title: Quality control for terms and definitions in ontologies and taxonomies.
abstract: BACKGROUND
  Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way.
  
  
  RESULTS
  We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO.
  
  
  CONCLUSIONS
  Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.
authors.affiliation: Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, UK. jacob.koehler@bbsrc.ac.uk
authors.forename: Jacob
authors.initials: J
authors.lastname: Köhler
authors.forename: Katherine
authors.initials: K
authors.lastname: Munn
authors.forename: Alexander
authors.initials: A
authors.lastname: Rüegg
authors.forename: Andre
authors.initials: A
authors.lastname: Skusa
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
mesh_terms: D001185:Artificial Intelligence; D002965:Classification / Q000379:methods; D030541:Databases, Genetic; D004282:Documentation / Q000379:methods* / Q000592:standards; D016247:Information Storage and Retrieval / Q000379:methods* / Q000592:standards; D009323:Natural Language Processing; D010802:Phylogeny; D011506:Proteins / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D011786:Quality Control; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins