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Repository: mapping-commons/sssom
Branch: master
Commit: 8cfba1099da4
Files: 129
Total size: 1004.5 KB
Directory structure:
gitextract_mofzv687/
├── .github/
│ ├── ISSUE_TEMPLATE/
│ │ └── new_sssom_element.md
│ ├── pull_request_template.md
│ └── workflows/
│ ├── build.yml
│ ├── codespell.yml
│ ├── deploy_documentation.yml
│ ├── main.yaml
│ └── pypi-publish.yaml
├── .gitignore
├── .prettierignore
├── CHANGELOG.md
├── CITATION.cff
├── CODE_OF_CONDUCT.md
├── CONTRIBUTING.md
├── LICENSE
├── Makefile
├── README.md
├── SSSOM.md
├── about.yaml
├── examples/
│ ├── README.md
│ ├── embedded/
│ │ ├── foodie-inc-2022-05-01.sssom.tsv
│ │ └── mp-hp-exact-0.0.1.sssom.tsv
│ ├── external/
│ │ ├── example1.sssom.tsv
│ │ ├── example1.sssom.yml
│ │ ├── mp-hp-exact-0.0.1.sssom.tsv
│ │ └── mp-hp-exact-0.0.1.sssom.yml
│ └── schema/
│ ├── cardinality-scope-empty.sssom.tsv
│ ├── cardinality-scope-predicate+object_source.sssom.tsv
│ ├── cardinality-scope-predicate.sssom.tsv
│ ├── cardinality-with-unmapped-entities.sssom.tsv
│ ├── cardinality.sssom.tsv
│ ├── composite-entities.sssom.tsv
│ ├── curation_rule-propagated.sssom.tsv
│ ├── curation_rule.sssom.tsv
│ ├── curation_rule_text-propagated.sssom.tsv
│ ├── curation_rule_text.sssom.tsv
│ ├── curation_rule_text2.sssom.tsv
│ ├── curie_map.sssom.tsv
│ ├── cxsmiles_pipe.sssom.tsv
│ ├── extension-slots.sssom.tsv
│ ├── issue_tracker.sssom.tsv
│ ├── issue_tracker_item.sssom.tsv
│ ├── literals.sssom.tsv
│ ├── mapping_set_confidence.sssom.tsv
│ ├── mapping_tool_id.sssom.tsv
│ ├── no_term_found.sssom.tsv
│ ├── pipe-escaping.sssom.tsv
│ ├── predicate-types.sssom.tsv
│ ├── record-ids.sssom.tsv
│ ├── review_date.sssom.tsv
│ ├── reviewer_agreement.sssom.tsv
│ ├── similarity_score.sssom.tsv
│ └── version.sssom.tsv
├── mkdocs.yml
├── project/
│ ├── excel/
│ │ └── sssom_schema.xlsx
│ ├── graphql/
│ │ └── sssom_schema.graphql
│ ├── jsonld/
│ │ ├── sssom_schema.context.jsonld
│ │ └── sssom_schema.jsonld
│ ├── jsonschema/
│ │ └── sssom_schema.schema.json
│ ├── prefixmap/
│ │ └── sssom_schema.yaml
│ ├── protobuf/
│ │ └── sssom_schema.proto
│ ├── shacl/
│ │ └── sssom_schema.shacl.ttl
│ ├── shex/
│ │ └── sssom_schema.shex
│ └── sqlschema/
│ └── sssom_schema.sql
├── project.Makefile
├── pyproject.toml
├── run.sh
├── scripts/
│ └── gh_table.pl
├── src/
│ ├── CONFIG.yaml
│ ├── doc-templates/
│ │ ├── class.md.jinja2
│ │ ├── class_diagram.md.jinja2
│ │ ├── common_metadata.md.jinja2
│ │ ├── frontpage.md.jinja2
│ │ ├── index.md.jinja2
│ │ └── slot.md.jinja2
│ ├── docs/
│ │ ├── 5star-mappings.md
│ │ ├── chaining-rules.md
│ │ ├── confidence-model.md
│ │ ├── contributing.md
│ │ ├── create-mapping-commons.md
│ │ ├── editors.md
│ │ ├── events/
│ │ │ ├── ccb2022.md
│ │ │ ├── mc2021.md
│ │ │ ├── mc2023.md
│ │ │ ├── oboacademy2022.md
│ │ │ ├── ohdsi2022.md
│ │ │ ├── ohdsi2023.md
│ │ │ ├── om2022.md
│ │ │ ├── pistoia2022.md
│ │ │ └── wsbo2021.md
│ │ ├── explanation/
│ │ │ └── mappings.md
│ │ ├── faq.md
│ │ ├── funding.md
│ │ ├── getting-started.md
│ │ ├── glossary.md
│ │ ├── introduction.md
│ │ ├── javascripts/
│ │ │ └── mathjax.js
│ │ ├── mapping-commons.md
│ │ ├── mapping-justifications.md
│ │ ├── mapping-predicates.md
│ │ ├── matching-tool-implementation-guide.md
│ │ ├── presentations.md
│ │ ├── record-identifiers.md
│ │ ├── related-documentation.md
│ │ ├── spec-formats-json.md
│ │ ├── spec-formats-owl.md
│ │ ├── spec-formats-rdf.md
│ │ ├── spec-formats-tsv.md
│ │ ├── spec-formats.md
│ │ ├── spec-intro.md
│ │ ├── spec-model.md
│ │ ├── spec-support-hashing.md
│ │ ├── spec-support.md
│ │ ├── toolkit.md
│ │ ├── training.md
│ │ ├── tutorial.md
│ │ ├── tutorials/
│ │ │ └── omop-mappings.md
│ │ ├── usecases.md
│ │ └── workshops.md
│ └── sssom_schema/
│ ├── __init__.py
│ ├── context/
│ │ ├── sssom_schema.context.jsonld
│ │ └── sssom_schema.jsonld
│ ├── datamodel/
│ │ ├── __init__.py
│ │ └── sssom_schema.py
│ └── schema/
│ └── sssom_schema.yaml
├── tests/
│ ├── __init__.py
│ ├── input/
│ │ ├── CONFIG.yaml
│ │ └── README.md
│ └── test_added_in_annotations.py
└── utils/
└── get-value.sh
================================================
FILE CONTENTS
================================================
================================================
FILE: .github/ISSUE_TEMPLATE/new_sssom_element.md
================================================
---
title: "[New metadata element]: "
name: Add new SSSOM metadata element
about: New metadata element suggestion for SSSOM
assignees: matentzn
labels: 'new metadata element request'
---
**Element id (e.g. creator_id, mapping_tool_version):**
(Must be lower case and contain only letters and underscores.)
```
element_id_example
```
**Value data type (e.g. URI, URL, text, xsd:boolean):**
```
xsd:string
```
**Description**
(Provide a human-readable description that clarifies the intended use of the metadata element.)
Example description.
**Complete example to a SSSOM file with this element**
(This example can be given as a markdown table or a linked SSSOM file, feel free to edit the markdown table below)
```
# curie_map:
# HP: http://purl.obolibrary.org/obo/FBbt_
# MP: http://purl.obolibrary.org/obo/UBERON_
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/ac9e1878-73f4-4767-8402-a6c40e1b0835
```
| subject_id | predicate_id | object_id | mapping_justification | element_id_example |
| ----------- | --------------- | ----------- | ----------------------- | ------------------- |
| HP:0009124 | skos:exactMatch | MP:0000003 | semapv:LexicalMatching | YOUR EXAMPLE VALUE |
| HP:0008551 | skos:exactMatch | MP:0000018 | semapv:LexicalMatching | YOUR EXAMPLE VALUE |
================================================
FILE: .github/pull_request_template.md
================================================
Resolves [#ISSUE, #ISSUE]
- [ ] `docs/` have been added/updated if necessary
- [ ] `make test` has been run locally
- [ ] tests have been added/updated (if applicable)
- [ ] [CHANGELOG.md](https://github.com/mapping-commons/sssom/blob/master/CHANGELOG.md) has been updated.
If you are proposing a change to the SSSOM metadata model, you must
- [ ] provide a full, working and valid example in `examples/`
- [ ] provide a link to the related GitHub issue in the `see_also` field of the linkml model
- [ ] provide a link to a valid example in the `see_also` field of the linkml model
- [ ] update the "Model changes across versions" (in `src/docs/spec-models.md`) accordingly
- [ ] run SSSOM-Py test suite against the updated model
[Add a description, mentioning at least relevant #ISSUE and how it was addressed. A bulleted list of all changes performed by the PR is is helpful.]
================================================
FILE: .github/workflows/build.yml
================================================
name: Build
on:
workflow_dispatch:
#push:
# branches: [ master ]
# paths:
# - 'src/linkml/sssom.yaml'
jobs:
build:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v4.2.2
with:
persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
- name: Install uv
uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
- name: Set up Python
run: uv python install 3.10
- name: Install dependencies
run: uv sync --all-groups
- name: Create local changes
run: |
make all
- name: Commit files
run: |
git config --local user.email "action@github.com"
git config --local user.name "GitHub Action"
git commit -m "Rebuilding documentation and generated files with Github Action" -a
- name: Push changes
uses: ad-m/github-push-action@master
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
branch: ${{ github.ref }}
================================================
FILE: .github/workflows/codespell.yml
================================================
# Codespell configuration is within pyproject.toml
---
name: Codespell
on:
push:
branches: [master]
pull_request:
branches: [master]
permissions:
contents: read
jobs:
codespell:
name: Check for spelling errors
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4.2.2
- name: Annotate locations with typos
uses: codespell-project/codespell-problem-matcher@9ba2c57125d4908eade4308f32c4ff814c184633
- name: Codespell
uses: codespell-project/actions-codespell@94259cd8be02ad2903ba34a22d9c13de21a74461
================================================
FILE: .github/workflows/deploy_documentation.yml
================================================
name: Deploy Documentation
# Controls when the action will run. Triggers the workflow on push
on:
workflow_dispatch:
push:
branches:
- master
paths:
- "src/docs/*"
- "src/sssom_schema/schema/sssom_schema.yaml"
- "mkdocs.yml"
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
build-docs:
# The type of runner that the job will run on
runs-on: ubuntu-latest
permissions:
contents: write
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
#----------------------------------------------
# check-out repo and set-up python
#----------------------------------------------
- name: Check out repository
uses: actions/checkout@v4.2.2
with:
# persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
- name: Install uv
uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
- name: Set up Python
run: uv python install 3.10
- name: Install dependencies
run: uv sync --all-groups
#----------------------------------------------
# generate markdown files
#----------------------------------------------
- name: Create local docs
run: |
mkdir -p docs
touch docs/.nojekyll
make gendoc
#----------------------------------------------
# deploy website to gh-pages
#----------------------------------------------
- name: Deploy web-based documentation to GitHub Pages
run: |
git config user.name mike-bot
git config user.email mike-bot@sssom.invalid
make deploy-doc
================================================
FILE: .github/workflows/main.yaml
================================================
# Built from:
# https://docs.github.com/en/actions/guides/building-and-testing-python
name: Build and test sssom
on:
pull_request:
branches: [master]
types: [opened, synchronize, reopened]
jobs:
test:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.10", "3.14"]
steps:
- name: Check out repository
uses: actions/checkout@v4.2.2
with:
fetch-depth: 0
- name: Install uv
uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
- name: Set up Python ${{ matrix.python-version }}
run: uv python install ${{ matrix.python-version }}
- name: Install dependencies
run: uv sync --all-groups
- name: Run tests
run: make test
#----------------------------------------------
# YAML linting
#----------------------------------------------
- name: Install Prettier
run: npm install prettier
- name: Lint YML
run: npx prettier --check --prose-wrap always "**/*.yml"
- name: Lint YAML
run: npx prettier --check --prose-wrap always "**/*.yaml"
================================================
FILE: .github/workflows/pypi-publish.yaml
================================================
name: Publish Python Package
# Upload to PyPI is triggered by creating & publishing a release in GitHub UI
on:
release:
# Run when a release is published or a prerelease is published (not on draft creation)
types: [published]
jobs:
build:
name: Build Python 🐍 distributions 📦 for publishing to PyPI
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4.2.2
with:
# Checkout the code including tags required for dynamic versioning
fetch-depth: 0
- name: Install uv
uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
- name: Set up Python
run: uv python install 3.10
- name: Build source and wheel archives
run: uv build
- name: Store built distribution
uses: actions/upload-artifact@v4.6.2
with:
name: distribution-files
path: dist/
pypi-publish:
name: Build and publish Python 🐍 package 📦 to PyPI
needs: build
runs-on: ubuntu-latest
# Uses trusted publishing. https://docs.pypi.org/trusted-publishers/adding-a-publisher/
environment:
name: pypi-release
url: https://pypi.org/p/sssom-schema
permissions:
id-token: write # This permission is mandatory for trusted publishing.
steps:
- name: Download built distribution
uses: actions/download-artifact@v4.3.0
with:
name: distribution-files
path: dist
- name: Publish package 📦 to PyPI
uses: pypa/gh-action-pypi-publish@v1.12.4
with:
verbose: true
skip-existing: true
================================================
FILE: .gitignore
================================================
/docs/
/project/docs/
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
# IPython
profile_default/
ipython_config.py
# pyenv
.python-version
# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock
# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/
# Celery stuff
celerybeat-schedule
celerybeat.pid
# SageMath parsed files
*.sage.py
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
.dmypy.json
dmypy.json
# Pyre type checker
.pyre/
.DS_Store
tmp/
/node_modules
package-lock.json
================================================
FILE: .prettierignore
================================================
project/prefixmap/sssom_schema.yaml
================================================
FILE: CHANGELOG.md
================================================
# Changelog for SSSOM
## Next
- Add `composed entity expression` as a new value in the `EntityType` enumeration ([issue](https://github.com/mapping-commons/sssom/issues/402)).
- Add `predicate_type` slot (previously defined but unused) to the `Mapping` and `MappingSet` classes ([issue](https://github.com/mapping-commons/sssom/issues/404)).
- Add `similarity_measure` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/411)).
- Add `sssom_version` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/439)).
- Change the type of the `see_also` slot to `xsd:anyURI` ([issue](https://github.com/mapping-commons/sssom/issues/422)).
- Add `mapping_set_confidence` slot to the `MappingSet` class ([issue](https://github.com/mapping-commons/sssom/issues/438)).
- Updated the RDF binding of sssom:publication_date from dcterms:created to dcterms:issued, which is the more appropriate property to use in this case.
- Add `mapping_tool_id` slot to the `Mapping` and `MappingSet` classes ([issue](https://github.com/mapping-commons/sssom/issues/449)).
- Add `record_id` slot to the `Mapping` class ([issue](https://github.com/mapping-commons/sssom/issues/359)).
- Change all URI-typed slots to clarify that they expect _non-relative_ URIs as values ([issue](https://github.com/mapping-commons/sssom/issues/448)).
- Add `curation_rule` and `curation_rule_text` to the `MappingSet` class and made propagatable ([issue](https://github.com/mapping-commons/sssom/issues/464)).
- Add `cardinality_scope` slot ([issue](https://github.com/mapping-commons/sssom/issues/467)).
- Add new value `0:0` to the `mapping_cardinality_enum` ([issue](https://github.com/mapping-commons/sssom/issues/477)).
- Add specification for the RDF serialisation ([discussion](https://github.com/mapping-commons/sssom/discussions/454)).
- Development snapshots of SSSOM schema can now be released using GitHub's pre-release feature ([issue](https://github.com/mapping-commons/sssom/issues/490)).
- Add `review_date` slot ([issue](https://github.com/mapping-commons/sssom/issues/511))
- Add `reviewer_agreement` slot ([issue](https://github.com/mapping-commons/sssom/issues/510))
- Allow encoding pipe characters in multi-valued slots in SSSOM/TSV format ([issue](https://github.com/mapping-commons/sssom/issues/429)).
- Specify a standard SSSOM hashing function ([issue](https://github.com/mapping-commons/sssom/issues/436)).
## SSSOM version 1.0.0
- Add the concept of "propagatable slots".
- Add the `curie_map` to the model (instead of it being a specificity of the SSSOM/TSV format).
- Add the concept of "extension slots".
- Add the concept of "literal mappings".
- Add the entity reference `sssom:NoTermFound` to express the concept of an "unmapped entity" ([issue](https://github.com/mapping-commons/sssom/issues/28))
- Replace `semantic_similarity_score` with `similarity_score` and `semantic_similarity_measure` with `similarity_measure` in the data model ([issue](https://github.com/mapping-commons/sssom/issues/385))
## SSSOM version 0.15.1
- Add recommendation to sort the keys in the YAML metadata block.
- Double-typed slots explicitly constrained to the [0.0,1.0] range, as per their description.
## SSSOM version 0.15.0
- Add issue_tracker_item and issue_tracker [model elements](https://github.com/mapping-commons/sssom/pull/259).
## SSSOM version 0.13.0
- The necessity of the "canonical column ordering" was downgraded from MUST to SHOULD (https://github.com/mapping-commons/sssom/pull/285)
- Documents clearly that built-in prefixes MUST NOT be redefined (https://github.com/mapping-commons/sssom/pull/285)
## SSSOM version 0.11.0
- see https://github.com/mapping-commons/sssom/releases/tag/0.11.0
### Summary
#### New elements:
- `mapping_set_title` to capture a human readable title for a mapping set
- `registry_title` and `registry_description` to capture the human readable title and description of an SSSOM mapping set registry
- `curation_rule` to capture a (potentially) complex (set of) condition(s) executed by an agent (usually human) that led to the establishment of a mapping.
#### Updated elements:
- Adding mapping_source slot to Mapping by @matentzn in #230
- Improve documentation for `subject_category` and `object_category` elements
#### Documentation
- Compiled a list of all SSSOM talks: https://mapping-commons.github.io/sssom/presentations/
- Document chaining rules: https://mapping-commons.github.io/sssom/chaining_rules/
#### Quality control and Technical infrastructure
- Make adding a concrete SSSOM example part of the new element request
- Adding QC checks for example SSSOM files hosted in the repo
## SSSOM version 0.10.1
- see https://github.com/mapping-commons/sssom/releases/tag/0.10.1
## SSSOM version 0.9.4
- see https://github.com/mapping-commons/sssom/releases/tag/0.9.4
## SSSOM version 0.9.3
- see https://github.com/mapping-commons/sssom/releases/tag/0.9.3
- Major change: Changed `match_type` logic to `mapping_justification` ([issue](https://github.com/mapping-commons/sssom/issues/150)).
## SSSOM version 0.9.2
- see https://github.com/mapping-commons/sssom/releases/tag/0.9.2
## SSSOM version 0.9.1
- see https://github.com/mapping-commons/sssom/releases/tag/0.9.1
## SSSOM version 0.9.0
- Initial release
- see https://github.com/mapping-commons/sssom/releases/tag/0.9.0
================================================
FILE: CITATION.cff
================================================
cff-version: '1.1.0'
message: 'Please cite the following works when using this software.'
abstract: "<jats:title>Abstract</jats:title>\n <jats:p>Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec.</jats:p>\n <jats:p>Database URL: http://w3id.org/sssom/spec</jats:p>"
authors:
- family-names: 'Matentzoglu'
given-names: 'Nicolas'
- family-names: 'Balhoff'
given-names: 'James P'
- family-names: 'Bello'
given-names: 'Susan M'
- family-names: 'Bizon'
given-names: 'Chris'
- family-names: 'Brush'
given-names: 'Matthew'
- family-names: 'Callahan'
given-names: 'Tiffany J'
- family-names: 'Chute'
given-names: 'Christopher G'
- family-names: 'Duncan'
given-names: 'William D'
- family-names: 'Evelo'
given-names: 'Chris T'
- family-names: 'Gabriel'
given-names: 'Davera'
- family-names: 'Graybeal'
given-names: 'John'
- family-names: 'Gray'
given-names: 'Alasdair'
- family-names: 'Gyori'
given-names: 'Benjamin M'
- family-names: 'Haendel'
given-names: 'Melissa'
- family-names: 'Harmse'
given-names: 'Henriette'
- family-names: 'Harris'
given-names: 'Nomi L'
- family-names: 'Harrow'
given-names: 'Ian'
- family-names: 'Hegde'
given-names: 'Harshad B'
- family-names: 'Hoyt'
given-names: 'Amelia L'
- family-names: 'Hoyt'
given-names: 'Charles T'
- family-names: 'Jiao'
given-names: 'Dazhi'
- family-names: 'Jiménez-Ruiz'
given-names: 'Ernesto'
- family-names: 'Jupp'
given-names: 'Simon'
- family-names: 'Kim'
given-names: 'Hyeongsik'
- family-names: 'Koehler'
given-names: 'Sebastian'
- family-names: 'Liener'
given-names: 'Thomas'
- family-names: 'Long'
given-names: 'Qinqin'
- family-names: 'Malone'
given-names: 'James'
- family-names: 'McLaughlin'
given-names: 'James A'
- family-names: 'McMurry'
given-names: 'Julie A'
- family-names: 'Moxon'
given-names: 'Sierra'
- family-names: 'Munoz-Torres'
given-names: 'Monica C'
- family-names: 'Osumi-Sutherland'
given-names: 'David'
- family-names: 'Overton'
given-names: 'James A'
- family-names: 'Peters'
given-names: 'Bjoern'
- family-names: 'Putman'
given-names: 'Tim'
- family-names: 'Queralt-Rosinach'
given-names: 'Núria'
- family-names: 'Shefchek'
given-names: 'Kent'
- family-names: 'Solbrig'
given-names: 'Harold'
- family-names: 'Thessen'
given-names: 'Anne'
- family-names: 'Tudorache'
given-names: 'Tania'
- family-names: 'Vasilevsky'
given-names: 'Nicole'
- family-names: 'Wagner'
given-names: 'Alex H'
- family-names: 'Mungall'
given-names: 'Christopher J'
doi: '10.1093/database/baac035'
identifiers:
- type: 'doi'
value: '10.1093/database/baac035'
- type: 'url'
value: 'http://dx.doi.org/10.1093/database/baac035'
- type: 'other'
value: 'urn:issn:1758-0463'
title: 'A Simple Standard for Sharing Ontological Mappings (SSSOM)'
url: 'http://dx.doi.org/10.1093/database/baac035'
================================================
FILE: CODE_OF_CONDUCT.md
================================================
# Contributor Covenant Code of Conduct
## Our Pledge
In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
## Our Standards
Examples of behavior that contributes to creating a positive environment include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
* The use of sexualized language or imagery and unwelcome sexual attention or advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a professional setting
## Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
## Scope
This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
## Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by [contacting the project team](contact.md). All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
## Attribution
This code of conduct has been derived from the excellent code of conduct of the [ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md) which in turn is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
[homepage]: https://contributor-covenant.org
[version]: https://contributor-covenant.org/version/1/4/
================================================
FILE: CONTRIBUTING.md
================================================
# Contributing to SSSOM
:+1: First of all: Thank you for taking the time to contribute!
The following is a set of guidelines for contributing to SSSOM. They are derived
from the excellent contribution guidelines for the
[ATOM Editor](https://github.com/atom/atom/blob/master/CONTRIBUTING.md) and are
mostly guidelines, not rules. Use your best judgment, and feel free to propose
changes to this document in a pull request.
#### Table Of Contents
[Code of Conduct](#code-of-conduct)
[I don't want to read this whole thing, I just have a question!!!](#i-dont-want-to-read-this-whole-thing-i-just-have-a-question)
[What should I know before I get started?](#what-should-i-know-before-i-get-started)
[How Can I Contribute?](#how-can-i-contribute)
- [Reporting Bugs](#reporting-bugs)
- [Your First Code Contribution](#your-first-code-contribution)
- [Pull Requests](#pull-requests)
- [Local Testing](#local-testing)
- [Making a release](#making-a-release)
[Style Guides](#styleguides)
- [Git Commit Messages](#git-commit-messages)
- [Documentation Styleguide](#documentation-styleguide)
[Additional Notes](#additional-notes)
- [Issue and Pull Request Labels](#issue-and-pull-request-labels)
## Code of Conduct
This project and everyone participating in it is governed by the
[SSSOM Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected
to uphold this code. Please report unacceptable behavior to
[a member of the SSSOM core team](https://mapping-commons.github.io/sssom/contact/).
## I don't want to read this whole thing I just have a question!!!
We have an official message board with a detailed FAQ and where the community
chimes in with helpful advice if you have questions.
- [GitGub Discussions](https://github.com/mapping-commons/sssom/discussions)
- [SSSOM FAQ](https://mapping-commons.github.io/sssom/faq/)
## What should I know before I get started?
- Read the [introduction](https://mapping-commons.github.io/sssom/introduction/)
- Do the [SSSOM tutorial](https://mapping-commons.github.io/sssom/tutorial/)
- Read about the [SSSOM toolkit](https://mapping-commons.github.io/sssom-py),
which is managed
[in a different repo](https://github.com/mapping-commons/sssom-py)
## How Can I Contribute?
### Reporting Bugs
This section guides you through submitting a bug report for SSSOM. Following
these guidelines helps maintainers and the community understand your report
:pencil:, reproduce the behavior :computer: :computer:, and find related reports
:mag_right:.
Before creating bug reports, please check
[this list](#before-submitting-a-bug-report) as you might find out that you
don't need to create one. When you are creating a bug report, please include as
many details as possible. Wherever available, use
[existing issue tracker templates](https://github.com/mapping-commons/sssom/issues/new/choose),
the information it asks for helps us resolve issues faster.
> **Note:** If you find a **Closed** issue that seems like it is the same thing
> that you're experiencing, open a new issue and include a link to the original
> issue in the body of your new one.
#### Before Submitting A Bug Report
- **Check the
[discussions](https://github.com/mapping-commons/sssom/discussions)** for a
list of common questions and problems.
- **Decide whether the issue should be reported in the tracker for the
[SSSOM data model](https://github.com/mapping-commons/sssom/issues) or the
tracker for the
[SSSOM toolkit](https://github.com/mapping-commons/sssom-py/issues)**.
- **Perform a
[cursory search](https://github.com/mapping-commons/sssom/issues)** to see if
the problem has already been reported. If it has **and the issue is still
open**, add a comment to the existing issue instead of opening a new one.
#### How Do I Submit A (Good) Bug Report or Feature request?
Bugs and feature requests are tracked as
[GitHub issues](https://guides.github.com/features/issues/). After you've
determined which repository your bug or feature is related to, create an issue
on that repository providing the information required by
[the appropriate template](https://github.com/mapping-commons/sssom/issues/new/choose).
Explain the problem and include additional details to help maintainers reproduce
the problem:
- **Use a clear and descriptive title** for the issue to identify the
problem/requests.
- **Describe the exact steps which reproduce the problem** in as many details as
possible. For example, start by explaining how you started SSSOM, e.g. which
command exactly you used in the terminal, or how you started SSSOM otherwise.
When listing steps, **don't just say what you did, but explain how you did
it**. For example, if you moved the cursor to the end of a line, explain if
you used the mouse, or a keyboard shortcut or an SSSOM command, and if so
which one?
- **Provide specific examples to demonstrate the steps**. Include links to files
or GitHub projects, or copy/pasteable snippets, which you use in those
examples. If you're providing snippets in the issue, use
[Markdown code blocks](https://help.github.com/articles/markdown-basics/#multiple-lines).
- **Describe the behavior you observed after following the steps** and point out
what exactly is the problem with that behavior.
- **Explain which behavior you expected to see instead and why.**
Include details about your configuration and environment:
- **Which version of SSSOM toolkit/model are you using?** You can get the exact
version by running `sssom --version` in your terminal
- **What's the name and version of the OS you're using**?
### Your First Code Contribution
Unsure where to begin contributing to SSSOM? You can start by looking through
these `beginner` and `help-wanted` issues:
- [Beginner issues][beginner] - issues which should only require a few lines of
code, and a test or two.
- [Help wanted issues][help-wanted] - issues which should be a bit more involved
than `beginner` issues.
### Considerations when proposing changes to the model
Now that SSSOM 1.0 has been released, and until we start working on a
hypothetical SSSOM 2.0, any proposed change to the SSSOM model must consider the
issue of backwards compatibility.
The key point is that _a set that is compliant with version 1.0 of the
specification must be usable “as is” with an implementation compliant with any
1.x version_.
This is automatically achieved if all the proposed changes do is _adding_ new
_optional_ slots, or _new_ enumeration values. For that reason, it is strongly
recommended that evolution of the 1.x branch be limited to this type of changes
only, and that other changes be reserved for a hypothetical version 2.0.
In addition, new slots must be marked with a `added_in` annotation indicating
the version in which the slot will be introduced, as in the following example:
```yaml
my_new_slot:
instantiates:
- sssom:Versionable
annotations:
added_in: "1.1"
```
### Pull Requests
The process described here has several goals:
- Maintain SSSOM's quality
- Fix problems that are important to users
- Engage the community in working toward the best possible data model and
toolkit
- Enable a sustainable system for SSSOM's maintainers to review contributions
Please follow these steps to have your contribution considered by the
maintainers:
1. Follow all instructions in the pull request template (you will see them when
you open a pull request).
2. Follow the [style guides](#styleguides)
3. After you submit your pull request, verify that all
[status checks](https://help.github.com/articles/about-status-checks/) are
passing <details><summary>What if the status checks are failing?</summary>If
a status check is failing, and you believe that the failure is unrelated to
your change, please leave a comment on the pull request explaining why you
believe the failure is unrelated. A maintainer will re-run the status check
for you. If we conclude that the failure was a false positive, then we will
open an issue to track that problem with our status check suite.</details>
While the prerequisites above must be satisfied prior to having your pull
request reviewed, the reviewer(s) may ask you to complete additional design
work, tests, or other changes before your pull request can be ultimately
accepted.
### Local testing
Contributors are strongly advised to run the test suite locally even before
submitting a pull request.
Prepare the testing environment by running:
```console
$ make install
```
This only needs to be run once after cloning the repository. After that, the
test suite can be run anytime with
```console
$ make test
```
If you are making a change to the documentation/specification, you should also
check how your changes are rendered, by running
```console
$ make serve
```
and opening `http://127.0.0.1:8000/sssom/` with your browser.
Furthermore, any change to the LinkML model should also be tested against
SSSOM-Py. To do so:
1. In the current `sssom` repository, build the Python files derived from the
LinkML:
```console
$ make all
```
2. Clone the SSSOM-Py repository somewhere (outside your current checkout of
`sssom`):
```console
$ git clone https://github.com/mapping-commons/sssom-py.git
```
3. Initialize environment inside the newly cloned repository:
```console
$ uv sync
```
4. Forcefully install your _local_ version of `sssom-schema` in the newly
initialized environment:
```sh
$ uv pip install /path/to/your/sssom/repository
```
You may get a warning about “incompatible sssom-schema versions”; this is due
to the fact that your local copy of `sssom` has a version number set to
`0.0.0` (the “real” version number is set at release time, when the package
is published to PyPI) and can be safely ignored.
5. Run SSSOM-Py’s test suite:
```sh
$ uv run --all-extras pytest
```
### Making a release
<a id="releasing"></a>
Before making a release, check that all the files that are derived from the
LinkML schema are up-to-date. If they are not:
- re-generate them by running `make all`;
- commit all the files that were modified as a result of that command.
Update any other file as needed (e.g. changelog, README, copyright notices,
etc.), and commit the corresponding changes.
Once the repository is ready for a release, tag the head commit of the main
branch with a version number tag. If the release is intended to be published on
the Python Package Index (which it normally should), the version tag MUST be of
the form `vVERSION` (`v` prefix followed by the actual intended version number).
Push all changes to the main GitHub repository (including the tag), and create
the release from the new tag.
Be careful that any new release that bumps either the major or the minor version
number, and that is not a _pre_ release, will be interpreted not merely as a new
version of the `sssom_schema` Python package, but as a new version of the SSSOM
specification!
## Styleguides
### Git Commit Messages
- Use the present tense ("Add feature" not "Added feature")
- Use the imperative mood ("Move cursor to..." not "Moves cursor to...")
- Limit the first line to 72 characters or less
- Reference issues and pull requests liberally after the first line
- Consider starting the commit message with an applicable emoji:
- :art: `:art:` when improving the format/structure of the code
- :racehorse: `:racehorse:` when improving performance
- :non-potable_water: `:non-potable_water:` when plugging memory leaks
- :memo: `:memo:` when writing docs
- :penguin: `:penguin:` when fixing something on Linux
- :apple: `:apple:` when fixing something on macOS
- :checkered_flag: `:checkered_flag:` when fixing something on Windows
- :bug: `:bug:` when fixing a bug
- :fire: `:fire:` when removing code or files
- :green_heart: `:green_heart:` when fixing the CI build
- :white_check_mark: `:white_check_mark:` when adding tests
- :lock: `:lock:` when dealing with security
- :arrow_up: `:arrow_up:` when upgrading dependencies
- :arrow_down: `:arrow_down:` when downgrading dependencies
- :shirt: `:shirt:` when removing linter warnings
### Documentation Styleguide
- Use [Markdown](https://daringfireball.net/projects/markdown).
## Additional Notes
### Issue and Pull Request Labels
This section lists the labels we use to help us track and manage issues and pull
requests. Most labels are used across all mapping commons repositories.
#### Type of Issue and Issue State
| Label name | `mapping-commons/sssom` :mag_right: | `sssom`‑org :mag_right: | Description |
| ------------------------- | --------------------------------------------------------- | ------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------- |
| `enhancement` | [search][search-sssom-repo-label-enhancement] | [search][search-mapping-commons-org-label-enhancement] | Feature requests. |
| `bug` | [search][search-sssom-repo-label-bug] | [search][search-mapping-commons-org-label-bug] | Confirmed bugs or reports that are very likely to be bugs. |
| `question` | [search][search-sssom-repo-label-question] | [search][search-mapping-commons-org-label-question] | Questions more than bug reports or feature requests (e.g. how do I do X). |
| `feedback` | [search][search-sssom-repo-label-feedback] | [search][search-mapping-commons-org-label-feedback] | General feedback more than bug reports or feature requests. |
| `help-wanted` | [search][search-sssom-repo-label-help-wanted] | [search][search-mapping-commons-org-label-help-wanted] | The SSSOM core team would appreciate help from the community in resolving these issues. |
| `beginner` | [search][search-sssom-repo-label-beginner] | [search][search-mapping-commons-org-label-beginner] | Less complex issues which would be good first issues to work on for users who want to contribute to SSSOM. |
| `more-information-needed` | [search][search-sssom-repo-label-more-information-needed] | [search][search-mapping-commons-org-label-more-information-needed] | More information needs to be collected about these problems or feature requests (e.g. steps to reproduce). |
| `needs-reproduction` | [search][search-sssom-repo-label-needs-reproduction] | [search][search-mapping-commons-org-label-needs-reproduction] | Likely bugs, but haven't been reliably reproduced. |
| `blocked` | [search][search-sssom-repo-label-blocked] | [search][search-mapping-commons-org-label-blocked] | Issues blocked on other issues. |
| `duplicate` | [search][search-sssom-repo-label-duplicate] | [search][search-mapping-commons-org-label-duplicate] | Issues which are duplicates of other issues, i.e. they have been reported before. |
| `wontfix` | [search][search-sssom-repo-label-wontfix] | [search][search-mapping-commons-org-label-wontfix] | The SSSOM core team has decided not to fix these issues for now, either because they're working as intended or for some other reason. |
[search-sssom-repo-label-enhancement]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aenhancement
[search-mapping-commons-org-label-enhancement]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aenhancement
[search-sssom-repo-label-bug]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Abug
[search-mapping-commons-org-label-bug]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Abug
[search-sssom-repo-label-question]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aquestion
[search-mapping-commons-org-label-question]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aquestion
[search-sssom-repo-label-feedback]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Afeedback
[search-mapping-commons-org-label-feedback]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Afeedback
[search-sssom-repo-label-help-wanted]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Ahelp-wanted
[search-mapping-commons-org-label-help-wanted]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Ahelp-wanted
[search-sssom-repo-label-beginner]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Abeginner
[search-mapping-commons-org-label-beginner]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Abeginner
[search-sssom-repo-label-more-information-needed]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Amore-information-needed
[search-mapping-commons-org-label-more-information-needed]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Amore-information-needed
[search-sssom-repo-label-needs-reproduction]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aneeds-reproduction
[search-mapping-commons-org-label-needs-reproduction]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aneeds-reproduction
[search-sssom-repo-label-triage-help-needed]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Atriage-help-needed
[search-mapping-commons-org-label-triage-help-needed]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Atriage-help-needed
[search-sssom-repo-label-windows]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Awindows
[search-mapping-commons-org-label-windows]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Awindows
[search-sssom-repo-label-linux]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Alinux
[search-mapping-commons-org-label-linux]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Alinux
[search-sssom-repo-label-mac]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Amac
[search-mapping-commons-org-label-mac]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Amac
[search-sssom-repo-label-documentation]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Adocumentation
[search-mapping-commons-org-label-documentation]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Adocumentation
[search-sssom-repo-label-performance]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aperformance
[search-mapping-commons-org-label-performance]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aperformance
[search-sssom-repo-label-security]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Asecurity
[search-mapping-commons-org-label-security]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Asecurity
[search-sssom-repo-label-ui]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aui
[search-mapping-commons-org-label-ui]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aui
[search-sssom-repo-label-api]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aapi
[search-mapping-commons-org-label-api]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aapi
[search-sssom-repo-label-crash]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Acrash
[search-mapping-commons-org-label-crash]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Acrash
[search-sssom-repo-label-auto-indent]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aauto-indent
[search-mapping-commons-org-label-auto-indent]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aauto-indent
[search-sssom-repo-label-encoding]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aencoding
[search-mapping-commons-org-label-encoding]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aencoding
[search-sssom-repo-label-network]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Anetwork
[search-mapping-commons-org-label-network]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Anetwork
[search-sssom-repo-label-uncaught-exception]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Auncaught-exception
[search-mapping-commons-org-label-uncaught-exception]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Auncaught-exception
[search-sssom-repo-label-git]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Agit
[search-mapping-commons-org-label-git]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Agit
[search-sssom-repo-label-blocked]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Ablocked
[search-mapping-commons-org-label-blocked]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Ablocked
[search-sssom-repo-label-duplicate]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aduplicate
[search-mapping-commons-org-label-duplicate]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aduplicate
[search-sssom-repo-label-wontfix]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Awontfix
[search-mapping-commons-org-label-wontfix]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Awontfix
[search-sssom-repo-label-invalid]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Ainvalid
[search-mapping-commons-org-label-invalid]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Ainvalid
[search-sssom-repo-label-package-idea]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Apackage-idea
[search-mapping-commons-org-label-package-idea]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Apackage-idea
[search-sssom-repo-label-wrong-repo]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Awrong-repo
[search-mapping-commons-org-label-wrong-repo]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Awrong-repo
[search-sssom-repo-label-editor-rendering]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aeditor-rendering
[search-mapping-commons-org-label-editor-rendering]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aeditor-rendering
[search-sssom-repo-label-build-error]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Abuild-error
[search-mapping-commons-org-label-build-error]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Abuild-error
[search-sssom-repo-label-error-from-pathwatcher]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aerror-from-pathwatcher
[search-mapping-commons-org-label-error-from-pathwatcher]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aerror-from-pathwatcher
[search-sssom-repo-label-error-from-save]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aerror-from-save
[search-mapping-commons-org-label-error-from-save]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aerror-from-save
[search-sssom-repo-label-error-from-open]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aerror-from-open
[search-mapping-commons-org-label-error-from-open]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aerror-from-open
[search-sssom-repo-label-installer]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Ainstaller
[search-mapping-commons-org-label-installer]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Ainstaller
[search-sssom-repo-label-auto-updater]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Aauto-updater
[search-mapping-commons-org-label-auto-updater]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aauto-updater
[search-sssom-repo-label-deprecation-help]:
https://github.com/search?q=is%3Aopen+is%3Aissue+repo%3Amapping-commons%2Fsssom+label%3Adeprecation-help
[search-mapping-commons-org-label-deprecation-help]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Adeprecation-help
[search-sssom-repo-label-electron]:
https://github.com/search?q=is%3Aissue+repo%3Amapping-commons%2Fsssom+is%3Aopen+label%3Aelectron
[search-mapping-commons-org-label-electron]:
https://github.com/search?q=is%3Aopen+is%3Aissue+user%3Amapping-commons+label%3Aelectron
[search-sssom-repo-label-work-in-progress]:
https://github.com/search?q=is%3Aopen+is%3Apr+repo%3Amapping-commons%2Fsssom+label%3Awork-in-progress
[search-mapping-commons-org-label-work-in-progress]:
https://github.com/search?q=is%3Aopen+is%3Apr+user%3Amapping-commons+label%3Awork-in-progress
[search-sssom-repo-label-needs-review]:
https://github.com/search?q=is%3Aopen+is%3Apr+repo%3Amapping-commons%2Fsssom+label%3Aneeds-review
[search-mapping-commons-org-label-needs-review]:
https://github.com/search?q=is%3Aopen+is%3Apr+user%3Amapping-commons+label%3Aneeds-review
[search-sssom-repo-label-under-review]:
https://github.com/search?q=is%3Aopen+is%3Apr+repo%3Amapping-commons%2Fsssom+label%3Aunder-review
[search-mapping-commons-org-label-under-review]:
https://github.com/search?q=is%3Aopen+is%3Apr+user%3Amapping-commons+label%3Aunder-review
[search-sssom-repo-label-requires-changes]:
https://github.com/search?q=is%3Aopen+is%3Apr+repo%3Amapping-commons%2Fsssom+label%3Arequires-changes
[search-mapping-commons-org-label-requires-changes]:
https://github.com/search?q=is%3Aopen+is%3Apr+user%3Amapping-commons+label%3Arequires-changes
[search-sssom-repo-label-needs-testing]:
https://github.com/search?q=is%3Aopen+is%3Apr+repo%3Amapping-commons%2Fsssom+label%3Aneeds-testing
[search-mapping-commons-org-label-needs-testing]:
https://github.com/search?q=is%3Aopen+is%3Apr+user%3Amapping-commons+label%3Aneeds-testing
[beginner]:
https://github.com/search?utf8=%E2%9C%93&q=is%3Aopen+is%3Aissue+label%3Abeginner+label%3Ahelp-wanted+user%3Amapping-commons+sort%3Acomments-desc
[help-wanted]:
https://github.com/search?q=is%3Aopen+is%3Aissue+label%3Ahelp-wanted+user%3Amapping-commons+sort%3Acomments-desc+-label%3Abeginner
[contributing-to-official-sssom-packages]:
https://flight-manual.sssom.io/hacking-sssom/sections/contributing-to-official-sssom-packages/
[hacking-on-sssom-core]:
https://flight-manual.sssom.io/hacking-sssom/sections/hacking-on-sssom-core/
================================================
FILE: LICENSE
================================================
BSD 3-Clause License
Copyright (c) 2022, Nico Matentzoglu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
================================================
FILE: Makefile
================================================
MAKEFLAGS += --warn-undefined-variables
SHELL := bash
.SHELLFLAGS := -eu -o pipefail -c
.DEFAULT_GOAL := help
.DELETE_ON_ERROR:
.SUFFIXES:
.SECONDARY:
RUN = uv run
# get values from about.yaml file
SCHEMA_NAME = sssom_schema
SOURCE_SCHEMA_PATH = src/sssom_schema/schema/sssom_schema.yaml
SRC = src
DEST = project
PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
DOCDIR = docs
TEMPLATE_DIR = $(SRC)/doc-templates
# basename of a YAML file in model/
.PHONY: all clean
help: status
@echo ""
@echo "make all -- makes site locally"
@echo "make install -- install dependencies"
@echo "make setup -- initial setup"
@echo "make test -- runs tests"
@echo "make testdoc -- builds docs and runs local test server"
@echo "make deploy -- deploys site"
@echo "make update -- updates linkml version"
@echo "make help -- show this help"
@echo ""
status: check-config
@echo "Project: $(SCHEMA_NAME)"
@echo "Source: $(SOURCE_SCHEMA_PATH)"
setup: install gen-project gendoc git-init-add
install:
uv sync
.PHONY: install
all: gen-project gendoc gen-excel get-context
%.yaml: gen-project
deploy: all mkd-gh-deploy
# generates all project files
gen-project: $(PYMODEL)
$(RUN) gen-project \
--exclude owl \
-d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
test: validate-schema
$(RUN) gen-project \
--exclude owl \
-d tmp $(SOURCE_SCHEMA_PATH)
$(RUN) pytest
validate-schema: $(SOURCE_SCHEMA_PATH)
$(RUN) linkml lint --validate --validate-only $<
check-config:
@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n - Remember to edit 'about.yaml'\n\n" || exit 0)
convert-examples-to-%:
$(patsubst %, $(RUN) linkml-convert % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell find src/data/examples -name "*.yaml"))
get-context:
mkdir -p $(SRC)/$(SCHEMA_NAME)/context
cp $(DEST)/jsonld/* $(SRC)/$(SCHEMA_NAME)/context
examples/%.yaml: src/data/examples/%.yaml
$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
examples/%.json: src/data/examples/%.yaml
$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
examples/%.ttl: src/data/examples/%.yaml
$(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
upgrade:
uv add linkml --upgrade-package linkml
# Test documentation locally
serve: mkd-serve
# Python datamodel
$(PYMODEL):
mkdir -p $@
$(DOCDIR):
mkdir -p $@
gendoc: $(DOCDIR)
cp -rf $(SRC)/docs/* $(DOCDIR) ; \
$(RUN) jinjanate $(SRC)/doc-templates/frontpage.md.jinja2 $(SOURCE_SCHEMA_PATH) -o $(DOCDIR)/index.md
$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) --template-directory $(TEMPLATE_DIR) --index-name linkml-index
testdoc: gendoc serve
MKDOCS = $(RUN) --all-groups mkdocs
mkd-%:
$(MKDOCS) $*
deploy-doc:
$(RUN) mike deploy --push dev
PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel
git-init-add: git-init git-add git-commit git-status
git-init:
git init
git-add:
git add .gitignore .github Makefile LICENSE *.md examples utils about.yaml mkdocs.yml uv.lock project.Makefile pyproject.toml src/linkml/*yaml src/*/datamodel/*py src/data
git add $(patsubst %, project/%, $(PROJECT_FOLDERS))
git-commit:
git commit -m 'Initial commit' -a
git-status:
git status
clean:
rm -rf $(DEST)
rm -rf tmp
yaml-lint-all:
npx --yes prettier --check --prose-wrap always --write "**/*.yaml"
npx --yes prettier --check --prose-wrap always --write "**/*.yml"
include project.Makefile
================================================
FILE: README.md
================================================
<!--[](https://zenodo.org/badge/latestdoi/13996/mapping-commons/sssom)-->
# A Simple Standard for Sharing Ontological Mappings (SSSOM)
<img src="src/docs/images/sssom-banner.png" />
SSSOM is a Simple Standard for Sharing Ontological Mappings, providing
1. a TSV-based representation for ontology term mappings
1. a comprehensive set of standard metadata elements to describe mappings and
1. a standard translation between the TSV and the Web Ontology Language (OWL).
