This is the accepted version of the paper.This version of the publication may differ from the final published version. The Gene Ontology (GO), a scientific vocabulary widely used in molecular biology databases, is examined by an analysis of its structure, a comparison of its principles to those of traditional controlled vocabularies, and by a detailed analysis of a single concept within it. It is found that the GO deviates in some respects from its principles of ontological realism, and that the two forms of vocabulary could benefit from adopting good practice from the other. In a companion paper, the ways in which the GO is used and maintained are examined by bibliometric analysis, content analysis and discourse analysis. Permanent repository link

This is the unspecified version of the paper.This version of the publication may differ from the final published version. The development and use of the Gene Ontology (GO), a scientific vocabulary widely used in molecular biology databases, is evaluated, with particular reference to the relation between the theoretical basis of the GO, and the pragmatics of its application. Permanent repository link MethodologyThe study uses a combination of bibliometric analysis, content analysis and discourse analysis. These analyses focus on details of the ways in which the terms of the ontology are amended and deleted, and in which they are applied by users. FindingsAlthough the GO is explicitly based on an objective realist epistemology, a considerable extent of subjectivity and social factors are evident in its development and use. It is concluded that bio-ontologies could beneficially be extended to be pluralist, while remaining objective, taking a view of concepts closer to that of more traditional controlled vocabularies. Originality/valueThis is one of very few studies which evaluate the development of a formal ontology in relation to its conceptual foundations, and the first to consider the GO in this way.