The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Identifieur interne : 000304 ( Pmc/Corpus ); précédent : 000303; suivant : 000305The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Auteurs : Barry Smith ; Michael Ashburner ; Cornelius Rosse ; Jonathan Bard ; William Bug ; Werner Ceusters ; Louis J. Goldberg ; Karen Eilbeck ; Amelia Ireland ; Christopher J. Mungall ; Neocles Leontis ; Philippe Rocca-Serra ; Alan Ruttenberg ; Susanna-Assunta Sansone ; Richard H. Scheuermann ; Nigam Shah ; Patricia L. Whetzel ; Suzanna LewisSource :
- 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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Goldberg</name><affiliation><nlm:aff id="A7">Department of Oral Biology and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</nlm:aff></affiliation></author><author><name sortKey="Eilbeck, Karen" sort="Eilbeck, Karen" uniqKey="Eilbeck K" first="Karen" last="Eilbeck">Karen Eilbeck</name><affiliation><nlm:aff id="A8">Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, Utah 84112, USA</nlm:aff></affiliation></author><author><name sortKey="Ireland, Amelia" sort="Ireland, Amelia" uniqKey="Ireland A" first="Amelia" last="Ireland">Amelia Ireland</name><affiliation><nlm:aff id="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Mungall, Christopher J" sort="Mungall, Christopher J" uniqKey="Mungall C" first="Christopher J" last="Mungall">Christopher J. Mungall</name><affiliation><nlm:aff id="A10">Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720, USA</nlm:aff></affiliation></author><author><name sortKey="Leontis, Neocles" sort="Leontis, Neocles" uniqKey="Leontis N" first="Neocles" last="Leontis">Neocles Leontis</name><affiliation><nlm:aff id="A12">Department of Chemistry, Bowling Green State University, 212 Physical Sciences Laboratory Building, 1001 East Wooster Street, Bowling Green, Ohio 43403, USA</nlm:aff></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><nlm:aff id="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Ruttenberg, Alan" sort="Ruttenberg, Alan" uniqKey="Ruttenberg A" first="Alan" last="Ruttenberg">Alan Ruttenberg</name><affiliation><nlm:aff id="A13">Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, Massachusetts 02139, USA</nlm:aff></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><nlm:aff id="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H" last="Scheuermann">Richard H. Scheuermann</name><affiliation><nlm:aff id="A14">Department of Pathology, University of Texas Southwestern Medical Center, Harry Hines Blvd., Dallas, Texas 75390 USA</nlm:aff></affiliation></author><author><name sortKey="Shah, Nigam" sort="Shah, Nigam" uniqKey="Shah N" first="Nigam" last="Shah">Nigam Shah</name><affiliation><nlm:aff id="A15">Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, California 94305, USA</nlm:aff></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><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></affiliation></author><author><name sortKey="Lewis, Suzanna" sort="Lewis, Suzanna" uniqKey="Lewis S" first="Suzanna" last="Lewis">Suzanna Lewis</name><affiliation><nlm:aff id="A10">Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17989687</idno><idno type="pmc">2814061</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814061</idno><idno type="RBID">PMC:2814061</idno><idno type="doi">10.1038/nbt1346</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">000304</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration</title><author><name sortKey="Smith, Barry" sort="Smith, Barry" uniqKey="Smith B" first="Barry" last="Smith">Barry Smith</name><affiliation><nlm:aff id="A1">Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</nlm:aff></affiliation></author><author><name sortKey="Ashburner, Michael" sort="Ashburner, Michael" uniqKey="Ashburner M" first="Michael" last="Ashburner">Michael Ashburner</name><affiliation><nlm:aff id="A2">Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK</nlm:aff></affiliation></author><author><name sortKey="Rosse, Cornelius" sort="Rosse, Cornelius" uniqKey="Rosse C" first="Cornelius" last="Rosse">Cornelius Rosse</name><affiliation><nlm:aff id="A3">Department of Biological Structure, Box 357420, University of Washington, Seattle, Washington 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Bard, Jonathan" sort="Bard, Jonathan" uniqKey="Bard J" first="Jonathan" last="Bard">Jonathan Bard</name><affiliation><nlm:aff id="A4">Department of Biomedical Sciences, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, Scotland, UK</nlm:aff></affiliation></author><author><name sortKey="Bug, William" sort="Bug, William" uniqKey="Bug