UMLS Community - User Contributions

A Collection of UMLS Tools

The UMLS community has developed APIs, automation scripts, and natural language processing tools that extend the functionality of the UMLS. Want to contribute? Submit your tool via our customer service form with subject: "UMLS Community" and a link to your source code. Please be aware that these tools cannot be guaranteed to function as-is on all platforms, and certain adjustments may be necessary to fit your local environment.

Name	Description	Publisher	Category
Lexical Tools	Lexical Tools is a set of fundamental core NLP tools for retrieving lexical variants. Includes LVG for lexical variant generation, Norm for string normalization, and WordInd for generating word indexes.	National Library of Medicine	Natural Language Processing Tools
Medical Text Indexer (MTI)	The NLM Medical Text Indexer (MTI) combines human NLM indexing expertise and Natural Language Processing technology to curate the biomedical literature more efficiently and consistently.	National Library of Medicine	Natural Language Processing Tools
MEDLINE Co-Occurrences (MRCOC) Files	The MEDLINE co-occurrences file summarizes the MeSH Descriptors that occur together in MEDLINE citations.	National Library of Medicine	Natural Language Processing Tools
MeSH on Demand	MeSH on Demand identifies MeSH terms in your submitted text (abstract or manuscript). MeSH on Demand also lists PubMed similar articles relevant to your submitted text.	National Library of Medicine	Natural Language Processing Tools
MetaMap	MetaMap is a highly configurable program developed by Dr. Alan (Lan) Aronson at the National Library of Medicine (NLM) to map biomedical text to the UMLS Metathesaurus or, equivalently, to discover Metathesaurus concepts referred to in text.	National Library of Medicine	Natural Language Processing Tools
MetaMapLite	The primary goal of MetaMapLite to provide a near real-time named-entity recognizer which is not a rigorous as MetaMap but is much faster while allowing users to customize and augment its behavior for specific purposes.	National Library of Medicine	Natural Language Processing Tools
File Downloads	Automate downloads of UMLS, RxNorm, and SNOMED CT release files.	National Library of Medicine	Automation Scripts
MYSQL Load Scripts	MYSQL load scripts are packaged with the UMLS release .	National Library of Medicine	Automation Scripts
Oracle Load Scripts	Oracle load scripts are packaged with the UMLS release .	National Library of Medicine	Automation Scripts
Semantic MEDLINE Database (SemMedDB)	The Semantic MEDLINE Database (SemMedDB) is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text.	National Library of Medicine	Natural Language Processing Tools
SemRep	SemRep is a UMLS-based program that extracts three-part propositions, called semantic predications, from sentences in biomedical text. Predications consist of a subject argument, an object argument, and the relation that binds them.	National Library of Medicine	Natural Language Processing Tools
UMLS REST API Postman Samples	A collection of UMLS API examples that can be run using the Postman application.	National Library of Medicine	APIs
Apache cTakes	cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text. Originally developed at the Mayo Clinic, it has expanded to being used by various institutions internationally.	Apache cTakes Community	Natural Language Processing Tools
becas	becas is a web application, API and widget for biomedical concept identification.	University of Aveiro Bioinformatics Group	Natural Language Processing Tools
BioMedICUS	The BioMedical Information Collection and Understanding System (BioMedICUS) is a system for large-scale text analysis and processing of biomedical and clinical reports.	University of Minnesota Institute for Health Informatics NLP/IE Group	Natural Language Processing Tools
BioPortal Annotator	Get annotations for biomedical text with classes from BioPortal ontologies. Filter by UMLS Semantic Type.	National Center for Biomedical Ontology	Natural Language Processing Tools
CLAMP	CLAMP is a comprehensive clinical Natural Language Processing (NLP) software that enables recognition and automatic encoding of clinical information in narrative patient reports.	University of Texas Health Science Center at Houston	Natural Language Processing Tools
GATE Bio-YODIE	Bio-YODIE is a named entity linking system. It links mentions in biomedical text to their referents in the UMLS.	GATE (General Architecture for Text Engineering)	Natural Language Processing Tools
C# Code Samples for UMLS REST API	C# code samples for the UMLS REST API.	Wesley Eastridge, MD	APIs
Health Vocabulary (HaVoc) REST API	A REST API for querying UMLS data.	Applied Informatics Inc.	APIs
