title: Semi-automated evaluation of biomedical ontologies for the biobanking domain based on competency questions.
abstract: BACKGROUND
  Biosample collections and biobank information systems have become a key enabler for medical research. Therefore it is important to identify potentially relevant ontologies to semantically enrich information related to the biobanking domain.
  
  
  OBJECTIVE
  We present a three-stage semi-automated evaluation approach which allows identifying relevant ontologies for the biobanking domain based on competency questions.
  
  
  METHODS
  After identifying candidate biobanking ontologies (Stage 1) and competency questions (Stage 2), a six-step lexical evaluation approach, which assesses the coverage of concepts, properties or instances defined by competency questions is suggested and described (Stage 3).
  
  
  RESULTS
  We were able to perform a proof-of-concept evaluation of the OMIABIS ontology using our proposed three-stage approach together with a sample competency question.
  
  
  CONCLUSIONS
  Our evaluation approach allows a swift evaluation of candidate ontology entities based on a search for higher hierarchy key terms that exist in comprehensive medical vocabularies in order to state the usability of specific ontologies for the biobanking domain.
authors.affiliation: Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
authors.forename: Philipp
authors.initials: P
authors.lastname: Hofer
authors.affiliation: Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Neururer
authors.affiliation: Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
authors.forename: Helga
authors.initials: H
authors.lastname: Hauffe
authors.affiliation: Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Insam
authors.affiliation: Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
authors.forename: Anette
authors.initials: A
authors.lastname: Zeilner
authors.affiliation: Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
authors.forename: Georg
authors.initials: G
authors.lastname: Göbel
mesh_terms: D001317:Austria; D064229:Biological Ontologies; D018070:Biological Specimen Banks / Q000145:classification*; D000069550:Machine Learning; D062527:Meaningful Use; D009323:Natural Language Processing; D009626:Terminology as Topic