The SSSOM TSV format in particular is geared towards the needs of the wider bioinformatics community as a way to safely exchange mappings in an easily readable yet semantically well-specified manner. Consider this example of a simple mapping file:
| subject_id | predicate_id | object_id | mapping_justification | subject_label | object_label |
| --- | --- | --- | --- | --- | --- |
| HP:0009124 | skos:exactMatch | MP:0000003 | semapv:LexicalMatching | Abnormal adipose tissue morphology | abnormal adipose tissue morphology |
| HP:0008551 | skos:exactMatch | MP:0000018 | semapv:LexicalMatching | Microtia | small ears |
| HP:0000411 | skos:exactMatch | MP:0000021 | semapv:LexicalMatching | Protruding ear | prominent ears |
SSSOM specifies all its metadata elements:
- subject_id
- predicate_id
- object_id
- mapping_justification (*NOTE: Since June 2022* `match_type` is being replaced by `mapping_justification` see [here](https://github.com/mapping-commons/sssom/issues/150))
- subject_label
- object_label
including clear definitions, examples of use and controlled vocabulary where necessary, along with 30 other optional metadata elements to provide additional provenance.
SSSOM further provides a standard way to
- augment the TSV file with mapping set - level metadata, such as creator_id, mapping_date or license and
- translate a SSSOM compliant TSV files into _OWL reified axioms_. This will allow the easy loading, and merging of SSSOM mapping tables into existing ontologies using standard tools such as ROBOT (under development).
Note that SSSOM is currently under development and subject to change. Please leave us a comment on the [issue tracker](https://github.com/OBOFoundry/SSSOM/issues) if you want to be involved. The full specification can be found [here](https://w3id.org/sssom/spec).
## Citation
If you have found SSSOM to be helpful in your work, please consider citing:
Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A McLaughlin, Julie A McMurry, Sierra Moxon, Monica C Munoz-Torres, David Osumi-Sutherland, James A Overton, Bjoern Peters, Tim Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher J Mungall, A Simple Standard for Sharing Ontological Mappings (SSSOM), Database, Volume 2022, 2022, baac035, https://doi.org/10.1093/database/baac035
```bibtex
@article{10.1093/database/baac035,
author = {Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and Graybeal, John and Gray, Alasdair and Gyori, Benjamin M and Haendel, Melissa and Harmse, Henriette and Harris, Nomi L and Harrow, Ian and Hegde, Harshad B and Hoyt, Amelia L and Hoyt, Charles T and Jiao, Dazhi and Jiménez-Ruiz, Ernesto and Jupp, Simon and Kim, Hyeongsik and Koehler, Sebastian and Liener, Thomas and Long, Qinqin and Malone, James and McLaughlin, James A and McMurry, Julie A and Moxon, Sierra and Munoz-Torres, Monica C and Osumi-Sutherland, David and Overton, James A and Peters, Bjoern and Putman, Tim and Queralt-Rosinach, Núria and Shefchek, Kent and Solbrig, Harold and Thessen, Anne and Tudorache, Tania and Vasilevsky, Nicole and Wagner, Alex H and Mungall, Christopher J},
title = "{A Simple Standard for Sharing Ontological Mappings (SSSOM)}",
journal = {Database},
volume = {2022},
year = {2022},
month = {05},
abstract = "{Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec.Database URL: http://w3id.org/sssom/spec}",
issn = {1758-0463},
doi = {10.1093/database/baac035},
url = {https://doi.org/10.1093/database/baac035},
note = {baac035},
eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf},
}
```
A [second report with updates since the primary SSSOM publication](https://ceur-ws.org/Vol-3324/om2022_LTpaper6.pdf) above was published as part of the proceedings of the Ontology Matching Workshop 2022.
## Copying
SSSOM is distributed under the terms of the 3-clause BSD license, as included in the [LICENSE](LICENSE) file of the source distribution.
By exception, the following files are _not_ covered by the 3-clause BSD license:
* [sssom-banner.png](src/docs/images/sssom-banner.png): That file may only be used by members of the internal Monarch team and collaborators on Monarch flagship products.
================================================
FILE: SSSOM.md
================================================
This page has moved here:
https://mapping-commons.github.io/sssom/spec/
================================================
FILE: about.yaml
================================================
name: sssom_schema
description: A Simple Standard for Sharing Ontology Mappings (SSSOM)
source_schema_path: src/sssom_schema/schema/sssom_schema.yaml
================================================
FILE: examples/README.md
================================================
# Examples of use of sssom
This folder contains example data conforming to sssom
The source for these is in [src/data](../src/data/examples)
================================================
FILE: examples/embedded/foodie-inc-2022-05-01.sssom.tsv
================================================
# comment: We could map to FOODON:00004187 instead which more specifically refers to
# 'raw' Pink apples. Decided against to be consistent with other mapping choices.
# curie_map:
# FOODON: http://purl.obolibrary.org/obo/FOODON_
# KF_FOOD: https://kewl-foodie.inc/food/
# orcid: https://orcid.org/
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# wikidata: https://www.wikidata.org/wiki/
# license: https://creativecommons.org/licenses/by/4.0/
# mapping_date: '2022-05-02'
# mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food
# and nutrition database with Food Ontology (FOODON). Intended to be used for ontological
# analysis and grouping of KEWL FOODIE INC related data.
# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
# mapping_set_version: '2022-05-01'
# object_source: wikidata:Q55118395
# object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
# subject_source: KF_FOOD:DB
subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment
KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F003 pink skos:exactMatch FOODON:00004187 Pink apple (whole, raw) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices."
KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
================================================
FILE: examples/embedded/mp-hp-exact-0.0.1.sssom.tsv
================================================
# curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_provider: http://purl.obolibrary.org/obo/upheno.owl
# mapping_set_id: https://w3id.org/sssom/mappings/27f85fe9-8a72-4e76-909b-7ba4244d9ede
subject_id subject_label predicate_id object_id object_label mapping_justification
HP:0000175 Cleft palate skos:exactMatch MP:0000111 cleft palate semapv:LexicalMatching
HP:0000252 Microcephaly skos:exactMatch MP:0000433 microcephaly semapv:LexicalMatching
HP:0000260 Wide anterior fontanel skos:exactMatch MP:0000085 large anterior fontanelle semapv:LexicalMatching
HP:0000375 Abnormal cochlea morphology skos:exactMatch MP:0000031 abnormal cochlea morphology semapv:LexicalMatching
HP:0000411 Protruding ear skos:exactMatch MP:0000021 prominent ears semapv:LexicalMatching
HP:0000822 Hypertension skos:exactMatch MP:0000231 hypertension semapv:LexicalMatching
HP:0001336 Myoclonus skos:exactMatch MP:0000243 myoclonus semapv:LexicalMatching
HP:0001363 Craniosynostosis skos:exactMatch MP:0000081 premature cranial suture closure semapv:LexicalMatching
HP:0001596 Alopecia skos:exactMatch MP:0000414 alopecia semapv:LexicalMatching
HP:0001627 Abnormal heart morphology skos:exactMatch MP:0000266 abnormal heart morphology semapv:LexicalMatching
HP:0001633 Abnormal mitral valve morphology skos:exactMatch MP:0000286 abnormal mitral valve morphology semapv:LexicalMatching
HP:0001667 Right ventricular hypertrophy skos:exactMatch MP:0000276 heart right ventricle hypertrophy semapv:LexicalMatching
HP:0001679 Abnormal aortic morphology skos:exactMatch MP:0000272 abnormal aorta morphology semapv:LexicalMatching
HP:0001719 Double outlet right ventricle skos:exactMatch MP:0000284 double outlet right ventricle semapv:LexicalMatching
HP:0001882 Leukopenia skos:exactMatch MP:0000221 decreased leukocyte cell number semapv:LexicalMatching
HP:0001913 Granulocytopenia skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching
HP:0001974 Leukocytosis skos:exactMatch MP:0000218 increased leukocyte cell number semapv:LexicalMatching
HP:0001978 Extramedullary hematopoiesis skos:exactMatch MP:0000240 extramedullary hematopoiesis semapv:LexicalMatching
HP:0001981 Schistocytosis skos:exactMatch MP:0000314 schistocytosis semapv:LexicalMatching
HP:0002212 Curly hair skos:exactMatch MP:0000410 waved hair semapv:LexicalMatching
HP:0002659 Increased susceptibility to fractures skos:exactMatch MP:0000061 fragile skeleton semapv:LexicalMatching
HP:0002763 Abnormal cartilage morphology skos:exactMatch MP:0000163 abnormal cartilage morphology semapv:LexicalMatching
HP:0003307 Hyperlordosis skos:exactMatch MP:0000162 lordosis semapv:LexicalMatching
HP:0004349 Reduced bone mineral density skos:exactMatch MP:0000063 decreased bone mineral density semapv:LexicalMatching
HP:0006288 Advanced eruption of teeth skos:exactMatch MP:0000122 premature tooth eruption semapv:LexicalMatching
HP:0008551 Microtia skos:exactMatch MP:0000018 small ears semapv:LexicalMatching
HP:0009124 Abnormal adipose tissue morphology skos:exactMatch MP:0000003 abnormal adipose tissue morphology semapv:LexicalMatching
HP:0009910 Aplasia of the middle ear ossicles skos:exactMatch MP:0000040 absent middle ear ossicles semapv:LexicalMatching
HP:0009939 Mandibular aplasia skos:exactMatch MP:0000087 absent mandible semapv:LexicalMatching
HP:0011002 Osteopetrosis skos:exactMatch MP:0000067 osteopetrosis semapv:LexicalMatching
HP:0011457 Loss of eyelashes skos:exactMatch MP:0000425 loss of eyelid cilia semapv:LexicalMatching
HP:0011897 Neutrophilia skos:exactMatch MP:0000219 increased neutrophil cell number semapv:LexicalMatching
HP:0012234 Agranulocytosis skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching
HP:0012543 Hemosiderinuria skos:exactMatch MP:0000327 hemosiderinuria semapv:LexicalMatching
HP:0025065 Abnormal mean corpuscular volume skos:exactMatch MP:0000226 abnormal mean corpuscular volume semapv:LexicalMatching
HP:0025084 Folliculitis skos:exactMatch MP:0000376 folliculitis semapv:LexicalMatching
HP:0031377 Abnormal cell proliferation skos:exactMatch MP:0000350 abnormal cell proliferation semapv:LexicalMatching
HP:0031851 Reduced hematocrit skos:exactMatch MP:0000208 decreased hematocrit semapv:LexicalMatching
HP:0032310 Granulocytosis skos:exactMatch MP:0000322 increased granulocyte number semapv:LexicalMatching
HP:0100629 Midline facial cleft skos:exactMatch MP:0000108 midline facial cleft semapv:LexicalMatching
HP:0100671 Abnormal trabecular bone morphology skos:exactMatch MP:0000130 abnormal trabecular bone morphology semapv:LexicalMatching
HP:0400001 Chin with vertical crease skos:exactMatch MP:0000114 cleft chin semapv:LexicalMatching
================================================
FILE: examples/external/example1.sssom.tsv
================================================
subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment
KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F003 pink skos:exactMatch FOODON:00004187 Pink apple (whole, raw) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices."
KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
================================================
FILE: examples/external/example1.sssom.yml
================================================
comment:
We could map to FOODON:00004187 instead which more specifically refers to
'raw' Pink apples. Decided against to be consistent with other mapping
choices.
curie_map:
FOODON: http://purl.obolibrary.org/obo/FOODON_
KF_FOOD: https://kewl-foodie.inc/food/
orcid: https://orcid.org/
owl: http://www.w3.org/2002/07/owl#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#
semapv: https://w3id.org/semapv/vocab/
skos: http://www.w3.org/2004/02/skos/core#
sssom: https://w3id.org/sssom/
wikidata: https://www.wikidata.org/wiki/
license: https://creativecommons.org/licenses/by/4.0/
mapping_date: "2022-05-02"
mapping_set_description:
Manually curated alignment of KEWL FOODIE INC internal food and nutrition
database with Food Ontology (FOODON). Intended to be used for ontological
analysis and grouping of KEWL FOODIE INC related data.
mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
mapping_set_version: "2022-05-01"
object_source: wikidata:Q55118395
object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
subject_source: KF_FOOD:DB
================================================
FILE: examples/external/mp-hp-exact-0.0.1.sssom.tsv
================================================
subject_id subject_label predicate_id object_id object_label mapping_justification
HP:0000175 Cleft palate skos:exactMatch MP:0000111 cleft palate semapv:LexicalMatching
HP:0000252 Microcephaly skos:exactMatch MP:0000433 microcephaly semapv:LexicalMatching
HP:0000260 Wide anterior fontanel skos:exactMatch MP:0000085 large anterior fontanelle semapv:LexicalMatching
HP:0000375 Abnormal cochlea morphology skos:exactMatch MP:0000031 abnormal cochlea morphology semapv:LexicalMatching
HP:0000411 Protruding ear skos:exactMatch MP:0000021 prominent ears semapv:LexicalMatching
HP:0000822 Hypertension skos:exactMatch MP:0000231 hypertension semapv:LexicalMatching
HP:0001336 Myoclonus skos:exactMatch MP:0000243 myoclonus semapv:LexicalMatching
HP:0001363 Craniosynostosis skos:exactMatch MP:0000081 premature cranial suture closure semapv:LexicalMatching
HP:0001596 Alopecia skos:exactMatch MP:0000414 alopecia semapv:LexicalMatching
HP:0001627 Abnormal heart morphology skos:exactMatch MP:0000266 abnormal heart morphology semapv:LexicalMatching
HP:0001633 Abnormal mitral valve morphology skos:exactMatch MP:0000286 abnormal mitral valve morphology semapv:LexicalMatching
HP:0001667 Right ventricular hypertrophy skos:exactMatch MP:0000276 heart right ventricle hypertrophy semapv:LexicalMatching
HP:0001679 Abnormal aortic morphology skos:exactMatch MP:0000272 abnormal aorta morphology semapv:LexicalMatching
HP:0001719 Double outlet right ventricle skos:exactMatch MP:0000284 double outlet right ventricle semapv:LexicalMatching
HP:0001882 Leukopenia skos:exactMatch MP:0000221 decreased leukocyte cell number semapv:LexicalMatching
HP:0001913 Granulocytopenia skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching
HP:0001974 Leukocytosis skos:exactMatch MP:0000218 increased leukocyte cell number semapv:LexicalMatching
HP:0001978 Extramedullary hematopoiesis skos:exactMatch MP:0000240 extramedullary hematopoiesis semapv:LexicalMatching
HP:0001981 Schistocytosis skos:exactMatch MP:0000314 schistocytosis semapv:LexicalMatching
HP:0002212 Curly hair skos:exactMatch MP:0000410 waved hair semapv:LexicalMatching
HP:0002659 Increased susceptibility to fractures skos:exactMatch MP:0000061 fragile skeleton semapv:LexicalMatching
HP:0002763 Abnormal cartilage morphology skos:exactMatch MP:0000163 abnormal cartilage morphology semapv:LexicalMatching
HP:0003307 Hyperlordosis skos:exactMatch MP:0000162 lordosis semapv:LexicalMatching
HP:0004349 Reduced bone mineral density skos:exactMatch MP:0000063 decreased bone mineral density semapv:LexicalMatching
HP:0006288 Advanced eruption of teeth skos:exactMatch MP:0000122 premature tooth eruption semapv:LexicalMatching
HP:0008551 Microtia skos:exactMatch MP:0000018 small ears semapv:LexicalMatching
HP:0009124 Abnormal adipose tissue morphology skos:exactMatch MP:0000003 abnormal adipose tissue morphology semapv:LexicalMatching
HP:0009910 Aplasia of the middle ear ossicles skos:exactMatch MP:0000040 absent middle ear ossicles semapv:LexicalMatching
HP:0009939 Mandibular aplasia skos:exactMatch MP:0000087 absent mandible semapv:LexicalMatching
HP:0011002 Osteopetrosis skos:exactMatch MP:0000067 osteopetrosis semapv:LexicalMatching
HP:0011457 Loss of eyelashes skos:exactMatch MP:0000425 loss of eyelid cilia semapv:LexicalMatching
HP:0011897 Neutrophilia skos:exactMatch MP:0000219 increased neutrophil cell number semapv:LexicalMatching
HP:0012234 Agranulocytosis skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching
HP:0012543 Hemosiderinuria skos:exactMatch MP:0000327 hemosiderinuria semapv:LexicalMatching
HP:0025065 Abnormal mean corpuscular volume skos:exactMatch MP:0000226 abnormal mean corpuscular volume semapv:LexicalMatching
HP:0025084 Folliculitis skos:exactMatch MP:0000376 folliculitis semapv:LexicalMatching
HP:0031377 Abnormal cell proliferation skos:exactMatch MP:0000350 abnormal cell proliferation semapv:LexicalMatching
HP:0031851 Reduced hematocrit skos:exactMatch MP:0000208 decreased hematocrit semapv:LexicalMatching
HP:0032310 Granulocytosis skos:exactMatch MP:0000322 increased granulocyte number semapv:LexicalMatching
HP:0100629 Midline facial cleft skos:exactMatch MP:0000108 midline facial cleft semapv:LexicalMatching
HP:0100671 Abnormal trabecular bone morphology skos:exactMatch MP:0000130 abnormal trabecular bone morphology semapv:LexicalMatching
HP:0400001 Chin with vertical crease skos:exactMatch MP:0000114 cleft chin semapv:LexicalMatching
================================================
FILE: examples/external/mp-hp-exact-0.0.1.sssom.yml
================================================
curie_map:
HP: http://purl.obolibrary.org/obo/HP_
MP: http://purl.obolibrary.org/obo/MP_
owl: http://www.w3.org/2002/07/owl#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#
semapv: https://w3id.org/semapv/vocab/
skos: http://www.w3.org/2004/02/skos/core#
sssom: https://w3id.org/sssom/
license: https://creativecommons.org/publicdomain/zero/1.0/
mapping_provider: http://purl.obolibrary.org/obo/upheno.owl
mapping_set_id: https://w3id.org/sssom/mappings/27f85fe9-8a72-4e76-909b-7ba4244d9ede
================================================
FILE: examples/schema/cardinality-scope-empty.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
# NETENT: https://example.net/entities/
# ORGENT: https://example.org/entities/
# SRC: https://example.org/sources/
#mapping_set_id: https://example.org/sets/cardinality-scope-empty
#license: https://creativecommons.org/licenses/by/4.0/
subject_id subject_label predicate_id object_id object_label mapping_justification object_source mapping_cardinality
ORGENT:0001 alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration SRC:com 1:n
ORGENT:0001 alice skos:closeMatch NETENT:0111 alpha semapv:ManualMappingCuration SRC:net 1:n
ORGENT:0002 bob skos:closeMatch COMENT:0012 beta semapv:ManualMappingCuration SRC:com 1:n
ORGENT:0002 bob skos:closeMatch NETENT:0112 bravo semapv:ManualMappingCuration SRC:net 1:n
ORGENT:0007 gavin skos:closeMatch NETENT:0117 golf semapv:ManualMappingCuration SRC:net 1:n
ORGENT:0007 gavin skos:exactMatch COMENT:0013 gamma semapv:ManualMappingCuration SRC:com 1:n
================================================
FILE: examples/schema/cardinality-scope-predicate+object_source.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
# NETENT: https://example.net/entities/
# ORGENT: https://example.org/entities/
# SRC: https://example.org/sources/
#mapping_set_id: https://example.org/sets/cardinality-scope-predicate+object_source
#license: https://creativecommons.org/licenses/by/4.0/
#cardinality_scope:
# - predicate_id
# - object_source
subject_id subject_label predicate_id object_id object_label mapping_justification object_source mapping_cardinality
ORGENT:0001 alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration SRC:com 1:1
ORGENT:0001 alice skos:closeMatch NETENT:0111 alpha semapv:ManualMappingCuration SRC:net 1:1
ORGENT:0002 bob skos:closeMatch COMENT:0012 beta semapv:ManualMappingCuration SRC:com 1:1
ORGENT:0002 bob skos:closeMatch NETENT:0112 bravo semapv:ManualMappingCuration SRC:net 1:1
ORGENT:0007 gavin skos:closeMatch NETENT:0117 golf semapv:ManualMappingCuration SRC:net 1:1
ORGENT:0007 gavin skos:exactMatch COMENT:0013 gamma semapv:ManualMappingCuration SRC:com 1:1
================================================
FILE: examples/schema/cardinality-scope-predicate.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
# NETENT: https://example.net/entities/
# ORGENT: https://example.org/entities/
# SRC: https://example.org/sources/
#mapping_set_id: https://example.org/sets/cardinality-scope-predicate
#license: https://creativecommons.org/licenses/by/4.0/
#cardinality_scope:
# - predicate_id
subject_id subject_label predicate_id object_id object_label mapping_justification object_source mapping_cardinality
ORGENT:0001 alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration SRC:com 1:n
ORGENT:0001 alice skos:closeMatch NETENT:0111 alpha semapv:ManualMappingCuration SRC:net 1:n
ORGENT:0002 bob skos:closeMatch COMENT:0012 beta semapv:ManualMappingCuration SRC:com 1:n
ORGENT:0002 bob skos:closeMatch NETENT:0112 bravo semapv:ManualMappingCuration SRC:net 1:n
ORGENT:0007 gavin skos:closeMatch NETENT:0117 golf semapv:ManualMappingCuration SRC:net 1:1
ORGENT:0007 gavin skos:exactMatch COMENT:0013 gamma semapv:ManualMappingCuration SRC:com 1:1
================================================
FILE: examples/schema/cardinality-with-unmapped-entities.sssom.tsv
================================================
#curie_map:
# OBJ: https://example.org/object/
# SRC: https://example.org/sources/
# SUBJ: https://example.org/subject/
#mapping_set_id: https://example.org/sets/cardinality-with-unmapped-entities
#license: https://creativecommons.org/licenses/by/4.0/
subject_id predicate_id object_id mapping_justification subject_source object_source mapping_cardinality comment
SUBJ:0001 skos:exactMatch sssom:NoTermFound semapv:ManualMappingCuration SRC:A SRC:B 1:0 S1 in vocabulary A has no exact match in vocabulary B
SUBJ:0001 skos:closeMatch OBJ:0001 semapv:ManualMappingCuration SRC:A SRC:B 1:1 S1 mapped only to O1, O1 mapped only to S1 -- the record involving sssom:NoTermFound does not count, as it is an absence of match rather than an actual mapping
sssom:NoTermFound skos:exactMatch OBJ:0002 semapv:ManualMappingCuration SRC:C SRC:D 0:1 O2 in vocabulary D has no exact match in vocabulary C
sssom:NoTermFound skos:exactMatch sssom:NoTermFound semapv:ManualMappingCuration SRC:E SRC:F 0:0 No exact match between any term from vocabulary E and any term for vocabulary F (in other words, the two vocabularies are completely disjoint, at least as far as exact matches are considered)
================================================
FILE: examples/schema/cardinality.sssom.tsv
================================================
#curie_map:
# OBJ: https://example.org/object/
# SUBJ: https://example.org/subject/
#mapping_set_id: https://example.org/sets/cardinality
#license: https://creativecommons.org/licenses/by/4.0/
subject_id predicate_id object_id mapping_justification mapping_cardinality comment
SUBJ:0001 skos:exactMatch OBJ:0001 semapv:LexicalMatching 1:1 S1 and O1 only mapped to each other
SUBJ:0001 skos:exactMatch OBJ:0001 semapv:MappingReview 1:1 S1 and O1 only mapped to each other
SUBJ:0002 skos:exactMatch OBJ:0002 semapv:LexicalMatching 1:n S2 mapped to both O2 and O3, O2 mapped only to S2
SUBJ:0002 skos:exactMatch OBJ:0003 semapv:LexicalMatching 1:n S2 mapped to both O2 and O3, O3 mapped only to S2
SUBJ:0003 skos:exactMatch OBJ:0004 semapv:LexicalMatching n:1 S3 and S4 both mapped to only O4
SUBJ:0004 skos:exactMatch OBJ:0004 semapv:LexicalMatching n:1 S3 and S4 both mapped to only O4
SUBJ:0005 skos:exactMatch OBJ:0005 semapv:LexicalMatching n:n S5 mapped to O5 and O6, O5 mapped to S5 and S6
SUBJ:0005 skos:exactMatch OBJ:0006 semapv:LexicalMatching 1:n S5 mapped to O5 and O6, O6 mapped only to S5
SUBJ:0006 skos:exactMatch OBJ:0005 semapv:LexicalMatching n:1 S6 mapped only to O5, O5 mapped to both S5 and S6
================================================
FILE: examples/schema/composite-entities.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MONDO: http://purl.obolibrary.org/obo/MONDO_
# MP: http://purl.obolibrary.org/obo/MP_
# SCHEMA: http://example.org/schema
#mapping_set_id: https://w3id.org/sssom/commons/examples/composite-entities.sssom.tsv
#license: https://creativecommons.org/publicdomain/zero/1.0/
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification subject_type
SCHEMA:0001/(disease:'MONDO:0005148',phenotype:'HP:0009124') skos:exactMatch MP:0000003 semapv:ManualMappingCuration composed entity expression
SCHEMA:0001/(disease:'MONDO:0005149',phenotype:'HP:0008551') skos:exactMatch MP:0000018 semapv:ManualMappingCuration composed entity expression
SCHEMA:0001/(disease:'MONDO:0005150',phenotype:'HP:0000411') skos:exactMatch MP:0000018 semapv:ManualMappingCuration composed entity expression
================================================
FILE: examples/schema/curation_rule-propagated.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule.sssom.tsv
#mapping_set_description: "This example illustrates how to express that all mappings in a mapping set have been curated according to a specific curation rule"
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#curation_rule:
# - DISEASE_MAPPING_COMMONS_RULES:MPR2
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration
================================================
FILE: examples/schema/curation_rule.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification curation_rule see_also
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration DISEASE_MAPPING_COMMONS_RULES:MPR2 https://github.com/mapping-commons/disease-mappings/issues/16
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration DISEASE_MAPPING_COMMONS_RULES:MPR3 https://github.com/mapping-commons/disease-mappings/issues/16
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration DISEASE_MAPPING_COMMONS_RULES:MPR3 https://github.com/mapping-commons/disease-mappings/issues/16
================================================
FILE: examples/schema/curation_rule_text-propagated.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule.sssom.tsv
#mapping_set_description: "This example illustrates how to express that all mappings in a mapping set have been curated according to a specific curation rule"
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#curation_rule_text:
# - Human and mouse phenotypes that inhere in homologous structures and exhibit the same phenotypic quality are considered exact matches.
