Measuring semantic similarity between Gene Ontology terms

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. (c) 2006 Elsevier B.V. All rights reserved.