Representation of roles in biomedical ontologies: a case study in functional genomics

OBJECTIVE Representing roles, i.e. functions of proteins, sequences and structures, is the cornerstone of knowledge representation in functional genomics. The objective of this study is to investigate representation of roles as functional categories or associative relations. We focus on GeneOntology (GO) and the UMLS and take examples from iron metabolism. METHODS The terms corresponding to the main proteins involved in iron metabolism were mapped to GO (including the annotations) and the UMLS. The representation of their biological roles was then analyzed. RESULTS Functional aspects are represented in both GO and the UMLS. However, the granularity may not be appropriate. DISCUSSION Advantages and limits of functional categories and associative relations are discussed.