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Bioinformatics Advance Access published online on October 16, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp597
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GeneE: Gene and protein query expansion with disambiguation

Martijn J. Schuemie 1,*, Ning Kang 1, Maarten L. Hekkelman 2 and Jan A. Kors 1

1Department of Medical Informatics, Erasmus University Medical Center Rotterdam,P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
2Nijmegen Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands

*To whom correspondence should be addressed. Dr. Martijn Schuemie, E-mail: m.schuemie{at}erasmusmc.nl


  Abstract

Summary: When referring to genes, authors often use synonyms instead of the official gene symbols. In order to accurately retrieve as many relevant documents as possible, we have developed GeneE, a web application that expands a gene query to include all known synonyms, and adds disambiguation information for ambiguous terms, before forwarding the query to either PubMed, Google, or Jane. The query expansion algorithm is also available as a web service.

Availability: http://biosemantics.org/geneE

Contact: m.schuemie{at}erasmusmc.nl

Associate Editor: Prof. Burkhard Rost

Received on September 14, 2009; revised on October 6, 2009; accepted on October 14, 2009

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