git clone --recursive https://github.com/amalic/bern-docker.git
- Lot's of disk space (~60 GB disk space)
- 32 GB Ram (see BERN project README)
- NVidia Docker
- Those files:
- GNormPlus.zip (~4GB)
- tmVarJava.zip
ftp://ftp.ncbi.nlm.nih.gov/pub/lu/Suppl/tmVar2/tmVarJava.zip(~40GB) - CRF++-0.58.tar.gz (~4 MB)
- biobert_ner_models.zip (~7GB)
- data.zip (~750 MB)
- resources.zip (~3 GB)
Download and extract all archives into externalData folder within this repository by running.
sh prerequisites.sh
You might want to get a coffee or learn a new programming language, depending on your internet connection.
docker build -t bern-docker .
docker run --name bern-docker --log-opt max-size=10m -d --rm --gpus all -p 80:8888 \
-v $PWD/externalData/GNormPlusJava/Dictionary/:/app/GNormPlusJava/Dictionary/ \
-v $PWD/externalData/tmVarJava/Database:/app/tmVarJava/Database \
-v $PWD/externalData/biobert_ner_models/pretrainedBERT:/app/biobert_ner/pretrainedBERT/ \
-v $PWD/externalData/biobert_ner_models/conf/:/app/biobert_ner/conf/ \
-v $PWD/externalData/biobert_ner_models/tmp/:/app/biobert_ner/tmp/ \
-v $PWD/externalData/biobert_ner_models/result/:/app/biobert_ner/result/ \
-v $PWD/externalData/data/:/app/normalization/data/ \
-v $PWD/externalData/resources/:/app/normalization/resources/ \
bern-docker
Usage PMID(s) (HTTP GET)
- http://<YOUR_SERVER_ADDRESS>:<PORT>/?pmid=<a PMID or comma seperate PMIDs>&format=<json or pubtator>
- Example: http://localhost/?pmid=30429607&format=json&indent=true
- Example: http://localhost/?pmid=30429607&format=pubtator
- Example: http://localhost/?pmid=30429607,29446767&format=json&indent=true
@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},
}