BERN

BERN is a BioBERT-based multi-type NER tool that also supports normalization of extracted entities. This repository contains the official implementation of BERN. You can use BERN at https://bern.korea.ac.kr, or host your own server by following the description below. Please refer to our paper (Kim et al., IEEE Access 2019) for more details. This project is done by DMIS Laboratory at Korea University.

[Updates]

Check out BERN2, an improved version of BERN with much faster and more accurate inference!

Fixed our gene normalizer to respond to issues between 2020-03-12 and 2020-03-13

Download gnormplus-normalization_19.jar at this URL and place (overwrite) the file under normalization/resources/normalizers/gene directory.
Stop normalizers by running stop_normalizers.sh
Start the normalizers by running load_dicts.sh

Done - Server down due to air conditioning problems in our server room 2019-10-10 - 2019-10-11 7:55 AM (UTC-0)

Fixed our disease normalizer 2019-08-19, 2019-08-10 and 2019-08-02 issues

Download disease_normalizer_19.jar at this URL and place the file under normalization/resources/normalizers/disease directory.
Stop normalizers by running stop_normalizers.sh and restart the normalizers by running load_dicts.sh

Done - Server check 2019-07-18 8:20 AM - 1:30 PM (UTC-0)

BERN

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

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://\<YOUR_SERVER_ADDRESS>:8888/?pmid=\<a PMID or comma seperate PMIDs>&format=\<json or pubtator>
        * Example: http://\<YOUR_SERVER_ADDRESS>:8888/?pmid=30429607&format=json&indent=true
        * Example: http://\<YOUR_SERVER_ADDRESS>:8888/?pmid=30429607&format=pubtator
        * Example: http://\<YOUR_SERVER_ADDRESS>:8888/?pmid=30429607,29446767&format=json&indent=true
    * Raw text (HTTP POST)
        * POST Address: http://\<YOUR_SERVER_ADDRESS>:8888
        * Set key, value of a body as follows:

    import requests
    import json
    body_data = {"param": json.dumps({"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."})}
    response = requests.post('http://<YOUR_SERVER_ADDRESS>:8888', data=body_data)
    result_dict = response.json()
    print(result_dict)
    ```

Result

See a result example in JSON (PMID:29446767)

[
    {
        "denotations": [
            {
                "id": [
                    "MESH:C567763",
                    "BERN:262813101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 0,
                    "end": 13
                }
            },
            {
                "id": [
                    "MIM:171834",
                    "HGNC:8975",
                    "Ensembl:ENSG00000121879",
                    "BERN:324295302"
                ],
                "obj": "gene",
                "span": {
                    "begin": 53,
                    "end": 58
                }
            },
            {
                "id": [
                    "MESH:C567763",
                    "BERN:262813101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 133,
                    "end": 146
                }
            },
            {
                "id": [
                    "MESH:D014652",
                    "BERN:256572101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 158,
                    "end": 174
                }
            },
            {
                "id": [
                    "MESH:C567763",
                    "BERN:262813101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 193,
                    "end": 231
                }
            },
            {
                "id": [
                    "MESH:C567763",
                    "BERN:262813101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 234,
                    "end": 288
                }
            },
            {
                "id": [
                    "MESH:C567763",
                    "BERN:262813101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 589,
                    "end": 593
                }
            },
            {
                "id": [
                    "MIM:171834",
                    "HGNC:8975",
                    "Ensembl:ENSG00000121879",
                    "BERN:324295302"
                ],
                "obj": "gene",
                "span": {
                    "begin": 748,
                    "end": 758
                }
            },
            {
                "id": [
                    "CUI-less"
                ],
                "mutationType": "ProteinMutation",
                "normalizedName": "p.F83S;CorrespondingGene:5290",
                "obj": "mutation",
                "span": {
                    "begin": 857,
                    "end": 866
                }
            },
            {
                "id": [
                    "BERN:257523801"
                ],
                "obj": "disease",
                "span": {
                    "begin": 906,
                    "end": 928
                }
            },
            {
                "id": [
                    "CUI-less"
                ],
                "obj": "gene",
                "span": {
                    "begin": 1009,
                    "end": 1024
                }
            },
            {
                "id": [
                    "MESH:C567763",
                    "BERN:262813101"
                ],
                "obj": "disease",
                "span": {
                    "begin": 1043,
                    "end": 1047
                }
            }
        ],
        "elapsed_time": {
            "ner": 0.611,
            "normalization": 0.218,
            "tmtool": 1.281,
            "total": 2.111
        },
        "project": "BERN",
        "sourcedb": "PubMed",
        "sourceid": "29446767",
        "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"
    }
]

