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

P. W. Lord, R. D. Stevens, A. Brass, C. A. Goble
2003 Bioinformatics  
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
more » ... ledge 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.
doi:10.1093/bioinformatics/btg153 pmid:12835272 fatcat:hxk6fl4d55dvpgbqrvhg4juto4