Development of FuGO: An Ontology for Functional Genomics Investigations
Identifieur interne : 000098 ( Pmc/Curation ); précédent : 000097; suivant : 000099Development 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><wicri:noCountry code="subfield">Pennsylvania.</wicri:noCountry></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><wicri:noCountry code="subfield">Pennsylvania.</wicri:noCountry></affiliation><affiliation><nlm:aff id="A13">Dana-Farber Cancer Institute, Boston, Massachusetts.</nlm:aff><wicri:noCountry code="subfield">Massachusetts.</wicri:noCountry></affiliation>Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Development of FuGO: An Ontology for Functional Genomics Investigations</title><author><name sortKey="Whetzel, Patricia L" sort="Whetzel, Patricia L" uniqKey="Whetzel P" first="Patricia L." last="Whetzel">Patricia L. Whetzel</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="Brinkman, Ryan R" sort="Brinkman, Ryan R" uniqKey="Brinkman R" first="Ryan R." last="Brinkman">Ryan R. Brinkman</name><affiliation wicri:level="1"><nlm:aff id="A2">Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC</wicri:regionArea></affiliation></author><author><name sortKey="Causton, Helen C" sort="Causton, Helen C" uniqKey="Causton H" first="Helen C." last="Causton">Helen C. Causton</name><affiliation wicri:level="1"><nlm:aff id="A3">MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London, United Kingdom.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country><wicri:regionArea>MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Liju" sort="Fan, Liju" uniqKey="Fan L" first="Liju" last="Fan">Liju Fan</name><affiliation><nlm:aff id="A4">Ontology Workshop LLC, Columbia, Maryland.</nlm:aff><wicri:noCountry code="subfield">Maryland.</wicri:noCountry></affiliation></author><author><name sortKey="Field, Dawn" sort="Field, Dawn" uniqKey="Field D" first="Dawn" last="Field">Dawn Field</name><affiliation wicri:level="1"><nlm:aff id="A5">Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom.</nlm:aff><country xml:lang="fr" 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code="subfield">California.</wicri:noCountry></affiliation></author><author><name sortKey="Morrison, Norman" sort="Morrison, Norman" uniqKey="Morrison N" first="Norman" last="Morrison">Norman Morrison</name><affiliation wicri:level="1"><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></affiliation><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Parkinson, Helen" sort="Parkinson, Helen" uniqKey="Parkinson H" 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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></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></affiliation></author><author><name sortKey="Smith, Barry" sort="Smith, Barry" uniqKey="Smith B" first="Barry" last="Smith">Barry Smith</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Stevens, Robert" sort="Stevens, Robert" uniqKey="Stevens R" first="Robert" last="Stevens">Robert Stevens</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Stoeckert, Christian J" sort="Stoeckert, Christian J" uniqKey="Stoeckert C" first="Christian J." last="Stoeckert">Christian J. 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Whetzel</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="Brinkman, Ryan R" sort="Brinkman, Ryan R" uniqKey="Brinkman R" first="Ryan R." last="Brinkman">Ryan R. Brinkman</name><affiliation wicri:level="1"><nlm:aff id="A2">Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Canada</country><wicri:regionArea>Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC</wicri:regionArea></affiliation></author><author><name sortKey="Causton, Helen C" sort="Causton, Helen C" uniqKey="Causton H" first="Helen C." last="Causton">Helen C. Causton</name><affiliation wicri:level="1"><nlm:aff id="A3">MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London, United Kingdom.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country><wicri:regionArea>MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Liju" sort="Fan, Liju" uniqKey="Fan L" first="Liju" last="Fan">Liju Fan</name><affiliation><nlm:aff id="A4">Ontology Workshop LLC, Columbia, Maryland.</nlm:aff><wicri:noCountry code="subfield">Maryland.</wicri:noCountry></affiliation></author><author><name sortKey="Field, Dawn" sort="Field, Dawn" uniqKey="Field D" first="Dawn" last="Field">Dawn Field</name><affiliation wicri:level="1"><nlm:aff id="A5">Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country><wicri:regionArea>Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Fostel, Jennifer" sort="Fostel, Jennifer" uniqKey="Fostel J" first="Jennifer" last="Fostel">Jennifer Fostel</name><affiliation><nlm:aff id="A6">NIEHS, Research Triangle Park, North Carolina.</nlm:aff><wicri:noCountry code="subfield">North Carolina.</wicri:noCountry></affiliation></author><author><name sortKey="Fragoso, Gilberto" sort="Fragoso, Gilberto" uniqKey="Fragoso G" first="Gilberto" last="Fragoso">Gilberto Fragoso</name><affiliation><nlm:aff id="A7">NCICB, NCI Center for Bioinformatics, Rockville, Maryland.</nlm:aff><wicri:noCountry code="subfield">Maryland.</wicri:noCountry></affiliation></author><author><name sortKey="Gray, Tanya" sort="Gray, Tanya" uniqKey="Gray T" first="Tanya" last="Gray">Tanya Gray</name><affiliation wicri:level="1"><nlm:aff id="A5">Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom.</nlm:aff><country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country><wicri:regionArea>Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford</wicri:regionArea></affiliation></author><author><name sortKey="Heiskanen, Mervi" sort="Heiskanen, Mervi" uniqKey="Heiskanen M" first="Mervi" last="Heiskanen">Mervi Heiskanen</name><affiliation><nlm:aff id="A7">NCICB, NCI Center for Bioinformatics, Rockville, Maryland.</nlm:aff><wicri:noCountry code="subfield">Maryland.</wicri:noCountry></affiliation></author><author><name sortKey="Hernandez Boussard, Tina" sort="Hernandez Boussard, Tina" uniqKey="Hernandez Boussard T" first="Tina" last="Hernandez-Boussard">Tina Hernandez-Boussard</name><affiliation><nlm:aff id="A8">Department of Genetics, Stanford University Medical Center, Stanford, California.</nlm:aff><wicri:noCountry code="subfield">California.