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Gaudet P, Lane L, Fey P, Bridge A, Poux S, Auchincloss A, Axelsen K, Braconi Quintaje S, Boutet E, Brown P, Coudert E, Datta RS, de Lima WC, de Oliveira Lima T, Duvaud S, Farriol-Mathis N, Ferro Rojas S, Feuermann M, Gateau A, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Moinat M, Nikolskaya A, Pedruzzi I, Rivoire C, Roechert B, Schneider M, Stanley E, Tognolli M, Sjölander K, Bougueleret L, Chisholm RL, Bairoch A. Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. Database (Oxford) 2009; 2009:bap016. [PMID: 20157489 PMCID: PMC2790310 DOI: 10.1093/database/bap016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/23/2009] [Accepted: 09/07/2009] [Indexed: 11/14/2022]
Abstract
UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the ‘Dicty annotation marathon’, a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations.
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Affiliation(s)
- P Gaudet
- dictyBase, Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, IL 60611, USA, Swiss-Prot group, Swiss Institute of Bioinformatics, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, The EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, QB3 Institute and Department of Bioengineering, University of California, Berkeley, CA, USA, Department of Cellular Physiology and Metabolism, University of Geneva, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland, Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven St NW, Suite 1200, Washington DC 20007, USA and Department of Structural Biology and Bioinformatics, University of Geneva, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
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