Combining hierarchical and associative gene ontology relations with textual evidence in estimating gene and gene product similarity

Antonio Sanfilippo, Christian Posse, Banu Gopalan, Rick Riensche, Nathaniel Beagley, Bob Baddeley, Stephen Tratz, Michelle Gregory

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)51-59
Number of pages9
JournalIEEE Transactions on Nanobioscience
Volume6
Issue number1
DOIs
Publication statusPublished - Mar 2007
Externally publishedYes

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Keywords

  • BLAST
  • Gene ontology
  • Gene product similarity
  • GoPubMed
  • Ontology alignment

ASJC Scopus subject areas

  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Pharmaceutical Science
  • Medicine (miscellaneous)
  • Biotechnology
  • Biomedical Engineering
  • Bioengineering

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