congenital Abnormality\n      - STY:T019\n       # Acquired Abnormality\n      - STY:T020\n       # Mental or Behavioral Dysfunction\n      - STY:T048\n       # Cell or Molecular Dysfunction\n      - STY:T049\n       # Anatomical Abnormality\n      - STY:T190\n       # Neoplastic Process\n      - STY:T191\n       # disease susceptibility\n      - MONDO:0042489\n    id_prefixes:\n      - MONDO\n      - DOID\n      - OMIM\n      - OMIM.PS\n      - orphanet\n      - EFO\n      - UMLS\n      - MESH\n      - MEDDRA\n      - NCIT\n      - SNOMEDCT\n      - medgen\n      - ICD10\n      - ICD9\n      - KEGG.DISEASE  ## H number\n      - HP\n      - MP\n      - PHARMGKB.DISEASE\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n  phenotypic feature:\n    aliases: ['sign', 'symptom', 'phenotype', 'trait', 'endophenotype']\n    is_a: disease or phenotypic feature\n    description: >-\n      A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an \n      individual resulting from the interaction of its genotype with its molecular and physical environment.\n    examples:\n      - value: MP:0001262\n        description: decreased body weight\n    exact_mappings:\n      - UPHENO:0001001\n      - SIO:010056\n      - WIKIDATA:Q104053\n      - UMLS:C4021819\n      - NCIT:C16977\n      - SNOMEDCT:8116006  # documented as phenotypic finding and phenotype, also referred to as \"SCTID:8116006\" at SNOMEDCT\n      - MESH:D010641  # phenotype\n    narrow_mappings:\n      - STY:T184  # Sign or Symptom\n      - WIKIDATA:Q169872  # Sign or Symptom\n       # presentation of a disease in clinical medicine\n      - WIKIDATA:Q25203551\n      - ZP:00000000  # zebrafish phenotype\n      - FBcv:0001347  # fly phenotype\n      - HP:0000118  # human phenotype\n      - MP:0000001  # mouse phenotype\n      - WBPhenotype:0000886  # worm phenotype\n      - XPO:00000000  # frog phenotype\n      - FYPO:0000001  # fission yeast phenotype\n      - APO:0000017  # phenotype\n      - TO:0000387  # more narrowly defined here for plants; our definition conflates trait and phenotype.\n    broad_mappings:\n      - BFO:0000019  # quality\n      - PATO:0000001  # quality\n    id_prefixes:\n      - HP\n      - EFO  # covered by BFO quality mapping\n      - NCIT\n      - UMLS\n      - MEDDRA  # can not find a mapping\n      - MP\n      - ZP\n      - UPHENO\n      - APO\n      - FBcv\n      - WBPhenotype\n      - SNOMEDCT\n      - MESH\n      - XPO\n      - FYPO\n      - TO\n    in_subset:\n      - model_organism_database\n\n  behavioral feature:\n    description: >-\n      A phenotypic feature which is behavioral in nature.\n    is_a: phenotypic feature\n    exact_mappings:\n      - NBO:0000243\n\n  anatomical entity:\n    is_a: organismal entity\n    mixins:\n      - physical essence\n    description: >-\n      A subcellular location, cell type or gross anatomical part\n    exact_mappings:\n      - UBERON:0001062\n      - WIKIDATA:Q4936952\n       # UMLS Semantic Group \"Anatomy\"\n      - UMLSSG:ANAT\n       # UMLS Semantic Type \"Anatomical Structure\"\n      - STY:T017\n      - FMA:62955  # anatomical entity\n      - CARO:0000000   # anatomical entity\n      - SIO:001262  # anatomical entity\n      - STY:T029  # Body Location or Region\n      - STY:T030  # Body Space or Junction\n    narrow_mappings:\n      - ZFA:0100000  # zebrafish anatomical entity\n      - FBbt:10000000  # fly anatomical entity\n      - EMAPA:0  # mouse anatomical entity\n      - MA:0000001  # mouse anatomical entity\n      - XAO:0000000  # frog anatomical entity\n      - WBbt:0000100  # c. elegans anatomical entity\n      - NCIT:C12219  # human anatomical entity\n      - GO:0110165  # cellular anatomical entity, also used directly in CL\n      - STY:T031  # Body Substance\n    related_mappings:\n      - SNOMEDCT:123037004  # body structure\n    id_prefixes:\n      - UBERON\n      - GO\n      - CL\n      - UMLS\n      - MESH\n      - NCIT\n      - EMAPA\n      - ZFA\n      - FBbt\n      - WBbt\n    in_subset:\n      - model_organism_database\n\n  cellular component:\n    aliases: ['cell component', 'cell part']\n    is_a: anatomical entity\n    description: >-\n      A location in or around a cell\n    exact_mappings:\n      - GO:0005575\n      - SIO:001400\n      - WIKIDATA:Q5058355\n       # Cell Component\n      - STY:T026\n    broad_mappings:\n      - WIKIDATA:P681\n    id_prefixes:\n      - GO\n      - MESH\n      - UMLS\n      - NCIT\n      - SNOMEDCT\n      - CL\n      - UBERON\n\n  cell:\n    is_a: anatomical entity\n    exact_mappings:\n      - GO:0005623\n      - CL:0000000\n      - SIO:010001\n      - WIKIDATA:Q7868\n       # UMLS Semantic Type \"Cell\"\n      - STY:T025\n      - MESH:D002477  # cells\n    id_prefixes:\n      - CL\n      - PO\n      - UMLS\n      - NCIT\n      - MESH\n      - UBERON\n      - SNOMEDCT\n      - MESH\n\n  cell line:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - CLO:0000031\n    id_prefixes:\n      - CLO\n\n  gross anatomical structure:\n    aliases: ['tissue', 'organ']\n    is_a: anatomical entity\n    exact_mappings:\n      - UBERON:0010000\n      - WIKIDATA:Q4936952\n    narrow_mappings:\n       # UMLS Semantic Type \"Body Part, Organ, or Organ Component\"\n      - STY:T023\n       # UMLS Semantic Type \"Tissue\"\n      - STY:T024\n       # Embryonic Structure\n      - STY:T018\n    id_prefixes:\n      - UBERON\n      - UMLS\n      - MESH\n      - NCIT\n      - PO\n      - FAO\n\n\n   ## entity mixins\n\n  chemical entity or gene or gene product:\n    description: >-\n      A union of chemical entities and children, and gene or gene product.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  chemical entity or protein or polypeptide:\n    description: >-\n      A union of chemical entities and children, and protein and polypeptide.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  macromolecular machine mixin:\n    description: >-\n      A union of gene locus, gene product, and macromolecular complex. These are\n      the basic units of function in a cell. They either carry out individual\n      biological activities, or they encode molecules which do this.\n    mixin: true\n    slots:\n      - name\n    slot_usage:\n      name:\n        range: symbol type\n        description: >-\n          genes are typically designated by a short symbol and a full name.\n          We map the symbol to the default display name\n          and use an additional slot for full name\n\n  gene or gene product:\n    description: >-\n      A union of gene loci or gene products.\n      Frequently an identifier for one will be used as proxy for another\n    is_a: macromolecular machine mixin\n    mixin: true\n    id_prefixes:\n      - CHEMBL.TARGET\n      - IUPHAR.FAMILY\n\n  gene:\n    description: >-\n      A region (or regions) that includes all of the sequence elements\n      necessary to encode a functional transcript. A gene locus may include\n      regulatory regions, transcribed regions and/or other\n      functional sequence regions.\n    is_a: biological entity\n    mixins:\n      - gene or gene product\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    slots:\n      - symbol\n      - synonym\n      - xref\n    exact_mappings:\n      - SO:0000704\n      - SIO:010035\n      - WIKIDATA:Q7187\n      - dcid:Gene\n    id_prefixes:\n      - NCBIGene\n      - ENSEMBL\n      - HGNC\n      - MGI\n      - ZFIN\n      - dictyBase\n      - WB\n      - WormBase  # we have two prefixes here as wormbase supports WormBase:WBGene00000898\n       # and alliancegenome.org and identifiers.org supports WB:WBGene00000898.\n      - FB\n      - RGD\n      - SGD\n      - PomBase\n      - OMIM\n      - KEGG.GENES  ## org:gene\n      - UMLS\n      - Xenbase\n      - AspGD\n      - PHARMGKB.GENE\n    in_subset:\n      - translator_minimal\n      - model_organism_database\n    narrow_mappings:\n      - bioschemas:gene\n    broad_mappings:\n      - NCIT:C45822\n\n\n  gene product mixin:\n    description: >-\n      The functional molecular product of a single gene locus.\n      Gene products are either proteins or functional RNA molecules.\n    is_a: gene or gene product\n    mixin: true\n    slots:\n      - synonym\n      - xref\n    exact_mappings:\n      - WIKIDATA:Q424689\n      - GENO:0000907\n      - NCIT:C26548\n    id_prefixes:\n      - UniProtKB\n      - gtpo\n      - PR\n\n  gene product isoform mixin:\n    description: >-\n      This is an abstract class that can be mixed in with different kinds of\n      gene products to indicate that the gene product is intended to represent\n      a specific isoform rather than a canonical or reference or generic\n      product. The designation of canonical or reference may be arbitrary,\n      or it may represent the superclass of all isoforms.\n    is_a: gene product mixin\n    mixin: true\n\n  macromolecular complex:\n    description: >-\n      A stable assembly of two or more macromolecules, i.e. proteins,\n      nucleic acids, carbohydrates or lipids, in which at least one\n      component is a protein and the constituent parts function together.\n    is_a: biological entity\n    mixins:\n      - macromolecular machine mixin\n    exact_mappings:\n      - GO:0032991\n      - WIKIDATA:Q22325163\n    id_prefixes:\n      - INTACT\n      - GO\n      - PR\n      - REACT\n      - ComplexPortal\n    in_subset:\n      - model_organism_database\n\n   ## Genomic Classes\n  nucleosome modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform.\n      e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.\n    mixins:\n      - gene product isoform mixin\n      - genomic entity\n      - epigenomic entity\n\n  genome:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A genome is the sum of genetic material within a cell or virion.\n    exact_mappings:\n      - SO:0001026\n      - SIO:000984\n      - WIKIDATA:Q7020\n    close_mappings:\n      - dcid:GenomeAssemblyUnit\n    in_subset:\n      - model_organism_database\n\n  exon:\n    is_a: nucleic acid entity\n    description: >-\n      A region of the transcript sequence within a gene which is not\n      removed from the primary RNA transcript by RNA splicing.\n    exact_mappings:\n      - SO:0000147\n      - SIO:010445\n      - WIKIDATA:Q373027\n\n  transcript:\n    is_a: nucleic acid entity\n    description: >-\n      An RNA synthesized on a DNA or RNA template by an RNA polymerase.\n    exact_mappings:\n      - SO:0000673\n      - SIO:010450\n      - WIKIDATA:Q7243183\n      - dcid:RNATranscript\n    id_prefixes:\n      - ENSEMBL  # ENSEMBL:ENST for human\n      - FB       # FlyBase:FBtr\n    in_subset:\n      - model_organism_database\n\n  coding sequence:\n    is_a: nucleic acid entity\n    exact_mappings:\n      - SO:0000316\n      - SIO:001390\n\n  polypeptide:\n    aliases: ['amino acid entity']\n    is_a: biological entity\n    description: >-\n      A polypeptide is a molecular entity characterized by availability\n      in protein databases of amino-acid-based sequence representations\n      of its precise primary structure; for convenience of representation,\n      partial sequences of various kinds are included, even if they do not\n      represent a physical molecule.\n    mixins:\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL  # ENSEMBL:ENSP*\n      - FB       # FlyBase FBpp*\n      - UMLS\n    in_subset:\n      - model_organism_database\n    narrow_mappings:\n      - SO:0000104  # polypeptide defined in SO conflates protein and polypeptide\n       # Amino Acid, Peptide, or Protein\n      - STY:T116\n       # Amino Acid Sequence\n      - STY:T087\n\n  protein:\n    description: >-\n      A gene product that is composed of a chain of amino acid sequences\n      and is produced by ribosome-mediated translation of mRNA\n    is_a: polypeptide\n    mixins:\n      - gene product mixin\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL  # ENSEMBL:ENSP*\n      - FB       # FlyBase FBpp*\n      - UMLS\n      - MESH\n      - ncats.drug\n    broad_mappings:\n      - bioschemas:Protein\n    exact_mappings:\n      - PR:000000001\n      - SIO:010043\n      - WIKIDATA:Q8054\n    narrow_mappings:\n       # Enzyme\n      - STY:T126\n       # Receptor\n      - STY:T192\n\n  protein isoform:\n    aliases: ['proteoform']\n    is_a: protein\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or\n      reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - UniProtKB  # UniProtKB:([A-Z0-9]+-\\d+)\n      - UNIPROT.ISOFORM\n      - PR\n      - ENSEMBL\n\n  protein domain:\n    is_a: biological entity\n    description: >-\n      A conserved part of protein sequence and (tertiary) structure that can evolve,\n      function, and exist independently of the rest of the protein chain.\n      Protein domains maintain their structure and function independently of the proteins in which they are found.\n      e.g. an SH3 domain.\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    exact_mappings:\n      - NCIT:C13379\n      - SIO:001379\n      - UMLS:C1514562\n  \n  posttranslational modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a polypeptide or protein that occurs after translation. \n      e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, \n      protein ubiquitination.\n    mixins:\n      - gene product isoform mixin\n  \n  protein family:\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n\n  nucleic acid sequence motif:\n    aliases: ['consensus sequence']\n    is_a: biological entity\n    description: >-\n      A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have,\n      a biological significance. e.g. the TATA box promoter motif, transcription factor binding\n      consensus sequences.\n\n  RNA product:\n    is_a: transcript\n    mixins:\n      - gene product mixin\n    exact_mappings:\n      - CHEBI:33697\n       # This SIO term here also mapped to 'biolink:Transcript'; however,\n       # since this 'biolink:RNAProduct' relates more to the biochemical\n       # essence of RNA, then map the SIO term instead to 'biolink:Transcript'\n       # - SIO:010450\n      - WIKIDATA:Q11053\n    id_prefixes:\n      - RNACENTRAL\n\n  RNA product isoform:\n    is_a: RNA product\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or reference RNA\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - RNACENTRAL\n\n  noncoding RNA product:\n    is_a: RNA product\n    id_prefixes:\n      - RNACENTRAL\n      - NCBIGene\n      - ENSEMBL\n    exact_mappings:\n      - SO:0000655\n      - SIO:001235\n\n  microRNA:\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000276\n      - SIO:001397\n      - WIKIDATA:Q310899\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  siRNA:\n    aliases: ['small interfering RNA', 'RNAi']\n    description: >-\n      A small RNA molecule that is the product of a longer exogenous or\n      endogenous dsRNA, which is either a bimolecular duplex or very long\n      hairpin, processed (via the Dicer pathway) such that numerous siRNAs\n      accumulate from both strands of the dsRNA. SRNAs trigger the cleavage\n      of their target molecules.\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000646\n      - WIKIDATA:Q203221\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  gene grouping mixin:\n    description: >-\n      any grouping of multiple genes or gene products\n    mixin: true\n    slots:\n      - has gene or gene product\n\n  gene family:\n    aliases: ['orthogroup', 'protein family']\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n       # These term definitions focus only on proteins;\n       # the 'biolink:GeneFamily' term would be more inclusive\n       # to describe gene loci, non-coding RNA, etc.\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    description: >-\n      any grouping of multiple genes or gene products related by common descent\n    id_prefixes:\n      - PANTHER.FAMILY\n      - HGNC.FAMILY\n      - FB        # FlyBase FBgg*\n      - interpro  # note: may be better to introduce a protein domain/family\n      - CATH\n      - CDD\n      - HAMAP\n      - PFAM\n      - PIRSF\n      - PRINTS\n      - PRODOM\n      - PROSITE\n      - SMART\n      - SUPFAM\n      - TIGRFAM\n      - CATH.SUPERFAMILY\n      - RFAM  ## RNAs only\n      - KEGG.ORTHOLOGY  ## aka KEGG.KO: K number\n      - EGGNOG\n      - COG\n    in_subset:\n      - model_organism_database\n\n  zygosity:\n    is_a: attribute\n    exact_mappings:\n      - GENO:0000133\n\n  genotype:\n    is_a: biological entity\n    mixins:\n      - physical essence\n      - genomic entity\n      - ontology class\n    description: >-\n      An information content entity that describes a genome by specifying the\n      total variation in genomic sequence and/or gene expression, relative to\n      some established background\n    comments:\n      - Consider renaming as genotypic entity\n    slots:\n      - has zygosity\n    exact_mappings:\n      - GENO:0000536\n      - SIO:001079\n    id_prefixes:\n      - ZFIN\n      - FB    # FlyBase FBba*\n    in_subset:\n      - model_organism_database\n\n  haplotype:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A set of zero or more Alleles on a single instance of a Sequence[VMC]\n     #    slots:\n     #      - completeness\n    exact_mappings:\n      - GENO:0000871\n      - SO:0001024\n      - VMC:Haplotype\n\n  sequence variant:\n    aliases: ['allele']\n    local_names:\n      agr: allele\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.\n    comments:\n      - This class is for modeling the specific state at a locus.\n        A single DBSNP rs ID could correspond to more than one sequence variants\n        (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\n    exact_mappings:\n       # slightly broader semantics than SO:0001059 - 'sequence alteration'\n       # describes a sequence feature that may have 1..* sequence alterations\n      - WIKIDATA:Q15304597\n    close_mappings:\n      - dcid:Allele\n      - SO:0001060\n      - VMC:Allele\n      - GENO:0000002\n      - SIO:010277\n      - SO:0001060\n    id_prefixes:\n      - CAID  # ClinGen Allele Registry\n      - CLINVAR\n      - WIKIDATA\n       # - CIViC needs IRI mapping\n      - DBSNP\n      - MGI\n      - ZFIN\n      - FB\n      - RGD\n      - AGRKB\n      - SPDI\n      - WB\n      - WormBase\n      - PHARMGKB.VARIANT\n    alt_descriptions:\n      AGR: >-\n        An entity that describes a single affected, endogenous allele.\n        These can be of any type that matches that definition\n      VMC: >-\n        A contiguous change at a Location\n    slots:\n      - has gene\n    slot_usage:\n      has gene:\n        multivalued: true\n        description: Each allele can be associated with any number of genes\n      has biological sequence:\n        description: >-\n          The state of the sequence w.r.t a reference sequence\n      id:\n        examples:\n          - value: ZFIN:ZDB-ALT-980203-1091\n            description: ti282a allele from ZFIN\n          - value: CLINVAR:17681\n            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\n    in_subset:\n      - model_organism_database\n\n  snv:\n    aliases: ['single nucleotide variant', 'single nucleotide polymorphism', 'snp']\n    is_a: sequence variant\n    description: >-\n      SNVs are single nucleotide positions in genomic DNA at\n      which different sequence alternatives exist\n    exact_mappings:\n      - SO:0001483\n\n  reagent targeted gene:\n    aliases: ['sequence targeting reagent']\n    is_a: biological entity\n    description: >-\n      A gene altered in its expression level in the context of some\n      experiment as a result of being targeted by gene-knockdown\n      reagent(s) such as a morpholino or RNAi.\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - GENO:0000504\n    in_subset:\n      - model_organism_database\n\n   ## --------------------\n   ## Clinical\n   ## Attributes, Cohort,\n   ## Exposures & Outcomes\n   ## --------------------\n\n   ## Clinical Attributes\n\n  clinical attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a clinical manifestation\n    exact_mappings:\n       # Clinical Attribute\n      - STY:T201\n\n  clinical measurement:\n    is_a: clinical attribute\n    description: >-\n      A clinical measurement is a special kind of attribute which results\n      from a laboratory observation from a subject individual or sample.\n      Measurements can be connected to their subject by the 'has attribute' slot.\n    slot_usage:\n      has attribute type:\n        required: true\n        multivalued: false\n        values_from:\n          - EFO\n          - LOINC\n    exact_mappings:\n      - EFO:0001444\n\n  clinical modifier:\n    is_a: clinical attribute\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the phenotypic abnormality sub-ontology, with respect\n      to severity, laterality, and other aspects\n    exact_mappings:\n\n\n  clinical course:\n    is_a: clinical attribute\n    description: >-\n      The course a disease typically takes from its onset, progression in time, and\n      eventual resolution or death of the affected individual\n    exact_mappings:\n      - HP:0031797\n\n  onset:\n    is_a: clinical course\n    description: >-\n      The age group in which (disease) symptom manifestations appear\n    exact_mappings:\n      - HP:0003674\n\n  clinical entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists in the clinical domain and outside the\n      biological realm. Diseases are placed under biological entities\n\n  clinical trial:\n    is_a: clinical entity\n\n  clinical intervention:\n    is_a: clinical entity\n\n  clinical finding:\n    is_a: phenotypic feature\n    description: >-\n      this category is currently considered broad enough to tag clinical lab\n      measurements and other biological attributes taken as 'clinical traits'\n      with some statistical score, for example, a p value in genetic associations.\n    slot_usage:\n      has attribute:\n        range: clinical attribute\n    id_prefixes:\n      - LOINC\n      - NCIT\n      - EFO\n\n  hospitalization:\n    is_a: clinical intervention\n    exact_mappings:\n      - SNOMEDCT:32485007\n      - WIKIDATA:Q3140971\n\n  socioeconomic attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a socioeconomic manifestation\n\n   ## Cohorts\n\n  case:\n    aliases: ['patient', 'proband']\n    is_a: individual organism\n    description: >-\n      An individual (human) organism that has a patient role in some clinical context.\n    mixins:\n      - subject of investigation\n\n  cohort:\n    is_a: study population\n    description: >-\n      A group of people banded together or treated as a group who share common characteristics.\n      A cohort 'study' is a particular form of longitudinal study that samples a cohort,\n      performing a cross-section at intervals through time.\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - WIKIDATA:Q1303415\n    narrow_mappings:\n       # Professional or Occupational Group\n      - STY:T097\n       # Family Group\n      - STY:T099\n       # Age Group\n      - STY:T100\n       # Patient or Disabled Group\n      - STY:T101\n\n   ## Exposures\n\n  exposure event:\n    is_a: ontology class\n    aliases: ['exposure', 'experimental condition']\n    mixin: true\n    slots:\n      - timepoint\n    description: >-\n      A (possibly time bounded) incidence of a feature of the environment of an organism that\n      influences one or more phenotypic features of that organism, potentially mediated by genes\n    exact_mappings:\n      - XCO:0000000\n    in_subset:\n      - model_organism_database\n\n   # TODO - confirm that genomic backgrounds are exposures\n  genomic background exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - gene grouping mixin\n      - physical essence\n      - genomic entity\n      - thing with taxon\n      - ontology class\n    description: >-\n      A genomic background exposure is where an individual's specific genomic background\n      of genes, sequence variants or other pre-existing genomic conditions constitute\n      a kind of 'exposure' to the organism, leading to or influencing an outcome.\n\n  pathological entity mixin:\n    description: >-\n      A pathological (abnormal) structure or process.\n    mixin: true\n    exact_mappings:\n      - MPATH:0\n    narrow_mappings:\n      - HP:0000118\n\n  pathological process:\n    description: >-\n      A biologic function or a process having an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: biological process\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - OBI:1110122\n      - NCIT:C16956\n      - MPATH:596\n    narrow_mappings:\n       # metastasis\n      - NCIT:C19151\n      - EFO:0009708\n      - STY:T046\n      - STY:T037\n\n  pathological process exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A pathological process, when viewed as an exposure, representing\n      a precondition, leading to or influencing an outcome,\n      e.g. autoimmunity leading to disease.\n\n  pathological anatomical structure:\n    description: >-\n      An anatomical structure with the potential of have an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: anatomical entity\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - MPATH:603\n\n  pathological anatomical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      An abnormal anatomical structure, when viewed as an exposure,\n      representing an precondition, leading to or influencing an outcome,\n      e.g. thrombosis leading to an ischemic disease outcome.\n\n  disease or phenotypic feature exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - pathological entity mixin\n    description: >-\n      A disease or phenotypic feature state, when viewed as an exposure,\n      represents an precondition, leading to or influencing an outcome,\n      e.g. HIV predisposing an individual to infections; a relative deficiency\n      of skin pigmentation predisposing an individual to skin cancer.\n\n  chemical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    slots:\n      - has quantitative value\n    description: >-\n      A chemical exposure is an intake of a particular\n      chemical entity.\n    exact_mappings:\n       # this ECTO term is not visibly defined but\n       # the 9000000-series identifiers seems to be the\n       # numeric space of chemical exposure definitions\n      - ECTO:9000000\n      - SIO:001399\n\n  complex chemical exposure:\n    is_a: attribute\n    description: >-\n      A complex chemical exposure is an intake of a chemical\n      mixture (e.g. gasoline), other than a drug.\n\n  drug exposure:\n    is_a: chemical exposure\n    aliases: ['drug intake', 'drug dose', 'medication intake']\n    description: >-\n      A drug exposure is an intake of a particular drug.\n    mixins:\n      - exposure event\n    broad_mappings:\n       # slightly broader than just drug effects on a biological system\n      - SIO:001005\n    exact_mappings:\n      - ECTO:0000509\n\n   # TODO: deprecate?\n  drug to gene interaction exposure:\n    description: >-\n      drug to gene interaction exposure is a drug exposure is where the\n      interactions of the drug with specific genes are known to constitute\n      an 'exposure' to the organism, leading to or influencing an outcome.\n    is_a: drug exposure\n    mixins:\n      - gene grouping mixin\n\n  treatment:\n    aliases: ['medical action', 'medical intervention']\n     # 'named thing' seems too generic here but not sure what applies better here\n    is_a: named thing\n    mixins:\n      - exposure event\n      - chemical or drug or treatment\n    description: >-\n      A treatment is targeted at a disease or phenotype and may involve\n      multiple drug 'exposures', medical devices and/or procedures\n    slots:\n      - has drug\n      - has device\n      - has procedure\n    exact_mappings:\n      - OGMS:0000090\n      - SIO:001398\n    broad_mappings:\n      - MAXO:0000058\n\n  biotic exposure:\n    is_a: attribute\n    aliases: ['viral exposure', 'bacterial exposure']\n    mixins:\n      - exposure event\n    description: >-\n      An external biotic exposure is an intake of (sometimes pathological)\n      biological organisms (including viruses).\n\n  geographic exposure:\n    is_a: environmental exposure\n    mixins:\n      - exposure event\n    description: >-\n      A geographic exposure is a factor relating to geographic\n      proximity to some impactful entity.\n    close_mappings:\n      - dcid:GeologicalEvent\n    narrow_mappings:\n      - dcid:IceStoremEvent\n      - dcid:LakeEffectSnowEvent\n      - dcid:LandslideEvent\n      - dcid:MarineDenseFogEvent\n      - dcid:MarineLighteningEvent\n      - dcid:MarineStrongWindEvent\n      - dcid:MarineThunderstormWindEvent\n      - dcid:StormEvent\n      - dcid:StormSurgeTideEvent\n      - dcid:StrongWindEvent\n      - dcid:ThunderstormWindEvent\n      - dcid:TornadoEvent\n      - dcid:TropicalDepressionEvent\n      - dcid:WinterStoremEvent\n\n  environmental exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A environmental exposure is a factor relating to abiotic processes\n      in the environment including sunlight (UV-B), atmospheric (heat,\n      cold, general pollution) and water-born contaminants.\n\n  behavioral exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A behavioral exposure is a factor relating to behavior impacting an individual.\n\n  socioeconomic exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A socioeconomic exposure is a factor relating to social and\n      financial status of an affected individual (e.g. poverty).\n    slot_usage:\n      has attribute:\n        range: socioeconomic attribute\n        required: true\n\n   ## Outcomes\n\n  outcome:\n    mixin: true\n    description: >-\n      An entity that has the role of being the consequence of an exposure event.\n      This is an abstract mixin grouping of various categories of possible\n      biological or non-biological (e.g. clinical) outcomes.\n\n  pathological process outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of a pathological process.\n\n  pathological anatomical outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of an abnormal anatomical structure.\n\n  disease or phenotypic feature outcome:\n    mixins:\n      - outcome\n    description: >-\n      Physiological outcomes resulting from an exposure event which\n      is the manifestation of a disease or other characteristic phenotype.\n\n  behavioral outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the manifestation of human behavior.\n\n  hospitalization outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the increased manifestation of acute (e.g. emergency\n      room visit) or chronic (inpatient) hospitalization.\n\n  mortality outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome of death from resulting from an exposure event.\n\n  epidemiological outcome:\n    mixins:\n      - outcome\n    description: >-\n      An epidemiological outcome, such as societal disease\n      burden, resulting from an exposure event.\n    related_mappings:\n      - NCIT:C19291\n\n  socioeconomic outcome:\n    mixins:\n      - outcome\n    description: >-\n      An general social or economic outcome, such as\n      healthcare costs, utilization, etc., resulting from an exposure event\n\n   ## ------------\n   ## ASSOCIATIONS\n   ## ------------\n\n  association:\n    is_a: entity\n    description: >-\n      A typed association between two entities, supported by evidence\n    comments:\n      - This is roughly the model used by biolink and ontobio at the moment\n    slots:\n      - subject\n      - predicate\n      - object\n      - negated\n      - qualifiers\n      - publications\n      - has evidence\n      - knowledge source\n      - primary knowledge source\n      - aggregator knowledge source\n      - timepoint\n      - original subject\n      - original predicate\n      - original object\n       # denormalized fields\n      - subject category\n      - object category\n      - subject closure\n      - object closure\n      - subject category closure\n      - object category closure\n      - subject namespace\n      - object namespace\n      - subject label closure\n      - object label closure\n      - retrieval source ids\n    slot_usage:\n      type:\n        description: rdf:type of biolink:Association should be fixed at rdf:Statement\n      category:\n        range: category type\n        required: false\n    exact_mappings:\n      - OBAN:association\n      - rdf:Statement\n      - owl:Axiom\n\n\n  chemical entity assesses named thing association:\n    is_a: association\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: assesses\n\n\n  contributor association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      Any association between an entity (such as a publication)\n      and various agents that contribute to its realisation\n    slot_usage:\n      subject:\n        range: information content entity\n        description: >-\n          information content entity which an agent has helped realise\n      predicate:\n        subproperty_of: contributor\n        description: >-\n          generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\n      object:\n        range: agent\n        description: >-\n          agent helping to realise the given entity (e.g. such as a publication)\n      qualifiers:\n        description: >-\n          this field can be used to annotate special characteristics of an\n          agent relationship, such as the fact that a given author agent of\n          a publication is the 'corresponding author'\n\n  genotype to genotype part association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a genotypic entity that is a sub-component of it\n    slot_usage:\n      predicate:\n        subproperty_of: has variant part\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: genotype\n        description: >-\n          child genotype\n\n  genotype to gene association:\n    description: >-\n      Any association between a genotype and a gene.\n      The genotype have have multiple variants in that gene or a single one.\n      There is no assumption of cardinality\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: gene\n        description: >-\n          gene implicated in genotype\n\n  genotype to variant association:\n    description: >-\n      Any association between a genotype and a sequence variant.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: sequence variant\n        description: >-\n          gene implicated in genotype\n\n  gene to gene association:\n    aliases: ['molecular or genetic interaction']\n    description: >-\n      abstract parent class for different kinds of gene-gene or gene product\n      to gene product relationships. Includes homology and interaction.\n    abstract: true\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          the subject gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n      object:\n        range: gene or gene product\n        description: >-\n          the object gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n\n  gene to gene homology association:\n    description: >-\n      A homology association between two genes. May be orthology (in which\n      case the species of subject and object should differ) or paralogy\n      (in which case the species may be the same)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n      predicate:\n        subproperty_of: homologous to\n        symmetric: true\n        description: >-\n          homology relationship type\n      object:\n        range: gene or gene product\n\n  gene to gene family association:\n    description: >-\n      Set membership of a gene in a family of genes related by common\n      evolutionary ancestry usually inferred by sequence comparisons.\n      The genes in a given family generally share common sequence motifs which\n      generally map onto shared gene product structure-function relationships.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene family\n      predicate:\n        subproperty_of: member of\n        symmetric: false\n        description: >-\n          membership of the gene in the given gene family.\n\n  gene expression mixin:\n    description: >-\n      Observed gene expression intensity, context (site, stage) and\n      associated phenotypic status within which the expression occurs.\n    mixin: true\n    slots:\n      - quantifier qualifier\n      - expression site\n      - stage qualifier\n      - phenotypic state\n    slot_usage:\n      quantifier qualifier:\n        description: >-\n          Optional quantitative value indicating degree of expression.\n\n  gene to gene coexpression association:\n    description: >-\n      Indicates that two genes are co-expressed,\n      generally under the same conditions.\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: coexpressed with\n        symmetric: true\n\n  pairwise gene to gene interaction:\n    description: >-\n      An interaction between two genes or two gene products.\n      May be physical (e.g. protein binding) or genetic (between genes).\n      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      predicate:\n        subproperty_of: interacts with\n        symmetric: true\n        description: \"interaction relationship type\"\n    narrow_mappings:\n      - dcid:ProteinProteinInteraction\n\n  pairwise molecular interaction:\n    description: >-\n      An interaction at the molecular level between two physical entities\n    is_a: pairwise gene to gene interaction\n    slots:\n      - interacting molecules category\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: molecular entity\n      id:\n        description: >-\n          identifier for the interaction. This may come from an interaction database such as IMEX.\n        examples:\n          - value: WB:WBInteraction000538741\n        values_from:\n          - IMEX\n          - BioGRID\n      predicate:\n        subproperty_of: interacts with\n        description: \"interaction relationship type\"\n        examples:\n          - value: RO:0002447\n            description: the subject molecular phosphorylates the object molecule\n      object:\n        range: molecular entity\n\n  cell line to entity association mixin:\n    description: >-\n      An relationship between a cell line and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: cell line\n\n   # TODO: figure out what gives with subject range\n  cell line to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - cell line to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    description: >-\n      An relationship between a cell line and a disease or a phenotype, where\n      the cell line is derived from an individual with that disease or phenotype.\n    slot_usage:\n      subject:\n         #        - range: cell line\n         #        - range: disease or phenotypic feature\n        range: disease or phenotypic feature\n\n  chemical entity to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity that is an interactor\"\n\n  drug to entity association mixin:\n    description: >-\n      An interaction between a drug and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: drug\n        description: \"the drug that is an interactor\"\n\n  chemical to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity or entity that is an interactor\"\n\n  case to entity association mixin:\n    description: >-\n      An abstract association for use where the case is the subject\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: case\n        description: \"the case (e.g. patient) that has the property\"\n\n  chemical to chemical association:\n    description: >-\n      A relationship between two chemical entities. This can encompass actual\n      interactions as well as temporal causal edges, e.g. one chemical converted to another.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: chemical entity\n        description: \"the chemical element that is the target of the statement\"\n\n  reaction to participant association:\n    description:\n    is_a: chemical to chemical association\n    slots:\n      - stoichiometry\n      - reaction direction\n      - reaction side\n    slot_usage:\n      subject:\n        range: molecular entity\n    defining_slots:\n      - subject\n      - predicate\n      - object\n\n  reaction to catalyst association:\n    description:\n    is_a: reaction to participant association\n    slot_usage:\n      object:\n        range: gene or gene product\n\n  chemical to chemical derivation association:\n    description: >-\n      A causal relationship between two chemical entities, where the subject\n      represents the upstream entity and the object represents the downstream.\n      For any such association there is an implicit reaction:\n        IF\n        R has-input C1 AND\n        R has-output C2 AND\n        R enabled-by P AND\n        R type Reaction\n        THEN\n        C1 derives-into C2 <>\n    is_a: chemical to chemical association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - catalyst qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: >-\n          the upstream chemical entity\n      object:\n        range: chemical entity\n        description: >-\n          the downstream chemical entity\n      predicate:\n        subproperty_of: derives into\n      catalyst qualifier:\n        description: >-\n          this connects the derivation edge to the chemical entity that\n          catalyzes the reaction that causes the subject chemical to\n          transform into the object chemical.\n\n  chemical to disease or phenotypic feature association:\n    description: >-\n      An interaction between a chemical entity and a phenotype or disease,\n      where the presence of the chemical gives rise to or exacerbates the phenotype.\n    is_a: association\n    narrow_mappings:\n      - SIO:000993\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"the disease or phenotype that is affected by the chemical\"\n\n  chemical or drug or treatment to disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary undesirable effect.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slots:\n      - FDA adverse event level\n    slot_usage:\n      predicate:\n        subproperty_of: has adverse event\n\n  chemical or drug or treatment side effect disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.\n    is_a: chemical or drug or treatment to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has side effect\n\n  gene to pathway association:\n    description: >-\n      An interaction between a gene or gene product and a biological process or pathway.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"the gene or gene product entity that participates or influences the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that includes or is affected by the gene or gene product\"\n\n  molecular activity to pathway association:\n    description: >-\n      Association that holds the relationship between a reaction and the pathway it participates in.\n    is_a: association\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: pathway\n      predicate:\n        subproperty_of: part of\n\n  chemical to pathway association:\n    description: >-\n      An interaction between a chemical entity and a biological process or pathway.\n    is_a: association\n    exact_mappings:\n      - SIO:001250\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: \"the chemical entity that is affecting the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that is affected by the chemical\"\n\n  named thing associated with likelihood of named thing association:\n     # TODO: better name\n    description: >-\n    is_a: association\n    defining_slots:\n      - subject\n      - subject aspect qualifier\n      - subject context qualifier\n      - predicate\n      - object\n      - object aspect qualifier\n      - object context qualifier\n      - population context qualifier\n    slot_usage:\n      predicate:\n        subproperty_of: associated with\n      subject aspect qualifier:\n       # TODO: range\n      subject context qualifier:\n        range: ontology class\n      object aspect qualifier:\n       # TODO: range\n      object context qualifier:\n        range: ontology class\n\n  chemical gene interaction association:\n    description: >-\n      describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical\n      effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type\n      (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)\n    is_a: association\n    exact_mappings:\n      - SIO:001257\n    mixins:\n      - chemical to entity association mixin\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object context qualifier\n      - anatomical context qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: gene or gene product\n      predicate:\n        subproperty_of: physically interacts with\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject context qualifier:\n        range: anatomical entity\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object context qualifier:\n        range: anatomical entity\n      anatomical context qualifier:\n        range: anatomical entity\n\n  chemical affects gene association:\n    description: >-\n      Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,\n      localization, processing, expression, etc.)\n    is_a: association\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject aspect qualifier\n      - subject context qualifier\n      - subject direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object aspect qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - qualified predicate\n    slot_usage:\n      subject:\n        range: chemical entity\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      subject context qualifier:\n        range: anatomical entity\n      subject direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n      qualified predicate:\n        subproperty_of: causes\n      object:\n        range: gene or gene product\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      object context qualifier:\n        range: anatomical entity\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      causal mechanism qualifier:\n        range: CausalMechanismQualifierEnum\n      anatomical context qualifier:\n        range: anatomical entity\n      species context qualifier:\n        range: organism taxon\n\n  drug to gene association:\n    description: >-\n      An interaction between a drug and a gene or gene product.\n    is_a: association\n    related_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - drug to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: \"the gene or gene product that is affected by the drug\"\n\n  material sample to entity association mixin:\n    description: >-\n      An association between a material sample and something.\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n\n  material sample derivation association:\n    description: >-\n      An association between a material sample and\n      the material entity from which it is derived.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n      object:\n        description: >-\n          the material entity the sample was derived from. This may be another\n          material sample, or any other material entity, including for example\n          an organism, a geographic feature, or some environmental material.\n      predicate:\n        description: >-\n          derivation relationship\n        subproperty_of: derives from\n\n  material sample to disease or phenotypic feature association:\n    description: >-\n      An association between a material sample and a disease or phenotype.\n    is_a: association\n    mixins:\n      - material sample to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    defining_slots:\n      - subject\n      - object\n\n  disease to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease\n        description: \"disease class\"\n        values_from: ['mondo', 'omim', 'orphanet', 'ncit', 'doid']\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n\n  entity to exposure event association mixin:\n    description: >-\n      An association between some entity and an exposure event.\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: exposure event\n\n  disease to exposure event association:\n    description: >-\n      An association between an exposure event and a disease.\n    is_a: association\n    mixins:\n      - disease to entity association mixin\n      - entity to exposure event association mixin\n    defining_slots:\n      - subject\n      - object\n\n\n  entity to outcome association mixin:\n    description: >-\n      An association between some entity and an outcome\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: outcome\n\n  exposure event to outcome association:\n    description: >-\n      An association between an exposure event and an outcome.\n    is_a: association\n    mixins:\n      - entity to outcome association mixin\n    slots:\n      - population context qualifier\n      - temporal context qualifier\n    defining_slots:\n      - subject\n      - object\n\n  frequency qualifier mixin:\n    mixin: true\n    description: >-\n      Qualifier for frequency type associations\n    slots:\n      - frequency qualifier\n\n  entity to feature or disease qualifiers mixin:\n    description: >-\n      Qualifiers for entity to disease or phenotype associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - severity qualifier\n      - onset qualifier\n\n  entity to phenotypic feature association mixin:\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    mixins:\n      - frequency quantifier\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: phenotypic feature\n        values_from: ['upheno', 'hp', 'mp', 'wbphenotype']\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n    slots:\n      - sex qualifier\n\n  information content entity to named thing association:\n    description: >-\n      association between a named thing and a information content entity where the specific context\n      of the relationship between that named thing and the publication is unknown. For\n      example, model organisms databases often capture the knowledge that a gene is found in a\n      journal article, but not specifically the context in which that gene was documented in the article.\n      In these cases, this association with the accompanying predicate 'mentions' could be used.\n      Conversely, for more specific associations (like 'gene to disease association', the publication should\n      be captured as an edge property).\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        domain: publication\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: mentions\n    in_subset:\n      - model_organism_database\n\n  entity to disease association mixin:\n    description: >-\n      mixin class for any association whose object (target node) is a disease\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease\n        description: \"disease\"\n        examples:\n          - value: MONDO:0020066\n            description: \"Ehlers-Danlos syndrome\"\n\n  disease or phenotypic feature to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  disease or phenotypic feature to location association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      an anatomical entity, where the disease/feature manifests in that site.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      object:\n        range: anatomical entity\n        description: >-\n          anatomical entity in which the disease or feature is found.\n        examples:\n          - value: UBERON:0002048\n            description: \"lung\"\n\n  disease or phenotypic feature to genetic inheritance association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      its mode of (genetic) inheritance.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has mode of inheritance\n      object:\n        range: genetic inheritance\n        description: >-\n          genetic inheritance associated with the specified disease or phenotypic feature.\n        examples:\n          - value: HP:0001417\n            description: \"X-linked inheritance\"\n\n  entity to disease or phenotypic feature association mixin:\n    mixin: true\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  genotype to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: genotype\n        description: \"genotype that is the subject of the association\"\n\n  genotype to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a phenotypic feature, where having\n      the genotype confers the phenotype, either in isolation or through environment\n    mixins:\n      - entity to phenotypic feature association mixin\n      - genotype to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has phenotype\n      subject:\n        range: genotype\n        description: >-\n          genotype that is associated with the phenotypic feature\n\n   # ie: smoke exposure to coughing phenotype? is this a denormalization?\n  exposure event to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between an environment and a phenotypic feature,\n      where being in the environment influences the phenotype.\n    mixins:\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: exposure event\n\n  disease to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      An association between a disease and a phenotypic feature in which the\n      phenotypic feature is associated with the disease in some way.\n    mixins:\n      - entity to phenotypic feature association mixin\n      - disease to entity association mixin\n    close_mappings:\n      - dcid:DiseaseSymptomAssociation\n    slot_usage:\n      subject:\n        range: disease\n      object:\n        range: phenotypic feature\n\n  case to phenotypic feature association:\n    description: >-\n      An association between a case (e.g. individual patient) and a phenotypic\n      feature in which the individual has or has had the phenotype.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - case to entity association mixin\n\n  behavior to behavioral feature association:\n    description: >-\n      An association between an mixture behavior and\n      a behavioral feature manifested by\n      the individual exhibited or has exhibited the behavior.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: behavior\n        description: >-\n          behavior that is the subject of the association\n      object:\n        range: behavioral feature\n        description: >-\n          behavioral feature that is the object of the association\n    mixins:\n      - entity to phenotypic feature association mixin\n\n  gene to entity association mixin:\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene that is the subject of the association\n\n  variant to entity association mixin:\n    local_names:\n      ga4gh: variant annotation\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is associated with some other entity\n        examples:\n          - value: CLINVAR:38077\n            description: \"CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n          - value: ClinGen:CA024716\n            description: \"chr13:g.32921033G>C (hg19) in ClinGen\"\n\n  gene to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    narrow_mappings:\n      - WBVocab:Gene-Phenotype-Association\n      - dcid:DiseaseGeneAssociation\n      - SIO:000983\n    slots:\n      - subject aspect qualifier\n      - object direction qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      object:\n        range: disease or phenotypic feature\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n      - for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype\n      - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.\n\n  gene to phenotypic feature association:\n    is_a: gene to disease or phenotypic feature association\n    exact_mappings:\n      - WBVocab:Gene-Phenotype-Association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      object:\n        range: phenotypic feature\n\n  gene to disease association:\n    is_a: gene to disease or phenotypic feature association\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n    exact_mappings:\n      - SIO:000983\n    close_mappings:\n      - dcid:DiseaseGeneAssociation\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease,\n          may be protective or causative or associative, or as a model\n      object:\n        range: disease\n\n  causal gene to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is shown to cause the disease.\n      object:\n        range: disease\n\n  correlated gene to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is shown to correlate with the disease.\n      object:\n        range: disease\n\n  druggable gene to disease association:\n    is_a: gene to disease association\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease\n          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and\n          this leads to a protective or improving disease state.\n      predicate:\n        subproperty_of: target for\n      has evidence:\n        range: DruggableGeneCategoryEnum\n    defining_slots:\n      - subject\n      - object\n      - predicate\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n\n  variant to gene association:\n    description: >-\n      An association between a variant and a gene, where the variant has\n      a genetic association with the gene (i.e. is in linkage disequilibrium)\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - variant to entity association mixin\n    slot_usage:\n      object:\n        range: gene\n      predicate:\n        subproperty_of: genetically associated with\n\n  variant to gene expression association:\n    description: >-\n      An association between a variant and expression of a gene (i.e. e-QTL)\n    is_a: variant to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: affects\n\n  variant to population association:\n    description: >-\n      An association between a variant and a population, where the variant has\n      particular frequency in the population\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - frequency quantifier\n      - frequency qualifier mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          an allele that has a certain frequency in a given population\n        examples:\n          - value: \"NC_000017.11:g.43051071A>T\"\n            description: >-\n              17:41203088 A/C in gnomad\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that is observed to have the frequency\n        examples:\n          - value: HANCESTRO:0010\n            description: African\n      has quotient:\n        description: >-\n          frequency of allele in population, expressed as a number with allele\n          divided by number in reference population, aka allele frequency\n        examples:\n          - value: \"0.0001666\"\n      has count:\n        description: >-\n          number in object population that carry a particular allele, aka allele count\n        examples:\n          - value: \"4\"\n            description: 4 individuals in gnomad set\n      has total:\n        description: >-\n          number all populations that carry a particular allele, aka allele number\n        examples:\n          - value: \"24014\"\n            description: 24014 individuals in gnomad set\n\n  population to population association:\n    description: >-\n      An association between a two populations\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: population of individual organisms\n        description: >-\n          the population that form the subject of the association\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that form the object of the association\n      predicate:\n         # subproperty_of: ???\n        description: >-\n          A relationship type that holds between the subject and object\n          populations. Standard mereological relations can be used.\n          E.g. subject part-of object, subject overlaps object.\n          Derivation relationships can also be used\n\n  variant to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is\n          associated in some way with the phenotype state\n\n  variant to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a sequence variant in which the allele state\n          is associated in some way with the disease state\n        examples:\n          - value: CLINVAR:52241\n            description: \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that variant\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  genotype to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - genotype to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a genotype that is associated in some way with a disease state\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that genotype\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  model to disease association mixin:\n    description: >-\n      This mixin is used for any association class for which the subject\n      (source node) plays the role of a 'model', in that it recapitulates some\n      features of the disease in a way that is useful for studying the disease\n      outside a patient carrying the disease\n    mixin: true\n    slot_usage:\n      subject:\n        description: >-\n          The entity that serves as the model of the disease. This may be\n          an organism, a strain of organism, a genotype or variant that exhibits\n          similar features, or a gene that when mutated exhibits features of the disease\n      predicate:\n        subproperty_of: model of\n        description: >-\n          The relationship to the disease\n\n  gene as a model of disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be a model\n          organism ortholog of a known disease gene, or it may be a gene whose\n          mutants recapitulate core features of the disease.\n\n  variant as a model of disease association:\n    is_a: variant to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          A variant that has a role in modeling the disease.\n\n  genotype as a model of disease association:\n    is_a: genotype to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: genotype\n        description: >-\n          A genotype that has a role in modeling the disease.\n\n  cell line as a model of disease association:\n    is_a: cell line to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: cell line\n        description: >-\n          A cell line derived from an organismal entity with a disease state that is used\n          as a model of that disease.\n\n  organismal entity as a model of disease association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: organismal entity\n        description: >-\n          A organismal entity (strain, breed) with a predisposition to a disease, or bred/created\n          specifically to model a disease.\n\n  organism to organism association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: individual organism\n      object:\n        range: individual organism\n        description: >-\n          An association between two individual organisms.\n\n  taxon to taxon association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n        description: >-\n          An association between individuals of different taxa.\n\n  gene has variant that contributes to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - subject form or variant qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be\n          a model organism ortholog of a known disease gene, or it may be\n          a gene whose mutants recapitulate core features of the disease.\n      object:\n        range: disease\n      predicate:\n        subproperty_of: contributes to\n\n  gene to expression site association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      An association between a gene and a gene expression site,\n      possibly qualified by stage/timing info.\n    notes:\n      - \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n    see_also: \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n    slots:\n      - stage qualifier\n      - quantifier qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          Gene or gene product positively within the specified\n          anatomical entity (or subclass, i.e. cellular component) location.\n      object:\n        range: anatomical entity\n        description: \"location in which the gene is expressed\"\n        examples:\n          - value: UBERON:0002037\n            description: cerebellum\n      predicate:\n        description: \"expression relationship\"\n        subproperty_of: expressed in\n      stage qualifier:\n        range: life stage\n        description: \"stage at which the gene is expressed in the site\"\n        examples:\n          - value: UBERON:0000069\n            description: larval stage\n      quantifier qualifier:\n        description: >-\n          can be used to indicate magnitude, or also ranking\n\n  sequence variant modulates treatment association:\n    is_a: association\n    description: >-\n      An association between a sequence variant and a treatment or health intervention.\n      The treatment object itself encompasses both the disease and the drug used.\n    comments:\n      - An alternate way to model the same information could be via a qualifier\n    defining_slots:\n      - subject\n      - object\n    abstract: true\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: \"variant that modulates the treatment of some disease\"\n      object:\n        range: treatment\n        description: \"treatment whose efficacy is modulated by the subject variant\"\n\n  functional association:\n    is_a: association\n    description: >-\n      An association between a macromolecular machine mixin (gene, gene product or\n      complex of gene products) and either a molecular activity, a biological\n      process or a cellular location in which a function is executed.\n    slot_usage:\n      subject:\n        range: macromolecular machine mixin\n        description: >-\n          gene, product or macromolecular complex that\n          has the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n          - value: GO:0045211\n            description: postsynaptic membrane\n\n  macromolecular machine to entity association mixin:\n    description: >-\n      an association which has a macromolecular machine mixin as a subject\n    mixin: true\n    slot_usage:\n      subject:\n        domain: macromolecular machine mixin\n\n  macromolecular machine to molecular activity association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a molecular activity (as represented\n      in the GO molecular function branch), where the entity\n      carries out the activity, or contributes to its execution.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: molecular activity\n\n  macromolecular machine to biological process association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a biological process or pathway\n      (as represented in the GO biological process branch), where the entity\n      carries out some part of the process, regulates it, or acts upstream of it.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: biological process\n\n  macromolecular machine to cellular component association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a cellular component (as represented\n      in the GO cellular component branch), where the entity\n      carries out its function in the cellular component.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: cellular component\n\n  molecular activity to chemical entity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: chemical entity\n\n  molecular activity to molecular activity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: molecular activity\n\n\n  gene to go term association:\n    aliases: ['functional association']\n    is_a: functional association\n    exact_mappings:\n      - WBVocab:Gene-GO-Association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene\n        description: >-\n          gene, product or macromolecular complex that has\n          the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n\n  entity to disease association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n  entity to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - FDA approval status\n    defining_slots:\n      - subject\n      - object\n\n   ## -----------------\n   ## SEQUENCE FEATURES\n   ## -----------------\n\n  sequence association:\n    is_a: association\n    description: >-\n      An association between a sequence feature and a nucleic acid entity it is localized to.\n\n  genomic sequence localization:\n    is_a: sequence association\n    description: >-\n      A relationship between a sequence feature and a nucleic acid entity\n      it is localized to. The reference entity may be a chromosome,\n      chromosome region or information entity such as a contig.\n    slot_usage:\n      subject:\n        aliases: ['sequence feature']\n        range: nucleic acid entity\n      object:\n        aliases: ['reference']\n        range: nucleic acid entity   # typically a chromosome use monochrom\n      predicate:\n        subproperty_of: has sequence location\n    slots:\n      - start interbase coordinate\n      - end interbase coordinate\n      - genome build\n      - strand\n      - phase\n    broad_mappings:\n      - dcid:Chromosome\n    exact_mappings:\n      - dcid:GenomeAnnotation\n\n  sequence feature relationship:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      For example, a particular exon is part of a particular transcript or gene\n    slot_usage:\n      subject:\n        range: nucleic acid entity\n      object:\n        range: nucleic acid entity   # typically a chromosome\n    exact_mappings:\n      - CHADO:feature_relationship\n\n  transcript to gene relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is a collection of transcripts\n    slot_usage:\n      subject:\n        range: transcript\n      object:\n        range: gene\n\n  gene to gene product relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is transcribed and potentially translated to a gene product\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene product mixin\n      predicate:\n        subproperty_of: has gene product\n\n  exon to transcript relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A transcript is formed from multiple exons\n    slot_usage:\n      subject:\n        range: exon\n      object:\n        range: transcript\n\n  chemical entity or gene or gene product regulates gene association:\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slots:\n      - object direction qualifier\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n        subproperty_of: regulates\n      subject:\n        range: chemical entity or gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n      object direction qualifier:\n        range: DirectionQualifierEnum\n\n  anatomical entity to anatomical entity association:   # schema: gocam\n    is_a: association\n    abstract: true\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: anatomical entity\n      object:\n        range: anatomical entity\n\n  anatomical entity to anatomical entity part of association:\n     #      schema: gocam\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is mereological, i.e the two entities are related by parthood. This\n      includes relationships between cellular components and cells, between\n      cells and tissues, tissues and whole organisms\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the part\n      object:\n        range: anatomical entity\n        description: >-\n          the whole\n      predicate:\n        subproperty_of: part of\n\n  anatomical entity to anatomical entity ontogenic association:\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is ontogenic, i.e. the two entities are related by development. A number\n      of different relationship types can be used to specify the precise\n      nature of the relationship.\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the structure at a later time\n      object:\n        range: anatomical entity\n        description: >-\n          the structure at an earlier time\n      predicate:\n        subproperty_of: develops from\n\n  organism taxon to entity association:\n    mixin: true\n    description: >-\n      An association between an organism taxon and another entity\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: organism taxon\n        description: >-\n          organism taxon that is the subject of the association\n\n  organism taxon to organism taxon association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    description: >-\n      A relationship between two organism taxon nodes\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n\n  organism taxon to organism taxon specialization:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      A child-parent relationship between two taxa.\n      For example: Homo sapiens subclass_of Homo\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: child taxon\n        description: >-\n          the more specific taxon\n      object:\n        range: organism taxon\n        role: parent taxon\n        description: >-\n          the more general taxon\n      predicate:\n        subproperty_of: subclass of\n\n  organism taxon to organism taxon interaction:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      An interaction relationship between two taxa. This may be a symbiotic\n      relationship (encompassing mutualism and parasitism), or it may be non-symbiotic.\n      Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens\n    defining_slots:\n      - predicate\n    slots:\n      - associated environmental context\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        range: organism taxon\n        role: interactee taxon\n        description: >-\n          the taxon that is the subject of the association\n      predicate:\n        subproperty_of: interacts with\n      associated environmental context:\n        description: >-\n          the environment in which the two taxa interact\n\n  organism taxon to environment association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        role: environmental context\n        description: >-\n          the environment in which the organism occurs\n      predicate:\n        description: >-\n          predicate describing the relationship between the taxon and the environment\n\n\nenums:\n\n  DirectionQualifierEnum:\n    permissible_values:\n      increased:\n      upregulated:\n        is_a: increased\n        close_mappings:\n          - RO:0002336\n        exact_mappings:\n          - RO:0002213\n        narrow_mappings:\n          - RO:0004032\n          - RO:0004034\n          - RO:0002629\n      decreased:\n      downregulated:\n        is_a: decreased\n        exact_mappings:\n          - RO:0004035\n          - RO:0002212\n        close_mappings:  # This RTX contributed term is tagged as an inverse of this Biolink predicate\n          - RO:0002335\n        broad_mappings:  # This term is slightly broader in that it includes that A acts within B as well\n          - RO:0004033\n\n  ChemicalEntityDerivativeEnum:\n    permissible_values:\n      metabolite:\n\n  ChemicalOrGeneOrGeneProductFormOrVariantEnum:\n    permissible_values:\n      genetic_variant_form:\n        is_a: modified_form\n      modified_form:\n      loss_of_function_variant_form:\n        is_a: genetic_variant_form\n      gain_of_function_variant_form:\n        is_a: genetic_variant_form\n      polymorphic_form:\n        is_a: genetic_variant_form\n      snp_form:\n        is_a: polymorphic_form\n      analog_form:\n        is_a: modified_form\n\n  GeneOrGeneProductOrChemicalPartQualifierEnum:\n    permissible_values:\n      3_prime_utr:\n      5_prime_utr:\n      polya_tail:\n      promoter:\n      enhancer:\n      exon:\n      intron:\n\n  GeneOrGeneProductOrChemicalEntityAspectEnum:\n    permissible_values:\n      activity_or_abundance:\n        description: >- \n          Used in cases where the specificity of the relationship can not be determined to be either activity \n          or abundance.  In general, a more specific value from this enumeration should be used.\n      abundance:\n        is_a: activity_or_abundance\n      activity:\n        is_a: activity_or_abundance\n      expression:\n        is_a: abundance\n      synthesis:\n        is_a: abundance\n      degradation:\n      cleavage:\n        is_a: degradation\n      hydrolysis:\n        is_a: degradation\n      metabolic_processing:\n      mutation_rate:\n      stability:\n      folding:\n      localization:\n      transport:\n      secretion:\n        is_a: transport\n      uptake:\n        is_a: transport\n      molecular_modification:\n      acetylation:\n        is_a: molecular_modification\n      acylation:\n        is_a: molecular_modification\n      alkylation:\n        is_a: molecular_modification\n      amination:\n        is_a: molecular_modification\n      carbamoylation:\n        is_a: molecular_modification\n      ethylation:\n        is_a: molecular_modification\n      glutathionylation:\n        is_a: molecular_modification\n      glycation:\n        is_a: molecular_modification\n      glycosylation:\n        is_a: molecular_modification\n      glucuronidation:\n        is_a: molecular_modification\n      n_linked_glycosylation:\n        is_a: molecular_modification\n      o_linked_glycosylation:\n        is_a: molecular_modification\n      hydroxylation:\n        is_a: molecular_modification\n      lipidation:\n        is_a: molecular_modification\n      farnesylation:\n        is_a: molecular_modification\n      geranoylation:\n        is_a: molecular_modification\n      myristoylation:\n        is_a: molecular_modification\n      palmitoylation:\n        is_a: molecular_modification\n      prenylation:\n        is_a: molecular_modification\n      methylation:\n        is_a: molecular_modification\n      nitrosation:\n        is_a: molecular_modification\n      nucleotidylation:\n        is_a: molecular_modification\n      phosphorylation:\n        is_a: molecular_modification\n      ribosylation:\n        is_a: molecular_modification\n      ADP-ribosylation:\n        is_a: molecular_modification\n      sulfation:\n        is_a: molecular_modification\n      sumoylation:\n        is_a: molecular_modification\n      ubiquitination:\n        is_a: molecular_modification\n      oxidation:\n        is_a: molecular_modification\n      reduction:\n        is_a: molecular_modification\n      carboxylation:\n        is_a: molecular_modification\n\n  CausalMechanismQualifierEnum:\n    permissible_values:\n      binding:\n        description: >-\n          A causal mechanism mediated by the direct contact between effector and target chemical or \n          biomolecular entity, which form a stable physical interaction.\n      inhibition:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to the target and negatively effects its normal function, \n          e.g. prevention of enzymatic reaction or activation of downstream pathway.\n        close_mappings:\n          - DGIdb:inhibitor\n          - SEMMEDDB:INHIBITS\n        narrow_mappings:\n          - DGIdb:blocker\n          - DGIdb:channel_blocker\n          - DGIdb:gating_inhibitor\n          - CHEMBL.MECHANISM:antisense_inhibitor\n          - CHEMBL.MECHANISM:blocker\n          - CHEMBL.MECHANISM:inhibitor\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - CHEMBL.MECHANISM:negative_modulator\n          - DGIdb:negative_modulator\n      antibody_inhibition:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which an antibody specifically binds to and interferes with the target.\n      antagonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist \n          through competing for the binding site.\n        close_mappings:\n          - DGIdb:antagonist\n          - CHEMBL.MECHANISM:antagonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:allosteric_antagonist\n      molecular_channel_blockage:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and prevents or reduces \n          transport of ions through it.\n      inverse_agonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes\n          its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.\n        close_mappings:\n          - CHEMBL.MECHANISM:inverse_agonist\n          - DGIdb:inverse_agonist\n      negative_allosteric_modulation:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a \n          receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - DGIdb:inhibitory_allosteric_modulator\n        narrow_mappings:\n          - DGIdb:negative_modulator\n      agonism:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an \n          endogenous ligand.\n        close_mappings:\n          - CHEMBL.MECHANISM:agonist\n          - DGIdb:agonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:partial_agonist\n          - DGIdb:partial_agonist\n      molecular_channel_opening:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and facilitates transport of \n          ions through it.\n        close_mappings:\n          - CHEMBL.MECHANISM:opener\n      positive_allosteric_modulation:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by \n          binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:positive_allosteric_modulator\n          - CHEMBL.MECHANISM:positive_modulator\n          - DGIdb:positive_allosteric_modulator\n        broad_mappings:\n          - DGIdb:modulator\n          - DGIdb:allosteric_modulator\n      potentiation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector  binds to and enhances or intensifies the effect of some \n          other chemical or drug on its target.\n        close_mappings:\n      activation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.\n        close_mappings:\n          - CHEMBL.MECHANISM:activator\n          - DGIdb:activator\n      inducer:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that \n          processes drugs in the body.\n        close_mappings:\n          - DGIdb:inducer\n      transcriptional_regulation:\n        description: >-\n          A causal mechanism mediated by through the control of target gene transcription\n      signaling_mediated_control:\n        description: >-\n          A causal mechanism mediated by the activation or control of signaling events that influence the some aspect \n          of the target entity (e.g. its activity, processing, transport, etc)\n      stabilization:\n        is_a: activation\n        close_mappings:\n          - CHEMBL.MECHANISM:stabiliser\n      stimulation:\n        is_a: activation\n        close_mappings:\n          - DGIdb:stimulator\n          - SEMMEDDB:STIMULATES\n          - DGIdb:stimulator\n      releasing_activity:\n        is_a: activation\n        close_mappings:\n          - CHEMBL:MECHANISM:releasing_agent\n\n  LogicalInterpretationEnum:\n    permissible_values:\n      some_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as a some-some statement\n        meaning: os:SomeSomeInterpretation\n      all_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as an all-some statement.\n        meaning: os:AllSomeInterpretation\n      inverse_all_some:\n\n  ReactionDirectionEnum:\n    permissible_values:\n      left_to_right:\n      right_to_left:\n      bidirectional:\n      neutral:\n\n  ReactionSideEnum:\n    permissible_values:\n      left:\n      right:\n\n  PhaseEnum:\n    description: phase\n    permissible_values:\n      0:\n      1:\n      2:\n\n  StrandEnum:\n    description: strand\n    permissible_values:\n      \"+\":\n        description: Positive\n      \"-\":\n        description: Negative\n      \".\":\n        description: Unstranded\n      \"?\":\n        description: Unknown\n\n  SequenceEnum:\n    description: type of sequence\n    permissible_values:\n      \"na\":\n        description: nucleic acid\n      \"aa\":\n        description: amino acid\n\n  DruggableGeneCategoryEnum:\n    permissible_values:\n      \"tclin\":\n        description: >-\n          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.\n      \"tbio\":\n        description: >-\n          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy\n          the activity thresholds detailed below.\n      \"tchem\":\n        description: >-\n          These targets do not have known drug or small molecule activities that satisfy the activity\n          thresholds detailed below AND satisfy one or more of the following criteria:\n          target is above the cutoff criteria for Tdark\n          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)\n          with an Experimental Evidence code\n      \"tdark\":\n        description: >-\n          These are targets about which virtually nothing is known. They do not have known drug or small\n          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or\n          more of the following criteria:\n          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or\n          less than or equal to 50 Antibodies available according to http://antibodypedia.com.\n\n  DrugAvailabilityEnum:\n    description: >-\n    permissible_values:\n      \"over_the_counter\":\n        description: >-\n          chemical entity is available over the counter without a prescription.\n      \"prescription\":\n        description:\n          chemical entity is available by prescription.\n\n  DrugDeliveryEnum:\n    permissible_values:\n      \"inhalation\":\n      \"oral\":\n      \"absorption_through_the_skin\":\n      \"intravenous_injection\":\n        \n  ResourceRoleEnum:\n    description: >-\n      The role played by the information reource in serving as a\n      source for an edge in a TRAPI message. Note that a given Edge should have one\n      and only one 'primary' source, and may have any number of\n      'aggregator' or 'supporting data' sources.  This enumeration\n      is found in Biolink Model, but is repeated here for convenience.\n    permissible_values:\n      \"primary_knowledge_source\":\n      \"aggregator_knowledge_source\":\n      \"supporting_data_source\":\n    in_subset:\n      - translator_minimal\n\n  FDAApprovalStatusEnum:\n    description: >-\n    permissible_values:\n      \"discovery_and_development_phase\":\n        description: >-\n          Discovery & Development Phase. Discovery involves researchers finding new possibilities\n          for medication through testing molecular compounds, noting unexpected effects from existing treatments,\n          or the creation of new technology that allows novel ways of targeting medical products to sites in the body.\n          Drug development occurs after researchers identify potential compounds for experiments.\n      \"preclinical_research_phase\":\n        description: >-\n          Preclinical Research Phase.  Once researchers have examined the possibilities a new drug may contain,\n          they must do preliminary research to determine its potential for harm (toxicity).\n          This is categorized as preclinical research and can be one of two types: in vitro or in vivo.\n      \"fda_clinical_research_phase\":\n        description: >-\n          Clinical Research Phase. Clinical research involves trials of the drug on people,\n          and it is one of the most involved stages in the drug development and approval process.\n          Clinical trials must answer specific questions and follow a protocol determined by\n          the drug researcher or manufacturer.\n      \"fda_review_phase_4\":\n        description: >-\n          FDA Review\n      \"fda_post_market_safety_review\":\n        description: >-\n          FDA Post-Market Safety Monitoring.  The last phase of drug approval is an ongoing one\n          while the drug is on the marketplace. If a developer wants to change anything about the\n          drug formulation or approve it for a new use, they must apply with the FDA. The FDA also\n          frequently reviews the drug’s advertising and its manufacturing facility to make sure\n          everything involved in its creation and marketing is in compliance with regulations.\n      \"fda_clinical_research_phase_1\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and\n          lasts several months. This phase is used to determine the safety and dosage of the drug,\n          and about 70% of these drugs move on to the next clinical research phase.\n      \"fda_clinical_research_phase_2\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people,\n          who must have the disease or condition the drug supposes to treat. This phase can last\n          from a few months to two years, and its purpose is to monitor the efficacy of the drug,\n          as well as note side effects that may occur.\n      \"fda_clinical_research_phase_3\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers\n          and can last up to four years. It is used to continue monitoring the efficacy of\n          the drug, as well as exploring any longer-term adverse reactions.\n      \"fda_clinical_research_phase_4\":\n        description: >-\n          In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of\n          volunteers who have the disease or condition and continues to monitor safety and efficacy.\n          If a drug passes this phase, it goes on to FDA review.\n      \"fda_fast_track\":\n        description: >-\n          Fast track is a process designed to facilitate the development, and expedite the\n          review of drugs to treat serious conditions and fill an unmet medical need.\n          The purpose is to get important new drugs to the patient earlier. Fast Track\n          addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track\n      \"fda_breakthrough_therapy\":\n        description: >-\n          Breakthrough Therapy designation is a process designed to expedite the\n          development and review of drugs that are intended to treat a serious\n          condition and preliminary clinical evidence indicates that the drug may\n          demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy\n      \"fda_accelerated_approval\":\n        description: >-\n          When studying a new drug, it can sometimes take many years to learn whether a drug actually\n          provides a real effect on how a patient survives, feels, or functions. A positive therapeutic\n          effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”.\n          Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical\n          benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs\n          for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint.\n          Using a surrogate endpoint enabled the FDA to approve these drugs faster.\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval\n      \"fda_priority_review\":\n        description: >-\n          Prior to approval, each drug marketed in the United States must go through a detailed FDA review process.\n          In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving\n          the drug review time and created a two-tiered system of review times – Standard Review and Priority\n          Review. A Priority Review designation means FDA’s goal is to take action on an application\n          within 6 months (compared to 10 months under standard review).\n          For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review\n      \"regular_fda_approval\":\n        description: >-\n          Regular FDA Approval.  The last phase of drug approval is an ongoing one while the drug is on the marketplace.\n          If a developer wants to change anything about the drug formulation or approve it for a new use,\n          they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its\n          manufacturing facility to make sure everything involved in its creation and marketing is in compliance\n          with regulations.\n      \"post_approval_withdrawal\":\n\n  FDAIDAAdverseEventEnum:\n    description: >-\n      please consult with the FDA guidelines as proposed in this document:\n      https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32\n    permissible_values:\n      \"life_threatening_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either \n          the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. \n          It does not include an adverse event or suspected adverse reaction that, had it occurred in a more \n          severe form, might have caused death.\n      \"serious_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the \n          investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event,\n          inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity \n          or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth \n          defect. Important medical events that may not result in death, be life-threatening, or require hospitalization\n          may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or \n          subject and may require medical or surgical intervention to prevent one of the outcomes listed in this \n          definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment \n          in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient \n          hospitalization, or the development of drug dependency or drug abuse.\n      \"suspected_adverse_reaction\":\n        description: >-\n           means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. \n           For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a \n           causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser \n           degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.\n      \"unexpected_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the \n          investigator brochure or is not listed at the specificity or severity that has been observed; or, if an \n          investigator brochure is not required or available, is not consistent with the risk information described \n          in the general investigational plan or elsewhere in the current application, as amended. For example, \n          under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the \n          investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral \n          thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the \n          investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, \n          also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure\n          as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but \n          are not specifically mentioned as occurring with the particular drug under investigation.\n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_3_5_2/semmed-exclude-list-model.yaml",
    "content": "---\nid: https://w3id.org/biolink/biolink-model\nname: semmed-exclude-list-model\ndescription: Model that represents a semmed exclude list object\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 3.5.2\n\n## ------------\n##\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  biolink: 'https://w3id.org/biolink/vocab/'\n  linkml: 'https://w3id.org/linkml/'\n  infores: 'https://w3id.org/biolink/vocab/'\n  sel: 'https://w3id.org/biolink/vocab/'\n\n\nimports:\n  - linkml:types\n\ndefault_prefix: sel\ndefault_range: string\n\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - oboInOwl\n\nclasses:\n  ExcludeListContainer:\n    tree_root: true\n    description: >-\n      A collection of exclusion objects\n    slots:\n      - excluded_semmedb_records\n\n  ExcludedSemmedbRecord:\n    slots:\n      - semmed_subject_code\n      - semmed_subject_t_code\n      - semmed_predicate\n      - semmed_object_code\n      - semmed_object_t_code\n      - exclusion_type\n\nslots:\n\n  semmed_subject_code:\n    description: >-\n      The subject code of the semmeddb record\n    range: string\n\n  semmed_subject_t_code:\n    description: >-\n      The subject t code of the semmeddb record\n    range: string\n\n  semmed_predicate:\n    description: >-\n      The predicate of the semmeddb record\n    range: string\n\n  semmed_object_code:\n    description: >-\n      The object code of the semmeddb record\n    range: string\n\n  semmed_object_t_code:\n    description: >-\n      The object t code of the semmeddb record\n    range: string\n\n  exclusion_type:\n    description: >-\n      The notes describing the kind of exclusion that generated this record.\n    range: string\n\n  excluded_semmedb_records:\n    description: >-\n      The list of semmeddb records that are excluded\n    multivalued: true\n    range: ExcludedSemmedbRecord\n    inlined_as_list: true"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_3_5_2/semmed-exclude-list.yaml",
    "content": "---\nexcluded_semmedb_records:\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: mosq\n  semmed_subject_t_code: T085\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: mosq\n  semmed_object_t_code: T085\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: acty\n  semmed_subject_t_code: T052\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: acty\n  semmed_object_t_code: T052\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: resd\n  semmed_object_t_code: T075\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: bhvr\n  semmed_object_t_code: T053\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: bmod\n  semmed_subject_t_code: T091\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: bmod\n  semmed_object_t_code: T091\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: clas\n  semmed_subject_t_code: T185\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: cnce\n  semmed_subject_t_code: T077\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: cnce\n  semmed_object_t_code: T077\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: crbs\n  semmed_subject_t_code: T088\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: crbs\n  semmed_object_t_code: T088\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: enty\n  semmed_subject_t_code: T071\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: enty\n  semmed_object_t_code: T071\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: evnt\n  semmed_subject_t_code: T051\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: evnt\n  semmed_object_t_code: T051\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: geoa\n  semmed_subject_t_code: T083\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: gora\n  semmed_subject_t_code: T064\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: gora\n  semmed_object_t_code: T064\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: grpa\n  semmed_subject_t_code: T102\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: grpa\n  semmed_object_t_code: T102\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: hcpp\n  semmed_subject_t_code: T068\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: hcpp\n  semmed_object_t_code: T068\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: lang\n  semmed_subject_t_code: T171\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: lang\n  semmed_object_t_code: T171\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: mcha\n  semmed_subject_t_code: T066\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: mcha\n  semmed_object_t_code: T066\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: ocac\n  semmed_object_t_code: T057\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: ocdi\n  semmed_subject_t_code: T090\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: ocdi\n  semmed_object_t_code: T090\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: phob\n  semmed_subject_t_code: T072\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: phob\n  semmed_object_t_code: T072\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: pros\n  semmed_subject_t_code: T094\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: pros\n  semmed_object_t_code: T094\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: rnlw\n  semmed_subject_t_code: T089\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: rnlw\n  semmed_object_t_code: T089\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: shro\n  semmed_subject_t_code: T095\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: shro\n  semmed_object_t_code: T095\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: N/A\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: N/A\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: semantic type exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: genf\n  semmed_subject_t_code: T045\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: diap\n  semmed_subject_t_code: T060\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: celc\n  semmed_subject_t_code: T026\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: irda\n  semmed_subject_t_code: T130\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bodm\n  semmed_subject_t_code: T122\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: emod\n  semmed_subject_t_code: T050\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rnlw\n  semmed_subject_t_code: T089\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: evnt\n  semmed_subject_t_code: T051\n  semmed_predicate: AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: AUGMENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: AUGMENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: AUGMENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: AUGMENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: genf\n  semmed_subject_t_code: T045\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fndg\n  semmed_subject_t_code: T033\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: aggp\n  semmed_subject_t_code: T100\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: emod\n  semmed_subject_t_code: T050\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: medd\n  semmed_subject_t_code: T074\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clas\n  semmed_subject_t_code: T185\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: geoa\n  semmed_subject_t_code: T083\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lang\n  semmed_subject_t_code: T171\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clas\n  semmed_subject_t_code: T185\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: acty\n  semmed_subject_t_code: T052\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: cnce\n  semmed_subject_t_code: T077\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: COMPLICATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: CONVERTS_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: CONVERTS_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: genf\n  semmed_subject_t_code: T045\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: neop\n  semmed_subject_t_code: T191\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fndg\n  semmed_subject_t_code: T033\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: geoa\n  semmed_subject_t_code: T083\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: acty\n  semmed_subject_t_code: T052\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lang\n  semmed_subject_t_code: T171\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clas\n  semmed_subject_t_code: T185\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: INHIBITS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: INHIBITS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: food\n  semmed_subject_t_code: T168\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: aggp\n  semmed_subject_t_code: T100\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: topp\n  semmed_subject_t_code: T061\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: medd\n  semmed_subject_t_code: T074\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: eehu\n  semmed_subject_t_code: T069\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mosq\n  semmed_subject_t_code: T085\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: geoa\n  semmed_subject_t_code: T083\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bmod\n  semmed_subject_t_code: T091\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocdi\n  semmed_subject_t_code: T090\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: acty\n  semmed_subject_t_code: T052\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: gora\n  semmed_subject_t_code: T064\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: pros\n  semmed_subject_t_code: T094\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phob\n  semmed_subject_t_code: T072\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mcha\n  semmed_subject_t_code: T066\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: shro\n  semmed_subject_t_code: T095\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: evnt\n  semmed_subject_t_code: T051\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clas\n  semmed_subject_t_code: T185\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mosq\n  semmed_subject_t_code: T085\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: aggp\n  semmed_subject_t_code: T100\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: shro\n  semmed_subject_t_code: T095\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: pros\n  semmed_subject_t_code: T094\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: emod\n  semmed_subject_t_code: T050\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bacs\n  semmed_subject_t_code: T123\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phsu\n  semmed_subject_t_code: T121\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: nnon\n  semmed_subject_t_code: T114\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: dsyn\n  semmed_subject_t_code: T047\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mosq\n  semmed_subject_t_code: T085\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: emod\n  semmed_subject_t_code: T050\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inbe\n  semmed_subject_t_code: T055\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: MEASUREMENT_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: MEASUREMENT_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mcha\n  semmed_subject_t_code: T066\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: gora\n  semmed_subject_t_code: T064\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rnlw\n  semmed_subject_t_code: T089\n  semmed_predicate: METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rnlw\n  semmed_subject_t_code: T089\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_AUGMENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_AUGMENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_DIAGNOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_DISRUPTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_INHIBITS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_INHIBITS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: geoa\n  semmed_subject_t_code: T083\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bmod\n  semmed_subject_t_code: T091\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocdi\n  semmed_subject_t_code: T090\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: acty\n  semmed_subject_t_code: T052\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: evnt\n  semmed_subject_t_code: T051\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: pros\n  semmed_subject_t_code: T094\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mcha\n  semmed_subject_t_code: T066\n  semmed_predicate: NEG_ISA\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mamm\n  semmed_subject_t_code: T015\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: anim\n  semmed_subject_t_code: T008\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vtbt\n  semmed_subject_t_code: T010\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: shro\n  semmed_subject_t_code: T095\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: pros\n  semmed_subject_t_code: T094\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: fish\n  semmed_subject_t_code: T013\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: amph\n  semmed_subject_t_code: T011\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bird\n  semmed_subject_t_code: T012\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rept\n  semmed_subject_t_code: T014\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: NEG_MANIFESTATION_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_MEASUREMENT_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: NEG_MEASUREMENT_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mcha\n  semmed_subject_t_code: T066\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: gora\n  semmed_subject_t_code: T064\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: NEG_PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: NEG_PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: NEG_USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: NOM\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phpr\n  semmed_subject_t_code: T067\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: elii\n  semmed_subject_t_code: T196\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: horm\n  semmed_subject_t_code: T125\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mosq\n  semmed_subject_t_code: T085\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: PART_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: PRECEDES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: PRECEDES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: PRECEDES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: PRECEDES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: PRECEDES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: nusq\n  semmed_subject_t_code: T086\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: diap\n  semmed_subject_t_code: T060\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: irda\n  semmed_subject_t_code: T130\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: PREVENTS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: socb\n  semmed_subject_t_code: T054\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: acty\n  semmed_subject_t_code: T052\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bhvr\n  semmed_subject_t_code: T053\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clas\n  semmed_subject_t_code: T185\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: evnt\n  semmed_subject_t_code: T051\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: spco\n  semmed_subject_t_code: T082\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: dsyn\n  semmed_subject_t_code: T047\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: genf\n  semmed_subject_t_code: T045\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: aggp\n  semmed_subject_t_code: T100\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hcro\n  semmed_subject_t_code: T093\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orgt\n  semmed_subject_t_code: T092\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ffas\n  semmed_subject_t_code: T021\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: pros\n  semmed_subject_t_code: T094\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clna\n  semmed_subject_t_code: T201\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: menp\n  semmed_subject_t_code: T041\n  semmed_predicate: PRODUCES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: tmco\n  semmed_subject_t_code: T079\n  semmed_predicate: SAME_AS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: nusq\n  semmed_subject_t_code: T086\n  semmed_predicate: STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: STIMULATES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: diap\n  semmed_subject_t_code: T060\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hops\n  semmed_subject_t_code: T131\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: irda\n  semmed_subject_t_code: T130\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: gngm\n  semmed_subject_t_code: T028\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bodm\n  semmed_subject_t_code: T122\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chem\n  semmed_subject_t_code: T103\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: gora\n  semmed_subject_t_code: T064\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ortf\n  semmed_subject_t_code: T042\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: celc\n  semmed_subject_t_code: T026\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ftcn\n  semmed_subject_t_code: T169\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mcha\n  semmed_subject_t_code: T066\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mnob\n  semmed_subject_t_code: T073\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: ocac\n  semmed_subject_t_code: T057\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resd\n  semmed_subject_t_code: T075\n  semmed_predicate: TREATS\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lbpr\n  semmed_subject_t_code: T059\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: resa\n  semmed_subject_t_code: T062\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hlca\n  semmed_subject_t_code: T058\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: popg\n  semmed_subject_t_code: T098\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: podg\n  semmed_subject_t_code: T101\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: mbrt\n  semmed_subject_t_code: T063\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: prog\n  semmed_subject_t_code: T097\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: aggp\n  semmed_subject_t_code: T100\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: grup\n  semmed_subject_t_code: T096\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: famg\n  semmed_subject_t_code: T099\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: aapp\n  semmed_subject_t_code: T116\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: orch\n  semmed_subject_t_code: T109\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: humn\n  semmed_subject_t_code: T016\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: bacs\n  semmed_subject_t_code: T123\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: gngm\n  semmed_subject_t_code: T028\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: horm\n  semmed_subject_t_code: T125\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: phsu\n  semmed_subject_t_code: T121\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: imft\n  semmed_subject_t_code: T129\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: nnon\n  semmed_subject_t_code: T114\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inch\n  semmed_subject_t_code: T197\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: nsba\n  semmed_subject_t_code: not_found\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: antb\n  semmed_subject_t_code: T195\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: enzy\n  semmed_subject_t_code: T126\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: hops\n  semmed_subject_t_code: T131\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: opco\n  semmed_subject_t_code: not_found\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: carb\n  semmed_subject_t_code: not_found\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: eico\n  semmed_subject_t_code: not_found\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: lipd\n  semmed_subject_t_code: not_found\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: clnd\n  semmed_subject_t_code: T200\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: elii\n  semmed_subject_t_code: T196\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: inpr\n  semmed_subject_t_code: T170\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qnco\n  semmed_subject_t_code: T081\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: dora\n  semmed_subject_t_code: T056\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvf\n  semmed_subject_t_code: T120\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: npop\n  semmed_subject_t_code: T070\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: genf\n  semmed_subject_t_code: T045\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: irda\n  semmed_subject_t_code: T130\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: edac\n  semmed_subject_t_code: T065\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: plnt\n  semmed_subject_t_code: T002\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: virs\n  semmed_subject_t_code: T005\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: chvs\n  semmed_subject_t_code: T104\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: idcn\n  semmed_subject_t_code: T078\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: qlco\n  semmed_subject_t_code: T080\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: rcpt\n  semmed_subject_t_code: T192\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: strd\n  semmed_subject_t_code: not_found\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: vita\n  semmed_subject_t_code: T127\n  semmed_predicate: USES\n  semmed_object_code: N/A\n  semmed_object_t_code: N/A\n  exclusion_type: Domain exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: invt\n  semmed_object_t_code: not_found\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: bact\n  semmed_object_t_code: T007\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: fngs\n  semmed_object_t_code: T004\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: plnt\n  semmed_object_t_code: T002\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: virs\n  semmed_object_t_code: T005\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: neop\n  semmed_object_t_code: T191\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: arch\n  semmed_object_t_code: T194\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: alga\n  semmed_object_t_code: not_found\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: rich\n  semmed_object_t_code: not_found\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ADMINISTERED_TO\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: orgm\n  semmed_object_t_code: T001\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: aggp\n  semmed_object_t_code: T100\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: bhvr\n  semmed_object_t_code: T053\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: diap\n  semmed_object_t_code: T060\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: shro\n  semmed_object_t_code: T095\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: pros\n  semmed_object_t_code: T094\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: acty\n  semmed_object_t_code: T052\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AFFECTS\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ASSOCIATED_WITH\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: AUGMENTS\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: fndg\n  semmed_object_t_code: T033\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: emod\n  semmed_object_t_code: T050\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: lbtr\n  semmed_object_t_code: T034\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: orga\n  semmed_object_t_code: T032\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CAUSES\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: medd\n  semmed_object_t_code: T074\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COEXISTS_WITH\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: lang\n  semmed_object_t_code: T171\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: COMPARED_WITH\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CONVERTS_TO\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: CONVERTS_TO\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DIAGNOSES\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: fndg\n  semmed_object_t_code: T033\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: DISRUPTS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: lang\n  semmed_object_t_code: T171\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: HIGHER_THAN\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INHIBITS\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INHIBITS\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INHIBITS\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: food\n  semmed_object_t_code: T168\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: aggp\n  semmed_object_t_code: T100\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: medd\n  semmed_object_t_code: T074\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: topp\n  semmed_object_t_code: T061\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: eehu\n  semmed_object_t_code: T069\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: INTERACTS_WITH\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: ocdi\n  semmed_object_t_code: T090\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: bmod\n  semmed_object_t_code: T091\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: evnt\n  semmed_object_t_code: T051\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: acty\n  semmed_object_t_code: T052\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: ocac\n  semmed_object_t_code: T057\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: hcpp\n  semmed_object_t_code: T068\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: mosq\n  semmed_object_t_code: T085\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: gora\n  semmed_object_t_code: T064\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: bhvr\n  semmed_object_t_code: T053\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: mcha\n  semmed_object_t_code: T066\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: pros\n  semmed_object_t_code: T094\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: resd\n  semmed_object_t_code: T075\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: shro\n  semmed_object_t_code: T095\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: ISA\n  semmed_object_code: phob\n  semmed_object_t_code: T072\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: genf\n  semmed_object_t_code: T045\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: medd\n  semmed_object_t_code: T074\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: hops\n  semmed_object_t_code: T131\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: ocac\n  semmed_object_t_code: T057\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: ocdi\n  semmed_object_t_code: T090\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: mcha\n  semmed_object_t_code: T066\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOCATION_OF\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: LOWER_THAN\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MANIFESTATION_OF\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASUREMENT_OF\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASUREMENT_OF\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: MEASURES\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: bmod\n  semmed_object_t_code: T091\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: ocdi\n  semmed_object_t_code: T090\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: mcha\n  semmed_object_t_code: T066\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: METHOD_OF\n  semmed_object_code: ocac\n  semmed_object_t_code: T057\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ADMINISTERED_TO\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: bhvr\n  semmed_object_t_code: T053\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: acty\n  semmed_object_t_code: T052\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AFFECTS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ASSOCIATED_WITH\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AUGMENTS\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AUGMENTS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_AUGMENTS\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_CAUSES\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_COEXISTS_WITH\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_DISRUPTS\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_DISRUPTS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_DISRUPTS\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_DISRUPTS\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_HIGHER_THAN\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INHIBITS\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_INTERACTS_WITH\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: ocdi\n  semmed_object_t_code: T090\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: evnt\n  semmed_object_t_code: T051\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: bmod\n  semmed_object_t_code: T091\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: acty\n  semmed_object_t_code: T052\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: hcpp\n  semmed_object_t_code: T068\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: ocac\n  semmed_object_t_code: T057\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: mosq\n  semmed_object_t_code: T085\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_ISA\n  semmed_object_code: bhvr\n  semmed_object_t_code: T053\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: ocac\n  semmed_object_t_code: T057\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOCATION_OF\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_LOWER_THAN\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASUREMENT_OF\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASUREMENT_OF\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_MEASURES\n  semmed_object_code: phpr\n  semmed_object_t_code: T067\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: ocdi\n  semmed_object_t_code: T090\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: bmod\n  semmed_object_t_code: T091\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_METHOD_OF\n  semmed_object_code: mcha\n  semmed_object_t_code: T066\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_OCCURS_IN\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PART_OF\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRECEDES\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRECEDES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRECEDES\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PROCESS_OF\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: resd\n  semmed_object_t_code: T075\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: rnlw\n  semmed_object_t_code: T089\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_PRODUCES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_SAME_AS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_STIMULATES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_TREATS\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: resd\n  semmed_object_t_code: T075\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: rnlw\n  semmed_object_t_code: T089\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: NEG_USES\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: OCCURS_IN\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: ffas\n  semmed_object_t_code: T021\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PART_OF\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: hlca\n  semmed_object_t_code: T058\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: edac\n  semmed_object_t_code: T065\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRECEDES\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PREDISPOSES\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PREP\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PREVENTS\n  semmed_object_code: fndg\n  semmed_object_t_code: T033\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PREVENTS\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: anim\n  semmed_object_t_code: T008\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: fish\n  semmed_object_t_code: T013\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: vtbt\n  semmed_object_t_code: T010\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: rept\n  semmed_object_t_code: T014\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: amph\n  semmed_object_t_code: T011\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PROCESS_OF\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: medd\n  semmed_object_t_code: T074\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: resd\n  semmed_object_t_code: T075\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: rnlw\n  semmed_object_t_code: T089\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: PRODUCES\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: chem\n  semmed_object_t_code: T103\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: geoa\n  semmed_object_t_code: T083\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: SAME_AS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: STIMULATES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: STIMULATES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: STIMULATES\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: podg\n  semmed_object_t_code: T101\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: mamm\n  semmed_object_t_code: T015\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: humn\n  semmed_object_t_code: T016\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: fndg\n  semmed_object_t_code: T033\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: popg\n  semmed_object_t_code: T098\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: aggp\n  semmed_object_t_code: T100\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: bact\n  semmed_object_t_code: T007\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: orga\n  semmed_object_t_code: T032\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: famg\n  semmed_object_t_code: T099\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: emod\n  semmed_object_t_code: T050\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: prog\n  semmed_object_t_code: T097\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: grup\n  semmed_object_t_code: T096\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: plnt\n  semmed_object_t_code: T002\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: ftcn\n  semmed_object_t_code: T169\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: menp\n  semmed_object_t_code: T041\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: euka\n  semmed_object_t_code: T204\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: nnon\n  semmed_object_t_code: T114\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: tmco\n  semmed_object_t_code: T079\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: bpoc\n  semmed_object_t_code: T023\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: clna\n  semmed_object_t_code: T201\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: idcn\n  semmed_object_t_code: T078\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: qlco\n  semmed_object_t_code: T080\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: bird\n  semmed_object_t_code: T012\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: dora\n  semmed_object_t_code: T056\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: socb\n  semmed_object_t_code: T054\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: TREATS\n  semmed_object_code: spco\n  semmed_object_t_code: T082\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: lbpr\n  semmed_object_t_code: T059\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: resd\n  semmed_object_t_code: T075\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: mnob\n  semmed_object_t_code: T073\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: mbrt\n  semmed_object_t_code: T063\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: rnlw\n  semmed_object_t_code: T089\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: clas\n  semmed_object_t_code: T185\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: chvf\n  semmed_object_t_code: T120\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: gngm\n  semmed_object_t_code: T028\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: inpr\n  semmed_object_t_code: T170\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: qnco\n  semmed_object_t_code: T081\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: hcro\n  semmed_object_t_code: T093\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: resa\n  semmed_object_t_code: T062\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: chvs\n  semmed_object_t_code: T104\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: npop\n  semmed_object_t_code: T070\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: gora\n  semmed_object_t_code: T064\n  exclusion_type: Range exclusion\n- semmed_subject_code: N/A\n  semmed_subject_t_code: N/A\n  semmed_predicate: USES\n  semmed_object_code: orgt\n  semmed_object_t_code: T092\n  exclusion_type: Range exclusion\n"
  },
  {
    "path": "medikanren2/neo/neo-biolink/biolink_4_2_1/biolink-model.yaml",
    "content": "---\nid: https://w3id.org/biolink/biolink-model\nname: Biolink-Model\ndescription: Entity and association taxonomy and datamodel for life-sciences data\nlicense: https://creativecommons.org/publicdomain/zero/1.0/\n\n# Version should be kept in sync with primary Git repository release tag\n\nversion: 4.2.1\n\n## ------------\n##\n## PREFIXES\n## ------------\n# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification\n# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld\n# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following\n# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's\n# which should ideally be repaired in one of the precedence lists.\n#\n# 1. The following 'prefixes:' delimited list has first precedence in resolution.\n#\nprefixes:\n  AGRKB: 'https://www.alliancegenome.org/'\n  apollo: 'https://github.com/GMOD/Apollo'\n  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='\n  biolink: 'https://w3id.org/biolink/vocab/'\n  bioschemas: 'https://bioschemas.org/'\n  linkml: 'https://w3id.org/linkml/'\n  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='\n   # Placeholder: just points to GMOD Chado wiki\n  CHADO: 'http://gmod.org/wiki/Chado/'\n   # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve\n  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='\n  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'\n  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'\n  CLINVAR: 'http://identifiers.org/clinvar'\n  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'\n  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'\n  ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'\n  CPT: 'https://www.ama-assn.org/practice-management/cpt/'\n  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='\n  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='\n  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='\n  CTD: 'http://ctdbase.org/'\n  DGIdb: 'https://www.dgidb.org/interaction_types'\n  dcat: 'http://www.w3.org/ns/dcat#'\n  dct: 'http://purl.org/dc/terms/'\n  dcid: 'https://datacommons.org/browser/'\n  doi: 'https://doi.org/'\n  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'\n  DrugCentral: 'http://drugcentral.org/drugcard/'\n  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'\n  EDAM-DATA: 'http://edamontology.org/data_'\n  EDAM-FORMAT: 'http://edamontology.org/format_'\n  EDAM-OPERATION: 'http://edamontology.org/operation_'\n  EDAM-TOPIC: 'http://edamontology.org/topic_'\n  EFO: 'http://www.ebi.ac.uk/efo/EFO_'\n  ExO: 'http://purl.obolibrary.org/obo/ExO_'\n  fabio: 'http://purl.org/spar/fabio/'\n  foaf: 'http://xmlns.com/foaf/0.1/'\n  foodb.compound: 'http://foodb.ca/compounds/'\n  foodb.food: 'http://foodb.ca/foods/'\n  FYECO: 'https://www.pombase.org/term/'\n  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'   # Fission Yeast Phenotype Ontology\n  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'\n  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'\n   # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)\n  GOP: 'http://purl.obolibrary.org/obo/go#'\n  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'\n  GSID: 'https://scholar.google.com/citations?user='\n  GTEx: 'https://www.gtexportal.org/home/gene/'\n  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='\n  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'\n  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'\n  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'\n  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'\n  ICD10: 'https://icd.codes/icd9cm/'\n  ICD9: 'http://translator.ncats.nih.gov/ICD9_'\n  interpro: 'https://www.ebi.ac.uk/interpro/entry/'\n  INO: 'http://purl.obolibrary.org/obo/INO_'\n  isbn: 'https://www.isbn-international.org/identifier/'  # note: a resolvable base URI not available from isbn-international\n  isni: 'https://isni.org/isni/'\n  issn: 'https://portal.issn.org/resource/ISSN/'\n  ncats.drug: 'https://drugs.ncats.io/drug/'\n  KEGG.BRITE: 'https://bioregistry.io/kegg.brite:'\n  KEGG: 'http://www.kegg.jp/entry/'\n  KEGG.GENES: 'https://bioregistry.io/kegg.genes:bsu:'\n  KEGG.PATHWAY: 'https://bioregistry.io/kegg.pathway:'\n  KEGG.RCLASS: 'https://www.genome.jp/dbget-bin/www_bget?rc:'\n  LOINC: 'http://loinc.org/rdf/'\n  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'\n  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'\n  metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'\n  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'\n  MESH: 'http://id.nlm.nih.gov/mesh/'\n  MI: 'http://purl.obolibrary.org/obo/MI_'\n  mirbase: 'http://identifiers.org/mirbase'\n  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'\n  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'\n  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'\n  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'\n  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='\n  NCBIGene: 'http://identifiers.org/ncbigene/'\n  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'\n  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'\n  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='\n  OBAN: 'http://purl.org/oban/'\n  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'\n  ORCID: 'https://orcid.org/'\n  orphanet: 'http://www.orpha.net/ORDO/Orphanet_'\n  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'\n  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='\n  PathWhiz: 'http://smpdb.ca/pathways/#'   #  See also https://smpdb.ca/pathwhiz/\n  pav: 'http://purl.org/pav/'\n  PHARMGKB.CHEMICAL: 'https://www.pharmgkb.org/chemical/'\n  PHARMGKB.DISEASE: 'https://www.pharmgkb.org/disease/'\n  PHARMGKB.GENE: 'https://www.pharmgkb.org/gene/'\n  PHARMGKB.PATHWAYS: 'https://www.pharmgkb.org/pathway/'\n  PHARMGKB.VARIANT: 'https://www.pharmgkb.org/variant/'\n  PHAROS: 'http://pharos.nih.gov'\n  PomBase: 'https://www.pombase.org/gene/'\n  prov: 'http://www.w3.org/ns/prov#'\n  qud: 'http://qudt.org/1.1/schema/qudt#'\n  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'\n  ResearchID: 'https://publons.com/researcher/'\n  RO: 'http://purl.obolibrary.org/obo/RO_'\n  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'\n  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='\n  schema: 'http://schema.org/'\n  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='\n  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'\n  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'\n  SIO: 'http://semanticscience.org/resource/SIO_'\n  SNOMEDCT: 'http://snomed.info/id/'\n  SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'\n  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'\n  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'\n  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'\n  STY: 'http://purl.bioontology.org/ontology/STY/'\n  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'\n  UniProtKB: 'http://purl.uniprot.org/uniprot/'\n  UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/'\n  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'\n  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'\n  VMC: 'https://github.com/ga4gh/vr-spec/'\n  WBls: 'http://purl.obolibrary.org/obo/WBls_'\n  WBbt: 'http://purl.obolibrary.org/obo/WBbt_'\n  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'\n  WIKIDATA: 'https://www.wikidata.org/entity/'             #  Wikidata Entity\n  WIKIDATA_PROPERTY: 'https://www.wikidata.org/prop/'\n  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'\n  XPO: 'http://purl.obolibrary.org/obo/XPO_'   #  Xenopus Phenotype Ontology\n  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='\n  PMC: 'http://europepmc.org/articles/PMC'\n\ndefault_prefix: biolink\ndefault_range: string\n\ndefault_curi_maps:\n  - obo_context\n  - idot_context\n  - monarch_context\n  - semweb_context\n\nemit_prefixes:\n  - rdf\n  - rdfs\n  - xsd\n  - skos\n  - oboInOwl\n  - BIOGRID\n  - SO\n\n## ------------\n## SUBSETS\n## ------------\n\n\nsubsets:\n\n  model_organism_database:\n    description: >-\n      Subset that is relevant for a typical Model Organism Database (MOD)\n\n  translator_minimal:\n    description: >-\n      Minimum subset of translator work\n\n  samples:\n    description: >-\n      Sample/biosample datamodel\n\n  testing:\n    description: >-\n      TBD\n\n\n## ------------\n## TYPES\n## ------------\n\nimports:\n  - linkml:types\n\ntypes:\n\n  chemical formula value:\n    uri: xsd:string\n    base: str\n    description: A chemical formula\n    notes:\n      - Should be implemented as a stronger type\n\n  iri type:\n    typeof: uriorcurie\n    description: >-\n      An IRI\n\n  label type:\n    typeof: string\n    description: >-\n      A string that provides a human-readable name for an entity\n\n  predicate type:\n    typeof: uriorcurie\n    description: >-\n      A CURIE from the biolink related_to hierarchy.\n      For example, biolink:related_to, biolink:causes, biolink:treats.\n\n  narrative text:\n    typeof: string\n    description: >-\n      A string that provides a human-readable description of something\n\n  symbol type:\n    typeof: string\n\n  frequency value:\n    typeof: string\n    uri: UO:0000105\n\n  percentage frequency value:\n    typeof: double\n    uri: UO:0000187\n\n  quotient:\n    aliases: ['ratio']\n    typeof: double\n    uri: UO:0010006\n\n  unit:\n    typeof: string\n    uri: UO:0000000\n    id_prefixes:\n      - UO\n    exact_mappings:\n      - qud:Unit\n\n  time type:\n    typeof: time\n\n  biological sequence:\n    typeof: string\n\n## ------------\n## SLOTS\n## ------------\n\nslots:\n\n  has attribute:\n    description: >-\n      connects any entity to an attribute\n    domain: entity\n    range: attribute\n    multivalued: true\n    in_subset:\n      - samples\n    close_mappings:\n       # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'\n      - OBI:0001927\n    exact_mappings:\n      - SIO:000008\n    narrow_mappings:\n       # if 'has attribute' annotates a NamedThing as subject or\n       # object of an association, these OBAN mappings may apply\n      - OBAN:association_has_subject_property\n      - OBAN:association_has_object_property\n      - CPT:has_possibly_included_panel_element\n      - DRUGBANK:category\n       # RTX contributed terms. Could perhaps review for more semantically precise mappings?\n      - EFO:is_executed_in\n      - HANCESTRO:0301\n      - LOINC:has_action_guidance\n      - LOINC:has_adjustment\n      - LOINC:has_aggregation_view\n      - LOINC:has_approach_guidance\n      - LOINC:has_divisor\n      - LOINC:has_exam\n      - LOINC:has_method\n      - LOINC:has_modality_subtype\n      - LOINC:has_object_guidance\n      - LOINC:has_scale\n      - LOINC:has_suffix\n      - LOINC:has_time_aspect\n      - LOINC:has_time_modifier\n      - LOINC:has_timing_of\n       # disease is stage\n      - NCIT:R88\n      - NCIT:eo_disease_has_property_or_attribute\n      - NCIT:has_data_element\n      - NCIT:has_pharmaceutical_administration_method\n      - NCIT:has_pharmaceutical_basic_dose_form\n      - NCIT:has_pharmaceutical_intended_site\n      - NCIT:has_pharmaceutical_release_characteristics\n      - NCIT:has_pharmaceutical_state_of_matter\n      - NCIT:has_pharmaceutical_transformation\n      - NCIT:is_qualified_by\n      - NCIT:qualifier_applies_to\n      - NCIT:role_has_domain\n      - NCIT:role_has_range\n      - INO:0000154\n      - HANCESTRO:0308\n      - OMIM:has_inheritance_type\n      - orphanet:C016\n      - orphanet:C017\n      - RO:0000053\n       # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here\n      - RO:0000086\n      - RO:0000087\n      - SNOMED:has_access\n      - SNOMED:has_clinical_course\n      - SNOMED:has_count_of_base_of_active_ingredient\n      - SNOMED:has_dose_form_administration_method\n      - SNOMED:has_dose_form_release_characteristic\n      - SNOMED:has_dose_form_transformation\n      - SNOMED:has_finding_context\n      - SNOMED:has_finding_informer\n      - SNOMED:has_inherent_attribute\n      - SNOMED:has_intent\n      - SNOMED:has_interpretation\n      - SNOMED:has_laterality\n      - SNOMED:has_measurement_method\n      - SNOMED:has_method\n      - SNOMED:has_priority\n      - SNOMED:has_procedure_context\n      - SNOMED:has_process_duration\n      - SNOMED:has_property\n      - SNOMED:has_revision_status\n      - SNOMED:has_scale_type\n      - SNOMED:has_severity\n      - SNOMED:has_specimen\n      - SNOMED:has_state_of_matter\n      - SNOMED:has_subject_relationship_context\n      - SNOMED:has_surgical_approach\n      - SNOMED:has_technique\n      - SNOMED:has_temporal_context\n      - SNOMED:has_time_aspect\n      - SNOMED:has_units\n      - UMLS:has_structural_class\n      - UMLS:has_supported_concept_property\n      - UMLS:has_supported_concept_relationship\n      - UMLS:may_be_qualified_by\n\n  has attribute type:\n    description: >-\n      connects an attribute to a class that describes it\n    domain: attribute\n    range: ontology class\n    multivalued: false\n    required: true\n    in_subset:\n      - samples\n    narrow_mappings:\n      - LOINC:has_modality_type\n      - LOINC:has_view_type\n\n   # TRAPI Attribute schema alignment:\n   # value: NamedThing.name\n   # value_type: NamedThing.category\n   # value_type_name: quantity_value.NamedThing.name\n  has qualitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: named thing\n    multivalued: false\n    in_subset:\n      - samples\n\n   # TRAPI Attribute schema alignment:\n   # value: quantity_value.has_numeric_value[double] - may be a vector?\n   # value_type: quantity_value.has_unit.unit.uri\n   # value_type_name: quantity_value.has_unit.unit.name[string]\n  has quantitative value:\n    description: >-\n      connects an attribute to a value\n    domain: attribute\n    range: quantity value\n    multivalued: true\n    exact_mappings:\n      - qud:quantityValue\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_numerator_value\n      - SNOMED:has_presentation_strength_denominator_value\n      - SNOMED:has_presentation_strength_numerator_value\n    in_subset:\n      - samples\n\n  has numeric value:\n    description: >-\n      connects a quantity value to a number\n    domain: quantity value\n    range: double\n    multivalued: false\n    exact_mappings:\n      - qud:quantityValue\n    in_subset:\n      - samples\n\n  has unit:\n    description: >-\n      connects a quantity value to a unit\n    domain: quantity value\n    range: unit\n    multivalued: false\n    close_mappings:\n       # These RTX contributed terms mean \"is unit of\" which is the semantic inverse of this biolink:has_unit term\n      - EFO:0001697\n      - UO-PROPERTY:is_unit_of\n    exact_mappings:\n      - qud:unit\n      - IAO:0000039\n    narrow_mappings:\n      - SNOMED:has_concentration_strength_denominator_unit\n      - SNOMED:has_concentration_strength_numerator_unit\n      - SNOMED:has_presentation_strength_denominator_unit\n      - SNOMED:has_presentation_strength_numerator_unit\n      - SNOMED:has_unit_of_presentation\n    in_subset:\n      - samples\n\n  base coordinate:\n    is_a: sequence localization attribute\n    aliases: ['one-based', 'fully-closed']\n    description: >-\n      A position in the base coordinate system.  Base coordinates start at position 1 instead of position 0.\n    range: integer\n\n   ## --------------------\n   ## NODE PROPERTY SLOTS\n   ## --------------------\n\n  node property:\n    description: >-\n      A grouping for any property that holds between a node and a value\n    domain: named thing\n\n  id:\n    identifier: true\n    domain: entity\n    description: >-\n      A unique identifier for an entity.\n      Must be either a CURIE shorthand for a URI or a complete URI\n    in_subset:\n      - translator_minimal\n    required: true\n    exact_mappings:\n      - AGRKB:primaryId\n      - gff3:ID\n      - gpi:DB_Object_ID\n\n  iri:\n    description: >-\n      An IRI for an entity. This is determined by the id using expansion rules.\n    range: iri type\n    in_subset:\n      - translator_minimal\n      - samples\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P854\n\n  type:\n    slot_uri: rdf:type\n    domain: entity\n    exact_mappings:\n      - gff3:type\n      - gpi:DB_Object_Type\n    multivalued: true\n\n  category:\n    is_a: type\n    domain: entity\n    range: uriorcurie\n    designates_type: true\n    description: >-\n      Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the\n      biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI.\n      This field is multi-valued. It should include values for ancestors of the biolink class; for example,\n      a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.\n      In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink\n      class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`\n      may have a rdf:type assertion to a SO class such as TF_binding_site,\n      which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,\n      biolink:MolecularEntity, biolink:NamedThing}\n    is_class_field: true\n    multivalued: true\n    in_subset:\n      - translator_minimal\n\n  publication type:\n    slot_uri: dct:type\n    description: >-\n      Ontology term for publication type may be drawn from\n      Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),\n      FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),\n      the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),\n      the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres\n      (http://vocabularies.coar-repositories.org/documentation/resource_types/),\n      Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or\n      equivalent publication type ontology. When a given publication type ontology term\n      is used within a given knowledge graph, then the CURIE identified term must be\n      documented in the graph as a concept node of biolink:category biolink:OntologyClass.\n    values_from:  # Not sure which takes precedence, if any...\n      - dctypes\n      - fabio\n      - MESH_PUB\n      - COAR_RESOURCE\n      - WIKIDATA\n    multivalued: true\n\n  name:\n    aliases: ['label', 'display name', 'title']\n    description: >-\n      A human-readable name for an attribute or entity.\n    domain: entity\n    range: label type\n    in_subset:\n      - translator_minimal\n      - samples\n    slot_uri: rdfs:label\n    exact_mappings:\n      - gff3:Name\n      - gpi:DB_Object_Name\n    narrow_mappings:\n      - dct:title\n      - WIKIDATA_PROPERTY:P1476\n\n  stoichiometry:\n    description: >-\n      the relationship between the relative quantities of substances taking part in a reaction or\n      forming a compound, typically a ratio of whole integers.\n    is_a: association slot\n    range: integer\n\n  reaction direction:\n    description: >-\n      the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)\n    is_a: association slot\n    range: ReactionDirectionEnum\n    narrow_mappings:\n      - NCIT:C42677\n\n  reaction balanced:\n    is_a: association slot\n    range: boolean\n\n  reaction side:\n    description: >-\n      the side of a reaction being modeled (ie: left or right)\n    is_a: association slot\n    range: ReactionSideEnum\n\n  symbol:\n    is_a: node property\n    domain: named thing\n    description: >-\n      Symbol for a particular thing\n    exact_mappings:\n      - AGRKB:symbol\n      - gpi:DB_Object_Symbol\n\n  synonym:\n    is_a: node property\n    aliases: ['alias']\n    domain: named thing\n    range: label type\n    description: >-\n      Alternate human-readable names for a thing\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n       # there is an interesting debate here: are these terms \"narrower\" a.k.a. more specialized instances of\n       # 'biolink:synonym' or should they be binned into their respective namesake class of mappings?\n       # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.\n      - skos:altLabel\n      - gff3:Alias\n      - AGRKB:synonyms\n      - gpi:DB_Object_Synonyms\n       # TODO: RTX contributed terms mapped here... May need review?\n      - HANCESTRO:0330\n      - IAO:0000136\n      - RXNORM:has_tradename\n\n  exact synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasExactSynonym\n\n  broad synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasBroadSynonym\n\n  narrow synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasNarrowSynonym\n\n  related synonym:\n    is_a: synonym\n    exact_mappings:\n      - oboInOwl:hasRelatedSynonym\n\n  deprecated:\n    range: boolean\n    exact_mappings:\n      - oboInOwl:ObsoleteClass\n    description: >-\n      A boolean flag indicating that an entity is no longer considered current or valid.\n\n  has topic:\n    aliases: ['topic', 'descriptors']\n    is_a: node property\n    range: ontology class\n    exact_mappings:\n      - foaf:topic\n    description: >-\n      Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.\n      See https://github.com/biolink/biolink-model/issues/238\n\n  xref:\n    aliases: ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls']\n    domain: named thing\n    range: uriorcurie\n    description: >-\n      A database cross reference or alternative identifier for a NamedThing or edge between two\n      NamedThings.  This property should point to a database record or webpage that supports the existence of the edge, or\n      gives more detail about the edge. This property can be used on a node or edge to provide multiple\n      URIs or CURIE cross references.\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - gff3:Dbxref\n      - gpi:DB_Xrefs\n\n  semmed agreement count:\n    is_a: association slot\n    range: integer\n    description: >-\n      The number of times this concept has been asserted in the SemMedDB literature database.\n    in_subset:\n      - translator_minimal\n\n  support graphs:\n    description: >-\n      A list of knowledge graphs that support the existence of this association.\n    multivalued: true\n    is_a: association slot\n    in_subset:\n      - translator_minimal\n\n  resource id:\n    is_a: node property\n    description: >-\n      The CURIE for an Information Resource that served as a source\n      of knowledge expressed in an Edge, or a source of data used to\n      generate this knowledge.\n    domain: retrieval source\n    range: uriorcurie\n    in_subset:\n      - translator_minimal\n\n  resource role:\n    is_a: node property\n    description: >-\n      The role played by the InformationResource in serving as a\n      source for an Edge. Note that a given Edge should have one\n      and only one 'primary' source, and may have any number of\n      'aggregator' or 'supporting data' sources.\n    domain: retrieval source\n    range: ResourceRoleEnum\n    in_subset:\n      - translator_minimal\n\n  retrieval source ids:\n    description: >-\n        A list of retrieval sources that served as a source of knowledge\n        expressed in an Edge, or a source of data used to generate this\n        knowledge.\n    multivalued: true\n    range: retrieval source\n    in_subset:\n      - translator_minimal\n\n  full name:\n    is_a: node property\n    domain: named thing\n    range: label type\n    description: >-\n      a long-form human readable name for a thing\n\n  upstream resource ids:\n    is_a: node property\n    description: >-\n      An upstream InformationResource from which the resource\n      being described directly retrieved a record of the knowledge\n      expressed in the Edge, or data used to generate this knowledge.\n      This is an array because there are cases where a merged Edge\n      holds knowledge that was retrieved from multiple sources. e.g.\n      an Edge provided by the ARAGORN ARA can expressing knowledge it\n      retrieved from both the automat-mychem-info and molepro KPs,\n      which both provided it with records of this single fact.\n    domain: retrieval source\n    range: uriorcurie\n\n  description:\n    aliases: ['definition']\n    range: narrative text\n    description: >-\n      a human-readable description of an entity\n    in_subset:\n      - translator_minimal\n    slot_uri: dct:description\n    exact_mappings:\n      - IAO:0000115\n      - skos:definitions\n    narrow_mappings:\n      - gff3:Description\n\n  systematic synonym:\n    is_a: node property\n    domain: named thing\n    range: label type\n    multivalued: true\n    slot_uri: GOP:systematic_synonym\n    description: >-\n      more commonly used for gene symbols in yeast\n\n  affiliation:\n    is_a: node property\n    description: >-\n      a professional relationship between one provider (often a person) within another provider (often an organization).\n      Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.\n    domain: agent\n    range: uriorcurie\n    multivalued: true\n\n  address:\n    is_a: node property\n    description: >-\n      the particulars of the place where someone or an organization is situated.  For now, this slot is a\n      simple text \"blob\" containing all relevant details of the given location for fitness of purpose.\n      For the moment, this \"address\" can include other contact details such as email and phone number(?).\n\n   ## Space\n\n  latitude:\n    is_a: node property\n    range: float\n    description: >-\n      latitude\n    exact_mappings:\n      - wgs:lat\n\n  longitude:\n    is_a: node property\n    range: float\n    description: >-\n      longitude\n    exact_mappings:\n      - wgs:long\n\n   ## Time\n\n  timepoint:\n    aliases: ['duration']\n    range: time type\n    description: >-\n      a point in time\n\n  creation date:\n    is_a: node property\n    aliases: ['publication date']\n    range: date\n    description: >-\n      date on which an entity was created. This can be applied to nodes or edges\n    exact_mappings:\n      - dct:createdOn\n      - WIKIDATA_PROPERTY:P577\n\n  update date:\n    is_a: node property\n    range: date\n    description: >-\n      date on which an entity was updated. This can be applied to nodes or edges\n\n   ## Statistics\n\n  aggregate statistic:\n    is_a: node property\n    abstract: true\n\n  has count:\n    description: >-\n      number of things with a particular property\n    is_a: aggregate statistic\n    range: integer\n    exact_mappings:\n      - LOINC:has_count\n\n  has total:\n    description: >-\n      total number of things in a particular reference set\n    is_a: aggregate statistic\n    range: integer\n\n  has quotient:\n    is_a: aggregate statistic\n    range: double\n\n  has percentage:\n    description: >-\n      equivalent to has quotient multiplied by 100\n    is_a: aggregate statistic\n    range: double\n\n   ## Properties for Information Content Entity and Publication Nodes\n\n  has taxonomic rank:\n    is_a: node property\n    range: taxonomic rank\n    multivalued: false\n    mappings:\n      - WIKIDATA:P105\n\n  has dataset:\n    is_a: node property\n    domain: dataset version\n    range: dataset\n    broad_mappings:\n      - dct:source\n\n  source web page:\n    is_a: node property\n    domain: dataset summary\n    broad_mappings:\n      - dct:source\n\n  source logo:\n    is_a: node property\n    domain: dataset summary\n    slot_uri: schema:logo\n\n  retrieved on:\n    is_a: node property\n    domain: dataset\n    range: date\n    exact_mappings:\n      - pav:retrievedOn\n\n  version of:\n    is_a: node property\n    domain: dataset version\n    range: dataset summary\n    exact_mappings:\n      - dct:isVersionOf\n\n  version:\n    is_a: node property\n    domain: dataset\n    broad_mappings:\n      - pav:version\n      - owl:versionInfo\n\n  license:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:license\n    narrow_mappings:\n      - WIKIDATA_PROPERTY:P275\n\n  rights:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:rights\n\n  format:\n    is_a: node property\n    domain: information content entity\n    exact_mappings:\n      - dct:format\n      - WIKIDATA_PROPERTY:P2701\n\n  created with:\n    is_a: node property\n    domain: dataset\n    exact_mappings:\n      - pav:createdWith\n\n  download url:\n    is_a: node property\n    domain: information content entity\n    slot_uri: dcat:downloadURL\n\n  dataset download url:\n    is_a: node property\n    domain: dataset\n    slot_uri: dcat:downloadURL\n\n  distribution download url:\n    is_a: node property\n    domain: dataset distribution\n    exact_mappings:\n      - dcat:downloadURL\n\n  ingest date:\n    is_a: node property\n    domain: dataset version\n    broad_mappings:\n      - dct:issued\n\n  has distribution:\n    is_a: node property\n    domain: dataset version\n    range: dataset distribution\n    slot_uri: dct:distribution\n\n  published in:\n    is_a: node property\n    description: >-\n      CURIE identifier of a broader publication context within which the publication may be placed,\n      e.g. a specified book or journal.\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - NLMID\n      - issn\n      - isbn\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1433\n\n  iso abbreviation:\n    is_a: node property\n    description: >-\n      Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system\n      See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,\n      then the iso abbreviation pertains to the broader publication context (the journal) within which the given\n      publication node is embedded, not the publication itself.\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P1160\n\n  authors:\n    is_a: node property\n    description: >-\n      connects an publication to the list of authors who contributed to the publication.\n      This property should be a comma-delimited list of author names. It is recommended that an author's name\n      be formatted as \"surname, firstname initial.\".   Note that this property is a node annotation expressing\n      the citation list of authorship which might typically otherwise be more completely documented in\n      biolink:PublicationToProviderAssociation defined edges which point to full details about an author\n      and possibly, some qualifiers which clarify the specific status of a given author in the publication.\n    multivalued: true\n    domain: publication\n    range: agent\n\n  volume:\n    is_a: node property\n    description: >-\n      volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P478\n\n  chapter:\n    is_a: node property\n    description: >-\n      chapter of a book\n    domain: book chapter\n    exact_mappings:\n      - WIKIDATA:Q1980247\n\n  issue:\n    is_a: node property\n    description: >-\n      issue of a newspaper, a scientific journal or magazine for reference purpose\n    domain: publication\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P433\n\n  pages:\n    is_a: node property\n    description: >-\n      page number of source referenced for statement or publication\n    domain: publication\n    multivalued: true\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P304\n\n  summary:\n    is_a: node property\n     # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot,\n     # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract'\n    aliases: ['abstract']\n    description: >-\n      executive  summary of a publication\n    domain: publication\n    exact_mappings:\n      - dct:abstract\n      - WIKIDATA:Q333291\n\n  keywords:\n    is_a: node property\n    description: >-\n      keywords tagging a publication\n    domain: publication\n    multivalued: true\n\n  mesh terms:\n    is_a: node property\n    description: >-\n      mesh terms tagging a publication\n    domain: publication\n    range: uriorcurie\n    values_from:\n      - MESH\n    multivalued: true\n    exact_mappings:\n      - dcid:MeSHTerm\n\n   ## Biology\n\n  has biological sequence:\n    is_a: node property\n    description: >-\n      connects a genomic feature to its sequence\n    range: biological sequence\n\n  has gene or gene product:\n    is_a: node property\n    description: >-\n      connects an entity with one or more gene or gene products\n    range: gene\n    multivalued: true\n\n  has gene:\n    is_a: has gene or gene product\n    description: >-\n      connects an entity associated with one or more genes\n    range: gene\n    multivalued: true\n\n  has zygosity:\n    is_a: node property\n    domain: nucleic acid entity\n    range: zygosity\n\n   ## Chemistry, drugs and food\n\n  has chemical formula:\n    is_a: node property\n    range: chemical formula value\n    description: >-\n      description of chemical compound based on element symbols\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P274\n\n  is metabolite:\n    is_a: node property\n    domain: molecular entity\n    range: boolean\n    description: >-\n      indicates whether a molecular entity is a metabolite\n    exact_mappings:\n      - CHEBI:25212\n\n  has constituent:\n    description: >-\n      one or more molecular entities within a chemical mixture\n    is_a: node property\n    range: molecular entity\n    multivalued: true\n\n  has drug:\n    is_a: node property\n    description: >-\n      connects an entity to one or more drugs\n    range: drug\n    multivalued: true\n\n  has device:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) devices\n    range: device\n    multivalued: true\n\n  has procedure:\n    is_a: node property\n    description: >-\n      connects an entity to one or more (medical) procedures\n    range: procedure\n    multivalued: true\n\n   ## Clinical exposures\n\n  has receptor:\n    is_a: node property\n    domain: exposure event\n    range: organismal entity\n    description: >-\n      the organism or organism part being exposed\n    exact_mappings:\n      - ExO:0000001\n\n  has stressor:\n    is_a: node property\n    domain: exposure event\n    aliases: ['has stimulus']\n    description: >-\n      the process or entity that the receptor is being exposed to\n    exact_mappings:\n      - ExO:0000000\n\n  has route:\n    is_a: node property\n    domain: exposure event\n    description: >-\n      the process that results in the stressor coming into direct contact with the receptor\n    exact_mappings:\n      - ExO:0000055\n    narrow_mappings:\n      - LOINC:has_pharmaceutical_route\n      - SNOMED:has_dose_form_intended_site\n      - SNOMED:has_route_of_administration\n\n\n  population context qualifier:\n    description: >-\n      a biological population (general, study, cohort, etc.) with a specific\n      set of characteristics to constrain an association.\n    is_a: qualifier\n    range: population of individual organisms\n\n  temporal context qualifier:\n    description: >-\n      a constraint of time placed upon the truth value of an association.\n      for time intervales, use temporal interval qualifier.\n    is_a: qualifier\n    range: time type\n\n  temporal interval qualifier:\n    is_a: temporal context qualifier\n    description: >-\n      a constraint of a time interval placed upon the truth value of an\n      association.\n\n  is supplement:\n    description: >-\n    is_a: node property\n    domain: chemical mixture\n\n  trade name:\n    description: >-\n    is_a: node property\n    domain: chemical entity\n\n  available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: DrugAvailabilityEnum\n\n  is toxic:\n    description: >-\n    is_a: node property\n    multivalued: false\n    range: boolean\n\n  has chemical role:\n    is_a: related to at concept level\n    description: >-\n      A role is particular behaviour which a chemical entity may exhibit.\n    range: chemical role\n    multivalued: true\n    id_prefixes:\n      - CHEBI\n    comments: >-\n      We expect primarily to use CHEBI chemical roles here; however, we are looking for a mapping between\n      CHEBI And ATC codes to support this slot.\n\n  max tolerated dose:\n    description: >-\n      The highest dose of a drug or treatment that does not cause unacceptable side effects.\n      The maximum tolerated dose is determined in clinical trials by testing increasing doses\n      on different groups of people until the highest dose with acceptable side effects is\n      found. Also called MTD.\n    is_a: node property\n    multivalued: false\n    range: string\n\n  animal model available from:\n    description: >-\n    is_a: node property\n    multivalued: true\n    range: disease or phenotypic feature\n\n  FDA adverse event level:\n    description: >-\n    is_a: association slot\n    range: FDAIDAAdverseEventEnum\n\n  highest FDA approval status:\n    description: >-\n      Should be the highest level of FDA approval this chemical entity or device has, regardless of which\n      disease, condition or phenotype it is currently being reviewed to treat.  For specific levels of FDA\n      approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'\n\n  drug regulatory status world wide:\n    aliases: ['max phase']\n    description: >-\n      An agglomeration of drug regulatory status worldwide. Not specific to FDA.\n    exact_mappings:\n      - NCIT:C172573\n    narrow_mappings:\n      - NCIT:R172\n      - NCIT:regimen_has_accepted_use_for_disease\n       # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n\n  routes of delivery:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    multivalued: true\n    range: DrugDeliveryEnum\n\n   ## -------------------\n   ## QUALIFIERS\n   ## -------------------\n\n  form or variant qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.\n    examples:\n      - value: mutation\n      - value: late stage\n      - value: severe\n      - value: transplant\n      - value: chemical analog\n    notes: >-\n      please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier'\n      terms in the gene->chemical association space.\n      the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’.\n      the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the  more specific concept ‘Late Stage forms of Disease X’\n      the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’\n      the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’\n    in_subset:\n      - translator_minimal\n\n  aspect qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.  The purpose of the aspect slot is to indicate what aspect is being affected in an\n      'affects' association.\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    notes: >-\n      for good examples of aspects in the gene-> chemical space, please see the\n      GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify\n      the gene making the full subject a different ontological type.\n      the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process)\n      the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process)\n      the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity)\n      the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event)\n      the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process)\n      the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality)\n      the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)\n    in_subset:\n      - translator_minimal\n\n  derivative qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.\n    examples:\n      - value: metabolite\n    in_subset:\n      - translator_minimal\n\n  part qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).\n    examples:\n      - value: polyA tail\n      - value: upstream control region\n    in_subset:\n      - translator_minimal\n\n  context qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.\n    examples:\n      - value: cohort x (e.g. a specific population, referenced by an identifier)\n      - value: gut microbiome  # OHMI:0000020\n    in_subset:\n      - translator_minimal\n\n  direction qualifier:\n    is_a: qualifier\n    abstract: true\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n    notes: >-\n      the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’\n      the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’\n    in_subset:\n      - translator_minimal\n\n  mapped predicate:\n    description: >-\n      The predicate that is being replaced by the fully qualified representation of predicate + subject and object\n      qualifiers.  Only to be used in test data and mapping data to help with the transition to the fully qualified\n      predicate model. Not to be used in knowledge graphs.\n\n  predicate mappings:\n    description: >-\n      A collection of relationships that are not used in biolink, but have biolink patterns that can\n      be used to replace them.  This is a temporary slot to help with the transition to the fully qualified predicate\n      model in Biolink3.\n    multivalued: true\n    range: predicate mapping\n    inlined_as_list: true\n\n  exact matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      an identical meaning. Such terms often describe the same concept from\n      different ontological perspectives.\n    multivalued: true\n\n  narrow matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a narrower meaning. Such terms often describe a more specific concept\n      from different ontological perspectives.\n    multivalued: true\n\n  broad matches:\n    description: >-\n      A list of terms from different schemas or terminology systems that have\n      a broader meaning. Such terms often describe a more general concept\n      from different ontological perspectives.\n    multivalued: true\n\n  subject aspect qualifier:\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.  The purpose of the aspect slot is to indicate what aspect is being affected in an\n      'affects' association.  This qualifier specifies a change in the subject of an association (aka: statement).\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    is_a: aspect qualifier\n    in_subset:\n      - translator_minimal\n\n  subject form or variant qualifier:\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.  This qualifier specifies a change in the subject of an association (aka: statement).\n    examples:\n      - value: mutation\n      - value: late stage\n      - value: severe\n      - value: transplant\n      - value: chemical analog\n    is_a: form or variant qualifier\n    in_subset:\n      - translator_minimal\n\n  subject part qualifier:\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).  This qualifier is for the \n      subject of an association (or statement).\n    is_a: part qualifier\n    in_subset:\n      - translator_minimal\n\n  subject derivative qualifier:\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.  This qualifier is for the subject of an association \n      (or statement).\n    examples:\n      - value: metabolite\n    is_a: derivative qualifier\n    in_subset:\n      - translator_minimal\n\n  subject context qualifier:\n    is_a: context qualifier\n    in_subset:\n      - translator_minimal\n\n  subject direction qualifier:\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n      This qualifier qualifies the subject of an association (aka: statement).\n    is_a: direction qualifier\n    range: DirectionQualifierEnum\n    in_subset:\n      - translator_minimal\n\n  object aspect qualifier:\n    description: >-\n      Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which\n      the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that\n      inheres in the core concept.  The purpose of the aspect slot is to indicate what aspect is being affected in an\n      'affects' association.  This qualifier specifies a change in the object of an association (aka: statement).\n    examples:\n      - value: stability\n      - value: abundance\n      - value: expression\n      - value: exposure\n    is_a: aspect qualifier\n    in_subset:\n      - translator_minimal\n\n  object form or variant qualifier:\n    description: >-\n      A qualifier that composes with a core subject/object concept to define a specific type, variant,\n      alternative version of this concept. The composed concept remains a subtype or instance of the core concept.\n      For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept\n      ‘a mutation of Gene X’.  This qualifier specifies a change in the object of an association (aka: statement).\n    examples:\n      - value: mutation\n      - value: late stage\n      - value: severe\n      - value: transplant\n      - value: chemical analog\n    is_a: form or variant qualifier\n    in_subset:\n      - translator_minimal\n\n  object part qualifier:\n    description: >-\n      defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can\n      use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).  This qualifier is for the \n      object of an association (or statement).\n    is_a: part qualifier\n    in_subset:\n      - translator_minimal\n\n  object derivative qualifier:\n    description: >-\n      A qualifier that composes with a core subject/object  concept to describe something that is derived from the\n      core concept.  For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express\n      the composed concept ‘a metabolite of Chemical X’.  This qualifier is for the object of an association \n      (or statement).\n    examples:\n      - value: metabolite\n    is_a: derivative qualifier\n    in_subset:\n      - translator_minimal\n\n  object context qualifier:\n    is_a: context qualifier\n    in_subset:\n      - translator_minimal\n\n  object direction qualifier:\n    description: >-\n      Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.\n      This qualifier qualifies the object of an association (aka: statement).\n    is_a: direction qualifier\n    range: DirectionQualifierEnum\n    in_subset:\n      - translator_minimal\n\n  qualified predicate:\n    is_a: qualifier\n    description: >-\n      Predicate to be used in an association when subject and object qualifiers are present and the full\n      reading of the statement requires a qualification to the predicate in use in order to refine or\n      increase the specificity of the full statement reading.  This qualifier holds a relationship to be used instead of that\n      expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based\n      semantics are included.  This is necessary only in cases where the primary predicate does not work in a\n      full statement reading.\n    notes: >-\n      to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read\n      using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using\n      the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression,\n      object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make\n      sense in the full statement reading  (because “Chemical X affects increased expression of Gene Y'' is not\n      what we mean to say here: it causes increased expression of Gene Y)\n\n  statement qualifier:\n    is_a: qualifier\n    description: >-\n      A property that qualifies the entirety of the statement made in an association.  It applies to both\n      a fully qualified subject and a fully qualified object as well as the predicate and qualified predicate\n      in an association.\n    in_subset:\n      - translator_minimal\n\n  causal mechanism qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a type of molecular control mechanism through which an\n      effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition',\n      'allosteric modulation', 'channel blocker')\n    range: CausalMechanismQualifierEnum\n    in_subset:\n      - translator_minimal\n\n  anatomical context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing an anatomical location where an relationship expressed in an\n      association took place (can be a tissue, cell type, or sub-cellular location).\n    notes: >-\n      Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’\n      combines with a core concept of ‘neuron’\n      to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies\n      taxonomic context, e.g. species-specific molecular activity.  Ontology CURIEs are expected as values\n      here, the examples below are intended to help clarify the content of the CURIEs.\n    examples:\n      - value: blood  # UBERON:0000178\n      - value: cerebral cortext  # UBERON:0000956\n    in_subset:\n      - translator_minimal\n\n  species context qualifier:\n    is_a: statement qualifier\n    description: >-\n      A statement qualifier representing a taxonomic category of species in which a relationship\n      expressed in an association took place.\n    range: organism taxon\n    examples:\n      - value: zebrafish  # NCBITaxon:7955\n      - value: human  # NCBITaxon:9606\n    notes:\n      - Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs.\n    in_subset:\n      - translator_minimal\n\n  qualifiers:\n    deprecated: true\n    description: >-\n      connects an association to qualifiers that modify or\n      qualify the meaning of that association\n    local_names:\n      ga4gh: annotation qualifier\n    is_a: association slot\n    multivalued: true\n    range: ontology class\n\n  frequency qualifier:\n    is_a: qualifier\n    description: >-\n      a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject\n    range: frequency value\n    in_subset:\n      - translator_minimal\n\n  severity qualifier:\n    deprecated: true\n    description: >-\n      a qualifier used in a phenotypic association to state\n      how severe the phenotype is in the subject\n    is_a: qualifier\n    range: severity value\n    in_subset:\n      - translator_minimal\n\n  sex qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state whether\n      the association is specific to a particular sex.\n    is_a: qualifier\n    range: biological sex\n    in_subset:\n      - translator_minimal\n\n  onset qualifier:\n    description: >-\n      a qualifier used in a phenotypic association to state\n      when the phenotype appears is in the subject.\n    notes: >-\n      This  is in Biolink to support HP ontology annotations which use \"onset\" (with terms from HP) \n      as an annotation on a disease to phenotypic feature association.  Please only use it for this\n      purpose.  If the intent is to describe the onset of a disease in the context of a treatment, \n      use object_aspect_qualifier and object_direction_qualifier to capture \"delayed onset\" or \"exacerbated onset\"\n      slot.\n    is_a: qualifier\n    range: onset\n    in_subset:\n      - translator_minimal\n\n  clinical modifier qualifier:\n    description: >-\n      the method or process of administering a pharmaceutical compound to achieve a therapeutic\n      effect in humans or animals.\n    is_a: association slot\n    range: clinical modifier\n\n  sequence variant qualifier:\n    description: >-\n      a qualifier used in an association with the variant\n    is_a: association slot\n    range: sequence variant\n\n  quantifier qualifier:\n    is_a: association slot\n    range: ontology class\n    description: >-\n      A measurable quantity for the object of the association\n    narrow_mappings:\n       # TODO: RTX contributed terms mapped here... May need review?\n      - LOINC:analyzes\n      - LOINC:measured_by\n      - LOINC:property_of\n      - SEMMEDDB:MEASURES\n      - UMLS:measures\n\n  catalyst qualifier:\n    is_a: association slot\n    multivalued: true\n    range: macromolecular machine mixin\n    description: >-\n      a qualifier that connects an association between two causally connected\n      entities (for example, two chemical entities, or a chemical entity in\n      that changes location) and the gene product, gene, or complex that\n      enables or catalyzes the change.\n\n  stage qualifier:\n    description: >-\n      stage during which gene or protein expression of takes place.\n    is_a: statement qualifier\n    range: life stage\n     # path: \"object/during\"\n    examples:\n      - value: UBERON:0000069\n        description: larval stage\n    in_subset:\n      - translator_minimal\n\n   ## --------------------\n   ## PREDICATES/RELATIONS\n   ## --------------------\n\n  related to:\n    description: >-\n      A relationship that is asserted between two named things\n    domain: named thing\n    range: named thing\n    multivalued: true\n    inherited: true\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - UMLS:related_to\n    broad_mappings:\n      - owl:topObjectProperty\n    narrow_mappings:\n      - SEMMEDDB:compared_with\n      - SEMMEDDB:higher_than\n      - SEMMEDDB:lower_than\n      - SEMMEDDB:ADMINISTERED_TO\n      - SEMMEDDB:ASSOCIATED_WITH\n      - BFO:0000054\n      - UBERON_CORE:protects\n      - GOREL:0002005\n      - GOREL:0012006\n       # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms\n      - BTO:related_to\n      - CHEBI:is_conjugate_acid_of\n      - CHEBI:is_conjugate_base_of\n      - CPT:has_add_on_code\n      - CPT:mapped_to\n      - EFO:0006351\n      - FMA:connected_to\n      - FMA:continuous_with\n      - FMA:homonym_of\n      - FMA:related_developmental_entity_of\n      - RO:0002093\n      - RO:0002092\n      - RO:0002084\n      - HCPCS:mapped_to\n       # RTX contributed terms, perhaps belong somewhere else with more precise semantics?\n      - HMDB:disease\n      - HMDB:has_protein_association\n      - IAO:0000136\n      - LOINC:has_answer\n      - LOINC:has_challenge\n      - LOINC:has_evaluation\n      - LOINC:mapped_to\n      - LOINC:mth_has_expanded_form\n      - MESH:RO\n      - MESH:has_mapping_qualifier\n      - MESH:mapped_to\n      - MONDO:disease_shares_features_of\n      - NCIT:disease_may_have_associated_disease\n      - NCIT:human_disease_maps_to_eo_disease\n      - NCIT:is_abnormal_cell_of_disease\n      - NCIT:is_related_to_endogenous_product\n      - UBERON_NONAMESPACE:connected_to\n      - UBERON_NONAMESPACE:innervated_by\n      - NBO-PROPERTY:is_about\n      - RO:0000053  # bearer_of\n      - PATO:reciprocal_of\n      - RO:0000052\n      - RO:0002001\n      - RO:0002002\n      - RO:0002003\n      - RO:0002008\n      - RO:0002134\n      - RO:0002150\n      - RO:0002159\n      - RO:0002176\n      - RO:0002177\n      - RO:0002178\n      - RO:0002179\n      - RO:0002314\n      - RO:0002322\n       # functionally related to\n      - RO:0002328\n      - RO:0002332\n      - RO:0002338\n      - RO:0002339\n      - RO:0002341\n      - RO:0002342\n      - RO:0002344\n      - RO:0002348\n      - RO:0002349\n      - RO:0002356\n      - RO:0002371\n      - RO:0002372\n      - RO:0002373\n      - RO:0002374\n      - RO:0002385\n      - RO:0002387\n      - RO:0002451\n      - RO:0002494\n      - RO:0002495\n      - RO:0002568\n      - RO:0002573\n      - RO:0004026\n      - RO:0004027\n      - RO:0009001\n      - RO:0009004\n      - RXNORM:has_form\n      - RXNORM:reformulated_to\n      - SNOMED:has_associated_morphology\n      - SNOMED:has_associated_procedure\n      - SNOMED:has_direct_morphology\n      - SNOMED:has_disposition\n      - SNOMED:has_indirect_morphology\n      - SNOMED:has_modification\n      - SNOMED:has_procedure_morphology\n      - SNOMED:has_specimen_source_morphology\n      - SNOMED:inheres_in\n      - SNOMED:is_interpreted_by\n      - SNOMED:relative_to_part_of\n      - UBERON:synapsed_by\n      - UMLS:RO\n      - UMLS:RQ\n      - UMLS:class_code_classified_by\n      - UMLS:exhibited_by\n      - UMLS:has_context_binding\n      - UMLS:has_form\n      - UMLS:has_mapping_qualifier\n      - UMLS:larger_than\n      - UMLS:mapped_to\n      - UMLS:owning_section_of\n\n  related to at concept level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between terminology components that describe the conceptual model of a domain.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  related to at instance level:\n    is_a: related to\n    description: >-\n      Represents a relationship held between two instances of a data classes.  Much like an assertion component,\n      in an ABox, these represent facts associated with the conceptual model.\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  associated with:\n    is_a: related to at instance level\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent,\n      'related to'. This relationship holds between two concepts represented by variables for which a statistical\n      dependence is demonstrated.  E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial\n      Infraction (MI)” asserts that having Afib is not statistically independent from whether a patient\n      will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to\n      the statistical variables, or represent related entities for which the variables serve as proxies in an\n      Association (e.g. diseases, chemical entities or processes).\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    domain: named thing\n    range: named thing\n    narrow_mappings:\n      - RO:0004029\n      - SNOMEDCT:47429007\n\n  superclass of:\n    is_a: related to at concept level\n    inverse: subclass of\n    description: >-\n      holds between two classes where the domain class is a super class of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q66088480\n      - CHEMBL.MECHANISM:superset_of\n      - GO:inverse_isa\n      - RXNORM:inverse_isa\n      - MESH:inverse_isa\n      - VANDF:inverse_isa\n    narrow_mappings:\n      - NCIT:cdrh_parent_of\n      - NCIT:ctcae_5_parent_of\n      - NCIT:subset_includes_concept\n      - OMIM:has_manifestation\n      - SNOMED:has_basic_dose_form\n      - UMLS:RB\n\n  subclass of:\n    is_a: related to at concept level\n    description: >-\n      holds between two classes where the domain class is a specialization of the range class\n    domain: ontology class\n    range: ontology class\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # RTX\n      - LOINC:class_of\n      - LOINC:has_class\n    exact_mappings:\n      - rdfs:subClassOf\n      - SEMMEDDB:ISA\n      - WIKIDATA_PROPERTY:P279\n      - CHEMBL.MECHANISM:subset_of\n      - GO:isa\n      - MESH:isa\n      - RXNORM:isa\n      - VANDF:isa\n    narrow_mappings:\n      - CHEBI:has_parent_hydride\n      - LOINC:has_archetype\n      - LOINC:has_parent_group\n      - LOINC:is_presence_guidance_for\n      - NCIT:gene_product_has_chemical_classification\n       # RTX mapped terms classes for biomarkers\n      - NCIT:R36\n      - NCIT:R42\n      - NCIT:A16\n      - NCIT:A11\n      - NCIT:A14\n      - NCIT:A3\n      - NDDF:has_dose_form\n      - RXNORM:has_dose_form\n      - RXNORM:has_doseformgroup\n      - SNOMED:entire_anatomy_structure_of\n      - SNOMED:has_dose_form\n       # RTX mapping\n      - rdfs:subPropertyOf\n\n  same as:\n    is_a: exact match\n    description: >-\n      holds between two entities that are considered equivalent to each other\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # identical class extension with identical sets of individuals\n      - owl:equivalentClass\n    exact_mappings:\n       # identical individual, or identical class concept/meaning\n      - owl:sameAs\n      - skos:exactMatch\n       # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n       # RTX suggests mapping this to proposed new \"biolink:close_match\" predicate instead\n       # - SEMMEDDB:same_as\n      - WIKIDATA_PROPERTY:P2888\n      - CHEMBL.MECHANISM:equivalent_to\n      - MONDO:equivalentTo\n    narrow_mappings:\n      - DRUGBANK:external-identifier\n\n  close match:\n    is_a: related to at concept level\n    description: >-\n      a list of terms from different schemas or terminology systems that have\n      a semantically similar but not strictly equivalent, broader, or narrower\n      meaning. Such terms often describe the same general concept from\n      different ontological perspectives (e.g. drug as a type of chemical\n      entity versus drug as a type of role borne by a chemical entity).\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:closeMatch\n       # Semantic Medline definition: \"comparative predicate\" where the equivalence could simply be functional\n      - SEMMEDDB:same_as\n    narrow_mappings:\n      - CHEBI:is_enantiomer_of\n      - CHEBI:is_tautomer_of\n      - MEDDRA:classified_as\n      - oboInOwl:hasDbXref\n      - RXNORM:has_quantified_form\n      - UMLS:SY\n\n  exact match:\n    is_a: close match\n    description: >-\n      holds between two entities that have strictly equivalent\n      meanings, with a high degree of confidence\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - skos:exactMatch\n      - WIKIDATA:Q39893449\n      - WIKIDATA:P2888\n\n  broad match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a broader, more general meaning. Broader terms are\n      typically shown as parents in a hierarchy or tree.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: narrow match\n    exact_mappings:\n      - skos:broadMatch\n      - WIKIDATA:Q39894595\n\n  narrow match:\n    description: >-\n      a list of terms from different schemas or terminology systems\n      that have a narrower, more specific meaning. Narrower terms are\n      typically shown as children in a hierarchy or tree.\n    is_a: related to at concept level\n    inverse: broad match\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - skos:narrowMatch\n      - WIKIDATA:Q39893967\n    annotations:\n      opposite_of: broad match\n\n  member of:\n    description: >-\n      Defines a mereological relation between a item and a collection.\n    is_a: related to at concept level\n    inverse: has member\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002350\n    close_mappings:\n      - skos:member\n\n  has member:\n    description: >-\n      Defines a mereological relation between a collection and an item.\n    is_a: related to at concept level\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002351\n      - skos:member\n\n  opposite of:\n    description: >-\n      x is the opposite of y if there exists some distance metric M, and there exists\n      no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002604\n    see_also:\n      - https://doi.org/10.1101/108977\n      - https://github.com/biolink/biolink-model/issues/657\n\n  affects likelihood of:\n    is_a: related to at instance level\n    description: >-\n      Holds between two entities where the presence or application of one alters the chance that the other will come\n      to be.\n    notes: >- \n      - This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the \n      actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used\n      for a statistical associations that describe correlations between two feature variables (use predicates\n      in the 'associated with likelihood of' hierarchy here.)\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  likelihood affected by:\n    is_a: related to at instance level\n    inverse: affects likelihood of\n\n  associated with likelihood of:\n    is_a: associated with\n    description: >-\n      A a relationship that holds between two concepts represented by variables for which a statistical\n      dependence is demonstrated, wherein the state or value of one variable predicts the future state\n      or value of the other.  E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated\n      with likelihood of a Myocardial Infraction (MI) diagnosis” asserts that the state of having Afib\n      is associated with an increased or decreased likelihood that a patient will later exhibit MI.\n    annotations:\n      canonical_predicate: true\n\n  likelihood associated with:\n    is_a: associated with\n    description: >-\n    inverse: associated with likelihood of\n\n  associated with increased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is more probable.\n    annotations:\n      canonical_predicate: true\n\n  increased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with increased likelihood of\n\n  associated with decreased likelihood of:\n    is_a: associated with likelihood of\n    description: >-\n      Expresses a relationship between two named things where the relationship is typically generated statistically\n      and the state or fact of something is less probable.\n    annotations:\n      canonical_predicate: true\n\n  decreased likelihood associated with:\n    is_a: likelihood associated with\n    description: >-\n    inverse: associated with decreased likelihood of\n\n  target for:\n    is_a: related to at instance level\n    description: >-\n      A gene is a target of a disease when its products are druggable and when a drug interaction with the gene\n      product could have a therapeutic effect\n    annotations:\n      canonical_predicate: true\n    domain: gene\n    range: disease\n\n  has target:\n    is_a: related to at instance level\n    inverse: target for\n    domain: disease\n    range: gene\n\n  active in:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: cellular component\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002432\n\n  has active component:\n    is_a: related to at instance level\n    inverse: active in\n    domain: cellular component\n    range: gene or gene product\n\n  acts upstream of:\n    is_a: related to at instance level\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002263\n\n  has upstream actor:\n    is_a: related to at instance level\n    inverse: acts upstream of\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of positive effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004034\n\n  has positive upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of negative effect:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004035\n\n  has negative upstream actor:\n    is_a: has upstream actor\n    inverse: acts upstream of negative effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within:\n    is_a: acts upstream of\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002264\n\n  has upstream or within actor:\n    is_a: has upstream actor\n    inverse: acts upstream of or within\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within positive effect:\n    is_a: acts upstream of or within\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004032\n\n  has positive upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within positive effect\n    domain: biological process\n    range: gene or gene product\n\n  acts upstream of or within negative effect:\n    is_a: acts upstream of or within\n    domain: gene or gene product\n    range: biological process\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0004033\n\n  has negative upstream or within actor:\n    is_a: has upstream or within actor\n    inverse: acts upstream of or within negative effect\n    domain: biological process\n    range: gene or gene product\n\n     ## Publication related predicates\n  mentions:\n    description: >-\n      refers to is a relation between one information content entity and the named thing\n      that it makes reference to.\n    is_a: related to at instance level\n    exact_mappings:\n      - IAO:0000142\n    narrow_mappings:\n      - SIO:000628\n\n  mentioned by:\n    description: >-\n      refers to is a relation between one named thing and the information content entity\n      that it makes reference to.\n    is_a: related to at instance level\n    inverse: mentions\n\n   ## Publication related predicates\n\n  contributor:\n    is_a: related to at instance level\n    domain: agent\n    range: information content entity\n    comments:\n      - This is a grouping for predicates relating entities to their associated contributors realizing them\n    abstract: true\n    exact_mappings:\n      - dct:contributor\n\n  has contributor:\n    inverse: contributor\n    is_a: related to at instance level\n    domain: information content entity\n    range: agent\n\n  provider:\n    is_a: contributor\n    description: >-\n      person, group, organization or project that provides a piece of information (e.g. a knowledge association).\n\n  has provider:\n    inverse: provider\n    is_a: has contributor\n    domain: information content entity\n    range: agent\n\n  publisher:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      organization or person responsible for publishing books, periodicals, podcasts, games or software.\n      Note that in the case of publications which have a containing \"published in\" node property, the publisher\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the publisher agent of the encompassing publication\n      (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).\n    exact_mappings:\n      - dct:publisher\n      - WIKIDATA_PROPERTY:P123\n\n  has publisher:\n    is_a: has contributor\n    inverse: publisher\n    domain: publication\n    range: agent\n\n  editor:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      editor of a compiled work such as a book or a periodical (newspaper or an academic journal).\n      Note that in the case of publications which have a containing \"published in\" node property, the editor\n      association may not be attached directly to the embedded child publication, but only made in between the\n      parent's publication node and the editorial agent of the encompassing publication\n      (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P98\n\n  has editor:\n    inverse: editor\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n  author:\n    is_a: contributor\n    domain: agent\n    range: publication\n    description: >-\n      an instance of one (co-)creator primarily responsible for a written work\n    exact_mappings:\n      - dct:creator\n      - WIKIDATA_PROPERTY:P50\n\n  has author:\n    inverse: author\n    is_a: has contributor\n    domain: publication\n    range: agent\n\n   ## end of Publication related predicates\n\n  assesses:\n    is_a: related to at instance level\n    aliases: ['was assayed against']\n    description: >-\n      The effect of a thing on a target was interrogated in some assay.\n      A relationship between some perturbing agent (usually a chemical compound) and some target entity,\n      where the affect of the perturbing agent on the target entity was interrogated in a particular assay.\n      The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type\n      of biological entity.\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n\n  is assessed by:\n    is_a: related to at instance level\n    inverse: assesses\n    domain: named thing\n    range: named thing\n\n  interacts with:\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between any two entities that directly or indirectly interact with each other\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    mixin: true\n    exact_mappings:\n      - SEMMEDDB:INTERACTS_WITH\n    notes: >-\n      please use a more specific child predicate of interacts with, either physically interacts with\n      or genetically interacts with.\n\n  physically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two entities that make physical contact as part of some interaction.\n      does not imply a causal relationship.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - WIKIDATA_PROPERTY:P129\n    close_mappings:\n      - CHEMBL.MECHANISM:binding_agent\n      - CHEMBL.MECHANISM:chelating_agent\n      - CHEMBL.MECHANISM:cross-linking_agent\n      - CHEMBL.MECHANISM:oxidative_enzyme\n      - CHEMBL.MECHANISM:sequestering_agent\n      - CHEMBL.MECHANISM:substrate\n      - DRUGBANK:target\n    narrow_mappings:\n       # Defined more narrowly as \"substance interaction\", thus specific applies to a subclass entities\n      - DRUGBANK:drug-interaction\n      - FMA:adheres_to\n      - NCIT:A7\n      - PR:non-covalently_bound_to\n    mixins:\n      - interacts with\n\n  directly physically interacts with:\n    is_a: physically interacts with\n    description: >-\n      A causal mechanism mediated by a direct contact between the effector and target entities (this contact may\n      be weak or strong, transient or stable).\n    symmetric: true\n    exact_mappings:\n      - RO:0002436\n    broad_mappings:\n       # Definition of this term is more generic than direct physical molecular interactions:\n       # A is connected to B iff there exists a fiat, material or temporal path between A and B.\n      - SIO:000203\n      - RO:0002578\n    narrow_mappings:\n      - PHAROS:drug_targets\n      - DRUGBANK:chelator\n      - CTD:affects_binding\n      - DGIdb:cofactor\n    annotations:\n      canonical_predicate: true\n\n  binds:\n    deprecated: true\n    is_a: directly physically interacts with\n    description: >-\n      A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity,\n      which form a stable physical interaction.\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - DGIdb:binder\n\n  indirectly physically interacts with:\n    is_a: physically interacts with\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  genetically interacts with:\n    is_a: interacts with\n    description: >-\n      holds between two genes whose phenotypic effects are dependent on each\n      other in some way - such that their combined phenotypic effects are the\n      result of some interaction between the activity of their gene products.\n      Examples include epistasis and synthetic lethality.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n    exact_mappings:\n      - RO:0002435\n\n  gene_fusion_with:\n    is_a: genetically interacts with\n    description: >-\n      holds between two independent genes that have fused through\n      translocation, interstitial deletion, or chromosomal inversion to\n      form a new, hybrid gene. Fusion genes are often implicated in various neoplasms\n      and cancers.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  genetic_neighborhood_of:\n    is_a: genetically interacts with\n    description: >-\n      holds between two genes located nearby one another on a chromosome.\n    domain: gene\n    range: gene\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    symmetric: true\n\n  affects:\n    is_a: related to at instance level\n    description: >-\n      Describes an entity that has an effect on the state or quality of another existing entity.\n    notes: >-\n      Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as\n      'affects likelihood of' and 'prevents' where the effect concerns whether or when something may or\n      may not come into existence.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n       # Contributed by RTX. Seems possible that a new predicate \"biolink:in_pathway\" could be justified?\n      - DRUGBANK:pathway\n    exact_mappings:\n      - SEMMEDDB:AFFECTS\n      - DGIdb:affects\n    narrow_mappings:\n      - CTD:prediction_hypothesis\n      - GOREL:0001006\n      - CTD:inferred\n      - UPHENO:0000001\n      - RO:0002263\n      - RO:0002264\n      - NCIT:R158\n      - NCIT:R160\n      - NCIT:R30\n      - NCIT:R150\n      - NCIT:R72\n      - NCIT:R146\n      - NCIT:R124\n      - NCIT:R173\n      - NCIT:R100\n      - NCIT:R102\n      - NCIT:R101\n      - NCIT:R113\n      - NCIT:R23\n      - NCIT:R25\n      - NCIT:gene_mapped_to_disease\n      - NCIT:R133\n      - RO:0002343\n      - RO:0002355\n      - RO:0002591\n      - RO:0002592\n      - RO:0012003\n      - SNOMED:has_pathological_process\n      - UBERGRAPH:is_increase_of  # talked to Jim Balhoff, this is a valid mapping\n      - UBERGRAPH:is_decrease_of  # talked to Jim Balhoff, this is a valid mapping\n\n  affected by:\n    is_a: related to at instance level\n    description: >-\n      describes an entity of which the state or quality is affected by\n      another existing entity.\n    inverse: affects\n\n  associated with sensitivity to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of sensitivity to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - PATO:0000085  # sensitivity toward\n    narrow_mappings:\n      - SNOMEDCT:418038007  # propensity to adverse reaction\n\n  sensitivity associated with:\n    is_a: associated with\n    inverse: associated with sensitivity to\n    range: named thing\n    domain: chemical entity\n\n  associated with resistance to:\n    is_a: associated with\n    description: >-\n      A relation that holds between a named thing and a chemical\n      that specifies that the change in the named\n      thing is found to be associated with the degree of resistance to treatment by the chemical.\n    domain: named thing\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n\n  resistance associated with:\n    is_a: associated with\n    inverse: associated with resistance to\n    range: named thing\n    domain: chemical entity\n\n  diagnoses:\n    is_a: related to at instance level\n    description: >-\n      a relationship that identifies the nature of (an illness or other problem) by examination\n      of the symptoms.\n    domain: diagnostic aid\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n      - NCIT:C15220  # diagnosis\n      - SIO:001331  # diagnosis\n    exact_mappings:\n      - DrugCentral:5271\n      - SEMMEDDB:DIAGNOSES\n\n  is diagnosed by:\n    is_a: related to at instance level\n    inverse: diagnoses\n    domain: disease or phenotypic feature\n    range: diagnostic aid\n\n  increases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that increase the amount\n      or activity of the object.\n\n  amount or activity increased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: increases amount or activity of\n\n  decreases amount or activity of:\n    deprecated: true\n    is_a: related to at instance level\n    mixin: true\n    description: >-\n      A grouping mixin to help with searching for all the predicates that decrease the amount\n      or activity of the object.\n\n  amount or activity decreased by:\n    deprecated: true\n    is_a: related to at instance level\n    inverse: decreases amount or activity of\n\n   ## role mixins for use in tagging corresponding role predicates\n\n  chemical role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a chemical context.\n    mixin: true\n    exact_mappings:\n      - CHEBI:51086\n\n  biological role mixin:\n    description: >-\n      A role played by the chemical entity or part thereof within a biological context.\n    mixin: true\n    narrow_mappings:\n      - CHEBI:24432\n\n  affects response to:\n    is_a: affects\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: response affected by\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - CTD:affects_response_to\n\n  response affected by:\n    description: >-\n      holds between two chemical entities where the susceptibility of a biological entity or system\n      (e.g. an organism, cell, cellular component, macromolecular machine mixin,\n      biological or pathological process) of one is affected by the action of the other.\n    is_a: affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  increases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      increases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: decreases response to\n    exact_mappings:\n      - CTD:increases_response_to\n\n  response increased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: increases response to\n\n  decreases response to:\n    description: >-\n      holds between two chemical entities where the action or effect of one\n      decreases the susceptibility of a biological entity or system (e.g. an\n      organism, cell, cellular component, macromolecular machine mixin, biological\n      or pathological process) to the other\n    is_a: affects response to\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n      opposite_of: increases response to\n    exact_mappings:\n      - CTD:decreases_response_to\n    narrow_mappings:\n      - CTD:decreases_response_to_substance\n\n  response decreased by:\n    is_a: response affected by\n    in_subset:\n      - translator_minimal\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    inverse: decreases response to\n\n  regulates:\n    is_a: affects\n    description: >-\n      A more specific form of affects, that implies the effect results from a biologically evolved control mechanism.\n      Gene-affects-gene relationships will (almost) always involve regulation.  Exogenous/environmental chemical-affects-gene relationships\n      are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or\n      possibly one of the 'interacts with' predicates depending on the nature of the interaction.\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002448\n    broad_mappings:\n       # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology)\n      - WIKIDATA_PROPERTY:P128\n      - CHEMBL.MECHANISM:modulator\n      - RO:0002295\n      - RO:0002332\n      - RO:0002448\n    notes: >-\n      The RO definition of 'directly regulates the activity of' is an exact_mapping here because\n      it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to\n      \"RO:0002211\" which describes process to process regulation.\n    mixins:\n      - interacts with\n\n  regulated by:\n    is_a: affected by\n    domain: physical essence or occurrent\n    range: physical essence or occurrent\n    inverse: regulates\n\n  disrupts:\n    is_a: affects\n    aliases: ['disease causes disruption of']\n    description: >-\n      describes a relationship where one entity degrades or interferes\n      with the structure, function, or occurrence of another.\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n      opposite_of: enables\n    exact_mappings:\n      - SEMMEDDB:DISRUPTS\n      - CHEMBL.MECHANISM:disrupting_agent\n    narrow_mappings:\n      - RO:0004024\n      - RO:0004025\n\n  disrupted by:\n    is_a: affected by\n    description: >-\n      describes a relationship where the structure, function, or occurrence\n      of one entity is degraded or interfered with by another.\n    inverse: disrupts\n\n  gene product of:\n    is_a: related to at instance level\n    description: >-\n      definition x has gene product of y if and only if y is a gene (SO:0000704)\n      that participates in some gene expression process (GO:0010467) where the output of thatf\n      process is either y or something that is ribosomally translated from x\n    exact_mappings:\n      - RO:0002204\n    domain: gene product mixin\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: has gene product\n    in_subset:\n      - translator_minimal\n\n  has gene product:\n    is_a: related to at instance level\n    description: >-\n      holds between a gene and a transcribed and/or\n      translated product generated from it\n    domain: gene\n    range: gene product mixin\n    inverse: gene product of\n    in_subset:\n      - translator_minimal\n    close_mappings:\n       # RTX term tagged as inverse mapping\n      - PR:has_gene_template\n    exact_mappings:\n      - RO:0002205\n      - WIKIDATA_PROPERTY:P688\n      - NCIT:gene_encodes_gene_product\n    narrow_mappings:\n      - NCIT:R178\n\n  transcribed to:\n    is_a: related to at instance level\n    domain: gene\n    range: transcript\n    description: >-\n      inverse of transcribed from\n    inverse: transcribed from\n    exact_mappings:\n      - RO:0002511\n      - SIO:010080\n\n  transcribed from:\n    is_a: related to at instance level\n    domain: transcript\n    range: gene\n    annotations:\n      canonical_predicate: true\n    inverse: transcribed to\n    description: >-\n      x is transcribed from y if and only if x is synthesized from template y\n    exact_mappings:\n      - RO:0002510\n      - SIO:010081\n\n  translates to:\n    is_a: related to at instance level\n    domain: transcript\n    range: protein\n    annotations:\n      canonical_predicate: true\n    inverse: translation of\n    description: >-\n      x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome\n      reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533)\n      and produces x (amino acid chain/polypeptide)\n    close_mappings:\n      - RO:0002513\n      - SIO:010082\n\n  translation of:\n    is_a: related to at instance level\n    domain: protein\n    range: transcript\n    description: >-\n      inverse of translates to\n    inverse: translates to\n    close_mappings:\n      - RO:0002512\n      - SIO:010083\n\n  homologous to:\n    is_a: similar to\n    aliases: ['in homology relationship with']\n    description: >-\n      holds between two biological entities that have common evolutionary origin\n    comments:\n      - typically used to describe homology relationships between genes or gene products\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000001\n      - SIO:010302\n    narrow_mappings:\n       # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158\n      - UBERON_CORE:sexually_homologous_to\n\n  paralogous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship that holds between entities (typically genes) that diverged after a duplication event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000011\n\n  orthologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship between entities (typically genes) that diverged after a speciation event.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000017\n      - WIKIDATA_PROPERTY:P684\n\n  xenologous to:\n    is_a: homologous to\n    description: >-\n      a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000018\n\n  coexists with:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n      - SEMMEDDB:COEXISTS_WITH\n    narrow_mappings:\n      - BSPO:0000096\n      - BSPO:0000097\n      - BSPO:0000098\n      - BSPO:0000099\n      - BSPO:0000100\n      - BSPO:0000102\n      - BSPO:0000104\n      - BSPO:0000110\n      - BSPO:0000113\n      - BSPO:0015001\n      - BSPO:0015002\n      - BSPO:0015003\n      - BSPO:0015005\n      - BSPO:0015006\n      - BSPO:0015007\n      - BSPO:0015008\n      - BSPO:0015009\n      - BSPO:0015012\n      - BSPO:0015014\n      - BSPO:parallel_to\n      - UBERON_CORE:anastomoses_with\n      - UBERON_CORE:anteriorly_connected_to\n      - UBERON_CORE:posteriorly_connected_to\n      - UBERON_CORE:channel_for\n      - UBERON_CORE:channels_from\n      - UBERON_CORE:channels_into\n      - UBERON_CORE:conduit_for\n      - UBERON_CORE:distally_connected_to\n      - UBERON_CORE:extends_fibers_into\n      - UBERON_CORE:filtered_through\n      - UBERON_CORE:indirectly_supplies\n      - UBERON_CORE:proximally_connected_to\n      - UBERON_CORE:synapsed_by\n      - UBERON_CORE:transitively_anteriorly_connected_to\n      - UBERON_CORE:transitively_connected_to\n      - UBERON_CORE:transitively_distally_connected_to\n      - UBERON_CORE:transitively_proximally_connected_to\n       # RTX contributed Environmental Ontology term meaning \"partially surrounded by\"\n      - ENVO:01001307\n      - FMA:adjacent_to\n      - FMA:afferent_to\n      - FMA:anterior_to\n      - FMA:anteroinferior_to\n      - FMA:anterolateral_to\n      - FMA:anteromedial_to\n      - FMA:anterosuperior_to\n       # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics?\n       # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink\n      - FMA:arterial_supply_of\n      - FMA:has_arterial_supply\n      - FMA:articulates_with\n      - FMA:attaches_to\n      - FMA:bounded_by\n      - FMA:bounds\n      - FMA:branch_of\n      - FMA:connection_type_of\n      - FMA:continuation_branch_of\n      - FMA:continuous_distally_with\n      - FMA:continuous_proximally_with\n      - FMA:corresponds_to\n      - FMA:development_type_of\n      - FMA:developmental_stage_of\n      - FMA:direct_cell_shape_of\n      - FMA:direct_left_of\n      - FMA:direct_right_of\n      - FMA:distal_to\n      - FMA:drains_into\n      - FMA:efferent_to\n      - FMA:external_to\n      - FMA:formed_by\n      - FMA:forms\n       # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:full_grown_phenotype_of\n      - FMA:has_full_grown_phenotype\n       # these next two RTX mapped terms also seem to be inverses of one another\n      - FMA:fuses_with\n      - FMA:fusion_of\n      - FMA:has_fusion\n      - FMA:germ_origin_of\n      - FMA:has_germ_origin\n      - FMA:has_adherent\n      - FMA:has_branch\n      - FMA:has_connection_type\n      - FMA:has_continuation_branch\n      - FMA:has_development_type\n      - FMA:has_developmental_stage\n      - FMA:has_direct_cell_shape\n      - FMA:has_inherent_3d_shape\n      - FMA:has_insertion\n      - FMA:has_lymphatic_drainage\n      - FMA:has_nerve_supply\n      - FMA:has_observed_anatomical_entity\n      - FMA:has_origin\n      - FMA:has_primary_segmental_supply\n      - FMA:has_projection\n      - FMA:has_regional_part\n      - FMA:has_related_developmental_entity\n      - FMA:has_secondary_segmental_supply\n      - FMA:has_segmental_composition\n      - FMA:has_segmental_supply\n      - FMA:has_tributary\n      - FMA:has_venous_drainage\n      - FMA:inferior_to\n      - FMA:inferolateral_to\n      - FMA:inferomedial_to\n      - FMA:inherent_3d_shape_of\n      - FMA:insertion_of\n      - FMA:internal_to\n      - FMA:lateral_to\n      - FMA:left_lateral_to\n      - FMA:left_medial_to\n      - FMA:lymphatic_drainage_of\n      - FMA:matures_from\n      - FMA:matures_into\n      - FMA:medial_to\n      - FMA:merges_with\n      - FMA:nerve_supply_of\n      - FMA:origin_of\n      - FMA:posterior_to\n      - FMA:posteroinferior_to\n      - FMA:posterolateral_to\n      - FMA:posteromedial_to\n      - FMA:posterosuperior_to\n      - FMA:primary_segmental_supply_of\n      - FMA:projects_from\n      - FMA:projects_to\n      - FMA:proximal_to\n      - FMA:receives_attachment_from\n      - FMA:receives_drainage_from\n      - FMA:receives_input_from\n      - FMA:receives_projection\n      - FMA:related_part\n      - FMA:right_lateral_to\n      - FMA:right_medial_to\n      - FMA:secondary_segmental_supply_of\n      - FMA:segmental_composition_of\n      - FMA:segmental_supply_of\n      - FMA:sends_output_to\n      - FMA:superior_to\n      - FMA:superolateral_to\n      - FMA:superomedial_to\n      - FMA:surrounded_by\n      - FMA:surrounds\n      - FMA:tributary_of\n      - FMA:venous_drainage_of\n       # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute'\n       # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now\n      - LOINC:has_lateral_anatomic_location\n      - LOINC:has_lateral_location_presence\n      - UBERON_NONAMESPACE:distally_connected_to\n      - UBERON_NONAMESPACE:subdivision_of\n       # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to'\n      - RO:0002219\n      - RO:0002220\n      - RO:0002221\n      - SO:has_origin\n       # RTX mapped these UBERON terms all here\n      - UBERON:anastomoses_with\n      - UBERON:anteriorly_connected_to\n      - UBERON:channel_for\n      - UBERON:channels_from\n      - UBERON:channels_into\n      - UBERON:conduit_for\n      - UBERON:distally_connected_to\n      - UBERON:existence_starts_and_ends_during\n      - UBERON:extends_fibers_into\n      - UBERON:filtered_through\n      - UBERON:in_central_side_of\n      - UBERON:in_innermost_side_of\n      - UBERON:in_outermost_side_of\n      - UBERON:indirectly_supplies\n      - UBERON:posteriorly_connected_to\n      - UBERON:protects\n      - UBERON:proximally_connected_to\n      - UBERON:sexually_homologous_to\n\n  in pathway with:\n    description: >-\n      holds between two genes or gene products that are part of in the same biological pathway\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n       # generally pertains to membership of a (subject) component - gene,\n       # metabolite, etc? - in an (object) metabolic pathway\n      - SIO:010532\n\n  in complex with:\n    description: >-\n      holds between two genes or gene products that are part of (or code for\n      products that are part of) in the same macromolecular complex\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n       # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though)\n      - SIO:010497\n    broad_mappings:\n       # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes)\n      - SIO:010285\n\n  in cell population with:\n    description: >-\n      holds between two genes or gene products that are expressed in the same cell type or population\n    is_a: coexists with\n    domain: gene or gene product\n    range: gene or gene product\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  colocalizes with:\n    description: >-\n      holds between two entities that are observed to be located in the same place.\n    is_a: coexists with\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002325\n\n   # Despite the name, note that this particular entity is\n   # NOT a biolink:Association but rather, a biolink:predicate\n  genetic association:\n    deprecated: true\n    deprecated_element_has_exact_replacement: biolink:genetically_associated_with\n    is_a: associated with\n    symmetric: true\n\n  genetically associated with:\n    is_a: associated with\n    description: >-\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      description: >-\n        Co-occurrence of a certain allele of a genetic marker and the phenotype\n        of interest in the same individuals at above-chance level\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2293\n    in_subset:\n      - translator_minimal\n\n  gene associated with condition:\n    is_a: genetically associated with\n    description: >-\n      holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,\n      contribute to, or correlate with\n    domain: gene\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - GENO:0000840  # broader than a single gene: 'genotype' pathogenic for condition\n      - GENO:0000841\n    narrow_mappings:\n       # narrower: just diseases, not phenotypic features as well\n      - NCIT:R38\n      - NCIT:R175\n      - NCIT:R48\n\n  condition associated with gene:\n    is_a: genetically associated with\n    aliases: ['disease associated with gene']\n    description: >-\n      holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products\n    domain: disease or phenotypic feature\n    range: gene\n    in_subset:\n      - translator_minimal\n    inverse: gene associated with condition\n    narrow_mappings:\n       # RO term implies causality making it narrower\n      - RO:0004000\n       # narrower since just diseases, not phenotypic features as well\n      - NCIT:R176\n\n\n  contributes to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one contributes to the\n      occurrence or generation of the other\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # RTX contributed mapping tagged as 'inverse' of this Biolink predicate\n      - IDO:0000664\n    exact_mappings:\n      - RO:0002326\n    narrow_mappings:\n      - CTD:marker_mechanism\n      - MONDO:predisposes_towards\n       # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002255\n       # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here\n      - RO:0003304\n\n  contribution from:\n    is_a: related to at instance level\n    in_subset:\n      - translator_minimal\n    inverse: contributes to\n\n  causes:\n    description: >-\n      holds between two entities where the occurrence, existence, or activity of one causes the occurrence\n      or generation of the other\n    is_a: contributes to\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SEMMEDDB:CAUSES\n      - WIKIDATA_PROPERTY:P1542\n      - SNOMED:cause_of\n      - RO:0003303\n    broad_mappings:\n      - RO:0002410\n      - RO:0002506\n    narrow_mappings:\n      - MONDO:disease_triggers\n      - GOREL:0000040\n      - MONDO:disease_causes_feature\n      - NCIT:allele_has_abnormality\n      - NCIT:biological_process_has_result_biological_process\n      - NCIT:chemical_or_drug_has_physiologic_effect\n       # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'?\n      - NCIT:chemical_or_drug_initiates_biological_process\n      - NCIT:process_initiates_biological_process\n      - NCIT:chromosome_mapped_to_disease\n      - NCIT:disease_has_normal_tissue_origin\n      - NBO-PROPERTY:in_response_to\n      - orphanet:317343\n      - orphanet:317344\n      - orphanet:317346\n      - orphanet:410295\n      - orphanet:410296\n       # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping\n      - RO:0002256\n      - RO:0002315\n      - RO:0002507\n      - RO:0002509\n      - RO:0004001\n      - SNOMED:causative_agent_of\n      - SNOMED:has_realization\n      - UMLS:has_physiologic_effect\n\n  caused by:\n    description: >-\n      holds between two entities where the occurrence, existence,\n      or activity of one is caused by the occurrence or generation of the other\n    is_a: contribution from\n    aliases: ['disease caused by disruption of', 'disease has basis in dysfunction of',\n              'realized in response to', 'realized in response to stimulus']\n    in_subset:\n      - translator_minimal\n    inverse: causes\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P828\n    narrow_mappings:\n      - RO:0001022\n      - RO:0002608\n      - RO:0004019\n      - RO:0004020\n      - RO:0004028\n      - RO:0009501\n\n   # TODO: ameliorates and exacerbates inverses.\n  ameliorates condition:\n    aliases: ['ameliorates', 'beneficial for condition', 'therapeutic for condition']\n    is_a: affects\n    description: >-\n      Holds between an entity and an existing medical condition (disease or phenotypic feature) where the entity is\n      able to ameliorate symptoms, stabilize progression, or cure the condition.\n    notes: >-\n      This predicate describes a narrower view of 'treats' - that covers interventions that are beneficial for existing\n      disease, and excludes interventions that prevent/reduce risk of developing a condition in the future.\n    mixins:\n      - treats\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: exacerbates condition\n    exact_mappings:\n      - RO:0003307\n\n  condition ameliorated by:\n    inverse: ameliorates condition\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  preventative for condition:\n    aliases: ['prophylactic for', 'prevents']\n    is_a: affects likelihood of\n    mixins:\n      - treats\n    description: >-\n      Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature),\n      and states that the  substance, procedure, or activity is able to prevent it manifesting in the first place.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: promotes condition\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - SEMMEDDB:PREVENTS\n\n  condition prevented by:\n    inverse: preventative for condition\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  promotes condition:\n    mixin: true\n    is_a: related to at instance level\n    description: >-\n      Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature),\n      and states that the  substance, procedure, or activity is able to promote it manifesting in the first place.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: preventative for condition\n    in_subset:\n      - translator_minimal\n\n  condition promoted by:\n    is_a: likelihood affected by\n    inverse: promotes condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  predisposes to condition:\n    aliases: ['risk factor for']\n    is_a: affects likelihood of\n    mixins:\n      - promotes condition\n    description: >-\n      Holds between two entities where the presence or application of one increases the chance that the\n      other will come to be.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    broad_mappings:\n      - SEMMEDDB:PREDISPOSES\n\n  condition predisposed by:\n    is_a: likelihood affected by\n    inverse: predisposes to condition\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  exacerbates condition:\n    aliases: ['exacerbates', 'detrimental for condition']\n    is_a: affects\n    description: >-\n       Holds between a substance, procedure, or activity and an existing medical condition (disease or phenotypic\n        feature) where the substance, procedure, or activity worsens some or all aspects of the condition.\n    mixins:\n      - promotes condition\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n      opposite_of: ameliorates condition\n    exact_mappings:\n      - RO:0003309\n    broad_mappings:\n      - SEMMEDDB:COMPLICATES\n\n  condition exacerbated by:\n    inverse: exacerbates condition\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    in_subset:\n      - translator_minimal\n\n  treats:\n    is_a: treats or applied or studied to treat\n    mixin: true\n    aliases: ['is substance that treats', 'indicated for', 'ameliorates or prevents condition']\n    description: >-\n      Holds between an intervention (substance, procedure, or activity) and a medical condition\n      (disease or phenotypic feature), and states that the intervention is able to ameliorate,\n      stabilize, or cure the condition or delay, prevent, or reduce the risk of it manifesting\n      in the first place.\n      ‘Treats’ edges should be asserted (knowledge_level: assertion) only in cases where there\n      is strong supporting evidence - i.e. the intervention is approved for the condition, passed\n      phase 3 or in phase 4 trials for the condition, or is an otherwise established \n      treatment in the medical community (e.g. a widely-accepted or formally recommended \n      off-label use). In the absence of such evidence, weaker predicates should be used in \n      asserted edges (e.g. ‘in clinical trials for’ or ‘beneficial in models of’). ‘Treats’ edges\n      based on weaker or indirect forms of evidence can however be created as predictions \n      (knowledge_level: prediction) and should point to the more foundational asserted edges that \n      support them.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    related_mappings:\n      - MONDO:disease_responds_to\n    exact_mappings:\n      - DRUGBANK:treats\n      - WIKIDATA_PROPERTY:P2175\n    narrow_mappings:\n       # \"is substance that treats\" constrains statements to\n       # a subset of the universe of all possible treatments\n      - RO:0002606\n      - NCIT:regimen_has_accepted_use_for_disease\n       # RTX mapped REPODB terms\n      - REPODB:clinically_tested_approved_unknown_phase\n      - REPODB:clinically_tested_suspended_phase_0\n      - REPODB:clinically_tested_suspended_phase_1\n      - REPODB:clinically_tested_suspended_phase_1_or_phase_2\n      - REPODB:clinically_tested_suspended_phase_2\n      - REPODB:clinically_tested_suspended_phase_2_or_phase_3\n      - REPODB:clinically_tested_suspended_phase_3\n      - REPODB:clinically_tested_terminated_phase_0\n      - REPODB:clinically_tested_terminated_phase_1\n      - REPODB:clinically_tested_terminated_phase_1_or_phase_2\n      - REPODB:clinically_tested_terminated_phase_2\n      - REPODB:clinically_tested_terminated_phase_2_or_phase_3\n      - REPODB:clinically_tested_terminated_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_0\n      - REPODB:clinically_tested_withdrawn_phase_1\n      - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2\n      - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\n      - REPODB:clinically_tested_withdrawn_phase_3\n      - SNOMED:plays_role\n    broad_mappings:\n      - DRUGBANK:treats\n      - SEMMEDDB:TREATS\n      - WIKIDATA_PROPERTY:P2175\n      - MONDO:disease_responds_to\n\n  treated by:\n    mixin: true\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    # range: chemical or drug or treatment\n    in_subset:\n      - translator_minimal\n    inverse: treats\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P2176\n      # RTX contributed term tagged as inverse of 'biolink:treats'\n      - MONDO:disease_responds_to\n    narrow_mappings:\n      # \"is treated by substance\" constrains statements to\n      # subset of the universe of all possible treatments\n      - RO:0002302\n\n  studied to treat:\n    is_a: related to at instance level\n    description: >-\n      Holds between an  substance, procedure, or activity and a medical condition, and reports that one or more\n      scientific study has been performed to specifically test the potential of the  substance, procedure, or\n      activity to treat the medical condition  (i.e. to ameliorate, stabilize, or cure the condition, or to delay,\n      prevent, or reduce the risk of it manifesting in the first place).\n    notes: >-\n      Predicates in this hierarchy are used in practice when a source reports performance of a study, but there is\n      not sufficient evidence or demonstrated efficacy against the condition to warrant creating a ‘treats’ assertion\n      edge. Note however that a 'studied to treat' edge may be used as evidence to support creation of a separate\n      'treats' prediction edge.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    mixins:\n      - treats or applied or studied to treat\n    annotations:\n      canonical_predicate: true\n\n  in clinical trials for:\n    is_a: studied to treat\n    description: >-\n      Holds between an intervention and a medical condition, and reports that a clinical trial  is being or has been\n      performed in human patients to test the potential of the intervention to treat the medical condition\n      (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it\n      manifesting in the first place).\n    notes: >-\n      This predicate should be used when a source reports a clinical trial where the intervention is being or was\n      interrogated, regardless of the phase of the trial, or its ultimate outcome.  Information about phase and outcome\n      can be capture using other modeling elements.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    mixins:\n      - treats or applied or studied to treat\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n  # TODO: add inverse\n\n  tested by clinical trials of:\n    is_a: treated in studies by\n    inverse: in clinical trials for\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  treated in studies by:\n    is_a: treated by\n    inverse: studied to treat\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  tested by preclinical trials of:\n    is_a: treated in studies by\n    inverse: in preclinical trials for\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  in preclinical trials for:\n    is_a: studied to treat\n    description: >-\n      Holds between an  substance, procedure, or activity and a medical condition, and reports that a pre-clinical\n      study has been performed specifically to test the potential of the  substance, procedure, or activity to treat\n      the medical condition  (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce\n      the risk of it manifesting in the first place).\n    mixins:\n      - treats or applied or studied to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    # TODO: inverse of in_preclincal_trials_for needed\n\n  beneficial in models for:\n    is_a: in preclinical trials for\n    description: >-\n      Holds between an  substance, procedure, or activity and a medical condition, and reports that the  substance,\n      procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/\n      phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).\n    notes: >-\n      This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention\n      alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease.\n      (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation\n      phenotype of zebrafish used to model the human disease Kabuki Syndrome) .\n    mixins:\n      - treats or applied or studied to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    # TODO: need inverse of beneficial_in_models_for\n\n  models demonstrating benefits for:\n    is_a: tested by preclinical trials of\n    inverse: beneficial in models for\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  applied to treat:\n    aliases: ['administered to treat', 'used to treat', 'given to treat']\n    is_a: related to at instance level\n    description: >-\n      Holds between an  substance, procedure, or activity and a medical condition, and reports that the  substance,\n      procedure, or activity was actually taken by one or more patients with the intent of treating the condition.\n    notes: >-\n      This predicate is used simply to report observations of use in the real world, and is agnostic to whether the\n      treatment is approved for or might be effective in treating the condition. The treatment could be taken by a\n      patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In\n      practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS\n      where patients directly report the condition for which they took a drug, or statements from a database cataloging\n      instances of off-label prescription of drugs for specific conditions (e.g. here, here, here).\n    mixins:\n      - treats or applied or studied to treat\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n   # TODO: need an inverse for taken to treat\n\n  treatment applications from:\n    is_a: related to at instance level\n    inverse: applied to treat\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n\n  treats or applied or studied to treat:\n    mixin: true\n    description: >-\n      Holds between an substance, procedure, or activity and a medical condition (disease or phenotypic feature),\n      and states that the substance, procedure, or activity is able to treat the condition, has been observed to be\n      taken/prescribed in practice with the intent of treating the condition, or has been interrogated in a scientific\n      study that hypothesized an ability to treat the condition (in humans or other biological systems/organisms).\n    notes: >-\n      This predicate is helpful both as a grouping predicate to aid in searching for broader senses of treating a\n      condition, and as a catch-all for representing sources that are not clear about the sense of treats that is\n      being reported. For example, text-mined statements concerning treatments for disease are based on sentences\n      that can report treatment in any of these different senses and thus require a broader predicate such as\n      this to safely report statement semantics.\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:TREATS\n\n  subject of treatment application or study for treatment by:\n    mixin: true\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: treats or applied or studied to treat\n\n  correlated with:\n    is_a: associated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical dependence is\n      demonstrated using a correlation analysis method.\n    notes: >-\n      These concepts may map exactly to the statistical variables, or represent related entities for which the\n      variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002610\n      - PATO:correlates_with\n\n   # proposed positive and negative semantic extensions to the general \"correlated with\" predicate\n\n  positively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation\n      is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or\n      presence of one correlates with an increase or presence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: negatively correlated with\n    exact_mappings:\n      - CTD:positive_correlation\n\n  negatively correlated with:\n    is_a: correlated with\n    description: >-\n      A relationship that holds between two concepts represented by variables for which a statistical correlation\n      is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of\n      one correlates with a decrease or absence of the other).\n    domain: named thing\n    range: named thing\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n      opposite_of: positively correlated with\n    exact_mappings:\n      - CTD:negative_correlation\n\n  occurs together in literature with:\n    is_a: correlated with\n    description: >-\n      holds between two entities where their co-occurrence is correlated by counts of publications\n      in which both occur, using some threshold of occurrence as defined by the edge provider.\n    domain: named thing\n    range: named thing\n    in_subset: translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  coexpressed with:\n    is_a: correlated with\n    description: >-\n      holds between any two genes or gene products, in which both are\n      generally expressed within a single defined experimental context.\n    domain: gene or gene product\n    range: gene or gene product\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n\n  has biomarker:\n    is_a: correlated with\n    description: >-\n      holds between a disease or phenotypic feature and a measurable\n      chemical entity that is used as an indicator of the presence\n      or state of the disease or feature.\n       # metabolite\n    domain: disease or phenotypic feature\n    range: chemical entity or gene or gene product\n    in_subset:\n      - translator_minimal\n    inverse: biomarker for\n    narrow_mappings:\n       # some RTX terms contributed as inverses of 'biolink:biomarker_for'\n      - NCIT:disease_has_molecular_abnormality\n      - NCIT:disease_is_marked_by_gene\n\n  biomarker for:\n    is_a: correlated with\n    description: >-\n      holds between a measurable chemical entity and a disease\n      or phenotypic feature, where the entity is used as an indicator\n      of the presence or state of the disease or feature.\n    domain: chemical entity or gene or gene product\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - NCIT:R39\n    broad_mappings:\n       # Generic marker definition not specific to biomarkers per say\n      - RO:0002607\n    narrow_mappings:\n      - NCIT:R47\n       # RTX term was tagged as 'biolink:actively_involved_in' but maps better here?\n      - NCIT:genetic_biomarker_related_to\n      - NCIT:is_molecular_abnormality_of_disease\n      - orphanet:465410\n\n   # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in'\n   # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates\n   # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others\n  expressed in:\n    is_a: located in\n    description: >-\n      holds between a gene or gene product and an anatomical entity in which it is expressed\n    domain: gene or gene product\n    range: anatomical entity\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002206\n    narrow_mappings:\n      - NCIT:R49\n      - NCIT:R46\n\n  expresses:\n    is_a: location of\n    aliases: ['anatomy expresses gene']\n    description: >-\n      holds between an anatomical entity and gene or gene product that is expressed there\n    domain: anatomical entity\n    range: gene or gene product\n    multivalued: true\n    in_subset:\n      - translator_minimal\n    inverse: expressed in\n    exact_mappings:\n      - RO:0002292\n\n  has phenotype:\n    is_a: related to at instance level\n    aliases: ['disease presents symptom']\n    description: >-\n      holds between a biological entity and a phenotype, where a phenotype\n      is construed broadly as any kind of quality of an organism part,\n      a collection of these qualities, or a change in quality or qualities\n      (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should\n      translate into this predicate.\n    domain: biological entity\n    range: phenotypic feature\n    multivalued: true\n    annotations:\n      canonical_predicate: true\n    notes:\n      - check the range\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002200\n    broad_mappings:\n      - NCIT:R115\n      - NCIT:R108\n    narrow_mappings:\n      - NCIT:R89\n      - DOID-PROPERTY:has_symptom\n      - RO:0004022\n      - RO:0004029\n\n  phenotype of:\n    is_a: related to at instance level\n    domain: phenotypic feature\n    range: biological entity\n    multivalued: true\n    inverse: has phenotype\n\n   # TODO: predicate inverse for occurs in\n  occurs in:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a material entity or site within which the process occurs\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # These RTX mapped terms tagged as the inverse of \"biolink:occurs_in\", i.e. Entity/Site contains Process\n      - BFO:0000067\n      - SNOMED:has_occurrence\n      - UBERON:site_of\n    exact_mappings:\n      - BFO:0000066\n      - PathWhiz:has_location\n      - SNOMED:occurs_in\n    narrow_mappings:\n       # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population\n      - SEMMEDDB:OCCURS_IN\n       # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity\n      - SEMMEDDB:PROCESS_OF\n       # Uberon term constrained to a 'site' as object concept\n      - UBERON_CORE:site_of\n      - LOINC:has_imaged_location\n      - PathWhiz:in_species\n      - RO:0002231\n      - RO:0002232\n      - SNOMED:has_direct_procedure_site\n      - SNOMED:has_direct_site\n      - SNOMED:has_procedure_site\n\n  contains process:\n    is_a: related to at instance level\n    inverse: occurs in\n\n  located in:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a material entity or site\n      within which it is located (but of which it is not considered a part)\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0001025\n      - FMA:has_location\n    narrow_mappings:\n      - GOREL:0001004\n      - BSPO:0000107\n      - BSPO:0000108\n      - BSPO:0000120\n      - BSPO:0000121\n      - BSPO:0000122\n      - BSPO:0000123\n      - BSPO:0000124\n      - BSPO:0000125\n      - BSPO:0000126\n      - BSPO:0001100\n      - BSPO:0001101\n      - BSPO:0001107\n      - BSPO:0015101\n      - BSPO:0015102\n      - BSPO:0015202\n      - UBERON_CORE:in_central_side_of\n      - UBERON_CORE:in_innermost_side_of\n      - UBERON_CORE:in_outermost_side_of\n      - NCIT:R100\n      - EFO:0000784\n      - FMA:has_location\n      - HMDB:at_cellular_location\n      - HMDB:at_tissue\n      - HMDB:in_biospecimen\n      - LOINC:has_imaging_focus\n      - NCIT:R156\n      - NCIT:R155\n      - NCIT:R145\n      - NCIT:R40\n      - NCIT:R171\n      - NCIT:R167\n      - NCIT:R165\n      - NCIT:R169\n      - NCIT:R170\n      - NCIT:R166\n      - NCIT:R168\n      - RO:0002303\n      - SNOMED:has_finding_site\n      - SNOMED:has_indirect_procedure_site\n      - SNOMED:has_inherent_location\n    domain: named thing\n    range: named thing\n\n  location of:\n    is_a: related to at instance level\n    aliases: ['site of']\n    domain: named thing\n    range: named thing\n    description: >-\n      holds between material entity or site and a material entity\n      that is located within it (but not considered a part of it)\n    in_subset:\n      - translator_minimal\n    inverse: located in\n    exact_mappings:\n      - RO:0001015\n      - SEMMEDDB:LOCATION_OF\n      - WIKIDATA_PROPERTY:P276\n       # RTX tagged this as an inverse of biolink:located_in\n      - FMA:location_of\n    narrow_mappings:\n      - SNOMED:inherent_location_of\n      - NCIT:Anatomic_Structure_Has_Location_Role\n\n  disease has location:\n    description: >-\n      A relationship between a disease and an anatomical entity where the\n      disease has one or more features that are located in that entity.\n    is_a: related to\n    exact_mappings:\n      - RO:0004026\n      - MONDO:disease_has_location\n\n  location of disease:\n    is_a: related to\n    inverse: disease has location\n\n  similar to:\n    is_a: related to at instance level\n    description: >-\n      holds between an entity and some other entity with similar features.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:HOM0000000\n      - SO:similar_to\n\n  chemically similar to:\n    is_a: similar to\n    description: >-\n      holds between one small molecule entity and another that it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - CHEBI:has_parent_hydride     # subproperty\n      - CHEBI:has_functional_parent  # subproperty\n      - CHEBI:is_conjugate_acid_of   # subproperty\n      - CHEBI:is_conjugate_base_of   # subproperty\n      - CHEBI:is_enantiomer_of       # subproperty\n      - CHEBI:is_tautomer_of         # subproperty\n      - NCIT:has_salt_form\n\n  has sequence location:\n    is_a: related to at instance level\n    description: >-\n      holds between two nucleic acid entities when the subject can be localized\n      in sequence coordinates on the object. For example, between\n      an exon and a chromosome/contig.\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - faldo:location\n\n  sequence location of:\n    is_a: related to at instance level\n    domain: nucleic acid entity\n    range: nucleic acid entity\n    inverse: has sequence location\n\n  model of:\n    is_a: related to at instance level\n    description: >-\n      holds between a thing and some other thing it approximates\n      for purposes of scientific study, in virtue of its exhibiting\n      similar features of the studied entity.\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0003301\n    narrow_mappings:\n      - FOODON:00001301\n\n  models:\n    is_a: related to at instance level\n    inverse: model of\n\n  overlaps:\n    is_a: related to at instance level\n    description: >-\n      holds between entities that overlap in their extents (materials or processes)\n    in_subset:\n      - translator_minimal\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002131\n    narrow_mappings:\n      - BSPO:0005001\n      - CHEMBL.MECHANISM:overlaps_with\n      - RO:0002100\n      - RO:0002102\n      - RO:0002433\n\n  has part:\n    is_a: overlaps\n    annotations:\n      canonical_predicate: true\n      opposite_of: lacks part\n    description: >-\n      holds between wholes and their parts (material entities or processes)\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000051\n       # term name seems to be 'realizes' but RTX maps this term here\n      - BFO:0000055\n      - WIKIDATA_PROPERTY:P527\n      - RO:0001019\n      - RXNORM:consists_of\n      - RXNORM:has_part\n    broad_mappings:\n       # To 'contain' is 'to have something inside or include something as a part'; slightly broader?\n      - RO:0001019\n      - FMA:contains\n      - RXNORM:contains\n    narrow_mappings:\n      - BFO:0000117\n       # RTX term originally mapped to 'biolink:coexists_with'?\n      - FMA:has_constitutional_part\n      - FMA:has_part\n       # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'?\n      - FMA:has_member\n      - FOODON:00001563\n      - FOODON:00002420\n      - LOINC:has_component\n      - LOINC:has_member\n      - MEDDRA:has_member\n      - MONDO:disease_has_major_feature\n      - NCIT:complex_has_physical_part\n      - NDDF:has_ingredient\n      - PathWhiz:has_element_in_bound\n       # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature\n      - NCIT:R50\n      - PathWhiz:has_protein_in_complex\n      - RO:0002104\n      - RO:0002180\n      - RO:0002351\n      - RO:0002473\n      - RO:0002524\n      - RO:0002551\n      - RXNORM:has_ingredient\n      - SNOMED:has_component\n      - UMLS:has_component\n\n  has plasma membrane part:\n    is_a: has part\n    description: >-\n      Holds between a cell c and a protein complex or protein p if\n      and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.\n    exact_mappings:\n      - RO:0002104\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  composed primarily of:\n    is_a: related to\n    description: >-\n      x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.\n    exact_mappings:\n      - RO:0002473\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  primarily composed of:\n    inverse: composed primarily of\n    is_a: related to\n\n  plasma membrane part of:\n    is_a: part of\n    inverse: has plasma membrane part\n\n  part of:\n    is_a: overlaps\n    description: >-\n      holds between parts and wholes (material entities or processes)\n    in_subset:\n      - translator_minimal\n    inverse: has part\n    exact_mappings:\n      - BFO:0000050\n      - SEMMEDDB:PART_OF\n      - WIKIDATA_PROPERTY:P361\n      - FMA:part_of\n      - RXNORM:constitutes\n      - RXNORM:part_of\n    broad_mappings:\n       # To 'contain' is 'to have something inside or include something as a part'\n      - RO:0001018\n      - FMA:contained_in\n      - RXNORM:contained_in\n    narrow_mappings:\n      - BSPO:0001106\n      - BSPO:0001108\n      - BSPO:0001113\n      - BSPO:0001115\n      - UBERON_CORE:layer_part_of\n      - UBERON_CORE:subdivision_of\n      - UBERON_CORE:trunk_part_of\n      - CHEBI:is_substituent_group_from\n      - CPT:panel_element_of\n      - CPT:panel_element_of_possibly_included\n      - DRUGBANK:component_of\n      - FMA:constitutional_part_of\n      - FMA:member_of\n      - FMA:regional_part_of\n      - FMA:related_developmental_entity_of\n      - LOINC:component_of\n      - LOINC:has_supersystem\n      - LOINC:member_of\n      - LOINC:multipart_of\n      - MEDDRA:member_of\n      - MONDO:part_of_progression_of_disease\n      - NCIT:R82\n      - NCIT:R27\n      - NCIT:is_component_of_chemotherapy_regimen\n      - NDDF:ingredient_of\n      - RO:0002007\n      - RO:0002350\n      - RO:0002376\n      - RO:0002380\n      - RO:0002571\n      - RO:0002572\n      - RO:0002576\n      - RXNORM:ingredient_of\n      - RXNORM:ingredients_of\n      - RXNORM:precise_ingredient_of\n      - SNOMED:active_ingredient_of\n      - SNOMED:basis_of_strength_substance_of\n      - SNOMED:component_of\n      - SNOMED:direct_substance_of\n      - SNOMED:during\n      - SNOMED:focus_of\n      - SNOMED:has_dependent\n      - SNOMED:part_anatomy_structure_of\n      - SNOMED:precise_active_ingredient_of\n      - UBERON:subdivision_of\n      - UMLS:component_of\n      - UMLS:has_owning_affiliate\n      - UMLS:owning_subsection_of\n      - VANDF:ingredient_of\n\n  has input:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an input into the process\n    domain: biological process or activity\n    range: named thing\n    annotations:\n      canonical_predicate: true\n      opposite_of: has output\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002233\n      - SEMMEDDB:USES\n    narrow_mappings:\n      - LOINC:has_fragments_for_synonyms\n      - LOINC:has_system\n      - PathWhiz:has_left_element\n      - RO:0002590\n      - RO:0004009\n      - SNOMED:has_finding_method\n      - SNOMED:has_precondition\n      - SNOMED:has_specimen_source_identity\n      - SNOMED:has_specimen_substance\n      - SNOMED:uses_access_device\n      - SNOMED:uses_device\n      - SNOMED:uses_energy\n      - SNOMED:uses_substance\n\n  is input of:\n    is_a: participates in\n    domain: named thing\n    range: biological process or activity\n    inverse: has input\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002352\n\n  has output:\n    is_a: has participant\n    description: >-\n      holds between a process and a continuant, where the continuant is an output of the process\n    domain: biological process or activity\n    range: named thing\n    annotations:\n      canonical_predicate: true\n      opposite_of: has input\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002234\n    narrow_mappings:\n      - NCIT:R31\n      - OBI:0000299\n      - PathWhiz:has_right_element\n      - RO:0002296\n      - RO:0002297\n      - RO:0002298\n      - RO:0002299\n      - RO:0002588\n      - RO:0004008\n\n  is output of:\n    is_a: participates in\n    domain: named thing\n    range: biological process or activity\n    inverse: has output\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002353\n    narrow_mappings:\n      - RO:0002354\n\n  has participant:\n    is_a: related to at instance level\n    description: >-\n      holds between a process and a continuant, where the continuant is somehow involved in the process\n    domain: biological process or activity\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    close_mappings:\n      - WIKIDATA_PROPERTY:P2283\n    exact_mappings:\n      - RO:0000057\n      - RO:has_participant\n    narrow_mappings:\n      - BFO:0000167\n       # Several of the following RTX terms tagged as inverse to 'biolink:participates_in'\n      - LOINC:has_subject\n      - NCIT:process_involves_gene\n      - NBO-PROPERTY:has_participant\n      - PathWhiz:has_bound\n      - PathWhiz:has_compound\n      - PathWhiz:has_element_collection\n      - PathWhiz:has_enzyme\n      - OBI:0000293\n      - PathWhiz:has_nucleic_acid\n      - PathWhiz:has_protein\n      - PathWhiz:has_reaction\n      - RO:0002565\n      - RO:0004007\n      - RO:0004020\n      - RO:0004021\n      - SNOMED:has_indirect_device\n      - SNOMED:has_procedure_device\n      - SNOMED:has_recipient_category\n\n  catalyzes:\n    is_a: participates in\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - RO:0002327\n\n  has catalyst:\n    is_a: has participant\n    inverse: catalyzes\n\n  has substrate:\n    is_a: has participant\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n    annotations:\n      canonical_predicate: true\n\n  is substrate of:\n    is_a: participates in\n    inverse: has substrate\n    domain: chemical entity or gene or gene product\n    range: chemical entity or gene or gene product\n\n  participates in:\n    is_a: related to at instance level\n    description: >-\n      holds between a continuant and a process, where the continuant is somehow involved\n      in the process\n    range: biological process or activity\n    domain: occurrent\n    inverse: has participant\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0000056\n      - BFO:0000056\n    narrow_mappings:\n      - DRUGBANK:pathway\n      - HMDB:in_pathway\n      - LOINC:is_given_pharmaceutical_substance_for\n      - NCIT:R130\n      - NCIT:R37\n      - NCIT:R131\n      - NCIT:R51\n      - NCIT:R53\n      - OBI:0000295\n      - RO:0002216\n      - RO:0002505\n      - SNOMED:has_direct_device\n\n  actively involved in:\n    is_a: participates in\n    aliases: ['involved in']\n    description: >-\n      holds between a continuant and a process or function, where\n      the continuant actively contributes to part or all of\n      the process or function it realizes\n    domain: named thing\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002331\n    narrow_mappings:\n      - NBO-PROPERTY:by_means\n      - orphanet:317348\n      - orphanet:317349\n      - orphanet:327767\n      - RO:0002503\n\n  actively involves:\n    is_a: has participant\n    domain: biological process or activity\n    range: named thing\n    inverse: actively involved in\n    in_subset:\n      - translator_minimal\n\n  capable of:\n    is_a: actively involved in\n    description: >-\n      holds between a physical entity and process or function, where the\n      continuant alone has the ability to carry out the process or function.\n    domain: named thing\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002215\n    narrow_mappings:\n      - NCIT:R52\n      - RO:0002500\n\n  can be carried out by:\n    is_a: actively involves\n    inverse: capable of\n    domain: occurrent\n    range: named thing\n\n  enables:\n    is_a: participates in\n    description: >-\n      holds between a physical entity and a process, where the physical entity executes the process\n    domain: physical entity\n    range: biological process or activity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    inverse: enabled by\n    exact_mappings:\n      - RO:0002327\n\n  enabled by:\n    is_a: has participant\n    description: >-\n      holds between a process and a physical entity, where the physical entity executes the process\n    domain: biological process or activity\n    range: physical entity\n    in_subset:\n      - translator_minimal\n    inverse: enables\n    exact_mappings:\n      - RO:0002333\n    annotations:\n      opposite_of: prevented by\n\n  derives into:\n    is_a: related to at instance level\n    aliases: ['is normal cell origin of disease', 'may be normal cell origin of disease']\n    description: >-\n      holds between two distinct material entities, the old entity and\n      the new entity, in which the new entity begins to exist when\n      the old entity ceases to exist, and the new entity inherits\n      the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n    inverse: derives from\n    exact_mappings:\n      - RO:0001001\n      - SEMMEDDB:CONVERTS_TO\n       # RTX posted terms as inverse of 'biolink:derives_from'\n      - FMA:derives\n\n  derives from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    description: >-\n      holds between two distinct material entities, the new entity\n      and the old entity, in which the new entity begins to exist\n      when the old entity ceases to exist, and the new entity\n      inherits the significant portion of the matter of the old entity\n    in_subset:\n      - translator_minimal\n      - samples\n    inverse: derives into\n    exact_mappings:\n      - RO:0001000\n      - FMA:derives_from\n      - DOID-PROPERTY:derives_from\n    narrow_mappings:\n      - CHEBI:has_functional_parent\n      - SNOMED:has_specimen_source_topography\n\n  is metabolite of:\n    is_a: derives from\n    description: >-\n      holds between two molecular entities in which the first one is derived\n      from the second one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    in_subset:\n      - translator_minimal\n    inverse: has metabolite\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  has metabolite:\n    is_a: derives into\n    description: >-\n      holds between two molecular entities in which the second one is derived from the first\n      one as a product of metabolism\n    domain: molecular entity\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    comments:\n      - The CHEBI ID represents a role rather than a predicate\n    exact_mappings:\n      - CHEBI:25212\n\n  food component of:\n    is_a: part of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has food component\n\n  has food component:\n    is_a: has part\n    description: >-\n      holds between food and one or more chemical entities composing it,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  nutrient of:\n    is_a: food component of\n    description: >-\n      holds between a one or more chemical entities present in food,\n      irrespective of nutritional value (i.e. could also be a contaminant or additive)\n    domain: chemical entity\n    range: chemical entity\n    in_subset:\n      - translator_minimal\n    inverse: has nutrient\n\n  has nutrient:\n    is_a: has food component\n    description: >-\n      one or more nutrients which are growth factors for a living organism\n    domain: chemical entity\n    range: chemical entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA:Q181394\n\n  is active ingredient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug, in which the former\n      is a part of the latter, and is a biologically active component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has active ingredient\n    mappings:\n      - RO:0002249\n\n  has active ingredient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entity in which the latter\n      is a part of the former, and is a biologically active component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: is excipient of\n    in_subset:\n      - translator_minimal\n    inverse: is active ingredient of\n    mappings:\n      - RO:0002248\n\n  is excipient of:\n    is_a: part of\n    description: >-\n      holds between a molecular entity and a drug in which the former is\n      a part of the latter, and is a biologically inactive component\n    domain: molecular entity\n    range: drug\n    in_subset:\n      - translator_minimal\n    inverse: has excipient\n    mappings:\n      - WIKIDATA:Q902638\n\n  has excipient:\n    is_a: has part\n    description: >-\n      holds between a drug and a molecular entities in which the latter\n      is a part of the former, and is a biologically inactive component\n    domain: drug\n    range: molecular entity\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    mappings:\n      - WIKIDATA:Q902638\n\n  manifestation of:\n    is_a: related to at instance level\n    description: >-\n      that part of a phenomenon which is directly observable or\n      visibly expressed, or which gives evidence to the underlying\n      process; used in SemMedDB for linking things like dysfunctions\n      and processes to some disease or syndrome\n    range: disease\n    annotations:\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - SEMMEDDB:MANIFESTATION_OF\n      - OMIM:manifestation_of\n    broad_mappings:\n       # Wikidata's definition is slightly broader: \"inherent and characteristic embodiment of a given concept\"\n      - WIKIDATA_PROPERTY:P1557\n    narrow_mappings:\n      - SNOMED:has_definitional_manifestation\n\n  has manifestation:\n    is_a: related to at instance level\n    domain: disease\n    inverse: manifestation of\n\n  mode of inheritance of:\n    is_a: manifestation of\n    domain: genetic inheritance\n    range: disease or phenotypic feature\n    inverse: has mode of inheritance\n\n  has mode of inheritance:\n    is_a: has manifestation\n    description: >-\n      Relates a disease or phenotypic feature to its observed genetic segregation and assumed\n      associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).\n    domain: disease or phenotypic feature\n    range: genetic inheritance\n    annotations:\n       # This canonical order reverses that of its parent 'has manifestation' class\n       # but seems a more natural direction in the pertinent edge relationships.\n      canonical_predicate: true\n    in_subset:\n      - translator_minimal\n\n  produces:\n    is_a: related to at instance level\n    description: >-\n      holds between a material entity and a product that is generated\n      through the intentional actions or functioning of the material entity\n    in_subset:\n      - translator_minimal\n    annotations:\n      canonical_predicate: true\n    related_mappings:\n      - GOREL:0001010\n    exact_mappings:\n      - RO:0003000\n      - WIKIDATA_PROPERTY:P1056\n      - SEMMEDDB:PRODUCES\n    narrow_mappings:\n      - NCIT:R29\n      - SNOMED:has_process_output\n      - SNOMED:specimen_procedure_of\n\n  produced by:\n    is_a: related to at instance level\n    inverse: produces\n    exact_mappings:\n      - RO:0003001\n\n  consumes:\n    is_a: has input\n    domain: named thing\n    range: named thing\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - RO:0004009\n\n  consumed by:\n    is_a: is input of\n    inverse: consumes\n    domain: named thing\n    range: named thing\n\n  temporally related to:\n    is_a: related to at instance level\n    description: >-\n      holds between two entities with a temporal relationship\n    domain: occurrent\n    range: occurrent\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SNOMED:temporally_related_to\n    narrow_mappings:\n       # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here\n      - RO:0002082\n      - RO:0002083\n      - RO:0002092\n      - RO:0002093\n      - RO:0002223\n      - RO:0002224\n      - RO:0002229\n      - RO:0002230\n      - RO:0002488\n      - RO:0002489\n      - RO:0002492\n      - RO:0002493\n      - RO:0002496\n      - RO:0002497\n\n  precedes:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where one completes before the other begins\n    domain: occurrent\n    range: occurrent\n    annotations:\n      canonical_predicate: true\n    inverse: preceded by\n    in_subset:\n      - translator_minimal\n    close_mappings:\n       # the subject of these terms is a material entity, not a process,\n       # but affects a process which causes a second process to occur\n      - RO:0002263\n      - RO:0002264\n    exact_mappings:\n      - BFO:0000063\n      - SEMMEDDB:PRECEDES\n      - SNOMED:occurs_before\n    broad_mappings:\n       # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature\n      - WIKIDATA_PROPERTY:P156\n    narrow_mappings:\n      - FMA:transforms_into\n      - RO:0002090\n      - RO:0002411\n      - RO:0002412\n\n  preceded by:\n    is_a: temporally related to\n    description: >-\n      holds between two processes, where the other is completed before the one begins\n    domain: occurrent\n    range: occurrent\n    inverse: precedes\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - BFO:0000062\n    broad_mappings:\n       # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'?\n      - GENEPIO:0001739\n    narrow_mappings:\n       # RTX contributed mapping was given as the inverse of 'biolink:precedes'\n      - FMA:transforms_from\n      - RO:0002087\n      - RO:0002285\n\n  has variant part:\n    is_a: has part\n    description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000382\n\n  variant part of:\n    is_a: part of\n    inverse: has variant part\n\n  related condition:\n    is_a: related to at instance level\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - GENO:0000790\n\n   ## Predicates relating variants to genes\n\n  is sequence variant of:\n    is_a: related to at instance level\n    aliases: ['gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product']\n    description: holds between a sequence variant and a nucleic acid entity\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - WIKIDATA:P3433\n\n  has sequence variant:\n    is_a: related to at instance level\n    inverse: is sequence variant of\n    domain: genomic entity\n    range: sequence variant\n\n  is missense variant of:\n    is_a: is sequence variant of\n    description: holds between a gene  and a sequence variant, such the sequence variant\n      results in a different amino acid sequence but where the length is preserved.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001583\n\n  has missense variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is missense variant of\n\n  is synonymous variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the coding sequence of the gene, but results in the same amino acid sequence\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001819\n\n  has synonymous variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is synonymous variant of\n    aliases: ['stop gained']\n\n  is nonsense variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      results in a premature stop codon\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    broad_mappings:\n       # Term definition broader than nonsense codon: A sequence variant whereby\n       # the gene product has diminished or abolished function.\n      - SO:0002054\n\n  has nonsense variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is nonsense variant of\n\n  is frameshift variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      causes a disruption of the translational reading frame, because the number of\n      nucleotides inserted or deleted is not a multiple of three.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001589\n    aliases: ['frameshift variant', 'start lost', 'stop lost']\n\n  has frameshift variant:\n    is_a: has sequence variant\n    inverse: is frameshift variant of\n    domain: genomic entity\n    range: sequence variant\n    aliases: ['splice region variant', 'splice acceptor variant', 'splice donor variant']\n\n  is splice site variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, such the sequence variant\n      is in the canonical splice site of one of the gene's exons.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - SO:0001629\n\n\n  has splice site variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is splice site variant of\n    aliases: ['downstream gene variant', 'upstream gene variant']\n\n  is nearby variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene sequence that the variant\n      is genomically close to.\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n\n  has nearby variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is nearby variant of\n    aliases: ['intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant']\n\n  is non coding variant of:\n    is_a: is sequence variant of\n    description: holds between a sequence variant and a gene, where the variant does\n      not affect the coding sequence\n    domain: sequence variant\n    range: genomic entity\n    annotations:\n      canonical_predicate: true\n\n  has non coding variant:\n    is_a: has sequence variant\n    domain: genomic entity\n    range: sequence variant\n    inverse: is non coding variant of\n\n   # relating disease to process\n\n  disease has basis in:\n    description: A relation that holds between a disease and an entity where the state\n      of the entity has contribution to the disease.\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n       # These two MONDO terms seem more particular than the predicate\n      - MONDO:disease_has_basis_in_development_of\n      - MONDO:disease_has_basis_in_accumulation_of\n\n  occurs in disease:\n    is_a: related to at instance level\n    inverse: disease has basis in\n\n\n  has adverse event:\n    is_a: affects\n    aliases: ['adverse effect']\n    description: >-\n      An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment\n      with a therapeutic agent. Adverse events may be caused by something\n      other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or\n      diseases temporally associated with the treatment, whether or not considered related to the treatment.\n      Adverse events are unintended effects that occur when a medication is administered correctly.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n\n  adverse event of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has adverse event\n\n  has side effect:\n    aliases: ['adverse drug reaction']\n    is_a: affects\n    description: >-\n      An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment.\n      Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of\n      the medication.\n    notes: >-\n      Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative.\n      Aeolus, Sider are both resources that provide side effects.\n    domain: chemical or drug or treatment\n    range: disease or phenotypic feature\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C2861  # side effect\n\n  is side effect of:\n    is_a: affected by\n    domain: disease or phenotypic feature\n    range: chemical or drug or treatment\n    inverse: has side effect\n\n  contraindicated in:\n    is_a: related to at instance level\n    description: >-\n      Holds between a substance, procedure, or activity and a medical condition or circumstance, where an authority\n      has established that the substance, procedure, or activity should not be applied as an intervention in patients\n      with the condition or circumstance because it can result in detrimental outcomes.\n    notes: >-\n      This predicate relates the intervention with a specific disease, phenotype, or other medical circumstance that\n      puts patients at high risk for detrimental outcomes.  This may be a different condition from the one that the\n      drug would be used to treat (e.g. pseudoephedrine is contraindicated in people with high-blood pressure as\n      a treatment for nasal congestion), a biological state (e.g. isotretinoin is contraindicated in people who\n      are pregnant as a treatment for acne), or being on a different medication (e.g. aspirin is contraindicated\n      in people taking warfarin as a preventative treatment for stroke).\n    domain: chemical or drug or treatment\n    range: biological entity\n    annotations:\n      canonical_predicate: true\n      opposite_of: treats\n    exact_mappings:\n      - NCIT:C37933\n\n  chemical entity or drug or treatment:\n    description: >-\n      A union of chemical entities and children, and drug or treatment.\n    mixin: true\n\n  has contraindication:\n    is_a: related to at instance level\n    domain: biological entity\n    range: chemical or drug or treatment\n    inverse: contraindicated in\n\n   # The remaining new slots are here because we ran across them somewhere and\n   # they didn't seem to map well to anything else.\n\n  has not completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of,\n      but has not completed\n    exact_mappings:\n      - CL:has_not_completed\n    annotations:\n      opposite_of: has completed\n      canonical_predicate: true\n\n  not completed by:\n    is_a: related to at instance level\n    inverse: has not completed\n\n  has completed:\n    is_a: related to at instance level\n    description: holds between an entity and a process that the entity is capable of\n      and has completed\n    annotations:\n      canonical_predicate: true\n      opposite_of: has not completed\n    exact_mappings:\n      - CL:has_completed\n\n  completed by:\n    is_a: related to at instance level\n    inverse: has completed\n\n\n  in linkage disequilibrium with:\n    is_a: related to at instance level\n    description: holds between two sequence variants, the presence of which are correlated\n      in a population\n    symmetric: true\n    annotations:\n      canonical_predicate: true\n    exact_mappings:\n      - NCIT:C16798\n\n  has increased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has decreased amount\n    narrow_mappings:\n      - CL:has_high_plasma_membrane_amount\n\n  increased amount of:\n    is_a: related to at instance level\n    inverse: has increased amount\n\n  has decreased amount:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has increased amount\n    narrow_mappings:\n      - CL:has_low_plasma_membrane_amount\n\n  decreased amount in:\n    is_a: related to at instance level\n    inverse: has decreased amount\n\n  lacks part:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n      opposite_of: has part\n    exact_mappings:\n      - CL:lacks_part\n      - PR:lacks_part\n    narrow_mappings:\n      - CL:lacks_plasma_membrane_part\n\n  missing from:\n    is_a: related to at instance level\n    inverse: lacks part\n\n  develops from:\n    is_a: related to at instance level\n    annotations:\n      canonical_predicate: true\n    close_mappings:\n       # RTX mapping seems to be inverse of 'biolink:develops_from'\n      - RO:0002203\n      - FMA:develops_into\n    exact_mappings:\n      - BTO:develops_from\n      - DDANAT:develops_from\n      - FMA:develops_from\n      - RO:0002202\n    narrow_mappings:\n      - RO:0002207\n      - RO:0002225  # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y\n      - RO:0002226  # x develops_in y if x is located in y whilst x is developing\n\n  develops into:\n    is_a: related to at instance level\n    inverse: develops from\n\n  in taxon:\n    aliases: ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source']\n    is_a: related to at instance level\n    domain: thing with taxon\n    range: organism taxon\n    annotations:\n      canonical_predicate: true\n    description: >-\n      connects an entity to its taxonomic classification. Only certain kinds\n      of entities can be taxonomically classified; see 'thing with taxon'\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - RO:0002162\n      - WIKIDATA_PROPERTY:P703\n    narrow_mappings:\n      - RO:0002160\n\n  in taxon label:\n    is_a: node property\n    domain: thing with taxon\n    range: label type\n    description: >-\n      The human readable scientific name for the taxon of the entity.\n    in_subset:\n      - translator_minimal\n    exact_mappings:\n      - WIKIDATA_PROPERTY:P225\n    annotations:\n      denormalized: true\n\n  taxon of:\n    is_a: related to at instance level\n    inverse: in taxon\n    domain: organism taxon\n    range: thing with taxon\n\n  has molecular consequence:\n    is_a: related to at instance level\n    aliases: ['allele has activity']\n    description: >-\n      connects a sequence variant to a class describing the molecular\n      consequence. E.g.  SO:0001583\n    range: ontology class\n    annotations:\n      canonical_predicate: true\n    narrow_mappings:\n      - NCIT:allele_has_activity\n\n  is molecular consequence of:\n    is_a: related to at instance level\n    domain: ontology class\n    inverse: has molecular consequence\n\n   ## --------------------\n   ## ASSOCIATION SLOTS\n   ## --------------------\n\n  association slot:\n    abstract: true\n    domain: association\n    aliases: ['edge property', 'statement property', 'node qualifier', 'edge qualifier', 'statement qualifier']\n    description: >-\n      any slot that relates an association to another entity\n\n  qualifier:\n    is_a: association slot\n    description: >-\n      grouping slot for all qualifiers on an edge.  useful for testing compliance with association classes\n    in_subset:\n      - translator_minimal\n\n  original subject:\n    is_a: association slot\n    description: >-\n      used to hold the original subject of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original object:\n    is_a: association slot\n    description: >-\n      used to hold the original object of a relation (or predicate) that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n\n  original predicate:\n    aliases: ['original relation', 'relation']\n    is_a: association slot\n    description: >-\n      used to hold the original relation/predicate that an external knowledge\n      source uses before transformation to match the biolink-model specification.\n    id_prefixes:\n      - RO\n      - BSPO\n      - SIO\n    domain: association\n    range: uriorcurie\n\n  subject closure:\n    is_a: association slot\n    description: >-\n      Used to hold the subject closure of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    annotations:\n      denormalized: true\n\n  object closure:\n    is_a: association slot\n    description: >-\n      Used to hold the object closure of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    examples:\n      - value: [\"MONDO:0000167\", \"MONDO:0005395\"]\n        description: >-\n          The object closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          diseases that are ancestors of 'breast cancer' in the\n          MONDO ontology.  Note: typically the \"subclass of\" and \"part of\"\n          relations are used to construct the closure, but other relations\n          may be used as well.\n    annotations:\n      denormalized: true\n\n  subject category:\n    is_a: association slot\n    description: >-\n      Used to hold the biolink class/category of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: ontology class\n    examples:\n      - value: \"biolink:Gene\"\n        description: >-\n          The subject category of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is 'biolink:Gene'.\n    annotations:\n      denormalized: true\n\n  object category:\n    is_a: association slot\n    description: >-\n      Used to hold the biolink class/category of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: ontology class\n    examples:\n      - value: \"biolink:Disease\"\n        description: >-\n            The object category of the association between the gene\n            'BRCA1' and the disease 'breast cancer' is 'biolink:Disease'.\n    annotations:\n      denormalized: true\n\n  subject category closure:\n    is_a: association slot\n    description: >-\n      Used to hold the subject category closure of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: ontology class\n    examples:\n      - value: ['biolink:Gene\", \"biolink:NamedThing']\n        description: >-\n          The subject category closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          biolink classes that are ancestors of 'biolink:Gene' in the\n          biolink model.  Note: typically the \"subclass of\" and \"part of\"\n          relations are used to construct the closure, but other relations\n          may be used as well.\n    annotations:\n      denormalized: true\n\n  object category closure:\n    is_a: association slot\n    description: >-\n      Used to hold the object category closure of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: ontology class\n    examples:\n      - value: ['biolink:Disease\", \"biolink:NamedThing']\n        description: >-\n          The object category closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          biolink classes that are ancestors of 'biolink:Disease' in the\n          biolink model.  Note: typically the \"subclass of\" and \"part of\"\n          relations are used to construct the closure, but other relations\n          may be used as well.\n    annotations:\n      denormalized: true\n\n  subject label closure:\n    is_a: association slot\n    description: >-\n      Used to hold the subject label closure of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: string\n    examples:\n      - value: [\"BRACA1\"]\n        description: >-\n          The subject label closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          labels that are ancestors of 'BRCA1' in the\n          biolink model.\n    annotations:\n      denormalized: true\n\n  object label closure:\n    is_a: association slot\n    description: >-\n      Used to hold the object label closure of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: true\n    domain: association\n    range: string\n    examples:\n      - value: \"breast cancer\"\n        description: >-\n          The object label closure of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is the set of all\n          labels that are ancestors of 'breast cancer' in the\n          biolink model.\n      - value: \"cancer\"\n    annotations:\n      denormalized: true\n\n  subject namespace:\n    aliases: [\"subject prefix\"]\n    is_a: association slot\n    description: >-\n      Used to hold the subject namespace of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: string\n    examples:\n      - value: \"NCBIGene\"\n        description: >-\n          The subject namespace of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is 'NCBIGene'.\n    annotations:\n      denormalized: true\n\n  object namespace:\n    aliases: [\"object prefix\"]\n    is_a: association slot\n    description: >-\n      Used to hold the object namespace of an association. This is a denormalized\n      field used primarily in the SQL serialization of a knowledge graph via KGX.\n    multivalued: false\n    domain: association\n    range: string\n    examples:\n      - value: \"MONDO\"\n        description: >-\n          The object namespace of the association between the gene\n          'BRCA1' and the disease 'breast cancer' is 'MONDO'.\n    annotations:\n      denormalized: true\n\n  subject:\n    is_a: association slot\n    local_names:\n      ga4gh: annotation subject\n      neo4j: node with outgoing relationship\n    description: >-\n      connects an association to the subject of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    domain: association\n    range: named thing\n    slot_uri: rdf:subject\n    exact_mappings:\n      - owl:annotatedSource\n      - OBAN:association_has_subject\n\n  object:\n    is_a: association slot\n    description: >-\n      connects an association to the object of the association.\n      For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.\n    required: true\n    domain: association\n    range: named thing\n    local_names:\n      ga4gh: descriptor\n      neo4j: node with incoming relationship\n    slot_uri: rdf:object\n    exact_mappings:\n      - owl:annotatedTarget\n      - OBAN:association_has_object\n\n  predicate:\n    is_a: association slot\n    description: >-\n      A high-level grouping for the relationship type. AKA minimal predicate.\n      This is analogous to category for nodes.\n    domain: association\n    notes: >-\n      Has a value from the Biolink related_to hierarchy. In RDF,  this\n      corresponds to rdf:predicate and in Neo4j this corresponds to the\n      relationship type. The convention is for an edge label in snake_case\n      form. For example, biolink:related_to, biolink:causes, biolink:treats\n    range: predicate type\n    required: true\n    local_names:\n      ga4gh: annotation predicate\n      translator: predicate\n    slot_uri: rdf:predicate\n    exact_mappings:\n      - owl:annotatedProperty\n      - OBAN:association_has_predicate\n\n  logical interpretation:\n    is_a: association slot\n    required: false\n    domain: association\n    range: LogicalInterpretationEnum\n    exact_mappings:\n      - os:LogicalInterpretation\n\n  relation:\n    deprecated: true\n\n  negated:\n    is_a: association slot\n    range: boolean\n    description: >-\n      if set to true, then the association is negated i.e. is not true\n\n  has confidence level:\n    is_a: association slot\n    range: confidence level\n    description: >-\n      connects an association to a qualitative term denoting the level of confidence\n\n  has evidence:\n    is_a: association slot\n    range: evidence type\n    description: >-\n      connects an association to an instance of supporting evidence\n    exact_mappings:\n      - RO:0002558\n    multivalued: true\n\n  has supporting study result:\n    is_a: association slot\n    description: >-\n      connects an association to an instance of supporting study result\n\n  log odds ratio:\n    is_a: association slot\n    description: >-\n      The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the\n      odds of event Y occurring in a non-exposed group.\n    range: float\n\n  log odds ratio 95 ci:\n    is_a: association slot\n    description: >-\n      The ninety-five percent confidence range in which the true log odds ratio for the sample population falls.\n    range: float\n\n  total sample size:\n    is_a: dataset count\n    description: >-\n      The total number of patients or participants within a sample population.\n    range: integer\n\n\n  mechanism of action:\n    is_a: association slot\n    range: boolean\n    description: >-\n      a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes\n      the mechanism of action for a result.\n    exact_mappings:\n      - NCIT:C54680\n      - MI:2044\n      - LOINC:MTHU019741\n\n  knowledge source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which the knowledge expressed in an Association was\n      retrieved, directly or indirectly. This can be any resource through which the\n      knowledge passed on its way to its currently serialized form. In practice,\n      implementers should use one of the more specific subtypes of this generic property.\n    close_mappings:\n      - pav:providedBy\n\n  provided by:\n    is_a: node property\n    description: >-\n      The value in this node property represents the knowledge provider that created or assembled the\n      node and all of its attributes.  Used internally to represent how a particular node made its way into a\n      knowledge provider or graph.\n    multivalued: true\n\n  primary knowledge source:\n    is_a: knowledge source\n    description: >-\n      The most upstream source of the knowledge expressed in an Association that an\n      implementer can identify.  Performing a rigorous analysis of upstream data providers is expected; every effort\n      is made to catalog the most upstream source of data in this property.  Only one data source should be declared\n      primary in any association.  \"aggregator knowledge source\" can be used to capture non-primary sources.\n    notes: >-\n      For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then\n      incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to\n      the NCATS ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   MolePro  --retrieved_from--> ChEMBL --retrieved_from-->  ClinicalTrials.gov\n      The \"primary knowledge source\" for this edge is \"infores:clinical-trials-gov\".  \"infores:chembl\" and \"infores:molecular_data_provider\"\n      are listed in the \"aggregator knowledge source\" property.\n    multivalued: false\n\n  aggregator knowledge source:\n    is_a: knowledge source\n    description: >-\n      An intermediate aggregator resource from which knowledge expressed in an Association was\n      retrieved downstream of the original source, on its path to its current serialized form.\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP,\n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse,\n      the Edge is passed to the Ranking Agent’s ARAGORN ARA,\n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of\n      data from which the knowledge was derived.\n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data source:\n    is_a: association slot\n    description: >-\n      An Information Resource from which data was retrieved and subsequently used as\n      evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    multivalued: true\n    notes: >-\n      For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP,\n      through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse,\n      the Edge is passed to the Ranking Agent’s ARAGORN ARA,\n      and then on to the ARS. The retrieval path for this Edge is as follows:\n      ARS--retrieved_from-->  ARAGORN  --retrieved_from-->   ICEES --supporting_data_from-->  UNC Data Warehouse\n      This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of\n      data from which the knowledge was derived.\n      The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP-\n      generated knowledge is \"infores:unc-cdw-health.\"  The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"\n\n  supporting data set:\n    is_a: association slot\n    description: >-\n      A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through\n      computation on, reasoning or inference over the retrieved data).\n    multivalued: true\n\n  chi squared statistic:\n    is_a: association slot\n    range: float\n    description: >-\n      represents the chi-squared statistic computed from observations\n    exact_mappings:\n      - STATO:0000030\n\n  p value:\n    aliases: ['unadjusted p value']\n    is_a: association slot\n    range: float\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    exact_mappings:\n      - OBI:0000175\n      - NCIT:C44185\n      - EDAM-DATA:1669\n\n  evidence count:\n    is_a: association slot\n    description: >-\n      The number of evidence instances that are connected to an association.\n    range: integer\n\n  dataset count:\n    is_a: association slot\n    description: >-\n      The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort.\n    range: integer\n    examples:\n      - value: 100000\n\n  concept count subject:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the subject slot of an association.\n    range: integer\n    examples:\n      - value: 489\n\n  concept count object:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      the concept in the object slot of an association.\n    range: integer\n\n  concept pair count:\n    is_a: association slot\n    description: >-\n      The number of instances in a dataset/cohort whose records contain\n      both the subject and object concept of an association.\n    range: integer\n    examples:\n      - value: 1731\n\n  expected count:\n    is_a: association slot\n    description: >-\n      The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and\n      object concept of an association if the subject and object concepts are independent.\n\n  relative frequency subject:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in\n      records within a dataset/cohort, relative to the frequency at which the subject\n      concept appears in these same records.\n    range: float\n    examples:\n      - value: 0.01840490798\n\n  relative frequency object:\n    is_a: association slot\n    description: >-\n      The frequency at which subject and object concepts co-occur in\n      records within a dataset/cohort, relative to the frequency at which the object\n      concept appears in these same records.\n    range: string\n\n  relative frequency subject confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_subject calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  relative frequency object confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the relative_frequency_object calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: string\n\n  adjusted p value:\n    is_a: p value\n    description: >-\n      The adjusted p-value is the probability of obtaining test results\n      at least as extreme as the results actually observed, under the assumption that\n      the null hypothesis is correct, adjusted for multiple comparisons.\n      P is always italicized and capitalized. The actual P value* should be expressed (P=. 04)\n      rather than expressing a statement of inequality (P<. 05), unless P<.\n    range: float\n\n  bonferonni adjusted p value:\n    is_a: adjusted p value\n    description: >-\n      The Bonferroni correction is an adjustment made to P values when several dependent or independent\n      statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni\n      correction, divide the critical P value (α) by the number of comparisons being made.  P is always italicized and\n      capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality\n      (P<. 05), unless P<.\n    range: float\n    examples:\n      - value: 0.018\n\n  supporting text:\n    is_a: association slot\n    description: The segment of text from a document that supports the mined assertion.\n    multivalued: true\n    range: string\n    examples:\n      - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer.\n\n  supporting documents:\n    deprecated: true\n    is_a: association slot\n    description: >-\n      One or more referenceable documents that report the statement expressed in an Association, or provide\n      information used as evidence supporting this statement.\n    range: uriorcurie\n    multivalued: true\n    examples:\n      - value: PMID:12345678\n\n  subject location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the subject concept of the extracted assertion.\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  object location in text:\n    is_a: association slot\n    description: >-\n      Character offsets for the text span(s) in the supporting text corresponding\n      to the object concept of the extracted assertion\n    range: integer\n    examples:\n      - value: 15\n    multivalued: true\n\n  extraction confidence score:\n    is_a: association slot\n    description: >-\n      A quantitative confidence value that represents the probability of\n      obtaining a result at least as extreme as that actually obtained,\n      assuming that the actual value was the result of chance alone.\n    range: integer\n    examples:\n      - value: 15\n\n  supporting document type:\n    is_a: association slot\n    description: >-\n      The document type (e.g., Journal Article, Case Study, Preprint) for\n      the supporting document used in a Text Mining Result.\n    range: string\n    examples:\n      - value: Journal Article\n\n  supporting document year:\n    is_a: association slot\n    description: >-\n      The document year (typically the publication year) for the supporting\n      document used in a Text Mining Result.\n    range: integer\n    examples:\n      - value: 1999\n\n  supporting text section type:\n    is_a: association slot\n    description: >-\n      The section of the supporting text of a Text Mining Result within\n      the supporting document. This is in the form of the name of the document section\n      (e.g., Abstract, Introduction) that contains the supporting text.\n    range: string\n    examples:\n      - value: Introduction\n\n  ln ratio:\n    is_a: association slot\n    description: the natural log of the ratio of co-occurrence to expected\n    range: float\n    examples:\n      - value: 2.922827136\n\n  ln ratio confidence interval:\n    is_a: association slot\n    description: >-\n      The 99% confidence interval for the ln_ratio calculation\n      (i.e. the range of values within which the true value has a 99% chance of falling)\n    range: float\n    examples:\n      - value: 2.922827136\n\n  interacting molecules category:\n    is_a: association slot\n    range: ontology class\n    exact_mappings:\n      - MI:1046\n    values_from:\n      - MI\n    examples:\n      - value: MI:1048\n        description: smallmolecule-protein\n\n  expression site:\n    description: >-\n      location in which gene or protein expression takes place.\n      May be cell, tissue, or organ.\n    is_a: association slot\n    range: anatomical entity\n    examples:\n      - value: UBERON:0002037\n        description: cerebellum\n\n  phenotypic state:\n    description: >-\n      in experiments (e.g. gene expression) assaying diseased or unhealthy\n      tissue, the phenotypic state can be put here, e.g. MONDO ID.\n      For healthy tissues, use XXX.\n    is_a: association slot\n    range: disease or phenotypic feature\n\n\n  publications:\n    aliases: ['supporting publications', 'supporting documents']\n    description: >-\n      One or more publications that report the statement expressed in an\n      Association, or provide information used as evidence supporting this statement.\n    comments: >-\n        The notion of a ‘Publication’ is considered broadly to include any\n        document made available for public consumption. It covers journal issues,\n        individual articles, and books - and also things like article pre-prints,\n        white papers, patents, drug labels, web pages, protocol documents, etc.\n    is_a: association slot\n    multivalued: true\n    range: publication\n\n  associated environmental context:\n    is_a: association slot\n    description: >-\n      An attribute that can be applied to an association where the association holds between two entities\n      located or occurring in a particular environment. For example, two microbial taxa may interact in the context of\n      a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure.\n       # TODO: add examples of values for this property.\n\n  sequence localization attribute:\n    is_a: association slot\n    domain: genomic sequence localization\n    description: >-\n      An attribute that can be applied to a genome sequence localization edge. These edges\n      connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used\n      to ascribe specific positional information and other metadata to the localization. In pragmatic terms\n      this can be thought of as columns in a GFF3 line.\n\n  interbase coordinate:\n    is_a: sequence localization attribute\n    aliases: ['zero-based', 'half-open', 'space-based']\n    description: >-\n      A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1.\n      This is applied to a sequence localization edge.\n    range: integer\n\n  start interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 0).\n    close_mappings:\n      - faldo:begin\n    annotations:\n      opposite_of: end interbase coordinate\n\n  end interbase coordinate:\n    is_a: interbase coordinate\n    description: >-\n      The position at which the subject nucleic acid entity ends\n      on the chromosome or other entity to which it is located on.\n    close_mappings:\n      - faldo:end\n    annotations:\n      opposite_of: start interbase coordinate\n\n  start coordinate:\n    is_a: base coordinate\n    aliases: ['start']\n    description: >-\n      The position at which the subject genomic entity starts\n      on the chromosome or other entity to which it is located on.\n      (ie: the start of the sequence being referenced is 1).\n    exact_mappings:\n      - gff3:start\n    close_mappings:\n      - faldo:begin\n\n  end coordinate:\n    is_a: base coordinate\n    aliases: ['end']\n    description: >-\n      The position at which the subject genomic entity ends\n      on the chromosome or other entity to which it is located on.\n    exact_mappings:\n      - gff3:end\n    close_mappings:\n      - faldo:end\n\n  genome build:\n    is_a: sequence localization attribute\n    description: >-\n      The version of the genome on which a feature is located.\n      For example, GRCh38 for Homo sapiens.\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  strand:\n    is_a: sequence localization attribute\n    description: >-\n      The strand on which a feature is located. Has a value of '+'\n      (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).\n    range: StrandEnum\n    exact_mappings:\n      - gff3:strand\n\n  phase:\n    is_a: sequence localization attribute\n    domain: coding sequence\n    description: >-\n      The phase for a coding sequence entity. For example, phase of a\n      CDS as represented in a GFF3 with a value of 0, 1 or 2.\n    range: PhaseEnum\n    exact_mappings:\n      - gff3:phase\n\n  clinical approval status:\n    is_a: association slot\n    description: >-\n    range: ClinicalApprovalStatusEnum\n\n  max research phase:\n    is_a: association slot\n    range: MaxResearchPhaseEnum\n\n  supporting study metadata:\n    is_a: association slot\n    description: >-\n      Information about a study used to generate information used as evidence to support the knowledge expressed in an\n      Association. In practice, data creators should use one of the more specific subtypes of this property.\n    abstract: true\n\n  supporting study method type:\n    is_a: supporting study metadata\n    description: >-\n      A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of\n      experimental assay, or statistical calculation, or computational analysis).\n    range: uriorcurie\n\n  supporting study method description:\n    is_a: supporting study metadata\n    description: >-\n      A uri or curie pointing to information about the methodology used to generate data supporting an Association.\n    range: uriorcurie\n\n  supporting study size:\n    is_a: supporting study metadata\n    description: >-\n      The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a\n      clinical study).\n    range: integer\n\n  supporting study cohort:\n    is_a: supporting study metadata\n    description: >-\n      A description of a study population/cohort that was interrogated to provide evidence for the association\n      (e.g. the inclusion and exclusion criteria).\n    range: string\n\n  supporting study date range:\n    is_a: supporting study metadata\n    description: >-\n      The date range over which data was collected in a study that provided evidence for an Association.\n    range: string\n\n  supporting study context:\n    is_a: supporting study metadata\n    description: >-\n      A term or terms describing the experimental setting/context in which evidence supporting the Association was\n      generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue\n      type, disease, etc.).\n    range: string\n\n  knowledge level:\n    aliases: ['knowledge type']\n    is_a: association slot\n    description: >-\n      Describes the level of knowledge expressed in a statement, based on the\n      reasoning or analysis methods used to generate the statement, or the\n      scope or specificity of what the statement expresses to be true.\n    notes: >-\n      The notion of a 'level' of knowledge can in one sense relate to the strength \n      of a statement - i.e. how confident we are that it says something true about\n      our domain of discourse. Here, we can generally consider Assertions to be \n      stronger than Entailments to be stronger than Predictions. \n      But in another sense, 'level' of knowledge can refer to the scope or specificity of\n      what a statement expresses - on a spectrum from context-specific results of a data\n      analysis, to generalized assertions of knowledge or fact. Here, Statistical \n      Associations and  Observations represent more foundational statements that are only \n      slightly removed from the data on which they are based (the former reporting the \n      direct results of  an analysis in terms of correlations between variables in the data,\n      and the latter describing phenomena that were observed/reported to have occurred).\n    domain: association\n    range: KnowledgeLevelEnum\n    multivalued: false\n    required: true\n    ifabsent: string(not_provided)\n    examples:\n      - value: knowledge_assertion\n      - value: prediction\n      - value: statistical_association\n\n  agent type:\n    is_a: association slot\n    description: >-\n        Describes the high-level category of agent who originally generated a \n        statement of knowledge or other type of information.\n    notes: >-\n        Note that this property indicates the type of agent who produced a \n        final statement of knowledge, which is often different from the \n        agent oragents who produced information used as evidence to \n        support generation of this knowledge. For example, if a human curator\n        concludes that a particular gene variant causes a medical condition -\n        based on their interpretation of information produced by computational \n        modeling tools, automated data analysis pipelines, and robotic laboratory\n        assay systems - the agent_type for this statement is 'manual agent' - \n        despite all of the evidence being created by automated agents. But if any\n        of these systems is programmed to generate knowledge statements \n        directly and without human assistance, the statement would be attributed \n        to an 'automated_agent'.\n    domain: association\n    range: AgentTypeEnum\n    multivalued: false\n    required: true\n    ifabsent: string(not_provided)\n    examples:\n      - value: manual_agent\n      - value: automated_agent\n      - value: computational_model\n      - value: text_mining_agent\n\nclasses:\n\n  mapping collection:\n    description: >-\n      A collection of deprecated mappings.\n    abstract: true\n    slots:\n      - predicate mappings\n    tree_root: true\n\n  predicate mapping:\n    description: >-\n      A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should\n      be done to use a qualified statement in its place.\n    slots:\n      - mapped predicate\n      - subject aspect qualifier\n      - subject direction qualifier\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - predicate\n      - qualified predicate\n      - object aspect qualifier\n      - object direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object derivative qualifier\n      - object context qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - species context qualifier\n      - exact match\n      - narrow match\n      - broad match\n\n\n   ## ----------\n   ## ATTRIBUTES\n   ## ----------\n\n   ## Ontology Classes\n\n  ontology class:\n    mixin: true\n    slots:\n      - id\n    description: >-\n      a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in\n      a biolink compatible KG can be considered both instances of biolink classes, and\n      OWL classes in their own right. In general you should not need to use this class directly.\n      Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897),\n      use bl:BiologicalProcess as the type.\n    exact_mappings:\n      - owl:Class\n      - schema:Class\n    comments:\n      - >-\n        This is modeled as a mixin. 'ontology class' should not be the primary type of a\n        node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity\n        (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\n      - >-\n        Note that formally this is a metaclass. Instances of this class are instances in the graph,\n        but can be the object of 'type' edges. For example, if we had a node in the graph representing\n        a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample,\n        and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\n    see_also:\n      - https://github.com/biolink/biolink-model/issues/486\n    examples:\n      - value: UBERON:0000955\n        description: >-\n          the class 'brain' from the Uberon anatomy ontology\n    id_prefixes:\n      - MESH\n      - UMLS\n      - KEGG.BRITE  ## br/ko number\n\n  annotation:\n    description: >-\n      Biolink Model root class for entity annotations.\n    abstract: true\n\n  quantity value:\n    is_a: annotation\n    description: >-\n      A value of an attribute that is quantitative and measurable,\n      expressed as a combination of a unit and a numeric value\n    slots:\n      - has unit\n      - has numeric value\n\n   # Alignment attempted of the biolink:Attribute model\n   # to the proposed TRAPI Release 1.1 Attribute schema, i.e.\n   #\n   # attribute_name: \"assertionAuthoredBy\",\n   # attribute_type: SEPIO:0000130,\n   # value: \"ORCID:12345\",\n   # value_type: \"wd:Q51044\",\n   # value_type_name: \"ORCID ID\"\n   # url: https://orcid.org/12345\n   # source: ORCID\n\n  attribute:\n    is_a: named thing\n    mixins:\n      - ontology class\n    description: >-\n      A property or characteristic of an entity.\n      For example, an apple may have properties such as color, shape, age, crispiness.\n      An environmental sample may have attributes such as depth, lat, long, material.\n    slots:\n      - name                    # 'attribute_name'\n      - has attribute type      # 'attribute_type'\n       # 'value', 'value_type', 'value_type_name'\n       # extracted from either of the next two slots\n      - has quantitative value\n      - has qualitative value\n      - iri                     # 'url'\n    slot_usage:\n      name:\n        description: >-\n          The human-readable 'attribute name' can be set to a string which reflects its context of\n          interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default\n          to the name associated with the 'has attribute type' slot ontology term.\n    id_prefixes:\n      - EDAM-DATA\n      - EDAM-FORMAT\n      - EDAM-OPERATION\n      - EDAM-TOPIC\n    exact_mappings:\n      - SIO:000614\n    in_subset:\n      - samples\n\n  chemical role:\n    is_a: attribute\n    description: >-\n      A role played by the molecular entity or part thereof within a chemical context.\n    id_prefixes:\n      - CHEBI\n    exact_mappings:\n      - CHEBI:51086\n    examples:\n      - value: CHEBI:35469  # antidepressant role\n\n  biological sex:\n    is_a: attribute\n    exact_mappings:\n      - PATO:0000047\n\n  phenotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the phenotypic sex of the individual,\n      based upon the reproductive organs present.\n    exact_mappings:\n      - PATO:0001894\n\n  genotypic sex:\n    is_a: biological sex\n    description: >-\n      An attribute corresponding to the genotypic sex of the individual,\n      based upon genotypic composition of sex chromosomes.\n    exact_mappings:\n      - PATO:0020000\n\n  severity value:\n    deprecated: true\n    is_a: attribute\n    description: >-\n      describes the severity of a phenotypic feature or disease\n\n  relationship quantifier:\n    mixin: true\n\n  sensitivity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  specificity quantifier:\n    is_a: relationship quantifier\n    mixin: true\n\n  pathognomonicity quantifier:\n    is_a: specificity quantifier\n    description: >-\n      A relationship quantifier between a variant or symptom and a disease, which is\n      high when the presence of the feature implies the existence of the disease\n    mixin: true\n\n  frequency quantifier:\n    is_a: relationship quantifier\n    mixin: true\n    slots:\n      - has count\n      - has total\n      - has quotient\n      - has percentage\n\n  chemical or drug or treatment:\n    mixin: true\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - CHEBI\n      - MAXO\n\n   ## ------\n   ## THINGS\n   ## ------\n\n  entity:\n    description: >-\n      Root Biolink Model class for all things and informational relationships, real or imagined.\n    abstract: true\n    slots:\n      - id\n      - iri\n      - category\n      - type    # rdf:type\n      - name\n      - description\n      - has attribute\n      - deprecated\n       # evidence code(s)?\n\n  named thing:\n    is_a: entity\n    description: \"a databased entity or concept/class\"\n    slots:\n      - provided by\n      - xref\n      - full name\n      - synonym\n    slot_usage:\n      category:\n        required: true\n    exact_mappings:\n      - BFO:0000001\n      - WIKIDATA:Q35120\n       # UMLS Semantic Group \"Objects\"\n      - UMLSSG:OBJC\n       # Entity\n      - STY:T071\n      - dcid:Thing\n\n  relationship type:\n    is_a: ontology class\n    description: >-\n      An OWL property used as an edge label\n\n  taxonomic rank:\n    description: >-\n      A descriptor for the rank within a taxonomic classification.\n      Example instance: TAXRANK:0000017 (kingdom)\n    is_a: ontology class\n    id_prefixes:\n      - TAXRANK\n    mappings:\n      - WIKIDATA:Q427626\n\n  organism taxon:\n    aliases: ['taxon', 'taxonomic classification']\n    description: >-\n      A classification of a set of organisms. Example instances:\n      NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria).\n      Can also be used to represent strains or subspecies.\n    is_a: named thing\n    slots:\n      - has taxonomic rank\n    slot_usage:\n      has taxonomic rank:\n        range: taxonomic rank\n        multivalued: false\n        mappings:\n          - WIKIDATA:P105\n    values_from:\n      - NCBITaxon\n    exact_mappings:\n      - WIKIDATA:Q16521\n      - STY:T001\n      - bioschemas:Taxon\n    narrow_mappings:\n      - dcid:BiologicalSpecies\n    id_prefixes:\n      - NCBITaxon\n      - MESH\n      - UMLS\n    in_subset:\n      - model_organism_database\n\n   ## Temporal Entities\n\n  event:\n    is_a: named thing\n    description: >-\n      Something that happens at a given place and time.\n    exact_mappings:\n      - NCIT:C25499\n       # UMLS \"Event\"\n      - STY:T051\n\n   ## Administrative Entities\n\n  administrative entity:\n    is_a: named thing\n    abstract: true\n\n  study result:\n    abstract: true\n    description: >-\n      A collection of data items from a study that are about a particular study subject or experimental unit (the\n      'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation\n      of this data as evidence.\n    notes:\n      The data/metadata included in a Study Result object are typically a subset of data from a larger study data set,\n      that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific\n      focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any\n      scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational\n      analyses, or a larger scale clinical trial or experimental research investigation.\n    is_a: information content entity\n\n  study:\n    description: a detailed investigation and/or analysis\n    is_a: activity\n    exact_mappings:\n      - NCIT:C63536\n    close_mappings:\n      - SIO:001066\n      - SEPIO:0000004\n    narrow_mappings:\n      - SIO:000994\n\n  study variable:\n    is_a: information content entity\n    description: a variable that is used as a measure in the investigation of a study\n    narrow_mappings:\n      - NCIT:C142192  # specifies clinical study\n    close_mappings:\n      - STATO:0000258\n      - SIO:000367\n\n  common data element:\n    is_a: information content entity\n    description: >-\n      A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable\n      responses, used systematically across different sites, studies, or clinical trials to ensure consistent\n      data collection. Multiple CDEs (from one or more Collections) can be curated into Forms.\n      (https://cde.nlm.nih.gov/home)\n    close_mappings:\n      - NCIT:C19984\n\n   ## epc result sets\n  concept count analysis result:\n    is_a: study result\n    description: >-\n      A result of a concept count analysis.\n\n  observed expected frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a observed expected frequency analysis.\n\n  relative frequency analysis result:\n    is_a: study result\n    description: >-\n      A result of a relative frequency analysis.\n\n  text mining result:\n    is_a: study result\n    description: >-\n      A result of text mining.\n\n  chi squared analysis result:\n    is_a: study result\n    description: >-\n      A result of a chi squared analysis.\n\n  log odds analysis result:\n    is_a: study result\n    description: >-\n      A result of a log odds ratio analysis.\n\n  agent:\n    is_a: administrative entity\n    aliases: ['group']\n    description: >-\n      person, group, organization or project that provides\n      a piece of information (i.e. a knowledge association)\n    slots:\n      - affiliation\n      - address\n    exact_mappings:\n      - prov:Agent\n      - dct:Agent\n    narrow_mappings:\n       # Organization\n      - UMLSSG:ORGA\n      - STY:T092\n       # Health Care Related Organization\n      - STY:T093\n       # Professional Society\n      - STY:T094\n       # Self-help or Relief Organization\n      - STY:T095\n       # Group\n      - STY:T096\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Different classes of agents have distinct preferred identifiers.\n          For publishers, use the ISBN publisher code.\n          See https://grp.isbn-international.org/ for publisher code lookups.\n          For editors, authors and  individual providers, use the individual's\n          ORCID if available; Otherwise, a ScopusID, ResearchID or\n          Google Scholar ID ('GSID') may be used if the author ORCID is unknown.\n          Institutional agents could be identified by an\n          International Standard Name Identifier ('ISNI') code.\n        values_from:\n           # CURIE space for publishers\n          - isbn\n           # CURIE space for authors\n          - ORCID\n          - ScopusID\n          - ResearchID\n          - GSID\n           # Institutional agents\n          - isni\n      name:\n        description: >-\n          it is recommended that an author's 'name' property\n          be formatted as \"surname, firstname initial.\"\n    id_prefixes:\n      - isbn\n      - ORCID\n      - ScopusID\n      - ResearchID\n      - GSID\n      - isni\n\n   ## General Information Entities\n\n  information content entity:\n    aliases: ['information', 'information artefact', 'information entity']\n    abstract: true\n    is_a: named thing\n    description: >-\n      a piece of information that typically describes\n      some topic of discourse or is used as support.\n    slots:\n      - license\n      - rights\n      - format\n      - creation date\n    id_prefixes:\n      - doi\n    exact_mappings:\n      - IAO:0000030\n    narrow_mappings:\n       # UMLS Semantic Group \"Concepts & Ideas\"\n      - UMLSSG:CONC\n       # Conceptual Entity\n      - STY:T077\n       # Idea or Concept\n      - STY:T078\n       # Temporal Concept\n      - STY:T079\n       # Qualitative Concept\n      - STY:T080\n       # Quantitative Concept\n      - STY:T081\n       # Spatial Concept\n      - STY:T082\n       # Regulation or Law\n      - STY:T089\n       # Group Attribute\n      - STY:T102\n       # Functional Concept\n      - STY:T169\n       # Language\n      - STY:T171\n       # Classification\n      - STY:T185\n\n  dataset:\n    description: >-\n      an item that refers to a collection of data from a data source.\n    is_a: information content entity\n    exact_mappings:\n      - IAO:0000100\n      - dctypes:Dataset\n      - schema:dataset\n      - dcid:Dataset\n\n  dataset distribution:\n    is_a: information content entity\n    description: >-\n      an item that holds distribution level information about a dataset.\n    slots:\n      - distribution download url\n    exact_mappings:\n      - dcat:Distribution\n\n  dataset version:\n    description: >-\n      an item that holds version level information about a dataset.\n    is_a: information content entity\n    slots:\n      - has dataset\n      - ingest date\n      - has distribution\n\n  dataset summary:\n    description: >-\n      an item that holds summary level information about a dataset.