Design of a data model for developing laboratory information management and analysis systems for protein production
Identifieur interne : 002604 ( Istex/Curation ); précédent : 002603; suivant : 002605Design of a data model for developing laboratory information management and analysis systems for protein production
Auteurs : Anne Pajon [Royaume-Uni] ; John Ionides [Royaume-Uni] ; Jon Diprose [Royaume-Uni] ; Joël Fillon [Royaume-Uni] ; Rasmus Fogh [Royaume-Uni] ; Alun W. Ashton [Royaume-Uni] ; Helen Berman [États-Unis] ; Wayne Boucher [Royaume-Uni] ; Miroslaw Cygler [Canada] ; Emeline Deleury [France] ; Robert Esnouf [Royaume-Uni] ; Joël Janin [France] ; Rosalind Kim [États-Unis] ; Isabelle Krimm [France] ; Catherine L. Lawson [États-Unis] ; Eric Oeuillet [France] ; Anne Poupon [France] ; Stéphane Raymond [Canada] ; Tim Stevens [Royaume-Uni] ; Herman Van Tilbeurgh [France] ; John Westbrook [États-Unis] ; Peter Wood [Royaume-Uni] ; Eldon Ulrich [États-Unis] ; Wim Vranken [Royaume-Uni] ; Li Xueli [Canada] ; Ernest Laue [Royaume-Uni] ; David I. Stuart [Royaume-Uni] ; Kim Henrick [Royaume-Uni]Source :
- Proteins: Structure, Function, and Bioinformatics [ 0887-3585 ] ; 2005-02-01.
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Abstract
Data management has emerged as one of the central issues in the high‐throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects. Proteins 2005. © 2004 Wiley‐Liss, Inc.
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DOI: 10.1002/prot.20303
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Jersey</region></placeName><wicri:cityArea>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway</wicri:cityArea></affiliation></author><author><name sortKey="Wood, Peter" sort="Wood, Peter" uniqKey="Wood P" first="Peter" last="Wood">Peter Wood</name><affiliation wicri:level="1"><mods:affiliation>Daresbury Laboratory, Daresbury, Warrington, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Daresbury Laboratory, Daresbury, Warrington</wicri:regionArea></affiliation></author><author><name sortKey="Ulrich, Eldon" sort="Ulrich, Eldon" uniqKey="Ulrich E" first="Eldon" last="Ulrich">Eldon Ulrich</name><affiliation wicri:level="2"><mods:affiliation>Department of Biochemistry, University Wisconsin Madison, Madison, Wisconsin</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Wisconsin</region></placeName><wicri:cityArea>Department of Biochemistry, University Wisconsin Madison, Madison</wicri:cityArea></affiliation></author><author><name sortKey="Vranken, Wim" sort="Vranken, Wim" uniqKey="Vranken W" first="Wim" last="Vranken">Wim Vranken</name><affiliation wicri:level="1"><mods:affiliation>EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Xueli, Li" sort="Xueli, Li" uniqKey="Xueli L" first="Li" last="Xueli">Li Xueli</name><affiliation wicri:level="1"><mods:affiliation>Biotechnology Research Institute, NRC, Montréal, Québec, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biotechnology Research Institute, NRC, Montréal, Québec</wicri:regionArea></affiliation></author><author><name sortKey="Laue, Ernest" sort="Laue, Ernest" uniqKey="Laue E" first="Ernest" last="Laue">Ernest Laue</name><affiliation wicri:level="1"><mods:affiliation>Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biochemistry, University of Cambridge, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Stuart, David I" sort="Stuart, David I" uniqKey="Stuart D" first="David I." last="Stuart">David I. 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Ashton</name><affiliation wicri:level="1"><mods:affiliation>Daresbury Laboratory, Daresbury, Warrington, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Daresbury Laboratory, Daresbury, Warrington</wicri:regionArea></affiliation></author><author><name sortKey="Berman, Helen" sort="Berman, Helen" uniqKey="Berman H" first="Helen" last="Berman">Helen Berman</name><affiliation wicri:level="2"><mods:affiliation>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">New Jersey</region></placeName><wicri:cityArea>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway</wicri:cityArea></affiliation></author><author><name sortKey="Boucher, Wayne" sort="Boucher, Wayne" uniqKey="Boucher