Anatomy Ontologies for Bioinformatics pp 59-117

Part of the Computational Biology book series (COBO, volume 6)

The Foundational Model of Anatomy Ontology

  • Cornelius Rosse
  • José L. V. MejinoJr

Summary

Anatomy is the structure of biological organisms. The term also denotes the scientific discipline devoted to the study of anatomical entities and the structural and developmental relations that obtain among these entities during the lifespan of an organism. Anatomical entities are the independent continuants of biomedical reality on which physiological and disease processes depend, and which, in response to etiological agents, can transform themselves into pathological entities. For these reasons, hard copy and in silico information resources in virtually all fields of biology and medicine, as a rule, make extensive reference to anatomical entities. Because of the lack of a generalizable, computable representation of anatomy, developers of computable terminologies and ontologies in clinical medicine and biomedical research represented anatomy from their own more or less divergent viewpoints. The resulting heterogeneity presents a formidable impediment to correlating human anatomy not only across computational resources but also with the anatomy of model organisms used in biomedical experimentation. The Foundational Model of Anatomy (FMA) ontology is being developed to fill the need for a generalizable anatomy ontology, which can be used and adapted by any computer-based application that requires anatomical information. Moreover it is evolving into a standard reference for divergent views of anatomy and a template for representing the anatomy of animals. A distinction is made between the FMA ontology as a theory of anatomy and the implementation of this theory as the FMA artifact. In either sense of the term, the FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Making use of explicit ontological principles and sound methods, it is designed to be understandable by human beings and navigable by computers. The FMA’s ontological structure provides for machine-based inference, enabling powerful computational tools of the future to reason with biomedical data.

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References

  1. 1.
    Adult mouse anatomical dictionary browser.http://www.informatics.jax.org/searches/AMA form.shtml.Google Scholar
  2. 2.
    A. Agoncillo, J.L.V. Mejino, and C. Rosse. Influence of the digital anatomist foundationalmodel on traditional representations of anatomical concepts. In AMIA Symposium Proceedings, pages 2–6, 1999.Google Scholar
  3. 3.
    B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P.Walter. Molecular Biology of the Cell. Garland Science, New York, 4th edition, 2002.Google Scholar
  4. 4.
    Aristotle. The categories.Harvard University Press, Cambridge, Mass., 1973.Google Scholar
  5. 5.
    A. Au, X. Li, and J.H. Gennari. Differences among cell structure ontologies: FMA, Goand CCO. In AMIA Symposium Proceedings, pages 16–20, 2006.Google Scholar
  6. 6.
    J. Bard, S.Y. Rhee, and M. Ashburner. An ontology for cell types. Genome Biology,6(R21), 2005.Google Scholar
  7. 7.
    J.B.L. Bard. Anatomics: the intersection of anatomy and bioinformatics. J Anat, pages1–16, 2005.Google Scholar
  8. 8.
    C.A. Bean, T.C. Rindflesh, and C.A. Sneiderman. Automatic semantic interpretation ofanatomic spatial relationships in clinical text. In AMIA Symposium Proceedings, pages897–901, 1998.Google Scholar
  9. 9.
    N. Benson, M. Whipple, and I.Kalet. A markov model approach to predicting regionaltumor spread in the lymphatic system of the head and neck. In AMIA Symposium Proceedings,pages 31–35, 2006.Google Scholar
  10. 10.
    J. Berg. Aristotle’s theory of definition. In AATI del Convegno Internationale di Storia della Logica San Gimignano, pages 19–30, Bologna, 4-8 December 1982 1983. CLUEB.Google Scholar
  11. 11.
    T. Bittner. Axioms for parthood and containment relations in bio-ontologies. In First International Workshop on Formal Biomedical Knowledge Representation, pages 4–11,Bethesda MD, 2004. American Medical Informatics Association.Google Scholar
  12. 12.
