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

Lookup NU author(s): Dr Phillip LordORCiD

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Abstract

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.

Publication metadata

Author(s): Lord PW, Stevens RD, Brass A, Goble CA

Publication type: Article

Publication status: Published

Journal: Bioinformatics

Year: 2003

Volume: 19

Issue: 10

Pages: 1275-1283

Print publication date: 01/01/2003

ISSN (print): 1367-4803

ISSN (electronic): 1460-2059

Publisher: Oxford University Press

URL: http://dx.doi.org/10.1093/bioinformatics/btg153

DOI: 10.1093/bioinformatics/btg153

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