IntelliGO: a new vector-based semantic similarity measure including annotation origin

Background: The Gene Ontology (GO) is a well known controlled vocabulary describing the biological process, molecular function and cellular component aspects of gene annotation. It has become a widely used knowledge source in bioinformatics for annotating genes and measuring their semantic similarity. These measures generally involve the GO graph structure, the information content of GO aspects, or a combination of both. However, only a few of the semantic similarity measures described so far can handle GO annotations differently according to their origin (i.e. their evidence codes). Results: We present here a new semantic similarity measure called IntelliGO which integrates several complementary properties in a novel vector space model. The coefficients associated with each GO term that annotates a given gene or protein include its information content as well as a customized value for each type of GO evidence code. The generalized cosine similarity measure, used for calculating the d...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes
• Keywords: BMCBI 2010, Business, IntelliGO Similarity Measure, Semantic Similarity, Similarity Measure