Gene ontology summarization to support visualization and quality assurance

Christopher Ochs, Yehoshua Perl, Michael Halper, James Geller, Jane Lomax

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

Abstract

The Gene Ontology (GO) is used extensively in the field of genomics. Like other large and complex ontologies, GO is difficult to maintain. In particular, quality assurance (QA) efforts for GO's content can be laborious and time consuming. Abstraction networks are summarization networks that reveal and highlight high-level structural and hierarchical aggregation patterns in an ontology. They have been shown to successfully support QA work in the context of OWL-format ontologies and SNOMED CT. A kind of abstraction network, called a partial-area taxonomy, is developed for GO hierarchies. The Biological process (BP) taxonomy is derived. Within this framework, several QA heuristics based on the identification of anomalous groups of terms are introduced. Such groups are expected to have higher error rates compared to the general population of terms. The results of a preliminary QA review, based on the BP taxonomy, are presented. It is observed that various inconsistencies in the modeling of GO are exposed with the use of the taxonomy-based QA heuristics. Some anomalies repeatedly revealed errors in the underlying GO.

Original languageEnglish (US)
Title of host publicationProceedings of the 7th International Conference on Bioinformatics and Computational Biology, BICOB 2015
EditorsNurit Haspel, Fahad Saeed
PublisherThe International Society for Computers and Their Applications (ISCA)
Pages167-174
Number of pages8
ISBN (Electronic)9781880843994
StatePublished - 2015
Event7th International Conference on Bioinformatics and Computational Biology, BICOB 2015 - Honolulu, United States
Duration: Mar 9 2015Mar 11 2015

Publication series

NameProceedings of the 7th International Conference on Bioinformatics and Computational Biology, BICOB 2015

Other

Other7th International Conference on Bioinformatics and Computational Biology, BICOB 2015
CountryUnited States
CityHonolulu
Period3/9/153/11/15

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Computer Science Applications
  • Health Information Management

Keywords

  • Abstraction network
  • Gene Ontology
  • OBO ontology
  • Ontology quality assurance

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