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration
================================================
FILE: examples/schema/curation_rule_text.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule_text.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification curation_rule_text see_also
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality https://github.com/mapping-commons/disease-mappings/issues/16
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality https://github.com/mapping-commons/disease-mappings/issues/16
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration The two phenotypes are associated with the exact same set of diseases https://github.com/mapping-commons/disease-mappings/issues/16
================================================
FILE: examples/schema/curation_rule_text2.sssom.tsv
================================================
#curie_map:
# WTO: http://purl.obolibrary.org/obo/WTO_
# CO321: "http://www.cropontology.org/rdf/CO_321:"
# ror: https://ror.org/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule_text2.sssom.tsv
#license: "https://www.etalab.gouv.fr/licence-ouverte-open-licence/"
#comment: This is an example file for the SSSOM for illustration only. This example was extracted from a real mapping set where the subject source (WTO) is an ontology used to annotate text (e.g. scientific literature) and the object source (CO321) is an ontology used to annotate the traits evaluated from observational data. The objective of the alignment is to allow information retrieval from both textual and experimental phenotypic dataset.
#creator_id: ror:02kvxyf05
#creator_label: "INRAE"
subject_id subject_label predicate_id object_id object_label mapping_justification curation_rule_text comment
WTO:0000304 cold resistance skos:closeMatch CO321:0000080 Cold tolerance semapv:ManualMappingCuration Rule 4: We consider that "tolerance" and "resistance" are almost equivalent when applied to abiotic environmental conditions.
WTO:0000450 aluminium toxicity skos:closeMatch CO321:0000079 Aluminum tolerance semapv:ManualMappingCuration Rule 3: We consider that the user of the information retrieval function interested in plant traits related to metal toxicity (WTO) also wants to retrieve observational data measuring the plant tolerance to the same metal (CO_321). The rule metal + toxicity (WTO) <-> metal + tolerance (CO321) is valid for any kind of metal.
WTO:0000065 anther extrusion skos:exactMatch CO321:0000982 Anther extrusion semapv:ManualMappingCuration
WTO:0000296 aphid resistance skos:closeMatch CO321:0000085 Aphid damage semapv:ManualMappingCuration Rule 2: We consider that the user of the information retrieval function interested in plant traits related to damages caused by some animal, insect, nematode, etc. also wants to retrieve observational data mentioning resistance to the same living organism.
WTO:0000281 Armyworm resistance skos:closeMatch CO321:0000086 Armyworm damage semapv:ManualMappingCuration Rule 2: We consider that the user of the information retrieval function interested in plant traits related to damages caused by some animal, insect, nematode, etc. also wants to retrieve observational data mentioning resistance to the same living organism.
WTO:0000125 awn color skos:exactMatch CO321:0000960 Awn color semapv:ManualMappingCuration
WTO:0000126 awn length skos:exactMatch CO321:0000026 Awn length semapv:ManualMappingCuration
WTO:0000452 bacterial leaf blight resistance skos:closeMatch CO321:0000932 Bacterial leaf blight severity semapv:ManualMappingCuration Rule 1.3: We consider that the user of the information retrieval function, given a pathogen or a disease, would like to retrieve all data, independently of the way the affection is observed. In observational data, a severity score is represented by two digits representing the vertical disease progress and an estimate of severity. The capacity of resistance to a disease would be deduced from the severity of this one on the plant.
================================================
FILE: examples/schema/curie_map.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curie_map.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration
================================================
FILE: examples/schema/cxsmiles_pipe.sssom.tsv
================================================
#curie_map:
# CHEBI: http://purl.obolibrary.org/obo/CHEBI_
# PUBCHEM.COMPOUND: http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID
# wikidata: http://www.wikidata.org/entity/
# orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/sssom/commons/examples/cxsmiles_pipe.sssom.tsv
#mapping_set_description: "Mappings between ChEBI and PubChem Compound established via structural matching. The ferrocene entry uses a CXSMILES match_string whose pipe-delimited extension block must be escaped to avoid being incorrectly split by a parser treating | as a multivalued separator."
#license: https://creativecommons.org/publicdomain/zero/1.0/
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: https://w3id.org/sssom/core_team
#comment: This is an example file for SSSOM for illustration only.
subject_id predicate_id object_id mapping_justification match_string subject_match_field object_match_field
CHEBI:30672 skos:exactMatch PUBCHEM.COMPOUND:7611 semapv:LexicalMatching c12c3c4c5c1[Fe]23451234c5c1c2c3c45 \|C:4.5,0.6,1.7,2.8,3.9,7.12,6.10,9.16,10.18,8.14\| wikidata:P10718 wikidata:P10718
================================================
FILE: examples/schema/extension-slots.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
# EXPROP: https://example.org/properties/
# ORGENT: https://example.org/entities/
#mapping_set_id: https://example.org/sets/exo2c-with-extensions
#mapping_set_title: Sample set EXO2C with extension slots
#license: https://creativecommons.org/licenses/by/4.0/
#extension_definitions:
# - slot_name: ext_bar
# property: EXPROP:barProperty
# type_hint: xsd:integer
# - slot_name: ext_baz
# property: EXPROP:bazProperty
# type_hint: linkml:Uriorcurie
# - slot_name: ext_foo
# property: EXPROP:fooProperty
#ext_foo: Foo A
#ext_undeclared_foo: Foo B
subject_id subject_label predicate_id object_id object_label mapping_justification ext_bar ext_baz ext_undeclared_baz
ORGENT:0001 alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration 111 ORGENT:BAZ_0001 BAZ A
ORGENT:0002 bob skos:closeMatch COMENT:0012 beta semapv:ManualMappingCuration 112 ORGENT:BAZ_0002
ORGENT:0004 daphne skos:closeMatch COMENT:0014 delta semapv:ManualMappingCuration 114 Baz C
ORGENT:0005 eve skos:closeMatch COMENT:0015 epsilon semapv:ManualMappingCuration 115 ORGENT:BAZ_0005 Baz E
================================================
FILE: examples/schema/issue_tracker.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# MH_MAPPINGS_GITHUB_ISSUES: https://github.com/mapping-commons/mh_mapping_initiative/issues/
#mapping_set_id: https://w3id.org/sssom/commons/examples/issue_tracker.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#issue_tracker: "https://github.com/mapping-commons/mh_mapping_initiative/issues"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification issue_tracker_item
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration MH_MAPPINGS_GITHUB_ISSUES:9123
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration MH_MAPPINGS_GITHUB_ISSUES:9125
================================================
FILE: examples/schema/issue_tracker_item.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# MH_MAPPINGS_GITHUB_ISSUES: https://github.com/mapping-commons/mh_mapping_initiative/issues/
#mapping_set_id: https://w3id.org/sssom/commons/examples/issue_tracker_item.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification issue_tracker_item
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration MH_MAPPINGS_GITHUB_ISSUES:9123
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration
HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration MH_MAPPINGS_GITHUB_ISSUES:9125
================================================
FILE: examples/schema/literals.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
#mapping_set_id: https://example.org/sets/literal-mappings
#license: https://creativecommons.org/licenses/by/4.0/
subject_label predicate_id object_id object_label mapping_justification subject_type
alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration rdfs literal
bob skos:closeMatch COMENT:0012 beta semapv:ManualMappingCuration rdfs literal
daphne skos:closeMatch COMENT:0014 delta semapv:ManualMappingCuration rdfs literal
eve skos:closeMatch COMENT:0015 epsilon semapv:ManualMappingCuration rdfs literal
================================================
FILE: examples/schema/mapping_set_confidence.sssom.tsv
================================================
#sssom_version: "1.1"
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/sssom/commons/examples/curie_map.sssom.tsv
#mapping_set_confidence: 0.8
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#mapping_tool: AgreementMakerLight
#comment: This is an example file for the SSSOM for illustration only. The mapping_set_confidence value expresses the confidence of the creator of the mapping into the agent that produced the mappings, i.e. AgreementMakerLight.
subject_id predicate_id object_id mapping_justification
HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalMatching
HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalMatching
================================================
FILE: examples/schema/mapping_tool_id.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# wikidata: https://www.wikidata.org/wiki/
#mapping_set_id: https://w3id.org/sssom/commons/examples/mapping_tool_id.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#issue_tracker: "https://github.com/mapping-commons/mh_mapping_initiative/issues"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification mapping_tool_id
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration wikidata:Q58057366
HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration wikidata:Q58057366
================================================
FILE: examples/schema/no_term_found.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# obo: http://purl.obolibrary.org/obo/
# orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/sssom/commons/examples/no_term_found.sssom.tsv
#creator_id:
# - orcid:0000-0002-7356-1779
#subject_source: obo:hp
#object_source: obo:mp
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#mapping_provider: "https://w3id.org/sssom/core_team"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification
HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration
HP:0000411 skos:exactMatch sssom:NoTermFound semapv:ManualMappingCuration
================================================
FILE: examples/schema/pipe-escaping.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
# ORGENT: https://example.org/entities/
#mapping_set_id: https://example.org/sets/test-escaping-pipe
#license: https://creativecommons.org/licenses/by/4.0/
#comment: >-
# This mapping set is intended to demonstrate the backslash-based
# escaping mechanism for multi-valued slots.
# In this set, the author_label slot of the first record has two values:
# "Alice|Bob" and "Charlie" (NOT "Alice\", "Bob", and "Charlie").
# The author_label slot of the second record has three values:
# "Alice\Bob", "Charlie\", and "David\|Eve\".
subject_id subject_label predicate_id object_id object_label mapping_justification author_label
ORGENT:0001 alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration Alice\|Bob|Charlie
ORGENT:0002 alice skos:closeMatch COMENT:0011 alpha semapv:ManualMappingCuration Alice\\Bob|Charlie\\|David\\\|Eve\\
================================================
FILE: examples/schema/predicate-types.sssom.tsv
================================================
#curie_map:
# COMENT: https://example.com/entities/
# ORGENT: https://example.org/entities/
# ORGPRO: https://example.org/properties/
#mapping_set_id: https://w3id.org/sssom/commons/examples/predicate-types.sssom.tsv
#license: https://creativecommons.org/licenses/by/4.0/
subject_id subject_label predicate_id object_id object_label mapping_justification predicate_type
ORGENT:0001 alice ORGPRO:example_annot_property COMENT:0011 alpha semapv:ManualMappingCuration owl annotation property
ORGENT:0002 bob ORGPRO:example_object_property COMENT:0012 beta semapv:ManualMappingCuration owl object property
ORGENT:0004 daphne ORGPRO:example_data_property COMENT:0014 delta semapv:ManualMappingCuration owl data property
ORGENT:0005 eve ORGPRO:example_rdf_property COMENT:0015 epsilon semapv:ManualMappingCuration rdf property
================================================
FILE: examples/schema/record-ids.sssom.tsv
================================================
# sssom_version: "1.1"
# curie_map:
# HP: http://purl.obolibrary.org/obo/FBbt_
# MP: http://purl.obolibrary.org/obo/UBERON_
# RI: https://example.org/sets/record-id#
# mapping_set_id: https://example.org/sets/record-id
# license: https://creativecommons.org/publicdomain/zero/1.0/
record_id subject_id predicate_id object_id mapping_justification
RI:0000001 HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalMatching
RI:0000002 HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalMatching
RI:0000003 HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration
================================================
FILE: examples/schema/review_date.sssom.tsv
================================================
# curie_map:
# CHEBI: http://purl.obolibrary.org/obo/CHEBI_
# mesh: http://id.nlm.nih.gov/mesh/
# orcid: https://orcid.org/
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/review_date.sssom.tsv
# creator_id:
# - orcid:0000-0003-4423-4370
# see_also:
# - https://github.com/mapping-commons/sssom/issues/511
# - https://github.com/mapping-commons/sssom/pull/514
# - https://mapping-commons.github.io/sssom/confidence-model
subject_id subject_label predicate_id object_id object_label mapping_justification author_id reviewer_id review_date
CHEBI:10001 Visnadin skos:exactMatch mesh:C067604 visnadin semapv:ManualMappingCuration orcid:0000-0001-9439-5346 orcid:0000-0003-4423-4370 2026-03-26
================================================
FILE: examples/schema/reviewer_agreement.sssom.tsv
================================================
# curie_map:
# CHEBI: http://purl.obolibrary.org/obo/CHEBI_
# mesh: http://id.nlm.nih.gov/mesh/
# orcid: https://orcid.org/
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/reviewer_agreement.sssom.tsv
# creator_id:
# - orcid:0000-0003-4423-4370
# see_also:
# - https://github.com/mapping-commons/sssom/issues/510
# - https://github.com/mapping-commons/sssom/pull/519
# - https://mapping-commons.github.io/sssom/confidence-model
subject_id subject_label predicate_id object_id object_label mapping_justification author_id reviewer_id reviewer_agreement comment
CHEBI:10001 Visnadin skos:exactMatch mesh:C067604 visnadin semapv:ManualMappingCuration orcid:0000-0001-9439-5346 orcid:0000-0003-4423-4370 0.99 the reviewer confidently agrees with the accuracy of the mapping
CHEBI:127105 tribromosalicylanilide skos:exactMatch mesh:C004361 tribromsalan semapv:LexicalMatching orcid:0000-0003-4423-4370 0.0 the reviewer is not sure whether the mapping is correct or incorrect
CHEBI:10057 9H-xanthene skos:exactMatch mesh:C002563 xanthan gum semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -0.99 the reviewer confidently disagrees with the accuracy of the mapping
================================================
FILE: examples/schema/similarity_score.sssom.tsv
================================================
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# orcid: https://orcid.org/
# wikidata: https://www.wikidata.org/entity/
#mapping_set_id: https://w3id.org/sssom/commons/examples/similarity_score.sssom.tsv
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#creator_id:
# - orcid:0000-0002-7356-1779
#mapping_provider: "https://w3id.org/sssom/core_team"
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification similarity_score similarity_measure
HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalSimilarityThresholdMatching 0.8 wikidata:Q865360
HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalSimilarityThresholdMatching 0.4 wikidata:Q865360
HP:0000411 skos:exactMatch MP:0000021 semapv:SemanticSimilarityThresholdMatching 1.0 wikidata:Q1784941
================================================
FILE: examples/schema/version.sssom.tsv
================================================
# sssom_version: "1.1"
# curie_map:
# HP: http://purl.obolibrary.org/obo/FBbt_
# MP: http://purl.obolibrary.org/obo/UBERON_
# license: https://w3id.org/sssom/license/unspecified
subject_id predicate_id object_id mapping_justification
HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalMatching
HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalMatching
================================================
FILE: mkdocs.yml
================================================
site_name: "A Simple Standard for Sharing Ontology Mappings (SSSOM)"
site_author: "The SSSOM Community"
theme:
name: material
analytics:
gtag: G-2SYBSJVZ23
# palette:
# scheme: slate
# primary: cyan
features:
- content.tabs.link
extra:
version:
provider: mike
plugins:
- search
- mermaid2
markdown_extensions:
- pymdownx.highlight:
use_pygments: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.tabbed:
- pymdownx.critic
- pymdownx.caret
- pymdownx.keys
- pymdownx.mark
- pymdownx.tilde
- pymdownx.arithmatex:
generic: true
- admonition
#- pymdownx.emoji:
# emoji_index: !!python/name:material.extensions.emoji.twemoji
# emoji_generator: !!python/name:material.extensions.emoji.to_svg
extra_javascript:
- javascripts/mathjax.js
- https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
nav:
- Home: index.md
- Introduction: introduction.md
- Getting started: getting-started.md
- Specification:
- Introduction: spec-intro.md
- Data model:
- Introduction: spec-model.md
- LinkML documentation: linkml-index.md
- Serialisations:
- Introduction: spec-formats.md
- SSSOM/TSV serialisation: spec-formats-tsv.md
- SSSOM/JSON serialisation: spec-formats-json.md
- SSSOM/RDF serialisation: spec-formats-rdf.md
- OWL/RDF serialisation: spec-formats-owl.md
- Support functions:
- Introduction: spec-support.md
- Hashing mapping records: spec-support-hashing.md
- Applying Chaining Rules: chaining-rules.md
- Resources for contributors: contributing.md
- Resources for users:
- FAQ: faq.md
- Community:
- Use Cases: usecases.md
- Workshops: workshops.md
- Presentations: presentations.md
- Training materials:
- Overview: training.md
- Basic Tutorial: tutorial.md
- How to:
- Mapping Justifications: mapping-justifications.md
- How to use mapping predicates: mapping-predicates.md
- Set up a mapping registry/commons: mapping-commons.md
- A basic guide for the SSSOM toolkit: toolkit.md
- 5-Star Entity Mappings - Cheatsheet: 5star-mappings.md
- Matching tool implementation guide: matching-tool-implementation-guide.md
- How to gradually enrich OMOP mappings with SSSOM: tutorials/omop-mappings.md
- How to assess mapping confidence: confidence-model.md
- Identifying mapping records: record-identifiers.md
- Reference:
- Glossary: glossary.md
- Related documentation: related-documentation.md
- Funding: funding.md
site_url: https://mapping-commons.github.io/sssom/
repo_url: https://github.com/mapping-commons/sssom/
edit_uri: "edit/master/src/docs/"
================================================
FILE: project/graphql/sssom_schema.graphql
================================================
# metamodel_version: 1.7.0
enum EntityTypeEnum
{
owl_class
owl_object_property
owl_data_property
owl_annotation_property
owl_named_individual
skos_concept
rdfs_resource
rdfs_class
rdfs_literal
rdfs_datatype
rdf_property
composed_entity_expression
}
enum MappingCardinalityEnum
{
__1__COLON__1
__1__COLON__n
n__COLON__1
n__COLON__n
__1__COLON__0
__0__COLON__1
__0__COLON__0
}
enum PredicateModifierEnum
{
Not
}
enum SssomVersionEnum
{
__1__FULL_STOP__0
__1__FULL_STOP__1
}
type ExtensionDefinition
{
slotName: String!
property: String
typeHint: String
}
type Mapping
{
recordId: EntityReference
subjectId: EntityReference
subjectLabel: String
subjectCategory: String
predicateId: EntityReference!
predicateLabel: String
predicateModifier: PredicateModifierEnum
objectId: EntityReference
objectLabel: String
objectCategory: String
mappingJustification: EntityReference!
authorId: [EntityReference]
authorLabel: [String]
reviewerId: [EntityReference]
reviewerLabel: [String]
creatorId: [EntityReference]
creatorLabel: [String]
license: NonRelativeURI
subjectType: EntityTypeEnum
subjectSource: EntityReference
subjectSourceVersion: String
objectType: EntityTypeEnum
objectSource: EntityReference
objectSourceVersion: String
predicateType: EntityTypeEnum
mappingProvider: NonRelativeURI
mappingSource: EntityReference
mappingCardinality: MappingCardinalityEnum
cardinalityScope: [String]
mappingTool: String
mappingToolId: EntityReference
mappingToolVersion: String
mappingDate: String
publicationDate: String
reviewDate: String
confidence: Float
reviewerAgreement: Float
curationRule: [EntityReference]
curationRuleText: [String]
subjectMatchField: [EntityReference]
objectMatchField: [EntityReference]
matchString: [String]
subjectPreprocessing: [EntityReference]
objectPreprocessing: [EntityReference]
similarityScore: Float
similarityMeasure: String
seeAlso: [NonRelativeURI]
issueTrackerItem: EntityReference
other: String
comment: String
}
type MappingRegistry
{
mappingRegistryId: EntityReference!
mappingRegistryTitle: String
mappingRegistryDescription: String
imports: [NonRelativeURI]
mappingSetReferences: [MappingSetReference]
documentation: NonRelativeURI
homepage: NonRelativeURI
issueTracker: NonRelativeURI
}
type MappingSet
{
sssomVersion: SssomVersionEnum
curieMap: [Prefix]
mappings: [Mapping]
mappingSetId: NonRelativeURI!
mappingSetVersion: String
mappingSetSource: [NonRelativeURI]
mappingSetTitle: String
mappingSetDescription: String
mappingSetConfidence: Float
creatorId: [EntityReference]
creatorLabel: [String]
license: NonRelativeURI!
subjectType: EntityTypeEnum
subjectSource: EntityReference
subjectSourceVersion: String
objectType: EntityTypeEnum
objectSource: EntityReference
objectSourceVersion: String
predicateType: EntityTypeEnum
mappingProvider: NonRelativeURI
cardinalityScope: [String]
mappingTool: String
mappingToolId: EntityReference
mappingToolVersion: String
mappingDate: String
publicationDate: String
subjectMatchField: [EntityReference]
objectMatchField: [EntityReference]
subjectPreprocessing: [EntityReference]
objectPreprocessing: [EntityReference]
similarityMeasure: String
curationRule: [EntityReference]
curationRuleText: [String]
seeAlso: [NonRelativeURI]
issueTracker: NonRelativeURI
other: String
comment: String
extensionDefinitions: [ExtensionDefinition]
}
type MappingSetReference
{
mappingSetId: NonRelativeURI!
mirrorFrom: NonRelativeURI
registryConfidence: Float
mappingSetGroup: String
lastUpdated: String
localName: String
}
type NoTermFound
{
}
type Prefix
{
prefixName: String!
