%0 Journal Article
%T Disjunctive shared information between ontology concepts: application to Gene Ontology
%A Francisco M Couto
%A M¨¢rio J Silva
%J Journal of Biomedical Semantics
%D 2011
%I BioMed Central
%R 10.1186/2041-1480-2-5
%X This paper proposes a novel method, dubbed DiShIn, that effectively exploits the multiple inheritance relationships present in many biomedical ontologies. DiShIn calculates the shared information content of two ontology concepts, based on the information content of the disjunctive common ancestors of the concepts being compared. DiShIn identifies these disjunctive ancestors through the number of distinct paths from the concepts to their common ancestors.DiShIn was applied to Gene Ontology and its performance was evaluated against state-of-the-art measures using CESSM, a publicly available evaluation platform of protein similarity measures. By modifying the way traditional semantic similarity measures calculate the shared information content, DiShIn was able to obtain a statistically significant higher correlation between semantic and sequence similarity. Moreover, the incorporation of DiShIn in existing applications that exploit multiple inheritance would reduce their execution time.Comparison techniques have always been essential tools for managing knowledge. For example, the study and analysis of a given protein often starts by comparing it with related proteins, and that characterization can be helpful to better understand it. However, the number of possible proteins that can be compared is huge and does not stop growing, due to contemporary high-throughput technologies. Thus, the quest for efficient advanced computational sequence comparison techniques to search for similar proteins is omnipresent in many fields of proteomics.The most straightforward comparison methods are sequence-based. They only require information on their internal structure (the sequence itself), but limit the analysis to proteins sharing a similar structure, independently of their biological role. This ignores ontological knowledge about the properties and relationships among proteins. For example, when looking for proteins with an oxidoreductase activity, we may be not only interested in
%U http://www.jbiomedsem.com/content/2/1/5