    T. Bittner, M. Donnelly, and L.J. Goldberg. Modeling principles and methodologiesspatial representation and reasoning. In Burger A., Davidson D., and Baldock R., editors,Anatomy Ontologies for Bioinformatics: Principles and Practice, New York, In press.Springer.Google Scholar
  13. 13.
    T. Bittner and B. Smith. A theory of granular partitions. In Duckham D., GoodchildMF, and Worboys MF., editors, Foundations of Geographic Information Science, pages117–151, London, 2003. Taylor & Francis.Google Scholar
  14. 14.
    O. Bodenreider and S. Zhang. Comparing the representation of anatomy in the FMAand SNOMED CT. In AMIA Symposium Proceedings, pages 46–50, 2006.Google Scholar
  15. 15.
    J.F. Brinkley, J.S. Prothero, J.W. Prothero, and C. Rosse. A framework for the designof knowledge-based systems in structural biology. In Proc. 13th Annual Symposium on Computer Application in Medical Care, pages 61–65, 1989.Google Scholar
  16. 16.
    J.F. Brinkley, B.A. Wong, K.P. Hinshaw, and C. Rosse. Design of an anatomy informationsystem. IEEE Comp Graphics Applic, 3:38–48, 1999.CrossRefGoogle Scholar
  17. 17.
    M.B. Carpenter and J. Sutin. Human Neuroanatomy. Wilkins &Wilkins, Baltimore, 8th edition, 1983.Google Scholar
  18. 18.
    Cell type ontology.http://www.sanbi.ac.za/evoc/ontologies html/latest/celltype.html.Google Scholar
  19. 19.
    D.L. Cook, J.L.V. Mejino, and C. Rosse. Evolution of a foundational model of physiology:symbolic representation for functional bioinformatics. In Proceedings of MedInfo,pages 336–340, 2004.4 The Foundational Model of Anatomy Ontology 107Google Scholar
  20. 20.
    O. Dameron, D.L. Rubin, and M. Musen. Challenges in converting frame-based ontologyinto OWL: the foundational model of anatomy case-study. In AMIA Symposium Proceedings, pages 181–185, 2005.Google Scholar
  21. 21.
    L.T. Detwiler, E. Chung, A. Li, J.L.V. Mejino, A.V. Agoncillo, J.F. Brinkley, C. Rosse,and L.G. Shapiro. A relation-centric query engine for the foundational model ofanatomy. In Proceedings of MedInfo, pages 341–345, 2004.Google Scholar
  22. 22.
    L.T. Detwiler, J.L.V. Mejino, C. Rosse, and J.F. Brinkley. Efficient web-based navigationof the foundational model of anatomy. In AMIA Symposium Proceedings, page 829,2003.Google Scholar
  23. 23.
    Digital anatomist project - interactive atlases.http://www9.biostr.washington.edu/da.html.Google Scholar
  24. 24.
    G. Distelhorst, V. Srivastava, C. Rosse, and J.F. Brinkley. A prototype natural languageinterface to a large complex knowledge base, the foundational model of anatomy. InAMIA Symposium Proceedings, pages 200–204, 2003.Google Scholar
  25. 25.
    M. Donnelly, T. Bittner, and C. Rosse. A formal theory for spatial representation andreasoning in biomedical ontologies. Artificial Intelligence in Medicine, 36:1–27, 2006.CrossRefGoogle Scholar
  26. 26.
    Dorland’s medical dictionary.http://www.dorlands.com/.Google Scholar
  27. 27.
    Edinburgh developmental anatomy.http://www.ana.ed.ac.uk/anatomy/database/humat/.Google Scholar
  28. 28.
    D.W. Fawcett. Bloom and Fawcett Textbook of Histology. Chapman & Hall, NewYork,12th edition, 1994.Google Scholar
  29. 29.
    Federative Committee on Anatomical Terminology (FCAT). Terminologia Anatomica.Thieme, Stuttgart, 1998.Google Scholar
  30. 30.
    FMA in OWL-full format. Published on the Web.http://webrum.uni-mannheim.de/math/lski/release.html.Google Scholar
  31. 31.