prefixUrl: String
}
type Propagatable
{
propagated: Boolean
}
type Versionable
{
addedIn: SssomVersionEnum
}
================================================
FILE: project/jsonld/sssom_schema.context.jsonld
================================================
{
"@context": {
"xsd": "http://www.w3.org/2001/XMLSchema#",
"dcterms": "http://purl.org/dc/terms/",
"linkml": "https://w3id.org/linkml/",
"oboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
"owl": "http://www.w3.org/2002/07/owl#",
"pav": "http://purl.org/pav/",
"prov": "http://www.w3.org/ns/prov#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"semapv": "https://w3id.org/semapv/vocab/",
"skos": "http://www.w3.org/2004/02/skos/core#",
"sssom": "https://w3id.org/sssom/",
"@vocab": "https://w3id.org/sssom/",
"author_id": {
"@type": "rdfs:Resource",
"@id": "pav:authoredBy"
},
"author_label": {
"@id": "author_label"
},
"cardinality_scope": {
"@id": "cardinality_scope"
},
"comment": {
"@id": "rdfs:comment"
},
"confidence": {
"@type": "xsd:double",
"@id": "confidence"
},
"creator_id": {
"@type": "rdfs:Resource",
"@id": "dcterms:creator"
},
"creator_label": {
"@id": "creator_label"
},
"curation_rule": {
"@type": "rdfs:Resource",
"@id": "curation_rule"
},
"curation_rule_text": {
"@id": "curation_rule_text"
},
"curie_map": {
"@type": "@id",
"@id": "curie_map"
},
"documentation": {
"@type": "xsd:anyURI",
"@id": "documentation"
},
"extension_definitions": {
"@type": "@id",
"@id": "extension_definitions"
},
"property": {
"@type": "xsd:anyURI",
"@id": "property"
},
"slot_name": {
"@id": "slot_name"
},
"type_hint": {
"@type": "xsd:anyURI",
"@id": "type_hint"
},
"homepage": {
"@type": "xsd:anyURI",
"@id": "homepage"
},
"imports": {
"@type": "xsd:anyURI",
"@id": "imports"
},
"issue_tracker": {
"@type": "xsd:anyURI",
"@id": "issue_tracker"
},
"issue_tracker_item": {
"@type": "rdfs:Resource",
"@id": "issue_tracker_item"
},
"last_updated": {
"@type": "xsd:date",
"@id": "last_updated"
},
"license": {
"@type": "xsd:anyURI",
"@id": "dcterms:license"
},
"local_name": {
"@id": "local_name"
},
"mapping_cardinality": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "mapping_cardinality"
},
"mapping_date": {
"@type": "xsd:date",
"@id": "dcterms:created"
},
"mapping_justification": {
"@type": "rdfs:Resource",
"@id": "mapping_justification"
},
"mapping_provider": {
"@type": "xsd:anyURI",
"@id": "mapping_provider"
},
"mapping_registry_description": {
"@id": "mapping_registry_description"
},
"mapping_registry_id": {
"@type": "rdfs:Resource",
"@id": "mapping_registry_id"
},
"mapping_registry_title": {
"@id": "mapping_registry_title"
},
"mapping_set_confidence": {
"@type": "xsd:double",
"@id": "mapping_set_confidence"
},
"mapping_set_description": {
"@id": "dcterms:description"
},
"mapping_set_group": {
"@id": "mapping_set_group"
},
"mapping_set_id": {
"@type": "xsd:anyURI",
"@id": "mapping_set_id"
},
"mapping_set_references": {
"@type": "@id",
"@id": "mapping_set_references"
},
"mapping_set_source": {
"@type": "xsd:anyURI",
"@id": "prov:wasDerivedFrom"
},
"mapping_set_title": {
"@id": "dcterms:title"
},
"mapping_set_version": {
"@id": "owl:versionInfo"
},
"mapping_source": {
"@type": "rdfs:Resource",
"@id": "mapping_source"
},
"mapping_tool": {
"@id": "mapping_tool"
},
"mapping_tool_id": {
"@type": "rdfs:Resource",
"@id": "mapping_tool_id"
},
"mapping_tool_version": {
"@id": "mapping_tool_version"
},
"mappings": {
"@type": "@id",
"@id": "mappings"
},
"match_string": {
"@id": "match_string"
},
"mirror_from": {
"@type": "xsd:anyURI",
"@id": "mirror_from"
},
"object_category": {
"@id": "object_category"
},
"object_id": {
"@type": "rdfs:Resource",
"@id": "owl:annotatedTarget"
},
"object_label": {
"@id": "object_label"
},
"object_match_field": {
"@type": "rdfs:Resource",
"@id": "object_match_field"
},
"object_preprocessing": {
"@type": "rdfs:Resource",
"@id": "object_preprocessing"
},
"object_source": {
"@type": "rdfs:Resource",
"@id": "object_source"
},
"object_source_version": {
"@id": "object_source_version"
},
"object_type": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "object_type"
},
"other": {
"@id": "other"
},
"predicate_id": {
"@type": "rdfs:Resource",
"@id": "owl:annotatedProperty"
},
"predicate_label": {
"@id": "predicate_label"
},
"predicate_modifier": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "predicate_modifier"
},
"predicate_type": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "predicate_type"
},
"prefix_name": {
"@id": "prefix_name"
},
"prefix_url": {
"@type": "xsd:anyURI",
"@id": "prefix_url"
},
"propagated": {
"@type": "xsd:boolean",
"@id": "propagated"
},
"publication_date": {
"@type": "xsd:date",
"@id": "dcterms:issued"
},
"record_id": {
"@type": "rdfs:Resource",
"@id": "record_id"
},
"registry_confidence": {
"@type": "xsd:double",
"@id": "registry_confidence"
},
"review_date": {
"@type": "xsd:date",
"@id": "review_date"
},
"reviewer_agreement": {
"@type": "xsd:double",
"@id": "reviewer_agreement"
},
"reviewer_id": {
"@type": "rdfs:Resource",
"@id": "reviewer_id"
},
"reviewer_label": {
"@id": "reviewer_label"
},
"see_also": {
"@type": "xsd:anyURI",
"@id": "rdfs:seeAlso"
},
"similarity_measure": {
"@id": "similarity_measure"
},
"similarity_score": {
"@type": "xsd:double",
"@id": "similarity_score"
},
"sssom_version": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "sssom_version"
},
"subject_category": {
"@id": "subject_category"
},
"subject_id": {
"@type": "rdfs:Resource",
"@id": "owl:annotatedSource"
},
"subject_label": {
"@id": "subject_label"
},
"subject_match_field": {
"@type": "rdfs:Resource",
"@id": "subject_match_field"
},
"subject_preprocessing": {
"@type": "rdfs:Resource",
"@id": "subject_preprocessing"
},
"subject_source": {
"@type": "rdfs:Resource",
"@id": "subject_source"
},
"subject_source_version": {
"@id": "subject_source_version"
},
"subject_type": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "subject_type"
},
"added_in": {
"@context": {
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
},
"@id": "added_in"
},
"ExtensionDefinition": {
"@id": "ExtensionDefinition"
},
"Mapping": {
"@id": "owl:Axiom"
},
"MappingRegistry": {
"@id": "MappingRegistry"
},
"MappingSet": {
"@id": "MappingSet"
},
"MappingSetReference": {
"@id": "MappingSetReference"
},
"NoTermFound": {
"@id": "NoTermFound"
},
"Prefix": {
"@id": "Prefix"
},
"Propagatable": {
"@id": "Propagatable"
},
"Versionable": {
"@id": "Versionable"
}
}
}
================================================
FILE: project/jsonld/sssom_schema.jsonld
================================================
{
"name": "sssom",
"description": "Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)",
"see_also": [
"https://github.com/mapping-commons/sssom",
"https://mapping-commons.github.io/sssom/home/"
],
"id": "https://w3id.org/sssom/schema/",
"imports": [
"linkml:types"
],
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"prefixes": [
{
"prefix_prefix": "dcterms",
"prefix_reference": "http://purl.org/dc/terms/"
},
{
"prefix_prefix": "linkml",
"prefix_reference": "https://w3id.org/linkml/"
},
{
"prefix_prefix": "sssom",
"prefix_reference": "https://w3id.org/sssom/"
},
{
"prefix_prefix": "rdfs",
"prefix_reference": "http://www.w3.org/2000/01/rdf-schema#"
},
{
"prefix_prefix": "rdf",
"prefix_reference": "http://www.w3.org/1999/02/22-rdf-syntax-ns#"
},
{
"prefix_prefix": "oboInOwl",
"prefix_reference": "http://www.geneontology.org/formats/oboInOwl#"
},
{
"prefix_prefix": "pav",
"prefix_reference": "http://purl.org/pav/"
},
{
"prefix_prefix": "prov",
"prefix_reference": "http://www.w3.org/ns/prov#"
},
{
"prefix_prefix": "skos",
"prefix_reference": "http://www.w3.org/2004/02/skos/core#"
},
{
"prefix_prefix": "xsd",
"prefix_reference": "http://www.w3.org/2001/XMLSchema#"
},
{
"prefix_prefix": "semapv",
"prefix_reference": "https://w3id.org/semapv/vocab/"
}
],
"default_curi_maps": [
"semweb_context",
"obo_context"
],
"default_prefix": "sssom",
"default_range": "string",
"types": [
{
"name": "EntityReference",
"definition_uri": "https://w3id.org/sssom/EntityReference",
"description": "A reference to an entity involved in the mapping.\n",
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://mapping-commons.github.io/sssom/spec/#tsv"
],
"typeof": "uriorcurie",
"base": "str",
"uri": "http://www.w3.org/2000/01/rdf-schema#Resource",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "NonRelativeURI",
"definition_uri": "https://w3id.org/sssom/NonRelativeURI",
"description": "A URI as per RFC 3986, that is a string that matches the production of the \"URI\" rule defined in Appendix A of that RFC. Contrary to the underlying LinkML type, this specifically excludes _relative URI references_, which do not start with a scheme component. Relative URI references are forbidden because SSSOM has no built-in mechanism to provide the base URI that would be needed to resolve relative URI references into non-relative ones.",
"examples": [
{
"value": "https://example.org/path/to/file.txt#L4",
"description": "A URI that is URL to a HTTP resource.",
"@type": "Example"
},
{
"value": "urn:oasis:names:tc:entity:xmlns:xml:catalog",
"description": "A URI that is the URN of the namespace for the OASIS XML Catalogs specification.",
"@type": "Example"
},
{
"value": "ldap://example.org/cn=Alice,dc=example,dc=org?mail",
"description": "A URI that is a LDAP query URL.",
"@type": "Example"
},
{
"value": "mailto:alice@example.org",
"description": "A URI that is an email address.",
"@type": "Example"
},
{
"value": "file.txt",
"description": "An _invalid_ example, as it a relative URI (path only, no scheme).",
"@type": "Example"
},
{
"value": "/path/to/file.txt",
"description": "An _invalid_ example; though it appears to be an _absolute path_, it is a _relative URI_ because of the absence of a scheme.",
"@type": "Example"
},
{
"value": "//example.org/path/to/file.txt",
"description": "An _invalid_ example; though it includes an authority component (example.org), it has no scheme and is therefore a _relative URI_.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/448"
],
"typeof": "uri",
"base": "URI",
"uri": "http://www.w3.org/2001/XMLSchema#anyURI",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "string",
"definition_uri": "https://w3id.org/linkml/String",
"description": "A character string",
"notes": [
"In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Text"
],
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"@type": "TypeDefinition"
},
{
"name": "integer",
"definition_uri": "https://w3id.org/linkml/Integer",
"description": "An integer",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Integer"
],
"base": "int",
"uri": "http://www.w3.org/2001/XMLSchema#integer",
"@type": "TypeDefinition"
},
{
"name": "boolean",
"definition_uri": "https://w3id.org/linkml/Boolean",
"description": "A binary (true or false) value",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Boolean"
],
"base": "Bool",
"uri": "http://www.w3.org/2001/XMLSchema#boolean",
"repr": "bool",
"@type": "TypeDefinition"
},
{
"name": "float",
"definition_uri": "https://w3id.org/linkml/Float",
"description": "A real number that conforms to the xsd:float specification",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Float"
],
"base": "float",
"uri": "http://www.w3.org/2001/XMLSchema#float",
"@type": "TypeDefinition"
},
{
"name": "double",
"definition_uri": "https://w3id.org/linkml/Double",
"description": "A real number that conforms to the xsd:double specification",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"close_mappings": [
"schema:Float"
],
"base": "float",
"uri": "http://www.w3.org/2001/XMLSchema#double",
"@type": "TypeDefinition"
},
{
"name": "decimal",
"definition_uri": "https://w3id.org/linkml/Decimal",
"description": "A real number with arbitrary precision that conforms to the xsd:decimal specification",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"broad_mappings": [
"schema:Number"
],
"base": "Decimal",
"uri": "http://www.w3.org/2001/XMLSchema#decimal",
"@type": "TypeDefinition"
},
{
"name": "time",
"definition_uri": "https://w3id.org/linkml/Time",
"description": "A time object represents a (local) time of day, independent of any particular day",
"notes": [
"URI is dateTime because OWL reasoners do not work with straight date or time",
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Time"
],
"base": "XSDTime",
"uri": "http://www.w3.org/2001/XMLSchema#time",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "date",
"definition_uri": "https://w3id.org/linkml/Date",
"description": "a date (year, month and day) in an idealized calendar",
"notes": [
"URI is dateTime because OWL reasoners don't work with straight date or time",
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:Date"
],
"base": "XSDDate",
"uri": "http://www.w3.org/2001/XMLSchema#date",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "datetime",
"definition_uri": "https://w3id.org/linkml/Datetime",
"description": "The combination of a date and time",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"exact_mappings": [
"schema:DateTime"
],
"base": "XSDDateTime",
"uri": "http://www.w3.org/2001/XMLSchema#dateTime",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "date_or_datetime",
"definition_uri": "https://w3id.org/linkml/DateOrDatetime",
"description": "Either a date or a datetime",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "https://w3id.org/linkml/DateOrDatetime",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "uriorcurie",
"definition_uri": "https://w3id.org/linkml/Uriorcurie",
"description": "a URI or a CURIE",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "URIorCURIE",
"uri": "http://www.w3.org/2001/XMLSchema#anyURI",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "curie",
"definition_uri": "https://w3id.org/linkml/Curie",
"conforms_to": "https://www.w3.org/TR/curie/",
"description": "a compact URI",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"."
],
"comments": [
"in RDF serializations this MUST be expanded to a URI",
"in non-RDF serializations MAY be serialized as the compact representation"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "Curie",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "uri",
"definition_uri": "https://w3id.org/linkml/Uri",
"conforms_to": "https://www.ietf.org/rfc/rfc3987.txt",
"description": "a complete URI",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"."
],
"comments": [
"in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"close_mappings": [
"schema:URL"
],
"base": "URI",
"uri": "http://www.w3.org/2001/XMLSchema#anyURI",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "ncname",
"definition_uri": "https://w3id.org/linkml/Ncname",
"description": "Prefix part of CURIE",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "NCName",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "objectidentifier",
"definition_uri": "https://w3id.org/linkml/Objectidentifier",
"description": "A URI or CURIE that represents an object in the model.",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"."
],
"comments": [
"Used for inheritance and type checking"
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "ElementIdentifier",
"uri": "http://www.w3.org/ns/shex#iri",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "nodeidentifier",
"definition_uri": "https://w3id.org/linkml/Nodeidentifier",
"description": "A URI, CURIE or BNODE that represents a node in a model.",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "NodeIdentifier",
"uri": "http://www.w3.org/ns/shex#nonLiteral",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "jsonpointer",
"definition_uri": "https://w3id.org/linkml/Jsonpointer",
"conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901",
"description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "jsonpath",
"definition_uri": "https://w3id.org/linkml/Jsonpath",
"conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html",
"description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
},
{
"name": "sparqlpath",
"definition_uri": "https://w3id.org/linkml/Sparqlpath",
"conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths",
"description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.",
"notes": [
"If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"."
],
"from_schema": "https://w3id.org/linkml/types",
"imported_from": "linkml:types",
"base": "str",
"uri": "http://www.w3.org/2001/XMLSchema#string",
"repr": "str",
"@type": "TypeDefinition"
}
],
"enums": [
{
"name": "sssom_version_enum",
"definition_uri": "https://w3id.org/sssom/SssomVersionEnum",
"from_schema": "https://w3id.org/sssom/schema/",
"permissible_values": [
{
"text": "1.0",
"description": "SSSOM specification version 1.0",
"meaning": "sssom:version1.0"
},
{
"text": "1.1",
"description": "SSSOM specification version 1.1",
"meaning": "sssom:version1.1"
}
]
},
{
"name": "entity_type_enum",
"definition_uri": "https://w3id.org/sssom/EntityTypeEnum",
"from_schema": "https://w3id.org/sssom/schema/",
"permissible_values": [
{
"text": "owl class",
"meaning": "owl:Class"
},
{
"text": "owl object property",
"meaning": "owl:ObjectProperty"
},
{
"text": "owl data property",
"meaning": "owl:DataProperty"
},
{
"text": "owl annotation property",
"meaning": "owl:AnnotationProperty"
},
{
"text": "owl named individual",
"meaning": "owl:NamedIndividual"
},
{
"text": "skos concept",
"meaning": "skos:Concept"
},
{
"text": "rdfs resource",
"meaning": "rdfs:Resource"
},
{
"text": "rdfs class",
"meaning": "rdfs:Class"
},
{
"text": "rdfs literal",
"description": "This value indicates that the entity being mapped is not a semantic entity with a distinct identifier, but is instead represented entirely by its literal label. This value MUST NOT be used in the predicate_type slot.",
"meaning": "rdfs:Literal",
"see_also": [
"https://mapping-commons.github.io/sssom/spec-model/#literal-mappings",
"https://github.com/mapping-commons/sssom/issues/234",
"https://github.com/mapping-commons/sssom/blob/master/examples/schema/literals.sssom.tsv"
]
},
{
"text": "rdfs datatype",
"meaning": "rdfs:Datatype"
},
{
"text": "rdf property",
"meaning": "rdf:Property"
},
{
"text": "composed entity expression",
"description": "This value indicates that the entity ID does not represent a single entity, but a composite involving several individual entities. This value MUST NOT be used in the predicate_type slot. This specifications does not prescribe how an ID representing a composite entity should be interpreted; this is left at the discretion of applications.",
"meaning": "sssom:ComposedEntityExpression",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/402",
"https://github.com/mapping-commons/sssom/blob/master/examples/schema/composite-entities.sssom.tsv"
]
}
]
},
{
"name": "predicate_modifier_enum",
"definition_uri": "https://w3id.org/sssom/PredicateModifierEnum",
"from_schema": "https://w3id.org/sssom/schema/",
"permissible_values": [
{
"text": "Not",
"description": "Negating the mapping predicate. The meaning of the triple becomes subject_id is not a predicate_id match to object_id.",
"meaning": "sssom:NegatedPredicate"
}
]
},
{
"name": "mapping_cardinality_enum",
"definition_uri": "https://w3id.org/sssom/MappingCardinalityEnum",
"from_schema": "https://w3id.org/sssom/schema/",
"permissible_values": [
{
"text": "1:1",
"description": "Indicates the mapping record is about a one-to-one mapping, that is, the subject and the object are only mapped to each other, exclusive of any other subject or object."
},
{
"text": "1:n",
"description": "Indicates the mapping record is about a one-to-many mapping, that is, the same subject is mapped to several different objects."
},
{
"text": "n:1",
"description": "Indicates the mapping record is about a many-to-one mapping, that is, several different subjects are mapped to the same object."
},
{
"text": "n:n",
"description": "Indicates the mapping record is about a many-to-many mapping, that is, the subject is mapped to several different objects and the object is mapped to several different subjects."
},
{
"text": "1:0",
"description": "Indicates that the subject has no match in the object vocabulary. This value MUST only be used when the object_id is sssom:NoTermFound."
},
{
"text": "0:1",
"description": "Indicates that the object has no match in the subject vocabulary. This value MUST only be used when the subject_id is sssom:NoTermFound."
},
{
"text": "0:0",
"description": "Indicates that there is no match between the subject vocabulary and the object vocabulary. This value MUST only be used when both the subject_id and the object_id are sssom:NoTermFound."
