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A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts

Gooch, P. and Roudsari, A. (2011). A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts. Paper presented at the IDAMAP Workshop at 13th Conference on Artificial Intelligence in Medicine (AIME'11), 02-07-2011 - 06-07-2011, Bled, Slovenia.

Abstract

We developed a tool that integrates the National Library of Medicine's MetaMap software with GATE, an open-source text an- alytics framework. The tool allows non-ASCII encoded documents of numerous formats to be annotated with UMLS concepts. We created a GATE pipeline to chunk cardiovascular disease guideline text into default segments (blank-line delimited), XML element content, sentences and phrases, which were sequentially submitted to MetaMap for annotation. XML element, sentence and phrase chunking allowed term extraction and mapping to be completed in around 1/3 of the time taken with de- fault chunking, although with slight loss of accuracy (F1.0s=0.94-0.99). However, phrase chunking allows more complex input to be processed in real time, which is not possible with the other approaches. We discuss the results in relation to use of MetaMap's --term processing option for generating pre- and post-coordinated mappings from composite phrases.

Publication Type: Conference or Workshop Item (Paper)
Subjects: R Medicine > RA Public aspects of medicine
Z Bibliography. Library Science. Information Resources > ZA Information resources > ZA4050 Electronic information resources
Departments: School of Mathematics, Computer Science & Engineering > Computer Science > Health Informatics
URI: http://openaccess.city.ac.uk/id/eprint/1036
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