Restart

# Start GNormPlusServer
cd ~/bern/GNormPlusJava
nohup java -Xmx16G -Xms16G -jar GNormPlusServer.jar 18895 >> ~/bern/logs/nohup_gnormplus.out 2>&1 &

# Start tmVar2Server
cd ~/bern/tmVarJava
nohup java -Xmx8G -Xms8G -jar tmVar2Server.jar 18896 >> ~/bern/logs/nohup_tmvar.out 2>&1 &

# Start normalizers
cd ~/bern/
sh load_dicts.sh

# Check your GPU number(s)
echo $CUDA_VISIBLE_DEVICES

# Set your GPU number(s)
export CUDA_VISIBLE_DEVICES=0

# Run BERN
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

Troubleshooting

Trouble: It takes a long time to get results.
- Solution: Make sure TensorFlow is using a GPU. For more details, visit https://stackoverflow.com/questions/42326748/tensorflow-on-gpu-no-known-devices-despite-cudas-devicequery-returning-a-pas/48079860#48079860

Monitoring

List processes (every 5s)

watch -n 5 "ps auxww | egrep 'python|java|node' | grep -v grep"

Periodic HTTPS GET checker

Permission setting
```
chmod +x scripts/bern_checker.sh
```

crontab (every 30 min)

crontab -e
*/30 * * * * /home/<YOUR_ACCOUNT>/bern/scripts/bern_checker.sh >> /home/<YOUR_ACCOUNT>/bern/logs/bern_checker.out 2>&1

Bug report

Add a new issue to https://github.com/dmis-lab/bern/issues

Contact

donghyeon@korea.ac.kr

Citation

Please cite the following two papers if you use BERN on your work.


@article{kim2019neural,
title={A Neural Named Entity Recognition and Multi-Type Normalization Tool for Biomedical Text Mining},
author={Kim, Donghyeon and Lee, Jinhyuk and So, Chan Ho and Jeon, Hwisang and Jeong, Minbyul and Choi, Yonghwa and Yoon, Wonjin and Sung, Mujeen and and Kang, Jaewoo},
journal={IEEE Access},
volume={7},
pages={73729--73740},
year={2019},
publisher={IEEE}
}

@article{10.1093/bioinformatics/btz682, author = {Lee, Jinhyuk and Yoon, Wonjin and Kim, Sungdong and Kim, Donghyeon and Kim, Sunkyu and So, Chan Ho and Kang, Jaewoo}, title = "{BioBERT: a pre-trained biomedical language representation model for biomedical text mining}", journal = {Bioinformatics}, year = {2019}, month = {09}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btz682}, url = {https://doi.org/10.1093/bioinformatics/btz682}, }

dmis-lab / bern

readme

BERN

Requirements

Installation

chmod 764 CRF/crf_test

Set FocusSpecies to 9606 (Human)

Download GNormPlusServer.jar

Start GNormPlusServer

Download tmVar2Server.jar

Download dependencies

Start tmVar2Server

Check your GPU number(s)

Set your GPU number(s)

Run BERN

Please check gnormplus_home directory and tmvar2_home directory.

Print logs

Result

Restart

Troubleshooting

Monitoring

Bug report

Contact

Citation