title: Combining hierarchical and associative gene ontology relations with textual evidence in estimating gene and gene product similarity.
abstract: Two approaches have recently emerged where the similarity between two genes or gene products is obtained by comparing Gene Ontology (GO) annotations associated with the genes or gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene subontology, while the other relies on associative relations across the three gene subontologies. We propose a novel methodology where the two approaches can be merged and enriched by textual evidence extracted from biomedical literature with ensuing benefits in coverage and stronger correlation with sequence-based similarity.
authors: Pacific Northwest National Laboratory, Richland, WA 99352, USA. antonio.sanfilippo@pnl.gov
authors: Antonio
authors: A
authors: Sanfilippo
authors: Christian
authors: C
authors: Posse
authors: Banu
authors: B
authors: Gopalan
authors: Rick
authors: R
authors: Riensche
authors: Nathaniel
authors: N
authors: Beagley
authors: Bob
authors: B
authors: Baddeley
authors: Stephen
authors: S
authors: Tratz
authors: Michelle
authors: M
authors: Gregory
mesh_terms: D001185:Artificial Intelligence; D016208:Databases, Factual; D005796:Genes / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods*; D011506:Proteins / Q000145:classification* / Q000378:metabolism*; D011642:Publications; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins