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Bioinformatics Advance Access originally published online on June 9, 2006
Bioinformatics 2006 22(17):2151-2157; doi:10.1093/bioinformatics/btl281
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Combination of text-mining algorithms increases the performance

Rainer Malik 1,*, Lude Franke 2 and Arno Siebes 1

1 Universiteit Utrecht, Department of Information and Computing Sciences Padualaan 14, 3584CH Utrecht, The Netherlands
2 Complex Genetics Section, Department of Medical Genetics UMC Utrecht, The Netherlands

*To whom correspondence should be addressed.

Motivation: Recently, several information extraction systems have been developed to retrieve relevant information out of biomedical text. However, these methods represent individual efforts. In this paper, we show that by combining different algorithms and their outcome, the results improve significantly. For this reason, CONAN has been created, a system which combines different programs and their outcome. Its methods include tagging of gene/protein names, finding interaction and mutation data, tagging of biological concepts and linking to MeSH and Gene Ontology terms.

Results: In this paper, we will present data that show that combining different text-mining algorithms significantly improves the results. Not only is CONAN a full-scale approach that will ultimately cover all of PubMed/MEDLINE, we also show that this universality has no effect on quality: our system performs as well as or better than existing systems.

Availability: The LDD corpus presented is available by request to the author. The system will be available shortly. For information and updates on CONAN please visit http://www.cs.uu.nl/people/rainer/conan.html

Contact: rainer{at}cs.uu.nl

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on January 9, 2006; revised on April 25, 2006; accepted on June 1, 2006

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