Measuring semantic similarity between Gene Ontology terms

Authors:
Francisco M. Couto;Mário J. Silva;Pedro M. Coutinho
Affiliations:
Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Portugal;Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Portugal;UMR 6098, CNRS and Universities Aix-Marseille I & II, Marseille, France
Venue:
Data & Knowledge Engineering
Year:
2007

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Abstract

Many bioinformatics applications would benefit from comparing proteins based on their biological role rather than their sequence. This paper adds two new contributions. First, a study of the correlation between Gene Ontology (GO) terms and family similarity demonstrates that protein families constitute an appropriate baseline for validating GO similarity. Secondly, we introduce GraSM, a novel method that uses all the information in the graph structure of the Gene Ontology, instead of considering it as a hierarchical tree. GraSM gives a consistently higher family similarity correlation on all aspects of GO than the original semantic similarity measures.