UMLS Community - User Contributions
A Collection of UMLS Tools
The UMLS community has developed APIs, automation scripts, and NLP tools that extend UMLS functionality. Want to contribute? Submit your tool via our customer service form with subject: UMLS Community and a link to your source code.
Name
Description
Publisher
APIs(11 items)
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
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
A collection of UMLS API examples that can be run using the
Postman
application.
National Library of Medicine
A basic UI that calls a set of REST APIs built around a UMLS data model.
West Coast Informatics
A Perl interface for the UMLS.
Bridget McInnes, Ted Pedersen, Serguei Pakhomov, Siddharth Patwardhan
Automation Scripts(14 items)
Automate downloads of UMLS, RxNorm, and SNOMED CT release files.
National Library of Medicine
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
Allows command-line execution of customizable MRCXT Builder configurations.
Brian Carlsen
Allows command-line execution of customizable MetamorphoSys configurations.
Brian Carlsen
Loads Metathesaurus .RRF files into a Microsoft SQL Server database.
Dr. Nader Elshehabi
MYSQL load scripts are packaged with the
UMLS release
.
National Library of Medicine
Oracle load scripts are packaged with the
UMLS release
.
National Library of Medicine
A script for changing | to a TAB delimiter. Useful for importing large files (such as MRCONSO.RRF) into FileMaker.
Dr. Daniel Hinostroza
Julian Maya
Julian Maya
Loads Metathesaurus .RRF files into a PostgreSQL database. Includes separate index creation script.
Steve Bedrick
Yeb Havinga
Yeb Havinga
Loads Semantic Network files into a Microsoft SQL Server database
Dr. Nader Elshehabi
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
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)
Natural Language Processing Tools(18 items)
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
becas is a web application, API and widget for biomedical concept identification.
University of Aveiro Bioinformatics Group
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
Get annotations for biomedical text with classes from BioPortal ontologies. Filter by UMLS Semantic Type.
National Center for Biomedical Ontology
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
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)
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
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
The MEDLINE co-occurrences file summarizes the MeSH Descriptors that occur together in MEDLINE citations.
National Library of Medicine
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
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
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
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
QuickUMLS (Soldaini and Goharian, 2016) is a tool for fast, unsupervised biomedical concept extraction from medical text.
Georgetown Information Retrieval Lab
A Python package containing spaCy models for processing biomedical, scientific or clinical text.
Allen Institute for Artificial Intelligence
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
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
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
Siddharth Patwardhan
Serguei Pakhomov
Ted Pedersen
Ying Liu
Disclaimer: Tools listed here are provided by third parties and are not officially endorsed by the National Library of Medicine (NLM).
Use at your own risk. Verify functionality and compatibility before using in production environments.
Last Reviewed: September 19, 2024