Development of FuGO: An Ontology for Functional Genomics Investigations
Identifieur interne : 000886 ( Main/Curation ); précédent : 000885; suivant : 000887Development of FuGO: An Ontology for Functional Genomics Investigations
Auteurs : Patricia L. Whetzel ; Ryan R. Brinkman [Canada] ; Helen C. Causton [Royaume-Uni] ; Liju Fan ; Dawn Field [Royaume-Uni] ; Jennifer Fostel ; Gilberto Fragoso ; Tanya Gray [Royaume-Uni] ; Mervi Heiskanen ; Tina Hernandez-Boussard ; Norman Morrison [Royaume-Uni] ; Helen Parkinson [Royaume-Uni] ; Philippe Rocca-Serra [Royaume-Uni] ; Susanna-Assunta Sansone [Royaume-Uni] ; Daniel Schober [Royaume-Uni] ; Barry Smith [Allemagne] ; Robert Stevens [Royaume-Uni] ; Christian J. Stoeckert ; Chris Taylor [Royaume-Uni] ; Joe White ; Andrew Wood [Royaume-Uni]Source :
- Omics : a journal of integrative biology [ 1536-2310 ] ; 2006.
Abstract
The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans.
Url:
DOI: 10.1089/omi.2006.10.199
PubMed: 16901226
PubMed Central: 2783628
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Patricia L. Whetzel<affiliation><nlm:aff id="A1">Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania.</nlm:aff>
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</affiliation>
<affiliation><nlm:aff id="A4">Ontology Workshop LLC, Columbia, Maryland.</nlm:aff>
<wicri:noCountry code="subfield">Maryland.</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A6">NIEHS, Research Triangle Park, North Carolina.</nlm:aff>
<wicri:noCountry code="subfield">North Carolina.</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A7">NCICB, NCI Center for Bioinformatics, Rockville, Maryland.</nlm:aff>
<wicri:noCountry code="subfield">Maryland.</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A7">NCICB, NCI Center for Bioinformatics, Rockville, Maryland.</nlm:aff>
<wicri:noCountry code="subfield">Maryland.</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A8">Department of Genetics, Stanford University Medical Center, Stanford, California.</nlm:aff>
<wicri:noCountry code="subfield">California.</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="A1">Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania.</nlm:aff>
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</affiliation>
<affiliation><nlm:aff id="A13">Dana-Farber Cancer Institute, Boston, Massachusetts.</nlm:aff>
<wicri:noCountry code="subfield">Massachusetts.</wicri:noCountry>
</affiliation>
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<author><name sortKey="Sansone, Susanna Assunta" sort="Sansone, Susanna Assunta" uniqKey="Sansone S" first="Susanna-Assunta" last="Sansone">Susanna-Assunta Sansone</name>
<affiliation wicri:level="1"><nlm:aff id="A11">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Schober, Daniel" sort="Schober, Daniel" uniqKey="Schober D" first="Daniel" last="Schober">Daniel Schober</name>
<affiliation wicri:level="1"><nlm:aff id="A11">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Smith, Barry" sort="Smith, Barry" uniqKey="Smith B" first="Barry" last="Smith">Barry Smith</name>
<affiliation wicri:level="4"><nlm:aff id="A12">Department of Philosophy, Center of Excellence in Bioinformatics and Life Sciences, and National Center for Biomedical Ontology, University at Buffalo, Buffalo, New York, and Institute for Formal Ontology and Medical Information Science, Saarbrücken, Germany.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Allemagne</country>
<wicri:regionArea>Department of Philosophy, Center of Excellence in Bioinformatics and Life Sciences, and National Center for Biomedical Ontology, University at Buffalo, Buffalo, New York, and Institute for Formal Ontology and Medical Information Science, Saarbrücken</wicri:regionArea>
<placeName><region type="land" nuts="2">Sarre (Land)</region>
<settlement type="city">Sarrebruck</settlement>
</placeName>
<orgName type="university">Université d'État de New York à Buffalo</orgName>
</affiliation>
</author>
<author><name sortKey="Stevens, Robert" sort="Stevens, Robert" uniqKey="Stevens R" first="Robert" last="Stevens">Robert Stevens</name>
<affiliation wicri:level="4"><nlm:aff id="A9">Department of Computer Science, University of Manchester, Manchester, United Kingdom.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>Department of Computer Science, University of Manchester, Manchester</wicri:regionArea>
<placeName><settlement type="city">Manchester</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Grand Manchester</region>
</placeName>
<orgName type="university">Université de Manchester</orgName>
</affiliation>
</author>
<author><name sortKey="Stoeckert, Christian J" sort="Stoeckert, Christian J" uniqKey="Stoeckert C" first="Christian J." last="Stoeckert">Christian J. Stoeckert</name>
<affiliation><nlm:aff id="A1">Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania.</nlm:aff>
<wicri:noCountry code="subfield">Pennsylvania.</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Taylor, Chris" sort="Taylor, Chris" uniqKey="Taylor C" first="Chris" last="Taylor">Chris Taylor</name>
<affiliation wicri:level="1"><nlm:aff id="A11">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge</wicri:regionArea>
<wicri:noRegion>Cambridge</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="White, Joe" sort="White, Joe" uniqKey="White J" first="Joe" last="White">Joe White</name>
<affiliation><nlm:aff id="A13">Dana-Farber Cancer Institute, Boston, Massachusetts.</nlm:aff>
<wicri:noCountry code="subfield">Massachusetts.</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Wood, Andrew" sort="Wood, Andrew" uniqKey="Wood A" first="Andrew" last="Wood">Andrew Wood</name>
<affiliation wicri:level="3"><nlm:aff id="A10">NERC Environmental Bioinformatics Centre, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom.</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>NERC Environmental Bioinformatics Centre, Oxford Centre for Ecology and Hydrology, Oxford</wicri:regionArea>
<placeName><settlement type="city">Oxford</settlement>
<region type="country">Angleterre</region>
<region type="comté" nuts="2">Oxfordshire</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Omics : a journal of integrative biology</title>
<idno type="ISSN">1536-2310</idno>
<idno type="eISSN">1557-8100</idno>
<imprint><date when="2006">2006</date>
</imprint>
</series>
</biblStruct>
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<profileDesc><textClass></textClass>
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<front><div type="abstract" xml:lang="en"><p id="P2">The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans.</p>
</div>
</front>
</TEI>
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