zhangzeyu/biore
Biomedical Relation Extraction Tool
369
zhangzeyu/biore repository overview
Biomedical relation extraction
BIORE is a relation extraction tool including 5 fine-tuned models (semantic 'type', 'typecode', 'group', 'groupabb', 'noentity') baesd on PubMedBERT with task-specific continued pre-training to extract relations between key entities from biomedical literatures.
Quick Start
Docker and nvidia-docker installation
If you don't have docker, you should Install Docker and nvidia-docker (Optional for GPU).
Pull BIORE image from Docker Hub
CPU: docker pull zhangzeyu/biore:cpu
GPU: docker pull zhangzeyu/biore:gpu
Setup
Start BIORE container:
CPU:
docker run -d --name=biore -it -v ~/biore:/root/biore -p 8888:8888 --ipc=host zhangzeyu/biore:cpu jupyter lab --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token= --notebook-dir='/root'
GPU:
docker run -d --name=biore --runtime=nvidia -it -v ~/biore:/root/biore -p 8888:8888 --ipc=host zhangzeyu/biore:gpu jupyter lab --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token= --notebook-dir='/root'
This will create a empty folder ~/biore from the host visible as /root/biore in the container, you can upload the pmid list file or NERed text data in PubTator format here. Such isolation reduces the chances of your containerized experiments overwriting or using wrong data.
Relation extracion usage
Login Jupyter lab at "host ip":8888 and open a terminal.
bin/bash
cd /root/biore
$ python
(optional) Get NERed text data from PubTator by pmids of interest, a folder named 'import' will be automatically generated:
Input: a file containing a column of pmids.
>>> from pmid2pubtator import *
>>> pmid2pubtator('input file')
Perform relation extraction on NERed text data in PubTator format:
Input: a folder containing PubTator format txt file.
>>> from bre_pubtator import *
>>> bre_pubtator('input folder','select model')
Citation
Zhang Z, Fang M, Wu R, et al. Large-Scale Biomedical Relation Extraction Across Diverse Relation Types: Model Development and Usability Study on COVID-19 [J]. J Med Internet Res, 2023, 25: e48115.
Licensing
BIORE is MIT licensed.
Tag summary
Content type
Image
Digest
sha256:46f700ef2…
Size
2.1 GB
Last updated
over 3 years ago
docker pull zhangzeyu/biore