How the gene ontology evolves

BMC Bioinformatics

Jane Lomax³  Midori A Harris³  Karen R Christie⁴  Alexander D Diehl²  Sabina Leonelli¹ 

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

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

关键词: ontology shifts;    curation;    maintenance;    knowledge;    Gene Ontology;   

Others  :  1125679
DOI  :  10.1186/1471-2105-12-325

 received in 2010-09-15, accepted in 2011-08-05,  发布年份 2011

【 摘 要 】

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.

【 授权许可】

   
2011 Leonelli et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Reviews: Genetics 2000, 25:25-29.
• [2]The Gene Ontology Consortium: The Gene Ontology (GO) project in 2008. Nucleic Acids Research 2007, 1-5.
• [3]Rubin DL, Shah NH, Noy NF: Biomedical ontologies: a functional perspective. Briefings in bioinformatics 2008, 9(1):75-90.
• [4]Lewis SE: Gene Ontology: Looking backwards and forwards. Genome Biology 2004, 6(1):103. BioMed Central Full Text
• [5]Hill DP, Smith B, McAndrews-Hill MS, Blake JA: Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics 2008, 9(Suppl 5):S2. BioMed Central Full Text
• [6]Smith B, et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 2007, 25(11):1251-1255.
• [7]Leonelli S: Documenting the Emergence of Bio-Ontologies: Or, Why Researching Bioinformatics Requires HPSSB. History and Philosophy of the Life Sciences 2010, 32(1):105-126.
• [8]Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, et al.: Ontology engineering. Nature biotechnology 2010, 28(2):128-30.
• [9]Minutes of Gene Ontology 2005 Meeting [http:/ / www.geneontology.org/ minutes/ 20051115_TIGR_Content/ 20051115_TIGR_Content.pdf] webcite
• [10]Diehl AD, Lee JA, Scheuermann RH, Blake JA: Ontology development for biological systems: immunology. Bioinformatics 2007, 23:913-915.
• [11]Nürnberger T, Brunner F, Kemmerling B, Piater L: Immunological Reviews. 2004, 198:249-266.
• [12]The Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research 2004, 32:D258-D261.
• [13]Michie KA, Löwe J: Dynamic filaments of the bacterial cytoskeleton. Annual Reviews of Biochemistry 2006, 75:467-492.
• [14]Shih YL, Rothfield L: The bacterial cytoskeleton. Microbiology and Molecular Biology Reviews 2006, 70:729-754.
• [15]Hu K, et al.: Cytoskeletal components of an invasion machine--the apical complex of Toxoplasma gondii. PloS Pathogens 2006, 2:e13.
• [16]Hu K, et al.: A novel polymer of tubulin forms the conoid of Toxoplasma gondii. Journal of Cell Biology 2002, 156:1039-1050.
• [17]Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, et al.: Relations in biomedical ontologies. Genome Biology 2005, 6(5):R46. BioMed Central Full Text
• [18]The Gene Ontology Consortium: The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Research 2010, (38 Database):D331-D335.