Clinical Concept Linking NLP Tools

Tools for extracting medical/clinical entities from text and linking them to standardized biomedical vocabularies (UMLS, ontologies, etc.). Does NOT include general medical NLP tasks like classification or document segmentation, nor does it include non-linking entity recognition tools.

There are 35 clinical concept linking tools tracked. 3 score above 50 (established tier). The highest-rated is Georgetown-IR-Lab/QuickUMLS at 59/100 with 436 stars.

Get all 35 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=nlp&subcategory=clinical-concept-linking&limit=20"

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Tool	Score	Tier	Stars	Language
1	Georgetown-IR-Lab/QuickUMLS System for Medical Concept Extraction and Linking	59	Established	436	Python
2	apache/ctakes Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.	55	Established	123	Java
3	CogStack/MedCAT Medical Concept Annotation Tool	50	Established	526	Python
4	medkit-lib/medkit Toolkit for a learning health system	47	Emerging	27	Python
5	OHNLP/MedTagger MedTagger is a light weight clinical NLP system built upon Apache UIMA.	46	Emerging	72	Java
6	CogStack/MedCATtrainer A simple interface to inspect, improve and add concepts to biomedical NER+L...	46	Emerging	85	Python
7	CogStack/MedCATtutorials General tutorials for the setup and use of MedCAT.	45	Emerging	42	HTML
8	nlpie/biomedicus BioMedICUS: A biomedical and clinical NLP engine.	45	Emerging	20	Java
9	noc-lab/clinical_concept_extraction Clinical Concept Extraction with Contextual Word Embedding	42	Emerging	41	Python
10	Bohdan-Khomtchouk/Biochat Natural language processing of Gene Expression Omnibus data	41	Emerging	54	Common Lisp
11	nlpie/biomedicus2 Code for the old version of BioMedICUS, for the new version see the...	41	Emerging	44	Java
12	CharlyWargnier/S4_wiki_topic_grapher Leverage the power of the Google Natural Language API NLP to retrieve entity...	38	Emerging	15	Python
13	NLPReViz/emr-vis-web An Interactive Tool for Natural Language Processing on Clinical Text	38	Emerging	23	JavaScript
14	NLPReViz/emr-nlp-server An Interactive Tool for Natural Language Processing on Clinical Text	38	Emerging	15	Java
15	liamca/medical-ner-search Leveraging Apache CTakes and Azure Search to Build and Medical Search App	36	Emerging	11	JavaScript
16	yugagarin/ctakesspark Attempt to integrate Apache cTakes with Apache Spark	33	Emerging	5	Java
17	eHealth-KD-PUCs-UFMG/pucrj-pucpr-ufmg Code presented by the PUCRJ-PUCPR-UFMG team in the eHealth Knowledge Discovery 2021.	33	Emerging	5	Python
18	CogStack/MedCAT2 MedCATv2	33	Emerging	5	Python
19	ExaNLP/sket This repository contains the source code for the Semantic Knowledge...	32	Emerging	13	Python
20	boxorange/LLM-GeneticTool-Extraction Official implementation of Bacterial hosts and Genetic tools Extraction from...	29	Experimental	1	Python
21	SDM-TIB/NSSC A Neuro-Symbolic AI System for Enhancing Accuracy of Named Entity...	29	Experimental	1	Python
22	zyocum/ptllm-events-extraction Demonstration of using OpenAI's pre-trained LLMs for the linguistic...	29	Experimental	1	Shell
23	boxorange/BioIE-LLM Biological Information Extraction from Large Language Models (LLMs) (Journal...	29	Experimental	13	Python
24	dabane-ghassan/cazy-little-helper Biocuration assistant for the CAZy database.	29	Experimental	1	Python
25	TPAFS/hicric Health Insurance Coverage Rules Interepretation Corpus	21	Experimental	4	Python
26	WadoodAbdul/clinical_ner_benchmark Run model evaluation and upload results on Clinical NER (NCER) leaderboard	20	Experimental	6	Python
27	shtrausslearning/biopylib Bioinformatics made simple 🧬	20	Experimental	5	Python
28	frankkramer-lab/DrNote DrNote is an open tagging tool for text annotation and entity linking based...	20	Experimental	5	Shell
29	scossin/RomediApp Set of programs on top of the Romedi terminology	20	Experimental	8	Java
30	jplasser/CNEP CNEP (Contrastive Notes Events Pre-training), Contrastive Learning with...	19	Experimental	3	Jupyter Notebook
31	0xcodemate/Med-annotation Medical Concept Annotation Tool	18	Experimental	1	Python
32	nlpie/biomedicus-measures A lightweight (small and dependency-free) Java 8 library for identifying and...	12	Experimental	3	Java
33	Advanced-Reality-Lab/MI-TAGS MI-TAGS is a dataset of English-language Motivational Interviewing therapy...	11	Experimental	3	HTML
34	kant2002/cTakes-mixed Clone of latest Apache cTakes	11	Experimental	—	Java
35	Manpreetkour95/LLM_Extraction_streamlit_app LLM end to end	10	Experimental	2	Python

Comparisons in this category

MedCAT and MedCATtrainer (50 vs 46) MedCAT and MedCAT2 (50 vs 33) ctakes and ctakesspark (55 vs 33) biomedicus and biomedicus2 (45 vs 41) emr-nlp-server and emr-vis-web (38 vs 38)