Foundations for a realism-based drug repurposing ontology

Several ontologies represent entities pertinent to the domain of medicinal drugs. An analysis of these ontologies and the related literature shows that they primarily do so from the perspective of treatment and that the definitions for many of the core entities fall short when applied to drug discovery in general and drug repurposing in particular. We therefore redefined or created new elucidations and definitions for terms which are most important to understanding what is meant by 'drug repurposing' using guidelines of ontological realism, thereby making judicious use of the Basic Formal Ontology, the Ontology for Biomedical Investigations, the Ontology for General Medical Science, and the Drug Ontology. We tested the appropriateness of these modifications for the description of a use case on what is involved, and inferred when using the Computational Analysis of Novel Drug Opportunities (CANDO) drug repurposing platform. We found that the definitions proposed remove some of the shortcomings of other ontologies but that still more work is needed to address all issues.