</wicri:noCountry></affiliation></author><author><name sortKey="Morrison, Norman" sort="Morrison, Norman" uniqKey="Morrison N" first="Norman" last="Morrison">Norman Morrison</name><affiliation wicri:level="1"><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></affiliation><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Parkinson, Helen" sort="Parkinson, Helen" uniqKey="Parkinson H" first="Helen" last="Parkinson">Helen Parkinson</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></affiliation></author><author><name sortKey="Rocca Serra, Philippe" sort="Rocca Serra, Philippe" uniqKey="Rocca Serra P" first="Philippe" last="Rocca-Serra">Philippe Rocca-Serra</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></affiliation></author><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></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></affiliation></author><author><name sortKey="Smith, Barry" sort="Smith, Barry" uniqKey="Smith B" first="Barry" last="Smith">Barry Smith</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Stevens, Robert" sort="Stevens, Robert" uniqKey="Stevens R" first="Robert" last="Stevens">Robert Stevens</name><affiliation wicri:level="1"><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></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></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="1"><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></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></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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><pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101131135</journal-id><journal-id journal-id-type="pubmed-jr-id">27023</journal-id><journal-id journal-id-type="nlm-ta">OMICS</journal-id><journal-title>Omics : a journal of integrative biology</journal-title><issn pub-type="ppub">1536-2310</issn><issn pub-type="epub">1557-8100</issn></journal-meta><article-meta><article-id pub-id-type="pmid">16901226</article-id><article-id pub-id-type="pmc">2783628</article-id><article-id pub-id-type="doi">10.1089/omi.2006.10.199</article-id><article-id pub-id-type="manuscript">NIHMS154515</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Development of FuGO: An Ontology for Functional Genomics Investigations</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Whetzel</surname><given-names>Patricia L.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Brinkman</surname><given-names>Ryan R.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Causton</surname><given-names>Helen C.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Fan</surname><given-names>Liju</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Field</surname><given-names>Dawn</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Fostel</surname><given-names>Jennifer</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Fragoso</surname><given-names>Gilberto</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Gray</surname><given-names>Tanya</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Heiskanen</surname><given-names>Mervi</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Hernandez-Boussard</surname><given-names>Tina</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Morrison</surname><given-names>Norman</given-names></name><xref ref-type="aff" rid="A9">9</xref><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Parkinson</surname><given-names>Helen</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Rocca-Serra</surname><given-names>Philippe</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Sansone</surname><given-names>Susanna-Assunta</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Schober</surname><given-names>Daniel</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Barry</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Stevens</surname><given-names>Robert</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Stoeckert</surname><given-names>Christian J.</given-names><suffix>Jr.</suffix></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Taylor</surname><given-names>Chris</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>White</surname><given-names>Joe</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Wood</surname><given-names>Andrew</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><collab>FuGO Working Group</collab><xref ref-type="author-notes" rid="FN1">14</xref></contrib></contrib-group><aff id="A1"><label>1</label>Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania.</aff><aff id="A2"><label>2</label>Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada.</aff><aff id="A3"><label>3</label>MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London, United Kingdom.</aff><aff id="A4"><label>4</label>Ontology Workshop LLC, Columbia, Maryland.</aff><aff id="A5"><label>5</label>Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom.</aff><aff id="A6"><label>6</label>NIEHS, Research Triangle Park, North Carolina.</aff><aff id="A7"><label>7</label>NCICB, NCI Center for Bioinformatics, Rockville, Maryland.</aff><aff id="A8"><label>8</label>Department of Genetics, Stanford University Medical Center, Stanford, California.</aff><aff id="A9"><label>9</label>Department of Computer Science, University of Manchester, Manchester, United Kingdom.</aff><aff id="A10"><label>10</label>NERC Environmental Bioinformatics Centre, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom.</aff><aff id="A11"><label>11</label>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.</aff><aff id="A12"><label>12</label>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.</aff><aff id="A13"><label>13</label>Dana-Farber Cancer Institute, Boston, Massachusetts.</aff><author-notes><corresp id="cor1">Address reprint requests to: Dr. Patricia L. Whetzel, Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, <email>whetzel@pcbi.upenn.edu</email></corresp><fn id="FN1"><label>14</label><p id="P1">See FuGO webpage for a complete list of contributing groups and their members: 〈<ext-link ext-link-type="uri" xlink:href="http://fugo.sf.net">http://fugo.sf.net</ext-link>〉.</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>27</day><month>10</month><year>2009</year></pub-date><pub-date pub-type="ppub"><season>Summer</season><year>2006</year></pub-date><pub-date pub-type="pmc-release"><day>26</day><month>11</month><year>2009</year></pub-date><volume>10</volume><issue>2</issue><fpage>199</fpage><lpage>204</lpage><permissions><copyright-statement>© Mary Ann Liebert, Inc.</copyright-statement></permissions><abstract><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></abstract><contract-num rid="EB1">R01 EB005034-02
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