Semi-automated evaluation of biomedical ontologies for the biobanking domain based on competency questions

Stud Health Technol Inform. 2015;212:65-72.


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.

Objectives: 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.

Conclusion: 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.

MeSH terms

  • Austria
  • Biological Ontologies*
  • Biological Specimen Banks / classification*
  • Machine Learning
  • Meaningful Use*
  • Natural Language Processing*
  • Terminology as Topic*