UMLS-Query: a perl module for querying the UMLS.
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.
Shah
Nigam H
NH
Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.
Shah
Nigam
N
Muse
Mark A
MA
Musen
Mark
M
D000465:Algorithms; D001185:Artificial Intelligence; D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods*; D012984:Software; D013358:Subject Headings; D017432:Unified Medical Language System; D014481:United States; D014584:User-Computer Interface