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Bioinformatics Vol. 19 no. 10 2003
Pages 1275-1283
© 2003 Oxford University Press

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation

P. W. Lord *, R. D. Stevens , A. Brass and C. A. Goble

Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK

Received on July 2, 2002 ; revised on October 23, 2002 and December 23, 2002 ; accepted on December 6, 2002

Motivation: Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientific natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or ‘semantic similarity’ between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repetoire of analyses.

Results: We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases.

Availability: Software available from http://www.russet.org.uk

Contact: p.lord{at}russet.org.uk

* To whom correspondence should be addressed.


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