UMLS-Query: A Perl Module for Querying the UMLS

Saturday, June 2, 2007

Shah N, Musen M. AMIA Annu Symp Proc. 2008 Nov 6:652-6.

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.