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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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References

  1. Yue, L. & Reisdorf, W.C. Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints. Curr. Mol. Med. 5, 11–21 (2005).

    Article  CAS  Google Scholar 

  2. Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34 (database issue), D322–D326 (2006).

  3. Camon, E. et al. The Gene Ontology Annotation (GOA) Project. Genome Res. 13, 662–672 (2003).

    Article  CAS  Google Scholar 

  4. Kohane, I.S. et al. Building national electronic medical record systems via the World Wide Web. J. Am. Med. Inform. Assoc. 3, 191–207 (1996).

    Article  CAS  Google Scholar 

  5. Bodenreider, O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32 (database issue), D267–D270 (2004).

    Article  CAS  Google Scholar 

  6. Ceusters, W., Smith, B., Kumar, A. & Dhaen, C. Mistakes in medical ontologies: where do they come from and how can they be detected? Stud. Health Technol. Inform. 102, 145–164 (2004).

    PubMed  Google Scholar 

  7. Ceusters, W., Smith, B. & Goldberg, L. A terminological and ontological analysis of the NCI Thesaurus. Methods Inf. Med. 44, 498–507 (2005).

    Article  CAS  Google Scholar 

  8. Campbell, K.E., Oliver, D.E. & Shortliffe, E.H. The Unified Medical Language System. Toward a collaborative approach for solving terminologic problems. J. Am. Med. Inform. Assoc. 5, 12–16 (1998).

    Article  CAS  Google Scholar 

  9. Buetow, K.H. Cyberinfrastructure: empowering a 'third way' in biomedical research. Science 308, 821–824 (2005).

    Article  CAS  Google Scholar 

  10. Smith, B. & Ceusters, W. HL7 RIM: an incoherent standard. Stud. Health Technol. Inform. 124, 133–138 (2006).

    PubMed  Google Scholar 

  11. Ashburner, M., Mungall, C.J. & Lewis, S.E. Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb. Symp. Quant. Biol. 68, 227–236 (2003).

    Article  CAS  Google Scholar 

  12. Rubin, D.L. et al. National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS 10, 185–198 (2006).

    Article  CAS  Google Scholar 

  13. Rosse, C. & Mejino, J.L.F. The Foundational Model of Anatomy ontology. In Anatomy Ontologies for Bioinformatics (eds. Burger, A. et al.) (Springer, New York, in the press).

  14. Haendel, M. et al. CARO: the Common Anatomy Reference Ontology. In Anatomy Ontologies for Bioinformatics (eds. Burger, A. et al.) (Springer, New York, in the press).

  15. Leontis, N.B. et al. The RNA Ontology Consortium: an open invitation to the RNA community. RNA 12, 533–541 (2006).

    Article  CAS  Google Scholar 

  16. Natale, D.A. et al. Framework for a protein ontology. BMC Bioinformatics [online] (in the press).

  17. Bard, J., Rhee, S.Y. & Ashburner, M. An ontology for cell types. Genome Biol. [online] 6, R21 (2005).

    Article  Google Scholar 

  18. Kelso, J. et al. eVOC: a controlled vocabulary for unifying gene expression data. Genome Res. 13, 1222–1230 (2003).

    Article  CAS  Google Scholar 

  19. Mabee, P.M. et al. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol. Evol. 22, 345–350 (2007).

    Article  Google Scholar 

  20. Whetzel, P.L. et al. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22, 866–873 (2006).

    Article  CAS  Google Scholar 

  21. Whetzel, P.L. et al. Development of FuGO: an ontology for functional genomics investigations. OMICS 10, 199–204 (2006).

    Article  CAS  Google Scholar 

  22. Golbreic, C. et al. OBO and OWL: leveraging semantic web technologies for the life sciences. In Proceedings 6th International Semantic Web Conference (ISWC 2007), (Springer, in the press).

    Google Scholar 

  23. Brinkley, J.F., Detwiler, L.T., Gennari, J.H., Rosse, C. & Suciu, D. A framework for using reference ontologies as a foundation for the semantic web. Proc. AMIA Fall Symposium, 2006, 95–100.

  24. Lacy, L.W. Owl: Representing Information Using the Web Ontology Language (Trafford Publishing, Victoria, BC, Canada, 2005).

