Overview of BERN.
\n\nThe description below gives instructions on hosting your own BERN. Please refer to https://bern.korea.ac.kr for the RESTful Web service of BERN.\n\n## Requirements\n* Environment\n * Python >= 3.6 \n * CUDA 9 or higher\n* Main components\n * [BioBERT NER models (Lee et al., 2019)](https://arxiv.org/abs/1901.08746)\n * [tmTool APIs (Wei et al., 2016)](https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/) \n * [GNormPlus (Wei et al., 2015)](https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/)\n * [tmVar 2.0 (Wei et al., 2018)](https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/tmvar/)\n * [TensorFlow 1.13.1](https://github.com/tensorflow/tensorflow/releases/tag/v1.13.1)\n\nNote that you will need at least 66 GB of free disk space and 32 GB or more RAM.\n\n## Installation\n* Clone this repo\n```\ncd\ngit clone https://github.com/dmis-lab/bern.git\n```\n\n* Install python packages\n```\npip3 install -r requirements.txt --user\n```\n\n* Install GNormPlus & run GNormPlusServer.jar\n * FYI: Download Google Drive files with WGET: https://gist.github.com/iamtekeste/3cdfd0366ebfd2c0d805#gistcomment-2316906\n```\ncd ~/bern\nwget https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/download/GNormPlus/GNormPlusJava.zip\nunzip GNormPlusJava.zip\n\ncd GNormPlusJava\nwget -O ./crfpp-0.58.tar.gz https://drive.google.com/uc?id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ\ntar xvfz crfpp-0.58.tar.gz\ncp -rf CRF++-0.58/* CRF\ncd CRF\nsh ./configure\nmake\nsudo make install\n\ncd ..\nchmod 764 Ab3P\n# chmod 764 CRF/crf_test\n\n# Set FocusSpecies to 9606 (Human)\nsed -i 's/= All/= 9606/g' setup.txt; echo \"FocusSpecies: from All to 9606 (Human)\"\nsh Installation.sh\n\nrm -r CRF++-0.58\nrm crfpp-0.58.tar.gz\n\n# Download GNormPlusServer.jar\nwget --load-cookies /tmp/cookies.txt \"https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1g-JlhqeDIlZX5YFk8Y27_M8BXUXcQRSX' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\\1\\n/p')&id=1g-JlhqeDIlZX5YFk8Y27_M8BXUXcQRSX\" -O GNormPlusServer.jar && rm -rf /tmp/cookies.txt\n\n# Start GNormPlusServer\nnohup java -Xmx16G -Xms16G -jar GNormPlusServer.jar 18895 >> ~/bern/logs/nohup_gnormplus.out 2>&1 &\n```\n\n\n* Install tmVar2 & run tmVar2Server.jar\n```\ncd ~/bern\nwget ftp://ftp.ncbi.nlm.nih.gov/pub/lu/Suppl/tmVar2/tmVarJava.zip\nunzip tmVarJava.zip\n\ncd tmVarJava\nwget -O ./crfpp-0.58.tar.gz https://drive.google.com/uc?id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ\ntar xvfz crfpp-0.58.tar.gz\ncp -rf CRF++-0.58/* CRF\ncd CRF\nsh ./configure\nmake\nsudo make install\n\ncd ..\nchmod 764 CRF/crf_test\n\nsh Installation.sh\n\nrm -r CRF++-0.58\nrm crfpp-0.58.tar.gz\n\n# Download tmVar2Server.jar\nwget --load-cookies /tmp/cookies.txt \"https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1kQYzLHLFLsU9qKpRRGjXkIYmaYK6bPJm' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\\1\\n/p')&id=1kQYzLHLFLsU9qKpRRGjXkIYmaYK6bPJm\" -O tmVar2Server.jar && rm -rf /tmp/cookies.txt\n\n# Download dependencies\nwget https://repo1.maven.org/maven2/org/xerial/sqlite-jdbc/3.20.0/sqlite-jdbc-3.20.0.jar\nwget https://repo1.maven.org/maven2/edu/stanford/nlp/stanford-corenlp/3.5.2/stanford-corenlp-3.5.2.jar\n\n# Start tmVar2Server\nnohup java -Xmx8G -Xms8G -jar tmVar2Server.jar 18896 >> ~/bern/logs/nohup_tmvar.out 2>&1 &\n```\n \n* Download normalization resources and pre-trained BioBERT NER models\n```\ncd ~/bern/scripts\nsh download_norm.sh\nsh download_biobert_ner_models.sh\n```\n\n* Run named entity normalizers\n```\ncd ..