W" first="William" last="Bug">William Bug</name><affiliation><nlm:aff id="A5">Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA</nlm:aff></affiliation></author><author><name sortKey="Ceusters, Werner" sort="Ceusters, Werner" uniqKey="Ceusters W" first="Werner" last="Ceusters">Werner Ceusters</name><affiliation><nlm:aff id="A6">Department of Psychiatry and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</nlm:aff></affiliation></author><author><name sortKey="Goldberg, Louis J" sort="Goldberg, Louis J" uniqKey="Goldberg L" first="Louis J" last="Goldberg">Louis J. Goldberg</name><affiliation><nlm:aff id="A7">Department of Oral Biology and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</nlm:aff></affiliation></author><author><name sortKey="Eilbeck, Karen" sort="Eilbeck, Karen" uniqKey="Eilbeck K" first="Karen" last="Eilbeck">Karen Eilbeck</name><affiliation><nlm:aff id="A8">Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, Utah 84112, USA</nlm:aff></affiliation></author><author><name sortKey="Ireland, Amelia" sort="Ireland, Amelia" uniqKey="Ireland A" first="Amelia" last="Ireland">Amelia Ireland</name><affiliation><nlm:aff id="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Mungall, Christopher J" sort="Mungall, Christopher J" uniqKey="Mungall C" first="Christopher J" last="Mungall">Christopher J. Mungall</name><affiliation><nlm:aff id="A10">Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720, USA</nlm:aff></affiliation></author><author><name sortKey="Leontis, Neocles" sort="Leontis, Neocles" uniqKey="Leontis N" first="Neocles" last="Leontis">Neocles Leontis</name><affiliation><nlm:aff id="A12">Department of Chemistry, Bowling Green State University, 212 Physical Sciences Laboratory Building, 1001 East Wooster Street, Bowling Green, Ohio 43403, USA</nlm:aff></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><nlm:aff id="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Ruttenberg, Alan" sort="Ruttenberg, Alan" uniqKey="Ruttenberg A" first="Alan" last="Ruttenberg">Alan Ruttenberg</name><affiliation><nlm:aff id="A13">Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, Massachusetts 02139, USA</nlm:aff></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><nlm:aff id="A9">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H" last="Scheuermann">Richard H. Scheuermann</name><affiliation><nlm:aff id="A14">Department of Pathology, University of Texas Southwestern Medical Center, Harry Hines Blvd., Dallas, Texas 75390 USA</nlm:aff></affiliation></author><author><name sortKey="Shah, Nigam" sort="Shah, Nigam" uniqKey="Shah N" first="Nigam" last="Shah">Nigam Shah</name><affiliation><nlm:aff id="A15">Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, California 94305, USA</nlm:aff></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><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></affiliation></author><author><name sortKey="Lewis, Suzanna" sort="Lewis, Suzanna" uniqKey="Lewis S" first="Suzanna" last="Lewis">Suzanna Lewis</name><affiliation><nlm:aff id="A10">Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720, USA</nlm:aff></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><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">9604648</journal-id><journal-id journal-id-type="pubmed-jr-id">20305</journal-id><journal-id journal-id-type="nlm-ta">Nat Biotechnol</journal-id><journal-title>Nature biotechnology</journal-title><issn pub-type="ppub">1087-0156</issn><issn pub-type="epub">1546-1696</issn></journal-meta><article-meta><article-id pub-id-type="pmid">17989687</article-id><article-id pub-id-type="pmc">2814061</article-id><article-id pub-id-type="doi">10.1038/nbt1346</article-id><article-id pub-id-type="manuscript">NIHMS169394</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Barry</given-names></name><xref rid="A1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Ashburner</surname><given-names>Michael</given-names></name><xref rid="A2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Rosse</surname><given-names>Cornelius</given-names></name><xref rid="A3" ref-type="aff">3</xref></contrib><contrib contrib-type="author"><name><surname>Bard</surname><given-names>Jonathan</given-names></name><xref rid="A4" ref-type="aff">4</xref></contrib><contrib contrib-type="author"><name><surname>Bug</surname><given-names>William</given-names></name><xref rid="A5" ref-type="aff">5</xref></contrib><contrib contrib-type="author"><name><surname>Ceusters</surname><given-names>Werner</given-names></name><xref rid="A6" ref-type="aff">6</xref></contrib><contrib contrib-type="author"><name><surname>Goldberg</surname><given-names>Louis