}
]
}
],
"slots": [
{
"name": "prefix_name",
"definition_uri": "https://w3id.org/sssom/prefix_name",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/prefix_name",
"key": true,
"owner": "Prefix",
"domain_of": [
"Prefix"
],
"range": "ncname",
"required": true,
"@type": "SlotDefinition"
},
{
"name": "prefix_url",
"definition_uri": "https://w3id.org/sssom/prefix_url",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/prefix_url",
"owner": "Prefix",
"domain_of": [
"Prefix"
],
"range": "uri",
"@type": "SlotDefinition"
},
{
"name": "sssom_version",
"definition_uri": "https://w3id.org/sssom/sssom_version",
"instantiates": [
"sssom:Versionable"
],
"annotations": [
{
"tag": "added_in",
"value": "1.1",
"@type": "Annotation"
}
],
"description": "The version of the SSSOM specification a mapping set is compliant with.",
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/439",
"https://github.com/mapping-commons/sssom/blob/master/examples/schema/version.sssom.tsv"
],
"slot_uri": "https://w3id.org/sssom/sssom_version",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "sssom_version_enum",
"@type": "SlotDefinition"
},
{
"name": "curie_map",
"definition_uri": "https://w3id.org/sssom/curie_map",
"description": "A dictionary that contains prefixes as keys and their URI expansions as values.",
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/225",
"https://github.com/mapping-commons/sssom/pull/349",
"https://github.com/mapping-commons/sssom/blob/master/examples/schema/curie_map.sssom.tsv"
],
"slot_uri": "https://w3id.org/sssom/curie_map",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "Prefix",
"multivalued": true,
"inlined": true,
"@type": "SlotDefinition"
},
{
"name": "mirror_from",
"definition_uri": "https://w3id.org/sssom/mirror_from",
"description": "A URL location from which to obtain a resource, such as a mapping set.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mirror_from",
"owner": "MappingSetReference",
"domain_of": [
"MappingSetReference"
],
"range": "NonRelativeURI",
"@type": "SlotDefinition"
},
{
"name": "registry_confidence",
"definition_uri": "https://w3id.org/sssom/registry_confidence",
"description": "This value is set by the creator/maintainer of the mapping registry and reflects the confidence the mapping registry has in the correctness (i.e., precision) of mappings in the mapping set.\nWhen not explicitly specified, confidence estimation algorithms should consider the registry confidence in a mapping set to be 1.0 by default.",
"examples": [
{
"value": "0.95",
"description": "A confidence score of 0.95, indicating 95% confidence.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://mapping-commons.github.io/sssom/confidence-model"
],
"slot_uri": "https://w3id.org/sssom/registry_confidence",
"owner": "MappingSetReference",
"domain_of": [
"MappingSetReference"
],
"range": "double",
"minimum_value": 0.0,
"maximum_value": 1.0,
"@type": "SlotDefinition"
},
{
"name": "last_updated",
"definition_uri": "https://w3id.org/sssom/last_updated",
"description": "The date this reference was last updated.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/last_updated",
"owner": "MappingSetReference",
"domain_of": [
"MappingSetReference"
],
"range": "date",
"@type": "SlotDefinition"
},
{
"name": "local_name",
"definition_uri": "https://w3id.org/sssom/local_name",
"description": "The local name assigned to file that corresponds to the downloaded mapping set.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/local_name",
"owner": "MappingSetReference",
"domain_of": [
"MappingSetReference"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_set_references",
"definition_uri": "https://w3id.org/sssom/mapping_set_references",
"description": "A list of mapping set references.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mapping_set_references",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "MappingSetReference",
"recommended": true,
"multivalued": true,
"inlined": true,
"inlined_as_list": true,
"@type": "SlotDefinition"
},
{
"name": "mapping_registry_id",
"definition_uri": "https://w3id.org/sssom/mapping_registry_id",
"description": "The unique identifier of a mapping registry.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mapping_registry_id",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "EntityReference",
"required": true,
"@type": "SlotDefinition"
},
{
"name": "mapping_registry_title",
"definition_uri": "https://w3id.org/sssom/mapping_registry_title",
"description": "The title of a mapping registry.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mapping_registry_title",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_registry_description",
"definition_uri": "https://w3id.org/sssom/mapping_registry_description",
"description": "The description of a mapping registry.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mapping_registry_description",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "imports",
"definition_uri": "https://w3id.org/sssom/imports",
"description": "A list of registries that should be imported into this one.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/imports",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "NonRelativeURI",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "documentation",
"definition_uri": "https://w3id.org/sssom/documentation",
"description": "A URL to the documentation of this mapping commons.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/documentation",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "NonRelativeURI",
"@type": "SlotDefinition"
},
{
"name": "homepage",
"definition_uri": "https://w3id.org/sssom/homepage",
"description": "A URL to a homepage of this mapping commons.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/homepage",
"owner": "MappingRegistry",
"domain_of": [
"MappingRegistry"
],
"range": "NonRelativeURI",
"@type": "SlotDefinition"
},
{
"name": "mappings",
"definition_uri": "https://w3id.org/sssom/mappings",
"description": "Contains a list of mapping objects.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mappings",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "Mapping",
"recommended": true,
"multivalued": true,
"inlined": true,
"inlined_as_list": true,
"@type": "SlotDefinition"
},
{
"name": "subject_id",
"definition_uri": "https://w3id.org/sssom/subject_id",
"description": "The ID of the subject of the mapping.",
"examples": [
{
"value": "HP:0009894",
"description": "The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://www.w3.org/2002/07/owl#annotatedSource",
"http://www.w3.org/2002/07/owl#annotatedSource"
],
"slot_uri": "http://www.w3.org/2002/07/owl#annotatedSource",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "EntityReference",
"@type": "SlotDefinition"
},
{
"name": "subject_label",
"definition_uri": "https://w3id.org/sssom/subject_label",
"description": "The label of subject of the mapping.",
"examples": [
{
"value": "Thickened ears",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/subject_label",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"recommended": true,
"@type": "SlotDefinition"
},
{
"name": "subject_category",
"definition_uri": "https://w3id.org/sssom/subject_category",
"description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.",
"examples": [
{
"value": "UBERON:0001062",
"description": "The CURIE of the Uberon term for \"anatomical entity\".",
"@type": "Example"
},
{
"value": "anatomical entity",
"description": "A string, rather than ID, describing the \"anatomical entity\" category. This is possible, but less preferred than using an ID.",
"@type": "Example"
},
{
"value": "biolink:Gene",
"description": "The CURIE of the biolink class for genes.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/13",
"https://github.com/mapping-commons/sssom/issues/256"
],
"slot_uri": "https://w3id.org/sssom/subject_category",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "subject_type",
"definition_uri": "https://w3id.org/sssom/subject_type",
"instantiates": [
"sssom:Propagatable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
}
],
"description": "The type of entity that is being mapped.",
"examples": [
{
"value": "owl:Class",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/subject_type",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "entity_type_enum",
"@type": "SlotDefinition"
},
{
"name": "predicate_id",
"definition_uri": "https://w3id.org/sssom/predicate_id",
"description": "The ID of the predicate or relation that relates the subject and object of this match.",
"examples": [
{
"value": "owl:sameAs",
"description": "The subject and the object are instances (owl individuals), and the two instances are the same.",
"@type": "Example"
},
{
"value": "owl:equivalentClass",
"description": "The subject and the object are classes (owl class), and the two classes are the same.",
"@type": "Example"
},
{
"value": "owl:equivalentProperty",
"description": "The subject and the object are properties (owl object, data, annotation properties), and the two properties are the same.",
"@type": "Example"
},
{
"value": "rdfs:subClassOf",
"description": "The subject and the object are classes (owl class), and the subject is a subclass of the object.",
"@type": "Example"
},
{
"value": "rdfs:subPropertyOf",
"description": "The subject and the object are properties (owl object, data, annotation properties), and the subject is a subproperty of the object.",
"@type": "Example"
},
{
"value": "skos:relatedMatch",
"description": "The subject and the object are associated in some unspecified way.",
"@type": "Example"
},
{
"value": "skos:closeMatch",
"description": "The subject and the object are sufficiently similar that they can be used interchangeably in some information retrieval applications.",
"@type": "Example"
},
{
"value": "skos:exactMatch",
"description": "The subject and the object can, with a high degree of confidence, be used interchangeably across a wide range of information retrieval applications.",
"@type": "Example"
},
{
"value": "skos:narrowMatch",
"description": "From the SKOS primer: A triple skos:narrower (and skos:narrowMatch) asserts that , the object of the triple, is a narrower concept than , the subject of the triple.",
"@type": "Example"
},
{
"value": "skos:broadMatch",
"description": "From the SKOS primer: A triple skos:broader (and skos:broadMatch) asserts that , the object of the triple, is a broader concept than , the subject of the triple.",
"@type": "Example"
},
{
"value": "oboInOwl:hasDbXref",
"description": "Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go).",
"@type": "Example"
},
{
"value": "rdfs:seeAlso",
"description": "The subject and the object are associated in some unspecified way. The object IRI often resolves to a resource on the web that provides additional information.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://www.w3.org/2002/07/owl#annotatedProperty",
"http://www.w3.org/2002/07/owl#annotatedProperty"
],
"slot_uri": "http://www.w3.org/2002/07/owl#annotatedProperty",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "EntityReference",
"required": true,
"@type": "SlotDefinition"
},
{
"name": "predicate_modifier",
"definition_uri": "https://w3id.org/sssom/predicate_modifier",
"description": "A modifier for negating the predicate. See https://github.com/mapping-commons/sssom/issues/40 for discussion",
"examples": [
{
"value": "Not",
"description": "Negates the predicate, see documentation of predicate_modifier_enum",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/107"
],
"slot_uri": "https://w3id.org/sssom/predicate_modifier",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "predicate_modifier_enum",
"@type": "SlotDefinition"
},
{
"name": "predicate_label",
"definition_uri": "https://w3id.org/sssom/predicate_label",
"description": "The label of the predicate/relation of the mapping.",
"examples": [
{
"value": "has cross-reference",
"description": "The label of the oboInOwl:hasDbXref property to represent cross-references.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/predicate_label",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "predicate_type",
"definition_uri": "https://w3id.org/sssom/predicate_type",
"instantiates": [
"sssom:Propagatable",
"sssom:Versionable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
},
{
"tag": "added_in",
"value": "1.1",
"@type": "Annotation"
}
],
"description": "The type of the predicate used to map the subject and object entities.",
"examples": [
{
"value": "owl:AnnotationProperty",
"@type": "Example"
},
{
"value": "owl:ObjectProperty",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/143",
"https://github.com/mapping-commons/sssom/blob/master/examples/schema/predicate-types.sssom.tsv"
],
"slot_uri": "https://w3id.org/sssom/predicate_type",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "entity_type_enum",
"@type": "SlotDefinition"
},
{
"name": "object_id",
"definition_uri": "https://w3id.org/sssom/object_id",
"description": "The ID of the object of the mapping.",
"examples": [
{
"value": "HP:0009894",
"description": "The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://www.w3.org/2002/07/owl#annotatedTarget",
"http://www.w3.org/2002/07/owl#annotatedTarget"
],
"slot_uri": "http://www.w3.org/2002/07/owl#annotatedTarget",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "EntityReference",
"@type": "SlotDefinition"
},
{
"name": "object_label",
"definition_uri": "https://w3id.org/sssom/object_label",
"description": "The label of object of the mapping.",
"examples": [
{
"value": "Thickened ears",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/object_label",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"recommended": true,
"@type": "SlotDefinition"
},
{
"name": "object_category",
"definition_uri": "https://w3id.org/sssom/object_category",
"description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.",
"examples": [
{
"value": "UBERON:0001062",
"description": "The CURIE of the Uberon term for \"anatomical entity\".",
"@type": "Example"
},
{
"value": "anatomical entity",
"description": "A string, rather than ID, describing the \"anatomical entity\" category. This is possible, but less preferred than using an ID.",
"@type": "Example"
},
{
"value": "biolink:Gene",
"description": "The CURIE of the biolink class for genes.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://github.com/mapping-commons/sssom/issues/13",
"https://github.com/mapping-commons/sssom/issues/256"
],
"slot_uri": "https://w3id.org/sssom/object_category",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_justification",
"definition_uri": "https://w3id.org/sssom/mapping_justification",
"description": "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.",
"examples": [
{
"value": "semapv:LexicalMatching",
"@type": "Example"
},
{
"value": "semapv:ManualMappingCuration",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://mapping-commons.github.io/semantic-mapping-vocabulary/",
"https://www.ebi.ac.uk/ols4/ontologies/semapv"
],
"slot_uri": "https://w3id.org/sssom/mapping_justification",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "EntityReference",
"required": true,
"pattern": "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining|MappingInversion|StructuralMatching|InstanceBasedMatching|BackgroundKnowledgeBasedMatching)$",
"any_of": [
{
"equals_string": "semapv:LexicalMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:LogicalReasoning",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:CompositeMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:UnspecifiedMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:SemanticSimilarityThresholdMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:LexicalSimilarityThresholdMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:MappingChaining",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:MappingReview",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:ManualMappingCuration",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:MappingInversion",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:StructuralMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:InstanceBasedMatching",
"@type": "AnonymousSlotExpression"
},
{
"equals_string": "semapv:BackgroundKnowledgeBasedMatching",
"@type": "AnonymousSlotExpression"
}
],
"@type": "SlotDefinition"
},
{
"name": "object_type",
"definition_uri": "https://w3id.org/sssom/object_type",
"instantiates": [
"sssom:Propagatable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
}
],
"description": "The type of entity that is being mapped.",
"examples": [
{
"value": "owl:Class",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/object_type",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "entity_type_enum",
"@type": "SlotDefinition"
},
{
"name": "mapping_set_id",
"definition_uri": "https://w3id.org/sssom/mapping_set_id",
"description": "A globally unique identifier for the mapping set (not each individual mapping). Should ideally be resolvable.",
"examples": [
{
"value": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_exactmatch_ncit.sssom.tsv",
"description": "A persistent URI pointing to the latest version of the Mondo - NCIT mapping in the Mondo namespace.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mapping_set_id",
"owner": "MappingSetReference",
"domain_of": [
"MappingSet",
"MappingSetReference"
],
"range": "NonRelativeURI",
"required": true,
"@type": "SlotDefinition"
},
{
"name": "mapping_set_version",
"definition_uri": "https://w3id.org/sssom/mapping_set_version",
"description": "A version string for the mapping.",
"examples": [
{
"value": "2020-01-01",
"description": "A date-based version that indicates that the mapping was published on the 1st January in 2021.",
"@type": "Example"
},
{
"value": "1.2.1",
"description": "(A semantic version tag that indicates that this is the 1st major, 2nd minor version, patch 1 (https://semver.org/).)",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://www.w3.org/2002/07/owl#versionInfo"
],
"slot_uri": "http://www.w3.org/2002/07/owl#versionInfo",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_set_group",
"definition_uri": "https://w3id.org/sssom/mapping_set_group",
"description": "Set by the owners of the mapping registry. A way to group related mapping sets for example for UI purposes.",
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/mapping_set_group",
"owner": "MappingSetReference",
"domain_of": [
"MappingSetReference"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_set_title",
"definition_uri": "https://w3id.org/sssom/mapping_set_title",
"description": "The display name of a mapping set.",
"examples": [
{
"value": "The Mondo-OMIM mappings by Monarch Initiative.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://purl.org/dc/terms/title"
],
"slot_uri": "http://purl.org/dc/terms/title",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_set_description",
"definition_uri": "https://w3id.org/sssom/mapping_set_description",
"description": "A description of the mapping set.",
"examples": [
{
"value": "This mapping set was produced to integrate human and mouse phenotype data at the IMPC. It is primarily used for making mouse phenotypes searchable by human synonyms at https://mousephenotype.org/.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://purl.org/dc/terms/description"
],
"slot_uri": "http://purl.org/dc/terms/description",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_set_confidence",
"definition_uri": "https://w3id.org/sssom/mapping_set_confidence",
"instantiates": [
"sssom:Versionable"
],
"annotations": [
{
"tag": "added_in",
"value": "1.1",
"@type": "Annotation"
}
],
"description": "Mapping-set level confidence is assigned by the creator of the mapping set to indicate their overall confidence in the correctness (i.e., precision) of mappings in the mapping set. Mapping set confidence is intended to be used in cases were the creator wants to express an overall confidence into the agent that curated the individual mappings, for example a lexical matching tool, or a group of students.\nWhen not explicitly specified, confidence estimation algorithms should consider the mapping set confidence to be 1.0 by default.",
"examples": [
{
"value": "0.95",
"description": "A confidence score of 0.95, indicating 95% confidence that the mappings in the mapping set are correct.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"see_also": [
"https://mapping-commons.github.io/sssom/confidence-model",
"https://github.com/mapping-commons/sssom/issues/438",
"https://github.com/mapping-commons/sssom/blob/master/examples/schema/mapping_set_confidence.sssom.tsv"
],
"slot_uri": "https://w3id.org/sssom/mapping_set_confidence",
"owner": "MappingSet",
"domain_of": [
"MappingSet"
],
"range": "double",
"minimum_value": 0.0,
"maximum_value": 1.0,
"@type": "SlotDefinition"
},
{
"name": "creator_id",
"definition_uri": "https://w3id.org/sssom/creator_id",
"description": "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a list of ORCIDs or otherwise identifying URIs.",
"examples": [
{
"value": "orcid:0000-0002-7356-1779|orcid:0000-0002-6601-2165",
"description": "The ORCID of the (multiple) creators of the mapping. Note that this is how the example would look like specifically in the SSSOM/TSV format, where multivalued slots such as `creator_id` are represented as single strings containing `|`-separated values.",
"@type": "Example"
},
{
"value": "orcid:0000-0002-7356-1779",
"description": "The ORCID of the creator of the mapping.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://purl.org/dc/terms/creator"
],
"slot_uri": "http://purl.org/dc/terms/creator",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "EntityReference",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "creator_label",
"definition_uri": "https://w3id.org/sssom/creator_label",
"description": "A string representing the creator of this mapping. This should only be used in the absence of a proper semantic identifier (which would be stored in creator_id) for that creator. It is not expected that there should be any link between creator_id and creator_label; in particular, creator_label is not intended to provide a human-friendly version of an identifier in creator_id.",
"examples": [
{
"value": "Nicolas Matentzoglu|Chris Mungall",
"description": "The human-readable names of the (multiple) creators of the mapping. Note that this is how the example would look like specifically in the SSSOM/TSV format, where multivalued slots such as `creator_label` are represented as single strings containing `|`-separated values.",
"@type": "Example"
},
{
"value": "Nicolas Matentzoglu",
"description": "The human-readable name of the creator of the mapping.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/creator_label",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "string",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "author_id",
"definition_uri": "https://w3id.org/sssom/author_id",
"description": "Identifies the persons or groups responsible for asserting the mappings. Recommended to be a list of ORCIDs or otherwise identifying URIs.",
"examples": [
{
"value": "orcid:0000-0002-7356-1779|orcid:0000-0002-6601-2165",
"description": "The ORCID of the (multiple) authors of the mapping. Note that this is how the example would look like specifically in the SSSOM/TSV format, where multivalued slots such as `author_id` are represented as single strings containing `|`-separated values.",
"@type": "Example"
},
{
"value": "orcid:0000-0002-7356-1779",
"description": "The ORCID of the author of the mapping.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://purl.org/pav/authoredBy"
],
"slot_uri": "http://purl.org/pav/authoredBy",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "EntityReference",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "author_label",
"definition_uri": "https://w3id.org/sssom/author_label",
"description": "A string representing the author of this mapping. This should only be used in the absence of a proper semantic identifier (which would be stored in author_id) for that author. It is not expected that there should be any link between author_id and author_label; in particular, author_label is not intended to provide a human-friendly version of an identifier in author_id.",
"examples": [
{
"value": "Nicolas Matentzoglu|Chris Mungall",
"description": "The human-readable names of the (multiple) authors of the mapping. Note that this is how the example would look like specifically in the SSSOM/TSV format, where multivalued slots such as `author_label` are represented as single strings containing `|`-separated values.",
"@type": "Example"
},
{
"value": "Nicolas Matentzoglu",
"description": "The human-readable name of the author of the mapping.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/author_label",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "reviewer_id",
"definition_uri": "https://w3id.org/sssom/reviewer_id",
"description": "Identifies the persons or groups that reviewed and confirmed the mapping. Recommended to be a list of ORCIDs or otherwise identifying URIs.",
"examples": [
{
"value": "orcid:0000-0002-7356-1779|orcid:0000-0002-6601-2165",
"description": "The ORCID of the (multiple) reviewers of the mapping. Note that this is how the example would look like specifically in the SSSOM/TSV format, where multivalued slots such as `reviewer_id` are represented as single strings containing `|`-separated values.",
"@type": "Example"
},
{
"value": "orcid:0000-0002-7356-1779",
"description": "The ORCID of the reviewer of the mapping.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/reviewer_id",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "EntityReference",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "reviewer_label",
"definition_uri": "https://w3id.org/sssom/reviewer_label",
"description": "A string representing the reviewer of this mapping. This should only be used in the absence of a proper semantic identifier (which would be stored in reviewer_id) for that reviewer. It is not expected that there should be any link between reviewer_id and reviewer_label; in particular, reviewer_label is not intended to provide a human-friendly version of an identifier in reviewer_id.",
"examples": [
{
"value": "Nicolas Matentzoglu|Chris Mungall",
"description": "The human-readable names of the (multiple) reviewers of the mapping. Note that this is how the example would look like specifically in the SSSOM/TSV format, where multivalued slots such as `reviewer_label` are represented as single strings containing `|`-separated values.",
"@type": "Example"
},
{
"value": "Nicolas Matentzoglu",
"description": "The human-readable name of the reviewer of the mapping.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/reviewer_label",
"owner": "Mapping",
"domain_of": [
"Mapping"
],
"range": "string",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "license",
"definition_uri": "https://w3id.org/sssom/license",
"description": "A url to the license of the mapping. In absence of a license we assume no license.",
"examples": [
{
"value": "https://creativecommons.org/licenses/by/4.0/",
"description": "The URI of the Creative Commons Attribution 4.0 International license.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"mappings": [
"http://purl.org/dc/terms/license"
],
"slot_uri": "http://purl.org/dc/terms/license",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "NonRelativeURI",
"@type": "SlotDefinition"
},
{
"name": "subject_source",
"definition_uri": "https://w3id.org/sssom/subject_source",
"instantiates": [
"sssom:Propagatable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
}
],
"description": "URI of vocabulary or identifier source for the subject.",
"examples": [
{
"value": "obo:mondo.owl",
"description": "A persistent OBO CURIE pointing to the latest version of the Mondo ontology.",
"@type": "Example"
},
{
"value": "wikidata:Q7876491",
"description": "A Wikidata identifier for the Uberon ontology resource.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/subject_source",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "EntityReference",
"@type": "SlotDefinition"
},
{
"name": "subject_source_version",
"definition_uri": "https://w3id.org/sssom/subject_source_version",
"instantiates": [
"sssom:Propagatable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
}
],
"description": "Version IRI or version string of the source of the subject term.",
"examples": [
{
"value": "http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl",
"description": "A persistent Version IRI pointing to the Mondo version '2021-01-30'",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/subject_source_version",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "object_source",
"definition_uri": "https://w3id.org/sssom/object_source",
"instantiates": [
"sssom:Propagatable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
}
],
"description": "URI of vocabulary or identifier source for the object.",
"examples": [
{
"value": "obo:mondo.owl",
"description": "A persistent OBO CURIE pointing to the latest version of the Mondo ontology.",
"@type": "Example"
},
{
"value": "wikidata:Q7876491",
"description": "A Wikidata identifier for the Uberon ontology resource.",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/object_source",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "EntityReference",
"@type": "SlotDefinition"
},
{
"name": "object_source_version",
"definition_uri": "https://w3id.org/sssom/object_source_version",
"instantiates": [
"sssom:Propagatable"
],
"annotations": [
{
"tag": "propagated",
"value": true,
"@type": "Annotation"
}
],
"description": "Version IRI or version string of the source of the object term.",
"examples": [
{
"value": "http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl",
"description": "A persistent Version IRI pointing to the Mondo version '2021-01-30'",
"@type": "Example"
}
],
"from_schema": "https://w3id.org/sssom/schema/",
"slot_uri": "https://w3id.org/sssom/object_source_version",
"owner": "Mapping",
"domain_of": [
"MappingSet",
"Mapping"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "mapping_provider",
"definition_uri": "https://w3id.org/sssom/mapping_provider",
"instantiates": [
"sssom:Propagatable"
gitextract_mofzv687/
├── .github/
│ ├── ISSUE_TEMPLATE/
│ │ └── new_sssom_element.md
│ ├── pull_request_template.md
│ └── workflows/
│ ├── build.yml
│ ├── codespell.yml
│ ├── deploy_documentation.yml
│ ├── main.yaml
│ └── pypi-publish.yaml
├── .gitignore
├── .prettierignore
├── CHANGELOG.md
├── CITATION.cff
├── CODE_OF_CONDUCT.md
├── CONTRIBUTING.md
├── LICENSE
├── Makefile
├── README.md
├── SSSOM.md
├── about.yaml
├── examples/
│ ├── README.md
│ ├── embedded/
│ │ ├── foodie-inc-2022-05-01.sssom.tsv
│ │ └── mp-hp-exact-0.0.1.sssom.tsv
│ ├── external/
│ │ ├── example1.sssom.tsv
│ │ ├── example1.sssom.yml
│ │ ├── mp-hp-exact-0.0.1.sssom.tsv
│ │ └── mp-hp-exact-0.0.1.sssom.yml
│ └── schema/
│ ├── cardinality-scope-empty.sssom.tsv
│ ├── cardinality-scope-predicate+object_source.sssom.tsv
│ ├── cardinality-scope-predicate.sssom.tsv
│ ├── cardinality-with-unmapped-entities.sssom.tsv
│ ├── cardinality.sssom.tsv
│ ├── composite-entities.sssom.tsv
│ ├── curation_rule-propagated.sssom.tsv
│ ├── curation_rule.sssom.tsv
│ ├── curation_rule_text-propagated.sssom.tsv
│ ├── curation_rule_text.sssom.tsv
│ ├── curation_rule_text2.sssom.tsv
│ ├── curie_map.sssom.tsv
│ ├── cxsmiles_pipe.sssom.tsv
│ ├── extension-slots.sssom.tsv
│ ├── issue_tracker.sssom.tsv
│ ├── issue_tracker_item.sssom.tsv
│ ├── literals.sssom.tsv
│ ├── mapping_set_confidence.sssom.tsv
│ ├── mapping_tool_id.sssom.tsv
│ ├── no_term_found.sssom.tsv
│ ├── pipe-escaping.sssom.tsv
│ ├── predicate-types.sssom.tsv
│ ├── record-ids.sssom.tsv
│ ├── review_date.sssom.tsv
│ ├── reviewer_agreement.sssom.tsv
│ ├── similarity_score.sssom.tsv
│ └── version.sssom.tsv
├── mkdocs.yml
├── project/
│ ├── excel/
│ │ └── sssom_schema.xlsx
│ ├── graphql/
│ │ └── sssom_schema.graphql
│ ├── jsonld/
│ │ ├── sssom_schema.context.jsonld
│ │ └── sssom_schema.jsonld
│ ├── jsonschema/
│ │ └── sssom_schema.schema.json
│ ├── prefixmap/
│ │ └── sssom_schema.yaml
│ ├── protobuf/
│ │ └── sssom_schema.proto
│ ├── shacl/
│ │ └── sssom_schema.shacl.ttl
│ ├── shex/
│ │ └── sssom_schema.shex
│ └── sqlschema/
│ └── sssom_schema.sql
├── project.Makefile
├── pyproject.toml
├── run.sh
├── scripts/
│ └── gh_table.pl
├── src/
│ ├── CONFIG.yaml
│ ├── doc-templates/
│ │ ├── class.md.jinja2
│ │ ├── class_diagram.md.jinja2
│ │ ├── common_metadata.md.jinja2
│ │ ├── frontpage.md.jinja2
│ │ ├── index.md.jinja2
│ │ └── slot.md.jinja2
│ ├── docs/
│ │ ├── 5star-mappings.md
│ │ ├── chaining-rules.md
│ │ ├── confidence-model.md
│ │ ├── contributing.md
│ │ ├── create-mapping-commons.md
│ │ ├── editors.md
│ │ ├── events/
│ │ │ ├── ccb2022.md
│ │ │ ├── mc2021.md
│ │ │ ├── mc2023.md
│ │ │ ├── oboacademy2022.md
│ │ │ ├── ohdsi2022.md
│ │ │ ├── ohdsi2023.md
│ │ │ ├── om2022.md
│ │ │ ├── pistoia2022.md
│ │ │ └── wsbo2021.md
│ │ ├── explanation/
│ │ │ └── mappings.md
│ │ ├── faq.md
│ │ ├── funding.md
│ │ ├── getting-started.md
│ │ ├── glossary.md
│ │ ├── introduction.md
│ │ ├── javascripts/
│ │ │ └── mathjax.js
│ │ ├── mapping-commons.md
│ │ ├── mapping-justifications.md
│ │ ├── mapping-predicates.md
│ │ ├── matching-tool-implementation-guide.md
│ │ ├── presentations.md
│ │ ├── record-identifiers.md
│ │ ├── related-documentation.md
│ │ ├── spec-formats-json.md
│ │ ├── spec-formats-owl.md
│ │ ├── spec-formats-rdf.md
│ │ ├── spec-formats-tsv.md
│ │ ├── spec-formats.md
│ │ ├── spec-intro.md
│ │ ├── spec-model.md
│ │ ├── spec-support-hashing.md
│ │ ├── spec-support.md
│ │ ├── toolkit.md
│ │ ├── training.md
│ │ ├── tutorial.md
│ │ ├── tutorials/
│ │ │ └── omop-mappings.md
│ │ ├── usecases.md
│ │ └── workshops.md
│ └── sssom_schema/
│ ├── __init__.py
│ ├── context/
│ │ ├── sssom_schema.context.jsonld
│ │ └── sssom_schema.jsonld
│ ├── datamodel/
│ │ ├── __init__.py
│ │ └── sssom_schema.py
│ └── schema/
│ └── sssom_schema.yaml
├── tests/
│ ├── __init__.py
│ ├── input/
│ │ ├── CONFIG.yaml
│ │ └── README.md
│ └── test_added_in_annotations.py
└── utils/
└── get-value.sh
SYMBOL INDEX (139 symbols across 3 files)
FILE: project/sqlschema/sssom_schema.sql
type "mapping set" (line 186) | CREATE TABLE "mapping set" (
type "mapping set" (line 214) | CREATE INDEX "ix_mapping set_id" ON "mapping set" (id)
type "mapping registry" (line 216) | CREATE TABLE "mapping registry" (
type "mapping registry" (line 226) | CREATE INDEX "ix_mapping registry_id" ON "mapping registry" (id)
type "mapping set reference" (line 228) | CREATE TABLE "mapping set reference" (
type "mapping set reference" (line 238) | CREATE INDEX "ix_mapping set reference_id" ON "mapping set reference" (id)
type "extension definition" (line 240) | CREATE TABLE "extension definition" (
type "extension definition" (line 247) | CREATE INDEX "ix_extension definition_id" ON "extension definition" (id)
type "Propagatable" (line 249) | CREATE TABLE "Propagatable" (
type "Propagatable" (line 254) | CREATE INDEX "ix_Propagatable_id" ON "Propagatable" (id)
type "Versionable" (line 256) | CREATE TABLE "Versionable" (
type "Versionable" (line 261) | CREATE INDEX "ix_Versionable_id" ON "Versionable" (id)
type "NoTermFound" (line 263) | CREATE TABLE "NoTermFound" (
type "NoTermFound" (line 267) | CREATE INDEX "ix_NoTermFound_id" ON "NoTermFound" (id)
type mapping (line 269) | CREATE TABLE mapping (
type mapping_record_id_idx (line 311) | CREATE INDEX mapping_record_id_idx ON mapping (record_id)
type ix_mapping_id (line 312) | CREATE INDEX ix_mapping_id ON mapping (id)
type prefix (line 314) | CREATE TABLE prefix (
type prefix (line 322) | CREATE INDEX "prefix_mapping set_id_prefix_name_idx" ON prefix ("mapping...
