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      The EMBRACE web service collection

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          Abstract

          The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry ( http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

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          Most cited references23

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          Gene Ontology: tool for the unification of biology

          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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            The Universal Protein Resource (UniProt) in 2010

            The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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              Taverna: a tool for building and running workflows of services

              Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from .
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                1 July 2010
                12 May 2010
                12 May 2010
                : 38
                : Web Server issue
                : W683-W688
                Affiliations
                1School of Computer Science, The University of Manchester, Manchester, M13 9PL, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK, 3Computational Biology Unit, Bergen Center for Computational Science, 5008 Bergen, Norway, 4Department of Informatics, University of Bergen, 5008 Bergen, Norway, 5Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK, 6Spanish National Cancer Research Centre (CNIO), Structural Biology and Biocomputing Programme, 28029 Madrid, Spain, 7Spanish National Bioinformatics Institute (INB), INB Central Node, 28029 Madrid, Spain, 8Université Lyon 1; CNRS, UMR 5086; IBCP, Institut de Biologie et Chimie des Protéines, Lyon, France, 9Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark, 10CMBI, Radboud University Medical Centre, 26-28 6525 GA, Nijmegen, The Netherlands, 11Service de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, B-1050, Belgium, 12Swiss Institute of Bioinformatics, Vital-IT group, CH-1015 Lausanne, Switzerland, 13Research Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK, 14The Linnaeus Centre for Bioinformatics Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden and 15Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP10448, F-63000 Clermont-Ferrand, France
                Author notes
                *To whom correspondence should be addressed. Tel: +44 161 275 6259; Fax: +44 161 275 6204; Email: steve.pettifer@ 123456manchester.ac.uk
                Article
                gkq297
                10.1093/nar/gkq297
                2896104
                20462862
                873c9b70-5aa8-4f0d-91ba-da3ee414a337
                © The Author(s) 2010. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 2 February 2010
                : 29 March 2010
                : 7 April 2010
                Categories
                Web Services

                Genetics
                Genetics

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