The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Identifieur interne : 000038 ( Ncbi/Curation ); précédent : 000037; suivant : 000039The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Auteurs : Barry Smith [États-Unis] ; Michael Ashburner [Royaume-Uni] ; Cornelius Rosse [États-Unis] ; Jonathan Bard [Royaume-Uni] ; William Bug [États-Unis] ; Werner Ceusters [États-Unis] ; Louis J. Goldberg [États-Unis] ; Karen Eilbeck [États-Unis] ; Amelia Ireland [Royaume-Uni] ; Christopher J. Mungall [États-Unis] ; Neocles Leontis [États-Unis] ; Philippe Rocca-Serra [Royaume-Uni] ; Alan Ruttenberg [États-Unis] ; Susanna-Assunta Sansone [Royaume-Uni] ; Richard H. Scheuermann [États-Unis] ; Nigam Shah [États-Unis] ; Patricia L. Whetzel [États-Unis] ; Suzanna Lewis [États-Unis]Source :
- Nature biotechnology [ 1087-0156 ] ; 2007.
Abstract
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.
Url:
DOI: 10.1038/nbt1346
PubMed: 17989687
PubMed Central: 2814061
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<author><name sortKey="Mungall, Christopher J" sort="Mungall, Christopher J" uniqKey="Mungall C" first="Christopher J" last="Mungall">Christopher J. Mungall</name>
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<author><name sortKey="Leontis, Neocles" sort="Leontis, Neocles" uniqKey="Leontis N" first="Neocles" last="Leontis">Neocles Leontis</name>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Bowling Green State University, 212 Physical Sciences Laboratory Building, 1001 East Wooster Street, Bowling Green, Ohio 43403</wicri:regionArea>
<wicri:noRegion>Ohio 43403</wicri:noRegion>
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<author><name sortKey="Rocca Serra, Philippe" sort="Rocca Serra, Philippe" uniqKey="Rocca Serra P" first="Philippe" last="Rocca-Serra">Philippe Rocca-Serra</name>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD</wicri:regionArea>
<wicri:noRegion>CB10 1SD</wicri:noRegion>
</affiliation>
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<author><name sortKey="Ruttenberg, Alan" sort="Ruttenberg, Alan" uniqKey="Ruttenberg A" first="Alan" last="Ruttenberg">Alan Ruttenberg</name>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, Massachusetts 02139</wicri:regionArea>
<wicri:noRegion>Massachusetts 02139</wicri:noRegion>
</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="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD</wicri:regionArea>
<wicri:noRegion>CB10 1SD</wicri:noRegion>
</affiliation>
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<author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H" last="Scheuermann">Richard H. Scheuermann</name>
<affiliation wicri:level="2"><nlm:aff id="A14">Department of Pathology, University of Texas Southwestern Medical Center, Harry Hines Blvd., Dallas, Texas 75390 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Texas</region>
</placeName>
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</affiliation>
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<author><name sortKey="Shah, Nigam" sort="Shah, Nigam" uniqKey="Shah N" first="Nigam" last="Shah">Nigam Shah</name>
<affiliation wicri:level="1"><nlm:aff id="A15">Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, California 94305, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, California 94305</wicri:regionArea>
<wicri:noRegion>California 94305</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Whetzel, Patricia L" sort="Whetzel, Patricia L" uniqKey="Whetzel P" first="Patricia L" last="Whetzel">Patricia L. Whetzel</name>
<affiliation wicri:level="1"><nlm:aff id="A16">Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, 423 Guardian Drive, Philadelphia, Pennsylvania 19104, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, 423 Guardian Drive, Philadelphia, Pennsylvania 19104</wicri:regionArea>
<wicri:noRegion>Pennsylvania 19104</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lewis, Suzanna" sort="Lewis, Suzanna" uniqKey="Lewis S" first="Suzanna" last="Lewis">Suzanna Lewis</name>
<affiliation wicri:level="1"><nlm:aff id="A10">Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720</wicri:regionArea>
<wicri:noRegion>California 94720</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Nature biotechnology</title>
<idno type="ISSN">1087-0156</idno>
<idno type="eISSN">1546-1696</idno>
<imprint><date when="2007">2007</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P1">The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.</p>
</div>
</front>
</TEI>
</record>
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