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Bioinformatics Advance Access published online on January 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl010
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 18, 2005
Revised January 12, 2006
Accepted January 15, 2006

Article

Automatic extension of gene ontology with flexible identification of candidate terms

Jin-Bok Lee 1, Jung-jae Kim 1, and Jong C. Park 1 *

1 Computer Science Division and AITrc, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701 South Korea

* To whom correspondence should be addressed.
Jong C. Park, E-mail: park{at}nlp.kaist.ac.kr


  Abstract

Motivation: Gene Ontology (GO) has been manually developed to provide a controlled vocabulary for gene product attributes. It continues to evolve with new concepts that are compiled mostly from existing concepts in a compositional way. If we consider the relatively slow growth rate of GO in the face of the fast accumulation of the biological data, it is much desirable to provide an automatic means for predicting new concepts from the existing ones.

Results: We present a novel method that predicts more detailed concepts by utilizing syntactic relations among the existing concepts. We propose a validation measure for the automatically predicted concepts by matching the concepts to biomedical articles. We also suggest how to find a suitable direction for the extension of a constantly-growing ontology such as GO.

Availability: http://autogo.biopathway.org/.

Supplementary information: Supplementary materials are available at Bioinformatics online.

Associate Editor: Alfonso Valencia
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