Describing knowledge domains : a case study of biological ontologies

Chapter 10: In the past decade, the development of standardised and machine-processable controlled vocabularies has been a fertile field of research in the life sciences. Understandably, development of the semantic web has attracted significant attention from parts of the medical and life science community. A nexus of government, academic and corporate sources has funded the construction of semantic web ontologies for a range of biomedical and biological vocabularies, including: clinical terms (SNOMED), genetic sequencing (Gene Ontology), proteins (PRotein Ontology) and general ontology repositories (Open Biological and Biomedical Ontologies). Even several of the upper-level ontologies surveyed in the preceding chapter were the beneficiaries of bioinformatics funding. The nature and scale of the classificatory structures of life sciences makes the semantic web, and ontologies in particular, seem especially well suited. This study seek to explore some of the trade-offs of taxonomic standardisation through a content analysis of ontologies and surrounding debates in the life science and bioinformatics communities. It begins by briefly examining some of the more successful ontologies used in biological research, including two of the most widely cited and noted: an umbrella biomedical ontology collaborative effort known as the ‘OBO Foundry’, and a particularly successful biological ontology, the Gene Ontology.