XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
Identifieur interne : 000125 ( Ncbi/Merge ); précédent : 000124; suivant : 000126XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
Auteurs : Morris A. Swertz [Pays-Bas, Royaume-Uni] ; K Joeri Van Der Velde [Pays-Bas] ; Bruno M. Tesson [Pays-Bas] ; Richard A. Scheltema [Pays-Bas] ; Danny Arends [Pays-Bas] ; Gonzalo Vera [Pays-Bas] ; Rudi Alberts [Allemagne] ; Martijn Dijkstra [Pays-Bas] ; Paul Schofield [Royaume-Uni] ; Klaus Schughart [Allemagne] ; John M. Hancock [Royaume-Uni] ; Damian Smedley [Royaume-Uni] ; Katy Wolstencroft [Royaume-Uni] ; Carole Goble [Royaume-Uni] ; Engbert O. De Brock [Pays-Bas] ; Andrew R. Jones [Royaume-Uni] ; Helen E. Parkinson [Royaume-Uni] ; Ritsert C. Jansen [Pays-Bas]Source :
- Genome Biology [ 1465-6906 ] ; 2010.
Abstract
XGAP, a software platform for the integration and analysis of genotype and phenotype data.
Url:
DOI: 10.1186/gb-2010-11-3-r27
PubMed: 20214801
PubMed Central: 2864567
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<series><title level="j">Genome Biology</title>
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<front><div type="abstract" xml:lang="en"><p>XGAP, a software platform for the integration and analysis of genotype and phenotype data.</p>
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<pmc article-type="product-review"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id>
<journal-title-group><journal-title>Genome Biology</journal-title>
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<issn pub-type="ppub">1465-6906</issn>
<issn pub-type="epub">1465-6914</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
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<article-meta><article-id pub-id-type="pmid">20214801</article-id>
<article-id pub-id-type="pmc">2864567</article-id>
<article-id pub-id-type="publisher-id">gb-2010-11-3-r27</article-id>
<article-id pub-id-type="doi">10.1186/gb-2010-11-3-r27</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Software</subject>
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<title-group><article-title>XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments</article-title>
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<given-names>Paul</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
<email>ps@mole.bio.cam.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A10"><name><surname>Schughart</surname>
<given-names>Klaus</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>klaus.schughart@helmholtz-hzi.de</email>
</contrib>
<contrib contrib-type="author" id="A11"><name><surname>Hancock</surname>
<given-names>John M</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>j.hancock@har.mrc.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A12"><name><surname>Smedley</surname>
<given-names>Damian</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>damian@ebi.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A13"><name><surname>Wolstencroft</surname>
<given-names>Katy</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>katherine.wolstencroft@manchester.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A14"><name><surname>Goble</surname>
<given-names>Carole</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>carole.goble@manchester.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A15"><name><surname>de Brock</surname>
<given-names>Engbert O</given-names>
</name>
<xref ref-type="aff" rid="I9">9</xref>
<email>e.o.de.brock@rug.nl</email>
</contrib>
<contrib contrib-type="author" id="A16"><name><surname>Jones</surname>
<given-names>Andrew R</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>andrew.jones@liverpool.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A17"><name><surname>Parkinson</surname>
<given-names>Helen E</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>parkinson@ebi.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A18"><collab>members of the Coordination of Mouse Informatics Resources (CASIMIR)</collab>
<xref ref-type="aff" rid="I6">6</xref>
<email>info@casimir.org.uk</email>
</contrib>
<contrib contrib-type="author" id="A19"><collab>Genotype-To-Phenotype (GEN2PHEN) Consortiums</collab>
<xref ref-type="aff" rid="I1">1</xref>
<email>info@gen2phen.org</email>
</contrib>
<contrib contrib-type="author" id="A20"><name><surname>Jansen</surname>
<given-names>Ritsert C</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>r.c.jansen@rug.nl</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, 9700 RB Groningen, The Netherlands</aff>
<aff id="I2"><label>2</label>
Groningen Bioinformatics Center, University of Groningen, 9750 AA Haren, The Netherlands</aff>
<aff id="I3"><label>3</label>
EMBL - European Bioinformatics Institute, Hinxton, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK</aff>
<aff id="I4"><label>4</label>
Experimental Mouse Genetics, Helmholtz Center for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany</aff>
<aff id="I5"><label>5</label>
Center for Medical Biomics, University of Groningen, Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands</aff>
<aff id="I6"><label>6</label>
Physiological Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK</aff>
<aff id="I7"><label>7</label>