    FMA open source.http://sig.biostr.washington.edu/cgi-bin/fma register.cgi.Google Scholar
  32. 32.
    Foundational Model Explorer.http://fme.biostr.washington.edu:8089/FME/index.html.Google Scholar
  33. 33.
    GALEN.http://www.opengalen.org/.Google Scholar
  34. 34.
    Gene Ontology.http://www.geneontology.org.Google Scholar
  35. 35.
    C. Golbreich, S. Zhang, and O. Bodenreider. The foundational model of anatomy inOWL: Experience and perspectives. Journal of Web Semantics, 4:181–195, 2006.Google Scholar
  36. 36.
    P. Grenon, B. Smith, and L. Goldberg. Biodynamic ontology: applying BFO in thebiomedical domain. In P.M. Pisannelli, editor, Ontologies in Medicine. Studies in Health technology and Informatics, volume 102, pages 20–38, Amsterdam, 2004. IOS Press.Google Scholar
  37. 37.
    M. Haendel, F. Neuhaus, J.L.E. Sutherland, J.L.V. Mejino(Jr), C. Mungall, and B. Smith.The common anatomy reference ontology. In A. Burger, D. Davidson, and R. Baldock,editors, Anatomy Ontologies for Bioinformatics: Principles and Practice, New York, Inpress. Springer.Google Scholar
  38. 38.
    T.F. Hayamizu, M. Mangan, J.P. Corradi, J.A. Kadin, and M. Ringwald. Adult mouseanatomy dictionary. Genome Biology, 6(R29), 2005.Google Scholar
  39. 39.
    W.H. Hollinshead. Anatomy for surgeons, volume 1–3. Harper and Row, Philadelphia,3rd edition, 1982.Google Scholar
  40. 40.
    International code of zoological nomenclature online; chapter 13: The type concept innomenclature; article 61: Principles of typification.http://www.iczn.org/iczn/indes.jsp.108 Cornelius Rosse and Jos’e L. V. Mejino Jr.Google Scholar
  41. 41.
    IUPS Physionome Project - body systems.http://www.bioeng.auckland.ac.nz/physiome/anatomy.php.Google Scholar
  42. 42.
    R. Jakobovits, J.F. Brinkley, C. Rosse, and E. Weinberger. Enabling clinicians, researchersand educators to build custom web-based biomedical information systems.In AMIA Symposium Proceedings, pages 279–283, 2001.Google Scholar
  43. 43.
    I. Johansson, B. Smith, K. Munn, N. Tsikolia, K. Elsner, D. Ernst, and D. Siebert. Functionalanatomy: a taxonomic proposal. Acta Biotheoretica, 53(3):153–166, 2005.CrossRefGoogle Scholar
  44. 44.
    I.J. Kalet, J.Wu,M. Lease, M.M. Austin Seymour, J.F. Brinkley, and C. Rosse. Anatomicalinformation in radiation treatment planning. In AMIA Symposium Proceedings, pages291–295, 1999.Google Scholar
  45. 45.
    R.C. Kerckhoffs, M.L. Neal, Q. Gu, J.B. Bassingthwaighte, J.H. Omens, and A.D. Mc-Culloch. Coupling of a 3d finite element model of cardiac ventricular mechanics tolumped systems models of the systemic and pulmonic circulation. Ann Biomed Eng,35(1):1–18, 2007.CrossRefGoogle Scholar
  46. 46.
    S. Kim, J.F. Brinkley, and C. Rosse. A profile of on-line anatomy information resources:design and instructional implications. Clin Anat., 16:55–71, 2003.CrossRefGoogle Scholar
  47. 47.
    K.L. Rickard KL, J.L.V. Mejino(Jr), R.F. Martin, A.V. Agoncillo, and C. Rosse. Problemsand solutions with integrating terminologies into evolving knowledge bases. InProceedings of MedInfo, pages 420–424, 2004.Google Scholar
  48. 48.
    A. Kumar, Y.L. Yip, B. Smith, D. Marwede, and D. Novotny. An ontology for carcinomaclassification for clinical bioinformatics. Stud Health Technol Inform., 116:635–40, 2005.Google Scholar
  49. 49.
    J.H. Martin. Neuroanatomy Text and Atlas. Appleton & Lange, Stamford, Connecticut,2nd edition, 1996.Google Scholar
  50. 50.
    R.F. Martin, J.L.V. Mejino, D.M. Bowden, J.F. Brinkley, and C. Rosse. Foundationalmodel of neuroanatomy: its implications for the Human Brain Project. In AMIA Symposium Proceedings, pages 438–442, 2001.Google Scholar
  51. 51.
    D. Marwede. RadiO. Personal Communication.Google Scholar
  52. 52.
    Medical Entities Dictionary.http://med.dmi.columbia.edu/.Google Scholar
  53. 53.
    J.L.V. Mejino(Jr), A.V. Agoncillo, K.L. Rickard, and C. Rosse. Representing complexityin part-whole relationships within the foundational model of anatomy. In AMIA Symposium Proceedings, pages 450–454, 2003.Google Scholar
  54. 54.
    J.L.V. Mejino(Jr) and C. Rosse. Interactive radiology exercises.http://www9.biostr.washington.edu/hubio511/.Google Scholar
  55. 55.
    J.L.V. Mejino(Jr) and C. Rosse. The potential of the digital anatomist foundationalmodel for assuring consistency in UMLS sources. In E.G. Chute, editor, AMIA Symposium Proceedings, pages 825–829, 1998.Google Scholar
  56. 56.
    J.L.V. Mejino(Jr) and C. Rosse. Conceptualizations of anatomical spatial entities in thedigital anatomist foundational model. In AMIA Symposium Proceedings, pages 112–116, 1999.Google Scholar
  57. 57.
    J.L.V. Mejino(Jr) and C. Rosse. Symbolic modeling of structural relationships in thefoundational model of anatomy. In First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), pages 48–62, Bethesda MD, 2004. AmericanMedical Informatics Association.Google Scholar
  58. 58.
    J. Michael, J.L.V. Mejino(Jr), and C. Rosse. The role of definitions in biomedical conceptrepresentation. In AMIA Symposium Proceedings, pages 463–467, 2001.Google Scholar
  59. 59.
    P. Mork and P.A. Bernstein. Adapting a generic match algorithm to align ontologies ofhuman anatomy. In ICDE, pages 787–790, 2004.4 The Foundational Model of Anatomy Ontology 109Google Scholar
  60. 60.
    P. Mork, J.F. Brinkley, and C. Rosse. OQAFMA querying agent for the foundationalmodel of anatomy: providing flexible and efficient access to a large semantic network. J Biomed Inform, 36:501–517, 2003.Google Scholar
  61. 61.
    C. Mungall. Personal Communication.Google Scholar
  62. 62.
    P.J. Neal, L.G. Shapiro, and C. Rosse. The digital anatomist spatial abstraction: a schemefor the spatial description of anatomical entities. In AMIA Symposium Proceedings,pages 423–427, 1998.Google Scholar
  63. 63.
    S. Nelson. Personal Communication.Google Scholar
  64. 64.
    F. Neuhaus and B. Smith. Modeling principles and methodologies – relations in anatomicalontologies. In A. Burger, D. Davidson, and R. Baldock R., editors, Anatomy Ontologies for Bioinformatics: Principles and Practice, New York, In press. Springer.Google Scholar
  65. 65.
    N.F. Noy, J.L.V. Mejino(Jr), M.A. Musen, and C. Rosse. Pushing the envelope: challengesin frame-based representation of human anatomy. Data & Knowledge Engineering,48:335–359, 2004.CrossRefGoogle Scholar
  66. 66.
    OBO - Open Biological Ontologies.htpp://obo.sourseforge.net.Google Scholar
  67. 67.
