CARO – The Common Anatomy Reference Ontology

  • Melissa A. Haendel
  • Fabian Neuhaus
  • David Osumi-Sutherland
  • Paula M. Mabee
  • Jos L.V. MejinoJr.
  • Chris J. Mungall
  • Barry Smith
Part of the Computational Biology book series (COBO, volume 6)


The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using the latter to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by crossreferencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized by other ontologies for cross-product generation.


Gene Ontology Anatomical Structure Anatomical Entity Anatomical Type Anatomy Ontology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    C. Berger, J. Urban, and G.M. Technau. Stage-specific inductive signals in the Drosophila neuroectoderm control the temporal sequence of neuroblast specification. Development, 128: 3243-3251, 2001.Google Scholar
  2. 2.
    J.A. Campos-Ortega and V. Hartenstein. TheEmbryonic Development of Drosophila melanogaster. (SecondEdition), Springer-Verlag, Berlin, 1999.Google Scholar
  3. 3.
    D.L. Cook, J.L.V. Mejino, and C. Rosse. Evolution of a foundational model of physiology: symbolic representation for functional bioinformatics.Medinfo, 11(1): 336-340, 2004.Google Scholar
  4. 4.
    D.H. Erwin and E.H. Davidson. The last common bilaterian ancestor. Development, 129:3021-3032, 2002.Google Scholar
  5. 5.
    Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res., 34: D322-6, 2006.Google Scholar
  6. 6.
    P.W.H. Holland. Major transitions in animal evolution: a developmental genetic perspective. American Zoologist, 38(6): 829-842,1998.MathSciNetGoogle Scholar
  7. 7.
    M. Jollie. Chordate Morphology. New York, Reinhold Books, 1962.Google Scholar
  8. 8.
    C.B. Kimmel, W.W. Ballard, S.R. Kimmel, B. Ullmann, and T.F. Schilling. Stages of embryonic development of the zebrafish.Dev. Dyn., 203: 253-310, 1995.Google Scholar
  9. 9.
    C. Mungall. Obol: integrating language and meaning in bio-ontologies. Comparative and Functional Genomics, 5 (6-7), 509-520, 2004.CrossRefGoogle Scholar
  10. 10.
    P.D. Nieuwkoop and J. Faber. Normal Table of Xenopus laevis. 3rd Ed, 1994.Google Scholar
  11. 11.
    C. Rosse and J.L.V. Mejino. A reference ontology for bioinformatics: The Foundational Model of Anatomy. Journal of BiomedicalInformatics, 36: 478-500, 2003.Google Scholar
  12. 12.
    C. Rosse, J.L.V. Mejino, B.R. Modayur, R. Jakobovits, K.P. Hinshaw, J.F. Brinkley. Motivation and organizational principles for anatomicalknowledge representation: the Digital Anatomist symbolic knowledgebase. Journal of the American Medical InformaticsAssociation, 5(1): 17-40, 1998.Google Scholar
  13. 13.
    H. P. Schultze and M. Arsenault. The panderichthyid fish Elpistostege: A close relative of tetrapods? Paleontology, 28: 293-309, 1985.Google Scholar
  14. 14.
    M.A. Selleck and C.D. Stern. Fate mapping and cell lineage analysis of Hensen’s node in the chick embryo. Development, 112(2): 615-626, 1991.Google Scholar
  15. 15.
    J. Slack. From egg to Embryo (2nd Ed). Cambridge University Press, 1991.Google Scholar
  16. 16.
    B. Smith. Fiat objects. Topoi, 20(2): 131-148, 2001.CrossRefGoogle Scholar
  17. 17.
    B. Smith, W. Ceusters, B. Klagges, J. KÖhler, A. Kumar, J. Lomax, C. Mungall, F. Neuhaus, A. Rector, and C. Rosse.Relations in biomedical ontologies. Genome Biology,6(5):r46, 2005.CrossRefGoogle Scholar
  18. 18.
    B. Smith, W. Ceusters, and C. Rosse. On carcinomas and other pathological entities. Comparative and FunctionalGenomics, vol 6, 7-8, 379-387, 2005.CrossRefGoogle Scholar

Copyright information

© Albert Burger, Duncan Davidson, Richard Baldock 2008

Authors and Affiliations

  • Melissa A. Haendel
  • Fabian Neuhaus
  • David Osumi-Sutherland
  • Paula M. Mabee
  • Jos L.V. MejinoJr.
  • Chris J. Mungall
  • Barry Smith

There are no affiliations available

Personalised recommendations