A guide to best practices for Gene Ontology (GO) manual annotation

Creators: Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael; Van Auken, Kimberly; Cherry, J. Michael

Abstract

The Gene Ontology Consortium (GOC) is a community-based bioinformatics project that classifies gene product function through the use of structured controlled vocabularies. A fundamental application of the Gene Ontology (GO) is in the creation of gene product annotations, evidence-based associations between GO definitions and experimental or sequence-based analysis. Currently, the GOC disseminates 126 million annotations covering >374 000 species including all the kingdoms of life. This number includes two classes of GO annotations: those created manually by experienced biocurators reviewing the literature or by examination of biological data (1.1 million annotations covering 2226 species) and those generated computationally via automated methods. As manual annotations are often used to propagate functional predictions between related proteins within and between genomes, it is critical to provide accurate consistent manual annotations. Toward this goal, we present here the conventions defined by the GOC for the creation of manual annotation. This guide represents the best practices for manual annotation as established by the GOC project over the past 12 years. We hope this guide will encourage research communities to annotate gene products of their interest to enhance the corpus of GO annotations available to all.

Additional Information

© 2013 The Author(s). Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Submitted 15 February 2013; Revised 11 June 2013; Accepted 17 June 2013. We thank D.P. Hill and D.G. Howe for assistance in preparing this article and The GOC Annotation Working Group and members from many projects, including UniProt and Swiss Institute of Bioinformatics, which assist in the maintenance of these annotation policies. In addition to the authors, the members of the Annotation Working Group include P. Fey, P. Gaudet (dictyBase, Northwestern University, Chicago, IL, USA); V.K. Khodiyar, R.C. Lovering (Institute of Cardiovascular Science, University College London, London, UK); J.C. Hu (EcoliWiki, Departments of Biology, and Biochemistry and Biophysics, Texas A&M Univ., College Station, TX, USA); D.G. Fisk, M. Costanzo, R. Nash, S. Engel (Saccharomyces Genome Database, Department of Genetics, Stanford University, CA, USA), S. Tweedie (FlyBase, Gurdon Institute, Department of Genetics, University of Cambridge, Cambridge, UK); R.R. Kishore (WormBase, California Institute of Technology, Pasadena, CA, USA); T.Z. Berardini, D. Li (The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA); V. Wood (PomBase, University of Cambridge, Cambridge, UK); A. Lock (PomBase, University College London, London, UK); R.E. Foulger, J. Lomax, P. Roncaglia (Gene Ontology, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK); Y. Alam-Faruque, P. Mutowo- Muellenet (UniProt: European Bioinformatics Institute, Hinxton, Cambridgeshire, UK); J. A. Blake, M. Dolan, H. Drabkin, D.P. Hill, L. Ni, K.R. Christie (Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA); P. D'Eustachio (Reactome, Department of Biochemistry, NYU School of Medicine, New York, NY, USA); S.J. Laulederkind (Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA); and D.G. Howe (Zebrafish Model Organism Database, University of Oregon, Eugene, OR, USA). Funding: National Human Genome Research Institute, National Institutes of Health, USA, for the Gene Ontology Consortium (U41HG002273) and to the European Bioinformatics Institute (U41HG006104); The British Heart Foundation to the University College of London, UK (SP/07/007/23671); Wellcome Trust to University of Cambridge, UK, for Pombase (WT090548MA). Conflict of interest. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health.

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