title: simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.
abstract: Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the semantic similarity of their GO terms; however, these measures are highly sensitive to modifications in the topological structure of GO, tend to be focused on specific analytical tasks and concentrate on the GO terms themselves rather than considering their textual definitions.
  
  
  
  We introduce simDEF, an efficient method for measuring semantic similarity of GO terms using their GO definitions, which is based on the Gloss Vector measure commonly used in natural language processing. The simDEF approach builds optimized definition vectors for all relevant GO terms, and expresses the similarity of a pair of proteins as the cosine of the angle between their definition vectors. Relative to existing similarity measures, when validated on a yeast reference database, simDEF improves correlation with sequence homology by up to 50%, shows a correlation improvement >4% with gene expression in the biological process hierarchy of GO and increases PPI predictability by > 2.5% in F1 score for molecular function hierarchy.
  
  
  
  Datasets, results and source code are available at http://kiwi.cs.dal.ca/Software/simDEF CONTACT: ahmad.pgh@dal.ca or beiko@cs.dal.ca
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada, Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Pesaranghader
authors.affiliation: Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada, Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada, Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland and.
authors.forename: Stan
authors.initials: S
authors.lastname: Matwin
authors.affiliation: Institute for Big Data Analytics, Halifax, NS B3H 4R2, Canada, Faculty of Medicine and Faculty of Engineering, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
authors.forename: Marina
authors.initials: M
authors.lastname: Sokolova
authors.affiliation: Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada.
authors.forename: Robert G
authors.initials: RG
authors.lastname: Beiko
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D063990:Gene Ontology; D006801:Humans; D011506:Proteins; D012660:Semantics
chemical_list: D011506:Proteins