Overview of BERN.
The description below gives instructions on hosting your own BERN. Please refer to https://bern.korea.ac.kr for the RESTful Web service of BERN. ## Requirements * Environment * Python >= 3.6 * CUDA 9 or higher * Main components * [BioBERT NER models (Lee et al., 2019)](https://arxiv.org/abs/1901.08746) * [tmTool APIs (Wei et al., 2016)](https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/) * [GNormPlus (Wei et al., 2015)](https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/) * [tmVar 2.0 (Wei et al., 2018)](https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/tmvar/) * [TensorFlow 1.13.1](https://github.com/tensorflow/tensorflow/releases/tag/v1.13.1) Note that you will need at least 66 GB of free disk space and 32 GB or more RAM. ## Installation * Clone this repo ``` cd git clone https://github.com/dmis-lab/bern.git ``` * Install python packages ``` pip3 install -r requirements.txt --user ``` * Install GNormPlus & run GNormPlusServer.jar * FYI: Download Google Drive files with WGET: https://gist.github.com/iamtekeste/3cdfd0366ebfd2c0d805#gistcomment-2316906 ``` cd ~/bern wget https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/download/GNormPlus/GNormPlusJava.zip unzip GNormPlusJava.zip cd GNormPlusJava wget -O ./crfpp-0.58.tar.gz https://drive.google.com/uc?id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ tar xvfz crfpp-0.58.tar.gz cp -rf CRF++-0.58/* CRF cd CRF sh ./configure make sudo make install cd .. chmod 764 Ab3P # chmod 764 CRF/crf_test # Set FocusSpecies to 9606 (Human) sed -i 's/= All/= 9606/g' setup.txt; echo "FocusSpecies: from All to 9606 (Human)" sh Installation.sh rm -r CRF++-0.58 rm crfpp-0.58.tar.gz # Download GNormPlusServer.jar wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1g-JlhqeDIlZX5YFk8Y27_M8BXUXcQRSX' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1g-JlhqeDIlZX5YFk8Y27_M8BXUXcQRSX" -O GNormPlusServer.jar && rm -rf /tmp/cookies.txt # Start GNormPlusServer nohup java -Xmx16G -Xms16G -jar GNormPlusServer.jar 18895 >> ~/bern/logs/nohup_gnormplus.out 2>&1 & ``` * Install tmVar2 & run tmVar2Server.jar ``` cd ~/bern wget ftp://ftp.ncbi.nlm.nih.gov/pub/lu/Suppl/tmVar2/tmVarJava.zip unzip tmVarJava.zip cd tmVarJava wget -O ./crfpp-0.58.tar.gz https://drive.google.com/uc?id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ tar xvfz crfpp-0.58.tar.gz cp -rf CRF++-0.58/* CRF cd CRF sh ./configure make sudo make install cd .. chmod 764 CRF/crf_test sh Installation.sh rm -r CRF++-0.58 rm crfpp-0.58.tar.gz # Download tmVar2Server.jar wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(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 # Download dependencies wget https://repo1.maven.org/maven2/org/xerial/sqlite-jdbc/3.20.0/sqlite-jdbc-3.20.0.jar wget https://repo1.maven.org/maven2/edu/stanford/nlp/stanford-corenlp/3.5.2/stanford-corenlp-3.5.2.jar # Start tmVar2Server nohup java -Xmx8G -Xms8G -jar tmVar2Server.jar 18896 >> ~/bern/logs/nohup_tmvar.out 2>&1 & ``` * Download normalization resources and pre-trained BioBERT NER models ``` cd ~/bern/scripts sh download_norm.sh sh download_biobert_ner_models.sh ``` * Run named entity normalizers ``` cd .. sh load_dicts.sh ``` * Run BERN server ``` # Check your GPU number(s) echo $CUDA_VISIBLE_DEVICES # Set your GPU number(s) export CUDA_VISIBLE_DEVICES=0 # Run BERN # Please check gnormplus_home directory and tmvar2_home directory. nohup 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 & # Print logs tail -F logs/nohup_BERN.out ``` * Usage * PMID(s) (HTTP GET) * http://\
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"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.",
"timestamp": "Thu Jul 04 06:15:27 +0000 2019"
}
]