Table of contents
Medical entity recognition, relationship extraction and labeling tools
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Harbin Institute of Technology Open Source Labeling Tool
This project not only provides medical data labeling tools for named entity recognition and relationship extraction, but also provides labeling specification documents and some electronic medical record samples that can be used to test labeling tools.
https://github.com/WILAB-HIT/Resources -
BRAT
official website: http://brat.nlplab.org/index.html
Installation package: https://github.com/nlplab/brat/releases/tag/v1.3_Crunchy_Frog
The visualization effect is very good, the configuration is also more convenient, and it feels good Use brat to label, and use Harbin Institute of Technology's labeling specifications as our reference for formulating labeling specifications. Brat needs to be installed in the linux system. I installed a virtual machine with vmware and tried it out in ubuntu. The effect is as follows
Labeling ideas
In the lectures related to medical knowledge graphs, the Institute of Mathematics introduced the idea of pre-labeling + manual proofreading they adopted when labeling entities and entity relationships. I feel that it is quite helpful to improve the efficiency of labeling.
https://mp.weixin.qq.com/s/gDMCfHP1xN7erjxvA-NZSw
BRAT
reference documents
Brat annotation tool (local) installation and use [including demo]
https://blog.csdn.net/p_jinsan/article/details/96152078
The use document of Brat text annotation tool
introduces the annotation method of event extraction
https://blog.csdn.net/Jay_Josby/article/details/103569721
Brat annotation system description
introduces shortcut keys
http://ws.nju.edu.cn/blog/2018/06/brat%E6%A0%87%E6%B3%A8%E7%B3%BB%E7%BB% 9F%E8%AF%B4%E6%98%8E/
The installation, configuration, and labeling operations of BRAT
are written in great detail. It describes the relevant content of the label attribute.
https://blog.csdn.net/weixin_42927998/article/details/106623370
Brat docker image
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https://hub.docker.com/r/heliex/docker-brat
is very useful, but the author canceled the sharing of the image. I exported the image uploaded by the author before, and the image download link is as follows:
Link: https://pan.baidu.com/s/11Z5LwtLowwb10xq1gomSSQ
Extraction code: fcp5
Image usage:
docker run -p 8080:80 -v /d/xx/ brat-v1.3_Crunchy_Frog/data_docker/:/var/www/brat/data/annotatordata -d heliex/docker-brat
Replace "/d/xx/brat-v1.3_Crunchy_Frog/data_docker/" in the above command with local storage data address is fine.
Put the brat config file and data in the same folder to take effect. -
https://hub.docker.com/r/cassj/brat
I haven't tried this
other
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HTML color codes
https://htmlcolorcodes.com/zh/ -
Add users Add USER_PASSWORD = { 'admn': 'admin', 'test': 'test', }
directly in the config.py file
error
Python sequence labeling platform brat, file wrapping line CRLF (\r\n) caused bug records
https://zhuanlan.zhihu.com/p/119316158