Integrating ontological knowledge and textual evidence in estimating gene and gene product similarity

Authors:
Antonio Sanfilippo;Christian Posse;Banu Gopalan;Stephen Tratz;Michelle Gregory
Affiliations:
Pacific Northwest National Laboratory, Richland, WA;Pacific Northwest National Laboratory, Richland, WA;Pacific Northwest National Laboratory, Richland, WA;Pacific Northwest National Laboratory, Richland, WA;Pacific Northwest National Laboratory, Richland, WA
Venue:
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Year:
2006

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Abstract

With the rising influence of the Gene Ontology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associated with them. So far, these approaches have solely relied on the knowledge encoded in the Gene Ontology and the gene annotations associated with the Gene Ontology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.