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Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation

Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation,10.1093/bioinformatics/btg153,Bi

Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation   (Citations: 333)
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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 natu- ral 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 on- tological annotation to measure the similarities in knowledge content or "semantic similarity" between entries in a data re- source. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those per- formed 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 inves- tigate 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 se- quence databases. Availability: Software available from http://www. russet.org.uk
Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 19, no. 10, pp. 1275-1283, 2003
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