A reference model for biomedical ontology evaluation: the perspective of granularity

Abstract

There have been many attempts using ontologies to develop systems that integrate data from the domains of medicine and biology, across levels of gravity. Such integration systems have not gained wide adoption and reuse. This is largely due to a lack of an approach with metrics as frame of reference to enable users evaluate these systems for their representation of biomedical structure, across levels of granularity. In this paper a reference ontology against which such evaluation of biomedical ontologies may be conducted is presented. Requirements for the reference ontology were validated in a descriptive study. Basic formal ontology with its support for representing biomedical structure across levels of granularity is adopted as the underlying theory for deriving the reference ontology. Metrics for determining the suitability of an ontology to integrate biomedical data across levels of granularity are derived using the reference ontology. The utility of the reference ontology was tested by a prototype tool that was used to evaluate the infectious disease ontology. The results were validated in a questionnaire based study with users.