Measuring semantic similarity between Gene Ontology terms

• DOI: 10.1016/j.datak.2006.05.003
• Publication Date: 2006-06-19T09:44:00Z
• Authors: Francisco M. Couto; Mário J. Silva; Pedro M. Coutinho
• Keywords: Computer Science; 0206 medical engineering; 02 engineering and technology

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.