type prefix (line 323) | CREATE INDEX "ix_prefix_mapping set_id" ON prefix ("mapping set_id")
type ix_prefix_prefix_url (line 324) | CREATE INDEX ix_prefix_prefix_url ON prefix (prefix_url)
type ix_prefix_prefix_name (line 325) | CREATE INDEX ix_prefix_prefix_name ON prefix (prefix_name)
type "mapping set_mapping_set_source" (line 327) | CREATE TABLE "mapping set_mapping_set_source" (
type "mapping set_mapping_set_source" (line 333) | CREATE INDEX "ix_mapping set_mapping_set_source_mapping_set_source" ON "...
type "mapping set_mapping_set_source" (line 334) | CREATE INDEX "ix_mapping set_mapping_set_source_mapping set_id" ON "mapp...
type "mapping set_creator_id" (line 336) | CREATE TABLE "mapping set_creator_id" (
type "mapping set_creator_id" (line 342) | CREATE INDEX "ix_mapping set_creator_id_creator_id" ON "mapping set_crea...
type "mapping set_creator_id" (line 343) | CREATE INDEX "ix_mapping set_creator_id_mapping set_id" ON "mapping set_...
type "mapping set_creator_label" (line 345) | CREATE TABLE "mapping set_creator_label" (
type "mapping set_creator_label" (line 351) | CREATE INDEX "ix_mapping set_creator_label_mapping set_id" ON "mapping s...
type "mapping set_creator_label" (line 352) | CREATE INDEX "ix_mapping set_creator_label_creator_label" ON "mapping se...
type "mapping set_cardinality_scope" (line 354) | CREATE TABLE "mapping set_cardinality_scope" (
type "mapping set_cardinality_scope" (line 360) | CREATE INDEX "ix_mapping set_cardinality_scope_mapping set_id" ON "mappi...
type "mapping set_cardinality_scope" (line 361) | CREATE INDEX "ix_mapping set_cardinality_scope_cardinality_scope" ON "ma...
type "mapping set_subject_match_field" (line 363) | CREATE TABLE "mapping set_subject_match_field" (
type "mapping set_subject_match_field" (line 369) | CREATE INDEX "ix_mapping set_subject_match_field_subject_match_field" ON...
type "mapping set_subject_match_field" (line 370) | CREATE INDEX "ix_mapping set_subject_match_field_mapping set_id" ON "map...
type "mapping set_object_match_field" (line 372) | CREATE TABLE "mapping set_object_match_field" (
type "mapping set_object_match_field" (line 378) | CREATE INDEX "ix_mapping set_object_match_field_object_match_field" ON "...
type "mapping set_object_match_field" (line 379) | CREATE INDEX "ix_mapping set_object_match_field_mapping set_id" ON "mapp...
type "mapping set_subject_preprocessing" (line 381) | CREATE TABLE "mapping set_subject_preprocessing" (
type "mapping set_subject_preprocessing" (line 387) | CREATE INDEX "ix_mapping set_subject_preprocessing_mapping set_id" ON "m...
type "mapping set_subject_preprocessing" (line 388) | CREATE INDEX "ix_mapping set_subject_preprocessing_subject_preprocessing...
type "mapping set_object_preprocessing" (line 390) | CREATE TABLE "mapping set_object_preprocessing" (
type "mapping set_object_preprocessing" (line 396) | CREATE INDEX "ix_mapping set_object_preprocessing_mapping set_id" ON "ma...
type "mapping set_object_preprocessing" (line 397) | CREATE INDEX "ix_mapping set_object_preprocessing_object_preprocessing" ...
type "mapping set_curation_rule" (line 399) | CREATE TABLE "mapping set_curation_rule" (
type "mapping set_curation_rule" (line 405) | CREATE INDEX "ix_mapping set_curation_rule_mapping set_id" ON "mapping s...
type "mapping set_curation_rule" (line 406) | CREATE INDEX "ix_mapping set_curation_rule_curation_rule" ON "mapping se...
type "mapping set_curation_rule_text" (line 408) | CREATE TABLE "mapping set_curation_rule_text" (
type "mapping set_curation_rule_text" (line 414) | CREATE INDEX "ix_mapping set_curation_rule_text_curation_rule_text" ON "...
type "mapping set_curation_rule_text" (line 415) | CREATE INDEX "ix_mapping set_curation_rule_text_mapping set_id" ON "mapp...
type "mapping set_see_also" (line 417) | CREATE TABLE "mapping set_see_also" (
type "mapping set_see_also" (line 423) | CREATE INDEX "ix_mapping set_see_also_mapping set_id" ON "mapping set_se...
type "mapping set_see_also" (line 424) | CREATE INDEX "ix_mapping set_see_also_see_also" ON "mapping set_see_also...
type "mapping set_extension_definitions" (line 426) | CREATE TABLE "mapping set_extension_definitions" (
type "mapping set_extension_definitions" (line 433) | CREATE INDEX "ix_mapping set_extension_definitions_mapping set_id" ON "m...
type "mapping set_extension_definitions" (line 434) | CREATE INDEX "ix_mapping set_extension_definitions_extension_definitions...
type "mapping registry_imports" (line 436) | CREATE TABLE "mapping registry_imports" (
type "mapping registry_imports" (line 442) | CREATE INDEX "ix_mapping registry_imports_mapping registry_id" ON "mappi...
type "mapping registry_imports" (line 443) | CREATE INDEX "ix_mapping registry_imports_imports" ON "mapping registry_...
type "mapping registry_mapping_set_references" (line 445) | CREATE TABLE "mapping registry_mapping_set_references" (
type "mapping registry_mapping_set_references" (line 452) | CREATE INDEX "ix_mapping registry_mapping_set_references_mapping_set_ref...
type "mapping registry_mapping_set_references" (line 453) | CREATE INDEX "ix_mapping registry_mapping_set_references_mapping registr...
type mapping_author_id (line 455) | CREATE TABLE mapping_author_id (
type ix_mapping_author_id_author_id (line 461) | CREATE INDEX ix_mapping_author_id_author_id ON mapping_author_id (author...
type ix_mapping_author_id_mapping_id (line 462) | CREATE INDEX ix_mapping_author_id_mapping_id ON mapping_author_id (mappi...
type mapping_author_label (line 464) | CREATE TABLE mapping_author_label (
type ix_mapping_author_label_author_label (line 470) | CREATE INDEX ix_mapping_author_label_author_label ON mapping_author_labe...
type ix_mapping_author_label_mapping_id (line 471) | CREATE INDEX ix_mapping_author_label_mapping_id ON mapping_author_label ...
type mapping_reviewer_id (line 473) | CREATE TABLE mapping_reviewer_id (
type ix_mapping_reviewer_id_reviewer_id (line 479) | CREATE INDEX ix_mapping_reviewer_id_reviewer_id ON mapping_reviewer_id (...
type ix_mapping_reviewer_id_mapping_id (line 480) | CREATE INDEX ix_mapping_reviewer_id_mapping_id ON mapping_reviewer_id (m...
type mapping_reviewer_label (line 482) | CREATE TABLE mapping_reviewer_label (
type ix_mapping_reviewer_label_mapping_id (line 488) | CREATE INDEX ix_mapping_reviewer_label_mapping_id ON mapping_reviewer_la...
type ix_mapping_reviewer_label_reviewer_label (line 489) | CREATE INDEX ix_mapping_reviewer_label_reviewer_label ON mapping_reviewe...
type mapping_creator_id (line 491) | CREATE TABLE mapping_creator_id (
type ix_mapping_creator_id_creator_id (line 497) | CREATE INDEX ix_mapping_creator_id_creator_id ON mapping_creator_id (cre...
type ix_mapping_creator_id_mapping_id (line 498) | CREATE INDEX ix_mapping_creator_id_mapping_id ON mapping_creator_id (map...
type mapping_creator_label (line 500) | CREATE TABLE mapping_creator_label (
type ix_mapping_creator_label_creator_label (line 506) | CREATE INDEX ix_mapping_creator_label_creator_label ON mapping_creator_l...
type ix_mapping_creator_label_mapping_id (line 507) | CREATE INDEX ix_mapping_creator_label_mapping_id ON mapping_creator_labe...
type mapping_cardinality_scope (line 509) | CREATE TABLE mapping_cardinality_scope (
type ix_mapping_cardinality_scope_cardinality_scope (line 515) | CREATE INDEX ix_mapping_cardinality_scope_cardinality_scope ON mapping_c...
type ix_mapping_cardinality_scope_mapping_id (line 516) | CREATE INDEX ix_mapping_cardinality_scope_mapping_id ON mapping_cardinal...
type mapping_curation_rule (line 518) | CREATE TABLE mapping_curation_rule (
type ix_mapping_curation_rule_mapping_id (line 524) | CREATE INDEX ix_mapping_curation_rule_mapping_id ON mapping_curation_rul...
type ix_mapping_curation_rule_curation_rule (line 525) | CREATE INDEX ix_mapping_curation_rule_curation_rule ON mapping_curation_...
type mapping_curation_rule_text (line 527) | CREATE TABLE mapping_curation_rule_text (
type ix_mapping_curation_rule_text_curation_rule_text (line 533) | CREATE INDEX ix_mapping_curation_rule_text_curation_rule_text ON mapping...
type ix_mapping_curation_rule_text_mapping_id (line 534) | CREATE INDEX ix_mapping_curation_rule_text_mapping_id ON mapping_curatio...
type mapping_subject_match_field (line 536) | CREATE TABLE mapping_subject_match_field (
type ix_mapping_subject_match_field_subject_match_field (line 542) | CREATE INDEX ix_mapping_subject_match_field_subject_match_field ON mappi...
type ix_mapping_subject_match_field_mapping_id (line 543) | CREATE INDEX ix_mapping_subject_match_field_mapping_id ON mapping_subjec...
type mapping_object_match_field (line 545) | CREATE TABLE mapping_object_match_field (
type ix_mapping_object_match_field_object_match_field (line 551) | CREATE INDEX ix_mapping_object_match_field_object_match_field ON mapping...
type ix_mapping_object_match_field_mapping_id (line 552) | CREATE INDEX ix_mapping_object_match_field_mapping_id ON mapping_object_...
type mapping_match_string (line 554) | CREATE TABLE mapping_match_string (
type ix_mapping_match_string_mapping_id (line 560) | CREATE INDEX ix_mapping_match_string_mapping_id ON mapping_match_string ...
type ix_mapping_match_string_match_string (line 561) | CREATE INDEX ix_mapping_match_string_match_string ON mapping_match_strin...
type mapping_subject_preprocessing (line 563) | CREATE TABLE mapping_subject_preprocessing (
type ix_mapping_subject_preprocessing_subject_preprocessing (line 569) | CREATE INDEX ix_mapping_subject_preprocessing_subject_preprocessing ON m...
type ix_mapping_subject_preprocessing_mapping_id (line 570) | CREATE INDEX ix_mapping_subject_preprocessing_mapping_id ON mapping_subj...
type mapping_object_preprocessing (line 572) | CREATE TABLE mapping_object_preprocessing (
type ix_mapping_object_preprocessing_object_preprocessing (line 578) | CREATE INDEX ix_mapping_object_preprocessing_object_preprocessing ON map...
type ix_mapping_object_preprocessing_mapping_id (line 579) | CREATE INDEX ix_mapping_object_preprocessing_mapping_id ON mapping_objec...
type mapping_see_also (line 581) | CREATE TABLE mapping_see_also (
type ix_mapping_see_also_see_also (line 587) | CREATE INDEX ix_mapping_see_also_see_also ON mapping_see_also (see_also)
type ix_mapping_see_also_mapping_id (line 588) | CREATE INDEX ix_mapping_see_also_mapping_id ON mapping_see_also (mapping...
FILE: src/sssom_schema/datamodel/sssom_schema.py
class EntityReference (line 82) | class EntityReference(Uriorcurie):
class NonRelativeURI (line 91) | class NonRelativeURI(Uri):
class PrefixPrefixName (line 100) | class PrefixPrefixName(NCName):
class MappingSet (line 105) | class MappingSet(YAMLRoot):
method __post_init__ (line 155) | def __post_init__(self, *_: str, **kwargs: Any):
class Mapping (line 286) | class Mapping(YAMLRoot):
method __post_init__ (line 348) | def __post_init__(self, *_: str, **kwargs: Any):
class MappingRegistry (line 522) | class MappingRegistry(YAMLRoot):
method __post_init__ (line 542) | def __post_init__(self, *_: str, **kwargs: Any):
class MappingSetReference (line 573) | class MappingSetReference(YAMLRoot):
method __post_init__ (line 592) | def __post_init__(self, *_: str, **kwargs: Any):
class Prefix (line 617) | class Prefix(YAMLRoot):
method __post_init__ (line 628) | def __post_init__(self, *_: str, **kwargs: Any):
class ExtensionDefinition (line 641) | class ExtensionDefinition(YAMLRoot):
method __post_init__ (line 656) | def __post_init__(self, *_: str, **kwargs: Any):
class Propagatable (line 672) | class Propagatable(YAMLRoot):
method __post_init__ (line 686) | def __post_init__(self, *_: str, **kwargs: Any):
class Versionable (line 694) | class Versionable(YAMLRoot):
method __post_init__ (line 707) | def __post_init__(self, *_: str, **kwargs: Any):
class NoTermFound (line 714) | class NoTermFound(YAMLRoot):
class SssomVersionEnum (line 729) | class SssomVersionEnum(EnumDefinitionImpl):
method _addvals (line 736) | def _addvals(cls):
class EntityTypeEnum (line 748) | class EntityTypeEnum(EnumDefinitionImpl):
method _addvals (line 755) | def _addvals(cls):
class PredicateModifierEnum (line 807) | class PredicateModifierEnum(EnumDefinitionImpl):
class MappingCardinalityEnum (line 818) | class MappingCardinalityEnum(EnumDefinitionImpl):
method _addvals (line 825) | def _addvals(cls):
class slots (line 856) | class slots:
FILE: tests/test_added_in_annotations.py
class TestAddedInAnnotationTestCase (line 9) | class TestAddedInAnnotationTestCase(unittest.TestCase):
method test_new_slots (line 12) | def test_new_slots(self):
Condensed preview — 129 files, each showing path, character count, and a content snippet. Download the .json file or copy for the full structured content (1,082K chars).
