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Published on: November 30, 2022
Semi-automated evaluation of biomedical ontologies for the biobanking domain based on competency questions
Philipp Hofer1, Sabrina Neururer1, Helga Hauffe1
1Department of Medical Informatics, Statistics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria.
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.
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