\n    is_a: information content entity\n    slots:\n      - source web page\n      - source logo\n\n  confidence level:\n    is_a: information content entity\n    description: >-\n      Level of confidence in a statement\n    values_from:\n      - cio\n    exact_mappings:\n      - CIO:0000028\n       # statement confidence\n      - SEPIO:0000187\n    close_mappings:\n       # assertion confidence levels\n      - SEPIO:0000167\n\n  evidence type:\n    is_a: information content entity\n    aliases: ['evidence code']\n    description: >-\n      Class of evidence that supports an association\n    values_from:\n      - eco\n    exact_mappings:\n      - ECO:0000000\n\n   ## Publications\n\n   # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies\n  publication:\n    is_a: information content entity\n    description: >-\n      Any ‘published’ piece of information. Publications are considered broadly\n      to include any document or document part made available in print or on the\n      web - which may include scientific journal issues, individual articles, and\n      books - as well as things like pre-prints, white papers, patents, drug\n      labels, web pages, protocol documents,  and even a part of a publication if\n      of significant knowledge scope (e.g. a figure, figure legend, or section\n      highlighted by NLP).\n    slots:\n      - authors\n      - pages\n      - summary\n      - keywords\n      - mesh terms\n      - xref\n      - publication type\n     # In addition to embedded slots, instances of 'contributor association'\n     # may be used to more extensively document publisher, editor and author details\n    slot_usage:\n      id:\n        description: >-\n          Different kinds of publication subtypes will have different preferred\n          identifiers (curies when feasible). Precedence of identifiers for\n          scientific articles is as follows: PMID if available; DOI if not; actual\n          alternate CURIE otherwise. Enclosing publications (i.e. referenced by\n          'published in' node property) such as books and journals, should have\n          industry-standard identifier such as from ISBN and ISSN.\n      name:\n        description: >-\n          the 'title' of the publication is generally recorded in the 'name'\n          property (inherited from NamedThing). The field name 'title' is now also\n          tagged as an acceptable alias for the node property 'name' (just in case).\n      publication type:\n        required: true\n      pages:\n        multivalued: true\n        description: >-\n          When a 2-tuple of page numbers are provided, they represent\n          the start and end page of the publication within its parent publication context.\n          For books, this may be set to the total number of pages of the book.\n    exact_mappings:\n      - IAO:0000311\n    narrow_mappings:\n      - IAO:0000013\n       # UMLS Semantic Type \"Intellectual Product\"\n      - STY:T170\n    id_prefixes:\n      - PMID\n      - PMC\n      - doi\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book:\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Books should have industry-standard identifier such as from ISBN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'book'.\n    id_prefixes:\n      - isbn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  book chapter:\n    is_a: publication\n    slots:\n      - published in\n      - volume\n      - chapter\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent book containing the chapter\n          should have industry-standard identifier from ISBN.\n    in_subset:\n      - model_organism_database\n\n  serial:\n    aliases: ['journal']\n    is_a: publication\n    description: >-\n      This class may rarely be instantiated except if use cases\n      of a given knowledge graph support its utility.\n    slots:\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      id:\n        required: true\n        description: >-\n          Serials (journals) should have industry-standard identifier such as from ISSN.\n      type:\n        description: >-\n          Should generally be set to an ontology class defined term for 'serial' or 'journal'.\n    id_prefixes:\n      - issn\n      - NLMID\n    in_subset:\n      - model_organism_database\n\n  article:\n    is_a: publication\n    description: >-\n      a piece of writing on a particular topic presented as a stand-alone\n      section of a larger publication\n    slots:\n      - published in\n      - iso abbreviation\n      - volume\n      - issue\n    slot_usage:\n      published in:\n        required: true\n        description: >-\n          The enclosing parent serial containing the article should\n          have industry-standard identifier from ISSN.\n      iso abbreviation:\n        description: >-\n          Optional value, if used locally as a convenience, is set\n          to the iso abbreviation of the 'published in' parent.\n    exact_mappings:\n      - SIO:000154\n      - fabio:article\n    id_prefixes:\n       # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces\n      - PMID\n    in_subset:\n      - model_organism_database\n\n  journal article:\n    is_a: article\n    description: >-\n      an article, typically presenting results of research, that is published\n      in an issue of a scientific journal.\n    exact_mappings:\n      - IAO:0000013\n      - fabio:JournalArticle\n    id_prefixes:\n      - PMID\n      - PMCID\n      - doi\n\n  patent:\n    is_a: publication\n    description: >-\n      a legal document granted by a patent issuing authority which confers upon\n      the patenter the sole right to make, use and sell an invention for a set\n      period of time.\n    exact_mappings:\n      - SIO:000153\n      - IAO:0000313\n      - fabio:Patent\n\n  web page:\n    is_a: publication\n    description: >-\n      a document that is published according to World Wide Web standards, which\n      may incorporate text, graphics, sound, and/or other features.\n    exact_mappings:\n      - SIO:000302\n      - NCIT-OBO:C142749\n      - fabio:WebPage\n\n  preprint publication:\n    is_a: publication\n    description: >-\n      a document reresenting an early version of an author's original scholarly work,\n      such as a research paper or a review, prior to formal peer review and publication\n      in a peer-reviewed scholarly or scientific journal.\n    exact_mappings:\n      - EFO:0010558\n      - fabio:Preprint\n\n  drug label:\n    is_a: publication\n    description: >-\n      a document accompanying a drug or its container that provides written, printed or\n      graphic information about the drug, including drug contents, specific instructions\n      or warnings for administration, storage and disposal instructions, etc.\n    broad_mappings:\n      - NCIT-OBO:C41203\n\n  retrieval source:\n    is_a: information content entity\n    description: >-\n      Provides information about how a particular InformationResource\n      served as a source from which knowledge expressed in an Edge, or\n      data used to generate this knowledge, was retrieved.\n    slots:\n      - resource id\n      - resource role\n      - upstream resource ids\n      - xref\n    slot_usage:\n      resource id:\n        required: true\n        description: >-\n          The InformationResource that served as a source for the\n          knowledge expressed in an Edge, or data used to generate this knowledge.\n      resource role:\n        required: true\n        description: >-\n            The role of the InformationResource in the retrieval of the\n            knowledge expressed in an Edge, or data used to generate this knowledge.\n      upstream resource ids:\n        description: >-\n          The InformationResources that served as a source for the\n          InformationResource that served as a source for the knowledge\n          expressed in an Edge, or data used to generate this knowledge.\n\n   ## Top Level Abstractions of Material & Process Entities\n\n  physical essence or occurrent:\n    description: >-\n      Either a physical or processual entity.\n    mixin: true\n\n  physical essence:\n    description: >-\n      Semantic mixin concept.  Pertains to entities that have\n      physical properties such as mass, volume, or charge.\n    is_a: physical essence or occurrent\n    mixin: true\n\n  physical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n    description: >-\n      An entity that has material reality (a.k.a. physical essence).\n    exact_mappings:\n       # Physical Object\n      - STY:T072\n    narrow_mappings:\n       # Manufactured Object\n      - STY:T073\n\n  occurrent:\n    description: >-\n      A processual entity.\n     # biolink:Occurrent is most consistently used as a mixin thus it should\n     # be declared as such and cannot inherit from the non-mixin biolink:NamedThing\n    is_a: physical essence or occurrent\n    mixin: true\n    exact_mappings:\n      - BFO:0000003\n\n  activity and behavior:\n    is_a: occurrent\n    mixin: true\n    description: >-\n      Activity or behavior of any independent integral living,\n      organization or mechanical actor in the world\n    exact_mappings:\n       # Activities & Behaviors\n      - UMLSSG:ACTI\n\n  activity:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      An activity is something that occurs over a period of time and acts upon\n      or with entities; it may include consuming, processing, transforming,\n      modifying, relocating, using, or generating entities.\n    exact_mappings:\n      - prov:Activity\n      - NCIT:C43431\n       # Activity\n      - STY:T052\n    narrow_mappings:\n       # Daily or Recreational Activity\n      - STY:T056\n       # Occupational Activity\n      - STY:T057\n       # Governmental or Regulatory Activity\n      - STY:T064\n       # Machine Activity\n      - STY:T066\n       # Research Activity\n      - STY:T062\n       # Educational Activity\n      - STY:T065\n       # Health Care Activity\n      - STY:T058\n\n  procedure:\n    is_a: named thing\n    mixins:\n      - activity and behavior\n    description: >-\n      A series of actions conducted in a certain order or manner\n    exact_mappings:\n       # Procedures\n      - UMLSSG:PROC\n      - dcid:MedicalProcedure\n    narrow_mappings:\n       # Laboratory Procedure\n      - STY:T059\n       # Diagnostic Procedure\n      - STY:T060\n       # Therapeutic or Preventive Procedure\n      - STY:T061\n       # Molecular Biology Research Technique\n      - STY:T063\n    id_prefixes:\n      - CPT\n\n  phenomenon:\n    is_a: named thing\n    mixins:\n      - occurrent\n    description: >-\n      a fact or situation that is observed to exist or happen,\n      especially one whose cause or explanation is in question\n    broad_mappings:\n       # the inclusion of 'process' in the definition of these\n       # terms broadens them, relative to 'phenomenon'\n       # Phenomenon or Process\n      - STY:T067\n       # Human-caused Phenomenon or Process\n      - STY:T068\n       # Natural Phenomenon or Process\n      - STY:T070\n    exact_mappings:\n       # Phenomena\n      - UMLSSG:PHEN\n    narrow_mappings:\n       # Laboratory or Test Result\n      - STY:T034\n       # Biologic Function\n      - STY:T038\n       # Environmental Effect of Humans\n      - STY:T069\n\n  device:\n    is_a: named thing\n    description: >-\n      A thing made or adapted for a particular purpose, especially\n      a piece of mechanical or electronic equipment\n    narrow_mappings:\n      # Devices\n      - UMLSSG:DEVI\n      # Medical Device\n      - STY:T074\n      # Research Device\n      - STY:T075\n      # Drug Delivery Device\n      - STY:T203\n      # Biomedical or Dental Material\n      - STY:T122\n\n  diagnostic aid:\n    is_a: named thing\n    description: >-\n      A device or substance used to help diagnose disease or injury\n    exact_mappings:\n      - STY:T130  # Diagnostic Aid\n      - SNOMED:2949005  # Diagnostic aid\n\n   ## Scientific Studies\n\n  study population:\n    is_a: population of individual organisms\n    description: >-\n      A group of people banded together or treated as a group as participants in a research study.\n    close_mappings:\n      - WIKIDATA:Q7229825\n\n  subject of investigation:\n    mixin: true\n    description: >-\n      An entity that has the role of being studied in an investigation, study, or experiment\n\n  material sample:\n    aliases: ['biospecimen', 'sample', 'biosample', 'physical sample']\n    is_a: physical entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A sample is a limited quantity of something (e.g. an individual or set of individuals\n      from a population, or a portion of a substance) to be used for testing, analysis,\n      inspection, investigation, demonstration, or trial use. [SIO]\n    exact_mappings:\n      - OBI:0000747\n      - SIO:001050\n    id_prefixes:\n      - BIOSAMPLE\n      - GOLD.META\n\n   ## Earth Sciences\n\n  planetary entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists at the level of the whole planet\n\n  environmental process:\n    is_a: planetary entity\n    mixins:\n      - occurrent\n    exact_mappings:\n      - ENVO:02500000\n\n  environmental feature:\n    is_a: planetary entity\n    exact_mappings:\n      - ENVO:01000254\n\n  geographic location:\n    is_a: planetary entity\n    description: >-\n      a location that can be described in lat/long coordinates\n    slots:\n      - latitude\n      - longitude\n    exact_mappings:\n       # Geographic Areas\n      - UMLSSG:GEOG\n       # Geographic Area\n      - STY:T083\n\n  geographic location at time:\n    is_a: geographic location\n    description: >-\n      a location that can be described in lat/long coordinates, for a particular time\n    slots:\n      - timepoint\n\n   ## Biological Sciences\n\n  thing with taxon:\n    mixin: true\n    description: >-\n      A mixin that can be used on any entity that can be taxonomically classified.\n      This includes individual organisms; genes, their products and other molecular\n      entities; body parts; biological processes\n    slots:\n      - in taxon\n      - in taxon label\n\n  biological entity:\n    is_a: named thing\n    aliases: ['bioentity']\n    abstract: true\n    mixins:\n      - thing with taxon\n    narrow_mappings:\n      - WIKIDATA:Q28845870\n       # UMLS Semantic Type \"Experimental Model of Disease\"\n      - STY:T050\n       # SIO term is 'biological entity' but less inclusive than the Biolink scope\n      - SIO:010046\n      - STY:T129  # (imft, full name: Immunologic Factor\n\n  genomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n      - STY:T028    # Gene or Genome\n      - GENO:0000897   # Genomic Entity\n\n  epigenomic entity:\n    mixin: true\n    slots:\n      - has biological sequence\n    in_subset:\n      - translator_minimal\n    narrow_mappings:\n\n  molecular entity:\n    is_a: chemical entity\n    description: >-\n      A molecular entity is a chemical entity composed of individual or\n      covalently bonded atoms.\n    slots:\n      - is metabolite\n    narrow_mappings:\n      - STY:T088  # Carbohydrate\n      - STY:T085  # Molecular Sequence\n      - CHEBI:23367  # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical,\n       # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.\n      - bioschemas:MolecularEntity\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.DRUG     # D number\n      - KEGG.ENVIRON  # E number\n      - KEGG\n      - UMLS\n\n  chemical entity:\n    is_a: named thing\n    mixins:\n      - physical essence\n      - chemical or drug or treatment  # issue 701\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    description: >-\n      A chemical entity is a physical entity that pertains to chemistry or\n      biochemistry.\n    slots:\n      - trade name\n      - available from\n      - max tolerated dose\n      - is toxic\n      - has chemical role\n    exact_mappings:\n      - CHEBI:24431\n      - SIO:010004  # Chemical entity\n      - WIKIDATA:Q79529  # Chemical substance\n      - STY:T103  # Chemical\n    broad_mappings:\n      - STY:T167  # Substance, children include food, body substance, chemical.\n    narrow_mappings:\n      - WIKIDATA:Q43460564\n      - STY:T123  # (bacs, full name: Biologically Active Substance)\n      - STY:T131  # (hops, full name: Hazardous or Poisonous Substance)\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS  # CAS numbers are given for things like plant extracts as well.\n      - ncats.drug\n      - PHARMGKB.CHEMICAL\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n      # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.DRUG     # D number\n      - KEGG.ENVIRON  # E number\n      - KEGG\n      - UMLS\n\n  small molecule:\n    is_a: molecular entity\n    aliases: ['chemical substance']\n    description: >-\n      A small molecule entity is a molecular entity characterized by availability\n      in small-molecule databases of SMILES, InChI, IUPAC, or other\n      unambiguous representation of its precise chemical structure; for\n      convenience of representation, any valid chemical representation is\n      included, even if it is not strictly molecular (e.g., sodium ion).\n    narrow_mappings:\n      - STY:T196  # Element, Ion, or Isotope\n      - CHEBI:59999\n      - bioschemas:ChemicalSubstance\n      - STY:T125  # (horm, full name: Hormone)\n      - STY:T197  # (inch, full name: Inorganic Chemical)\n      - STY:T109  # (orch, full name: Organic Chemical)\n      - STY:T118  # (carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files)\n      - STY:T111  # (eico, full name: Eicosanoid) - same note as above\n      - STY:T119  # (lipd, full name: Lipid) - same note as above\n      - STY:T124  # (nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above\n      - STY:T115  # (opco, full name: Organophosphorus Compound) - same note as above\n      - STY:T110  # (strd, full name: Steroid) - same note as above\n      - STY:T127  # vitamin\n    id_prefixes:\n      - CHEBI\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - BIGG.METABOLITE\n      - UMLS\n      - foodb.compound\n      - KEGG.GLYCAN   # G number\n      - KEGG.DRUG     # D number\n      - KEGG.ENVIRON  # E number\n      - KEGG\n      - UMLS\n    slot_usage:\n      id:\n        examples:\n          - value: CHEBI:29101\n            description: sodium ion\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n\n  chemical mixture:\n    is_a: chemical entity\n    description: >-\n      A chemical mixture is a chemical entity composed of two or more\n      molecular entities.\n    slots:\n      - is supplement\n      - highest FDA approval status\n      - drug regulatory status world wide\n      - routes of delivery\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG\n      - KEGG.ENVIRON  ## E number\n      - UMLS\n    close_mappings:\n      - dcid:ChemicalCompound\n    narrow_mappings:\n      - NCIT:C20401  # monoclonal antibody\n      - SNOMEDCT:49616005  # monoclonal antibody (substance)\n\n  nucleic acid entity:\n    is_a: molecular entity\n    description: >-\n      A nucleic acid entity is a molecular entity characterized by\n      availability in gene databases of nucleotide-based sequence\n      representations of its precise sequence; for convenience of\n      representation, partial sequences of various kinds are included.\n    aliases: ['sequence feature', 'genomic entity']\n    mixins:\n      - genomic entity\n      - thing with taxon\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000110\n    narrow_mappings:\n      - STY:T086    # Nucleotide Sequence\n      - STY:T114    # Nucleic Acid, Nucleoside, or Nucleotide\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n      - ChemBank\n      - SIDER.DRUG\n      - BIGG.METABOLITE\n      - foodb.compound\n      - UMLS\n\n  regulatory region:\n    aliases: ['regulatory element']\n    description: >-\n      A region (or regions) of the genome that contains known or putative regulatory elements\n      that act in cis- or trans- to affect the transcription of gene\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0005836\n      - SIO:001225\n      - WIKIDATA:Q3238407\n\n  accessible dna region:\n    aliases: ['dnase-seq accessible region', 'atac-seq accessible region']\n    description: >-\n      A region (or regions) of a chromatinized genome that has been measured to be more\n      accessible to an enzyme such as DNase-I or Tn5 Transpose\n    is_a: regulatory region\n    mixins:\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0002231\n\n  transcription factor binding site:\n    aliases: ['tf binding site', 'binding site']\n    description: >-\n      A region (or regions) of the genome that contains a region of DNA known or predicted\n      to bind a protein that modulates gene transcription\n    is_a: regulatory region\n    mixins:\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - SO:0000235\n\n  molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A molecular mixture is a chemical mixture composed of two or more\n      molecular entities with known concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG\n      - KEGG.ENVIRON  ## E number\n      - UMLS\n      - ncats.drug\n\n  complex molecular mixture:\n    is_a: chemical mixture\n    description: >-\n      A complex molecular mixture is a chemical mixture composed of two or\n      more molecular entities with unknown concentration and stoichiometry.\n    in_subset:\n      - translator_minimal\n    id_prefixes:\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - DRUGBANK\n      - MESH\n      - CAS\n      - DrugCentral\n      - GTOPDB\n      - HMDB\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - SIDER.DRUG\n      - INCHI\n      - INCHIKEY\n       # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n       # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   ## G number\n      - KEGG.DRUG     ## D number\n      - KEGG\n      - KEGG.ENVIRON  ## E number\n      - UMLS\n\n  biological process or activity:\n    description: >-\n      Either an individual molecular activity, or a collection of\n      causally connected molecular activities in a biological system.\n    is_a: biological entity\n    mixins:\n      - occurrent\n      - ontology class\n    id_prefixes:\n      - GO\n      - REACT\n    slots:\n      - has input\n      - has output\n      - enabled by\n\n  molecular activity:\n    description: >-\n      An execution of a molecular function carried out by a\n      gene product or macromolecular complex.\n    is_a: biological process or activity\n    aliases: ['molecular function', 'molecular event', 'reaction']\n    mixins:\n      - occurrent\n      - ontology class\n    slot_usage:\n      has input:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the input for the reaction\n      has output:\n        range: molecular entity\n        description: >-\n          A chemical entity that is the output for the reaction\n      enabled by:\n        range: macromolecular machine mixin\n        description: >-\n          The gene product, gene, or complex that catalyzes the reaction\n    exact_mappings:\n      - GO:0003674\n      # UMLS Semantic Type \"Molecular Function\"\n      - STY:T044\n    broad_mappings:\n      - STY:T045  # Genetic Function\n    id_prefixes:\n      - GO\n      - REACT\n      - RHEA\n      - metacyc.reaction\n      - EC\n      - TCDB\n      - KEGG.REACTION   ## R number\n      - KEGG\n      - KEGG.ORTHOLOGY  ## in particular for gut microbiome use case in issue  #888\n      - UMLS\n      - BIGG.REACTION\n      - SEED.REACTION\n      - METANETX.REACTION\n\n  biological process:\n    is_a: biological process or activity\n    mixins:\n      - occurrent\n      - ontology class\n    description: >-\n      One or more causally connected executions of molecular functions\n    exact_mappings:\n      - GO:0008150\n      - SIO:000006\n      - WIKIDATA:Q2996394\n    broad_mappings:\n      - WIKIDATA:P682\n    id_prefixes:\n      - GO\n      - REACT\n      - metacyc.reaction\n      - KEGG.MODULE  ## M number\n      - KEGG\n\n  pathway:\n    is_a: biological process\n    mixins:\n      - ontology class\n    exact_mappings:\n      - PW:0000001\n      - WIKIDATA:Q4915012\n    narrow_mappings:\n      - SIO:010526\n      - GO:0007165\n    id_prefixes:\n      - GO\n      - REACT\n      - KEGG\n      - SMPDB\n      - MSigDB\n      - PHARMGKB.PATHWAYS\n      - WIKIPATHWAYS\n      - FB   # FlyBase FBgg*\n      - PANTHER.PATHWAY\n      - KEGG.PATHWAY\n      - ncats.bioplanet\n\n  physiological process:\n    aliases: ['physiology']\n    is_a: biological process\n    mixins:\n      - ontology class\n    close_mappings:\n    exact_mappings:\n       # Physiologic Function\n      - STY:T039\n      - WIKIDATA:Q30892994\n    narrow_mappings:\n       # Organism Function\n      - STY:T040\n       # Organ or Tissue Function\n      - STY:T042\n       # Cell Function\n      - STY:T043\n       # Genetic Function\n      - STY:T045\n    id_prefixes:\n      - GO\n      - REACT\n\n  behavior:\n    is_a: biological process\n    mixins:\n      - ontology class\n      - activity and behavior\n    exact_mappings:\n      - GO:0007610\n       # Behavior\n      - STY:T053\n    narrow_mappings:\n       # Mental Process\n      - STY:T041\n       # Social Behavior\n      - STY:T054\n       # Individual Behavior\n      - STY:T055\n\n   ## (Bio)chemistry\n\n  processed material:\n    is_a: chemical mixture\n    description: >-\n      A chemical entity (often a mixture) processed\n      for consumption for nutritional, medical or technical use.\n      Is a material entity that is created or changed during material processing.\n    exact_mappings:\n      - OBI:0000047\n    id_prefixes:\n      - UMLS\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n      - ChemBank\n      - SIDER.DRUG\n      - BIGG.METABOLITE\n      - foodb.compound\n      - UMLS\n      - foodb.food\n\n  drug:\n    is_a: molecular mixture\n    mixins:\n      - chemical or drug or treatment\n      - ontology class\n    description: >-\n      A substance intended for use in the diagnosis, cure,\n      mitigation, treatment, or prevention of disease\n    comments:\n      - The CHEBI ID represents a role rather than a substance\n    broad_mappings:\n       # Pharmacologic Substance: Any natural, endogenously-derived,\n       # synthetic or semi synthetic compound with pharmacologic activity.\n      - STY:T121\n    exact_mappings:\n      - WIKIDATA:Q12140\n      - CHEBI:23888\n       # UMLS Semantic Type \"Clinical Drug\"\n      - STY:T200\n      - dcid:Drug\n    narrow_mappings:\n       # Antibiotic\n      - STY:T195\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n      - ChemBank\n      - SIDER.DRUG\n      - BIGG.METABOLITE\n      - foodb.compound\n\n   ## Food\n\n  environmental food contaminant:\n    is_a: chemical entity\n    related_mappings:\n       # substance role\n      - CHEBI:78299\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n      - ChemBank\n      - SIDER.DRUG\n      - BIGG.METABOLITE\n      - foodb.compound\n\n  food additive:\n    is_a: chemical entity\n    related_mappings:\n       # substance role\n      - CHEBI:64047\n    id_prefixes:\n      - ncats.drug\n      - RXCUI\n      - NDC\n      - UMLS\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n      - ChemBank\n      - SIDER.DRUG\n      - BIGG.METABOLITE\n      - foodb.compound\n\n  food:\n    is_a: chemical mixture\n    description: >-\n      A substance consumed by a living organism as a source of nutrition\n    id_prefixes:\n      - foodb.food\n      - foodb.compound\n      - FOODON\n      - UMLS\n      - NCIT\n      - PUBCHEM.COMPOUND\n      - CHEMBL.COMPOUND\n      - UNII\n      - CHEBI\n      - MESH\n      - CAS\n      - GTOPDB\n      - HMDB\n      - KEGG\n      - KEGG.COMPOUND\n      - ChemBank\n      - PUBCHEM.SUBSTANCE\n      - INCHI\n      - INCHIKEY\n      # - iupac  # is not actually a CURIE namespace but only a naming convention for chemistry\n      # - SMILES   # is not actually a CURIE namespace but only a query language for chemistry\n      - KEGG.GLYCAN   # G number\n      - KEGG.ENVIRON  # E number\n      - ChemBank\n      - SIDER.DRUG\n      - BIGG.METABOLITE\n    exact_mappings:\n       # Food\n      - STY:T168\n\n   ## Biology and Biomedical Sciences\n\n   ## Biological Attributes\n\n  organism attribute:\n    is_a: attribute\n    description: >-\n      describes a characteristic of an organismal entity.\n    exact_mappings:\n       # Organism Attribute\n      - STY:T032\n\n  phenotypic quality:\n    aliases: ['phenotypic properties']\n    is_a: organism attribute\n    description: >-\n      A property of a phenotype\n    examples:\n      - value: weight\n    mappings:\n      - PATO:0000001\n\n  genetic inheritance:\n    aliases: ['inheritance']\n    is_a: biological entity\n    description: >-\n      The pattern or 'mode' in which a particular genetic trait or disorder is passed from one\n      generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\n    exact_mappings:\n      - HP:0000005\n      - GENO:0000141\n      - NCIT:C45827\n    close_mappings:\n      - STY:T045\n    id_prefixes:\n      - HP\n      - GENO\n      - NCIT\n\n    ## Biological Entities\n\n  organismal entity:\n    description: >-\n      A named entity that is either a part of an organism, a whole organism,\n      population or clade of organisms, excluding chemical entities\n    abstract: true\n    is_a: biological entity\n    mixins:\n      - subject of investigation\n    slot_usage:\n      has attribute:\n        description: >-\n          may often be an organism attribute\n    exact_mappings:\n      - WIKIDATA:Q7239\n        # UMLS Semantic Group \"Living Beings\"\n        # Several of the associated semantic types here are probably not\n      # that relevant to the Biolink world, but we keep them here for now.\n      - UMLSSG:LIVB\n      - CARO:0001010\n    narrow_mappings:\n      - STY:T008  # animal\n\n  bacterium:\n    is_a: organismal entity\n    description: >-\n      A member of a group of unicellular microorganisms lacking a nuclear membrane,\n      that reproduce by binary fission and are often motile.\n    exact_mappings:\n      - NCBITaxon:1869227\n      - STY:T007  # Bacterium\n\n  virus:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n      A virus is a microorganism that replicates itself as a microRNA\n      and infects the host cell.\n    exact_mappings:\n      - NCBITaxon:10239\n      - STY:T005  # Virus\n\n  cellular organism:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    description: >-\n    exact_mappings:\n      - NCBITaxon:131567\n\n  mammal:\n    is_a: cellular organism\n    mixins:\n      - subject of investigation\n    description: >-\n      A member of the class Mammalia, a clade of endothermic amniotes\n      distinguished from reptiles and birds by the possession of hair,\n      three middle ear bones, mammary glands, and a neocortex\n    exact_mappings:\n      - NCBITaxon:40674  # mammal\n      - STY:T015  # mammal\n      - NCIT:C14234  # Mamalia\n      - FOODON:03411134  # mammal\n\n  human:\n    is_a: mammal\n    mixins:\n      - subject of investigation\n    description: >-\n      A member of the the species Homo sapiens.\n    exact_mappings:\n      - STY:T016\n      - NCBITaxon:9606\n      - SIO:000485\n      - NCIT:C14225\n\n  plant:\n    is_a: cellular organism\n    description: >-\n    exact_mappings:\n      - NCIT:C14258  # plant\n      - STY:T002  # plant\n      - PO:0000003  # whole plant\n      - NCIT:C79659  # plant, whole\n\n  invertebrate:\n    is_a: cellular organism\n    description: >-\n      An animal lacking a vertebral column. This group consists of 98% of all animal species.\n    exact_mappings:\n      - NCIT:C14228  # invertebrate\n      - OMIT:0008565  # invertebrates\n      - FOODON:00002452  # invertebrate animals\n      - STY:T011\n    related_mappings:\n      - NCBITaxon:1767184  # unidentified invertebrate\n\n  vertebrate:\n    is_a: cellular organism\n    description: >-\n      A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.\n    exact_mappings:\n      - STY:T010\n      - NCBITaxon:7742  # vertebrata\n      - OMIT:0015545  # vertebrates\n    related_mappings:\n      - NCBITaxon:2662825  # unclassified vertebrata (in:vertebrates)\n\n  fungus:\n    is_a: cellular organism\n    description: >-\n      A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites,\n      including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or\n      asexually, and have life cycles that range from simple to complex. Filamentous\n      fungi refer to those that grow as multicellular colonies (mushrooms and molds).\n    exact_mappings:\n      - STY:T004\n      - NCIT:C14209\n      - FOODON:03411261\n    narrow_mappings:\n      - FOODON:03315605  # fungus (edible)\n      - NCBITaxon:1670606  # fungus metagenome\n\n  life stage:\n    is_a: organismal entity\n    description: >-\n      A stage of development or growth of an organism,\n      including post-natal adult stages\n    exact_mappings:\n      - UBERON:0000105\n    narrow_mappings:\n      # constrained to human life cycles\n      - HsapDv:0000000\n    in_subset:\n      - model_organism_database\n    id_prefixes:\n      - HsapDv\n      - MmusDv\n      - ZFS\n      - FBdv\n      - WBls\n      - UBERON\n\n  individual organism:\n    aliases: ['organism']\n    description: >-\n      An instance of an organism. For example, Richard Nixon,\n      Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - SIO:010000\n      # Organism\n      - STY:T001\n    narrow_mappings:\n      # Wikidata considers its definition of 'individual' to be constrained to human persons?\n      - WIKIDATA:Q795052\n      - foaf:Person\n    id_prefixes:\n      - ORCID\n\n  population of individual organisms:\n    description: >-\n      A collection of individuals from the same taxonomic class\n      distinguished by one or more characteristics.  Characteristics can\n      include, but are not limited to, shared geographic location, genetics,\n      phenotypes.\n    local_names:\n      ga4gh: population\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - PCO:0000001\n      - SIO:001061\n      # UMLS Semantic Type \"Population Group\"\n      - STY:T098\n      - OBI:0000181\n    id_prefixes:\n      - HANCESTRO\n    in_subset:\n      - model_organism_database\n\n  disease or phenotypic feature:\n    aliases: ['phenome']\n    is_a: biological entity\n    description: >-\n      Either one of a disease or an individual phenotypic feature.\n      Some knowledge resources such as Monarch treat these as\n      distinct, others such as MESH conflate.  Please see definitions of phenotypic feature and disease in this model\n      for their independent descriptions.  This class is helpful to enforce domains and ranges\n      that may involve either a disease or a phenotypic feature.\n    union_of:\n      - disease\n      - phenotypic feature\n    narrow_mappings:\n      # UMLS Semantic Type \"Finding\" - more specialized use of 'disease or phenotypic feature'\n      - STY:T033\n\n  disease:\n    aliases: ['condition', 'disorder', 'medical condition']\n    description: >-\n      A disorder of structure or function, especially one that produces specific\n      signs, phenotypes or symptoms or that affects a specific location and is not simply a\n      direct result of physical injury.  A disposition to undergo pathological processes that exists in an\n      organism because of one or more disorders in that organism.\n    is_a: disease or phenotypic feature\n    exact_mappings:\n      - MONDO:0000001\n      - DOID:4\n      - NCIT:C2991\n      - WIKIDATA:Q12136\n      - SIO:010299\n      - UMLSSG:DISO\n      - STY:T047\n      - dcid:Disease\n    narrow_mappings:\n      - STY:T019\n       # Acquired Abnormality\n      - STY:T020\n       # Mental or behavioral disfunction\n      - STY:T048\n      # (Cell or Molecular Dysfunction)\n      - STY:T049\n      # (Neoplastic Process)\n      - STY:T191\n      # disease susceptibility\n      - MONDO:0042489\n    id_prefixes:\n      - MONDO\n      - DOID\n      - OMIM\n      - OMIM.PS\n      - orphanet\n      - EFO\n      - UMLS\n      - MESH\n      - MEDDRA\n      - NCIT\n      - SNOMEDCT\n      - medgen\n      - ICD10\n      - ICD9\n      - KEGG.DISEASE  ## H number\n      - HP\n      - MP\n      - PHARMGKB.DISEASE\n    in_subset:\n      - model_organism_database\n      - translator_minimal\n\n  phenotypic feature:\n    aliases: ['sign', 'symptom', 'phenotype', 'trait', 'endophenotype']\n    is_a: disease or phenotypic feature\n    description: >-\n      A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an\n      individual resulting from the interaction of its genotype with its molecular and physical environment.\n    examples:\n      - value: MP:0001262\n        description: decreased body weight\n    exact_mappings:\n      - UPHENO:0001001\n      - SIO:010056\n      - WIKIDATA:Q104053\n      - UMLS:C4021819\n      - NCIT:C16977\n      - SNOMEDCT:8116006  # documented as phenotypic finding and phenotype, also referred to as \"SCTID:8116006\" at SNOMEDCT\n      - MESH:D010641  # phenotype\n    narrow_mappings:\n      - STY:T184  # Sign or Symptom\n      - WIKIDATA:Q169872  # Sign or Symptom\n       # presentation of a disease in clinical medicine\n      - WIKIDATA:Q25203551\n      - ZP:00000000  # zebrafish phenotype\n      - FBcv:0001347  # fly phenotype\n      - HP:0000118  # human phenotype\n      - MP:0000001  # mouse phenotype\n      - WBPhenotype:0000886  # worm phenotype\n      - XPO:00000000  # frog phenotype\n      - FYPO:0000001  # fission yeast phenotype\n      - APO:0000017  # phenotype\n      - TO:0000387  # more narrowly defined here for plants; our definition conflates trait and phenotype.\n      - STY:T190\n    broad_mappings:\n      - BFO:0000019  # quality\n      - PATO:0000001  # quality\n    id_prefixes:\n      - HP\n      - EFO  # covered by BFO quality mapping\n      - NCIT\n      - UMLS\n      - MEDDRA  # can not find a mapping\n      - MP\n      - ZP\n      - UPHENO\n      - APO\n      - FBcv\n      - WBPhenotype\n      - SNOMEDCT\n      - MESH\n      - XPO\n      - FYPO\n      - TO\n    in_subset:\n      - model_organism_database\n\n  behavioral feature:\n    description: >-\n      A phenotypic feature which is behavioral in nature.\n    is_a: phenotypic feature\n    exact_mappings:\n      - NBO:0000243\n\n  anatomical entity:\n    is_a: organismal entity\n    mixins:\n      - physical essence\n    description: >-\n      A subcellular location, cell type or gross anatomical part\n    exact_mappings:\n      - UBERON:0001062\n      - WIKIDATA:Q4936952\n       # UMLS Semantic Group \"Anatomy\"\n      - UMLSSG:ANAT\n       # UMLS Semantic Type \"Anatomical Structure\"\n      - STY:T017\n      - FMA:62955  # anatomical entity\n      - CARO:0000000   # anatomical entity\n      - SIO:001262  # anatomical entity\n      - STY:T029  # Body Location or Region\n      - STY:T030  # Body Space or Junction\n    narrow_mappings:\n      - ZFA:0100000  # zebrafish anatomical entity\n      - FBbt:10000000  # fly anatomical entity\n      - EMAPA:0  # mouse anatomical entity\n      - MA:0000001  # mouse anatomical entity\n      - XAO:0000000  # frog anatomical entity\n      - WBbt:0000100  # c. elegans anatomical entity\n      - NCIT:C12219  # human anatomical entity\n      - GO:0110165  # cellular anatomical entity, also used directly in CL\n      - STY:T031  # Body Substance\n    related_mappings:\n      - SNOMEDCT:123037004  # body structure\n    id_prefixes:\n      - UBERON\n      - GO\n      - CL\n      - UMLS\n      - MESH\n      - NCIT\n      - EMAPA\n      - ZFA\n      - FBbt\n      - WBbt\n    in_subset:\n      - model_organism_database\n\n  cellular component:\n    aliases: ['cell component', 'cell part']\n    is_a: anatomical entity\n    description: >-\n      A location in or around a cell\n    exact_mappings:\n      - GO:0005575\n      - SIO:001400\n      - WIKIDATA:Q5058355\n       # Cell Component\n      - STY:T026\n    broad_mappings:\n      - WIKIDATA:P681\n    id_prefixes:\n      - GO\n      - MESH\n      - UMLS\n      - NCIT\n      - SNOMEDCT\n      - CL\n      - UBERON\n\n  cell:\n    is_a: anatomical entity\n    exact_mappings:\n      - GO:0005623\n      - CL:0000000\n      - SIO:010001\n      - WIKIDATA:Q7868\n       # UMLS Semantic Type \"Cell\"\n      - STY:T025\n      - MESH:D002477  # cells\n    id_prefixes:\n      - CL\n      - PO\n      - UMLS\n      - NCIT\n      - MESH\n      - UBERON\n      - SNOMEDCT\n      - MESH\n\n  cell line:\n    is_a: organismal entity\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - CLO:0000031\n    id_prefixes:\n      - CLO\n\n  gross anatomical structure:\n    aliases: ['tissue', 'organ']\n    is_a: anatomical entity\n    exact_mappings:\n      - UBERON:0010000\n      - WIKIDATA:Q4936952\n    narrow_mappings:\n       # UMLS Semantic Type \"Body Part, Organ, or Organ Component\"\n      - STY:T023\n       # UMLS Semantic Type \"Tissue\"\n      - STY:T024\n       # Embryonic Structure\n      - STY:T018\n    id_prefixes:\n      - UBERON\n      - UMLS\n      - MESH\n      - NCIT\n      - PO\n      - FAO\n\n\n   ## entity mixins\n\n  chemical entity or gene or gene product:\n    description: >-\n      A union of chemical entities and children, and gene or gene product.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  chemical entity or protein or polypeptide:\n    description: >-\n      A union of chemical entities and children, and protein and polypeptide.\n      This mixin is helpful to use when searching across\n      chemical entities that must include genes and their children as chemical entities.\n    mixin: true\n\n  macromolecular machine mixin:\n    description: >-\n      A union of gene locus, gene product, and macromolecular complex. These are\n      the basic units of function in a cell. They either carry out individual\n      biological activities, or they encode molecules which do this.\n    mixin: true\n    slots:\n      - name\n    slot_usage:\n      name:\n        range: symbol type\n        description: >-\n          genes are typically designated by a short symbol and a full name.\n          We map the symbol to the default display name\n          and use an additional slot for full name\n\n  gene or gene product:\n    description: >-\n      A union of gene loci or gene products.\n      Frequently an identifier for one will be used as proxy for another\n    is_a: macromolecular machine mixin\n    mixin: true\n    id_prefixes:\n      - CHEMBL.TARGET\n      - IUPHAR.FAMILY\n\n  gene:\n    description: >-\n      A region (or regions) that includes all of the sequence elements\n      necessary to encode a functional transcript. A gene locus may include\n      regulatory regions, transcribed regions and/or other\n      functional sequence regions.\n    is_a: biological entity\n    mixins:\n      - gene or gene product\n      - genomic entity\n      - chemical entity or gene or gene product\n      - physical essence\n      - ontology class\n    slots:\n      - symbol\n      - xref\n    exact_mappings:\n      - SO:0000704\n      - SIO:010035\n      - WIKIDATA:Q7187\n      - dcid:Gene\n    id_prefixes:\n      - NCBIGene\n      - ENSEMBL\n      - HGNC\n      - MGI\n      - ZFIN\n      - dictyBase\n      - WB\n      - WormBase  # we have two prefixes here as wormbase supports WormBase:WBGene00000898\n       # and alliancegenome.org and identifiers.org supports WB:WBGene00000898.\n      - FB\n      - RGD\n      - SGD\n      - PomBase\n      - OMIM\n      - KEGG.GENES  ## org:gene\n      - UMLS\n      - Xenbase\n      - AspGD\n      - PHARMGKB.GENE\n    in_subset:\n      - translator_minimal\n      - model_organism_database\n    narrow_mappings:\n      - bioschemas:gene\n    broad_mappings:\n      - NCIT:C45822\n\n\n  gene product mixin:\n    description: >-\n      The functional molecular product of a single gene locus.\n      Gene products are either proteins or functional RNA molecules.\n    is_a: gene or gene product\n    mixin: true\n    slots:\n      - synonym\n      - xref\n    exact_mappings:\n      - WIKIDATA:Q424689\n      - GENO:0000907\n      - NCIT:C26548\n    id_prefixes:\n      - UniProtKB\n      - gtpo\n      - PR\n\n  gene product isoform mixin:\n    description: >-\n      This is an abstract class that can be mixed in with different kinds of\n      gene products to indicate that the gene product is intended to represent\n      a specific isoform rather than a canonical or reference or generic\n      product. The designation of canonical or reference may be arbitrary,\n      or it may represent the superclass of all isoforms.\n    is_a: gene product mixin\n    mixin: true\n\n  macromolecular complex:\n    description: >-\n      A stable assembly of two or more macromolecules, i.e. proteins,\n      nucleic acids, carbohydrates or lipids, in which at least one\n      component is a protein and the constituent parts function together.\n    is_a: biological entity\n    mixins:\n      - macromolecular machine mixin\n    exact_mappings:\n      - GO:0032991\n      - WIKIDATA:Q22325163\n    id_prefixes:\n      - INTACT\n      - GO\n      - PR\n      - REACT\n      - ComplexPortal\n    in_subset:\n      - model_organism_database\n\n   ## Genomic Classes\n  nucleosome modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform.\n      e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.\n    mixins:\n      - gene product isoform mixin\n      - genomic entity\n      - epigenomic entity\n\n  genome:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A genome is the sum of genetic material within a cell or virion.\n    exact_mappings:\n      - SO:0001026\n      - SIO:000984\n      - WIKIDATA:Q7020\n    close_mappings:\n      - dcid:GenomeAssemblyUnit\n    in_subset:\n      - model_organism_database\n\n  exon:\n    is_a: biological entity\n    description: >-\n      A region of the transcript sequence within a gene which is not\n      removed from the primary RNA transcript by RNA splicing.\n    exact_mappings:\n      - SO:0000147\n      - SIO:010445\n      - WIKIDATA:Q373027\n\n  transcript:\n    is_a: biological entity\n    description: >-\n      An RNA synthesized on a DNA or RNA template by an RNA polymerase.\n    exact_mappings:\n      - SO:0000673\n      - SIO:010450\n      - WIKIDATA:Q7243183\n      - dcid:RNATranscript\n    id_prefixes:\n      - ENSEMBL  # ENSEMBL:ENST for human\n      - FB       # FlyBase:FBtr\n    in_subset:\n      - model_organism_database\n\n  coding sequence:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n    exact_mappings:\n      - SO:0000316\n      - SIO:001390\n\n  polypeptide:\n    aliases: ['amino acid entity']\n    is_a: biological entity\n    description: >-\n      A polypeptide is a molecular entity characterized by availability\n      in protein databases of amino-acid-based sequence representations\n      of its precise primary structure; for convenience of representation,\n      partial sequences of various kinds are included, even if they do not\n      represent a physical molecule.\n    mixins:\n      - chemical entity or gene or gene product\n      - chemical entity or protein or polypeptide\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL  # ENSEMBL:ENSP*\n      - FB       # FlyBase FBpp*\n      - UMLS\n    in_subset:\n      - model_organism_database\n    narrow_mappings:\n      - SO:0000104  # polypeptide defined in SO conflates protein and polypeptide\n       # Amino Acid, Peptide, or Protein\n      - STY:T116\n       # Amino Acid Sequence\n      - STY:T087\n\n  protein:\n    description: >-\n      A gene product that is composed of a chain of amino acid sequences\n      and is produced by ribosome-mediated translation of mRNA\n    is_a: polypeptide\n    mixins:\n      - gene product mixin\n    id_prefixes:\n      - UniProtKB\n      - PR\n      - ENSEMBL  # ENSEMBL:ENSP*\n      - FB       # FlyBase FBpp*\n      - UMLS\n      - MESH\n      - ncats.drug\n    broad_mappings:\n      - bioschemas:Protein\n    exact_mappings:\n      - PR:000000001\n      - SIO:010043\n      - WIKIDATA:Q8054\n    narrow_mappings:\n       # Enzyme\n      - STY:T126\n       # Receptor\n      - STY:T192\n\n  protein isoform:\n    aliases: ['proteoform']\n    is_a: protein\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or\n      reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - UniProtKB  # UniProtKB:([A-Z0-9]+-\\d+)\n      - UNIPROT.ISOFORM\n      - PR\n      - ENSEMBL\n\n  protein domain:\n    is_a: biological entity\n    description: >-\n      A conserved part of protein sequence and (tertiary) structure that can evolve,\n      function, and exist independently of the rest of the protein chain.\n      Protein domains maintain their structure and function independently of the proteins in which they are found.\n      e.g. an SH3 domain.\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    exact_mappings:\n      - NCIT:C13379\n      - SIO:001379\n      - UMLS:C1514562\n\n  posttranslational modification:\n    is_a: biological entity\n    description: >-\n      A chemical modification of a polypeptide or protein that occurs after translation.\n      e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids,\n      protein ubiquitination.\n    mixins:\n      - gene product isoform mixin\n\n  protein family:\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n\n  nucleic acid sequence motif:\n    aliases: ['consensus sequence']\n    is_a: biological entity\n    description: >-\n      A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have,\n      a biological significance. e.g. the TATA box promoter motif, transcription factor binding\n      consensus sequences.\n\n  RNA product:\n    is_a: transcript\n    mixins:\n      - gene product mixin\n    exact_mappings:\n      - CHEBI:33697\n       # This SIO term here also mapped to 'biolink:Transcript'; however,\n       # since this 'biolink:RNAProduct' relates more to the biochemical\n       # essence of RNA, then map the SIO term instead to 'biolink:Transcript'\n       # - SIO:010450\n      - WIKIDATA:Q11053\n    id_prefixes:\n      - RNACENTRAL\n\n  RNA product isoform:\n    is_a: RNA product\n    description: >-\n      Represents a protein that is a specific isoform of the canonical or reference RNA\n    mixins:\n      - gene product isoform mixin\n    id_prefixes:\n      - RNACENTRAL\n\n  noncoding RNA product:\n    is_a: RNA product\n    id_prefixes:\n      - RNACENTRAL\n      - NCBIGene\n      - ENSEMBL\n    exact_mappings:\n      - SO:0000655\n      - SIO:001235\n\n  microRNA:\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000276\n      - SIO:001397\n      - WIKIDATA:Q310899\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  siRNA:\n    aliases: ['small interfering RNA', 'RNAi']\n    description: >-\n      A small RNA molecule that is the product of a longer exogenous or\n      endogenous dsRNA, which is either a bimolecular duplex or very long\n      hairpin, processed (via the Dicer pathway) such that numerous siRNAs\n      accumulate from both strands of the dsRNA. SRNAs trigger the cleavage\n      of their target molecules.\n    is_a: noncoding RNA product\n    exact_mappings:\n      - SO:0000646\n      - WIKIDATA:Q203221\n    id_prefixes:\n      - MIR\n      - HGNC\n      - WormBase\n    in_subset:\n      - model_organism_database\n\n  gene grouping mixin:\n    description: >-\n      any grouping of multiple genes or gene products\n    mixin: true\n    slots:\n      - has gene or gene product\n\n  gene family:\n    aliases: ['orthogroup', 'protein family']\n    is_a: biological entity\n    exact_mappings:\n      - NCIT:C26004\n      - WIKIDATA:Q2278983\n    narrow_mappings:\n       # These term definitions focus only on proteins;\n       # the 'biolink:GeneFamily' term would be more inclusive\n       # to describe gene loci, non-coding RNA, etc.\n      - SIO:001380\n      - NCIT:C20130\n      - WIKIDATA:Q417841\n    mixins:\n      - gene grouping mixin\n      - chemical entity or gene or gene product\n    description: >-\n      any grouping of multiple genes or gene products related by common descent\n    id_prefixes:\n      - PANTHER.FAMILY\n      - HGNC.FAMILY\n      - FB        # FlyBase FBgg*\n      - interpro  # note: may be better to introduce a protein domain/family\n      - CATH\n      - CDD\n      - HAMAP\n      - PFAM\n      - PIRSF\n      - PRINTS\n      - PRODOM\n      - PROSITE\n      - SMART\n      - SUPFAM\n      - TIGRFAM\n      - CATH.SUPERFAMILY\n      - RFAM  ## RNAs only\n      - KEGG.ORTHOLOGY  ## aka KEGG.KO: K number\n      - EGGNOG\n      - COG\n    in_subset:\n      - model_organism_database\n\n  zygosity:\n    is_a: attribute\n    exact_mappings:\n      - GENO:0000133\n\n  genotype:\n    is_a: biological entity\n    mixins:\n      - physical essence\n      - genomic entity\n      - ontology class\n    description: >-\n      An information content entity that describes a genome by specifying the\n      total variation in genomic sequence and/or gene expression, relative to\n      some established background\n    comments:\n      - Consider renaming as genotypic entity\n    slots:\n      - has zygosity\n    exact_mappings:\n      - GENO:0000536\n      - SIO:001079\n    id_prefixes:\n      - ZFIN\n      - FB    # FlyBase FBba*\n    in_subset:\n      - model_organism_database\n\n  haplotype:\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A set of zero or more Alleles on a single instance of a Sequence[VMC]\n     #    slots:\n     #      - completeness\n    exact_mappings:\n      - GENO:0000871\n      - SO:0001024\n      - VMC:Haplotype\n\n  sequence variant:\n    aliases: ['allele']\n    local_names:\n      agr: allele\n    is_a: biological entity\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    description: >-\n      A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.\n    comments:\n      - This class is for modeling the specific state at a locus.\n        A single DBSNP rs ID could correspond to more than one sequence variants\n        (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)\n    exact_mappings:\n       # slightly broader semantics than SO:0001059 - 'sequence alteration'\n       # describes a sequence feature that may have 1..* sequence alterations\n      - WIKIDATA:Q15304597\n    close_mappings:\n      - dcid:Allele\n      - SO:0001060\n      - VMC:Allele\n      - GENO:0000002\n      - SIO:010277\n      - SO:0001060\n    id_prefixes:\n      - CAID  # ClinGen Allele Registry\n      - CLINVAR\n      - WIKIDATA\n       # - CIViC needs IRI mapping\n      - DBSNP\n      - MGI\n      - ZFIN\n      - FB\n      - RGD\n      - AGRKB\n      - SPDI\n      - WB\n      - WormBase\n      - PHARMGKB.VARIANT\n    alt_descriptions:\n      AGR: >-\n        An entity that describes a single affected, endogenous allele.\n        These can be of any type that matches that definition\n      VMC: >-\n        A contiguous change at a Location\n    slots:\n      - has gene\n    slot_usage:\n      has gene:\n        multivalued: true\n        description: Each allele can be associated with any number of genes\n      has biological sequence:\n        description: >-\n          The state of the sequence w.r.t a reference sequence\n      id:\n        examples:\n          - value: ZFIN:ZDB-ALT-980203-1091\n            description: ti282a allele from ZFIN\n          - value: CLINVAR:17681\n            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)\n    in_subset:\n      - model_organism_database\n\n  snv:\n    aliases: ['single nucleotide variant', 'single nucleotide polymorphism', 'snp']\n    is_a: sequence variant\n    description: >-\n      SNVs are single nucleotide positions in genomic DNA at\n      which different sequence alternatives exist\n    exact_mappings:\n      - SO:0001483\n\n  reagent targeted gene:\n    aliases: ['sequence targeting reagent']\n    is_a: biological entity\n    description: >-\n      A gene altered in its expression level in the context of some\n      experiment as a result of being targeted by gene-knockdown\n      reagent(s) such as a morpholino or RNAi.\n    mixins:\n      - genomic entity\n      - physical essence\n      - ontology class\n    exact_mappings:\n      - GENO:0000504\n    in_subset:\n      - model_organism_database\n\n   ## --------------------\n   ## Clinical\n   ## Attributes, Cohort,\n   ## Exposures & Outcomes\n   ## --------------------\n\n   ## Clinical Attributes\n\n  clinical attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a clinical manifestation\n    exact_mappings:\n       # Clinical Attribute\n      - STY:T201\n\n  clinical measurement:\n    is_a: clinical attribute\n    description: >-\n      A clinical measurement is a special kind of attribute which results\n      from a laboratory observation from a subject individual or sample.\n      Measurements can be connected to their subject by the 'has attribute' slot.\n    slot_usage:\n      has attribute type:\n        required: true\n        multivalued: false\n        values_from:\n          - EFO\n          - LOINC\n    exact_mappings:\n      - EFO:0001444\n\n  clinical modifier:\n    is_a: clinical attribute\n    description: >-\n      Used to characterize and specify the phenotypic abnormalities\n      defined in the phenotypic abnormality sub-ontology, with respect\n      to severity, laterality, and other aspects\n    exact_mappings:\n\n\n  clinical course:\n    is_a: clinical attribute\n    description: >-\n      The course a disease typically takes from its onset, progression in time, and\n      eventual resolution or death of the affected individual\n    exact_mappings:\n      - HP:0031797\n\n  onset:\n    is_a: clinical course\n    description: >-\n      The age group in which (disease) symptom manifestations appear.\n    notes: >-\n      This class is in Biolink to support HP ontology annotations which use \"onset\" (with terms from HP) \n      as an annotation on a disease to phenotypic feature association.  This should be the primary use\n      case for this class.\n    exact_mappings:\n      - HP:0003674\n\n  clinical entity:\n    is_a: named thing\n    description: >-\n      Any entity or process that exists in the clinical domain and outside the\n      biological realm. Diseases are placed under biological entities\n\n  clinical trial:\n    is_a: clinical entity\n\n  clinical intervention:\n    is_a: clinical entity\n\n  clinical finding:\n    is_a: phenotypic feature\n    description: >-\n      this category is currently considered broad enough to tag clinical lab\n      measurements and other biological attributes taken as 'clinical traits'\n      with some statistical score, for example, a p value in genetic associations.\n    slot_usage:\n      has attribute:\n        range: clinical attribute\n    id_prefixes:\n      - LOINC\n      - NCIT\n      - EFO\n\n  hospitalization:\n    is_a: clinical intervention\n    exact_mappings:\n      - SNOMEDCT:32485007\n      - WIKIDATA:Q3140971\n\n  socioeconomic attribute:\n    is_a: attribute\n    description: >-\n      Attributes relating to a socioeconomic manifestation\n\n   ## Cohorts\n\n  case:\n    aliases: ['patient', 'proband']\n    is_a: individual organism\n    description: >-\n      An individual (human) organism that has a patient role in some clinical context.\n    mixins:\n      - subject of investigation\n\n  cohort:\n    is_a: study population\n    description: >-\n      A group of people banded together or treated as a group who share common characteristics.\n      A cohort 'study' is a particular form of longitudinal study that samples a cohort,\n      performing a cross-section at intervals through time.\n    mixins:\n      - subject of investigation\n    exact_mappings:\n      - WIKIDATA:Q1303415\n    narrow_mappings:\n       # Professional or Occupational Group\n      - STY:T097\n       # Family Group\n      - STY:T099\n       # Age Group\n      - STY:T100\n       # Patient or Disabled Group\n      - STY:T101\n\n   ## Exposures\n\n  exposure event:\n    is_a: ontology class\n    aliases: ['exposure', 'experimental condition']\n    mixin: true\n    slots:\n      - timepoint\n    description: >-\n      A (possibly time bounded) incidence of a feature of the environment of an organism that\n      influences one or more phenotypic features of that organism, potentially mediated by genes\n    exact_mappings:\n      - XCO:0000000\n    in_subset:\n      - model_organism_database\n\n   # TODO - confirm that genomic backgrounds are exposures\n  genomic background exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - gene grouping mixin\n      - physical essence\n      - genomic entity\n      - thing with taxon\n      - ontology class\n    description: >-\n      A genomic background exposure is where an individual's specific genomic background\n      of genes, sequence variants or other pre-existing genomic conditions constitute\n      a kind of 'exposure' to the organism, leading to or influencing an outcome.\n\n  pathological entity mixin:\n    description: >-\n      A pathological (abnormal) structure or process.\n    mixin: true\n    exact_mappings:\n      - MPATH:0\n    narrow_mappings:\n      - HP:0000118\n\n  pathological process:\n    description: >-\n      A biologic function or a process having an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: biological process\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - OBI:1110122\n      - NCIT:C16956\n      - MPATH:596\n    narrow_mappings:\n       # metastasis\n      - NCIT:C19151\n      - EFO:0009708\n      - STY:T046\n      - STY:T037\n\n  pathological process exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A pathological process, when viewed as an exposure, representing\n      a precondition, leading to or influencing an outcome,\n      e.g. autoimmunity leading to disease.\n\n  pathological anatomical structure:\n    description: >-\n      An anatomical structure with the potential of have an abnormal or deleterious\n      effect at the subcellular, cellular, multicellular, or organismal level.\n    is_a: anatomical entity\n    mixins:\n      - pathological entity mixin\n    exact_mappings:\n      - MPATH:603\n\n  pathological anatomical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      An abnormal anatomical structure, when viewed as an exposure,\n      representing an precondition, leading to or influencing an outcome,\n      e.g. thrombosis leading to an ischemic disease outcome.\n\n  disease or phenotypic feature exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n      - pathological entity mixin\n    description: >-\n      A disease or phenotypic feature state, when viewed as an exposure,\n      represents an precondition, leading to or influencing an outcome,\n      e.g. HIV predisposing an individual to infections; a relative deficiency\n      of skin pigmentation predisposing an individual to skin cancer.\n\n  chemical exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    slots:\n      - has quantitative value\n    description: >-\n      A chemical exposure is an intake of a particular\n      chemical entity.\n    exact_mappings:\n       # this ECTO term is not visibly defined but\n       # the 9000000-series identifiers seems to be the\n       # numeric space of chemical exposure definitions\n      - ECTO:9000000\n      - SIO:001399\n\n  complex chemical exposure:\n    is_a: attribute\n    description: >-\n      A complex chemical exposure is an intake of a chemical\n      mixture (e.g. gasoline), other than a drug.\n\n  drug exposure:\n    is_a: chemical exposure\n    aliases: ['drug intake', 'drug dose', 'medication intake']\n    description: >-\n      A drug exposure is an intake of a particular drug.\n    mixins:\n      - exposure event\n    broad_mappings:\n       # slightly broader than just drug effects on a biological system\n      - SIO:001005\n    exact_mappings:\n      - ECTO:0000509\n\n   # TODO: deprecate?\n  drug to gene interaction exposure:\n    description: >-\n      drug to gene interaction exposure is a drug exposure is where the\n      interactions of the drug with specific genes are known to constitute\n      an 'exposure' to the organism, leading to or influencing an outcome.\n    is_a: drug exposure\n    mixins:\n      - gene grouping mixin\n\n  treatment:\n    aliases: ['medical action', 'medical intervention']\n     # 'named thing' seems too generic here but not sure what applies better here\n    is_a: named thing\n    mixins:\n      - exposure event\n      - chemical or drug or treatment\n    description: >-\n      A treatment is targeted at a disease or phenotype and may involve\n      multiple drug 'exposures', medical devices and/or procedures\n    slots:\n      - has drug\n      - has device\n      - has procedure\n    exact_mappings:\n      - OGMS:0000090\n      - SIO:001398\n    broad_mappings:\n      - MAXO:0000058\n\n  biotic exposure:\n    is_a: attribute\n    aliases: ['viral exposure', 'bacterial exposure']\n    mixins:\n      - exposure event\n    description: >-\n      An external biotic exposure is an intake of (sometimes pathological)\n      biological organisms (including viruses).\n\n  geographic exposure:\n    is_a: environmental exposure\n    mixins:\n      - exposure event\n    description: >-\n      A geographic exposure is a factor relating to geographic\n      proximity to some impactful entity.\n    close_mappings:\n      - dcid:GeologicalEvent\n    narrow_mappings:\n      - dcid:IceStoremEvent\n      - dcid:LakeEffectSnowEvent\n      - dcid:LandslideEvent\n      - dcid:MarineDenseFogEvent\n      - dcid:MarineLighteningEvent\n      - dcid:MarineStrongWindEvent\n      - dcid:MarineThunderstormWindEvent\n      - dcid:StormEvent\n      - dcid:StormSurgeTideEvent\n      - dcid:StrongWindEvent\n      - dcid:ThunderstormWindEvent\n      - dcid:TornadoEvent\n      - dcid:TropicalDepressionEvent\n      - dcid:WinterStoremEvent\n\n  environmental exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A environmental exposure is a factor relating to abiotic processes\n      in the environment including sunlight (UV-B), atmospheric (heat,\n      cold, general pollution) and water-born contaminants.\n\n  behavioral exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A behavioral exposure is a factor relating to behavior impacting an individual.\n\n  socioeconomic exposure:\n    is_a: attribute\n    mixins:\n      - exposure event\n    description: >-\n      A socioeconomic exposure is a factor relating to social and\n      financial status of an affected individual (e.g. poverty).\n    slot_usage:\n      has attribute:\n        range: socioeconomic attribute\n        required: true\n\n   ## Outcomes\n\n  outcome:\n    mixin: true\n    description: >-\n      An entity that has the role of being the consequence of an exposure event.\n      This is an abstract mixin grouping of various categories of possible\n      biological or non-biological (e.g. clinical) outcomes.\n\n  pathological process outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of a pathological process.\n\n  pathological anatomical outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which\n      is the manifestation of an abnormal anatomical structure.\n\n  disease or phenotypic feature outcome:\n    mixins:\n      - outcome\n    description: >-\n      Physiological outcomes resulting from an exposure event which\n      is the manifestation of a disease or other characteristic phenotype.\n\n  behavioral outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the manifestation of human behavior.\n\n  hospitalization outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome resulting from an exposure event which is\n      the increased manifestation of acute (e.g. emergency\n      room visit) or chronic (inpatient) hospitalization.\n\n  mortality outcome:\n    mixins:\n      - outcome\n    description: >-\n      An outcome of death from resulting from an exposure event.\n\n  epidemiological outcome:\n    mixins:\n      - outcome\n    description: >-\n      An epidemiological outcome, such as societal disease\n      burden, resulting from an exposure event.\n    related_mappings:\n      - NCIT:C19291\n\n  socioeconomic outcome:\n    mixins:\n      - outcome\n    description: >-\n      An general social or economic outcome, such as\n      healthcare costs, utilization, etc., resulting from an exposure event\n\n   ## ------------\n   ## ASSOCIATIONS\n   ## ------------\n\n  association:\n    is_a: entity\n    description: >-\n      A typed association between two entities, supported by evidence\n    comments:\n      - This is roughly the model used by biolink and ontobio at the moment\n    slots:\n      - subject\n      - predicate\n      - object\n      - negated\n      - qualifier\n      - qualifiers  # deprecated\n      - publications\n      - has evidence\n      - knowledge source\n      - primary knowledge source\n      - aggregator knowledge source\n      - knowledge level\n      - agent type\n      - timepoint\n      - original subject\n      - original predicate\n      - original object\n       # denormalized fields\n      - subject category\n      - object category\n      - subject closure\n      - object closure\n      - subject category closure\n      - object category closure\n      - subject namespace\n      - object namespace\n      - subject label closure\n      - object label closure\n      - retrieval source ids\n    slot_usage:\n      type:\n        description: rdf:type of biolink:Association should be fixed at rdf:Statement\n      category:\n        range: uriorcurie\n        required: false\n    exact_mappings:\n      - OBAN:association\n      - rdf:Statement\n      - owl:Axiom\n\n\n  chemical entity assesses named thing association:\n    is_a: association\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: assesses\n\n\n  contributor association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      Any association between an entity (such as a publication)\n      and various agents that contribute to its realisation\n    slot_usage:\n      subject:\n        range: information content entity\n        description: >-\n          information content entity which an agent has helped realise\n      predicate:\n        subproperty_of: contributor\n        description: >-\n          generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\n      object:\n        range: agent\n        description: >-\n          agent helping to realise the given entity (e.g. such as a publication)\n      qualifiers:\n        description: >-\n          this field can be used to annotate special characteristics of an\n          agent relationship, such as the fact that a given author agent of\n          a publication is the 'corresponding author'\n\n  genotype to genotype part association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a genotypic entity that is a sub-component of it\n    slot_usage:\n      predicate:\n        subproperty_of: has variant part\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: genotype\n        description: >-\n          child genotype\n\n  genotype to gene association:\n    description: >-\n      Any association between a genotype and a gene.\n      The genotype have have multiple variants in that gene or a single one.\n      There is no assumption of cardinality\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: gene\n        description: >-\n          gene implicated in genotype\n\n  genotype to variant association:\n    description: >-\n      Any association between a genotype and a sequence variant.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      predicate:\n        description: >-\n          the relationship type used to connect genotype to gene\n      subject:\n        range: genotype\n        description: >-\n          parent genotype\n      object:\n        range: sequence variant\n        description: >-\n          gene implicated in genotype\n\n  gene to gene association:\n    aliases: ['molecular or genetic interaction']\n    description: >-\n      abstract parent class for different kinds of gene-gene or gene product\n      to gene product relationships. Includes homology and interaction.\n    abstract: true\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          the subject gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n      object:\n        range: gene or gene product\n        description: >-\n          the object gene in the association. If the relation is symmetric,\n          subject vs object is arbitrary. We allow a gene product to stand\n          as a proxy for the gene or vice versa.\n\n  gene to gene homology association:\n    description: >-\n      A homology association between two genes. May be orthology (in which\n      case the species of subject and object should differ) or paralogy\n      (in which case the species may be the same)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene or gene product\n      predicate:\n        subproperty_of: homologous to\n        symmetric: true\n        description: >-\n          homology relationship type\n      object:\n        range: gene or gene product\n\n  gene to gene family association:\n    description: >-\n      Set membership of a gene in a family of genes related by common\n      evolutionary ancestry usually inferred by sequence comparisons.\n      The genes in a given family generally share common sequence motifs which\n      generally map onto shared gene product structure-function relationships.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene family\n      predicate:\n        subproperty_of: member of\n        symmetric: false\n        description: >-\n          membership of the gene in the given gene family.\n\n  gene expression mixin:\n    description: >-\n      Observed gene expression intensity, context (site, stage) and\n      associated phenotypic status within which the expression occurs.\n    mixin: true\n    slots:\n      - quantifier qualifier\n      - expression site\n      - stage qualifier\n      - phenotypic state\n    slot_usage:\n      quantifier qualifier:\n        description: >-\n          Optional quantitative value indicating degree of expression.\n\n  gene to gene coexpression association:\n    description: >-\n      Indicates that two genes are co-expressed,\n      generally under the same conditions.\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: coexpressed with\n        symmetric: true\n\n  pairwise gene to gene interaction:\n    description: >-\n      An interaction between two genes or two gene products.\n      May be physical (e.g. protein binding) or genetic (between genes).\n      May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)\n    is_a: gene to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      predicate:\n        subproperty_of: interacts with\n        symmetric: true\n        description: \"interaction relationship type\"\n    narrow_mappings:\n      - dcid:ProteinProteinInteraction\n\n  pairwise molecular interaction:\n    description: >-\n      An interaction at the molecular level between two physical entities\n    is_a: pairwise gene to gene interaction\n    slots:\n      - interacting molecules category\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: molecular entity\n      id:\n        description: >-\n          identifier for the interaction. This may come from an interaction database such as IMEX.\n        examples:\n          - value: WB:WBInteraction000538741\n        values_from:\n          - IMEX\n          - BioGRID\n      predicate:\n        subproperty_of: interacts with\n        description: \"interaction relationship type\"\n        examples:\n          - value: RO:0002447\n            description: the subject molecular phosphorylates the object molecule\n      object:\n        range: molecular entity\n\n  cell line to entity association mixin:\n    description: >-\n      An relationship between a cell line and another entity\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: cell line\n\n   # TODO: figure out what gives with subject range\n  cell line to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - cell line to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    description: >-\n      An relationship between a cell line and a disease or a phenotype, where\n      the cell line is derived from an individual with that disease or phenotype.\n    slot_usage:\n      subject:\n         #        - range: cell line\n         #        - range: disease or phenotypic feature\n        range: disease or phenotypic feature\n\n  chemical entity to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity that is an interactor\"\n\n  drug to entity association mixin:\n    description: >-\n      An interaction between a drug and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: drug\n        description: \"the drug that is an interactor\"\n\n  chemical to entity association mixin:\n    description: >-\n      An interaction between a chemical entity and another entity\n    is_a: chemical entity to entity association mixin\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: chemical entity or gene or gene product\n        description: \"the chemical entity or entity that is an interactor\"\n\n  case to entity association mixin:\n    description: >-\n      An abstract association for use where the case is the subject\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: case\n        description: \"the case (e.g. patient) that has the property\"\n\n  chemical to chemical association:\n    description: >-\n      A relationship between two chemical entities. This can encompass actual\n      interactions as well as temporal causal edges, e.g. one chemical converted to another.\n    is_a: association\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      object:\n        range: chemical entity\n        description: \"the chemical element that is the target of the statement\"\n\n  reaction to participant association:\n    description:\n    is_a: chemical to chemical association\n    slots:\n      - stoichiometry\n      - reaction direction\n      - reaction side\n    slot_usage:\n      subject:\n        range: molecular entity\n    defining_slots:\n      - subject\n      - predicate\n      - object\n\n  reaction to catalyst association:\n    description:\n    is_a: reaction to participant association\n    slot_usage:\n      object:\n        range: gene or gene product\n\n  chemical to chemical derivation association:\n    description: >-\n      A causal relationship between two chemical entities, where the subject\n      represents the upstream entity and the object represents the downstream.\n      For any such association there is an implicit reaction: IF R has-input C1 AND\n      R has-output C2 AND R enabled-by P AND\n      R type Reaction THEN C1 derives-into C2 catalyst qualifier P\n    is_a: chemical to chemical association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - catalyst qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: >-\n          the upstream chemical entity\n      object:\n        range: chemical entity\n        description: >-\n          the downstream chemical entity\n      predicate:\n        subproperty_of: derives into\n      catalyst qualifier:\n        description: >-\n          this connects the derivation edge to the chemical entity that\n          catalyzes the reaction that causes the subject chemical to\n          transform into the object chemical.\n\n  chemical to disease or phenotypic feature association:\n    description: >-\n      An interaction between a chemical entity and a phenotype or disease,\n      where the presence of the chemical gives rise to or exacerbates the phenotype.\n    is_a: association\n    narrow_mappings:\n      - SIO:000993\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"the disease or phenotype that is affected by the chemical\"\n\n  chemical or drug or treatment to disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary undesirable effect.\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slots:\n      - FDA adverse event level\n    slot_usage:\n      predicate:\n        subproperty_of: has adverse event\n\n  chemical or drug or treatment side effect disease or phenotypic feature association:\n    description: >-\n      This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature\n      where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.\n    is_a: chemical or drug or treatment to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - chemical to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has side effect\n\n  gene to pathway association:\n    description: >-\n      An interaction between a gene or gene product and a biological process or pathway.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"the gene or gene product entity that participates or influences the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that includes or is affected by the gene or gene product\"\n\n  molecular activity to pathway association:\n    description: >-\n      Association that holds the relationship between a reaction and the pathway it participates in.\n    is_a: association\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: pathway\n      predicate:\n        subproperty_of: part of\n\n  chemical to pathway association:\n    description: >-\n      An interaction between a chemical entity and a biological process or pathway.\n    is_a: association\n    exact_mappings:\n      - SIO:001250\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - chemical to entity association mixin\n    slot_usage:\n      subject:\n        range: chemical entity\n        description: \"the chemical entity that is affecting the pathway\"\n      object:\n        range: pathway\n        description: \"the pathway that is affected by the chemical\"\n\n  named thing associated with likelihood of named thing association:\n     # TODO: better name\n    description: >-\n    is_a: association\n    slots:\n      - subject\n      - subject aspect qualifier\n      - subject context qualifier\n      - predicate\n      - object\n      - object aspect qualifier\n      - object context qualifier\n      - population context qualifier\n    defining_slots:\n      - subject\n      - subject aspect qualifier\n      - subject context qualifier\n      - predicate\n      - object\n      - object aspect qualifier\n      - object context qualifier\n      - population context qualifier\n    slot_usage:\n      predicate:\n        subproperty_of: associated with\n      subject aspect qualifier:\n       # TODO: range\n      subject context qualifier:\n        range: ontology class\n      object aspect qualifier:\n       # TODO: range\n      object context qualifier:\n        range: ontology class\n\n  chemical gene interaction association:\n    description: >-\n      describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical\n      effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type\n      (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)\n    is_a: association\n    exact_mappings:\n      - SIO:001257\n    mixins:\n      - chemical to entity association mixin\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject context qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object context qualifier\n      - anatomical context qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n      object:\n        range: gene or gene product\n      predicate:\n        subproperty_of: physically interacts with\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject context qualifier:\n        range: anatomical entity\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object context qualifier:\n        range: anatomical entity\n      anatomical context qualifier:\n        range: anatomical entity\n\n  chemical affects gene association:\n    description: >-\n      Describes an effect that a chemical has on a gene or gene product (e.g. an impact\n      of on its abundance, activity,localization, processing, expression, etc.)\n    is_a: association\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject aspect qualifier\n      - subject context qualifier\n      - subject direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object aspect qualifier\n      - object context qualifier\n      - object direction qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - qualified predicate\n      - species context qualifier\n    slot_usage:\n      subject:\n        range: chemical entity\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      subject context qualifier:\n        range: anatomical entity\n      subject direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n      qualified predicate:\n        subproperty_of: causes\n      object:\n        range: gene or gene product\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      object context qualifier:\n        range: anatomical entity\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      causal mechanism qualifier:\n        range: CausalMechanismQualifierEnum\n      anatomical context qualifier:\n        range: anatomical entity\n      species context qualifier:\n        range: organism taxon\n\n  gene affects chemical association:\n    description: >-\n      Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact\n      of on its abundance, activity, localization, processing, transport, etc.)\n    examples:\n      value:\n        subject: TRPC4\n        predicate: affects\n        qualified_predicte: causes\n        object: Barium\n        object_aspect_qualifier: transport\n        object_direction_qualifier: increased\n    is_a: association\n    slots:\n      - subject form or variant qualifier\n      - subject part qualifier\n      - subject derivative qualifier\n      - subject aspect qualifier\n      - subject context qualifier\n      - subject direction qualifier\n      - object form or variant qualifier\n      - object part qualifier\n      - object aspect qualifier\n      - object context qualifier\n      - object direction qualifier\n      - object derivative qualifier\n      - causal mechanism qualifier\n      - anatomical context qualifier\n      - qualified predicate\n      - species context qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n      subject form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      subject part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      subject context qualifier:\n        range: anatomical entity\n      subject direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n      qualified predicate:\n        subproperty_of: causes\n      object:\n        range: chemical entity\n      object form or variant qualifier:\n        range: ChemicalOrGeneOrGeneProductFormOrVariantEnum\n      object part qualifier:\n        range: GeneOrGeneProductOrChemicalPartQualifierEnum\n      object derivative qualifier:\n        range: ChemicalEntityDerivativeEnum\n      object aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      object context qualifier:\n        range: anatomical entity\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      causal mechanism qualifier:\n        range: CausalMechanismQualifierEnum\n      anatomical context qualifier:\n        range: anatomical entity\n      species context qualifier:\n        range: organism taxon\n\n  drug to gene association:\n    description: >-\n      An interaction between a drug and a gene or gene product.\n    is_a: association\n    related_mappings:\n      - SIO:001257\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - drug to entity association mixin\n    slot_usage:\n      object:\n        range: gene or gene product\n        description: \"the gene or gene product that is affected by the drug\"\n\n  material sample to entity association mixin:\n    description: >-\n      An association between a material sample and something.\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n\n  material sample derivation association:\n    description: >-\n      An association between a material sample and\n      the material entity from which it is derived.\n    is_a: association\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n      - predicate\n    slot_usage:\n      subject:\n        range: material sample\n        description: >-\n          the material sample being described\n      object:\n        description: >-\n          the material entity the sample was derived from. This may be another\n          material sample, or any other material entity, including for example\n          an organism, a geographic feature, or some environmental material.\n      predicate:\n        description: >-\n          derivation relationship\n        subproperty_of: derives from\n\n  material sample to disease or phenotypic feature association:\n    description: >-\n      An association between a material sample and a disease or phenotype.\n    is_a: association\n    mixins:\n      - material sample to entity association mixin\n      - entity to disease or phenotypic feature association mixin\n    defining_slots:\n      - subject\n      - object\n\n  disease to entity association mixin:\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease\n        description: \"disease class\"\n        values_from: ['mondo', 'omim', 'orphanet', 'ncit', 'doid']\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n\n  entity to exposure event association mixin:\n    description: >-\n      An association between some entity and an exposure event.\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: exposure event\n\n  disease to exposure event association:\n    description: >-\n      An association between an exposure event and a disease.\n    is_a: association\n    mixins:\n      - disease to entity association mixin\n      - entity to exposure event association mixin\n    defining_slots:\n      - subject\n      - object\n\n\n  entity to outcome association mixin:\n    description: >-\n      An association between some entity and an outcome\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: outcome\n\n  exposure event to outcome association:\n    description: >-\n      An association between an exposure event and an outcome.\n    is_a: association\n    mixins:\n      - entity to outcome association mixin\n    slots:\n      - population context qualifier\n      - temporal context qualifier\n    defining_slots:\n      - subject\n      - object\n\n  frequency qualifier mixin:\n    mixin: true\n    description: >-\n      Qualifier for frequency type associations\n    slots:\n      - frequency qualifier\n      - subject\n      - predicate\n      - object\n\n  entity to feature or disease qualifiers mixin:\n    description: >-\n      Qualifiers for entity to disease or phenotype associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - subject aspect qualifier\n      - subject direction qualifier\n      - object aspect qualifier\n      - object direction qualifier\n      - qualified predicate\n\n  feature or disease qualifiers to entity mixin:\n    description: >-\n      Qualifiers for disease or phenotype to entity associations.\n    mixin: true\n    is_a: frequency qualifier mixin\n    slots:\n      - subject aspect qualifier\n      - subject direction qualifier\n      - object aspect qualifier\n      - object direction qualifier\n      - qualified predicate\n\n  entity to phenotypic feature association mixin:\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    mixins:\n      - frequency quantifier\n    slots:\n      - subject\n      - predicate\n      - object\n      - sex qualifier\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: phenotypic feature\n        values_from: ['upheno', 'hp', 'mp', 'wbphenotype']\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n\n  phenotypic feature to entity association mixin:\n    mixin: true\n    is_a: feature or disease qualifiers to entity mixin\n    mixins:\n      - frequency quantifier\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: phenotypic feature\n        values_from: ['upheno', 'hp', 'mp', 'wbphenotype']\n        examples:\n          - value: HP:0002487\n            description: Hyperkinesis\n          - value: WBPhenotype:0000180\n            description: axon morphology variant\n          - value: MP:0001569\n            description: abnormal circulating bilirubin level\n    slots:\n      - sex qualifier\n\n  information content entity to named thing association:\n    description: >-\n      association between a named thing and a information content entity where the specific context\n      of the relationship between that named thing and the publication is unknown. For\n      example, model organisms databases often capture the knowledge that a gene is found in a\n      journal article, but not specifically the context in which that gene was documented in the article.\n      In these cases, this association with the accompanying predicate 'mentions' could be used.\n      Conversely, for more specific associations (like 'gene to disease association', the publication should\n      be captured as an edge property).\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        domain: publication\n      object:\n        range: named thing\n      predicate:\n        subproperty_of: mentions\n    in_subset:\n      - model_organism_database\n\n  entity to disease association mixin:\n    description: >-\n      mixin class for any association whose object (target node) is a disease\n    mixin: true\n    is_a: entity to feature or disease qualifiers mixin\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease\n        description: \"disease\"\n        examples:\n          - value: MONDO:0020066\n            description: \"Ehlers-Danlos syndrome\"\n\n  disease or phenotypic feature to entity association mixin:\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  disease or phenotypic feature to location association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      an anatomical entity, where the disease/feature manifests in that site.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      object:\n        range: anatomical entity\n        description: >-\n          anatomical entity in which the disease or feature is found.\n        examples:\n          - value: UBERON:0002048\n            description: \"lung\"\n\n  disease or phenotypic feature to genetic inheritance association:\n    description: >-\n      An association between either a disease or a phenotypic feature and\n      its mode of (genetic) inheritance.\n    is_a: association\n    mixins:\n      - disease or phenotypic feature to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has mode of inheritance\n      object:\n        range: genetic inheritance\n        description: >-\n          genetic inheritance associated with the specified disease or phenotypic feature.\n        examples:\n          - value: HP:0001417\n            description: \"X-linked inheritance\"\n\n  entity to disease or phenotypic feature association mixin:\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - object\n    slot_usage:\n      object:\n        range: disease or phenotypic feature\n        description: \"disease or phenotype\"\n        examples:\n          - value: MONDO:0017314\n            description: \"Ehlers-Danlos syndrome, vascular type\"\n          - value: MP:0013229\n            description: \"abnormal brain ventricle size\"\n\n  genotype to entity association mixin:\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: genotype\n        description: \"genotype that is the subject of the association\"\n\n  genotype to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between one genotype and a phenotypic feature, where having\n      the genotype confers the phenotype, either in isolation or through environment\n    mixins:\n      - entity to phenotypic feature association mixin\n      - genotype to entity association mixin\n    slot_usage:\n      predicate:\n        subproperty_of: has phenotype\n      subject:\n        range: genotype\n        description: >-\n          genotype that is associated with the phenotypic feature\n\n   # ie: smoke exposure to coughing phenotype? is this a denormalization?\n  exposure event to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      Any association between an environment and a phenotypic feature,\n      where being in the environment influences the phenotype.\n    mixins:\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: exposure event\n\n  disease to phenotypic feature association:\n    is_a: association\n    slots:\n      - onset qualifier\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      An association between a disease and a phenotypic feature in which the\n      phenotypic feature is associated with the disease in some way.\n    mixins:\n      - frequency quantifier\n      - entity to phenotypic feature association mixin\n      - disease to entity association mixin\n    close_mappings:\n      - dcid:DiseaseSymptomAssociation\n    slot_usage:\n      subject:\n        range: disease\n      object:\n        range: phenotypic feature\n\n  case to phenotypic feature association:\n    description: >-\n      An association between a case (e.g. individual patient) and a phenotypic\n      feature in which the individual has or has had the phenotype.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - case to entity association mixin\n\n  behavior to behavioral feature association:\n    description: >-\n      An association between an mixture behavior and\n      a behavioral feature manifested by\n      the individual exhibited or has exhibited the behavior.\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: behavior\n        description: >-\n          behavior that is the subject of the association\n      object:\n        range: behavioral feature\n        description: >-\n          behavioral feature that is the object of the association\n    mixins:\n      - entity to phenotypic feature association mixin\n\n  gene to entity association mixin:\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene that is the subject of the association\n\n  variant to entity association mixin:\n    slots:\n      - subject\n      - predicate\n      - object\n    local_names:\n      ga4gh: variant annotation\n    mixin: true\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is associated with some other entity\n        examples:\n          - value: CLINVAR:38077\n            description: \"CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)\"\n          - value: ClinGen:CA024716\n            description: \"chr13:g.32921033G>C (hg19) in ClinGen\"\n\n  gene to disease or phenotypic feature association:\n    is_a: association\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    narrow_mappings:\n      - WBVocab:Gene-Phenotype-Association\n      - dcid:DiseaseGeneAssociation\n      - SIO:000983\n    slots:\n      - subject aspect qualifier\n      - object direction qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      subject aspect qualifier:\n        range: GeneOrGeneProductOrChemicalEntityAspectEnum\n      object:\n        range: disease or phenotypic feature\n      object direction qualifier:\n        range: DirectionQualifierEnum\n      predicate:\n        subproperty_of: affects\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n      - for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype\n      - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.\n\n  gene to phenotypic feature association:\n    is_a: gene to disease or phenotypic feature association\n    exact_mappings:\n      - WBVocab:Gene-Phenotype-Association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to phenotypic feature association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: \"gene in which variation is correlated with the phenotypic feature\"\n        examples:\n          - value: HGNC:2197\n            description: \"COL1A1 (Human)\"\n      object:\n        range: phenotypic feature\n\n  gene to disease association:\n    is_a: gene to disease or phenotypic feature association\n    comments:\n      - NCIT:R176 refers to the inverse relationship\n    exact_mappings:\n      - SIO:000983\n    close_mappings:\n      - dcid:DiseaseGeneAssociation\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease,\n          may be protective or causative or associative, or as a model\n      object:\n        range: disease\n\n  causal gene to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is shown to cause the disease.\n      object:\n        range: disease\n\n  correlated gene to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is shown to correlate with the disease.\n      object:\n        range: disease\n\n  druggable gene to disease association:\n    is_a: gene to disease association\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          gene in which variation is correlated with the disease\n          in a protective manner, or if the product produced by the gene can be targeted by a small molecule and\n          this leads to a protective or improving disease state.\n      predicate:\n        subproperty_of: target for\n      has evidence:\n        range: DruggableGeneCategoryEnum\n    defining_slots:\n      - subject\n      - object\n      - predicate\n    mixins:\n      - entity to disease association mixin\n      - gene to entity association mixin\n\n  phenotypic feature to disease association:\n    is_a: association\n    slot_usage:\n      predicate:\n        subproperty_of: associated with\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - entity to disease association mixin\n      - phenotypic feature to entity association mixin\n\n  variant to gene association:\n    description: >-\n      An association between a variant and a gene, where the variant has\n      a genetic association with the gene (i.e. is in linkage disequilibrium)\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - variant to entity association mixin\n    slot_usage:\n      object:\n        range: gene\n      predicate:\n        subproperty_of: genetically associated with\n\n  variant to gene expression association:\n    description: >-\n      An association between a variant and expression of a gene (i.e. e-QTL)\n    is_a: variant to gene association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - gene expression mixin\n    slot_usage:\n      predicate:\n        subproperty_of: affects\n\n  variant to population association:\n    description: >-\n      An association between a variant and a population, where the variant has\n      particular frequency in the population\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - frequency quantifier\n      - frequency qualifier mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          an allele that has a certain frequency in a given population\n        examples:\n          - value: \"NC_000017.11:g.43051071A>T\"\n            description: >-\n              17:41203088 A/C in gnomad\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that is observed to have the frequency\n        examples:\n          - value: HANCESTRO:0010\n            description: African\n      has quotient:\n        description: >-\n          frequency of allele in population, expressed as a number with allele\n          divided by number in reference population, aka allele frequency\n        examples:\n          - value: \"0.0001666\"\n      has count:\n        description: >-\n          number in object population that carry a particular allele, aka allele count\n        examples:\n          - value: \"4\"\n            description: 4 individuals in gnomad set\n      has total:\n        description: >-\n          number all populations that carry a particular allele, aka allele number\n        examples:\n          - value: \"24014\"\n            description: 24014 individuals in gnomad set\n\n  population to population association:\n    description: >-\n      An association between a two populations\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: population of individual organisms\n        description: >-\n          the population that form the subject of the association\n      object:\n        range: population of individual organisms\n        description: >-\n          the population that form the object of the association\n      predicate:\n         # subproperty_of: ???\n        description: >-\n          A relationship type that holds between the subject and object\n          populations. Standard mereological relations can be used.\n          E.g. subject part-of object, subject overlaps object.\n          Derivation relationships can also be used\n\n  variant to phenotypic feature association:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to phenotypic feature association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          a sequence variant in which the allele state is\n          associated in some way with the phenotype state\n\n  variant to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - variant to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a sequence variant in which the allele state\n          is associated in some way with the disease state\n        examples:\n          - value: CLINVAR:52241\n            description: \"NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)\"\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that variant\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  genotype to disease association:\n    is_a: association\n    comments:\n      - TODO decide no how to model pathogenicity\n    defining_slots:\n      - subject\n      - object\n    mixins:\n      - genotype to entity association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        description: >-\n          a genotype that is associated in some way with a disease state\n      predicate:\n        description: >-\n          E.g. is pathogenic for\n        subproperty_of: related condition\n      object:\n        description: >-\n          a disease that is associated with that genotype\n        examples:\n          - value: MONDO:0016419\n            description: hereditary breast cancer\n\n  model to disease association mixin:\n    description: >-\n      This mixin is used for any association class for which the subject\n      (source node) plays the role of a 'model', in that it recapitulates some\n      features of the disease in a way that is useful for studying the disease\n      outside a patient carrying the disease\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        description: >-\n          The entity that serves as the model of the disease. This may be\n          an organism, a strain of organism, a genotype or variant that exhibits\n          similar features, or a gene that when mutated exhibits features of the disease\n      predicate:\n        subproperty_of: model of\n        description: >-\n          The relationship to the disease\n\n  gene as a model of disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be a model\n          organism ortholog of a known disease gene, or it may be a gene whose\n          mutants recapitulate core features of the disease.\n\n  variant as a model of disease association:\n    is_a: variant to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: >-\n          A variant that has a role in modeling the disease.\n\n  genotype as a model of disease association:\n    is_a: genotype to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: genotype\n        description: >-\n          A genotype that has a role in modeling the disease.\n\n  cell line as a model of disease association:\n    is_a: cell line to disease or phenotypic feature association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: cell line\n        description: >-\n          A cell line derived from an organismal entity with a disease state that is used\n          as a model of that disease.\n\n  organismal entity as a model of disease association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    mixins:\n      - model to disease association mixin\n      - entity to disease association mixin\n    slot_usage:\n      subject:\n        range: organismal entity\n        description: >-\n          A organismal entity (strain, breed) with a predisposition to a disease, or bred/created\n          specifically to model a disease.\n\n  organism to organism association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: individual organism\n      object:\n        range: individual organism\n        description: >-\n          An association between two individual organisms.\n\n  taxon to taxon association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n        description: >-\n          An association between individuals of different taxa.\n\n  gene has variant that contributes to disease association:\n    is_a: gene to disease association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    slots:\n      - subject form or variant qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          A gene that has a role in modeling the disease. This may be\n          a model organism ortholog of a known disease gene, or it may be\n          a gene whose mutants recapitulate core features of the disease.\n      object:\n        range: disease\n      predicate:\n        subproperty_of: contributes to\n\n  gene to expression site association:\n    is_a: association\n    defining_slots:\n      - subject\n      - predicate\n      - object\n    description: >-\n      An association between a gene and a gene expression site,\n      possibly qualified by stage/timing info.\n    notes:\n      - \"TBD: introduce subclasses for distinction between wild-type and experimental conditions?\"\n    see_also: \"https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee\"\n    slots:\n      - stage qualifier\n      - quantifier qualifier\n    slot_usage:\n      subject:\n        range: gene or gene product\n        description: >-\n          Gene or gene product positively within the specified\n          anatomical entity (or subclass, i.e. cellular component) location.\n      object:\n        range: anatomical entity\n        description: \"location in which the gene is expressed\"\n        examples:\n          - value: UBERON:0002037\n            description: cerebellum\n      predicate:\n        description: \"expression relationship\"\n        subproperty_of: expressed in\n      stage qualifier:\n        range: life stage\n        description: \"stage at which the gene is expressed in the site\"\n        examples:\n          - value: UBERON:0000069\n            description: larval stage\n      quantifier qualifier:\n        description: >-\n          can be used to indicate magnitude, or also ranking\n\n  sequence variant modulates treatment association:\n    is_a: association\n    description: >-\n      An association between a sequence variant and a treatment or health intervention.\n      The treatment object itself encompasses both the disease and the drug used.\n    comments:\n      - An alternate way to model the same information could be via a qualifier\n    defining_slots:\n      - subject\n      - object\n    abstract: true\n    slot_usage:\n      subject:\n        range: sequence variant\n        description: \"variant that modulates the treatment of some disease\"\n      object:\n        range: treatment\n        description: \"treatment whose efficacy is modulated by the subject variant\"\n\n  functional association:\n    is_a: association\n    description: >-\n      An association between a macromolecular machine mixin (gene, gene product or\n      complex of gene products) and either a molecular activity, a biological\n      process or a cellular location in which a function is executed.\n    slot_usage:\n      subject:\n        range: macromolecular machine mixin\n        description: >-\n          gene, product or macromolecular complex that\n          has the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n          - value: GO:0045211\n            description: postsynaptic membrane\n\n  macromolecular machine to entity association mixin:\n    description: >-\n      an association which has a macromolecular machine mixin as a subject\n    mixin: true\n    slots:\n      - subject\n      - predicate\n      - object\n    slot_usage:\n      subject:\n        domain: macromolecular machine mixin\n\n  macromolecular machine to molecular activity association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a molecular activity (as represented\n      in the GO molecular function branch), where the entity\n      carries out the activity, or contributes to its execution.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: molecular activity\n\n  macromolecular machine to biological process association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a biological process or pathway\n      (as represented in the GO biological process branch), where the entity\n      carries out some part of the process, regulates it, or acts upstream of it.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: biological process\n\n  macromolecular machine to cellular component association:\n    description: >-\n      A functional association between a macromolecular machine (gene,\n      gene product or complex) and a cellular component (as represented\n      in the GO cellular component branch), where the entity\n      carries out its function in the cellular component.\n    is_a: functional association\n    mixins:\n      - macromolecular machine to entity association mixin\n    slot_usage:\n      object:\n        range: cellular component\n\n  molecular activity to chemical entity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: chemical entity\n\n  molecular activity to molecular activity association:\n    is_a: association\n    description: >-\n      Added in response to capturing relationship between microbiome activities as measured via\n      measurements of blood analytes as collected via blood and stool samples\n    slot_usage:\n      subject:\n        range: molecular activity\n      object:\n        range: molecular activity\n\n\n  gene to go term association:\n    aliases: ['functional association']\n    is_a: functional association\n    exact_mappings:\n      - WBVocab:Gene-GO-Association\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: gene\n        description: >-\n          gene, product or macromolecular complex that has\n          the function associated with the GO term\n        examples:\n          - value: ZFIN:ZDB-GENE-050417-357\n            description: twist1b\n      object:\n        range: ontology class\n        description: >-\n          class describing the activity, process or\n          localization of the gene product\n        values_from:\n          - go\n        examples:\n          - value: GO:0016301\n            description: kinase activity\n\n  entity to disease association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - clinical approval status\n      - max research phase\n    defining_slots:\n      - subject\n      - object\n\n  entity to phenotypic feature association:\n    is_a: association\n    exact_mappings:\n    slots:\n      - clinical approval status\n      - max research phase\n    defining_slots:\n      - subject\n      - object\n\n   ## -----------------\n   ## SEQUENCE FEATURES\n   ## -----------------\n\n  sequence association:\n    is_a: association\n    description: >-\n      An association between a sequence feature and a nucleic acid entity it is localized to.\n\n  genomic sequence localization:\n    is_a: sequence association\n    description: >-\n      A relationship between a sequence feature and a nucleic acid entity\n      it is localized to. The reference entity may be a chromosome,\n      chromosome region or information entity such as a contig.\n    slot_usage:\n      subject:\n        aliases: ['sequence feature']\n        range: nucleic acid entity\n      object:\n        aliases: ['reference']\n        range: nucleic acid entity   # typically a chromosome use monochrom\n      predicate:\n        subproperty_of: has sequence location\n    slots:\n      - start interbase coordinate\n      - end interbase coordinate\n      - genome build\n      - strand\n      - phase\n    broad_mappings:\n      - dcid:Chromosome\n    exact_mappings:\n      - dcid:GenomeAnnotation\n\n  sequence feature relationship:\n    is_a: association\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      For example, a particular exon is part of a particular transcript or gene\n    slot_usage:\n      subject:\n        range: nucleic acid entity\n      object:\n        range: nucleic acid entity   # typically a chromosome\n    exact_mappings:\n      - CHADO:feature_relationship\n\n  transcript to gene relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is a collection of transcripts\n    slot_usage:\n      subject:\n        range: transcript\n      object:\n        range: gene\n\n  gene to gene product relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A gene is transcribed and potentially translated to a gene product\n    slot_usage:\n      subject:\n        range: gene\n      object:\n        range: gene product mixin\n      predicate:\n        subproperty_of: has gene product\n\n  exon to transcript relationship:\n    is_a: sequence feature relationship\n    defining_slots:\n      - subject\n      - object\n    description: >-\n      A transcript is formed from multiple exons\n    slot_usage:\n      subject:\n        range: exon\n      object:\n        range: transcript\n\n  chemical entity or gene or gene product regulates gene association:\n    is_a: association\n    description: >-\n      A regulatory relationship between two genes\n    slots:\n      - object direction qualifier\n    slot_usage:\n      predicate:\n        description: >-\n          the direction is always from regulator to regulated\n        subproperty_of: regulates\n      subject:\n        range: chemical entity or gene or gene product\n        role: regulatory gene\n      object:\n        range: gene or gene product\n        role: regulated gene\n      object direction qualifier:\n        range: DirectionQualifierEnum\n\n  anatomical entity to anatomical entity association:   # schema: gocam\n    is_a: association\n    abstract: true\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: anatomical entity\n      object:\n        range: anatomical entity\n\n  anatomical entity to anatomical entity part of association:\n     #      schema: gocam\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is mereological, i.e the two entities are related by parthood. This\n      includes relationships between cellular components and cells, between\n      cells and tissues, tissues and whole organisms\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the part\n      object:\n        range: anatomical entity\n        description: >-\n          the whole\n      predicate:\n        subproperty_of: part of\n\n  anatomical entity to anatomical entity ontogenic association:\n    is_a: anatomical entity to anatomical entity association\n    description: >-\n      A relationship between two anatomical entities where the relationship\n      is ontogenic, i.e. the two entities are related by development. A number\n      of different relationship types can be used to specify the precise\n      nature of the relationship.\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: anatomical entity\n        description: >-\n          the structure at a later time\n      object:\n        range: anatomical entity\n        description: >-\n          the structure at an earlier time\n      predicate:\n        subproperty_of: develops from\n\n  organism taxon to entity association:\n    mixin: true\n    description: >-\n      An association between an organism taxon and another entity\n    slots:\n      - subject\n      - predicate\n      - object\n    defining_slots:\n      - subject\n    slot_usage:\n      subject:\n        range: organism taxon\n        description: >-\n          organism taxon that is the subject of the association\n\n  organism taxon to organism taxon association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    description: >-\n      A relationship between two organism taxon nodes\n    defining_slots:\n      - subject\n      - object\n    slot_usage:\n      subject:\n        range: organism taxon\n      object:\n        range: organism taxon\n\n  organism taxon to organism taxon specialization:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      A child-parent relationship between two taxa.\n      For example: Homo sapiens subclass_of Homo\n    defining_slots:\n      - predicate\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: child taxon\n        description: >-\n          the more specific taxon\n      object:\n        range: organism taxon\n        role: parent taxon\n        description: >-\n          the more general taxon\n      predicate:\n        subproperty_of: subclass of\n\n  organism taxon to organism taxon interaction:\n    is_a: organism taxon to organism taxon association\n    description: >-\n      An interaction relationship between two taxa. This may be a symbiotic\n      relationship (encompassing mutualism and parasitism), or it may be non-symbiotic.\n      Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens\n    defining_slots:\n      - predicate\n    slots:\n      - associated environmental context\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        range: organism taxon\n        role: interactee taxon\n        description: >-\n          the taxon that is the subject of the association\n      predicate:\n        subproperty_of: interacts with\n      associated environmental context:\n        description: >-\n          the environment in which the two taxa interact\n\n  organism taxon to environment association:\n    is_a: association\n    abstract: true\n    mixins:\n      - organism taxon to entity association\n    slot_usage:\n      subject:\n        range: organism taxon\n        role: interactor taxon\n        description: >-\n          the taxon that is the subject of the association\n      object:\n        role: environmental context\n        description: >-\n          the environment in which the organism occurs\n      predicate:\n        description: >-\n          predicate describing the relationship between the taxon and the environment\n\n\nenums:\n\n  ClinicalApprovalStatusEnum:\n    description:\n    permissible_values:\n      approved_for_condition:\n      fda_approved_for_condition:\n        is_a: approved_for_condition\n      not_approved_for_condition:\n      post_approval_withdrawal:\n        is_a: not_approved_for_condition\n      off_label_use:\n        is_a: not_approved_for_condition\n      not_provided:\n\n  MaxResearchPhaseEnum:\n    permissible_values:\n      pre_clinical_research_phase:\n        description: >-\n          Biolink 'pre_clinical_research' is the union of both the `FDA discovery and development phase` and\n          `FDA preclinical research phase`. Discovery involves researchers finding new possibilities for medication\n          through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of\n          new technology that allows novel ways of targeting medical products to sites in the body. Drug development\n          occurs after researchers identify potential compounds for experiments Preclinical Research Phase.\n          Once researchers have examined the possibilities a new drug may contain, they must do preliminary research\n          to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of\n          two types: in vitro or in vivo.\n        notes: >-\n          DrugBank calls this 'experimental'.\n      clinical_trial_phase:\n        description: >-\n          Clinical research involves trials of the drug on people,\n          and it is one of the most involved stages in the drug development and approval process.\n          Clinical trials must answer specific questions and follow a protocol determined by\n          the drug researcher or manufacturer.\n      clinical_trial_phase_1:\n        is_a: clinical_trial_phase\n        description: >-\n          In the FDA Clinical Trial Phase, the Clinical Trial Phase 1 involves 20 – 100 study participants and\n          lasts several months. This phase is used to determine the safety and dosage of the drug,\n          and about 70% of these drugs move on to the next clinical research phase.\n      clinical_trial_phase_2:\n        is_a: clinical_trial_phase\n        description: >-\n          In the FDA Clinical Trial Phase, the Clinical Trial Phase 2 involves up to several hundred people,\n          who must have the disease or condition the drug supposes to treat. This phase can last\n          from a few months to two years, and its purpose is to monitor the efficacy of the drug,\n          as well as note side effects that may occur.\n      clinical_trial_phase_3:\n        is_a: clinical_trial_phase\n        description: >-\n          In the FDA Clinical Trial Phase, the Clinical Trial Phase 3 involves 300 – 3000 volunteers\n          and can last up to four years. It is used to continue monitoring the efficacy of\n          the drug, as well as exploring any longer-term adverse reactions.\n      clinical_trial_phase_4:\n        is_a: clinical_trial_phase\n        description: >-\n          In the FDA Clinical Trial Phase, the Clinical Trial Phase 4 involves several thousands of\n          volunteers who have the disease or condition and continues to monitor safety and efficacy.\n          If a drug passes this phase, it goes on to FDA review.\n      not_provided:\n\n  DirectionQualifierEnum:\n    permissible_values:\n      increased:\n      upregulated:\n        is_a: increased\n        close_mappings:\n          - RO:0002336\n        exact_mappings:\n          - RO:0002213\n        narrow_mappings:\n          - RO:0004032\n          - RO:0004034\n          - RO:0002629\n      decreased:\n      downregulated:\n        is_a: decreased\n        exact_mappings:\n          - RO:0004035\n          - RO:0002212\n        close_mappings:\n          - RO:0002335\n        broad_mappings:\n          - RO:0004033\n\n  ChemicalEntityDerivativeEnum:\n    permissible_values:\n      metabolite:\n\n  ChemicalOrGeneOrGeneProductFormOrVariantEnum:\n    permissible_values:\n      genetic_variant_form:\n        is_a: modified_form\n      modified_form:\n      loss_of_function_variant_form:\n        is_a: genetic_variant_form\n      gain_of_function_variant_form:\n        is_a: genetic_variant_form\n      polymorphic_form:\n        is_a: genetic_variant_form\n      snp_form:\n        is_a: polymorphic_form\n      analog_form:\n        is_a: modified_form\n\n  GeneOrGeneProductOrChemicalPartQualifierEnum:\n    permissible_values:\n      3_prime_utr:\n      5_prime_utr:\n      polya_tail:\n      promoter:\n      enhancer:\n      exon:\n      intron:\n\n  GeneOrGeneProductOrChemicalEntityAspectEnum:\n    permissible_values:\n      activity_or_abundance:\n        description: >-\n          Used in cases where the specificity of the relationship can not be determined to be either activity\n          or abundance.  In general, a more specific value from this enumeration should be used.\n      abundance:\n        is_a: activity_or_abundance\n      activity:\n        is_a: activity_or_abundance\n      expression:\n        is_a: abundance\n      synthesis:\n        is_a: abundance\n      degradation:\n      cleavage:\n        is_a: degradation\n      hydrolysis:\n        is_a: degradation\n      metabolic_processing:\n      mutation_rate:\n      stability:\n      folding:\n      localization:\n      transport:\n      secretion:\n        is_a: transport\n      uptake:\n        is_a: transport\n      splicing:\n      molecular_interaction:\n      molecular_modification:\n      acetylation:\n        is_a: molecular_modification\n      acylation:\n        is_a: molecular_modification\n      alkylation:\n        is_a: molecular_modification\n      amination:\n        is_a: molecular_modification\n      carbamoylation:\n        is_a: molecular_modification\n      ethylation:\n        is_a: molecular_modification\n      glutathionylation:\n        is_a: molecular_modification\n      glycation:\n        is_a: molecular_modification\n      glycosylation:\n        is_a: molecular_modification\n      glucuronidation:\n        is_a: molecular_modification\n      n_linked_glycosylation:\n        is_a: molecular_modification\n      o_linked_glycosylation:\n        is_a: molecular_modification\n      hydroxylation:\n        is_a: molecular_modification\n      lipidation:\n        is_a: molecular_modification\n      farnesylation:\n        is_a: molecular_modification\n      geranoylation:\n        is_a: molecular_modification\n      myristoylation:\n        is_a: molecular_modification\n      palmitoylation:\n        is_a: molecular_modification\n      prenylation:\n        is_a: molecular_modification\n      methylation:\n        is_a: molecular_modification\n      nitrosation:\n        is_a: molecular_modification\n      nucleotidylation:\n        is_a: molecular_modification\n      phosphorylation:\n        is_a: molecular_modification\n      ribosylation:\n        is_a: molecular_modification\n      ADP-ribosylation:\n        is_a: molecular_modification\n      sulfation:\n        is_a: molecular_modification\n      sumoylation:\n        is_a: molecular_modification\n      ubiquitination:\n        is_a: molecular_modification\n      oxidation:\n        is_a: molecular_modification\n      reduction:\n        is_a: molecular_modification\n      carboxylation:\n        is_a: molecular_modification\n\n  CausalMechanismQualifierEnum:\n    permissible_values:\n      binding:\n        description: >-\n          A causal mechanism mediated by the direct contact between effector and target chemical or\n          biomolecular entity, which form a stable physical interaction.\n      inhibition:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to the target and negatively effects its normal function,\n          e.g. prevention of enzymatic reaction or activation of downstream pathway.\n        close_mappings:\n          - DGIdb:inhibitor\n          - SEMMEDDB:INHIBITS\n        narrow_mappings:\n          - DGIdb:blocker\n          - DGIdb:channel_blocker\n          - DGIdb:gating_inhibitor\n          - CHEMBL.MECHANISM:antisense_inhibitor\n          - CHEMBL.MECHANISM:blocker\n          - CHEMBL.MECHANISM:inhibitor\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - CHEMBL.MECHANISM:negative_modulator\n          - DGIdb:negative_modulator\n      antibody_inhibition:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which an antibody specifically binds to and interferes with the target.\n      antagonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist\n          through competing for the binding site.\n        close_mappings:\n          - DGIdb:antagonist\n          - CHEMBL.MECHANISM:antagonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:allosteric_antagonist\n      molecular_channel_blockage:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and prevents or reduces\n          transport of ions through it.\n      inverse_agonism:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes\n          its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.\n        close_mappings:\n          - CHEMBL.MECHANISM:inverse_agonist\n          - DGIdb:inverse_agonist\n      negative_allosteric_modulation:\n        is_a: inhibition\n        description: >-\n          A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a\n          receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:negative_allosteric_modulator\n          - DGIdb:inhibitory_allosteric_modulator\n        narrow_mappings:\n          - DGIdb:negative_modulator\n      agonism:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an\n          endogenous ligand.\n        close_mappings:\n          - CHEMBL.MECHANISM:agonist\n          - DGIdb:agonist\n        narrow_mappings:\n          - CHEMBL.MECHANISM:partial_agonist\n          - DGIdb:partial_agonist\n      molecular_channel_opening:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector binds to a molecular channel and facilitates transport of\n          ions through it.\n        close_mappings:\n          - CHEMBL.MECHANISM:opener\n      positive_allosteric_modulation:\n        is_a: activation\n        description: >-\n          A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by\n          binding to a site distinct from that ligand (i.e. non-competitive inhibition)\n        close_mappings:\n          - CHEMBL.MECHANISM:positive_allosteric_modulator\n          - CHEMBL.MECHANISM:positive_modulator\n          - DGIdb:positive_allosteric_modulator\n        broad_mappings:\n          - DGIdb:modulator\n          - DGIdb:allosteric_modulator\n      potentiation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector  binds to and enhances or intensifies the effect of some\n          other chemical or drug on its target.\n        close_mappings:\n      activation:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.\n        close_mappings:\n          - CHEMBL.MECHANISM:activator\n          - DGIdb:activator\n      inducer:\n        is_a: binding\n        description: >-\n          A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that\n          processes drugs in the body.\n        close_mappings:\n          - DGIdb:inducer\n      transcriptional_regulation:\n        description: >-\n          A causal mechanism mediated by through the control of target gene transcription\n      signaling_mediated_control:\n        description: >-\n          A causal mechanism mediated by the activation or control of signaling events that influence the some aspect\n          of the target entity (e.g. its activity, processing, transport, etc)\n      stabilization:\n        is_a: activation\n        close_mappings:\n          - CHEMBL.MECHANISM:stabiliser\n      stimulation:\n        is_a: activation\n        close_mappings:\n          - DGIdb:stimulator\n          - SEMMEDDB:STIMULATES\n          - DGIdb:stimulator\n      releasing_activity:\n        is_a: activation\n        close_mappings:\n          - CHEMBL:MECHANISM:releasing_agent\n\n  LogicalInterpretationEnum:\n    permissible_values:\n      some_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as a some-some statement\n        meaning: os:SomeSomeInterpretation\n      all_some:\n        description: >-\n          A modifier on a triple that causes the triple to be interpreted as an all-some statement.\n        meaning: os:AllSomeInterpretation\n      inverse_all_some:\n\n  ReactionDirectionEnum:\n    permissible_values:\n      left_to_right:\n      right_to_left:\n      bidirectional:\n      neutral:\n\n  ReactionSideEnum:\n    permissible_values:\n      left:\n      right:\n\n  PhaseEnum:\n    description: phase\n    permissible_values:\n      0:\n      1:\n      2:\n\n  StrandEnum:\n    description: strand\n    permissible_values:\n      \"+\":\n        description: Positive\n      \"-\":\n        description: Negative\n      \".\":\n        description: Unstranded\n      \"?\":\n        description: Unknown\n\n  SequenceEnum:\n    description: type of sequence\n    permissible_values:\n      \"na\":\n        description: nucleic acid\n      \"aa\":\n        description: amino acid\n\n  DruggableGeneCategoryEnum:\n    permissible_values:\n      \"tclin\":\n        description: >-\n          These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.\n      \"tbio\":\n        description: >-\n          These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy\n          the activity thresholds detailed below.\n      \"tchem\":\n        description: >-\n          These targets do not have known drug or small molecule activities that satisfy the activity\n          thresholds detailed below AND satisfy one or more of the following criteria:\n          target is above the cutoff criteria for Tdark\n          target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)\n          with an Experimental Evidence code\n      \"tdark\":\n        description: >-\n          These are targets about which virtually nothing is known. They do not have known drug or small\n          molecule activities that satisfy the activity thresholds detailed below AND satisfy two or\n          more of the following criteria:\n          A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or\n          less than or equal to 50 Antibodies available according to http://antibodypedia.com.\n\n  DrugAvailabilityEnum:\n    description: >-\n    permissible_values:\n      \"over_the_counter\":\n        description: >-\n          chemical entity is available over the counter without a prescription.\n      \"prescription\":\n        description:\n          chemical entity is available by prescription.\n\n  DrugDeliveryEnum:\n    permissible_values:\n      \"inhalation\":\n      \"oral\":\n      \"absorption_through_the_skin\":\n      \"intravenous_injection\":\n\n  ResourceRoleEnum:\n    description: >-\n      The role played by the information reource in serving as a\n      source for an edge in a TRAPI message. Note that a given Edge should have one\n      and only one 'primary' source, and may have any number of\n      'aggregator' or 'supporting data' sources.  This enumeration\n      is found in Biolink Model, but is repeated here for convenience.\n    permissible_values:\n      \"primary_knowledge_source\":\n      \"aggregator_knowledge_source\":\n      \"supporting_data_source\":\n    in_subset:\n      - translator_minimal\n\n\n  FDAIDAAdverseEventEnum:\n    description: >-\n      please consult with the FDA guidelines as proposed in this document:\n      https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32\n    permissible_values:\n      \"life_threatening_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either\n          the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death.\n          It does not include an adverse event or suspected adverse reaction that, had it occurred in a more\n          severe form, might have caused death.\n      \"serious_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the\n          investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event,\n          inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity\n          or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth\n          defect. Important medical events that may not result in death, be life-threatening, or require hospitalization\n          may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or\n          subject and may require medical or surgical intervention to prevent one of the outcomes listed in this\n          definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment\n          in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient\n          hospitalization, or the development of drug dependency or drug abuse.\n      \"suspected_adverse_reaction\":\n        description: >-\n           means any adverse event for which there is a reasonable possibility that the drug caused the adverse event.\n           For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a\n           causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser\n           degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.\n      \"unexpected_adverse_event\":\n        description: >-\n          An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the\n          investigator brochure or is not listed at the specificity or severity that has been observed; or, if an\n          investigator brochure is not required or available, is not consistent with the risk information described\n          in the general investigational plan or elsewhere in the current application, as amended. For example,\n          under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the\n          investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral\n          thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the\n          investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition,\n          also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure\n          as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but\n          are not specifically mentioned as occurring with the particular drug under investigation.\n    in_subset:\n      - translator_minimal\n\n  AgentTypeEnum:\n    permissible_values:\n      manual_agent:\n        description: >-\n          A human agent who is responsible for generating a statement of\n          knowledge. The human may utilize computationally generated\n          information as evidence for the resulting knowledge, \n          but the human is the one who ultimately interprets/reasons with \n          this evidence to produce a statement of knowledge.\n      automated_agent:\n        description: >-\n          An automated agent, typically a software program or tool, that is \n          responsible for generating a statement of knowledge. Human contribution \n          to the knowledge creation process ends with the definition and coding\n          of algorithms or analysis pipelines that get executed by the automated\n          agent.\n      data_analysis_pipeline:\n        is_a: automated_agent\n        description: >-\n          An automated agent that executes an analysis workflow over data and \n          reports the direct results of the analysis. These typically report \n          statistical associations/correlations between variables in the input\n          dataset, and do not interpret/infer broader conclusions from associations\n          the analysis reveals in the data.\n        notes: >-\n          If an analysis pipeline includes any rules for generating broader \n          conclusions based on the dataset-specific statistical correlations\n          it calculates (e.g. create a 'treats' edge when the analysis reveals a \n          drug-disease correlation in the data with statistical scores that meet a \n          certain threshold) - we would consider this agent to be a Computational Model\n          rather than just a Data Analysis Pipeline.\n      computational_model:\n        is_a: automated_agent\n        description: >-\n          An automated agent that generates knowledge statements (typically\n          predictions) based on rules/logic explicitly encoded in an algorithm\n          (e.g. heuristic models, supervised classifiers), or learned from patterns \n          observed in data (e.g. ML models, unsupervised classifiers).\n        notes: >-\n          The bar is quite low relatively for what is considered to be a \n          ‘computational model’ by our definition. Even agents/tools that apply \n          simple rules or logic to the output of an ingest or analysis pipeline\n          to allow for a stronger or more general conclusion to be stated can \n          qualify an agent as a model. For example, an ingest pipeline that applies rules to its ingest of \n          clinical trials data to create a 'treats' prediction edge when the \n          source reports a drug to be in phase 2 or 3 trials represents a\n          computational model because it is automatically drawing a stronger\n          conclusion than the source reports, based on logic encoded in the ingest\n          pipeline. Similarly, a data analysis pipeline that is extended with rules to \n          automatically generate broader conclusions based on dataset-specific\n          statistical correlations (e.g. create a 'treats' edge when the analysis\n          reveals a drug-disease correlation in the data with statistical scores \n          that meet a certain threshold), would also qualify as a computational \n          model by our definition.\n      text_mining_agent:\n        is_a: automated_agent\n        description: >-\n          An automated agent that uses Natural Language Processing to recognize\n          concepts and/or relationships in text, and report them using formally\n          encoded semantics (e.g. as an edge in a knowledge graph).\n        notes: >-\n          The original statement in the source text is typically made by a human / \n          manual agent, but if a specific encoding of this knowledge is produced\n          by a text-mining tool, it has an agent_type of 'text_mining_agent'.\n          Examples of text mining agents include SemmedDB, and the Translator\n          Text-Mining Knowledge Provider. Note that text-mining tools are prone to erroneous interpretation of \n          concepts and relationships, and can fail to provide important details \n          about the context in which the original knowledge was reported - so\n          users should always consult the source text for a text-mined statement\n          to assess its veracity and relevance.\n      image_processing_agent:\n        is_a: automated_agent\n        description: >-\n          An automated agent that processes images to generate textual statements of \n          knowledge derived from the image and/or expressed in text the image \n          depicts (e.g. via OCR).\n      manual_validation_of_automated_agent:\n        description: >-\n          A human agent reviews and validates/approves the veracity of knowledge \n          that is initially generated by an automated agent.\n        notes: >-\n          This term applies when a human was only involved in evaluating the veracity\n          of a knowledge statement that was generated by an automated agent. It is \n          important to indicate when such manual review has occurred, because it can\n          give a user more confidence in an automated statement.\n      not_provided:\n        description: >-\n          The agent type is not provided, typically because it cannot be determined\n          from available information if the agent that generated the knowledge is \n          manual or automated.\n    in_subset:\n      - translator_minimal\n\n  KnowledgeLevelEnum:\n    permissible_values:\n      knowledge_assertion:\n        aliases: ['assertion']\n        description: >-\n          A statement of purported fact that is put forth by an agent as true,\n          based on assessment of direct evidence. Assertions are likely but not \n          definitively true.\n        notes: >-\n          Knowledge Assertions are supported by direct evidence deemed sufficient\n          by some agent to support a confidence assertion of truth. Our certainty \n          in this truth is not absolute, but is typically higher than for Predictions.\n      logical_entailment:\n        aliases: ['deductive_inference']\n        description: >-\n          A statement reporting a conclusion that follows logically from premises\n          representing established facts or knowledge assertions (e.g. fingernail\n          part of finger, finger part of hand --> fingernail part of hand).\n        notes: >-\n          These statements report entailed conclusions derived through dedictive inference.\n          They are not directly asserted by a source, but logically follow from statement(s) \n          a source does make - and are necessarily true if their supporting premises are true. \n          In practice, these will primarily be entailments based on logic encoded in ontologies. \n          Examples include propagation of annotated knowledge to hierarchically-related concepts,\n          across paths through a graph constructed from transitive relationships, or sets of \n          relationships that support property chain inference.\n      prediction:\n        aliases: ['hypothesis']\n        description: >-\n          A statement of a possible fact based on probabilistic forms of reasoning over\n          more indirect forms of evidence, that lead to more speculative conclusions.\n        notes: >-\n          Predictions typically result from non-deductive forms of reasoning - e.g.\n          inductive and deductive inference, or statistical inference where conclusions\n          are drawn about a broader/global population based on data from a representative\n          cohort. For example, a prediction that a drug may treat a particular disease based on its chemical\n          similarity to known drugs that treat the disease, and the fact that it can inhibit proteins \n          in a pathway that is associated with the disease\n          As Predictions are based on weaker forms of inference and evidence, they are typically \n          considered lower confidence statements as compared to Knowledge Assertions and Logical\n          Entailments.\n      statistical_association:\n        description: >-\n          A statement that reports concepts representing variables in a dataset to be statistically\n          associated with each other in a particular cohort (e.g. 'Metformin Treatment (variable 1)\n          is correlated with Diabetes Diagnosis (variable 2) in EHR dataset X').\n        notes: >-\n          Such statements report the direct results of some statistical analysis. Their scope is limited\n          tp the cohort/dataset interrogated in the analysis, and they do not make broader claims or draw \n          more meaningful conclusions about the domain of discourse. Note however that such Statistical \n          Associations can be used as evidence to support a more pointed/precise Prediction or Assertion \n          of knowledge. For example, e.g. a Statistical Association between 'Metformin Prescription' and\n          'Diabetes Diagnosis' in EHR records could support a Prediction that 'Metformin treats Diabetes', \n          or 'Metformin causes Diabetes'. This 'treats' edge may have a knowledge_level of 'Prediction', \n          but the provider could use the 'evidence_type' edge property to indicate that this prediction is \n          based on a 'Statistical Association'. Because Statistical Associations directly report analysis-specific \n          results, we can consider them to be inherently true statements, whose broader utility is dependent on \n          subsequent generalization of the reported result to a broader population, and/or interpretation of the \n          result as support for a more meaningful statements about the domain of discourse.\n      observation:\n        description: >-\n          A statement reporting (and possibly quantifying) a phenomenon that was observed to occur - \n          absent any analysis or interpretation that generates a statistical association or supports\n          a broader conclusion or inference.\n        notes: >-\n          An observation that \"56362 people self-reported taking melatonin to treat migraines\"\n          is agnostic to whether melatonin is an effective or approved treatment - it only claims that it was\n          taken for this purpose. Such observations, however, may be used as the basis for predicting that a \n          drug may be efficacious against a disease.\n      not_provided:\n        description: >-\n          The knowledge level is not provided, typically because it cannot be determined from available.\n          information.\n        notes: >-\n          This term is most often applied for text-mined edges, as NLP tools are typically not able to detect\n          a specific knowledge level for the concept relationships they extract (e.g. whether the author \n          was predicting or asserting a relationship, or merely observed it to occur).\n    in_subset:\n      - translator_minimal\n"
  },
  {
    "path": "medikanren2/neo/neo-command-line-interface/README.md",
    "content": "# mediKanren Command-Line Interface\n\nThis command-line interface (CLI) allows users to query the mediKanren biomedical reasoning system to explore relationships between medical concepts, such as identifying drug targets that activate or inhibit specific genes.\n\n## Prerequisites\n\n- [Racket](https://racket-lang.org/) programming language installed on your system.\n- Access to the mediKanren knowledge graph database.\n\n## Installation\n\n1. **Clone the Repository**:\n   ```bash\n   git clone https://github.com/webyrd/mediKanren.git \n   ```\n2. **Navigate to the Directory**:\n   ```bash\n   cd mediKanren/medikanren2/neo/neo-command-line-interface\n   ```\n3. **Run the Script**:\n   ```bash\n   racket command-line-interface.rkt\n   ```\n\n## Usage\n\nUpon running the script, you'll be prompted to enter commands. The available commands are:\n\n- `activates CURIE ... > output-file`: Identifies entities that activate the specified CURIE(s).\n- `inhibits CURIE ... > output-file`: Identifies entities that inhibit the specified CURIE(s).\n- `synonyms CURIE ...`: Retrieves synonyms for the specified CURIE(s).\n- `all relations CURIE ... > output-file`: Retrieves all relations for the specified CURIE(s).\n- `with predicates -predicate PREDICATE ... -curie CURIE ... > output-file`: Retrieves relations for the specified CURIE(s) with given predicates.\n\n## Example Query\n\nTo identify drug targets that activate or inhibit a gene of interest:\n\n1. **Identify the CURIE for the Gene**: Determine the CURIE for the gene. For example, the CURIE for the gene *TP53* might be `HGNC:11998`.\n\n2. **Run the `synonyms` Command**:\n   ```bash\n   synonyms HGNC:11998\n   ```\n   **Expected Output**:\n   ```\n   The synonyms of (HGNC:11998) are (HGNC:11998 NCBIGene:7157 UMLS:C0079419 OMIM:191170 REACT:R-HSA-6797244 ENSEMBL:LRG_321 ENSEMBL:ENSG00000141510)\n   ```\n   You may find the details about the returned entities in the file `synonyms-details.tsv` under the same directory.\n\n3. **Run the `activates` Command**:\n   ```bash\n   activates HGNC:11998 NCBIGene:7157 UMLS:C0079419 OMIM:191170 REACT:R-HSA-6797244 ENSEMBL:LRG_321 ENSEMBL:ENSG00000141510 > activates_TP53.tsv\n   ```\n   This command will generate a file named `activates_TP53.tsv` containing entities that activate *TP53* with information about the enities and the relationships.\n\n   *Please note that `HGNC:11998` and all its synonyms retrieved via the `synonyms` command are included in the command.* \n\n5. **Run the `inhibits` Command**:\n   ```bash\n   inhibits HGNC:11998 NCBIGene:7157 UMLS:C0079419 OMIM:191170 REACT:R-HSA-6797244 ENSEMBL:LRG_321 ENSEMBL:ENSG00000141510 > inhibits_TP53.tsv\n   ```\n   This command will generate a file named `inhibits_TP53.tsv` containing entities that inhibit *TP53*.\n"
  },
  {
    "path": "medikanren2/neo/neo-command-line-interface/command-line-interface.rkt",
    "content": "#lang racket\n\n(require\n  \"../neo-low-level/query-low-level-multi-db.rkt\"\n  \"utils.rkt\"\n  racket/string\n  readline\n  )\n\n;; TODO:\n;; sentence column in output\n\n(define (mediKanren-activates curie* path)\n  (write-out-prepared-answers\n   (filter\n    activate-edge-filter\n   (query:X->Known\n    #f\n    '(\"biolink:has_increased_amount\"\n      \"biolink:affects\"\n      \"biolink:produces\"\n      \"biolink:regulates\"\n      \"biolink:regulates\"\n      \"biolink:enables\"\n      \"biolink:treats\"\n      \"biolink:positively_correlated_with\"\n      \"biolink:produces\"\n      \"biolink:ameliorates\")\n    curie*))\n   path))\n\n(define (mediKanren-inhibits curie* path)\n  (write-out-prepared-answers\n   (filter\n    inhibite-edge-filter\n    (query:X->Known\n     #f\n     '(\"biolink:prevents\"\n       \"biolink:affects\"\n       \"biolink:regulates\"\n       \"biolink:has_decreased_amount\"\n       \"biolink:disrupts\"\n       \"biolink:negatively_correlated_with\")\n     curie*))\n   path))\n\n(define (mediKanren-all-relations curie* path)\n  (write-out-prepared-answers\n   (append\n    (query:X->Known\n     #f\n     #f\n     curie*)\n    (query:Known->X\n     curie*\n     #f\n     #f))\n   path))\n\n(define (mediKanren-with-predicates curie* predicate* path)\n  (write-out-prepared-answers\n   (append\n    (query:X->Known\n     #f\n     predicate*\n     curie*)\n    (query:Known->X\n     curie*\n     predicate*\n     #f))\n   path))   \n\n(define (mediKanren-synonyms curie*)\n  (write-list-to-tsv\n   '(\"curie\" \"curie-name\" \"curie-properties\")\n   (synonym-format curie*)\n   \"synonyms-details.tsv\"))\n\n; Main loop for CLI\n(define (main-loop)\n  (display \"Enter your command: \")\n  (let ([input (read-line)])\n    (cond\n      [(string-prefix? input \"activates\")\n       (let ([arug* (string-split (substring input (string-length \"activates\")))])\n         (match arug*\n           [`(,c ... \">\" ,file-name)\n            (let ((curie* c)\n                  (path file-name))\n              (printf \"The input curies are ~a\\n\" c)\n              (mediKanren-activates curie* path)\n              (printf \"The results are written in file ~a\\n\" path)\n              )]\n           [else\n            (displayln \"Incomplete command. Please use 'activates CURIE ... > name-of-the-file'\")]))]\n      [(string-prefix? input \"inhibits\")\n       (let ([arug* (string-split (substring input (string-length \"inhibits\")))])\n         (match arug*\n           [`(,c ... \">\" ,file-name)\n            (let ((curie* c)\n                  (path file-name))\n              (printf \"The input curies are ~a\\n\" c)\n              (mediKanren-inhibits curie* path)\n              (printf \"The results are written in file ~a\\n\" path)\n              )]\n           [else\n            (displayln \"Incomplete command. Please use 'inhibits CURIE ... > name-of-the-file'\")]))]\n      [(string-prefix? input \"synonyms\")\n       (let* ([arug* (string-split (substring input (string-length \"synonyms\")))])\n         (match arug*\n           [`(,c ,c* ...) \n            (let* ((synonym* (curies->synonyms (list* c c*)))\n                   (synonym* (curie->gene/protein-conflation synonym*)))\n              (printf \"The synonyms of ~a are ~a\\n\" arug* synonym*)\n              (mediKanren-synonyms synonym*)\n              (printf \"You may find the details in the file synonyms-details.tsv.\\n\"))]\n           [else (displayln \"Incomplete command. Please use 'synonyms CURIE ...'\")]))]\n      [(string-prefix? input \"all relations\")\n       (let* ([arug* (string-split (substring input (string-length \"all relations\")))])\n         (match arug*\n           [`(,c ... \">\" ,file-name)\n            (let ((curie* c)\n                  (path file-name))\n              (printf \"The input curies are ~a\\n\" c)\n              (mediKanren-all-relations curie* path)\n              (printf \"The results are written in file ~a\\n\" path)\n              )]\n           [else\n            (displayln \"Incomplete command. Please use 'all relations CURIE ... > name-of-the-file'\")]))]\n      [(string-prefix? input \"with predicates\")\n       (let* ([arug* (string-split (substring input (string-length \"with predicates\")))])\n         (match arug*\n           [`(\"-predicate\",p ... \"-curie\" ,c ... \">\" ,file-name)\n            (let ((curie* c)\n                  (predicate* p)\n                  (path file-name))\n              (printf \"The input predicates are ~a and the input curies are ~a\\n\" p c)\n              (mediKanren-with-predicates curie* predicate* path)\n              (printf \"The results are written in file ~a\\n\" path)\n              )]\n           [else\n            (displayln \"Incomplete command. Please use 'with predicates -predicate PREDICATE ... -curie CURIE ... > name-of-the-file'\")]))]\n      [else (displayln \"Unknown command. Please use\n'activates CURIE ... > name-of-the-file' or\n'inhibits CURIE ... > name-of-the-file' or\n'synonyms CURIE ...' or\n'all relations CURIE ... > name-of-the-file'\n'with predicates -predicate PREDICATE ... -curie CURIE ... > name-of-the-file'\")])\n    (main-loop)))\n\n; Start the program\n(main-loop)"
  },
  {
    "path": "medikanren2/neo/neo-command-line-interface/utils.rkt",
    "content": "#lang racket/base\n\n(require\n  \"../neo-low-level/query-low-level-multi-db.rkt\"\n  \"../neo-utils/neo-helpers-without-db.rkt\"\n  racket/string\n  racket/list\n  racket/match\n  racket/set\n  )\n\n(provide get-publications\n         write-out-prepared-answers\n         activate-edge-filter\n         inhibite-edge-filter\n         write-list-to-tsv\n         curie->gene/protein-conflation\n         synonym-format\n         curie->name-remember\n         get-assoc\n         curie->categories-remember\n         )\n\n(define (get-assoc k m)\n  (let ((r (assoc k m)))\n    (if r\n        (cadr r)\n        #f)))\n\n(define (list-assoc k m)\n  (let ((r (assoc k m)))\n    (if r\n        (cdr r)\n        '())))\n\n(define get-publications\n  (lambda props\n    (define (helper props pubs)\n      (cond\n        [(null? props) pubs]\n        [else\n         (let ((publication (or (get-assoc \"publications\" (car props))\n                                (get-assoc \"supporting_publications\" (car props))\n                                (get-assoc \"publications:string[]\" (car props)))))\n           (if publication\n               (helper (cdr props)\n                       (append \n                        (cond\n                          [(string-prefix? publication \"(\")\n                           (string-split (string-trim (string-trim publication \"(\") \")\"))]\n                          [(string-contains? publication \"|\") (string-split publication \"|\")]\n                          [(string-contains? publication \";\") (string-split publication \"; \")]\n                          [else (string-split publication)])\n                        pubs))\n               (helper (cdr props) pubs)))]))\n    (define pubs (filter\n                  (lambda (p) (not (equal? \"PMID:\" p)))\n                  (remove-duplicates (helper props '()))))\n    pubs))\n\n(define (get-mediKanren-score props)\n  (string->number (get-assoc \"mediKanren-score\" props)))\n\n(define write-list-to-tsv\n  (lambda (header-ls lol path)\n    (with-output-to-file path\n      ;; thunk -- procedure that takes no arguments\n      (lambda ()\n        (for-each\n          (lambda (l)\n            (let loop ([l l])\n              (cond\n                ((null? l)\n                 (error 'output-to-tsv \"where's the data!?\"))\n                ((null? (cdr l)) ;; l contains exactly 1 element\n                 (display (car l))\n                 (display #\\newline))\n                (else\n                 (display (car l))\n                 (display #\\tab)\n                 (loop (cdr l))))))\n          (cons header-ls lol)))\n      #:mode 'text\n      #:exists 'replace)))\n\n(define (concept->name curie)\n  (let ((id-name-val\n         (remove-duplicates (filter (lambda (cl)\n                                      (and (equal? (car cl) curie)\n                                           (equal? (cadr cl) \"name\")))\n                                    (query:Concept (list curie))))))\n        (if (null? id-name-val)\n            curie\n            (caddar id-name-val))))\n\n(define (concept->categories curie)\n  (let* ((props (curie->properties curie))\n         (categories (list-assoc \"category\" props)))\n    categories))\n\n(define build-remember\n  (lambda (curie->b hash)\n    (lambda (curie)\n      (let ((b (hash-ref hash curie #f)))\n        (if b\n            b\n            (let ((b^ (curie->b curie)))\n              (if (> (hash-count hash) 10000)\n                  (begin (set! hash (make-hash)) b^)\n                  (begin (hash-set! hash curie b^) b^))))))))\n\n(define curie-names (make-hash))\n(define curie->name-remember (build-remember concept->name curie-names))\n\n(define curie-categories (make-hash))\n(define curie->categories-remember (build-remember concept->categories curie-categories))\n\n\n(define (write-out-prepared-answers edge* path)\n  (write-list-to-tsv\n   '(\"subject\"\n     \"subject properties\"\n     \"predicate\"\n     \"object\"\n     \"object properties\"\n     \"publications\"\n     \"mediKanren score\"\n     \"edge properties\")\n   (map (lambda (e)\n          (match e\n            [`(,sub ,pred ,obj . ,prop)\n             (list* (curie->name-remember sub)\n                    (curie->properties sub)\n                    pred\n                    (curie->name-remember obj)\n                    (curie->properties obj)\n                    (get-publications prop)\n                    (get-mediKanren-score prop)\n                    prop)]\n            [else '()]))\n        (remove-duplicates edge*))\n   path))\n\n(define activate-edge-filter\n  (lambda (e)\n    (match e\n      [`(,sub ,pred ,obj . ,prop)\n       (let ((qualified-pred (get-assoc \"qualified_predicate\" prop))\n             (object-aspect-qualifier\n              (or (get-assoc \"object_aspect_qualifier\" prop)\n                  (get-assoc \"qualified_object_aspect\" prop)))\n             (object-direction-qualifier\n              (or (get-assoc \"object_direction_qualifier\" prop)\n                  (get-assoc \"qualified_object_direction\" prop))))\n         (if (member pred (list \"biolink:affects\" \"biolink:regulates\"))\n             (member (list pred qualified-pred object-aspect-qualifier object-direction-qualifier)\n                     (list (list \"biolink:regulates\" #f #f \"upregulated\")\n                           (list \"biolink:regulates\" \"biolink:causes\" \"expression\" \"increased\")\n                           (list \"biolink:regulates\" \"biolink:causes\" #f \"increased\")\n                           (list \"biolink:regulates\" \"biolink:causes\" #f \"upregulated\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"expression\" #f)\n                           (list \"biolink:affects\" \"biolink:causes\" \"expression\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"transport\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"activity_or_abundance\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"activity\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"secretion\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"synthesis\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"molecular_interaction\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"degradation\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"localization\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"uptake\" \"increased\")))\n             #t))]\n      [else (error \"the edge format seems not correct\")])))\n\n(define inhibite-edge-filter\n  (lambda (e)\n    (match e\n      [`(,sub ,pred ,obj . ,prop)\n       (let ((qualified-pred (get-assoc \"qualified_predicate\" prop))\n             (object-aspect-qualifier\n              (or (get-assoc \"object_aspect_qualifier\" prop)\n                  (get-assoc \"qualified_object_aspect\" prop)))\n             (object-direction-qualifier\n              (or (get-assoc \"object_direction_qualifier\" prop)\n                  (get-assoc \"qualified_object_direction\" prop))))\n         (if (member pred (list \"biolink:affects\" \"biolink:regulates\"))\n             (member (list pred qualified-pred object-aspect-qualifier object-direction-qualifier)\n                     (list (list \"biolink:regulates\" #f\t#f \"decreased\")\n                           (list \"biolink:regulates\" \"biolink:causes\" #f \"decreased\")\n                           (list \"biolink:regulates\" \"biolink:causes\" #f \"downregulated\")\n                           (list \"biolink:regulates\" #f\t#f \"downregulated\")\n                           (list \"biolink:regulates\" \"biolink:causes\" \"expression\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"degradation\" #f)\n                           (list \"biolink:affects\" \"biolink:causes\" \"expression\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"activity\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"activity_or_abundance\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"secretion\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"molecular_interaction\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"degradation\" \"increased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"transport\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"localization\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"synthesis\" \"decreased\")\n                           (list \"biolink:affects\" \"biolink:causes\" \"uptake\" \"decreased\")))       \n             #t))]\n      [else (error \"the edge format seems not correct\")])))\n\n(define (curie->gene/protein-conflation curies)\n  (set->list \n   (set-union (list->set curies)\n              (set-fixed-point\n               (list->set\n                (curies->synonyms \n                 (append \n                  (map car\n                       (query:X->Known-scored\n                        #f\n                        '(\"biolink:gene_product_of\")\n                        curies\n                        (list (list 1112) #f (list 0))))\n                  (map caddr\n                       (query:Known->X-scored\n                        curies\n                        '(\"biolink:gene_product_of\")\n                        #f\n                        (list (list 1112) #f (list 0)))))))\n               (lambda (new-curies)\n                 (list->set\n                  (curies->synonyms \n                   (append \n                    (map car\n                         (query:X->Known-scored\n                          #f\n                          '(\"biolink:gene_product_of\")\n                          (set->list curies)\n                          (list (list 1112) #f (list 0))))\n                    (map caddr\n                         (query:Known->X-scored\n                          (set->list curies)\n                          '(\"biolink:gene_product_of\")\n                          #f\n                          (list (list 1112) #f (list 0))))))))))))\n\n(define (synonym-format curie*)\n  (map (lambda (c)\n          (list* c (curie->name-remember c) (curie->properties c)))\n        curie*))\n  \n           \n      \n  "
  },
  {
    "path": "medikanren2/neo/neo-data/place_processed_data_here.txt",
    "content": "place processed data in this directory!\n\nFor example, this directory (`neo-data`) might contain:\n\nkgx-synonym.db/\n\nand\n\nrtx-kg2pre_7.6.db/\n"
  },
  {
    "path": "medikanren2/neo/neo-data/raw_downloads_from_kge_archive/place_raw_2tsv_kge_downloads_here.txt",
    "content": "place raw 2tsv kge downloads in this directory!\n\nfor example, the uncompressed `rtx-kg2pre_7.6` directory, containing `edges.tsv` and `nodes.tsv`\n"
  },
  {
    "path": "medikanren2/neo/neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/4tsv_versions_of_kgs_will_be_generated_here.txt",
    "content": "Running the transformation scripts in `neo/neo-data-import/transform-2tsv-to-4tsv-kgs/` will generate directories (in this directory) containing 4 TSV files, which in turn can be processed using the scripts in `neo/neo-data-import/build-mediKanren2-kg-from-4tsv/`.\n\n\nFor example, running the script\n\nneo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2pre_7.6.rkt\n\nwill transform the 2 TSV rtx-kg2pre_7.6 files here:\n\nneo-data/\n  raw_downloads_from_kge_archive/\n    rtx-kg2pre_7.6/\n      edges.tsv\n      nodes.tsv\n      ...\n\ninto the 4 TSV files here:\n\nneo-data/\n  raw_downloads_from_kge_archive_transformed_to_4tsv/\n    rtx-kg2pre_7.6/\n      rtx-kg2pre_7.6.edge.tsv\n      rtx-kg2pre_7.6.edgeprop.tsv\n      rtx-kg2pre_7.6.node.tsv\n      rtx-kg2pre_7.6.nodeprop.tsv\n\n\nAfterwards, running the script\n\nneo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2pre_7.6.rkt\n\nwill generate the fully-processed dbKanren database here:\n\n\nneo-data/\n  rtx-kg2pre_7.6.db/\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/an_important_note_on_pre_processing_kgs.txt",
    "content": "There is an issue with the data in `rtx-kg2pre_7.6`, and perhaps in\nother KGs.\n\nIn the `nodes.tsv` file of `rtx-kg2pre_7.6`, some lines contain the\ncarriage return character ^M, presumably from DOS.\n\nAlas, the mediKanren processing scripts for the KGs do not handle this\nproperly, which can result in a \"wrong number of columns\" error during\nprocessing or use of the KG.\n\nSo, we must remove the offending carriage return characters before\nrunning a script in `../neo-data-import/transform-2tsv-to-4tsv-kgs/`\nto transform the 2 TSV KG into the 4 TSV format (which then will be\nimported into a dbKanren-compatible database).\n\nThese two pages describe the ^M carriage return character:\n\nhttps://www.atechtown.com/remove-ctrl-m-character/\n\nhttps://stackoverflow.com/questions/2613800/how-to-convert-dos-windows-newline-crlf-to-unix-newline-lf\n\n***\nImportant: the standard `dos2unix` utility does *not* appear to process the file correctly!\nWhich is why we use the `sed` approach instead.\n***\n\n\nTo check if a file contains the offending carriage return character, you can run from the terminal (in the directory containing the TSV files):\n\n```\nack ^M \n```\n\nFor example, `ack ^M nodes.tsv`\n\nHowever, you need to enter the ^M character correctly on the command line, as control-v followed by control-m\n\n\nIf the file contains the offending carriage return character, we must create a version of the TSV file without the carriage return:\n\n```\nsed  -e \"s/^M//g\" nodes.tsv > nodes_dos_free.tsv\n```\n\nOnce again, you need to enter the ^M character correctly on the command line, as control-v followed by control-m\n\nAfter running the `sed` script, the command\n\n```\nack ^M nodes_dos_free.tsv\n```\n\nshould not find any lines with the offending carriage return (once again, please enter ^M as command-v followed by command-m)\n\nAlso, we should check that the only difference between the two versions of the TSV files are the lines containing ^M:\n\n```\ndiff nodes.tsv nodes_dos_free.tsv > out.diff.txt\n```\n\n\nThe script\n\n`./transform-2tsv-to-4tsv-kgs/transform-rtx-kg2pre_7.6.rkt`\n\nlooks for the file `edges.tsv`, but looks for `nodes_dos_free.tsv` rather than `nodes.tsv`.\n\n\nIt would be good to automate this checking/fixing of the TSV files, as part of automated KG processing.\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/bucket-setting/README.md",
    "content": "The Bash script, **`run.sh`**, performs the following tasks in order:\n\n1. Runs a Racket file (`rtx-kg2-publication-distribution.rkt`).\n2. Checks if the Python package `pandas` is installed; if not, installs it.\n3. Runs a Python file (`generate-publication-dist.py`).\n\nUse this script to automate your workflow without having to manually execute each command.\n\n---\n\n## Prerequisites\n\n- **Bash** (or a Bash-compatible shell)  \n  - If you’re on macOS or a Linux distribution, Bash is usually installed by default.  \n  - On Windows, you can use [Git Bash](https://git-scm.com/downloads) or the Windows Subsystem for Linux (WSL).\n- **Racket**  \n  - Make sure the `racket` command is available on your system path.\n- **Python 3**  \n  - Confirm you can run `python3` in your terminal.\n- **pip3**  \n  - If you can run `pip3 --version`, it’s installed.\n\n---\n\n## Getting Started\n\n1. **Ensure the data is ready:** Please ensure that the data is stored in the directories specified in the Racket and Python files.\n\n2. **Make the script executable** (if it isn’t already):\n   ```bash\n   chmod +x run.sh\n\n3. **Run the script:**\n   ```bash\n   ./run.sh\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/bucket-setting/generate-publication-dist.py",
    "content": "import pandas as pd\nimport math\nimport csv\n\nfile_base = '../../neo-data/raw_downloads_from_kge_archive/rtx-kg2-v2.10.0/'\n\nfile_path = file_base + 'scores.tsv'\nmax_bucket_size_percentage = 0.02\nmin_bucket_size_percentage = max_bucket_size_percentage * 0.7\nmax_bucket_size_min = 20000\nmin_bucket_size_min = max_bucket_size_min * 0.7\n\ndef export_to_tsv(data, filename):\n    with open(filename, 'w', newline='') as file:\n        writer = csv.writer(file, delimiter='\\t')\n\n        for record, nested_dict in data.items():\n            for column, value in nested_dict.items():\n                writer.writerow([record, column, value])\n\n# Load the TSV file\ndata = pd.read_csv(file_path, sep='\\t')\n\n# Calculate the total number of edges for each predicate\ntotal_edges_per_predicate = data.groupby('predicate')['num-edges'].sum()\n\n# Define the maximum and minimum bucket size thresholds\nmax_bucket_size = total_edges_per_predicate.apply(lambda x: max(x * max_bucket_size_percentage, max_bucket_size_min))\nmin_bucket_size = total_edges_per_predicate.apply(lambda x: max(x * min_bucket_size_percentage, min_bucket_size_min))\n\n# Calculate the number of buckets needed for each score of each predicate\nbuckets_needed = {}\n\nfor predicate, group in data.groupby('predicate'):\n    scores_sorted = group.sort_values('score').reset_index(drop=True)\n    handled_scores = set()  # To keep track of scores that have been handled\n\n    for index, row in scores_sorted.iterrows():\n        score = row['score']\n        num_edges = row['num-edges']\n\n        if score in handled_scores:\n            continue  # Skip this score because it's already been handled\n\n        if num_edges > max_bucket_size[predicate]:\n            # Split into multiple buckets if more than 5% of the total edges\n            num_buckets = math.ceil(num_edges / max_bucket_size[predicate])\n            buckets_needed.setdefault(predicate, {})[score] = num_buckets\n        elif num_edges >= min_bucket_size[predicate]:\n            # Assign a single bucket if between 3.5% and 5%\n            buckets_needed.setdefault(predicate, {})[score] = 1\n        else:\n            # Attempt to combine with subsequent scores if less than 3.5%\n            current_total = num_edges\n            start_score = score  # Track the starting score of the bucket\n\n            for j in range(index + 1, len(scores_sorted)):\n                next_score = scores_sorted.at[j, 'score']\n                next_num_edges = scores_sorted.at[j, 'num-edges']\n\n                if next_score in handled_scores:\n                    continue  # Skip already handled scores\n\n                if current_total + next_num_edges <= max_bucket_size[predicate]:\n                    current_total += next_num_edges\n                    handled_scores.add(next_score)  # Mark this score as handled\n                    buckets_needed.setdefault(predicate, {})[next_score] = 0\n\n                    if current_total >= min_bucket_size[predicate]:\n                        break  # Stop combining if we reach the minimum size\n\n            # Assign a bucket to the starting score of the combination\n            buckets_needed.setdefault(predicate, {})[start_score] = 1\n            handled_scores.add(start_score)  # Mark the starting score as handled\n\nstart_bucket_numbers = {predicate: {} for predicate in buckets_needed.keys()}\nfor predicate, scores in buckets_needed.items():\n    start_number = 1\n    last_start_number = start_number\n    for score, num_buckets in sorted(scores.items(), key=lambda x: x[0]):\n        if num_buckets==0:\n            start_bucket_numbers[predicate][score] = last_start_number\n        else:\n            start_bucket_numbers[predicate][score] = start_number\n            last_start_number = start_number\n        start_number += num_buckets\n\nexport_to_tsv(buckets_needed, file_base + \"buckets-needed.tsv\")\nexport_to_tsv(start_bucket_numbers, file_base + \"start-bucket-numbers.tsv\")\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/bucket-setting/predicate-publication-statistics.rkt",
    "content": "#lang racket\n\n(require json\n         \"../transform-2tsv-to-4tsv-kgs/transform-utils.rkt\")\n\n(provide get-pub-dist-tsv\n         get-pred-tsv\n         get-pub-dist-jsonl\n         get-pubs-counts-jsonl\n         get-pred-jsonl)\n\n\n(define get-pub-dist-tsv\n  (lambda (tsv factor?)\n    (define pub (make-hash))\n    (define in (open-input-file tsv))\n    (define header (efficient-no-trim-tab-string-split (read-line in 'any)))\n    (define (helper i)\n      (when (zero? (modulo i 1000000))\n          (printf \"processing edges line ~s\\n\" i))\n      (define line-str (read-line in 'any))\n      (when (not (eof-object? line-str))\n        (define line (efficient-no-trim-tab-string-split line-str))\n\n        (define pub-idx (find-index header \"publications\"))\n        (define pred-idx (find-index header \"predicate\"))\n        (define factor-idx (if factor? (find-index header \"score\") #f))\n        (define pubs (list-ref line pub-idx))\n        (define pred (list-ref line pred-idx))\n        (define factor (if factor? (list-ref line factor-idx) 1))\n\n        (if (equal? pubs \"\")\n            (hash-update! pub pred (lambda (oldh) (hash-update oldh 0 add1 0)) (hash))\n            (let ((pub-len (length (string-split pubs \"|\"))))\n              (hash-update! pub\n                            pred\n                            (lambda (oldh)\n                              (hash-update oldh\n                                           (exact-round (* factor pub-len))\n                                           add1\n                                           0))\n                            (hash))))\n        (helper (add1 i))))\n    (helper 1)\n    (close-input-port in)\n    (hash->list pub)))\n\n(define get-pred-tsv\n  (lambda (jsonl)\n    (define pred-t (make-hash))\n    (define in (open-input-file jsonl))\n    (define (helper i)\n      (when (zero? (modulo i 1000000))\n          (printf \"processing edges line ~s\\n\" i))\n      (define line-str (read-line in 'any))\n      (when (not (eof-object? line-str))\n        (define line (efficient-no-trim-tab-string-split line-str))\n        #|\n        (define pred (list-ref line 1)) ;text mining\n        (define qualified-pred (list-ref line 3)) ;text mining\n        (define object-direction-qualifier (list-ref line 9)) ;text mining\n        (define object-aspect-qualifier (list-ref line 8)) ;text mining\n        |#\n        (define pred (list-ref line 15)) ;rtx-kg2\n        (define qualified-pred (list-ref line 10)) ;rtx-kg2\n        (define object-direction-qualifier (list-ref line 9)) ;rtx-kg2\n        (define object-aspect-qualifier (list-ref line 8)) ;rtx-kg2\n        (when pred\n            (hash-update! pred-t\n                          pred\n                          (lambda (accu)\n                            (remove-duplicates\n                             (cons\n                              (list qualified-pred object-aspect-qualifier object-direction-qualifier)\n                              accu)))\n                          '()))\n        (helper (add1 i))))\n    (helper 1)\n    (close-input-port in)\n    (hash->list pred-t)))\n\n(define get-pub-dist-jsonl\n  (lambda (jsonl)\n    (define pub (make-hash))\n    (define in (open-input-file jsonl))\n    (define (helper i)\n      (when (zero? (modulo i 1000000))\n          (printf \"processing edges line ~s\\n\" i))\n      (define line (read-json in))\n      (when (not (eof-object? line))\n        (define pubs (hash-ref line 'publications #f))\n        (define pred (hash-ref line 'predicate #f))\n        (if pubs\n            (let ((pub-len (cond\n                             [(string? pubs) 1]\n                             [(list? pubs) (length pubs)]\n                             [else (display pubs) \"not seen\"])))\n              (hash-update! pub\n                            pred\n                            (lambda (oldh)\n                              (hash-update oldh\n                                           pub-len \n                                           add1\n                                           0))\n                            (hash)))\n            (hash-update! pub pred (lambda (oldh) (hash-update oldh 0 add1 0)) (hash)))\n        (helper (add1 i))))\n    (helper 1)\n    (close-input-port in)\n    (hash->list pub)))\n\n(define get-pubs-counts-jsonl\n  (lambda (jsonl pub-sym)\n    (define pub-count-dict (make-hash))\n    (define in (open-input-file jsonl))\n    (define helper\n      (lambda ()\n        (define json (read-json in))\n        (when (not (eof-object? json))    \n          (define pubs (hash-ref json pub-sym #f))\n          (if pubs\n              (let ((pub-len (cond\n                               [(string? pubs)\n                                 (max (length (string-split pubs \"|\")) (length (string-split pubs)))]\n                               [(list? pubs) (length pubs)]\n                               [else (display pubs) \"not seen\"])))\n                (hash-update! pub-count-dict pub-len add1 0))\n              (hash-update! pub-count-dict 0 add1 0))\n          (helper))))\n    (helper)\n    (close-input-port in)\n    (hash->list pub-count-dict)))\n\n(define get-pred-jsonl\n  (lambda (jsonl)\n    (define pred-t (make-hash))\n    (define in (open-input-file jsonl))\n    (define (helper i)\n      (when (zero? (modulo i 1000000)) ;; print the lines and number after 73000000\n          (printf \"processing edges line ~s\\n\" i))\n      (define line (read-json in))\n      (when (not (eof-object? line))\n        (define pred (hash-ref line 'predicate \"\"))\n        (define qualified-pred (hash-ref line 'qualified_predicate \"\"))\n        (define object-direction-qualifier (hash-ref line 'object_direction_qualifier \"\"))\n        (define object-aspect-qualifier (hash-ref line  'object_aspect_qualifier \"\"))\n        (when pred\n            (hash-update! pred-t\n                          pred\n                          (lambda (accu)\n                            (remove-duplicates\n                             (cons\n                              (list qualified-pred object-aspect-qualifier object-direction-qualifier)\n                              accu)))\n                          '()))\n        (helper (add1 i))))\n    (helper 1)\n    (close-input-port in)\n    (hash->list pred-t)))\n\n\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/bucket-setting/rtx-kg2-publication-distribution.rkt",
    "content": "#lang racket\n\n(require \"predicate-publication-statistics.rkt\"\n         \"../transform-2tsv-to-4tsv-kgs/transform-utils.rkt\")\n\n(define KG_DIRECTORY \"../../neo-data/raw_downloads_from_kge_archive/rtx-kg2-v2.10.0/\")\n(define KG_EDGE_File \"data_01_RAW_KGs_rtx_kg2_v2.10.0_validated_rtx-kg2_2.10.0_edges.tsv\")\n(define KG_PATH (string-append KG_DIRECTORY KG_EDGE_File))\n(define FILE_TYPE \"tsv\")\n(define SCORE_FACTOR #f)\n\n(define pub-distribution\n  (cond\n    ((equal? FILE_TYPE \"jsonl\") (get-pub-dist-jsonl KG_PATH))\n    ((equal? FILE_TYPE \"tsv\") (get-pub-dist-tsv KG_PATH SCORE_FACTOR))\n    (else (error \"mediKanren does not support the file type ~a.\" FILE_TYPE))))\n\n(define formated-pub-distribution\n  (unwrap (map (lambda (p)\n                 (map\n                  (lambda (pub/count)\n                    (list (car p) (car pub/count) (cdr pub/count)))\n                  (hash->list (cdr p))))\n               pub-distribution)))\n\n(write-list-to-tsv\n '(\"predicate\"\n   \"score\"\n   \"num-edges\")\n formated-pub-distribution\n (string-append KG_DIRECTORY \"scores.tsv\"))"
  },
  {
    "path": "medikanren2/neo/neo-data-import/bucket-setting/run.sh",
    "content": "#!/usr/bin/env bash\n\n# Exit immediately if a command exits with a non-zero status\nset -e\n\necho \"===== Step 1: Calculating the predicate and score distribution for RTX-KG2=====\"\nracket rtx-kg2-publication-distribution.rkt\n\necho \"===== Step 2: Checking for pandas in Python =====\"\n# Check if pandas is installed\nif ! python3 -c \"import pandas\" &> /dev/null; then\n  echo \"pandas is not installed. Installing now...\"\n  pip3 install pandas\nelse\n  echo \"pandas is already installed.\"\nfi\n\necho \"===== Step 3: Assigning buckets =====\"\npython3 generate-publication-dist.py\n\necho \"===== The bucket setting is completed. =====\"\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-full-Robokop.rkt",
    "content": "#lang racket/base\n(require \"../../dbKanren/dbk/database.rkt\"\n         racket/list racket/pretty racket/runtime-path)\n\n(define BASE \"../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/robokop-july-31-2024/\")\n\n(define EDGEPROP_PATH (string-append BASE \"Robokop.edgeprop.tsv\"))\n(define EDGE_PATH (string-append BASE \"Robokop.edge.tsv\"))\n(define SCORED_EDGE_PATH (string-append BASE \"Robokop.scorededge.tsv\"))\n(define NODEPROP_PATH (string-append BASE \"Robokop.nodeprop.tsv\"))\n;;\n(define OUTPUT_DATABASE_PATH \"../../neo-data/robokop.db\")\n\n(define-runtime-path path.here \".\")\n\n(pretty-write `(current-batch-size: ,(current-batch-size)))\n\n(define relation-specs `(\n                         (eprop\n                           ,EDGEPROP_PATH\n                           (int text text)\n                           (eid key value)\n                           ((eid key value)\n                            (key value eid)))\n                         (edge\n                           ,EDGE_PATH\n                           (int text text)\n                           (eid subject object)\n                           ((eid)\n                            (subject object)\n                            (object  subject)\n                            (subject eid object)\n                            (object  eid subject)))\n                         (scored-edge\n                           ,SCORED_EDGE_PATH\n                           (int text text text int)\n                           (eid predicate subject object score)\n                           ((score predicate subject object eid)\n                            (score predicate object subject eid)\n                            #;(predicate score subject object eid)\n                            #;(predicate score object subject eid)))\n                         (cprop\n                           ,NODEPROP_PATH\n                           (text text text)\n                           (curie key value)\n                           ((curie key value)\n                            (key value curie)))\n                         ))\n(pretty-write `(relation-specs: . ,relation-specs))\n\n(define db (database (build-path path.here OUTPUT_DATABASE_PATH)))\n\n(define relation-names   (map car             relation-specs))\n(define relation-files   (map cadr            relation-specs))\n(define relation-types   (map caddr           relation-specs))\n(define relation-attrs   (map cadddr          relation-specs))\n(define relation-indexes (map car (map cddddr relation-specs)))\n\n(for-each (lambda (name file-name type attrs)\n            (unless (database-relation-name? db name)\n              (pretty-write `(building ,name from ,file-name))\n              (define R (build-tsv-relation db type file-name))\n              (relation-name-set! R name)\n              (relation-attributes-set! R attrs)\n              (database-commit! db)))\n          relation-names\n          relation-files\n          relation-types\n          relation-attrs)\n(database-trash-empty! db)\n\n(pretty-write '(compacting full database))\n(for-each (lambda (name)\n            (define R (database-relation db name))\n            (relation-full-compact! R))\n          relation-names)\n(database-commit! db)\n(database-trash-empty! db)\n\n(for-each (lambda (name indexes)\n            (define R (database-relation db name))\n            (for-each (lambda (index)\n                        (pretty-write `(indexing ,name for ,index))\n                        (relation-index-add! R index)\n                        (database-commit! db))\n                      indexes))\n          relation-names\n          relation-indexes)\n(database-trash-empty! db)\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2.rkt",
    "content": "#lang racket/base\n(require \"../../dbKanren/dbk/database.rkt\"\n         racket/list racket/pretty racket/runtime-path)\n\n(define BASE \"../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/rtx-kg2-v2.10.0/\")\n\n(define EDGEPROP_PATH (string-append BASE \"rtx_kg2.edgeprop.tsv\"))\n(define EDGE_PATH (string-append BASE \"rtx_kg2.edge.tsv\"))\n(define SCORED_EDGE_PATH (string-append BASE  \"rtx_kg2.scorededge.tsv\"))\n(define NODEPROP_PATH (string-append BASE \"rtx_kg2.nodeprop.tsv\"))\n;;\n(define OUTPUT_DATABASE_PATH \"../../neo-data/rtx-kg2.db\")\n\n(define-runtime-path path.here \".\")\n\n(pretty-write `(current-batch-size: ,(current-batch-size)))\n\n(define relation-specs `(\n                         (eprop\n                           ,EDGEPROP_PATH\n                           (int text text)\n                           (eid key value)\n                           ((eid key value)\n                            (key value eid)))\n                         (edge\n                           ,EDGE_PATH\n                           (int text text)\n                           (eid subject object)\n                           ((eid)\n                            (subject object)\n                            (object  subject)\n                            (subject eid object)\n                            (object  eid subject)))\n                         (scored-edge\n                           ,SCORED_EDGE_PATH\n                           (int text text text int)\n                           (eid predicate subject object score)\n                           ((score predicate subject object eid)\n                            (score predicate object subject eid)\n                            #;(predicate score subject object eid)\n                            #;(predicate score object subject eid)))\n                         (cprop\n                           ,NODEPROP_PATH\n                           (text text text)\n                           (curie key value)\n                           ((curie key value)\n                            (key value curie)))\n                         ))\n(pretty-write `(relation-specs: . ,relation-specs))\n\n(define db (database (build-path path.here OUTPUT_DATABASE_PATH)))\n\n(define relation-names   (map car             relation-specs))\n(define relation-files   (map cadr            relation-specs))\n(define relation-types   (map caddr           relation-specs))\n(define relation-attrs   (map cadddr          relation-specs))\n(define relation-indexes (map car (map cddddr relation-specs)))\n\n(for-each (lambda (name file-name type attrs)\n            (unless (database-relation-name? db name)\n              (pretty-write `(building ,name from ,file-name))\n              (define R (build-tsv-relation db type file-name))\n              (relation-name-set! R name)\n              (relation-attributes-set! R attrs)\n              (database-commit! db)))\n          relation-names\n          relation-files\n          relation-types\n          relation-attrs)\n(database-trash-empty! db)\n\n(pretty-write '(compacting full database))\n(for-each (lambda (name)\n            (define R (database-relation db name))\n            (relation-full-compact! R))\n          relation-names)\n(database-commit! db)\n(database-trash-empty! db)\n\n(for-each (lambda (name indexes)\n            (define R (database-relation db name))\n            (for-each (lambda (index)\n                        (pretty-write `(indexing ,name for ,index))\n                        (relation-index-add! R index)\n                        (database-commit! db))\n                      indexes))\n          relation-names\n          relation-indexes)\n(database-trash-empty! db)\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/build-mediKanren2-kg-from-4tsv/import-text_mining.rkt",
    "content": "#lang racket/base\n(require \"../../dbKanren/dbk/database.rkt\"\n         racket/pretty racket/runtime-path)\n\n(define BASE \"../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/text-mining-aug-5-2024/\")\n\n(define EDGEPROP_PATH (string-append BASE \"text_mining.edgeprop.tsv\"))\n(define EDGE_PATH (string-append BASE \"text_mining.edge.tsv\"))\n(define SCORED_EDGE_PATH (string-append BASE \"text_mining.scorededge.tsv\"))\n(define NODEPROP_PATH (string-append BASE \"text_mining.nodeprop.tsv\"))\n;;\n(define OUTPUT_DATABASE_PATH \"../../neo-data/text_mining.db\")\n\n(define-runtime-path path.here \".\")\n\n(pretty-write `(current-batch-size: ,(current-batch-size)))\n\n(define relation-specs `(\n                         (eprop\n                           ,EDGEPROP_PATH\n                           (int text text)\n                           (eid key value)\n                           ((eid key value)\n                            (key value eid)))\n                         (edge\n                           ,EDGE_PATH\n                           (int text text)\n                           (eid subject object)\n                           ((eid)\n                            (subject object)\n                            (object  subject)\n                            (subject eid object)\n                            (object  eid subject)))\n                         (scored-edge\n                           ,SCORED_EDGE_PATH\n                           (int text text text int)\n                           (eid predicate subject object score)\n                           ((score predicate subject object eid)\n                            (score predicate object subject eid)\n                            #;(predicate score subject object eid)\n                            #;(predicate score object subject eid)))\n                         (cprop\n                           ,NODEPROP_PATH\n                           (text text text)\n                           (curie key value)\n                           ((curie key value)\n                            (key value curie)))\n                         ))\n(pretty-write `(relation-specs: . ,relation-specs))\n\n(define db (database (build-path path.here OUTPUT_DATABASE_PATH)))\n\n(define relation-names   (map car             relation-specs))\n(define relation-files   (map cadr            relation-specs))\n(define relation-types   (map caddr           relation-specs))\n(define relation-attrs   (map cadddr          relation-specs))\n(define relation-indexes (map car (map cddddr relation-specs)))\n\n(for-each (lambda (name file-name type attrs)\n            (unless (database-relation-name? db name)\n              (pretty-write `(building ,name from ,file-name))\n              (define R (build-tsv-relation db type file-name))\n              (relation-name-set! R name)\n              (relation-attributes-set! R attrs)\n              (database-commit! db)))\n          relation-names\n          relation-files\n          relation-types\n          relation-attrs)\n(database-trash-empty! db)\n\n(pretty-write '(compacting full database))\n(for-each (lambda (name)\n            (define R (database-relation db name))\n            (relation-full-compact! R))\n          relation-names)\n(database-commit! db)\n(database-trash-empty! db)\n\n(for-each (lambda (name indexes)\n            (define R (database-relation db name))\n            (for-each (lambda (index)\n                        (pretty-write `(indexing ,name for ,index))\n                        (relation-index-add! R index)\n                        (database-commit! db))\n                      indexes))\n          relation-names\n          relation-indexes)\n(database-trash-empty! db)\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-edge-jsonl.rkt",
    "content": "#lang racket\n\n(require json\n         \"transform-utils.rkt\")\n(provide transform-edge-jsonl)\n\n#|\nOutput edge and edge-props file formats:\n.edge.tsv\n:ID :START :END\nex-row: 1 ENSEMBL:ENSG00000004059 ENSEMBL:ENSP00000000233\n\n.edgeprops.tsv\n:ID propname value\nex-rows:\n1\tid\tdf6920caa6087ee642b8016b55776432\n1\tsubject\tGO:0061729\n1\tpredicate\tbiolink:same_as\n1\tobject\tREACT:R-HSA-446205\n\n.scorededge.tsv\n:ID predicate subject object score\n|#\n\n\n(define counters (hash))\n(define build-buckets-with-distribution\n  (lambda (predicate score buckets-needed start-bucket-numbers)\n    (set! counters\n          (hash-update counters\n                       predicate\n                       (lambda(pred-h)\n                         (hash-update pred-h score add1 0))\n                       (hash)))\n    (let* ((edge-count (hash-ref (hash-ref counters predicate) score))\n           (num-buckets (hash-ref (hash-ref buckets-needed predicate) score))\n           (start-bucket-number (hash-ref (hash-ref start-bucket-numbers predicate) score))\n           (specific-bucket (modulo (- edge-count 1) (max num-buckets 1)))\n           (bucket-assignment (+ start-bucket-number specific-bucket)))\n      bucket-assignment)))  \n\n(define transform-edge-jsonl\n  (lambda (edges-file-import-path\n           bucket-needed-path\n           start-bucket-numbers-path\n           edge-file-export-path\n           edge-props-file-export-path\n           scored-edge-file-export-path\n           which-kg)\n\n    (define buckets-needed (build-pred-score-amount-hash bucket-needed-path))\n     \n    (define start-bucket-numbers (build-pred-score-amount-hash start-bucket-numbers-path))\n\n    (printf \"transform-edge-jsonl called\\n\")\n    (printf \"input edges jsonl: ~s\\n\" edges-file-import-path)\n    (printf \"output edge tsv: ~s\\n\" edge-file-export-path)\n    (printf \"output edge props tsv: ~s\\n\" edge-props-file-export-path)\n    (printf \"output edge tsv: ~s\\n\" scored-edge-file-export-path)\n\n    (define edges-export-out\n      (open-output-file edge-file-export-path))\n    (fprintf edges-export-out \":ID\\t:START\\t:END\\n\")\n    (define edge-props-out\n      (open-output-file edge-props-file-export-path))\n    (fprintf edge-props-out \":ID\\tpropname\\tvalue\\n\")\n    (define scored-edge-out\n      (open-output-file scored-edge-file-export-path))\n    (fprintf scored-edge-out \":ID\\tpredicate\\tsubject\\tobject\\tscore\\n\")\n\n    (define edges-in\n      (open-input-file edges-file-import-path))\n\n    (let loop ((id 0)\n               (line (read-json edges-in)))\n      (when (zero? (modulo id 100000))\n        (printf \"processing edges line ~s\\n\" id))\n      (cond\n        [(eof-object? line)\n         (close-input-port edges-in)\n         (close-output-port edges-export-out)\n         (close-output-port edge-props-out)\n         (close-output-port scored-edge-out)\n         (printf \"finished processing edges\\n\")\n         (printf \"the current counters ~s\\n\\n\" counters)]\n        [else\n         (let* ((subject (hash-ref line 'subject #f))\n                (object (hash-ref line 'object #f))\n                (predicate (hash-ref line 'predicate #f))\n                ; the following line is for a fix for rtx-kg2 2.10.1pre\n                (predicate (if (and (string? predicate) (string-contains? predicate \"biolink:biolink_\"))\n                               (string-replace predicate \"biolink:biolink_\" \"biolink:\")\n                               predicate)) \n                (robokop-primary_knowledge_source (hash-ref line 'primary_knowledge_source #f)))\n           (if (equal? robokop-primary_knowledge_source \"infores:text-mining-provider-targeted\")\n               (loop id (read-json edges-in))\n               (begin\n                 (when (and subject object predicate)\n                   (fprintf edges-export-out \"~a\\t~a\\t~a\\n\" id subject object)\n                   (let* ((pubs (hash-ref line 'publications #f))\n                          (score (cond\n                                   [(not pubs) 0]\n                                   [(string? pubs) 1]\n                                   [(list? pubs) (length pubs)]\n                                   [else (error \"not seen\")]))\n                          (bucket-num\n                           (cond\n                             [(equal? predicate \"biolink:subclass_of\") 1111]\n                             [(equal? predicate \"biolink:gene_product_of\") 1112]\n                             [else (build-buckets-with-distribution\n                                    predicate score buckets-needed start-bucket-numbers)])))\n                     (fprintf scored-edge-out \"~a\\t~a\\t~a\\t~a\\t~a\\n\"\n                              id predicate subject object bucket-num)\n                     (let loop-inner (;; all the properties, including the subject and onbject. The order might be various.\n                                      (propnames (hash-keys line)))\n                       (when (not (null? propnames))\n                         (let* ((propname (car propnames))\n                                (value (hash-ref line propname))\n                                (value (if (hash? value)\n                                           (jsexpr->string value)\n                                           value)))\n                           (unless (or (equal? \"\" value) (equal? 'null value))\n                             (cond\n                               ; the following line is for a fix for rtx-kg2 2.10.1pre\n                               ((and (equal? propname 'predicate) (string-contains? value \"biolink:biolink_\"))\n                                (fprintf edge-props-out \"~a\\t~a\\t~a\\n\" id propname (string-replace value \"biolink:biolink_\" \"biolink:\")))\n                               ((equal? propname 'qualified_object_aspect)\n                                (fprintf edge-props-out \"~a\\tobject_aspect_qualifier\\t~a\\n\" id value))\n                               ((equal? propname 'qualified_object_direction)\n                                (fprintf edge-props-out \"~a\\tobject_direction_qualifier\\t~a\\n\" id value))\n                               ((equal? propname 'biolink:primary_knowledge_source)\n                                (fprintf edge-props-out \"~a\\tprimary_knowledge_source\\t~a\\n\" id value))\n                               (else\n                                (fprintf edge-props-out \"~a\\t~a\\t~a\\n\" id propname value)))))\n                         (loop-inner (cdr propnames))))\n                     (fprintf edge-props-out \"~a\\tmediKanren-score\\t~a\\n\" id score)))\n                 (loop\n                  (add1 id)\n                  (read-json edges-in)))))]))))\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-edge-tsv.rkt",
    "content": "#lang racket\n(require \"transform-utils.rkt\")\n(provide transform-edge-tsv)\n\n#|\nOutput edge and edge-props file formats:\n\n.edge.tsv\n:ID :START :END\n\n.edge-props.tsv\n:ID propname value\n\n.qualifiededge.tsv\n:ID predicate object-aspect object-direction subject object\n\n|#\n\n\n(define counters (hash))\n(define build-buckets-with-distribution\n  (lambda (predicate score buckets-needed start-bucket-numbers)\n    (set! counters\n          (hash-update counters\n                       predicate\n                       (lambda(pred-h)\n                         (hash-update pred-h score add1 0))\n                       (hash)))\n    (let* ((edge-count (hash-ref (hash-ref counters predicate) score))\n           (num-buckets (hash-ref (hash-ref buckets-needed predicate) score))\n           (start-bucket-number (hash-ref (hash-ref start-bucket-numbers predicate) score))\n           (specific-bucket (modulo (- edge-count 1) (max num-buckets 1)))\n           (bucket-assignment (+ start-bucket-number specific-bucket)))\n      bucket-assignment)))\n\n(define transform-edge-tsv\n  (lambda (edges-file-import-path\n           bucket-needed-path\n           start-bucket-numbers-path\n           edge-file-export-path\n           edge-props-file-export-path\n           scored-edge-file-export-path\n           which-kg)\n    \n    (define buckets-needed (build-pred-score-amount-hash bucket-needed-path))\n\n    (define start-bucket-numbers (build-pred-score-amount-hash start-bucket-numbers-path))\n\n    (printf \"transform-edge-tsv\\n\")\n    (printf \"transform-edge-tsv called\\n\")\n    (printf \"input edges tsv: ~s\\n\" edges-file-import-path)\n    (printf \"output edge tsv: ~s\\n\" edge-file-export-path)\n    (printf \"output edge props tsv: ~s\\n\" edge-props-file-export-path)\n    (printf \"output scored edge tsv: ~s\\n\" scored-edge-file-export-path)\n    \n    (define edges-export-out\n      (open-output-file edge-file-export-path))\n    (fprintf edges-export-out \":ID\\t:START\\t:END\\n\")\n    (define edge-props-out\n      (open-output-file edge-props-file-export-path))\n    (fprintf edge-props-out \":ID\\tpropname\\tvalue\\n\")\n    (define scored-edge-out\n      (open-output-file scored-edge-file-export-path))\n    (fprintf scored-edge-out \":ID\\tpredicate\\tsubject\\tobject\\tscore\\n\")\n\n    (define edges-in\n      (open-input-file edges-file-import-path))\n    \n    (let* ((header (read-line edges-in 'any))\n           (header (string-split header \"\\t\" #:trim? #f)))\n      (let loop ((id 0)\n                 (line-str (read-line edges-in 'any)))\n        (when (zero? (modulo id 100000))\n          (printf \"processing edges line ~s\\n\" id))\n        (cond\n          ((eof-object? line-str)\n           (close-input-port edges-in)\n           (close-output-port edges-export-out)\n           (close-output-port edge-props-out)\n           (close-output-port scored-edge-out)\n           (printf \"finished processing edges\\n\\n\")\n           (printf \"the current counters ~s\\n\" counters))\n          (else\n           (let ((line (efficient-no-trim-tab-string-split line-str)))\n             (match-define (list predicate subject object score bucket-num)\n               (cond\n                 [(eq? which-kg 'text-mining)\n                  (let* ((predicate (list-ref line 1))\n                         (subject (list-ref line 0))\n                         (object (list-ref line 2))\n                         (pubs (list-ref line 17))\n                         (pub-len (if (equal? pubs \"\")\n                                    0\n                                    (length (string-split pubs \"|\"))))\n                         (TM-score (string->number (list-ref line 15)))\n                         (score (exact-round (* TM-score pub-len)))\n                         (bucket-num (build-buckets-with-distribution\n                                      predicate score buckets-needed start-bucket-numbers)))\n                    (list predicate subject object score bucket-num))]\n                 [(eq? which-kg 'rtx-kg2)\n                  (let* ((predicate (list-ref line (find-index header \"predicate\")))\n                         (subject (list-ref line (find-index header \"subject\")))\n                         (object (list-ref line (find-index header \"object\")))\n                         (pubs (list-ref line (find-index header \"publications\")))\n                         (score (if (equal? pubs \"\")\n                                    0\n                                    (length (string-split pubs \"|\"))))\n                         (bucket-num (cond\n                                       [(equal? predicate \"biolink:subclass_of\") 1111]\n                                       [(equal? predicate \"biolink:gene_product_of\") 1112]\n                                       [else (build-buckets-with-distribution\n                                              predicate score buckets-needed start-bucket-numbers)])))\n                    (list predicate subject object score bucket-num))]\n                 [else (error \"unknown KG\")]))\n             (unless (or (string=? \"\" subject) (string=? \"\" object))\n               (fprintf edges-export-out \"~a\\t~a\\t~a\\n\" id subject object)\n               (unless (string=? \"\" predicate)\n                 (fprintf scored-edge-out \"~a\\t~a\\t~a\\t~a\\t~a\\n\" id predicate subject object bucket-num)))\n               \n             (let loop-inner ((props line) ;; all the properties, including the subject and object\n                              (headers header))\n               (when (not (null? props))\n                 (unless (string=? \"\" (car props))\n                   (let ((propname (car headers))\n                         (value (car props)))\n                     (fprintf edge-props-out \"~a\\t~a\\t~a\\n\" id propname value)))\n                 (loop-inner (cdr props) (cdr headers))))\n             (fprintf edge-props-out \"~a\\tmediKanren-score\\t~a\\n\" id score)\n             #;(fprintf edge-props-out \"~a\\tprimary_knowledge_source\\tinfores:text-mining-provider-targeted\\n\" id)\n             (loop\n              (add1 id)\n              (read-line edges-in 'any)))))))))\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-full-Robokop.rkt",
    "content": "#lang racket\n\n(require \"transform-generic.rkt\"\n         \"transform-edge-jsonl.rkt\"\n         json\n         \"../../neo-reasoning/neo-biolink-reasoning-low-level.rkt\")\n\n(define transform-node-jsonl\n  (lambda (nodes-file-import-path\n           node-file-export-path\n           node-props-file-export-path\n           which-kg)\n\n    (printf \"transform-node-jsonl called\\n\")\n    (printf \"input nodes jsonl: ~s\\n\" nodes-file-import-path)\n    (printf \"output node tsv: ~s\\n\" node-file-export-path)\n    (printf \"output node props tsv: ~s\\n\" node-props-file-export-path)\n    \n    (define node-out\n      (open-output-file node-file-export-path))\n    (fprintf node-out \":ID\\n\")\n    (define node-props-out\n      (open-output-file node-props-file-export-path))\n    (fprintf node-props-out \":ID\\tpropname\\tvalue\\n\")\n\n    (define nodes-in\n      (open-input-file nodes-file-import-path))\n\n    (let loop ((i 0)\n               (seen-nodes (set))\n               (line-json (read-json nodes-in)))\n      (when (zero? (modulo i 100000))\n        (printf \"processing nodes line ~s\\n\" i))\n\n      (cond\n        [(eof-object? line-json)\n         (close-input-port nodes-in)\n         (close-output-port node-out)\n         (close-output-port node-props-out)\n         (printf \"finished processing nodes\\n\\n\")]\n        [else\n         (let ((id (hash-ref line-json 'id #f)))\n           (if id\n               (begin\n                 (when (set-member? seen-nodes id)\n                   (error 'make-kg-node (format \"already seen node: ~a\" id)))\n                 (fprintf node-out \"~a\\n\" id)\n                 (let* ((name (hash-ref line-json 'name \"N/A\"))\n                        (categories (hash-ref line-json 'category #f))\n                        (categories-smallest-nonmixin (and categories\n                                                           (list? categories)\n                                                           (get-smallest-nonmixin-class* categories))))\n                   (fprintf node-props-out \"~a\\tname\\t~a\\n\" id name)\n                   (cond\n                     ((and categories-smallest-nonmixin\n                           (not (null? categories-smallest-nonmixin)))\n                      (for-each\n                       (lambda (c)\n                         (fprintf node-props-out \"~a\\tcategory\\t~a\\n\" id c))\n                       categories-smallest-nonmixin))\n                     ((and categories-smallest-nonmixin\n                           (null? categories-smallest-nonmixin))\n                      (let ((categories-samllest (find-leaf-classes categories)))\n                        (for-each\n                         (lambda (c)\n                           (fprintf node-props-out \"~a\\tcategory\\t~a\\n\" id c))\n                         categories-samllest)))\n                     ((and categories (string? categories))\n                      (fprintf node-props-out \"~a\\tcategory\\t~a\\n\" id categories))\n                     (else\n                      (printf \"unseen format\" categories))))\n                 (loop\n                  (add1 i)\n                  (set-add seen-nodes id)\n                  (read-json nodes-in)))\n               (loop\n                (add1 i)\n                seen-nodes\n                (read-json nodes-in))))]))))\n\n(define BASE \"robokop-july-31-2024/\")\n\n(transform-generic\n (string-append \"../../neo-data/raw_downloads_from_kge_archive/\" BASE)\n (string-append \"../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/\" BASE)\n \"nodes.jsonl\"\n \"edges.jsonl\"\n \"Robokop\"\n 'robokop\n (cons transform-node-jsonl transform-edge-jsonl))\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-generic.rkt",
    "content": "#lang racket/base\n\n(provide transform-generic)\n\n;; transform-node-and-edge is a pair (transform-node . transform-edge) containing\n;; - a transform node function/procedure (transform-node-jsonl or transform-node-tsv)\n;; - a transform edge function/procedure (transform-edge-jsonl or transform-edge-tsv)\n\n(define transform-generic\n  (lambda (import-directory-path\n           export-directory-path\n           nodes-import-file-name\n           edges-import-file-name\n           export-base-file-name\n           which-kg\n           transform-node-and-edge)\n    \n    (define node-export-file-name\n      (string-append\n       export-base-file-name\n       \".node.tsv\"))\n    (define node-props-export-file-name\n      (string-append\n       export-base-file-name\n       \".nodeprop.tsv\"))\n\n    (define edge-export-file-name\n      (string-append\n       export-base-file-name\n       \".edge.tsv\"))\n    (define edge-props-export-file-name\n      (string-append\n       export-base-file-name\n       \".edgeprop.tsv\"))\n    (define scored-edge-export-file-name\n      (string-append\n       export-base-file-name\n       \".scorededge.tsv\"))\n\n        ;; --- nodes ---\n    (define nodes-file-import-path\n      (string-append\n       import-directory-path\n       nodes-import-file-name))\n\n    (define node-file-export-path\n      (string-append\n       export-directory-path\n       node-export-file-name))\n    (define node-props-file-export-path\n      (string-append\n       export-directory-path\n       node-props-export-file-name))\n\n        ;; --- edges ---\n    (define edges-file-import-path\n      (string-append\n       import-directory-path\n       edges-import-file-name))\n\n    (define edge-file-export-path\n      (string-append\n       export-directory-path\n       edge-export-file-name))\n    (define edge-props-file-export-path\n      (string-append\n       export-directory-path\n       edge-props-export-file-name))\n    (define scored-edge-file-export-path\n      (string-append\n       export-directory-path\n       scored-edge-export-file-name))\n\n    ;; --- precomputed distribution ---\n    (define bucket-needed-path\n      (string-append\n       import-directory-path\n       \"buckets-needed.tsv\"))\n\n    (define start-bucket-numbers-path\n      (string-append\n       import-directory-path\n       \"start-bucket-numbers.tsv\"))\n\n    (let ((transform-node (car transform-node-and-edge))\n          (transform-edge (cdr transform-node-and-edge)))\n      (transform-node nodes-file-import-path\n                      node-file-export-path\n                      node-props-file-export-path\n                      which-kg)\n\n      (transform-edge edges-file-import-path\n                      bucket-needed-path\n                      start-bucket-numbers-path\n                      edge-file-export-path\n                      edge-props-file-export-path\n                      scored-edge-file-export-path\n                      which-kg)\n\n    )))"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-node-jsonl.rkt",
    "content": "#lang racket\n\n(require json)\n(provide transform-node-jsonl)\n\n#|\nOutput node and node-props file formats:\n.node.scm\n:ID\n.node-props.scm\n:ID propname value\n|#\n\n(define (sanitize-string str)\n  (regexp-replace* #rx\"\\t|\\n|\\r\" str \" \"))\n\n(define transform-node-jsonl\n  (lambda (nodes-file-import-path\n           node-file-export-path\n           node-props-file-export-path\n           which-kg)\n\n    (printf \"transform-node-jsonl called\\n\")\n    (printf \"input nodes jsonl: ~s\\n\" nodes-file-import-path)\n    (printf \"output node tsv: ~s\\n\" node-file-export-path)\n    (printf \"output node props tsv: ~s\\n\" node-props-file-export-path)\n    \n    (define node-out\n      (open-output-file node-file-export-path))\n    (fprintf node-out \":ID\\n\")\n    (define node-props-out\n      (open-output-file node-props-file-export-path))\n    (fprintf node-props-out \":ID\\tpropname\\tvalue\\n\")\n\n    (define nodes-in\n      (open-input-file nodes-file-import-path))\n\n    (let loop ((i 0)\n               (seen-nodes (set))\n               (line-json (read-json nodes-in)))\n      (when (zero? (modulo i 100000))\n        (printf \"processing nodes line ~s\\n\" i))\n\n      (cond\n        [(eof-object? line-json)\n         (close-input-port nodes-in)\n         (close-output-port node-out)\n         (close-output-port node-props-out)\n         (printf \"finished processing nodes\\n\\n\")]\n        [else\n         (let ((id (hash-ref line-json 'id #f)))\n           (when id\n             (when (set-member? seen-nodes id)\n               (error 'make-kg-node (format \"already seen node: ~a\" id)))\n             (fprintf node-out \"~a\\n\" id)\n             (let loop-inner ((propnames (remove 'id (hash-keys line-json))))\n               (when (not (null? propnames)) \n                 (let* ((propname (car propnames))\n                        (value (hash-ref line-json propname #f))\n                        (value (cond\n                                 ((string? value) (sanitize-string value))\n                                 ((list? value) (if (andmap string? value)\n                                                    (map sanitize-string value)\n                                                    value))\n                                 (else value))))\n                   (unless (equal? \"\" value)\n                     (fprintf node-props-out \"~a\\t~a\\t~a\\n\" id propname value)))\n                 (loop-inner (cdr propnames)))))\n           (loop\n            (add1 i)\n            (set-add seen-nodes id)\n            (read-json nodes-in)))]))))\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-node-tsv.rkt",
    "content": "#lang racket\n(require \"transform-utils.rkt\")\n(provide transform-node-tsv)\n\n#|\nOutput node and node-props file formats:\n\n.node.scm\n:ID\n\n.node-props.scm\n:ID propname value\n|#\n\n(define transform-node-tsv\n  (lambda (nodes-file-import-path\n           node-file-export-path\n           node-props-file-export-path\n           which-kg)\n\n    (printf \"transform-node-tsv called\\n\")\n    (printf \"input nodes tsv: ~s\\n\" nodes-file-import-path)\n    (printf \"output node tsv: ~s\\n\" node-file-export-path)\n    (printf \"output node props tsv: ~s\\n\" node-props-file-export-path)\n    \n    (define node-out\n      (open-output-file node-file-export-path))\n    (fprintf node-out \":ID\\n\")\n    (define node-props-out\n      (open-output-file node-props-file-export-path))\n    (fprintf node-props-out \":ID\\tpropname\\tvalue\\n\")\n\n    (define nodes-in\n      (open-input-file nodes-file-import-path))\n    \n    (let* ((header (read-line nodes-in 'any))\n           (header (string-split header \"\\t\" #:trim? #f)))\n      (let loop ((i 0)\n                 (seen-nodes (set))\n                 (line-str (read-line nodes-in 'any)))\n        (when (zero? (modulo i 100000))\n          (printf \"processing nodes line ~s\\n\" i))\n\n        (cond\n          ((eof-object? line-str)\n           (close-input-port nodes-in)\n           (close-output-port node-out)\n           (close-output-port node-props-out)\n           (printf \"finished processing nodes\\n\\n\"))\n          (else\n           (let ((line (efficient-no-trim-tab-string-split line-str)))               \n             (let ((id (cond\n                         [(eq? which-kg 'text-mining) (car line)]\n                         [(eq? which-kg 'rtx-kg2) (list-ref line 7)])))\n               (when (set-member? seen-nodes id)\n                 (error 'make-kg-node (format \"already seen node: ~a\" id)))\n               (fprintf node-out \"~a\\n\" id)\n               (let loop-inner ((props (cdr line))\n                                (headers (cdr header)))                   \n                 (when (not (null? props))\n                   (unless (string=? \"\" (car props))\n                     (let ((propname (car headers))\n                           (value (car props)))\n                       (fprintf node-props-out \"~a\\t~a\\t~a\\n\" id propname value)))\n                   (loop-inner (cdr props) (cdr headers))))\n               (loop\n                (add1 i)\n                (set-add seen-nodes id)\n                (read-line nodes-in 'any))))))))))\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2.rkt",
    "content": "#lang racket\n\n(require \"transform-generic.rkt\"\n         \"transform-edge-tsv.rkt\"\n         \"transform-node-tsv.rkt\")\n\n(define BASE \"rtx-kg2-v2.10.0/\")\n\n(transform-generic (string-append \"../../neo-data/raw_downloads_from_kge_archive/\" BASE)\n                   (string-append \"../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/\" BASE)\n                   \"data_01_RAW_KGs_rtx_kg2_v2.10.0_validated_rtx-kg2_2.10.0_nodes.tsv\"\n                   \"data_01_RAW_KGs_rtx_kg2_v2.10.0_validated_rtx-kg2_2.10.0_edges.tsv\"\n                   \"rtx_kg2\"\n                   'rtx-kg2\n                   (cons transform-node-tsv transform-edge-tsv))\n"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-text_mining.rkt",
    "content": "#lang racket\n\n(require \"transform-generic.rkt\"\n         \"transform-edge-tsv.rkt\"\n         \"transform-node-tsv.rkt\")\n\n(define BASE \"text-mining-aug-5-2024/\")\n\n(transform-generic (string-append \"../../neo-data/raw_downloads_from_kge_archive/\" BASE)\n                   (string-append \"../../neo-data/raw_downloads_from_kge_archive_transformed_to_4tsv/\" BASE)\n                   \"nodes_with_header.tsv\"\n                   \"edges_with_header.tsv\"\n                   \"text_mining\"\n                   'text-mining\n                   (cons transform-node-tsv transform-edge-tsv))"
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform-utils.rkt",
    "content": "#lang racket\n(provide efficient-no-trim-tab-string-split\n         build-pred-score-amount-hash\n         find-index\n         write-list-to-tsv\n         unwrap)\n\n#|\n\nRacket's `string-split` function has lots of functionality, but can be\n*extremely* slow for very long strings (with millions of characters, for\nexample):\n\nhttps://docs.racket-lang.org/reference/strings.html#%28def._%28%28lib._racket%2Fstring..rkt%29._string-split%29%29\n\nFor example, splitting a single extremely long string may take minutes\nor even hours.\n\nInstead of using `string-split`, the KG TSV processing code for the\nneo server uses a more limited, but far more efficient, function for\nsplitting a string into substrings, based on the tab character as a\ndelimiter.\n\n|#\n\n(define efficient-no-trim-tab-string-split\n  (lambda (str)\n    (let ((len (string-length str)))\n      (let loop ((i 0)\n                 (indices '(-1)))\n        (cond\n          [(= i len)\n           ;; create substrings from the numeric offsets, and return a\n           ;; list of these substrings\n           (let inner-loop ((indices (reverse (cons (string-length str) indices)))\n                            (strings '()))\n             (cond\n               [(null? indices)\n                (error 'efficient-no-trim-tab-string-split\n                       (format \"unexpected unmatched indices\"))]\n               [(null? (cdr indices))\n                (reverse strings)]\n               [else\n                (inner-loop\n                 (cdr indices)\n                 (cons (substring str (add1 (car indices)) (cadr indices))\n                       strings))]))]\n          [(char=? (string-ref str i) #\\tab)\n           (loop\n            (add1 i)\n            (cons i indices))]\n          [else\n           (loop\n            (add1 i)\n            indices)])))))\n\n(define (build-pred-score-amount-hash path)\n  (define in\n      (open-input-file path))\n  (define return (make-hash))\n  (let loop ((line (read-line in 'any)))\n    (cond\n      ((eof-object? line)\n       (close-input-port in)\n        return)\n      (else\n        (let* ((line (efficient-no-trim-tab-string-split line))\n               (predicate (list-ref line 0))\n               (score (string->number  (list-ref line 1)))\n               (amount (string->number (list-ref line 2))))\n          (hash-set! return predicate (hash-set (hash-ref return predicate (hash))\n                                                score\n                                                amount))\n          (loop (read-line in 'any)))))))\n                                \n\n(define (find-index lst ele)\n  (let loop ((lst lst) (idx 0))\n    (cond\n      [(null? lst) #f]\n      [(equal? (car lst) ele) idx]\n      [else (loop (cdr lst) (add1 idx))])))\n\n(define write-list-to-tsv\n  (lambda (header-ls lol path)\n    (with-output-to-file path\n      ;; thunk -- procedure that takes no arguments\n      (lambda ()\n        (for-each\n          (lambda (l)\n            (let loop ([l l])\n              (cond\n                ((null? l)\n                 (error 'output-to-tsv \"where's the data!?\"))\n                ((null? (cdr l)) ;; l contains exactly 1 element\n                 (display (car l))\n                 (display #\\newline))\n                (else\n                 (display (car l))\n                 (display #\\tab)\n                 (loop (cdr l))))))\n          (cons header-ls lol)))\n      #:mode 'text\n      #:exists 'replace)))\n\n(define unwrap\n  (lambda (lol)\n    (let loop ((lol lol) (accu '()))\n      (cond\n        ((null? lol) accu)\n        ((not (pair? (car lol))) (cons lol accu))\n        (else (append (loop (car lol) accu) (loop (cdr lol) accu)))))))\n             \n    "
  },
  {
    "path": "medikanren2/neo/neo-data-import/transform-2tsv-to-4tsv-kgs/transform.rkt",
    "content": "#lang racket\n(provide transform)\n(require \"transform-node-tsv.rkt\"\n         \"transform-edge-tsv.rkt\")\n\n(define transform\n  (lambda (import-directory-path\n           export-directory-path\n           nodes-import-file-name\n           edges-import-file-name\n           export-base-file-name)\n\n    (define node-export-file-name\n      (string-append\n       export-base-file-name\n       \".node.tsv\"))\n    (define node-props-export-file-name\n      (string-append\n       export-base-file-name\n       \".nodeprop.tsv\"))\n\n    (define edge-export-file-name\n      (string-append\n       export-base-file-name\n       \".edge.tsv\"))\n    (define edge-props-export-file-name\n      (string-append\n       export-base-file-name\n       \".edgeprop.tsv\"))\n\n    ;; --- nodes ---\n    (define nodes-file-import-path\n      (string-append\n       import-directory-path\n       nodes-import-file-name))\n\n    (define node-file-export-path\n      (string-append\n       export-directory-path\n       node-export-file-name))\n    (define node-props-file-export-path\n      (string-append\n       export-directory-path\n       node-props-export-file-name))\n\n\n    ;; --- edges ---\n    (define edges-file-import-path\n      (string-append\n       import-directory-path\n       edges-import-file-name))\n\n    (define edge-file-export-path\n      (string-append\n       export-directory-path\n       edge-export-file-name))\n    (define edge-props-file-export-path\n      (string-append\n       export-directory-path\n       edge-props-export-file-name))\n\n    (transform-node-tsv nodes-file-import-path\n                        node-file-export-path\n                        node-props-file-export-path)\n\n    (transform-edge-tsv edges-file-import-path\n                        edge-file-export-path\n                        edge-props-file-export-path)\n\n    ))\n\n"
  },
  {
    "path": "medikanren2/neo/neo-low-level/make-query-low-level.rkt",
    "content": "#lang racket/base\n\n;; adapted from\n;;\n;; https://github.com/gregr/dbKanren/blob/master/test/test-low-level.rkt\n\n(provide\n make-query-low-level)\n(require\n  \"../dbKanren/dbk/database.rkt\"\n  \"../dbKanren/dbk/enumerator.rkt\"\n  \"../dbKanren/dbk/logging.rkt\"\n  \"../dbKanren/dbk/stream.rkt\"\n  \"../neo-utils/neo-helpers-without-db.rkt\"\n  racket/fixnum racket/match racket/pretty racket/runtime-path racket/set racket/list)\n\n(define-runtime-path path.here \"../neo-data\")\n\n(define NAME_NOT_FOUND_STRING \"N/A\")\n\n\n(define (make-query-low-level\n         db-path-under-parent ;; for example, \"rtx-kg2/pre_2.8.0/rtx-kg2pre_2.8.0.db\"\n         kg-infores\n         )\n\n  (pretty-log `(In make-query-low-level for)\n              db-path-under-parent)\n  \n  (define str.predicate \"predicate\")\n  ;;(define str.predicate \"edge_label\")\n\n  (define (curie-in-db? curie)\n    (initialize-text!)\n    (dict-ref (thread-cell-ref tcell.text=>id)\n              (string->bytes/utf-8 curie)\n              (lambda (id) #t)\n              (lambda () #f)))\n\n  (define (curies-in-db curie*)\n    (initialize-text!)\n    (define curie-text*=>1\n      (let* ((text* (map string->bytes/utf-8 curie*))\n             (text* (list->vector (sort (remove-duplicates text*) bytes1 (thread-cell-ref tcell.text=>id))\n       (lambda (text.curie __ ___)\n         (yield (bytes->string/utf-8 text.curie)))))\n    (enumerator->rlist helper))\n\n  (define (dict-get d key)\n    (dict-ref d key (lambda (v) v) (lambda () (error \"dict-get failed\" key))))\n\n  (define (dict-get-safe d key not-found-value)\n    (dict-ref d key (lambda (v) v) (lambda () not-found-value)))\n\n  (define (get-name-from-dict-safe d k)\n    (if d\n        (let* ((name? (dict-get-safe d k #f))\n               (name (if name? (dict-min name?) #f)))\n          (if name (id->string name) NAME_NOT_FOUND_STRING))\n        NAME_NOT_FOUND_STRING))\n  \n  (define (string*->id=>1 str*) (bytes*->id=>1 (map string->bytes/utf-8 str*)))\n  (define (bytes*->id=>1 text*)\n    (let* ((text* (sort (set->list (list->set text*)) bytesvector (map text->id text*))))\n      (dict:ref (lambda (i) (vector-ref id* i)) fx<\n                (lambda (_) '()) 0 (vector-length id*))))\n\n  (define (int*->id=>1 int*)\n    (let ((id* (list->vector (sort (remove-duplicates int*) fx<))))\n      (dict:ref (lambda (i) (vector-ref id* i)) fx<\n                (lambda (_) '()) 0 (vector-length id*))))\n\n  (define (string->id str) (text->id (string->bytes/utf-8 str)))\n  (define (id->string id)  (bytes->string/utf-8 (id->text id)))\n  (define (text->id   b)   (initialize-text!) (dict-get (thread-cell-ref tcell.text=>id) b))\n  (define (id->text   id)  (initialize-text!) (dict-get (thread-cell-ref tcell.id=>text) id))\n\n  (define (concept-properties)          (map id->string (enumerator->list\n                                                         (dict-key-enumerator ckey=>cvalue=>curie=>1))))\n  (define (edge-properties)             (map id->string (enumerator->list\n                                                         (dict-key-enumerator ekey=>evalue=>eid=>1))))\n  (define (concept-property-values key) (s-map id->string (enumerator->s\n                                                           (dict-key-enumerator\n                                                            (dict-get ckey=>cvalue=>curie=>1\n                                                                      (string->id key))))))\n  (define (edge-property-values    key) (s-map id->string (enumerator->s\n                                                           (dict-key-enumerator\n                                                            (dict-get ekey=>evalue=>eid=>1\n                                                                      (string->id key))))))\n  (define (curie->properties curie)\n    (enumerator->list\n     (lambda (yield)\n       ((dict-enumerator (dict-get-safe curie=>ckey=>cvalue=>1 (string->id curie) dict.empty))\n        (lambda (ckey cvalue=>1)\n          (yield (map id->string (cons ckey (enumerator->list\n                                             (dict-key-enumerator cvalue=>1))))))))))\n  (define (edge-id->properties eid)\n    (cons (list \"upstream_resource_ids\" (list kg-infores))\n          (enumerator->list\n           (lambda (yield)\n             ((dict-enumerator (dict-get eid=>ekey=>evalue=>1 eid))\n              (lambda (ekey evalue=>1)\n                (yield (map id->string (cons ekey (enumerator->list\n                                                   (dict-key-enumerator evalue=>1)))))))))))\n\n  (define (query:Known->X curie*.K predicate*.K->X category*.X)\n    (define (query. yield)\n      (let* ((ekey.predicate (string->id str.predicate))\n             (K=>1           (string*->id=>1 curie*.K)))\n        ((merge-join fx< K=>1 subject=>object=>eid=>1)\n         (lambda (id.K __ X=>eid=>1)\n           (let* ((K      (id->string id.K)))\n             ((dict-enumerator X=>eid=>1)\n              (lambda (id.X eid=>1)\n                (let* ((X      (id->string id.X)))\n                  ((dict-key-enumerator eid=>1)\n                   (lambda (eid)\n                     (let ((predicate.K->X\n                            (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                            ekey.predicate)))))\n                       (yield (list* K predicate.K->X X (edge-id->properties eid))))))))))))))\n    (define (query.c yield)\n      (let* ((ekey.predicate     (string->id str.predicate))\n             (ckey.category      (string->id \"category\"))\n             (K=>1               (string*->id=>1 curie*.K))\n             (category=>1        (string*->id=>1 category*.X))\n             (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n        ((merge-join fx< K=>1 subject=>object=>eid=>1)\n         (lambda (id.K __ X=>eid=>1)\n           (let* ((K      (id->string id.K)))\n             ((merge-join fx< category=>1 category=>curie=>1)\n              (lambda (__ ___ X=>1.cprop)\n                ((merge-join fx< X=>eid=>1 X=>1.cprop)\n                 (lambda (id.X eid=>1 __)\n                   (let* ((X      (id->string id.X)))\n                     ((dict-key-enumerator eid=>1)\n                      (lambda (eid)\n                        (let ((predicate.K->X\n                               (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                               ekey.predicate)))))\n                          (yield (list* K predicate.K->X X (edge-id->properties eid))))))))))))))))\n    (define (query.p yield)\n      (let* ((ekey.predicate     (string->id str.predicate))\n             (K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.K->X))\n             (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1 ekey.predicate)))\n        ((merge-join fx< K=>1 subject=>eid=>object=>1)\n         (lambda (id.K __ eid=>X=>1)\n           (let* ((K         (id->string id.K)))\n             ((merge-join fx< predicate=>1 predicate=>eid=>1)\n              (lambda (id.predicate.K->X __ eid=>1)\n                (let ((predicate.K->X (id->string id.predicate.K->X)))\n                  ((merge-join fx< eid=>1 eid=>X=>1)\n                   (lambda (eid __ X=>1.edge)\n                     ((dict-key-enumerator X=>1.edge)\n                      (lambda (id.X)\n                        (let* ((X      (id->string id.X)))\n                          (yield (list* K predicate.K->X X (edge-id->properties eid))))))))))))))))\n    (define (query.p&c yield)\n      (let* ((ekey.predicate     (string->id str.predicate))\n             (ckey.category      (string->id \"category\"))\n             (K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.K->X))\n             (category=>1        (string*->id=>1 category*.X))\n             (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1   ekey.predicate))\n             (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n        ((merge-join fx< K=>1 subject=>eid=>object=>1)\n         (lambda (id.K __ eid=>X=>1)\n           (let* ((K         (id->string id.K)))\n             ((merge-join fx< predicate=>1 predicate=>eid=>1)\n              (lambda (id.predicate.K->X __ eid=>1)\n                (let ((predicate.K->X (id->string id.predicate.K->X)))\n                  ((merge-join fx< eid=>1 eid=>X=>1)\n                   (lambda (eid __ X=>1.edge)\n                     ((merge-join fx< category=>1 category=>curie=>1)\n                      (lambda (__ ___ X=>1.cprop)\n                        ((merge-join fx< X=>1.cprop X=>1.edge)\n                         (lambda (id.X __ ___)\n                           (let* ((X      (id->string id.X)))\n                             (yield (list* K predicate.K->X X (edge-id->properties eid))))))))))))))))))\n    (maybe-time (enumerator->rlist (if predicate*.K->X\n                                       (if category*.X query.p&c query.p)\n                                       (if category*.X query.c   query.)))))\n\n  (define (query:Known->X-scored curie*.K predicate*.K->X category*.X score*)\n\n    (define (query.p yield)\n      (let* ((K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.K->X))\n             (score=>1           (int*->id=>1 score*)))\n        ((merge-join fx< score=>1 score=>pred=>sub=>obj=>eid=>1)\n         (lambda (__ ___ pred=>sub=>obj=>eid=>1)\n           ((merge-join fx< predicate=>1 pred=>sub=>obj=>eid=>1)\n            (lambda (id.predicate.K->X __ sub=>obj=>eid=>1)\n              (let ((predicate.K->X (id->string id.predicate.K->X)))\n                ((merge-join fx< K=>1 sub=>obj=>eid=>1)\n                 (lambda (id.K __ obj=>eid=>1)\n                   (let ((K         (id->string id.K)))\n                     ((dict-enumerator obj=>eid=>1)\n                      (lambda (id.X eid=>1)\n                        (let ((X      (id->string id.X)))\n                          ((dict-key-enumerator eid=>1)\n                              (lambda (eid)\n                                (yield (list* K predicate.K->X X (edge-id->properties eid))))))))))))))))))\n    (define (query.p&c yield)\n      (let* ((ckey.category      (string->id \"category\"))\n             (K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.K->X))\n             (score=>1           (int*->id=>1 score*))\n             (category=>1        (string*->id=>1 category*.X))\n             (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n        ((merge-join fx< score=>1 score=>pred=>sub=>obj=>eid=>1)\n         (lambda (__ ___ pred=>sub=>obj=>eid=>1)\n           ((merge-join fx< predicate=>1 pred=>sub=>obj=>eid=>1)\n            (lambda (id.predicate.K->X __ sub=>obj=>eid=>1)\n              (let* ((predicate.K->X (id->string id.predicate.K->X)))\n                ((merge-join fx< K=>1 sub=>obj=>eid=>1)\n                    (lambda (id.K __ obj=>eid=>1)\n                      (let* ((K         (id->string id.K)))\n                        ((merge-join fx< category=>1 category=>curie=>1)\n                         (lambda (__ ___ X=>1.cprop)\n                           ((merge-join fx< X=>1.cprop obj=>eid=>1)\n                            (lambda (id.X __ eid=>1)\n                              (let* ((X      (id->string id.X)))\n                                ((dict-key-enumerator eid=>1)\n                                 (lambda (eid)\n                                   (yield (list* K predicate.K->X X (edge-id->properties eid))))))))))))))))))))\n    (if score*\n        (if category*.X\n            (maybe-time (enumerator->rlist query.p&c))\n            (maybe-time (enumerator->rlist query.p)))\n        '()))\n\n  (define (query:X->Known category*.X predicate*.X->K curie*.K)\n    (define (query. yield)\n      (let* ((ekey.predicate (string->id str.predicate))\n             (K=>1           (string*->id=>1 curie*.K)))\n        ((merge-join fx< K=>1 object=>subject=>eid=>1)\n         (lambda (id.K __ X=>eid=>1)\n           (let* ((K      (id->string id.K)))\n             ((dict-enumerator X=>eid=>1)\n              (lambda (id.X eid=>1)\n                (let* ((X      (id->string id.X)))\n                  ((dict-key-enumerator eid=>1)\n                   (lambda (eid)\n                     (let ((predicate.X->K\n                            (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                            ekey.predicate)))))\n                       (yield (list* X predicate.X->K K (edge-id->properties eid))))))))))))))\n    (define (query.c yield)\n      (let* ((ekey.predicate     (string->id str.predicate))\n             (ckey.category      (string->id \"category\"))\n             (K=>1               (string*->id=>1 curie*.K))\n             (category=>1        (string*->id=>1 category*.X))\n             (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n        ((merge-join fx< K=>1 object=>subject=>eid=>1)\n         (lambda (id.K __ X=>eid=>1)\n           (let* ((K      (id->string id.K)))\n             ((merge-join fx< category=>1 category=>curie=>1)\n              (lambda (__ ___ X=>1.cprop)\n                ((merge-join fx< X=>eid=>1 X=>1.cprop)\n                 (lambda (id.X eid=>1 __)\n                   (let* ((X      (id->string id.X)))\n                     ((dict-key-enumerator eid=>1)\n                      (lambda (eid)\n                        (let ((predicate.X->K\n                               (id->string (dict-min (dict-get (dict-get eid=>ekey=>evalue=>1 eid)\n                                                               ekey.predicate)))))\n                          (yield (list* X predicate.X->K K (edge-id->properties eid))))))))))))))))\n    (define (query.p yield)\n      (let* ((ekey.predicate     (string->id str.predicate))\n             (K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.X->K))\n             (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1   ekey.predicate)))\n        ((merge-join fx< K=>1 object=>eid=>subject=>1)\n         (lambda (id.K __ eid=>X=>1)\n           (let* ((K      (id->string id.K)))\n             ((merge-join fx< predicate=>1 predicate=>eid=>1)\n              (lambda (id.predicate.X->K __ eid=>1)\n                (let ((predicate.X->K (id->string id.predicate.X->K)))\n                  ((merge-join fx< eid=>1 eid=>X=>1)\n                   (lambda (eid __ X=>1.edge)\n                     ((dict-key-enumerator X=>1.edge)\n                      (lambda (id.X)\n                        (let* ((X      (id->string id.X)))\n                          (yield (list* X predicate.X->K K (edge-id->properties eid))))))))))))))))\n    (define (query.p&c yield)\n      (let* ((ekey.predicate     (string->id str.predicate))\n             (ckey.category      (string->id \"category\"))\n             (K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.X->K))\n             (category=>1        (string*->id=>1 category*.X))\n             (predicate=>eid=>1  (dict-get ekey=>evalue=>eid=>1   ekey.predicate))\n             (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n        ((merge-join fx< K=>1 object=>eid=>subject=>1)\n         (lambda (id.K __ eid=>X=>1)\n           (let* ((K      (id->string id.K)))\n             ((merge-join fx< predicate=>1 predicate=>eid=>1)\n              (lambda (id.predicate.X->K __ eid=>1)\n                (let ((predicate.X->K (id->string id.predicate.X->K)))\n                  ((merge-join fx< eid=>1 eid=>X=>1)\n                   (lambda (eid __ X=>1.edge)\n                     ((merge-join fx< category=>1 category=>curie=>1)\n                      (lambda (__ ___ X=>1.cprop)\n                        ((merge-join fx< X=>1.cprop X=>1.edge)\n                         (lambda (id.X __ ___)\n                           (let* ((X      (id->string id.X)))\n                             (yield (list* X predicate.X->K K (edge-id->properties eid))))))))))))))))))\n    (maybe-time (enumerator->rlist (if predicate*.X->K\n                                       (if category*.X query.p&c query.p)\n                                       (if category*.X query.c   query.)))))\n\n  (define (query:X->Known-scored category*.X predicate*.X->K curie*.K score*)\n    (define (query.p yield)\n      (let* ((K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.X->K))\n             (score=>1           (int*->id=>1 score*)))\n        ((merge-join fx< score=>1 score=>pred=>obj=>sub=>eid=>1)\n         (lambda (__ ___ pred=>obj=>sub=>eid=>1)\n           ((merge-join fx< predicate=>1 pred=>obj=>sub=>eid=>1)\n            (lambda (id.predicate.X->K __ obj=>sub=>eid=>1)\n              (let ((predicate.X->K (id->string id.predicate.X->K)))\n                ((merge-join fx< K=>1 obj=>sub=>eid=>1)\n                 (lambda (id.K __ sub=>eid=>1)\n                   (let ((K         (id->string id.K)))\n                     ((dict-enumerator sub=>eid=>1)\n                      (lambda (id.X eid=>1)\n                        (let ((X      (id->string id.X)))\n                          ((dict-key-enumerator eid=>1)\n                              (lambda (eid)\n                                (yield (list* X predicate.X->K K (edge-id->properties eid))))))))))))))))))\n    (define (query.p&c yield)\n      (let* ((ckey.category      (string->id \"category\"))\n             (K=>1               (string*->id=>1 curie*.K))\n             (predicate=>1       (string*->id=>1 predicate*.X->K))\n             (score=>1           (int*->id=>1 score*))\n             (category=>1        (string*->id=>1 category*.X))\n             (category=>curie=>1 (dict-get ckey=>cvalue=>curie=>1 ckey.category)))\n        ((merge-join fx< score=>1 score=>pred=>obj=>sub=>eid=>1)\n         (lambda (__ ___ pred=>obj=>sub=>eid=>1)\n           ((merge-join fx< predicate=>1 pred=>obj=>sub=>eid=>1)\n            (lambda (id.predicate.X->K __ obj=>sub=>eid=>1)\n              (let ((predicate.X->K (id->string id.predicate.X->K)))\n                ((merge-join fx< K=>1 obj=>sub=>eid=>1)\n                 (lambda (id.K __ sub=>eid=>1)\n                   (let ((K         (id->string id.K)))\n                     ((merge-join fx< category=>1 category=>curie=>1)\n                      (lambda (__ ___ X=>1.cprop)\n                        ((merge-join fx< X=>1.cprop sub=>eid=>1)\n                         (lambda (id.X __ eid=>1)\n                           (let ((X      (id->string id.X)))\n                             ((dict-key-enumerator eid=>1)\n                              (lambda (eid)\n                                (yield (list* X predicate.X->K K (edge-id->properties eid))))))))))))))))))))\n    (if score*\n        (if category*.X\n            (maybe-time (enumerator->rlist query.p&c))\n            (maybe-time (enumerator->rlist query.p)))\n        '()))\n\n\n  (define (query:Known<-X->Known curie*.K1 predicate*.K1<-X category*.X predicate*.X->K2 curie*.K2)\n    (error 'query:Known<-X->Known \"obsolete\"))\n\n  (define (query:Known->X->Known curie*.K1 predicate*.K1->X category*.X predicate*.X->K2 curie*.K2)\n    (error 'query:Known->X->Known \"obsolete\"))\n\n  (define (query:X->Y->Known category*.X predicate*.X->Y category*.Y predicate*.Y->K curie*.K)\n    (error 'query:X->Y->Known \"obsolete\"))\n\n  (define (query:Known->Known curie*.S predicate*.S->O curie*.O)\n    (if (> (length curie*.S) (length curie*.O))\n        (query:dict.Known->dict.Known\n         (string*->id=>1 curie*.S) predicate*.S->O (string*->id=>1 curie*.O) 'obj->sub)\n        (query:dict.Known->dict.Known\n         (string*->id=>1 curie*.S) predicate*.S->O (string*->id=>1 curie*.O) 'sub->obj)))\n\n  (define (query:dict.Known->dict.Known curie=>1.S predicate*.S->O curie=>1.O direction-tag)\n    (define (query.sub->obj yield)\n      (let* ((ekey.predicate    (string->id str.predicate))\n             (predicate=>1      (string*->id=>1 predicate*.S->O))\n             (predicate=>eid=>1 (dict-get ekey=>evalue=>eid=>1 ekey.predicate)))\n        ((merge-join fx< curie=>1.S subject=>eid=>object=>1)\n         (lambda (id.S __ eid=>O=>1)\n           (let* ((S      (id->string id.S)))\n             ((merge-join fx< predicate=>1 predicate=>eid=>1)\n              (lambda (id.predicate.S->O __ eid=>1)\n                (let ((predicate.S->O (id->string id.predicate.S->O)))\n                  ((merge-join fx< eid=>1 eid=>O=>1)\n                   (lambda (eid __ O=>1)\n                     ((merge-join fx< curie=>1.O O=>1)\n                      (lambda (id.O __ ___)\n                        (let* ((O      (id->string id.O)))\n                          (yield (list* S predicate.S->O O (edge-id->properties eid))))))))))))))))\n    (define (query.obj->sub yield)\n      (let* ((ekey.predicate    (string->id str.predicate))\n             (predicate=>1      (string*->id=>1 predicate*.S->O))\n             (predicate=>eid=>1 (dict-get ekey=>evalue=>eid=>1 ekey.predicate)))\n        ((merge-join fx< curie=>1.O object=>eid=>subject=>1)\n         (lambda (id.O __ eid=>S=>1)\n           (let* ((O      (id->string id.O)))\n             ((merge-join fx< predicate=>1 predicate=>eid=>1)\n              (lambda (id.predicate.O->S __ eid=>1)\n                (let ((predicate.O->S (id->string id.predicate.O->S)))\n                  ((merge-join fx< eid=>1 eid=>S=>1)\n                   (lambda (eid __ S=>1)\n                     ((merge-join fx< curie=>1.S S=>1)\n                      (lambda (id.S __ ___)\n                        (let* ((S      (id->string id.S)))\n                          (yield (list* S predicate.O->S O (edge-id->properties eid))))))))))))))))\n    (cond\n      [(eq? direction-tag 'obj->sub) (maybe-time (enumerator->rlist query.obj->sub))]\n      [(eq? direction-tag 'sub->obj) maybe-time (enumerator->rlist query.sub->obj)]\n      [else (error \"unknown direction tag\")]))\n\n  (define (query:Concept curie*)\n    (define (query yield)\n      (let ((curie=>1 (string*->id=>1 curie*)))\n        ((merge-join fx< curie=>1 curie=>ckey=>cvalue=>1)\n         (lambda (id.curie _ ckey=>cvalue=>1)\n           (let ((curie (id->string id.curie)))\n             ((dict-enumerator ckey=>cvalue=>1)\n              (lambda (id.key cvalue=>1)\n                (yield (list curie (id->string id.key) (id->string (dict-min cvalue=>1)))))))))))\n    (maybe-time (enumerator->list query)))\n\n  (define (get-highest-bucket-number)\n    (define (helper yield)\n      ((dict-key-enumerator score=>pred=>sub=>obj=>eid=>1)\n       (lambda (score)\n         (yield (list score)))))\n    (let* ((score* (remove-duplicates (enumerator->rlist helper)))\n           (score* (sort (apply append score*) >)))\n      (let loop ((s* score*))\n        (if (or (eq? (car s*) 1111) (eq? (car s*) 1112))\n            (loop (cdr s*))\n            (car s*)))))\n\n  (pretty-log `(defining db for)\n              path.here\n              db-path-under-parent)\n  (define db (database (build-path path.here db-path-under-parent)))\n  (pretty-log `(defined db for)\n              path.here\n              db-path-under-parent)\n\n\n  (pretty-log `(defining r.cprop for)\n              path.here\n              db-path-under-parent)\n  (define r.cprop (database-relation db 'cprop))\n  (pretty-log `(defining r.edge for)\n              path.here\n              db-path-under-parent)  \n  (define r.edge  (database-relation db 'edge))\n  (pretty-log `(defining r.eprop for)\n              path.here\n              db-path-under-parent)\n  (define r.eprop (database-relation db 'eprop))\n\n  (define r.scored-edge (database-relation db 'scored-edge))  \n\n  (pretty-log `(defining tcells for)\n              path.here\n              db-path-under-parent)\n  (define tcell.text=>id (make-thread-cell #f))\n  (define tcell.id=>text (make-thread-cell #f))\n\n  (define (initialize-text!)\n    (unless (thread-cell-ref tcell.text=>id)\n      (define-values (text=>id id=>text) (relation-text-dicts r.cprop #f))\n      (thread-cell-set! tcell.text=>id text=>id)\n      (thread-cell-set! tcell.id=>text id=>text)))\n  \n  (pretty-log `(loading relation index dictionaries for db)\n              path.here\n              db-path-under-parent)\n  (define subject=>object=>eid=>1 (maybe-time (relation-index-dict r.edge  '(subject object eid) #f))) ;; #f\n  (define object=>subject=>eid=>1 (maybe-time (relation-index-dict r.edge  '(object subject eid) #f))) ;; #f\n  (define subject=>eid=>object=>1 (maybe-time (relation-index-dict r.edge  '(subject eid object) #f))) ;; #t\n  (define object=>eid=>subject=>1 (maybe-time (relation-index-dict r.edge  '(object eid subject) #f))) ;; #t\n  (define ekey=>evalue=>eid=>1    (maybe-time (relation-index-dict r.eprop '(key value eid)      #f))) ;; #f\n  (define eid=>ekey=>evalue=>1    (maybe-time (relation-index-dict r.eprop '(eid key value)      #f))) ;; #f\n  (define ckey=>cvalue=>curie=>1  (maybe-time (relation-index-dict r.cprop '(key value curie)    #t))) ;; #t\n  (define curie=>ckey=>cvalue=>1  (maybe-time (relation-index-dict r.cprop '(curie key value)    #f))) ;; #f\n  (define score=>pred=>sub=>obj=>eid=>1 (maybe-time\n                                         (relation-index-dict r.scored-edge '(score predicate subject object eid) #t)))\n  (define score=>pred=>obj=>sub=>eid=>1 (maybe-time\n                                         (relation-index-dict r.scored-edge '(score predicate object subject eid) #t)))\n  (pretty-log `(loaded relation index dictionaries for db)\n              path.here\n              db-path-under-parent)\n \n  (list\n   query:Known->Known\n   query:Known->X-scored\n   query:Known->X\n   query:X->Known-scored\n   query:X->Known\n   query:Known<-X->Known\n   query:Known->X->Known\n   query:X->Y->Known\n   query:Concept\n   concept-properties\n   concept-property-values\n   curie-in-db?\n   curies-in-db\n   curie->properties\n   edge-properties\n   edge-property-values\n   edge-id->properties\n   get-highest-bucket-number\n   )\n  )\n"
  },
  {
    "path": "medikanren2/neo/neo-low-level/query-low-level-equivalence.rkt",
    "content": "#lang racket/base\n\n(require \"../dbKanren/dbk/database.rkt\"\n         \"../dbKanren/dbk/enumerator.rkt\"\n         \"../dbKanren/dbk/logging.rkt\"\n         racket/runtime-path\n         racket/fixnum\n         racket/list\n         racket/set)\n\n(provide curie->representative\n         curies->synonyms\n         curie->synonyms\n         build-curies-representative-hash\n         add-curies-representative-to-hash)\n\n(define (curie->representative curie)\n  (define (helper yield)\n    (let* ((id.curie (string->id curie))\n           (representative=>1 (dict-get curie=>representative=>1 id.curie)))\n      ((dict-key-enumerator representative=>1)\n       (lambda (id.representative)\n         (let ((representative (id->string id.representative)))\n           (yield representative))))))\n  (if (null? (curies-in-db (list curie)))\n      curie\n      (car (enumerator->rlist helper))))\n\n(define (curies->synonyms curie*)\n  (define (helper yield)\n    (let ((curie*=>1 (string*->id=>1\n                      (curies-in-db curie*)\n                      #;(filter curie-in-db? curie*))))\n      ((merge-join fx< curie*=>1 curie=>representative=>1)\n       (lambda (__ ___ representative=>1)\n         ((merge-join fx< representative=>1 representative=>curie=>1)\n          (lambda (__ ___ curie=>1)\n            ((dict-key-enumerator curie=>1)\n             (lambda (id.curie)\n               (let ((curie (id->string id.curie)))\n                 (yield curie))))))))))\n  (let ((synonyms (enumerator->rlist helper)))\n    (remove-duplicates (append curie* synonyms))))\n\n(define (curie->synonyms curie)\n  (curies->synonyms (list curie)))\n\n(define build-curie-representative-hash\n      (lambda (hash curie)\n        (if (hash-has-key? hash curie)\n            hash\n            (let* ((synonyms (curie->synonyms curie))\n                   (representative (find-smallest-string synonyms)))\n              (let loop ((h hash) (s* synonyms))\n                (cond\n                  ((null? s*) h)\n                  (else (loop (hash-set h (car s*) representative) (cdr s*)))))))))\n\n(define build-curies-representative-hash\n  (lambda (curie*)\n    (let loop ((h (hash)) (c* curie*))\n      (cond\n        ((null? c*) h)\n        (else (loop (build-curie-representative-hash h (car c*)) (cdr c*)))))))\n\n(define add-curies-representative-to-hash\n  (lambda (representative-hash curie*)\n    (let loop ((h representative-hash) (c* curie*))\n      (cond\n        ((null? c*) h)\n        (else (loop (build-curie-representative-hash h (car c*)) (cdr c*)))))))\n\n(define find-smallest-string\n  (lambda (string*)\n    (let loop ((s* (cdr string*)) (smallest (car string*)))\n      (cond\n        ((null? s*) smallest)\n        (else\n         (if (stringid\n              (string->bytes/utf-8 curie)\n              (lambda (id) #t)\n              (lambda () #f)))\n\n(define (curies-in-db curie*)\n    (define curie-text*=>1\n      (let* ((text* (map string->bytes/utf-8 curie*))\n             (text* (list->vector (sort (remove-duplicates text*) bytes1 text=>id)\n       (lambda (text.curie __ ___)\n         (yield (bytes->string/utf-8 text.curie)))))\n    (enumerator->rlist helper))                      \n\n(define (dict-get d key)\n    (dict-ref d key (lambda (v) v) (lambda () (error \"dict-get failed\" key))))\n\n\n\n(define-runtime-path path.here \"../neo-data\")\n(define db-path-under-parent \"equivalence-dec-6-2023/dec_3_2023/equivalence.db\")\n(pretty-log `(loading relation index dictionaries for db)\n              path.here\n              db-path-under-parent)\n(define name.equiv-class-member 'equivalence-class-member)\n(define db.equiv (database (build-path path.here db-path-under-parent)))\n(define r.equiv-class-member (database-relation db.equiv name.equiv-class-member))\n(define representative=>curie=>1 (relation-index-dict r.equiv-class-member '(representative member) #f))\n(define curie=>representative=>1 (relation-index-dict r.equiv-class-member '(member representative) #f))\n\n(define-values (text=>id id=>text) (relation-text-dicts r.equiv-class-member #f))\n(define (text->id text) (dict-ref text=>id text (lambda (v) v)\n                                  (lambda () (error \"invalid text\" text))))\n(define (id->text id)   (dict-ref id=>text id (lambda (v) v)\n                                  (lambda () (error \"invalid text id\" id))))\n\n(define (string*->id=>1 str*) (bytes*->id=>1 (map string->bytes/utf-8 str*)))\n(define (bytes*->id=>1 text*)\n    (let* ((text* (sort (set->list (list->set text*)) bytesvector (map text->id text*))))\n      (dict:ref (lambda (i) (vector-ref id* i)) fx<\n                (lambda (_) '()) 0 (vector-length id*))))\n\n(define (string->id str) (text->id (string->bytes/utf-8 str)))\n(define (id->string id)  (bytes->string/utf-8 (id->text id)))\n"
  },
  {
    "path": "medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt",
    "content": "#lang racket/base\n\n(provide\n query:Known->Known\n query:Known->X\n query:Known->X-scored\n query:X->Known\n query:X->Known-scored\n query:Known<-X->Known\n query:Known->X->Known\n query:X->Y->Known\n query:X->Y->Known-scored\n query:Known->Y->X\n query:Known->Y->X-scored\n query:Concept\n concept-properties\n ;;concept-property-values\n curie-in-db?\n curies-in-db\n curie->properties\n edge-properties\n ;;edge-property-values\n ;;edge-id->properties\n curie->synonyms\n curies->synonyms\n curie->representative\n build-curies-representative-hash\n add-curies-representative-to-hash\n query:Known->Y->X-auto-grow\n query:X->Y->Known-auto-grow\n get-highest-bucket-number-robokop\n get-highest-bucket-number-text-mining\n get-highest-bucket-number-rtx-kg2\n)\n\n(require\n\n  (rename-in \"query-low-level-robokop.rkt\"\n             (query:Known->Known query:Known->Known-robokop)\n             (query:Known->X query:Known->X-robokop)\n             (query:Known->X-scored query:Known->X-scored-robokop)\n             (query:X->Known query:X->Known-robokop)\n             (query:X->Known-scored  query:X->Known-scored-robokop)\n             (query:Known<-X->Known query:Known<-X->Known-robokop)\n             (query:Known->X->Known query:Known->X->Known-robokop)\n             (query:X->Y->Known query:X->Y->Known-robokop)\n             (query:Concept query:Concept-robokop)\n             (concept-properties concept-properties-robokop)\n             (concept-property-values concept-property-values-robokop)\n             (curie-in-db? curie-in-db?-robokop)\n             (curies-in-db curies-in-db-robokop)\n             (curie->properties curie->properties-robokop)\n             (edge-properties edge-properties-robokop)\n             (edge-property-values edge-property-values-robokop)\n             (edge-id->properties edge-id->properties-robokop)\n             (get-highest-bucket-number get-highest-bucket-number-robokop)\n             )\n\n  (rename-in \"query-low-level-text-mining.rkt\"\n             (query:Known->Known query:Known->Known-text-mining)\n             (query:Known->X query:Known->X-text-mining)\n             (query:Known->X-scored query:Known->X-scored-text-mining)\n             (query:X->Known query:X->Known-text-mining)\n             (query:X->Known-scored  query:X->Known-scored-text-mining)\n             (query:Known<-X->Known query:Known<-X->Known-text-mining)\n             (query:Known->X->Known query:Known->X->Known-text-mining)\n             (query:X->Y->Known query:X->Y->Known-text-mining)\n             (query:Concept query:Concept-text-mining)\n             (concept-properties concept-properties-text-mining)\n             (concept-property-values concept-property-values-text-mining)\n             (curie-in-db? curie-in-db?-text-mining)\n             (curies-in-db curies-in-db-text-mining)\n             (curie->properties curie->properties-text-mining)\n             (edge-properties edge-properties-text-mining)\n             (edge-property-values edge-property-values-text-mining)\n             (edge-id->properties edge-id->properties-text-mining)\n             (get-highest-bucket-number get-highest-bucket-number-text-mining)\n             )\n\n  (rename-in \"query-low-level-rtx-kg2.rkt\"\n             (query:Known->Known query:Known->Known-rtx-kg2)\n             (query:Known->X query:Known->X-rtx-kg2)\n             (query:Known->X-scored query:Known->X-scored-rtx-kg2)\n             (query:X->Known query:X->Known-rtx-kg2)\n             (query:X->Known-scored  query:X->Known-scored-rtx-kg2)\n             (query:Known<-X->Known query:Known<-X->Known-rtx-kg2)\n             (query:Known->X->Known query:Known->X->Known-rtx-kg2)\n             (query:X->Y->Known query:X->Y->Known-rtx-kg2)\n             (query:Concept query:Concept-rtx-kg2)\n             (concept-properties concept-properties-rtx-kg2)\n             (concept-property-values concept-property-values-rtx-kg2)\n             (curie-in-db? curie-in-db?-rtx-kg2)\n             (curies-in-db curies-in-db-rtx-kg2)\n             (curie->properties curie->properties-rtx-kg2)\n             (edge-properties edge-properties-rtx-kg2)\n             (edge-property-values edge-property-values-rtx-kg2)\n             (edge-id->properties edge-id->properties-rtx-kg2)\n             (get-highest-bucket-number get-highest-bucket-number-rtx-kg2)\n             )\n  \"query-low-level-equivalence.rkt\"\n  \"../neo-utils/neo-helpers-without-db.rkt\"\n  \"../dbKanren/dbk/database.rkt\"\n  \"../dbKanren/dbk/enumerator.rkt\"\n  \"../dbKanren/dbk/stream.rkt\"\n  ;;racket/fixnum\n  racket/match\n  racket/math\n  racket/set\n  racket/list\n  )\n\n(define (query:Known->Known curie*.S predicate*.S->O curie*.O)\n  (append\n   (query:Known->Known-robokop\n    (curies-in-db-robokop curie*.S)\n    (curies-in-db-robokop predicate*.S->O)\n    (curies-in-db-robokop curie*.O))\n   (query:Known->Known-text-mining\n    (curies-in-db-text-mining curie*.S)\n    (curies-in-db-text-mining predicate*.S->O)\n    (curies-in-db-text-mining curie*.O))\n   (query:Known->Known-rtx-kg2\n    (curies-in-db-rtx-kg2 curie*.S)\n    (curies-in-db-rtx-kg2 predicate*.S->O)\n    (curies-in-db-rtx-kg2 curie*.O))))\n\n(define (query:Known->X curie*.K predicate*.K->X category*.X)\n  (append\n   (query:Known->X-robokop\n    (curies-in-db-robokop curie*.K)\n    (and predicate*.K->X\n         (curies-in-db-robokop predicate*.K->X))\n    (and category*.X\n         (curies-in-db-robokop category*.X)))\n   (query:Known->X-text-mining\n    (curies-in-db-text-mining curie*.K)\n    (and predicate*.K->X\n         (curies-in-db-text-mining predicate*.K->X))\n    (and category*.X\n         (curies-in-db-text-mining category*.X)))\n   (query:Known->X-rtx-kg2\n    (curies-in-db-rtx-kg2 curie*.K)\n    (and predicate*.K->X\n         (curies-in-db-rtx-kg2 predicate*.K->X))\n    (and category*.X\n         (curies-in-db-rtx-kg2 category*.X)))))\n\n(define (query:Known->X-scored curie*.K predicate*.K->X category*.X score*)\n  (append\n   (query:Known->X-scored-robokop\n    (curies-in-db-robokop curie*.K)\n    (curies-in-db-robokop predicate*.K->X)\n    (and category*.X\n         (curies-in-db-robokop category*.X))\n    (list-ref score* 0))\n   (query:Known->X-scored-text-mining\n    (curies-in-db-text-mining curie*.K)\n    (curies-in-db-text-mining predicate*.K->X)\n    (and category*.X\n         (curies-in-db-text-mining category*.X))\n    (list-ref score* 1))\n   (query:Known->X-scored-rtx-kg2\n    (curies-in-db-rtx-kg2 curie*.K)\n    (curies-in-db-rtx-kg2 predicate*.K->X)\n    (and category*.X\n         (curies-in-db-rtx-kg2 category*.X))\n    (list-ref score* 2))))\n\n(define (query:X->Known category*.X predicate*.X->K curie*.K)\n  (append\n   (query:X->Known-robokop\n    (and category*.X\n         (curies-in-db-robokop category*.X))\n    (and predicate*.X->K\n         (curies-in-db-robokop predicate*.X->K))\n    (curies-in-db-robokop curie*.K))\n   (query:X->Known-text-mining\n    (and category*.X\n         (curies-in-db-text-mining category*.X))\n    (and predicate*.X->K\n         (curies-in-db-text-mining predicate*.X->K))\n    (curies-in-db-text-mining curie*.K))\n   (query:X->Known-rtx-kg2\n    (and category*.X\n         (curies-in-db-rtx-kg2 category*.X))\n    (and predicate*.X->K\n         (curies-in-db-rtx-kg2 predicate*.X->K))\n    (curies-in-db-rtx-kg2 curie*.K))))\n\n(define (query:X->Known-scored category*.X predicate*.X->K curie*.K score*)\n  (append\n   (query:X->Known-scored-robokop\n    (and category*.X\n         (curies-in-db-robokop category*.X))\n    (curies-in-db-robokop predicate*.X->K)\n    (curies-in-db-robokop curie*.K)\n    (list-ref score* 0))\n   (query:X->Known-scored-text-mining\n    (and category*.X\n         (curies-in-db-text-mining category*.X))\n    (curies-in-db-text-mining predicate*.X->K)\n    (curies-in-db-text-mining curie*.K)\n    (list-ref score* 1))\n   (query:X->Known-scored-rtx-kg2\n    (and category*.X\n         (curies-in-db-rtx-kg2 category*.X))\n    (curies-in-db-rtx-kg2 predicate*.X->K)\n    (curies-in-db-rtx-kg2 curie*.K)\n    (list-ref score* 2))))\n\n;; query:Known<-X->Known is analogous to a miniKanren-style query with this shape:\n;;(run* (K1 name.K1 predicates.K1<-X X name.X predicates.X->K1 K2 name.K2)\n;;  (fresh (id1 id2 category.X)\n;;    (edge id1 X K1)\n;;    (edge id2 X K2)\n;;    (cprop X   \"category\" category.X)\n;;    (cprop X   \"name\" name.X)\n;;    (cprop K1  \"name\" name.K1)\n;;    (cprop K2  \"name\" name.K2)\n;;    (eprop id1 \"predicate\" K1<-X)\n;;    (eprop id2 \"predicate\" X->K2)\n;;    (membero category.X categories.X)\n;;    (membero K1         curies.K1)\n;;    (membero K1<-X      predicates.K1<-X)\n;;    (membero K2         curies.K2)\n;;    (membero X->K2      predicates.X->K2)))\n\n;; Question:  Are we missing potential answers, either between KGs or within a single KG,\n;; due to 'X' using more than one CURIE (HGNC vs. ENSMBL, for example)?\n(define (query:Known<-X->Known curie*.K1 predicate*.K1<-X category*.X predicate*.X->K2 curie*.K2)\n  (query:Known<-X->Known-helper\n   (filter curie-in-db? curie*.K1)\n   (filter curie-in-db? predicate*.K1<-X)\n   (and category*.X\n        (filter curie-in-db? category*.X))\n   (filter curie-in-db? predicate*.X->K2)\n   (filter curie-in-db? curie*.K2)))\n\n(define (query:Known<-X->Known-helper curie*.K1 predicate*.K1<-X category*.X predicate*.X->K2 curie*.K2)\n  (define (candidate*->dict candidate*)\n    (let* ((candidate* (sort candidate* (lambda (a b) (stringvector (s-group candidate* equal? car)))\n           (ref.value  (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (caar (ref.value i))) stringXK1=>1 (candidate*->dict (query:X->Known category*.X predicate*.K1<-X curie*.K1)))\n         (X=>XK2=>1 (candidate*->dict (query:X->Known category*.X predicate*.X->K2 curie*.K2))))\n    (maybe-time (enumerator->list\n                 (lambda (yield)\n                   ((merge-join stringXK1=>1 X=>XK2=>1)\n                    (lambda (X XK1* XK2*)\n                      (for-each\n                       (lambda (XK1)\n                         (match-define (list* _ predicate.X->K1 K1 props1) XK1)\n                         (for-each\n                          (lambda (XK2)\n                            (match-define (list* _ X->K2 K2 props2) XK2)\n                            (yield (append (list K1 predicate.X->K1 X X->K2 K2)\n                                           (append props1 props2))))\n                          XK2*))\n                       XK1*))))))))\n\n\n(define (query:Known->X->Known curie*.K1 predicate*.K1->X category*.X predicate*.X->K2 curie*.K2)\n  (query:Known->X->Known-helper\n   (filter curie-in-db? curie*.K1)\n   (filter curie-in-db? predicate*.K1->X)\n   (and category*.X\n        (filter curie-in-db? category*.X))\n   (filter curie-in-db? predicate*.X->K2)\n   (filter curie-in-db? curie*.K2)))\n\n(define (query:Known->X->Known-helper curie*.K1 predicate*.K1->X category*.X predicate*.X->K2 curie*.K2)\n  (define (KX*->dict candidate*)\n    (let* ((candidate* (sort candidate* (lambda (a b) (stringvector (s-group candidate* equal? caddr)))\n           (ref.value  (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (caddr (car (ref.value i)))) stringdict candidate*)\n    (let* ((candidate* (sort candidate* (lambda (a b) (stringvector (s-group candidate* equal? car)))\n           (ref.value  (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (caar (ref.value i))) stringK1X* (KX*->dict (query:Known->X curie*.K1 predicate*.K1->X category*.X)))\n         (X=>XK2* (XK*->dict (query:X->Known category*.X predicate*.X->K2 curie*.K2))))\n    (maybe-time (enumerator->list\n                 (lambda (yield)\n                   ((merge-join stringK1X* X=>XK2*)\n                    (lambda (X K1X* XK2*)\n                      (for-each\n                       (lambda (K1X)\n                         (match-define (list* K1 predicate.X->K1 _ props1) K1X)\n                         (for-each\n                          (lambda (XK2)\n                            (match-define (list* _ X->K2 K2 props2) XK2)\n                            (yield (append (list K1 predicate.X->K1 X X->K2 K2)\n                                           (append props1 props2))))\n                          XK2*))\n                       K1X*))))))))\n\n(define (result*->dict key result* curie-rep-hash)\n    (let* ((get-representative (lambda (tuple) (hash-ref curie-rep-hash (key tuple))))\n           (rep/result* (map (lambda (tuple) (cons (get-representative tuple) tuple)) result*))\n           (rep/key car)\n           (rep/result*  (sort rep/result* (lambda (a b) (stringvector (s-group rep/result* equal? rep/key)))\n           (ref.value (lambda (i) (vector-ref group* i))))\n      (dict:ref (lambda (i) (rep/key (car (ref.value i)))) stringY->Known category*.X predicate*.X->Y category*.Y predicate*.Y->K curie*.K)\n  (query:X->Y->Known-helper\n   (and category*.X\n        (curies-in-db category*.X))\n   (and predicate*.X->Y\n        (curies-in-db predicate*.X->Y))\n   (and category*.Y\n        (curies-in-db category*.Y))\n   (and predicate*.Y->K\n        (curies-in-db predicate*.Y->K))\n   (curies-in-db curie*.K)\n   #f))\n\n(define (query:X->Y->Known-scored category*.X predicate*.X->Y category*.Y predicate*.Y->K curie*.K score*)\n  (query:X->Y->Known-helper\n   (and category*.X\n        (curies-in-db category*.X))\n   (curies-in-db predicate*.X->Y)\n   (and category*.Y\n        (curies-in-db category*.Y))\n   (curies-in-db predicate*.Y->K)\n   (curies-in-db curie*.K)\n   score*))\n\n(define (query:X->Y->Known-helper category*.X predicate*.X->Y category*.Y predicate*.Y->K curie*.K score*)\n  (let* ((YK (if score*\n                 (query:X->Known-scored category*.Y predicate*.Y->K curie*.K score*)\n                 (query:X->Known category*.Y predicate*.Y->K curie*.K)))\n         (curie-rep-hash (build-curies-representative-hash (remove-duplicates (map car YK))))\n         (Y=>YK=>1 (result*->dict car YK curie-rep-hash))\n         (curie*.Y (hash-keys curie-rep-hash))\n         (XY (if score*\n                 (query:X->Known-scored category*.X predicate*.X->Y curie*.Y score*)\n                 (query:X->Known category*.X predicate*.X->Y curie*.Y)))\n         (Y=>XY=>1 (result*->dict caddr XY curie-rep-hash)))\n    (maybe-time (enumerator->list\n                 (lambda (yield)\n                   ((merge-join stringXY=>1 Y=>YK=>1)\n                    (lambda (rep XY* YK*)\n                      (for-each\n                       (lambda (XY)\n                         (match-define (list* _ X predicate.X->Y _ props.X->Y) XY)\n                         (for-each\n                          (lambda (YK)\n                            (match-define (list* _ Y Y->K K props.Y->K) YK)\n                            (yield (list X predicate.X->Y Y Y->K K props.X->Y props.Y->K)))\n                          YK*))\n                       XY*))))))))\n\n(define (query:Known->Y->X curie*.K predicate*.K->Y category*.Y predicate*.Y->X category*.X)\n  (query:Known->Y->X-helper\n   (curies-in-db curie*.K)\n   (and predicate*.K->Y\n        (curies-in-db predicate*.K->Y))\n   (and category*.Y\n        (curies-in-db category*.Y))\n   (and predicate*.Y->X\n        (curies-in-db predicate*.Y->X))\n   (and category*.X\n        (curies-in-db category*.X))\n   #f))\n\n(define (query:Known->Y->X-scored curie*.K predicate*.K->Y category*.Y predicate*.Y->X category*.X score*)\n  (query:Known->Y->X-helper\n   (curies-in-db curie*.K)\n   (curies-in-db predicate*.K->Y)\n   (and category*.Y\n        (curies-in-db category*.Y))\n   (curies-in-db predicate*.Y->X)\n   (and category*.X\n        (curies-in-db category*.X))\n   score*))\n\n(define (query:Known->Y->X-helper curie*.K predicate*.K->Y category*.Y predicate*.Y->X category*.X score*)\n  (let* ((KY (if score*\n                 (query:Known->X-scored curie*.K predicate*.K->Y category*.Y score*)\n                 (query:Known->X curie*.K predicate*.K->Y category*.Y)))\n         (curie-rep-hash (build-curies-representative-hash (remove-duplicates (map caddr KY))))\n         (Y=>KY=>1 (result*->dict caddr KY curie-rep-hash))\n         (curie*.Y (hash-keys curie-rep-hash))\n         (YX (if score*\n                 (query:Known->X-scored curie*.Y predicate*.Y->X category*.X score*)\n                 (query:Known->X curie*.Y predicate*.Y->X category*.X)))\n         (Y=>YX=>1 (result*->dict car YX curie-rep-hash)))\n    (maybe-time (enumerator->list\n                 (lambda (yield)\n                   ((merge-join stringYX=>1 Y=>KY=>1)\n                    (lambda (rep YX* KY*)\n                      (for-each\n                       (lambda (YX)\n                         (match-define (list* _ _ predicate.Y->X X props.Y->X) YX)\n                         (for-each\n                          (lambda (KY)\n                            (match-define (list* _ K K->Y Y props.K->Y) KY)\n                            (yield (list K K->Y Y predicate.Y->X X props.K->Y props.Y->X)))\n                          KY*))\n                       YX*))))))))\n\n(define (query:X->Y->Known-auto-grow\n         category*.X predicate*.X->Y category*.Y predicate*.Y->K curie*.K score* result_amount result-filter)\n  (define (helper YK XY curie-rep-hash score*)\n    (let* ((Y=>YK=>1 (result*->dict car YK curie-rep-hash))\n           (Y=>XY=>1 (result*->dict caddr XY curie-rep-hash))\n           (result (enumerator->list\n                    (lambda (yield)\n                      ((merge-join stringXY=>1 Y=>YK=>1)\n                       (lambda (rep XY* YK*)\n                         (for-each\n                          (lambda (XY)\n                            (match-define (list* _ X predicate.X->Y _ props.X->Y) XY)\n                            (for-each\n                             (lambda (YK)\n                               (match-define (list* _ Y Y->K K props.Y->K) YK)\n                               (yield (list X predicate.X->Y Y Y->K K props.X->Y props.Y->K)))\n                             YK*))\n                          XY*))))))\n           (result (result-filter result)))\n      (cond\n        [(> (length result) result_amount)\n         (printf \"return ~a answers\\n\" (length result))\n         result]\n        [(andmap not score*)\n         (printf \"return ~a answers\\n\" (length result))\n         result]\n        [else\n         (let* ((score* (list (minus-one-before-zero (list-ref score* 0))\n                              (minus-one-before-zero (list-ref score* 1))\n                              (minus-one-before-zero (list-ref score* 2))))\n                (YK-new (query:X->Known-scored category*.Y predicate*.Y->K curie*.K score*))\n                (YK (append YK YK-new))\n                (curie-rep-hash (add-curies-representative-to-hash curie-rep-hash (remove-duplicates (map car YK-new))))\n                (curie*.Y (hash-keys curie-rep-hash))\n                (XY (append XY (query:X->Known-scored category*.X predicate*.X->Y curie*.Y score*))))\n           (helper YK XY curie-rep-hash score*))])))\n  (let* ((YK (query:X->Known-scored category*.Y predicate*.Y->K curie*.K score*))\n         (curie-rep-hash (build-curies-representative-hash (remove-duplicates (map car YK))))\n         (curie*.Y (hash-keys curie-rep-hash))\n         (XY (query:X->Known-scored category*.X predicate*.X->Y curie*.Y score*)))\n    (helper YK XY curie-rep-hash score*)))\n\n(define (query:Known->Y->X-auto-grow\n         curie*.K predicate*.K->Y category*.Y predicate*.Y->X category*.X score* result_amount result-filter)\n  (define (helper KY YX curie-rep-hash score*)\n    (let* ((Y=>KY=>1 (result*->dict caddr KY curie-rep-hash))\n           (Y=>YX=>1 (result*->dict car YX curie-rep-hash))\n           (result (enumerator->list\n                    (lambda (yield)\n                      ((merge-join stringYX=>1 Y=>KY=>1)\n                       (lambda (rep YX* KY*)\n                         (for-each\n                          (lambda (YX)\n                            (match-define (list* _ _ predicate.Y->X X props.Y->X) YX)\n                            (for-each\n                             (lambda (KY)\n                               (match-define (list* _ K K->Y Y props.K->Y) KY)\n                               (yield (list K K->Y Y predicate.Y->X X props.K->Y props.Y->X)))\n                             KY*))\n                          YX*))))))\n           (result (result-filter result)))\n      (cond\n        [(> (length result) result_amount)\n         (printf \"return ~a answers\\n\" (length result))\n         result]\n        [(andmap not score*)\n         (printf \"return ~a answers\\n\" (length result))\n         result]\n        [else\n         (let* ((score* (list (minus-one-before-zero (list-ref score* 0))\n                              (minus-one-before-zero (list-ref score* 1))\n                              (minus-one-before-zero (list-ref score* 2))))\n                (KY-new (query:Known->X-scored curie*.K predicate*.K->Y category*.Y score*))\n                (KY (append KY KY-new))\n                (curie-rep-hash (add-curies-representative-to-hash curie-rep-hash (remove-duplicates (map caddr KY-new))))\n                (curie*.Y (hash-keys curie-rep-hash))\n                (YX (append YX (query:Known->X-scored curie*.Y predicate*.Y->X category*.X score*))))\n           (helper KY YX curie-rep-hash score*))])))\n  (let* ((KY (query:Known->X-scored curie*.K predicate*.K->Y category*.Y score*))\n         (curie-rep-hash (build-curies-representative-hash (remove-duplicates (map caddr KY))))\n         (curie*.Y (hash-keys curie-rep-hash))\n         (YX (query:Known->X-scored curie*.Y predicate*.Y->X category*.X score*)))\n    (helper KY YX curie-rep-hash score*)))\n\n(define (query:Concept curie*)\n  (append\n   (query:Concept-robokop (filter curie-in-db?-robokop curie*))\n   (query:Concept-text-mining (filter curie-in-db?-text-mining curie*))\n   (query:Concept-rtx-kg2 (filter curie-in-db?-rtx-kg2 curie*))))\n\n(define (concept-properties)\n  (append\n   (concept-properties-robokop)\n   (concept-properties-text-mining)\n   (concept-properties-rtx-kg2)))\n\n;;(define (concept-property-values key) 'TODO)\n\n(define (curie-in-db? curie)\n  (or\n   (curie-in-db?-robokop curie)\n   (curie-in-db?-text-mining curie)\n   (curie-in-db?-rtx-kg2 curie)))\n\n(define (curies-in-db curie*)\n  (remove-duplicates\n   (append\n    (curies-in-db-robokop curie*)\n    (curies-in-db-text-mining curie*)\n    (curies-in-db-rtx-kg2 curie*))))\n\n(define (curie->properties curie)\n  (append\n   (if (curie-in-db?-text-mining curie)\n       (curie->properties-text-mining curie)\n       '())\n   (if (curie-in-db?-rtx-kg2 curie)\n       (curie->properties-rtx-kg2 curie)\n       '())\n   (if (curie-in-db?-robokop curie)\n       (curie->properties-robokop curie)\n       '())))\n\n(define (edge-properties)\n  (append\n   (edge-properties-robokop)\n   (edge-properties-text-mining)\n   (edge-properties-rtx-kg2)))\n\n;;(define (edge-property-values key) 'TODO)\n;;(define (edge-id->properties eid) 'TODO)\n"
  },
  {
    "path": "medikanren2/neo/neo-low-level/query-low-level-node-normalization.rkt",
    "content": "#lang racket/base\n\n(provide\n  query:Known->X\n  query:X->Known  \n  curie-in-db?\n  )\n(require\n \"make-query-low-level.rkt\"\n racket/match)\n\n(define db-path-under-parent \"kgx-synonym/neo/node_normalization.db\")\n\n(match-define\n  (list\n    query:Known->Known\n    query:Known->X\n    query:X->Known\n    query:Known<-X->Known\n    query:Known->X->Known\n    query:X->Y->Known\n    query:Concept\n    concept-properties\n    concept-property-values\n    curie-in-db?\n    curie->properties\n    edge-properties\n    edge-property-values\n    edge-id->properties)\n  (make-query-low-level db-path-under-parent))"
  },
  {
    "path": "medikanren2/neo/neo-low-level/query-low-level-robokop.rkt",
    "content": "#lang racket/base\n\n(provide\n  query:Known->Known\n  query:Known->X\n  query:Known->X-scored\n  query:X->Known\n  query:X->Known-scored\n  query:Known<-X->Known\n  query:Known->X->Known\n  query:X->Y->Known\n  query:Concept\n  concept-properties\n  concept-property-values\n  curie-in-db?\n  curies-in-db\n  curie->properties\n  edge-properties\n  edge-property-values\n  edge-id->properties\n  get-highest-bucket-number)\n(require\n \"make-query-low-level.rkt\"\n racket/match)\n \n#;(define db-path-under-parent \"robokop-may-9-2024/march-7-2024/robokop.db\")\n(define db-path-under-parent \"robokop-aug-6-2024/july-31-2024/robokop.db\")\n\n(match-define\n  (list\n   query:Known->Known\n   query:Known->X-scored\n   query:Known->X\n   query:X->Known-scored\n   query:X->Known\n   query:Known<-X->Known\n   query:Known->X->Known\n   query:X->Y->Known\n   query:Concept\n   concept-properties\n   concept-property-values\n   curie-in-db?\n   curies-in-db\n   curie->properties\n   edge-properties\n   edge-property-values\n   edge-id->properties\n   get-highest-bucket-number\n   )\n  (make-query-low-level db-path-under-parent \"infores:robokop-kg\"))\n"
  },
  {
    "path": "medikanren2/neo/neo-low-level/query-low-level-rtx-kg2.rkt",
    "content": "#lang racket/base\n\n(provide\n  query:Known->Known\n  query:Known->X\n  query:Known->X-scored\n  query:X->Known\n  query:X->Known-scored\n  query:Known<-X->Known\n  query:Known->X->Known\n  query:X->Y->Known\n  query:Concept\n  concept-properties\n  concept-property-values\n  curie-in-db?\n  curies-in-db\n  curie->properties\n  edge-properties\n  edge-property-values\n  edge-id->properties\n  get-highest-bucket-number)\n(require\n \"make-query-low-level.rkt\"\n racket/match)\n\n#;(define db-path-under-parent \"rtx-kg2-may-9-2024/rtx-kg2-2.9.0pre/rtx-kg2.db\")\n(define db-path-under-parent \"rtx-kg2-oct-30-2024/rtx-kg2-2.10.1pre/rtx-kg2.db\")\n\n(match-define\n  (list\n   query:Known->Known\n   query:Known->X-scored\n   query:Known->X\n   query:X->Known-scored\n   query:X->Known\n   query:Known<-X->Known\n   query:Known->X->Known\n   query:X->Y->Known\n   query:Concept\n   concept-properties\n   concept-property-values\n   curie-in-db?\n   curies-in-db\n   curie->properties\n   edge-properties\n   edge-property-values\n   edge-id->properties\n   get-highest-bucket-number\n   )\n  (make-query-low-level db-path-under-parent \"infores:rtx-kg2\"))\n"
  },
  {
    "path": "medikanren2/neo/neo-low-level/query-low-level-text-mining.rkt",
    "content": "#lang racket/base\n\n(provide\n  query:Known->Known\n  query:Known->X\n  query:Known->X-scored\n  query:X->Known\n  query:X->Known-scored\n  query:Known<-X->Known\n  query:Known->X->Known\n  query:X->Y->Known\n  query:Concept\n  concept-properties\n  concept-property-values\n  curie-in-db?\n  curies-in-db\n  curie->properties\n  edge-properties\n  edge-property-values\n  edge-id->properties\n  get-highest-bucket-number)\n(require\n \"make-query-low-level.rkt\"\n racket/match)\n\n(define db-path-under-parent \"text-mining-aug-5-2024/aug_5_2024/text_mining.db\")\n#;(define db-path-under-parent \"text-mining-apr-5-2024/apr_2_2024/text_mining.db\")\n\n(match-define\n  (list\n   query:Known->Known\n   query:Known->X-scored\n   query:Known->X\n   query:X->Known-scored\n   query:X->Known\n   query:Known<-X->Known\n   query:Known->X->Known\n   query:X->Y->Known\n   query:Concept\n   concept-properties\n   concept-property-values\n   curie-in-db?\n   curies-in-db\n   curie->properties\n   edge-properties\n   edge-property-values\n   edge-id->properties\n   get-highest-bucket-number\n   )\n  (make-query-low-level db-path-under-parent  \"infores:text-mining-provider-targeted\"))\n"
  },
  {
    "path": "medikanren2/neo/neo-open-api/mediKanrenSmartAPI_1_4.json",
    "content": "{\n  \"openapi\": \"3.0.3\",\n  \"info\": {\n    \"contact\": {\n      \"email\": \"webyrd@gmail.com\",\n      \"name\": \"William E. Byrd\",\n      \"url\": \"https://github.com/webyrd\",\n      \"x-role\": \"responsible developer\"\n    },\n    \"description\": \"TRAPI 1.4 Endpoint for Team Unsecret Agent's mediKanren ARA\",\n    \"license\": {\n      \"name\": \"MIT License\",\n      \"url\": \"https://github.com/webyrd/mediKanren/blob/master/LICENSE\"\n    },\n    \"title\": \"mediKanren\",\n    \"version\": \"2.0 neo TRAPI 1.4\",\n    \"x-translator\": {\n      \"biolink-version\": \"3.1.2\",\n      \"component\": \"ARA\",\n      \"externalDocs\": {\n        \"description\": \"The values for component and team are restricted according to this external JSON schema. See schema and examples at url\",\n        \"url\": \"https://github.com/NCATSTranslator/translator_extensions/blob/\\\\ production/x-translator/\"\n      },\n      \"infores\": \"infores:unsecret-agent\",\n      \"team\": [\n        \"Unsecret Agent\"\n      ]\n    },\n    \"x-trapi\": {\n      \"asyncquery\": false,\n      \"batch_size_limit\": 500,\n      \"externalDocs\": {\n        \"description\": \"The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url\",\n        \"url\": \"https://github.com/NCATSTranslator/translator_extensions/blob/\\\\ production/x-trapi/\"\n      },\n      \"operations\": [\n        \"lookup\"\n      ],\n      \"version\": \"1.4.0\"\n    }\n  },\n  \"servers\": [\n    {\n      \"description\": \"Team Unsecret Agent mediKanren 1.4 Production server\",\n      \"url\": \"https://medikanren-trapi.transltr.io\",\n      \"x-location\": \"ITRB\",\n      \"x-maturity\": \"production\"\n    },\n    {\n      \"description\": \"Team Unsecret Agent mediKanren 1.4 Test server\",\n      \"url\": \"https://medikanren-trapi.test.transltr.io\",\n      \"x-location\": \"ITRB\",\n      \"x-maturity\": \"testing\"\n    }\n  ],\n  \"externalDocs\": {\n    \"description\": \"Documentation for the NCATS Biomedical Translator Reasoners web services\",\n    \"url\": \"https://github.com/NCATSTranslator/ReasonerAPI\"\n  },\n  \"tags\": [\n    {\n      \"description\": \"Initiate a query and wait to receive the response\",\n      \"name\": \"query\"\n    },\n    {\n      \"description\": \"Required for SmartAPI validation of x-translator\",\n      \"name\": \"translator\"\n    },\n    {\n      \"description\": \"Required for SmartAPI validation of x-trapi\",\n      \"name\": \"trapi\"\n    }\n  ],\n  \"paths\": {\n    \"/query\": {\n      \"post\": {\n        \"description\": \"Query Team Unsecret Agent's mediKanren ARA API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI).\",\n        \"operationId\": \"query\",\n        \"requestBody\": {\n          \"content\": {\n            \"application/json\": {\n              \"example\": \"{\\\"message\\\": {\\\"query_graph\\\": {\\\"nodes\\\": {\\\"n0\\\": {\\\"ids\\\": [\\\"MONDO:0004975\\\"], \\\"categories\\\": [\\\"biolink:Disease\\\"]}, \\\"n1\\\": {\\\"categories\\\":[\\\"biolink:ChemicalEntity\\\"]}}, \\\"edges\\\": {\\\"e0\\\": {\\\"subject\\\": \\\"n1\\\", \\\"object\\\": \\\"n0\\\", \\\"predicates\\\":[\\\"biolink:treats\\\"], \\\"knowledge_type\\\": \\\"inferred\\\"}}}}}\",\n              \"schema\": {\n                \"$ref\": \"#/components/schemas/Query\"\n              }\n            }\n          },\n          \"description\": \"Query information to be submitted\",\n          \"required\": true\n        },\n        \"responses\": {\n          \"200\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"$ref\": \"#/components/schemas/Response\"\n                }\n              }\n            },\n            \"description\": \"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized.\"\n          },\n          \"400\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"type\": \"string\"\n                }\n              }\n            },\n            \"description\": \"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized).\"\n          },\n          \"500\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"type\": \"string\"\n                }\n              }\n            },\n            \"description\": \"Internal server error.\"\n          },\n          \"501\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"type\": \"string\"\n                }\n              }\n            },\n            \"description\": \"Not implemented.\"\n          }\n        },\n        \"summary\": \"Initiate a query and wait to receive a Response\",\n        \"tags\": [\n          \"query\"\n        ],\n        \"x-swagger-router-controller\": \"swagger_server.controllers.query_controller\"\n      }\n    }\n  },\n  \"components\": {\n    \"schemas\": {\n      \"AsyncQuery\": {\n        \"additionalProperties\": true,\n        \"description\": \"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.\",\n        \"properties\": {\n          \"callback\": {\n            \"description\": \"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.\",\n            \"format\": \"uri\",\n            \"pattern\": \"^https?://\",\n            \"type\": \"string\"\n          },\n          \"log_level\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/LogLevel\"\n              }\n            ],\n            \"description\": \"The least critical level of logs to return\",\n            \"nullable\": true\n          },\n          \"message\": {\n            \"$ref\": \"#/components/schemas/Message\",\n            \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n          },\n          \"workflow\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n              }\n            ],\n            \"description\": \"List of workflow steps to be executed.\",\n            \"nullable\": true\n          }\n        },\n        \"required\": [\n          \"callback\",\n          \"message\"\n        ],\n        \"type\": \"object\",\n        \"x-body-name\": \"request_body\"\n      },\n      \"Attribute\": {\n        \"additionalProperties\": false,\n        \"description\": \"Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with a SubAttribute (for example to provide confidence intervals on a value).\",\n        \"properties\": {\n          \"attribute_source\": {\n            \"description\": \"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.\",\n            \"example\": \"UniProtKB\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"attribute_type_id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.\",\n            \"example\": \"Biolink:has_p-value_evidence, Biolink:has_original_source\"\n          },\n          \"attributes\": {\n            \"description\": \"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/SubAttribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"description\": {\n            \"description\": \"Human-readable description for the attribute and its value.\",\n            \"example\": \"Assertion Authored By Dr. Trans L. Ator\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"original_attribute_name\": {\n            \"description\": \"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.\",\n            \"example\": \"p-value\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"value\": {\n            \"description\": \"Value of the attribute. May be any data type, including a list.\",\n            \"example\": 0.000153\n          },\n          \"value_type_id\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/CURIE\"\n              }\n            ],\n            \"description\": \"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n            \"example\": \"EDAM:data_1187\",\n            \"nullable\": true\n          },\n          \"value_url\": {\n            \"description\": \"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).\",\n            \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"attribute_type_id\",\n          \"value\"\n        ],\n        \"type\": \"object\"\n      },\n      \"BiolinkEntity\": {\n        \"description\": \"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.\",\n        \"example\": \"biolink:PhenotypicFeature\",\n        \"externalDocs\": {\n          \"description\": \"Biolink model entities\",\n          \"url\": \"https://biolink.github.io/biolink-model/docs/NamedThing.html\"\n        },\n        \"pattern\": \"^biolink:[A-Z][a-zA-Z]*$\",\n        \"type\": \"string\"\n      },\n      \"BiolinkPredicate\": {\n        \"description\": \"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.\",\n        \"example\": \"biolink:interacts_with\",\n        \"externalDocs\": {\n          \"description\": \"Biolink model predicates\",\n          \"url\": \"https://biolink.github.io/biolink-model/docs/related_to.html\"\n        },\n        \"pattern\": \"^biolink:[a-z][a-z_]*$\",\n        \"type\": \"string\"\n      },\n      \"CURIE\": {\n        \"description\": \"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.\",\n        \"externalDocs\": {\n          \"url\": \"https://www.w3.org/TR/2010/NOTE-curie-20101216/\"\n        },\n        \"type\": \"string\"\n      },\n      \"Edge\": {\n        \"additionalProperties\": false,\n        \"description\": \"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \\\"thought\\\" graph resulting from a query upon the underlying knowledge source.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"A list of additional attributes for this edge\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Attribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"object\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"Corresponds to the map key CURIE of the object concept node of this relationship edge.\",\n            \"example\": \"UniProtKB:P00738\"\n          },\n          \"predicate\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n              }\n            ],\n            \"nullable\": true\n          },\n          \"subject\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"Corresponds to the map key CURIE of the subject concept node of this relationship edge.\",\n            \"example\": \"OMIM:603903\"\n          }\n        },\n        \"required\": [\n          \"subject\",\n          \"object\"\n        ],\n        \"type\": \"object\"\n      },\n      \"EdgeBinding\": {\n        \"additionalProperties\": true,\n        \"description\": \"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized).\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Attribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"id\": {\n            \"description\": \"The key identifier of a specific KnowledgeGraph Edge.\",\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"id\"\n        ],\n        \"type\": \"object\"\n      },\n      \"KnowledgeGraph\": {\n        \"additionalProperties\": true,\n        \"description\": \"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.\",\n        \"properties\": {\n          \"edges\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/Edge\"\n            },\n            \"description\": \"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n            \"type\": \"object\"\n          },\n          \"nodes\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/Node\"\n            },\n            \"description\": \"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n            \"type\": \"object\"\n          }\n        },\n        \"required\": [\n          \"nodes\",\n          \"edges\"\n        ],\n        \"type\": \"object\"\n      },\n      \"LogEntry\": {\n        \"additionalProperties\": true,\n        \"description\": \"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.\",\n        \"properties\": {\n          \"code\": {\n            \"description\": \"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"level\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/LogLevel\"\n              }\n            ],\n            \"nullable\": true\n          },\n          \"message\": {\n            \"description\": \"A human-readable log message\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"timestamp\": {\n            \"description\": \"Timestamp in ISO 8601 format\",\n            \"example\": \"2020-09-03T18:13:49+00:00\",\n            \"format\": \"date-time\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"LogLevel\": {\n        \"description\": \"Logging level\",\n        \"enum\": [\n          \"ERROR\",\n          \"WARNING\",\n          \"INFO\",\n          \"DEBUG\"\n        ],\n        \"type\": \"string\"\n      },\n      \"Message\": {\n        \"additionalProperties\": false,\n        \"description\": \"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.\",\n        \"properties\": {\n          \"knowledge_graph\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/KnowledgeGraph\"\n              }\n            ],\n            \"description\": \"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message\",\n            \"nullable\": true\n          },\n          \"query_graph\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/QueryGraph\"\n              }\n            ],\n            \"description\": \"QueryGraph object that contains a serialization of a query in the form of a graph\",\n            \"nullable\": true\n          },\n          \"results\": {\n            \"description\": \"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property,\\n if present, MAY be used to infer result rankings.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Result\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"MetaAttribute\": {\n        \"properties\": {\n          \"attribute_source\": {\n            \"description\": \"Source of an attribute provided by this TRAPI web service.\",\n            \"example\": \"infores:chembl\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"attribute_type_id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)\",\n            \"example\": \"biolink:p_value\"\n          },\n          \"constraint_name\": {\n            \"description\": \"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.\",\n            \"example\": \"p-value\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"constraint_use\": {\n            \"default\": false,\n            \"description\": \"Indicates whether this attribute can be used as a query constraint.\",\n            \"type\": \"boolean\"\n          },\n          \"original_attribute_names\": {\n            \"description\": \"Names of an the attribute as provided by the source.\",\n            \"items\": {\n              \"type\": \"string\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          }\n        },\n        \"required\": [\n          \"attribute_type_id\"\n        ],\n        \"type\": \"object\"\n      },\n      \"MetaEdge\": {\n        \"additionalProperties\": false,\n        \"description\": \"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"Edge attributes provided by this TRAPI web service.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/MetaAttribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"object\": {\n            \"$ref\": \"#/components/schemas/BiolinkEntity\",\n            \"description\": \"Object node category of this relationship edge.\",\n            \"example\": \"biolink:Protein\"\n          },\n          \"predicate\": {\n            \"$ref\": \"#/components/schemas/BiolinkPredicate\",\n            \"description\": \"Biolink relationship between the subject and object categories.\",\n            \"example\": \"biolink:affects\"\n          },\n          \"subject\": {\n            \"$ref\": \"#/components/schemas/BiolinkEntity\",\n            \"description\": \"Subject node category of this relationship edge.\",\n            \"example\": \"biolink:ChemicalSubstance\"\n          }\n        },\n        \"required\": [\n          \"subject\",\n          \"predicate\",\n          \"object\"\n        ],\n        \"type\": \"object\"\n      },\n      \"MetaKnowledgeGraph\": {\n        \"description\": \"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.\",\n        \"properties\": {\n          \"edges\": {\n            \"description\": \"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/MetaEdge\"\n            },\n            \"type\": \"array\"\n          },\n          \"nodes\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/MetaNode\"\n            },\n            \"description\": \"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.\",\n            \"type\": \"object\"\n          }\n        },\n        \"required\": [\n          \"nodes\",\n          \"edges\"\n        ],\n        \"type\": \"object\"\n      },\n      \"MetaNode\": {\n        \"additionalProperties\": false,\n        \"description\": \"Description of a node category provided by this TRAPI web service.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"Node attributes provided by this TRAPI web service.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/MetaAttribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"id_prefixes\": {\n            \"description\": \"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.\",\n            \"example\": [\n              \"CHEMBL.COMPOUND\",\n              \"INCHIKEY\"\n            ],\n            \"items\": {\n              \"type\": \"string\"\n            },\n            \"minItems\": 1,\n            \"type\": \"array\"\n          }\n        },\n        \"required\": [\n          \"id_prefixes\"\n        ],\n        \"type\": \"object\"\n      },\n      \"Node\": {\n        \"additionalProperties\": false,\n        \"description\": \"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"A list of attributes describing the node\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Attribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"categories\": {\n            \"items\": {\n              \"$ref\": \"#/components/schemas/BiolinkEntity\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"name\": {\n            \"description\": \"Formal name of the entity\",\n            \"example\": \"Haptoglobin\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"NodeBinding\": {\n        \"additionalProperties\": true,\n        \"properties\": {\n          \"id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation (such annotation is not yet fully standardized).\"\n          }\n        },\n        \"required\": [\n          \"id\"\n        ],\n        \"type\": \"object\"\n      },\n      \"QEdge\": {\n        \"additionalProperties\": true,\n        \"description\": \"An edge in the QueryGraph used as an filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.\",\n        \"properties\": {\n          \"constraints\": {\n            \"default\": [],\n            \"description\": \"A list of contraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/QueryConstraint\"\n            },\n            \"type\": \"array\"\n          },\n          \"object\": {\n            \"description\": \"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.\",\n            \"example\": \"https://www.uniprot.org/uniprot/P00738\",\n            \"type\": \"string\"\n          },\n          \"predicates\": {\n            \"items\": {\n              \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"subject\": {\n            \"description\": \"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.\",\n            \"example\": \"https://omim.org/entry/603903\",\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"subject\",\n          \"object\"\n        ],\n        \"type\": \"object\"\n      },\n      \"QNode\": {\n        \"additionalProperties\": true,\n        \"description\": \"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.\",\n        \"properties\": {\n          \"categories\": {\n            \"items\": {\n              \"$ref\": \"#/components/schemas/BiolinkEntity\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"constraints\": {\n            \"default\": [],\n            \"description\": \"A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/QueryConstraint\"\n            },\n            \"type\": \"array\"\n          },\n          \"ids\": {\n            \"description\": \"CURIE identifier for this node\",\n            \"example\": [\n              \"OMIM:603903\"\n            ],\n            \"items\": {\n              \"$ref\": \"#/components/schemas/CURIE\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"is_set\": {\n            \"default\": false,\n            \"description\": \"Boolean that if set to true, indicates that this QNode MAY have multiple KnowledgeGraph Nodes bound to it within each Result. The nodes in a set should be considered as a set of independent nodes, rather than a set of dependent nodes, i.e., the answer would still be valid if the nodes in the set were instead returned individually. Multiple QNodes may have is_set=True. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=False, each n1 must be connected to n2. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True, each n1 must be connected to at least one n2.\",\n            \"type\": \"boolean\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"Query\": {\n        \"additionalProperties\": true,\n        \"description\": \"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.\",\n        \"properties\": {\n          \"log_level\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/LogLevel\"\n              }\n            ],\n            \"description\": \"The least critical level of logs to return\",\n            \"nullable\": true\n          },\n          \"message\": {\n            \"$ref\": \"#/components/schemas/Message\",\n            \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n          },\n          \"workflow\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n              }\n            ],\n            \"description\": \"List of workflow steps to be executed.\",\n            \"nullable\": true\n          }\n        },\n        \"required\": [\n          \"message\"\n        ],\n        \"type\": \"object\",\n        \"x-body-name\": \"request_body\"\n      },\n      \"QueryConstraint\": {\n        \"additionalProperties\": false,\n        \"description\": \"Generic query constraint for a query node or query edge\",\n        \"properties\": {\n          \"id\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/CURIE\"\n              }\n            ],\n            \"description\": \"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n            \"example\": \"EDAM:data_0844\"\n          },\n          \"name\": {\n            \"description\": \"Human-readable name or label for the constraint concept. If appropriate, it SHOULD be the term name of the CURIE used as the 'id'. This is redundant but required for human readability.\",\n            \"example\": \"molecular mass\",\n            \"type\": \"string\"\n          },\n          \"not\": {\n            \"default\": false,\n            \"type\": \"boolean\"\n          },\n          \"operator\": {\n            \"description\": \"Relationship between the database value and the constraint value for the specified id. The operators ==, >, and < mean is exactly equal to, is greater than, and is less than, respectively. The 'matches' operator indicates that the value is a regular expression to be evaluated. If value is a list type, then at least one evaluation must be true (equivalent to OR). This means that the == operator with a list acts like a SQL 'IN' clause. The 'not' property negates the operator such that not and == means 'not equal to' (or 'not in' for a list), and not > means <=, and not < means >=, and not matches means does not match. The '==' operator SHOULD NOT be used in a manner that describes an \\\"is a\\\" subclass relationship for the parent QNode.\",\n            \"enum\": [\n              \"==\",\n              \">\",\n              \"<\",\n              \"matches\"\n            ],\n            \"type\": \"string\"\n          },\n          \"unit_id\": {\n            \"description\": \"CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units.\",\n            \"example\": \"UO:0000222\",\n            \"nullable\": true\n          },\n          \"unit_name\": {\n            \"description\": \"Term name that is associated with the CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability.\",\n            \"example\": \"kilodalton\",\n            \"nullable\": true\n          },\n          \"value\": {\n            \"description\": \"Value of the attribute. May be any data type, including a list. If the value is a list and there are multiple items, at least one comparison must be true (equivalent to OR). If 'value' is of data type 'object', the keys of the object MAY be treated as a list. A 'list' data type paired with the '>' or '<' operators will encode extraneous comparisons, but this is permitted as it is in SQL and other languages.\",\n            \"example\": 57\n          }\n        },\n        \"required\": [\n          \"name\",\n          \"id\",\n          \"operator\",\n          \"value\"\n        ],\n        \"type\": \"object\"\n      },\n      \"QueryGraph\": {\n        \"additionalProperties\": true,\n        \"description\": \"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.\",\n        \"properties\": {\n          \"edges\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/QEdge\"\n            },\n            \"description\": \"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.\",\n            \"type\": \"object\"\n          },\n          \"nodes\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/QNode\"\n            },\n            \"description\": \"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.\",\n            \"type\": \"object\"\n          }\n        },\n        \"required\": [\n          \"nodes\",\n          \"edges\"\n        ],\n        \"type\": \"object\"\n      },\n      \"Response\": {\n        \"additionalProperties\": true,\n        \"description\": \"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.\",\n        \"properties\": {\n          \"description\": {\n            \"description\": \"A brief human-readable description of the outcome\",\n            \"example\": \"Success. 42 results found.\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"logs\": {\n            \"description\": \"Log entries containing errors, warnings, debugging information, etc\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/LogEntry\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"message\": {\n            \"$ref\": \"#/components/schemas/Message\",\n            \"description\": \"Contains the knowledge of the response (query graph, knowledge graph, and results).\"\n          },\n          \"status\": {\n            \"description\": \"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable\",\n            \"example\": \"Success\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"workflow\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n              }\n            ],\n            \"description\": \"List of workflow steps that were executed.\",\n            \"nullable\": true\n          }\n        },\n        \"required\": [\n          \"message\"\n        ],\n        \"type\": \"object\"\n      },\n      \"Result\": {\n        \"additionalProperties\": true,\n        \"description\": \"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings).\",\n        \"properties\": {\n          \"edge_bindings\": {\n            \"additionalProperties\": {\n              \"items\": {\n                \"$ref\": \"#/components/schemas/EdgeBinding\"\n              },\n              \"type\": \"array\"\n            },\n            \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple knowledge graph edges in the result.\",\n            \"type\": \"object\"\n          },\n          \"node_bindings\": {\n            \"additionalProperties\": {\n              \"items\": {\n                \"$ref\": \"#/components/schemas/NodeBinding\"\n              },\n              \"type\": \"array\"\n            },\n            \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.\",\n            \"type\": \"object\"\n          },\n          \"score\": {\n            \"description\": \"A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better.\",\n            \"example\": 163.233,\n            \"format\": \"float\",\n            \"nullable\": true,\n            \"type\": \"number\"\n          }\n        },\n        \"required\": [\n          \"node_bindings\",\n          \"edge_bindings\"\n        ],\n        \"type\": \"object\"\n      },\n      \"SubAttribute\": {\n        \"additionalProperties\": false,\n        \"description\": \"Second-level attribute that can be used to qualify information contained in a primary Attribute attached to a Node or Edge.\",\n        \"properties\": {\n          \"attribute_source\": {\n            \"description\": \"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.\",\n            \"example\": \"UniProtKB\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"attribute_type_id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.\",\n            \"example\": \"Biolink:has_p-value_evidence, Biolink:has_original_source\"\n          },\n          \"description\": {\n            \"description\": \"Human-readable description for the attribute and its value.\",\n            \"example\": \"Assertion Authored By Dr. Trans L. Ator\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"original_attribute_name\": {\n            \"description\": \"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.\",\n            \"example\": \"p-value\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"value\": {\n            \"description\": \"Value of the attribute. May be any data type, including a list.\",\n            \"example\": 0.000153\n          },\n          \"value_type_id\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/CURIE\"\n              }\n            ],\n            \"description\": \"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n            \"example\": \"EDAM:data_1187\",\n            \"nullable\": true\n          },\n          \"value_url\": {\n            \"description\": \"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).\",\n            \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"attribute_type_id\",\n          \"value\"\n        ],\n        \"type\": \"object\"\n      }\n    }\n  }\n}"
  },
  {
    "path": "medikanren2/neo/neo-open-api/mediKanrenSmartAPI_1_4.yaml",
