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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Nature Biotechnology volume 25, pages 1251–1255 (2007)Cite this article

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.

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Acknowledgements

The Foundry is receiving ad hoc funding under the BISC Gen e Ontology Consortium, MGED, NCBO and RNA Ontology grants. We are grateful to all of these sources, and also to the ACGT Project of the European Union and to the Humboldt and Volkswagen Foundations.

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Authors and Affiliations

  1. Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, 14203, New York, USA

    Barry Smith

  2. Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

    Michael Ashburner

  3. Department of Biological Structure, Box 357420, University of Washington, Seattle, 98195, Washington, USA

    Cornelius Rosse

  4. Department of Biomedical Sciences, The University of Edinburgh, 1 George Square, Edinburgh, EH8 9JZ, Scotland, UK

    Jonathan Bard

  5. Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, 19129, Pennsylvania, USA

    William Bug

  6. Department of Psychiatry and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, 14203, New York, USA

    Werner Ceusters

  7. Department of Oral Biology and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 701 Ellicott Street, Buffalo, 14203, New York, USA

    Louis J Goldberg

  8. Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, 84112, Utah, USA

    Karen Eilbeck

  9. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK

    Amelia Ireland, Philippe Rocca-Serra & Susanna-Assunta Sansone

  10. Life Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, 94720, California, USA

    Christopher J Mungall & Suzanna Lewis

  11. Department of Chemistry, Bowling Green State University, 212 Physical Sciences Laboratory Building, 1001 East Wooster Street, Bowling Green, 43403, Ohio, USA

    Neocles Leontis

  12. Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, 02139, Massachusetts, USA

    Alan Ruttenberg

  13. Department of Pathology, University of Texas Southwestern Medical Center, Harry Hines Blvd., Dallas, 75390, Texas, USA

    Richard H Scheuermann

  14. Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, 94305, California, USA

    Nigam Shah

  15. Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, 423 Guardian Drive, Philadelphia, 19104, Pennsylvania, USA

    Patricia L Whetzel

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  1. Barry Smith
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  15. Richard H Scheuermann
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  18. Suzanna Lewis
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The OBI Consortium

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Correspondence to Barry Smith.

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http://obi.sourceforge.net/community/index.php

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Smith, B., Ashburner, M., Rosse, C. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25, 1251–1255 (2007). https://doi.org/10.1038/nbt1346

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