J</given-names></name><xref rid="A7" ref-type="aff">7</xref></contrib><contrib contrib-type="author"><name><surname>Eilbeck</surname><given-names>Karen</given-names></name><xref rid="A8" ref-type="aff">8</xref></contrib><contrib contrib-type="author"><name><surname>Ireland</surname><given-names>Amelia</given-names></name><xref rid="A9" ref-type="aff">9</xref></contrib><contrib contrib-type="author"><name><surname>Mungall</surname><given-names>Christopher J</given-names></name><xref rid="A10" ref-type="aff">10</xref></contrib><contrib contrib-type="author"><collab>the OBI Consortium</collab><xref rid="A11" ref-type="aff">11</xref></contrib><contrib contrib-type="author"><name><surname>Leontis</surname><given-names>Neocles</given-names></name><xref rid="A12" ref-type="aff">12</xref></contrib><contrib contrib-type="author"><name><surname>Rocca-Serra</surname><given-names>Philippe</given-names></name><xref rid="A9" ref-type="aff">9</xref></contrib><contrib contrib-type="author"><name><surname>Ruttenberg</surname><given-names>Alan</given-names></name><xref rid="A13" ref-type="aff">13</xref></contrib><contrib contrib-type="author"><name><surname>Sansone</surname><given-names>Susanna-Assunta</given-names></name><xref rid="A9" ref-type="aff">9</xref></contrib><contrib contrib-type="author"><name><surname>Scheuermann</surname><given-names>Richard H</given-names></name><xref rid="A14" ref-type="aff">14</xref></contrib><contrib contrib-type="author"><name><surname>Shah</surname><given-names>Nigam</given-names></name><xref rid="A15" ref-type="aff">15</xref></contrib><contrib contrib-type="author"><name><surname>Whetzel</surname><given-names>Patricia L</given-names></name><xref rid="A16" ref-type="aff">16</xref></contrib><contrib contrib-type="author"><name><surname>Lewis</surname><given-names>Suzanna</given-names></name><xref rid="A10" ref-type="aff">10</xref></contrib></contrib-group><aff id="A1"><label>1</label>Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</aff><aff id="A2"><label>2</label>Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK</aff><aff id="A3"><label>3</label>Department of Biological Structure, Box 357420, University of Washington, Seattle, Washington 98195, USA</aff><aff id="A4"><label>4</label>Department of Biomedical Sciences, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, Scotland, UK</aff><aff id="A5"><label>5</label>Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA</aff><aff id="A6"><label>6</label>Department of Psychiatry and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</aff><aff id="A7"><label>7</label>Department of Oral Biology and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, New York 14203, USA</aff><aff id="A8"><label>8</label>Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, Utah 84112, USA</aff><aff id="A9"><label>9</label>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</aff><aff id="A10"><label>10</label>Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, California 94720, USA</aff><aff id="A11"><label>11</label><ext-link ext-link-type="uri" xlink:href="http://obi.sourceforge.net/community/index.php">http://obi.sourceforge.net/community/index.php</ext-link></aff><aff id="A12"><label>12</label>Department of Chemistry, Bowling Green State University, 212 Physical Sciences Laboratory Building, 1001 East Wooster Street, Bowling Green, Ohio 43403, USA</aff><aff id="A13"><label>13</label>Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, Massachusetts 02139, USA</aff><aff id="A14"><label>14</label>Department of Pathology, University of Texas Southwestern Medical Center, Harry Hines Blvd., Dallas, Texas 75390 USA</aff><aff id="A15"><label>15</label>Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, California 94305, USA</aff><aff id="A16"><label>16</label>Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, 423 Guardian Drive, Philadelphia, Pennsylvania 19104, USA</aff><author-notes><corresp id="FN1">Correspondence should be addressed to B.S. (<email>phismith@buffalo.edu</email>)</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>21</day><month>1</month><year>2010</year></pub-date><pub-date pub-type="ppub"><month>11</month><year>2007</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>1</month><year>2010</year></pub-date><volume>25</volume><issue>11</issue><fpage>1251</fpage><permissions><copyright-statement>© 2007 Nature Publishing Group</copyright-statement><copyright-year>2007</copyright-year></permissions><abstract><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></abstract><contract-num rid="HG1">U54 HG004028-02
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