UMLS-Interface and UMLS-Similarity: open source software for measuring paths and semantic similarity.

Bridget T. McInnes, Ted Pedersen, Serguei V.S. Pakhomov

Research output: Contribution to journalArticlepeer-review

102 Scopus citations

Abstract

A number of computational measures for determining semantic similarity between pairs of biomedical concepts have been developed using various standards and programming platforms. In this paper, we introduce two new open-source frameworks based on the Unified Medical Language System (UMLS). These frameworks consist of the UMLS-Similarity and UMLS-Interface packages. UMLS-Interface provides path information about UMLS concepts. UMLS-Similarity calculates the semantic similarity between UMLS concepts using several previously developed measures and can be extended to include new measures. We validate the functionality of these frameworks by reproducing the results from previous work. Our frameworks constitute a significant contribution to the field of biomedical Natural Language Processing by providing a common development and testing platform for semantic similarity measures based on the UMLS.

Original languageEnglish (US)
Pages (from-to)431-435
Number of pages5
JournalAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium
Volume2009
StatePublished - 2009

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