{"id":13834522,"url":"https://github.com/OHNLP/awesome-clinical-nlp","last_synced_at":"2025-07-10T07:30:41.353Z","repository":{"id":115500321,"uuid":"247758411","full_name":"OHNLP/awesome-clinical-nlp","owner":"OHNLP","description":null,"archived":false,"fork":false,"pushed_at":"2020-10-30T21:16:46.000Z","size":54,"stargazers_count":15,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-05-02T03:02:11.142Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OHNLP.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2020-03-16T16:05:21.000Z","updated_at":"2025-04-27T16:44:06.000Z","dependencies_parsed_at":null,"dependency_job_id":"334c5ae1-a680-4abb-a613-1540918d1b0c","html_url":"https://github.com/OHNLP/awesome-clinical-nlp","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/OHNLP/awesome-clinical-nlp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OHNLP%2Fawesome-clinical-nlp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OHNLP%2Fawesome-clinical-nlp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OHNLP%2Fawesome-clinical-nlp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OHNLP%2Fawesome-clinical-nlp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OHNLP","download_url":"https://codeload.github.com/OHNLP/awesome-clinical-nlp/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OHNLP%2Fawesome-clinical-nlp/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264545157,"owners_count":23625403,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-04T14:00:36.875Z","updated_at":"2025-07-10T07:30:41.069Z","avatar_url":"https://github.com/OHNLP.png","language":null,"funding_links":[],"categories":["Related Topics"],"sub_categories":[],"readme":"# awesome-clinical-nlp\n\n# Contents\n- Overview Articles\n- COVID 19\n- Tools\n- Workshops\n\nIf you are interested particular in Biomedical Information Extraction, there is a good resource at https://github.com/caufieldjh/awesome-bioie.\n\n# Overview Articles\n- [Clinical concept extraction: A methodology review](https://doi.org/10.1016/j.jbi.2020.103526) Fu S et al, 2020\n- [SECNLP: A survey of embeddings in clinical natural language processing](https://www.sciencedirect.com/science/article/pii/S1532046419302436)  Kalyan K et al, 2020\n- [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\n- [Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review](https://www.sciencedirect.com/science/article/pii/S1532046418302016#!), Sheikhalishahi S et al, 2019\n- [Clinical information extraction applications: A literature review](https://www.sciencedirect.com/science/article/pii/S1532046417302563), Wang Y et al, 2018\n- [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\n- [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\n\n# COVID 19\n- [covid19nlp.org](http://covid19nlp.org/index.php)\n  - NLP to support Coronavirus disease (COVID-19) research\n- [MedTagger COVID 19 demo](http://167.114.144.164/)\n  - A demo site for COVID 19 symptom extraction from clinical texts using MedTagger\n- [LitCovid](https://www.ncbi.nlm.nih.gov/research/coronavirus/)\n  - \"LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus.\" \n- [ACT-COVID-Ontology](https://github.com/shyamvis/ACT-COVID-Ontology)\n\n\n# Tools\n- NLP systems \n  - [Apache cTAKES](https://ctakes.apache.org/)\n  - [CLAMP](https://clamp.uth.edu/) \n  - [MedTagger](https://github.com/ohnlp/MedTagger)\n  - [MetaMap](https://metamap.nlm.nih.gov/)\n  - [CD2H NLP Sandbox](https://github.com/data2health/nlp-sandbox)\n- EHR Systems for Texts\n  - [EMERSE](http://project-emerse.org/index.html)\n  - [SemEHR](https://github.com/CogStack/CogStack-SemEHR)\n  - [EliIE](https://github.com/Tian312/ELIIE)\n- Manual Annotation Tools\n  - [Brat](https://brat.nlplab.org/)\n  - [Anafora](https://github.com/weitechen/anafora)\n  - [MEA](http://keighrim.github.io/mae-annotation/)\n\n# Workshops and Resources\n\n- [BioNLP](https://aclweb.org/aclwiki/SIGBIOMED)  \n- ClinicalNLP: [2019](https://clinical-nlp.github.io/2019/), [2020](https://clinical-nlp.github.io/2020/)\n  - [Resources](https://clinical-nlp.github.io/2019/resources.html)\n- Health NLP [2018](https://ohnlp.github.io/HealthNLP2018/healthnlp2018), [2019](https://ohnlp.github.io/HealthNLP2019/healthnlp2019), [2020](https://ohnlp.github.io/HealthNLP2020/healthnlp2020)\n- [BioCreative/OHNLP 2018](https://sites.google.com/view/ohnlp2018/home)\n- [n2c2 NLP Research Data Sets](https://portal.dbmi.hms.harvard.edu/projects/n2c2-nlp/)\n  - \"Unstructured notes from the Research Patient Data Repository at Partners Healthcare.\"\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FOHNLP%2Fawesome-clinical-nlp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FOHNLP%2Fawesome-clinical-nlp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FOHNLP%2Fawesome-clinical-nlp/lists"}