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Bioinformatics Advance Access originally published online on February 2, 2009
Bioinformatics 2009 25(6):815-821; doi:10.1093/bioinformatics/btp071
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

High-performance gene name normalization with GENO

Joachim Wermter *, Katrin Tomanek and Udo Hahn

Jena University Language and Information Engineering (JULIE) Lab, Friedrich-Schiller-Universität Jena, Fürstengraben 30, 07743 Jena, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging. Its importance lies in the fact that they constitute the crucial conceptual entities in biomedicine. Their recognition and normalization remains a challenging task because of widespread gene name ambiguities within species, across species, with common English words and with medical sublanguage terms.

Results: We present GENO, a highly competitive system for gene name normalization, which obtains an F-measure performance of 86.4% (precision: 87.8%, recall: 85.0%) on the BIOCREATIVE-II test set, thus being on a par with the best system on that task. Our system tackles the complex gene normalization problem by employing a carefully crafted suite of symbolic and statistical methods, and by fully relying on publicly available software and data resources, including extensive background knowledge based on semantic profiling. A major goal of our work is to present GENO's architecture in a lucid and perspicuous way to pave the way to full reproducibility of our results.

Availability: GENO, including its underlying resources, will be available from www.julielab.de. It is also currently deployed in the Semedico search engine at www.semedico.org.

Contact: joachim.wermter{at}uni-jena.de

Associate Editor: Jonathan Wren

Received on December 11, 2008; revised on January 21, 2009; accepted on January 28, 2009

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