humumls (UMLS in Python with MongoDB)	This package allows for the conversion of UMLS .RRF files to a document-level MongoDB database. Note that the goal of this package is not to provide a 1-to-1 mapping from the UMLS .RRF mapping to a MongoDB, but rather to provide useful abstractions where necessary.	Computational Linguistics Research Group, University of Antwerp	Automation Scripts
MetamorphoSys Batch MRCXT Builder	Allows command-line execution of customizable MRCXT Builder configurations.	Brian Carlsen	Automation Scripts
MELODI	MELODI (Mining Enriched Literature Objects to Derive Intermediates) is a hypothesis generator. It identifies enriched overlapping objects which have been assigned to scientific literature and uses these to derive intermediate mechanisms.	Benjamin Elsworth, Karen Dawe, Emma E Vincent, Ryan Langdon, Brigid M Lynch, Richard M Martin, Caroline Relton, Julian P T Higgins, Tom R Gaunt	Natural Language Processing Tools
MetamorphoSys Batch Run Script	Allows command-line execution of customizable MetamorphoSys configurations.	Brian Carlsen	Automation Scripts
Microsoft SQL Server load script for Metathesaurus subset.	Loads Metathesaurus .RRF files into a Microsoft SQL Server database.	Dr. Nader Elshehabi	Automation Scripts
Pipe (\|) to tab substitution for RRF files	A script for changing \| to a TAB delimiter. Useful for importing large files (such as MRCONSO.RRF) into FileMaker.	Dr. Daniel Hinostroza Julian Maya	Automation Scripts
PostgreSQL load & index scripts	Loads Metathesaurus .RRF files into a PostgreSQL database. Includes separate index creation script.	Steve Bedrick Yeb Havinga	Automation Scripts
py-umls	Basic tools to interact with UMLS lexica, namely UMLS, SNOMED and RxNorm, using Python 3 scripts. Includes a sqlite load script .	Boston Children's Hospital	APIs
PyMedTermino	A Python module for easy access to the main medical terminologies in Python, including SNOMED CT, ICD10, MedDRA, CDF, UMLS and VCM icons.	Jean-Baptiste Lamy	APIs
QuickUMLS	QuickUMLS (Soldaini and Goharian, 2016) is a tool for fast, unsupervised biomedical concept extraction from medical text.	Georgetown Information Retrieval Lab	Natural Language Processing Tools
RxNorm PostgreSQL Load Scripts	Scripts to import RxNorm into a PostgreSQL database.	Joseph Nahmias	Automation Scripts
rUMLS	An R wrapper for the UMLS REST API.	Matthew Pancia	APIs
umlsr	An R package for interfacing with the UMLS API.	David Kincaid	APIs
SciSpacy	A Python package containing spaCy models for processing biomedical, scientific or clinical text.	Allen Institute for Artificial Intelligence	Natural Language Processing Tools
sqlite load script	Quickly loads the UMLS Metathesaurus into sqlite. To implement, download the UMLS Metathesaurus Files and modify the script to point to the META folder.	Boston Children's Hospital	Automation Scripts
SQL load script for Semantic Network	Loads Semantic Network files into a Microsoft SQL Server database	Dr. Nader Elshehabi	Automation Scripts
umls2rdf	This project takes a MySQL Unified Medical Language System (UMLS) database and converts the ontologies to RDF using OWL and SKOS as the main schemas.	National Center for Biomedical Ontology (NCBO)	Automation Scripts
umls-to-graph	Converts UMLS to a graph structure.	Bethany Percha	Automation Scripts
UMLS::Interface	A Perl interface for the UMLS.	Bridget McInnes, Ted Pedersen, Serguei Pakhomov, Siddharth Patwardhan	APIs
umls-rat (UMLS Rest API Tool)	A Python interface for the UMLS API.	Russell Klopfer	APIs
UMLS::Similarity	A suite of Perl modules that implement a number of semantic similarity measures in order to calculate the similarity between two concepts in the UMLS. The measures use the UMLS-Interface module to access the UMLS present in a mysql database.	Bridget McInnes Siddharth Patwardhan Serguei Pakhomov Ted Pedersen Ying Liu	Natural Language Processing Tools
UMLS Terminology Server	A basic UI that calls a set of REST APIs built around a UMLS data model.	West Coast Informatics	APIs

Disclaimer: Neither the author(s) nor the National Library of Medicine (NLM) makes any warranty, expressed or implied, or assumes any liability or responsibility for the use of this information, scripts, or software described here. It is the sole responsibility of the end-user to verify compatibility, safety, and functionality of any third-party contribution before attempting to incorporate it into a production-level environment. NLM shall not be held responsible for any claims of data loss, system damage, or other unexpected outcomes resulting from incorporating these contributions into real-world applications. The posting of these contributions does not constitute endorsement by the NLM.

Last Reviewed: February 21, 2023

Unified Medical Language System® (UMLS®)

A Collection of UMLS Tools

Unified Medical Language System^® (UMLS^®)