Combining hierarchical and associative gene ontology relations with textual evidence in estimating gene and gene product similarity.
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.
Sanfilippo
Antonio
A
Pacific Northwest National Laboratory, Richland, WA 99352, USA. antonio.sanfilippo@pnl.gov
Posse
Christian
C
Gopalan
Banu
B
Riensche
Rick
R
Beagley
Nathaniel
N
Baddeley
Bob
B
Tratz
Stephen
S
Gregory
Michelle
M
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
D011506:Proteins