Determining the semantic similarities of GO terms based on their existence dependencies

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We introduce in this paper a system called EDGT, which determines the semantic relationships among Gene Ontology terms. EDGT accepts Keyword-based queries with the form Q ("t1", "t2", .., "tn") and Loosely Structured queries with the form Q( "t1",..., "tn", R1?,..., Rn?), where ti denotes a GO search term and Ri denotes a return/result GO term. The result of the Keyword-based query Q("t1", "t2") is a set of GO terms, where each term in the set is semantically related to both t1 and t2. The framework of EDGT determines the relationships among GO terms using the concept of existence dependency. EDGT resides between user application and Gene Ontology database. We experimentally evaluated EDGT and compared it with four existing methods. The results showed marked improvement.

Original languageBritish English
Title of host publicationProceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012
Pages118-122
Number of pages5
DOIs
StatePublished - 2012
Event2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012 - Bali, Indonesia
Duration: 12 Jul 201214 Jul 2012

Publication series

NameProceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012

Conference

Conference2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012
Country/TerritoryIndonesia
CityBali
Period12/07/1214/07/12

Keywords

  • Gene Ontology
  • gene products
  • semantic similarity

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