    Google Scholar 

  25. Smith, B., Köhler, J. & Kumar, A. On the application of formal principles to life science data: a case study in the Gene Ontology. Data Integration in the Life Sciences (DILS) Workshop 2004, 79–94.

    Chapter  Google Scholar 

  26. Smith, B. et al. Relations in biomedical ontologies. Genome Biol. [online] 6, R46 (2005).

    Article  Google Scholar 

  27. Bittner, T. & Goldberg, L.J. Spatial location and its relevance for terminological inferences in bio-ontologies. BMC Bioinformatics 23, 1674–1682 (2007).

    Article  CAS  Google Scholar 

  28. Ramírez, M.J. et al. Linking of digital images to phylogenetic data matrices using a morphological ontology. Syst. Biol. 56, 283–294 (2007).

    Article  Google Scholar 

  29. Schober, D., et al. Towards naming conventions for use in controlled vocabulary and ontology engineering. Bio-Ontologies Workshop, ISMB/ECCB, Vienna, 20 July 2007, 87–90.

    Google Scholar 

  30. Ruttenberg, A., Rees, J., & Zucker, J. What BioPAX communicates and how to extend OWL to help it. OWL: Experiences and Directions Workshop Series <http://owl-workshop.man.ac.uk/acceptedLong/submission_26.pdf> (2006).

    Google Scholar 

  31. Hunter, L. & Bada. M. Enrichment of OBO ontologies. J. Biomed. Inform. 40, 300–315 (2007).

    Article  Google Scholar 

  32. Hill, D.P., Blake, J.A., Richardson, J.E. & Ringwald, M. Extension and integration of the Gene Ontology (GO): combining GO vocabularies with external vocabularies. Genome Res. 12, 1982–1991 (2002).

    Article  CAS  Google Scholar 

  33. Mungall, C.J. Obol: integrating language and meaning in bio-ontologies. Comp. Funct. Genomics 5, 509–520 (2004).

    Article  CAS  Google Scholar 

  34. Camon, E. et al. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32 (database issue), D262–D266 (2004).

    Article  CAS  Google Scholar 

  35. Blake, J., Hill, D.P. & Smith, B. Gene Ontology annotations: what they mean and where they come from. Bio-Ontologies Workshop, ISMB/ECCB, Vienna, 20 July 2007, 79–82.

    Google Scholar 

  36. Sjoblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006).

    Article  Google Scholar 

  37. Lee, J.A. et al. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics [online] 7, 237 (2006).

    Article  Google Scholar 

  38. Rebholz-Schuhmann, D., Kirsch, H. & Couto, F. Facts from text—is text mining ready to deliver? PLoS Biol. [online] 3, e65 (2005).

    Article  Google Scholar 

  39. Witte, R., Kappler, T. & Baker, C.J.O. Ontology design for biomedical text mining. In Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. Baker C.J.O. & Cheung, K.-H.) 281–313 (Springer, New York, 2007).

    Chapter  Google Scholar 

  40. Zhang, S. & Bodenreider, O. Aligning multiple anatomical ontologies through a reference. International Workshop on Ontology Matching (OM 2006) 193–197 (2006).

  41. Luo, F. et al. Modular organization of protein interaction networks. Bioinformatics 23, 207–214 (2007).

    Article  CAS  Google Scholar 

  42. Martone, M.E., Gupta, A. & Ellisman, M.H. E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat. Neurosci. 7, 467–472 (2004).

    Article  CAS  Google Scholar 

  43. Fong, L. et al. An ontology-driven knowledge environment for subcellular neuroanatomy. OWL Experiences and Directions, 3rd International Workshop, Innsbruck, Austria, June 6–7, 2007 (in the press).

    Google Scholar 

  44. Taylor, C.F. et al. Promoting coherent minimum reporting requirements for biological and biomedical investigations: the MIBBI Project. Nat. Biotechnol. (in the press).

  45. Brazma, A. et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat. Genet. 29, 365–371 (2001).

    Article  CAS  Google Scholar 

  46. Sansone, S.A. et al. A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS 10, 164–171 (2006).

    Article  CAS  Google Scholar 

  47. Grenon, P., Smith, B. & Goldberg, L. Biodynamic ontology: applying BFO in the biomedical domain. In Ontologies in Medicine (ed. Pisanelli, D.M.) 20–38 (IOS, Amsterdam, 2004).

    Google Scholar 

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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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The OBI Consortium

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Correspondence to Barry Smith.

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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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