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      FlyBase: enhancing Drosophila Gene Ontology annotations

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          Abstract

          FlyBase ( http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project—a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Evolution of genes and genomes on the Drosophila phylogeny.

            Andrew G Clark, Michael B Eisen, Douglas R Smith … (2007)
            Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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              The Gene Ontology project in 2008

              (2008)
              The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of ‘reference’ genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2009
                Publication date (Print): January 2009
                Publication date (Electronic): 23 October 2008
                Publication date PMC-release: 23 October 2008
                Volume: 37
                Issue: Database issue , Database issue
                Pages: D555-D559
                Affiliations
                1Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK and 2The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 333 963; Fax: +44 1223 333 992; Email: s.tweedie@ 123456gen.cam.ac.uk

                Present address: Ruth Seal, EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK

                †The FlyBase Consortium comprises: FlyBase-Harvard: W. Gelbart, L. Bitsoi, M. Crosby, A. Dirkmaat, D. Emmert, L. S. Gramates, K. Falls, R. Kulathinal, B. Matthews, M. Roark, S. Russo, A. Schroeder, S. St Pierre, H. Zhang, P. Zhou and M. Zytkovicz; FlyBase-Cambridge: M. Ashburner, N. Brown, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland, R. Stefancsik, S. Tweedie and M. Williams; and FlyBase-Indiana: T. Kaufman, K. Matthews, J. Goodman, G. Grumbling, V. Strelets and R. Wilson.

                Article
                Publisher ID: gkn788
                DOI: 10.1093/nar/gkn788
                PMC ID: 2686450
                PubMed ID: 18948289
                SO-VID: ad47e4d1-0764-40c7-b334-dd26f15d7743
                Copyright © © 2008 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 19 September 2008
                Date revision received : 8 October 2008
                Date accepted : 9 October 2008
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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