A network-theoretic approach for decompositional translation across Open Biological Ontologies

Authors:
Chintan O. Patel;James J. Cimino
Affiliations:
Department of Biomedical Informatics, Columbia University, New York, NY, United States;Department of Biomedical Informatics, Columbia University, New York, NY, United States and Laboratory for Informatics Development, NIH Clinical Center, Bethesda, MD, United States
Venue:
Journal of Biomedical Informatics
Year:
2010

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Abstract

Biological ontologies are now being widely used for annotation, sharing and retrieval of the biological data. Many of these ontologies are hosted under the umbrella of the Open Biological Ontologies Foundry. In order to support interterminology mapping, composite terms in these ontologies need to be translated into atomic or primitive terms in other, orthogonal ontologies, for example, gluconeogenesis (biological process term) to glucose (chemical ontology term). Identifying such decompositional ontology translations is a challenging problem. In this paper, we propose a network-theoretic approach based on the structure of the integrated OBO relationship graph. We use a network-theoretic measure, called the clustering coefficient, to find relevant atomic terms in the neighborhood of a composite term. By eliminating the existing GO to ChEBI Ontology mappings from OBO, we evaluate whether the proposed approach can re-identify the corresponding relationships. The results indicate that the network structure provides strong cues for decompositional ontology translation and the existing relationships can be used to identify new translations.