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This article is part of the supplement: Proceedings of the 2009 AMIA Summit on Translational Bioinformatics

Open Access Proceedings

The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers

Casey Lynnette Overby14, Peter Tarczy-Hornoch123 and Dina Demner-Fushman4*

Author Affiliations

1 Department of Medical Education & Biomedical Informatics, University of Washington, Seattle, WA, USA

2 Department of Pediatrics, University of Washington, Seattle, WA, USA

3 Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA

4 Lister Hill National Center for Biomedical Communications, National Library of Medicine, NIH, BHHS, Bethesda, MD, USA

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BMC Bioinformatics 2009, 10(Suppl 9):S8  doi:10.1186/1471-2105-10-S9-S8

Published: 17 September 2009


Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to therapy. These scientific discoveries need to be translated into practical applications to optimize patient care. Translating research into practice can be facilitated by supplying clinicians with research evidence. We assessed the role of existing tools in extracting answers to translational research questions in the area of genomic medicine. We: evaluate the coverage of translational research terms in the Unified Medical Language Systems (UMLS) Metathesaurus; determine where answers are most often found in full-text articles; and determine common answer patterns. Findings suggest that we will be able to leverage the UMLS in development of natural language processing algorithms for automated extraction of answers to translational research questions from biomedical text in the area of genomic medicine.