Research article

How the gene ontology evolves

Sabina Leonelli^1*, Alexander D Diehl², Karen R Christie³, Midori A Harris⁴ and Jane Lomax⁴

• * Corresponding author: Sabina Leonelli s.leonelli@exeter.ac.uk

Author Affiliations

¹ ESRC Centre for Genomics in Society, University of Exeter, St Germans Road, EX4 4PJ Exeter, UK

² The Jacobs Neurological Institute, University at Buffalo School of Medicine and Biomedical Sciences, 100 High Street, Buffalo, NY 14203, USA

³ Department of Genetics, Stanford University, 1501 S. California Ave, Palo Alto, CA 94304-5577, USA

⁴ EMBL--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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BMC Bioinformatics 2011, 12:325 doi:10.1186/1471-2105-12-325

Published: 5 August 2011

Abstract

Background

Maintaining a bio-ontology in the long term requires improving and updating its contents so that it adequately captures what is known about biological phenomena. This paper illustrates how these processes are carried out, by studying the ways in which curators at the Gene Ontology have hitherto incorporated new knowledge into their resource.

Results

Five types of circumstances are singled out as warranting changes in the ontology: (1) the emergence of anomalies within GO; (2) the extension of the scope of GO; (3) divergence in how terminology is used across user communities; (4) new discoveries that change the meaning of the terms used and their relations to each other; and (5) the extension of the range of relations used to link entities or processes described by GO terms.

Conclusion

This study illustrates the difficulties involved in applying general standards to the development of a specific ontology. Ontology curation aims to produce a faithful representation of knowledge domains as they keep developing, which requires the translation of general guidelines into specific representations of reality and an understanding of how scientific knowledge is produced and constantly updated. In this context, it is important that trained curators with technical expertise in the scientific field(s) in question are involved in supervising ontology shifts and identifying inaccuracies.