    "content": "openapi: 3.0.3\ninfo:\n  contact:\n    email: webyrd@gmail.com\n    name: William E. Byrd\n    url: https://github.com/webyrd\n    x-role: responsible developer\n  description: TRAPI 1.4 Endpoint for Team Unsecret Agent's mediKanren ARA\n  license:\n    name: MIT License\n    url: https://github.com/webyrd/mediKanren/blob/master/LICENSE\n  title: mediKanren\n  version: '2.0 neo TRAPI 1.4'\n  x-translator:\n    biolink-version: 3.1.2\n    component: ARA\n    externalDocs:\n      description: The values for component and team are restricted according to this\n        external JSON schema. See schema and examples at url\n      url: https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-translator/    \n    infores: infores:unsecret-agent\n    team:\n    - Unsecret Agent\n  x-trapi:\n    asyncquery: false\n    batch_size_limit: 500\n    externalDocs:\n      description: The values for version are restricted according to the regex in\n        this external JSON schema. See schema and examples at url\n      url: https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-trapi/    \n    operations:\n    - lookup\n    version: 1.4.0\nservers:\n- description: Team Unsecret Agent mediKanren 1.4 Production server\n  url: https://medikanren-trapi.transltr.io\n  x-location: ITRB\n  x-maturity: production\n- description: Team Unsecret Agent mediKanren 1.4 Test server\n  url: https://medikanren-trapi.test.transltr.io\n  x-location: ITRB\n  x-maturity: testing\nexternalDocs:\n  description: Documentation for the NCATS Biomedical Translator Reasoners web services\n  url: https://github.com/NCATSTranslator/ReasonerAPI\ntags:\n- description: Initiate a query and wait to receive the response\n  name: query\n- description: Required for SmartAPI validation of x-translator\n  name: translator\n- description: Required for SmartAPI validation of x-trapi\n  name: trapi\npaths:\n  /query:\n    post:\n      description: \"Query Team Unsecret Agent's mediKanren ARA API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI).\"\n      operationId: query\n      requestBody:\n        content:\n          application/json:\n            example: \"{\\\"message\\\": {\\\"query_graph\\\": {\\\"nodes\\\": {\\\"n0\\\": {\\\"ids\\\": [\\\"MONDO:0004975\\\"], \\\"categories\\\": [\\\"biolink:Disease\\\"]}, \\\"n1\\\": {\\\"categories\\\":[\\\"biolink:ChemicalEntity\\\"]}}, \\\"edges\\\": {\\\"e0\\\": {\\\"subject\\\": \\\"n1\\\", \\\"object\\\": \\\"n0\\\", \\\"predicates\\\":[\\\"biolink:treats\\\"], \\\"knowledge_type\\\": \\\"inferred\\\"}}}}}\"\n            schema:\n              $ref: '#/components/schemas/Query'\n        description: Query information to be submitted\n        required: true\n      responses:\n        '200':\n          content:\n            application/json:\n              schema:\n                $ref: '#/components/schemas/Response'\n          description: OK. There may or may not be results. Note that some of the\n            provided identifiers may not have been recognized.\n        '400':\n          content:\n            application/json:\n              schema:\n                type: string\n          description: Bad request. The request is invalid according to this OpenAPI\n            schema OR a specific identifier is believed to be invalid somehow (not\n            just unrecognized).\n        '500':\n          content:\n            application/json:\n              schema:\n                type: string\n          description: Internal server error.\n        '501':\n          content:\n            application/json:\n              schema:\n                type: string\n          description: Not implemented.\n      summary: Initiate a query and wait to receive a Response\n      tags:\n      - query\n      x-swagger-router-controller: swagger_server.controllers.query_controller\ncomponents:\n  schemas:\n    AsyncQuery:\n      additionalProperties: true\n      description: The AsyncQuery class is effectively the same as the Query class\n        but it requires a callback property.\n      properties:\n        callback:\n          description: 'Upon completion, this server will send a POST request to the\n            callback URL with `Content-Type: application/json` header and request\n            body containing a JSON-encoded `Response` object. The server MAY POST\n            `Response` objects before work is fully complete to provide interim results\n            with a Response.status value of ''Running''. If a POST operation to the\n            callback URL does not succeed, the server SHOULD retry the POST at least\n            once.'\n          format: uri\n          pattern: ^https?://\n          type: string\n        log_level:\n          allOf:\n          - $ref: '#/components/schemas/LogLevel'\n          description: The least critical level of logs to return\n          nullable: true\n        message:\n          $ref: '#/components/schemas/Message'\n          description: The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For example,\n            the fill operation requires a non-empty query_graph field as part of the\n            Message, whereas other operations, e.g. overlay, require non-empty results\n            and knowledge_graph fields.\n        workflow:\n          allOf:\n          - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          description: List of workflow steps to be executed.\n          nullable: true\n      required:\n      - callback\n      - message\n      type: object\n      x-body-name: request_body\n    Attribute:\n      additionalProperties: false\n      description: Generic attribute for a node or an edge that expands the key-value\n        pair concept by including fields for additional metadata. These fields can\n        be used to describe the source of the statement made in a key-value pair of\n        the attribute object, or describe the attribute's value itself including its\n        semantic type, or a url providing additional information about it. An attribute\n        may be further qualified with a SubAttribute (for example to provide confidence\n        intervals on a value).\n      properties:\n        attribute_source:\n          description: The source of the core assertion made by the key-value pair\n            of an attribute object. Use a CURIE or namespace designator for this resource\n            where possible.\n          example: UniProtKB\n          nullable: true\n          type: string\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: The 'key' of the attribute object, holding a CURIE of an ontology\n            property defining the attribute (preferably the CURIE of a Biolink association\n            slot). This property captures the relationship asserted to hold between\n            the value of the attribute, and the node or edge from  which it hangs.\n            For example, that a value of '0.000153' represents a p-value supporting\n            an edge, or that a value of 'ChEMBL' represents the original source of\n            the knowledge expressed in the edge.\n          example: Biolink:has_p-value_evidence, Biolink:has_original_source\n        attributes:\n          description: A list of attributes providing further information about the\n            parent attribute (for example to provide provenance information about\n            the parent attribute).\n          items:\n            $ref: '#/components/schemas/SubAttribute'\n          nullable: true\n          type: array\n        description:\n          description: Human-readable description for the attribute and its value.\n          example: Assertion Authored By Dr. Trans L. Ator\n          nullable: true\n          type: string\n        original_attribute_name:\n          description: The term used by the original source of an attribute to describe\n            the meaning or significance of the value it captures. This may be a column\n            name in a source tsv file, or a key in a source json document for the\n            field in the data that held the attribute's value. Capturing this information  where\n            possible lets us preserve what the original source said. Note that the\n            data type is string' but the contents of the field could also be a CURIE\n            of a third party ontology term.\n          example: p-value\n          nullable: true\n          type: string\n        value:\n          description: Value of the attribute. May be any data type, including a list.\n          example: 0.000153\n        value_type_id:\n          allOf:\n          - $ref: '#/components/schemas/CURIE'\n          description: CURIE describing the semantic type of an  attribute's value.\n            Use a Biolink class if possible, otherwise a term from an external ontology.\n            If a suitable CURIE/identifier does not exist, enter a descriptive phrase\n            here and submit the new type for consideration by the appropriate authority.\n          example: EDAM:data_1187\n          nullable: true\n        value_url:\n          description: Human-consumable URL linking to a web document that provides\n            additional information about an  attribute's value (not the node or the\n            edge fom which it hangs).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n          type: string\n      required:\n      - attribute_type_id\n      - value\n      type: object\n    BiolinkEntity:\n      description: Compact URI (CURIE) for a Biolink class, biolink:NamedThing or\n        a child thereof. The CURIE must use the prefix 'biolink:' followed by the\n        PascalCase class name.\n      example: biolink:PhenotypicFeature\n      externalDocs:\n        description: Biolink model entities\n        url: https://biolink.github.io/biolink-model/docs/NamedThing.html\n      pattern: ^biolink:[A-Z][a-zA-Z]*$\n      type: string\n    BiolinkPredicate:\n      description: CURIE for a Biolink 'predicate' slot, taken from the Biolink slot\n        ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate\n        defines the Biolink relationship between the subject and object nodes of a\n        biolink:Association defining a knowledge graph edge.\n      example: biolink:interacts_with\n      externalDocs:\n        description: Biolink model predicates\n        url: https://biolink.github.io/biolink-model/docs/related_to.html\n      pattern: ^biolink:[a-z][a-z_]*$\n      type: string\n    CURIE:\n      description: A Compact URI, consisting of a prefix and a reference separated\n        by a colon, such as UniProtKB:P00738. Via an external context definition,\n        the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/,\n        to form a full URI.\n      externalDocs:\n        url: https://www.w3.org/TR/2010/NOTE-curie-20101216/\n      type: string\n    Edge:\n      additionalProperties: false\n      description: A specification of the semantic relationship linking two concepts\n        that are expressed as nodes in the knowledge \"thought\" graph resulting from\n        a query upon the underlying knowledge source.\n      properties:\n        attributes:\n          description: A list of additional attributes for this edge\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n          type: array\n        object:\n          $ref: '#/components/schemas/CURIE'\n          description: Corresponds to the map key CURIE of the object concept node\n            of this relationship edge.\n          example: UniProtKB:P00738\n        predicate:\n          allOf:\n          - $ref: '#/components/schemas/BiolinkPredicate'\n          nullable: true\n        subject:\n          $ref: '#/components/schemas/CURIE'\n          description: Corresponds to the map key CURIE of the subject concept node\n            of this relationship edge.\n          example: OMIM:603903\n      required:\n      - subject\n      - object\n      type: object\n    EdgeBinding:\n      additionalProperties: true\n      description: A instance of EdgeBinding is a single KnowledgeGraph Edge mapping,\n        identified by the corresponding 'id' object key identifier of the Edge within\n        the Knowledge Graph. Instances of EdgeBinding may include extra annotation\n        (such annotation is not yet fully standardized).\n      properties:\n        attributes:\n          description: A list of attributes providing further information about the\n            edge binding. This is not intended for capturing edge attributes and should\n            only be used for properties that vary from result to result.\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n          type: array\n        id:\n          description: The key identifier of a specific KnowledgeGraph Edge.\n          type: string\n      required:\n      - id\n      type: object\n    KnowledgeGraph:\n      additionalProperties: true\n      description: The knowledge graph associated with a set of results. The instances\n        of Node and Edge defining this graph represent instances of biolink:NamedThing\n        (concept nodes) and biolink:Association (relationship edges) representing\n        (Attribute) annotated knowledge returned from the knowledge sources and inference\n        agents wrapped by the given TRAPI implementation.\n      properties:\n        edges:\n          additionalProperties:\n            $ref: '#/components/schemas/Edge'\n          description: Dictionary of Edge instances used in the KnowledgeGraph, referenced\n            elsewhere in the TRAPI output by the dictionary key.\n          type: object\n        nodes:\n          additionalProperties:\n            $ref: '#/components/schemas/Node'\n          description: Dictionary of Node instances used in the KnowledgeGraph, referenced\n            elsewhere in the TRAPI output by the dictionary key.\n          type: object\n      required:\n      - nodes\n      - edges\n      type: object\n    LogEntry:\n      additionalProperties: true\n      description: The LogEntry object contains information useful for tracing and\n        debugging across Translator components.  Although an individual component\n        (for example, an ARA or KP) may have its own logging and debugging infrastructure,\n        this internal information is not, in general, available to other components.\n        In addition to a timestamp and logging level, LogEntry includes a string intended\n        to be read by a human, along with one of a standardized set of codes describing\n        the condition of the component sending the message.\n      properties:\n        code:\n          description: One of a standardized set of short codes e.g. QueryNotTraversable,\n            KPNotAvailable, KPResponseMalformed\n          nullable: true\n          type: string\n        level:\n          allOf:\n          - $ref: '#/components/schemas/LogLevel'\n          nullable: true\n        message:\n          description: A human-readable log message\n          nullable: true\n          type: string\n        timestamp:\n          description: Timestamp in ISO 8601 format\n          example: '2020-09-03T18:13:49+00:00'\n          format: date-time\n          nullable: true\n          type: string\n      type: object\n    LogLevel:\n      description: Logging level\n      enum:\n      - ERROR\n      - WARNING\n      - INFO\n      - DEBUG\n      type: string\n    Message:\n      additionalProperties: false\n      description: 'The message object holds the main content of a Query or a Response\n        in three properties: query_graph, results, and knowledge_graph. The query_graph\n        property contains the query configuration, the results property contains any\n        answers that are returned by the service, and knowledge_graph property contains\n        lists of edges and nodes in the thought graph corresponding to this message.\n        The content of these properties is context-dependent to the encompassing object\n        and the TRAPI operation requested.'\n      properties:\n        knowledge_graph:\n          allOf:\n          - $ref: '#/components/schemas/KnowledgeGraph'\n          description: KnowledgeGraph object that contains lists of nodes and edges\n            in the thought graph corresponding to the message\n          nullable: true\n        query_graph:\n          allOf:\n          - $ref: '#/components/schemas/QueryGraph'\n          description: QueryGraph object that contains a serialization of a query\n            in the form of a graph\n          nullable: true\n        results:\n          description: \"List of all returned Result objects for the query posed. The\\\n            \\ list SHOULD NOT be assumed to be ordered. The 'score' property,\\n if\\\n            \\ present, MAY be used to infer result rankings.\"\n          items:\n            $ref: '#/components/schemas/Result'\n          nullable: true\n          type: array\n      type: object\n    MetaAttribute:\n      properties:\n        attribute_source:\n          description: Source of an attribute provided by this TRAPI web service.\n          example: infores:chembl\n          nullable: true\n          type: string\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: Type of an attribute provided by this TRAPI web service (preferably\n            the CURIE of a Biolink association slot)\n          example: biolink:p_value\n        constraint_name:\n          description: Human-readable name or label for the constraint concept. Required\n            whenever constraint_use is true.\n          example: p-value\n          nullable: true\n          type: string\n        constraint_use:\n          default: false\n          description: Indicates whether this attribute can be used as a query constraint.\n          type: boolean\n        original_attribute_names:\n          description: Names of an the attribute as provided by the source.\n          items:\n            type: string\n          minItems: 1\n          nullable: true\n          type: array\n      required:\n      - attribute_type_id\n      type: object\n    MetaEdge:\n      additionalProperties: false\n      description: Edge in a meta knowledge map describing relationship between a\n        subject Biolink class and an object Biolink class.\n      properties:\n        attributes:\n          description: Edge attributes provided by this TRAPI web service.\n          items:\n            $ref: '#/components/schemas/MetaAttribute'\n          nullable: true\n          type: array\n        object:\n          $ref: '#/components/schemas/BiolinkEntity'\n          description: Object node category of this relationship edge.\n          example: biolink:Protein\n        predicate:\n          $ref: '#/components/schemas/BiolinkPredicate'\n          description: Biolink relationship between the subject and object categories.\n          example: biolink:affects\n        subject:\n          $ref: '#/components/schemas/BiolinkEntity'\n          description: Subject node category of this relationship edge.\n          example: biolink:ChemicalSubstance\n      required:\n      - subject\n      - predicate\n      - object\n      type: object\n    MetaKnowledgeGraph:\n      description: Knowledge-map representation of this TRAPI web service. The meta\n        knowledge graph is composed of the union of most specific categories and predicates\n        for each node and edge.\n      properties:\n        edges:\n          description: List of the most specific edges/predicates provided by this\n            TRAPI web service. A predicate is only exposed here if there is an edge\n            for which the predicate is the most specific available.\n          items:\n            $ref: '#/components/schemas/MetaEdge'\n          type: array\n        nodes:\n          additionalProperties:\n            $ref: '#/components/schemas/MetaNode'\n          description: Collection of the most specific node categories provided by\n            this TRAPI web service, indexed by Biolink class CURIEs. A node category\n            is only exposed here if there is node for which that is the most specific\n            category available.\n          type: object\n      required:\n      - nodes\n      - edges\n      type: object\n    MetaNode:\n      additionalProperties: false\n      description: Description of a node category provided by this TRAPI web service.\n      properties:\n        attributes:\n          description: Node attributes provided by this TRAPI web service.\n          items:\n            $ref: '#/components/schemas/MetaAttribute'\n          nullable: true\n          type: array\n        id_prefixes:\n          description: List of CURIE prefixes for the node category that this TRAPI\n            web service understands and accepts on the input.\n          example:\n          - CHEMBL.COMPOUND\n          - INCHIKEY\n          items:\n            type: string\n          minItems: 1\n          type: array\n      required:\n      - id_prefixes\n      type: object\n    Node:\n      additionalProperties: false\n      description: A node in the KnowledgeGraph which represents some biomedical concept.\n        Nodes are identified by the keys in the KnowledgeGraph Node mapping.\n      properties:\n        attributes:\n          description: A list of attributes describing the node\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n          type: array\n        categories:\n          items:\n            $ref: '#/components/schemas/BiolinkEntity'\n          nullable: true\n          type: array\n        name:\n          description: Formal name of the entity\n          example: Haptoglobin\n          nullable: true\n          type: string\n      type: object\n    NodeBinding:\n      additionalProperties: true\n      properties:\n        id:\n          $ref: '#/components/schemas/CURIE'\n          description: An instance of NodeBinding is a single KnowledgeGraph Node\n            mapping, identified by the corresponding 'id' object key identifier of\n            the Node within the Knowledge Graph. Instances of NodeBinding may include\n            extra annotation (such annotation is not yet fully standardized).\n      required:\n      - id\n      type: object\n    QEdge:\n      additionalProperties: true\n      description: An edge in the QueryGraph used as an filter pattern specification\n        in a query. If the optional predicate property is not specified, it is assumed\n        to be a wildcard match to the target knowledge space. If specified, the ontological\n        inheritance hierarchy associated with the term provided is assumed, such that\n        edge bindings returned may be an exact match to the given QEdge predicate\n        term, or to a term that is a descendant of the QEdge predicate term.\n      properties:\n        constraints:\n          default: []\n          description: A list of contraints applied to a query edge. If there are\n            multiple items, they must all be true (equivalent to AND)\n          items:\n            $ref: '#/components/schemas/QueryConstraint'\n          type: array\n        object:\n          description: Corresponds to the map key identifier of the object concept\n            node anchoring the query filter pattern for the query relationship edge.\n          example: https://www.uniprot.org/uniprot/P00738\n          type: string\n        predicates:\n          items:\n            $ref: '#/components/schemas/BiolinkPredicate'\n          minItems: 1\n          nullable: true\n          type: array\n        subject:\n          description: Corresponds to the map key identifier of the subject concept\n            node anchoring the query filter pattern for the query relationship edge.\n          example: https://omim.org/entry/603903\n          type: string\n      required:\n      - subject\n      - object\n      type: object\n    QNode:\n      additionalProperties: true\n      description: A node in the QueryGraph used to represent an entity in a query.\n        If a CURIE is not specified, any nodes matching the category of the QNode\n        will be returned in the Results.\n      properties:\n        categories:\n          items:\n            $ref: '#/components/schemas/BiolinkEntity'\n          minItems: 1\n          nullable: true\n          type: array\n        constraints:\n          default: []\n          description: A list of contraints applied to a query node. If there are\n            multiple items, they must all be true (equivalent to AND)\n          items:\n            $ref: '#/components/schemas/QueryConstraint'\n          type: array\n        ids:\n          description: CURIE identifier for this node\n          example:\n          - OMIM:603903\n          items:\n            $ref: '#/components/schemas/CURIE'\n          minItems: 1\n          nullable: true\n          type: array\n        is_set:\n          default: false\n          description: Boolean that if set to true, indicates that this QNode MAY\n            have multiple KnowledgeGraph Nodes bound to it within each Result. The\n            nodes in a set should be considered as a set of independent nodes, rather\n            than a set of dependent nodes, i.e., the answer would still be valid if\n            the nodes in the set were instead returned individually. Multiple QNodes\n            may have is_set=True. If a QNode (n1) with is_set=True is connected to\n            a QNode (n2) with is_set=False, each n1 must be connected to n2. If a\n            QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True,\n            each n1 must be connected to at least one n2.\n          type: boolean\n      type: object\n    Query:\n      additionalProperties: true\n      description: The Query class is used to package a user request for information.\n        A Query object consists of a required Message object with optional additional\n        properties. Additional properties are intended to convey implementation-specific\n        or query-independent parameters. For example, an additional property specifying\n        a log level could allow a user to override the default log level in order\n        to receive more fine-grained log information when debugging an issue.\n      properties:\n        log_level:\n          allOf:\n          - $ref: '#/components/schemas/LogLevel'\n          description: The least critical level of logs to return\n          nullable: true\n        message:\n          $ref: '#/components/schemas/Message'\n          description: The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For example,\n            the fill operation requires a non-empty query_graph field as part of the\n            Message, whereas other operations, e.g. overlay, require non-empty results\n            and knowledge_graph fields.\n        workflow:\n          allOf:\n          - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          description: List of workflow steps to be executed.\n          nullable: true\n      required:\n      - message\n      type: object\n      x-body-name: request_body\n    QueryConstraint:\n      additionalProperties: false\n      description: Generic query constraint for a query node or query edge\n      properties:\n        id:\n          allOf:\n          - $ref: '#/components/schemas/CURIE'\n          description: CURIE of the concept being constrained. For properties defined\n            by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible,\n            from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive\n            phrase here and submit the new type for consideration by the appropriate\n            authority.\n          example: EDAM:data_0844\n        name:\n          description: Human-readable name or label for the constraint concept. If\n            appropriate, it SHOULD be the term name of the CURIE used as the 'id'.\n            This is redundant but required for human readability.\n          example: molecular mass\n          type: string\n        not:\n          default: false\n          type: boolean\n        operator:\n          description: Relationship between the database value and the constraint\n            value for the specified id. The operators ==, >, and < mean is exactly\n            equal to, is greater than, and is less than, respectively. The 'matches'\n            operator indicates that the value is a regular expression to be evaluated.\n            If value is a list type, then at least one evaluation must be true (equivalent\n            to OR). This means that the == operator with a list acts like a SQL 'IN'\n            clause. The 'not' property negates the operator such that not and == means\n            'not equal to' (or 'not in' for a list), and not > means <=, and not <\n            means >=, and not matches means does not match. The '==' operator SHOULD\n            NOT be used in a manner that describes an \"is a\" subclass relationship\n            for the parent QNode.\n          enum:\n          - ==\n          - '>'\n          - <\n          - matches\n          type: string\n        unit_id:\n          description: CURIE of the units of the value or list of values in the 'value'\n            property. The Units of Measurement Ontology (UO) should be used if possible.\n            The unit_id MUST be provided for (lists of) numerical values that correspond\n            to a quantity that has units.\n          example: UO:0000222\n          nullable: true\n        unit_name:\n          description: Term name that is associated with the CURIE of the units of\n            the value or list of values in the 'value' property. The Units of Measurement\n            Ontology (UO) SHOULD be used if possible. This property SHOULD be provided\n            if a unit_id is provided. This is redundant but recommended for human\n            readability.\n          example: kilodalton\n          nullable: true\n        value:\n          description: Value of the attribute. May be any data type, including a list.\n            If the value is a list and there are multiple items, at least one comparison\n            must be true (equivalent to OR). If 'value' is of data type 'object',\n            the keys of the object MAY be treated as a list. A 'list' data type paired\n            with the '>' or '<' operators will encode extraneous comparisons, but\n            this is permitted as it is in SQL and other languages.\n          example: 57.0\n      required:\n      - name\n      - id\n      - operator\n      - value\n      type: object\n    QueryGraph:\n      additionalProperties: true\n      description: A graph representing a biomedical question. It serves as a template\n        for each result (answer), where each bound knowledge graph node/edge is expected\n        to obey the constraints of the associated query graph element.\n      properties:\n        edges:\n          additionalProperties:\n            $ref: '#/components/schemas/QEdge'\n          description: The edge specifications. The keys of this map are unique edge\n            identifiers and the corresponding values include the constraints on bound\n            edges, in addition to specifying the subject and object QNodes.\n          type: object\n        nodes:\n          additionalProperties:\n            $ref: '#/components/schemas/QNode'\n          description: The node specifications. The keys of this map are unique node\n            identifiers and the corresponding values include the constraints on bound\n            nodes.\n          type: object\n      required:\n      - nodes\n      - edges\n      type: object\n    Response:\n      additionalProperties: true\n      description: The Response object contains the main payload when a TRAPI query\n        endpoint interprets and responds to the submitted query successfully (i.e.,\n        HTTP Status Code 200). The message property contains the knowledge of the\n        response (query graph, knowledge graph, and results). The status, description,\n        and logs properties provide additional details about the response.\n      properties:\n        description:\n          description: A brief human-readable description of the outcome\n          example: Success. 42 results found.\n          nullable: true\n          type: string\n        logs:\n          description: Log entries containing errors, warnings, debugging information,\n            etc\n          items:\n            $ref: '#/components/schemas/LogEntry'\n          nullable: true\n          type: array\n        message:\n          $ref: '#/components/schemas/Message'\n          description: Contains the knowledge of the response (query graph, knowledge\n            graph, and results).\n        status:\n          description: One of a standardized set of short codes, e.g. Success, QueryNotTraversable,\n            KPsNotAvailable\n          example: Success\n          nullable: true\n          type: string\n        workflow:\n          allOf:\n          - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          description: List of workflow steps that were executed.\n          nullable: true\n      required:\n      - message\n      type: object\n    Result:\n      additionalProperties: true\n      description: A Result object specifies the nodes and edges in the knowledge\n        graph that satisfy the structure or conditions of a user-submitted query graph.\n        It must contain a NodeBindings object (list of query graph node to knowledge\n        graph node mappings) and an EdgeBindings object (list of query graph edge\n        to knowledge graph edge mappings).\n      properties:\n        edge_bindings:\n          additionalProperties:\n            items:\n              $ref: '#/components/schemas/EdgeBinding'\n            type: array\n          description: The dictionary of Input Query Graph to Result Knowledge Graph\n            edge bindings where the dictionary keys are the key identifiers of the\n            Query Graph edges and the associated values of those keys are instances\n            of EdgeBinding schema type (see below). This value is an array of EdgeBindings\n            since a given query edge may resolve to multiple knowledge graph edges\n            in the result.\n          type: object\n        node_bindings:\n          additionalProperties:\n            items:\n              $ref: '#/components/schemas/NodeBinding'\n            type: array\n          description: The dictionary of Input Query Graph to Result Knowledge Graph\n            node bindings where the dictionary keys are the key identifiers of the\n            Query Graph nodes and the associated values of those keys are instances\n            of NodeBinding schema type (see below). This value is an array of NodeBindings\n            since a given query node may have multiple knowledge graph Node bindings\n            in the result.\n          type: object\n        score:\n          description: A numerical score associated with this result indicating the\n            relevance or confidence of this result relative to others in the returned\n            set. Higher MUST be better.\n          example: 163.233\n          format: float\n          nullable: true\n          type: number\n      required:\n      - node_bindings\n      - edge_bindings\n      type: object\n    SubAttribute:\n      additionalProperties: false\n      description: Second-level attribute that can be used to qualify information\n        contained in a primary Attribute attached to a Node or Edge.\n      properties:\n        attribute_source:\n          description: The source of the core assertion made by the key-value pair\n            of an attribute object. Use a CURIE or namespace designator for this resource\n            where possible.\n          example: UniProtKB\n          nullable: true\n          type: string\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: The 'key' of the attribute object, holding a CURIE of an ontology\n            property defining the attribute (preferably the CURIE of a Biolink association\n            slot). This property captures the relationship asserted to hold between\n            the value of the attribute, and the node or edge from  which it hangs.\n            For example, that a value of '0.000153' represents a p-value supporting\n            an edge, or that a value of 'ChEMBL' represents the original source of\n            the knowledge expressed in the edge.\n          example: Biolink:has_p-value_evidence, Biolink:has_original_source\n        description:\n          description: Human-readable description for the attribute and its value.\n          example: Assertion Authored By Dr. Trans L. Ator\n          nullable: true\n          type: string\n        original_attribute_name:\n          description: The term used by the original source of an attribute to describe\n            the meaning or significance of the value it captures. This may be a column\n            name in a source tsv file, or a key in a source json document for the\n            field in the data that held the attribute's value. Capturing this information  where\n            possible lets us preserve what the original source said. Note that the\n            data type is string' but the contents of the field could also be a CURIE\n            of a third party ontology term.\n          example: p-value\n          nullable: true\n          type: string\n        value:\n          description: Value of the attribute. May be any data type, including a list.\n          example: 0.000153\n        value_type_id:\n          allOf:\n          - $ref: '#/components/schemas/CURIE'\n          description: CURIE describing the semantic type of an  attribute's value.\n            Use a Biolink class if possible, otherwise a term from an external ontology.\n            If a suitable CURIE/identifier does not exist, enter a descriptive phrase\n            here and submit the new type for consideration by the appropriate authority.\n          example: EDAM:data_1187\n          nullable: true\n        value_url:\n          description: Human-consumable URL linking to a web document that provides\n            additional information about an  attribute's value (not the node or the\n            edge fom which it hangs).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n          type: string\n      required:\n      - attribute_type_id\n      - value\n      type: object\n"
  },
  {
    "path": "medikanren2/neo/neo-open-api/mediKanrenSmartAPI_1_5.json",
    "content": "{\n  \"openapi\": \"3.0.3\",\n  \"info\": {\n    \"contact\": {\n      \"email\": \"webyrd@gmail.com\",\n      \"name\": \"William E. Byrd\",\n      \"url\": \"https://github.com/webyrd\",\n      \"x-role\": \"responsible developer\"\n    },\n    \"description\": \"TRAPI 1.5 Endpoint for Team Unsecret Agent's mediKanren ARA\",\n    \"license\": {\n      \"name\": \"MIT License\",\n      \"url\": \"https://github.com/webyrd/mediKanren/blob/master/LICENSE\"\n    },\n    \"title\": \"mediKanren\",\n    \"version\": \"2.0 neo TRAPI 1.5\",\n    \"x-translator\": {\n      \"biolink-version\": \"3.1.2\",\n      \"component\": \"ARA\",\n      \"externalDocs\": {\n        \"description\": \"The values for component and team are restricted according to this external JSON schema. See schema and examples at url\",\n        \"url\": \"https://github.com/NCATSTranslator/translator_extensions/blob/\\\\ production/x-translator/\"\n      },\n      \"infores\": \"infores:unsecret-agent\",\n      \"team\": [\n        \"Unsecret Agent\"\n      ]\n    },\n    \"x-trapi\": {\n      \"asyncquery\": false,\n      \"batch_size_limit\": 500,\n      \"externalDocs\": {\n        \"description\": \"The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url\",\n        \"url\": \"https://github.com/NCATSTranslator/translator_extensions/blob/\\\\ production/x-trapi/\"\n      },\n      \"operations\": [\n        \"lookup\"\n      ],\n      \"version\": \"1.5.0\"\n    }\n  },\n  \"servers\": [\n    {\n      \"description\": \"Team Unsecret Agent mediKanren 1.5 Production server\",\n      \"url\": \"https://medikanren-trapi.transltr.io\",\n      \"x-location\": \"ITRB\",\n      \"x-maturity\": \"production\"\n    },\n    {\n      \"description\": \"Team Unsecret Agent mediKanren 1.5 Test server\",\n      \"url\": \"https://medikanren-trapi.test.transltr.io\",\n      \"x-location\": \"ITRB\",\n      \"x-maturity\": \"testing\"\n    },\n    {\n      \"description\": \"Team Unsecret Agent mediKanren 1.5 CI server\",\n      \"url\": \"https://medikanren-trapi.ci.transltr.io\",\n      \"x-location\": \"ITRB\",\n      \"x-maturity\": \"staging\"\n    }\n  ],\n  \"externalDocs\": {\n    \"description\": \"Documentation for the NCATS Biomedical Translator Reasoners web services\",\n    \"url\": \"https://github.com/NCATSTranslator/ReasonerAPI\"\n  },\n  \"tags\": [\n    {\n      \"description\": \"Initiate a query and wait to receive the response\",\n      \"name\": \"query\"\n    },\n    {\n      \"description\": \"Required for SmartAPI validation of x-translator\",\n      \"name\": \"translator\"\n    },\n    {\n      \"description\": \"Required for SmartAPI validation of x-trapi\",\n      \"name\": \"trapi\"\n    }\n  ],\n  \"paths\": {\n    \"/query\": {\n      \"post\": {\n        \"description\": \"Query Team Unsecret Agent's mediKanren ARA API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI).\",\n        \"operationId\": \"query\",\n        \"requestBody\": {\n          \"content\": {\n            \"application/json\": {\n              \"example\": \"{\\\"message\\\": {\\\"query_graph\\\": {\\\"nodes\\\": {\\\"n0\\\": {\\\"ids\\\": [\\\"MONDO:0004975\\\"], \\\"categories\\\": [\\\"biolink:Disease\\\"]}, \\\"n1\\\": {\\\"categories\\\":[\\\"biolink:ChemicalEntity\\\"]}}, \\\"edges\\\": {\\\"e0\\\": {\\\"subject\\\": \\\"n1\\\", \\\"object\\\": \\\"n0\\\", \\\"predicates\\\":[\\\"biolink:treats\\\"], \\\"knowledge_type\\\": \\\"inferred\\\"}}}}}\",\n              \"schema\": {\n                \"$ref\": \"#/components/schemas/Query\"\n              }\n            }\n          },\n          \"description\": \"Query information to be submitted\",\n          \"required\": true\n        },\n        \"responses\": {\n          \"200\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"$ref\": \"#/components/schemas/Response\"\n                }\n              }\n            },\n            \"description\": \"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized.\"\n          },\n          \"400\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"type\": \"string\"\n                }\n              }\n            },\n            \"description\": \"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized).\"\n          },\n          \"500\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"type\": \"string\"\n                }\n              }\n            },\n            \"description\": \"Internal server error.\"\n          },\n          \"501\": {\n            \"content\": {\n              \"application/json\": {\n                \"schema\": {\n                  \"type\": \"string\"\n                }\n              }\n            },\n            \"description\": \"Not implemented.\"\n          }\n        },\n        \"summary\": \"Initiate a query and wait to receive a Response\",\n        \"tags\": [\n          \"query\"\n        ],\n        \"x-swagger-router-controller\": \"swagger_server.controllers.query_controller\"\n      }\n    }\n  },\n  \"components\": {\n    \"schemas\": {\n      \"AsyncQuery\": {\n        \"additionalProperties\": true,\n        \"description\": \"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.\",\n        \"properties\": {\n          \"callback\": {\n            \"description\": \"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.\",\n            \"format\": \"uri\",\n            \"pattern\": \"^https?://\",\n            \"type\": \"string\"\n          },\n          \"log_level\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/LogLevel\"\n              }\n            ],\n            \"description\": \"The least critical level of logs to return\",\n            \"nullable\": true\n          },\n          \"message\": {\n            \"$ref\": \"#/components/schemas/Message\",\n            \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n          },\n          \"workflow\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n              }\n            ],\n            \"description\": \"List of workflow steps to be executed.\",\n            \"nullable\": true\n          }\n        },\n        \"required\": [\n          \"callback\",\n          \"message\"\n        ],\n        \"type\": \"object\",\n        \"x-body-name\": \"request_body\"\n      },\n      \"Attribute\": {\n        \"additionalProperties\": false,\n        \"description\": \"Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with a SubAttribute (for example to provide confidence intervals on a value).\",\n        \"properties\": {\n          \"attribute_source\": {\n            \"description\": \"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.\",\n            \"example\": \"UniProtKB\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"attribute_type_id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.\",\n            \"example\": \"Biolink:has_p-value_evidence, Biolink:has_original_source\"\n          },\n          \"attributes\": {\n            \"description\": \"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/SubAttribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"description\": {\n            \"description\": \"Human-readable description for the attribute and its value.\",\n            \"example\": \"Assertion Authored By Dr. Trans L. Ator\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"original_attribute_name\": {\n            \"description\": \"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.\",\n            \"example\": \"p-value\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"value\": {\n            \"description\": \"Value of the attribute. May be any data type, including a list.\",\n            \"example\": 0.000153\n          },\n          \"value_type_id\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/CURIE\"\n              }\n            ],\n            \"description\": \"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n            \"example\": \"EDAM:data_1187\",\n            \"nullable\": true\n          },\n          \"value_url\": {\n            \"description\": \"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).\",\n            \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"attribute_type_id\",\n          \"value\"\n        ],\n        \"type\": \"object\"\n      },\n      \"BiolinkEntity\": {\n        \"description\": \"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.\",\n        \"example\": \"biolink:PhenotypicFeature\",\n        \"externalDocs\": {\n          \"description\": \"Biolink model entities\",\n          \"url\": \"https://biolink.github.io/biolink-model/docs/NamedThing.html\"\n        },\n        \"pattern\": \"^biolink:[A-Z][a-zA-Z]*$\",\n        \"type\": \"string\"\n      },\n      \"BiolinkPredicate\": {\n        \"description\": \"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.\",\n        \"example\": \"biolink:interacts_with\",\n        \"externalDocs\": {\n          \"description\": \"Biolink model predicates\",\n          \"url\": \"https://biolink.github.io/biolink-model/docs/related_to.html\"\n        },\n        \"pattern\": \"^biolink:[a-z][a-z_]*$\",\n        \"type\": \"string\"\n      },\n      \"CURIE\": {\n        \"description\": \"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.\",\n        \"externalDocs\": {\n          \"url\": \"https://www.w3.org/TR/2010/NOTE-curie-20101216/\"\n        },\n        \"type\": \"string\"\n      },\n      \"Edge\": {\n        \"additionalProperties\": false,\n        \"description\": \"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \\\"thought\\\" graph resulting from a query upon the underlying knowledge source.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"A list of additional attributes for this edge\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Attribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"object\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"Corresponds to the map key CURIE of the object concept node of this relationship edge.\",\n            \"example\": \"UniProtKB:P00738\"\n          },\n          \"predicate\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n              }\n            ],\n            \"nullable\": true\n          },\n          \"subject\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"Corresponds to the map key CURIE of the subject concept node of this relationship edge.\",\n            \"example\": \"OMIM:603903\"\n          }\n        },\n        \"required\": [\n          \"subject\",\n          \"object\"\n        ],\n        \"type\": \"object\"\n      },\n      \"EdgeBinding\": {\n        \"additionalProperties\": true,\n        \"description\": \"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized).\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Attribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"id\": {\n            \"description\": \"The key identifier of a specific KnowledgeGraph Edge.\",\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"id\"\n        ],\n        \"type\": \"object\"\n      },\n      \"KnowledgeGraph\": {\n        \"additionalProperties\": true,\n        \"description\": \"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.\",\n        \"properties\": {\n          \"edges\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/Edge\"\n            },\n            \"description\": \"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n            \"type\": \"object\"\n          },\n          \"nodes\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/Node\"\n            },\n            \"description\": \"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n            \"type\": \"object\"\n          }\n        },\n        \"required\": [\n          \"nodes\",\n          \"edges\"\n        ],\n        \"type\": \"object\"\n      },\n      \"LogEntry\": {\n        \"additionalProperties\": true,\n        \"description\": \"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.\",\n        \"properties\": {\n          \"code\": {\n            \"description\": \"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"level\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/LogLevel\"\n              }\n            ],\n            \"nullable\": true\n          },\n          \"message\": {\n            \"description\": \"A human-readable log message\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"timestamp\": {\n            \"description\": \"Timestamp in ISO 8601 format\",\n            \"example\": \"2020-09-03T18:13:49+00:00\",\n            \"format\": \"date-time\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"LogLevel\": {\n        \"description\": \"Logging level\",\n        \"enum\": [\n          \"ERROR\",\n          \"WARNING\",\n          \"INFO\",\n          \"DEBUG\"\n        ],\n        \"type\": \"string\"\n      },\n      \"Message\": {\n        \"additionalProperties\": false,\n        \"description\": \"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.\",\n        \"properties\": {\n          \"knowledge_graph\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/KnowledgeGraph\"\n              }\n            ],\n            \"description\": \"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message\",\n            \"nullable\": true\n          },\n          \"query_graph\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/QueryGraph\"\n              }\n            ],\n            \"description\": \"QueryGraph object that contains a serialization of a query in the form of a graph\",\n            \"nullable\": true\n          },\n          \"results\": {\n            \"description\": \"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property,\\n if present, MAY be used to infer result rankings.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Result\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"MetaAttribute\": {\n        \"properties\": {\n          \"attribute_source\": {\n            \"description\": \"Source of an attribute provided by this TRAPI web service.\",\n            \"example\": \"infores:chembl\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"attribute_type_id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)\",\n            \"example\": \"biolink:p_value\"\n          },\n          \"constraint_name\": {\n            \"description\": \"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.\",\n            \"example\": \"p-value\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"constraint_use\": {\n            \"default\": false,\n            \"description\": \"Indicates whether this attribute can be used as a query constraint.\",\n            \"type\": \"boolean\"\n          },\n          \"original_attribute_names\": {\n            \"description\": \"Names of an the attribute as provided by the source.\",\n            \"items\": {\n              \"type\": \"string\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          }\n        },\n        \"required\": [\n          \"attribute_type_id\"\n        ],\n        \"type\": \"object\"\n      },\n      \"MetaEdge\": {\n        \"additionalProperties\": false,\n        \"description\": \"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"Edge attributes provided by this TRAPI web service.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/MetaAttribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"object\": {\n            \"$ref\": \"#/components/schemas/BiolinkEntity\",\n            \"description\": \"Object node category of this relationship edge.\",\n            \"example\": \"biolink:Protein\"\n          },\n          \"predicate\": {\n            \"$ref\": \"#/components/schemas/BiolinkPredicate\",\n            \"description\": \"Biolink relationship between the subject and object categories.\",\n            \"example\": \"biolink:affects\"\n          },\n          \"subject\": {\n            \"$ref\": \"#/components/schemas/BiolinkEntity\",\n            \"description\": \"Subject node category of this relationship edge.\",\n            \"example\": \"biolink:ChemicalSubstance\"\n          }\n        },\n        \"required\": [\n          \"subject\",\n          \"predicate\",\n          \"object\"\n        ],\n        \"type\": \"object\"\n      },\n      \"MetaKnowledgeGraph\": {\n        \"description\": \"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.\",\n        \"properties\": {\n          \"edges\": {\n            \"description\": \"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/MetaEdge\"\n            },\n            \"type\": \"array\"\n          },\n          \"nodes\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/MetaNode\"\n            },\n            \"description\": \"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.\",\n            \"type\": \"object\"\n          }\n        },\n        \"required\": [\n          \"nodes\",\n          \"edges\"\n        ],\n        \"type\": \"object\"\n      },\n      \"MetaNode\": {\n        \"additionalProperties\": false,\n        \"description\": \"Description of a node category provided by this TRAPI web service.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"Node attributes provided by this TRAPI web service.\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/MetaAttribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"id_prefixes\": {\n            \"description\": \"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.\",\n            \"example\": [\n              \"CHEMBL.COMPOUND\",\n              \"INCHIKEY\"\n            ],\n            \"items\": {\n              \"type\": \"string\"\n            },\n            \"minItems\": 1,\n            \"type\": \"array\"\n          }\n        },\n        \"required\": [\n          \"id_prefixes\"\n        ],\n        \"type\": \"object\"\n      },\n      \"Node\": {\n        \"additionalProperties\": false,\n        \"description\": \"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.\",\n        \"properties\": {\n          \"attributes\": {\n            \"description\": \"A list of attributes describing the node\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/Attribute\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"categories\": {\n            \"items\": {\n              \"$ref\": \"#/components/schemas/BiolinkEntity\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"name\": {\n            \"description\": \"Formal name of the entity\",\n            \"example\": \"Haptoglobin\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"NodeBinding\": {\n        \"additionalProperties\": true,\n        \"properties\": {\n          \"id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation (such annotation is not yet fully standardized).\"\n          }\n        },\n        \"required\": [\n          \"id\"\n        ],\n        \"type\": \"object\"\n      },\n      \"QEdge\": {\n        \"additionalProperties\": true,\n        \"description\": \"An edge in the QueryGraph used as an filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.\",\n        \"properties\": {\n          \"constraints\": {\n            \"default\": [],\n            \"description\": \"A list of contraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/QueryConstraint\"\n            },\n            \"type\": \"array\"\n          },\n          \"object\": {\n            \"description\": \"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.\",\n            \"example\": \"https://www.uniprot.org/uniprot/P00738\",\n            \"type\": \"string\"\n          },\n          \"predicates\": {\n            \"items\": {\n              \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"subject\": {\n            \"description\": \"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.\",\n            \"example\": \"https://omim.org/entry/603903\",\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"subject\",\n          \"object\"\n        ],\n        \"type\": \"object\"\n      },\n      \"QNode\": {\n        \"additionalProperties\": true,\n        \"description\": \"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.\",\n        \"properties\": {\n          \"categories\": {\n            \"items\": {\n              \"$ref\": \"#/components/schemas/BiolinkEntity\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"constraints\": {\n            \"default\": [],\n            \"description\": \"A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/QueryConstraint\"\n            },\n            \"type\": \"array\"\n          },\n          \"ids\": {\n            \"description\": \"CURIE identifier for this node\",\n            \"example\": [\n              \"OMIM:603903\"\n            ],\n            \"items\": {\n              \"$ref\": \"#/components/schemas/CURIE\"\n            },\n            \"minItems\": 1,\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"is_set\": {\n            \"default\": false,\n            \"description\": \"Boolean that if set to true, indicates that this QNode MAY have multiple KnowledgeGraph Nodes bound to it within each Result. The nodes in a set should be considered as a set of independent nodes, rather than a set of dependent nodes, i.e., the answer would still be valid if the nodes in the set were instead returned individually. Multiple QNodes may have is_set=True. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=False, each n1 must be connected to n2. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True, each n1 must be connected to at least one n2.\",\n            \"type\": \"boolean\"\n          }\n        },\n        \"type\": \"object\"\n      },\n      \"Query\": {\n        \"additionalProperties\": true,\n        \"description\": \"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.\",\n        \"properties\": {\n          \"log_level\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/LogLevel\"\n              }\n            ],\n            \"description\": \"The least critical level of logs to return\",\n            \"nullable\": true\n          },\n          \"message\": {\n            \"$ref\": \"#/components/schemas/Message\",\n            \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n          },\n          \"workflow\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n              }\n            ],\n            \"description\": \"List of workflow steps to be executed.\",\n            \"nullable\": true\n          }\n        },\n        \"required\": [\n          \"message\"\n        ],\n        \"type\": \"object\",\n        \"x-body-name\": \"request_body\"\n      },\n      \"QueryConstraint\": {\n        \"additionalProperties\": false,\n        \"description\": \"Generic query constraint for a query node or query edge\",\n        \"properties\": {\n          \"id\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/CURIE\"\n              }\n            ],\n            \"description\": \"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n            \"example\": \"EDAM:data_0844\"\n          },\n          \"name\": {\n            \"description\": \"Human-readable name or label for the constraint concept. If appropriate, it SHOULD be the term name of the CURIE used as the 'id'. This is redundant but required for human readability.\",\n            \"example\": \"molecular mass\",\n            \"type\": \"string\"\n          },\n          \"not\": {\n            \"default\": false,\n            \"type\": \"boolean\"\n          },\n          \"operator\": {\n            \"description\": \"Relationship between the database value and the constraint value for the specified id. The operators ==, >, and < mean is exactly equal to, is greater than, and is less than, respectively. The 'matches' operator indicates that the value is a regular expression to be evaluated. If value is a list type, then at least one evaluation must be true (equivalent to OR). This means that the == operator with a list acts like a SQL 'IN' clause. The 'not' property negates the operator such that not and == means 'not equal to' (or 'not in' for a list), and not > means <=, and not < means >=, and not matches means does not match. The '==' operator SHOULD NOT be used in a manner that describes an \\\"is a\\\" subclass relationship for the parent QNode.\",\n            \"enum\": [\n              \"==\",\n              \">\",\n              \"<\",\n              \"matches\"\n            ],\n            \"type\": \"string\"\n          },\n          \"unit_id\": {\n            \"description\": \"CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units.\",\n            \"example\": \"UO:0000222\",\n            \"nullable\": true\n          },\n          \"unit_name\": {\n            \"description\": \"Term name that is associated with the CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability.\",\n            \"example\": \"kilodalton\",\n            \"nullable\": true\n          },\n          \"value\": {\n            \"description\": \"Value of the attribute. May be any data type, including a list. If the value is a list and there are multiple items, at least one comparison must be true (equivalent to OR). If 'value' is of data type 'object', the keys of the object MAY be treated as a list. A 'list' data type paired with the '>' or '<' operators will encode extraneous comparisons, but this is permitted as it is in SQL and other languages.\",\n            \"example\": 57\n          }\n        },\n        \"required\": [\n          \"name\",\n          \"id\",\n          \"operator\",\n          \"value\"\n        ],\n        \"type\": \"object\"\n      },\n      \"QueryGraph\": {\n        \"additionalProperties\": true,\n        \"description\": \"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.\",\n        \"properties\": {\n          \"edges\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/QEdge\"\n            },\n            \"description\": \"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.\",\n            \"type\": \"object\"\n          },\n          \"nodes\": {\n            \"additionalProperties\": {\n              \"$ref\": \"#/components/schemas/QNode\"\n            },\n            \"description\": \"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.\",\n            \"type\": \"object\"\n          }\n        },\n        \"required\": [\n          \"nodes\",\n          \"edges\"\n        ],\n        \"type\": \"object\"\n      },\n      \"Response\": {\n        \"additionalProperties\": true,\n        \"description\": \"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.\",\n        \"properties\": {\n          \"description\": {\n            \"description\": \"A brief human-readable description of the outcome\",\n            \"example\": \"Success. 42 results found.\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"logs\": {\n            \"description\": \"Log entries containing errors, warnings, debugging information, etc\",\n            \"items\": {\n              \"$ref\": \"#/components/schemas/LogEntry\"\n            },\n            \"nullable\": true,\n            \"type\": \"array\"\n          },\n          \"message\": {\n            \"$ref\": \"#/components/schemas/Message\",\n            \"description\": \"Contains the knowledge of the response (query graph, knowledge graph, and results).\"\n          },\n          \"status\": {\n            \"description\": \"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable\",\n            \"example\": \"Success\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"workflow\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n              }\n            ],\n            \"description\": \"List of workflow steps that were executed.\",\n            \"nullable\": true\n          }\n        },\n        \"required\": [\n          \"message\"\n        ],\n        \"type\": \"object\"\n      },\n      \"Result\": {\n        \"additionalProperties\": true,\n        \"description\": \"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings).\",\n        \"properties\": {\n          \"edge_bindings\": {\n            \"additionalProperties\": {\n              \"items\": {\n                \"$ref\": \"#/components/schemas/EdgeBinding\"\n              },\n              \"type\": \"array\"\n            },\n            \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple knowledge graph edges in the result.\",\n            \"type\": \"object\"\n          },\n          \"node_bindings\": {\n            \"additionalProperties\": {\n              \"items\": {\n                \"$ref\": \"#/components/schemas/NodeBinding\"\n              },\n              \"type\": \"array\"\n            },\n            \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.\",\n            \"type\": \"object\"\n          },\n          \"score\": {\n            \"description\": \"A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better.\",\n            \"example\": 163.233,\n            \"format\": \"float\",\n            \"nullable\": true,\n            \"type\": \"number\"\n          }\n        },\n        \"required\": [\n          \"node_bindings\",\n          \"edge_bindings\"\n        ],\n        \"type\": \"object\"\n      },\n      \"SubAttribute\": {\n        \"additionalProperties\": false,\n        \"description\": \"Second-level attribute that can be used to qualify information contained in a primary Attribute attached to a Node or Edge.\",\n        \"properties\": {\n          \"attribute_source\": {\n            \"description\": \"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.\",\n            \"example\": \"UniProtKB\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"attribute_type_id\": {\n            \"$ref\": \"#/components/schemas/CURIE\",\n            \"description\": \"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.\",\n            \"example\": \"Biolink:has_p-value_evidence, Biolink:has_original_source\"\n          },\n          \"description\": {\n            \"description\": \"Human-readable description for the attribute and its value.\",\n            \"example\": \"Assertion Authored By Dr. Trans L. Ator\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"original_attribute_name\": {\n            \"description\": \"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.\",\n            \"example\": \"p-value\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          },\n          \"value\": {\n            \"description\": \"Value of the attribute. May be any data type, including a list.\",\n            \"example\": 0.000153\n          },\n          \"value_type_id\": {\n            \"allOf\": [\n              {\n                \"$ref\": \"#/components/schemas/CURIE\"\n              }\n            ],\n            \"description\": \"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n            \"example\": \"EDAM:data_1187\",\n            \"nullable\": true\n          },\n          \"value_url\": {\n            \"description\": \"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).\",\n            \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n            \"nullable\": true,\n            \"type\": \"string\"\n          }\n        },\n        \"required\": [\n          \"attribute_type_id\",\n          \"value\"\n        ],\n        \"type\": \"object\"\n      }\n    }\n  }\n}"
  },
  {
    "path": "medikanren2/neo/neo-open-api/mediKanrenSmartAPI_1_5.yaml",
    "content": "openapi: 3.0.3\ninfo:\n  contact:\n    email: webyrd@gmail.com\n    name: William E. Byrd\n    url: https://github.com/webyrd\n    x-role: responsible developer\n  description: TRAPI 1.5 Endpoint for Team Unsecret Agent's mediKanren ARA\n  license:\n    name: MIT License\n    url: https://github.com/webyrd/mediKanren/blob/master/LICENSE\n  title: mediKanren\n  version: '2.0 neo TRAPI 1.5'\n  x-translator:\n    biolink-version: 3.1.2\n    component: ARA\n    externalDocs:\n      description: The values for component and team are restricted according to this\n        external JSON schema. See schema and examples at url\n      url: https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-translator/    \n    infores: infores:unsecret-agent\n    team:\n    - Unsecret Agent\n  x-trapi:\n    asyncquery: false\n    batch_size_limit: 500\n    externalDocs:\n      description: The values for version are restricted according to the regex in\n        this external JSON schema. See schema and examples at url\n      url: https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-trapi/    \n    operations:\n    - lookup\n    version: 1.5.0\nservers:\n- description: Team Unsecret Agent mediKanren 1.5 Production server\n  url: https://medikanren-trapi.transltr.io\n  x-location: ITRB\n  x-maturity: production\n- description: Team Unsecret Agent mediKanren 1.5 Test server\n  url: https://medikanren-trapi.test.transltr.io\n  x-location: ITRB\n  x-maturity: testing\n- description: Team Unsecret Agent mediKanren 1.5 CI server\n  url: https://medikanren-trapi.ci.transltr.io\n  x-location: ITRB\n  x-maturity: staging\nexternalDocs:\n  description: Documentation for the NCATS Biomedical Translator Reasoners web services\n  url: https://github.com/NCATSTranslator/ReasonerAPI\ntags:\n- description: Initiate a query and wait to receive the response\n  name: query\n- description: Required for SmartAPI validation of x-translator\n  name: translator\n- description: Required for SmartAPI validation of x-trapi\n  name: trapi\npaths:\n  /query:\n    post:\n      description: \"Query Team Unsecret Agent's mediKanren ARA API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI).\"\n      operationId: query\n      requestBody:\n        content:\n          application/json:\n            example: \"{\\\"message\\\": {\\\"query_graph\\\": {\\\"nodes\\\": {\\\"n0\\\": {\\\"ids\\\": [\\\"MONDO:0004975\\\"], \\\"categories\\\": [\\\"biolink:Disease\\\"]}, \\\"n1\\\": {\\\"categories\\\":[\\\"biolink:ChemicalEntity\\\"]}}, \\\"edges\\\": {\\\"e0\\\": {\\\"subject\\\": \\\"n1\\\", \\\"object\\\": \\\"n0\\\", \\\"predicates\\\":[\\\"biolink:treats\\\"], \\\"knowledge_type\\\": \\\"inferred\\\"}}}}}\"\n            schema:\n              $ref: '#/components/schemas/Query'\n        description: Query information to be submitted\n        required: true\n      responses:\n        '200':\n          content:\n            application/json:\n              schema:\n                $ref: '#/components/schemas/Response'\n          description: OK. There may or may not be results. Note that some of the\n            provided identifiers may not have been recognized.\n        '400':\n          content:\n            application/json:\n              schema:\n                type: string\n          description: Bad request. The request is invalid according to this OpenAPI\n            schema OR a specific identifier is believed to be invalid somehow (not\n            just unrecognized).\n        '500':\n          content:\n            application/json:\n              schema:\n                type: string\n          description: Internal server error.\n        '501':\n          content:\n            application/json:\n              schema:\n                type: string\n          description: Not implemented.\n      summary: Initiate a query and wait to receive a Response\n      tags:\n      - query\n      x-swagger-router-controller: swagger_server.controllers.query_controller\ncomponents:\n  schemas:\n    AsyncQuery:\n      additionalProperties: true\n      description: The AsyncQuery class is effectively the same as the Query class\n        but it requires a callback property.\n      properties:\n        callback:\n          description: 'Upon completion, this server will send a POST request to the\n            callback URL with `Content-Type: application/json` header and request\n            body containing a JSON-encoded `Response` object. The server MAY POST\n            `Response` objects before work is fully complete to provide interim results\n            with a Response.status value of ''Running''. If a POST operation to the\n            callback URL does not succeed, the server SHOULD retry the POST at least\n            once.'\n          format: uri\n          pattern: ^https?://\n          type: string\n        log_level:\n          allOf:\n          - $ref: '#/components/schemas/LogLevel'\n          description: The least critical level of logs to return\n          nullable: true\n        message:\n          $ref: '#/components/schemas/Message'\n          description: The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For example,\n            the fill operation requires a non-empty query_graph field as part of the\n            Message, whereas other operations, e.g. overlay, require non-empty results\n            and knowledge_graph fields.\n        workflow:\n          allOf:\n          - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          description: List of workflow steps to be executed.\n          nullable: true\n      required:\n      - callback\n      - message\n      type: object\n      x-body-name: request_body\n    Attribute:\n      additionalProperties: false\n      description: Generic attribute for a node or an edge that expands the key-value\n        pair concept by including fields for additional metadata. These fields can\n        be used to describe the source of the statement made in a key-value pair of\n        the attribute object, or describe the attribute's value itself including its\n        semantic type, or a url providing additional information about it. An attribute\n        may be further qualified with a SubAttribute (for example to provide confidence\n        intervals on a value).\n      properties:\n        attribute_source:\n          description: The source of the core assertion made by the key-value pair\n            of an attribute object. Use a CURIE or namespace designator for this resource\n            where possible.\n          example: UniProtKB\n          nullable: true\n          type: string\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: The 'key' of the attribute object, holding a CURIE of an ontology\n            property defining the attribute (preferably the CURIE of a Biolink association\n            slot). This property captures the relationship asserted to hold between\n            the value of the attribute, and the node or edge from  which it hangs.\n            For example, that a value of '0.000153' represents a p-value supporting\n            an edge, or that a value of 'ChEMBL' represents the original source of\n            the knowledge expressed in the edge.\n          example: Biolink:has_p-value_evidence, Biolink:has_original_source\n        attributes:\n          description: A list of attributes providing further information about the\n            parent attribute (for example to provide provenance information about\n            the parent attribute).\n          items:\n            $ref: '#/components/schemas/SubAttribute'\n          nullable: true\n          type: array\n        description:\n          description: Human-readable description for the attribute and its value.\n          example: Assertion Authored By Dr. Trans L. Ator\n          nullable: true\n          type: string\n        original_attribute_name:\n          description: The term used by the original source of an attribute to describe\n            the meaning or significance of the value it captures. This may be a column\n            name in a source tsv file, or a key in a source json document for the\n            field in the data that held the attribute's value. Capturing this information  where\n            possible lets us preserve what the original source said. Note that the\n            data type is string' but the contents of the field could also be a CURIE\n            of a third party ontology term.\n          example: p-value\n          nullable: true\n          type: string\n        value:\n          description: Value of the attribute. May be any data type, including a list.\n          example: 0.000153\n        value_type_id:\n          allOf:\n          - $ref: '#/components/schemas/CURIE'\n          description: CURIE describing the semantic type of an  attribute's value.\n            Use a Biolink class if possible, otherwise a term from an external ontology.\n            If a suitable CURIE/identifier does not exist, enter a descriptive phrase\n            here and submit the new type for consideration by the appropriate authority.\n          example: EDAM:data_1187\n          nullable: true\n        value_url:\n          description: Human-consumable URL linking to a web document that provides\n            additional information about an  attribute's value (not the node or the\n            edge fom which it hangs).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n          type: string\n      required:\n      - attribute_type_id\n      - value\n      type: object\n    BiolinkEntity:\n      description: Compact URI (CURIE) for a Biolink class, biolink:NamedThing or\n        a child thereof. The CURIE must use the prefix 'biolink:' followed by the\n        PascalCase class name.\n      example: biolink:PhenotypicFeature\n      externalDocs:\n        description: Biolink model entities\n        url: https://biolink.github.io/biolink-model/docs/NamedThing.html\n      pattern: ^biolink:[A-Z][a-zA-Z]*$\n      type: string\n    BiolinkPredicate:\n      description: CURIE for a Biolink 'predicate' slot, taken from the Biolink slot\n        ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate\n        defines the Biolink relationship between the subject and object nodes of a\n        biolink:Association defining a knowledge graph edge.\n      example: biolink:interacts_with\n      externalDocs:\n        description: Biolink model predicates\n        url: https://biolink.github.io/biolink-model/docs/related_to.html\n      pattern: ^biolink:[a-z][a-z_]*$\n      type: string\n    CURIE:\n      description: A Compact URI, consisting of a prefix and a reference separated\n        by a colon, such as UniProtKB:P00738. Via an external context definition,\n        the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/,\n        to form a full URI.\n      externalDocs:\n        url: https://www.w3.org/TR/2010/NOTE-curie-20101216/\n      type: string\n    Edge:\n      additionalProperties: false\n      description: A specification of the semantic relationship linking two concepts\n        that are expressed as nodes in the knowledge \"thought\" graph resulting from\n        a query upon the underlying knowledge source.\n      properties:\n        attributes:\n          description: A list of additional attributes for this edge\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n          type: array\n        object:\n          $ref: '#/components/schemas/CURIE'\n          description: Corresponds to the map key CURIE of the object concept node\n            of this relationship edge.\n          example: UniProtKB:P00738\n        predicate:\n          allOf:\n          - $ref: '#/components/schemas/BiolinkPredicate'\n          nullable: true\n        subject:\n          $ref: '#/components/schemas/CURIE'\n          description: Corresponds to the map key CURIE of the subject concept node\n            of this relationship edge.\n          example: OMIM:603903\n      required:\n      - subject\n      - object\n      type: object\n    EdgeBinding:\n      additionalProperties: true\n      description: A instance of EdgeBinding is a single KnowledgeGraph Edge mapping,\n        identified by the corresponding 'id' object key identifier of the Edge within\n        the Knowledge Graph. Instances of EdgeBinding may include extra annotation\n        (such annotation is not yet fully standardized).\n      properties:\n        attributes:\n          description: A list of attributes providing further information about the\n            edge binding. This is not intended for capturing edge attributes and should\n            only be used for properties that vary from result to result.\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n          type: array\n        id:\n          description: The key identifier of a specific KnowledgeGraph Edge.\n          type: string\n      required:\n      - id\n      type: object\n    KnowledgeGraph:\n      additionalProperties: true\n      description: The knowledge graph associated with a set of results. The instances\n        of Node and Edge defining this graph represent instances of biolink:NamedThing\n        (concept nodes) and biolink:Association (relationship edges) representing\n        (Attribute) annotated knowledge returned from the knowledge sources and inference\n        agents wrapped by the given TRAPI implementation.\n      properties:\n        edges:\n          additionalProperties:\n            $ref: '#/components/schemas/Edge'\n          description: Dictionary of Edge instances used in the KnowledgeGraph, referenced\n            elsewhere in the TRAPI output by the dictionary key.\n          type: object\n        nodes:\n          additionalProperties:\n            $ref: '#/components/schemas/Node'\n          description: Dictionary of Node instances used in the KnowledgeGraph, referenced\n            elsewhere in the TRAPI output by the dictionary key.\n          type: object\n      required:\n      - nodes\n      - edges\n      type: object\n    LogEntry:\n      additionalProperties: true\n      description: The LogEntry object contains information useful for tracing and\n        debugging across Translator components.  Although an individual component\n        (for example, an ARA or KP) may have its own logging and debugging infrastructure,\n        this internal information is not, in general, available to other components.\n        In addition to a timestamp and logging level, LogEntry includes a string intended\n        to be read by a human, along with one of a standardized set of codes describing\n        the condition of the component sending the message.\n      properties:\n        code:\n          description: One of a standardized set of short codes e.g. QueryNotTraversable,\n            KPNotAvailable, KPResponseMalformed\n          nullable: true\n          type: string\n        level:\n          allOf:\n          - $ref: '#/components/schemas/LogLevel'\n          nullable: true\n        message:\n          description: A human-readable log message\n          nullable: true\n          type: string\n        timestamp:\n          description: Timestamp in ISO 8601 format\n          example: '2020-09-03T18:13:49+00:00'\n          format: date-time\n          nullable: true\n          type: string\n      type: object\n    LogLevel:\n      description: Logging level\n      enum:\n      - ERROR\n      - WARNING\n      - INFO\n      - DEBUG\n      type: string\n    Message:\n      additionalProperties: false\n      description: 'The message object holds the main content of a Query or a Response\n        in three properties: query_graph, results, and knowledge_graph. The query_graph\n        property contains the query configuration, the results property contains any\n        answers that are returned by the service, and knowledge_graph property contains\n        lists of edges and nodes in the thought graph corresponding to this message.\n        The content of these properties is context-dependent to the encompassing object\n        and the TRAPI operation requested.'\n      properties:\n        knowledge_graph:\n          allOf:\n          - $ref: '#/components/schemas/KnowledgeGraph'\n          description: KnowledgeGraph object that contains lists of nodes and edges\n            in the thought graph corresponding to the message\n          nullable: true\n        query_graph:\n          allOf:\n          - $ref: '#/components/schemas/QueryGraph'\n          description: QueryGraph object that contains a serialization of a query\n            in the form of a graph\n          nullable: true\n        results:\n          description: \"List of all returned Result objects for the query posed. The\\\n            \\ list SHOULD NOT be assumed to be ordered. The 'score' property,\\n if\\\n            \\ present, MAY be used to infer result rankings.\"\n          items:\n            $ref: '#/components/schemas/Result'\n          nullable: true\n          type: array\n      type: object\n    MetaAttribute:\n      properties:\n        attribute_source:\n          description: Source of an attribute provided by this TRAPI web service.\n          example: infores:chembl\n          nullable: true\n          type: string\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: Type of an attribute provided by this TRAPI web service (preferably\n            the CURIE of a Biolink association slot)\n          example: biolink:p_value\n        constraint_name:\n          description: Human-readable name or label for the constraint concept. Required\n            whenever constraint_use is true.\n          example: p-value\n          nullable: true\n          type: string\n        constraint_use:\n          default: false\n          description: Indicates whether this attribute can be used as a query constraint.\n          type: boolean\n        original_attribute_names:\n          description: Names of an the attribute as provided by the source.\n          items:\n            type: string\n          minItems: 1\n          nullable: true\n          type: array\n      required:\n      - attribute_type_id\n      type: object\n    MetaEdge:\n      additionalProperties: false\n      description: Edge in a meta knowledge map describing relationship between a\n        subject Biolink class and an object Biolink class.\n      properties:\n        attributes:\n          description: Edge attributes provided by this TRAPI web service.\n          items:\n            $ref: '#/components/schemas/MetaAttribute'\n          nullable: true\n          type: array\n        object:\n          $ref: '#/components/schemas/BiolinkEntity'\n          description: Object node category of this relationship edge.\n          example: biolink:Protein\n        predicate:\n          $ref: '#/components/schemas/BiolinkPredicate'\n          description: Biolink relationship between the subject and object categories.\n          example: biolink:affects\n        subject:\n          $ref: '#/components/schemas/BiolinkEntity'\n          description: Subject node category of this relationship edge.\n          example: biolink:ChemicalSubstance\n      required:\n      - subject\n      - predicate\n      - object\n      type: object\n    MetaKnowledgeGraph:\n      description: Knowledge-map representation of this TRAPI web service. The meta\n        knowledge graph is composed of the union of most specific categories and predicates\n        for each node and edge.\n      properties:\n        edges:\n          description: List of the most specific edges/predicates provided by this\n            TRAPI web service. A predicate is only exposed here if there is an edge\n            for which the predicate is the most specific available.\n          items:\n            $ref: '#/components/schemas/MetaEdge'\n          type: array\n        nodes:\n          additionalProperties:\n            $ref: '#/components/schemas/MetaNode'\n          description: Collection of the most specific node categories provided by\n            this TRAPI web service, indexed by Biolink class CURIEs. A node category\n            is only exposed here if there is node for which that is the most specific\n            category available.\n          type: object\n      required:\n      - nodes\n      - edges\n      type: object\n    MetaNode:\n      additionalProperties: false\n      description: Description of a node category provided by this TRAPI web service.\n      properties:\n        attributes:\n          description: Node attributes provided by this TRAPI web service.\n          items:\n            $ref: '#/components/schemas/MetaAttribute'\n          nullable: true\n          type: array\n        id_prefixes:\n          description: List of CURIE prefixes for the node category that this TRAPI\n            web service understands and accepts on the input.\n          example:\n          - CHEMBL.COMPOUND\n          - INCHIKEY\n          items:\n            type: string\n          minItems: 1\n          type: array\n      required:\n      - id_prefixes\n      type: object\n    Node:\n      additionalProperties: false\n      description: A node in the KnowledgeGraph which represents some biomedical concept.\n        Nodes are identified by the keys in the KnowledgeGraph Node mapping.\n      properties:\n        attributes:\n          description: A list of attributes describing the node\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n          type: array\n        categories:\n          items:\n            $ref: '#/components/schemas/BiolinkEntity'\n          nullable: true\n          type: array\n        name:\n          description: Formal name of the entity\n          example: Haptoglobin\n          nullable: true\n          type: string\n      type: object\n    NodeBinding:\n      additionalProperties: true\n      properties:\n        id:\n          $ref: '#/components/schemas/CURIE'\n          description: An instance of NodeBinding is a single KnowledgeGraph Node\n            mapping, identified by the corresponding 'id' object key identifier of\n            the Node within the Knowledge Graph. Instances of NodeBinding may include\n            extra annotation (such annotation is not yet fully standardized).\n      required:\n      - id\n      type: object\n    QEdge:\n      additionalProperties: true\n      description: An edge in the QueryGraph used as an filter pattern specification\n        in a query. If the optional predicate property is not specified, it is assumed\n        to be a wildcard match to the target knowledge space. If specified, the ontological\n        inheritance hierarchy associated with the term provided is assumed, such that\n        edge bindings returned may be an exact match to the given QEdge predicate\n        term, or to a term that is a descendant of the QEdge predicate term.\n      properties:\n        constraints:\n          default: []\n          description: A list of contraints applied to a query edge. If there are\n            multiple items, they must all be true (equivalent to AND)\n          items:\n            $ref: '#/components/schemas/QueryConstraint'\n          type: array\n        object:\n          description: Corresponds to the map key identifier of the object concept\n            node anchoring the query filter pattern for the query relationship edge.\n          example: https://www.uniprot.org/uniprot/P00738\n          type: string\n        predicates:\n          items:\n            $ref: '#/components/schemas/BiolinkPredicate'\n          minItems: 1\n          nullable: true\n          type: array\n        subject:\n          description: Corresponds to the map key identifier of the subject concept\n            node anchoring the query filter pattern for the query relationship edge.\n          example: https://omim.org/entry/603903\n          type: string\n      required:\n      - subject\n      - object\n      type: object\n    QNode:\n      additionalProperties: true\n      description: A node in the QueryGraph used to represent an entity in a query.\n        If a CURIE is not specified, any nodes matching the category of the QNode\n        will be returned in the Results.\n      properties:\n        categories:\n          items:\n            $ref: '#/components/schemas/BiolinkEntity'\n          minItems: 1\n          nullable: true\n          type: array\n        constraints:\n          default: []\n          description: A list of contraints applied to a query node. If there are\n            multiple items, they must all be true (equivalent to AND)\n          items:\n            $ref: '#/components/schemas/QueryConstraint'\n          type: array\n        ids:\n          description: CURIE identifier for this node\n          example:\n          - OMIM:603903\n          items:\n            $ref: '#/components/schemas/CURIE'\n          minItems: 1\n          nullable: true\n          type: array\n        is_set:\n          default: false\n          description: Boolean that if set to true, indicates that this QNode MAY\n            have multiple KnowledgeGraph Nodes bound to it within each Result. The\n            nodes in a set should be considered as a set of independent nodes, rather\n            than a set of dependent nodes, i.e., the answer would still be valid if\n            the nodes in the set were instead returned individually. Multiple QNodes\n            may have is_set=True. If a QNode (n1) with is_set=True is connected to\n            a QNode (n2) with is_set=False, each n1 must be connected to n2. If a\n            QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True,\n            each n1 must be connected to at least one n2.\n          type: boolean\n      type: object\n    Query:\n      additionalProperties: true\n      description: The Query class is used to package a user request for information.\n        A Query object consists of a required Message object with optional additional\n        properties. Additional properties are intended to convey implementation-specific\n        or query-independent parameters. For example, an additional property specifying\n        a log level could allow a user to override the default log level in order\n        to receive more fine-grained log information when debugging an issue.\n      properties:\n        log_level:\n          allOf:\n          - $ref: '#/components/schemas/LogLevel'\n          description: The least critical level of logs to return\n          nullable: true\n        message:\n          $ref: '#/components/schemas/Message'\n          description: The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For example,\n            the fill operation requires a non-empty query_graph field as part of the\n            Message, whereas other operations, e.g. overlay, require non-empty results\n            and knowledge_graph fields.\n        workflow:\n          allOf:\n          - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          description: List of workflow steps to be executed.\n          nullable: true\n      required:\n      - message\n      type: object\n      x-body-name: request_body\n    QueryConstraint:\n      additionalProperties: false\n      description: Generic query constraint for a query node or query edge\n      properties:\n        id:\n          allOf:\n          - $ref: '#/components/schemas/CURIE'\n          description: CURIE of the concept being constrained. For properties defined\n            by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible,\n            from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive\n            phrase here and submit the new type for consideration by the appropriate\n            authority.\n          example: EDAM:data_0844\n        name:\n          description: Human-readable name or label for the constraint concept. If\n            appropriate, it SHOULD be the term name of the CURIE used as the 'id'.\n            This is redundant but required for human readability.\n          example: molecular mass\n          type: string\n        not:\n          default: false\n          type: boolean\n        operator:\n          description: Relationship between the database value and the constraint\n            value for the specified id. The operators ==, >, and < mean is exactly\n            equal to, is greater than, and is less than, respectively. The 'matches'\n            operator indicates that the value is a regular expression to be evaluated.\n            If value is a list type, then at least one evaluation must be true (equivalent\n            to OR). This means that the == operator with a list acts like a SQL 'IN'\n            clause. The 'not' property negates the operator such that not and == means\n            'not equal to' (or 'not in' for a list), and not > means <=, and not <\n            means >=, and not matches means does not match. The '==' operator SHOULD\n            NOT be used in a manner that describes an \"is a\" subclass relationship\n            for the parent QNode.\n          enum:\n          - ==\n          - '>'\n          - <\n          - matches\n          type: string\n        unit_id:\n          description: CURIE of the units of the value or list of values in the 'value'\n            property. The Units of Measurement Ontology (UO) should be used if possible.\n            The unit_id MUST be provided for (lists of) numerical values that correspond\n            to a quantity that has units.\n          example: UO:0000222\n          nullable: true\n        unit_name:\n          description: Term name that is associated with the CURIE of the units of\n            the value or list of values in the 'value' property. The Units of Measurement\n            Ontology (UO) SHOULD be used if possible. This property SHOULD be provided\n            if a unit_id is provided. This is redundant but recommended for human\n            readability.\n          example: kilodalton\n          nullable: true\n        value:\n          description: Value of the attribute. May be any data type, including a list.\n            If the value is a list and there are multiple items, at least one comparison\n            must be true (equivalent to OR). If 'value' is of data type 'object',\n            the keys of the object MAY be treated as a list. A 'list' data type paired\n            with the '>' or '<' operators will encode extraneous comparisons, but\n            this is permitted as it is in SQL and other languages.\n          example: 57.0\n      required:\n      - name\n      - id\n      - operator\n      - value\n      type: object\n    QueryGraph:\n      additionalProperties: true\n      description: A graph representing a biomedical question. It serves as a template\n        for each result (answer), where each bound knowledge graph node/edge is expected\n        to obey the constraints of the associated query graph element.\n      properties:\n        edges:\n          additionalProperties:\n            $ref: '#/components/schemas/QEdge'\n          description: The edge specifications. The keys of this map are unique edge\n            identifiers and the corresponding values include the constraints on bound\n            edges, in addition to specifying the subject and object QNodes.\n          type: object\n        nodes:\n          additionalProperties:\n            $ref: '#/components/schemas/QNode'\n          description: The node specifications. The keys of this map are unique node\n            identifiers and the corresponding values include the constraints on bound\n            nodes.\n          type: object\n      required:\n      - nodes\n      - edges\n      type: object\n    Response:\n      additionalProperties: true\n      description: The Response object contains the main payload when a TRAPI query\n        endpoint interprets and responds to the submitted query successfully (i.e.,\n        HTTP Status Code 200). The message property contains the knowledge of the\n        response (query graph, knowledge graph, and results). The status, description,\n        and logs properties provide additional details about the response.\n      properties:\n        description:\n          description: A brief human-readable description of the outcome\n          example: Success. 42 results found.\n          nullable: true\n          type: string\n        logs:\n          description: Log entries containing errors, warnings, debugging information,\n            etc\n          items:\n            $ref: '#/components/schemas/LogEntry'\n          nullable: true\n          type: array\n        message:\n          $ref: '#/components/schemas/Message'\n          description: Contains the knowledge of the response (query graph, knowledge\n            graph, and results).\n        status:\n          description: One of a standardized set of short codes, e.g. Success, QueryNotTraversable,\n            KPsNotAvailable\n          example: Success\n          nullable: true\n          type: string\n        workflow:\n          allOf:\n          - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          description: List of workflow steps that were executed.\n          nullable: true\n      required:\n      - message\n      type: object\n    Result:\n      additionalProperties: true\n      description: A Result object specifies the nodes and edges in the knowledge\n        graph that satisfy the structure or conditions of a user-submitted query graph.\n        It must contain a NodeBindings object (list of query graph node to knowledge\n        graph node mappings) and an EdgeBindings object (list of query graph edge\n        to knowledge graph edge mappings).\n      properties:\n        edge_bindings:\n          additionalProperties:\n            items:\n              $ref: '#/components/schemas/EdgeBinding'\n            type: array\n          description: The dictionary of Input Query Graph to Result Knowledge Graph\n            edge bindings where the dictionary keys are the key identifiers of the\n            Query Graph edges and the associated values of those keys are instances\n            of EdgeBinding schema type (see below). This value is an array of EdgeBindings\n            since a given query edge may resolve to multiple knowledge graph edges\n            in the result.\n          type: object\n        node_bindings:\n          additionalProperties:\n            items:\n              $ref: '#/components/schemas/NodeBinding'\n            type: array\n          description: The dictionary of Input Query Graph to Result Knowledge Graph\n            node bindings where the dictionary keys are the key identifiers of the\n            Query Graph nodes and the associated values of those keys are instances\n            of NodeBinding schema type (see below). This value is an array of NodeBindings\n            since a given query node may have multiple knowledge graph Node bindings\n            in the result.\n          type: object\n        score:\n          description: A numerical score associated with this result indicating the\n            relevance or confidence of this result relative to others in the returned\n            set. Higher MUST be better.\n          example: 163.233\n          format: float\n          nullable: true\n          type: number\n      required:\n      - node_bindings\n      - edge_bindings\n      type: object\n    SubAttribute:\n      additionalProperties: false\n      description: Second-level attribute that can be used to qualify information\n        contained in a primary Attribute attached to a Node or Edge.\n      properties:\n        attribute_source:\n          description: The source of the core assertion made by the key-value pair\n            of an attribute object. Use a CURIE or namespace designator for this resource\n            where possible.\n          example: UniProtKB\n          nullable: true\n          type: string\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: The 'key' of the attribute object, holding a CURIE of an ontology\n            property defining the attribute (preferably the CURIE of a Biolink association\n            slot). This property captures the relationship asserted to hold between\n            the value of the attribute, and the node or edge from  which it hangs.\n            For example, that a value of '0.000153' represents a p-value supporting\n            an edge, or that a value of 'ChEMBL' represents the original source of\n            the knowledge expressed in the edge.\n          example: Biolink:has_p-value_evidence, Biolink:has_original_source\n        description:\n          description: Human-readable description for the attribute and its value.\n          example: Assertion Authored By Dr. Trans L. Ator\n          nullable: true\n          type: string\n        original_attribute_name:\n          description: The term used by the original source of an attribute to describe\n            the meaning or significance of the value it captures. This may be a column\n            name in a source tsv file, or a key in a source json document for the\n            field in the data that held the attribute's value. Capturing this information  where\n            possible lets us preserve what the original source said. Note that the\n            data type is string' but the contents of the field could also be a CURIE\n            of a third party ontology term.\n          example: p-value\n          nullable: true\n          type: string\n        value:\n          description: Value of the attribute. May be any data type, including a list.\n          example: 0.000153\n        value_type_id:\n          allOf:\n          - $ref: '#/components/schemas/CURIE'\n          description: CURIE describing the semantic type of an  attribute's value.\n            Use a Biolink class if possible, otherwise a term from an external ontology.\n            If a suitable CURIE/identifier does not exist, enter a descriptive phrase\n            here and submit the new type for consideration by the appropriate authority.\n          example: EDAM:data_1187\n          nullable: true\n        value_url:\n          description: Human-consumable URL linking to a web document that provides\n            additional information about an  attribute's value (not the node or the\n            edge fom which it hangs).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n          type: string\n      required:\n      - attribute_type_id\n      - value\n      type: object\n"
  },
  {
    "path": "medikanren2/neo/neo-open-api/neo-api-query.rkt",
    "content": "#lang racket\n(provide\n ;;\n api-query\n path.query\n ;;\n url.genetics.prod\n url.genetics.test\n url.genetics.ci\n ;;\n )\n(require\n json\n net/url)\n\n(define url.genetics.prod\n  \"https://genetics-kp.transltr.io/genetics_provider/trapi/v1.3\")\n(define url.genetics.test\n  \"https://genetics-kp.test.transltr.io/genetics_provider/trapi/v1.3\")\n(define url.genetics.ci\n  \"https://genetics-kp.ci.transltr.io/genetics_provider/trapi/v1.3\")\n\n(define path.query\n  \"/query\")\n\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (printf \"##### making api-query call to url:\\n~s\\n\" url-string) \n  (define-values (status headers in)\n    (time (if (void? optional-post-jsexpr)\n              (http-sendrecv/url\n               (string->url url-string)\n               #:method \"GET\")\n              (http-sendrecv/url\n               (string->url url-string)\n               #:method \"POST\"\n               #:data (jsexpr->string optional-post-jsexpr)\n               #:headers '(\"Content-Type: application/json; charset=utf-8\")))))\n  (define response-string (time (port->string in)))\n  (printf \"status:\\n~s\\n\" status)\n  (define OK-status? (bytes=? #\"HTTP/1.1 200 OK\" status))\n  (if OK-status?\n      (hash 'status status\n            'headers headers\n            'response (string->jsexpr response-string))\n      (begin\n        (printf \"!!!!!! unexpected non-OK status returned from ~s:\\n\" url-string)\n        (pretty-print `(,status ,headers ,response-string))\n        (hash 'status status\n              'headers headers\n              'response (hash)))))\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n"
  },
  {
    "path": "medikanren2/neo/neo-open-api/unsecret-source-consume.yaml",
    "content": "'ROBOKOP KG':\n  infores_curie: infores:robokop-kg\n'Text Mining KG':\n  infores_curie: infores:text-mining-provider-targeted\n'RTX-KG2 KG':\n  infores_curie: infores:rtx-kg2\n"
  },
  {
    "path": "medikanren2/neo/neo-open-api/unsecret_metaKG.json",
    "content": "{\n \"edges\": [\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:process_positively_regulates_process\",\n   \"subject\": \"biolink:BiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:process_positively_regulates_process\",\n   \"subject\": \"biolink:BiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:process_positively_regulates_process\",\n   \"subject\": \"biolink:BiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:BiologicalProcess\",\n   \"predicate\": \"biolink:process_positively_regulates_process\",\n   \"subject\": \"biolink:BiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": 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\"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:MolecularEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Agent\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": 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\"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:manifestation_of\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:manifestation_of\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:manifestation_of\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:InformationContentEntity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:InformationContentEntity\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:precedes\",\n   \"subject\": \"biolink:InformationContentEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:precedes\",\n   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\"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:BiologicalProcess\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Event\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:ClinicalIntervention\",\n   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\"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  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\"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:predisposes\",\n   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\"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Vitamin\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   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},\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:IndividualOrganism\"\n  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\"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:treats\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:treats\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:treats\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:treats\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:ProteinFamily\"\n  },\n  {\n   \"object\": \"biolink:ProteinDomain\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:ProteinFamily\"\n  },\n  {\n   \"object\": \"biolink:BiologicalProcess\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:RNAProduct\"\n  },\n  {\n   \"object\": 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\"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": 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\"predicate\": \"biolink:chemically_similar_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:MolecularEntity\",\n   \"predicate\": \"biolink:chemically_similar_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:chemically_similar_to\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:BiologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": 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\"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Pathway\",\n   \"predicate\": 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 \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": 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\"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Phenomenon\"\n  },\n  {\n   \"object\": \"biolink:Event\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": 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\"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Cohort\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": 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\"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:GeographicLocation\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": 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{\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PathologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:located_in\",\n 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\"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": 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{\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": 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\"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": 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\"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NucleicAcidEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NucleicAcidEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NucleicAcidEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NucleicAcidEntity\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:molecularly_interacts_with\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:molecularly_interacts_with\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": 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\"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": 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\"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n 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\"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Agent\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": 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 \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:has_part\",\n   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{\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Disease\"\n  },\n  {\n   \"object\": 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{\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:physically_interacts_with\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:physically_interacts_with\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:physically_interacts_with\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:physically_interacts_with\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:physically_interacts_with\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:physically_interacts_with\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": 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\"biolink:Drug\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:molecularly_interacts_with\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:MolecularEntity\",\n   \"predicate\": 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\"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": 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\"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": 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\"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": 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{\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n  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\"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": 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\"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:NoncodingRNAProduct\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   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\"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:ChemicalMixture\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:CellLine\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:MolecularEntity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": 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\"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:OrganismalEntity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": 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\"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:Vitamin\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:Vitamin\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:Vitamin\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:Vitamin\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:Vitamin\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:Vitamin\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:derives_from\",\n   \"subject\": \"biolink:InformationContentEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:derives_from\",\n   \"subject\": \"biolink:InformationContentEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:predisposes\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:derives_from\",\n   \"subject\": \"biolink:MolecularEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:Agent\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:Agent\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   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\"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": 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\"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": 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{\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:LifeStage\",\n  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\"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:GeographicLocation\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": 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  },
  {
    "path": "medikanren2/neo/neo-open-api/unsecret_metaKG_May_2023.json",
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\"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:OrganismTaxon\"\n  },\n  {\n   \"object\": \"biolink:BiologicalProcess\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Event\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:ClinicalIntervention\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Agent\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": 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\"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  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\"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Vitamin\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Activity\"\n  },\n 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\"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Cell\"\n  },\n  {\n   \"object\": 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{\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": 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\"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:located_in\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   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\"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Drug\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Drug\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Drug\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Drug\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Drug\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:Drug\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   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\"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:disrupts\",\n   \"subject\": \"biolink:PhysiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:EnvironmentalProcess\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:has_input\",\n   \"subject\": \"biolink:EnvironmentalProcess\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n 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{\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Agent\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": \"biolink:Device\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:related_to\",\n   \"subject\": 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\"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:causes\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:composed_primarily_of\",\n   \"subject\": \"biolink:PhysicalEntity\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": 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\"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   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\"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:NucleicAcidEntity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": 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{\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": 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\"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Agent\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:IndividualOrganism\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": 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 \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:affects\",\n   \"subject\": \"biolink:Behavior\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:has_part\",\n   \"subject\": \"biolink:Gene\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": 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\"predicate\": \"biolink:affects_transport_of\",\n   \"subject\": \"biolink:MolecularActivity\"\n  },\n  {\n   \"object\": \"biolink:PhysiologicalProcess\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:BiologicalEntity\"\n  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\"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Behavior\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:SmallMolecule\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:produces\",\n   \"subject\": \"biolink:DiseaseOrPhenotypicFeature\"\n 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\"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:prevents\",\n   \"subject\": \"biolink:Publication\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:PathologicalProcess\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:DiseaseOrPhenotypicFeature\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:diagnoses\",\n   \"subject\": \"biolink:ChemicalEntity\"\n  },\n  {\n   \"object\": \"biolink:BiologicalProcess\",\n   \"predicate\": \"biolink:same_as\",\n   \"subject\": \"biolink:BiologicalProcess\"\n  },\n  {\n   \"object\": \"biolink:Treatment\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Treatment\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Treatment\"\n  },\n  {\n   \"object\": \"biolink:Publication\",\n   \"predicate\": \"biolink:subclass_of\",\n   \"subject\": \"biolink:Treatment\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_positively_regulates_entity\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:SmallMolecule\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:Food\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": 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\"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Event\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Food\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:ChemicalMixture\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:CellularComponent\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n 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{\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Device\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:NucleicAcidEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Polypeptide\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:ChemicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Drug\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:PhysicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:coexists_with\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:MolecularActivity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:InformationContentEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:BiologicalEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Phenomenon\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:PhenotypicFeature\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Activity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:Procedure\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:Procedure\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": 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{\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:entity_negatively_regulates_entity\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:Protein\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:gene_product_of\",\n   \"subject\": \"biolink:Protein\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:NamedThing\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:PopulationOfIndividualOrganisms\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:OrganismTaxon\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Cohort\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:GrossAnatomicalStructure\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Cell\",\n   \"predicate\": \"biolink:occurs_in\",\n   \"subject\": \"biolink:Polypeptide\"\n  },\n  {\n   \"object\": \"biolink:Disease\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:AnatomicalEntity\",\n   \"predicate\": \"biolink:interacts_with\",\n   \"subject\": \"biolink:AnatomicalEntity\"\n  },\n  {\n   \"object\": \"biolink:Gene\",\n   \"predicate\": \"biolink:close_match\",\n   \"subject\": \"biolink:NamedThing\"\n  },\n  {\n   \"object\": \"biolink:LifeStage\",\n  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],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_mesenchymal_cell_neoplasm\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_agonist\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_dysostosis\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_bone_marrow_disorder\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      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\"MONDO_SUPERCLASS_familial_hypertrophic_cardiomyopathy\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_hemorrhagic_disease\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_enzyme_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_inborn_disorder_of_amino_acid_transport\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_parasitic_infectious_disease\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": 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},\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_myeloid_neoplasm\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_posterior_fossa_malformation\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_hormone_receptor_modulator\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_genetic_head_and_neck_malformation\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_inflammatory_diarrhea\"\n    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 {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_muscular_disorder\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_breast_cancer\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_anemia\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_nervous_system_disorder\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_primary_immunodeficiency_due_to_a_defect_in_adaptive_immunity\"\n     ],\n 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 {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_NMDA_receptor_antagonist\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_beta_adrenergic_agonist\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_chemical_hybridisation_agent\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_ophthalmology_drug\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:same_as\",\n     \"original_attribute_names\": [\n      \"equivalent_identifiers\"\n     ],\n     \"value_type_id\": 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{\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_food_humectant\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_vitamin_B1_antagonist\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_cathepsin_B_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_1.3.5_oxidoreductase_acting_on_CH_CH_of_donor_with_a_quinone_or_related_compound_as_acceptor_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      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},\n  \"biolink:Disease\": {\n   \"attributes\": [\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_cardiac_rhythm_disease\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_thyroid_gland_disorder\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_bone_marrow_cancer\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_gram-negative_bacterial_infections\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      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{\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_nervous_system_benign_neoplasm\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_developmental_defect_of_the_eye\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_reproductive_system_cancer\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_retinal_disorder\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"MONDO_SUPERCLASS_acute_diarrhea\"\n     ],\n     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   \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_neuroprotective_agent\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_survivin_dimerisation_modulator\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_glycine_transporter_2_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_6.3.5.5_[carbamoyl_phosphate_synthase_glutamine_hydrolysing_]_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_vesicular_glutamate_transport_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_4.2.1.20_tryptophan_synthase_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_vitamin_B1_antagonist\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_quinone_outside_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_anxiogenic\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_Daphnia_metabolite\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_1.13.11.11_tryptophan_2,3_dioxygenase_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_4.1.1_carboxy_lyase_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_food_additive\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_3.2.1.1_alpha_amylase_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_sodium_channel_modulator\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_2.7.11.1_non_specific_serine/threonine_protein_kinase_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_H2_receptor_antagonist\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_salt_inducible_kinase_2_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_EC_2.5.1.59_protein_geranylgeranyltransferase_type_I_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_antiviral_drug\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_antiparkinson_drug\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    },\n    {\n     \"attribute_type_id\": \"biolink:Attribute\",\n     \"original_attribute_names\": [\n      \"CHEBI_ROLE_sterol_biosynthesis_inhibitor\"\n     ],\n     \"value_type_id\": \"EDAM:data_0006\"\n    }\n   ],\n   \"id_prefixes\": [\n    \"ATC\",\n    \"CHEBI\",\n    \"CHEMBL.COMPOUND\",\n    \"CHEMBL.TARGET\",\n    \"DRUGBANK\",\n    \"FOODON\",\n    \"HMDB\",\n    \"KEGG.COMPOUND\",\n    \"KEGG.GLYCAN\",\n    \"LOINC\",\n    \"MESH\",\n    \"NCIT\",\n    \"NDDF\",\n    \"PSY\",\n    \"PathWhiz.Compound\",\n    \"REACT\",\n    \"UMLS\",\n    \"VANDF\",\n    \"ttd.target\",\n    \"PUBCHEM.COMPOUND\",\n    \"UNII\",\n    \"DrugCentral\",\n    \"GTOPDB\"\n   ]\n  },\n  \"biolink:Transcript\": {\n   \"id_prefixes\": [\n    \"ENSEMBL\",\n    \"NCIT\"\n   ]\n  },\n  \"biolink:Treatment\": {\n   \"id_prefixes\": [\n    \"MAXO\",\n    \"NCIT\"\n   ]\n  },\n  \"biolink:Vitamin\": {\n   \"id_prefixes\": [\n    \"ATC\",\n    \"MESH\",\n    \"NCIT\",\n    \"NDDF\",\n    \"UMLS\",\n    \"VANDF\"\n   ]\n  }\n }\n}"
  },
  {
    "path": "medikanren2/neo/neo-reasoning/neo-biolink-reasoning-low-level.rkt",
    "content": "#lang racket/base\n(provide\n ;;\n get-biolink-version\n ;;\n predicate-deprecated?\n class-deprecated?\n predicate-mixin?\n predicate-abstract?\n class-mixin?\n class-abstract?\n predicate-symmetric?\n ;;\n all-predicates\n all-classes\n ;;\n get-inverse-predicate\n ;;\n get-predicate-children\n get-class-children\n ;;\n get-predicate-descendents \n get-class-descendents\n ;;\n get-predicate-descendents*\n get-class-descendents*\n ;;\n get-predicate-proper-descendents \n get-class-proper-descendents\n ;;\n get-predicates-from-mixin\n get-classes-from-mixin\n ;;\n get-mixed-ins-and-descendent-predicates*\n ;;\n get-mixed-ins-and-descendent-classes*\n ;;\n UMLS-biolink-class-mapper\n UMLS-biolink-pred-mapper\n ;;\n find-leaf-classes\n get-smallest-nonmixin-class*\n )\n(require\n racket/pretty\n racket/runtime-path\n racket/set\n racket/string\n yaml\n \"../neo-utils/neo-helpers-without-db.rkt\")\n\n;; (define BIOLINK_YAML_FILE \"../neo-biolink/biolink_2_4_8/biolink-model.yaml\")\n;; (define BIOLINK_YAML_FILE \"../neo-biolink/biolink_3_0_3/biolink-model.yaml\")\n;; (define BIOLINK_YAML_FILE \"../neo-biolink/biolink_3_1_1/biolink-model.yaml\")\n;;(define BIOLINK_YAML_FILE \"../neo-biolink/biolink_3_1_2/biolink-model.yaml\")\n;;(define BIOLINK_YAML_FILE \"../neo-biolink/biolink_3_5_2/biolink-model.yaml\")\n(define BIOLINK_YAML_FILE \"../neo-biolink/biolink_4_2_1/biolink-model.yaml\")\n\n(define-runtime-path path.here \".\")\n(define bl-path (build-path path.here BIOLINK_YAML_FILE))\n\n(printf \"loading biolink YAML file from '~s'...\\n\" bl-path)\n\n(define ip (open-input-file bl-path))\n(define biolink (time (read-yaml ip)))\n\n(define (get-biolink-version)\n  (hash-ref biolink \"version\"))\n\n(printf \"finished loading biolink YAML file from '~s'\\n\" BIOLINK_YAML_FILE)\n(printf \"loaded biolink version '~s'\\n\" (get-biolink-version))\n\n(define yaml-predicate-name-to-biolink-name\n  (lambda (str)\n    (string-append \"biolink:\" (string-replace str \" \" \"_\"))))\n\n(define (string-titlecase-title-only str)\n  (if (string? str)\n      (string-append (string-upcase (substring str 0 1))\n                     (substring str 1 (string-length str)))\n      (error \"invalid string\" str)))\n\n(define yaml-class-name-to-biolink-name\n  (lambda (str)\n    (apply string-append (cons \"biolink:\" (map string-titlecase-title-only (string-split str))))))\n\n#;(define yaml-class-name-to-biolink-name\n  (lambda (str)\n    (string-append \"biolink:\" (string-replace (string-titlecase str) \" \" \"\"))))\n\n(define slots-h (hash-ref biolink \"slots\"))\n(define classes-h (hash-ref biolink \"classes\"))\n\n;; list of predicates\n(define slots (hash-keys slots-h))\n\n;; list of classes\n(define classes (hash-keys classes-h))\n\n(define all-predicates (list->set (map yaml-predicate-name-to-biolink-name slots)))\n(define all-classes (list->set (map yaml-class-name-to-biolink-name classes)))\n\n(define predicate-deprecated?\n  (let ((predicate-deprecated-hash (make-hash)))\n    (for-each\n      (lambda (pred-yaml-str)\n        (let ((deprecated-flag (hash-ref (hash-ref (hash-ref biolink \"slots\") pred-yaml-str) \"deprecated\" #f)))\n          (when deprecated-flag\n            (let ((pred-biolink-name (yaml-predicate-name-to-biolink-name pred-yaml-str)))\n              (hash-set! predicate-deprecated-hash pred-biolink-name #t)))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicate-deprecated-hash pred #f))))\n\n(define class-deprecated?\n  (let ((class-deprecated-hash (make-hash)))\n    (for-each\n      (lambda (class-yaml-str)\n        (let ((deprecated-flag (hash-ref (hash-ref (hash-ref biolink \"classes\") class-yaml-str) \"deprecated\" #f)))\n          (when deprecated-flag\n            (let ((class-biolink-name (yaml-class-name-to-biolink-name class-yaml-str)))\n              (hash-set! class-deprecated-hash class-biolink-name #t)))))\n      classes)\n    (lambda (class)\n      (hash-ref class-deprecated-hash class #f))))\n\n(define predicate-mixin?\n  (let ((predicate-mixin-hash (make-hash)))\n    (for-each\n      (lambda (pred-yaml-str)\n        (let ((mixin-flag (hash-ref (hash-ref (hash-ref biolink \"slots\") pred-yaml-str) \"mixin\" #f)))\n          (when mixin-flag\n            (let ((pred-biolink-name (yaml-predicate-name-to-biolink-name pred-yaml-str)))\n              (hash-set! predicate-mixin-hash pred-biolink-name #t)))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicate-mixin-hash pred #f))))\n\n(define predicate-abstract?\n  (let ((predicate-abstract-hash (make-hash)))\n    (for-each\n      (lambda (pred-yaml-str)\n        (let ((abstract-flag (hash-ref (hash-ref (hash-ref biolink \"slots\") pred-yaml-str) \"abstract\" #f)))\n          (when abstract-flag\n            (let ((pred-biolink-name (yaml-predicate-name-to-biolink-name pred-yaml-str)))\n              (hash-set! predicate-abstract-hash pred-biolink-name #t)))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicate-abstract-hash pred #f))))\n\n(define class-mixin-hash\n  (let ((class-mixin-hash (make-hash)))\n    (for-each\n      (lambda (class-yaml-str)\n        (let ((mixin-flag (hash-ref (hash-ref (hash-ref biolink \"classes\") class-yaml-str) \"mixin\" #f)))\n          (when mixin-flag\n            (let ((class-biolink-name (yaml-class-name-to-biolink-name class-yaml-str)))\n              (hash-set! class-mixin-hash class-biolink-name #t)))))\n      classes)\n    class-mixin-hash))\n\n(define class-mixin?\n    (lambda (class)\n      (hash-ref class-mixin-hash class #f)))\n\n(define class-abstract?\n  (let ((class-abstract-hash (make-hash)))\n    (for-each\n      (lambda (class-yaml-str)\n        (let ((abstract-flag (hash-ref (hash-ref (hash-ref biolink \"classes\") class-yaml-str) \"abstract\" #f)))\n          (when abstract-flag\n            (let ((class-biolink-name (yaml-class-name-to-biolink-name class-yaml-str)))\n              (hash-set! class-abstract-hash class-biolink-name #t)))))\n      classes)\n    (lambda (class)\n      (hash-ref class-abstract-hash class #f))))\n\n(define predicate-symmetric?\n  (let ((predicate-symmetric-hash (make-hash)))\n    (for-each\n      (lambda (pred-yaml-str)\n        (let ((symmetric-flag (hash-ref (hash-ref (hash-ref biolink \"slots\") pred-yaml-str) \"symmetric\" #f)))\n          (when symmetric-flag\n            (let ((pred-biolink-name (yaml-predicate-name-to-biolink-name pred-yaml-str)))\n              (hash-set! predicate-symmetric-hash pred-biolink-name #t)))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicate-symmetric-hash pred #f))))\n\n(define get-inverse-predicate\n  (let ((inverse-predicate-hash (make-hash)))\n    (for-each\n      (lambda (pred-yaml-str)\n        (let ((inverse-pred-yaml-str (hash-ref (hash-ref (hash-ref biolink \"slots\") pred-yaml-str) \"inverse\" #f)))\n          (when inverse-pred-yaml-str\n            (let ((pred-biolink-name (yaml-predicate-name-to-biolink-name pred-yaml-str))\n                  (inverse-pred-biolink-name (yaml-predicate-name-to-biolink-name inverse-pred-yaml-str)))\n              (hash-set! inverse-predicate-hash pred-biolink-name inverse-pred-biolink-name)\n              (hash-set! inverse-predicate-hash inverse-pred-biolink-name pred-biolink-name)))))\n      slots)\n    (lambda (pred)\n      (hash-ref inverse-predicate-hash pred #f))))\n\n(define get-predicate-children\n  (let ((predicate-children-hash (make-hash)))\n    (for-each\n      (lambda (child-yaml-str)\n        (let ((parent-yaml-str (hash-ref (hash-ref (hash-ref biolink \"slots\") child-yaml-str) \"is_a\" #f)))\n          (when parent-yaml-str\n            (let ((child-biolink-name (yaml-predicate-name-to-biolink-name child-yaml-str))\n                  (parent-biolink-name (yaml-predicate-name-to-biolink-name parent-yaml-str)))\n              (let ((children-set (hash-ref predicate-children-hash parent-biolink-name (set))))\n                (hash-set! predicate-children-hash parent-biolink-name\n                           (set-union (set child-biolink-name) children-set)))))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicate-children-hash pred (set)))))\n\n(define get-predicate-descendents*\n  (lambda (preds)\n    (let loop ((preds preds)\n               (desc (set)))\n      (cond\n        [(null? preds) desc]\n        [else (let ((pred (car preds)))\n                (let ((d (get-predicate-descendents pred)))\n                  (loop (cdr preds) (set-union d desc))))]))))\n\n(define get-predicate-descendents\n  (lambda (pred)\n    (set-add\n     (get-predicate-proper-descendents pred)\n     pred)))\n\n(define get-predicate-proper-descendents\n  (let ((predicate-proper-descendents-hash (make-hash)))\n    (for-each\n      (lambda (parent-yaml-str)\n        (let ((parent-biolink-name (yaml-predicate-name-to-biolink-name parent-yaml-str)))\n          (let loop ((to-process-set (get-predicate-children parent-biolink-name))\n                     (processed-set (set parent-biolink-name))\n                     (descendents-set (set)))\n            (cond\n              [(set-empty? to-process-set)\n               (hash-set! predicate-proper-descendents-hash parent-biolink-name descendents-set)]\n              [else\n               (let ((process-element (set-first to-process-set))\n                     (to-process-set (set-rest to-process-set)))\n                 (cond\n                   [(set-member? processed-set process-element)\n                    (loop to-process-set processed-set descendents-set)]\n                   [else\n                    (let ((children-set (get-predicate-children process-element))\n                          (descendents-set (set-add descendents-set process-element)))\n                      (let ((to-process-set\n                             (set-union\n                              (set-subtract children-set processed-set)\n                              to-process-set)))\n                        (loop to-process-set\n                              (set-add processed-set process-element)\n                              descendents-set)))]))]))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicate-proper-descendents-hash pred (set)))))\n\n(define class-children-hash\n  (let ((class-children-hash (make-hash)))\n    (for-each\n      (lambda (child-yaml-str)\n        (let ((parent-yaml-str (hash-ref (hash-ref (hash-ref biolink \"classes\") child-yaml-str) \"is_a\" #f)))\n          (when parent-yaml-str\n            (let ((child-biolink-name (yaml-class-name-to-biolink-name child-yaml-str))\n                  (parent-biolink-name (yaml-class-name-to-biolink-name parent-yaml-str)))\n              (let ((children-set (hash-ref class-children-hash parent-biolink-name (set))))\n                (hash-set! class-children-hash parent-biolink-name\n                           (set-union (set child-biolink-name) children-set)))))))\n      classes)\n    class-children-hash))\n\n(define get-class-children\n  (lambda (class)\n    (hash-ref class-children-hash class (set))))\n\n(define (find-leaf-classes class*)\n  (let ((sub-hierarchy (make-hash)))\n    (for-each\n     (lambda (class)\n       (let* ((child* (set->list (hash-ref class-children-hash class (set))))\n              (child* (filter (lambda (c) (member c class*)) child*)))\n        (hash-set! sub-hierarchy class child*)))\n     class*)\n    (filter (lambda (class) (null? (hash-ref sub-hierarchy class)))\n            (hash-keys sub-hierarchy))))\n\n(define (get-smallest-nonmixin-class* class*)\n  (find-leaf-classes (filter (lambda (c) (not (class-mixin? c))) class*)))\n\n(define get-class-descendents*\n  (lambda (classes)\n    (let loop ((classes classes)\n               (desc (set)))\n      (cond\n        [(null? classes) desc]\n        [else (let ((class (car classes)))\n                (let ((d (get-class-descendents class)))\n                  (loop (cdr classes) (set-union d desc))))]))))\n\n(define get-class-descendents\n  (lambda (class)\n    (set-add\n     (get-class-proper-descendents class)\n     class)))\n\n(define get-class-proper-descendents\n  (let ((class-proper-descendents-hash (make-hash)))\n    (for-each\n      (lambda (parent-yaml-str)\n        (let ((parent-biolink-name (yaml-class-name-to-biolink-name parent-yaml-str)))\n          (let loop ((to-process-set (get-class-children parent-biolink-name))\n                     (processed-set (set parent-biolink-name))\n                     (descendents-set (set)))\n            (cond\n              [(set-empty? to-process-set)\n               (hash-set! class-proper-descendents-hash parent-biolink-name descendents-set)]\n              [else\n               (let ((process-element (set-first to-process-set))\n                     (to-process-set (set-rest to-process-set)))\n                 (cond\n                   [(set-member? processed-set process-element)\n                    (loop to-process-set processed-set descendents-set)]\n                   [else\n                    (let ((children-set (get-class-children process-element))\n                          (descendents-set (set-add descendents-set process-element)))\n                      (let ((to-process-set\n                             (set-union\n                              (set-subtract children-set processed-set)\n                              to-process-set)))\n                        (loop to-process-set\n                              (set-add processed-set process-element)\n                              descendents-set)))]))]))))\n      classes)\n    (lambda (class)\n      (hash-ref class-proper-descendents-hash class (set)))))\n\n\n(define get-predicates-from-mixin\n  (let ((predicates-from-mixin (make-hash)))\n    (for-each\n      (lambda (pred-yaml-str)\n        (let ((mixins (hash-ref (hash-ref (hash-ref biolink \"slots\") pred-yaml-str) \"mixins\" #f)))\n          (when mixins\n            (let ((pred-biolink-name (yaml-predicate-name-to-biolink-name pred-yaml-str))\n                  (mixin* (map yaml-predicate-name-to-biolink-name mixins)))\n              (for-each\n                (lambda (mixin-biolink-name)\n                  (let ((pred-set-for-mixin (hash-ref predicates-from-mixin mixin-biolink-name (set))))\n                    (hash-set! predicates-from-mixin mixin-biolink-name\n                               (set-union (set pred-biolink-name) pred-set-for-mixin))))\n                mixin*)))))\n      slots)\n    (lambda (pred)\n      (hash-ref predicates-from-mixin pred (set)))))\n\n\n(define get-classes-from-mixin\n  (let ((classes-from-mixin (make-hash)))\n    (for-each\n      (lambda (class-yaml-str)\n        (let ((mixins (hash-ref (hash-ref (hash-ref biolink \"classes\") class-yaml-str) \"mixins\" #f)))\n          (when mixins\n            (let ((class-biolink-name (yaml-class-name-to-biolink-name class-yaml-str))\n                  (mixin* (map yaml-class-name-to-biolink-name mixins)))\n              (for-each\n                (lambda (mixin-biolink-name)\n                  (let ((class-set-for-mixin (hash-ref classes-from-mixin mixin-biolink-name (set))))\n                    (hash-set! classes-from-mixin mixin-biolink-name\n                               (set-union (set class-biolink-name) class-set-for-mixin))))\n                mixin*)))))\n      classes)\n    (lambda (class)\n      (hash-ref classes-from-mixin class (set)))))\n\n\n;; Return descendent predicates and mixins,\n;; and predicates that include any of those\n;; mixins, from a given list of predicates\n;; and/or mixins.\n(define get-mixed-ins-and-descendent-predicates*\n  (lambda (predicate*)\n    (set-fixed-point\n     (set-intersect\n      (list->set predicate*)\n      all-predicates)\n     (lambda (new-predicate-set)\n       (let ((updated-set\n              (apply set-union\n                     (set->list\n                      (for/set ([c new-predicate-set])\n                               (if (predicate-mixin? c)\n                                   (set-union\n                                    (get-predicates-from-mixin c)\n                                    (get-predicate-descendents c))\n                                   (get-predicate-descendents c)))))))\n         (set-subtract updated-set new-predicate-set))))))\n\n;; Return descendent classes and mixins,\n;; and classes that include any of those\n;; mixins, from a given list of classes\n;; and/or mixins.\n(define get-mixed-ins-and-descendent-classes*\n  (lambda (class*)\n    (set-fixed-point\n      (set-intersect\n       (list->set class*)\n       all-classes)\n      (lambda (new-class-set)\n        (let ((updated-set\n               (apply set-union\n                      (set->list\n                       (for/set ([c new-class-set])\n                                (if (class-mixin? c)\n                                    (set-union\n                                     (get-classes-from-mixin c)\n                                     (get-class-descendents c))\n                                    (get-class-descendents c)))))))\n          (set-subtract updated-set new-class-set))))))\n\n\n\n(define build-UMLS-biolink-hash\n  (lambda (kind)\n    (define return (make-hash))\n    (define (helper! kind-hash name-mapper prefix)\n      (for-each\n       (lambda (k)\n         #;(displayln k)\n         (let* ((v (hash-ref kind-hash k))\n                (exact-map-code* (hash-ref v \"exact_mappings\" '()))\n                (exact-map-code* (if (eq? exact-map-code* 'null) '() exact-map-code*))\n                (close-map-code* (hash-ref v \"close_mappings\" '()))\n                (close-map-code* (if (eq? close-map-code* 'null) '() close-map-code*))\n                (narrow-map-code* (hash-ref v \"narrow_mappings\" '()))\n                (narrow-map-code* (if (eq? narrow-map-code* 'null) '() narrow-map-code*))\n                (umls-code* (filter\n                             (lambda (code) (string-prefix? code prefix))\n                             (append exact-map-code* close-map-code* narrow-map-code*))))\n           (for-each\n            (lambda (code)\n              (hash-set! return\n                         (string-trim code prefix)\n                         (name-mapper k)))\n            umls-code*)))\n       (hash-keys kind-hash)))\n    (cond\n      ((eq? kind 'predicate) (helper! slots-h yaml-predicate-name-to-biolink-name \"SEMMEDDB:\"))\n      ((eq? kind 'class) (helper! classes-h yaml-class-name-to-biolink-name \"STY:\"))\n      (else (error \"unknown kind\" kind)))\n    return))\n    \n(define UMLS-biolink-class-hash (build-UMLS-biolink-hash 'class))\n(define (UMLS-biolink-class-mapper class) (hash-ref UMLS-biolink-class-hash class #f))\n(define UMLS-biolink-pred-hash (build-UMLS-biolink-hash 'predicate))\n(define (UMLS-biolink-pred-mapper predicate) (hash-ref UMLS-biolink-pred-hash predicate #f))\n\n"
  },
  {
    "path": "medikanren2/neo/neo-reasoning/neo-biolink-reasoning.rkt",
    "content": "#lang racket/base\n(provide\n ;;\n get-biolink-version\n ;;\n class-deprecated?\n predicate-mixin?\n predicate-abstract?\n class-mixin?\n class-abstract?\n predicate-symmetric?\n ;;\n all-predicates\n all-classes\n ;;\n get-inverse-predicate\n ;;\n get-non-deprecated-mixed-ins-and-descendent-predicates*\n ;;\n get-non-deprecated-mixed-ins-and-descendent-classes*\n ;;\n )\n(require\n racket/set\n \"../neo-utils/neo-helpers-without-db.rkt\"\n \"neo-biolink-reasoning-low-level.rkt\")\n\n;; Return non-deprecated descendent predicates and mixins, and\n;; non-deprecated predicates that include any of those mixins, from a\n;; given list of predicates and/or mixins.\n(define get-non-deprecated-mixed-ins-and-descendent-predicates*\n  (lambda (predicate*)\n    (list->set\n     (filter (lambda (c) (not (predicate-deprecated? c)))\n             (set->list (get-mixed-ins-and-descendent-predicates* predicate*))))))\n\n;; Return non-deprecated descendent classes and mixins, and\n;; non-deprecated classes that include any of those mixins, from a\n;; given list of classes and/or mixins.\n(define get-non-deprecated-mixed-ins-and-descendent-classes*\n  (lambda (class*)\n    (list->set\n     (filter (lambda (c) (not (class-deprecated? c)))\n             (set->list (get-mixed-ins-and-descendent-classes* class*))))))\n"
  },
  {
    "path": "medikanren2/neo/neo-reasoning/semmed-exclude.rkt",
    "content": "#lang racket/base\n\n(provide semantic-exclude* domain-exclude* range-exclude*)\n\n(require racket/runtime-path\n         yaml\n         racket/match\n         racket/list\n         \"neo-biolink-reasoning-low-level.rkt\")\n\n(define SEMMED_EXCLUDE_LIST_FILE \"../neo-biolink/biolink_3_5_2/semmed-exclude-list.yaml\")\n\n(define-runtime-path path.here \".\")\n(define semmed-exclude-path (build-path path.here SEMMED_EXCLUDE_LIST_FILE))\n\n(printf \"loading semmed exclude list YAML file from '~s'...\\n\" semmed-exclude-path)\n\n(define ip (open-input-file semmed-exclude-path))\n(define exclude-orig (time (read-yaml ip)))\n(define exclude-recd* (hash-ref exclude-orig \"excluded_semmedb_records\"))\n\n(match-define-values (semantic-exclude* domain-exclude* range-exclude*)\n  (let loop ((h exclude-recd*) (s '()) (d '()) (r '()))\n    (if (null? h)\n        (values (remove-duplicates s)\n                (remove-duplicates d)\n                (remove-duplicates r))\n        (let* ((hs (car h))\n               (type (hash-ref hs \"exclusion_type\"))\n               (sub-t (hash-ref hs \"semmed_subject_t_code\"))\n               (pred (hash-ref hs \"semmed_predicate\"))\n               (obj-t (hash-ref hs \"semmed_object_t_code\")))\n          (cond\n            ((equal? type \"semantic type exclusion\")\n             (let ((sub-b (UMLS-biolink-class-mapper sub-t))\n                   (obj-b (UMLS-biolink-class-mapper obj-t)))\n               (if (or sub-b obj-b)\n                   (loop (cdr h) (cons (list sub-b #f obj-b) s) d r)\n                   (loop (cdr h) s d r))))\n            ((equal? type \"Domain exclusion\")\n             (let ((sub-b (UMLS-biolink-class-mapper sub-t))\n                   (pred-b (UMLS-biolink-pred-mapper pred)))\n               (if (and sub-b pred-b)\n                   (loop (cdr h) s (cons (list sub-b pred-b #f) d) r)\n                   (loop (cdr h) s d r))))\n            ((equal? type \"Range exclusion\")\n             (let ((obj-b (UMLS-biolink-class-mapper obj-t))\n                   (pred-b (UMLS-biolink-pred-mapper pred)))\n               (if (and pred-b obj-b)\n                   (loop (cdr h) s d (cons (list #f pred-b obj-b) r))\n                   (loop (cdr h) s d r)))))))))\n           \n \n\n\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-1.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n;; This version does successfully kill thread t1 by calling\n;; kill-thread\n\n(define n 0)\n\n(printf \"*** 1 n: ~s\\n\" n)\n(define t1-thunk\n  (lambda ()\n    (let loop ()\n      (set! n (add1 n))\n      (loop))))\n\n(printf \"*** 2 n: ~s\\n\" n)\n(define t1\n  (thread t1-thunk))\n\n(printf \"*** 3 n: ~s\\n\" n)\n(sleep 1)\n(printf \"*** 4 n: ~s\\n\" n)\n(kill-thread t1)\n(printf \"*** 5 n: ~s\\n\" n)\n(sleep 1)\n(printf \"*** 6 n: ~s\\n\" n)\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-2.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n;; This version *does not* shut down the infinite loop!\n\n(define *n* 0)\n(define *cust* #f)\n\n(printf \"*** 1 *n*: ~s\\n\" *n*)\n(define t1-thunk\n  (lambda ()\n    (define t1-thunk-cust (make-custodian))\n    (set! *cust* t1-thunk-cust)\n    (parameterize ((current-custodian t1-thunk-cust))\n      (let loop ()\n        (set! *n* (add1 *n*))\n        (loop)))))\n\n(printf \"*** 2 *n*: ~s\\n\" *n*)\n(define t1\n  (thread t1-thunk))\n\n(printf \"*** 3 *n*: ~s\\n\" *n*)\n(sleep 1)\n(printf \"*** 4 *n*: ~s\\n\" *n*)\n(custodian-shutdown-all *cust*)\n(printf \"*** 5 *n*: ~s\\n\" *n*)\n(sleep 1)\n(printf \"*** 6 *n*: ~s\\n\" *n*)\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-3.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n;; This version seems to successfully kill the t1 thread by shutting\n;; down the custodian *cust*\n\n(define *n* 0)\n(define *cust* #f)\n\n(printf \"*** 1 *n*: ~s\\n\" *n*)\n(define t1-thunk\n  (lambda ()\n    (let loop ()\n      (set! *n* (add1 *n*))\n      (loop))))\n\n(printf \"*** 2 *n*: ~s\\n\" *n*)\n(define t1\n  (let ()\n    (define t1-thunk-cust (make-custodian))\n    (set! *cust* t1-thunk-cust)\n    (parameterize ((current-custodian t1-thunk-cust))\n      (thread t1-thunk))))\n\n(printf \"*** 3 *n*: ~s\\n\" *n*)\n(sleep 1)\n(printf \"*** 4 *n*: ~s\\n\" *n*)\n(custodian-shutdown-all *cust*)\n(printf \"*** 5 *n*: ~s\\n\" *n*)\n(sleep 1)\n(printf \"*** 6 *n*: ~s\\n\" *n*)\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-4.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n;; This version seems to successfully kill the t1 thread by shutting\n;; down the custodian cust\n\n(define *n* 0)\n\n(printf \"*** 1 *n*: ~s\\n\" *n*)\n(define t1-thunk\n  (lambda ()\n    (let loop ()\n      (set! *n* (add1 *n*))\n      (loop))))\n\n(printf \"*** 2 *n*: ~s\\n\" *n*)\n(define-values (t1 cust)\n  (let ()\n    (define t1-thunk-cust (make-custodian))\n    (parameterize ((current-custodian t1-thunk-cust))\n      (values (thread t1-thunk) t1-thunk-cust))))\n\n(printf \"*** 3 *n*: ~s\\n\" *n*)\n(sleep 1)\n(printf \"*** 4 *n*: ~s\\n\" *n*)\n(custodian-shutdown-all cust)\n(printf \"*** 5 *n*: ~s\\n\" *n*)\n(sleep 1)\n(printf \"*** 6 *n*: ~s\\n\" *n*)\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-5.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n;; This version seems to successfully kill the t1 thread by shutting\n;; down the custodian cust, and shut down the t2 thread as well.\n;; The done! message is never displayed.\n\n(define *chan* (make-channel))\n(define *n* 0)\n\n(printf \"*** 1 *n*: ~s\\n\" *n*)\n(define t1-thunk\n  (lambda ()\n    (printf \"t1-thunk invoked\\n\")\n    (let loop ()\n      (set! *n* (add1 *n*))\n      (loop))))\n\n(printf \"*** 2 *n*: ~s\\n\" *n*)\n\n(define t1\n  (let ()\n    (define t1-thunk-cust (make-custodian))    \n    (parameterize ((current-custodian t1-thunk-cust))\n      (thread (lambda ()\n                (printf \"about to put t1-thunk-cust into channel *chan*\\n\")\n                (channel-put *chan* t1-thunk-cust)\n                (printf \"done putting t1-thunk-cust into channel *chan*\\n\")\n                (t1-thunk))))))\n\n(define-values (t2 cust)\n  (let ()\n    (define t2-cust (make-custodian))\n    (parameterize ((current-custodian t2-cust))\n      (values\n        (thread\n         (lambda ()\n           (printf \"*** 3 *n*: ~s\\n\" *n*)\n           (sleep 1)\n           (printf \"*** 4 *n*: ~s\\n\" *n*)\n           (define cust (channel-get *chan*))\n           (printf \"*** 5 *n*: ~s\\n\" *n*)\n           (sleep 1)\n           (printf \"*** 6 *n*: ~s\\n\" *n*)\n           (custodian-shutdown-all cust)\n           (printf \"*** 7 *n*: ~s\\n\" *n*)\n           (sleep 1)\n           (printf \"*** 8 *n*: ~s\\n\" *n*)\n           (printf \"shutting down t2 cust\\n\")\n           (custodian-shutdown-all t2-cust)\n           (printf \"done!\\n\")))\n        t2-cust))))\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-6.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n;; This version seems nice!\n\n#|\nWelcome to Racket v8.6 [cs].\n> (load \"experiment-6.rkt\")\n*** 1 *n*: 0\n*** 2 *n*: 0\nabout to put t1-thunk-cust into channel *chan*\nabout to sleep\n*** 3 *n*: 0\n*** 4 *n*: 0\n*** 5 *n*: 0\ndone putting t1-thunk-cust into channel *chan*\nt1-thunk invoked\n*** 6 *n*: 201695745\n*** 7 *n*: 201695745\n*** 8 *n*: 201695745\n*** 9 (looping) *n*: 201695745\n*** 9 (looping) *n*: 201695745\n*** 9 (looping) *n*: 201695745\nshutting down t2 cust\ndone!\n> \n|#\n\n(define *chan* (make-channel))\n(define *n* 0)\n\n(printf \"*** 1 *n*: ~s\\n\" *n*)\n(define t1-thunk\n  (lambda ()\n    (printf \"t1-thunk invoked\\n\")\n    (let loop ()\n      (set! *n* (add1 *n*))\n      (loop))))\n\n(printf \"*** 2 *n*: ~s\\n\" *n*)\n\n(define t1\n  (let ()\n    (define t1-thunk-cust (make-custodian))    \n    (parameterize ((current-custodian t1-thunk-cust))\n      (thread (lambda ()\n                (printf \"about to put t1-thunk-cust into channel *chan*\\n\")\n                (channel-put *chan* t1-thunk-cust)\n                (printf \"done putting t1-thunk-cust into channel *chan*\\n\")\n                (t1-thunk))))))\n\n(define-values (t2 cust)\n  (let ()\n    (define t2-cust (make-custodian))\n    (parameterize ((current-custodian t2-cust))\n      (values\n        (thread\n         (lambda ()\n           (printf \"*** 3 *n*: ~s\\n\" *n*)\n           (sleep 1)\n           (printf \"*** 4 *n*: ~s\\n\" *n*)\n           (define cust (channel-get *chan*))\n           (printf \"*** 5 *n*: ~s\\n\" *n*)\n           (sleep 1)\n           (printf \"*** 6 *n*: ~s\\n\" *n*)\n           (custodian-shutdown-all cust)\n           (printf \"*** 7 *n*: ~s\\n\" *n*)\n           (sleep 1)\n           (printf \"*** 8 *n*: ~s\\n\" *n*)\n           (let loop ()\n             (printf \"*** 9 (looping) *n*: ~s\\n\" *n*)\n             (sleep 1)\n             (loop))))\n        t2-cust))))\n\n(printf \"about to sleep\\n\")\n(sleep 6)\n(printf \"shutting down t2 cust\\n\")\n(custodian-shutdown-all cust)\n(printf \"done!\\n\")\n"
  },
  {
    "path": "medikanren2/neo/neo-server/experiments/experiment-7.rkt",
    "content": ";; Custodian, thread, channel experiments\n\n(define CONNECTION_TIMEOUT_SECONDS 10)\n\n;; Beware!  Various Racket time operations, such as syncing on alarm\n;; events, uses elapsed CPU time, rather than elapsed real time (\"wall\n;; clock\" time/\"walltime\").\n;;\n;; When a job is in a queue waiting to be run, the CPU time doesn't\n;; advance, which can lead to apparently bizarre timeout behavior.\n;;\n;; For Translator timeouts, we should use walltime.\n\n(thread\n (lambda ()\n   (printf \"@@@ hello from watcher-thread\\n\")\n   (define alarm (alarm-evt (+ (current-inexact-milliseconds)\n                               (* CONNECTION_TIMEOUT_SECONDS 1000))))\n   (let ((evt (sync (thread-dead-evt handler-thread)\n                    alarm)))\n     (cond\n       (evt\n        (cond\n          ((eq? (thread-dead-evt handler-thread) evt)\n           (printf \"@@@ Watcher thread got a thread-dead-evt for handler-thread\\n\")\n           (semaphore-post sem))\n          ((eq? alarm evt)\n           (printf \"!!! Watcher thread got an alarm event after ~s seconds\\n\"\n                   CONNECTION_TIMEOUT_SECONDS)\n           (semaphore-post sem))\n          (else\n           (printf \"!!! Watcher thread received unexpected event ~s\\n\" evt)\n           (semaphore-post sem))))\n       (else\n        (printf \"!!! Watcher thread received unexpected #f value\\n\")\n        (semaphore-post sem))))))\n"
  },
  {
    "path": "medikanren2/neo/neo-server/neo-server-utils.rkt",
    "content": "#lang racket/base\n\n(provide get-assoc\n         list-assoc\n         get-publications\n         mvp2-1hop-filter\n         mvp2-2hop-filter\n         merge-list\n         merge-hash\n         minus-one-before-zero\n         find-max-number\n         get-source\n         UNSECRET-SOURCE\n         num-pubs\n         get-score-from-result\n         set-score-in-result\n         normalize-scores\n         edge-has-source?\n         publication-attributes\n         auxiliary-graph-attribute\n         qualifier-attribute*\n         merge-trapi-responses\n         semantic-exclude*\n         domain-exclude*\n         range-exclude*\n         get-object\n         get-and-print-qualifiers\n         Unsecret-agent-type-attribute\n         Unsecret-knowledge-level-attribute\n         agent-type-attribute\n         knowledge-level-attribute\n         )\n\n(require racket/list\n         racket/math\n         racket/string\n         json\n         racket/match\n         \"../neo-reasoning/semmed-exclude.rkt\"\n         \"../neo-utils/neo-helpers-without-db.rkt\"\n         )\n\n(define (merge-list xs ys)\n  (if (null? xs)\n      ys\n      (cons (car xs) (merge-list ys (cdr xs)))))\n\n(define (merge-hash h1 h2)\n  (define h h2)\n  (hash-for-each h1 (lambda (k v) (set! h (hash-set h k v))))\n  h)\n\n(define (get-assoc k m)\n  (let ((r (assoc k m)))\n    (if r\n        (cadr r)\n        #f)))\n\n(define (list-assoc k m)\n  (let ((r (assoc k m)))\n    (if r\n        (cdr r)\n        '())))\n\n(define mvp2-filter\n  (lambda (target-eprop direction care-aspect?)\n    (let* ((aspect (get-assoc \"object_aspect_qualifier\" target-eprop))\n           (direction^ (get-assoc \"object_direction_qualifier\" target-eprop)))\n      (if care-aspect?\n          (and\n           aspect\n           direction^\n           (member aspect '(\"activity\" \"abundance\" \"activity_or_abundance\" \"expression\" \"synthesis\"))\n           (equal? direction direction^))\n          (and\n           direction^\n           (equal? direction direction^))))))\n\n#|\nA increases B increases C = A increases C\nA decreases B deceases C = A increases C\nA increases B decreases C = A decreases C\nA decreases B increases C = A decreases C\n|#\n\n(define mvp2-2hop-filter\n  (lambda (e* direction)\n    (filter\n     (lambda (e)\n       (match e\n         [`(,curie_x\n            ,pred_xy\n            ,curie_y\n            ,(? string? pred_yz)\n            ,(? string? curie_z)\n            ,props_xy\n            ,props_yz)\n          (if (equal? pred_xy \"biolink:affects\")\n              (if (equal? direction \"increased\")\n                  (or\n                   (and (mvp2-filter props_xy \"increased\" #f)\n                        (mvp2-filter props_yz \"increased\" #t))\n                   (and (mvp2-filter props_xy \"decreased\" #f)\n                        (mvp2-filter props_yz \"decreased\" #t)))\n                  (or\n                   (and (mvp2-filter props_xy \"increased\" #f)\n                        (mvp2-filter props_yz \"decreased\" #t))\n                   (and (mvp2-filter props_xy \"decreased\" #f)\n                        (mvp2-filter props_yz \"increased\" #t))))\n              (if (equal? direction \"increased\")\n                  (mvp2-filter props_yz \"increased\" #t)\n                  (mvp2-filter props_yz \"decreased\" #t)))]\n         [else #f]))\n     e*)))\n\n(define mvp2-1hop-filter\n  (lambda (q direction)\n    (filter\n     (lambda (e)\n       (let-values ([(_ eprop) (split-at e 3)])\n         (mvp2-filter eprop direction #t)))\n     q)))\n\n(define find-max-number\n  (lambda (num*)\n    (let loop ((n* (cdr num*)) (greatest (car num*)))\n      (cond\n        ((null? n*) greatest)\n        (else\n         (if (> (car n*) greatest)\n             (loop (cdr n*) (car n*))\n             (loop (cdr n*) greatest)))))))\n\n(define (get-source-helper props)\n  (get-assoc \"primary_knowledge_source\" props))\n\n(define (get-source props)\n  (hash\n   'type \"biolink:RetrievalSource\"\n   'resource_id (get-source-helper props)\n   'resource_role \"primary_knowledge_source\"))\n\n(define (num-pubs props)\n  (let ((score (string->number (get-assoc \"mediKanren-score\" props)))\n        (source (get-source-helper props)))\n    (cond\n      ((equal? source \"infores:semmeddb\") (* 0.1 score))\n      ((equal? source \"infores:text-mining-provider-targeted\") (* 10 score))\n      (else score))))\n\n(define (UNSECRET-SOURCE prop)\n  (hash\n   'type \"biolink:RetrievalSource\"\n   'resource_id \"infores:unsecret-agent\"\n   'resource_role \"aggregator_knowledge_source\"\n   'upstream_resource_ids (get-assoc \"upstream_resource_ids\" prop)))\n\n(define (get-score-from-result result)\n  (let ((analyses (hash-ref result 'analyses #f)))\n    (if analyses\n        (hash-ref (car analyses) 'score)\n        (error \"check the implementation of results.analyses\"))))\n\n(define (set-score-in-result result score)\n  (let ((analyses (hash-ref result 'analyses #f)))\n    (if analyses\n        (hash-set result 'analyses\n                  (map (lambda (a) (hash-set a 'score score)) analyses))\n        (error \"check the implementation of results.analyses\"))))\n\n\n\n(define (normalize-scores results)\n  (if (null? results)\n      results\n      (let ((max-score (get-score-from-result (car results))))\n        (if (zero? max-score)\n            results\n            (map (lambda (x) (set-score-in-result x (/ (get-score-from-result x) (* 1.0 max-score)))) results)))))\n\n(define (edge-has-source? props)\n  (get-source-helper props))\n\n(define (publication-attributes props has-pub?)\n  (if has-pub?\n    (list (get-publications props))\n    (list)))\n\n(define get-publications\n  (lambda props\n    (define (helper props pubs)\n      (cond\n        [(null? props) pubs]\n        [else\n         (let ((publication (get-assoc \"publications\" (car props))))\n           (helper (cdr props)\n                   (append \n                    (cond\n                      [(string-prefix? publication \"(\")\n                       (string-split (string-trim (string-trim publication \"(\") \")\"))] ;rtx-kg2 & robokop\n                      [(string-contains? publication \"|\") (string-split publication \"|\")] ;text-mining\n                      [(string-contains? publication \";\") (string-split publication \"; \")]\n                      [else (string-split publication)])\n                    pubs)))]))\n    (define pubs (filter\n                  (lambda (p) (not (equal? \"PMID:\" p)))\n                  (remove-duplicates (helper props '()))))\n    (hash\n     'attribute_type_id \"biolink:publications\"\n     'value pubs\n     'value_type_id \"biolink:Uriorcurie\")))\n\n(define auxiliary-graph-attribute\n  (lambda (id)\n    (hash\n     'attribute_type_id \"biolink:support_graphs\"\n     'value (list id))))\n\n(define (qualifier-attribute* qualifier-name props)\n  (let ((qualifer (get-assoc qualifier-name props)))\n    (if qualifer\n        (list (hash 'qualifier_type_id (string-append \"biolink:\" qualifier-name)\n              'qualifier_value qualifer))\n        '())))\n        \n\n(define Unsecret-agent-type-attribute\n  (hash\n   'attribute_type_id \"biolink:agent_type\"\n   'value \"computational_model\"\n   'attribute_source \"infores:unsecret-agent\"))\n\n(define Unsecret-knowledge-level-attribute\n  (hash\n   'attribute_type_id \"biolink:knowledge_level\"\n   'value \"prediction\"\n   'attribute_source \"infores:unsecret-agent\"))\n\n(define (agent-type-attribute prop)\n  (let* ((edge-from-tmkg? (get-assoc \"json_attributes\" prop))\n         (agent-type (if edge-from-tmkg? \"text_mining_agent\" (get-assoc \"agent_type\" prop))))\n        (hash\n         'attribute_type_id \"biolink:agent_type\"\n         'value agent-type)))\n\n(define (knowledge-level-attribute prop)\n  (let* ((edge-from-tmkg? (get-assoc \"json_attributes\" prop))\n         (knowledge-level (if edge-from-tmkg? \"not_provided\" (get-assoc \"knowledge_level\" prop))))\n        (hash\n         'attribute_type_id \"biolink:knowledge_level\"\n         'value knowledge-level)))\n\n;; TODO: test it with calling out Genetics KP\n(define (merge-trapi-responses r1 r2 original-query_graph)\n  (let* ((message1 (hash-ref r1 'message))\n         (message2 (hash-ref r2 'message))\n         (auxiliary_graphs1 (hash-ref message1 'auxiliary_graphs))\n         (auxiliary_graphs2 (hash-ref message2 'auxiliary_graphs))\n         (knowledge_graph1 (hash-ref message1 'knowledge_graph))\n         (knowledge_graph2 (hash-ref message2 'knowledge_graph))\n         (nodes1 (hash-ref knowledge_graph1 'nodes))\n         (nodes2 (hash-ref knowledge_graph2 'nodes))\n         (edges1 (hash-ref knowledge_graph1 'edges))\n         (edges2 (hash-ref knowledge_graph2 'edges))\n         (results1 (hash-ref message1 'results))\n         (results2 (hash-ref message2 'results)))\n    ;; POSSIBLE TODO\n    ;; Might want to check that 'original-query_graph'\n    ;; is 'equal?' to the 'query_graph' in 'r1' and the\n    ;; 'query_graph' in 'r2' (to ensure we aren't trying\n    ;; to merge a response that modifies the 'query_graph'\n    ;; in creative mode, for example).\n    (hash 'message\n          (hash\n           ;;\n           'query_graph\n           original-query_graph\n           ;;\n           'knowledge_graph\n           (hash\n            'edges (merge-hash edges1 edges2)\n            ;;\n            'nodes (merge-hash nodes1 nodes2))\n           ;;\n           'auxiliary_graphs\n           (merge-hash auxiliary_graphs1 auxiliary_graphs2)\n           ;; TODO: merge results when they have the same node binding sub/obj depends on mvp\n           ;; similar with the metaKG merge\n           'results\n           (merge-list results1 results2)\n           ))))\n\n(define get-object\n  (lambda (e)\n    (match e\n      [`(,score\n         ,curie_x\n         ,pred_xy\n         ,curie_y\n         ,(? string? pred_yz)\n         ,(? string? curie_z)\n         ,props_xy\n         ,props_yz)\n       curie_z]\n      [`(,score\n         ,curie_x\n         ,pred_xy\n         ,curie_y\n         .\n         ,props_xy)\n       curie_y]\n      [else (error \"invalid form of returned edge\" e)])))\n\n(define (get-and-print-qualifiers qualifier)\n  (define qualifier-type (hash-ref qualifier 'qualifier_type_id #f))\n  (printf \"qualifier-type: ~s\\n\" qualifier-type)\n  (define qualifier-value (hash-ref qualifier 'qualifier_value #f))\n  (printf \"qualifier-value: ~s\\n\" qualifier-value)\n  (list qualifier-type qualifier-value))\n\n  \n  \n"
