UMLS-Query: a perl module for querying the UMLS

AMIA Annu Symp Proc. 2008 Nov 6;2008:652-6.

Abstract

The Metathesaurus from the Unified Medical Language System (UMLS) is a widely used ontology resource, which is mostly used in a relational database form for terminology research, mapping and information indexing. A significant section of UMLS users use a MySQL installation of the metathesaurus and Perl programming language as their access mechanism. We describe UMLS-Query, a Perl module that provides functions for retrieving concept identifiers, mapping text-phrases to Metathesaurus concepts and graph traversal in the Metathesaurus stored in a MySQL database. UMLS-Query can be used to build applications for semi-automated sample annotation, terminology based browsers for tissue sample databases and for terminology research. We describe the results of such uses of UMLS-Query and present the module for others to use.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Artificial Intelligence
  • Database Management Systems*
  • Information Storage and Retrieval / methods*
  • Natural Language Processing*
  • Pattern Recognition, Automated / methods*
  • Software*
  • Subject Headings*
  • Unified Medical Language System*
  • United States
  • User-Computer Interface