simDEF

simDEF is a software tool for measuring semantic similarity of Gene Ontology (GO) terms based on their textual definitions. The tool utilizes an optimized definition vector approach and expresses the similarity of a pair of proteins as the cosine of the angle between their definition vectors. Compared to existing methods, simDEF improves correlation with sequence homology by up to 50%, shows correlation improvement with gene expression in the biological process hierarchy of GO and increases PPI predictability by > 2.5% in F1 score for molecular function hierarchy. The software is available along with datasets and source code online.

Topic

Genetics;Ontology and terminology;Natural language processing

Detail

  • Operation: Document similarity calculation

  • Software interface: Command-line user interface

  • Language: Perl

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Natural Sciences and Engineering Research Council of Canada, Poland's National Scientific Center, the Canada Research Chairs program.

  • Input: -

  • Output: -

  • Contact: ahmad.pgh@dal.ca

  • Collection: -

  • Maturity: -

Publications

  • simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.
  • Pesaranghader A, et al. simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes. simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes. 2016; 32:1380-7. doi: 10.1093/bioinformatics/btv755
  • https://doi.org/10.1093/bioinformatics/btv755
  • PMID: 26708333
  • PMC: -

Download and documentation

    Currently not available or not maintained.

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