  },
  {
    "path": "medikanren2/neo/neo-server/neo-server.rkt",
    "content": "#lang racket/base\n\n(provide serve\n         DEFAULT_PORT)\n(require\n  \"../../logging2.rkt\"\n  \"../neo-low-level/query-low-level-multi-db.rkt\"\n  \"../neo-open-api/neo-api-query.rkt\"\n  \"../neo-reasoning/neo-biolink-reasoning.rkt\"\n  \"../neo-utils/neo-helpers-multi-db.rkt\"\n  \"neo-server-utils.rkt\"\n  racket/file\n  racket/match\n  racket/engine\n  racket/set\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  racket/tcp\n  json\n  xml\n  net/url\n  racket/list\n  racket/math\n  )\n\n;; Team Unsecret Agent mediKanren 2 neo server\n\n(define DEFAULT_PORT 8384)\n\n(define NEO_SERVER_VERSION \"1.54\")\n\n;; Maximum number of results to be returned from *each individual* KP,\n;; or from mediKanren itself.\n(define MAX_RESULTS_FROM_COMPONENT 250)\n\n;; Maximum number of results to score and then sort.\n(define MAX_RESULTS_TO_SCORE_AND_SORT 100000)\n\n(define MAX_DESCENDENT 100)\n\n;; Number of seconds before a connection times out, collecting all\n;; resources from the connection (was 10 seconds in the original\n;; tutorial).\n(define CONNECTION_TIMEOUT_SECONDS (* 58 60))\n(define API_CALL_CONNECTION_TIMEOUT_SECONDS (* 1 60))\n\n;; Numbers of the top bucket of the RoboKop KG, Text Mining KG, and RTX-KG2 KG.\n(define TOP_BUCKET_NUMBERS (list (list (get-highest-bucket-number-robokop))\n                                 (list (get-highest-bucket-number-text-mining))\n                                 (list (get-highest-bucket-number-rtx-kg2))))\n\n(define GENERAL-NODES\n  (curies->synonyms\n   '(\"UMLS:C0017337\" ; Genes\n     \"UMLS:C0005522\" ; Biological Products\n     \"UMLS:C1611640\" ; Therapeutic agent (substance)\n     \"MESH:D020218\" ; Response elements\n     \"UMLS:C0162327\" ; RNA Sequence\n     \"PUBCHEM.COMPOUND:135499568\" ; Double stranded RNA\n     \"UMLS:C1099354\" ; RNA, Small Interfering\n     \"UMLS:C0376613\" ; \"Vaccines, DNA\"\n     \"MESH:D004798\" ; Enzymes\n     )))\n\n;; Unsecret-level excluded MVP1 results - answers that is obviously wrong/useless\n(define UNWELCOME-TREATMENT\n  (append \n   (curies->synonyms\n    '(\n      \"MESH:D001335\" ; Vehicle emissions\n      \"UMLS:C0013227\" ; Pharmaceutical preparations\n      \"MESH:D014028\" ; tobacco smoke pollution\n      ))\n   GENERAL-NODES\n   ))\n\n\n\n\n;; ** `tcp-listen` settings **\n;;\n;; From the Racket documentation for `tcp-listen` in\n;; https://docs.racket-lang.org/reference/tcp.html:\n;;\n;; \"The max-allow-wait argument determines the maximum number of\n;; client connections that can be waiting for acceptance. (When\n;; max-allow-wait clients are waiting acceptance, no new client\n;; connections can be made.)\"\n(define MAX_ALLOW_WAIT 5)\n;; \"If the reuse? argument is true, then tcp-listen will create a\n;; listener even if the port is involved in a TIME_WAIT state. Such a\n;; use of reuse? defeats certain guarantees of the TCP protocol; see\n;; Stevens’s book for details. Furthermore, on many modern platforms,\n;; a true value for reuse? overrides TIME_WAIT only if the listener\n;; was previously created with a true value for reuse?.\"\n(define REUSE_LISTENER_WHILE_IN_TIME_WAIT_STATE #f)\n;; \"If hostname is #f (the default), then the listener accepts\n;; connections to all of the listening machine’s addresses. Otherwise,\n;; the listener accepts connections only at the interface(s)\n;; associated with the given hostname. For example, providing\n;; \"127.0.0.1\" as hostname creates a listener that accepts only\n;; connections to \"127.0.0.1\" (the loopback interface) from the local\n;; machine.\"\n(define ONLY_ACCEPT_CONNECTIONS_FROM_GIVEN_HOSTNAME #f)\n\n(define MAX_POST_REQUEST_CONTENT_LENGTH 100000)\n\n;; HTTP header strings\n(define HTTP_VERSION_STRING \"HTTP/1.0\")\n(define SERVER_STRING \"Server: k\")\n(define 200_OK_STRING \"200 OK\")\n(define 408_ERROR_STRING \"408 Request Timeout\")\n(define 500_ERROR_STRING \"500 Internal Server Error\")\n(define 501_ERROR_STRING \"501 Not Implemented Error\")\n\n(define-runtime-path path:root \".\")\n(define (path/root relative-path) (build-path path:root relative-path))\n\n(define schema.json.txt\n  (file->string (path/root \"../neo-open-api/mediKanrenSmartAPI_1_4.json\")))\n(define schema.yaml.txt\n  (file->string (path/root \"../neo-open-api/mediKanrenSmartAPI_1_4.yaml\")))\n(define metaKG.json.txt\n  (file->string (path/root \"../neo-open-api/unsecret_metaKG_May_2023.json\")))\n\n;; Environment variables (contained in boxes)\n(define ENVIRONMENT_TAG_BOX (box #f)) ;; Should be one of \"CI\", \"TEST\", or \"PROD\", if not #f\n(define MK_STAGE_BOX (box #f)) ;; deprecated (5 April 2023)\n;; (should be removed, once ENVIRONMENT_TAG_BOX is shown to work)\n\n(struct job-failure (message))\n\n(define job-request (make-channel))\n(define *jobs-waiting* 0)\n\n(define (work-safely work)\n  (printf \"entered work-safely\\n\")\n  (let ((result (work)))\n    ;; (printf \"work-safely returning result ~s\\n\" result)\n    result))\n\n;; Run multiple jobs concurrently\n;(define (job work) (work-safely work))\n\n;; Run multiple jobs sequentially\n(define (job work)\n  (define job-response (make-channel))\n  (printf \"job is calling channel-put on job-request channel\\n\")\n  (set! *jobs-waiting* (add1 *jobs-waiting*))\n  (printf \"^ ~s job(s) in job queue\\n\"\n          *jobs-waiting*)\n  (channel-put job-request (cons job-response work))\n  (printf \"job is calling channel-get on job-response channel\\n\")\n  (let ((response (channel-get job-response)))\n    (set! *jobs-waiting* (sub1 *jobs-waiting*))\n    (printf \"work returned response from job-reponse channel\\n\")\n    (printf \"^ ~s job(s) remaining in job queue\\n\"\n            *jobs-waiting*)\n    response))\n\n(define (serve port-no)\n  (define listener\n    (tcp-listen port-no\n                MAX_ALLOW_WAIT\n                REUSE_LISTENER_WHILE_IN_TIME_WAIT_STATE\n                ONLY_ACCEPT_CONNECTIONS_FROM_GIVEN_HOSTNAME))\n  (define (worker)\n    (let loop ()\n      (printf \"worker is about to call channel-get on job-request\\n\")\n      (match-define (cons job-response work) (channel-get job-request))\n      (printf \"worker is about to call channel-put on job-response\\n\")\n      (channel-put job-response (work-safely work))\n      (loop)))\n  (define (loop)\n    (accept-and-handle listener)\n    (loop))\n  (thread worker)\n  (thread loop))\n\n(define (accept-and-handle listener)\n  (define cust.accept-and-handle (make-custodian))\n  (parameterize ((current-custodian cust.accept-and-handle))\n    (define-values (in out) (tcp-accept listener))\n    (printf \"\\ntcp-accept accepted connection\\n\")\n\n    ;; main accept-and-handle thread\n    (thread\n     (lambda ()\n\n       (define start-time-ms-realtime (current-inexact-milliseconds))\n       (define timeout-ms-realtime\n         (+ start-time-ms-realtime (* CONNECTION_TIMEOUT_SECONDS 1000)))\n\n       (let ((result\n              (call/cc\n               (lambda (break)\n                 (with-handlers\n                     ;; Don't send HTTP replies with these\n                     ;; unexpected errors, to avoid errors from\n                     ;; writing to ports which are closed.\n                     ((exn:fail:network:errno?\n                       (lambda (ex)\n                         (cond\n                           ((equal? '(110 . posix) (exn:fail:network:errno-errno ex))\n                            (printf \"!!! Error: TCP keepalive failed.\\n\")\n                            (printf \"    Presuming half-open TCP connection.\\n\")\n                            (break 'tcp-keepalive-failed))\n                           (else\n                            (printf \"!!! Error: Unknown network error ~a.\\n\" ex)\n                            (break 'unknown-network-error)))))\n                      (exn:fail?\n                       (lambda (v)\n                         (printf \"!! exn:fail? handler called\\n\")\n                         ((error-display-handler) (exn-message v) v)\n                         (break 'exn:fail?-handler-called)))\n                      ((lambda _ #t)\n                       (lambda (v)\n                         (printf \"!! Unknown error handler called from job engine\\n\")\n                         (printf \"Unknown error: ~s\\n\" v)\n                         (break 'unknown-error))))\n                   (let ((result\n                          (handle in out\n                                  start-time-ms-realtime\n                                  timeout-ms-realtime\n                                  (lambda ()\n                                    (printf \"** Connection failure continuation invoked!\\n\")\n                                    (break 'connection-failure))\n                                  (lambda ()\n                                    (printf \"** Request failure continuation invoked!\\n\")\n                                    (break 'request-failure)))))\n                     (printf \"`handle` call in `engine-proc` finished cleanly\\n\")\n                     result))))))\n\n         (printf \"handle returned result ~s\\n\" result)\n\n         (printf \"(current-memory-use): ~s\\n\"\n                 (current-memory-use))\n         (printf \"calling (collect-garbage)\\n\")\n         (collect-garbage)\n         (printf \"(current-memory-use): ~s\\n\"\n                 (current-memory-use))\n\n         (printf \"main accept-and-handle thread about to shut-down cust.accept-and-handle\\n\")\n         (custodian-shutdown-all cust.accept-and-handle)\n\n         (printf \"(current-memory-use): ~s\\n\"\n                 (current-memory-use))\n         (printf \"calling (collect-garbage)\\n\")\n         (collect-garbage)\n         (printf \"(current-memory-use): ~s\\n\"\n                 (current-memory-use)))))))\n\n(define (get-request-headers in)\n  (define request-headers (make-hash))\n  (printf \"getting request headers\\n\")\n  (let loop ()\n    (define current-line-match (regexp-match #rx\"[^\\r\\n]*\\r\\n\" in))\n    (if (not current-line-match)\n        (begin\n          (printf \"** error parsing request headers: current line doesn't end properly\\n\")\n          #f)\n        (let ((current-line (list-ref current-line-match 0)))\n          (printf \"current-line:\\n~s\\n\" current-line)\n          (cond\n            [(regexp-match #rx\"^([^:]+:) (.+)\\r\\n\" current-line)\n             =>\n             (lambda (header)\n               ;(printf \"== header:\\n~s\\n\" header)\n               ;(printf \"== (list-ref header 1):\\n~s\\n\" (list-ref header 1))\n               ;(printf \"== (list-ref header 2):\\n~s\\n\" (list-ref header 1))\n               (hash-set! request-headers\n                          (bytes->string/utf-8 (list-ref header 1))\n                          (bytes->string/utf-8 (list-ref header 2)))\n               (printf \"== request-headers:\\n~s\\n\\n\" request-headers)\n               (loop))]\n            [(regexp-match #px\"^[[:space:]]*\\r\\n\" current-line)\n             (printf \"parsed request headers:\\n~s\\n\" request-headers)\n             request-headers]\n            [else\n             (printf \"** error parsing request headers: ~s\\n\" current-line)\n             #f])))))\n\n(define (get-request-body in content-length)\n  (define bytes (read-bytes content-length in))\n  (if (eof-object? bytes)\n      #f\n      (bytes->string/utf-8 bytes)))\n\n(define (send-reply dispatch-result out)\n  (begin\n    (match dispatch-result\n      [`(text ,respose-code ,text)\n       (printf \"sending text reply\\n\")\n       (display HTTP_VERSION_STRING out)\n       (display \" \" out)\n       (display respose-code out)\n       (display \"\\r\\n\" out)\n       (display SERVER_STRING out)\n       (display \"\\r\\n\" out)\n       (display \"Content-Type: text/plain\\r\\n\\r\\n\" out)\n       (display text out)]\n      [`(json ,respose-code ,jsexpr)\n       (printf \"sending JSON reply\\n\")\n       (display HTTP_VERSION_STRING out)\n       (display \" \" out)\n       (display respose-code out)\n       (display \"\\r\\n\" out)\n       (display SERVER_STRING out)\n       (display \"\\r\\n\" out)\n       (display \"Content-Type: application/json\\r\\n\\r\\n\" out)\n       (display (jsexpr->string jsexpr) out)\n       #;(pretty-print-json-string (jsexpr->string jsexpr) out)]\n      [`(xexpr ,respose-code ,xexpr)\n       (printf \"sending HTML reply\\n\")\n       (display HTTP_VERSION_STRING out)\n       (display \" \" out)\n       (display respose-code out)\n       (display \"\\r\\n\" out)\n       (display SERVER_STRING out)\n       (display \"\\r\\n\" out)\n       (display \"Content-Type: text/html\\r\\n\\r\\n\" out)\n       (display (xexpr->string xexpr) out)]\n      [else\n       (printf \"unknown dispatch-result type:\\n~s\\n\" dispatch-result)\n       (display HTTP_VERSION_STRING out)\n       (display \" \" out)\n       (display 500_ERROR_STRING out)\n       (display \"\\r\\n\" out)])\n    (flush-output out)))\n\n;; Try to get the value for a given key from the hash table of\n;; headers.  This is a little subtle, since the header keys are case\n;; insensitive, yet hash table lookup is case senstitive.  This\n;; function returns #f if no entry could be found for the given key\n;; string (in a case-insensitive manner).  Otherwise, the function\n;; returns the value.\n(define (get-key/value-from-headers key-name-str req-headers-hash)\n  (define keys (hash-keys req-headers-hash))\n  (define lowercase/original-keys\n    (map (lambda (key) (cons (string-downcase key) key)) keys))\n  (define pr (assoc (string-downcase key-name-str) lowercase/original-keys))\n  (if pr\n      (let ((actual-key (cdr pr)))\n        (let ((value (hash-ref req-headers-hash actual-key)))\n          value))\n      #f))\n\n;; `conn-fk` is a failure continuation to be invoked upon unexpected\n;; closing of the TCP connection, or due to a networking error.  The\n;; failure continuation should not be invoked for request that can not\n;; be handled due to an unknown request type or to a failure to\n;; respond to the request that can be handled gracefully (with a\n;; response error code and message).\n;;\n;; `request-fk` is a failure continuation to be invoked if the request\n;; is malformed, incomplete, or non-sensical, such as a request not\n;; being parsable, or a `query` POST not containing `Content-Type` or\n;; `Content-Length` information, `Content-Length` that isn't legal, or\n;; a body that can't be parsed as JSON.\n(define (handle in out\n                start-time-ms-realtime\n                timeout-ms-realtime\n                conn-fk request-fk)\n  (define first-input-line (read-line in))\n  (printf \"handling request:\\n~s\\n\" first-input-line)\n\n  (define get/post-req\n    (regexp-match #rx\"^(GET|POST) (.+) HTTP/[0-9]+\\\\.[0-9]+\"\n                  first-input-line))\n\n  (when get/post-req\n    (let ((request-type (list-ref get/post-req 1))\n          (str-path (list-ref get/post-req 2)))\n      (define req-headers (get-request-headers in))\n      (when req-headers\n        ;; Detect half-closed TCP connections with eof-evt on the input port\n        (with-handlers\n            ((exn:fail:network:errno?\n              (lambda (ex)\n                (cond\n                  ((equal? '(110 . posix) (exn:fail:network:errno-errno ex))\n                   (printf \"Error: TCP keepalive failed.  Presuming half-open TCP connection.\\n\")\n                   (conn-fk))\n                  (else\n                   (printf \"Error: Unknown network error ~a.\\n\" ex)\n                   (conn-fk))))))\n          (match request-type\n            [\"GET\"\n             ;; Dispatch GET request:\n             (let ([dispatch-result (dispatch-request 'GET\n                                                      str-path\n                                                      req-headers\n                                                      in out\n                                                      start-time-ms-realtime\n                                                      timeout-ms-realtime\n                                                      request-fk)])\n               (printf \"dispatch-result:\\n~s\\n\" dispatch-result)\n\n               ;; Send reply:\n               (send-reply dispatch-result out))]\n            [\"POST\"\n             (printf \"handling POST request\\n\")\n\n             (printf \"req-headers:\\n~s\\n\" req-headers)\n\n             (define content-length-string\n               (get-key/value-from-headers \"Content-Length:\" req-headers))\n\n             (unless content-length-string\n               (printf \"** error: POST request doesn't include 'Content-Length:'\\n\")\n               (request-fk))\n\n             (define content-length (string->number content-length-string))\n             (printf \"Content-Length as a number:\\n~s\\n\" content-length)\n\n             (unless (and (integer? content-length)\n                          (<= 0 content-length)\n                          (<= content-length MAX_POST_REQUEST_CONTENT_LENGTH))\n               (printf \"** error: bad POST content length: ~s\\n\" content-length)\n               (request-fk))\n\n             (define content-type-string\n               (get-key/value-from-headers \"Content-Type:\" req-headers))\n\n             (unless content-type-string\n               (printf \"** error: POST request doesn't include 'Content-Type:'\\n\")\n               (request-fk))\n\n             (printf \"Content-Type:\\n~s\\n\" content-type-string)\n\n             (define body-str (get-request-body in content-length))\n             (printf \"body-str:\\n~s\\n\" body-str)\n\n             (unless body-str\n               (printf \"** error: unable to get the body of POST request\\n\")\n               (request-fk))\n\n             (let ([dispatch-result (dispatch-request 'POST\n                                                      str-path\n                                                      req-headers\n                                                      in out\n                                                      start-time-ms-realtime\n                                                      timeout-ms-realtime\n                                                      request-fk\n                                                      ;;\n                                                      content-type-string\n                                                      content-length-string\n                                                      body-str)])\n               ;; (printf \"dispatch-result:\\n~s\\n\" dispatch-result)\n               (printf \"about to send reply\\n\")\n\n               ;; Send reply:\n               (send-reply dispatch-result out))]))))))\n\n;; dispatch for HTTP GET and POST requests\n(define (dispatch-request request-type\n                          str-path\n                          req-headers\n                          in out\n                          start-time-ms-realtime\n                          timeout-ms-realtime\n                          request-fk\n                          . rest-args)\n\n  ;; Parse the request as a URL:\n  (define url (string->url str-path))\n  ;; Extract the path part:\n  (define path (map path/param-path (url-path url)))\n  ;; Find a handler based on the path's first element:\n  (define dispatch-key (list request-type (car path)))\n  (define h/safe? (hash-ref dispatch-table dispatch-key #f))\n  (define h (and h/safe? (car h/safe?)))\n  (define safe-for-concurrent-use?\n    (and h/safe?\n         (eq? (cdr h/safe?) 'safe-for-concurrent-use)))\n  (printf \"dispatch-key: ~s\\n\" dispatch-key)\n  ;(printf \"dispatch-table: ~s\\n\" dispatch-table)\n  (printf \"h/safe?: ~s\\n\" h/safe?)\n  (printf \"h: ~s\\n\" h)\n  (printf \"safe-for-concurrent-use?: ~s\\n\" safe-for-concurrent-use?)\n  (printf \"url: ~s\\n\" url)\n  (printf \"path: ~s\\n\" path)\n  (printf \"url-query: ~s\\n\" (url-query url))\n  ;(printf \"req-headers: ~s\\n\" req-headers)\n  ;(printf \"rest-args: ~s\\n\" rest-args)\n  (newline)\n\n  (cond\n    ((not h)\n     (printf \"!! No handler found !!\\n\")\n     (list\n       'xexpr\n       `(html (head (title \"Error\"))\n              (body\n               (font ((color \"red\"))\n                     \"Unknown page: \"\n                     ,str-path)))))\n    (safe-for-concurrent-use?\n     (printf \"handler is safe for concurrent use\\n\")\n     ;; Call the handler, without using the job channels:\n     (apply h (url-query url) req-headers request-fk rest-args))\n    (else\n     (printf \"handler is *not* safe for concurrent use\\n\")\n     ;; Call the handler, using the job channels:\n     (define result/cust.job\n       (job\n        (lambda ()\n          (printf \"job-thunk invoked\\n\")\n\n          (printf \"(current-memory-use): ~s\\n\"\n                  (current-memory-use))\n          (printf \"calling (collect-garbage)\\n\")\n          (collect-garbage)\n          (printf \"(current-memory-use): ~s\\n\"\n                  (current-memory-use))\n\n          (define cust.job (make-custodian))\n          (parameterize ((current-custodian cust.job))\n\n            (define ENGINE_GAS_MS (* 1 1000))\n\n            (define eng\n              (engine\n               (lambda (suspend-proc)\n                 ;; apply the request handler\n                 (apply h (url-query url) req-headers request-fk rest-args))))\n\n            (with-handlers\n                ((exn:fail:network:errno?\n                  (lambda (ex)\n                    (cond\n                      ((equal? '(110 . posix) (exn:fail:network:errno-errno ex))\n                       (printf \"!!! Error: TCP keepalive failed.\\n\")\n                       (printf \"    Presuming half-open TCP connection.\\n\")\n                       (engine-kill eng)\n                       (cons\n                        (list\n                          'xexpr\n                          `(html (head (title \"Error\"))\n                                 (body\n                                  (font ((color \"red\"))\n                                        \"Error: TCP keepalive failed for: \"\n                                        ,str-path))))\n                        cust.job))\n                      (else\n                       (printf \"!!! Error: Unknown network error ~a.\\n\" ex)\n                       (engine-kill eng)\n                       (cons\n                        (list\n                          'xexpr\n                          `(html (head (title \"Error\"))\n                                 (body\n                                  (font ((color \"red\"))\n                                        \"Unknown network error for: \"\n                                        ,str-path))))\n                        cust.job)))\n                    ))\n                 (exn:fail?\n                  (lambda (v)\n                    (printf \"!! exn:fail? handler called from job engine\\n\")\n                    ((error-display-handler) (exn-message v) v)\n                    (engine-kill eng)\n                    (cons\n                     (list\n                       'xexpr\n                       `(html (head (title \"Error\"))\n                              (body\n                               (font ((color \"red\"))\n                                     \"Internal error for: \"\n                                     ,str-path))))\n                     cust.job)))\n                 ((lambda _ #t)\n                  (lambda (v)\n                    (printf \"!! Unknown error handler called from job engine\\n\")\n                    (printf \"Unknown error: ~s\\n\" v)\n                    (engine-kill eng)\n                    (cons\n                     (list\n                       'xexpr\n                       `(html (head (title \"Error\"))\n                              (body\n                               (font ((color \"red\"))\n                                     \"Internal error for: \"\n                                     ,str-path))))\n                     cust.job))))\n\n              (define unexpected-eof-evt\n                (eof-evt in))\n\n              (let loop-forever ()\n\n                (define engine-ran-out-of-gas-evt\n                  (alarm-evt (+ (current-inexact-milliseconds)\n                                ENGINE_GAS_MS)))\n\n                (define end-evt\n                  (choice-evt\n                   unexpected-eof-evt\n                   engine-ran-out-of-gas-evt))\n\n                (let* ((finished? (engine-run end-evt eng))\n                       (now-ms-realtime (current-inexact-milliseconds))\n                       (elapsed-seconds-realtime\n                        (inexact->exact\n                         (round\n                          (/ (- now-ms-realtime start-time-ms-realtime) 1000.0))))\n                       (current-mem (current-memory-use)))\n                  (cond\n                    (finished?\n                     (printf \"- Engine ran to completion (~s ~s)\\n\"\n                             elapsed-seconds-realtime\n                             current-mem)\n                     ;; Make sure to stop the engine.\n                     (engine-kill eng)\n                     (cons (engine-result eng) cust.job))\n                    (else\n                     ;; Engine returned because an event in\n                     ;; end-evt became ready for\n                     ;; synchronization, rather than from the\n                     ;; engine's procedure running to\n                     ;; completion.  Perform a case analysis on\n                     ;; the event that became ready for\n                     ;; synchronization.\n                     (let ((evt (sync end-evt)))\n                       (cond\n                         ((or (eof-object? evt)\n                              (eq? unexpected-eof-evt evt))\n                          (printf\n                           \"!!! Error: Detected half-closed TCP connection (~s ~s)\\n\"\n                           elapsed-seconds-realtime\n                           current-mem)\n                          (engine-kill eng)\n                          (cons\n                           (list\n                             'xexpr\n                             500_ERROR_STRING\n                             `(html\n                               (body\n                                \"Error: TCP keepalive failed.  Presuming half-open TCP connection.\")))\n                           cust.job))\n                         ((eq? engine-ran-out-of-gas-evt evt)\n                          (cond\n                            ((> now-ms-realtime timeout-ms-realtime)\n                             (printf\n                              \"!!! Computation timed out (~s ~s)\\n\"\n                              elapsed-seconds-realtime\n                              current-mem)\n                             (engine-kill eng)\n                             (cons\n                              (list\n                                'xexpr\n                                408_ERROR_STRING\n                                `(html\n                                  (body\n                                   \"Error: Request timeout.\")))\n                              cust.job))\n                            (else\n                             (printf \".(~s ~s) \"\n                                     elapsed-seconds-realtime\n                                     current-mem)\n                             (flush-output)\n                             (loop-forever))))\n                         (else\n                          (printf \"Unexpected value of `(sync end-evt)` (~s ~s): ~s\"\n                                  elapsed-seconds-realtime\n                                  current-mem\n                                  evt)\n                          (engine-kill eng)\n                          (cons\n                           (list\n                             'xexpr\n                             `(html (head (title \"Error\"))\n                                    (body\n                                     (font ((color \"red\"))\n                                           \"Internal error for: \"\n                                           ,str-path))))\n                           cust.job)))))))))))))\n     (define result (car result/cust.job))\n     (define cust.job (cdr result/cust.job))\n     (printf \"about to call (custodian-shutdown-all cust.job)\\n\")\n     (custodian-shutdown-all cust.job)\n     (if result\n         result\n         (begin\n           (printf \"job returned #f as the result\\n\")\n           (list\n             'xexpr\n             `(html (head (title \"Error\"))\n                    (body\n                     (font ((color \"red\"))\n                           \"Internal error for : \"\n                           ,str-path)))))))))\n\n(define (mvp-creative-query? edges nodes)\n\n  (define edge* (hash->list edges))\n  (printf \"edge*: ~s\\n\" edge*)\n\n  (match edge*\n    ;; exactly one edge\n    [`((,edge-id . ,edge-hash))\n     (define knowledge_type (hash-ref edge-hash 'knowledge_type #f))\n     (printf \"knowledge_type: ~s\\n\" knowledge_type)\n\n     (define predicates (hash-ref edge-hash 'predicates #f))\n     (printf \"predicates: ~s\\n\" predicates)\n\n     (define subject-id (hash-ref edge-hash 'subject #f))\n     (define object-id (hash-ref edge-hash 'object #f))\n\n     (define subject-node (hash-ref nodes (string->symbol subject-id) #f))\n     (define object-node (hash-ref nodes (string->symbol object-id) #f))\n\n     (printf \"subject-node: ~s\\n\" subject-node)\n     (printf \"object-node: ~s\\n\" object-node)\n\n     (cond\n       [(and (equal? \"inferred\" knowledge_type)\n             (list? predicates)\n             (member \"biolink:treats\" predicates)\n             subject-node\n             object-node\n             (let ()\n               (define object-ids (hash-ref object-node 'ids #f))\n               (printf \"object-ids: ~s\\n\" object-ids)\n               (and (list? object-ids)\n                    (not (null? object-ids))\n                    (let ()\n                      (define subject-categories (hash-ref subject-node 'categories #f))\n                      (printf \"subject-categories: ~s\\n\" subject-categories)\n                      (and (list? subject-categories)\n                           (member \"biolink:ChemicalEntity\" subject-categories)\n                           (let ()\n                             (define object-categories (hash-ref object-node 'categories #f))\n                             (printf \"object-categories: ~s\\n\" object-categories)\n\n                             (or (not object-categories)\n                                 (and (list? object-categories)\n                                      (member \"biolink:Disease\" object-categories)))))))))\n        'mvp1]\n       [(and (equal? \"inferred\" knowledge_type)\n             (list? predicates)\n             (member \"biolink:affects\" predicates)\n             subject-node\n             object-node\n             (let ()\n               (define object-ids (hash-ref object-node 'ids #f))\n               (and (list? object-ids)\n                    (not (null? object-ids))\n                    (let ()\n                      (printf \"object-ids: ~s\\n\" object-ids)\n                      (define subject-categories (hash-ref subject-node 'categories #f))\n                      (printf \"subject-categories: ~s\\n\" subject-categories)\n\n                      (and (list? subject-categories)\n                           (member \"biolink:ChemicalEntity\" subject-categories)\n                           (let ()\n                             (define object-categories (hash-ref object-node 'categories #f))\n                             (printf \"object-categories: ~s\\n\" object-categories)\n                             (and (list? object-categories)\n                                  (member \"biolink:Gene\" object-categories)\n                                  (let ()\n                                    (define qualifier-constraints (hash-ref edge-hash 'qualifier_constraints #f))\n                                    (and qualifier-constraints\n                                         (list? qualifier-constraints)\n                                         ; only one type of qualifier-constraints and it is the qualifer set\n                                         (eq? 1 (length qualifier-constraints))\n                                         (let ()\n                                           (define qualifier-set (hash-ref (car qualifier-constraints) 'qualifier_set #f))\n                                           (and qualifier-set\n                                                (list? qualifier-set)\n                                                (eq? 3 (length qualifier-set))\n                                                (let ()\n                                                  (match-define\n                                                    (list qualifier-a-type qualifier-a-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 0)))\n                                                  (match-define\n                                                    (list qualifier-b-type qualifier-b-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 1)))\n                                                  (match-define\n                                                    (list qualifier-c-type qualifier-c-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 2)))\n                                                  (define expected-qualifiers (list \"biolink:object_aspect_qualifier\"\n                                                                                    \"biolink:object_direction_qualifier\"\n                                                                                    \"biolink:qualified_predicate\"))\n                                                  (and qualifier-a-type\n                                                       qualifier-a-value\n                                                       qualifier-b-type\n                                                       qualifier-b-value\n                                                       qualifier-c-type\n                                                       qualifier-c-value\n                                                       (member qualifier-a-type expected-qualifiers)\n                                                       (member qualifier-b-type expected-qualifiers)\n                                                       (member qualifier-c-type expected-qualifiers))))))))))))))\n        'mvp2-gene]\n       [(and (equal? \"inferred\" knowledge_type)\n             (list? predicates)\n             (member \"biolink:affects\" predicates)\n             subject-node\n             object-node\n             (let ()\n               (define object-ids (hash-ref object-node 'ids #f))\n               (and (list? object-ids)\n                    (not (null? object-ids))\n                    (let ()\n                      (printf \"object-ids: ~s\\n\" object-ids)\n                      (define subject-categories (hash-ref subject-node 'categories #f))\n                      (printf \"subject-categories: ~s\\n\" subject-categories)\n\n                      (and (list? subject-categories)\n                           (member \"biolink:ChemicalEntity\" subject-categories)\n                           (let ()\n                             (define object-categories (hash-ref object-node 'categories #f))\n                             (printf \"object-categories: ~s\\n\" object-categories)\n                             (and (list? object-categories)\n                                  (member \"biolink:Gene\" object-categories)\n                                  (let ()\n                                    (define qualifier-constraints (hash-ref edge-hash 'qualifier_constraints #f))\n                                    (and qualifier-constraints\n                                         (list? qualifier-constraints)\n                                         ; only one type of qualifier-constraints and it is the qualifer set\n                                         (eq? 1 (length qualifier-constraints))\n                                         (let ()\n                                           (define qualifier-set (hash-ref (car qualifier-constraints) 'qualifier_set #f))\n                                           (and qualifier-set\n                                                (list? qualifier-set)\n                                                (eq? 2 (length qualifier-set))\n                                                (let ()\n                                                  (match-define\n                                                    (list qualifier-a-type qualifier-a-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 0)))\n                                                  (match-define\n                                                    (list qualifier-b-type qualifier-b-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 1)))\n                                                  (define expected-qualifiers (list \"biolink:object_aspect_qualifier\"\n                                                                                    \"biolink:object_direction_qualifier\"))\n                                                  (and qualifier-a-type\n                                                       qualifier-a-value\n                                                       qualifier-b-type\n                                                       qualifier-b-value\n                                                       (member qualifier-a-type expected-qualifiers)\n                                                       (member qualifier-b-type expected-qualifiers))))))))))))))\n        'mvp2-gene]\n       [(and (equal? \"inferred\" knowledge_type)\n             (list? predicates)\n             (member \"biolink:affects\" predicates)\n             subject-node\n             object-node\n             (let ()\n               (define subject-ids (hash-ref subject-node 'ids #f))\n               (and (list? subject-ids)\n                    (not (null? subject-ids))\n                    (let ()\n                      (printf \"subject-ids: ~s\\n\" subject-ids)\n                      (define subject-categories (hash-ref subject-node 'categories #f))\n                      (printf \"subject-categories: ~s\\n\" subject-categories)\n\n                      (and (list? subject-categories)\n                           (member \"biolink:ChemicalEntity\" subject-categories)\n                           (let ()\n                             (define object-categories (hash-ref object-node 'categories #f))\n                             (printf \"object-categories: ~s\\n\" object-categories)\n\n                             (and (list? object-categories)\n                                  (member \"biolink:Gene\" object-categories)\n                                  (let ()\n                                    (define qualifier-constraints (hash-ref edge-hash 'qualifier_constraints #f))\n                                    (and qualifier-constraints\n                                         (list? qualifier-constraints)\n                                         ; only one type of qualifier-constraints and it is the qualifer set\n                                         (eq? 1 (length qualifier-constraints))\n                                         (let ()\n                                           (define qualifier-set (hash-ref (car qualifier-constraints) 'qualifier_set #f))\n                                           (and qualifier-set\n                                                (list? qualifier-set)\n                                                (eq? 3 (length qualifier-set))\n                                                (let ()\n                                                  (match-define\n                                                    (list qualifier-a-type qualifier-a-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 0)))\n                                                  (match-define\n                                                    (list qualifier-b-type qualifier-b-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 1)))\n                                                  (match-define\n                                                    (list qualifier-c-type qualifier-c-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 2)))\n                                                  (define expected-qualifiers (list \"biolink:object_aspect_qualifier\"\n                                                                                    \"biolink:object_direction_qualifier\"\n                                                                                    \"biolink:qualified_predicate\"))       \n                                                  (and qualifier-a-type\n                                                       qualifier-a-value\n                                                       qualifier-b-type\n                                                       qualifier-b-value\n                                                       qualifier-c-type\n                                                       qualifier-c-value\n                                                       (member qualifier-a-type expected-qualifiers)\n                                                       (member qualifier-b-type expected-qualifiers)\n                                                       (member qualifier-c-type expected-qualifiers))))))))))))))\n        'mvp2-chem]\n       [(and (equal? \"inferred\" knowledge_type)\n             (list? predicates)\n             (member \"biolink:affects\" predicates)\n             subject-node\n             object-node\n             (let ()\n               (define subject-ids (hash-ref subject-node 'ids #f))\n               (and (list? subject-ids)\n                    (not (null? subject-ids))\n                    (let ()\n                      (printf \"subject-ids: ~s\\n\" subject-ids)\n                      (define subject-categories (hash-ref subject-node 'categories #f))\n                      (printf \"subject-categories: ~s\\n\" subject-categories)\n\n                      (and (list? subject-categories)\n                           (member \"biolink:ChemicalEntity\" subject-categories)\n                           (let ()\n                             (define object-categories (hash-ref object-node 'categories #f))\n                             (printf \"object-categories: ~s\\n\" object-categories)\n\n                             (and (list? object-categories)\n                                  (member \"biolink:Gene\" object-categories)\n                                  (let ()\n                                    (define qualifier-constraints (hash-ref edge-hash 'qualifier_constraints #f))\n                                    (and qualifier-constraints\n                                         (list? qualifier-constraints)\n                                         ; only one type of qualifier-constraints and it is the qualifer set\n                                         (eq? 1 (length qualifier-constraints))\n                                         (let ()\n                                           (define qualifier-set (hash-ref (car qualifier-constraints) 'qualifier_set #f))\n                                           (and qualifier-set\n                                                (list? qualifier-set)\n                                                (eq? 2 (length qualifier-set))\n                                                (let ()\n                                                  (match-define\n                                                    (list qualifier-a-type qualifier-a-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 0)))\n                                                  (match-define\n                                                    (list qualifier-b-type qualifier-b-value)\n                                                    (get-and-print-qualifiers (list-ref qualifier-set 1)))\n                                                  (define expected-qualifiers (list \"biolink:object_aspect_qualifier\"\n                                                                                    \"biolink:object_direction_qualifier\"))\n                                                  (and qualifier-a-type\n                                                       qualifier-a-value\n                                                       qualifier-b-type\n                                                       qualifier-b-value\n                                                       (member qualifier-a-type expected-qualifiers)\n                                                       (member qualifier-b-type expected-qualifiers))))))))))))))\n        'mvp2-chem]\n       [else #f])]\n\n    [else #f]))\n\n(define (make-empty-trapi-response)\n    (hash\n     'message\n     (hash\n      ;;\n      'auxiliary_graphs\n      (hash)\n      ;;\n      'query_graph\n      (hash)\n      ;;\n      'knowledge_graph\n      (hash 'nodes (hash)\n            'edges (hash))\n      ;;\n      ;;'results\n      ;;'()\n      )))\n\n(define (make-score-result num-results)\n  (lambda (result index)\n    (- num-results index)))\n\n(define (score-results results)\n  (let ((n (length results)))\n    (let ((score-one-result (make-score-result n)))\n      (map (lambda (h i) (set-score-in-result h (score-one-result h i))) results (iota n)))))\n\n(define (excluded-semmed-edge? prop)\n  (let ((source (get-assoc \"primary_knowledge_source\" prop))) ;only rkx-kg2 has semmed edge\n    (and (equal? source \"infores:semmeddb\")\n         (let* ((sub (get-assoc \"subject\" prop))\n                (sub-cat (car (list-assoc \"category\" (curie->properties sub))))\n                (obj (get-assoc \"object\" prop))\n                (obj-cat (car (list-assoc \"category\" (curie->properties obj))))\n                (pred (get-assoc \"predicate\" prop))\n                (semantic-pat-obj (list #f #f obj-cat))\n                (semantic-pat-sub (list sub-cat #f #f))\n                (domain-pat (list sub-cat pred #f))\n                (range-pat (list #f pred obj-cat)))\n           (or (member semantic-pat-obj semantic-exclude*)\n               (member semantic-pat-sub semantic-exclude*)\n               (member domain-pat domain-exclude*)\n               (member range-pat range-exclude*))))))\n\n(define (not-semmed-excluded? e)\n  (match e\n    [`(,curie_x\n       ,pred_xy\n       ,curie_y\n       ,(? string? pred_yz)\n       ,(? string? curie_z)\n       ,props_xy\n       ,props_yz)\n     (and (not (excluded-semmed-edge? props_xy))\n          (not (excluded-semmed-edge? props_yz)))]\n    [`(,curie_x\n       ,pred_xy\n       ,curie_y\n       .\n       ,props_xy)\n     (not (excluded-semmed-edge? props_xy))]))\n\n(define (not-general-connector? e)\n  (match e\n    [`(,curie_x\n       ,pred_xy\n       ,curie_y\n       ,(? string? pred_yz)\n       ,(? string? curie_z)\n       ,props_xy\n       ,props_yz)\n     (not (member curie_y GENERAL-NODES))]))\n\n(define (not-unwelcome-answer-as-subject? e)\n  (not (member (car e) UNWELCOME-TREATMENT)))\n\n(define (not-unwelcome-answer-as-object? e)\n  (let ((object (match e\n                  [`(,curie_x\n                     ,pred_xy\n                     ,curie_y\n                     ,(? string? pred_yz)\n                     ,(? string? curie_z)\n                     ,props_xy\n                     ,props_yz)\n                   curie_z]\n                  [`(,score\n                     ,curie_x\n                     ,pred_xy\n                     ,curie_y\n                     .\n                     ,props_xy)\n                   curie_y]\n                  [else \"UMLS:C0017337\"])))\n    (not (member object GENERAL-NODES))))\n\n(define (node-has-cat? curie)\n  (let* ((props (curie->properties curie))\n         (categories (list-assoc \"category\" props))\n         (categories (filter\n                      (lambda (c)\n                        (not (or\n                              (class-mixin? c)\n                              (class-abstract? c))))\n                      categories)))\n    (not (null? categories))))\n\n(define (same-concept? c1 c2)\n  (equal? (curie->representative c1) (curie->representative c2)))\n\n(define (handle-mvp-creative-query body-json message query_graph edges nodes which-mvp)\n\n  (printf \"++ handling MVP mode creative query for Neo Server ~a\\n\" NEO_SERVER_VERSION)\n\n  (define disable-external-requests\n    (hash-ref message 'disable_external_requests #f))\n\n  (define our-trapi-response\n    (let ()\n\n      (define query_graph (hash-ref message 'query_graph))\n      (define qg_nodes (hash-ref query_graph 'nodes))\n      (define qg_edges (hash-ref query_graph 'edges))\n      (define qg_edge* (hash->list qg_edges))\n\n      (match-define (list qg_edge-id qg_edge-hash)\n        (match qg_edge*\n          ;; exactly one edge\n          [`((,edge-id . ,edge-hash))\n           (list edge-id edge-hash)]))\n\n      (define qg_object-node-str (hash-ref qg_edge-hash 'object))\n      (define qg_object-node-id (string->symbol qg_object-node-str))\n\n      (define qg_subject-node-str (hash-ref qg_edge-hash 'subject))\n      (define qg_subject-node-id (string->symbol qg_subject-node-str))\n\n      ; TODO: Would new mvp support more than one predicates?\n      (define qg_predicate-str (car (hash-ref qg_edge-hash 'predicates)))\n\n      (match-define (list input-id* q-1hop-results q-2hop-results)\n        (time\n         (cond\n           [(eq? 'mvp1 which-mvp)\n            ;;\n            (define disease-ids\n              ;; TODO write a chainer in utils, and also check for errors\n              (hash-ref (hash-ref qg_nodes qg_object-node-id) 'ids))\n            (define disease-ids+ (curies->synonyms-in-db disease-ids))\n            \n            (define chemical-catogory+\n              (set->list\n               (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                '(\"biolink:ChemicalEntity\"))))\n            ;;\n            (define 1-hop-proc\n              (lambda (curies)\n                (lambda (score*)\n                  (filter (lambda (r)\n                            (and (not-semmed-excluded? r)\n                                 (not-unwelcome-answer-as-subject? r)))\n                          (query:X->Known-scored\n                           chemical-catogory+\n                           '(\"biolink:treats\"\n                             \"biolink:treats_or_applied_or_studied_to_treat\"\n                             \"biolink:ameliorates_condition\")\n                           curies\n                           score*)))))\n            (define 2-hop-proc\n              (lambda (curies)\n                (lambda (score* result-amount)\n                  (query:X->Y->Known-auto-grow\n                   chemical-catogory+\n                   '(\"biolink:affects\" \"biolink:regulates\")\n                   (set->list\n                    (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                     '(\"biolink:Gene\" \"biolink:GeneOrGeneProduct\" \"biolink:Protein\")))\n                   '(\"biolink:contributes_to\"\n                     \"biolink:gene_associated_with_condition\"\n                     \"biolink:causes\"\n                     \"biolink:target_for\")\n                   curies\n                   score*\n                   result-amount\n                   (lambda (r*) (filter (lambda (r)\n                                          (and (not-semmed-excluded? r)\n                                               (not-general-connector? r)\n                                               (not-unwelcome-answer-as-subject? r)))\n                                        r*))))))\n            ;;\n            (let ((q-1hop (auto-grow-with-class-hierarchy #t 1-hop-proc TOP_BUCKET_NUMBERS disease-ids+ (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2))))\n                  (q-2hop (auto-grow-with-class-hierarchy #f 2-hop-proc TOP_BUCKET_NUMBERS disease-ids+ (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2)))))\n              (list disease-ids q-1hop q-2hop))]\n           [(eq? 'mvp2-chem which-mvp)\n            ;;\n            (define chemical-ids\n              (hash-ref (hash-ref qg_nodes qg_subject-node-id) 'ids))\n            (define chemical-ids+ (curies->synonyms-in-db chemical-ids))\n            \n            (define direction\n              (let ((qualifer-set\n                     (hash-ref (car (hash-ref qg_edge-hash 'qualifier_constraints)) 'qualifier_set)))\n                (let loop ((l qualifer-set))\n                  (if (equal? (hash-ref (car l) 'qualifier_type_id) \"biolink:object_direction_qualifier\")\n                      (hash-ref (car l) 'qualifier_value)\n                      (loop (cdr l))))))\n            (define gene-category+\n              (set->list\n               (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                '(\"biolink:Gene\" \"biolink:Protein\"))))\n            ;;\n            (define 1-hop-proc\n              (lambda (curies)\n                (lambda (score*)\n                  (filter (lambda (r)\n                            (and (not-semmed-excluded? r)\n                                 (not-unwelcome-answer-as-object? r)))\n                          (mvp2-1hop-filter\n                           (query:Known->X-scored\n                            curies\n                            '(\"biolink:affects\")\n                            gene-category+\n                            score*)\n                           direction)))))\n            (define 2-hop-proc\n              (lambda (curies)\n                (lambda (score* result-amount)\n                  (query:Known->Y->X-auto-grow\n                   curies\n                   '(\"biolink:affects\"\n                     \"biolink:physically_interacts_with\"\n                     \"biolink:indirectly_physically_interacts_with\"\n                     \"biolink:directly_physically_interacts_with\")\n                   (set->list\n                    (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                     '(\"biolink:Gene\" \"biolink:GeneOrGeneProduct\" \"biolink:Protein\")))\n                   '(\"biolink:affects\")\n                   gene-category+\n                   score*\n                   result-amount\n                   (lambda (r*) (filter (lambda (r) (and (not-semmed-excluded? r)\n                                                         (not-general-connector? r)\n                                                         (not-unwelcome-answer-as-object? r)))\n                                        (mvp2-2hop-filter r* direction)))))))\n  \n            (let* ((qualified-q-1hop (auto-grow-with-class-hierarchy #t 1-hop-proc TOP_BUCKET_NUMBERS chemical-ids+ (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2))))\n                   (qualified-q-2hop (auto-grow-with-class-hierarchy #f 2-hop-proc TOP_BUCKET_NUMBERS chemical-ids+ (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2)))))\n              (list chemical-ids qualified-q-1hop qualified-q-2hop))]\n           [(eq? 'mvp2-gene which-mvp)\n            ;;\n            (define gene-ids\n              (hash-ref (hash-ref qg_nodes qg_object-node-id) 'ids))\n            (define gene-ids-syns (curies->synonyms-in-db gene-ids))\n            (define protein-ids\n              (remove-duplicates\n               (map car\n                    (query:X->Known-scored\n                     (set->list\n                      (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                       '(\"biolink:Protein\")))\n                     '(\"biolink:gene_product_of\")\n                     gene-ids-syns\n                     (list (list 1112) #f (list 1112))))))\n            (define gene-ids+ (remove-duplicates (append gene-ids-syns (curies->synonyms-in-db protein-ids))))\n            \n            (define chemical-catogory+\n              (set->list\n               (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                '(\"biolink:ChemicalEntity\"))))\n            (define direction\n              (let ((qualifer-set\n                     (hash-ref (car (hash-ref qg_edge-hash 'qualifier_constraints)) 'qualifier_set)))\n                (let loop ((l qualifer-set))\n                  (if (equal? (hash-ref (car l) 'qualifier_type_id) \"biolink:object_direction_qualifier\")\n                      (hash-ref (car l) 'qualifier_value)\n                      (loop (cdr l))))))\n            ;;\n            (define 1-hop-proc\n              (lambda (curies)\n                (lambda (score*)\n                  (filter (lambda (r)\n                            (and (not-semmed-excluded? r)\n                                 (not-unwelcome-answer-as-subject? r)))\n                          (mvp2-1hop-filter\n                           (query:X->Known-scored\n                            chemical-catogory+\n                            '(\"biolink:affects\")\n                            curies\n                            score*)\n                           direction)))))\n            (define 2-hop-proc\n              (lambda (curies)\n                (lambda (score* result-amount)\n                  (query:X->Y->Known-auto-grow\n                   chemical-catogory+\n                   '(\"biolink:affects\"\n                     \"biolink:physically_interacts_with\"\n                     \"biolink:indirectly_physically_interacts_with\"\n                     \"biolink:directly_physically_interacts_with\")\n                   (set->list\n                    (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                     '(\"biolink:Gene\" \"biolink:GeneOrGeneProduct\" \"biolink:Protein\")))\n                   '(\"biolink:affects\")\n                   curies\n                   score*\n                   result-amount\n                   (lambda (r*) (filter (lambda (r)\n                                          (and (not-semmed-excluded? r)\n                                               (not-general-connector? r)\n                                               (not-unwelcome-answer-as-subject? r)))\n                                        (mvp2-2hop-filter r* direction)))))))\n            ;;\n            (let* ((qualified-q-1hop (auto-grow-with-class-hierarchy #t 1-hop-proc TOP_BUCKET_NUMBERS gene-ids+ (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2))))\n                   (qualified-q-2hop (auto-grow-with-class-hierarchy #f 2-hop-proc TOP_BUCKET_NUMBERS gene-ids+ (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2)))))\n              (list gene-ids qualified-q-1hop qualified-q-2hop))])))\n\n      (define q-1hop-unique-results (remove-duplicates q-1hop-results))\n      (define q-2hop-unique-results (remove-duplicates q-2hop-results))\n\n      (printf \"computed ~s look-up edges and ~s inferred edges for MVP mode creative query\\n\"\n              (length q-1hop-unique-results) (length q-2hop-unique-results))\n\n      #|\n       weights = {\n        'class-hierarchy': 0.3,\n        'edge-score: 0.3,\n        'hop-count': 0.2,\n        'predicate-type': 0.2\n       }\n      class-hierarchy-values = 10 * 1/level. self: 10*1/1=10; child: 10*1/2=5; grandchild: 10*1/3=3.33 ...\n      hop-count-values = mvp1: {'look-up': 3, '1 hops': 2, ' 2 hops': 1}\n                         mvp2: {'look-up': 50, '1 hops': 40, ' 2 hops': 1}\n      predicate-type-values = {'causation': 3, 'association': 2, 'other': 1}\n      |#\n      (define causation-prediates (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db '(\"biolink:contributes_to\" \"biolink:affects\" \"biolink:target_for\")))\n      (define association-predicates (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db '(\"biolink:gene_associated_with_condition\" \"biolink:interacts_with\")))\n      (define (score-mvp-edge e)\n        (match e\n          [`(,hierarchy\n             ,curie_x\n             ,pred_xy\n             ,curie_y\n             ,(? string? pred_yz)\n             ,(? string? curie_z)\n             ,props_xy\n             ,props_yz)\n           (if (and (edge-has-source? props_xy)\n                    (edge-has-source? props_yz))\n               (let ((class-hierarchy-values (* 10 (/ 1  hierarchy)))\n                     (hop-count-values 1)\n                     (predicate-type-values (if (eq? which-mvp 'mvp1)\n                                                (cond\n                                                  [(set-member? causation-prediates pred_yz) 3]\n                                                  [(set-member? association-predicates pred_yz) 2]\n                                                  [else 1])\n                                                (cond\n                                                  [(set-member? causation-prediates pred_xy) 3]\n                                                  [(set-member? association-predicates pred_xy) 2]\n                                                  [else 1])))\n                     (edge-score (sqrt (* (num-pubs props_xy) (num-pubs props_yz)))))\n                 (+ (* 0.3 class-hierarchy-values) (* 0.3 edge-score) (* 0.2 hop-count-values) (* 0.2 predicate-type-values)))\n               #f)]\n          [`(,hierarchy\n             ,curie_x\n             ,pred_xy\n             ,curie_y\n             .\n             ,props_xy)\n           (if (edge-has-source? props_xy)\n               (let ((class-hierarchy-values (* 10 (/ 1  hierarchy)))\n                     (hop-count-values\n                      (if (eq? which-mvp 'mvp1)\n                          (if (equal? pred_xy qg_predicate-str) 3 2)\n                          (let ((aspect (get-assoc \"object_aspect_qualifier\" props_xy)))\n                            (if (member aspect '(\"activity\" \"abundance\" \"activity_or_abundance\")) 50 40))))                  \n                     (predicate-type-values 3)\n                     (edge-score (num-pubs props_xy)))\n                 (+ (* 0.3 class-hierarchy-values) (* 0.3 edge-score) (* 0.2 hop-count-values) (* 0.2 predicate-type-values)))\n               #f)]))\n\n      (define scored/q-1hop-unsorted-long\n        (filter (lambda (scored/r) (car scored/r))\n                (map\n                 (lambda (e) (cons (score-mvp-edge e) (cdr e)))\n                 q-1hop-unique-results)))\n\n      (define scored/q-2hop-unsorted-long\n        (filter (lambda (scored/r) (car scored/r))\n                (map\n                 (lambda (e) (cons (score-mvp-edge e) (cdr e)))\n                 q-2hop-unique-results)))\n\n      (define by-score\n        (lambda (score1/e1 score2/e2)\n          (let ((score1 (car score1/e1))\n                (score2 (car score2/e2)))\n            (> score1 score2))))\n\n      (define scored/q-1hop-sorted-long\n        (sort scored/q-1hop-unsorted-long by-score))\n\n      (define scored/q-2hop-sorted-long\n        (sort scored/q-2hop-unsorted-long by-score))\n\n      (define scored/q-1hop-sorted-short (take-at-most scored/q-1hop-sorted-long (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2.0))))\n      (define scored/q-2hop-sorted-short (take-at-most scored/q-2hop-sorted-long (exact-round (/ MAX_RESULTS_FROM_COMPONENT 2.0))))\n\n      (printf \"computed ~s valid 1 hop edges for MVP mode creative query\\n\" (length scored/q-1hop-sorted-short))\n      (printf \"computed ~s valid 2 hop edges for MVP mode creative query\\n\" (length scored/q-2hop-sorted-short))\n\n      (define scored/q-unsorted-short (append scored/q-1hop-sorted-short scored/q-2hop-sorted-short))\n\n      (printf \"computed total ~s valid edges for MVP mode creative query\\n\"\n              (length scored/q-unsorted-short))\n\n      (define old-scored/q-sorted-short\n        (sort scored/q-unsorted-short by-score))\n\n      #;(define old-scored/q-sorted-short (take-at-most scored/q-sorted-long MAX_RESULTS_FROM_COMPONENT))\n\n      (define subjs-from-2hop-results (remove-duplicates (map cadr scored/q-2hop-sorted-short)))\n      (define objs-from-2hop-results (remove-duplicates (map (lambda (e) (get-object e)) scored/q-2hop-sorted-short)))\n      \n      (when (eq? which-mvp 'mvp1)\n        (let* ((chemicals (remove-duplicates (curies->synonyms-in-db subjs-from-2hop-results)))\n               (disease-id+ (remove-duplicates (curies->synonyms-in-db objs-from-2hop-results)))\n               (chem-worsen-disease (remove-duplicates\n                                     (curies->synonyms-in-db\n                                      (map car \n                                           (time (query:Known->Known\n                                            chemicals\n                                            '(\"biolink:causes\"\n                                              \"biolink:exacerbates\"\n                                              \"biolink:has_adverse_event\"\n                                              \"biolink:contributes_to\")\n                                            disease-id+))))))\n               (not-cause-old-scored/q-sorted-short\n                (filter (lambda (e) (not (member (cadr e) chem-worsen-disease))) old-scored/q-sorted-short)))\n          (set! old-scored/q-sorted-short not-cause-old-scored/q-sorted-short)))\n\n      (printf \"Toke the best ~s edges for MVP mode creative query\\n\"\n              (length old-scored/q-sorted-short))\n\n      (define subjs-from-results (remove-duplicates (map cadr old-scored/q-sorted-short)))\n      (define objs-from-results (remove-duplicates (map (lambda (e) (get-object e)) old-scored/q-sorted-short)))\n      \n      (define curie-representative-table (add-curies-representative-to-hash\n                                          (build-curies-representative-hash subjs-from-results)\n                                          objs-from-results))\n\n      (define representative-canonical-table\n        (let ((t (make-hash)))\n          (define helper\n            (lambda (c*)\n                (cond\n                  ((null? c*) t)\n                  ((hash-has-key? t (hash-ref curie-representative-table (car c*)))\n                   (helper (cdr c*)))\n                  (else\n                    (hash-set! t (hash-ref curie-representative-table (car c*)) (car c*))\n                    (helper (cdr c*))))))\n           (helper (append subjs-from-results objs-from-results))))\n\n      (define curie->canonical\n        (lambda (c)\n          (hash-ref representative-canonical-table\n                    (hash-ref curie-representative-table c))))\n\n      (define scored/q-sorted-short\n        (map\n         (lambda (e)\n                 (match e\n                   [`(,score\n                      ,curie_x\n                      ,pred_xy\n                      ,curie_y\n                      ,(? string? pred_yz)\n                      ,(? string? curie_z)\n                      ,props_xy\n                      ,props_yz)\n                    (list score\n                          (curie->canonical curie_x)\n                          pred_xy\n                          curie_y\n                          pred_yz\n                          (curie->canonical curie_z)\n                          props_xy\n                          props_yz)]\n                   [`(,score\n                      ,curie_x\n                      ,pred_xy\n                      ,curie_y\n                      .\n                      ,props_xy)\n                    (list* score\n                           (curie->canonical curie_x)\n                           pred_xy\n                           (curie->canonical curie_y)\n                           props_xy)]\n                   [else (error \"invalid form of returned edge\" e)]))\n         old-scored/q-sorted-short))\n\n      (define representative-score-table\n        (cond\n          [(or (eq? which-mvp 'mvp1) (eq? which-mvp 'mvp2-gene))\n            (let ((subject-score-table (make-hash)))\n              (for-each\n               (lambda (e)\n                 (hash-update! subject-score-table\n                               (hash-ref curie-representative-table (cadr e))\n                               (lambda (old-socre)\n                                 (+ (car e) old-socre))\n                               0))\n               scored/q-sorted-short)\n              subject-score-table)]\n          [(eq? which-mvp 'mvp2-chem)\n           (let ((object-score-table (make-hash)))\n             (for-each\n              (lambda (e)\n                (hash-update! object-score-table\n                              (hash-ref curie-representative-table (get-object e))\n                              (lambda (old-socre)\n                                (+ (car e) old-socre))\n                              0))\n              scored/q-sorted-short)\n             object-score-table)]\n          [else (error \"unknown MVP\" which-mvp)]))\n\n      (printf \"There are ~a unique results/entities for the MVP query.\\n\" (hash-count representative-score-table))\n\n      (define nodes (make-hash))\n\n      (define edges (make-hash))\n\n      (define auxiliary-graph (make-hash))\n\n      (define unmerged-results (make-hash))\n\n      (define (add-node! curie)\n        (let ((props (curie->properties curie)))\n          (let* ((categories (list-assoc \"category\" props))\n                 (categories (filter\n                              (lambda (c)\n                                (not (or\n                                      (class-mixin? c)\n                                      (class-abstract? c))))\n                              categories))\n                 (name (get-assoc \"name\" props)))\n            (if name\n                (hash-set! nodes (string->symbol curie)\n                           (hash 'categories categories\n                                 'name name\n                                 'attributes (list)))\n                (hash-set! nodes (string->symbol curie)\n                           (hash 'categories categories\n                                 'attributes (list)\n                                 ))))))\n\n      (define (add-edge! subj obj props n)\n        (let* ((id (number->string n))\n               (id (string-append \"medik:edge#\" id))\n               (id-sym (string->symbol id))\n               (object obj)\n               (subject subj)\n               (predicate (get-assoc \"predicate\" props))\n               (aspect-qualifier (qualifier-attribute* \"object_aspect_qualifier\" props))\n               (direction-qualifier (qualifier-attribute* \"object_direction_qualifier\" props))\n               (qualifed-predicate (qualifier-attribute* \"qualified_predicate\" props))\n               (qualifiers-attr* (append aspect-qualifier direction-qualifier qualifed-predicate))\n               (has-pub? (> (num-pubs props) 0)))\n          (add-node! object)\n          (add-node! subject)\n          (if (not (null? qualifiers-attr*))\n              (hash-set! edges id-sym\n                         (hash 'attributes\n                               (or\n                                #;(and (get-assoc \"json_attributes\" props)\n                                     (string->jsexpr (get-assoc \"json_attributes\" props)))\n                                (list* (agent-type-attribute props)\n                                       (knowledge-level-attribute props)\n                                       (publication-attributes props has-pub?)))\n                               'object object\n                               'predicate predicate\n                               'subject subject\n                               'sources (list (get-source props) (UNSECRET-SOURCE props))\n                               'qualifiers qualifiers-attr*))\n              (hash-set! edges id-sym\n                         (hash 'attributes\n                               (or\n                                #;(and (get-assoc \"json_attributes\" props)\n                                     (string->jsexpr (get-assoc \"json_attributes\" props)))\n                                (list* (agent-type-attribute props)\n                                       (knowledge-level-attribute props)\n                                       (publication-attributes props has-pub?)))\n                               'object object\n                               'predicate predicate\n                               'subject subject\n                               'sources (list (get-source props) (UNSECRET-SOURCE props)))))\n          id))\n\n      (define (add-creative-edge! sub obj pred n aux-id)\n        (let ((id (string-append \"medik:creative_edge#\" (number->string n))))\n          (if (or (eq? which-mvp 'mvp2-gene) (eq? which-mvp 'mvp2-chem))\n              (hash-set! edges (string->symbol id)\n                         (hash 'attributes\n                               (list\n                                (auxiliary-graph-attribute aux-id)\n                                Unsecret-agent-type-attribute\n                                Unsecret-knowledge-level-attribute)\n                               'object obj\n                               'predicate pred\n                               'subject sub\n                               'qualifiers\n                               (let ((exist-qualifiers (hash-ref (car (hash-ref qg_edge-hash 'qualifier_constraints)) 'qualifier_set))\n                                     (qualified_pred (hash 'qualifier_type_id \"biolink:qualified_predicate\"\n                                                           'qualifier_value \"biolink:causes\")))\n                                 (if (member qualified_pred exist-qualifiers)\n                                     exist-qualifiers\n                                     (cons qualified_pred exist-qualifiers)))\n                               'sources (list\n                                         (hash\n                                          'resource_id \"infores:unsecret-agent\"\n                                          'resource_role \"primary_knowledge_source\"))))\n              (hash-set! edges (string->symbol id)\n                         (hash 'attributes\n                               (list\n                                (auxiliary-graph-attribute aux-id)\n                                Unsecret-agent-type-attribute\n                                Unsecret-knowledge-level-attribute)\n                               'object obj\n                               'predicate pred\n                               'subject sub\n                               'sources (list\n                                         (hash\n                                          'resource_id \"infores:unsecret-agent\"\n                                          'resource_role \"primary_knowledge_source\")))))\n          id))\n\n      (define (add-auxiliary! edge* n)\n        (let ((id (string-append \"medik:auxiliary_graph#\" (number->string n))))\n          (hash-set! auxiliary-graph (string->symbol id)\n                     (hash 'edges edge*\n                           'attributes (list)))\n          id))\n\n      (define (add-unmerged-result! r)\n        (hash-update! unmerged-results (hash-ref r 'result_id)\n                      (lambda (r-old)\n                        (let* ((a*-old (hash-ref r-old 'analyses))\n                               (a-old (car a*-old))\n                               (edge-old (hash-ref (hash-ref a-old 'edge_bindings) qg_edge-id))\n                               (edge-new (hash-ref  (hash-ref r 'edge_bindings) qg_edge-id)))\n                          (hash-set r-old 'analyses\n                                    (list (hash-set (car (hash-ref r-old 'analyses))\n                                                    'edge_bindings\n                                                    (hash qg_edge-id (remove-duplicates (append edge-old edge-new))))))))\n                      (hash\n                       'node_bindings (hash-ref r 'node_bindings)\n                       'analyses (list (hash 'edge_bindings (hash-ref r 'edge_bindings)\n                                             'resource_id \"infores:unsecret-agent\"\n                                             'score (hash-ref representative-score-table (hash-ref r 'score_id)))))))\n\n      (let loop ((en 0) (an 0) (score*/e* scored/q-sorted-short))\n        (cond\n          ((null? score*/e*) '())\n          (else\n           (define score/e (car score*/e*))\n           (define score (car score/e))\n           (define e (cdr score/e))\n           (match e\n             [`(,curie_x\n                ,pred_xy\n                ,curie_y\n                ,(? string? pred_yz)\n                ,(? string? curie_z)\n                ,props_xy\n                ,props_yz)\n              (if (and (node-has-cat? curie_x)\n                       (node-has-cat? curie_y)\n                       (node-has-cat? curie_z)\n                       (not (same-concept? curie_y curie_z)))\n                  (let* ((edge_xy (add-edge! curie_x curie_y props_xy en))\n                         (edge_yz (add-edge! curie_y curie_z props_yz (+ en 1)))\n                         (auxiliary_id (add-auxiliary! (list edge_xy edge_yz) an))\n                         (edge_creative (add-creative-edge! curie_x\n                                                            curie_z\n                                                            qg_predicate-str\n                                                            an\n                                                            auxiliary_id)))\n                    (add-unmerged-result!\n                     (cond\n                       [(or (eq? which-mvp 'mvp1) (eq? which-mvp 'mvp2-gene))\n                        (hash 'node_bindings\n                              (if (equal? curie_z (car input-id*))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_z\n                                                                 'attributes (list))))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_z\n                                                                 'query_id (car input-id*)\n                                                                 'attributes (list)))))\n                              'result_id (string-append curie_x curie_z)\n                              'score_id (hash-ref curie-representative-table curie_x)\n                              'edge_bindings (hash qg_edge-id (list (hash 'id edge_creative\n                                                                          'attributes (list))))\n                              )]\n                       [(eq? which-mvp 'mvp2-chem)\n                        (hash 'node_bindings\n                              (if (equal? curie_x (car input-id*))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_z\n                                                                 'attributes (list))))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'query_id (car input-id*)\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_z\n                                                                 'attributes (list)))))\n                              'result_id (string-append curie_x curie_z)\n                              'score_id (hash-ref curie-representative-table curie_z)\n                              'edge_bindings (hash qg_edge-id (list (hash 'id edge_creative\n                                                                          'attributes (list))))\n                              )]\n                       [else (error \"unknown MVP\" which-mvp)]))\n                    (loop (+ en 2) (+ an 1) (cdr score*/e*)))\n                  (loop en an (cdr score*/e*)))]\n             [`(,curie_x\n                ,pred_xy\n                ,curie_y\n                .\n                ,props_xy)\n              (if (and (node-has-cat? curie_x)\n                       (node-has-cat? curie_y))\n                  (let ((edge_xy (add-edge! curie_x curie_y props_xy en)))\n                    (add-unmerged-result!\n                     (cond\n                       [(and (eq? which-mvp 'mvp1) (not (equal? pred_xy qg_predicate-str)))\n                        (let* ((auxiliary_id (add-auxiliary! (list edge_xy) an))\n                               (edge_creative (add-creative-edge! curie_x\n                                                                  curie_y\n                                                                  qg_predicate-str\n                                                                  an\n                                                                  auxiliary_id)))\n                          (hash 'node_bindings\n                                (if (equal? curie_y (car input-id*))\n                                    (hash\n                                     qg_subject-node-id (list (hash 'id curie_x\n                                                                    'attributes (list)))\n                                     qg_object-node-id (list (hash 'id curie_y\n                                                                   'attributes (list))))\n                                    (hash\n                                     qg_subject-node-id (list (hash 'id curie_x\n                                                                    'attributes (list)))\n                                     qg_object-node-id (list (hash 'id curie_y\n                                                                   'query_id (car input-id*)\n                                                                   'attributes (list)))))\n                                'result_id (string-append curie_x curie_y)\n                                'score_id (hash-ref curie-representative-table curie_x)\n                                'edge_bindings (hash qg_edge-id (list (hash 'id edge_creative\n                                                                            'attributes (list))))\n                                ))]\n                       [(or (and (eq? which-mvp 'mvp1) (equal? pred_xy qg_predicate-str))\n                            (eq? which-mvp 'mvp2-gene))\n                        (hash 'node_bindings\n                              (if (equal? curie_y (car input-id*))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_y\n                                                                 'attributes (list))))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_y\n                                                                 'query_id (car input-id*)\n                                                                 'attributes (list)))))\n                              'result_id (string-append curie_x curie_y)\n                              'score_id (hash-ref curie-representative-table curie_x)\n                              'edge_bindings (hash qg_edge-id (list (hash 'id edge_xy\n                                                                          'attributes (list))))\n                              )]\n                       [(eq? which-mvp 'mvp2-chem)\n                        (hash 'node_bindings\n                              (if (equal? curie_x (car input-id*))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_y\n                                                                 'attributes (list))))\n                                  (hash\n                                   qg_subject-node-id (list (hash 'id curie_x\n                                                                  'query_id (car input-id*)\n                                                                  'attributes (list)))\n                                   qg_object-node-id (list (hash 'id curie_y\n                                                                 'attributes (list)))))\n                              'result_id (string-append curie_x curie_y)\n                              'score_id (hash-ref curie-representative-table curie_y)\n                              'edge_bindings (hash qg_edge-id (list (hash 'id edge_xy\n                                                                          'attributes (list))))\n                              )]))\n                    (if (equal? pred_xy qg_predicate-str)\n                        (loop (+ en 1) an (cdr score*/e*))\n                        (loop (+ en 1) (+ an 1) (cdr score*/e*))))\n                  (loop en an (cdr score*/e*)))]\n             ))))\n\n      (define merged-results\n        (let loop ((id* (hash-keys unmerged-results))\n                   (r '()))\n          (cond\n            [(null? id*) r]\n            [else (loop (cdr id*)\n                        (cons (hash-ref unmerged-results (car id*)) r))])))\n\n      (define results (sort merged-results (lambda (a b) (> (get-score-from-result a) (get-score-from-result b)))))\n\n      ;; add the input curie/id from query graph to nodes if mediKanren returns answer\n      (unless (null? results)\n        (add-node! (car input-id*)))\n\n      (hash\n       'message\n       (hash\n        ;;\n        'query_graph\n        query_graph\n        ;;\n        'knowledge_graph\n        (hash 'edges edges\n              'nodes nodes)\n        ;;\n        'auxiliary_graphs\n        auxiliary-graph\n        ;;\n        'results\n        (normalize-scores results)))\n      ))\n\n  (define gp-trapi-response\n    ;; Disable Genetics Provider TRAPI calls for now, until Genetics\n    ;; Provider KP is handling TRAPI 1.4 Creative Mode queries.\n    #f\n    #;(if disable-external-requests\n          #f\n          (let ()\n\n            (define res #f)\n\n            (printf \"making sync/timeout API call with timeout of ~s seconds\\n\"\n                    API_CALL_CONNECTION_TIMEOUT_SECONDS)\n\n            (sync/timeout\n             API_CALL_CONNECTION_TIMEOUT_SECONDS\n             (thread\n              (lambda ()\n                ;; use 'url.genetics.prod', 'url.genetics.test', or 'url.genetics.ci'\n                ;; based on the environment the Unsecret server is running in.\n                (let ((kp-url (case (unbox ENVIRONMENT_TAG_BOX)\n                                ((\"CI\") url.genetics.ci)\n                                ((\"TEST\") url.genetics.test)\n                                ((\"PROD\") url.genetics.prod)\n                                (else\n                                 (lognew-info\n                                  (hash 'event\n                                        (format\n                                         \"unexpected ENVIRONMENT_TAG_BOX value: '~s'\"\n                                         (unbox ENVIRONMENT_TAG_BOX))))\n                                 url.genetics.prod))))\n                  (lognew-info\n                   (hash 'event (format \"kp-url for Genetics Provider call: '~s'\" kp-url)))\n                  (set! res\n                        (api-query (string-append kp-url path.query)\n                                   body-json))))))\n\n            (if res\n                (printf \"API call returned\\n\")\n                (printf \"API call timed out\\n\"))\n\n            (if (hash? res)\n                (let ()\n                  (define upstream-status\n                    (hash-ref res 'status #f))\n\n                  (printf \"status from API call:\\n~s\\n\" upstream-status)\n\n                  (if upstream-status\n                      (let ()\n                        (define upstream-headers\n                          (hash-ref res 'headers #f))\n\n                        (printf \"headers from API call:\\n~s\\n\" upstream-headers)\n\n                        (if (string-contains?\n                             (bytes->string/utf-8 upstream-status)\n                             200_OK_STRING)\n                            (let ()\n                              (printf \"API returned an OK status...processing results\\n\")\n\n                              (define upstream-response\n                                (hash-ref res 'response #f))\n\n                              (define res-message\n                                (hash-ref upstream-response 'message))\n\n                              (define results\n                                (let ((results\n                                       (hash-ref res-message 'results)))\n                                  (take-at-most results MAX_RESULTS_FROM_COMPONENT)))\n\n                              (define scored-results\n                                (score-results results))\n\n                              (define knowledge_graph\n                                (hash-ref res-message 'knowledge_graph))\n\n                              (define edges\n                                (hash-ref knowledge_graph 'edges))\n\n                              (define stamped-edges\n                                (hash-map/copy\n                                 edges\n                                 (lambda (k v)\n                                   (values\n                                    k\n                                    (hash-set v\n                                              'sources\n                                              (cons unsecret-source\n                                                    (hash-ref v 'sources)))))))\n\n                              (define stamped-knowledge_graph\n                                (hash-set knowledge_graph 'edges stamped-edges))\n\n                              (hash-set upstream-response\n                                        'message\n                                        (hash-set (hash-set res-message\n                                                            'results\n                                                            (normalize-scores scored-results))\n                                                  'knowledge_graph\n                                                  stamped-knowledge_graph)))\n                            (begin\n                              (printf \"API returned a non-OK status...ignoring results\\n\")\n                              #f)))\n                      #f))\n                #f))))\n\n  (define trapi-response\n    (if gp-trapi-response\n        (merge-trapi-responses our-trapi-response gp-trapi-response query_graph)\n        our-trapi-response))\n\n  (define merged-results\n    (hash-ref (hash-ref trapi-response 'message) 'results))\n\n  (define merged-scored-results\n    (normalize-scores (score-results merged-results)))\n\n  (define scored-trapi-response\n    (hash-set trapi-response 'message\n              (hash-set (hash-ref trapi-response 'message)\n                        'results merged-scored-results)))\n\n  (define versioned-trapi-response\n    (hash-set* scored-trapi-response\n               'logs (list)\n               'schema_version \"1.5.0\"\n               'biolink_version (get-biolink-version)))\n\n  (list\n   'json\n   200_OK_STRING\n   versioned-trapi-response)\n  )\n\n\n(define (handle-trapi-query body-json request-fk)\n\n  (define (empty-reply)\n    (let ()\n\n      (printf \"-- handling non-MVP mode query\\n\")\n\n      (define trapi-response\n        (make-empty-trapi-response))\n\n      (list\n       'json\n       501_ERROR_STRING\n       trapi-response)\n      ))\n\n  (define message (hash-ref body-json 'message #f))\n  (if message\n      (let()\n        (define query_graph (hash-ref message 'query_graph #f))\n        (if query_graph\n            (let ()\n              (define edges (hash-ref query_graph 'edges #f))\n              (define nodes (hash-ref query_graph 'nodes #f))\n              (if (and edges nodes)\n                  (let ()\n                    (define creative-mvp? (mvp-creative-query? edges nodes))\n                    (printf \"creative-mvp?: ~s\\n\" creative-mvp?)\n                    (if creative-mvp?\n                        (handle-mvp-creative-query body-json message query_graph edges nodes creative-mvp?)\n                        (empty-reply)))\n                  (let ()\n                    (printf \"** missing `nodes` or `edges` in `query_graph`: ~s\\n\" query_graph)\n                    (empty-reply))))\n            (let ()\n              (printf \"** missing `query_graph` in `message`: ~s\\n\" message)\n              (empty-reply))))\n      (let ()\n        (printf \"** missing `message` in `body-json`: ~s\\n\" body-json)\n        (empty-reply)))\n  )\n\n(define (handle-trapi-asyncquery body-json request-fk)\n\n  (define (empty-reply)\n    (let ()\n\n      (printf \"-- handling non-MVP mode asyncquery\\n\")\n\n      (define trapi-response\n        (make-empty-trapi-response))\n\n      (list\n       'json\n       501_ERROR_STRING\n       trapi-response)\n      ))\n\n  (define message (hash-ref body-json 'message #f))\n  (if message\n      (let()\n        (define query_graph (hash-ref message 'query_graph #f))\n        (if query_graph\n            (let ()\n              (define edges (hash-ref query_graph 'edges #f))\n              (define nodes (hash-ref query_graph 'nodes #f))\n              (if (and edges nodes)\n                  (let ()\n                    (define creative-mvp? (mvp-creative-query? edges nodes))\n                    (printf \"creative-mvp?: ~s\\n\" creative-mvp?)\n                    (if creative-mvp?\n                        (handle-mvp-creative-query body-json message query_graph edges nodes creative-mvp?)\n                        (empty-reply)))\n                  (let ()\n                    (printf \"** missing `nodes` or `edges` in `query_graph`: ~s\\n\" query_graph)\n                    (empty-reply))))\n            (let ()\n              (printf \"** missing `query_graph` in `message`: ~s\\n\" message)\n              (empty-reply))))\n      (let ()\n        (printf \"** missing `message` in `body-json`: ~s\\n\" body-json)\n        (empty-reply)))\n  )\n\n\n\n\n(define dispatch-table (make-hash))\n\n;; servlet stuff\n\n;; dispatch functions\n(define (query query\n               headers\n               request-fk\n               ;;\n               content-type-string\n               content-length-string\n               body-str)\n  (printf \"received TRAPI `query` POST request\\n\")\n\n  (unless (string-contains? (string-downcase content-type-string) \"application/json\")\n    (printf \"** unexpected content-type-string for query\\nexpected 'application/json', received '~s'\\n\"\n            content-type-string)\n    (request-fk))\n\n  (define body-json (string->jsexpr body-str))\n  ;(printf \"body-json:\\n~s\\n\" body-json)\n\n  (handle-trapi-query body-json request-fk))\n\n\n(define (asyncquery query\n                    headers\n                    request-fk\n                    ;;\n                    content-type-string\n                    content-length-string\n                    body-str)\n  (printf \"received TRAPI `asyncquery` POST request\\n\")\n\n  (unless (string-contains? (string-downcase content-type-string) \"application/json\")\n    (printf \"** unexpected content-type-string for query\\nexpected 'application/json', received '~s'\\n\"\n            content-type-string)\n    (request-fk))\n\n  (define body-json (string->jsexpr body-str))\n  (printf \"body-json:\\n~s\\n\" body-json)\n\n  (handle-trapi-asyncquery body-json request-fk))\n\n\n(define (meta_knowledge_graph query headers request-fk)\n  (printf \"received TRAPI meta knowledge graph query:\\n~s\\n\" query)\n  (list\n   'text\n   200_OK_STRING\n   metaKG.json.txt))\n\n(define (health query headers request-fk)\n  (printf \"received health status query:\\n~s\\n\" query)\n  (list\n   'json\n   200_OK_STRING\n   (string->jsexpr \"{}\")))\n\n(define (schema.json query headers request-fk)\n  (printf \"received GET request for schema.json:\\n~s\\n\" query)\n  (list\n   'text\n   200_OK_STRING\n   schema.json.txt))\n\n(define (schema.yaml query headers request-fk)\n  (printf \"received GET request for schema.yaml:\\n~s\\n\" query)\n  (list\n   'text\n   200_OK_STRING\n   schema.yaml.txt))\n\n\n;; Dispatch table request handlers that are safe for concurrent use,\n;; without synchronization through the job channels:\n(hash-set! dispatch-table '(GET \"schema.json\") (cons schema.json 'safe-for-concurrent-use))\n(hash-set! dispatch-table '(GET \"schema.yaml\") (cons schema.yaml 'safe-for-concurrent-use))\n\n(hash-set! dispatch-table '(GET \"meta_knowledge_graph\")\n           (cons meta_knowledge_graph 'safe-for-concurrent-use))\n\n(hash-set! dispatch-table '(GET \"health\") (cons health 'safe-for-concurrent-use))\n\n(hash-set!\n dispatch-table\n '(GET \"hello\")\n (cons\n   (lambda (query headers request-fk)\n     (printf \"received hello query:\\n~s\\n\" query)\n     (list\n       'xexpr\n       200_OK_STRING\n       `(html (body ,(format \"Hello, World! from Neo Server ~a. Current amount of jobs waiting: ~a\" NEO_SERVER_VERSION *jobs-waiting*)))))\n   'safe-for-concurrent-use))\n\n\n;; Dispatch table request handlers that are *not* safe for concurrent\n;; use, and whose use must be synchronized through the job channels:\n(hash-set! dispatch-table '(POST \"query\") (cons query #f))\n(hash-set! dispatch-table '(POST \"asyncquery\") (cons asyncquery #f))\n\n(hash-set!\n dispatch-table\n '(GET \"syn\")\n (cons\n   (lambda (query headers request-fk)\n     (printf \"received syn query:\\n~s\\n\" query)\n     (list\n       'xexpr\n       200_OK_STRING\n       `(html\n         (body\n          ,(format\n            \"~s\"\n            (curie->synonyms-in-db \"HGNC:1101\"))))))\n   #f))\n\n(hash-set!\n dispatch-table\n '(GET \"simple\")\n (cons\n   (lambda (query headers request-fk)\n     (printf \"received simple query:\\n~s\\n\" query)\n     (list\n       'xexpr\n       200_OK_STRING\n       `(html\n         (body\n          ,(format\n            \"~s\"\n            (car\n             (query:X->Known\n              (set->list\n               (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n                '(\"biolink:ChemicalEntity\")))\n              (set->list\n               (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n                '(\"biolink:treats\")))\n              (set->list\n               (get-n-descendent-curies*-in-db\n                (curie->synonyms-in-db \"DOID:9351\")\n                MAX_DESCENDENT)))))))))\n   #f))\n\n(module+ main\n  (lognew-info\n   (hash 'event \"About to check server environment variables\"))\n  (set-box! ENVIRONMENT_TAG_BOX (getenv \"ENVIRONMENT_TAG\"))\n  (lognew-info\n   (hash 'event (format \"ENVIRONMENT_TAG_BOX value = '~s'\" (unbox ENVIRONMENT_TAG_BOX))))\n  (set-box! MK_STAGE_BOX (getenv \"MK_STAGE\"))\n  (lognew-info\n   (hash 'event (format \"MK_STAGE_BOX value = '~s'\" (unbox MK_STAGE_BOX))))\n  (lognew-info\n   (hash 'event \"starting_server\"))\n  (lognew-info\n   (hash 'event (format \"(Neo Server ~a)\" NEO_SERVER_VERSION)))\n  (serve DEFAULT_PORT)\n  (lognew-info\n   (hash 'event \"started_server\"))\n  (let forever ()\n    (sleep 10)\n    (forever)))\n\n\n\n;;; Ensure the data is loaded by running an example query:\n(define q3 (query:X->Known-scored\n            (set->list\n             (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n              '(\"biolink:ChemicalEntity\")))\n            (set->list\n             (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n              '(\"biolink:treats\")))\n            (set->list\n             (get-n-descendent-curies*-in-db\n              (curie->synonyms-in-db \"MONDO:0007827\")\n              MAX_DESCENDENT))\n            TOP_BUCKET_NUMBERS))\n\n(length q3)\n(length UNWELCOME-TREATMENT)\n(length GENERAL-NODES)\n"
  },
  {
    "path": "medikanren2/neo/neo-tests/test-mvps-TRAPI-response.rkt",
    "content": "#lang racket\n\n(require\n  net/url\n  json\n  rackunit)\n\n(define MEDIKANREN-LOCAL-URL (string->url \"http://127.0.0.1:8384/query\"))\n\n(define HEADER\n  (list \"accept: application/json\" \n        \"Content-Type: application/json\"))\n\n(define build-mvp-query\n  (lambda (which-mvp known-id direction)\n    (cond\n      [(eq? which-mvp 'mvp1)\n       (hash 'message\n             (hash \n              'disable_external_requests \"true\"\n              'query_graph (hash\n                            'nodes (hash \n                                    'n0 (hash\n                                         'ids (list known-id)\n                                         'categories (list \"biolink:Disease\"))\n                                    'n1 (hash\n                                         'categories (list \"biolink:ChemicalEntity\")))\n                            'edges (hash\n                                    'e0 (hash\n                                         'subject \"n1\"\n                                         'object \"n0\"\n                                         'predicates (list \"biolink:treats\")\n                                         'knowledge_type \"inferred\")))))]\n      [(eq? which-mvp 'mvp2-gene)\n       (hash 'message\n             (hash\n              'disable_external_requests \"true\"\n              'query_graph\n              (hash 'edges\n                    (hash 't_edge\n                          (hash 'knowledge_type \"inferred\"\n                                'object \"gene\"\n                                'predicates (list \"biolink:affects\")\n                                'qualifier_constraints\n                                (list (hash\n                                       'qualifier_set\n                                       (list\n                                        (hash 'qualifier_type_id \"biolink:object_aspect_qualifier\"\n                                              'qualifier_value \"activity_or_abundance\")\n                                        (hash 'qualifier_type_id \"biolink:object_direction_qualifier\"\n                                              'qualifier_value direction))))\n                                'subject \"chemical\"))\n                    'nodes (hash\n                            'chemical (hash\n                                       'categories (list \"biolink:ChemicalEntity\"))\n                            'gene (hash 'categories (list \"biolink:Gene\")\n                                        'ids (list known-id))))))]\n      [(eq? which-mvp 'mvp2-chem)\n       (hash 'message\n             (hash\n              'disable_external_requests \"true\"\n              'query_graph\n              (hash 'edges\n                    (hash 't_edge\n                          (hash 'knowledge_type \"inferred\"\n                                'object \"gene\"\n                                'predicates (list \"biolink:affects\")\n                                'qualifier_constraints\n                                (list (hash\n                                       'qualifier_set\n                                       (list\n                                        (hash 'qualifier_type_id \"biolink:object_aspect_qualifier\"\n                                              'qualifier_value \"activity_or_abundance\")\n                                        (hash 'qualifier_type_id \"biolink:object_direction_qualifier\"\n                                              'qualifier_value direction))))\n                                'subject \"chemical\"))\n                    'nodes (hash\n                            'chemical (hash\n                                       'categories (list \"biolink:ChemicalEntity\")\n                                       'ids (list known-id))\n                            'gene (hash 'categories (list \"biolink:Gene\")\n                                        )))))]\n      [else (error \"unknown mvp\")])))\n\n\n;; TODO: how to get the body and http_code for one call\n;; https://gist.github.com/branneman/8a018e39e993328be1cf25cf9035e7d6\n(define get-response\n  (lambda (which-mvp known-id direction)\n    (call/input-url\n     MEDIKANREN-LOCAL-URL\n     (lambda (url) (post-pure-port\n                    url\n                    (jsexpr->bytes (build-mvp-query which-mvp known-id direction))\n                    HEADER))\n     read-json)))\n\n(define (check-X-in-list X)\n    (lambda (lt) (member X lt)))\n\n(define (missing-string x)\n  (if (string? x)\n      (string-append x \" is missing\")\n      (error \"x is missing and x should be a string\")))\n\n(define (test-reply response)\n\n  (check-pred (check-X-in-list 'message) (hash-keys response) (missing-string \"\\\"message\\\"\"))\n  (define message-from-response (hash-ref response 'message (hash)))\n  (define message-key* (hash-keys message-from-response))\n  (check-pred (check-X-in-list 'results) message-key* (missing-string \"\\\"results\\\"\"))\n  (check-pred (check-X-in-list 'query_graph) message-key* (missing-string \"\\\"query_graph\\\"\"))\n  (check-pred (check-X-in-list 'knowledge_graph) message-key* (missing-string \"\\\"knowledge_graph\\\"\"))\n  (check-pred (check-X-in-list 'auxiliary_graphs) message-key* (missing-string \"\\\"auxiliary_graphs\\\"\"))\n\n\n  (define query-graph-from-response (hash-ref message-from-response 'query_graph (hash)))\n  (define query-graph-key* (hash-keys query-graph-from-response))\n  (check-pred (check-X-in-list 'nodes) query-graph-key* (missing-string \"\\\"query_graph.nodes\\\"\"))\n  (check-pred (check-X-in-list 'edges) query-graph-key* (missing-string \"\\\"query_graph.edges\\\"\"))\n\n  (define Qedge-from-response (hash-ref query-graph-from-response 'edges (hash)))\n  (for-each\n   (lambda (Qedge-key)\n     (define Qedge-dic (hash-ref Qedge-from-response Qedge-key))\n     (check-pred (check-X-in-list 'subject) (hash-keys Qedge-dic) (missing-string \"\\\"query_graph.edges.subject\\\"\"))\n     (check-pred (check-X-in-list 'object) (hash-keys Qedge-dic) (missing-string \"\\\"query_graph.edges.object\\\"\"))\n     )\n   (hash-keys Qedge-from-response))\n\n  (define auxiliary-graphs-from-response (hash-ref message-from-response 'auxiliary_graphs (hash)))\n  (for-each\n   (lambda (auxiliary_graph-key)\n     (define auxiliary_graph (hash-ref auxiliary-graphs-from-response auxiliary_graph-key))\n     (check-pred (check-X-in-list 'edges) (hash-keys auxiliary_graph) (missing-string \"\\\"auxiliary_graphs.edges\\\"\")))\n   (hash-keys auxiliary-graphs-from-response))\n\n  (define knowledge-graph-from-response (hash-ref message-from-response 'knowledge_graph (hash)))\n  (define knowledge-graph-key* (hash-keys knowledge-graph-from-response))\n  (check-pred (check-X-in-list 'nodes) knowledge-graph-key* (missing-string \"\\\"knowledge_graph.nodes\\\"\"))\n  (check-pred (check-X-in-list 'edges) knowledge-graph-key* (missing-string \"\\\"knowledge_graph.edges\\\"\"))\n\n  (define Kedge-from-response (hash-ref knowledge-graph-from-response 'edges (hash)))\n  (for-each\n   (lambda (Kedge-key)\n     (define Kedge-dic (hash-ref Kedge-from-response Kedge-key))\n     (check-pred (check-X-in-list 'subject) (hash-keys Kedge-dic) (missing-string \"\\\"knowledge_graph.edges.subject\\\"\"))\n     (check-pred (check-X-in-list 'object) (hash-keys Kedge-dic) (missing-string \"\\\"knowledge_graph.edges.object\\\"\"))\n     (check-pred (check-X-in-list 'predicate) (hash-keys Kedge-dic) (missing-string \"\\\"knowledge_graph.edges.predicate\\\"\"))\n     (check-pred (check-X-in-list 'sources) (hash-keys Kedge-dic) (missing-string \"\\\"knowledge_graph.edges.sources\\\"\")))\n   (hash-keys Kedge-from-response))\n\n  (define result*-from-response (hash-ref message-from-response 'results '()))\n  (for-each \n   (lambda (result-from-response)\n     (define results-key* (hash-keys result-from-response))\n     (check-pred (check-X-in-list 'node_bindings) results-key* (missing-string \"\\\"results.node_bindings\\\"\"))\n     (check-pred (check-X-in-list 'analyses) results-key* (missing-string \"\\\"results.analyses\\\"\"))\n     (for-each\n      (lambda (analyses)\n        (define analyses-key* (hash-keys analyses))\n        (check-pred (check-X-in-list 'resource_id) analyses-key*\n                    (missing-string \"\\\"results.analyses.resource_id\\\"\"))\n        (check-pred (check-X-in-list 'edge_bindings) analyses-key*\n                    (missing-string \"\\\"results.analyses.edge_bindings\\\"\"))\n        (define edge_bindings (hash-ref analyses 'edge_bindings (hash)))\n        (for-each\n         (lambda (edge-binding-key)\n           (define edge_binding* (hash-ref edge_bindings edge-binding-key))\n           (for-each\n            (lambda (edge_binding)\n              (check-pred (check-X-in-list 'id) (hash-keys edge_binding) (missing-string \"\\\"results.analyses.edge_bindings.id\\\"\")))\n            edge_binding*))\n         (hash-keys edge_bindings))\n        (define node_bindings (hash-ref result-from-response 'node_bindings))\n        (for-each\n         (lambda (node-binding-key)\n           (define node-binding* (hash-ref node_bindings node-binding-key))\n           (for-each\n            (lambda (node-binding)\n              (check-pred (check-X-in-list 'id) (hash-keys node-binding)\n                          (missing-string \"\\\"results.node_bindings.id\\\"\")))\n            node-binding*))\n         (hash-keys node_bindings)))\n      (hash-ref result-from-response 'analyses '()))\n     )\n   result*-from-response)\n  )\n\n(define (test-and-timer which-mvp known-id)\n  (printf \"About to call the ~a query with input id ~a\\n\" which-mvp known-id)\n  (if (or (eq? which-mvp 'mvp2-chem) (eq? which-mvp 'mvp2-gene))\n      (begin\n        (printf \"increased: \")\n        (test-reply (time (get-response which-mvp known-id \"increased\")))\n        (printf \"decreased: \")\n        (test-reply (time (get-response which-mvp known-id \"decreased\"))))\n      (test-reply (time (get-response which-mvp known-id #f)))))\n\n#|\n(test-and-timer 'mvp2-chem \"PUBCHEM.COMPOUND:3007\") ;Amphetamine ;Amphetamine\n(test-and-timer 'mvp2-chem \"PUBCHEM.COMPOUND:5826\") ;Dextroamphetamine\n(test-and-timer 'mvp2-chem \"PUBCHEM.COMPOUND:44246724\") ;Methylphenidate\n(test-and-timer 'mvp2-gene \"NCBIGene:1594\") ;P450\n(test-and-timer 'mvp2-gene \"NCBIGene:3075\") ;FHL1\n(test-and-timer 'mvp2-gene \"NCBIGene:7157\") ;TP53\n(test-and-timer 'mvp1 \"MONDO:0005148\") ;\"type 2 diabetes mellitus\"\n(test-and-timer 'mvp1 \"MONDO:0005302\") ;\"attention deficit hyperactivity disorder, inattentive type\"\n(test-and-timer 'mvp1 \"MONDO:0018956\") ;\"idiopathic bronchiectasis\"\n(test-and-timer 'mvp1 \"MONDO:0007254\") ;breast cancer\n(test-and-timer 'mvp1 \"MONDO:0005147\") ;type 1 diabetes mellitus\n(test-and-timer 'mvp1 \"MONDO:0020066\") ;Ehlers-Danlos syndrome\n(test-and-timer 'mvp1 \"MONDO:0007827\") ;inclusion body myositis\n(test-and-timer 'mvp1 \"MONDO:0001302\") ;hypertensive heart disease\n|#\n\n(test-and-timer 'mvp1 \"MONDO:0005301\")\n(test-and-timer 'mvp1 \"MONDO:0015564\")\n(test-and-timer 'mvp1 \"MONDO:0100345\")\n(test-and-timer 'mvp1 \"MONDO:0005799\")\n(test-and-timer 'mvp1 \"MONDO:0009265\")\n(test-and-timer 'mvp1 \"MONDO:0018982\")\n\n(test-and-timer 'mvp2-gene \"NCBIGene:1636\")\n(test-and-timer 'mvp2-gene \"NCBIGene:1565\")\n(test-and-timer 'mvp2-gene \"NCBIGene:154\")\n\n(test-and-timer 'mvp2-chem \"CHEBI:34648\")\n(test-and-timer 'mvp2-chem \"CHEBI:34911\")\n(test-and-timer 'mvp2-chem \"CHEBI:167574\")"
  },
  {
    "path": "medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt",
    "content": "#lang racket/base\n\n(provide\n curie->synonyms-in-db\n curies->synonyms-in-db\n ;;\n all-predicates-in-db\n all-classes-in-db\n ;;\n get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db\n get-non-deprecated-mixed-ins-and-descendent-classes*-in-db\n ;;\n get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db\n get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db\n ;;\n get-descendent-curies-in-db\n get-descendent-curies*-in-db\n get-n-descendent-curies*-in-db\n ;;\n iota\n pretty-print-json-string\n take-at-most\n ;;\n auto-grow\n auto-grow-with-class-hierarchy\n )\n(require\n \"../neo-low-level/query-low-level-multi-db.rkt\"\n \"../neo-reasoning/neo-biolink-reasoning.rkt\"\n racket/set\n \"neo-helpers-without-db.rkt\"\n racket/list\n racket/string)\n\n(define (curie->synonyms-in-db curie)\n  (curies-in-db (curie->synonyms curie)))\n\n(define (curies->synonyms-in-db curies)\n  (curies-in-db (curies->synonyms curies)))\n\n(define all-predicates-in-db\n  (list->set\n    (filter curie-in-db?\n            (set->list all-predicates))))\n(define all-classes-in-db\n  (list->set\n    (filter curie-in-db?\n            (set->list all-classes))))\n\n(define (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db preds)\n  (list->set\n   (curies-in-db\n    (set->list\n     (get-non-deprecated-mixed-ins-and-descendent-predicates* preds)))))\n\n(define (get-non-deprecated/mixin/abstract-ins-and-descendent-predicates*-in-db preds)\n  (list->set\n   (filter (lambda (p)\n             (not (or\n                   (predicate-mixin? p)\n                   (predicate-abstract? p))))\n           (set->list (get-non-deprecated-mixed-ins-and-descendent-predicates*-in-db preds)))))\n\n(define (get-non-deprecated-mixed-ins-and-descendent-classes*-in-db classes)\n  (list->set\n    (curies-in-db\n            (set->list\n              (get-non-deprecated-mixed-ins-and-descendent-classes* classes)))))\n\n(define (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db classes)\n  (list->set\n   (filter (lambda (c)\n             (not (or\n                   (class-mixin? c)\n                   (class-abstract? c))))\n           (set->list (get-non-deprecated-mixed-ins-and-descendent-classes*-in-db classes)))))\n\n(define (get-descendent-curies-in-db curie)\n  (get-descendent-curies*-in-db (list curie)))\n\n(define (get-descendent-curies*-in-db curies)\n  (set-union (list->set curies)\n   (set-fixed-point\n    (list->set\n     (map car\n          (query:X->Known-scored\n           #f\n           (list \"biolink:subclass_of\")\n           curies\n           (list (list 1111) #f (list 1111)))))\n    (lambda (new-curies)\n      (list->set\n       (map car\n            (query:X->Known-scored\n             #f\n             (list \"biolink:subclass_of\")\n             (set->list new-curies)\n             (list (list 1111) #f (list 1111)))))))))\n\n(define (curie-is-type? curie type)\n  (let* ((node-prop (curie->properties curie))\n        (umls-description (assoc \"description\" node-prop)))\n    (and umls-description (string-contains? (cadr umls-description) type))))\n\n(define (edge-from-source edge source^)\n  (let* ((props (cdddr edge))\n         (source (assoc \"primary_knowledge_source\" props))\n         (source (and source (cadr source))))\n    (and source (equal? source source^))))\n\n(define (get-n-descendent-curies*-in-db curies n)\n  (list->set\n   (append curies\n           (let loop ((r '()) (c curies))\n             (if (or (> (length r) n) (= (length r) n))\n                 r\n                 (let* ((children (remove-duplicates\n                                   (map car\n                                        (filter\n                                         (lambda (e) (not (edge-from-source e \"infores:medrt-umls\")))\n                                         (query:X->Known-scored\n                                          #f\n                                          (list \"biolink:subclass_of\")\n                                          c\n                                          (list (list 1111) #f (list 1111)))))))\n                        (not-classification-type (filter (lambda (c) (not (curie-is-type? c \"STY:T185\"))) children))\n                        (new-r (remove-duplicates (append r not-classification-type))))\n                   (if (= (length r) (length new-r))\n                       r\n                       (loop new-r not-classification-type))))))))\n\n(define (get-next-descendent-curies* curies)\n  (let* ((children (remove-duplicates\n                    (map car\n                         (filter\n                          (lambda (e) (not (edge-from-source e \"infores:medrt-umls\")))\n                          (query:X->Known-scored\n                           #f\n                           (list \"biolink:subclass_of\")\n                           curies\n                           (list (list 1111) #f (list 1111)))))))\n         (not-classification-type-children (filter (lambda (c) (not (curie-is-type? c \"STY:T185\"))) children)))\n    not-classification-type-children))\n\n(define (auto-grow-with-class-hierarchy 1hop? proc-template score* self-curie* result-amount)\n  (let loop ((r '()) (hierarchy 1) (desired-size result-amount) (c* self-curie*) (seen-curies '()))\n    (cond\n      [(or (< desired-size 0) (= desired-size 0)) r]\n      [(null? c*) r]\n      [else\n       (let* ((proc (proc-template c*))\n              (new-results (if 1hop? (auto-grow proc score* desired-size) (proc score* desired-size)))\n              (new-results-with-hierarchy-property (map (lambda (r) (cons hierarchy r)) new-results))\n              (new-results-size (length new-results-with-hierarchy-property))\n              (next-descendent (get-next-descendent-curies* c*))\n              (next-descendent (filter (lambda (c) (not (member c seen-curies))) next-descendent)))\n         (loop (append r new-results-with-hierarchy-property)\n               (+ hierarchy 1)\n               (- desired-size new-results-size)\n               next-descendent\n               (append seen-curies next-descendent)\n               ))])))\n"
  },
  {
    "path": "medikanren2/neo/neo-utils/neo-helpers-without-db.rkt",
    "content": "#lang racket/base\n\n(require\n racket/set\n racket/unsafe/ops\n racket/list)\n\n(provide\n maybe-time\n iota\n pretty-print-json-string\n take-at-most\n ;;\n bytes<=?\n set-fixed-point\n unsafe-bytes-split-tab\n bytes-base10->fxnat\n ;;\n minus-one-before-zero\n auto-grow)\n\n;; Use the second definition of 'maybe-time' to see the time use for\n;; low-level query calls.\n(define maybe-time (lambda (x) x)) ;; no-op\n;; (define maybe-time time)\n\n\n(define (iota n)\n  (define (iter i)\n    (if (>= i n)\n        '()\n        (cons i (iter (+ 1 i)))))\n  (iter 0))\n\n(define (pretty-print-json-string json-string port)\n  (define len (string-length json-string))\n  (define (display-indent-spaces n port)\n    (let loop ([i 0])\n      (cond\n        [(< i n)\n         (display #\\space port)\n         (loop (add1 i))]\n        [else (void)])))\n  (let loop ([i 0]\n             [indent 0]\n             [in-quote #f])\n    (cond\n      [(< i len)\n       (let ((c (string-ref json-string i)))\n         (case c\n           [(#\\\")\n            (display c port)\n            (loop (add1 i) indent (not in-quote))]\n           ;;\n           [(#\\:)\n            (display c port)\n            (unless in-quote\n              (display #\\space port))\n            (loop (add1 i) indent in-quote)]\n           ;;\n           [(#\\,)\n            (display c port)\n            (unless in-quote\n              (newline port)\n              (display-indent-spaces indent port))\n            (loop (add1 i) indent in-quote)]\n           ;;\n           [(#\\{ #\\[)\n            (display c port)\n            (if in-quote\n                (loop (add1 i) indent in-quote)                \n                (let ((indent (add1 indent)))\n                  (newline port)\n                  (display-indent-spaces indent port)\n                  (loop (add1 i) indent in-quote)))]\n           ;;\n           [(#\\} #\\])\n            (if in-quote\n                (begin\n                  (display c port)\n                  (loop (add1 i) indent in-quote))\n                (let ((indent (sub1 indent)))\n                  (newline port)\n                  (display-indent-spaces indent port)\n                  (display c port)\n                  (loop (add1 i) indent in-quote)))]\n           ;;\n           [else\n            (display c port)\n            (loop (add1 i) indent in-quote)]))]\n      [else (void)])))\n\n(define (take-at-most ls n)\n  (if (<= (length ls) n)\n      ls\n      (let loop ((ls ls)\n                 (n n))\n        (cond\n          [(<= n 0) '()]\n          [(null? ls) '()]\n          [else\n           (cons (car ls)\n                 (loop (cdr ls) (sub1 n)))]))))\n\n;; copied from 'database.rkt'\n(define (bytes<=? a b) (not (bytesfxnat bs)\n  (define len (bytes-length bs))\n  (unless (< 0 len 19)\n    (when (= len 0)  (error \"natural number must contain at least one digit\" bs))\n    (when (< 18 len) (error \"natural number must contain at most 18 digits (to safely fit in a fixnum)\" bs)))\n  (let loop ((i 0) (n 0))\n    (if (unsafe-fx< i len)\n      (let ((b (unsafe-bytes-ref bs i)))\n        (unless (unsafe-fx<= 48 b 57)\n          (error \"natural number must contain only base10 digits\" bs))\n        (loop (unsafe-fx+ i 1)\n              (unsafe-fx+ (unsafe-fx* n 10)\n                          (unsafe-fx- b 48))))\n      n)))\n\n(define minus-one-before-zero\n  (lambda (n*)\n    (and n*\n        (if (eq? (car n*) 0)\n            #f\n            (list (- (car n*) 1))))))\n\n(define (auto-grow hop-proc score* result_amount)\n  (let loop ((r '()) (sl score*))\n    (cond\n      [(> (length r) result_amount)\n       (printf \"return ~a answers\\n\" (length r))\n       r]\n      [(andmap not sl)\n       (printf \"return ~a answers\\n\" (length r))\n       r]\n      [else\n       #;(printf \"number of answers: ~a, take next round\\n\" (length r))\n       (loop (remove-duplicates  (append r (hop-proc sl)))\n             (list (minus-one-before-zero (list-ref sl 0))\n                   (minus-one-before-zero (list-ref sl 1))\n                   (minus-one-before-zero (list-ref sl 2))))])))\n"
  },
  {
    "path": "medikanren2/neo/readme.md",
    "content": "# mediKanren 2 neo TRAPI server\n\nThis directory contains the new, or `neo`, server for mediKanren 2, supporting the Translator Reasoner API (TRAPI) described at https://github.com/NCATSTranslator/ReasonerAPI\n\n\n## Racket install and raco package install\n\nLike the rest of mediKanren, the neo server requires that [DrRacket](https://racket-lang.org) be installed.  As of September 12, 2022, we are using Racket 8.6 on production.\n\nYou may receive an error from Racket when trying to start the neo server, saying that a required package is missing.  If so, you will need to install the package using the `raco` command-line tool.  For example, to install the `yaml` package, you can run the `raco` command:\n\n```\nraco pkg install yaml\n```\n\n(You will need to ensure that `raco` is on your `$PATH`)\n\nYou can see the packages already installed using `raco pkg show`.  On Will's laptop, these packages are installed:\n\n```\nwebyrd@Williams-MacBook-Pro neo % raco pkg show\nInstallation-wide:\n Package            Checksum             Source\n main-distribution  9481f7ced1cb2dea...  catalog...tribution\n racket-lib         9019e19592f3c3fd...  catalog racket-lib\n [205 auto-installed packages not shown]\nUser-specific for installation \"8.6\":\n Package         Checksum              Source\n aws             94a16a6875ac585a1...  catalog...aws/master\n chk             32fb635e19fa2dc2d...  catalog...k?path=chk\n memoize         02a647d7fec308f84...  catalog...ize#master\n shell-pipeline  116529759e06c850b...  catalog...l-pipeline\n yaml            b60a1e4a01979ed44...  catalog...aml/master\n [7 auto-installed packages not shown]\n```\n\n## dbKanren\n\nThe neo server uses the the dbKanren engine from `https://github.com/gregr/dbKanren`\n\nFor now, a snapshot of dbKanren is included in the top-level `neo` directory.  It may be better to use a symlink and to checkout from `git` a specific version of dbKanren.  For simplicity of deployment, though, it is easier to just include the correct `dbKanren` code locally.\n\n\n## Basic organization\n\nTODO\n\n\n## Data and \n\nThe neo server expects processed data to be located in the `neo-data` directory:\n\n`mediKanren/medikanren2/neo/neo-data/`\n\n\n## Processing of raw downloaded 2-TSV-file KGX formatted KGs from KGE\n\nTo process a \"raw\" 2-TSV-file KGX formatted KGs from KGE, first download the and uncompress the KG in the\n\n`neo-data/raw_downloads_from_kge_archive/`\n\ndirectory.  For example,\n\n`neo-data/raw_downloads_from_kge_archive/rtx-kg2pre_7.6/`\n\n\nNext, please read and follow the instructions in \n\n`./neo-data-import/an_important_note_on_pre_processing_kgs.txt`\n\nbefore running any of the scripts in `./neo-data-import/transform-2tsv-to-4tsv-kgs/` on a KG, to detect and fix a possible problem with DOS-style carriage returns (^M) that can appear in some of the KG TSVs.  This is critical, in order to avoid import errors.\n\n\nThen, running the transformation script in `neo/neo-data-import/transform-2tsv-to-4tsv-kgs/` to generate a directory containing 4 TSV files, which in turn can be processed using the scripts in `neo/neo-data-import/build-mediKanren2-kg-from-4tsv/`.\n\nFor example, running the script\n\n`./neo-data-import/transform-2tsv-to-4tsv-kgs/transform-rtx-kg2pre_7.6.rkt`\n\nwill transform the 2 TSV `rtx-kg2pre_7.6` files here:\n\n```\nneo-data/\n  raw_downloads_from_kge_archive/\n    rtx-kg2pre_7.6/\n      edges.tsv\n      nodes.tsv\n      ...\n```\n\ninto the 4 TSV files here:\n\n```\nneo-data/\n  raw_downloads_from_kge_archive_transformed_to_4tsv/\n    rtx-kg2pre_7.6/\n      rtx-kg2pre_7.6.edge.tsv\n      rtx-kg2pre_7.6.edgeprop.tsv\n      rtx-kg2pre_7.6.node.tsv\n      rtx-kg2pre_7.6.nodeprop.tsv\n```\n\nAfterwards, running the script\n\n`./neo-data-import/build-mediKanren2-kg-from-4tsv/import-rtx-kg2pre_7.6.rkt`\n\nwill generate the fully-processed dbKanren database here:\n\n```\nneo-data/\n  rtx-kg2pre_7.6.db/\n```\n\n\n## Starting the server\n\nTODO\n\n`neo-server.rkt` in `./neo-server/`\n\n\n`racket neo-server.rkt`\n\n```\n> (require \"neo-server.rkt\")\n```\n\n```\n> ,en neo-server.rkt\n```\n\n```\n> (stop)\n```\n\n```\n> (define stop (serve DEFAULT_PORT))\n```\n\n```\n> (stop)\n```\n"
  },
  {
    "path": "medikanren2/open-api/ISB-KG-api.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require net/url)\n(require net/http-client)\n(require json)\n\n(define api-query\n  (lambda (api-url)\n    (call/input-url\n     (string->url api-url)\n     get-pure-port\n     (lambda (port)\n       (string->jsexpr (port->string port))))))\n\n;; ISB KP\n(define url-ISB\n  \"https://biothings.ncats.io/tcga_mut_freq_kp/metadata/fields\")\n\n(define ISB-query1\n  \"https://biothings.ncats.io/drug_response_kp/query?q=subject.SYMBOL:EGFR%20AND%20association.effect_size:%3C0%20AND%20association.pvalue:%3C0.05%20AND%20association.median_ic50_mut:%3C0&size=1000\")\n\n(api-query ISB-query1)\n\n#|\nTODO: modify Greg's code below to query ISB with structured\ncontents Subject, Object, pvalue, ic50\n\n;; Broad Institute KP\n(define url.broad\n  \"https://translator.broadinstitute.org/molepro_reasoner\")\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n(define path.predicates\n  \"/predicates\")\n(define path.query\n  \"/query\")\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (define-values (status headers in)\n    (if (void? optional-post-jsexpr)\n      (http-sendrecv/url\n        (string->url url-string)\n        #:method \"GET\")\n      (http-sendrecv/url\n        (string->url url-string)\n        #:method \"POST\"\n        #:data (jsexpr->string optional-post-jsexpr)\n        #:headers '(\"Content-Type: application/json; charset=utf-8\"))))\n  (hash 'status status\n        'headers headers\n        'response (string->jsexpr (port->string in))))\n\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n;; test predicates available on Broad Institute KG\n;(pretty-print\n  ;(api-query (string-append url.broad path.predicates)))\n\n;(pretty-print\n  ;(api-query (string-append url.broad path.query)\n             ;(js-query (list (hash 'id        \"e00\"\n                                   ;'source_id \"n00\"\n                                   ;'target_id \"n01\"\n                                   ;'type      \"affects\"))\n                       ;(list (hash 'curie \"CID:2244\"\n                                   ;'id    \"n00\"\n                                   ;'type  \"chemical_substance\")\n                             ;(hash 'id    \"n01\"\n                                   ;'type  \"gene\")))))\n\n;(pretty-print\n  ;(api-query (string-append url.unsecret path.predicates)))\n\n(pretty-print\n  (api-query (string-append url.unsecret path.query)\n             (js-query (list (hash 'id        \"e00\"\n                                   'source_id \"n00\"\n                                   'target_id \"n01\"\n                                   'type      \"affects\"))\n                       (list (hash 'curie \"CHEBI:15365\"\n                                   'id    \"n00\"\n                                   'type  \"chemical_substance\")\n                             (hash 'id    \"n01\"\n                                   'type  \"gene\")))))\n\n\ndef buildQuery(genes):\n    # empty response\n    response = { \"query_graph\": dict(),\n                 \"knowledge_graph\": dict(),\n                 \"response\": dict()\n               }\n\n    # empty query graph\n    response[\"query_graph\"] = { \"edges\": [],\n                                \"nodes\": []\n                              }\n\n    # empty knowledge graph\n    response[\"knowledge_graph\"] = { \"edges\": [],\n                                    \"nodes\": []\n                                  }\n\n    # empty response graph\n    response[\"results\"] = { \"node_bindings\": [],\n                            \"edge_bindings\": []\n                          }\n\n    # nodes\n    nodeCount = 0\n    # edges\n    edgeCount = 0\n\n    # add in evidence genes\n    \n    for g in genes:\n        response['query_graph']['nodes'].append({ 'id':'n{}'.format(nodeCount),\n                                                  'type':'Gene',\n                                                  'name':'{}'.format(g[0]),\n                                                  'curie':'{}'.format(g[1])\n                                               })\n        nodeCount += 1\n\n    # grouping for genes\n    response['query_graph']['nodes'].append({ 'id':'n{}'.format(nodeCount),\n                                              'type':'gene_grouping'\n                                           })\n    nodeCount += 1\n    \n    # link genes over grouping\n    for n in response['query_graph']['nodes'][:-1]:\n        response['query_graph']['edges'].append({ 'id':'e{}'.format(edgeCount),\n                                                  'type':'part_of',\n                                                  'curie':['SEMMEDDB:PART_OF'],\n                                                  'source_id':n['id'],\n                                                  'target_id':'n{}'.format(nodeCount-1)\n                                               })\n        edgeCount += 1\n\n    # patient node\n    response['query_graph']['nodes'].append({ 'id':'n{}'.format(nodeCount),\n                                              'type':'patient',\n                                              'curie':['UMLSSC:T101']\n                                           })\n    nodeCount += 1\n\n    # link gene group to patient\n    response['query_graph']['edges'].append({ 'id':'e{}'.format(edgeCount),\n                                              'type':'expressed_in',\n                                              'curie':['RO:0002206'],\n                                              'source_id':'n{}'.format(nodeCount-2),\n                                              'target_id':'n{}'.format(nodeCount-1)\n                                           })\n    edgeCount += 1\n\n    # survival node\n    response['query_graph']['nodes'].append({ 'id': 'n{}'.format(nodeCount),\n                                              'type': 'PhenotypicFeature',\n                                              'curie': 'CHPDART:SURVIVAL',\n                                              'operator': '>=',\n                                              'value': '1000'\n                                           })\n    nodeCount += 1\n\n    # link patient to survival\n    response['query_graph']['edges'].append({ 'id':'e{}'.format(edgeCount),\n                                              'type':'has_phenotype',\n                                              'source_id':'n{}'.format(nodeCount-2),\n                                              'target_id':'n{}'.format(nodeCount-1)\n                                           })\n    edgeCount += 1\n\n    # BKB target\n    response['probability_targets'] = [('Survival_Time', '>=', 1000)]\n\n    return response\n\n\n\n\n\n\n|#\n"
  },
  {
    "path": "medikanren2/open-api/TranslatorReasonersAPI.json",
    "content": "{\n    \"openapi\": \"3.0.3\",\n    \"info\": {\n        \"contact\": {\n            \"email\": \"webyrd@gmail.com\",\n            \"name\": \"William E. Byrd\",\n            \"url\": \"https://github.com/webyrd\"\n        },\n        \"description\": \"A ReasonerStdAPI for mediKanren\",\n        \"license\": {\n            \"name\": \"MIT License\",\n            \"url\": \"https://github.com/webyrd/mediKanren/blob/master/LICENSE\"\n        },\n        \"title\": \"mediKanren\",\n        \"version\": \"2.0-alpha\",\n        \"x-trapi\": {\n            \"version\": \"1.1.0\",\n            \"operations\": [\n                \"lookup\"\n            ]\n        },\n        \"x-translator\": {\n            \"infores\": \"infores:unsecret-agent\",\n            \"biolink-version\": \"2.2.11\",\n            \"component\": \"ARA\",\n            \"team\": [\n                \"Unsecret Agent\"\n            ]\n        }\n    },\n    \"servers\": [\n        {\n            \"url\": \"https://medikanren-trapi.ci.transltr.io/v2\",\n            \"description\": \"Production server\",\n            \"x-maturity\": \"production\"\n        }\n    ],\n    \"tags\": [\n        {\n            \"name\": \"query\"\n        },\n        {\n            \"name\": \"translator\"\n        },\n        {\n            \"name\": \"trapi\"\n        }\n    ],\n    \"paths\": {\n        \"/query\": {\n            \"post\": {\n                \"tags\": [\n                    \"query\"\n                ],\n                \"summary\": \"Initiate a query and wait to receive a Response\",\n                \"description\": \"\",\n                \"requestBody\": {\n                    \"description\": \"Query information to be submitted\",\n                    \"required\": true,\n                    \"content\": {\n                        \"application/json\": {\n                            \"example\": {\n                                \"message\": {\n                                    \"disable_external_requests\": true,\n                                    \"query_graph\": {\n                                        \"edges\": {\n                                            \"e00\": {\n                                                \"object\": \"n01\",\n                                                \"subject\": \"n00\",\n                                                \"predicates\": [\n                                                    \"biolink:physically_interacts_with\"\n                                                ]\n                                            }\n                                        },\n                                        \"nodes\": {\n                                            \"n00\": {\n                                                \"ids\": [\n                                                    \"CHEMBL.COMPOUND:CHEMBL112\"\n                                                ]\n                                            },\n                                            \"n01\": {\n                                                \"categories\": [\n                                                    \"biolink:Protein\"\n                                                ]\n                                            }\n                                        }\n                                    }\n                                }\n                            },\n                            \"schema\": {\n                                \"$ref\": \"#/components/schemas/Query\"\n                            }\n                        }\n                    }\n                },\n                \"responses\": {\n                    \"200\": {\n                        \"description\": \"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized.\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"$ref\": \"#/components/schemas/Response\"\n                                }\n                            }\n                        }\n                    },\n                    \"400\": {\n                        \"description\": \"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized).\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"type\": \"string\"\n                                }\n                            }\n                        }\n                    },\n                    \"500\": {\n                        \"description\": \"Internal server error.\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"type\": \"string\"\n                                }\n                            }\n                        }\n                    },\n                    \"501\": {\n                        \"description\": \"Not implemented.\",\n                        \"content\": {\n                            \"application/json\": {\n                                \"schema\": {\n                                    \"type\": \"string\"\n                                }\n                            }\n                        }\n                    }\n                },\n                \"x-swagger-router-controller\": \"swagger_server.controllers.query_controller\"\n            }\n        }\n    },\n    \"components\": {\n        \"schemas\": {\n            \"Query\": {\n                \"description\": \"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.\",\n                \"x-body-name\": \"request_body\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"message\": {\n                        \"$ref\": \"#/components/schemas/Message\",\n                        \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n                    },\n                    \"log_level\": {\n                        \"description\": \"The least critical level of logs to return\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/LogLevel\"\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"workflow\": {\n                        \"description\": \"List of workflow steps to be executed.\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n                            }\n                        ],\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"message\"\n                ]\n            },\n            \"AsyncQuery\": {\n                \"description\": \"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.\",\n                \"x-body-name\": \"request_body\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"callback\": {\n                        \"type\": \"string\",\n                        \"format\": \"uri\",\n                        \"pattern\": \"^https?://\",\n                        \"description\": \"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.\"\n                    },\n                    \"message\": {\n                        \"$ref\": \"#/components/schemas/Message\",\n                        \"description\": \"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.\"\n                    },\n                    \"log_level\": {\n                        \"description\": \"The least critical level of logs to return\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/LogLevel\"\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"workflow\": {\n                        \"description\": \"List of workflow steps to be executed.\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n                            }\n                        ],\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"callback\",\n                    \"message\"\n                ]\n            },\n            \"Response\": {\n                \"type\": \"object\",\n                \"description\": \"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.\",\n                \"properties\": {\n                    \"message\": {\n                        \"description\": \"Contains the knowledge of the response (query graph, knowledge graph, and results).\",\n                        \"$ref\": \"#/components/schemas/Message\"\n                    },\n                    \"status\": {\n                        \"description\": \"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable\",\n                        \"type\": \"string\",\n                        \"example\": \"Success\",\n                        \"nullable\": true\n                    },\n                    \"description\": {\n                        \"description\": \"A brief human-readable description of the outcome\",\n                        \"type\": \"string\",\n                        \"example\": \"Success. 42 results found.\",\n                        \"nullable\": true\n                    },\n                    \"logs\": {\n                        \"description\": \"Log entries containing errors, warnings, debugging information, etc\",\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/LogEntry\"\n                        },\n                        \"nullable\": true\n                    },\n                    \"workflow\": {\n                        \"description\": \"List of workflow steps that were executed.\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"http://standards.ncats.io/workflow/1.0.0/schema\"\n                            }\n                        ],\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"message\"\n                ]\n            },\n            \"Message\": {\n                \"description\": \"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"results\": {\n                        \"description\": \"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property,\\n if present, MAY be used to infer result rankings.\",\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Result\"\n                        },\n                        \"nullable\": true\n                    },\n                    \"query_graph\": {\n                        \"description\": \"QueryGraph object that contains a serialization of a query in the form of a graph\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/QueryGraph\"\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"knowledge_graph\": {\n                        \"description\": \"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message\",\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/KnowledgeGraph\"\n                            }\n                        ],\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": false\n            },\n            \"LogEntry\": {\n                \"description\": \"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.\",\n                \"type\": \"object\",\n                \"properties\": {\n                    \"timestamp\": {\n                        \"type\": \"string\",\n                        \"format\": \"date-time\",\n                        \"description\": \"Timestamp in ISO 8601 format\",\n                        \"example\": \"2020-09-03T18:13:49+00:00\",\n                        \"nullable\": true\n                    },\n                    \"level\": {\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/LogLevel\"\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"code\": {\n                        \"type\": \"string\",\n                        \"description\": \"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed\",\n                        \"nullable\": true\n                    },\n                    \"message\": {\n                        \"type\": \"string\",\n                        \"description\": \"A human-readable log message\",\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true\n            },\n            \"LogLevel\": {\n                \"type\": \"string\",\n                \"description\": \"Logging level\",\n                \"enum\": [\n                    \"ERROR\",\n                    \"WARNING\",\n                    \"INFO\",\n                    \"DEBUG\"\n                ]\n            },\n            \"Result\": {\n                \"type\": \"object\",\n                \"description\": \"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings).\",\n                \"properties\": {\n                    \"node_bindings\": {\n                        \"type\": \"object\",\n                        \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.\",\n                        \"additionalProperties\": {\n                            \"type\": \"array\",\n                            \"items\": {\n                                \"$ref\": \"#/components/schemas/NodeBinding\"\n                            }\n                        }\n                    },\n                    \"edge_bindings\": {\n                        \"type\": \"object\",\n                        \"description\": \"The dictionary of Input Query Graph to Result Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple knowledge graph edges in the result.\",\n                        \"additionalProperties\": {\n                            \"type\": \"array\",\n                            \"items\": {\n                                \"$ref\": \"#/components/schemas/EdgeBinding\"\n                            }\n                        }\n                    },\n                    \"score\": {\n                        \"type\": \"number\",\n                        \"format\": \"float\",\n                        \"example\": 163.233,\n                        \"description\": \"A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better.\",\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"node_bindings\",\n                    \"edge_bindings\"\n                ]\n            },\n            \"NodeBinding\": {\n                \"type\": \"object\",\n                \"properties\": {\n                    \"id\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"description\": \"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation (such annotation is not yet fully standardized).\"\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"id\"\n                ]\n            },\n            \"EdgeBinding\": {\n                \"type\": \"object\",\n                \"description\": \"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized).\",\n                \"properties\": {\n                    \"id\": {\n                        \"type\": \"string\",\n                        \"description\": \"The key identifier of a specific KnowledgeGraph Edge.\"\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Attribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"id\"\n                ]\n            },\n            \"KnowledgeGraph\": {\n                \"type\": \"object\",\n                \"description\": \"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.\",\n                \"properties\": {\n                    \"nodes\": {\n                        \"type\": \"object\",\n                        \"description\": \"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/Node\"\n                        }\n                    },\n                    \"edges\": {\n                        \"type\": \"object\",\n                        \"description\": \"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/Edge\"\n                        }\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"nodes\",\n                    \"edges\"\n                ]\n            },\n            \"QueryGraph\": {\n                \"type\": \"object\",\n                \"description\": \"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.\",\n                \"properties\": {\n                    \"nodes\": {\n                        \"type\": \"object\",\n                        \"description\": \"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/QNode\"\n                        }\n                    },\n                    \"edges\": {\n                        \"type\": \"object\",\n                        \"description\": \"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/QEdge\"\n                        }\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"nodes\",\n                    \"edges\"\n                ]\n            },\n            \"QNode\": {\n                \"type\": \"object\",\n                \"description\": \"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.\",\n                \"properties\": {\n                    \"ids\": {\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/CURIE\"\n                        },\n                        \"minItems\": 1,\n                        \"example\": [\n                            \"OMIM:603903\"\n                        ],\n                        \"description\": \"CURIE identifier for this node\",\n                        \"nullable\": true\n                    },\n                    \"categories\": {\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/BiolinkEntity\"\n                        },\n                        \"minItems\": 1,\n                        \"nullable\": true\n                    },\n                    \"is_set\": {\n                        \"type\": \"boolean\",\n                        \"description\": \"Boolean that if set to true, indicates that this QNode MAY have multiple KnowledgeGraph Nodes bound to it within each Result. The nodes in a set should be considered as a set of independent nodes, rather than a set of dependent nodes, i.e., the answer would still be valid if the nodes in the set were instead returned individually. Multiple QNodes may have is_set=True. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=False, each n1 must be connected to n2. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True, each n1 must be connected to at least one n2.\",\n                        \"default\": false\n                    },\n                    \"constraints\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/QueryConstraint\"\n                        },\n                        \"default\": []\n                    }\n                },\n                \"additionalProperties\": true\n            },\n            \"QEdge\": {\n                \"type\": \"object\",\n                \"description\": \"An edge in the QueryGraph used as an filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.\",\n                \"properties\": {\n                    \"predicates\": {\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n                        },\n                        \"minItems\": 1,\n                        \"nullable\": true\n                    },\n                    \"subject\": {\n                        \"type\": \"string\",\n                        \"example\": \"https://omim.org/entry/603903\",\n                        \"description\": \"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.\"\n                    },\n                    \"object\": {\n                        \"type\": \"string\",\n                        \"example\": \"https://www.uniprot.org/uniprot/P00738\",\n                        \"description\": \"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.\"\n                    },\n                    \"constraints\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of contraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/QueryConstraint\"\n                        },\n                        \"default\": []\n                    }\n                },\n                \"additionalProperties\": true,\n                \"required\": [\n                    \"subject\",\n                    \"object\"\n                ]\n            },\n            \"Node\": {\n                \"type\": \"object\",\n                \"description\": \"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.\",\n                \"properties\": {\n                    \"name\": {\n                        \"type\": \"string\",\n                        \"example\": \"Haptoglobin\",\n                        \"description\": \"Formal name of the entity\",\n                        \"nullable\": true\n                    },\n                    \"categories\": {\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/BiolinkEntity\"\n                        },\n                        \"nullable\": true\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of attributes describing the node\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Attribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": false\n            },\n            \"Attribute\": {\n                \"type\": \"object\",\n                \"description\": \"Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with a SubAttribute (for example to provide confidence intervals on a value).\",\n                \"properties\": {\n                    \"attribute_type_id\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"description\": \"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.\",\n                        \"example\": \"Biolink:has_p-value_evidence, Biolink:has_original_source\"\n                    },\n                    \"original_attribute_name\": {\n                        \"type\": \"string\",\n                        \"description\": \"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.\",\n                        \"example\": \"p-value\",\n                        \"nullable\": true\n                    },\n                    \"value\": {\n                        \"description\": \"Value of the attribute. May be any data type, including a list.\",\n                        \"example\": 0.000153\n                    },\n                    \"value_type_id\": {\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/CURIE\"\n                            }\n                        ],\n                        \"description\": \"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n                        \"example\": \"EDAM:data_1187\",\n                        \"nullable\": true\n                    },\n                    \"attribute_source\": {\n                        \"type\": \"string\",\n                        \"description\": \"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.\",\n                        \"example\": \"UniProtKB\",\n                        \"nullable\": true\n                    },\n                    \"value_url\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).\",\n                        \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n                        \"nullable\": true\n                    },\n                    \"description\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-readable description for the attribute and its value.\",\n                        \"example\": \"Assertion Authored By Dr. Trans L. Ator\",\n                        \"nullable\": true\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/SubAttribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"attribute_type_id\",\n                    \"value\"\n                ],\n                \"additionalProperties\": false\n            },\n            \"SubAttribute\": {\n                \"type\": \"object\",\n                \"description\": \"Second-level attribute that can be used to qualify information contained in a primary Attribute attached to a Node or Edge.\",\n                \"properties\": {\n                    \"attribute_type_id\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"description\": \"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.\",\n                        \"example\": \"Biolink:has_p-value_evidence, Biolink:has_original_source\"\n                    },\n                    \"original_attribute_name\": {\n                        \"type\": \"string\",\n                        \"description\": \"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.\",\n                        \"example\": \"p-value\",\n                        \"nullable\": true\n                    },\n                    \"value\": {\n                        \"description\": \"Value of the attribute. May be any data type, including a list.\",\n                        \"example\": 0.000153\n                    },\n                    \"value_type_id\": {\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/CURIE\"\n                            }\n                        ],\n                        \"description\": \"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n                        \"example\": \"EDAM:data_1187\",\n                        \"nullable\": true\n                    },\n                    \"attribute_source\": {\n                        \"type\": \"string\",\n                        \"description\": \"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.\",\n                        \"example\": \"UniProtKB\",\n                        \"nullable\": true\n                    },\n                    \"value_url\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).\",\n                        \"example\": \"https://pubmed.ncbi.nlm.nih.gov/32529952\",\n                        \"nullable\": true\n                    },\n                    \"description\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-readable description for the attribute and its value.\",\n                        \"example\": \"Assertion Authored By Dr. Trans L. Ator\",\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"attribute_type_id\",\n                    \"value\"\n                ],\n                \"additionalProperties\": false\n            },\n            \"Edge\": {\n                \"type\": \"object\",\n                \"description\": \"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \\\"thought\\\" graph resulting from a query upon the underlying knowledge source.\",\n                \"properties\": {\n                    \"predicate\": {\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/BiolinkPredicate\"\n                            }\n                        ],\n                        \"nullable\": true\n                    },\n                    \"subject\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"example\": \"OMIM:603903\",\n                        \"description\": \"Corresponds to the map key CURIE of the subject concept node of this relationship edge.\"\n                    },\n                    \"object\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"example\": \"UniProtKB:P00738\",\n                        \"description\": \"Corresponds to the map key CURIE of the object concept node of this relationship edge.\"\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"A list of additional attributes for this edge\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/Attribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"additionalProperties\": false,\n                \"required\": [\n                    \"subject\",\n                    \"object\"\n                ]\n            },\n            \"BiolinkEntity\": {\n                \"description\": \"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.\",\n                \"type\": \"string\",\n                \"pattern\": \"^biolink:[A-Z][a-zA-Z]*$\",\n                \"externalDocs\": {\n                    \"description\": \"Biolink model entities\",\n                    \"url\": \"https://biolink.github.io/biolink-model/docs/NamedThing.html\"\n                },\n                \"example\": \"biolink:PhenotypicFeature\"\n            },\n            \"BiolinkPredicate\": {\n                \"description\": \"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.\",\n                \"type\": \"string\",\n                \"pattern\": \"^biolink:[a-z][a-z_]*$\",\n                \"externalDocs\": {\n                    \"description\": \"Biolink model predicates\",\n                    \"url\": \"https://biolink.github.io/biolink-model/docs/related_to.html\"\n                },\n                \"example\": \"biolink:interacts_with\"\n            },\n            \"CURIE\": {\n                \"type\": \"string\",\n                \"description\": \"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.\",\n                \"externalDocs\": {\n                    \"url\": \"https://www.w3.org/TR/2010/NOTE-curie-20101216/\"\n                }\n            },\n            \"MetaKnowledgeGraph\": {\n                \"type\": \"object\",\n                \"description\": \"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.\",\n                \"properties\": {\n                    \"nodes\": {\n                        \"type\": \"object\",\n                        \"description\": \"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.\",\n                        \"additionalProperties\": {\n                            \"$ref\": \"#/components/schemas/MetaNode\"\n                        }\n                    },\n                    \"edges\": {\n                        \"type\": \"array\",\n                        \"description\": \"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/MetaEdge\"\n                        }\n                    }\n                },\n                \"required\": [\n                    \"nodes\",\n                    \"edges\"\n                ]\n            },\n            \"MetaNode\": {\n                \"type\": \"object\",\n                \"description\": \"Description of a node category provided by this TRAPI web service.\",\n                \"properties\": {\n                    \"id_prefixes\": {\n                        \"type\": \"array\",\n                        \"description\": \"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.\",\n                        \"items\": {\n                            \"type\": \"string\"\n                        },\n                        \"minItems\": 1,\n                        \"example\": [\n                            \"CHEMBL.COMPOUND\",\n                            \"INCHIKEY\"\n                        ]\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"Node attributes provided by this TRAPI web service.\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/MetaAttribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"id_prefixes\"\n                ],\n                \"additionalProperties\": false\n            },\n            \"MetaEdge\": {\n                \"type\": \"object\",\n                \"description\": \"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.\",\n                \"properties\": {\n                    \"subject\": {\n                        \"$ref\": \"#/components/schemas/BiolinkEntity\",\n                        \"description\": \"Subject node category of this relationship edge.\",\n                        \"example\": \"biolink:ChemicalSubstance\"\n                    },\n                    \"predicate\": {\n                        \"$ref\": \"#/components/schemas/BiolinkPredicate\",\n                        \"description\": \"Biolink relationship between the subject and object categories.\",\n                        \"example\": \"biolink:affects\"\n                    },\n                    \"object\": {\n                        \"$ref\": \"#/components/schemas/BiolinkEntity\",\n                        \"description\": \"Object node category of this relationship edge.\",\n                        \"example\": \"biolink:Protein\"\n                    },\n                    \"attributes\": {\n                        \"type\": \"array\",\n                        \"description\": \"Edge attributes provided by this TRAPI web service.\",\n                        \"items\": {\n                            \"$ref\": \"#/components/schemas/MetaAttribute\"\n                        },\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"subject\",\n                    \"predicate\",\n                    \"object\"\n                ],\n                \"additionalProperties\": false\n            },\n            \"MetaAttribute\": {\n                \"type\": \"object\",\n                \"properties\": {\n                    \"attribute_type_id\": {\n                        \"$ref\": \"#/components/schemas/CURIE\",\n                        \"description\": \"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)\",\n                        \"example\": \"biolink:p_value\"\n                    },\n                    \"attribute_source\": {\n                        \"type\": \"string\",\n                        \"description\": \"Source of an attribute provided by this TRAPI web service.\",\n                        \"example\": \"infores:chembl\",\n                        \"nullable\": true\n                    },\n                    \"original_attribute_names\": {\n                        \"type\": \"array\",\n                        \"items\": {\n                            \"type\": \"string\"\n                        },\n                        \"description\": \"Names of an the attribute as provided by the source.\",\n                        \"nullable\": true,\n                        \"minItems\": 1\n                    },\n                    \"constraint_use\": {\n                        \"type\": \"boolean\",\n                        \"description\": \"Indicates whether this attribute can be used as a query constraint.\",\n                        \"default\": false\n                    },\n                    \"constraint_name\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.\",\n                        \"example\": \"p-value\",\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"attribute_type_id\"\n                ]\n            },\n            \"QueryConstraint\": {\n                \"type\": \"object\",\n                \"description\": \"Generic query constraint for a query node or query edge\",\n                \"properties\": {\n                    \"id\": {\n                        \"allOf\": [\n                            {\n                                \"$ref\": \"#/components/schemas/CURIE\"\n                            }\n                        ],\n                        \"description\": \"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.\",\n                        \"example\": \"EDAM:data_0844\"\n                    },\n                    \"name\": {\n                        \"type\": \"string\",\n                        \"description\": \"Human-readable name or label for the constraint concept. If appropriate, it SHOULD be the term name of the CURIE used as the 'id'. This is redundant but required for human readability.\",\n                        \"example\": \"molecular mass\"\n                    },\n                    \"not\": {\n                        \"type\": \"boolean\",\n                        \"default\": false\n                    },\n                    \"operator\": {\n                        \"type\": \"string\",\n                        \"description\": \"Relationship between the database value and the constraint value for the specified id. The operators ==, >, and < mean is exactly equal to, is greater than, and is less than, respectively. The 'matches' operator indicates that the value is a regular expression to be evaluated. If value is a list type, then at least one evaluation must be true (equivalent to OR). This means that the == operator with a list acts like a SQL 'IN' clause. The 'not' property negates the operator such that not and == means 'not equal to' (or 'not in' for a list), and not > means <=, and not < means >=, and not matches means does not match. The '==' operator SHOULD NOT be used in a manner that describes an \\\"is a\\\" subclass relationship for the parent QNode.\",\n                        \"enum\": [\n                            \"==\",\n                            \">\",\n                            \"<\",\n                            \"matches\"\n                        ]\n                    },\n                    \"value\": {\n                        \"example\": 57.0,\n                        \"description\": \"Value of the attribute. May be any data type, including a list. If the value is a list and there are multiple items, at least one comparison must be true (equivalent to OR). If 'value' is of data type 'object', the keys of the object MAY be treated as a list. A 'list' data type paired with the '>' or '<' operators will encode extraneous comparisons, but this is permitted as it is in SQL and other languages.\"\n                    },\n                    \"unit_id\": {\n                        \"example\": \"UO:0000222\",\n                        \"description\": \"CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units.\",\n                        \"nullable\": true\n                    },\n                    \"unit_name\": {\n                        \"example\": \"kilodalton\",\n                        \"description\": \"Term name that is associated with the CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability.\",\n                        \"nullable\": true\n                    }\n                },\n                \"required\": [\n                    \"name\",\n                    \"id\",\n                    \"operator\",\n                    \"value\"\n                ],\n                \"additionalProperties\": false\n            }\n        }\n    }\n}\n"
  },
  {
    "path": "medikanren2/open-api/TranslatorReasonersAPI.yaml",
    "content": "openapi: 3.0.3\ninfo:\n  contact:\n    email: webyrd@gmail.com\n    name: William E. Byrd\n    url: https://github.com/webyrd\n  description: A ReasonerStdAPI for mediKanren\n  license:\n    name: MIT License\n    url: https://github.com/webyrd/mediKanren/blob/master/LICENSE\n  title: mediKanren \n  version: \"2.0-alpha\"\n  x-trapi:\n    ## there's a plan to update the trapi server to fit the latest spec\n    version: 1.1.0\n    operations:\n      - lookup\n  x-translator:\n    infores: \"infores:unsecret-agent\"\n    ## using biolink version from rtx-kg2 so look there\n    biolink-version: \"2.2.11\"\n    component: ARA\n    team:\n      - Unsecret Agent\nservers:\n- url: https://medikanren-trapi.ci.transltr.io/v2\n  description: Production server\n  x-maturity: production\ntags:\n#- name: meta_knowledge_graph\n- name: query\n- name: translator\n- name: trapi\npaths:\n#  /meta_knowledge_graph:\n#    get:\n#      tags:\n#        - meta_knowledge_graph\n#      summary: Meta knowledge graph representation of this TRAPI web service.\n#      description: Returns meta knowledge graph representation of this TRAPI web service.\n#      responses:\n#        '200':\n#          description: Successful Response\n#          content:\n#            application/json:\n#              schema:\n#                $ref: '#/components/schemas/MetaKnowledgeGraph'\n  /query:\n    post:\n      tags:\n        - query\n      summary: Initiate a query and wait to receive a Response\n      description: ''\n      requestBody:\n        description: Query information to be submitted\n        required: true\n        content:\n          application/json:\n            ## used for registry's uptime status so should be a quick one\n            example:\n              message:\n                disable_external_requests: true\n                query_graph:\n                  edges:\n                    e00:\n                      object: \"n01\"\n                      subject: \"n00\"\n                      predicates:\n                      - \"biolink:physically_interacts_with\"\n                  nodes:\n                    n00:\n                      ids:\n                      - \"CHEMBL.COMPOUND:CHEMBL112\"\n                    n01:\n                      categories:\n                      - \"biolink:Protein\"\n            schema:\n              $ref: '#/components/schemas/Query'\n      responses:\n        '200':\n          description: >-\n            OK. There may or may not be results. Note that some of the provided\n            identifiers may not have been recognized.\n          content:\n            application/json:\n              schema:\n                $ref: '#/components/schemas/Response'\n        '400':\n          description: >-\n            Bad request. The request is invalid according to this OpenAPI\n            schema OR a specific identifier is believed to be invalid somehow\n            (not just unrecognized).\n          content:\n            application/json:\n              schema:\n                type: string\n        '500':\n          description: >-\n            Internal server error.\n          content:\n            application/json:\n              schema:\n                type: string\n        '501':\n          description: >-\n            Not implemented.\n          content:\n            application/json:\n              schema:\n                type: string\n      x-swagger-router-controller: swagger_server.controllers.query_controller\ncomponents:\n  schemas:\n    Query:\n      description: >-\n        The Query class is used to package a user request for information. A\n        Query object consists of a required Message object with optional\n        additional properties. Additional properties are intended to convey\n        implementation-specific or query-independent parameters. For example,\n        an additional property specifying a log level could allow a user to\n        override the default log level in order to receive more fine-grained\n        log information when debugging an issue.\n      x-body-name: request_body\n      type: object\n      properties:\n        message:\n          $ref: '#/components/schemas/Message'\n          description: >-\n            The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For\n            example, the fill operation requires a non-empty query_graph field\n            as part of the Message, whereas other operations, e.g. overlay,\n            require non-empty results and knowledge_graph fields.\n        log_level:\n          description: The least critical level of logs to return\n          allOf:\n            - $ref: '#/components/schemas/LogLevel'\n          nullable: true\n        workflow:\n          description: List of workflow steps to be executed.\n          allOf:\n            - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          nullable: true\n      additionalProperties: true\n      required:\n        - message\n    AsyncQuery:\n      description: >-\n        The AsyncQuery class is effectively the same as the Query class but\n        it requires a callback property.\n      x-body-name: request_body\n      type: object\n      properties:\n        callback:\n          type: string\n          format: uri\n          pattern: ^https?://\n          description: >-\n            Upon completion, this server will send a POST request to the\n            callback URL with `Content-Type: application/json` header and\n            request body containing a JSON-encoded `Response` object.\n            The server MAY POST `Response` objects before work is fully\n            complete to provide interim results with a Response.status\n            value of 'Running'. If a POST operation to the callback URL\n            does not succeed, the server SHOULD retry the POST at least\n            once.\n        message:\n          $ref: '#/components/schemas/Message'\n          description: >-\n            The query Message is a serialization of the user request. Content\n            of the Message object depends on the intended TRAPI operation. For\n            example, the fill operation requires a non-empty query_graph field\n            as part of the Message, whereas other operations, e.g. overlay,\n            require non-empty results and knowledge_graph fields.\n        log_level:\n          description: The least critical level of logs to return\n          allOf:\n            - $ref: '#/components/schemas/LogLevel'\n          nullable: true\n        workflow:\n          description: List of workflow steps to be executed.\n          allOf:\n            - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          nullable: true\n      additionalProperties: true\n      required:\n        - callback\n        - message\n    Response:\n      type: object\n      description: >-\n        The Response object contains the main payload when a TRAPI query\n        endpoint interprets and responds to the submitted query successfully\n        (i.e., HTTP Status Code 200). The message property contains the\n        knowledge of the response (query graph, knowledge graph, and results).\n        The status, description, and logs properties provide additional details\n        about the response.\n      properties:\n        message:\n          description: >-\n            Contains the knowledge of the response (query graph, knowledge\n            graph, and results).\n          $ref: '#/components/schemas/Message'\n        status:\n          description: >-\n            One of a standardized set of short codes,\n            e.g. Success, QueryNotTraversable, KPsNotAvailable\n          type: string\n          example: Success\n          nullable: true\n        description:\n          description: A brief human-readable description of the outcome\n          type: string\n          example: Success. 42 results found.\n          nullable: true\n        logs:\n          description: >-\n            Log entries containing errors, warnings, debugging information, etc\n          type: array\n          items:\n            $ref: '#/components/schemas/LogEntry'\n          nullable: true\n        workflow:\n          description: List of workflow steps that were executed.\n          allOf:\n            - $ref: http://standards.ncats.io/workflow/1.0.0/schema\n          nullable: true\n      additionalProperties: true\n      required:\n        - message\n    Message:\n      description: >-\n        The message object holds the main content of a Query or a Response in\n        three properties: query_graph, results, and knowledge_graph.\n        The query_graph property contains the query configuration, the results\n        property contains any answers that are returned by the service,\n        and knowledge_graph property contains lists of edges and nodes in the\n        thought graph corresponding to this message. The content of these\n        properties is context-dependent to the encompassing object and\n        the TRAPI operation requested.\n      type: object\n      properties:\n        results:\n          description: >-\n            List of all returned Result objects for the query posed.\n            The list SHOULD NOT be assumed to be ordered. The 'score' property,\n             if present, MAY be used to infer result rankings.\n          type: array\n          items:\n            $ref: '#/components/schemas/Result'\n          nullable: true\n        query_graph:\n          description: >-\n            QueryGraph object that contains a serialization of a query in the\n            form of a graph\n          allOf:\n            - $ref: '#/components/schemas/QueryGraph'\n          nullable: true\n        knowledge_graph:\n          description: >-\n            KnowledgeGraph object that contains lists of nodes and edges\n            in the thought graph corresponding to the message\n          allOf:\n            - $ref: '#/components/schemas/KnowledgeGraph'\n          nullable: true\n      additionalProperties: false\n    LogEntry:\n      description: >-\n        The LogEntry object contains information useful for tracing\n        and debugging across Translator components.  Although an\n        individual component (for example, an ARA or KP) may have its\n        own logging and debugging infrastructure, this internal\n        information is not, in general, available to other components.\n        In addition to a timestamp and logging level, LogEntry\n        includes a string intended to be read by a human, along with\n        one of a standardized set of codes describing the condition of\n        the component sending the message.\n      type: object\n      properties:\n        timestamp:\n          type: string\n          format: date-time\n          description: Timestamp in ISO 8601 format\n          example: '2020-09-03T18:13:49+00:00'\n          nullable: true\n        level:\n          allOf:\n            - $ref: '#/components/schemas/LogLevel'\n          nullable: true\n        code:\n          type: string\n          description: >-\n            One of a standardized set of short codes\n            e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed\n          nullable: true\n        message:\n          type: string\n          description: A human-readable log message\n          nullable: true\n      additionalProperties: true\n    LogLevel:\n      type: string\n      description: Logging level\n      enum:\n        - ERROR\n        - WARNING\n        - INFO\n        - DEBUG\n    Result:\n      type: object\n      description: >-\n        A Result object specifies the nodes and edges in the knowledge graph\n        that satisfy the structure or conditions of a user-submitted query\n        graph. It must contain a NodeBindings object (list of query graph node\n        to knowledge graph node mappings) and an EdgeBindings object (list of\n        query graph edge to knowledge graph edge mappings).\n      properties:\n        node_bindings:\n          type: object\n          description: >-\n            The dictionary of Input Query Graph to Result Knowledge Graph node\n            bindings where the dictionary keys are the key identifiers of the\n            Query Graph nodes and the associated values of those keys are\n            instances of NodeBinding schema type (see below). This value is an\n            array of NodeBindings since a given query node may have multiple\n            knowledge graph Node bindings in the result.\n          additionalProperties:\n            type: array\n            items:\n              $ref: '#/components/schemas/NodeBinding'\n        edge_bindings:\n          type: object\n          description: >-\n            The dictionary of Input Query Graph to Result Knowledge Graph edge\n            bindings where the dictionary keys are the key identifiers of the\n            Query Graph edges and the associated values of those keys are\n            instances of EdgeBinding schema type (see below). This value is an\n            array of EdgeBindings since a given query edge may resolve to\n            multiple knowledge graph edges in the result.\n          additionalProperties:\n            type: array\n            items:\n              $ref: '#/components/schemas/EdgeBinding'\n        score:\n          type: number\n          format: float\n          example: 163.233\n          description: >-\n            A numerical score associated with this result indicating the\n            relevance or confidence of this result relative to others in the\n            returned set. Higher MUST be better.\n          nullable: true\n      additionalProperties: true\n      required:\n        - node_bindings\n        - edge_bindings\n    NodeBinding:\n      type: object\n      properties:\n        id:\n          $ref: '#/components/schemas/CURIE'\n          description: >-\n            An instance of NodeBinding is a single KnowledgeGraph Node mapping,\n            identified by the corresponding 'id' object key identifier of the\n            Node within the Knowledge Graph. Instances of NodeBinding may\n            include extra annotation (such annotation is not yet fully\n            standardized).\n      additionalProperties: true\n      required:\n        - id\n    EdgeBinding:\n      type: object\n      description: >-\n        A instance of EdgeBinding is a single KnowledgeGraph Edge mapping,\n        identified by the corresponding 'id' object key identifier of the\n        Edge within the Knowledge Graph. Instances of EdgeBinding may include\n        extra annotation (such annotation is not yet fully standardized).\n      properties:\n        id:\n          type: string\n          description: The key identifier of a specific KnowledgeGraph Edge.\n        attributes:\n          type: array\n          description: >-\n            A list of attributes providing further information about the\n            edge binding. This is not intended for capturing edge attributes\n            and should only be used for properties that vary from result to\n            result.\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n      additionalProperties: true\n      required:\n        - id\n    KnowledgeGraph:\n      type: object\n      description: >-\n        The knowledge graph associated with a set of results. The instances\n        of Node and Edge defining this graph represent instances of\n        biolink:NamedThing (concept nodes) and biolink:Association\n        (relationship edges) representing (Attribute) annotated knowledge\n        returned from the knowledge sources and inference agents wrapped by\n        the given TRAPI implementation.\n      properties:\n        nodes:\n          type: object\n          description: >-\n            Dictionary of Node instances used in the KnowledgeGraph,\n            referenced elsewhere in the TRAPI output by the dictionary key.\n          additionalProperties:\n            $ref: '#/components/schemas/Node'\n        edges:\n          type: object\n          description: >-\n            Dictionary of Edge instances used in the KnowledgeGraph,\n            referenced elsewhere in the TRAPI output by the dictionary key.\n          additionalProperties:\n            $ref: '#/components/schemas/Edge'\n      additionalProperties: true\n      required:\n        - nodes\n        - edges\n    QueryGraph:\n      type: object\n      description: >-\n        A graph representing a biomedical question. It serves as a template for\n        each result (answer), where each bound knowledge graph node/edge is\n        expected to obey the constraints of the associated query graph element.\n      properties:\n        nodes:\n          type: object\n          description: >-\n            The node specifications. The keys of this map are unique node\n            identifiers and the corresponding values include the constraints\n            on bound nodes.\n          additionalProperties:\n            $ref: '#/components/schemas/QNode'\n        edges:\n          type: object\n          description: >-\n            The edge specifications. The keys of this map are unique edge\n            identifiers and the corresponding values include the constraints\n            on bound edges, in addition to specifying the subject and object\n            QNodes.\n          additionalProperties:\n            $ref: '#/components/schemas/QEdge'\n      additionalProperties: true\n      required:\n        - nodes\n        - edges\n    QNode:\n      type: object\n      description: A node in the QueryGraph used to represent an entity in a\n        query. If a CURIE is not specified, any nodes matching the category\n        of the QNode will be returned in the Results.\n      properties:\n        ids:\n          type: array\n          items:\n            $ref: '#/components/schemas/CURIE'\n          minItems: 1\n          example: [OMIM:603903]\n          description: CURIE identifier for this node\n          nullable: true\n        categories:\n          type: array\n          items:\n            $ref: '#/components/schemas/BiolinkEntity'\n          minItems: 1\n          nullable: true\n        is_set:\n          type: boolean\n          description: >-\n            Boolean that if set to true, indicates that this QNode MAY have\n            multiple KnowledgeGraph Nodes bound to it within each Result.\n            The nodes in a set should be considered as a set of independent\n            nodes, rather than a set of dependent nodes, i.e., the answer\n            would still be valid if the nodes in the set were instead returned\n            individually. Multiple QNodes may have is_set=True. If a QNode\n            (n1) with is_set=True is connected to a QNode (n2) with\n            is_set=False, each n1 must be connected to n2. If a QNode (n1)\n            with is_set=True is connected to a QNode (n2) with is_set=True,\n            each n1 must be connected to at least one n2.\n          default: false\n        constraints:\n          type: array\n          description: >-\n            A list of contraints applied to a query node.\n            If there are multiple items, they must all be true (equivalent\n            to AND)\n          items:\n            $ref: '#/components/schemas/QueryConstraint'\n          default: []\n      additionalProperties: true\n    QEdge:\n      type: object\n      description: >-\n        An edge in the QueryGraph used as an filter pattern specification in a\n        query. If the optional predicate property is not specified,\n        it is assumed to be a wildcard match to the target knowledge space.\n        If specified, the ontological inheritance hierarchy associated with\n        the term provided is assumed, such that edge bindings returned may be\n        an exact match to the given QEdge predicate term,\n        or to a term that is a descendant of the QEdge predicate term.\n      properties:\n        predicates:\n          type: array\n          items:\n            $ref: '#/components/schemas/BiolinkPredicate'\n          minItems: 1\n          nullable: true\n        subject:\n          type: string\n          example: https://omim.org/entry/603903\n          description: >-\n            Corresponds to the map key identifier of the\n            subject concept node anchoring the query filter\n            pattern for the query relationship edge.\n        object:\n          type: string\n          example: https://www.uniprot.org/uniprot/P00738\n          description: >-\n            Corresponds to the map key identifier of the\n            object concept node anchoring the query filter\n            pattern for the query relationship edge.\n        constraints:\n          type: array\n          description: >-\n            A list of contraints applied to a query edge.\n            If there are multiple items, they must all be true (equivalent\n            to AND)\n          items:\n            $ref: '#/components/schemas/QueryConstraint'\n          default: []\n      additionalProperties: true\n      required:\n        - subject\n        - object\n    Node:\n      type: object\n      description: >-\n        A node in the KnowledgeGraph which represents some biomedical\n        concept. Nodes are identified by the keys in the KnowledgeGraph\n        Node mapping.\n      properties:\n        name:\n          type: string\n          example: Haptoglobin\n          description: Formal name of the entity\n          nullable: true\n        categories:\n          type: array\n          items:\n            $ref: '#/components/schemas/BiolinkEntity'\n          nullable: true\n        attributes:\n          type: array\n          description: A list of attributes describing the node\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n      additionalProperties: false\n    Attribute:\n      type: object\n      description: >-\n        Generic attribute for a node or an edge that expands the key-value\n        pair concept by including fields for additional metadata. These fields\n        can be used to describe the source of the statement made in a key-value\n        pair of the attribute object, or describe the attribute's value itself\n        including its semantic type, or a url providing additional information\n        about it. An attribute may be further qualified with a SubAttribute\n        (for example to provide confidence intervals on a value).\n      properties:\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: >-\n            The 'key' of the attribute object, holding a CURIE of an ontology\n            property defining the attribute (preferably the CURIE of a\n            Biolink association slot). This property captures the relationship\n            asserted to hold between the value of the attribute, and the node\n            or edge from  which it hangs. For example, that a value of\n            '0.000153' represents a p-value supporting an edge, or that\n            a value of 'ChEMBL' represents the original source of the knowledge\n            expressed in the edge.\n          example: Biolink:has_p-value_evidence, Biolink:has_original_source\n        original_attribute_name:\n          type: string\n          description: >-\n            The term used by the original source of an attribute to describe\n            the meaning or significance of the value it captures. This may be\n            a column name in a source tsv file, or a key in a source json\n            document for the field in the data that held the attribute's\n            value. Capturing this information  where possible lets us preserve\n            what the original source said. Note that the data type is string'\n            but the contents of the field could also be a CURIE of a third\n            party ontology term.\n          example: p-value\n          nullable: true\n        value:\n          description: >-\n            Value of the attribute. May be any data type, including a list.\n          example: 0.000153\n        value_type_id:\n          allOf:\n            - $ref: '#/components/schemas/CURIE'\n          description: >-\n            CURIE describing the semantic type of an  attribute's value. Use\n            a Biolink class if possible, otherwise a term from an external\n            ontology. If a suitable CURIE/identifier does not exist, enter a\n            descriptive phrase here and submit the new type for consideration\n            by the appropriate authority.\n          example: EDAM:data_1187\n          nullable: true\n        attribute_source:\n          type: string\n          description: >-\n            The source of the core assertion made by the key-value pair of an\n            attribute object. Use a CURIE or namespace designator for this\n            resource where possible.\n          example: UniProtKB\n          nullable: true\n        value_url:\n          type: string\n          description: >-\n            Human-consumable URL linking to a web document that provides\n            additional information about an  attribute's value (not the node\n            or the edge fom which it hangs).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n        description:\n          type: string\n          description: >-\n            Human-readable description for the attribute and its value.\n          example: Assertion Authored By Dr. Trans L. Ator\n          nullable: true\n        attributes:\n          type: array\n          description: >-\n            A list of attributes providing further information about the\n            parent attribute (for example to provide provenance\n            information about the parent attribute).\n          items:\n            $ref: '#/components/schemas/SubAttribute'\n          nullable: true\n      required:\n        - attribute_type_id\n        - value\n      additionalProperties: false\n    SubAttribute:\n      type: object\n      description: >-\n        Second-level attribute that can be used to qualify information\n        contained in a primary Attribute attached to a Node or Edge.\n      properties:\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: >-\n            The 'key' of the attribute object, holding a CURIE of an ontology\n            property defining the attribute (preferably the CURIE of a\n            Biolink association slot). This property captures the relationship\n            asserted to hold between the value of the attribute, and the node\n            or edge from  which it hangs. For example, that a value of\n            '0.000153' represents a p-value supporting an edge, or that\n            a value of 'ChEMBL' represents the original source of the knowledge\n            expressed in the edge.\n          example: Biolink:has_p-value_evidence, Biolink:has_original_source\n        original_attribute_name:\n          type: string\n          description: >-\n            The term used by the original source of an attribute to describe\n            the meaning or significance of the value it captures. This may be\n            a column name in a source tsv file, or a key in a source json\n            document for the field in the data that held the attribute's\n            value. Capturing this information  where possible lets us preserve\n            what the original source said. Note that the data type is string'\n            but the contents of the field could also be a CURIE of a third\n            party ontology term.\n          example: p-value\n          nullable: true\n        value:\n          description: >-\n            Value of the attribute. May be any data type, including a list.\n          example: 0.000153\n        value_type_id:\n          allOf:\n            - $ref: '#/components/schemas/CURIE'\n          description: >-\n            CURIE describing the semantic type of an  attribute's value. Use\n            a Biolink class if possible, otherwise a term from an external\n            ontology. If a suitable CURIE/identifier does not exist, enter a\n            descriptive phrase here and submit the new type for consideration\n            by the appropriate authority.\n          example: EDAM:data_1187\n          nullable: true\n        attribute_source:\n          type: string\n          description: >-\n            The source of the core assertion made by the key-value pair of an\n            attribute object. Use a CURIE or namespace designator for this\n            resource where possible.\n          example: UniProtKB\n          nullable: true\n        value_url:\n          type: string\n          description: >-\n            Human-consumable URL linking to a web document that provides\n            additional information about an  attribute's value (not the node\n            or the edge fom which it hangs).\n          example: https://pubmed.ncbi.nlm.nih.gov/32529952\n          nullable: true\n        description:\n          type: string\n          description: >-\n            Human-readable description for the attribute and its value.\n          example: Assertion Authored By Dr. Trans L. Ator\n          nullable: true\n      required:\n        - attribute_type_id\n        - value\n      additionalProperties: false\n    Edge:\n      type: object\n      description: >-\n        A specification of the semantic relationship linking two concepts\n        that are expressed as nodes in the knowledge \"thought\" graph\n        resulting from a query upon the underlying knowledge source.\n      properties:\n        predicate:\n          allOf:\n            - $ref: '#/components/schemas/BiolinkPredicate'\n          nullable: true\n        subject:\n          $ref: '#/components/schemas/CURIE'\n          example: OMIM:603903\n          description: >-\n            Corresponds to the map key CURIE of the\n            subject concept node of this relationship edge.\n        object:\n          $ref: '#/components/schemas/CURIE'\n          example: UniProtKB:P00738\n          description: >-\n            Corresponds to the map key CURIE of the\n            object concept node of this relationship edge.\n        attributes:\n          type: array\n          description: A list of additional attributes for this edge\n          items:\n            $ref: '#/components/schemas/Attribute'\n          nullable: true\n      additionalProperties: false\n      required:\n        - subject\n        - object\n    BiolinkEntity:\n      description: >-\n        Compact URI (CURIE) for a Biolink class, biolink:NamedThing\n        or a child thereof. The CURIE must use the prefix 'biolink:'\n        followed by the PascalCase class name.\n      type: string\n      pattern: ^biolink:[A-Z][a-zA-Z]*$\n      externalDocs:\n        description: Biolink model entities\n        url: https://biolink.github.io/biolink-model/docs/NamedThing.html\n      example: biolink:PhenotypicFeature\n    BiolinkPredicate:\n      description: >-\n        CURIE for a Biolink 'predicate' slot, taken from the Biolink slot\n        ('is_a') hierarchy rooted in biolink:related_to (snake_case). This\n        predicate defines the Biolink relationship between the subject and\n        object nodes of a biolink:Association defining a knowledge graph edge.\n      type: string\n      pattern: ^biolink:[a-z][a-z_]*$\n      externalDocs:\n        description: Biolink model predicates\n        url: https://biolink.github.io/biolink-model/docs/related_to.html\n      example: biolink:interacts_with\n    CURIE:\n      type: string\n      description: >-\n        A Compact URI, consisting of a prefix and a reference separated\n        by a colon, such as UniProtKB:P00738. Via an external context\n        definition, the CURIE prefix and colon may be replaced by a URI\n        prefix, such as http://identifiers.org/uniprot/, to form a full\n        URI.\n      externalDocs:\n        url: https://www.w3.org/TR/2010/NOTE-curie-20101216/\n    MetaKnowledgeGraph:\n      type: object\n      description: >-\n        Knowledge-map representation of this TRAPI web service. The meta\n        knowledge graph is composed of the union of most specific categories\n        and predicates for each node and edge.\n      properties:\n        nodes:\n          type: object\n          description: >-\n            Collection of the most specific node categories provided by\n            this TRAPI web service, indexed by Biolink class CURIEs.\n            A node category is only exposed here if there is\n            node for which that is the most specific category available.\n          additionalProperties:\n            $ref: '#/components/schemas/MetaNode'\n        edges:\n          type: array\n          description: >-\n            List of the most specific edges/predicates provided by this TRAPI\n            web service. A predicate is only exposed here if there is an edge\n            for which the predicate is the most specific available.\n          items:\n            $ref: '#/components/schemas/MetaEdge'\n      required:\n        - nodes\n        - edges\n    MetaNode:\n      type: object\n      description: >-\n        Description of a node category provided by this TRAPI web service.\n      properties:\n        id_prefixes:\n          type: array\n          description: >-\n            List of CURIE prefixes for the node category that this TRAPI web\n            service understands and accepts on the input.\n          items:\n            type: string\n          minItems: 1\n          example: [CHEMBL.COMPOUND, INCHIKEY]\n        attributes:\n          type: array\n          description: >-\n            Node attributes provided by this TRAPI web service.\n          items:\n            $ref: '#/components/schemas/MetaAttribute'\n          nullable: true\n      required:\n        - id_prefixes\n      additionalProperties: false\n    MetaEdge:\n      type: object\n      description: >-\n        Edge in a meta knowledge map describing relationship between a subject\n        Biolink class and an object Biolink class.\n      properties:\n        subject:\n          $ref: '#/components/schemas/BiolinkEntity'\n          description: >-\n            Subject node category of this relationship edge.\n          example: biolink:ChemicalSubstance\n        predicate:\n          $ref: '#/components/schemas/BiolinkPredicate'\n          description: >-\n            Biolink relationship between the subject and object categories.\n          example: biolink:affects\n        object:\n          $ref: '#/components/schemas/BiolinkEntity'\n          description: >-\n            Object node category of this relationship edge.\n          example: biolink:Protein\n        attributes:\n          type: array\n          description: >-\n            Edge attributes provided by this TRAPI web service.\n          items:\n            $ref: '#/components/schemas/MetaAttribute'\n          nullable: true\n      required:\n        - subject\n        - predicate\n        - object\n      additionalProperties: false\n    MetaAttribute:\n      type: object\n      properties:\n        attribute_type_id:\n          $ref: '#/components/schemas/CURIE'\n          description: >-\n            Type of an attribute provided by this TRAPI web service\n            (preferably the CURIE of a Biolink association slot)\n          example: biolink:p_value\n        attribute_source:\n          type: string\n          description: >-\n            Source of an attribute provided by this TRAPI web service.\n          example: infores:chembl\n          nullable: true\n        original_attribute_names:\n          type: array\n          items:\n            type: string\n          description: >-\n            Names of an the attribute as provided by the source.\n          nullable: true\n          minItems: 1\n        constraint_use:\n          type: boolean\n          description: >-\n            Indicates whether this attribute can be used as a query\n            constraint.\n          default: false\n        constraint_name:\n          type: string\n          description: >-\n            Human-readable name or label for the constraint concept.\n            Required whenever constraint_use is true.\n          example: p-value\n          nullable: true\n      required:\n        - attribute_type_id\n    QueryConstraint:\n      type: object\n      description: >-\n        Generic query constraint for a query node or query edge\n      properties:\n        id:\n          allOf:\n            - $ref: '#/components/schemas/CURIE'\n          description: >-\n            CURIE of the concept being constrained. For properties\n            defined by the Biolink model this SHOULD be a biolink CURIE.\n            otherwise, if possible, from the EDAM ontology. If a suitable\n            CURIE does not exist, enter a descriptive phrase here and\n            submit the new type for consideration by the appropriate\n            authority.\n          example: EDAM:data_0844\n        name:\n          type: string\n          description: >-\n            Human-readable name or label for the constraint concept.\n            If appropriate, it SHOULD be the term name of the CURIE used\n            as the 'id'. This is redundant but required for human\n            readability.\n          example: molecular mass\n        not:\n          type: boolean\n          default: false\n        operator:\n          type: string\n          description: >-\n            Relationship between the database value and the constraint value\n            for the specified id. The operators ==, >, and < mean\n            is exactly equal to, is greater than, and is less than,\n            respectively. The 'matches' operator indicates that the value\n            is a regular expression to be evaluated. If value is a list type,\n            then at least one evaluation must be true (equivalent to OR).\n            This means that the == operator with a list acts like a SQL 'IN'\n            clause. The 'not' property negates the operator such that not\n            and == means 'not equal to' (or 'not in' for a list), and not >\n            means <=, and not < means >=, and not matches means does not\n            match. The '==' operator SHOULD NOT be used in a manner that\n            describes an \"is a\" subclass relationship for the parent QNode.\n          enum:\n            - ==\n            - '>'\n            - <\n            - matches\n        value:\n          example: 57.0\n          description: >-\n            Value of the attribute. May be any data type, including a list.\n            If the value is a list and there are multiple items, at least one\n            comparison must be true (equivalent to OR). If 'value' is of data\n            type 'object', the keys of the object MAY be treated as a list.\n            A 'list' data type paired with the '>' or '<' operators will\n            encode extraneous comparisons, but this is permitted as it is in\n            SQL and other languages.\n        unit_id:\n          example: UO:0000222\n          description: >-\n            CURIE of the units of the value or list of values in the 'value'\n            property. The Units of Measurement Ontology (UO) should be used\n            if possible. The unit_id MUST be provided for (lists of)\n            numerical values that correspond to a quantity that has units.\n          nullable: true\n        unit_name:\n          example: kilodalton\n          description: >-\n            Term name that is associated with the CURIE of the units\n            of the value or list of values in the 'value'\n            property. The Units of Measurement Ontology (UO) SHOULD be used\n            if possible. This property SHOULD be provided if a unit_id is\n            provided. This is redundant but recommended for human readability.\n          nullable: true\n      required:\n        - name\n        - id\n        - operator\n        - value\n      additionalProperties: false\n"
  },
  {
    "path": "medikanren2/open-api/api-query.rkt",
    "content": "#lang racket\n(provide (all-defined-out))\n(require \"../common.rkt\" json net/url)\n\n(define (js-count js)\n  (cond ((pair? js) (foldl + 0 (map js-count js)))\n        ((hash? js) (foldl + 0 (hash-map js (lambda (k v) (js-count v)))))\n        (else       1)))\n\n;; BKB Pathway Provider (currently uses a non-standard query path)\n(define url.bkbp-query\n  \"http://chp.thayer.dartmouth.edu/submitQuery/\")\n\n;; Broad Institute KP\n(define url.broad\n  \"https://translator.broadinstitute.org/molepro/trapi/v1.1\")\n\n;; Broad Institute KP specific for CHEMBL queries\n(define url.broad_chembl\n  \"https://translator.broadinstitute.org/chembl\")\n\n(define chembl-drug-indications/transform\n  \"/indications/transform\")\n\n(define url.unsecret\n  \"https://unsecret.ncats.io\")\n(define path.predicates\n  \"/predicates\")\n(define path.query\n  \"/query\")\n\n\n(define (api-query url-string (optional-post-jsexpr (void)))\n  (printf \"##### making api-query call to url:\\n~s\\n\" url-string) \n  (define-values (status headers in)\n    (time (if (void? optional-post-jsexpr)\n              (http-sendrecv/url\n               (string->url url-string)\n               #:method \"GET\")\n              (http-sendrecv/url\n               (string->url url-string)\n               #:method \"POST\"\n               #:data (jsexpr->string optional-post-jsexpr)\n               #:headers '(\"Content-Type: application/json; charset=utf-8\")))))\n  (define response-string (time (port->string in)))\n  (printf \"status:\\n~s\\n\" status)\n  (define OK-status? (bytes=? #\"HTTP/1.1 200 OK\" status))\n  (if OK-status?\n      (hash 'status status\n            'headers headers\n            'response (string->jsexpr response-string))\n      (begin\n        (printf \"!!!!!! unexpected non-OK status returned from ~s:\\n\" url-string)\n        (pretty-print `(,status ,headers ,response-string))\n        (hash 'status status\n              'headers headers\n              'response (hash)))))\n(define (js-query edges nodes)\n  (hash 'message\n        (hash 'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n\n(define (js-query/bkbp edges nodes)\n  (hash 'query\n        (hash 'reasoner_id \"unsecret\"\n              'query_graph\n              (hash 'edges edges\n                    'nodes nodes))))\n(define (bkbp-query edges nodes)\n  (api-query url.bkbp-query (js-query/bkbp edges nodes)))\n\n(define (bkbp-g2d e s o)  (hash 'id e  'type \"gene_to_disease_association\"      'source_id s 'target_id o))\n(define (bkbp-d2p e s o)  (hash 'id e  'type \"disease_to_phenotype_association\" 'source_id s 'target_id o 'value 1000))\n(define (bkbp-g id curie) (hash 'id id 'type \"Gene\"              'curie curie))\n(define (bkbp-d id curie) (hash 'id id 'type \"disease\"           'curie curie))\n(define (bkbp-p id curie) (hash 'id id 'type \"PhenotypicFeature\" 'curie curie))\n\n;{'query':\n;  {'query_graph':\n;    {'edges':\n;      [{'id': 'e0', 'type': 'gene_to_disease_association', 'source_id': 'n0', 'target_id': 'n2'},\n;       {'id': 'e1', 'type': 'gene_to_disease_association', 'source_id': 'n1', 'target_id': 'n2'},\n;       {'id': 'e2', 'type': 'disease_to_phenotype_association', 'value': 1000, 'source_id': 'n2', 'target_id': 'n3'}],\n;     'nodes':\n;      [{'id': 'n0', 'type': 'Gene', 'curie':              'ENSEMBL:ENSG00000132155'},\n;       {'id': 'n1', 'type': 'Gene', 'curie':              'ENSEMBL:ENSG00000073803'},\n;       {'id': 'n2', 'type': 'disease', 'curie':           'MONDO:0007254'},\n;       {'id': 'n3', 'type': 'PhenotypicFeature', 'curie': 'EFO:0000714'}]},\n;  'reasoner_id': 'unsecret'}}\n(define bkbp-edges\n  (list (bkbp-g2d \"e0\" \"n0\" \"n2\")\n        (bkbp-g2d \"e1\" \"n1\" \"n2\")\n        (bkbp-d2p \"e2\" \"n2\" \"n3\")))\n(define bkbp-nodes\n  (list (bkbp-g \"n0\" \"ENSEMBL:ENSG00000132155\")\n        (bkbp-g \"n1\" \"ENSEMBL:ENSG00000073803\")\n        (bkbp-d \"n2\" \"MONDO:0007254\")\n        (bkbp-p \"n3\" \"EFO:0000714\")))\n;(define response (bkbp-query bkbp-edges bkbp-nodes))\n\n;\n;{\"query\":\n;  {\"query_graph\":\n;    {\"edges\":\n;      [{\"target_id\":\"d00\",\"type\":\"gene_to_disease_association\",\"source_id\":\"g00\",\"id\":\"e00\"}],\n;     \"nodes\":\n;      [{\"type\":\"Gene\",\"curie\":\"ENSEMBLE:ENSG00000132155\",\"id\":\"g00\"},\n;       {\"type\":\"disease\",\"curie\":\"MONDO:0007254\",\"id\":\"d00\"}]},\n;  \"reasoner_id\": \"unsecret\"}}\n\n;; (define RAF1 (hash 'id \"g00\" 'type \"Gene\" 'curie \"ENSEMBLE:ENSG00000132155\"))\n;; (define (g2d e s o) (hash 'id e 'type \"gene_to_disease_association\" 'source_id s 'target_id o))\n;; (define breast-cancer (hash 'id \"d00\" 'type \"disease\" 'curie \"MONDO:0007254\"))\n;; (define MAP3K13 (hash 'id \"g01\" 'type \"Gene\" 'curie \"ENSEMBL:ENSG00000073803\"))\n;; (displayln (jsexpr->string (apply js-query/bkbp (reverse (list (list RAF1 breast-cancer) (list (g2d \"e00\" \"g00\" \"d00\")))))))\n;; (bkbp-query (list (g2d \"e00\" \"g00\" \"d00\") (list RAF1 breast-cancer))\n\n;(define (bkb-pathwayo subject subject-type verb object object-type)\n  ;(project (subject subject-type verb object object-type)\n    ;(let ()\n      ;(when (or (var? verb) (var? subject-type) (var? object-type)\n                ;(and (var? subject) (var? object)))\n        ;(error \"verb, types, and subject or object curie must be ground\"))\n      ;(define edges (list (hash 'id        \"e00\"\n                                ;'source_id \"n00\"\n                                ;'target_id \"n01\"\n                                ;'type      verb)))\n      ;(define subject-node\n        ;(make-immutable-hash\n          ;(append (if (var? subject) '() `((curie . ,subject)))\n                  ;`((id . \"n00\") (type . ,subject-type)))))\n      ;(define object-node\n        ;(make-immutable-hash\n          ;(append (if (var? object) '() `((curie . ,object)))\n                  ;`((id . \"n01\") (type . ,object-type)))))\n      ;(define nodes (list subject-node object-node))\n      ;(define results\n        ;(hash-ref\n          ;(hash-ref\n            ;(hash-ref (api-query (string-append url.broad path.query)\n                                 ;(js-query edges nodes))\n                      ;'response)\n            ;'knowledge_graph)\n          ;'edges))\n      ;;(pretty-print results)\n      ;;(pretty-print edges)\n      ;;(pretty-print nodes)\n      ;(let loop ((results results))\n        ;(if (null? results) (== #t #f)\n          ;(let ((e (car results)))\n            ;;; NOTE: this conditional equality constraint is due to the fact\n            ;;; that molepro doesn't return the same curies you put in.\n            ;(conde ((if (var? subject) (== subject (hash-ref e 'source_id))\n                      ;(== #t #t))\n                    ;(if (var? object) (== object  (hash-ref e 'target_id))\n                      ;(== #t #t)))\n                   ;((loop (cdr results))))))))))\n\n;; (define (molepro-edgeo subject subject-type verb object object-type)\n;;   (project (subject subject-type verb object object-type)\n;;     (let ()\n;;       (when (or (var? verb) (var? subject-type) (var? object-type)\n;;                 (and (var? subject) (var? object)))\n;;         (error \"verb, types, and subject or object curie must be ground\"))\n;;       (define edges (list (hash 'id        \"e00\"\n;;                                 'source_id \"n00\"\n;;                                 'target_id \"n01\"\n;;                                 'type      verb)))\n;;       (define subject-node\n;;         (make-immutable-hash\n;;           (append (if (var? subject) '() `((curie . ,subject)))\n;;                   `((id . \"n00\") (type . ,subject-type)))))\n;;       (define object-node\n;;         (make-immutable-hash\n;;           (append (if (var? object) '() `((curie . ,object)))\n;;                   `((id . \"n01\") (type . ,object-type)))))\n;;       (define nodes (list subject-node object-node))\n;;       (define results\n;;         (hash-ref\n;;           (hash-ref\n;;             (hash-ref (api-query (string-append url.broad path.query)\n;;                                  (js-query edges nodes))\n;;                       'response)\n;;             'knowledge_graph)\n;;           'edges))\n;;       ;(pretty-print results)\n;;       ;(pretty-print edges)\n;;       ;(pretty-print nodes)\n;;       (let loop ((results results))\n;;         (if (null? results) (== #t #f)\n;;           (let ((e (car results)))\n;;             ;; NOTE: this conditional equality constraint is due to the fact\n;;             ;; that molepro doesn't return the same curies you put in.\n;;             (conde ((if (var? subject) (== subject (hash-ref e 'source_id))\n;;                       (== #t #t))\n;;                     (if (var? object) (== object  (hash-ref e 'target_id))\n;;                       (== #t #t)))\n;;                    ((loop (cdr results))))))))))\n\n;; (module+ main\n;;   (pretty-print (api-query (string-append url.broad path.predicates)))\n\n;;   (run* (g) (molepro-edgeo \"CID:2244\" \"chemical_substance\" \"affects\" g \"gene\"))\n;;   ;(run 1 (g) (molepro-edgeo \"CHEBI:15365\" \"chemical_substance\" \"affects\" g \"gene\"))\n;;   ;(run 1 (c) (molepro-edgeo c \"chemical_substance\" \"affects\" \"HGNC:7645\" \"gene\"))\n;;   (run* (c) (molepro-edgeo \"HGNC:7645\" \"gene\" \"affected_by\" c \"chemical_substance\"))\n\n;;   ;(pretty-print\n;;      ;(api-query (string-append url.broad path.query)\n;;               ;(js-query (list (hash 'id        \"e00\"\n;;                                     ;'source_id \"n00\"\n;;                                     ;'target_id \"n01\"\n;;                                     ;'type      \"affects\"))\n;;                         ;(list (hash 'curie \"CID:2244\"\n;;                                     ;'id    \"n00\"\n;;                                     ;'type  \"chemical_substance\"\n;;                                     ;)\n;;                               ;(hash 'id    \"n01\"\n;;                                     ;'type  \"gene\")))))\n;;   )\n\n;; (module+ old-main\n;;   ;; test predicates available on Broad Institute KG\n;;  #;(pretty-print\n;;    (api-query (string-append url.broad path.predicates)))\n\n;;   #;(pretty-print\n;;      (api-query (string-append url.broad path.query)\n;;               (js-query (list (hash 'id        \"e00\"\n;;                                     'source_id \"n00\"\n;;                                     'target_id \"n01\"\n;;                                     'type      \"affects\"))\n;;                         (list (hash 'curie \"CID:2244\"\n;;                                     'id    \"n00\"\n;;                                     'type  \"chemical_substance\")\n;;                               (hash 'id    \"n01\"\n;;                                     'type  \"gene\")))))\n\n;;   #;(js-count\n;;     (time (api-query (string-append url.unsecret path.predicates))))\n\n;;   #;(pretty-print\n;;     (time\n;;       (api-query (string-append url.unsecret path.query)\n;;                 (js-query (list (hash 'id        \"e00\"\n;;                                        'source_id \"n00\"\n;;                                        'target_id \"n01\"\n;;                                        'type      \"causes\"))\n;;                            (list (hash 'curie \"UMLS:C0004096\"\n;;                                        'id    \"n01\"\n;;                                        'type  \"disease\")\n;;                                  (hash 'id    \"n00\"\n;;                                        'type  \"gene\"))))))\n\n;;   #;(pretty-print\n;;     (time\n;;        (api-query (string-append url.broad path.query)\n;;                   (js-query (list (hash 'id        \"e00\"\n;;                                         'source_id \"n00\"\n;;                                         'target_id \"n01\"\n;;                                         'type      \"causes\"))\n;;                             (list (hash 'curie \"UMLS:C0004096\"\n;;                                         'id    \"n01\"\n;;                                         'type  \"disease\")\n;;                                   (hash 'id    \"n00\"\n;;                                         'type  \"gene\"))))))\n\n;;   #;(pretty-print\n;;     (time (api-query (string-append url.unsecret path.query)\n;;                      (js-query (list (hash 'id        \"e00\"\n;;                                            'source_id \"n00\"\n;;                                            'target_id \"n01\"\n;;                                            'type      \"affects\"))\n;;                                (list (hash 'curie \"CID:2244\"\n;;                                            'id    \"n00\"\n;;                                            'type  \"chemical_substance\")\n;;                                      (hash 'id    \"n01\"\n;;                                            'type  \"gene\"))))))\n\n\n\n;; #|NOTES FOR SEPTEMBER 2020 RELAY API CALLS|#\n\n;; #|\n\n;; 1. all \"NO-evidence/provenance\" queries are to the base broad.url\n;; \"https://translator.broadinstitute.org/molepro_reasoner\n\n;; 2. all \"LIMITED evidence/provenance\" queries are to the chembl url\n;; \"https://translator.broadinstitute.org/chembl\"\n\n;; |#\n\n;; ;;MOLEPRO drug --treats--> disease query w/ NO EVIDENCE\n;; (pretty-print\n;;  (time (api-query (string-append url.broad path.query)\n;;                   (js-query (list (hash 'id        \"e00\"\n;;                                         'source_id \"n00\"\n;;                                         'target_id \"n01\"\n;;                                         'type      \"treats\"))\n;;                             (list (hash 'curie \"ChEMBL:CHEMBL25\"\n;;                                         'id    \"n00\"\n;;                                         'type  \"chemical_substance\")\n;;                                   (hash 'id    \"n01\"\n;;                                         'type  \"disease\"))))))\n\n;; ;; new query structure for chembl specific provenance/evidence queries\n;; (define (js-query/transform curie)\n;;   (hash 'collection\n;;         (list\n;;          (hash\n;;           'id \"\"\n;;           'identifiers\n;;           (hash\n;;            'chembl curie)))\n;;         'controls '()))\n\n;; #|\n;; ;; {} = hash                            ;\n;; ;; [] = list                            ;\n;; ;; key:value                            ;\n;;                                         ;\n;; QUERY/TRANSFORM QUERY STRUCTURE         ;\n;; ------------------------------\n\n;; query = {\n;;     'collection': [{\n;;             'id':'',\n;;             'identifiers': {'chembl':'ChEMBL:CHEMBL25'}\n;;         }],\n;;     'controls':[]\n;; }\n;; |#\n\n;; ;; addition provenance/evidence for drug indication query\n;; (pretty-print\n;;  (time\n;;   (api-query\n;;    (string-append (string-append url.broad_chembl chembl-drug-indications/transform))\n;;    (js-query/transform\n;;     \"ChEMBL:CHEMBL25\"))))\n\n\n;; ;; STRING gene->gene edge\n;; (pretty-print\n;;  (time (api-query (string-append url.broad path.query)\n;;                   (js-query (list (hash 'id        \"e00\"\n;;                                         'source_id \"n00\"\n;;                                         'target_id \"n01\"\n;;                                         'type      \"related_to\"))\n;;                             (list (hash 'curie \"HGNC:4556\"\n;;                                         'id    \"n00\"\n;;                                         'type  \"gene\")\n;;                                   (hash 'id    \"n01\"\n;;                                         'type  \"gene\"))))))\n\n;; ;; CMAP gene-to-compound query\n;; (pretty-print\n;;  (time (api-query (string-append url.broad path.query)\n;;                   (js-query (list (hash 'id        \"e00\"\n;;                                         'source_id \"n00\"\n;;                                         'target_id \"n01\"\n;;                                         'type      \"correlated_with\"))\n;;                             (list (hash 'curie \"HGNC:4556\"\n;;                                         'id    \"n00\"\n;;                                         'type  \"gene\")\n;;                                   (hash 'id    \"n01\"\n;;                                         'type  \"chemical_substance\"))))))\n\n;; ;; CMAP gene-to-gene query\n;; (pretty-print\n;;  (time (api-query (string-append url.broad path.query)\n;;                   (js-query (list (hash 'id        \"e00\"\n;;                                         'source_id \"n00\"\n;;                                         'target_id \"n01\"\n;;                                         'type      \"correlated_with\"))\n;;                             (list (hash 'curie \"HGNC:4556\"\n;;                                         'id    \"n00\"\n;;                                         'type  \"gene\")\n;;                                   (hash 'id    \"n01\"\n;;                                         'type  \"gene\"))))))\n\n;; ;; CMAP gene-to-gene query\n;; (pretty-print\n;;  (time (api-query (string-append url.broad path.query)\n;;                   (js-query (list (hash 'id        \"e00\"\n;;                                         'source_id \"n00\"\n;;                                         'target_id \"n01\"\n;;                                         'type      \"correlated_with\"))\n;;                             (list (hash 'curie \"HGNC:4556\"\n;;                                         'id    \"n00\"\n;;                                         'type  \"gene\")\n;;                                   (hash 'id    \"n01\"\n;;                                         'type  \"gene\"))))))\n\n;; )\n"
  },
  {
    "path": "medikanren2/open-api/yaml-to-json.sh",
    "content": "#!/bin/bash\nset -eufo pipefail\n\nhere=\"$( cd \"$( dirname \"${BASH_SOURCE[0]}\" )\" && pwd )\"\n\npython3 \"$here/yaml2json.py\" < \"$here/TranslatorReasonersAPI.yaml\" > \"$here/TranslatorReasonersAPI.json\"\n"
  },
  {
    "path": "medikanren2/open-api/yaml2json.py",
    "content": "import sys, json, yaml\n\ndata = yaml.load(sys.stdin, Loader=yaml.SafeLoader)\nprint(json.dumps(data, indent=4))\n"
  },
  {
    "path": "medikanren2/readme.md",
    "content": "# mediKanren 2\n\n## Prerequisites\n\n## Loading databases\n\n## Running queries\n\n## Lightweight reasoning\n\nRelations for lightweight reasoning are defined in `lw-reasoning.rkt`, and are currently under development and subject to change.\n\nHere is an example of getting synonyms and subclasses:\n\n```\n(require \"lw-reasoning.rkt\")\n\n(define meformin \"CHEBI:6801\")\n\n;; get diseases/phenotypes treated by meformin and its synonyms\n(define treated-diseases\n  (run* disease-or-phen\n    (fresh (drug)\n      (kgx-synonym drug meformin)\n      (triple drug \"biolink:treats\" disease-or-phen)\n      (conde ((is-a disease-or-phen \"biolink:PhenotypicFeature\")) ; *\n             ((is-a disease-or-phen \"biolink:Disease\"))))))\n\n(get-names-ls treated-diseases)\n\n;; get subclasses\n(get-names-ls\n (apply append\n        (map (lambda (disease)\n               (run* d (subclass-of+ d disease)))\n             treated-diseases)))\n\n```\n\n## TRAPI service\n\nRunning the [TRAPI](https://github.com/NCATSTranslator/ReasonerAPI)  service:\n\n```\nracket server.rkt\n```\n\nexposes the following endpoints on port `8384`:\n\n**/pmi/v1/query**, duplicated on **/query**\n\nMain TRAPI endpoint, accepts [TRAPI 1.1](https://github.com/NCATSTranslator/ReasonerAPI) requests. Requests are run one at a time, on a first-received basis, and are limited to 10 minutes query time.\n\n**/**\n\nSimple Web UI for testing queries.\n\n**/health**\n\nSimple health check: runs a trivial query and reports on query time. If other queries are running and/or queued to be run, this query will return only after the others have terminated or timed out.\n\n"
  },
  {
    "path": "medikanren2/server.rkt",
    "content": "#lang racket/base\n(require\n \"common.rkt\"   \n  \"trapi.rkt\"\n  \"logging2.rkt\"\n  \"lw-reasoning.rkt\"\n  \"open-api/api-query.rkt\"\n  \"ingest-pipeline-status.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/format\n  racket/date\n  racket/runtime-path\n  racket/string\n  json\n  web-server/servlet\n  web-server/servlet-env\n  web-server/managers/none\n  web-server/private/gzip\n  xml\n  web-server/safety-limits\n  racket/sandbox\n  )\n\n(define query-time-limit (make-parameter 600))\n\n(define (alist-ref alist key default)\n  (define kv (assoc key alist))\n  (if kv (cdr kv) default))\n\n(print-as-expression #f)\n(pretty-print-abbreviate-read-macros #f)\n(define argv (current-command-line-arguments))\n(define argv-optional '#(CONFIG_FILE))\n(when (not (<= (vector-length argv) (vector-length argv-optional)))\n  (error (format \"optional arguments ~s; given ~s\" argv-optional argv)))\n;; Loading will occur at first use if not explicitly forced like this.\n(load-config #t)\n;; (load-databases #t)\n\n(define-runtime-path path:root \".\")\n(define (path/root relative-path) (build-path path:root relative-path))\n\n(define schema.json.txt\n  (file->string (path/root \"open-api/TranslatorReasonersAPI.json\")))\n(define schema.yaml.txt\n  (file->string (path/root \"open-api/TranslatorReasonersAPI.yaml\")))\n(define schema.json\n  (call-with-input-file (path/root \"open-api/TranslatorReasonersAPI.json\")\n                        read-json))\n\n;; (pretty-print (list 'openapi:      (hash-ref schema.json 'openapi)))\n;; (pretty-print (list 'info:         (hash-ref schema.json 'info)))\n;; (pretty-print (list 'externalDocs: (hash-ref schema.json 'externalDocs)))\n;; (pretty-print (list 'tags:         (hash-ref schema.json 'tags)))\n;; (pretty-print (list 'paths:        (hash-keys (hash-ref schema.json 'paths))))\n;; (pretty-print (list 'components:   (hash-keys (hash-ref schema.json 'components))))\n\n(define (xexpr->html-string xe)\n  (string-append \"\" (xexpr->string xe)))\n(define mime:text (string->bytes/utf-8 \"text/plain;charset=utf-8\"))\n(define mime:html (string->bytes/utf-8 \"text/html; charset=utf-8\"))\n(define mime:js   (string->bytes/utf-8 \"text/javascript;charset=utf-8\"))\n(define mime:json (string->bytes/utf-8 \"application/json; charset=utf-8\"))\n\n(define index.js \"\nwindow.addEventListener('load', function(){\nvar find_concepts_form           = document.getElementById('find-concepts-form');\nvar find_concepts_text           = document.getElementById('find-concepts-text');\nvar find_concepts_submit         = document.getElementById('find-concepts-submit');\nvar find_concepts_result         = document.getElementById('find-concepts-result');\nvar find_concepts_result_clear   = document.getElementById('find-concepts-result-clear');\nvar find_categories_form         = document.getElementById('find-categories-form');\nvar find_categories_text         = document.getElementById('find-categories-text');\nvar find_categories_submit       = document.getElementById('find-categories-submit');\nvar find_categories_result       = document.getElementById('find-categories-result');\nvar find_categories_result_clear = document.getElementById('find-categories-result-clear');\nvar find_predicates_form         = document.getElementById('find-predicates-form');\nvar find_predicates_text         = document.getElementById('find-predicates-text');\nvar find_predicates_submit       = document.getElementById('find-predicates-submit');\nvar find_predicates_result       = document.getElementById('find-predicates-result');\nvar find_predicates_result_clear = document.getElementById('find-predicates-result-clear');\nvar query_result       = document.getElementById('query-result');\nvar query_form         = document.getElementById('query-form');\nvar query_text         = document.getElementById('query-text');\nvar query_submit       = document.getElementById('query-submit');\nfunction pretty_json(json_text) {\n  try { return JSON.stringify(JSON.parse(json_text), null, 2); }\n  catch (_) { return json_text; }\n}\nfunction show(element, result) { element.textContent = pretty_json(result); }\n\nfunction find_concepts_show(result)     { show(find_concepts_result,   result); }\nfunction find_categories_show(result)   { show(find_categories_result, result); }\nfunction find_predicates_show(result)   { show(find_predicates_result, result); }\nfunction find_concepts_clear_result()   { find_concepts_result.textContent = ''; }\nfunction find_categories_clear_result() { find_categories_result.textContent = ''; }\nfunction find_predicates_clear_result() { find_predicates_result.textContent = ''; }\nfunction find_concepts(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ find_concepts_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ find_concepts_show('POST error'); });\n  xhr.open('POST', '/find-concepts');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction find_categories(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ find_categories_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ find_categories_show('POST error'); });\n  xhr.open('POST', '/find-categories');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction find_predicates(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ find_predicates_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ find_predicates_show('POST error'); });\n  xhr.open('POST', '/find-predicates');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfind_concepts_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  find_concepts('\\\"'+find_concepts_text.value+'\\\"');\n}, false);\nfind_categories_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  find_categories('\\\"'+find_categories_text.value+'\\\"');\n}, false);\nfind_predicates_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  find_predicates('\\\"'+find_predicates_text.value+'\\\"');\n}, false);\nfind_concepts_result_clear.addEventListener('click', function(){\n  find_concepts_clear_result();\n}, false);\nfind_categories_result_clear.addEventListener('click', function(){\n  find_categories_clear_result();\n}, false);\nfind_predicates_result_clear.addEventListener('click', function(){\n  find_predicates_clear_result();\n}, false);\n\nfunction query(data) {\n  var xhr = new XMLHttpRequest();\n  xhr.addEventListener('load',  function(event){ query_show(xhr.responseText); });\n  xhr.addEventListener('error', function(event){ query_show('POST error'); });\n  xhr.open('POST', '/pmi/v2/query');\n  xhr.setRequestHeader('Content-Type', 'application/json; charset=utf-8');\n  xhr.send(data);\n}\nfunction query_show(result)   { show(query_result, result); }\nfunction query_clear_result() { query_result.textContent = ''; }\nquery_text.textContent = pretty_json(query_text.textContent);\nquery_form.addEventListener('submit', function(event){\n  event.preventDefault();\n  query_result.textContent = 'Querying...';\n  query(query_text.value);\n}, false);\nquery_result_clear.addEventListener('click', function(){\n  query_clear_result();\n}, false);\n\n});\")\n(define (not-found.html uri)\n  `(html (head (title \"mediKanren: 404\"))\n         (body (h1 \"What are you looking for?\")\n               (p \"There was nothing found at\")\n               (pre ,uri))))\n(define index.html\n  `(html (head (title \"mediKanren Reasoner API\")\n               (script ((src \"/index.js\"))))\n         (body (h1 \"mediKanren Reasoner API\")\n               (p (a ((href \"https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI\"))\n                     \"NCATS Biomedical Translator Reasoners Standard API\"))\n               (ul (li (a ((href \"/schema.yaml\")) \"schema.yaml\"))\n                   (li (a ((href \"/schema.json\")) \"schema.json\")))\n               (div ((style \"display:none\"))\n                    (form ((method \"post\") (id \"find-concepts-form\"))\n                          (div (input ((type \"text\")\n                                       (id \"find-concepts-text\")\n                                       (value \"UMLS:C0935989\"))))\n                          (div (button ((type \"submit\") (id \"find-concepts-submit\"))\n                                       \"Find concepts\")))\n                    (div (button ((id \"find-concepts-result-clear\")) \"Clear\"))\n                    (div (pre ((id \"find-concepts-result\")) \"Concepts will appear here.\"))\n                    (form ((method \"post\") (id \"find-categories-form\"))\n                          (div (input ((type \"text\")\n                                       (id \"find-categories-text\")\n                                       (value \"gene\"))))\n                          (div (button ((type \"submit\") (id \"find-categories-submit\"))\n                                       \"Find categories\")))\n                    (div (button ((id \"find-categories-result-clear\")) \"Clear\"))\n                    (div (pre ((id \"find-categories-result\")) \"Categories will appear here.\"))\n                    (form ((method \"post\") (id \"find-predicates-form\"))\n                          (div (input ((type \"text\")\n                                       (id \"find-predicates-text\")\n                                       (value \"negatively_regulates\"))))\n                          (div (button ((type \"submit\") (id \"find-predicates-submit\"))\n                                       \"Find predicates\")))\n                    (div (button ((id \"find-predicates-result-clear\")) \"Clear\"))\n                    (div (pre ((id \"find-predicates-result\")) \"Predicates will appear here.\"))\n                    (p (a ((href \"/predicates\")) \"GET /predicates\")))\n               (form ((method \"post\") (action \"/pmi/v2/query\") (id \"query-form\"))\n                     (div (textarea\n                            ((id \"query-text\")(rows \"40\") (cols \"60\"))\n                            #<attributes alist)\n  ;; TODO: provide standard types for\n  ;; * negated, publications, provided_by\n  ;; * ngd_score, association_type, id\n  ;; * update_date, publications_info\n  ;; * is_defined_by, pmids, n_pmids, SEMMED_PRED\n  (map (lambda (kv) (hash 'name  (car kv)\n                          'type  \"miscellaneous\"\n                          'value (cdr kv)))\n       alist))\n\n;; (define (concept->result c)\n;;   (define attrs\n;;     (alist->attributes\n;;       (cons (cons \"mediKanren-source\" (symbol->string (concept->dbname c)))\n;;             (concept->props c))))\n;;   (cons (string->symbol (concept->curie c))\n;;         (hash 'name       (concept->name c)\n;;               'category   (cdr (concept->category c))\n;;               'attributes attrs)))\n;; (define (edge->result e)\n;;   (define id (string-append (symbol->string (edge->dbname e)) \".\"\n;;                             (number->string (edge->eid e))))\n;;   (define props (make-immutable-hash (edge->props e)))\n;;   (define relation (hash-ref props \"relation\" #f))\n;;   (define attrs\n;;     (alist->attributes\n;;       (hash->list\n;;         (foldl (lambda (k ps) (hash-remove ps k)) props\n;;                '(\"relation\" \"subject\" \"object\"\n;;                  \"simplified_relation\" \"simplified_edge_label\")))))\n;;   (define obj\n;;     (hash 'predicate  (cdr (edge->pred e))\n;;           'subject    (concept->curie (edge->subject e))\n;;           'object     (concept->curie (edge->object e))\n;;           'attributes attrs))\n;;   (cons (string->symbol id) (if relation\n;;                               (hash-set obj 'relation relation)\n;;                               obj)))\n\n\n(define (message->response msg)\n  (define broad-response (if (or\n                                (hash-ref msg 'disable_external_requests #f)\n                                (not (cfg:config-ref 'trapi-enable-external-requests?)))\n                             (hash 'response hash-empty 'status #\"disabled\" 'headers '())\n                             (time (api-query (string-append url.broad path.query)\n                                              (hash 'message msg)))))\n  (define broad-results (hash-ref broad-response 'response))\n  (define broad-results-count (length (hash-ref (hash-ref broad-results 'message hash-empty) 'results '())))\n  (define broad-error-message (hash-ref broad-results 'detail #f)) ; not sure if this is stable - it isn't TRAPI\n  (lognew-info\n    (hasheq\n      'event \"broad-response\"\n      'status (bytes->string/utf-8 (hash-ref broad-response 'status))\n      'headers (map bytes->string/utf-8 (hash-ref broad-response 'headers))\n      'result-size broad-results-count))\n\n  ;; (log-info log-key (format \"Broad results: ~s\" broad-results))\n  \n  ;; (with-handlers ((exn:fail? (lambda (exn) \n  ;;                              (hash 'error (exn-message exn)))))\n  (lognew-info\n      (hasheq 'event \"query_received\"\n              'msg msg))\n\n  (with-handlers ((exn:fail:resource?\n                   (lambda (exn) \n                     (lognew-error (format \"Error: ~a\" exn))\n                     (error \"Max query time exceded\"))))\n    (call-with-limits (query-time-limit) #f\n      (lambda ()\n        (let-values (((result cpu real gc) (time-apply (lambda () (trapi-response msg)) '())))\n          (let* ((local-results (car result))\n                 (length-local (length (hash-ref  local-results 'results '()))))\n            (lognew-info\n              (hasheq\n                'event \"query_finished\"\n                'cpu-time cpu\n                'real-time real\n                'num-results length-local))\n            (values (hash-set*\n                     (merge-results\n                      (list (hash-ref (olift broad-results) 'message hash-empty)\n                            local-results)))\n                    (list (hash 'level \"INFO\"\n                                'message (format \"Query time: ~ams\" cpu))\n                          (if broad-error-message\n                              (hash 'level \"WARNING\"\n                                    'message (format \"MolePro error: ~s\" broad-error-message))\n                              (hash 'level \"INFO\"\n                                    'message (format \"MolePro results: ~a\" broad-results-count)))\n                          (hash 'level \"INFO\"\n                                'message (format \"MolePro response status: ~s\" (hash-ref broad-response 'status)))\n                          ))))))))\n    \n(define (merge-results rs)\n  (let loop ((rs rs) (results '()) (nodes '()) (edges '()))\n    (cond ((null? rs) (hash 'results         results\n                            'knowledge_graph (hash 'nodes (make-immutable-hash nodes)\n                                                   'edges (make-immutable-hash edges))))\n          (else (define r (car rs))\n                (define kg (hash-ref r 'knowledge_graph hash-empty))\n                (loop (cdr rs)\n                      (append (hash-ref r 'results '()) results)\n                      (append (hash->list (hash-ref kg 'nodes hash-empty))\n                              nodes)\n                      (append (hash->list (hash-ref kg 'edges hash-empty))\n                              edges))))))\n\n;; (define (predicates)\n;;   ;; TODO: at greater expense, we could restrict each list of predicates\n;;   ;; to those reflected by existing edges for the corresponding categories.\n;;   (define cs (run* (c) (categoryo c)))\n;;   (define ps (run* (p) (predicateo p)))\n;;   (define dbs (map car cs))\n;;   (make-immutable-hash\n;;     (append*\n;;       (map (lambda (db)\n;;              (define dcs\n;;                (filter-not\n;;                  not (map (lambda (c) (and (eq? (car c) db) (cddr c)))\n;;                           cs)))\n;;              (define dps\n;;                (filter-not\n;;                  not (map (lambda (p) (and (eq? (car p) db) (cddr p)))\n;;                           ps)))\n;;              (define dcps\n;;                (make-immutable-hash\n;;                  (map (lambda (c) (cons (string->symbol c) dps)) dcs)))\n;;              (map (lambda (c) (cons (string->symbol c) dcps)) dcs))\n;;            dbs))))\n\n;; (define predicates-cached (string->bytes/utf-8 (jsexpr->string (predicates))))\n;; (define predicates-cached-gzip (gzip/bytes predicates-cached))\n\n(define (query-impl jsdata)\n  (cond ((or (eof-object? jsdata) (not (hash? jsdata))) 'null)\n        (else (let* ((data (olift jsdata))\n                     (request-msg (olift (hash-ref data 'message hash-empty))))\n                (let-values (((message logs) (message->response request-msg)))\n                  (let ((length-local (length (hash-ref message 'results))))\n                    (hash 'message message\n                          'query_graph (hash-ref request-msg 'query_graph '#hash())\n                          'status \"Success\"\n                          'description (format \"Success. ~s result~a.\" length-local (if (= length-local 1) \"\" \"s\"))\n                          'logs logs)))))))\n(define ((query requestid0) jsdata)\n  (parameterize ((requestid requestid0))\n    (query-impl jsdata)))\n\n;; Load balancer health checks can be very numerous and drown out useful logs\n(define (squelch-noisy-request-log? req)\n  (define path (url->string (request-uri req)))\n  (cond\n    ((equal? path \"/health\") #t)\n    (else #f)))\n\n; Loosely adapted from:\n;   https://stackoverflow.com/questions/53911162/how-to-show-http-status-code-in-web-server-logs\n(define (headers->hasheq hs)\n  (for/hasheq ([h (in-list hs)])\n    (values (string->symbol (~a (header-field h)))\n            (~a (header-value h)))))\n(define (dict-request-fields req)\n    (hasheq 'method  (~a (request-method req))\n            'ip      (request-client-ip req)\n            'path    (url->string (request-uri req))\n            'headers (headers->hasheq (request-headers/raw req))))\n(define (logwrap-lazy-impl handler req t0 requestid0)\n  (define resp\n    (parameterize ((requestid requestid0))\n      (handler req)))\n  (unless (squelch-noisy-request-log? req)\n    (lognew-info\n        (hasheq 'request  (dict-request-fields req))))\n\n  (struct-copy response resp (output\n    (lambda (fd)\n      (define tmp\n        (parameterize ((requestid requestid0))\n          ((response-output resp) fd)))\n      (define t1 (current-milliseconds))\n      (define dur (- t1 t0))\n\n      ;; Let's use \"structured logging\" here to make it easier to search,\n      ;; and do things like create CloudWatch metrics from CloudWatch Logs\n      ;; filters (they have a syntax to extract things from JSON.)\n      (unless (squelch-noisy-request-log? req)\n        (lognew-info\n            (hasheq 'request  (dict-request-fields req)\n                    'response (hasheq 'code     (response-code resp)\n                                      'headers  (headers->hasheq (response-headers resp))\n                                      'duration dur))))\n      tmp))))\n\n(define ((logwrap-lazy handler) req)\n  (define t0 (current-milliseconds))\n  (define requestid0 (+ (* t0 1000) (random 1000)))\n  (logwrap-lazy-impl handler req t0 requestid0))\n\n\n(define (accepts-gzip? req)\n  (member \"gzip\" (map string-trim\n                      (string-split (alist-ref (request-headers req)\n                                               'accept-encoding \"\") \",\"))))\n(define (respond code message headers mime-type body)\n  (response/full code (string->bytes/utf-8 message)\n                 (current-seconds) mime-type headers\n                 (list body)))\n(define (OK req extra-headers mime-type body (body-gzipped? #f))\n  (define gzip? (accepts-gzip? req))\n  (define headers (if gzip? (cons (make-header #\"Content-Encoding\" #\"gzip\")\n                                  extra-headers)\n                    extra-headers))\n  (define bytes.body (if (string? body) (string->bytes/utf-8 body) body))\n  (define payload (if (and gzip? (not body-gzipped?)) (gzip/bytes bytes.body)\n                    bytes.body))\n  (respond 200 \"OK\" headers mime-type payload))\n(define (not-found req)\n  (respond 404 \"Not Found\" '() mime:html\n           (string->bytes/utf-8\n             (xexpr->html-string\n               (not-found.html (url->string (request-uri req)))))))\n(define (OK/jsexpr f req)\n  (define input (bytes->jsexpr (request-post-data/raw req)))\n  (define result (job (thunk (f input))))\n  (if (job-failure? result)\n    (respond 400 \"Bad Request\" '() mime:text\n             (string->bytes/utf-8 (job-failure-message result)))\n    (OK req '() mime:json (jsexpr->string result))))\n\n(define (/index req)\n  (OK req '() mime:html (xexpr->html-string index.html)))\n\n(define (/schema.json  req) (OK req '() mime:text schema.json.txt))\n(define (/schema.yaml  req) (OK req '() mime:text schema.yaml.txt))\n;; (define (/predicates   req) (if (accepts-gzip? req)\n;;                               (OK req '() mime:json predicates-cached-gzip #t)\n;;                               (OK req '() mime:json predicates-cached #f)))\n\n;; (define (/query        req) (OK/jsexpr query req))\n\n(define (group-by-db xs)\n  (foldl (lambda (x db=>id)\n           (hash-update db=>id (car x) (lambda (xs) (cons (cdr x) xs)) '()))\n         (hash) xs))\n\n(define (pretty-synonyms ss)\n  (if (and (pair? ss) (not (cdar ss))) '()\n    (make-immutable-hash\n      (map (lambda (kv) (cons (string->symbol (car kv)) (cdr kv))) ss))))\n\n;; (define (find-concepts/any str)\n;;   (hash 'synonyms (pretty-synonyms (curie-synonyms/names str))\n;;         'concepts\n;;         (make-immutable-hash\n;;           (hash-map\n;;             (group-by-db\n;;               (map (lambda (c)\n;;                      (define r (concept->result c))\n;;                      (define attrs (hash-ref (cdr r) 'attributes))\n;;                      (define dbnames\n;;                        (map (lambda (attr) (hash-ref attr 'value))\n;;                             (filter (lambda (attr) (equal? (hash-ref attr 'name)\n;;                                                            \"mediKanren-source\"))\n;;                                     attrs)))\n;;                      (define dbname (if (null? dbnames) 'unknown\n;;                                       (string->symbol (car dbnames))))\n;;                      (cons dbname r))\n;;                    (append (find-concepts #t (list str))\n;;                            (find-concepts #f (list str)))))\n;;             (lambda (db cs) (cons db (make-immutable-hash cs)))))))\n\n;; (define ((find/db-id find) data)\n;;   (group-by-db (map (lambda (x) (cons (car x) (cddr x))) (find (list data)))))\n(define (/health req)\n  (OK req '() mime:json (jsexpr->string '#hasheq()))\n  #;(let-values (((result cpu real gc) (time-apply (lambda () (run 1 () (triple \"NCIT:C18585\" \"biolink:actively_involved_in\" \"NCIT:C45399\"))) '())))\n    (let ((response\n           (if (null? result)\n               (hash 'status \"corrupt\"\n                     'reason \"no data\"\n                     'real_time real\n                     'cpu_time cpu)\n               (hash 'status \"online\"\n                     'real_time real\n                     'cpu_time cpu))))\n   (OK req '() mime:json (jsexpr->string response)))))\n\n(define (/index.js req)  (OK req '() mime:js index.js))\n;; (define (/health req)    (OK health                        req))\n(define (/query req)\n  (OK/jsexpr (query (requestid))                        req))\n;; (define (/v2/find-concepts   req) (OK/jsexpr find-concepts/any            req))\n;; (define (/v2/find-categories req) (OK/jsexpr (find/db-id find-categories) req))\n;; (define (/v2/find-predicates req) (OK/jsexpr (find/db-id find-predicates) req))\n\n\n(struct job-failure (message))\n\n(define (work-safely work)\n  (define custodian.work (make-custodian))\n  (define result\n    ;; current-custodian will collect all file handles opened during work\n    (parameterize ((current-custodian custodian.work))\n      (with-handlers ((exn:fail?\n                        (lambda (v)\n                          ((error-display-handler) (exn-message v) v)\n                          (job-failure (exn-message v))))\n                      ((lambda _ #t)\n                       (lambda (v)\n                         (define message\n                           (string-append \"unknown error: \"\n                                          (with-output-to-string (thunk (write v)))))\n                         (pretty-write message)\n                         (job-failure message))))\n        (work))))\n  (custodian-shutdown-all custodian.work) ; close all file handles opened during work\n  result)\n\n;; Run multiple jobs concurrently\n;(define (job work) (work-safely work))\n\n;; Run multiple jobs sequentially\n(define (job work)\n  (define job-response (make-channel))\n  (channel-put job-request (cons job-response work))\n  (channel-get job-response))\n\n(define job-request (make-channel))\n\n(define worker\n  (thread\n    (thunk (let loop ()\n             (match-define (cons job-response work) (channel-get job-request))\n             (channel-put job-response (work-safely work))\n             (loop)))))\n\n(define (start)\n  (define-values (dispatch _)\n    (dispatch-rules\n     ((\"\")                     #:method \"get\"  /index)\n     ((\"index.js\")             #:method \"get\"  /index.js)\n     ((\"schema.json\")          #:method \"get\"  /schema.json)\n     ((\"schema.yaml\")          #:method \"get\"  /schema.yaml)\n     ;; ((\"predicates\")           #:method \"get\"  /predicates)\n\n     ;; Legacy endpoint - unversioned - TRAPI 1.0 - TODO: Delete\n     ((\"query\")                #:method \"post\" /query)\n\n     ;; Current (versioned) endpoint for NCATS - TRAPI 1.1\n     ((\"v2\" \"query\")     #:method \"post\" /query)\n\n     ;; Endpoint for Andy's webapp\n     ((\"pmi\" \"v2\" \"query\")     #:method \"post\" /query)\n     ;; TODO: restore text search\n     ;; ((\"pmi\" \"v2\" \"query\" \"find-concepts\")   #:method \"post\" /v2/find-concepts)\n     ;; ((\"pmi\" \"v2\" \"query\" \"find-categories\") #:method \"post\" /v2/find-categories)\n     ;; ((\"pmi\" \"v2\" \"query\" \"find-predicates\") #:method \"post\" /v2/find-predicates)\n\n     ((\"pmi\" \"v2\" \"ingest-pipeline\" \"status\") #:method \"get\" /ingest-pipeline-status)\n\n     ((\"health\")               #:method \"get\" /health)\n\n     (else                                     not-found)))\n\n\n  (serve/servlet (logwrap-lazy dispatch)\n                 ;; none-manager for better performance:\n                 ;; only possible because we're not using web continuations.\n                 #:manager (create-none-manager #f)\n                 #:servlet-regexp #rx\"\"\n                 #:listen-ip #f  ;; comment this to disable external connection\n                 #:port 8384\n                 #:launch-browser? #f\n                 #:safety-limits (make-safety-limits #:response-send-timeout (* 2 (query-time-limit))\n                                                     #:response-timeout (* 2 (query-time-limit)))\n                                                     ;; Avoid (query-time-limit) getting enforced\n                                                     ;; in multiple locations.\n                 ))\n\n(module+ main (start))\n\n;; Notes for exercising multi-threaded file handle usage to stress-test work-safely:\n;; Start a long query, then repeatedly run short queries while the long query runs.\n;; Query results should be deterministic and produce no errors.\n\n;; A long query for semmed:\n#|\n{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n0\": {\n          \"ids\": [\n            \"UMLS:C0520909\"\n          ]\n        },\n        \"n1\": {\n          \"categories\": [\n            \"disease_or_phenotypic_feature\"\n          ]\n        },\n        \"n2\": {\n          \"categories\": [\n            \"gene\"\n          ]\n        }\n      },\n      \"edges\": {\n        \"e01\": {\n          \"subject\": \"n0\",\n          \"object\": \"n1\"\n        },\n        \"e21\": {\n          \"subject\": \"n2\",\n          \"object\": \"n1\"\n        }\n      }\n    }\n  }\n}\n|#\n\n;; A short query for semmed:\n#|\n{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n0\": {\n          \"ids\": [\n            \"UMLS:C0520909\"\n          ]\n        },\n        \"n1\": {\n          \"categories\": [\n            \"disease_or_phenotypic_feature\"\n          ]\n        }\n      },\n      \"edges\": {\n        \"e01\": {\n          \"subject\": \"n0\",\n          \"object\": \"n1\"\n        }\n      }\n    }\n  }\n}\n|#\n"
  },
  {
    "path": "medikanren2/string-search-config.rkt",
    "content": "#lang racket\n;; This file is private to string-search.rkt.\n;; Applications should include string-search.rkt instead.\n(provide\n    field-indexed\n    schema-pri\n    name-ornull-from-pri\n    name-from-pri\n    uri-from-pri\n    fn-concept-name-corpus\n    fn-concept-name-index\n    fn-cprop-primary\n)\n\n;;;; Isolate here the configuration of string-search (currently hard-coded).\n\n;; For now, we only index the field called \"name\"\n(define field-indexed \"name\")\n\n(define schema-pri '(string string string))\n\n;;; *** data transformation for ingest ***\n(define (name-ornull-from-pri v)\n  (let* (\n      (fd (list-ref v 1))\n      (name (list-ref v 2)))\n    (if (equal? fd field-indexed)\n      `(,name)\n      '())))\n\n;;; *** data transformation for egress ***\n(define (name-from-pri pri)\n  (list-ref pri 2))\n\n(define (uri-from-pri pri)\n  (list-ref pri 0))\n\n\n;;;; Filenames\n\n(define fn-concept-name-corpus \"concept-name-corpus.scm\")     ; only for build-name-string-search-v1\n(define fn-concept-name-index  \"concept-name-index.bytes\")\n(define fn-cprop-primary \"primary.value.table\")\n\n"
  },
  {
    "path": "medikanren2/string-search-impl.rkt",
    "content": "#lang racket/base\n;; This file is private to string-search.rkt.\n;; Applications should include string-search.rkt instead.\n(provide\n  string/searchable\n  suffix:corpus-find*/disk\n  bytes->suffix-key\n  suffix-key->bytes\n  param-fd-input-binary\n  ensure-fd-input-binary\n  test:parameterize-defaults\n\n  ;; The following are internals used in string-search.rkt\n  suffixsuffix-key index i))\n(define (suffix-key->bytes s)\n  (define cid (car s))\n  (define pos (cdr s))\n  (bytes (byte-at -40 cid) (byte-at -32 cid) \n         (byte-at -24 cid) (byte-at -16 cid) (byte-at -8 cid) (byte-at 0 cid)\n         (byte-at -8 pos) (byte-at 0 pos)))\n(define (bytes->suffix-key bs start)\n  (define i (* start suffix-key-byte-size))\n  (define (bref-to j offset) (arithmetic-shift (bytes-ref bs (+ i j)) offset))\n  (cons (+ (bref-to 0 40) (bref-to 1 32) (bref-to 2 24) (bref-to 3 16) (bref-to 4 8) (bref-to 5 0))\n        (+ (bref-to 6 8) (bref-to 7 0))))\n(define (read-suffix-key-bytes in) (read-bytes suffix-key-byte-size in))\n(define (write-suffix-keys out v)\n  (for ((s (in-vector v))) (write-bytes (suffix-key->bytes s) out)))\n(define (suffix-index->suffix-key in si)\n  (file-position in (* suffix-key-byte-size si))\n  (bytes->suffix-key (read-suffix-key-bytes in) 0))\n;; ...\n(define (write-scm out scm) (fprintf out \"~s\\n\" scm))\n;; END:excerpted from medikanren/repr.rkt\n\n(define (nlist-intersection nlists)\n  (if (null? nlists) '()\n    (let loop ((i** nlists))\n      (cond ((ormap null? i**) '())\n            (else (define i0* (map car i**))\n                  (define next (apply max i0*))\n                  (if (andmap (lambda (i) (= i next)) i0*)\n                    (cons next (loop (map cdr i**)))\n                    (loop (map (lambda (i*) (dropf i* (lambda (i) (< i next))))\n                               i**))))))))\n\n(define i0              (char->integer #\\0))\n(define i9              (char->integer #\\9))\n(define iA              (char->integer #\\A))\n(define iZ              (char->integer #\\Z))\n(define (searchable? c) (and (<= i0 c) (<= c iZ) (or (<= c i9) (<= iA c))))\n(define (string/searchable s)\n  (define cs (map char->integer (string->list (string-upcase s))))\n  (list->string (map integer->char (filter searchable? cs))))\n\n(define (string? (string-ref a ai) (string-ref b bi)) #f)\n          (else (loop (- k 1) (+ ai 1) (+ bi 1))))))\n(define (suffixsuffix-key bin-a 0))\n         (b (bytes->suffix-key bin-b 0))\n         (c (hash-ref hashcorpus (car a)))\n         (d (hash-ref hashcorpus (car b))))\n    (stringconcept in-index str)\n  (define needle (string/searchable str))\n  (define (compare si needle)\n    (match-define (cons cid pos) (suffix-index->suffix-key in-index si))\n    (define hay (substring (string/searchable (concept-name (cid->concept cid))) pos))\n    (cond ((string-prefix? hay needle) 0)\n          ((stringconcept in-index str*)\n  (define (rz r) (- (cdr r) (car r)))\n  (define rs (map (lambda (s) (suffix:corpus-find-range/disk cid->concept in-index s)) str*))\n  (define zmin (* 2 (if (null? rs) 0 (foldl (lambda (r z) (min z (rz r)))\n                                            (rz (car rs)) (cdr rs)))))\n  (nlist-intersection\n    (map (lambda (r) (dedup/< (map (lambda (i) (car (suffix-index->suffix-key in-index i)))\n                                   (range (car r) (cdr r)))))\n         (filter (lambda (r) (<= (rz r) zmin)) rs))))\n\n;;;; Provisions for efficient safe use of file handles\n\n;;; param-fd-input-binary:\n;;;   A context for caching file descriptors.\n;;;   To preserve context, (make-hash), keep a reference, and pass\n;;;   via parameterize.\n(define param-fd-input-binary\n  (make-parameter\n    'initialize-me-via-make-hash\n    #f))\n\n;;; ensure-fd-input-binary:\n;;;   Provide the cached file handle for fn, or open a file handle\n;;;   if one hasn't been created.\n(define (ensure-fd-input-binary absf)\n  (define (ensure-fd h)\n    (dict-ref! h absf (lambda () (open-input-file absf #:mode 'binary))))\n  (define h (param-fd-input-binary))\n  (if (dict? h)\n    (ensure-fd h)\n    (let* (\n        (h (make-hash))\n        (fd (ensure-fd h)))\n      (param-fd-input-binary h)\n      fd)))\n\n;;; test:parameterize-defaults\n;;;   A helper for automated tests to be able to open string indexes.\n;;;   Applications should implement a similar but usually more complicated\n;;;   function.  Call (make-hash) as we do here to trigger allocation of a\n;;;   new hash of file handles, or supply a previously allocated hash\n;;;   of file handles for reuse.\n(define (test:parameterize-defaults thunk)\n  (parameterize\n    ((param-fd-input-binary (make-hash)))\n    (thunk)))\n"
  },
  {
    "path": "medikanren2/string-search-impl2.rkt",
    "content": "#lang racket\n;; This file is private to string-search.rkt.\n;; Applications should include string-search.rkt instead.\n(provide\n    (all-defined-out)\n )\n(require racket/dict)\n(require racket/vector)\n(require \"base.rkt\")\n(require \"string-search-config.rkt\")\n(require \"string-search-impl.rkt\")\n\n\n;;; schema-aware wrapping for string-search-impl.rkt functions\n\n(define (foffs->concept fd-corpus foffs)\n  (file-position fd-corpus foffs)\n  (decode fd-corpus schema-pri))\n\n(define (make-~name*->value* absdOut fn-cprop-primary fn-concept-name-index)\n  (define fd-corpus\n    (ensure-fd-input-binary (expand-user-path (build-path absdOut fn-cprop-primary))))\n  (define fd-index\n    (ensure-fd-input-binary (expand-user-path (build-path absdOut fn-concept-name-index))))\n  (define (cid->concept foffs)\n    (let ((v (foffs->concept fd-corpus foffs)))\n;      (printf \"found file offset offs=~a v=~a\\n\" offs v)\n      (list '() (name-from-pri v))\n      ))\n  (lambda (~name*)\n    (map\n      (lambda (foffs)\n        (let ((v (foffs->concept fd-corpus foffs)))\n          v))\n      (suffix:corpus-find*/disk cid->concept fd-index ~name*))))\n\n;;; string search options\n(struct stsopt (\n  case-sensitive? ;; case sensitivity flag\n  chars:ignore    ;; ignored characters ('chars:ignore-typical' is pre-defined)\n  chars:split     ;; characters to split target name on for exact matching ('chars:split-typical' is pre-defined)\n) #:constructor-name new-stsopt\n  #:name stsopt-t\n  #:transparent)\n\n(define (make-stsopt\n    #:case-sensitive? (case-sensitive? #f)\n    #:chars:ignore (chars:ignore \"\")\n    #:chars:split (chars:split \"\")\n  )\n  (new-stsopt case-sensitive? chars:ignore chars:split))\n\n(define stsopt-default (make-stsopt))\n\n;;; from gui-simple-v2.rkt\n;; :77\n(define (split-name-string name)\n  (string-split name #px\"\\\\s+\"))\n\n;;; :242\n(define chars:ignore-typical \"-\")\n(define chars:split-typical \"\\t\\n\\v\\f\\r !\\\"#$%&'()*+,./:;<=>?@\\\\[\\\\\\\\\\\\]\\\\^_`{|}~\")\n\n;;; :245\n(define (smart-string-matches? stsopt str* hay)\n  (match stsopt\n      ( (struct stsopt-t (case-sensitive? chars:ignore chars:split))\n        (smart-string-matches-impl? case-sensitive? chars:ignore chars:split str* hay))))\n(define (smart-string-matches-impl? case-sensitive? chars:ignore chars:split str* hay)\n  (define re:ignore (and (non-empty-string? chars:ignore)\n                         (pregexp (string-append \"[\" chars:ignore \"]\"))))\n  (define re:split (and (non-empty-string? chars:split)\n                        (pregexp (string-append \"[\" chars:split \"]\"))))\n  (define (normalize s case-sensitive?)\n    (define pruned (if re:ignore (string-replace s re:ignore \"\") s))\n    (if case-sensitive? pruned (string-downcase pruned)))\n  (define (contains-upcase? s) (not (string=? s (string-downcase s))))\n  (define case-sensitive?*\n    (map (lambda (s) (or case-sensitive? (contains-upcase? s))) str*))\n  (define needles\n    (map (lambda (v case-sensitive?) (normalize v case-sensitive?))\n         str* case-sensitive?*))\n  (and hay\n       (andmap\n        (if re:split\n            (lambda (n case-sensitive?)\n              (ormap (lambda (s) (string=? s n))\n                     (string-split (normalize hay case-sensitive?) re:split)))\n            (lambda (n case-sensitive?)\n              (string-contains? (normalize hay case-sensitive?) n)))\n        needles case-sensitive?*)))\n;;; :269\n(define (~string*->offset&value*\n          stsopt value* str*)\n  (define (p? v)\n    (define hay (name-from-pri v))\n    (smart-string-matches? stsopt str* hay))\n  (filter p? value*))\n;;; :295\n(define (db:~name*->concept*/options\n          stsopt absdOut fn-cprop-primary fn-concept-name-index ~name*)\n  (define fd-corpus\n    (ensure-fd-input-binary (expand-user-path (build-path absdOut fn-cprop-primary))))\n  (define lookup (make-~name*->value* absdOut fn-cprop-primary fn-concept-name-index))\n  (define value* (lookup ~name*))\n  (~string*->offset&value* stsopt\n                           value* ~name*))\n"
  },
  {
    "path": "medikanren2/string-search.rkt",
    "content": "#lang racket\n(provide\n find-ids-named\n find-concepts-named\n string-search-init-rel\n make-stsopt\n stsopt-t\n param-fd-input-binary\n\n test:read-name-corpus\n test:suffix:corpus2->index-suffixes\n (prefix-out test: build-string-index-via-codec-and-write)\n (prefix-out test: build-string-index-via-codec)\n (prefix-out test: ensure-name-index-built)\n test:verify-corpus-index\n )\n(require racket/dict)\n(require racket/vector)\n(require \"base.rkt\")\n(require \"string-search-config.rkt\")\n(require \"string-search-impl.rkt\")\n(require \"string-search-impl2.rkt\")\n\n;;; *** routines for index building ***\n(define (report-memory)\n  (collect-garbage 'major)\n  (printf \"current-memory-use ~aMB\\n\" (exact->inexact (/ (current-memory-use) 1000000))))\n\n(define (suffix:corpus2->index-suffixes hashcorpus)\n  (for*/vector (((foffs s-searchable) (in-hash hashcorpus))\n              (soffs (range (string-length s-searchable))))\n    (suffix-key->bytes (cons foffs soffs))))\n\n(define (suffix:corpus2->index hashcorpus)\n  (define (suffixindex-suffixes hashcorpus))\n  (report-memory)\n  (printf \"sorting suffixes\\n\")\n  (vector-sort! suffixes suffixindex-suffixes veccorpus)\n  (define hashcorpus (in-pairs->hash veccorpus))\n  (suffix:corpus2->index-suffixes hashcorpus))\n\n;;; in-name-corpus\n;;;   Opens a sequence produced by decoding a primary index file.  Auto-closes upon encountering eof.\n(define (in-name-corpus fname absdOut)\n  (define fdIn (open-input-file (expand-user-path (build-path absdOut fname)) #:mode 'binary))\n  (define (read-decode fdIn)\n    (if (port-closed? fdIn)\n        eof\n        (if (eof-object? (peek-byte fdIn))\n            (begin\n              (close-input-port fdIn)\n              eof)\n            (let* ((foffs (file-position fdIn))\n                   (v (decode fdIn schema-pri)))\n              (match (name-ornull-from-pri v)\n                (`(,name)\n                 (let ((s-searchable (string/searchable name)))\n                   (cons s-searchable foffs)))\n                (_ (read-decode fdIn)))))))\n  (in-port read-decode fdIn))\n\n(define (in-pairs->hash in-pairs)\n  (let ((h (make-hasheqv))) ; TODO perf?\n    (for ((kv in-pairs))\n      (match kv\n        ((cons s-searchable foffs)\n          (hash-set! h foffs s-searchable))))\n    h))\n\n(define (read-name-corpus fname absdOut)\n  (let ((in-corpus (in-name-corpus fname absdOut)))\n    (in-pairs->hash in-corpus)))\n\n(define (test:read-name-corpus fname absdOut)\n  (let ((in-corpus (in-name-corpus fname absdOut)))\n    (for*/vector ((kv in-corpus))\n      kv)))\n\n\n;;; build-string-index-via-codec\n;; Name+id corpus must live on disk so as to possess file offsets.\n(define (build-string-index-via-codec fname absdOut)\n  (let ((hashcorpus (read-name-corpus fname absdOut)))\n    (report-memory)\n    (printf \"building name search index...\\n\")\n    (values hashcorpus (suffix:corpus2->index hashcorpus))))\n\n(define (build-string-index-via-codec-and-write fn-pri fn-index absdOut)\n  (define-values (hashcorpus name-index) (build-string-index-via-codec fn-pri absdOut))\n  (printf \"indexed ~a suffixes, now writing...\\n\" (vector-length name-index))\n  (call-with-atomic-output-file\n    (expand-user-path (build-path absdOut fn-index))\n    (lambda (fd-index adir-junk)\n      (for* ((ni name-index))\n          (write-bytes ni fd-index)\n          ))))\n\n(define (ensure-name-index-built absd-index fn-concept-name-index)\n  (let* (\n         (absf-index (path->string (simplify-path (build-path absd-index fn-concept-name-index)))))\n    ; (printf \"checking for index ~a\\n\" absf-index)\n    (unless (file-exists? absf-index)\n      (build-string-index-via-codec-and-write fn-cprop-primary fn-concept-name-index absd-index))))\n\n(define (assert-name-index-built absd-index fn-concept-name-index)\n  (let* (\n         (absf-index (path->string (simplify-path (build-path absd-index fn-concept-name-index)))))\n    ; (printf \"checking for index ~a\\n\" absf-index)\n    (unless (file-exists? absf-index)\n      (error (format \"Use of string search requires index preparation.  Call string-search-init-rel: ~a\" absf-index)))))\n\n(define (test:verify-corpus-index hashcorpus index)\n  (define (<=? c d) (not (stringsuffix-key (vector-ref index (- i 1)) 0))\n        (skey (bytes->suffix-key (vector-ref index i) 0))\n        (ss-prev (substring (hash-ref hashcorpus (car skey-prev)) (cdr skey-prev)))\n        (ss (substring (hash-ref hashcorpus (car skey)) (cdr skey))))\n      (unless (<=? ss-prev ss)\n        (error (format \"index out of sequence: ~a should be < ~a\\n\" (shorten ss-prev) (shorten ss)))))\n    ))\n\n;;; find-ids-named\n;; Consult the string index associated with rel to find the ids\n;; in rel with a (name) string matching every substr in substrs,\n;; according to options stsopt.  If the associated string index\n;; has not been previously prepared, fail.\n(define (find-ids-named rel substrs (stsopt stsopt-default))\n  (unless (andmap string? substrs)\n    (error \"find-ids-named: substrs must be a list of strings\"))\n  (define absd-index (hash-ref (relation-definition-info rel) 'path))\n  (assert-name-index-built absd-index fn-concept-name-index)\n    (let* ((pris (db:~name*->concept*/options stsopt absd-index fn-cprop-primary fn-concept-name-index substrs)))\n      (map uri-from-pri pris)))\n\n;;; find-ids-named\n;; Consult the string index associated with rel to find the concepts\n;; in rel with a (name) string matching every substr in substrs,\n;; according to options stsopt.  If the associated string index\n;; has not been previously prepared, fail.\n(define (find-concepts-named rel substrs (stsopt stsopt-default))\n  (let ((uris (find-ids-named rel substrs stsopt)))\n    (define-relation/table (found xxx)\n      'source-stream (map list uris))\n    (define-relation (found2 id subj object)\n      (found id)                                     ;; logical AND, as in fresh\n      (rel id subj object))\n    found2))\n\n;;; string-search-init-rel\n;; Prepare a string search index, if it has not already been prepared.\n;; If the the string search index has already been prepared, string-search-init-rel\n;; will exit quickly.  If no string search index is prepared, calls\n;; to find-ids-named and find-concepts-named will fail.\n(define (string-search-init-rel rel)\n  (let* ((absd-index (hash-ref (relation-definition-info rel) 'path))\n         (absf-primary (path->string (simplify-path (build-path absd-index fn-cprop-primary)))))\n    ;; We check for the file to exist so that individual db/foo.rkt files can call\n    ;; string-search-init-rel, and so that common.rkt can require db/foo.rkt\n    ;; without crashing, even when the data for db/foo.rkt is not installed.\n    (when (file-exists? absf-primary)\n      (ensure-name-index-built absd-index fn-concept-name-index)\n  )))\n"
  },
  {
    "path": "medikanren2/synonyms.rkt",
    "content": "#lang racket/base\n(require\n \"common.rkt\" \n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  racket/set\n  json\n  memoize)\n\n(provide direct-synonym direct-synonym* direct-synonym+ synonym close-match-synonym\n         synonyms/step synonym-of/step synonyms/breadth synonym-of/breadth\n         synonym synonym-path kgx-synonym\n         simple-synonym\n         get-synonyms-ls get-names-ls get-names-set)\n\n(define (equivalence-relation node link)\n  (define-relation (equiv=/= a b)\n    (=/= a b)\n    (fresh (x)\n      (conde ((link a x))\n             ((link x a)))\n      (conde ((==       x b))\n             ((equiv=/= x b)))))\n  (define-relation (equiv a b)\n    (conde ((==       a b) (node a))\n           ((equiv=/= a b))))\n  equiv)\n\n(define (simple-node x) (fresh (k v) (cprop x k v)))\n\n(define (simple-link a b)\n  (fresh (id pred)\n    (edge a b)\n    (eprop id \"predicate\" pred)\n    (membero pred '(\"biolink:same_as\"))))\n\n(define simple-synonym (equivalence-relation simple-node simple-link))\n\n\n(define synonyms-preds '(\"biolink:same_as\"\n                         ;; \"biolink:close_match\"   ; too risky un-constrained\n                         \"biolink:gene_product_of\"))\n\n(define rtx2-drug-categories '(\"biolink:ChemicalEntity\"\n                              \"biolink:ChemicalMixture\"\n                              \"biolink:MolecularEnity\"\n                              \"biolink:SmallMolecule\"\n                              \"biolink:Protein\"\n                              \"biolink:SmallMolecule\"\n                               \"biolink:ClinicalIntervention\"\n                               \"biolink:ClinicalModifier\"\n                               \"biolink:Drug\"\n                               \"biolink:Treatment\"))\n\n(define semmed-drug-categories '(\"chemical_substance\"))\n\n(define drug-categories (append rtx2-drug-categories semmed-drug-categories))\n\n(define drug-categories/set (list->set drug-categories))\n\n(define disease-categories '(\"biolink:Disease\"\n                             \"biolink:DiseaseOrPhenotypicFeature\"\n                             \"biolink:PhenotypicFeature\"))\n\n(define disease-categories/set (list->set disease-categories))\n\n(define inhibit-preds '(\"biolink:decreases_activity_of\"\n                        \"biolink:decreases_expression_of\"\n                        \"biolink:disrupts\"\n                        \"biolink:entity_negatively_regulates_entity\"\n                        \"biolink:process_negatively_regulates_process\"\n                        \"biolink:treats\"\n                        \"negatively_regulates\" ; semmed\n                        \"treats\" ; semmed\n                        )) \n\n(define gene-or-protein '(\"biolink:Gene\"\n                          \"biolink:GeneFamily\"\n                          \"biolink:GenomicEntity\"\n                          \"biolink:MacromolecularComplex\"\n                          \"biolink:MolecularEntity\"\n                          \"biolink:Protein\"))\n\n(define gene-or-protein/set (list->set gene-or-protein))\n\n; Cached synonyms from the kgx-synonym knowledge graph\n(define (kgx-synonym a b)\n  (fresh (predicate id source_database)\n    (conde\n      [(kgx:synonym a b predicate id source_database)]\n      [(kgx:synonym b a predicate id source_database)])))\n\n;; Query synonyms from loaded graphs\n(define-relation (direct-synonym a b)\n  (fresh (id sp)\n    (edge id a b)\n    (eprop id \"predicate\" sp)\n    (membero sp synonyms-preds)))\n\n;; More constrained approach\n;; (define-relation (close-match-syn a b)\n;;   (fresh (id)\n;;     (any<=o \"HGNC:\" a)\n;;     (any<=o a \"HGND\")\n;;     (any<=o \"UMLS:\" b)\n;;     (any<=o b \"UMLT\")\n;;     (edge id a b)\n;;     (:== #t (a) (not (null? (run 1 () (eprop id \"predicate\" \"biolink:close_match\")))))\n;;     (:== #t (a) (string-prefix? a \"HGNC:\"))\n;;     (:== #t (b) (string-prefix? b \"UMLS:\"))))\n\n(define (non-empty-intersection/ls ls1 ls2)\n  (not (set-empty? (set-intersect (list->set ls1) (list->set ls2)))))\n\n(define (non-empty-intersection set1 set2)\n  (not (set-empty? (set-intersect set1 set2))))\n\n(define-relation (close-match-synonym a b)\n  (fresh (id cat-a cat-b)\n    (edge id a b)\n    (eprop id \"predicate\" \"biolink:close_match\")\n    (:== cat-a (a) (run*/set c (is-a a c)))\n    (:== cat-b (b) (run*/set c (is-a b c)))\n    (conde ((:== #t (cat-a) (non-empty-intersection cat-a disease-categories/set) )\n            (:== #t (cat-b) (non-empty-intersection cat-b disease-categories/set)))\n           ((:== #t (cat-a) (non-empty-intersection cat-a drug-categories/set) )\n            (:== #t (cat-b) (non-empty-intersection cat-b drug-categories/set)))\n           ((:== #t (cat-a) (non-empty-intersection cat-a gene-or-protein/set))\n            (:== #t (cat-b) (non-empty-intersection cat-b gene-or-protein/set))\n            (conde ((:== #t (a) (string-prefix? a \"HGNC:\")))\n                   ((:== #t (a) (string-prefix? a \"NCBIGene:\")))\n                   ((:== #t (a) (string-prefix? a \"UniProtKB:\")))\n                   ((:== #t (a) (string-prefix? a \"ENSEMBL:\"))))))))\n\n(define-relation (direct-synonym* a b)\n  (conde ((== a b))\n         ((direct-synonym+ a b))))\n\n(define-relation (direct-synonym+ a b)\n  (conde ((direct-synonym a b))\n         ((fresh (mid)\n            (direct-synonym a mid)\n            (direct-synonym+ mid b)))))\n\n(define-relation (exact-synonym a b)\n  (conde ((== a b))\n         ((direct-synonym+ a b))\n         ((direct-synonym+ b a))))\n\n(define-relation (synonym a b)\n  (conde ((== a b))\n         ((close-match-synonym a b))\n         ((close-match-synonym b a))\n         ((direct-synonym a b))\n         ((direct-synonym b a))\n         ((fresh (mid)\n            (conde ((close-match-synonym a mid)) ((close-match-synonym mid a)))\n            (synonym mid b)))\n         ((fresh (mid)\n            (conde ((close-match-synonym b mid)) ((close-match-synonym mid b)))\n            (synonym mid a)))         \n         ((fresh (mid)\n            (conde ((direct-synonym a mid)) ((direct-synonym mid a)))\n            (synonym mid b)))\n         ((fresh (mid)\n            (conde ((direct-synonym b mid)) ((direct-synonym mid b)))\n            (synonym mid a)))))\n\n(define-relation (synonym-path a b path)\n  (conde\n    ((== a b) (== path `(,a)))\n    ((direct-synonym a b) (== path `(,a = ,b)))\n    ((direct-synonym b a) (== path `(,a = ,b)))\n    ((close-match-synonym a b) (== path `(,a ~ ,b)))\n    ((close-match-synonym b a) (== path `(,a ~ ,b)))\n    ((fresh (mid path-rest)\n       (conde      \n         ((conde ((direct-synonym a mid)) ((direct-synonym mid a)))\n          (synonym-path mid b path-rest)\n          (not-membero a path-rest)\n          (== path `(,a = . ,path-rest)))\n         ((conde ((direct-synonym b mid)) ((direct-synonym mid b)))\n          (synonym-path a mid path-rest)\n          (not-membero b path-rest)\n          (appendo path-rest (list '= b) path))\n         ((conde ((close-match-synonym a mid)) ((close-match-synonym mid a)))\n          (synonym-path mid b path-rest)\n          (not-membero a path-rest)\n          (== path `(,a ~ . ,path-rest)))\n         ((conde ((close-match-synonym b mid)) ((close-match-synonym mid b)))\n          (synonym-path a mid path-rest)\n          (not-membero b path-rest)\n          (appendo path-rest (list '~ b) path)))))))\n\n;; Different ways of actually getting a useful amount of synonyms in a reasonable amount of time\n\n(define (synonyms/step term (n 500) (categories '()))\n  (if (pair? categories)\n      (set->list\n       (run*/set/steps n s\n         (synonym s term)\n         (fresh (cat)\n           (cprop s \"category\" cat)\n           (membero cat categories))))\n      (set->list (run*/set/steps n s (synonym s term)))))\n\n;; relation for use in mk queries\n;; n is required\n;; (run* s ((synonym-of/set autism 1000) s)))\n(define/memo* (synonym-of/step term n)\n  (let ((synonyms (set->list (synonyms/step term n))))\n    (relation synonym-of/step^ (s)\n      (membero s synonyms))))\n\n(define (synonyms/breadth term (n 2) (categories '()))\n  (let loop ((n (- n 1)) (synonyms (set term)) (terms (list term)) )\n    (let ((new-synonyms\n           (run*/set s (fresh (term)\n                         (membero term terms)\n                         (conde ((direct-synonym s term))\n                                ((direct-synonym term s))\n                                ((close-match-synonym s term))\n                                ((close-match-synonym term s)))\n                         (if (pair? categories)\n                             (fresh (cat)\n                               (cprop s \"category\" cat)\n                               (membero cat categories))\n                             (== #t #t))\n                         (:== #f (s) (set-member? synonyms s))\n                         ;; (not-membero s (set->list synonyms))     ; purer but slower\n                         ))))\n      (cond ((set-empty? new-synonyms) (set->list synonyms))\n            ((= n 0) (set->list (set-union new-synonyms synonyms)))\n            (else\n             (loop (- n 1) (set-union new-synonyms synonyms) \n                   (set->list new-synonyms)))))))\n\n;; relation for use in mk queries\n;; n is required\n;; (run* s ((synonym-of/breadth autism 2) s)))\n(define/memo* (synonym-of/breadth term n)\n  (let ((synonyms (synonyms/breadth term n)))\n    (relation synonym-of/breadth^ (s)\n      (membero s synonyms))))\n\n;; used in TRAPI interpreter\n;; implements basic logic: KGX-syn for genes/proteins, and KGs for others\n(define/memo* (get-synonyms-ls curies)\n  (remove-duplicates\n   (append curies\n           (apply append\n                  (map (lambda (curie)\n                         (let ((cats (run*/set c (cprop curie \"category\" c))))\n                           (if (non-empty-intersection cats gene-or-protein/set)\n                               (synonyms/breadth curie 1)\n                               (run* s (kgx-synonym curie s)))))\n                       curies)))))\n\n; get-names-ls function takes a list of curies and return the curies with their coresponding names\n(define (get-names-ls curie-ls)\n  (run* (curie name)\n    (cprop curie \"name\" name)\n    (membero curie curie-ls)))\n\n(define (get-names-set curie-set)\n  (get-names-ls (set->list curie-set)))\n\n\n  \n"
  },
  {
    "path": "medikanren2/test/10GB-CI/require-common-spec.rkt",
    "content": "#lang racket\n(require chk)\n(require \"../../common.rkt\")\n\n; test that we can require common.rkt without problems\n(chk\n    (#:t #t))\n"
  },
  {
    "path": "medikanren2/test/10GB-CI/string-search-build-spec.rkt",
    "content": "#lang racket\n;(require racket)\n;(require racket/match)\n(require chk)\n(require \"../../string-search-config.rkt\")\n(require \"../../string-search-impl.rkt\")\n(require \"../../string-search.rkt\")\n(require racket/pretty)\n(require \"../../db/yeast-micro-sri-reference-kg-0.3.0.rkt\")\n(require \"../../base.rkt\")\n\n\n(chk\n    (#:do\n        (let* (\n                (relp-index (hash-ref (relation-definition-info nodes) 'path))\n                (absd-index (dbk:current-config-relation-path relp-index))\n                (name-corpus (test:read-name-corpus fn-cprop-primary absd-index))\n                (nbytes-total\n                    (time (for/sum ((v name-corpus))\n                        (string-length (car v)))))\n                (nbytes-avg (exact->inexact (/ nbytes-total (vector-length name-corpus)))))\n            (printf \"found ~a bytes, ~a items, ~a bytes/item\\n\" nbytes-total (vector-length name-corpus) nbytes-avg)\n        ))\n    (#:t #t))\n\n\n(define fn-perftest (format \"~a-perftest\" fn-concept-name-index))\n\n(define (absf-perftest rel)\n    (let* (\n            (relp-index (hash-ref (relation-definition-info nodes) 'path))\n            (absd-index (dbk:current-config-relation-path relp-index)))\n        (path->string (simplify-path (build-path absd-index fn-perftest)))))\n\n(chk\n    (#:do\n        (test:ensure-name-index-built (hash-ref (relation-definition-info nodes) 'path) fn-perftest))\n    (#:do\n        (time (length (find-ids-named nodes '(\"CACNA1\")))))\n    (#:do\n        (delete-file (absf-perftest nodes)))\n    (#:t #t))\n"
  },
  {
    "path": "medikanren2/test/10GB-CI/string-search-spec.rkt",
    "content": "#lang racket\n(require chk)\n(require \"../../base.rkt\")\n(require \"../../string-search-config.rkt\")\n(require \"../../string-search-impl.rkt\")\n(require \"../../string-search-impl2.rkt\")\n(require \"../../string-search.rkt\")\n(require racket/pretty)\n\n;; *** Utilities ***\n\n(define (with-finally thunk-run thunk-cleanup)\n  (with-handlers\n      ((exn:fail? (lambda (ex)\n        (thunk-cleanup)\n        (raise ex))))\n    (let ((x (thunk-run)))\n      (thunk-cleanup)\n      x)))\n\n(chk\n (#:=\n  (with-finally\n    (lambda () 7)\n    (lambda () 'no-opp))\n  7))\n\n(chk\n (#:do (define t 1))\n (#:do\n  (with-finally\n    (lambda () 8)\n    (lambda () (set! t 2))))\n (#:= t 2))\n\n(chk\n (#:do (define t 1))\n (#:do\n  (with-handlers ([exn? (lambda (ex)\n                   'no-op)]) ; \"swallow\" exception\n    (with-finally\n      (lambda () (error \"foobaaar!!\"))\n      (lambda () (set! t 2)))))\n (#:= t 2))\n\n\n(define (with-temporary-dir-cleanup template fn)\n  (define adirTemp (make-temporary-file template 'directory #f))\n  (with-finally\n    (lambda ()\n      (test:parameterize-defaults (lambda ()\n        (fn adirTemp))))\n    (lambda ()\n      (with-handlers ([exn:fail?\n                       'no-op]) ; \"swallow\" exception\n        (delete-directory/files adirTemp)))))\n\n;; No cleanup, in case manual inspection is required\n(define (with-temporary-dir template fn)\n  (define adirTemp (make-temporary-file template 'directory #f))\n  (printf \"populating ~a\\n\" adirTemp)\n  (test:parameterize-defaults (lambda ()\n    (fn adirTemp))))\n  \n;; We count both work ticks (w) and results (i).  Make a version\n;; parametreized by numTicksMax?\n(define (run-stream numMax s)\n  (define (iter i w xs s)\n    (cond\n      ((and (>= numMax 0) (>= i numMax)) xs)\n      ((null? s) xs)\n      ((procedure? s)\n       (iter i (+ w 1) xs (s)))\n      ((pair? s)\n       (let* ((x (car s))\n              (t (current-milliseconds))\n              )\n         (iter (+ i 1) (+ w 1) (cons x xs) ((cdr s)))))\n      (else (raise (format \"unexpected type: ~a\" s)))))\n  (reverse (iter 0 0 '() s)))\n\n\n(chk\n  (#:do\n    (for ((xp (range 0 46)))\n      (let* ((foffs (arithmetic-shift 1 xp))\n              (foffs2 (car (bytes->suffix-key (suffix-key->bytes (cons foffs 7)) 0))))\n        (unless (equal? foffs foffs2)\n          (error (format \"could not round trip file offset expected=~a actual=~a\" foffs foffs2))))))\n  (#:t #t))\n\n(chk\n  (#:do\n    (for ((xp (range 0 14)))\n      (let* ((soffs (arithmetic-shift 1 xp))\n              (soffs2 (cdr (bytes->suffix-key (suffix-key->bytes (cons 7 soffs)) 0))))\n        (unless (equal? soffs soffs2)\n          (error (format \"could not round trip string offset expected=~a actual=~a\" soffs soffs2))))))\n  (#:t #t))\n\n;; generalize suffix:corpus->index\n\n(chk\n (#:=\n  (list->set (map (lambda (b) (bytes->suffix-key b 0)) (vector->list (test:suffix:corpus2->index-suffixes\n   (vector\n    (cons \"the\" 7)\n    (cons \"the\" 9)\n    )))))\n  (list->set '((7 . 0) (7 . 1) (7 . 2) (9 . 0) (9 . 1) (9 . 2)))))\n\n(chk\n (#:=\n  (list->set (map (lambda (b) (bytes->suffix-key b 0)) (vector->list (test:suffix:corpus2->index-suffixes\n   (vector\n    (cons \"the\" 7))))))\n  (list->set '((7 . 2) (7 . 1) (7 . 0)))))\n\n\n(chk\n (#:=\n  (list->set (map (lambda (b) (bytes->suffix-key b 0)) (vector->list (test:suffix:corpus2->index-suffixes\n   (vector\n    (cons \"the\" 7)\n    (cons \"the\" 9)\n    )))))\n  (list->set '((7 . 2) (9 . 2) (7 . 1) (9 . 1) (7 . 0) (9 . 0)))\n  ))\n\n\n;; Can we pass names to the index?\n\n(define concept*-example-1\n  (list->vector\n   '(((\"OMIM:MTHU026069\" \"\\\"'Swiss-cheese\\\\\\\" appearance of cartilage\\\"\")\n   \"cartilage\")\n ((\"CHEMBL.COMPOUND:CHEMBL2271031\"\n   \"\\\"(+/-)-[1S*,2R*,5R*,6S*,(2\\\\\\\\\\\\\\\"S*,3\\\\\\\\\\\\\\\"R*)/(2\\\\\\\\\\\\\\\"R*,3\\\\\\\\\\\\\\\"S*)]-2-(2',6'-dimethoxyphenoxy)-1-hydroxy-6-[7\\\\\\\\\\\\\\\"-methoxy-3\\\\\\\\\\\\\\\"-methoxymethyl-2\\\\\\\\\\\\\\\"-(3,4-methylenedioxyphenyl)chroman-6\\\\\\\\\\\\\\\"-yl]-3,7-dioxabicyclo[3.3.0]octane\\\"\")\n  \"methoxy-3\")\n ((\"CHEBI:139029\"\n   \"\\\"(1S,3R)-dihydroxy-(20S)-[(5'R)-(2\\\\\\\"-hydroxy-2\\\\\\\"-propyl)-(2'S)-tetrahydrofuryl]-22,23,24,25,26,27-hexanor-1alpha-hydroxyvitamin D3\\\"\")\n  \"hexanor\")\n ((\"CHEMBL.COMPOUND:CHEMBL2426108\"\n   \"\\\"(3R',5S')-3,5-dihydroxy-1-(4'-hydroxy-3',5'-dimethoxyphenyl)-7-(4\\\\\\\\\\\\\\\"-hydroxy-3'-methoxyphenyl)heptane\\\"\")\n  \"hydroxy-3'-m\")\n ((\"CHEMBL.COMPOUND:CHEMBL2426107\"\n   \"\\\"(3R',5S')-3,5-dihydroxy-1-(4'-hydroxy-3',5'-dimethoxyphenyl)-7-(4\\\\\\\\\\\\\\\"-hydroxyphenyl)heptane\\\"\")\n  \"hydroxyphenyl)heptane\")\n ((\"CHEMBL.COMPOUND:CHEMBL2426106\"\n   \"\\\"(3S)-1-(3'-methoxy-4'-hydroxyphenyl)-7-(4\\\\\\\\\\\\\\\"-hydroxyphenyl)-(6E)-6-hepten-3-ol\\\"\")\n  \"hepten\")\n ((\"CHEMBL.COMPOUND:CHEMBL3735273\"\n   \"\\\"(Clarithromycin-(4\\\\\\\\\\\\\\\"-(methylamino)-N(methyl)(4-benzyltriazolyl))-N-hydroxyacetamide\\\"\")\n  \"hydroxya\"))))\n\n\n\n(define (build-test-corpus concept* absdOut)\n  (let ((fd (open-output-file (expand-user-path (build-path absdOut fn-cprop-primary)))))\n    (for/vector ((c concept*))\n      (let ((id (car c))\n            (name (cadr c)))\n        (encode fd schema-pri `(,id ,field-indexed ,name))))\n    (close-output-port fd)))\n\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (build-test-corpus (vector-map car concept*-example-1) adirTemp))))\n (#:t #t))\n\n\n;; can we build an index in a format that returns file offsets?\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (let ((fn-primary (expand-user-path (build-path adirTemp fn-cprop-primary))))\n        (build-test-corpus (vector-map car concept*-example-1) adirTemp)\n        (test:build-string-index-via-codec-and-write fn-cprop-primary fn-concept-name-index adirTemp)))))\n (#:t #t))\n\n\n\n;;; print-index-v2: print a human-readable form of the index for debugging purposes\n(define (print-index-v2 index-v2 adirTemp)\n  (define (string-left str end)\n    (substring str 0 (min (string-length str) end)))\n  (let* ((fn-primary (expand-user-path (build-path adirTemp fn-cprop-primary)))\n         (fd-primary (open-input-file fn-primary #:mode 'binary)))\n    (for ((i (range (vector-length index-v2))))\n      (let* ((s-n (vector-ref index-v2 i)))\n          (let* ((foffs (car s-n))\n                 (soffs (cdr s-n))\n                 (concept (foffs->concept fd-primary foffs))\n                 (id (list-ref concept 0))\n                 (name (list-ref concept 2))\n                 (st-hit (substring (string/searchable name) soffs))\n                 (st-hit-short (string-left st-hit 30)))\n            (printf \"~a (~a,~a) ~a len=~a id=~a\\n\" i foffs soffs st-hit-short (string-length st-hit) id))))\n    (close-input-port fd-primary)))\n\n\n;; Can we the sort an index without crashing?  If we print the index does it look right?\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (let* ((corpus2 #((\"ANIMALS:0123\" \"brown fox\"))))\n        (build-test-corpus corpus2 adirTemp)\n        (let-values (((hashcorpus index) (test:build-string-index-via-codec fn-cprop-primary adirTemp)))\n          (test:verify-corpus-index hashcorpus index)\n;          (printf \"about to print-index from corpus v2:\\n\")\n;          (print-index-v2 index adirTemp)\n          '()\n        )))))\n (#:t #t))\n\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (let* ((corpus2 #((\"JOBS:0123\" \"bookkeeper\"))))\n        (build-test-corpus corpus2 adirTemp)\n        (let-values (((hashcorpus index) (test:build-string-index-via-codec fn-cprop-primary adirTemp)))\n          (test:verify-corpus-index hashcorpus index)\n;          (printf \"about to print-index from corpus v2:\\n\")\n;          (print-index-v2 index adirTemp)\n          '()\n        )))))\n (#:t #t))\n\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (let* ((corpus2 #((\"JOBS:0123\" \"bookkeeper\")\n                        (\"JOBS:0123\" \"bookbinder\"))))\n        (build-test-corpus corpus2 adirTemp)\n        (let-values (((hashcorpus index) (test:build-string-index-via-codec fn-cprop-primary adirTemp)))\n          (test:verify-corpus-index hashcorpus index)\n;          (printf \"about to print-index from corpus v2:\\n\")\n;          (print-index-v2 index adirTemp)\n          '()\n        )))))\n (#:t #t))\n\n\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (let* ((corpus2 (vector-map car concept*-example-1)))\n        (build-test-corpus corpus2 adirTemp)\n        (let-values (((hashcorpus index) (test:build-string-index-via-codec fn-cprop-primary adirTemp)))\n          (test:verify-corpus-index hashcorpus index)\n;          (printf \"about to print-index from corpus v2:\\n\")\n;          (print-index-v2 index adirTemp)\n          '()\n        )))))\n (#:t #t))\n\n\n\n\n;; can we perform lookups in the new index format?\n(chk\n (#:do\n  (with-temporary-dir-cleanup\n    \"mediKanren-test-~a\"\n    (lambda (adirTemp)\n      (let ((fn-primary (expand-user-path (build-path adirTemp fn-cprop-primary))))\n        (build-test-corpus (vector-map car concept*-example-1) adirTemp)\n        (test:build-string-index-via-codec-and-write fn-cprop-primary fn-concept-name-index adirTemp)\n        (let ((lookup (lambda (name*)\n            (map uri-from-pri (db:~name*->concept*/options stsopt-default adirTemp fn-cprop-primary fn-concept-name-index name*)))))\n          (for ((i (range (vector-length concept*-example-1))))\n            (let* ((a-q (vector-ref concept*-example-1 i))\n                   (q (cdr a-q))\n                   (a (car a-q))\n                   (ids-expected (list (car a)))\n                   (ids (lookup q)))\n              (if (equal? ids ids-expected)\n                '() ;(displayln \"PASS\")\n                (displayln (format \"FAIL: name*->cid* i=~a ids-expected=~a ids=~a\" i ids-expected ids))))))))))\n (#:t #t))\n\n"
  },
  {
    "path": "medikanren2/test/10GB-CI/string-search-yeast-spec.rkt",
    "content": "#lang racket\n;(require racket)\n(require chk)\n(require \"../../db/yeast-sri-reference-kg-0.3.0.rkt\")\n(require \"../../base.rkt\")\n(require \"../../string-search.rkt\")\n\n;;; Can we perform lookups with the string search API?\n\n;; Does CACNA1 have at least 500 IDs?  (Most recent has 1185)\n(chk\n (#:t\n  (>=\n   (length (find-ids-named nodes '(\"CACNA1\")))\n   200)))\n\n(define cacna1-names\n  `((\"ClinVarVariant:11615\" \"NM_001256789.3(CACNA1F):c.2872C>T (p.Arg958Ter)\")\n    (\"ClinVarVariant:17623\" \"NM_000069.3(CACNA1S):c.3716G>A (p.Arg1239His)\")\n    (\"ClinVarVariant:17624\" \"NM_000069.3(CACNA1S):c.3715C>G (p.Arg1239Gly)\")\n    (\"ClinVarVariant:17625\" \"NM_000069.3(CACNA1S):c.1583G>A (p.Arg528His)\")\n    (\"ClinVarVariant:17626\" \"NM_000069.3(CACNA1S):c.3257G>A (p.Arg1086His)\")))\n\n;; find-ids-named: Do we find familiar IDs named CACNA1?\n(chk\n (#:=\n  (take\n   (sort\n    (find-ids-named nodes '(\"CACNA1\"))\n    string (length res-a) 0))\n  (#:t (> (length res-b) 0))\n  (#:t (> (length res-ab) 0))\n  (#:t (> (length res-a) (length res-ab)))\n  (#:t (> (length res-b) (length res-ab)))\n  )\n\n(chk\n  (#:do (define a \"cacna\"))\n  (#:do (define b \"2d1\"))\n  (#:do (define stsopt1 (make-stsopt #:case-sensitive? #t)))\n  (#:do (define res-a (find-ids-named nodes `(,a) stsopt1)))\n  (#:do (define res-b (find-ids-named nodes `(,b) stsopt1)))\n  (#:do (define res-ab (find-ids-named nodes `(,a ,b) stsopt1)))\n  (#:do (printf \"found ~s ~s ~s\\n\" (length res-a) (length res-b) (length res-ab)))\n  ; .../yeast-sri-reference/0.3.0\n  ; found 650 736 21\n  (#:t #t))\n"
  },
  {
    "path": "medikanren2/test/10GB-CI/with-yeast-sri-reference-kg-spec.rkt",
    "content": "#lang racket\n(require \"../../base.rkt\"\n         \"../../db/yeast-sri-reference-kg-0.3.0.rkt\"\n         chk)\n\n\n(define uri-scn4a \"ENSEMBL:ENSBTAG00000004770\")\n\n(chk\n (#:= (run* (p o)\n            (fresh (id)\n                   (== id uri-scn4a)\n                   (membero p '(\"in_taxon\" \"description\"))\n                   (nodes id p o)))\n  '((\"in_taxon\" \"NCBITaxon:9913|NCBITaxon:9913\")\n    (\"description\" \"Sodium channel protein\"))))\n\n\n(define uri-ion-transport \"GO:0034765\")\n\n(chk\n (#:= (run* (p o)\n            (fresh (id)\n                   (== id uri-ion-transport)\n                   (membero p '(\"iri\" \"name\"))\n                   (nodes id p o)))\n  '((\"iri\" \"http://purl.obolibrary.org/obo/GO_0034765\")\n    (\"name\" \"regulation of ion transmembrane transport\"))))\n"
  },
  {
    "path": "medikanren2/test/example_mk2_queries.rkt",
    "content": "#lang racket/base\n(require\n \"../base.rkt\"\n (prefix-in semmed: \"../db/semmed.rkt\")\n (prefix-in rtx: \"../db/rtx2-20210204.rkt\")\n (prefix-in kgx: \"../db/kgx-synonym.rkt\")\n (prefix-in sri: \"../db/sri-reference-kg-0.3.0.rkt\")\n \"../synonyms.rkt\"\n racket/pretty)\n\n#|\n### Loading and Providing ###\n\n- (prefix-in ...) appends the symbol prefix given (ie \"semmed:\") onto the materialized relations built in the /db/semmed.rkt file, allowing the user\nto define specific relations from specific knowledge graphs for querying. Relations in both the rtx2-20210204.rkt and semmed.rkt files are named\ncprop, eprop, edge, meaning that without a prefix, use of  the (cprop ...) relation will query both rtx2 and semmed KGs. \n\n### KG Specific Relations ### \n* Note: for all KGs with a prefix in the require statement above, the corresponding prefix must be appended to relation for the query to run. \nShown below are the native relations from each KG *\n\nsemmed.rkt\n - cprop\n - eprop\n - edge\n\nrtx2-20210204.rkt\n - cprop\n - eprop\n - edge\n\nsri-reference-kg-0.3.0.rkt\n- nodes\n- edges\n\nsri-reference-kg-0.3.0.rkt\n- synonym\n\n\n|#\n\n \n;; relation cprop exists in rtx2, semmed\n(run 5\n     (c k v)\n     ;(rtx:cprop c k v)\n     (semmed:cprop c k v)\n     )\n\n;; relation eprop exists in rtx2, semmed\n(run 5\n     (c k v)\n     ;(rtx:eprop c k v)\n     (semmed:eprop c k v)\n     )\n\n;; relation edge exists in rtx2, semmed\n(run 5\n     (c k v)\n     ;(rtx:edge c k v)\n     (semmed:edge c k v)\n     )\n\n\n;; relation synonym should exist in kgx-synonym\n;; Question: Has anyone gotten a response/working query with this KG? \n(run 5\n     (a b)\n     (kgx:synonym '(a) \"CHEBI:28304\"))\n\n;; relation nodes should exist in sri-reference KG\n(run 5\n     (c k v)\n     (sri:nodes c k v)\n     )\n\n;; relation edges should exist in sri-reference KG\n(run 5\n     (c k v)\n     (sri:edges c k v)\n     )\n\n\n#|Using synonyms.rkt to get concept synonyms|#\n\n;;synonyms.rkt\n(run* s (direct-synonym s \"MONDO:0005260\"))\n\n;;(run* x (kgx:synonym x '(\"DOID:9351\")))\n\n"
  },
  {
    "path": "medikanren2/test/query_clinical_kg.rkt",
    "content": "#lang racket/base\n(require \"../base.rkt\" \"../db/clinical_kg.rkt\" racket/pretty)\n(provide (all-from-out \"../base.rkt\") (all-defined-out))\n\n(define-syntax-rule (test name e expected)\n  (begin (printf \"Testing ~s:\\n\" name)\n         (let ((answer (time e)))\n           (unless (equal? answer expected)\n             (pretty-write 'e)\n             (printf \"FAILED ~s:\\n\" name)\n             (printf \"  ANSWER:\\n\")\n             (pretty-write answer)\n             (printf \"  EXPECTED:\\n\")\n             (pretty-write expected)))))\n\n;; test query\n(define c19-test\n  (list \"LOINC:94500-6\" \"LOINC:41458-1\" \"LOINC:94756-4\" \"LOINC:94533-7\" \"LOINC:94507-1\" \"LOINC:94309-2\"))\n\n(define c19-test-positive-result\n  (list \"Positive\" \"Detected\"))\n\n(define thrombotic-event-curies\n  (list \"ICD-10-CM:I21.A1\" \"ICD-10-CM:I21.A9\" \"ICD-10-CM:I21.0\"\n\t\"ICD-10-CM:I21.21\" \"ICD-10-CM:I21.1\" \"ICD-10-CM:I21.4\"\n\t\"ICD-10-CM:I21.9\" \"ICD-10-CM:I21.A\" \"ICD-10-CM:I21.3\"\n\t)\n  )\n\n#;(define c19-cohort\n  (run* (id date curie string value units)\n     (membero curie c19-test)\n     (membero value c19-test-positive-result)\n     (patient-clinical-data\n      id\n      date\n      curie\n      string\n      value\n      units)\n     ))\n\n#;(pretty-print (length c19-cohort))\n\n(define c19-cohort-with-thrombotic-event\n  (run 50 (id date curie string value units thrombotic-events)\n\t(membero curie c19-test)\n\t(membero value c19-test-positive-result)\n\t(=/= thrombotic-events '())\n \t(patient-clinical-data\n\t id\n\t date\n\t curie\n\t string\n\t value\n\t units)\n\t(:==  thrombotic-events (id date)\n\t      (run* (thrombotic-event-date curie string)\n\t\t    (fresh (value units)\n\t\t\t   (<=o date thrombotic-event-date)\n\t\t\t   (membero curie thrombotic-event-curies)\n\t\t\t   (patient-clinical-data\n\t\t\t    id\n\t\t\t    thrombotic-event-date\n\t\t\t    curie\n\t\t\t    string\n\t\t\t    value\n\t\t\t    units))))))\n\n(pretty-print c19-cohort-with-thrombotic-event)\n"
  },
  {
    "path": "medikanren2/test/rtx2-20210204.rkt",