[
{
"path": ".github/ISSUE_TEMPLATE/new_sssom_element.md",
"chars": 1616,
"preview": "---\ntitle: \"[New metadata element]: \"\nname: Add new SSSOM metadata element\nabout: New metadata element suggestion for SS"
},
{
"path": ".github/pull_request_template.md",
"chars": 885,
"preview": "Resolves [#ISSUE, #ISSUE]\n\n- [ ] `docs/` have been added/updated if necessary\n- [ ] `make test` has been run locally\n- ["
},
{
"path": ".github/workflows/build.yml",
"chars": 1193,
"preview": "name: Build\non:\n workflow_dispatch:\n #push:\n # branches: [ master ]\n # paths:\n # - 'src/linkml/sssom.yaml'\n\njo"
},
{
"path": ".github/workflows/codespell.yml",
"chars": 591,
"preview": "# Codespell configuration is within pyproject.toml\n---\nname: Codespell\n\non:\n push:\n branches: [master]\n pull_reques"
},
{
"path": ".github/workflows/deploy_documentation.yml",
"chars": 1894,
"preview": "name: Deploy Documentation\n\n# Controls when the action will run. Triggers the workflow on push\non:\n workflow_dispatch:\n"
},
{
"path": ".github/workflows/main.yaml",
"chars": 1167,
"preview": "# Built from:\n# https://docs.github.com/en/actions/guides/building-and-testing-python\n\nname: Build and test sssom\n\non:\n "
},
{
"path": ".github/workflows/pypi-publish.yaml",
"chars": 1624,
"preview": "name: Publish Python Package\n# Upload to PyPI is triggered by creating & publishing a release in GitHub UI\n\non:\n releas"
},
{
"path": ".gitignore",
"chars": 1869,
"preview": "/docs/\n/project/docs/\n\n# Byte-compiled / optimized / DLL files\n__pycache__/\n*.py[cod]\n*$py.class\n\n# C extensions\n*.so\n\n#"
},
{
"path": ".prettierignore",
"chars": 36,
"preview": "project/prefixmap/sssom_schema.yaml\n"
},
{
"path": "CHANGELOG.md",
"chars": 5402,
"preview": "# Changelog for SSSOM\n\n## Next\n\n- Add `composed entity expression` as a new value in the `EntityType` enumeration ([issu"
},
{
"path": "CITATION.cff",
"chars": 4979,
"preview": "cff-version: '1.1.0'\nmessage: 'Please cite the following works when using this software.'\nabstract: \"<jats:title>Abstrac"
},
{
"path": "CODE_OF_CONDUCT.md",
"chars": 3364,
"preview": "# Contributor Covenant Code of Conduct\n\n## Our Pledge\n\nIn the interest of fostering an open and welcoming environment, w"
},
{
"path": "CONTRIBUTING.md",
"chars": 29007,
"preview": "# Contributing to SSSOM\n\n:+1: First of all: Thank you for taking the time to contribute!\n\nThe following is a set of guid"
},
{
"path": "LICENSE",
"chars": 1523,
"preview": "BSD 3-Clause License\n\nCopyright (c) 2022, Nico Matentzoglu\nAll rights reserved.\n\nRedistribution and use in source and bi"
},
{
"path": "Makefile",
"chars": 3484,
"preview": "MAKEFLAGS += --warn-undefined-variables\nSHELL := bash\n.SHELLFLAGS := -eu -o pipefail -c\n.DEFAULT_GOAL := help\n.DELETE_ON"
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{
"path": "README.md",
"chars": 7361,
"preview": "<!--[](https://zenodo.org/badge/latestdoi/13996/mapping-"
},
{
"path": "SSSOM.md",
"chars": 72,
"preview": "This page has moved here:\n\nhttps://mapping-commons.github.io/sssom/spec/"
},
{
"path": "about.yaml",
"chars": 150,
"preview": "name: sssom_schema\ndescription: A Simple Standard for Sharing Ontology Mappings (SSSOM)\nsource_schema_path: src/sssom_sc"
},
{
"path": "examples/README.md",
"chars": 142,
"preview": "# Examples of use of sssom\n\nThis folder contains example data conforming to sssom\n\nThe source for these is in [src/data]"
},
{
"path": "examples/embedded/foodie-inc-2022-05-01.sssom.tsv",
"chars": 2644,
"preview": "# comment: We could map to FOODON:00004187 instead which more specifically refers to\n# 'raw' Pink apples. Decided agai"
},
{
"path": "examples/embedded/mp-hp-exact-0.0.1.sssom.tsv",
"chars": 5072,
"preview": "# curie_map:\n# HP: http://purl.obolibrary.org/obo/HP_\n# MP: http://purl.obolibrary.org/obo/MP_\n# owl: http://www.w"
},
{
"path": "examples/external/example1.sssom.tsv",
"chars": 1445,
"preview": "subject_id\tsubject_label\tpredicate_id\tobject_id\tobject_label\tmapping_justification\tauthor_id\tobject_source_version\tmappi"
},
{
"path": "examples/external/example1.sssom.yml",
"chars": 1164,
"preview": "comment:\n We could map to FOODON:00004187 instead which more specifically refers to\n 'raw' Pink apples. Decided agains"
},
{
"path": "examples/external/mp-hp-exact-0.0.1.sssom.tsv",
"chars": 4538,
"preview": "subject_id\tsubject_label\tpredicate_id\tobject_id\tobject_label\tmapping_justification\r\nHP:0000175\tCleft palate\tskos:exactMa"
},
{
"path": "examples/external/mp-hp-exact-0.0.1.sssom.yml",
"chars": 552,
"preview": "curie_map:\n HP: http://purl.obolibrary.org/obo/HP_\n MP: http://purl.obolibrary.org/obo/MP_\n owl: http://www.w3.org/20"
},
{
"path": "examples/schema/cardinality-scope-empty.sssom.tsv",
"chars": 962,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n# NETENT: https://example.net/entities/\n# ORGENT: https://example"
},
{
"path": "examples/schema/cardinality-scope-predicate+object_source.sssom.tsv",
"chars": 1037,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n# NETENT: https://example.net/entities/\n# ORGENT: https://example"
},
{
"path": "examples/schema/cardinality-scope-predicate.sssom.tsv",
"chars": 1004,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n# NETENT: https://example.net/entities/\n# ORGENT: https://example"
},
{
"path": "examples/schema/cardinality-with-unmapped-entities.sssom.tsv",
"chars": 1182,
"preview": "#curie_map:\n# OBJ: https://example.org/object/\n# SRC: https://example.org/sources/\n# SUBJ: https://example.org/subjec"
},
{
"path": "examples/schema/cardinality.sssom.tsv",
"chars": 1215,
"preview": "#curie_map:\n# OBJ: https://example.org/object/\n# SUBJ: https://example.org/subject/\n#mapping_set_id: https://example.o"
},
{
"path": "examples/schema/composite-entities.sssom.tsv",
"chars": 938,
"preview": "#curie_map:\n# HP: http://purl.obolibrary.org/obo/HP_\n# MONDO: http://purl.obolibrary.org/obo/MONDO_\n# MP: http://purl"
},
{
"path": "examples/schema/curation_rule-propagated.sssom.tsv",
"chars": 1056,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/curation_rule.sssom.tsv",
"chars": 1151,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/curation_rule_text-propagated.sssom.tsv",
"chars": 1069,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/curation_rule_text.sssom.tsv",
"chars": 1308,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/curation_rule_text2.sssom.tsv",
"chars": 3148,
"preview": "#curie_map:\n# WTO: http://purl.obolibrary.org/obo/WTO_\n# CO321: \"http://www.cropontology.org/rdf/CO_321:\"\n# ror: http"
},
{
"path": "examples/schema/curie_map.sssom.tsv",
"chars": 743,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/cxsmiles_pipe.sssom.tsv",
"chars": 1104,
"preview": "#curie_map:\n# CHEBI: http://purl.obolibrary.org/obo/CHEBI_\n# PUBCHEM.COMPOUND: http://rdf.ncbi.nlm.nih.gov/pubchem/com"
},
{
"path": "examples/schema/extension-slots.sssom.tsv",
"chars": 1141,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n# EXPROP: https://example.org/properties/\n# ORGENT: https://examp"
},
{
"path": "examples/schema/issue_tracker.sssom.tsv",
"chars": 1008,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/issue_tracker_item.sssom.tsv",
"chars": 930,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/literals.sssom.tsv",
"chars": 578,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n#mapping_set_id: https://example.org/sets/literal-mappings\n#license"
},
{
"path": "examples/schema/mapping_set_confidence.sssom.tsv",
"chars": 871,
"preview": "#sssom_version: \"1.1\"\r\n#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_"
},
{
"path": "examples/schema/mapping_tool_id.sssom.tsv",
"chars": 863,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/no_term_found.sssom.tsv",
"chars": 760,
"preview": "#curie_map:\n# HP: http://purl.obolibrary.org/obo/HP_\n# MP: http://purl.obolibrary.org/obo/MP_\n# obo: http://purl.obol"
},
{
"path": "examples/schema/pipe-escaping.sssom.tsv",
"chars": 901,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n# ORGENT: https://example.org/entities/\n#mapping_set_id: https://e"
},
{
"path": "examples/schema/predicate-types.sssom.tsv",
"chars": 824,
"preview": "#curie_map:\n# COMENT: https://example.com/entities/\n# ORGENT: https://example.org/entities/\n# ORGPRO: https://example"
},
{
"path": "examples/schema/record-ids.sssom.tsv",
"chars": 575,
"preview": "# sssom_version: \"1.1\"\n# curie_map:\n# HP: http://purl.obolibrary.org/obo/FBbt_\n# MP: http://purl.obolibrary.org/obo/"
},
{
"path": "examples/schema/review_date.sssom.tsv",
"chars": 890,
"preview": "# curie_map:\n# CHEBI: http://purl.obolibrary.org/obo/CHEBI_\n# mesh: http://id.nlm.nih.gov/mesh/\n# orcid: https://o"
},
{
"path": "examples/schema/reviewer_agreement.sssom.tsv",
"chars": 1367,
"preview": "# curie_map:\n# CHEBI: http://purl.obolibrary.org/obo/CHEBI_\n# mesh: http://id.nlm.nih.gov/mesh/\n# orcid: https://o"
},
{
"path": "examples/schema/similarity_score.sssom.tsv",
"chars": 937,
"preview": "#curie_map:\r\n# HP: http://purl.obolibrary.org/obo/HP_\r\n# MP: http://purl.obolibrary.org/obo/MP_\r\n# orcid: https://orc"
},
{
"path": "examples/schema/version.sssom.tsv",
"chars": 361,
"preview": "# sssom_version: \"1.1\"\n# curie_map:\n# HP: http://purl.obolibrary.org/obo/FBbt_\n# MP: http://purl.obolibrary.org/obo/"
},
{
"path": "mkdocs.yml",
"chars": 2855,
"preview": "site_name: \"A Simple Standard for Sharing Ontology Mappings (SSSOM)\"\nsite_author: \"The SSSOM Community\"\ntheme:\n name: m"
},
{
"path": "project/graphql/sssom_schema.graphql",
"chars": 4237,
"preview": "# metamodel_version: 1.7.0\nenum EntityTypeEnum\n {\n owl_class\n owl_object_property\n owl_data_property\n owl_a"
},
{
"path": "project/jsonld/sssom_schema.context.jsonld",
"chars": 9279,
"preview": "{\n \"@context\": {\n \"xsd\": \"http://www.w3.org/2001/XMLSchema#\",\n \"dcterms\": \"http://purl.org/dc/terms/\",\n "
},
{
"path": "project/jsonld/sssom_schema.jsonld",
"chars": 126014,
"preview": "{\n \"name\": \"sssom\",\n \"description\": \"Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)\",\n \"see_a"
},
{
"path": "project/jsonschema/sssom_schema.schema.json",
"chars": 58207,
"preview": "{\n \"$defs\": {\n \"EntityTypeEnum\": {\n \"description\": \"\",\n \"enum\": [\n \"owl c"
},
{
"path": "project/prefixmap/sssom_schema.yaml",
"chars": 610,
"preview": "{\n \"dcterms\": \"http://purl.org/dc/terms/\",\n \"linkml\": \"https://w3id.org/linkml/\",\n \"oboInOwl\": \"http://www.geneont"
},
{
"path": "project/protobuf/sssom_schema.proto",
"chars": 4676,
"preview": " syntax=\"proto3\";\n package\n// metamodel_version: 1.7.0\n// A definition of an extension (non-standard) slot.\nmessage Exte"
},
{
"path": "project/shacl/sssom_schema.shacl.ttl",
"chars": 44412,
"preview": "@prefix dcterms: <http://purl.org/dc/terms/> .\n@prefix owl: <http://www.w3.org/2002/07/owl#> .\n@prefix pav: <http://purl"
},
{
"path": "project/shex/sssom_schema.shex",
"chars": 8727,
"preview": "# metamodel_version: 1.7.0\nBASE <https://w3id.org/sssom/>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX skos: <http:/"
},
{
"path": "project/sqlschema/sssom_schema.sql",
"chars": 44281,
"preview": "-- # Class: mapping set Description: Represents a set of mappings.\n-- * Slot: id\n-- * Slot: sssom_version Descri"
},
{
"path": "project.Makefile",
"chars": 1475,
"preview": "## Add your own custom Makefile targets here\n# Added by H2\nEXCEL_DIR = $(DEST)/excel\n\ngen-excel:\n\tmkdir -p $(EXCEL_DIR)\n"
},
{
"path": "pyproject.toml",
"chars": 1726,
"preview": "[build-system]\nrequires = [\"poetry-core>=1.0.0\", \"poetry-dynamic-versioning\"]\nbuild-backend = \"poetry_dynamic_versioning"
},
{
"path": "run.sh",
"chars": 498,
"preview": "#!/bin/sh\n# Wrapper script for docker.\n#\n# This is used primarily for wrapping the GNU Make workflow.\n# Instead of typin"
},
{
"path": "scripts/gh_table.pl",
"chars": 626,
"preview": "#!/usr/bin/perl\n\nmy $n=0;\nmy $len;\nmy $hlen;\nwhile(<>) {\n chomp;\n if ($n==0 && m@^\\#@) {\n s@^\\#@@;\n }\n "
},
{
"path": "src/CONFIG.yaml",
"chars": 1968,
"preview": "model_organization: mapping-commons # Name of github individual organization where this cone exists (e.g. linkml / mygit"
},
{
"path": "src/doc-templates/class.md.jinja2",
"chars": 3014,
"preview": "# Class: {{ gen.name(element) }}\n\n{%- if header -%}\n{{header}}\n{%- endif -%}\n\n\n{% if element.description %}\n{% set eleme"
},
{
"path": "src/doc-templates/class_diagram.md.jinja2",
"chars": 2542,
"preview": "{% if schemaview.class_parents(element.name) and schemaview.class_children(element.name) %}\n```{{ gen.mermaid_directive("
},
{
"path": "src/doc-templates/common_metadata.md.jinja2",
"chars": 1321,
"preview": "{% if element.aliases %}\n## Aliases\n\n{% for alias in element.aliases %}\n* {{ alias }}\n{%- endfor %}\n{% endif %}\n\n\n{% if "
},
{
"path": "src/doc-templates/frontpage.md.jinja2",
"chars": 13656,
"preview": "---\nhide:\n - edit\n---\n\n[edit page](https://github.com/mapping-commons/sssom/edit/master/src/doc-templates/frontpage.md."
},
{
"path": "src/doc-templates/index.md.jinja2",
"chars": 5668,
"preview": "# SSSOM Official Data Model Documentation\n\n\n\n{% if schema.description %}{{ schem"
},
{
"path": "src/doc-templates/slot.md.jinja2",
"chars": 3026,
"preview": "# {{ gen.name(element) }}\n\n**URI**: {{ gen.uri_link(element) }}\n\n**Applicable to**: {% for c in schemaview.get_classes_b"
},
{
"path": "src/docs/5star-mappings.md",
"chars": 4850,
"preview": "# 5-Star Entity Mappings - Cheatsheet\n\n[Download as PDF](resources/sssom_5star_mappings.pdf).\n\nThis document is under de"
},
{
"path": "src/docs/chaining-rules.md",
"chars": 4253,
"preview": "## SSSOM Mapping Chains\n\nThe goal of this document is to capture all obvious mapping chaining rules that could be applie"
},
{
"path": "src/docs/confidence-model.md",
"chars": 9429,
"preview": "# Confidence\n\nSSSOM enables annotating confidence in several ways for individual mappings\nrecords and for mapping sets.\n"
},
{
"path": "src/docs/contributing.md",
"chars": 216,
"preview": "# Contributing to SSSOM\n\n- [Contribution guidelines](https://github.com/mapping-commons/sssom/blob/master/CONTRIBUTING.m"
},
{
"path": "src/docs/create-mapping-commons.md",
"chars": 2733,
"preview": "## Getting started\n\n- First, create a virtual environment of your choice. If you need assistance with virtual environmen"
},
{
"path": "src/docs/editors.md",
"chars": 836,
"preview": "# Simple Standard for Sharing Ontological Mappings (SSSOM)\n\n## How to make a new release\n* Automated:\n * On the main co"
},
{
"path": "src/docs/events/ccb2022.md",
"chars": 1189,
"preview": "## CCB Seminar Series: Open SSSOM - Unlocking the wealth of biomedical data using shared standardized entity mappings\n\nW"
},
{
"path": "src/docs/events/mc2021.md",
"chars": 13707,
"preview": "# 1st Mapping Commons Workshop on Simple Standard for Sharing Ontology Mappings\n\nWhen: 03.09.2021\n\nFor a *list of partic"
},
{
"path": "src/docs/events/mc2023.md",
"chars": 3850,
"preview": "# 2nd Mapping Commons Workshop on Simple Standard for Sharing Ontology Mappings (SSSOM)\n\n**When**: Sunday, 23rd April, 2"
},
{
"path": "src/docs/events/oboacademy2022.md",
"chars": 564,
"preview": "## OBO Academy 2022: Introduction to manual mapping curation\n\nWhere: Virtual, https://oboacademy.github.io/obook/courses"
},
{
"path": "src/docs/events/ohdsi2022.md",
"chars": 1380,
"preview": "## OHDSI Symposium 2022: There are no \"good\" mappings.\n\nWhere:\n\n- https://www.ohdsi.org/ohdsi2022symposium/\n- https://ww"
},
{
"path": "src/docs/events/ohdsi2023.md",
"chars": 592,
"preview": "## Poster presentation at OHDSI 2023 Symposium, Rotterdam\n\n*Title*: \"Synergizing Simple Standard for Sharing Ontology Ma"
},
{
"path": "src/docs/events/om2022.md",
"chars": 889,
"preview": "## OM 2022: A Simple Standard for Ontological Mappings 2022 - Updates of data model and outlook\n\nWhere: Virtual, co-loca"
},
{
"path": "src/docs/events/pistoia2022.md",
"chars": 286,
"preview": "## Pistoia Seminar 2022: A Simple Standard for Sharing Ontological Mappings (SSSOM)\n\nWhere: Virtual\n\nWhen: 28th April 20"
},
{
"path": "src/docs/events/wsbo2021.md",
"chars": 467,
"preview": "## WSBO-2021: Workshop on Synergizing Biomedical Ontologies\n\nWhere: https://github.com/OntoloBridge/WSBO/\n\n[Slides](http"
},
{
"path": "src/docs/explanation/mappings.md",
"chars": 10126,
"preview": "# What is a mapping?\n\nThe word \"mapping\" is pretty\noverloaded in practice: for some people, it simply means \"a correspon"
},
{
"path": "src/docs/faq.md",
"chars": 5752,
"preview": "# Frequently Asked Questions (FAQ)\n\n<a id=\"why\"></a>\n## Why should our mappings be FAIR and carefully standardised?\n\nMap"
},
{
"path": "src/docs/funding.md",
"chars": 3382,
"preview": "## Funding\n\nThe Simple Standard for Sharing Ontological Mappings (SSSOM) is a community-driven project which has receive"
},
{
"path": "src/docs/getting-started.md",
"chars": 15497,
"preview": "## Getting Started with SSSOM\n\nPre-requisites:\n\n- You know [what a mapping is](explanation/mappings.md).\n\n### Creating S"
},
{
"path": "src/docs/glossary.md",
"chars": 159,
"preview": "# Glossary\n\nThe glossary is currently being developed [here](https://docs.google.com/document/d/1QqR8j7szjaq6wzE9YLBnZ2k"
},
{
"path": "src/docs/introduction.md",
"chars": 18613,
"preview": "# Introduction\n\nThis section overs an overview of SSSOM. If you are looking for a fast way to [get started, see here](ge"
},
{
"path": "src/docs/javascripts/mathjax.js",
"chars": 384,
"preview": "window.MathJax = {\n tex: {\n inlineMath: [[\"\\\\(\", \"\\\\)\"]],\n displayMath: [[\"\\\\[\", \"\\\\]\"]],\n processEscapes: tru"
},
{
"path": "src/docs/mapping-commons.md",
"chars": 1622,
"preview": "# How to set up a Mapping Commons\n\nA mapping commons is an open, collaborative space for managing and reconciling mappin"
},
{
"path": "src/docs/mapping-justifications.md",
"chars": 12291,
"preview": "# Guide to using Mapping Justifications\n\nThe goal of this document is to provide the user with a few pointers into the a"
},
{
"path": "src/docs/mapping-predicates.md",
"chars": 21093,
"preview": "# How to pick the right mapping predicates\n\nA mapping predicate such as skos:exactMatch specifies the semantics of the m"
},
{
"path": "src/docs/matching-tool-implementation-guide.md",
"chars": 14857,
"preview": "# Matching Tools: Implementation Guide for SSSOM\n\n*Summary**: The goal of this document is to advice matching tool devel"
},
{
"path": "src/docs/presentations.md",
"chars": 6922,
"preview": "# Presentations\n\n## Building Bridges with FAIR Mappings: An RDA Perspective (GA4GH 13th Plenary)\n\n- October 6<sup>th</su"
},
{
"path": "src/docs/record-identifiers.md",
"chars": 11506,
"preview": "# Identifying mapping records\n\nSince version 1.1, the SSSOM specification allows to explicitly assign an\nidentifier to e"
},
{
"path": "src/docs/related-documentation.md",
"chars": 954,
"preview": "## Related documentation\n\n- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/index.html#): A toolkit and libra"
},
{
"path": "src/docs/spec-formats-json.md",
"chars": 334,
"preview": "# The JSON serialisation format\n\nThe JSON serialisation format is currently unspecified.\n\nIt is intended as a more-or-le"
},
{
"path": "src/docs/spec-formats-owl.md",
"chars": 3782,
"preview": "# The OWL/RDF serialisation format\n\nThis section defines a way to serialise SSSOM mappings as _reified OWL axioms_. This"
},
{
"path": "src/docs/spec-formats-rdf.md",
"chars": 17644,
"preview": "# The SSSOM/RDF serialisation format\n\nThis section defines how to represent a SSSOM mapping set as a\n[RDF model](https:/"
},
{
"path": "src/docs/spec-formats-tsv.md",
"chars": 20312,
"preview": "# The SSSOM/TSV serialisation format\n\nThe SSSOM/TSV format is intended as the main format for exchanging SSSOM mapping s"
},
{
"path": "src/docs/spec-formats.md",
"chars": 416,
"preview": "# SSSOM serialisation formats\n\nThe SSSOM standard defines the following serialisation formats for storing and exchanging"
},
{
"path": "src/docs/spec-intro.md",
"chars": 1539,
"preview": "# Specification of the SSSOM standard\n\nThis document is the official specification for the SSSOM standard.\n\nIt is divide"
},
{
"path": "src/docs/spec-model.md",
"chars": 24134,
"preview": "# The SSSOM data model\n\nThe SSSOM data model (hereafter “the model”) defines the data structure to represent and manipul"
},
{
"path": "src/docs/spec-support-hashing.md",
"chars": 13500,
"preview": "# Hashing a SSSOM mapping record\n\nSSSOM implementations SHOULD provide a function to compute a hash on a SSSOM\nmapping r"
},
{
"path": "src/docs/spec-support.md",
"chars": 540,
"preview": "# SSSOM supporting functions\n\nThis section defines functions and behaviours that SSSOM implementations should\nsupport to"
},
{
"path": "src/docs/toolkit.md",
"chars": 6092,
"preview": "# The SSSOM Toolkit\n\nIn the following we will give a brief introduction into the SSSOM toolkit. For more detailed docume"
},
{
"path": "src/docs/training.md",
"chars": 1712,
"preview": "## SSSOM Training materials\n\n- [Elevator pitch](#elevator)\n- [Tutorials and Guides](#guides)\n- [Related tutorials](#rela"
},
{
"path": "src/docs/tutorial.md",
"chars": 49488,
"preview": "# Introduction to mapping curation with SSSOM\n\nMappings between entities from ontologies, terminologies and databases ar"
},
{
"path": "src/docs/tutorials/omop-mappings.md",
"chars": 7567,
"preview": "# How to gradually enrich OMOP mappings with SSSOM\n\nThis document is a guide for OMOP ETL developers to think about grad"
},
{
"path": "src/docs/usecases.md",
"chars": 1141,
"preview": "# Use cases and case studies\n\n## Mondo disease mappings\n\n- [Mondo mappings](https://github.com/monarch-initiative/mondo/"
},
{
"path": "src/docs/workshops.md",
"chars": 301,
"preview": "# Workshops\n\n## Mapping Commons Workshop Series\n\nWikidata: https://www.wikidata.org/wiki/Q108394475\n\n- [1st Mapping Comm"
},
{
"path": "src/sssom_schema/__init__.py",
"chars": 37,
"preview": "from .datamodel.sssom_schema import *"
},
{
"path": "src/sssom_schema/context/sssom_schema.context.jsonld",
"chars": 9279,
"preview": "{\n \"@context\": {\n \"xsd\": \"http://www.w3.org/2001/XMLSchema#\",\n \"dcterms\": \"http://purl.org/dc/terms/\",\n "
},
{
"path": "src/sssom_schema/context/sssom_schema.jsonld",
"chars": 126014,
"preview": "{\n \"name\": \"sssom\",\n \"description\": \"Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)\",\n \"see_a"
},
{
"path": "src/sssom_schema/datamodel/__init__.py",
"chars": 0,
"preview": ""
},
{
"path": "src/sssom_schema/datamodel/sssom_schema.py",
"chars": 61590,
"preview": "# Auto generated from sssom_schema.yaml by pythongen.py version: 0.0.1\n# Generation date: 2026-04-14T16:00:32\n# Schema: "
},
{
"path": "src/sssom_schema/schema/sssom_schema.yaml",
"chars": 58960,
"preview": "id: https://w3id.org/sssom/schema/\nname: sssom\ndescription:\n Datamodel for Simple Standard for Sharing Ontological Mapp"
},
{
"path": "tests/__init__.py",
"chars": 0,
"preview": ""
},
{
"path": "tests/input/CONFIG.yaml",
"chars": 1628,
"preview": "model_name: template-config-model\nroot_schema: config_model\n\nmodel_organization: linkml\nmodel_author: Harold Solbrig\nmod"
},
{
"path": "tests/input/README.md",
"chars": 734,
"preview": "# Tests input directory\nThis file contains samples of your schema. Samples can written in yaml, json, rdf or any other l"
},
{
"path": "tests/test_added_in_annotations.py",
"chars": 4678,
"preview": "import unittest\nfrom jsonasobj2 import as_dict\n\nfrom linkml_runtime.utils.schemaview import SchemaView, load_schema_wrap"
},
{
"path": "utils/get-value.sh",
"chars": 230,
"preview": "#!/usr/bin/bash\n# get the value of a key in the about.yaml file\n# https://stackoverflow.com/questions/1221833/pipe-outpu"
}
]
// ... and 1 more files (download for full content)
About this extraction
This page contains the full source code of the mapping-commons/sssom GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 129 files (1004.5 KB), approximately 252.8k tokens, and a symbol index with 139 extracted functions, classes, methods, constants, and types. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.
Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.