W" first="Wayne" last="Boucher">Wayne Boucher</name><affiliation wicri:level="1"><mods:affiliation>Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biochemistry, University of Cambridge, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Cygler, Miroslaw" sort="Cygler, Miroslaw" uniqKey="Cygler M" first="Miroslaw" last="Cygler">Miroslaw Cygler</name><affiliation wicri:level="1"><mods:affiliation>Biotechnology Research Institute, NRC, Montréal, Québec, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biotechnology Research Institute, NRC, Montréal, Québec</wicri:regionArea></affiliation></author><author><name sortKey="Deleury, Emeline" sort="Deleury, Emeline" uniqKey="Deleury E" first="Emeline" last="Deleury">Emeline Deleury</name><affiliation wicri:level="1"><mods:affiliation>Plateforme Transcriptome CNRS/INRA de Sophia Antipolis, Sophia Antipolis, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Plateforme Transcriptome CNRS/INRA de Sophia Antipolis, Sophia Antipolis</wicri:regionArea></affiliation></author><author><name sortKey="Esnouf, Robert" sort="Esnouf, Robert" uniqKey="Esnouf R" first="Robert" last="Esnouf">Robert Esnouf</name><affiliation wicri:level="1"><mods:affiliation>Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Headington, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Janin, Joel" sort="Janin, Joel" uniqKey="Janin J" first="Joël" last="Janin">Joël Janin</name><affiliation wicri:level="1"><mods:affiliation>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Rosalind" sort="Kim, Rosalind" uniqKey="Kim R" first="Rosalind" last="Kim">Rosalind Kim</name><affiliation wicri:level="2"><mods:affiliation>Lawrence Berkeley National Laboratory, Berkeley, California</mods:affiliation><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation></author><author><name sortKey="Krimm, Isabelle" sort="Krimm, Isabelle" uniqKey="Krimm I" first="Isabelle" last="Krimm">Isabelle Krimm</name><affiliation wicri:level="1"><mods:affiliation>Laboratoire de RMN Biomoléculaire, Université Claude Bernard, Lyon, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de RMN Biomoléculaire, Université Claude Bernard, Lyon</wicri:regionArea></affiliation></author><author><name sortKey="Lawson, Catherine L" sort="Lawson, Catherine L" uniqKey="Lawson C" first="Catherine L." last="Lawson">Catherine L. Lawson</name><affiliation wicri:level="2"><mods:affiliation>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">New Jersey</region></placeName><wicri:cityArea>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway</wicri:cityArea></affiliation></author><author><name sortKey="Oeuillet, Eric" sort="Oeuillet, Eric" uniqKey="Oeuillet E" first="Eric" last="Oeuillet">Eric Oeuillet</name><affiliation wicri:level="1"><mods:affiliation>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette</wicri:regionArea></affiliation></author><author><name sortKey="Poupon, Anne" sort="Poupon, Anne" uniqKey="Poupon A" first="Anne" last="Poupon">Anne Poupon</name><affiliation wicri:level="1"><mods:affiliation>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette</wicri:regionArea></affiliation></author><author><name sortKey="Raymond, Stephane" sort="Raymond, Stephane" uniqKey="Raymond S" first="Stéphane" last="Raymond">Stéphane Raymond</name><affiliation wicri:level="1"><mods:affiliation>Biotechnology Research Institute, NRC, Montréal, Québec, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biotechnology Research Institute, NRC, Montréal, Québec</wicri:regionArea></affiliation></author><author><name sortKey="Stevens, Tim" sort="Stevens, Tim" uniqKey="Stevens T" first="Tim" last="Stevens">Tim Stevens</name><affiliation wicri:level="1"><mods:affiliation>Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biochemistry, University of Cambridge, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Van Tilbeurgh, Herman" sort="Van Tilbeurgh, Herman" uniqKey="Van Tilbeurgh H" first="Herman" last="Van Tilbeurgh">Herman Van Tilbeurgh</name><affiliation wicri:level="1"><mods:affiliation>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LEBS, Equipe Génomique Structurale, Gif‐sur‐Yvette</wicri:regionArea></affiliation></author><author><name sortKey="Westbrook, John" sort="Westbrook, John" uniqKey="Westbrook