    "content": "#lang racket/base\n(require \"../base.rkt\" \"../db/rtx2-20210204.rkt\" racket/pretty)\n\n(define-syntax-rule (test name e expected)\n  (begin (printf \"Testing ~s:\\n\" name)\n         (let ((answer (time e)))\n           (unless (equal? answer expected)\n             (pretty-write 'e)\n             (printf \"FAILED ~s:\\n\" name)\n             (printf \"  ANSWER:\\n\")\n             (pretty-write answer)\n             (printf \"  EXPECTED:\\n\")\n             (pretty-write expected)))))\n\n(test 'various-concept-properties\n  (run 5 (id k v) (cprop id k v))\n  '((\"MEDDRA:10001490\" \"category\" \"biolink:Activity\")\n    (\"MEDDRA:10001494\" \"category\" \"biolink:Activity\")\n    (\"MEDDRA:10001535\" \"category\" \"biolink:Activity\")\n    (\"MEDDRA:10001846\" \"category\" \"biolink:Activity\")\n    (\"MEDDRA:10003536\" \"category\" \"biolink:Activity\")))\n\n(test 'various-edges\n  (run 5 (id s o) (edge id s o))\n  '((12605868 \"EHDAA2:0004546\" \"AEO:0000013\")\n    (12606986 \"EHDAA2:0000152\" \"AEO:0000078\")\n    (12606988 \"EHDAA2:0000503\" \"AEO:0000078\")\n    (12606984 \"EHDAA2:0000935\" \"AEO:0000078\")\n    (12606994 \"EHDAA2:0001051\" \"AEO:0000078\")))\n\n(test 'various-edge-properties\n  (run 5 (id k v) (eprop id k v))\n  '((0 \"negated\" \"False\")\n    (1 \"negated\" \"False\")\n    (2 \"negated\" \"False\")\n    (3 \"negated\" \"False\")\n    (4 \"negated\" \"False\")))\n\n(test 'all-concept-properties\n  (run* k\n    (fresh (curie v)\n      (cprop curie k v)))\n  '(\"category\"\n    \"category_label\"\n    \"creation_date\"\n    \"deprecated\"\n    \"description\"\n    \"full_name\"\n    \"id\"\n    \"iri\"\n    \"name\"\n    \"provided_by\"\n    \"publications\"\n    \"replaced_by\"\n    \"synonym\"\n    \"update_date\"))\n\n(test 'all-edge-properties\n  (run* k\n    (fresh (eid v)\n      (eprop eid k v)))\n  '(\"negated\"\n    \"object\"\n    \"predicate\"\n    \"predicate_label\"\n    \"provided_by\"\n    \"publications\"\n    \"publications_info\"\n    \"relation\"\n    \"relation_label\"\n    \"subject\"\n    \"update_date\"))\n\n(test 'all-concept-categories\n  (run* category\n    (fresh (curie)\n      (cprop curie \"category\" category)))\n  '(\"biolink:Activity\"\n    \"biolink:Agent\"\n    \"biolink:AnatomicalEntity\"\n    \"biolink:Attribute\"\n    \"biolink:BiologicalEntity\"\n    \"biolink:BiologicalProcess\"\n    \"biolink:BiologicalProcessOrActivity\"\n    \"biolink:Carbohydrate\"\n    \"biolink:Cell\"\n    \"biolink:CellularComponent\"\n    \"biolink:ChemicalSubstance\"\n    \"biolink:ClinicalIntervention\"\n    \"biolink:ClinicalModifier\"\n    \"biolink:DataFile\"\n    \"biolink:Device\"\n    \"biolink:Disease\"\n    \"biolink:DiseaseOrPhenotypicFeature\"\n    \"biolink:Drug\"\n    \"biolink:EnvironmentalFeature\"\n    \"biolink:EnvironmentalProcess\"\n    \"biolink:Exon\"\n    \"biolink:ExposureEvent\"\n    \"biolink:FrequencyValue\"\n    \"biolink:Gene\"\n    \"biolink:GeneFamily\"\n    \"biolink:GeneProduct\"\n    \"biolink:GenomicEntity\"\n    \"biolink:GeographicLocation\"\n    \"biolink:GrossAnatomicalStructure\"\n    \"biolink:IndividualOrganism\"\n    \"biolink:InformationContentEntity\"\n    \"biolink:LifeStage\"\n    \"biolink:MacromolecularComplex\"\n    \"biolink:MaterialSample\"\n    \"biolink:Metabolite\"\n    \"biolink:MolecularActivity\"\n    \"biolink:MolecularEntity\"\n    \"biolink:NamedThing\"\n    \"biolink:OntologyClass\"\n    \"biolink:OrganismTaxon\"\n    \"biolink:OrganismalEntity\"\n    \"biolink:Pathway\"\n    \"biolink:Phenomenon\"\n    \"biolink:PhenotypicFeature\"\n    \"biolink:PhysicalEntity\"\n    \"biolink:PhysiologicalProcess\"\n    \"biolink:PopulationOfIndividualOrganisms\"\n    \"biolink:Procedure\"\n    \"biolink:Protein\"\n    \"biolink:Publication\"\n    \"biolink:QuantityValue\"\n    \"biolink:RelationshipType\"\n    \"biolink:Treatment\"))\n\n(test 'all-predicates\n  (run* predicate\n    (fresh (eid)\n      (eprop eid \"predicate\" predicate)))\n  '(\"biolink:actively_involved_in\"\n    \"biolink:affects\"\n    \"biolink:affects_activity_of\"\n    \"biolink:affects_degradation_of\"\n    \"biolink:affects_localization_of\"\n    \"biolink:affects_transport_of\"\n    \"biolink:biomarker_for\"\n    \"biolink:capable_of\"\n    \"biolink:causes\"\n    \"biolink:chemically_similar_to\"\n    \"biolink:close_match\"\n    \"biolink:coexists_with\"\n    \"biolink:colocalizes_with\"\n    \"biolink:contraindicated_for\"\n    \"biolink:contributes_to\"\n    \"biolink:correlated_with\"\n    \"biolink:decreases_activity_of\"\n    \"biolink:decreases_expression_of\"\n    \"biolink:derives_from\"\n    \"biolink:derives_into\"\n    \"biolink:develops_from\"\n    \"biolink:directly_interacts_with\"\n    \"biolink:disease_has_basis_in\"\n    \"biolink:disrupts\"\n    \"biolink:enables\"\n    \"biolink:expressed_in\"\n    \"biolink:expresses\"\n    \"biolink:gene_associated_with_condition\"\n    \"biolink:has_attribute\"\n    \"biolink:has_attribute_type\"\n    \"biolink:has_completed\"\n    \"biolink:has_count\"\n    \"biolink:has_decreased_amount\"\n    \"biolink:has_gene_product\"\n    \"biolink:has_increased_amount\"\n    \"biolink:has_input\"\n    \"biolink:has_molecular_consequence\"\n    \"biolink:has_not_completed\"\n    \"biolink:has_output\"\n    \"biolink:has_part\"\n    \"biolink:has_participant\"\n    \"biolink:has_phenotype\"\n    \"biolink:has_quantitative_value\"\n    \"biolink:has_route\"\n    \"biolink:has_unit\"\n    \"biolink:homologous_to\"\n    \"biolink:in_taxon\"\n    \"biolink:increases_activity_of\"\n    \"biolink:increases_degradation_of\"\n    \"biolink:increases_expression_of\"\n    \"biolink:increases_metabolic_processing_of\"\n    \"biolink:increases_stability_of\"\n    \"biolink:interacts_with\"\n    \"biolink:is_sequence_variant_of\"\n    \"biolink:lacks_part\"\n    \"biolink:located_in\"\n    \"biolink:location_of\"\n    \"biolink:manifestation_of\"\n    \"biolink:model_of\"\n    \"biolink:molecularly_interacts_with\"\n    \"biolink:negatively_regulates\"\n    \"biolink:negatively_regulates,_entity_to_entity\"\n    \"biolink:negatively_regulates,_process_to_process\"\n    \"biolink:occurs_in\"\n    \"biolink:overlaps\"\n    \"biolink:part_of\"\n    \"biolink:participates_in\"\n    \"biolink:physically_interacts_with\"\n    \"biolink:positively_regulates\"\n    \"biolink:positively_regulates,_entity_to_entity\"\n    \"biolink:positively_regulates,_process_to_process\"\n    \"biolink:preceded_by\"\n    \"biolink:precedes\"\n    \"biolink:predisposes\"\n    \"biolink:prevents\"\n    \"biolink:produces\"\n    \"biolink:quantifier_qualifier\"\n    \"biolink:regulates\"\n    \"biolink:regulates,_process_to_process\"\n    \"biolink:related_to\"\n    \"biolink:same_as\"\n    \"biolink:subclass_of\"\n    \"biolink:synonym\"\n    \"biolink:temporally_related_to\"\n    \"biolink:treats\"))\n\n(test 'all-relations\n  (run* relation\n    (fresh (eid)\n      (eprop eid \"relation\" relation)))\n  '(\"BFO:0000050\"\n    \"BFO:0000051\"\n    \"BFO:0000054\"\n    \"BFO:0000055\"\n    \"BFO:0000056\"\n    \"BFO:0000062\"\n    \"BFO:0000063\"\n    \"BFO:0000066\"\n    \"BFO:0000067\"\n    \"BFO:0000068\"\n    \"BFO:0000069\"\n    \"BFO:0000117\"\n    \"BFO:0000167\"\n    \"BSPO:0000096\"\n    \"BSPO:0000097\"\n    \"BSPO:0000098\"\n    \"BSPO:0000099\"\n    \"BSPO:0000100\"\n    \"BSPO:0000102\"\n    \"BSPO:0000104\"\n    \"BSPO:0000107\"\n    \"BSPO:0000108\"\n    \"BSPO:0000110\"\n    \"BSPO:0000113\"\n    \"BSPO:0000120\"\n    \"BSPO:0000121\"\n    \"BSPO:0000122\"\n    \"BSPO:0000123\"\n    \"BSPO:0000124\"\n    \"BSPO:0000125\"\n    \"BSPO:0000126\"\n    \"BSPO:0001100\"\n    \"BSPO:0001101\"\n    \"BSPO:0001106\"\n    \"BSPO:0001107\"\n    \"BSPO:0001108\"\n    \"BSPO:0001113\"\n    \"BSPO:0001115\"\n    \"BSPO:0005001\"\n    \"BSPO:0015001\"\n    \"BSPO:0015002\"\n    \"BSPO:0015003\"\n    \"BSPO:0015005\"\n    \"BSPO:0015006\"\n    \"BSPO:0015007\"\n    \"BSPO:0015008\"\n    \"BSPO:0015009\"\n    \"BSPO:0015012\"\n    \"BSPO:0015014\"\n    \"BSPO:0015101\"\n    \"BSPO:0015102\"\n    \"BSPO:0015202\"\n    \"BTO:develops_from\"\n    \"BTO:related_to\"\n    \"CHEBI:has_functional_parent\"\n    \"CHEBI:has_parent_hydride\"\n    \"CHEBI:is_conjugate_acid_of\"\n    \"CHEBI:is_conjugate_base_of\"\n    \"CHEBI:is_enantiomer_of\"\n    \"CHEBI:is_substituent_group_from\"\n    \"CHEBI:is_tautomer_of\"\n    \"CHEMBL.MECHANISM:activator\"\n    \"CHEMBL.MECHANISM:agonist\"\n    \"CHEMBL.MECHANISM:allosteric_antagonist\"\n    \"CHEMBL.MECHANISM:antagonist\"\n    \"CHEMBL.MECHANISM:antisense_inhibitor\"\n    \"CHEMBL.MECHANISM:binding_agent\"\n    \"CHEMBL.MECHANISM:blocker\"\n    \"CHEMBL.MECHANISM:chelating_agent\"\n    \"CHEMBL.MECHANISM:cross-linking_agent\"\n    \"CHEMBL.MECHANISM:degrader\"\n    \"CHEMBL.MECHANISM:disrupting_agent\"\n    \"CHEMBL.MECHANISM:equivalent_to\"\n    \"CHEMBL.MECHANISM:hydrolytic_enzyme\"\n    \"CHEMBL.MECHANISM:inhibitor\"\n    \"CHEMBL.MECHANISM:inverse_agonist\"\n    \"CHEMBL.MECHANISM:modulator\"\n    \"CHEMBL.MECHANISM:negative_allosteric_modulator\"\n    \"CHEMBL.MECHANISM:negative_modulator\"\n    \"CHEMBL.MECHANISM:opener\"\n    \"CHEMBL.MECHANISM:overlaps_with\"\n    \"CHEMBL.MECHANISM:oxidative_enzyme\"\n    \"CHEMBL.MECHANISM:partial_agonist\"\n    \"CHEMBL.MECHANISM:positive_allosteric_modulator\"\n    \"CHEMBL.MECHANISM:positive_modulator\"\n    \"CHEMBL.MECHANISM:proteolytic_enzyme\"\n    \"CHEMBL.MECHANISM:reducing_agent\"\n    \"CHEMBL.MECHANISM:releasing_agent\"\n    \"CHEMBL.MECHANISM:sequestering_agent\"\n    \"CHEMBL.MECHANISM:stabiliser\"\n    \"CHEMBL.MECHANISM:subset_of\"\n    \"CHEMBL.MECHANISM:substrate\"\n    \"CHEMBL.MECHANISM:superset_of\"\n    \"CL:has_completed\"\n    \"CL:has_high_plasma_membrane_amount\"\n    \"CL:has_low_plasma_membrane_amount\"\n    \"CL:has_not_completed\"\n    \"CL:lacks_part\"\n    \"CL:lacks_plasma_membrane_part\"\n    \"CPT:has_add_on_code\"\n    \"CPT:has_possibly_included_panel_element\"\n    \"CPT:mapped_to\"\n    \"CPT:panel_element_of\"\n    \"CPT:panel_element_of_possibly_included\"\n    \"DDANAT:develops_from\"\n    \"DGIdb:activator\"\n    \"DGIdb:adduct\"\n    \"DGIdb:affects\"\n    \"DGIdb:agonist\"\n    \"DGIdb:allosteric_modulator\"\n    \"DGIdb:antagonist\"\n    \"DGIdb:antibody\"\n    \"DGIdb:antisense_oligonucleotide\"\n    \"DGIdb:binder\"\n    \"DGIdb:blocker\"\n    \"DGIdb:chaperone\"\n    \"DGIdb:cleavage\"\n    \"DGIdb:cofactor\"\n    \"DGIdb:inducer\"\n    \"DGIdb:inhibitor\"\n    \"DGIdb:inhibitory_allosteric_modulator\"\n    \"DGIdb:inverse_agonist\"\n    \"DGIdb:ligand\"\n    \"DGIdb:modulator\"\n    \"DGIdb:multitarget\"\n    \"DGIdb:negative_modulator\"\n    \"DGIdb:partial_agonist\"\n    \"DGIdb:partial_antagonist\"\n    \"DGIdb:positive_modulator\"\n    \"DGIdb:potentiator\"\n    \"DGIdb:product_of\"\n    \"DGIdb:stimulator\"\n    \"DGIdb:substrate\"\n    \"DGIdb:suppressor\"\n    \"DGIdb:vaccine\"\n    \"DRUGBANK:category\"\n    \"DRUGBANK:drug-interaction\"\n    \"DRUGBANK:external-identifier\"\n    \"DRUGBANK:pathway\"\n    \"DRUGBANK:target\"\n    \"EFO:0000784\"\n    \"EFO:0001697\"\n    \"EFO:0006351\"\n    \"EFO:is_executed_in\"\n    \"ENVO:01001307\"\n    \"FMA:adheres_to\"\n    \"FMA:adjacent_to\"\n    \"FMA:afferent_to\"\n    \"FMA:anterior_to\"\n    \"FMA:anteroinferior_to\"\n    \"FMA:anterolateral_to\"\n    \"FMA:anteromedial_to\"\n    \"FMA:anterosuperior_to\"\n    \"FMA:arterial_supply_of\"\n    \"FMA:articulates_with\"\n    \"FMA:attaches_to\"\n    \"FMA:bounded_by\"\n    \"FMA:bounds\"\n    \"FMA:branch_of\"\n    \"FMA:connected_to\"\n    \"FMA:connection_type_of\"\n    \"FMA:constitutional_part_of\"\n    \"FMA:contained_in\"\n    \"FMA:contains\"\n    \"FMA:continuation_branch_of\"\n    \"FMA:continuous_distally_with\"\n    \"FMA:continuous_proximally_with\"\n    \"FMA:continuous_with\"\n    \"FMA:corresponds_to\"\n    \"FMA:derives\"\n    \"FMA:derives_from\"\n    \"FMA:development_type_of\"\n    \"FMA:developmental_stage_of\"\n    \"FMA:develops_from\"\n    \"FMA:develops_into\"\n    \"FMA:direct_cell_shape_of\"\n    \"FMA:direct_left_of\"\n    \"FMA:direct_right_of\"\n    \"FMA:distal_to\"\n    \"FMA:drains_into\"\n    \"FMA:efferent_to\"\n    \"FMA:external_to\"\n    \"FMA:formed_by\"\n    \"FMA:forms\"\n    \"FMA:full_grown_phenotype_of\"\n    \"FMA:fuses_with\"\n    \"FMA:fusion_of\"\n    \"FMA:germ_origin_of\"\n    \"FMA:has_adherent\"\n    \"FMA:has_arterial_supply\"\n    \"FMA:has_branch\"\n    \"FMA:has_connection_type\"\n    \"FMA:has_constitutional_part\"\n    \"FMA:has_continuation_branch\"\n    \"FMA:has_development_type\"\n    \"FMA:has_developmental_stage\"\n    \"FMA:has_direct_cell_shape\"\n    \"FMA:has_full_grown_phenotype\"\n    \"FMA:has_fusion\"\n    \"FMA:has_germ_origin\"\n    \"FMA:has_inherent_3d_shape\"\n    \"FMA:has_insertion\"\n    \"FMA:has_location\"\n    \"FMA:has_lymphatic_drainage\"\n    \"FMA:has_member\"\n    \"FMA:has_nerve_supply\"\n    \"FMA:has_observed_anatomical_entity\"\n    \"FMA:has_origin\"\n    \"FMA:has_part\"\n    \"FMA:has_primary_segmental_supply\"\n    \"FMA:has_projection\"\n    \"FMA:has_regional_part\"\n    \"FMA:has_related_developmental_entity\"\n    \"FMA:has_secondary_segmental_supply\"\n    \"FMA:has_segmental_composition\"\n    \"FMA:has_segmental_supply\"\n    \"FMA:has_tributary\"\n    \"FMA:has_venous_drainage\"\n    \"FMA:homonym_of\"\n    \"FMA:inferior_to\"\n    \"FMA:inferolateral_to\"\n    \"FMA:inferomedial_to\"\n    \"FMA:inherent_3d_shape_of\"\n    \"FMA:insertion_of\"\n    \"FMA:internal_to\"\n    \"FMA:lateral_to\"\n    \"FMA:left_lateral_to\"\n    \"FMA:left_medial_to\"\n    \"FMA:location_of\"\n    \"FMA:lymphatic_drainage_of\"\n    \"FMA:matures_from\"\n    \"FMA:matures_into\"\n    \"FMA:medial_to\"\n    \"FMA:member_of\"\n    \"FMA:merges_with\"\n    \"FMA:nerve_supply_of\"\n    \"FMA:origin_of\"\n    \"FMA:part_of\"\n    \"FMA:posterior_to\"\n    \"FMA:posteroinferior_to\"\n    \"FMA:posterolateral_to\"\n    \"FMA:posteromedial_to\"\n    \"FMA:posterosuperior_to\"\n    \"FMA:primary_segmental_supply_of\"\n    \"FMA:projects_from\"\n    \"FMA:projects_to\"\n    \"FMA:proximal_to\"\n    \"FMA:receives_attachment_from\"\n    \"FMA:receives_drainage_from\"\n    \"FMA:receives_input_from\"\n    \"FMA:receives_projection\"\n    \"FMA:regional_part_of\"\n    \"FMA:related_developmental_entity_of\"\n    \"FMA:related_object\"\n    \"FMA:related_part\"\n    \"FMA:right_lateral_to\"\n    \"FMA:right_medial_to\"\n    \"FMA:secondary_segmental_supply_of\"\n    \"FMA:segmental_composition_of\"\n    \"FMA:segmental_supply_of\"\n    \"FMA:sends_output_to\"\n    \"FMA:superior_to\"\n    \"FMA:superolateral_to\"\n    \"FMA:superomedial_to\"\n    \"FMA:surrounded_by\"\n    \"FMA:surrounds\"\n    \"FMA:transforms_from\"\n    \"FMA:transforms_into\"\n    \"FMA:tributary_of\"\n    \"FMA:venous_drainage_of\"\n    \"FOODON:00001301\"\n    \"FOODON:00001563\"\n    \"FOODON:00002420\"\n    \"GENEPIO:0001739\"\n    \"GO:acts_upstream_of\"\n    \"GO:acts_upstream_of_negative_effect\"\n    \"GO:acts_upstream_of_or_within\"\n    \"GO:acts_upstream_of_or_within_negative_effect\"\n    \"GO:acts_upstream_of_or_within_positive_effect\"\n    \"GO:acts_upstream_of_positive_effect\"\n    \"GO:colocalizes_with\"\n    \"GO:contributes_to\"\n    \"GO:enables\"\n    \"GO:ends_during\"\n    \"GO:happens_during\"\n    \"GO:has_occurrence\"\n    \"GO:has_part\"\n    \"GO:inverse_ends_during\"\n    \"GO:inverse_isa\"\n    \"GO:involved_in\"\n    \"GO:is_active_in\"\n    \"GO:isa\"\n    \"GO:negatively_regulated_by\"\n    \"GO:negatively_regulates\"\n    \"GO:occurs_in\"\n    \"GO:part_of\"\n    \"GO:positively_regulated_by\"\n    \"GO:positively_regulates\"\n    \"GO:regulated_by\"\n    \"GO:regulates\"\n    \"GOREL:0000040\"\n    \"GOREL:0002003\"\n    \"GOREL:0002004\"\n    \"GOREL:0002005\"\n    \"GOREL:0012006\"\n    \"HANCESTRO:0301\"\n    \"HANCESTRO:0330\"\n    \"HCPCS:mapped_to\"\n    \"HMDB:at_cellular_location\"\n    \"HMDB:at_tissue\"\n    \"HMDB:disease\"\n    \"HMDB:has_protein_association\"\n    \"HMDB:in_biospecimen\"\n    \"HMDB:in_pathway\"\n    \"IAO:0000039\"\n    \"IAO:0000136\"\n    \"IAO:0000219\"\n    \"IDO:0000664\"\n    \"LOINC:analyzes\"\n    \"LOINC:associated_with\"\n    \"LOINC:class_of\"\n    \"LOINC:component_of\"\n    \"LOINC:has_action_guidance\"\n    \"LOINC:has_adjustment\"\n    \"LOINC:has_aggregation_view\"\n    \"LOINC:has_answer\"\n    \"LOINC:has_approach_guidance\"\n    \"LOINC:has_archetype\"\n    \"LOINC:has_challenge\"\n    \"LOINC:has_class\"\n    \"LOINC:has_component\"\n    \"LOINC:has_count\"\n    \"LOINC:has_divisor\"\n    \"LOINC:has_evaluation\"\n    \"LOINC:has_exam\"\n    \"LOINC:has_fragments_for_synonyms\"\n    \"LOINC:has_imaged_location\"\n    \"LOINC:has_imaging_focus\"\n    \"LOINC:has_lateral_anatomic_location\"\n    \"LOINC:has_lateral_location_presence\"\n    \"LOINC:has_member\"\n    \"LOINC:has_method\"\n    \"LOINC:has_modality_subtype\"\n    \"LOINC:has_modality_type\"\n    \"LOINC:has_object_guidance\"\n    \"LOINC:has_parent_group\"\n    \"LOINC:has_pharmaceutical_route\"\n    \"LOINC:has_scale\"\n    \"LOINC:has_subject\"\n    \"LOINC:has_suffix\"\n    \"LOINC:has_supersystem\"\n    \"LOINC:has_system\"\n    \"LOINC:has_time_aspect\"\n    \"LOINC:has_time_modifier\"\n    \"LOINC:has_timing_of\"\n    \"LOINC:has_view_type\"\n    \"LOINC:is_given_pharmaceutical_substance_for\"\n    \"LOINC:is_presence_guidance_for\"\n    \"LOINC:mapped_to\"\n    \"LOINC:measured_by\"\n    \"LOINC:member_of\"\n    \"LOINC:mth_has_expanded_form\"\n    \"LOINC:multipart_of\"\n    \"LOINC:property_of\"\n    \"MEDDRA:classified_as\"\n    \"MEDDRA:has_member\"\n    \"MEDDRA:member_of\"\n    \"MESH:RO\"\n    \"MESH:has_mapping_qualifier\"\n    \"MESH:inverse_isa\"\n    \"MESH:isa\"\n    \"MESH:mapped_to\"\n    \"MONDO:disease_causes_feature\"\n    \"MONDO:disease_has_basis_in_accumulation_of\"\n    \"MONDO:disease_has_basis_in_development_of\"\n    \"MONDO:disease_has_major_feature\"\n    \"MONDO:disease_responds_to\"\n    \"MONDO:disease_shares_features_of\"\n    \"MONDO:disease_triggers\"\n    \"MONDO:equivalentTo\"\n    \"MONDO:has_onset\"\n    \"MONDO:part_of_progression_of_disease\"\n    \"MONDO:predisposes_towards\"\n    \"NCIT:allele_absent_from_wild-type_chromosomal_location\"\n    \"NCIT:allele_has_abnormality\"\n    \"NCIT:allele_has_activity\"\n    \"NCIT:allele_in_chromosomal_location\"\n    \"NCIT:allele_plays_altered_role_in_process\"\n    \"NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug\"\n    \"NCIT:anatomic_structure_is_physical_part_of\"\n    \"NCIT:biological_process_has_associated_location\"\n    \"NCIT:biological_process_has_result_anatomy\"\n    \"NCIT:biological_process_has_result_biological_process\"\n    \"NCIT:biological_process_has_result_chemical_or_drug\"\n    \"NCIT:biological_process_involves_chemical_or_drug\"\n    \"NCIT:cdrh_parent_of\"\n    \"NCIT:chemical_or_drug_affects_abnormal_cell\"\n    \"NCIT:chemical_or_drug_affects_cell_type_or_tissue\"\n    \"NCIT:chemical_or_drug_affects_gene_product\"\n    \"NCIT:chemical_or_drug_has_mechanism_of_action\"\n    \"NCIT:chemical_or_drug_has_physiologic_effect\"\n    \"NCIT:chemical_or_drug_initiates_biological_process\"\n    \"NCIT:chromosome_mapped_to_disease\"\n    \"NCIT:complex_has_physical_part\"\n    \"NCIT:conceptual_part_of\"\n    \"NCIT:ctcae_5_parent_of\"\n    \"NCIT:cytogenetic_abnormality_involves_chromosome\"\n    \"NCIT:disease_has_associated_anatomic_site\"\n    \"NCIT:disease_has_finding\"\n    \"NCIT:disease_has_metastatic_anatomic_site\"\n    \"NCIT:disease_has_molecular_abnormality\"\n    \"NCIT:disease_has_normal_tissue_origin\"\n    \"NCIT:disease_has_primary_anatomic_site\"\n    \"NCIT:disease_is_grade\"\n    \"NCIT:disease_is_marked_by_gene\"\n    \"NCIT:disease_is_stage\"\n    \"NCIT:disease_may_have_abnormal_cell\"\n    \"NCIT:disease_may_have_associated_disease\"\n    \"NCIT:disease_may_have_finding\"\n    \"NCIT:disease_may_have_molecular_abnormality\"\n    \"NCIT:enzyme_metabolizes_chemical_or_drug\"\n    \"NCIT:eo_disease_has_associated_cell_type\"\n    \"NCIT:eo_disease_has_associated_eo_anatomy\"\n    \"NCIT:eo_disease_has_property_or_attribute\"\n    \"NCIT:gene_associated_with_disease\"\n    \"NCIT:gene_encodes_gene_product\"\n    \"NCIT:gene_found_in_organism\"\n    \"NCIT:gene_has_physical_location\"\n    \"NCIT:gene_in_chromosomal_location\"\n    \"NCIT:gene_involved_in_molecular_abnormality\"\n    \"NCIT:gene_involved_in_pathogenesis_of_disease\"\n    \"NCIT:gene_is_biomarker_of\"\n    \"NCIT:gene_is_biomarker_type\"\n    \"NCIT:gene_is_element_in_pathway\"\n    \"NCIT:gene_mapped_to_disease\"\n    \"NCIT:gene_mutant_encodes_gene_product_sequence_variation\"\n    \"NCIT:gene_plays_role_in_process\"\n    \"NCIT:gene_product_expressed_in_tissue\"\n    \"NCIT:gene_product_has_abnormality\"\n    \"NCIT:gene_product_has_associated_anatomy\"\n    \"NCIT:gene_product_has_biochemical_function\"\n    \"NCIT:gene_product_has_chemical_classification\"\n    \"NCIT:gene_product_has_organism_source\"\n    \"NCIT:gene_product_has_structural_domain_or_motif\"\n    \"NCIT:gene_product_is_biomarker_of\"\n    \"NCIT:gene_product_is_biomarker_type\"\n    \"NCIT:gene_product_is_element_in_pathway\"\n    \"NCIT:gene_product_is_physical_part_of\"\n    \"NCIT:gene_product_malfunction_associated_with_disease\"\n    \"NCIT:gene_product_plays_role_in_biological_process\"\n    \"NCIT:gene_product_sequence_variation_encoded_by_gene_mutant\"\n    \"NCIT:gene_product_variant_of_gene_product\"\n    \"NCIT:genetic_biomarker_related_to\"\n    \"NCIT:has_data_element\"\n    \"NCIT:has_inc_parent\"\n    \"NCIT:has_nichd_parent\"\n    \"NCIT:has_pharmaceutical_administration_method\"\n    \"NCIT:has_pharmaceutical_basic_dose_form\"\n    \"NCIT:has_pharmaceutical_intended_site\"\n    \"NCIT:has_pharmaceutical_release_characteristics\"\n    \"NCIT:has_pharmaceutical_state_of_matter\"\n    \"NCIT:has_pharmaceutical_transformation\"\n    \"NCIT:has_salt_form\"\n    \"NCIT:has_target\"\n    \"NCIT:human_disease_maps_to_eo_disease\"\n    \"NCIT:is_abnormal_cell_of_disease\"\n    \"NCIT:is_associated_disease_of\"\n    \"NCIT:is_component_of_chemotherapy_regimen\"\n    \"NCIT:is_cytogenetic_abnormality_of_disease\"\n    \"NCIT:is_location_of_anatomic_structure\"\n    \"NCIT:is_molecular_abnormality_of_disease\"\n    \"NCIT:is_normal_cell_origin_of_disease\"\n    \"NCIT:is_organism_source_of_gene_product\"\n    \"NCIT:is_qualified_by\"\n    \"NCIT:is_related_to_endogenous_product\"\n    \"NCIT:may_be_normal_cell_origin_of_disease\"\n    \"NCIT:neoplasm_has_special_category\"\n    \"NCIT:organism_has_gene\"\n    \"NCIT:pathway_has_gene_element\"\n    \"NCIT:procedure_has_completely_excised_anatomy\"\n    \"NCIT:procedure_has_excised_anatomy\"\n    \"NCIT:procedure_has_imaged_anatomy\"\n    \"NCIT:procedure_has_partially_excised_anatomy\"\n    \"NCIT:procedure_has_target_anatomy\"\n    \"NCIT:procedure_may_have_completely_excised_anatomy\"\n    \"NCIT:procedure_may_have_excised_anatomy\"\n    \"NCIT:procedure_may_have_partially_excised_anatomy\"\n    \"NCIT:process_includes_biological_process\"\n    \"NCIT:process_initiates_biological_process\"\n    \"NCIT:process_involves_gene\"\n    \"NCIT:qualifier_applies_to\"\n    \"NCIT:regimen_has_accepted_use_for_disease\"\n    \"NCIT:role_has_domain\"\n    \"NCIT:role_has_parent\"\n    \"NCIT:role_has_range\"\n    \"NCIT:subset_includes_concept\"\n    \"NDDF:has_dose_form\"\n    \"NDDF:has_ingredient\"\n    \"NDDF:ingredient_of\"\n    \"OBI:0000293\"\n    \"OBI:0000295\"\n    \"OBI:0000299\"\n    \"OBI:0001927\"\n    \"OBO:INO_0000154\"\n    \"OBO:core#connected_to\"\n    \"OBO:core#distally_connected_to\"\n    \"OBO:core#innervated_by\"\n    \"OBO:core#subdivision_of\"\n    \"OBO:doid#derives_from\"\n    \"OBO:doid#has_symptom\"\n    \"OBO:envo#has_increased_levels_of\"\n    \"OBO:exo.obo#interacts_with\"\n    \"OBO:exo.obo#interacts_with_an_exposure_receptor_via\"\n    \"OBO:exo.obo#interacts_with_an_exposure_stressor_via\"\n    \"OBO:hancestro_0308\"\n    \"OBO:has_role\"\n    \"OBO:intersection_of\"\n    \"OBO:nbo#by_means\"\n    \"OBO:nbo#has_participant\"\n    \"OBO:nbo#in_response_to\"\n    \"OBO:nbo#is_about\"\n    \"OBO:uo#is_unit_of\"\n    \"OBO:xref\"\n    \"OBOREL:bearer_of\"\n    \"OMIM:allelic_variant_of\"\n    \"OMIM:has_inheritance_type\"\n    \"OMIM:has_manifestation\"\n    \"OMIM:has_phenotype\"\n    \"OMIM:manifestation_of\"\n    \"OMIM:phenotype_of\"\n    \"ORPHANET:317343\"\n    \"ORPHANET:317344\"\n    \"ORPHANET:317345\"\n    \"ORPHANET:317346\"\n    \"ORPHANET:317348\"\n    \"ORPHANET:317349\"\n    \"ORPHANET:327767\"\n    \"ORPHANET:410295\"\n    \"ORPHANET:410296\"\n    \"ORPHANET:465410\"\n    \"ORPHANET:C016\"\n    \"ORPHANET:C017\"\n    \"PATO:correlates_with\"\n    \"PATO:decreased_in_magnitude_relative_to\"\n    \"PATO:has_cross_section\"\n    \"PATO:has_relative_magnitude\"\n    \"PATO:increased_in_magnitude_relative_to\"\n    \"PATO:reciprocal_of\"\n    \"PATO:towards\"\n    \"PDQ:associated_disease\"\n    \"PDQ:component_of\"\n    \"PDQ:has_component\"\n    \"PR:has_gene_template\"\n    \"PR:lacks_part\"\n    \"PR:non-covalently_bound_to\"\n    \"PathWhiz:has_bound\"\n    \"PathWhiz:has_compound\"\n    \"PathWhiz:has_element_collection\"\n    \"PathWhiz:has_element_in_bound\"\n    \"PathWhiz:has_enzyme\"\n    \"PathWhiz:has_left_element\"\n    \"PathWhiz:has_location\"\n    \"PathWhiz:has_nucleic_acid\"\n    \"PathWhiz:has_protein\"\n    \"PathWhiz:has_protein_in_complex\"\n    \"PathWhiz:has_reaction\"\n    \"PathWhiz:has_right_element\"\n    \"PathWhiz:in_species\"\n    \"REPODB:clinically_tested_approved_unknown_phase\"\n    \"REPODB:clinically_tested_suspended_phase_0\"\n    \"REPODB:clinically_tested_suspended_phase_1\"\n    \"REPODB:clinically_tested_suspended_phase_1_or_phase_2\"\n    \"REPODB:clinically_tested_suspended_phase_2\"\n    \"REPODB:clinically_tested_suspended_phase_2_or_phase_3\"\n    \"REPODB:clinically_tested_suspended_phase_3\"\n    \"REPODB:clinically_tested_terminated_phase_0\"\n    \"REPODB:clinically_tested_terminated_phase_1\"\n    \"REPODB:clinically_tested_terminated_phase_1_or_phase_2\"\n    \"REPODB:clinically_tested_terminated_phase_2\"\n    \"REPODB:clinically_tested_terminated_phase_2_or_phase_3\"\n    \"REPODB:clinically_tested_terminated_phase_3\"\n    \"REPODB:clinically_tested_withdrawn_phase_0\"\n    \"REPODB:clinically_tested_withdrawn_phase_1\"\n    \"REPODB:clinically_tested_withdrawn_phase_1_or_phase_2\"\n    \"REPODB:clinically_tested_withdrawn_phase_2\"\n    \"REPODB:clinically_tested_withdrawn_phase_2_or_phase_3\"\n    \"REPODB:clinically_tested_withdrawn_phase_3\"\n    \"RO:0000052\"\n    \"RO:0000053\"\n    \"RO:0000056\"\n    \"RO:0000057\"\n    \"RO:0000086\"\n    \"RO:0000087\"\n    \"RO:0001000\"\n    \"RO:0001015\"\n    \"RO:0001019\"\n    \"RO:0001022\"\n    \"RO:0001025\"\n    \"RO:0002001\"\n    \"RO:0002002\"\n    \"RO:0002005\"\n    \"RO:0002007\"\n    \"RO:0002008\"\n    \"RO:0002082\"\n    \"RO:0002083\"\n    \"RO:0002087\"\n    \"RO:0002090\"\n    \"RO:0002092\"\n    \"RO:0002093\"\n    \"RO:0002100\"\n    \"RO:0002102\"\n    \"RO:0002103\"\n    \"RO:0002104\"\n    \"RO:0002120\"\n    \"RO:0002130\"\n    \"RO:0002131\"\n    \"RO:0002134\"\n    \"RO:0002150\"\n    \"RO:0002159\"\n    \"RO:0002160\"\n    \"RO:0002162\"\n    \"RO:0002170\"\n    \"RO:0002176\"\n    \"RO:0002177\"\n    \"RO:0002178\"\n    \"RO:0002179\"\n    \"RO:0002180\"\n    \"RO:0002200\"\n    \"RO:0002202\"\n    \"RO:0002203\"\n    \"RO:0002211\"\n    \"RO:0002212\"\n    \"RO:0002213\"\n    \"RO:0002215\"\n    \"RO:0002216\"\n    \"RO:0002219\"\n    \"RO:0002220\"\n    \"RO:0002221\"\n    \"RO:0002223\"\n    \"RO:0002224\"\n    \"RO:0002225\"\n    \"RO:0002226\"\n    \"RO:0002229\"\n    \"RO:0002230\"\n    \"RO:0002231\"\n    \"RO:0002232\"\n    \"RO:0002233\"\n    \"RO:0002234\"\n    \"RO:0002254\"\n    \"RO:0002256\"\n    \"RO:0002285\"\n    \"RO:0002292\"\n    \"RO:0002295\"\n    \"RO:0002296\"\n    \"RO:0002297\"\n    \"RO:0002298\"\n    \"RO:0002299\"\n    \"RO:0002303\"\n    \"RO:0002309\"\n    \"RO:0002313\"\n    \"RO:0002314\"\n    \"RO:0002315\"\n    \"RO:0002322\"\n    \"RO:0002328\"\n    \"RO:0002331\"\n    \"RO:0002332\"\n    \"RO:0002334\"\n    \"RO:0002338\"\n    \"RO:0002339\"\n    \"RO:0002340\"\n    \"RO:0002341\"\n    \"RO:0002342\"\n    \"RO:0002343\"\n    \"RO:0002344\"\n    \"RO:0002345\"\n    \"RO:0002348\"\n    \"RO:0002349\"\n    \"RO:0002350\"\n    \"RO:0002351\"\n    \"RO:0002352\"\n    \"RO:0002353\"\n    \"RO:0002354\"\n    \"RO:0002355\"\n    \"RO:0002356\"\n    \"RO:0002371\"\n    \"RO:0002372\"\n    \"RO:0002373\"\n    \"RO:0002374\"\n    \"RO:0002376\"\n    \"RO:0002380\"\n    \"RO:0002385\"\n    \"RO:0002387\"\n    \"RO:0002411\"\n    \"RO:0002412\"\n    \"RO:0002433\"\n    \"RO:0002451\"\n    \"RO:0002473\"\n    \"RO:0002488\"\n    \"RO:0002489\"\n    \"RO:0002491\"\n    \"RO:0002492\"\n    \"RO:0002494\"\n    \"RO:0002495\"\n    \"RO:0002496\"\n    \"RO:0002497\"\n    \"RO:0002500\"\n    \"RO:0002505\"\n    \"RO:0002507\"\n    \"RO:0002509\"\n    \"RO:0002524\"\n    \"RO:0002551\"\n    \"RO:0002565\"\n    \"RO:0002568\"\n    \"RO:0002571\"\n    \"RO:0002572\"\n    \"RO:0002573\"\n    \"RO:0002576\"\n    \"RO:0002578\"\n    \"RO:0002588\"\n    \"RO:0002590\"\n    \"RO:0002591\"\n    \"RO:0002592\"\n    \"RO:0002608\"\n    \"RO:0002629\"\n    \"RO:0002630\"\n    \"RO:0003000\"\n    \"RO:0003001\"\n    \"RO:0003304\"\n    \"RO:0004001\"\n    \"RO:0004007\"\n    \"RO:0004008\"\n    \"RO:0004009\"\n    \"RO:0004019\"\n    \"RO:0004020\"\n    \"RO:0004021\"\n    \"RO:0004022\"\n    \"RO:0004024\"\n    \"RO:0004025\"\n    \"RO:0004026\"\n    \"RO:0004027\"\n    \"RO:0004028\"\n    \"RO:0004029\"\n    \"RO:0004030\"\n    \"RO:0009001\"\n    \"RO:0009004\"\n    \"RO:0009501\"\n    \"RO:0012003\"\n    \"RO:derives_from\"\n    \"RO:has_participant\"\n    \"RO:participates_in\"\n    \"RTXKG1:affects\"\n    \"RTXKG1:associated_with_disease\"\n    \"RTXKG1:capable_of\"\n    \"RTXKG1:capable_of_part_of\"\n    \"RTXKG1:contains_process\"\n    \"RTXKG1:contraindicated_for\"\n    \"RTXKG1:disease_caused_by_disruption_of\"\n    \"RTXKG1:disease_causes_disruption_of\"\n    \"RTXKG1:disease_has_basis_in_dysfunction_of\"\n    \"RTXKG1:disease_has_location\"\n    \"RTXKG1:expressed_in\"\n    \"RTXKG1:gene_associated_with_condition\"\n    \"RTXKG1:gene_mutations_contribute_to\"\n    \"RTXKG1:has_phenotype\"\n    \"RTXKG1:has_plasma_membrane_part\"\n    \"RTXKG1:indicated_for\"\n    \"RTXKG1:involved_in\"\n    \"RTXKG1:lacks_part\"\n    \"RTXKG1:participates_in\"\n    \"RTXKG1:physically_interacts_with\"\n    \"RTXKG1:realized_in_response_to\"\n    \"RTXKG1:realized_in_response_to_stimulus\"\n    \"RTXKG1:regulates_activity_of\"\n    \"RTXKG1:regulates_expression_of\"\n    \"RTXKG1:site_of\"\n    \"RTXKG1:subclass_of\"\n    \"RTXKG1:targets\"\n    \"RXNORM:consists_of\"\n    \"RXNORM:constitutes\"\n    \"RXNORM:contained_in\"\n    \"RXNORM:contains\"\n    \"RXNORM:has_dose_form\"\n    \"RXNORM:has_doseformgroup\"\n    \"RXNORM:has_form\"\n    \"RXNORM:has_ingredient\"\n    \"RXNORM:has_part\"\n    \"RXNORM:has_quantified_form\"\n    \"RXNORM:has_tradename\"\n    \"RXNORM:ingredient_of\"\n    \"RXNORM:ingredients_of\"\n    \"RXNORM:inverse_isa\"\n    \"RXNORM:isa\"\n    \"RXNORM:part_of\"\n    \"RXNORM:precise_ingredient_of\"\n    \"RXNORM:reformulated_to\"\n    \"SEMMEDDB:administered_to\"\n    \"SEMMEDDB:affects\"\n    \"SEMMEDDB:associated_with\"\n    \"SEMMEDDB:augments\"\n    \"SEMMEDDB:causes\"\n    \"SEMMEDDB:coexists_with\"\n    \"SEMMEDDB:compared_with\"\n    \"SEMMEDDB:complicates\"\n    \"SEMMEDDB:converts_to\"\n    \"SEMMEDDB:diagnoses\"\n    \"SEMMEDDB:disrupts\"\n    \"SEMMEDDB:inhibits\"\n    \"SEMMEDDB:interacts_with\"\n    \"SEMMEDDB:isa\"\n    \"SEMMEDDB:location_of\"\n    \"SEMMEDDB:manifestation_of\"\n    \"SEMMEDDB:measures\"\n    \"SEMMEDDB:occurs_in\"\n    \"SEMMEDDB:part_of\"\n    \"SEMMEDDB:precedes\"\n    \"SEMMEDDB:predisposes\"\n    \"SEMMEDDB:prevents\"\n    \"SEMMEDDB:process_of\"\n    \"SEMMEDDB:produces\"\n    \"SEMMEDDB:same_as\"\n    \"SEMMEDDB:stimulates\"\n    \"SEMMEDDB:treats\"\n    \"SEMMEDDB:uses\"\n    \"SNOMED:active_ingredient_of\"\n    \"SNOMED:associated_with\"\n    \"SNOMED:basis_of_strength_substance_of\"\n    \"SNOMED:causative_agent_of\"\n    \"SNOMED:cause_of\"\n    \"SNOMED:characterized_by\"\n    \"SNOMED:component_of\"\n    \"SNOMED:direct_substance_of\"\n    \"SNOMED:during\"\n    \"SNOMED:entire_anatomy_structure_of\"\n    \"SNOMED:focus_of\"\n    \"SNOMED:has_access\"\n    \"SNOMED:has_associated_finding\"\n    \"SNOMED:has_associated_morphology\"\n    \"SNOMED:has_associated_procedure\"\n    \"SNOMED:has_basic_dose_form\"\n    \"SNOMED:has_clinical_course\"\n    \"SNOMED:has_component\"\n    \"SNOMED:has_concentration_strength_denominator_unit\"\n    \"SNOMED:has_concentration_strength_numerator_unit\"\n    \"SNOMED:has_concentration_strength_numerator_value\"\n    \"SNOMED:has_count_of_base_of_active_ingredient\"\n    \"SNOMED:has_definitional_manifestation\"\n    \"SNOMED:has_dependent\"\n    \"SNOMED:has_direct_device\"\n    \"SNOMED:has_direct_morphology\"\n    \"SNOMED:has_direct_procedure_site\"\n    \"SNOMED:has_direct_site\"\n    \"SNOMED:has_disposition\"\n    \"SNOMED:has_dose_form\"\n    \"SNOMED:has_dose_form_administration_method\"\n    \"SNOMED:has_dose_form_intended_site\"\n    \"SNOMED:has_dose_form_release_characteristic\"\n    \"SNOMED:has_dose_form_transformation\"\n    \"SNOMED:has_finding_context\"\n    \"SNOMED:has_finding_informer\"\n    \"SNOMED:has_finding_method\"\n    \"SNOMED:has_finding_site\"\n    \"SNOMED:has_indirect_device\"\n    \"SNOMED:has_indirect_morphology\"\n    \"SNOMED:has_indirect_procedure_site\"\n    \"SNOMED:has_inherent_attribute\"\n    \"SNOMED:has_inherent_location\"\n    \"SNOMED:has_intent\"\n    \"SNOMED:has_interpretation\"\n    \"SNOMED:has_laterality\"\n    \"SNOMED:has_measurement_method\"\n    \"SNOMED:has_method\"\n    \"SNOMED:has_modification\"\n    \"SNOMED:has_occurrence\"\n    \"SNOMED:has_pathological_process\"\n    \"SNOMED:has_precondition\"\n    \"SNOMED:has_presentation_strength_denominator_unit\"\n    \"SNOMED:has_presentation_strength_denominator_value\"\n    \"SNOMED:has_presentation_strength_numerator_unit\"\n    \"SNOMED:has_presentation_strength_numerator_value\"\n    \"SNOMED:has_priority\"\n    \"SNOMED:has_procedure_context\"\n    \"SNOMED:has_procedure_device\"\n    \"SNOMED:has_procedure_morphology\"\n    \"SNOMED:has_procedure_site\"\n    \"SNOMED:has_process_duration\"\n    \"SNOMED:has_process_output\"\n    \"SNOMED:has_property\"\n    \"SNOMED:has_realization\"\n    \"SNOMED:has_recipient_category\"\n    \"SNOMED:has_revision_status\"\n    \"SNOMED:has_route_of_administration\"\n    \"SNOMED:has_scale_type\"\n    \"SNOMED:has_severity\"\n    \"SNOMED:has_specimen\"\n    \"SNOMED:has_specimen_source_identity\"\n    \"SNOMED:has_specimen_source_morphology\"\n    \"SNOMED:has_specimen_source_topography\"\n    \"SNOMED:has_specimen_substance\"\n    \"SNOMED:has_state_of_matter\"\n    \"SNOMED:has_subject_relationship_context\"\n    \"SNOMED:has_surgical_approach\"\n    \"SNOMED:has_technique\"\n    \"SNOMED:has_temporal_context\"\n    \"SNOMED:has_time_aspect\"\n    \"SNOMED:has_unit_of_presentation\"\n    \"SNOMED:has_units\"\n    \"SNOMED:inherent_location_of\"\n    \"SNOMED:inheres_in\"\n    \"SNOMED:is_interpreted_by\"\n    \"SNOMED:occurs_before\"\n    \"SNOMED:occurs_in\"\n    \"SNOMED:part_anatomy_structure_of\"\n    \"SNOMED:plays_role\"\n    \"SNOMED:precise_active_ingredient_of\"\n    \"SNOMED:relative_to_part_of\"\n    \"SNOMED:specimen_procedure_of\"\n    \"SNOMED:temporally_related_to\"\n    \"SNOMED:uses_access_device\"\n    \"SNOMED:uses_device\"\n    \"SNOMED:uses_energy\"\n    \"SNOMED:uses_substance\"\n    \"SO:adjacent_to\"\n    \"SO:contains\"\n    \"SO:derives_from\"\n    \"SO:guided_by\"\n    \"SO:has_origin\"\n    \"SO:has_part\"\n    \"SO:has_quality\"\n    \"SO:member_of\"\n    \"SO:non_functional_homolog_of\"\n    \"SO:overlaps\"\n    \"SO:transcribed_from\"\n    \"SO:transcribed_to\"\n    \"UBERON:anastomoses_with\"\n    \"UBERON:anteriorly_connected_to\"\n    \"UBERON:channel_for\"\n    \"UBERON:channels_from\"\n    \"UBERON:channels_into\"\n    \"UBERON:conduit_for\"\n    \"UBERON:distally_connected_to\"\n    \"UBERON:extends_fibers_into\"\n    \"UBERON:filtered_through\"\n    \"UBERON:in_central_side_of\"\n    \"UBERON:in_innermost_side_of\"\n    \"UBERON:in_outermost_side_of\"\n    \"UBERON:indirectly_supplies\"\n    \"UBERON:posteriorly_connected_to\"\n    \"UBERON:protects\"\n    \"UBERON:proximally_connected_to\"\n    \"UBERON:sexually_homologous_to\"\n    \"UBERON:site_of\"\n    \"UBERON:subdivision_of\"\n    \"UBERON:synapsed_by\"\n    \"UMLS:RB\"\n    \"UMLS:RO\"\n    \"UMLS:RQ\"\n    \"UMLS:SY\"\n    \"UMLS:class_code_classified_by\"\n    \"UMLS:component_of\"\n    \"UMLS:exhibited_by\"\n    \"UMLS:has_component\"\n    \"UMLS:has_context_binding\"\n    \"UMLS:has_form\"\n    \"UMLS:has_mapping_qualifier\"\n    \"UMLS:has_owning_affiliate\"\n    \"UMLS:has_physiologic_effect\"\n    \"UMLS:has_structural_class\"\n    \"UMLS:has_supported_concept_property\"\n    \"UMLS:has_supported_concept_relationship\"\n    \"UMLS:larger_than\"\n    \"UMLS:mapped_to\"\n    \"UMLS:may_be_qualified_by\"\n    \"UMLS:measures\"\n    \"UMLS:owning_section_of\"\n    \"UMLS:owning_subsection_of\"\n    \"UMLS:related_to\"\n    \"VANDF:has_ingredient\"\n    \"VANDF:ingredient_of\"\n    \"VANDF:inverse_isa\"\n    \"VANDF:isa\"\n    \"biolink:has_gene_product\"\n    \"biolink:in_taxon\"\n    \"biolink:part_of\"\n    \"biolink:physically_interacts_with\"\n    \"biolink:related_to\"\n    \"biolink:same_as\"\n    \"biolink:subclass_of\"\n    \"biolink:treats\"\n    \"oboFormat:xref\"\n    \"owl:sameAs\"\n    \"rdfs:subClassOf\"\n    \"rdfs:subPropertyOf\"))\n\n(test 'single-concept-properties\n  (run* (k v)\n    (cprop \"UMLS:C0000137\" k v))\n  '((\"category\" \"biolink:ChemicalSubstance\")\n    (\"category_label\" \"chemical_substance\")\n    (\"deprecated\" \"False\")\n    (\"description\"\n     \"The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)\")\n    (\"id\" \"UMLS:C0000137\")\n    (\"iri\" \"https://identifiers.org/umls:C0000137\")\n    (\"name\" \"RNA, Ribosomal\")\n    (\"provided_by\" \"identifiers_org_registry:umls\")\n    (\"update_date\" \"2015\")))\n\n(test 'single-subject-edges\n  (run 5 (id s o) (== s \"UMLS:C0005767\") (edge id s o))\n  '((17304173 \"UMLS:C0005767\" \"NCBIGene:102723407\")\n    (15656350 \"UMLS:C0005767\" \"NCBIGene:10312\")\n    (19424627 \"UMLS:C0005767\" \"NCBIGene:11168\")\n    (26022613 \"UMLS:C0005767\" \"NCBIGene:1154\")\n    (29233569 \"UMLS:C0005767\" \"NCBIGene:115727\")))\n\n(test 'single-object-edges\n  (run 5 (id s o) (== o \"UMLS:C0005767\") (edge id s o))\n  '((75693 \"FMA:9670\" \"UMLS:C0005767\")\n    (48607873 \"HMDB:HMDB0000001\" \"UMLS:C0005767\")\n    (48607894 \"HMDB:HMDB0000002\" \"UMLS:C0005767\")\n    (48607928 \"HMDB:HMDB0000005\" \"UMLS:C0005767\")\n    (48607976 \"HMDB:HMDB0000008\" \"UMLS:C0005767\")))\n\n(test 'single-edge\n  (run* (id s o)\n    (== s \"UMLS:C0005767\")\n    (== o \"NCBIGene:3688\")\n    (edge id s o))\n  '((25672055 \"UMLS:C0005767\" \"NCBIGene:3688\")))\n\n(test 'single-edge-properties\n  (run* (id k v)\n    (edge id \"UMLS:C0005767\" \"NCBIGene:3688\")\n    (eprop id k v))\n  '((25672055 \"negated\" \"False\")\n    (25672055 \"object\" \"NCBIGene:3688\")\n    (25672055 \"predicate\" \"biolink:produces\")\n    (25672055 \"predicate_label\" \"produces\")\n    (25672055 \"provided_by\" \"\\\"(\\\\\\\"\\\\\\\"SEMMEDDB:\\\\\\\"\\\\\\\")\\\"\")\n    (25672055 \"publications\" \"\\\"(\\\\\\\"\\\\\\\"PMID:21182179\\\\\\\"\\\\\\\")\\\"\")\n    (25672055\n     \"publications_info\"\n     \"{'PMID:21182179': {'publication date': '2011 Jan', 'sentence': 'In particular, although CD34(Pos)CD45(Dim)CD38(Pos) HSCs from both hEPCB and hTCB expressed relatively higher amounts of CD29, CD71, and CD135 compared with CD34(Pos)CD45(Dim)CD38(Neg) cells, a higher expression of CD31 was restricted to CD34(Pos)CD45(Dim)CD38(Pos) cells from hEPCB samples, and a higher expression of CD117 was demonstrated in CD34(Pos)CD45(Dim)CD38(Pos) cells from hTCB samples.', 'subject score': 762, 'object score': 1000}}\")\n    (25672055 \"relation\" \"SEMMEDDB:produces\")\n    (25672055 \"relation_label\" \"produces\")\n    (25672055 \"subject\" \"UMLS:C0005767\")\n    (25672055 \"update_date\" \"2019-05-01 15:34:14\")))\n\n(test 'concept-descriptions\n  (run 3 (c cat n desc)\n    (cprop c \"category\" cat)\n    (cprop c \"name\" n)\n    (cprop c \"description\" desc))\n  '((\"VT:0002292\"\n     \"biolink:InformationContentEntity\"\n     \"gestation period duration\"\n     \"         The length of time between when a fertilized egg implants in the wall of the uterus and the birth of offspring.         \")\n    (\"RO:0001902\"\n     \"biolink:RelationshipType\"\n     \"relation has no temporal argument\"\n     \"  ## Elucidation  This is used when the first-order logic form of the relation is binary, and takes no temporal argument.  ## Example:      Class: limb     SubClassOf: develops_from some lateral-plate-mesoderm       forall t, t2:       forall x :         instance_of(x,Limb,t)          implies         exists y :           instance_of(y,LPM,t2)           develops_from(x,y)   \")\n    (\"PathWhiz:PW000166\"\n     \"biolink:Pathway\"\n     \"Threonine and 2-Oxobutanoate Degradation\"\n     \"  2-oxobutanoate, also known as 2-Ketobutyric acid, is a 2-keto acid that is commonly produced in the metabolism of amino acids such as methionine and threonine.  Like other 2-keto acids, degradation of 2-oxobutanoate occurs in the mitochondrial matrix and begins with oxidative decarboxylation to its acyl coenzyme A derivative, propionyl-CoA.  This reaction is mediated by a class of large, multienzyme complexes called 2-oxo acid dehydrogenase complexes.  While no 2-oxo acid dehydrogenase complex is specific to 2-oxobutanoate, numerous complexes can catalyze its reaction.  In this pathway the branched-chain alpha-keto acid dehydrogenase complex is depicted.  All 2-oxo acid dehydrogenase complexes consist of three main components: a 2-oxo acid dehydrogenase (E1) with a thiamine pyrophosphate cofactor, a dihydrolipoamide acyltransferase (E2) with a lipoate cofactor, and a dihydrolipoamide dehydrogenase (E3) with a flavin cofactor.  E1 binds the 2-oxobutanoate to the lipoate on E2, which then transfers the propionyl group to coenzyme A, producing propionyl-CoA and reducing the lipoate.  E3 then transfers protons to NAD in order to restore the lipoate.  Propionyl-CoA carboxylase transforms the propionyl-CoA to S-methylmalonyl-CoA, which is then converted to R-methylmalonyl-CoA via methylmalonyl-CoA epimerase.  In the final step, methylmalonyl-CoA mutase acts on the R-methylmalonyl-CoA to produce succinyl-CoA. \")))\n\n(test 'chemical-substance-names\n  (run 10 (curie name)\n    (cprop curie \"category\" \"biolink:ChemicalSubstance\")\n    (cprop curie \"name\" name))\n  '((\"ATC:A01AA02\" \"sodium monofluorophosphate\")\n    (\"ATC:A01AA03\" \"olaflur\")\n    (\"ATC:A01AB02\" \"hydrogen peroxide\")\n    (\"ATC:A01AB03\" \"chlorhexidine\")\n    (\"ATC:A01AB04\" \"amphotericin B\")\n    (\"ATC:A01AB05\" \"polynoxylin\")\n    (\"ATC:A01AB06\" \"domiphen\")\n    (\"ATC:A01AB07\" \"oxyquinoline\")\n    (\"ATC:A01AB08\" \"neomycin\")\n    (\"ATC:A01AB09\" \"miconazole\")))\n\n(test 'gene-names\n  (run 10 (c n)\n    (cprop c \"name\"     n)\n    (cprop c \"category\" \"biolink:Gene\"))\n  '((\"AraPort:AT1G01010\" \"NAC001 (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01020\" \"ARV1 (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01030\" \"NGA3 (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01040\" \"DCL1 (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01050\" \"PPA1 (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01060\" \"LHY (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01070\" \"At1g01070 (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01090\" \"PDH-E1 ALPHA (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01100\" \"RPP1A (Arabidopsis thaliana)\")\n    (\"AraPort:AT1G01120\" \"KCS1 (Arabidopsis thaliana)\")))\n\n(test 'concept-relationships\n  (run 5 (curie1 predicate curie2)\n    (fresh (eid)\n      (eprop eid \"predicate\" predicate)\n      (edge eid curie1 curie2)))\n  '((\"NCIT:C18585\" \"biolink:actively_involved_in\" \"NCIT:C45399\")\n    (\"NCIT:C18363\" \"biolink:actively_involved_in\" \"NCIT:C158854\")\n    (\"NCIT:C24399\" \"biolink:actively_involved_in\" \"NCIT:C158823\")\n    (\"NCIT:C24399\" \"biolink:actively_involved_in\" \"NCIT:C158822\")\n    (\"NCIT:C20719\" \"biolink:actively_involved_in\" \"NCIT:C158822\")))\n\n(test 'concept-regulators\n  (run 5 (curie1 predicate curie2)\n    (fresh (eid)\n      (membero predicate '(\"biolink:negatively_regulates\"\n                           \"biolink:negatively_regulates,_entity_to_entity\"\n                           \"biolink:negatively_regulates,_process_to_process\"\n                           \"biolink:positively_regulates\"\n                           \"biolink:positively_regulates,_entity_to_entity\"\n                           \"biolink:positively_regulates,_process_to_process\"\n                           \"biolink:regulates\"\n                           \"biolink:regulates,_process_to_process\"))\n      (eprop eid \"predicate\" predicate)\n      (edge eid curie1 curie2)))\n  '((\"GO:0002862\" \"biolink:negatively_regulates\" \"GO:0002437\")\n    (\"GO:0002875\" \"biolink:negatively_regulates\" \"GO:0002439\")\n    (\"GO:0002865\" \"biolink:negatively_regulates\" \"GO:0002438\")\n    (\"GO:0002632\" \"biolink:negatively_regulates\" \"GO:0002432\")\n    (\"GO:0002707\" \"biolink:negatively_regulates\" \"GO:0002449\")))\n\n(test 'specific-concept-regulators\n  (run 20 (curie1 predicate curie2)\n    (fresh (eid)\n      (membero predicate '(\"biolink:negatively_regulates\"\n                           \"biolink:negatively_regulates,_entity_to_entity\"\n                           \"biolink:negatively_regulates,_process_to_process\"\n                           \"biolink:positively_regulates\"\n                           \"biolink:positively_regulates,_entity_to_entity\"\n                           \"biolink:positively_regulates,_process_to_process\"\n                           \"biolink:regulates\"\n                           \"biolink:regulates,_process_to_process\"))\n      (eprop eid \"predicate\" predicate)\n      (== curie2 \"GO:0002437\")\n      (edge eid curie1 curie2)))\n  '((\"GO:0002862\" \"biolink:negatively_regulates\" \"GO:0002437\")\n    (\"GO:0002862\" \"biolink:negatively_regulates,_process_to_process\" \"GO:0002437\")\n    (\"GO:0002863\" \"biolink:positively_regulates\" \"GO:0002437\")\n    (\"GO:0002863\" \"biolink:positively_regulates,_process_to_process\" \"GO:0002437\")\n    (\"GO:0002861\" \"biolink:regulates\" \"GO:0002437\")\n    (\"GO:0002861\" \"biolink:regulates,_process_to_process\" \"GO:0002437\")))\n\n(test 'named-negative-regulators\n  (run 5 (curie1 name1 curie2 name2)\n    (fresh (eid)\n      (eprop eid \"predicate\" \"biolink:negatively_regulates\")\n      (edge eid curie1 curie2)\n      (cprop curie1 \"name\" name1)\n      (cprop curie2 \"name\" name2)))\n  '((\"GO:0002862\"\n     \"negative regulation of inflammatory response to antigenic stimulus\"\n     \"GO:0002437\"\n     \"inflammatory response to antigenic stimulus\")\n    (\"GO:0002875\"\n     \"negative regulation of chronic inflammatory response to antigenic stimulus\"\n     \"GO:0002439\"\n     \"chronic inflammatory response to antigenic stimulus\")\n    (\"GO:0002865\"\n     \"negative regulation of acute inflammatory response to antigenic stimulus\"\n     \"GO:0002438\"\n     \"acute inflammatory response to antigenic stimulus\")\n    (\"GO:0002632\"\n     \"negative regulation of granuloma formation\"\n     \"GO:0002432\"\n     \"granuloma formation\")\n    (\"GO:0002707\"\n     \"negative regulation of lymphocyte mediated immunity\"\n     \"GO:0002449\"\n     \"lymphocyte mediated immunity\")))\n\n(test 'nausea-properties\n  (run* (k v)\n    (cprop \"UMLS:C0520909\" k v))\n  '((\"category\" \"biolink:Disease\")\n    (\"category_label\" \"disease\")\n    (\"deprecated\" \"False\")\n    (\"description\" \"Emesis and queasiness occurring after anesthesia.\")\n    (\"id\" \"UMLS:C0520909\")\n    (\"iri\" \"https://identifiers.org/umls:C0520909\")\n    (\"name\" \"Postoperative nausea and vomiting\")\n    (\"provided_by\" \"identifiers_org_registry:umls\")\n    (\"update_date\" \"2017\")))\n\n(test 'nausea-object-edges\n  (run 5 (s cat name p)\n    (fresh (eid)\n      (edge eid s \"UMLS:C0520909\")\n      (cprop s \"category\" cat)\n      (cprop s \"name\" name)\n      (eprop eid \"predicate\" p)))\n  '((\"DRUGBANK:DB00184\" \"biolink:Drug\" \"Nicotine\" \"biolink:treats\")\n    (\"MESH:D020250\"\n     \"biolink:NamedThing\"\n     \"Postoperative Nausea and Vomiting\"\n     \"biolink:close_match\")\n    (\"NCBIGene:166\"\n     \"biolink:Gene\"\n     \"TLE family member 5, transcriptional modulator\"\n     \"biolink:related_to\")\n    (\"NCBIGene:1814\" \"biolink:Gene\" \"dopamine receptor D3\" \"biolink:related_to\")\n    (\"NCBIGene:2770\"\n     \"biolink:Gene\"\n     \"G protein subunit alpha i1\"\n     \"biolink:related_to\")))\n\n(test 'nausea-treatments\n  (run* (s cat name)\n    (fresh (eid)\n      (edge eid s \"UMLS:C0520909\")\n      (cprop s \"category\" cat)\n      (cprop s \"name\" name)\n      (eprop eid \"predicate\" \"biolink:treats\")))\n  '((\"DRUGBANK:DB00184\" \"biolink:Drug\" \"Nicotine\")\n    (\"UMLS:C0001425\" \"biolink:Procedure\" \"Adenoid excision\")\n    (\"UMLS:C0001563\" \"biolink:Procedure\" \"Medication administration: oral\")\n    (\"UMLS:C0001617\" \"biolink:ChemicalSubstance\" \"Adrenal corticosteriods\")\n    (\"UMLS:C0002428\" \"biolink:Procedure\" \"Ambulatory surgery\")\n    (\"UMLS:C0002766\" \"biolink:Procedure\" \"Pain management\")\n    (\"UMLS:C0002769\" \"biolink:Procedure\" \"epidural analgesia\")\n    (\"UMLS:C0002903\" \"biolink:Procedure\" \"Administration of anesthesia\")\n    (\"UMLS:C0002912\" \"biolink:Procedure\" \"Anesthesia, Dental\")\n    (\"UMLS:C0002915\" \"biolink:Procedure\" \"General anesthesia\")\n    (\"UMLS:C0002917\" \"biolink:Procedure\" \"Anesthesia, Inhalation\")\n    (\"UMLS:C0002928\" \"biolink:Procedure\" \"Spinal anesthesia\")\n    (\"UMLS:C0002932\" \"biolink:ChemicalSubstance\" \"Anesthetics\")\n    (\"UMLS:C0003297\" \"biolink:ChemicalSubstance\" \"Antiemetics\")\n    (\"UMLS:C0003893\" \"biolink:Procedure\" \"Arthroplasty\")\n    (\"UMLS:C0004933\" \"biolink:Procedure\" \"Behavioral therapy\")\n    (\"UMLS:C0005064\" \"biolink:NamedThing\" \"Benzodiazepine\")\n    (\"UMLS:C0008320\" \"biolink:Procedure\" \"Cholecystectomy\")\n    (\"UMLS:C0009014\" \"biolink:ChemicalSubstance\" \"Clonidine\")\n    (\"UMLS:C0009429\" \"biolink:Procedure\" \"Combination therapy\")\n    (\"UMLS:C0009653\" \"biolink:Device\" \"Condom\")\n    (\"UMLS:C0010280\" \"biolink:Procedure\" \"Craniotomy\")\n    (\"UMLS:C0011331\" \"biolink:Procedure\" \"Dental care\")\n    (\"UMLS:C0011777\" \"biolink:ChemicalSubstance\" \"Dexamethasone\")\n    (\"UMLS:C0012358\" \"biolink:Procedure\" \"Dilation and curettage of uterus\")\n    (\"UMLS:C0012381\" \"biolink:ChemicalSubstance\" \"Dimenhydrinate\")\n    (\"UMLS:C0013136\" \"biolink:ChemicalSubstance\" \"Droperidol\")\n    (\"UMLS:C0013216\" \"biolink:Procedure\" \"Drug therapy\")\n    (\"UMLS:C0013227\"\n     \"biolink:ChemicalSubstance\"\n     \"Pharmaceutical / biologic product\")\n    (\"UMLS:C0013973\" \"biolink:ChemicalSubstance\" \"Emetics\")\n    (\"UMLS:C0017118\" \"biolink:Procedure\" \"Gastrectomy\")\n    (\"UMLS:C0018546\" \"biolink:ChemicalSubstance\" \"Haloperidol\")\n    (\"UMLS:C0020591\" \"biolink:ChemicalSubstance\" \"Hypnotic agent\")\n    (\"UMLS:C0020699\" \"biolink:Procedure\" \"Hysterectomy\")\n    (\"UMLS:C0020700\" \"biolink:Procedure\" \"Vaginal hysterectomy\")\n    (\"UMLS:C0021778\"\n     \"biolink:Procedure\"\n     \"Intermittent positive pressure ventilation\")\n    (\"UMLS:C0021925\" \"biolink:Procedure\" \"Intubation - action\")\n    (\"UMLS:C0022237\" \"biolink:ChemicalSubstance\" \"Alcohol,isopropyl\")\n    (\"UMLS:C0024881\" \"biolink:Procedure\" \"Mastectomies\")\n    (\"UMLS:C0024883\" \"biolink:Procedure\" \"Modified radical mastectomy\")\n    (\"UMLS:C0025619\" \"biolink:ChemicalSubstance\" \"Mesylates\")\n    (\"UMLS:C0025853\" \"biolink:ChemicalSubstance\" \"Metoclopramide\")\n    (\"UMLS:C0026056\" \"biolink:ChemicalSubstance\" \"Midazolam\")\n    (\"UMLS:C0026549\" \"biolink:ChemicalSubstance\" \"Morphine\")\n    (\"UMLS:C0026868\" \"biolink:Procedure\" \"Music therapy\")\n    (\"UMLS:C0027136\" \"biolink:Procedure\" \"Myringoplasty\")\n    (\"UMLS:C0030054\" \"biolink:ChemicalSubstance\" \"Oxygen\")\n    (\"UMLS:C0032042\" \"biolink:Procedure\" \"Placebos\")\n    (\"UMLS:C0033229\" \"biolink:ChemicalSubstance\" \"Prochlorperazine\")\n    (\"UMLS:C0033231\" \"biolink:ChemicalSubstance\" \"Prochlorperazine maleate\")\n    (\"UMLS:C0033405\" \"biolink:ChemicalSubstance\" \"Promethazine\")\n    (\"UMLS:C0033487\" \"biolink:ChemicalSubstance\" \"Propofol\")\n    (\"UMLS:C0036442\" \"biolink:ChemicalSubstance\" \"Scopolamine\")\n    (\"UMLS:C0036751\" \"biolink:NamedThing\" \"Serotonin\")\n    (\"UMLS:C0038901\" \"biolink:Procedure\" \"Surgical procedure on eye proper\")\n    (\"UMLS:C0038902\" \"biolink:Procedure\" \"Operation on female genital organs\")\n    (\"UMLS:C0038910\"\n     \"biolink:Procedure\"\n     \"Otorhinolaryngologic Surgical Procedures\")\n    (\"UMLS:C0040145\" \"biolink:Procedure\" \"Thyroidectomy\")\n    (\"UMLS:C0040423\" \"biolink:Procedure\" \"Tonsillectomy\")\n    (\"UMLS:C0040508\" \"biolink:Procedure\" \"Total replacement of hip\")\n    (\"UMLS:C0040610\" \"biolink:ChemicalSubstance\" \"Tramadol\")\n    (\"UMLS:C0040654\"\n     \"biolink:Procedure\"\n     \"Percutaneous electrical nerve stimulation\")\n    (\"UMLS:C0040808\" \"biolink:NamedThing\" \"Abdominal Wall\")\n    (\"UMLS:C0041447\" \"biolink:Procedure\" \"Repair of middle ear\")\n    (\"UMLS:C0051162\" \"biolink:NamedThing\" \"Alizapride\")\n    (\"UMLS:C0053139\" \"biolink:ChemicalSubstance\" \"Benzamide\")\n    (\"UMLS:C0061851\" \"biolink:ChemicalSubstance\" \"Ondansetron\")\n    (\"UMLS:C0061863\" \"biolink:ChemicalSubstance\" \"Granisetron\")\n    (\"UMLS:C0063322\" \"biolink:NamedThing\" \"Tropisetron\")\n    (\"UMLS:C0065818\" \"biolink:ChemicalSubstance\" \"Dolasetron mesylate\")\n    (\"UMLS:C0078944\" \"biolink:Procedure\" \"Patient controlled analgesia\")\n    (\"UMLS:C0086511\" \"biolink:Procedure\" \"Arthroplasty of knee\")\n    (\"UMLS:C0086930\" \"biolink:Procedure\" \"Risk assessment\")\n    (\"UMLS:C0087111\" \"biolink:Procedure\" \"Therapy\")\n    (\"UMLS:C0103045\" \"biolink:NamedThing\" \"Amisulpride-containing product\")\n    (\"UMLS:C0150521\" \"biolink:Procedure\" \"Comfort measures\")\n    (\"UMLS:C0162522\" \"biolink:Procedure\" \"Laparoscopic cholecystectomy\")\n    (\"UMLS:C0162561\" \"biolink:Procedure\" \"Catheter Ablation\")\n    (\"UMLS:C0163712\" \"biolink:ChemicalSubstance\" \"Relate - vinyl resin\")\n    (\"UMLS:C0180288\" \"biolink:Publication\" \"Anesthesia information system\")\n    (\"UMLS:C0184625\" \"biolink:Activity\" \"Normal diet\")\n    (\"UMLS:C0184661\" \"biolink:Procedure\" \"Procedure\")\n    (\"UMLS:C0185624\" \"biolink:IndividualOrganism\" \"Orthognathic Surgery\")\n    (\"UMLS:C0188970\" \"biolink:Procedure\" \"Operation on nose\")\n    (\"UMLS:C0191922\" \"biolink:Procedure\" \"Reduction mammoplasty\")\n    (\"UMLS:C0192817\" \"biolink:Procedure\" \"Operation on colon\")\n    (\"UMLS:C0192866\" \"biolink:Procedure\" \"Sigmoid colectomy\")\n    (\"UMLS:C0193769\" \"biolink:Procedure\" \"Operation on thyroid gland\")\n    (\"UMLS:C0193788\" \"biolink:Procedure\" \"Total thyroidectomy\")\n    (\"UMLS:C0197981\" \"biolink:Procedure\" \"Strabismus surgery\")\n    (\"UMLS:C0198154\" \"biolink:Procedure\" \"Mastoidectomy\")\n    (\"UMLS:C0198482\" \"biolink:Procedure\" \"Operation on abdominal region\")\n    (\"UMLS:C0199176\" \"biolink:Procedure\" \"Prophylaxis - intent\")\n    (\"UMLS:C0206046\" \"biolink:NamedThing\" \"Zofran\")\n    (\"UMLS:C0206058\" \"biolink:Procedure\" \"Optional surgery\")\n    (\"UMLS:C0209210\" \"biolink:ChemicalSubstance\" \"Dolasetron\")\n    (\"UMLS:C0209337\" \"biolink:NamedThing\" \"Rocuronium\")\n    (\"UMLS:C0220578\" \"biolink:ChemicalSubstance\" \"Palonosetron\")\n    (\"UMLS:C0242402\" \"biolink:NamedThing\" \"Opioid receptor agonist\")\n    (\"UMLS:C0242702\"\n     \"biolink:ChemicalSubstance\"\n     \"Dopamine receptor antagonist-containing product\")\n    (\"UMLS:C0242897\" \"biolink:ChemicalSubstance\" \"Anticholinergic Agent\")\n    (\"UMLS:C0243076\" \"biolink:ChemicalSubstance\" \"antagonists & inhibitors\")\n    (\"UMLS:C0278259\" \"biolink:Procedure\" \"Local excision\")\n    (\"UMLS:C0282046\" \"biolink:Procedure\" \"Ambulatory Surgical Procedures\")\n    (\"UMLS:C0282493\" \"biolink:Procedure\" \"Endoscopy with surgical procedure\")\n    (\"UMLS:C0282614\" \"biolink:Procedure\" \"Acupressure\")\n    (\"UMLS:C0360055\"\n     \"biolink:NamedThing\"\n     \"5-HT3 receptor antagonist-containing product\")\n    (\"UMLS:C0376547\" \"biolink:Procedure\" \"Aromatherapy\")\n    (\"UMLS:C0394663\" \"biolink:Procedure\" \"Cupping\")\n    (\"UMLS:C0394664\" \"biolink:Procedure\" \"Acupuncture\")\n    (\"UMLS:C0404077\" \"biolink:Procedure\" \"Abdominal hysterectomy\")\n    (\"UMLS:C0404079\" \"biolink:Procedure\" \"Total abdominal hysterectomy\")\n    (\"UMLS:C0404088\"\n     \"biolink:Procedure\"\n     \"Laparoscopic-assisted vaginal hysterectomy\")\n    (\"UMLS:C0404089\" \"biolink:Procedure\" \"Laparoscopic hysterectomy\")\n    (\"UMLS:C0404090\" \"biolink:Procedure\" \"Laparoscopic total hysterectomy\")\n    (\"UMLS:C0408578\" \"biolink:Procedure\" \"Operation on lumbar spine\")\n    (\"UMLS:C0420172\" \"biolink:Procedure\" \"Drug prophylaxis\")\n    (\"UMLS:C0442968\" \"biolink:Procedure\" \"Functional endoscopic sinus surgery\")\n    (\"UMLS:C0450442\" \"biolink:ChemicalSubstance\" \"Agent\")\n    (\"UMLS:C0473965\" \"biolink:Procedure\" \"Total intravenous anesthesia\")\n    (\"UMLS:C0520483\" \"biolink:Procedure\" \"Ligation of fallopian tube\")\n    (\"UMLS:C0524850\" \"biolink:Procedure\" \"Operation on nervous system\")\n    (\"UMLS:C0526950\" \"biolink:ChemicalSubstance\" \"ramosetron\")\n    (\"UMLS:C0543467\" \"biolink:Procedure\" \"Surgery\")\n    (\"UMLS:C0543476\" \"biolink:ChemicalSubstance\" \"Granisetron hydrochloride\")\n    (\"UMLS:C0677616\" \"biolink:Procedure\" \"Plastic operation\")\n    (\"UMLS:C0700478\" \"biolink:ChemicalSubstance\" \"Ondansetron hydrochloride\")\n    (\"UMLS:C0728940\" \"biolink:Procedure\" \"Surgical removal\")\n    (\"UMLS:C0750934\" \"biolink:Procedure\" \"Arthroscopy with surgical procedure\")\n    (\"UMLS:C0751429\" \"biolink:Procedure\" \"laparoscopic surgery\")\n    (\"UMLS:C0752217\" \"biolink:Procedure\" \"Acupuncture, Ear\")\n    (\"UMLS:C0843593\"\n     \"biolink:Procedure\"\n     \"Laparoscopically Assisted Vaginal Hysterectomy\")\n    (\"UMLS:C0851312\" \"biolink:IndividualOrganism\" \"Breast surgery\")\n    (\"UMLS:C0853389\" \"biolink:Procedure\" \"Postoperative pain relief\")\n    (\"UMLS:C0886296\" \"biolink:Procedure\" \"Nursing interventions\")\n    (\"UMLS:C0920347\" \"biolink:Procedure\" \"Procedure on spinal cord\")\n    (\"UMLS:C0937846\" \"biolink:ChemicalSubstance\" \"Esomeprazole\")\n    (\"UMLS:C0949216\" \"biolink:NamedThing\" \"Complementary Therapies\")\n    (\"UMLS:C0972314\" \"biolink:NamedThing\" \"Etoricoxib\")\n    (\"UMLS:C1137094\" \"biolink:Activity\" \"Risk Reduction\")\n    (\"UMLS:C1176306\" \"biolink:ChemicalSubstance\" \"Aprepitant\")\n    (\"UMLS:C1261322\" \"biolink:Procedure\" \"Evaluation - action\")\n    (\"UMLS:C1268547\" \"biolink:NamedThing\" \"Patient chart\")\n    (\"UMLS:C1273869\" \"biolink:Procedure\" \"Intervention regime\")\n    (\"UMLS:C1327728\" \"biolink:Procedure\" \"Operation on female genital organs\")\n    (\"UMLS:C1328580\" \"biolink:Procedure\" \"Microvascular Decompression Surgery\")\n    (\"UMLS:C1445610\" \"biolink:Device\" \"Acupressure wrist band\")\n    (\"UMLS:C1456587\" \"biolink:Procedure\" \"Bariatric Surgery\")\n    (\"UMLS:C1515885\" \"biolink:Procedure\" \"Acustimulation Therapy\")))\n\n;(test 'all-concept-category-counts\n;  (run* (category count)\n;    (fresh (curie)\n;      (cprop curie \"category\" category)\n;      (:== count (category)\n;           (s-length (run^ (curie)\n;                           (cprop curie \"category\" category))))))\n;\n;  '?)\n"
  },
  {
    "path": "medikanren2/test/semmed.rkt",
    "content": "#lang racket/base\n(require \"../base.rkt\" \"../db/semmed.rkt\" racket/pretty)\n\n(define-syntax-rule (test name e expected)\n  (begin (printf \"Testing ~s:\\n\" name)\n         (let ((answer (time e)))\n           (unless (equal? answer expected)\n             (pretty-write 'e)\n             (printf \"FAILED ~s:\\n\" name)\n             (printf \"  ANSWER:\\n\")\n             (pretty-write answer)\n             (printf \"  EXPECTED:\\n\")\n             (pretty-write expected)))))\n\n(test 'various-edge-properties\n  (run 20 (id k v) (eprop id k v))\n  '((0 \"SEMMED_PRED\" \"AFFECTS\")\n    (1 \"SEMMED_PRED\" \"AFFECTS\")\n    (119 \"SEMMED_PRED\" \"AFFECTS\")\n    (502 \"SEMMED_PRED\" \"AFFECTS\")\n    (503 \"SEMMED_PRED\" \"AFFECTS\")\n    (504 \"SEMMED_PRED\" \"AFFECTS\")\n    (505 \"SEMMED_PRED\" \"AFFECTS\")\n    (2639 \"SEMMED_PRED\" \"AFFECTS\")\n    (2641 \"SEMMED_PRED\" \"AFFECTS\")\n    (2645 \"SEMMED_PRED\" \"AFFECTS\")\n    (2648 \"SEMMED_PRED\" \"AFFECTS\")\n    (2649 \"SEMMED_PRED\" \"AFFECTS\")\n    (2651 \"SEMMED_PRED\" \"AFFECTS\")\n    (2652 \"SEMMED_PRED\" \"AFFECTS\")\n    (2653 \"SEMMED_PRED\" \"AFFECTS\")\n    (2654 \"SEMMED_PRED\" \"AFFECTS\")\n    (2657 \"SEMMED_PRED\" \"AFFECTS\")\n    (2659 \"SEMMED_PRED\" \"AFFECTS\")\n    (2660 \"SEMMED_PRED\" \"AFFECTS\")\n    (2661 \"SEMMED_PRED\" \"AFFECTS\")))\n\n(test 'various-names\n  (run 17 (c n) (cprop c \"name\" n))\n  '((\"UMLS:C1156332\" \"'de novo' GDP-L-fucose biosynthetic process\")\n    (\"UMLS:C1157653\" \"'de novo' IMP biosynthetic process\")\n    (\"UMLS:C1523107\" \"'de novo' cotranslational protein folding\")\n    (\"UMLS:C1158942\" \"'de novo' protein folding\")\n    (\"UMLS:C0761898\" \"(((4-chloromethyl)benzoyl)amino)-tetramethylrhodamine\")\n    (\"UMLS:C1260101\"\n     \"(((4-nitrophenyl)amino)(2,2,4,4-tetramethyl thiochroman-6-yl)amino) methane-1-thione\")\n    (\"UMLS:C0643014\" \"((2-azido-4-benzyl)phenoxy)-N-ethylmorpholine\")\n    (\"UMLS:C0635089\"\n     \"((3-(bis(2-chloroethyl)amino)-4-methylphenyl)hydroxymethane)bisphosphonic acid\")\n    (\"UMLS:C1312836\"\n     \"((3Z)-N-(3-chlorophenyl)-3-((3,5-dimethyl-4-((4-methylpiperazin-1-yl)carbonyl)-1H-pyrrol-2-yl)methylene)-N-methyl-2-oxo-2,3-dihydro-1H-indole-5-sulfonamide)\")\n    (\"UMLS:C0378071\"\n     \"((5,6-dichloro-2,3,9,9a-tetrahydro-3-oxo-9a-propyl-1H-fluoren-7-yl)oxy)acetic acid\")\n    (\"UMLS:C0961234\"\n     \"((6-acetyl-3,4-dihydro-2,5,7,8-tetramethyl-2H-1-benzopyran-2yl)carbonyl)-3(aminoethyl)indole\")\n    (\"UMLS:C0915106\"\n     \"((E)-(5)-(3,5-di-tert-butyl-4-hydroxybenzylidene)- 2-ethyl-1,2-isothiazolidine-1,1-dioxide)\")\n    (\"UMLS:C1565913\"\n     \"((S)-2-acetylamino-3-((R)-(1-(3-(piperidin-4-yl)propionyl)piperidin-3-ylcarbonyl))amino) propionic acid trihydrate\")\n    (\"UMLS:C0043560\" \"((dihydroindenyl)oxy)alkanoic acid\")\n    (\"UMLS:C0967118\" \"((n-nitroveratryl)oxy)chlorocarbamate-caged thymosin beta4\")\n    (\"UMLS:C0257864\" \"((nitroveratryl)oxy)chlorocarbamate\")\n    (\"UMLS:C1158357\" \"(+)-camphor metabolic process\")))\n\n(test 'single-concept-properties\n  (run 10 (k v)\n    (cprop \"UMLS:C0000137\" k v))\n  '((\"category\" \"chemical_substance\")\n    (\"id\" \"UMLS:C0000137\")\n    (\"name\" \"15S RNA\")\n    (\"umls_type\" \"(\\\"T114\\\" \\\"T123\\\")\")\n    (\"umls_type_label\"\n     \"(\\\"Nucleic Acid, Nucleoside, or Nucleotide\\\" \\\"Biologically Active Substance\\\")\")\n    (\"xrefs\" \"(\\\"MESH:D012335\\\")\")))\n\n(test 'single-subject-edges\n  (run 20 (id o) (edge id \"UMLS:C0005767\" o))\n  '((11582417 \"UMLS:C0000039\")\n    (4175774 \"UMLS:C0000084\")\n    (3396436 \"UMLS:C0000103\")\n    (3475411 \"UMLS:C0000119\")\n    (9750416 \"UMLS:C0000163\")\n    (6336638 \"UMLS:C0000165\")\n    (7906789 \"UMLS:C0000167\")\n    (1604793 \"UMLS:C0000173\")\n    (9276373 \"UMLS:C0000215\")\n    (2443460 \"UMLS:C0000248\")\n    (11125423 \"UMLS:C0000257\")\n    (5177191 \"UMLS:C0000266\")\n    (12962849 \"UMLS:C0000294\")\n    (769969 \"UMLS:C0000343\")\n    (6609976 \"UMLS:C0000376\")\n    (6784014 \"UMLS:C0000379\")\n    (448326 \"UMLS:C0000392\")\n    (1110409 \"UMLS:C0000407\")\n    (13525868 \"UMLS:C0000473\")\n    (10823557 \"UMLS:C0000477\")))\n\n(test 'single-object-edges\n  (run 20 (id s) (edge id s \"UMLS:C0005767\"))\n  '((6463675 \"UMLS:C0000119\")\n    (6463674 \"UMLS:C0000163\")\n    (6466559 \"UMLS:C0000163\")\n    (6466558 \"UMLS:C0000167\")\n    (6463673 \"UMLS:C0000340\")\n    (6466556 \"UMLS:C0000379\")\n    (6466557 \"UMLS:C0000379\")\n    (6463672 \"UMLS:C0000392\")\n    (6463671 \"UMLS:C0000464\")\n    (6466555 \"UMLS:C0000503\")\n    (6463670 \"UMLS:C0000530\")\n    (6466554 \"UMLS:C0000530\")\n    (6463669 \"UMLS:C0000545\")\n    (6466553 \"UMLS:C0000545\")\n    (6463668 \"UMLS:C0000578\")\n    (6463667 \"UMLS:C0000608\")\n    (6463666 \"UMLS:C0000617\")\n    (6466551 \"UMLS:C0000617\")\n    (6466552 \"UMLS:C0000617\")\n    (6463665 \"UMLS:C0000779\")))\n\n(test 'single-edge\n  (run* (id) (edge id \"UMLS:C0005767\" \"UMLS:C1121571\"))\n  '((10012443)))\n\n(test 'single-edge-properties\n  (run* (id k v)\n    (edge id \"UMLS:C0005767\" \"UMLS:C1121571\")\n    (eprop id k v))\n  '((10012443 \"SEMMED_PRED\" \"LOCATION_OF\")\n    (10012443 \"edge_label\" \"location_of\")\n    (10012443 \"is_defined_by\" \"semmeddb\")\n    (10012443 \"n_pmids\" \"14\")\n    (10012443 \"negated\" \"False\")\n    (10012443\n     \"pmids\"\n     \"19402156;21663591;23551806;23551806;23551806;23551806;27062891;27253267;24048877;28903084;17297611;22683313;22172068;26418915\")\n    (10012443 \"provided_by\" \"semmeddb_sulab\")\n    (10012443 \"relation\" \"semmeddb:location_of\")))\n\n(test 'chemical-substance-names\n  (run 10 (curie name)\n    (cprop curie \"category\" \"chemical_substance\")\n    (cprop curie \"name\" name))\n  '((\"UMLS:C0000039\" \"1,2-dipalmitoylphosphatidylcholine\")\n    (\"UMLS:C0000096\" \"1-Methyl-3-isobutylxanthine\")\n    (\"UMLS:C0000097\" \"1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine\")\n    (\"UMLS:C0000098\" \"1-Methyl-4-phenylpyridinium\")\n    (\"UMLS:C0000102\" \"1-Naphthylamine\")\n    (\"UMLS:C0000103\" \"1-Naphthylisothiocyanate\")\n    (\"UMLS:C0000119\" \"11-Hydroxycorticosteroids\")\n    (\"UMLS:C0000137\" \"15S RNA\")\n    (\"UMLS:C0000151\" \"17 beta-Hydroxy-5 beta-Androstan-3-One\")\n    (\"UMLS:C0000163\" \"17-Hydroxycorticosteroids\")))\n\n(test 'gene-names\n  (run 10 (c n)\n    (cprop c \"name\"     n)\n    (cprop c \"category\" \"gene\"))\n  '((\"UMLS:C0002085\" \"Alleles\")\n    (\"UMLS:C0008288\" \"CIPC gene\")\n    (\"UMLS:C0008844\" \"Cistron\")\n    (\"UMLS:C0017258\" \"Gene Clusters\")\n    (\"UMLS:C0017272\" \"Gene Library\")\n    (\"UMLS:C0017337\" \"Genes\")\n    (\"UMLS:C0017338\" \"Genes, araC\")\n    (\"UMLS:C0017339\" \"Genes, Bacterial\")\n    (\"UMLS:C0017340\" \"Genes, Developmental\")\n    (\"UMLS:C0017342\" \"Genes, Dominant\")))\n\n(test 'concept-relationships\n  (run 10 (curie1 predicate curie2)\n    (fresh (eid)\n      (eprop eid \"edge_label\" predicate)\n      (edge eid curie1 curie2)))\n  '((\"UMLS:C1368111\" \"affects\" \"UMLS:C1523610\")\n    (\"UMLS:C1414313\" \"affects\" \"UMLS:C1523610\")\n    (\"UMLS:C0001962\" \"affects\" \"UMLS:C0333440\")\n    (\"UMLS:C0687133\" \"affects\" \"UMLS:C1332412\")\n    (\"UMLS:C0687133\" \"affects\" \"UMLS:C1332412\")\n    (\"UMLS:C0017262\" \"affects\" \"UMLS:C1332412\")\n    (\"UMLS:C0017262\" \"affects\" \"UMLS:C1332412\")\n    (\"UMLS:C1522575\" \"affects\" \"UMLS:C0002940\")\n    (\"UMLS:C1513016\" \"affects\" \"UMLS:C0002940\")\n    (\"UMLS:C1456820\" \"affects\" \"UMLS:C0002940\")))\n\n(test 'named-negative-regulators\n  (run 10 (curie1 name1 curie2 name2)\n    (fresh (eid)\n      (eprop eid \"edge_label\" \"negatively_regulates\")\n      (edge eid curie1 curie2)\n      (cprop curie1 \"name\" name1)\n      (cprop curie2 \"name\" name2)))\n  '((\"UMLS:C1537740\" \"MIR30D gene\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C1537740\" \"MIR30D gene\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C1422386\" \"HDAC9 gene\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0935996\" \"Signaling Pathway Gene\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0809183\" \"CDKN2B gene\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0809183\" \"CDKN2B gene\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0699251\" \"Fluimucil\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0288472\" \"oncoprotein p21\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0288472\" \"oncoprotein p21\" \"UMLS:C1332698\" \"CCNE2 gene\")\n    (\"UMLS:C0286651\" \"atorvastatin\" \"UMLS:C1332698\" \"CCNE2 gene\")))\n\n(test 'all-concept-properties\n  (run* (k)\n    (fresh (curie v)\n      (cprop curie k v)))\n  '((\"category\") (\"id\") (\"name\") (\"umls_type\") (\"umls_type_label\") (\"xrefs\")))\n\n(test 'all-edge-properties\n  (run* (k)\n    (fresh (eid v)\n      (eprop eid k v)))\n  '((\"SEMMED_PRED\")\n    (\"edge_label\")\n    (\"is_defined_by\")\n    (\"n_pmids\")\n    (\"negated\")\n    (\"pmids\")\n    (\"provided_by\")\n    (\"relation\")))\n\n(test 'all-concept-categories\n  (run* (category)\n    (fresh (curie)\n      (cprop curie \"category\" category)))\n  '((\"activity_and_behavior\")\n    (\"anatomical_entity\")\n    (\"biological_entity\")\n    (\"biological_process_or_activity\")\n    (\"cell\")\n    (\"cell_component\")\n    (\"chemical_substance\")\n    (\"disease_or_phenotypic_feature\")\n    (\"gene\")\n    (\"genomic_entity\")\n    (\"gross_anatomical_structure\")\n    (\"phenotypic_feature\")\n    (\"protein\")))\n\n(test 'all-predicates\n  (run* (predicate)\n    (fresh (eid)\n      (eprop eid \"edge_label\" predicate)))\n  '((\"affects\")\n    (\"causes\")\n    (\"coexists_with\")\n    (\"derives_into\")\n    (\"gene_associated_with_condition\")\n    (\"interacts_with\")\n    (\"location_of\")\n    (\"manifestation_of\")\n    (\"negatively_regulates\")\n    (\"part_of\")\n    (\"positively_regulates\")\n    (\"precedes\")\n    (\"predisposes\")\n    (\"prevents\")\n    (\"produces\")\n    (\"related_to\")\n    (\"subclass_of\")\n    (\"treats\")))\n\n(test 'nausea-properties\n  (run* (k v)\n    (cprop \"UMLS:C0520909\" k v))\n  '((\"category\" \"disease_or_phenotypic_feature\")\n    (\"id\" \"UMLS:C0520909\")\n    (\"name\" \"Postoperative Nausea and Vomiting\")\n    (\"umls_type\" \"(\\\"T184\\\")\")\n    (\"umls_type_label\" \"(\\\"Sign or Symptom\\\")\")\n    (\"xrefs\"\n     \"(\\\"SNMI:F-52846\\\" \\\"SNOMEDCT_US:1488000\\\" \\\"RCD:Xa0Ka\\\" \\\"CHV:0000037809\\\" \\\"MESH:D020250\\\" \\\"LCH_NW:sh99001642\\\" \\\"NDFRT:N0000004075\\\")\")))\n\n(test 'nausea-subject-edges\n  (run* (o cat name p)\n    (fresh (eid)\n      (edge eid \"UMLS:C0520909\" o)\n      (cprop o \"category\" cat)\n      (cprop o \"name\" name)\n      (eprop eid \"edge_label\" p)))\n  '((\"UMLS:C0004364\"\n     \"disease_or_phenotypic_feature\"\n     \"Autoimmune Diseases\"\n     \"related_to\")\n    (\"UMLS:C0009566\"\n     \"disease_or_phenotypic_feature\"\n     \"Complication\"\n     \"subclass_of\")\n    (\"UMLS:C0020450\"\n     \"disease_or_phenotypic_feature\"\n     \"Hyperemesis Gravidarum\"\n     \"causes\")\n    (\"UMLS:C0026603\"\n     \"disease_or_phenotypic_feature\"\n     \"Motion Sickness\"\n     \"related_to\")\n    (\"UMLS:C0027497\" \"disease_or_phenotypic_feature\" \"Nausea\" \"subclass_of\")\n    (\"UMLS:C0027497\" \"disease_or_phenotypic_feature\" \"Nausea\" \"causes\")\n    (\"UMLS:C0027497\" \"disease_or_phenotypic_feature\" \"Nausea\" \"coexists_with\")\n    (\"UMLS:C0027498\"\n     \"disease_or_phenotypic_feature\"\n     \"Nausea and vomiting\"\n     \"causes\")\n    (\"UMLS:C0030201\"\n     \"disease_or_phenotypic_feature\"\n     \"Pain, Postoperative\"\n     \"coexists_with\")\n    (\"UMLS:C0032290\"\n     \"disease_or_phenotypic_feature\"\n     \"Aspiration Pneumonia\"\n     \"predisposes\")\n    (\"UMLS:C0032787\"\n     \"disease_or_phenotypic_feature\"\n     \"Postoperative Complications\"\n     \"subclass_of\")\n    (\"UMLS:C0042963\" \"disease_or_phenotypic_feature\" \"Vomiting\" \"subclass_of\")\n    (\"UMLS:C0042963\" \"disease_or_phenotypic_feature\" \"Vomiting\" \"causes\")\n    (\"UMLS:C0042963\" \"disease_or_phenotypic_feature\" \"Vomiting\" \"coexists_with\")\n    (\"UMLS:C0232602\" \"disease_or_phenotypic_feature\" \"Retching\" \"coexists_with\")\n    (\"UMLS:C0234119\"\n     \"disease_or_phenotypic_feature\"\n     \"Neuromuscular inhibition\"\n     \"related_to\")\n    (\"UMLS:C0278134\"\n     \"disease_or_phenotypic_feature\"\n     \"Absence of sensation\"\n     \"causes\")\n    (\"UMLS:C0278134\"\n     \"disease_or_phenotypic_feature\"\n     \"Absence of sensation\"\n     \"coexists_with\")\n    (\"UMLS:C0344307\"\n     \"disease_or_phenotypic_feature\"\n     \"Absence of pain sensation\"\n     \"coexists_with\")\n    (\"UMLS:C0520905\"\n     \"disease_or_phenotypic_feature\"\n     \"Vomiting, Postoperative\"\n     \"coexists_with\")\n    (\"UMLS:C0879626\"\n     \"disease_or_phenotypic_feature\"\n     \"Adverse effects\"\n     \"subclass_of\")\n    (\"UMLS:C1306597\"\n     \"disease_or_phenotypic_feature\"\n     \"Psychiatric problem\"\n     \"manifestation_of\")))\n\n;; ~20 seconds\n;(test 'single-object-affects-edges\n;  (length (run* (s id)\n;            (edge id s \"UMLS:C0005767\")\n;            (eprop id \"edge_label\" \"affects\")))\n;  2414)\n\n;; ~190 seconds\n;(test 'all-concept-category-counts\n;  (run* (category count)\n;    (fresh (curie)\n;      (cprop curie \"category\" category)\n;      (:== count (category)\n;           (s-length (run^ (curie)\n;                           (cprop curie \"category\" category))))))\n;\n;  '((\"activity_and_behavior\" 935)\n;    (\"anatomical_entity\" 2750)\n;    (\"biological_entity\" 14905)\n;    (\"biological_process_or_activity\" 6887)\n;    (\"cell\" 1099)\n;    (\"cell_component\" 1644)\n;    (\"chemical_substance\" 58812)\n;    (\"disease_or_phenotypic_feature\" 36248)\n;    (\"gene\" 20695)\n;    (\"genomic_entity\" 174)\n;    (\"gross_anatomical_structure\" 8472)\n;    (\"phenotypic_feature\" 393)\n;    (\"protein\" 12644)))\n"
  },
  {
    "path": "medikanren2/trapi-cli.rkt",
    "content": "#lang racket\n\n#|\n    Reads TRAPI filenames from stdin and runs them.  Example (run all Dec 2021 queries):\n\n        git clone https://github.com/NCATSTranslator/minihackathons\n        find minihackathons -maxdepth 3 -type f -path \\*2021-12_demo\\* -name \\*.json \\\n            | racket -l errortrace -u medikanren2/trapi-cli.rkt\n\n|#\n\n(require\n \"common.rkt\"   \n  \"trapi.rkt\"\n  \"logging.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/pretty\n  racket/runtime-path\n  racket/dict\n  racket/async-channel\n  http/request\n  json\n)\n\n(define seconds-per-query (make-parameter 60))\n(define seconds-idle-between-queries (make-parameter 15))\n(define uri-trapi (make-parameter #f))\n\n(define (with-timeout seconds thunk)\n  (define ach (make-async-channel))\n  (define t (thread\n              (lambda ()\n                (async-channel-put\n                    ach\n                    (list (thunk))))))    ; nonempty list indicates success\n  ; Watcher thread:\n  (thread (lambda ()\n            (sleep seconds)\n            (kill-thread t)\n            (async-channel-put ach '()))) ; empty list indicates timeout\n  (sync ach))\n\n(define (run-query-without-network-impl fn msg)\n    (flush-output (current-output-port))\n    (define maybe-out (with-timeout (seconds-per-query) (lambda () (trapi-response msg))))\n    (flush-output (current-output-port))\n    (if (null? maybe-out)\n        (hasheq 'results '())\n        (let* ((out (car maybe-out))\n                (r (dict-ref out 'results)))\n            (dict-set out 'results r))))\n\n\n(define (run-query-without-network fn json1)\n    (define jsexpr (string->jsexpr json1))\n    (define trapimsg (hash-ref jsexpr 'message))\n    (define out (run-query-without-network-impl fn trapimsg))\n    (hasheq 'message out))\n\n(define http-version \"1.1\")\n(define (run-query-with-network fn json1)\n    (define uri (format \"~a~a\" (uri-trapi) \"/query\"))\n    (define headers '((#\"Content-Type\" . \"application/json\")))\n    (define bytes-out (call/output-request http-version\n                            \"POST\"\n                            uri\n                            (string->bytes/utf-8 json1)\n                            #f\n                            headers\n                            read-entity/bytes\n                            #:redirects 0))\n    (define tmp (bytes->jsexpr bytes-out))\n    (sleep (seconds-idle-between-queries))\n    tmp)\n\n(define (run-query fn json1)\n    (displayln (jsexpr->string (hasheq\n        'event \"request\"\n        'fn fn)))\n    (define out\n        (if (uri-trapi)\n            (run-query-with-network fn json1)\n            (run-query-without-network fn json1)))\n    (displayln (jsexpr->string (hasheq\n        'event \"response\"\n        'fn fn\n        'out out\n    )))\n    out)\n\n(define (read-and-run-by-filename fd)\n    (define (iter inouts)\n        (define l (read-line fd 'any))\n        (if (eof-object? l)\n            inouts\n            (let ((fn (string-trim l)))\n            (if (or (<= (string-length fn) 1) (not (file-exists? fn)))\n                '()\n                (let* (\n                    (t0 (current-milliseconds))\n                    (json1 (file->string fn))\n                    (out (run-query fn json1))\n                    (dt (exact->inexact (/ (- (current-milliseconds) t0) 1000)))\n                    (inout `((fn . ,fn) (dt . ,dt) (json . ,json1) (out . ,out))))\n                (iter (cons inout inouts)))))))\n    (iter '()))\n\n(define (num-results-from-out a1)\n;    (printf \"a1=\\n\")\n;    (pretty-write a1)\n    (if (null? a1)\n        -1                               ; -1 indicates timeout\n        (length (dict-ref (dict-ref a1 'message) 'results))))\n\n(define (run-main)\n    (let ((inouts (read-and-run-by-filename (current-input-port))))\n        (for ((inout inouts))\n            (let* (\n                    (n (num-results-from-out (dict-ref inout 'out))))\n                (displayln\n                    (jsexpr->string\n                        (hasheq\n                            'event \"summary\"\n                            'num-answers n\n                            'dt (dict-ref inout 'dt)\n                            'fn (dict-ref inout 'fn)))))))\n)\n\n(define (parse-configuration)\n  (command-line\n   #:program \"trapi-cli.rkt\"\n   #:usage-help \"trapi-cli.rkt \"\n   #:once-each\n   [(\"--seconds-per-query\") sec\n                    \"Number of seconds to allow for each query\"\n                    (seconds-per-query (string->number (string-trim #:left? #f sec)))]\n   [(\"--uri-trapi\") adir\n                    \"A URI to a TRAPI service\"\n                    (uri-trapi (string-trim #:left? #f adir))]\n   #:args ()\n   '())\n   ;\"\"  ; We don't care about the return value because configuration lives in mutatable racket parameters\n  )\n\n(module+ main\n  (parse-configuration)\n  (run-main)\n  )\n\n\n"
  },
  {
    "path": "medikanren2/trapi.rkt",
    "content": "#lang racket/base\n(provide trapi-response)\n(require\n \"common.rkt\" \n \"lw-reasoning.rkt\"\n \"logging.rkt\"\n  racket/file racket/function racket/list racket/hash\n  (except-in racket/match ==)\n  racket/port\n  racket/pretty\n  racket/runtime-path\n  racket/string\n  json\n  memoize\n  racket/format\n  racket/dict\n  racket/set\n  )\n\n\n;; QUESTION\n;; - Do we return all attributes, or only specified ones?\n;; - How is knowledge_graph used in queries?\n\n;; TODO (trapi.rkt and server.rkt)\n;; - status - logs - description\n;; - Understand Attribute types\n;; - QEdge constraints\n;; - QNode is_set:\n;;       Boolean that if set to true, indicates that this QNode MAY\n;;       have multiple KnowledgeGraph Nodes bound to it wi;; thin each\n;;       Result. The nodes in a set should be considered as a set of\n;;       independent nodes, rather than a set of dependent nodes,\n;;       i.e., the answer would still be valid if the nodes in the set\n;;       were instead returned individually. Multiple QNodes may have\n;;       is_set=True. If a QNode (n1) with is_set=True is connected to\n;;       a QNode (n2) with is_set=False, each n1 must be connected to\n;;       n2. If a QNode (n1) with is_set=True is connected to a QNode\n;;       (n2) with is_set=True, each n1 must be connected to at least\n;;       one n2.\n\n(define use-reasoning? (make-parameter #f))\n\n(define trapi-response-node-properties '(\"category\" \"name\"))\n(define trapi-response-node-attributes '((\"umls_type_label\" . \"miscellaneous\")\n                                         (\"umls_type\" . \"miscellaneous\")\n                                         (\"xrefs\" . \"miscellaneous\")))\n(define trapi-response-edge-properties '(\"predicate\" \"relation\" \"subject\" \"object\"))\n(define trapi-response-edge-attributes '((\"negated\" . \"miscellaneous\")\n                                         (\"provided_by\" . \"miscellaneous\")\n                                         (\"publications\" . \"miscellaneous\")))\n\n(define (alist-ref alist key default)\n  ;; WEB  FIXME unchecked 'assoc' result\n  (define kv (assoc key alist))\n  (if kv (cdr kv) default))\n\n(define hash-empty (hash))\n(define (str   v) (if (string? v) v (error (format \"invalid string: ~s\" v))))\n(define (olift v) (if (hash?   v) v (error (format \"invalid object: ~s\" v))))\n(define (slift v) (cond ((pair?   v) v)\n                        ((string? v) (list v))\n                        ((null?   v) '())\n                        (else        (error (format \"invalid string or list of strings: ~s\" v)))))\n(define (alist-of-hashes->lists v)\n  (map (lambda (pair)\n         (cons (car pair) (hash->list (olift (cdr pair)))))\n       v))\n(define (symlift v) \n  (cond ((number? v) (string->symbol (number->string v)))\n        ((string? v) (string->symbol v))\n        ((symbol? v) v)\n        (else (error (format \"Must be a number, string or symbol: ~s.\" v)))))\n\n(define (strlift v)\n  (cond ((number? v) (number->string v))\n        ((string? v) v)\n        ((symbol? v) (symbol->string v))\n        (error (format \"Must be a number, string or symbol: ~s\" v))))\n\n(define (trapi-response msg)\n  (define log-key \"[query]\")\n  (define max-results (hash-ref msg 'max_results #f))\n  (define qgraph (hash-ref msg 'query_graph #f))\n  (define kgraph (hash-ref msg 'knowledge_graph #f))\n  (define request-valid? (not (not qgraph)))\n\n  (if (not request-valid?)\n    (hash 'results '()\n          'knowledge_graph\n          (hash 'nodes '#hash()\n                'edges '#hash()))\n    (let ((results (if max-results\n                          (run max-results bindings (trapi-query qgraph kgraph bindings log-key))\n                          (run* bindings (trapi-query qgraph kgraph bindings log-key)))))\n      (hash 'results (trapi-response-results results qgraph)\n            'knowledge_graph\n            (hash 'nodes (trapi-response-knodes results)\n                  'edges (trapi-response-kedges results))))))\n\n(define (trapi-query qgraph kgraph bindings log-key)\n  (define nodes  (hash->list (olift (hash-ref qgraph 'nodes hash-empty))))\n  (define edges  (hash->list (olift (hash-ref qgraph 'edges hash-empty))))\n\n  ;; Interpret included KnowledgeGraph element\n  (define knodes (and kgraph\n                      (alist-of-hashes->lists\n                       (hash->list (olift (hash-ref kgraph 'nodes hash-empty))))))\n  (define kedges (and kgraph (alist-of-hashes->lists\n                              (hash->list (olift (hash-ref kgraph 'edges hash-empty))))))\n  (define-relation (k-is-a concept category)\n    (fresh (props concept-sym category-sym)\n      (membero `(,concept-sym . ,props) knodes)\n      (membero `(category . ,category) props)\n      (:== concept-sym (concept) (string->symbol concept))\n      (:== category-sym (category) (string->symbol category))))\n  (define-relation (k-triple eid s p o)\n    (fresh (props)\n      (membero `(,eid . ,props) kedges)\n      (membero `(subject . ,s) props)\n      (membero `(predicate . ,p) props)\n      (membero `(object . ,o) props)))\n\n    (let ((full-reasoning? (hash-ref qgraph 'use_reasoning #t)))\n      (fresh (node-bindings edge-bindings)\n        (== bindings `((node_bindings . ,node-bindings) \n                       (edge_bindings . ,edge-bindings)))\n        ((trapi-nodes nodes k-is-a full-reasoning? log-key) node-bindings)\n        ((trapi-edges edges k-triple full-reasoning? log-key) node-bindings edge-bindings))))\n\n(define (trapi-nodes nodes k-is-a full-reasoning? log-key)\n  (relation trapi-nodes-o (bindings)\n    (begin\n      (printf \"entering trapi-nodes loop...\\n\")\n      (let loop ((nodes nodes)\n                 (bindings bindings))\n        (if (null? nodes)\n            (== bindings '())\n            (let* ((id+n        (car nodes))\n                   (id          (car id+n))\n                   (n           (cdr id+n))\n                   (curie       (hash-ref n 'id #f)) ; deprecated v1.1\n                   (curies      (hash-ref n 'ids (and curie \n                                                      (if (pair? curie) curie\n                                                          (list curie)))))\n                   (category   (hash-ref n 'category #f)) ; deprecated v1.1\n                   (categories  (hash-ref n 'categories (and category \n                                                             (if (pair? category) category\n                                                                 (list category)))))\n                   (constraints (hash-ref n 'constraints '()))\n                   (is-set?     (hash-ref n 'is_set #f))\n                   (reasoning?  (hash-ref n 'use_reasoning #f)))\n              (printf \"--------------\\n\")\n              (printf \"id: ~s\\n\" id)\n              (printf \"n: ~s\\n\" n)\n              (printf \"curie (deprecated): ~s\\n\" curie)\n              (printf \"curies: ~s\\n\" curies)\n              (printf \"category (deprecated): ~s\\n\" category)\n              (printf \"categories: ~s\\n\" categories)\n              (printf \"constraints: ~s\\n\" constraints)\n              (printf \"is-set?: ~s\\n\" is-set?)\n              (printf \"reasoning?: ~s\\n\" reasoning?)\n              (printf \"--------------\\n\")\n              (if curies\n                  (if (pair? curies)\n                      ;; WEB TODO FIXME Shouldn't we be\n                      ;; simulataneously checking for subclasses of\n                      ;; categories (as in the code below, for when no\n                      ;; curies are specified), if categories are\n                      ;; present for the node, and reasoning? or\n                      ;; full-reasoning? is true?\n                      (let ((curies\n                             (if (or reasoning? full-reasoning?)\n                                 (log-time log-once log-key \n                                           (format \"Subclasses/synonyms of ~s\" curies)\n                                           (get-synonyms-ls (subclasses/set curies)))\n                                 curies)))\n                        (fresh (curie k+v bindings-rest)\n                          (== bindings `(,k+v . ,bindings-rest))\n                          (== k+v `(,id . ,curie))\n                          (membero curie curies)\n                          ((trapi-constraints constraints) curie)\n                          (loop (cdr nodes) bindings-rest)))\n                      (error (format\n                              \"Field: 'QNode/ids' must be array of CURIEs (TRAPI 1.1), but given ~s\\n\"\n                              curies)))\n                  (if categories\n                      (if (pair? categories)\n                          (let ((categories (if (or reasoning? full-reasoning?)\n                                                (log-time log-once log-key \n                                                          (format \"Subclasses of ~s\" categories)\n                                                          (subclasses/set categories))\n                                                categories)))\n                            (fresh (cat curie k+v bindings-rest)\n                              (== k+v `(,id . ,curie))\n                              (== bindings `(,k+v . ,bindings-rest))\n                              ((trapi-constraints constraints) curie)\n                              (membero cat categories)\n                              (conde ((is-a curie cat))\n                                     ((k-is-a curie cat)))\n                              (loop (cdr nodes) bindings-rest)))\n                          (error (format\n                                  \"Field: 'QNode/categories' must be array of CURIEs (TRAPI 1.1), but given ~s\\n\"\n                                  categories)))\n                      ;; No ids (CURIEs) or categories specified for the node:\n                      (fresh (curie k+v bindings-rest)\n                          (== bindings `(,k+v . ,bindings-rest))\n                          (== k+v `(,id . ,curie))\n                          ((trapi-constraints constraints) curie)\n                          (loop (cdr nodes) bindings-rest))))))))))\n\n(define (trapi-edges edges k-triple full-reasoning? log-key)\n  (relation trapi-edges-o (node-bindings edge-bindings)\n    (let loop ((edges edges) (bindings edge-bindings))\n      (if (null? edges)\n          (== bindings '()) \n          (let* ((id+e        (car edges))\n                 (id          (car id+e))\n                 (e           (cdr id+e))\n                 (predicate   (hash-ref e 'predicate #f)) ; deprecated v1.1\n                 (predicates  (hash-ref e 'predicates (and predicate\n                                                           (if (pair? predicate) predicate\n                                                               (list predicate)))))\n                 (subject-symbol (hash-ref e 'subject #f))\n                 (subject     (if subject-symbol\n                                  (string->symbol subject-symbol)\n                                  (error (format \"subject not found in e:\\n~s\" e))))\n                 (relation    (hash-ref e 'relation #f))\n                 (object-symbol (hash-ref e 'object #f))\n                 (object      (if object-symbol\n                                  (string->symbol object-symbol)\n                                  (error (format \"object not found in e:\\n~s\" e))))\n                 (constraints (hash-ref e 'constraints '()))\n                 (reasoning?  (hash-ref e 'use_reasoning #f)))\n            (if (and predicates (not (pair? predicates)))\n                (error (format\n                         \"Field: 'QEdge/predicates' must be an array of CURIEs (TRAPI 1.1).  Given ~s\\n\"\n                         predicates))\n                (let ((predicates (if (and (or reasoning? full-reasoning?) predicates)\n                                      (log-time log-once log-key \n                                                (format \"Subclasses of ~s\" predicates)\n                                                (subclasses/set predicates))\n                                      predicates)))\n                  (fresh (db+id s p o bindings-rest)\n                    (membero `(,subject . ,s) node-bindings)\n                    (membero `(,object . ,o) node-bindings)\n                    (conde ((== predicates #f))\n                           ((== predicates '()))\n                           ((membero p predicates)))\n                    (conde ((triple/eid db+id s p o)\n                            (conde ((== relation #f))\n                                   ((stringo relation) \n                                    (eprop db+id \"relation\" relation))))\n                           ((fresh (id)\n                              (k-triple id s p o)\n                              (== db+id `(kg . ,id)))))\n                    (== bindings `((,id . ,db+id) . ,bindings-rest))\n                    (loop (cdr edges) bindings-rest)))))))))\n\n(define (trapi-constraints constraints)\n  (relation trapi-node-constraints-o (node)\n    (let loop ((constraints constraints))\n      (if (null? constraints)\n          (== #t #t)\n          (let* ((constraint (car constraints))\n                 (id        (hash-ref constraint 'id #f))\n                 (not?      (hash-ref constraint 'not #f))\n                 (operator  (hash-ref constraint 'operator #f))\n                 (enum      (hash-ref constraint 'enum #f))\n                 (value     (hash-ref constraint 'value #f))\n                 (unit-id   (hash-ref constraint 'unit_id #f))) ;?\n            (fresh (val)\n              (triple node id val)\n              (case operator\n                ((\">\")  (if not?\n                            (<=o val value)\n                            (list (hash-ref qgraph 'nodes)))))\n    (if (null? is-set-nodes) \n        (transform-trapi-results results)\n        (transform-trapi-results (group-sets results (map car singleton-nodes))))))\n\n(define (transform-trapi-results results)\n  (map (lambda (bindings)\n         (hash 'node_bindings\n               (make-hash\n                (map (lambda (binding) \n                       (let ((node/s (cdr binding)))\n                         `(,(car binding)\n                           . ,(map (lambda (id) (hash 'id id))\n                                   (if (list? node/s) node/s\n                                       (list node/s))))))\n                     (alist-ref bindings 'node_bindings '())))\n               'edge_bindings\n               (make-hash\n                (map (lambda (ebinding)\n                       (let ((edge/s (cdr ebinding)))\n                         `(,(car ebinding)\n                           . ,(map (lambda (db+id)\n                                     (hash 'id (edge-id/reported db+id)))\n                                   (if (list? edge/s) edge/s\n                                       (list edge/s))))))\n                     (alist-ref bindings 'edge_bindings '())))\n\n               ;;; WEB: dummy score, until I implement a scoring algorithm\n               'score\n               42.01\n               \n               ))\n       results))\n\n(define (unique-bindings-values results key)\n  (remove-duplicates\n   (apply append\n          (map\n           (lambda (nb) (map cdr (alist-ref nb key #f)))\n           results))))\n\n(define (snake->camel str (capitalize? #f)) \n  (if (non-empty-string? str)\n      (let ((first-letter (substring str 0 1))\n            (rest-str (substring str 1 (string-length str))))\n        (if (equal? first-letter \"_\")\n            (snake->camel rest-str #t)\n            (string-append (if capitalize?\n                               (string-upcase first-letter) \n                               first-letter)\n                           (snake->camel rest-str))))\n      \"\"))\n\n;; hack to ensure Biolink compliance for rtx2-20210204 and semmeddb\n(define (biolinkify/predicate curie)\n  (let ((curie (string-replace curie \",\" \"\")))\n    (if (string-prefix? curie \"biolink:\") curie\n        (string-append \"biolink:\" curie))))\n\n;; hack to ensure Biolink compliance for rtx2-20210204 and semmeddb\n(define (biolinkify/category curie)\n  (if (string-prefix? curie \"biolink:\") curie\n      (string-append \"biolink:\" \n                     (string-replace (snake->camel curie #t) \"_\" \"\"))))\n\n(define (props-kv k+v)\n  (let ((k (car k+v)) (v (cdr k+v)))\n    (cond ((eq? k \"predicate\")\n           `(predicate . ,(biolinkify/predicate v)))\n          (else\n           (cons (string->symbol k) v)))))\n\n(define (attributes-kv keys)\n  (lambda (k+v)\n    (let ((k (car k+v)) (v (cdr k+v)))\n      (make-hash\n       `((attribute_type_id . ,(alist-ref keys k \"miscellaneous\"))\n         (value_type_id . ,(alist-ref keys k \"miscellaneous\"))\n         (original_attribute_name . ,(strlift k))\n         (value . ,(strlift v)))))))\n\n(define (trapi-response-knodes/edges results key new-key query attributes-query attributes-keys)\n  (make-hash\n   (map (lambda (node)\n          `(,(new-key node)\n            . ,(make-hash\n                (append (let ((attributes (attributes-query node)))\n                          (if (pair? attributes)\n                              `((attributes . ,(map (attributes-kv attributes-keys) attributes))) '()))\n                        (map props-kv (query node))))))\n        (unique-bindings-values results key))))\n\n(define (trapi-response-knodes results)\n  (trapi-response-knodes/edges\n   results 'node_bindings string->symbol\n   ;; (lambda (node) \n   ;;   (run* prop\n   ;;     (fresh (k v)\n   ;;       (membero k trapi-response-node-properties)\n   ;;       (== `(,k . ,v) prop)\n   ;;       (cprop node k v))))\n   (lambda (node)\n     `((\"name\" . ,(car (run 1 v (cprop node \"name\" v)))) ; hack: only gets 1!\n       (\"categories\" . ,(remove-duplicates\n                         (map biolinkify/category (run* v (cprop node \"category\" v)))))))\n   (lambda (node)\n     (run* attribute\n       (fresh (k v)\n         (membero k (map car trapi-response-node-attributes))\n         (== `(,k . ,v) attribute)\n         (cprop node k v))))\n   trapi-response-node-attributes))\n\n(define (trapi-response-kedges results)\n  (trapi-response-knodes/edges \n   results 'edge_bindings (compose symlift edge-id/reported)\n   (lambda (node) \n     (let ((properties\n            (run* prop\n              (fresh (k v)\n                (membero k trapi-response-edge-properties)\n                (== `(,k . ,v) prop)\n                (eprop node k v)))))\n       (if (and (memf (lambda (k+v) (eq? (car k+v) \"subject\")) properties)\n                (memf (lambda (k+v) (eq? (car k+v) \"object\")) properties))\n           properties\n           (let ((s+p (car (run 1 (s o) (edge node s o)))))\n             `((\"subject\" . ,(car s+p))\n               (\"object\" . ,(cadr s+p))\n               . ,properties)))))\n   (lambda (node)\n     (run* attribute\n       (fresh (k v)\n         (membero k (map car trapi-response-edge-attributes))\n         (== `(,k . ,v) attribute)\n         (eprop node k v))))\n   trapi-response-edge-attributes))\n\n(define (group-sets results singleton-nodes)\n  (define (get-nodes result)\n    (sort (filter (lambda (node)\n                    (member (car node) singleton-nodes))\n                  ;; WEB  FIXME taking 'cdr' of unchecked 'assoc' result\n                  (cdr (assoc 'node_bindings result)))\n          stringstring (car e)))))\n  (define (nodes-equal? a b)\n    (equal? (get-nodes a) (get-nodes b)))\n  (define (combine-bindings results key)\n    (foldl\n     (lambda (result rst) \n       (dict-map result (lambda (id curie)\n                          (remove-duplicates\n                           (cons id (cons curie (alist-ref rst id '())))))))\n     '()\n     (map (lambda (result)\n            ;; WEB  FIXME taking 'cdr' of unchecked 'assoc' result\n            (cdr (assoc key result)))\n          results)))\n  (map (lambda (results)\n         `((node_bindings . ,(combine-bindings results 'node_bindings))\n           (edge_bindings . ,(combine-bindings results 'edge_bindings))))\n       (group-by values results nodes-equal?)))\n"
  },
  {
    "path": "medikanren2/util/data-import-workaround/remove_cr.pl",
    "content": "use strict;\n\n# Remedy to a data corruption problem in one upstream file.  Repro:\n# \n# input file:\n#         3f8f7c80dc9c39dc291468fc1ab6ae9b80b5630c  sri-reference-kg-0.3.0.tar.gz\n# \n# Run this in a terminal:\n# \n#     cat medikanren2/data/sri-reference/0.3.0/upstream/sri-reference-kg-0.3.0_nodes.tsv | perl -e 'binmode(STDOUT); while($_ = <>) {$a=$_; chomp($_); $a =~ s/\\t/\\|/g; @F=split(\"|\",$a); $s=scalar(@F); $i+=1; print \"$i: \"; $x=$a; $x =~ s/\\t/\\\\t/g; print \"$i\\t$x\";}' | tail -n+849 | head -5 \n#     849: 849\tFlyBase:FBgn0004623|Gbeta76C|biolink:NamedThing|biolink:GenomicEntity|biolink:Gene|G protein beta-subunit 76C||ncbigene|panther|flybase|go|CG8770|DGqbeta|eGbeta|eye Gbeta|Galpha76C|gbe|Gbe|G[[beta]]|Gbeta|Gbeta76c|G[[beta76C]]|G[[beta]]e|Gbeta[[e]]|Gbeta{e}|Gbetae|G[[beta]] eye|G[q]|Gqbeta|Gqbetae|guanine nucleotide regulatory protein beta subunit||True||||||||||NCBITaxon:7227|NCBITaxon:7227||||||||||SO:0000704|owl:Class|SO:0000704|\n#     850: 850\tFlyBase:FBgn0004629|Cys|biolink:NamedThing|biolink:GenomicEntity|biolink:Gene|Cystatin-like||ncbigene|flybase|go|anon-EST:Liang-2.34|BcDNA:RH72992|CG8050|clone 2.34|cys|cystatin|Cystatin||True||||||||||NCBITaxon:7227||||||||||owl:Class|SO:0000704|\n#     ho|Dmrho|DMRHO|DmRho1|DMRHOa|DMRHOb|DRORHO|iks|Rho|RHO|rho-1|rho1|Rho-1|Rho1|RHOb|rhom|Rhomboid|RHOMBOID|rhomboid-1|rhomboid1|Rhomboid 1|Rhomboid-1|Rhomboid-I|rhomboid/veinlet|ve|Ve|veinlet|Veinlet||True||||||||||NCBITaxon:7227|NCBITaxon:7227||||||||||SO:0000704|owl:Class|SO:0000704|\n#     852: 852\tFlyBase:FBgn0004636|Rap1|biolink:NamedThing|biolink:GenomicEntity|biolink:Gene|Rap1 GTPase||ncbigene|panther|flybase|go|BEST:GH18528|CG1956|C-ras3|DRap|D-Rap1|DRap1|Dras3|Dras62B|EC3-7|E(faf)|Enhancer of faf|FCG-C|l(3)62Bf|l(3)R|P08645|R|Rap|rap1|RAP1|ras 3|ras3|Ras3|RasIII|roughened|Roughened||True||||||||||NCBITaxon:7227|NCBITaxon:7227||||||||||SO:0000704|owl:Class|SO:0000704|\n#     853: 853\tFlyBase:FBgn0004638|drk|biolink:NamedThing|biolink:GenomicEntity|biolink:Gene|downstream of receptor kinase||ncbigene|panther|flybase|go|24/1|CG6033|crkl|Downstream of receptor kinase|downstream of receptor kinases|downstream receptor kinase|Drk|DRK|Drk/Grb2|Enhancer of sevenless-2B|E(sev)2B|Grb-2|Grb2|GRB2|Grb2/drk|Grb/drk|l(2)10626|l(2)k13809|P1112|Su(sev)R1||True||||||||||NCBITaxon:7227|NCBITaxon:7227||||||||||SO:0000704|owl:Class|SO:0000704|\n# \n# The numbering appears corrupted due to a spurious CR character on line 851.\n#\n# Note that there really is a line 851 there, but if the output reaches the screen\n# as shown above, most terminals will overwrite it.\n# \n# Pipe the file through this script to remedy: \n#\n# cat medikanren2/data/sri-reference/0.3.0/upstream/sri-reference-kg-0.3.0_nodes.tsv \\\n#   | perl util/data-import/remove_cr.pl \\\n#   > medikanren2/data/sri-reference/0.3.0/upstream/sri-reference-kg-0.3.0_nodes_nocr.tsv \n\nbinmode(STDOUT);\nwhile($_ = <>) {\n    $a=$_; \n    $a =~ s/\\x0d//g; \n    print \"$a\";\n}\n"
  },
  {
    "path": "medikanren2/util/storage-size-workaround/s-cerevisiae-kg-ref-ll.py",
    "content": "\nimport os\n\nrfile_nodes = \"medikanren2/data/sri-reference/0.3.0/upstream/sri-reference-kg-0.3.0_nodes_nocr.tsv\"\nrfile_edges = \"medikanren2/data/sri-reference/0.3.0/upstream/sri-reference-kg-0.3.0_edges_nocr.tsv\"\n# When used as configured, requires ~9GB RAM (\"RES = Resident Size\" in top)\n\nconfigs = {\n    'small': {\n        'level_max': 4,\n        'rel_blacklist':{\n            \"biolink:related_to\":1,\n            \"biolink:actively_involved_in\":1,\n            \"biolink:enables\":1,\n            \"biolink:part_of\":1\n        },\n        'prefix_output': 'medikanren2/data/yeast-sri-reference/0.3.0b/simulation-of-upstream'\n    },\n    'micro': {\n        'level_max': 0,\n        'rel_blacklist':{\n            \"biolink:related_to\":1,\n            \"biolink:actively_involved_in\":1,\n            \"biolink:enables\":1,\n            \"biolink:part_of\":1\n        },\n        'prefix_output': 'medikanren2/data/yeast-micro-sri-reference/0.3.0/simulation-of-upstream'\n    }\n}\n\nkconfig='small'\ndo_write = True\n\nlevel_max = configs[kconfig]['level_max']\nrel_blacklist = configs[kconfig]['rel_blacklist']\nprefix_output = configs[kconfig]['prefix_output']\n\ndef dictappend(d,k,v):\n    if not k in d:\n        d[k]=[v]\n    else:\n        vs=d[k]\n        vs.append(v)\n        d[k]=vs\n\nnodes = {}\n\nedges_fw = {}\nedges_rev = {}\n\ncNodes=0\nwith open(rfile_nodes) as fin: \n    iline=0\n    for line in fin:\n        iline += 1\n        if iline == 1:\n            continue # skip header\n        cNodes += 1\n        xs = line.split(\"\\t\")\n        nodeid = xs[0]\n        if nodeid.startswith(\"SGD\"):\n            node = 0\n            nodes[nodeid]=node\n\nprint(\"{} of {} nodes are SGD\".format(len(nodes), cNodes))\n\nwith open(rfile_edges) as fin: \n    iline=0\n    for line in fin:\n        iline += 1\n        if iline == 1:\n            continue # skip header\n        xs = line.split(\"\\t\")\n        srcid = xs[1]\n        destid = xs[3]\n        rel = xs[2]\n        if not rel in rel_blacklist:\n            dictappend(edges_fw, srcid, (destid, rel))\n            dictappend(edges_rev, destid, (srcid, rel))\n\n\ncFw=0\ncRev=0\nfor level in range(0,level_max+1):\n    print(\"SGD level {} has {} nodes ({} found searching forward, {} found searching reverse)\".format(level, len(nodes), cFw, cRev))\n    cFw=0\n    cRev=0\n    if level < level_max:\n        for nodeid1 in list(nodes.keys()):\n            for edge in edges_fw[nodeid1] if nodeid1 in edges_fw else []:\n                nodeid2 = edge[0]\n                if not (nodeid2 in nodes):\n                    nodes[nodeid2] = level\n                    cFw += 1\n                    # if (cFw % 1024) == 0:\n                    #     print(\"cFw={} rel={}\".format(cFw, edge[1]))\n            for edge in edges_rev[nodeid1] if nodeid1 in edges_rev else []:\n                nodeid2 = edge[0]\n                if not (nodeid2 in nodes):\n                    nodes[nodeid2] = level\n                    cRev += 1\n                    # if (cRev % 1024) == 0:\n                    #     print(\"cRev={} rel={}\".format(cRev, edge[1]))\n\ndef path_prefix(prefix,rfile):\n    return os.path.join(prefix, os.path.basename(rfile))\n\nif do_write:\n    os.makedirs(prefix_output, exist_ok=True)\n    with open(rfile_nodes) as fin: \n        with open(path_prefix(prefix_output, rfile_nodes), \"w\") as fout:\n            fout.seek(0)\n            fout.truncate()\n            iline=0\n            for line in fin:\n                iline += 1\n                if iline == 1:\n                    fout.write(line)\n                else:\n                    cNodes += 1\n                    xs = line.split(\"\\t\")\n                    nodeid = xs[0]\n                    if nodeid in nodes:\n                        fout.write(line)\n\n    with open(rfile_edges) as fin: \n        with open(path_prefix(prefix_output, rfile_edges), \"w\") as fout:\n            fout.seek(0)\n            fout.truncate()\n            iline=0\n            for line in fin:\n                iline += 1\n                if iline == 1:\n                    fout.write(line)\n                else:\n                    xs = line.split(\"\\t\")\n                    srcid = xs[1]\n                    destid = xs[3]\n                    rel = xs[2]\n                    if srcid in nodes and destid in nodes:\n                        fout.write(line)\n\n\n\n"
  },
  {
    "path": "stuff/cmd-helpers.rkt",
    "content": "#lang racket\n(provide\n adir-temp\n with-adir-temp-root\n sha1sum\n dry-run\n run-cmds\n dry-runify)\n(require \"run-shell-pipelines.rkt\")\n\n;;;; begin racket parameters\n(define adir-temp \n  (make-parameter \n   'adir-temp-placeholder))\n\n(define (with-adir-temp-root thunk-run)\n  (let ((adir (path->string (make-temporary-file \"medikanren_~a\" 'directory #f))))\n    (dynamic-wind\n      (lambda ()\n        #f)\n      (lambda ()\n        (parameterize ([adir-temp adir]) (thunk-run)))\n      (lambda ()\n        #f\n        (delete-directory/files adir)\n        ))))\n\n(define dry-run\n  (make-parameter #t))\n\n(define verbose\n  (make-parameter #t))\n\n;;;; end racket parameters\n\n(define (run-cmds cmds)\n  (when (or (dry-run) (verbose))\n    (displayln cmds))\n  (when (not (dry-run))\n    (run-pipelines cmds)))\n#|  (if (dry-run)\n(displayln cmds)\n(run-pipelines cmds)))\n|#\n\n(define (dry-runify thunk name)\n  (lambda args\n    (when (or (dry-run) (verbose))\n      (displayln (cons name args))\n      (flush-output))\n    (when (not (dry-run))\n      (apply thunk args))))\n#|\n(if (dry-run)\n    (displayln (cons name args))\n    (apply thunk args))))\n|#\n\n(define (sha1sum afile)\n  (run-cmds\n    `(((#:out) ()\n              (\"sha1sum\" ,afile)\n              (\"head\" \"-c40\")\n              ))))\n\n"
  },
  {
    "path": "stuff/install-data-files.rkt",
    "content": "#!/usr/bin/env racket\n#lang racket\n;;(require racket)\n(require racket/cmdline)\n(require yaml)\n(require shell/pipeline)\n(require net/url-string)\n(require \"run-shell-pipelines.rkt\")\n(require (prefix-in cmd: \"cmd-helpers.rkt\"))\n(require \"symlink-tree.rkt\")\n(require racket/pretty)\n(require chk)\n\n;; logging approach 1: Actually try to make a log receiver and make it work.  AFAICT\n;;   involves creating a thread, configuring flushing, etc.  Probably better, but complicated.\n;; logging approach 2: KISS but abuse the API.\n;;\n;; This is approach 2:\n(define (log-warning . args)\n  (apply displayln args)\n  (flush-output))\n\n;; *** generic utilities ***\n\n(define (with-finally thunk-cleanup thunk-run)\n  (dynamic-wind\n    (lambda () #f)\n    thunk-run\n    thunk-cleanup))\n\n;; *** application configuration ***\n\n(define afile-yaml (make-parameter #f))\n(define uri-yaml (make-parameter #f))\n(define uri-remote-archive (make-parameter #f))\n(define adir-local-archive (make-parameter #f))\n(define adir-storage (make-parameter #f))\n(define adir-install (make-parameter #f))\n(define adir-data-dir (make-parameter #f))\n(define do-config-scm (make-parameter #f))\n(define delete-data-cache (make-parameter #f))\n(define omit-aws-workaround (make-parameter #f))\n(define config-ardbs (make-parameter #f))     ; mutable\n(define config-adir-temp (make-parameter #f)) ; mutable\n\n;;; Mnemonic: \"ARchive of DataBase\"\n(struct ardb \n  (\n   kgid\n   versionOfKg\n   configkey             ; For --write-config-scm.  Leave configkey blank\n   ; to prevent the ardb from adding to config.scm.\n   reldir\n   isUpstream\n   sha1sum\n   versionOfMedikanren\n   filename\n   format\n   ) #:transparent\n  #:name ardb-t\n  #:constructor-name ardb-new\n  )\n\n(define (prefer-string v)\n  (cond\n    ((number? v) (number->string v))\n    (else v)))\n\n;; wow lots of work to have the file be yaml\n(define (construct-ardb node)\n  (define mapping (construct-mapping node))\n  (ardb-new\n   (hash-ref mapping \"kgid\" (lambda () 'null))\n   (prefer-string (hash-ref mapping \"versionOfKg\" (lambda () 'null)))\n   (hash-ref mapping \"configkey\" (lambda () 'null))\n   (hash-ref mapping \"reldir\" (lambda () 'null))\n   (hash-ref mapping \"isUpstream\" (lambda () #f))\n   (hash-ref mapping \"sha1sum\")\n   (hash-ref mapping \"versionOfMedikanren\")\n   (hash-ref mapping \"filename\")\n   (hash-ref mapping \"format\")))\n(define (represent-ardb p)\n  (define mapping (make-hash))\n  (hash-set! mapping \"kgid\" (ardb-kgid p))\n  (hash-set! mapping \"versionOfKg\" (ardb-versionOfKg p))\n  (hash-set! mapping \"configkey\" (ardb-configkey p))\n  (hash-set! mapping \"reldir\" (ardb-reldir p))\n  (hash-set! mapping \"isUpstream\" (ardb-isUpstream p))\n  (hash-set! mapping \"sha1sum\" (ardb-sha1sum p))\n  (hash-set! mapping \"versionOfMedikanren\" (ardb-versionOfMedikanren p))\n  (hash-set! mapping \"filename\" (ardb-filename p))\n  (hash-set! mapping \"format\" (ardb-format p))\n  (represent-mapping \"!ardb\" mapping))\n(define ardb-representer\n  (yaml-representer ardb? represent-ardb))\n(define ardb-constructor\n  (yaml-constructor ardb? \"!ardb\" construct-ardb))\n\n(define (ardb->yaml ardb)\n  (parameterize (\n                 [yaml-representers (list ardb-representer)]\n                 [yaml-constructors (list ardb-constructor)]\n                 )\n    (yaml->string ardb)))\n\n(define (styaml->ardbs styaml)\n  (parameterize (\n                 [yaml-representers (list ardb-representer)]\n                 [yaml-constructors (list ardb-constructor)]\n                 )\n    (string->yaml* styaml #:allow-undefined? #t)))\n\n(define (yamlfile->ardbs absfile)\n  (parameterize (\n                 [yaml-representers (list ardb-representer)]\n                 [yaml-constructors (list ardb-constructor)]\n                 )\n    (append-map (lambda (x) x)\n      (file->yaml* absfile))))\n\n(define (sturl-dirname sturl)\n  (define url1 (string->url sturl))\n  (define path1 (url-path url1))\n  (define path2 (take path1 (- (length path1) 1)))\n  (url->string (struct-copy url url1 (path path2))))\n\n(define (implicit-uri-remote?)\n  (and (not (uri-remote-archive))\n          (uri-yaml)))\n\n(define (uri-remote)\n  (if (implicit-uri-remote?)\n    (sturl-dirname (uri-yaml))\n    (uri-remote-archive)))\n\n(define (yamluri->ardbs uri-yaml)\n  (define afile-yaml-temp (path->string (build-path (string->path (config-adir-temp)) \"tmp.yaml\")))\n  (parameterize\n      ((cmd:dry-run #f))\n    (cmd:run-cmds\n    `(((#:out) () (,@(prefix-for-aws-workaround)\n              \"aws\" \"s3\" \"cp\" \"--quiet\"\n              ,uri-yaml\n              ,afile-yaml-temp\n              ))))\n    (yamlfile->ardbs afile-yaml-temp)))\n\n(define (dataconfig)\n  (cond\n    ((afile-yaml) (yamlfile->ardbs (afile-yaml)))\n    ((uri-yaml) (yamluri->ardbs (uri-yaml)))\n    (else (error \"internal error\"))))\n\n(define (path-ver-from-st v)\n  (match (map string->number (string-split (string-trim v \"v\") \".\"))\n    (`(1 . ,_) \"medikanren1\")\n    (`(2 . ,_) \"medikanren2\")\n    (else (error (format \"unknown versionOfMedikanren: ~a\" v)))))\n\n(define (path-ver ardb)\n  (let ((v (ardb-versionOfMedikanren ardb)))\n    (path-ver-from-st v)))\n\n(define (dir-cat-temp dir-archive ardb)\n  (if (implicit-uri-remote?)\n    (format \"~a/~a\" dir-archive (ardb-filename ardb))\n    (format \"~a/~a/~a\" dir-archive (path-ver ardb)\n            (ardb-filename ardb))))\n\n(define (dir-cat-temp-* dir-archive ardb)\n  (format \"~a*\" (dir-cat-temp dir-archive ardb)))\n\n;; *** commands for extracting, checking, and installing ***\n(define (cmd-to-cat ardb dir-archive)\n  (cond\n    ((member \"split\" (ardb-format ardb))\n     `(\"sh\" \"-c\" ,(format \"cat ~a\" (dir-cat-temp-* dir-archive ardb))))\n    (else `(\"cat\" ,(dir-cat-temp dir-archive ardb)))))\n\n(define (cmds-to-sha1 ardb dir-archive)\n  `(((#:out) ()\n             ,(cmd-to-cat ardb dir-archive)\n             (\"sha1sum\")\n             (\"cut\" \"-c1-40\")\n             )))\n\n(define (dirname afile)\n  (path->string (simplify-path (build-path (string->path afile) 'up))))\n\n(define (cmds-to-extract sha1 ardb dir-archive)\n  (let* ((adir-target (format \"~a/~a\" (adir-storage) sha1))\n         (adir-target-parent (dirname adir-target))\n         (adir-target-temp (format \"~a/~a-temp\" (adir-storage) sha1)))\n    `((() ()\n          (\"rm\" \"-rf\" ,adir-target-temp))\n      (() ()\n          (\"mkdir\" \"-p\" ,adir-target-temp))\n      (() ()\n          ,(cmd-to-cat ardb dir-archive)\n          (\"tar\" \"xzf\" \"-\" \"-C\" ,adir-target-temp)\n          )\n      (() ()\n          (\"mkdir\" \"-p\" ,adir-target-parent))\n      (() ()\n          (\"mv\" ,adir-target-temp ,adir-target)))))\n\n(define (label-sha1-dir sha1 ardb dir-archive)\n  (when (new-format? ardb)\n    (let* ((afile-kgid (build-path (adir-storage) sha1 \"kgid\" (ardb-kgid ardb)))\n          (afile-ver (build-path (adir-storage) sha1 \"ver\" (ardb-versionOfKg ardb))))\n      (make-parent-directory* afile-kgid)\n      (display-to-file \"\" afile-kgid)\n      (make-parent-directory* afile-ver)\n      (display-to-file \"\" afile-ver))))\n\n(define dr-label-sha1-dir (cmd:dry-runify label-sha1-dir 'label-sha1-dir))\n\n(define (reldir-from-ardb ardb)\n  (if (not (new-format? ardb))\n    `(,(ardb-reldir ardb)) ; This is now the only bona fide usage of ardb-reldir\n    (if (ardb-isUpstream ardb)\n      `(\"upstream\" ,(ardb-kgid ardb) ,(ardb-versionOfKg ardb))\n      `(,(ardb-kgid ardb) ,(ardb-versionOfKg ardb)))))\n\n(define (append-path path patels)\n  (apply build-path (cons path patels)))\n\n(define (do-symlink-impl path-src path-dest)\n  (make-directory* path-dest)\n  (make-directory* path-src)\n  (symlink-tree path-src path-dest))\n\n(define dr-do-symlink-impl (cmd:dry-runify do-symlink-impl 'do-symlink))\n\n(define (do-symlink sha1 ardb)\n  (printf \"*** entering do-symlink\\n\")\n  (printf \"*** sha1: ~s\\n\" sha1)\n  (printf \"*** ardb: ~s\\n\" ardb)\n  ;;\n  (printf \"*** (ardb-kgid ardb): ~s\\n\" (ardb-kgid ardb))\n  (printf \"*** (ardb-versionOfKg ardb): ~s\\n\" (ardb-versionOfKg ardb))\n  (printf \"*** (ardb-configkey ardb): ~s\\n\" (ardb-configkey ardb))\n  (printf \"*** (ardb-reldir ardb): ~s\\n\" (ardb-reldir ardb))\n  (printf \"*** (ardb-isUpstream ardb): ~s\\n\" (ardb-isUpstream ardb))\n  (printf \"*** (ardb-versionOfMedikanren ardb): ~s\\n\" (ardb-versionOfMedikanren ardb))\n  (printf \"*** (ardb-filename ardb): ~s\\n\" (ardb-filename ardb))\n  (printf \"*** (ardb-format ardb): ~s\\n\" (ardb-format ardb))\n  ;;\n  (printf \"*** (adir-local-archive): ~s\\n\" (adir-local-archive))\n  (printf \"*** (adir-storage): ~s\\n\" (adir-storage))\n  ;;\n  (printf \"*** (adir-data-dir): ~s\\n\" (adir-data-dir))\n  (printf \"*** (adir-install): ~s\\n\" (adir-install))\n  (printf \"*** (path-ver ardb): ~s\\n\" (path-ver ardb))\n  (let ((data-dir (if (adir-data-dir) (adir-data-dir) \"data\")))\n    (printf \"*** data-dir: ~s\\n\" data-dir)\n    (let* ((path-dest (append-path (build-path (adir-install) (path-ver ardb) data-dir)\n                                   (reldir-from-ardb ardb)))\n           (_ (printf \"*** path-dest: ~s\\n\" path-dest))\n           (path-src (build-path (adir-storage) sha1 (ardb-kgid ardb) (ardb-versionOfKg ardb)))\n           (_ (printf \"*** path-src: ~s\\n\" path-src)))\n      (printf \"calling dr-do-symlink-impl:\\n\")\n      (printf \"~s\\n\\n\" `(dr-do-symlink-impl ,path-src ,path-dest))\n      (dr-do-symlink-impl path-src path-dest))))\n\n(define (ardb-already-installed? ardb)\n  ;; cmds-to-extract owns adir-ardb-storage and writes atomically.  Manual\n  ;; manipulation of adir-storage is not supported.  Therefore,\n  ;; if we find that adir-ardb-storage already exists, it must have been\n  ;; the byproduct of a previous successful sha1 verification and install.\n  ;; Therefore, we may \"short circuit\" by not repeating the installation.\n  ;; Instead, we run an echo command to signal to the user.\n  (let* ((adir (path->string (build-path (adir-storage) (ardb-sha1sum ardb)))))\n    (directory-exists? adir)))\n\n(define (cmds-echo-already-installed ardb)\n  (let* ((adir (path->string (build-path (adir-storage) (ardb-sha1sum ardb)))))\n    `((() () (\"echo\" ,adir \" appears to be already installed, skipping\")))))\n\n(define (run-check-extract-link dir-archive)\n  (for ((ardb (config-ardbs)))\n    (let* ((sha1-expected (ardb-sha1sum ardb)))\n      (cond \n        ((ardb-already-installed? ardb)\n         (begin\n           (cmd:run-cmds (cmds-echo-already-installed ardb))\n           (do-symlink sha1-expected ardb)))\n        ((cmd:dry-run)\n         (let ((sha1 (ardb-sha1sum ardb)))\n           (cmd:run-cmds (cmds-to-extract sha1-expected ardb dir-archive))\n           (do-symlink sha1-expected ardb)))\n        (else\n         (let ((sha1 (string-trim\n                      #:left? #f\n                      (cmd:run-cmds (cmds-to-sha1 ardb dir-archive)))))\n           (if (equal? sha1 sha1-expected)\n               (begin\n                 (cmd:run-cmds (cmds-to-extract sha1 ardb dir-archive))\n                 (dr-label-sha1-dir sha1 ardb dir-archive)\n                 (do-symlink sha1 ardb))\n               (error (format \"sha1 ~a != expected ~a\" sha1 sha1-expected)))))))))\n\n;; *** commands for syncing from a remote source ***\n(define (include-for-sync ardb)\n  (if (ardb-already-installed? ardb)\n      '()\n      (if (implicit-uri-remote?)\n        `(\"--include\" ,(format \"*~a*\" (ardb-filename ardb)))\n        `(\"--include\" ,(format \"*~a/~a*\" (path-ver ardb) (ardb-filename ardb))))))\n\n(define (includes-for-sync)\n  (append-map (lambda (ardb) (include-for-sync ardb)) (config-ardbs)))\n\n(define (prefix-for-aws-workaround)\n  (if (omit-aws-workaround)\n    '()\n    '(\"env\" \"AWS_EC2_METADATA_DISABLED=true\")\n        ;; fix: \"\"\n        ;; https://github.com/aws/aws-cli/issues/5262\n  ))\n\n;; interpret --write-config-scm to indicate unattended installation, otherwise show progress for the user\n(define (verbosity-options)\n  (if (do-config-scm)\n    '(\"--quiet\")\n    '()))\n\n(define (cmds-to-sync)\n  `((() () (,@(prefix-for-aws-workaround)\n            \"aws\" \"s3\" \"sync\" ,@(verbosity-options)\n            \"--exclude\" \"*\"\n            ,@(includes-for-sync)\n            ,(uri-remote)\n            ,(config-adir-temp)\n            ))))\n\n(define (path-remove-wildcards path)\n  (let* ((path1 (string-replace path \"*\" \"\" #:all? #t)))\n    (string-replace path1 \"?\" \"\" #:all? #t)))\n\n(define (cmds-rm-r absd)\n  `((() () (\"rm\" \"-rf\" ,(path-remove-wildcards absd)))))\n\n;;; TEMPORARY: migrated-to-new-db-versioning\n;;; BEGIN functions that do compatibility between the new kgid based config keys and the\n;;; older configkey field.\n\n(define (new-format? ardb)\n  (cond\n    ((equal? (ardb-kgid ardb) 'null) #f)\n    ((equal? (ardb-versionOfKg ardb) 'null) #f)\n    (else #t)))\n\n(define (get-configkey ardb)\n  (cond\n    ((not (ardb-configkey ardb)) #f)\n    ((eq? (ardb-configkey ardb) 'null) #f)\n    ((new-format? ardb) (ardb-kgid ardb))\n    (else (ardb-configkey ardb))))\n\n(define (idver-from-ardb ardb)\n  (if (new-format? ardb)\n    (values (ardb-kgid ardb) (ardb-versionOfKg ardb))\n    (values #f #f)))\n\n;;; END compatibility\n\n(define (gen-config-scm ver ardbs)\n  (let* (\n         (ardbs1\n          (filter\n           (lambda (ardb) (string-prefix? (ardb-versionOfMedikanren ardb) ver))\n           ardbs)))\n    `((databases ,@(append-map (lambda (ardb)\n                                 (if (get-configkey ardb) (list (string->symbol (get-configkey ardb))) '()))\n                               ardbs1)))))\n\n;; *** commands to automatically populate config.scm ***\n(define (write-config-scm ver)\n  (define cfg (gen-config-scm ver (config-ardbs)))\n  (pretty-write `((generated-config-scm . ,cfg)))\n  (unless (cmd:dry-run)\n    (let* (\n          (absf (format \"~a/~a/etc/config.scm\" (adir-install) (path-ver-from-st ver)))\n          (_ (make-parent-directory* absf))\n          (fout1 (open-output-file absf #:exists 'replace)))\n      (writeln cfg fout1)\n      (close-output-port fout1))))\n\n(define (write-configs-scm)\n  (write-config-scm \"v1.\")\n  (write-config-scm \"v2.\"))\n\n(define (update-vfd vfd ardbs)\n  (if (null? ardbs)\n    vfd\n    (let-values (((id ver) (idver-from-ardb (car ardbs))))\n      (update-vfd\n        (if id\n          (dict-set vfd (string->symbol id) (string->symbol ver))\n          vfd)\n        (cdr ardbs)))))\n\n(define (rewrite-config-installer-scm)\n  (let* ((ver \"v2.\")\n         (absf (format \"~a/~a/etc/config.installer.scm\" (adir-install) (path-ver-from-st ver)))\n         (_ (make-parent-directory* absf))\n         (fin1 (if (file-exists? absf) (open-input-file absf) (open-input-string \"()\")))\n         (h (read fin1))\n         (vfd (dict-ref h 'version-for-database '()))\n         (vfd2 (update-vfd vfd (config-ardbs)))\n         (h3 (dict-set h 'version-for-database vfd2)))\n    (if (cmd:dry-run)\n      (begin\n        (pretty-write `((rewrite-config-installer-scm . ,h)))\n        (newline))\n      (let ((fout1 (open-output-file absf #:exists 'replace)))\n        (pretty-write `((rewrite-config-installer-scm . ,h3)))\n        (pretty-write h3 fout1)\n        (newline fout1)\n        (close-output-port fout1)))))\n\n(define (cmds-delete-data-cache)\n  `((() ()\n        (\"rm\" \"-rf\" ,(adir-storage)))))\n\n;; *** main program ***\n(define (validate-env )\n  (define s3-id (getenv \"ncats_s3_id\"))\n  (define s3-secret (getenv \"ncats_s3_secret\"))\n\n  (unless s3-id (log-warning \"environment variable ncats_s3_id is missing.  awscli may be confused.\"))\n  (unless s3-secret (log-warning \"environment variable ncats_s3_secret is missing.  awscli may be confused.\")))\n\n(define (setup-teardown-run-install)\n  (validate-env)\n  (cmd:run-cmds (cmds-to-sync))\n  (run-check-extract-link (config-adir-temp)))\n\n;; TODO: inline\n(define (run-from-local-archive)\n  (run-check-extract-link (adir-local-archive)))\n\n(define (run-main)\n  (cmd:with-adir-temp-root\n    (lambda ()\n      (run-main-impl))))\n\n(define (run-main-impl)\n  (cond\n    ((not (or (afile-yaml) (uri-yaml))) (error \"--dir-root required\"))\n    ((not (adir-install)) (error \"--dir-install required\"))\n    ((not (adir-storage)) (error \"--dir-storage required\"))\n    ((not (or (uri-remote-archive) (implicit-uri-remote?) (adir-local-archive)))\n     (error \"either --uri-remote-archive or --dir-local-archive is required\"))\n    (else\n     (config-adir-temp (cmd:adir-temp)) ; parameter set!\n     (config-ardbs (dataconfig)) ; parameter set!\n     (when (delete-data-cache)\n       (cmd:run-cmds (cmds-delete-data-cache)))\n     (cond\n       ((implicit-uri-remote?) (setup-teardown-run-install))\n       ((uri-remote-archive) (setup-teardown-run-install))\n       ((adir-local-archive) (run-from-local-archive))\n       (else (error \"Nothing to do.  Pass --help for usage.\")))\n     (when (do-config-scm)\n       (write-configs-scm))\n     (rewrite-config-installer-scm)\n     )))\n\n;; *** CLI parsing ***\n(define (parse-configuration)\n  (cmd:dry-run #f)\n  (command-line\n   #:program \"install-data-files.rkt\"\n   #:usage-help \"install-data-files.rkt \"\n   #:once-each\n   [(\"--file-yaml\") adir\n                    \"The absolute path to a data.yaml file\"\n                    (afile-yaml (string-trim #:left? #f adir))]\n   [(\"--uri-yaml\") adir\n                    \"An S3 URI to a data.yaml file with data accessible at a relative path\"\n                    (uri-yaml (string-trim #:left? #f adir))]\n   [(\"--uri-remote-archive\") uri\n                             \"The base URI of the remote data repository\"\n                             (uri-remote-archive (string-trim #:left? #f uri))]\n   [(\"--dir-local-archive\") adir\n                            \"The base URI of the remote data repository\"\n                            (adir-local-archive (string-trim #:left? #f adir))]\n   [(\"--dir-storage\") adir\n                      \"The base absolute directory for storing data\"\n                      (adir-storage (string-trim #:left? #f adir))]\n   [(\"--dir-install\") adir\n                      \"The base absolute directory for installing data\"\n                      (adir-install (string-trim #:left? #f adir))]\n   [(\"--data-dir\") adir\n                   \"The remainder of the base path to the directory for installing data\"\n                   (adir-data-dir (string-trim #:left? #f adir))]   \n   [(\"--write-config-scm\")\n    \"Generate and overwrite config.scm files for extracted data\"\n    (do-config-scm #t)]\n   [(\"--omit-aws-workaround\")\n    \"Generate and overwrite config.scm files for extracted data\"\n    (omit-aws-workaround #t)]\n   [(\"--delete-data-cache\")\n    \"In case of full disk or invalid state, delete existing cache\"\n    (delete-data-cache #t)]\n   [(\"--dry-run\")\n    \"Print commands to run.  Do not run.\"\n    (cmd:dry-run #t)]\n   #:args ()\n   '())\n   ;\"\"  ; We don't care about the return value because configuration lives in mutatable racket parameters\n  )\n\n(module+ main\n  (parse-configuration)\n  (run-main)\n  )\n\n(module+ test\n  (define ardb-sample (ardb-new \"rtx\" \"1.0-kge\"\n                                \"rtx2-20210204\" \"rtx2\"\n                                \"d56c1a0507b4e2c16f941214576af052f1279500\" \n                                \"v2.0\"\n                                \"rtx2_2021_02_04.tar.gz\"\n                                '()))\n\n  (define (with-config-sample-1 thunk)\n    (uri-remote-archive \"s3://bucket\")\n    (adir-storage \"/path/to/storage\")\n    (adir-install \"/path/to/install\")\n    (config-ardbs (list ardb-sample))\n    (thunk))\n\n  (chk\n   (#:do (ardb->yaml ardb-sample))\n   (#:t #t)\n   )\n  (chk\n   #:=\n   (styaml->ardbs (ardb->yaml ardb-sample))\n   (list ardb-sample)\n   )\n\n  (chk\n   (#:do\n    (define ardb (car (styaml->ardbs\n                       (string-join '(\n                                      \"!ardb\"\n                                      \"sha1sum: d56c1a0507b4e2c16f941214576af052f1279500\"\n                                      \"format: []\"\n                                      \"versionOfMedikanren: v2.0\"\n                                      \"filename: rtx2_2021_02_04.tar.gz\"\n                                      \"kgid: rtx\"\n                                      \"versionOfKg: 1.0-kge\"\n                                      \"reldir: rtx2\")\n                                    \"\\n\"\n                                    )))))\n   (#:= (ardb-configkey ardb) 'null)\n   )\n\n  (chk\n   (#:do\n    (define configscm\n      (gen-config-scm \"v2.\" (car (styaml->ardbs\n                                  (string-join '(\n                                                 \"---\"\n                                                 \"- !ardb\"\n                                                 \"  versionOfMedikanren: v2.\"\n                                                 \"  configkey: yeast-sri-reference\"\n                                                 \"  reldir: nonempty\"\n                                                 \"  sha1sum: nonempty\"\n                                                 \"  size: 0\"\n                                                 \"  filename: nonempty\"\n                                                 \"  kgid: rtx\"\n                                                 \"  versionOfKg: 1.0-kge\"\n                                                 \"  format:\")\n                                               \"\\n\"\n                                               ))))))\n   (#:do (pretty-write configscm))\n   (#:= (length (dict-ref configscm 'databases)) 1)\n   )\n\n  (chk\n   (#:do\n    (define configscm\n      (gen-config-scm \"v2.\" (car (styaml->ardbs\n                                  (string-join '(\n                                                 \"---\"\n                                                 \"- !ardb\"\n                                                 \"  versionOfMedikanren: v2.\"\n                                                 \"  reldir: nonempty\"\n                                                 \"  sha1sum: nonempty\"\n                                                 \"  size: 0\"\n                                                 \"  filename: nonempty\"\n                                                 \"  kgid: rtx\"\n                                                 \"  versionOfKg: 1.0-kge\"\n                                                 \"  format:\")\n                                               \"\\n\"\n                                               ))))))\n   (#:do (pretty-write configscm))\n   (#:= (length (dict-ref configscm 'databases)) 0)\n   )\n\n  (chk\n   (#:do\n    (define configscm\n      (gen-config-scm \"v2.\" (car (styaml->ardbs\n                                  (string-join '(\n                                                 \"---\"\n                                                 \"- !ardb\"\n                                                 \"  versionOfMedikanren: v2.\"\n                                                 \"  configkey:\"\n                                                 \"  reldir: nonempty\"\n                                                 \"  sha1sum: nonempty\"\n                                                 \"  size: 0\"\n                                                 \"  filename: nonempty\"\n                                                 \"  kgid: rtx\"\n                                                 \"  versionOfKg: 1.0-kge\"\n                                                 \"  format:\")\n                                               \"\\n\"\n                                               ))))))\n   (#:do (pretty-write configscm))\n   (#:= (length (dict-ref configscm 'databases)) 0)\n   )\n\n  (chk\n   #:=\n   (with-config-sample-1\n    (lambda ()\n      (config-adir-temp \"/tmp/dir\")\n      (cmds-to-sync)))\n   `((() () (\n             \"env\" \"AWS_EC2_METADATA_DISABLED=true\"\n             \"aws\" \"s3\" \"sync\" \"--quiet\"\n             \"--exclude\" \"*\"\n             \"--include\" \"*medikanren2/rtx2_2021_02_04.tar.gz*\" \n             \"s3://bucket\" \"/tmp/dir\")))\n   )\n\n  (chk\n   #:do (run-pipelines `((() () (\"echo\"))))\n   #t)\n\n  (chk\n   #:do (run-pipelines `((() () (\"echo\" \"-e\"))))\n   #t)\n\n  (chk\n   #:do (with-handlers ((exn:fail? (lambda (ex) #t))) (delete-file \"echo-out.tmp\"))\n   #:do (run-pipelines `(((#:out) (\"echo-out.tmp\") (\"echo\" \"hello\"))))\n   #:t (file-exists? \"echo-out.tmp\"))\n\n  (chk\n   #:do (define fout (open-output-string))\n   #:do (run-pipelines `(((#:out) (,fout) (\"echo\" \"-ne\" \"foo\\\\nbar\\\\n\") (\"sort\"))))\n   #:do (close-output-port fout)\n   #:do (define st (get-output-string fout))\n   #:= st \"bar\\nfoo\\n\")\n\n  (chk\n   #:do (define st (run-pipelines `(((#:out) () (\"echo\" \"-ne\" \"hello\")))))\n   #:= st \"hello\")\n\n  (chk\n   #:do (with-config-sample-1\n    (lambda ()\n      (run-check-extract-link (config-adir-temp))))\n   #:t #t)\n\n  (chk\n   #:= (path-remove-wildcards \"/foo/*bar*\") \"/foo/bar\"\n   #:= (path-remove-wildcards \"/foo/?bar?\") \"/foo/bar\")\n\n  (chk\n    (#:= (dirname \"/foo/bar/baz\")\n      \"/foo/bar/\"))\n\n  (chk\n    (#:= (dirname \"/foo/bar/baz/\")\n      \"/foo/bar/\"))\n  )\n"
  },
  {
    "path": "stuff/run-shell-pipelines.rkt",
    "content": "#lang racket\n(provide \n    run-pipelines\n    report-invalid-pipelines)\n(require shell/pipeline)\n(require chk)\n\n;; shell/pipelines can represent a pipeline step without\n;; running it, via pipeline-member-spec.  However, it seems to\n;; lack ability to represent a whole pipeline without running it.\n;; So as a workaround we'll use a list of lists to be able\n;; to test command generation without running commands.\n\n(define (report-invalid-pipelines pipelines)\n  (for ((pipeline pipelines))\n    (unless (list? pipeline)\n      (error \"pipeline must be a list:\" pipeline))\n    (unless (and (>= (length pipeline) 3) (andmap list? pipeline))\n      (error \"pipeline must contain at least three lists:\" pipeline))\n    (unless (andmap (lambda (cmd) (> (length cmd) 0)) (list-tail pipeline 2))\n      (error \"each command must be nonempty:\" pipeline))))\n\n\n;;; Run a list of prepared pipelines\n(define (run-pipelines pipelines)\n  (report-invalid-pipelines pipelines)\n  (define ret #f)\n  (for* ((pipeline pipelines))\n    (let* (\n           (ks (car pipeline))\n           (vs (cadr pipeline))\n           (fout (if (and\n                      (not (null? ks))\n                      (equal? (last ks) '#:out)\n                      (equal? (- (length ks) 1) (length vs)))\n                     (open-output-string)\n                     #f))\n           (vs (if fout\n                   (append vs (list fout))\n                   vs))\n           (p (keyword-apply run-subprocess-pipeline\n                             ks\n                             vs\n                             (pipeline-member-spec (caddr pipeline))\n                             (map (lambda (cmd) (pipeline-member-spec cmd)) (cdddr pipeline)))))\n      (if (not (equal? 0 (pipeline-status p)))\n          (raise (format \"status ~a attempting to run ~s\" (pipeline-status p) pipeline))\n          (printf \"status ok\\n\"))\n      (when fout (set! ret (get-output-string fout)))))\n  ret)\n\n(module+ test\n  ;; How to run a simple command\n  (chk\n   #:do (run-pipelines `((() () (\"echo\"))))\n   #t)\n\n  ;; How to run a simple command with parameters\n  (chk\n   #:do (run-pipelines `((() () (\"echo\" \"-e\"))))\n   #t)\n\n  ;; How to capture stdout to a file\n  (chk\n   #:do (with-handlers ((exn:fail? (lambda (ex) #t))) (delete-file \"echo-out.tmp\"))\n   #:do (run-pipelines `(((#:out) (\"echo-out.tmp\") (\"echo\" \"hello\"))))\n   #:t (file-exists? \"echo-out.tmp\"))\n\n  ;; How to capture stdout to a port\n  (chk\n   #:do (define fout (open-output-string))\n   #:do (run-pipelines `(((#:out) (,fout) (\"echo\" \"-ne\" \"foo\\\\nbar\\\\n\") (\"sort\"))))\n   #:do (close-output-port fout)\n   #:do (define st (get-output-string fout))\n   #:= st \"bar\\nfoo\\n\")\n\n  ;; How to capture capture stdout to a string\n  (chk\n   #:do (define st (run-pipelines `(((#:out) () (\"echo\" \"-ne\" \"hello\")))))\n   #:= st \"hello\")\n\n  ;; How to source stdin from a port and capture stdout to a string\n  (chk\n   #:do (define fin (open-input-string \"foo\\nbar\\nbaz\\n\"))\n   #:do (define st (string-trim (run-pipelines `(((#:in #:out) (,fin) (\"wc\" \"-l\"))))))\n   #:do (close-input-port fin)\n   #:= st \"3\")\n\n  ;; How to source stdin from a port and capture stdout to a port\n  (chk\n   #:do (define fin (open-input-string \"foo\\nbar\\nbaz\\n\"))\n   #:do (define fout (open-output-string))\n   #:do (run-pipelines `(((#:in #:out) (,fin ,fout) (\"wc\" \"-l\"))))\n   #:do (close-input-port fin)\n   #:do (close-output-port fout)\n   #:do (define st (string-trim (get-output-string fout)))\n   #:= st \"3\"))\n"
  },
  {
    "path": "stuff/symlink-tree.rkt",
    "content": "#lang racket\n(provide\n  symlink-tree)\n(require chk)\n\n(define (redirect path path-src path-dst)\n  (let* ((ep-dst (explode-path path-dst))\n         (len-src (length (explode-path path-src)))\n         (ep-src-tail (list-tail (explode-path path) len-src))\n         (ep (append ep-dst ep-src-tail)))\n    (apply build-path ep)))\n\n\n(define (ensure-directory path)\n  (when (file-exists? path)\n    (delete-file path))\n  (unless (directory-exists? path)\n    (make-directory path)))\n\n(define (symlink-tree path-src path-dst)\n  (unless (directory-exists? path-src)\n    (error \"path-src must be a directory\"))\n  (unless (directory-exists? path-dst)\n    (error \"path-dst must be a directory\"))\n  (for ((path (find-files (lambda (x) #t) path-src)))\n    (let ((path-new (redirect path path-src path-dst)))\n      (cond\n        ((directory-exists? path) (ensure-directory path-new))\n        ((file-exists? path)\n         (begin\n           (when (file-exists? path-new)\n             (delete-file path-new))\n           (when (directory-exists? path-new)\n             (error \"not implemented: directory must be replaced by file\"))\n           (make-file-or-directory-link path path-new)))))))\n\n(chk\n (#:=\n  (path->string\n   (redirect\n    (build-path \"/src/foo/bar\")\n    (build-path \"/src\")\n    (build-path \"/dst\")))\n  \"/dst/foo/bar\"))\n\n(define (prepare-test path-0)\n  (make-directory path-0)\n  (make-directory (build-path path-0 \"src\"))\n  (make-directory (build-path path-0 \"src\" \"foo\"))\n  (display-to-file \"\" (build-path path-0 \"src\" \"foo\" \"bar\"))\n  (make-directory (build-path path-0 \"dst\"))\n  (list (build-path path-0 \"src\") (build-path path-0 \"dst\")))\n\n(chk\n (#:do (define path-tmp1 (build-path (current-directory) \"tmp1\")))\n (#:do (define paths (prepare-test path-tmp1)))\n (#:do (define path-src (list-ref paths 0)))\n (#:do (define path-dst (list-ref paths 1)))\n (#:do (symlink-tree path-src path-dst))\n (#:t (link-exists? (build-path path-tmp1 \"dst\" \"foo\" \"bar\")))\n (#:=\n  (resolve-path (build-path path-tmp1 \"dst\" \"foo\" \"bar\"))\n  (build-path path-tmp1 \"src\" \"foo\" \"bar\"))\n (#:do (delete-directory/files path-tmp1)))\n"
  },
  {
    "path": "trace-pathways-by-tissue-type.rkt",
    "content": "#lang racket\n(require \"query.rkt\")\n\n(define gene-list (list->set '(\"ENSEMBL:ENSG00000167972\"\n                               \"ENSEMBL:ENSG00000198691\"\n                               \"ENSEMBL:ENSG00000175164\"\n                               \"ENSEMBL:ENSG00000278540\"\n                               \"ENSEMBL:ENSG00000100412\"\n                               \"ENSEMBL:ENSG00000162104\"\n                               \"ENSEMBL:ENSG00000204305\"\n                               \"ENSEMBL:ENSG00000135744\"\n                               \"ENSEMBL:ENSG00000144891\"\n                               \"ENSEMBL:ENSG00000180772\"\n                               \"ENSEMBL:ENSG00000142208\"\n                               \"ENSEMBL:ENSG00000148218\"\n                               \"ENSEMBL:ENSG00000163631\"\n                               \"ENSEMBL:ENSG00000085662\"\n                               \"ENSEMBL:ENSG00000154188\"\n                               \"ENSEMBL:ENSG00000091879\"\n                               \"ENSEMBL:ENSG00000182718\"\n                               \"ENSEMBL:ENSG00000134982\"\n                               \"ENSEMBL:ENSG00000132703\"\n                               \"ENSEMBL:ENSG00000023445\"\n                               \"ENSEMBL:ENSG00000142515\"\n                               \"ENSEMBL:ENSG00000026103\"\n                               \"ENSEMBL:ENSG00000117560\"\n                               \"ENSEMBL:ENSG00000240583\"\n                               \"ENSEMBL:ENSG00000161798\"\n                               \"ENSEMBL:ENSG00000006756\"\n                               \"ENSEMBL:ENSG00000117601\"\n                               \"ENSEMBL:ENSG00000149311\"\n                               \"ENSEMBL:ENSG00000164904\"\n                               \"ENSEMBL:ENSG00000171791\"\n                               \"ENSEMBL:ENSG00000101144\"\n                               \"ENSEMBL:ENSG00000010671\"\n                               \"ENSEMBL:ENSG00000100300\"\n                               \"ENSEMBL:ENSG00000149131\"\n                               \"ENSEMBL:ENSG00000171860\"\n                               \"ENSEMBL:ENSG00000106804\"\n                               \"ENSEMBL:ENSG00000197405\"\n                               \"ENSEMBL:ENSG00000149823\"\n                               \"ENSEMBL:ENSG00000063180\"\n                               \"ENSEMBL:ENSG00000164305\"\n                               \"ENSEMBL:ENSG00000121691\"\n                               \"ENSEMBL:ENSG00000105974\"\n                               \"ENSEMBL:ENSG00000124813\"\n                               \"ENSEMBL:ENSG00000149257\"\n                               \"ENSEMBL:ENSG00000134057\"\n                               \"ENSEMBL:ENSG00000170458\"\n                               \"ENSEMBL:ENSG00000121594\"\n                               \"ENSEMBL:ENSG00000101017\"\n                               \"ENSEMBL:ENSG00000102245\"\n                               \"ENSEMBL:ENSG00000026508\"\n                               \"ENSEMBL:ENSG00000085063\"\n                               \"ENSEMBL:ENSG00000129226\"\n                               \"ENSEMBL:ENSG00000179776\"\n                               \"ENSEMBL:ENSG00000100526\"\n                               \"ENSEMBL:ENSG00000170835\"\n                               \"ENSEMBL:ENSG00000001626\"\n                               \"ENSEMBL:ENSG00000133019\"\n                               \"ENSEMBL:ENSG00000196811\"\n                               \"ENSEMBL:ENSG00000099622\"\n                               \"ENSEMBL:ENSG00000122705\"\n                               \"ENSEMBL:ENSG00000183813\"\n                               \"ENSEMBL:ENSG00000188153\"\n                               \"ENSEMBL:ENSG00000115966\"\n                               \"ENSEMBL:ENSG00000167193\"\n                               \"ENSEMBL:ENSG00000132693\"\n                               \"ENSEMBL:ENSG00000118231\"\n                               \"ENSEMBL:ENSG00000112062\"\n                               \"ENSEMBL:ENSG00000101439\"\n                               \"ENSEMBL:ENSG00000118523\"\n                               \"ENSEMBL:ENSG00000168036\"\n                               \"ENSEMBL:ENSG00000100448\"\n                               \"ENSEMBL:ENSG00000166347\"\n                               \"ENSEMBL:ENSG00000140465\"\n                               \"ENSEMBL:ENSG00000140505\"\n                               \"ENSEMBL:ENSG00000138061\"\n                               \"ENSEMBL:ENSG00000160870\"\n                               \"ENSEMBL:ENSG00000106258\"\n                               \"ENSEMBL:ENSG00000196730\"\n                               \"ENSEMBL:ENSG00000011465\"\n                               \"ENSEMBL:ENSG00000159640\"\n                               \"ENSEMBL:ENSG00000164825\"\n                               \"ENSEMBL:ENSG00000197766\"\n                               \"ENSEMBL:ENSG00000181019\"\n                               \"ENSEMBL:ENSG00000213918\"\n                               \"ENSEMBL:ENSG00000197635\"\n                               \"ENSEMBL:ENSG00000164330\"\n                               \"ENSEMBL:ENSG00000213694\"\n                               \"ENSEMBL:ENSG00000078401\"\n                               \"ENSEMBL:ENSG00000138798\"\n                               \"ENSEMBL:ENSG00000197561\"\n                               \"ENSEMBL:ENSG00000021355\"\n                               \"ENSEMBL:ENSG00000066044\"\n                               \"ENSEMBL:ENSG00000116016\"\n                               \"ENSEMBL:ENSG00000133216\"\n                               \"ENSEMBL:ENSG00000120915\"\n                               \"ENSEMBL:ENSG00000130427\"\n                               \"ENSEMBL:ENSG00000157554\"\n                               \"ENSEMBL:ENSG00000157557\"\n                               \"ENSEMBL:ENSG00000180210\"\n                               \"ENSEMBL:ENSG00000117525\"\n                               \"ENSEMBL:ENSG00000198734\"\n                               \"ENSEMBL:ENSG00000117480\"\n                               \"ENSEMBL:ENSG00000166147\"\n                               \"ENSEMBL:ENSG00000151422\"\n                               \"ENSEMBL:ENSG00000140285\"\n                               \"ENSEMBL:ENSG00000160867\"\n                               \"ENSEMBL:ENSG00000111206\"\n                               \"ENSEMBL:ENSG00000115414\"\n                               \"ENSEMBL:ENSG00000170345\"\n                               \"ENSEMBL:ENSG00000154727\"\n                               \"ENSEMBL:ENSG00000163288\"\n                               \"ENSEMBL:ENSG00000128683\"\n                               \"ENSEMBL:ENSG00000141448\"\n                               \"ENSEMBL:ENSG00000168621\"\n                               \"ENSEMBL:ENSG00000134812\"\n                               \"ENSEMBL:ENSG00000265107\"\n                               \"ENSEMBL:ENSG00000173221\"\n                               \"ENSEMBL:ENSG00000147437\"\n                               \"ENSEMBL:ENSG00000186810\"\n                               \"ENSEMBL:ENSG00000167701\"\n                               \"ENSEMBL:ENSG00000113580\"\n                               \"ENSEMBL:ENSG00000082701\"\n                               \"ENSEMBL:ENSG00000132518\"\n                               \"ENSEMBL:ENSG00000145649\"\n                               \"ENSEMBL:ENSG00000100453\"\n                               \"ENSEMBL:ENSG00000148702\"\n                               \"ENSEMBL:ENSG00000084754\"\n                               \"ENSEMBL:ENSG00000019991\"\n                               \"ENSEMBL:ENSG00000100644\"\n                               \"ENSEMBL:ENSG00000189403\"\n                               \"ENSEMBL:ENSG00000100292\"\n                               \"ENSEMBL:ENSG00000125798\"\n                               \"ENSEMBL:ENSG00000135486\"\n                               \"ENSEMBL:ENSG00000257017\"\n                               \"ENSEMBL:ENSG00000113905\"\n                               \"ENSEMBL:ENSG00000176387\"\n                               \"ENSEMBL:ENSG00000204389\"\n                               \"ENSEMBL:ENSG00000204388\"\n                               \"ENSEMBL:ENSG00000170606\"\n                               \"ENSEMBL:ENSG00000070614\"\n                               \"ENSEMBL:ENSG00000041982\"\n                               \"ENSEMBL:ENSG00000090339\"\n                               \"ENSEMBL:ENSG00000185745\"\n                               \"ENSEMBL:ENSG00000171855\"\n                               \"ENSEMBL:ENSG00000111537\"\n                               \"ENSEMBL:ENSG00000006652\"\n                               \"ENSEMBL:ENSG00000017427\"\n                               \"ENSEMBL:ENSG00000146674\"\n                               \"ENSEMBL:ENSG00000167779\"\n                               \"ENSEMBL:ENSG00000104365\"\n                               \"ENSEMBL:ENSG00000115008\"\n                               \"ENSEMBL:ENSG00000125538\"\n                               \"ENSEMBL:ENSG00000115594\"\n                               \"ENSEMBL:ENSG00000136689\"\n                               \"ENSEMBL:ENSG00000109471\"\n                               \"ENSEMBL:ENSG00000134460\"\n                               \"ENSEMBL:ENSG00000113520\"\n                               \"ENSEMBL:ENSG00000136244\"\n                               \"ENSEMBL:ENSG00000168685\"\n                               \"ENSEMBL:ENSG00000169429\"\n                               \"ENSEMBL:ENSG00000136634\"\n                               \"ENSEMBL:ENSG00000169194\"\n                               \"ENSEMBL:ENSG00000112115\"\n                               \"ENSEMBL:ENSG00000150782\"\n                               \"ENSEMBL:ENSG00000169245\"\n                               \"ENSEMBL:ENSG00000125347\"\n                               \"ENSEMBL:ENSG00000005884\"\n                               \"ENSEMBL:ENSG00000169896\"\n                               \"ENSEMBL:ENSG00000160255\"\n                               \"ENSEMBL:ENSG00000115474\"\n                               \"ENSEMBL:ENSG00000128052\"\n                               \"ENSEMBL:ENSG00000171345\"\n                               \"ENSEMBL:ENSG00000172037\"\n                               \"ENSEMBL:ENSG00000148346\"\n                               \"ENSEMBL:ENSG00000115850\"\n                               \"ENSEMBL:ENSG00000131981\"\n                               \"ENSEMBL:ENSG00000138039\"\n                               \"ENSEMBL:ENSG00000105370\"\n                               \"ENSEMBL:ENSG00000226979\"\n                               \"ENSEMBL:ENSG00000160932\"\n                               \"ENSEMBL:ENSG00000183918\"\n                               \"ENSEMBL:ENSG00000277443\"\n                               \"ENSEMBL:ENSG00000166949\"\n                               \"ENSEMBL:ENSG00000165471\"\n                               \"ENSEMBL:ENSG00000143384\"\n                               \"ENSEMBL:ENSG00000014641\"\n                               \"ENSEMBL:ENSG00000110492\"\n                               \"ENSEMBL:ENSG00000095015\"\n                               \"ENSEMBL:ENSG00000240972\"\n                               \"ENSEMBL:ENSG00000138755\"\n                               \"ENSEMBL:ENSG00000087245\"\n                               \"ENSEMBL:ENSG00000149968\"\n                               \"ENSEMBL:ENSG00000100985\"\n                               \"ENSEMBL:ENSG00000005381\"\n                               \"ENSEMBL:ENSG00000130830\"\n                               \"ENSEMBL:ENSG00000125148\"\n                               \"ENSEMBL:ENSG00000087250\"\n                               \"ENSEMBL:ENSG00000171100\"\n                               \"ENSEMBL:ENSG00000210195\"\n                               \"ENSEMBL:ENSG00000185499\"\n                               \"ENSEMBL:ENSG00000215182\"\n                               \"ENSEMBL:ENSG00000136997\"\n                               \"ENSEMBL:ENSG00000172936\"\n                               \"ENSEMBL:ENSG00000109063\"\n                               \"ENSEMBL:ENSG00000065534\"\n                               \"ENSEMBL:ENSG00000116044\"\n                               \"ENSEMBL:ENSG00000109320\"\n                               \"ENSEMBL:ENSG00000100906\"\n                               \"ENSEMBL:ENSG00000001167\"\n                               \"ENSEMBL:ENSG00000089250\"\n                               \"ENSEMBL:ENSG00000164867\"\n                               \"ENSEMBL:ENSG00000161270\"\n                               \"ENSEMBL:ENSG00000135318\"\n                               \"ENSEMBL:ENSG00000111331\"\n                               \"ENSEMBL:ENSG00000112038\"\n                               \"ENSEMBL:ENSG00000089041\"\n                               \"ENSEMBL:ENSG00000185624\"\n                               \"ENSEMBL:ENSG00000007168\"\n                               \"ENSEMBL:ENSG00000117450\"\n                               \"ENSEMBL:ENSG00000106366\"\n                               \"ENSEMBL:ENSG00000126759\"\n                               \"ENSEMBL:ENSG00000197249\"\n                               \"ENSEMBL:ENSG00000124102\"\n                               \"ENSEMBL:ENSG00000121879\"\n                               \"ENSEMBL:ENSG00000051382\"\n                               \"ENSEMBL:ENSG00000171608\"\n                               \"ENSEMBL:ENSG00000105851\"\n                               \"ENSEMBL:ENSG00000170890\"\n                               \"ENSEMBL:ENSG00000188257\"\n                               \"ENSEMBL:ENSG00000116711\"\n                               \"ENSEMBL:ENSG00000118495\"\n                               \"ENSEMBL:ENSG00000011422\"\n                               \"ENSEMBL:ENSG00000115896\"\n                               \"ENSEMBL:ENSG00000075651\"\n                               \"ENSEMBL:ENSG00000178209\"\n                               \"ENSEMBL:ENSG00000266964\"\n                               \"ENSEMBL:ENSG00000115138\"\n                               \"ENSEMBL:ENSG00000186951\"\n                               \"ENSEMBL:ENSG00000122862\"\n                               \"ENSEMBL:ENSG00000100030\"\n                               \"ENSEMBL:ENSG00000107643\"\n                               \"ENSEMBL:ENSG00000169032\"\n                               \"ENSEMBL:ENSG00000115718\"\n                               \"ENSEMBL:ENSG00000184500\"\n                               \"ENSEMBL:ENSG00000189002\"\n                               \"ENSEMBL:ENSG00000135406\"\n                               \"ENSEMBL:ENSG00000041357\"\n                               \"ENSEMBL:ENSG00000197170\"\n                               \"ENSEMBL:ENSG00000011304\"\n                               \"ENSEMBL:ENSG00000073756\"\n                               \"ENSEMBL:ENSG00000169398\"\n                               \"ENSEMBL:ENSG00000105894\"\n                               \"ENSEMBL:ENSG00000081237\"\n                               \"ENSEMBL:ENSG00000113456\"\n                               \"ENSEMBL:ENSG00000069974\"\n                               \"ENSEMBL:ENSG00000080823\"\n                               \"ENSEMBL:ENSG00000112619\"\n                               \"ENSEMBL:ENSG00000173039\"\n                               \"ENSEMBL:ENSG00000143839\"\n                               \"ENSEMBL:ENSG00000102032\"\n                               \"ENSEMBL:ENSG00000163914\"\n                               \"ENSEMBL:ENSG00000067900\"\n                               \"ENSEMBL:ENSG00000149489\"\n                               \"ENSEMBL:ENSG00000196218\"\n                               \"ENSEMBL:ENSG00000196154\"\n                               \"ENSEMBL:ENSG00000163220\"\n                               \"ENSEMBL:ENSG00000031698\"\n                               \"ENSEMBL:ENSG00000111319\"\n                               \"ENSEMBL:ENSG00000108691\"\n                               \"ENSEMBL:ENSG00000108688\"\n                               \"ENSEMBL:ENSG00000163735\"\n                               \"ENSEMBL:ENSG00000110876\"\n                               \"ENSEMBL:ENSG00000168878\"\n                               \"ENSEMBL:ENSG00000168484\"\n                               \"ENSEMBL:ENSG00000133661\"\n                               \"ENSEMBL:ENSG00000064651\"\n                               \"ENSEMBL:ENSG00000197208\"\n                               \"ENSEMBL:ENSG00000166311\"\n                               \"ENSEMBL:ENSG00000075618\"\n                               \"ENSEMBL:ENSG00000125835\"\n                               \"ENSEMBL:ENSG00000142168\"\n                               \"ENSEMBL:ENSG00000112096\"\n                               \"ENSEMBL:ENSG00000109610\"\n                               \"ENSEMBL:ENSG00000125398\"\n                               \"ENSEMBL:ENSG00000100883\"\n                               \"ENSEMBL:ENSG00000168610\"\n                               \"ENSEMBL:ENSG00000126561\"\n                               \"ENSEMBL:ENSG00000173757\"\n                               \"ENSEMBL:ENSG00000087586\"\n                               \"ENSEMBL:ENSG00000067715\"\n                               \"ENSEMBL:ENSG00000231925\"\n                               \"ENSEMBL:ENSG00000006638\"\n                               \"ENSEMBL:ENSG00000118526\"\n                               \"ENSEMBL:ENSG00000120156\"\n                               \"ENSEMBL:ENSG00000164362\"\n                               \"ENSEMBL:ENSG00000003436\"\n                               \"ENSEMBL:ENSG00000105329\"\n                               \"ENSEMBL:ENSG00000198959\"\n                               \"ENSEMBL:ENSG00000178726\"\n                               \"ENSEMBL:ENSG00000116001\"\n                               \"ENSEMBL:ENSG00000102265\"\n                               \"ENSEMBL:ENSG00000136352\"\n                               \"ENSEMBL:ENSG00000137462\"\n                               \"ENSEMBL:ENSG00000164342\"\n                               \"ENSEMBL:ENSG00000136869\"\n                               \"ENSEMBL:ENSG00000127324\"\n                               \"ENSEMBL:ENSG00000149809\"\n                               \"ENSEMBL:ENSG00000232810\"\n                               \"ENSEMBL:ENSG00000118503\"\n                               \"ENSEMBL:ENSG00000067182\"\n                               \"ENSEMBL:ENSG00000118194\"\n                               \"ENSEMBL:ENSG00000131747\"\n                               \"ENSEMBL:ENSG00000111669\"\n                               \"ENSEMBL:ENSG00000128311\"\n                               \"ENSEMBL:ENSG00000125482\"\n                               \"ENSEMBL:ENSG00000155657\"\n                               \"ENSEMBL:ENSG00000136810\"\n                               \"ENSEMBL:ENSG00000198431\"\n                               \"ENSEMBL:ENSG00000149021\"\n                               \"ENSEMBL:ENSG00000174607\"\n                               \"ENSEMBL:ENSG00000111424\"\n                               \"ENSEMBL:ENSG00000112715\"\n                               \"ENSEMBL:ENSG00000146469\"\n                               \"ENSEMBL:ENSG00000110799\"\n                               \"ENSEMBL:ENSG00000158125\"\n                               \"ENSEMBL:ENSG00000164924\"\n                               \"ENSEMBL:ENSG00000121966\"\n                               \"ENSEMBL:ENSG00000146070\"\n                               \"ENSEMBL:ENSG00000106305\"\n                               \"ENSEMBL:ENSG00000050327\"\n                               \"ENSEMBL:ENSG00000083168\"\n                               \"ENSEMBL:ENSG00000118972\"\n                               \"ENSEMBL:ENSG00000206561\"\n                               \"ENSEMBL:ENSG00000184381\"\n                               \"ENSEMBL:ENSG00000069764\"\n                               \"ENSEMBL:ENSG00000108528\"\n                               \"ENSEMBL:ENSG00000117461\"\n                               \"ENSEMBL:ENSG00000134107\"\n                               \"ENSEMBL:ENSG00000136908\"\n                               \"ENSEMBL:ENSG00000171720\"\n                               \"ENSEMBL:ENSG00000176170\"\n                               \"ENSEMBL:ENSG00000111602\"\n                               \"ENSEMBL:ENSG00000173805\"\n                               \"ENSEMBL:ENSG00000131023\"\n                               \"ENSEMBL:ENSG00000157456\"\n                               \"ENSEMBL:ENSG00000162889\"\n                               \"ENSEMBL:ENSG00000103671\"\n                               \"ENSEMBL:ENSG00000133116\"\n                               \"ENSEMBL:ENSG00000181092\"\n                               \"ENSEMBL:ENSG00000100351\"\n                               \"ENSEMBL:ENSG00000136156\"\n                               \"ENSEMBL:ENSG00000102230\"\n                               \"ENSEMBL:ENSG00000057663\"\n                               \"ENSEMBL:ENSG00000134318\"\n                               \"ENSEMBL:ENSG00000117592\"\n                               \"ENSEMBL:ENSG00000187608\"\n                               \"ENSEMBL:ENSG00000103335\"\n                               \"ENSEMBL:ENSG00000165733\"\n                               \"ENSEMBL:ENSG00000079999\"\n                               \"ENSEMBL:ENSG00000044090\"\n                               \"ENSEMBL:ENSG00000117020\"\n                               \"ENSEMBL:ENSG00000105835\"\n                               \"ENSEMBL:ENSG00000105246\"\n                               \"ENSEMBL:ENSG00000131477\"\n                               \"ENSEMBL:ENSG00000127528\"\n                               \"ENSEMBL:ENSG00000167315\"\n                               \"ENSEMBL:ENSG00000140092\"\n                               \"ENSEMBL:ENSG00000101000\"\n                               \"ENSEMBL:ENSG00000100591\"\n                               \"ENSEMBL:ENSG00000160999\"\n                               \"ENSEMBL:ENSG00000162493\"\n                               \"ENSEMBL:ENSG00000048740\"\n                               \"ENSEMBL:ENSG00000173083\"\n                               \"ENSEMBL:ENSG00000196843\"\n                               \"ENSEMBL:ENSG00000126264\"\n                               \"ENSEMBL:ENSG00000137959\"\n                               \"ENSEMBL:ENSG00000269821\"\n                               \"ENSEMBL:ENSG00000083807\"\n                               \"ENSEMBL:ENSG00000167114\"\n                               \"ENSEMBL:ENSG00000129465\"\n                               \"ENSEMBL:ENSG00000136110\"\n                               \"ENSEMBL:ENSG00000256525\"\n                               \"ENSEMBL:ENSG00000142082\"\n                               \"ENSEMBL:ENSG00000096717\"\n                               \"ENSEMBL:ENSG00000136859\"\n                               \"ENSEMBL:ENSG00000172828\"\n                               \"ENSEMBL:ENSG00000123415\"\n                               \"ENSEMBL:ENSG00000025800\"\n                               \"ENSEMBL:ENSG00000154589\"\n                               \"ENSEMBL:ENSG00000177663\"\n                               \"ENSEMBL:ENSG00000034677\"\n                               \"ENSEMBL:ENSG00000196141\"\n                               \"ENSEMBL:ENSG00000004142\"\n                               \"ENSEMBL:ENSG00000113249\"\n                               \"ENSEMBL:ENSG00000007952\"\n                               \"ENSEMBL:ENSG00000086232\"\n                               \"ENSEMBL:ENSG00000138744\"\n                               \"ENSEMBL:ENSG00000163106\"\n                               \"ENSEMBL:ENSG00000138375\"\n                               \"ENSEMBL:ENSG00000086991\"\n                               \"ENSEMBL:ENSG00000219430\"\n                               \"ENSEMBL:ENSG00000138303\"\n                               \"ENSEMBL:ENSG00000126524\"\n                               \"ENSEMBL:ENSG00000167772\"\n                               \"ENSEMBL:ENSG00000165682\"\n                               \"ENSEMBL:ENSG00000101916\"\n                               \"ENSEMBL:ENSG00000172458\"\n                               \"ENSEMBL:ENSG00000124731\"\n                               \"ENSEMBL:ENSG00000011426\"\n                               \"ENSEMBL:ENSG00000135766\"\n                               \"ENSEMBL:ENSG00000241635\"\n                               \"ENSEMBL:ENSG00000104835\"\n                               \"ENSEMBL:ENSG00000185480\"\n                               \"ENSEMBL:ENSG00000110075\"\n                               \"ENSEMBL:ENSG00000079691\"\n                               \"ENSEMBL:ENSG00000171109\"\n                               \"ENSEMBL:ENSG00000151849\"\n                               \"ENSEMBL:ENSG00000126970\"\n                               \"ENSEMBL:ENSG00000169241\"\n                               \"ENSEMBL:ENSG00000074842\"\n                               \"ENSEMBL:ENSG00000185115\"\n                               \"ENSEMBL:ENSG00000136688\"\n                               \"ENSEMBL:ENSG00000115350\"\n                               \"ENSEMBL:ENSG00000111666\"\n                               \"ENSEMBL:ENSG00000198074\"\n                               \"ENSEMBL:ENSG00000283122\"\n                               \"ENSEMBL:ENSG00000139946\"\n                               \"ENSEMBL:ENSG00000175482\"\n                               \"ENSEMBL:ENSG00000117569\"\n                               \"ENSEMBL:ENSG00000130234\"\n                               \"ENSEMBL:ENSG00000198026\"\n                               \"ENSEMBL:ENSG00000132429\"\n                               \"ENSEMBL:ENSG00000114745\"\n                               \"ENSEMBL:ENSG00000060237\"\n                               \"ENSEMBL:ENSG00000262246\"\n                               \"ENSEMBL:ENSG00000104518\"\n                               \"ENSEMBL:ENSG00000153395\"\n                               \"ENSEMBL:ENSG00000146094\"\n                               \"ENSEMBL:ENSG00000125779\"\n                               \"ENSEMBL:ENSG00000197496\"\n                               \"ENSEMBL:ENSG00000169612\"\n                               \"ENSEMBL:ENSG00000138496\"\n                               \"ENSEMBL:ENSG00000169962\"\n                               \"ENSEMBL:ENSG00000130363\"\n                               \"ENSEMBL:ENSG00000103510\"\n                               \"ENSEMBL:ENSG00000106125\"\n                               \"ENSEMBL:ENSG00000131653\"\n                               \"ENSEMBL:ENSG00000145794\"\n                               \"ENSEMBL:ENSG00000163702\"\n                               \"ENSEMBL:ENSG00000100410\"\n                               \"ENSEMBL:ENSG00000137691\"\n                               \"ENSEMBL:ENSG00000160188\"\n                               \"ENSEMBL:ENSG00000151148\"\n                               \"ENSEMBL:ENSG00000137033\"\n                               \"ENSEMBL:ENSG00000178473\"\n                               \"ENSEMBL:ENSG00000162711\"\n                               \"ENSEMBL:ENSG00000161544\"\n                               \"ENSEMBL:ENSG00000153391\"\n                               \"ENSEMBL:ENSG00000205359\"\n                               \"ENSEMBL:ENSG00000168724\"\n                               \"ENSEMBL:ENSG00000229140\"\n                               \"ENSEMBL:ENSG00000165953\"\n                               \"ENSEMBL:ENSG00000172967\"\n                               \"ENSEMBL:ENSG00000163803\"\n                               \"ENSEMBL:ENSG00000197272\"\n                               \"ENSEMBL:ENSG00000175311\"\n                               \"ENSEMBL:ENSG00000170782\"\n                               \"ENSEMBL:ENSG00000189195\"\n                               \"ENSEMBL:ENSG00000161911\"\n                               \"ENSEMBL:ENSG00000197448\"\n                               \"ENSEMBL:ENSG00000251562\"\n                               \"ENSEMBL:ENSG00000187258\"\n                               \"ENSEMBL:ENSG00000248131\"\n                               \"ENSEMBL:ENSG00000284520\"\n                               \"ENSEMBL:ENSG00000199133\"\n                               \"ENSEMBL:ENSG00000284440\"\n                               \"ENSEMBL:ENSG00000199161\"\n                               \"ENSEMBL:ENSG00000207608\"\n                               \"ENSEMBL:ENSG00000207625\"\n                               \"ENSEMBL:ENSG00000207782\"\n                               \"ENSEMBL:ENSG00000283904\"\n                               \"ENSEMBL:ENSG00000283815\"\n                               \"ENSEMBL:ENSG00000284204\"\n                               \"ENSEMBL:ENSG00000207607\"\n                               \"ENSEMBL:ENSG00000199038\"\n                               \"ENSEMBL:ENSG00000207702\"\n                               \"ENSEMBL:ENSG00000207590\"\n                               \"ENSEMBL:ENSG00000207798\"\n                               \"ENSEMBL:ENSG00000207870\"\n                               \"ENSEMBL:ENSG00000284567\"\n                               \"ENSEMBL:ENSG00000199075\"\n                               \"ENSEMBL:ENSG00000199121\"\n                               \"ENSEMBL:ENSG00000207808\"\n                               \"ENSEMBL:ENSG00000207864\"\n                               \"ENSEMBL:ENSG00000207827\"\n                               \"ENSEMBL:ENSG00000207582\"\n                               \"ENSEMBL:ENSG00000284357\"\n                               \"ENSEMBL:ENSG00000207638\"\n                               \"ENSEMBL:ENSG00000199059\"\n                               \"ENSEMBL:ENSG00000199151\"\n                               \"ENSEMBL:ENSG00000199104\"\n                               \"ENSEMBL:ENSG00000198982\"\n                               \"ENSEMBL:ENSG00000199020\"\n                               \"ENSEMBL:ENSG00000208001\"\n                               \"ENSEMBL:ENSG00000202569\"\n                               \"ENSEMBL:ENSG00000194717\"\n                               \"ENSEMBL:ENSG00000207731\"\n                               \"ENSEMBL:ENSG00000122852\"\n                               \"ENSEMBL:ENSG00000207571\"\n                               \"ENSEMBL:ENSG00000185303\"\n                               \"ENSEMBL:ENSG00000211590\"\n                               \"ENSEMBL:ENSG00000285427\"\n                               \"ENSEMBL:ENSG00000228750\"\n                               \"ENSEMBL:ENSG00000280634\"\n                               \"ENSEMBL:ENSG00000243438\"\n                               \"ENSEMBL:ENSG00000201796\"\n                               \"ENSEMBL:ENSG00000240160\")))\n\n(define (unwrap lst)\n  (if (null? lst) lst\n      (append (car lst) (unwrap (cdr lst)))))\n\n(define (predicate e)\n  (cdr (list-ref e 4)))\n\n(define (summary-obj edge-sum)\n  (car (list-ref edge-sum 4)))\n\n(define (summary-subj edge-sum)\n  (car (list-ref edge-sum 3)))\n\n(define ((edge/db? db) e) (eq? db (car e)))\n\n(define (sort-inner-hash h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (set-count (cdr x)))))\n\n(define (sort-outer-hash h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (length (cdr x)))))\n\n(define (sort-counter h)\n  (sort\n   (hash-map h (lambda (k v) (cons k v)))\n   >\n   #:key (lambda (x) (cdr x))))\n\n#|getting uniprots using run/graph\n(define encodes (find-predicates '(\"encodes\")))\n(define gene-curie?\n  (lambda (x)\n    (or\n     (string-prefix? x \"HGNC:\")\n     (string-prefix? x \"ENSEMBL:\")\n     (string-prefix? x \"NCBIGene:\"))))\n\n(define encodes-us (remove-duplicates (unwrap (filter (lambda (x) (not (null? x))) (set-map gene-list\n                                                                         (lambda (g) (time\n                                                                                      (define S (filter (lambda (x) (eq? (car x) 'rtx2)) (find-concepts #t (filter gene-curie? (map car (curie-synonyms/names g))))))\n                                                                                      (match-define\n                                                                                        (list name=>concepts name=>edges)\n                                                                                        (run/graph\n                                                                                         ((G S)\n                                                                                          (U #f))\n                                                                                         ((G->U encodes))\n                                                                                         (G G->U U)))\n                                                                                      (map concept->curie (hash-ref name=>concepts 'U))\n                                                                                      ))\n                                                                         )))))\n|#\n\n(define uniprot-curie?\n  (lambda (x)\n    (string-prefix? x \"UniProtKB:\")))\n\n;;Converting ENSEMBL curies to UniProtKB curies using synonymization in order to pass into count-downstream\n(define uniprots (remove-duplicates (filter uniprot-curie? (map car (unwrap (set-map gene-list curie-synonyms/names))))))\n\n#|\ntakes: list of UniProt curies (prot-list), list of GO predicates** (preds)\n** note: preds should only contain \"positively_regulates\", \"negatively_regulates\", \"subclass_of\", or any combination\n**       of those three predicates depending on what type of relationshion you want to count\n\nreturns: a list of the hash tables in this order: go-processes, go-process-members, cell-expression-hash, regulated-cell-expression-hash\n         The contents of these hashes are documented inside the function\n|#\n(define (count-downstream prot-list preds)\n  ;;maps each Uniprot curie (key) in prot-list -> a set of all GO pathways (value) that the UniProt (key) regulates\n  (define go-processes (make-hash))\n  ;;maps GO pathway curies (key) -> a set of all UniProts (value) that are members of the GO pathway (key) (not intersected with prot-list)\n  (define go-process-members (make-hash))\n  ;;maps each Uniprot in prot-list (key) -> a set of cell/tissue types (value) they're expressed in\n  (define cell-expression-hash (make-hash))\n  ;;maps each regulated gene (key) found from the 2-hop query -> a set of cell/tissue types (value) they're expressed in\n  (define regulated-genes-cell-expression-hash (make-hash))\n  (define involved_in (keep 1 (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"involved_in\")))))\n  (define regulators (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates preds)))\n  (define expressed_in (filter (lambda (x) (equal? (car x) 'rtx2)) (find-exact-predicates '(\"expressed_in\"))))\n  (for-each\n   (lambda (u)\n     (define S (filter (lambda (x) (equal? (car x) 'rtx2)) (find-concepts #t (list u))))\n     ;;G->M->X 1.1 + 1.3\n     ;;G->C - 1.2\n     ;;rG->X - 1.4\n     ;;rG->rC - 1.5\n     (unless (empty? S)\n       (match-define\n         (list name=>concepts name=>edges)\n         (time (run/graph\n                ((G S)\n                 (M #f)\n                 (X #f)\n                 (C #f)\n                 (rG #f)\n                 (rC #f))\n                ((G->M involved_in)\n                 (G->C expressed_in)\n                 (M->X regulators)\n                 (rG->X involved_in)\n                 (rG->rC expressed_in))\n                (G G->M M)\n                (G G->C C)\n                (M M->X X)\n                (rG rG->X X)\n                (rG rG->rC rC))))\n       ;;go-processes (k=>v): G=>X\n       (hash-set! go-processes u (list->set (map concept->curie (hash-ref name=>concepts 'X))))\n       ;;cell-expression-hash (k=>v): G=>C\n       (hash-set! cell-expression-hash u (list->set (filter (lambda (x) (string-prefix? x \"UBERON:\")) (map concept->curie (hash-ref name=>concepts 'C)))))\n       ;;regulated-genes-cell-expression-hash (k=>v): rG=>rC\n       (for-each\n        (lambda (e)\n          (unless (not (string-prefix? (concept->curie (edge->object e)) \"UBERON:\"))\n            (hash-update! regulated-genes-cell-expression-hash (concept->curie (edge->subject e)) (lambda (v) (set-add v (concept->curie (edge->object e)))) (set))\n            )\n          )\n        (hash-ref name=>edges 'rG->rC)\n        )\n       ;;go-process-members (k=>v): X=>rG\n       (for-each\n        (lambda (e)\n          (unless (set-member? S (concept->curie (edge->subject e)))\n            (hash-update! go-process-members (concept->curie (edge->object e)) (lambda (v) (set-add v (concept->curie (edge->subject e)))) (set))\n            )\n          )\n        (hash-ref name=>edges 'rG->X)\n        )\n       )\n     )\n   prot-list\n   )\n  (list go-processes go-process-members cell-expression-hash regulated-genes-cell-expression-hash)\n  )\n#|Examples\n(define ards-pos-reg (count-downstream uniprots '(\"positively_regulates\")))\n(define ards-neg-reg (count-downstream uniprots '(\"negatively_regulates\")))\n(define ards-subclass_of (count-downstream uniprots '(\"subclass_of\")))\n(define ards-all-regulation (count-downstream uniprots '(\"positively_regulates\" \"negatively_regulates\" \"subclass_of\")))\n|#\n\n\n#|\ntakes: a list of 4 hash tables returned by the count-downstream function above\n\nManipulates the given hash tables to provide a ranked list of the genes of interest (given as argument prot-list in count-downstream function) by the number of\nother genes they regulate within each cell/tissue type thet they're expressed in. Also gives a ranked list of the cell/tissue types by the number of the genes\nof interest that are expressed in them. This is to make finding possible cells/tissues of interest easier.\n\nreturns: A list of 2 assoc lists - overview of the structure: (list\n                                                                (list (C' . int)\n                                                                      (C\" . int)\n                                                                        ...\n                                                                  )\n                                                                (list (C' (G . (set rG's))\n                                                                          (G . (set rG's))\n                                                                           ...\n                                                                        )\n                                                                      (C\" (G . (set rG's))\n                                                                          (G . (set rG's))\n                                                                           ...\n                                                                        )\n                                                                       ...\n                                                                  )\n                                                                )\nThe first assoc list (key . value): the key is the cell/tissue type (C), the value is (int) the number of genes of interest that are expressed in that\n                                    cell/tissue type. The first assoc is sorted from highest to lowest int\nThe second assoc list (key . (key . value)): the first key is the cell/tissue type (C), the value is another assoc list where the keys are the genes of interest (G)\n  (a nested assoc list)                      expressed in the cell/tissue type (C) and the values are sets of other genes (rG) that are expressed in the cell/tissue type (C)\n                                             AND regulated by the gene of interest (G)\n                                             The inner assoc list is sorted (high->low) by the number of regulated genes (rG). The outer assoc list is given in the same order as\n                                             the first assoc list above.\n|#\n(define (count-by-cell-expressed-in count-downstream-results)\n  (define G=>X (list-ref count-downstream-results 0))\n  (define X=>rG (list-ref count-downstream-results 1))\n  (define G=>C (list-ref count-downstream-results 2))\n  (define rG=>rC (list-ref count-downstream-results 3))\n  (define cell-expression-ranks (make-hash))\n  (define counter (make-hash))\n  ;;populate cell-expression-ranks\n  (hash-for-each\n   G=>X\n   (lambda (G X)\n     (set-for-each\n      X\n      (lambda (x)\n        (set-for-each\n         (set-intersect (hash-ref X=>rG x (set)) (list->set uniprots));;filters for just ARDS genes, remove set-intersect for no filter\n         (lambda (rg)\n           (set-for-each\n            (set-intersect (hash-ref G=>C G (set)) (hash-ref rG=>rC rg (set)))\n            (lambda (c)\n              (hash-update! cell-expression-ranks c\n                            (lambda (h)\n                              (hash-update! h G (lambda (v) (set-add v rg)) (set))\n                              h\n                              )\n                            (make-hash)\n                            )\n              )\n            )\n           )\n         )\n        )\n      )\n     )\n   )\n  (hash-for-each cell-expression-ranks\n                 (lambda (k v)\n                   (hash-set! cell-expression-ranks k (sort-inner-hash v))\n                   (hash-set! counter k (hash-count v))\n                   )\n                 )\n  (list (sort-counter counter) (sort-outer-hash cell-expression-ranks))\n  )\n#|Examples\n(define ards-cell-type-count (count-by-cell-expressed-in ards-pos-reg))\n\n(car ards-cell-type-count) ;;gives the ranked count of the number of genes expressed in each cell type\n(cadr ards-cell-type-count) ;;gives the second (more meaningful) assoc list\n\n;;To get the ranked assoc list of regulating genes for the liver (\"UBERON:0002107\")\n(define liver-genes (cdr (assoc \"UBERON:0002107\" (cadr ards-cell-type-count))))\n;;for the lung (\"UBERON:0002048\")\n(define lung-genes (cdr (assoc \"UBERON:0002048\" (cadr ards-cell-type-count))))\n|#\n\n#|\n(make-hash 'ARDS-Genelist\n           (make-hash 'Gene1-ARDS\n                      (make-hash 'Gene1-UBERON-cell-location\n                                 (make-hash 'pos-reg-GO1\n                                            (make-hash 'GO1\n                                                       (make-hash 'GO1-members\n                                                                  (make-hash 'GO1-member-UBERON-Cell-locations\n                                                                             (make-hash 'GO1-ARDS-members)\n                                                                             )))))))\n|#"
  }
]