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Bioinformatics Advance Access originally published online on January 21, 2006
Bioinformatics 2006 22(6):665-670; 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

Automatic extension of Gene Ontology with flexible identification of candidate terms

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

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

*To whom correspondence should be addressed.

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

Contact: park{at}nlp.kaist.ac.kr

Supplementary information: Supplementary materials are available at Bioinformatics online.

Received on April 18, 2005; revised on January 12, 2006; accepted on January 15, 2006

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