J" first="John" last="Westbrook">John Westbrook</name><affiliation wicri:level="2"><mods:affiliation>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">New Jersey</region></placeName><wicri:cityArea>Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway</wicri:cityArea></affiliation></author><author><name sortKey="Wood, Peter" sort="Wood, Peter" uniqKey="Wood P" first="Peter" last="Wood">Peter Wood</name><affiliation wicri:level="1"><mods:affiliation>Daresbury Laboratory, Daresbury, Warrington, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Daresbury Laboratory, Daresbury, Warrington</wicri:regionArea></affiliation></author><author><name sortKey="Ulrich, Eldon" sort="Ulrich, Eldon" uniqKey="Ulrich E" first="Eldon" last="Ulrich">Eldon Ulrich</name><affiliation wicri:level="2"><mods:affiliation>Department of Biochemistry, University Wisconsin Madison, Madison, Wisconsin</mods:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Wisconsin</region></placeName><wicri:cityArea>Department of Biochemistry, University Wisconsin Madison, Madison</wicri:cityArea></affiliation></author><author><name sortKey="Vranken, Wim" sort="Vranken, Wim" uniqKey="Vranken W" first="Wim" last="Vranken">Wim Vranken</name><affiliation wicri:level="1"><mods:affiliation>EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Xueli, Li" sort="Xueli, Li" uniqKey="Xueli L" first="Li" last="Xueli">Li Xueli</name><affiliation wicri:level="1"><mods:affiliation>Biotechnology Research Institute, NRC, Montréal, Québec, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Biotechnology Research Institute, NRC, Montréal, Québec</wicri:regionArea></affiliation></author><author><name sortKey="Laue, Ernest" sort="Laue, Ernest" uniqKey="Laue E" first="Ernest" last="Laue">Ernest Laue</name><affiliation wicri:level="1"><mods:affiliation>Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biochemistry, University of Cambridge, Cambridge</wicri:regionArea></affiliation></author><author><name sortKey="Stuart, David I" sort="Stuart, David I" uniqKey="Stuart D" first="David I." last="Stuart">David I. Stuart</name><affiliation wicri:level="1"><mods:affiliation>Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Headington, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Henrick, Kim" sort="Henrick, Kim" uniqKey="Henrick K" first="Kim" last="Henrick">Kim Henrick</name><affiliation wicri:level="1"><mods:affiliation>EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</mods:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea></affiliation><affiliation wicri:level="1"><mods:affiliation>Macromolecular Structures Database, EMBL‐EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK===</mods:affiliation><country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country><wicri:regionArea>Macromolecular Structures Database, EMBL‐EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD</wicri:regionArea></affiliation></author></analytic><monogr></monogr><series><title level="j">Proteins: Structure, Function, and Bioinformatics</title><title level="j" type="abbrev">Proteins</title><idno type="ISSN">0887-3585</idno><idno type="eISSN">1097-0134</idno><imprint><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><pubPlace>Hoboken</pubPlace><date type="published" when="2005-02-01">2005-02-01</date><biblScope unit="volume">58</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="278">278</biblScope><biblScope unit="page" to="284">284</biblScope></imprint><idno type="ISSN">0887-3585</idno></series><idno type="istex">8D6E95898AA8051A750541550C87E2FC0D3E47E7</idno><idno type="DOI">10.1002/prot.20303</idno><idno type="ArticleID">PROT20303</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0887-3585</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>LIMS</term><term>UML data model</term><term>database schema</term><term>protein production</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Data management has emerged as one of the central issues in the high‐throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects. Proteins 2005. © 2004 Wiley‐Liss, Inc.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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