Bioinformatics Group, MRC Harwell, Harwell, Oxfordshire OX11 0RD, UK</aff>
<aff id="I8"><label>8</label>
Information Management Group, School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester M13 9PL, UK</aff>
<aff id="I9"><label>9</label>
Department of Business and ICT, Faculty of Economics and Business, University of Groningen, 9700 AV Groningen, The Netherlands</aff>
<aff id="I10"><label>10</label>
Department of Pre-Clinical Veterinary Science and Veterinary Pathology, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK</aff>
<pub-date pub-type="ppub"><year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>9</day>
<month>3</month>
<year>2010</year>
</pub-date>
<volume>11</volume>
<issue>3</issue>
<fpage>R27</fpage>
<lpage>R27</lpage>
<history><date date-type="received"><day>14</day>
<month>7</month>
<year>2009</year>
</date>
<date date-type="rev-recd"><day>17</day>
<month>12</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>9</day>
<month>3</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2010 Swertz et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2010</copyright-year>
<copyright-holder>Swertz et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://genomebiology.com/2010/11/3/R27"></self-uri>
<abstract abstract-type="short"><p>XGAP, a software platform for the integration and analysis of genotype and phenotype data.</p>
</abstract>
<abstract><p>We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (<ext-link ext-link-type="uri" xlink:href="http://www.xgap.org">http://www.xgap.org</ext-link>
) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.</p>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Allemagne</li>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
</country>
<region><li>Angleterre</li>
<li>Angleterre de l'Est</li>
<li>Grand Manchester</li>
<li>Groningue (province)</li>
</region>
<settlement><li>Cambridge</li>
<li>Groningue (ville)</li>
<li>Manchester</li>
</settlement>
<orgName><li>Université de Cambridge</li>
<li>Université de Groningue</li>
<li>Université de Manchester</li>
</orgName>
</list>
<tree><country name="Pays-Bas"><noRegion><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A" last="Swertz">Morris A. Swertz</name>
</noRegion>
<name sortKey="Arends, Danny" sort="Arends, Danny" uniqKey="Arends D" first="Danny" last="Arends">Danny Arends</name>
<name sortKey="Arends, Danny" sort="Arends, Danny" uniqKey="Arends D" first="Danny" last="Arends">Danny Arends</name>
<name sortKey="De Brock, Engbert O" sort="De Brock, Engbert O" uniqKey="De Brock E" first="Engbert O" last="De Brock">Engbert O. De Brock</name>
<name sortKey="Dijkstra, Martijn" sort="Dijkstra, Martijn" uniqKey="Dijkstra M" first="Martijn" last="Dijkstra">Martijn Dijkstra</name>
<name sortKey="Jansen, Ritsert C" sort="Jansen, Ritsert C" uniqKey="Jansen R" first="Ritsert C" last="Jansen">Ritsert C. Jansen</name>
<name sortKey="Jansen, Ritsert C" sort="Jansen, Ritsert C" uniqKey="Jansen R" first="Ritsert C" last="Jansen">Ritsert C. Jansen</name>
<name sortKey="Scheltema, Richard A" sort="Scheltema, Richard A" uniqKey="Scheltema R" first="Richard A" last="Scheltema">Richard A. Scheltema</name>
<name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A" last="Swertz">Morris A. Swertz</name>
<name sortKey="Tesson, Bruno M" sort="Tesson, Bruno M" uniqKey="Tesson B" first="Bruno M" last="Tesson">Bruno M. Tesson</name>
<name sortKey="Velde, K Joeri Van Der" sort="Velde, K Joeri Van Der" uniqKey="Velde K" first="K Joeri Van Der" last="Velde">K Joeri Van Der Velde</name>
<name sortKey="Velde, K Joeri Van Der" sort="Velde, K Joeri Van Der" uniqKey="Velde K" first="K Joeri Van Der" last="Velde">K Joeri Van Der Velde</name>
<name sortKey="Vera, Gonzalo" sort="Vera, Gonzalo" uniqKey="Vera G" first="Gonzalo" last="Vera">Gonzalo Vera</name>
</country>
<country name="Royaume-Uni"><noRegion><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A" last="Swertz">Morris A. Swertz</name>
</noRegion>
<name sortKey="Goble, Carole" sort="Goble, Carole" uniqKey="Goble C" first="Carole" last="Goble">Carole Goble</name>
<name sortKey="Hancock, John M" sort="Hancock, John M" uniqKey="Hancock J" first="John M" last="Hancock">John M. Hancock</name>
<name sortKey="Jones, Andrew R" sort="Jones, Andrew R" uniqKey="Jones A" first="Andrew R" last="Jones">Andrew R. Jones</name>
<name sortKey="Parkinson, Helen E" sort="Parkinson, Helen E" uniqKey="Parkinson H" first="Helen E" last="Parkinson">Helen E. Parkinson</name>
<name sortKey="Schofield, Paul" sort="Schofield, Paul" uniqKey="Schofield P" first="Paul" last="Schofield">Paul Schofield</name>
<name sortKey="Smedley, Damian" sort="Smedley, Damian" uniqKey="Smedley D" first="Damian" last="Smedley">Damian Smedley</name>
<name sortKey="Wolstencroft, Katy" sort="Wolstencroft, Katy" uniqKey="Wolstencroft K" first="Katy" last="Wolstencroft">Katy Wolstencroft</name>
</country>
<country name="Allemagne"><noRegion><name sortKey="Alberts, Rudi" sort="Alberts, Rudi" uniqKey="Alberts R" first="Rudi" last="Alberts">Rudi Alberts</name>
</noRegion>
<name sortKey="Schughart, Klaus" sort="Schughart, Klaus" uniqKey="Schughart K" first="Klaus" last="Schughart">Klaus Schughart</name>
</country>
</tree>
</affiliations>
</record>
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