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https://github.com/OHNLP/awesome-clinical-nlp

List: awesome-clinical-nlp

Last synced: 3 months ago
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Host: GitHub
URL: https://github.com/OHNLP/awesome-clinical-nlp
Owner: OHNLP
License: gpl-3.0
Created: 2020-03-16T16:05:21.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2020-10-30T21:16:46.000Z (about 4 years ago)
Last Synced: 2024-05-20T12:00:34.995Z (6 months ago)
Size: 52.7 KB
Stars: 11
Watchers: 5
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

awesome-icd-coding - OHNLP/awesome-clinical-nlp

README

        # awesome-clinical-nlp

# Contents

- Overview Articles

- COVID 19

- Tools

- Workshops

If you are interested particular in Biomedical Information Extraction, there is a good resource at https://github.com/caufieldjh/awesome-bioie.

# Overview Articles

- [Clinical concept extraction: A methodology review](https://doi.org/10.1016/j.jbi.2020.103526) Fu S et al, 2020

- [SECNLP: A survey of embeddings in clinical natural language processing](https://www.sciencedirect.com/science/article/pii/S1532046419302436)  Kalyan K et al, 2020

- [Deep learning in clinical natural language processing: a methodical review](https://academic.oup.com/jamia/article-abstract/27/3/457/5651084), Wu S et al, 2019

- [Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review](https://www.sciencedirect.com/science/article/pii/S1532046418302016#!), Sheikhalishahi S et al, 2019

- [Clinical information extraction applications: A literature review](https://www.sciencedirect.com/science/article/pii/S1532046417302563), Wang Y et al, 2018

- [Using clinical Natural Language Processing for health outcomes research: Overview and actionable suggestions for future advances](https://www.sciencedirect.com/science/article/pii/S1532046418302016), Velupillai S et al, 2018

- [Clinical Natural Language Processing in languages other than English: opportunities and challenges](https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-018-0179-8), Névéol A et al, 2018

# COVID 19

- [covid19nlp.org](http://covid19nlp.org/index.php)

  - NLP to support Coronavirus disease (COVID-19) research

- [MedTagger COVID 19 demo](http://167.114.144.164/)

  - A demo site for COVID 19 symptom extraction from clinical texts using MedTagger

- [LitCovid](https://www.ncbi.nlm.nih.gov/research/coronavirus/)

  - "LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus." 

- [ACT-COVID-Ontology](https://github.com/shyamvis/ACT-COVID-Ontology)

# Tools

- NLP systems 

  - [Apache cTAKES](https://ctakes.apache.org/)

  - [CLAMP](https://clamp.uth.edu/) 

  - [MedTagger](https://github.com/ohnlp/MedTagger)

  - [MetaMap](https://metamap.nlm.nih.gov/)

  - [CD2H NLP Sandbox](https://github.com/data2health/nlp-sandbox)

- EHR Systems for Texts

  - [EMERSE](http://project-emerse.org/index.html)

  - [SemEHR](https://github.com/CogStack/CogStack-SemEHR)

  - [EliIE](https://github.com/Tian312/ELIIE)

- Manual Annotation Tools

  - [Brat](https://brat.nlplab.org/)

  - [Anafora](https://github.com/weitechen/anafora)

  - [MEA](http://keighrim.github.io/mae-annotation/)

# Workshops and Resources

- [BioNLP](https://aclweb.org/aclwiki/SIGBIOMED)  

- ClinicalNLP: [2019](https://clinical-nlp.github.io/2019/), [2020](https://clinical-nlp.github.io/2020/)

  - [Resources](https://clinical-nlp.github.io/2019/resources.html)

- Health NLP [2018](https://ohnlp.github.io/HealthNLP2018/healthnlp2018), [2019](https://ohnlp.github.io/HealthNLP2019/healthnlp2019), [2020](https://ohnlp.github.io/HealthNLP2020/healthnlp2020)

- [BioCreative/OHNLP 2018](https://sites.google.com/view/ohnlp2018/home)

- [n2c2 NLP Research Data Sets](https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/)

  - "Unstructured notes from the Research Patient Data Repository at Partners Healthcare."