Detecting role errors in the gene hierarchy of the NCI thesaurus

Hua Min, Barry Cohen, Michael Halper, Marc Oren, Yehoshua Perl

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Gene terminologies are playing an increasingly important role in the ever-growing field of genomic research. While errors in large, complex terminologies are inevitable, gene terminologies are even more susceptible to them due to the rapid growth of genomic knowledge and the nature of its discovery. It is therefore very important to establish qualityassurance protocols for such genomic-knowledge repositories. Different kinds of terminologies oftentimes require auditing methodologies adapted to their particular structures. In light of this, an auditing methodology tailored to the characteristics of the NCI Thesaurus's (NCIT's) Gene hierarchy is presented. The Gene hierarchy is of particular interest to the NCIT's designers due to the primary role of genomics in current cancer research. This multiphase methodology focuses on detecting role-errors, such as missing roles or roles with incorrect or incomplete target structures, occurring within that hierarchy. The methodology is based on two kinds of abstraction networks, called taxonomies, that highlight the role distribution among concepts within the IS-A (subsumption) hierarchy. These abstract views tend to highlight portions of the hierarchy having a higher concentration of errors. The errors found during an application of the methodology are reported. Hypotheses pertaining to the efficacy of our methodology are investigated.

Original languageEnglish (US)
Pages (from-to)293-313
Number of pages21
JournalCancer Informatics
Volume6
DOIs
StatePublished - 2008

All Science Journal Classification (ASJC) codes

  • Oncology
  • Cancer Research

Keywords

  • Abstraction network
  • Auditing
  • Gene hierarchy
  • Gene terminology
  • National Cancer Institute Thesaurus (NCIT)
  • Role error
  • Taxonomy

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