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 33 clinical concept linking tools tracked. 2 score above 50 (established tier). The highest-rated is Georgetown-IR-Lab/QuickUMLS at 59/100 with 436 stars and 896 monthly downloads.

Get all 33 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.	51	Established	123	Java
3	medkit-lib/medkit Toolkit for a learning health system	44	Emerging	27	Python
4	CogStack/MedCAT Medical Concept Annotation Tool	43	Emerging	526	Python
5	CogStack/MedCATtrainer A simple interface to inspect, improve and add concepts to biomedical NER+L...	39	Emerging	85	Python
6	OHNLP/MedTagger MedTagger is a light weight clinical NLP system built upon Apache UIMA.	39	Emerging	72	Java
7	nlpie/biomedicus BioMedICUS: A biomedical and clinical NLP engine.	38	Emerging	20	Java
8	CogStack/MedCATtutorials General tutorials for the setup and use of MedCAT.	38	Emerging	42	HTML
9	noc-lab/clinical_concept_extraction Clinical Concept Extraction with Contextual Word Embedding	35	Emerging	41	Python
10	nlpie/biomedicus2 Code for the old version of BioMedICUS, for the new version see the...	34	Emerging	44	Java
11	Bohdan-Khomtchouk/Biochat Natural language processing of Gene Expression Omnibus data	34	Emerging	54	Common Lisp
12	NLPReViz/emr-vis-web An Interactive Tool for Natural Language Processing on Clinical Text	31	Emerging	23	JavaScript
13	CharlyWargnier/S4_wiki_topic_grapher Leverage the power of the Google Natural Language API NLP to retrieve entity...	31	Emerging	15	Python
14	NLPReViz/emr-nlp-server An Interactive Tool for Natural Language Processing on Clinical Text	31	Emerging	15	Java
15	liamca/medical-ner-search Leveraging Apache CTakes and Azure Search to Build and Medical Search App	29	Experimental	11	JavaScript
16	eHealth-KD-PUCs-UFMG/pucrj-pucpr-ufmg Code presented by the PUCRJ-PUCPR-UFMG team in the eHealth Knowledge Discovery 2021.	26	Experimental	5	Python
17	CogStack/MedCAT2 MedCATv2	26	Experimental	5	Python
18	yugagarin/ctakesspark Attempt to integrate Apache cTakes with Apache Spark	26	Experimental	5	Java
19	ExaNLP/sket This repository contains the source code for the Semantic Knowledge...	25	Experimental	13	Python
20	boxorange/BioIE-LLM Biological Information Extraction from Large Language Models (LLMs) (Journal...	22	Experimental	13	Python
21	zyocum/ptllm-events-extraction Demonstration of using OpenAI's pre-trained LLMs for the linguistic...	22	Experimental	1	Shell
22	SDM-TIB/NSSC A Neuro-Symbolic AI System for Enhancing Accuracy of Named Entity...	22	Experimental	1	Python
23	boxorange/LLM-GeneticTool-Extraction Official implementation of Bacterial hosts and Genetic tools Extraction from...	22	Experimental	1	Python
24	dabane-ghassan/cazy-little-helper Biocuration assistant for the CAZy database.	22	Experimental	1	Python
25	TPAFS/hicric Health Insurance Coverage Rules Interepretation Corpus	14	Experimental	4	Python
26	frankkramer-lab/DrNote DrNote is an open tagging tool for text annotation and entity linking based...	13	Experimental	5	Shell
27	scossin/RomediApp Set of programs on top of the Romedi terminology	13	Experimental	8	Java
28	shtrausslearning/biopylib Bioinformatics made simple 🧬	13	Experimental	5	Python
29	WadoodAbdul/clinical_ner_benchmark Run model evaluation and upload results on Clinical NER (NCER) leaderboard	13	Experimental	6	Python
30	nlpie/biomedicus-measures A lightweight (small and dependency-free) Java 8 library for identifying and...	12	Experimental	3	Java
31	jplasser/CNEP CNEP (Contrastive Notes Events Pre-training), Contrastive Learning with...	12	Experimental	3	Jupyter Notebook
32	0xcodemate/Med-annotation Medical Concept Annotation Tool	12	Experimental	1	Python
33	kant2002/cTakes-mixed Clone of latest Apache cTakes	11	Experimental	—	Java

Comparisons in this category

ctakes and ctakesspark (51 vs 26) biomedicus and biomedicus2 (38 vs 34) emr-nlp-server and emr-vis-web (31 vs 31)