\nsh load_dicts.sh\n```\n\n* Run BERN server\n```\n# Check your GPU number(s)\necho $CUDA_VISIBLE_DEVICES\n\n# Set your GPU number(s)\nexport CUDA_VISIBLE_DEVICES=0\n\n# Run BERN\n# Please check gnormplus_home directory and tmvar2_home directory.\nnohup python3 -u server.py --port 8888 --gnormplus_home ~/bern/GNormPlusJava --gnormplus_port 18895 --tmvar2_home ~/bern/tmVarJava --tmvar2_port 18896 >> logs/nohup_BERN.out 2>&1 &\n\n# Print logs\ntail -F logs/nohup_BERN.out\n```\n\n* Usage\n * PMID(s) (HTTP GET)\n * http://\\\n[\n {\n \"denotations\": [\n {\n \"id\": [\n \"MESH:C567763\",\n \"BERN:262813101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 0,\n \"end\": 13\n }\n },\n {\n \"id\": [\n \"MIM:171834\",\n \"HGNC:8975\",\n \"Ensembl:ENSG00000121879\",\n \"BERN:324295302\"\n ],\n \"obj\": \"gene\",\n \"span\": {\n \"begin\": 53,\n \"end\": 58\n }\n },\n {\n \"id\": [\n \"MESH:C567763\",\n \"BERN:262813101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 133,\n \"end\": 146\n }\n },\n {\n \"id\": [\n \"MESH:D014652\",\n \"BERN:256572101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 158,\n \"end\": 174\n }\n },\n {\n \"id\": [\n \"MESH:C567763\",\n \"BERN:262813101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 193,\n \"end\": 231\n }\n },\n {\n \"id\": [\n \"MESH:C567763\",\n \"BERN:262813101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 234,\n \"end\": 288\n }\n },\n {\n \"id\": [\n \"MESH:C567763\",\n \"BERN:262813101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 589,\n \"end\": 593\n }\n },\n {\n \"id\": [\n \"MIM:171834\",\n \"HGNC:8975\",\n \"Ensembl:ENSG00000121879\",\n \"BERN:324295302\"\n ],\n \"obj\": \"gene\",\n \"span\": {\n \"begin\": 748,\n \"end\": 758\n }\n },\n {\n \"id\": [\n \"CUI-less\"\n ],\n \"mutationType\": \"ProteinMutation\",\n \"normalizedName\": \"p.F83S;CorrespondingGene:5290\",\n \"obj\": \"mutation\",\n \"span\": {\n \"begin\": 857,\n \"end\": 866\n }\n },\n {\n \"id\": [\n \"BERN:257523801\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 906,\n \"end\": 928\n }\n },\n {\n \"id\": [\n \"CUI-less\"\n ],\n \"obj\": \"gene\",\n \"span\": {\n \"begin\": 1009,\n \"end\": 1024\n }\n },\n {\n \"id\": [\n \"MESH:C567763\",\n \"BERN:262813101\"\n ],\n \"obj\": \"disease\",\n \"span\": {\n \"begin\": 1043,\n \"end\": 1047\n }\n }\n ],\n \"elapsed_time\": {\n \"ner\": 0.611,\n \"normalization\": 0.218,\n \"tmtool\": 1.281,\n \"total\": 2.111\n },\n \"project\": \"BERN\",\n \"sourcedb\": \"PubMed\",\n \"sourceid\": \"29446767\",\n \"text\": \"CLAPO syndrome: identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype. PURPOSE: CLAPO syndrome is a rare vascular disorder characterized by capillary malformation of the lower lip, lymphatic malformation predominant on the face and neck, asymmetry, and partial/generalized overgrowth. Here we tested the hypothesis that, although the genetic cause is not known, the tissue distribution of the clinical manifestations in CLAPO seems to follow a pattern of somatic mosaicism. METHODS: We clinically evaluated a cohort of 13 patients with CLAPO and screened 20 DNA blood/tissue samples from 9 patients using high-throughput, deep sequencing. RESULTS: We identified five activating mutations in the PIK3CA gene in affected tissues from 6 of the 9 patients studied; one of the variants (NM_006218.2:c.248T>C; p.Phe83Ser) has not been previously described in developmental disorders. CONCLUSION: We describe for the first time the presence of somatic activating PIK3CA mutations in patients with CLAPO. We also report an update of the phenotype and natural history of the syndrome.\",\n \"timestamp\": \"Thu Jul 04 06:15:27 +0000 2019\"\n }\n]\n\n