The role of ontologies in biological and biomedical research: A functional perspective

Abstract

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of fourmain features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision ofmetadata that describes the intended meaning of the classes and relations in ontologies; and the provision ofmachine-readable axioms and definitions that enable computational access to some aspects of themeaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation ofmultimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured datamining andmachine learning applications.