A literature-based similarity metric for biological processes

Background: Recent analyses in systems biology pursue the discovery of functional modules within the cell. Recognition of such modules requires the integrative analysis of genome-wide experimental data together with available functional schemes. In this line, methods to bridge the een the abstract definitions of cellular processes in current schemes and the interlinked nature of biological networks are required. Results: This work explores the use of the scientific literature to establish potential relationships among cellular processes. To this end we haveused a document based similarity method to compute pair-wise similarities of the biological processes described in the Gene Ontology (GO). The method has been applied to the biological processes annotated for the Saccharomyces cerevisiae genome. We compared our results with similarities obtained with two ontology-based metrics, as well as with gene product annotation relationships. We show that the literature-based metric conserves ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, José María Carazo, Alberto D. Pascual-Montano
• Keywords: Biological, BMCBI 2006, Cellular Processes, Functional Schemes