Biomedical term normalization of EHRs with UMLS

Authors: Naiara Perez Miguel Montserrat Cuadros Oller German Rigau Claramunt

Date: 23.01.2019


Abstract

This paper presents a novel prototype for biomedical term normalization of electronic health record excerpts with the Unified Medical Language System (UMLS) Metathesaurus, a large, multi-lingual compendium of biomedical and health-related terminologies. Despite the prototype being multilingual and cross-lingual by design, we first focus on processing clinical text in Spanish because there is no existing tool for this language and for this specific purpose. The tool is based on Apache Lucene to index the Metathesaurus and generate mapping candidates from input text. It uses the IXA pipeline for basic language processing and resolves lexical ambiguities with the UKB toolkit. It has been evaluated by measuring its agreement with MetaMap --a mature software to discover UMLS concepts in English texts-- in two English-Spanish parallel corpora. In addition, we present a web-based interface for the tool.

BIB_text

@Article {
title = {Biomedical term normalization of EHRs with UMLS},
pages = {2045-2051},
keywds = {
term normalization, UMLS, information extraction, biomedical text
}
abstract = {

This paper presents a novel prototype for biomedical term normalization of electronic health record excerpts with the Unified Medical Language System (UMLS) Metathesaurus, a large, multi-lingual compendium of biomedical and health-related terminologies. Despite the prototype being multilingual and cross-lingual by design, we first focus on processing clinical text in Spanish because there is no existing tool for this language and for this specific purpose. The tool is based on Apache Lucene to index the Metathesaurus and generate mapping candidates from input text. It uses the IXA pipeline for basic language processing and resolves lexical ambiguities with the UKB toolkit. It has been evaluated by measuring its agreement with MetaMap --a mature software to discover UMLS concepts in English texts-- in two English-Spanish parallel corpora. In addition, we present a web-based interface for the tool.


}
isbn = {979-10-95546-00-9},
date = {2019-01-23},
}
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