    T.C. Rindflesch, C.A. Bean, and C.A. Sneiderman. Argument identification for arterialbranching predications asserted in cardiac catheterization reports. In AMIA Symposium Proceedings, pages 704–8, 2000.Google Scholar
  68. 68.
    C. Rosse. Terminologia anatomica; considered from the perspective of next-generationknowledge sources. Clin. Anat., 14:120–133, 2001.CrossRefGoogle Scholar
  69. 69.
    C. Rosse and P. Gaddum-Rosse. Hollinshead’s textbook of anatomy.Lippincott-Raven,Philadelphia, 5th edition, 1997.Google Scholar
  70. 70.
    C. Rosse, A. Kumar, J.L.V. Mejino(Jr), D.L. Cook, L.T. Detwiler, and B. Smith. Astrategy for improving and integrating biomedical ontologies. In AMIA Symposium Proceedings,pages 639–643, 2005.Google Scholar
  71. 71.
    C. Rosse and J.L.V. Mejino(Jr). A reference ontology for biomedical informatics: thefoundational model of anatomy. J Biomed Inform., 36:478–500, 2003.CrossRefGoogle Scholar
  72. 72.
    C. Rosse, J.L.V. Mejino(Jr), B.R. Modayur, R. Jakobovits, K.P. Hinshaw, and J.F. Brinkley.Motivation and organizational principles for anatomical knowledge representation:the digital anatomist symbolic knowledge base. J. Am. Med. Informatics Assoc., 5:17–40, 1998.Google Scholar
  73. 73.
    M.J. Schleiden. Beiträge zur Phytogenesis 1838. In Transactions in Sydenham Society,volume 12, London, 1838. Müller’s Archive 1838.Google Scholar
  74. 74.
    S. Schulz and U. Hahn. Toward a computational paradigm for biomedical structure. In Proceedings of First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004)., pages 63–71, Bethesda MD, 2004. American MedicalInformatics Association.Google Scholar
  75. 75.
    T. Schwann. Mikroskopische Untersuchungen über die Übereinstimmung in der Strukturund demWachsthum der Thiere und Pflanzen, pages 1845–1856. Reimer, Berlin, 1837.Microscopical Researches into the Accordance in the Structure and Growth of Animalsand Plants, translated by H. Smith, Sydenham Society, London, 1847.Google Scholar
  76. 76.
    L.G. Shapiro, E. Chung, T. Detwiler, J.L.V. Mejino(Jr), A.W. Agoncillo, J.F. Brinkley,and C. Rosse. Processes and problems in the formative evaluation of an interface to thefoundational model of anatomy knowledge base. J Am Med Inform Assoc., 12:35–46,2005.CrossRefGoogle Scholar
  77. 77.
    B. Smith. Mereotopology: a theory of parts and boundaries. Data & Knowledge Engineering,20:287–303, 1996.MATHCrossRefGoogle Scholar
  78. 78.
    B. Smith. From concepts to clinical reality: an essay on the benchmarking of biomedicalterminologies. J Biomed Inform., In press.110 Cornelius Rosse and Jos’e L. V. Mejino Jr.Google Scholar
  79. 79.
    B. Smith, W. Ceusters, B. Klagges, J. Kohler, A. Kumar, J. Lomax, C. Mungall,F. Neuhaus, A. Rector, and C. Rosse. Relations in biomedical ontologies. Genome Biology, 6(R46), 2005.Google Scholar
  80. 80.
    B. Smith, J. Kohler, and A. Kumar. On the application of formal principles to life sciencedata: a case study in the gene ontology. In Proceedings of DILS 2004 (Data Integration in the Life Sciences), Lecture Notes in Bioinformatics, pages 79–94, Berlin, 2004. Springer.Google Scholar
  81. 81.
    B. Smith, A. Kumar, W. Ceusters, and C. Rosse. On carcinomas and other pathologicalenitities. Comp Funct Genom, 6:379–387, 2005.CrossRefGoogle Scholar
  82. 82.
    B. Smith, J.L.V. Mejino(Jr), S. Schulz, A. Kumar, and C. Rosse. Anatomical informationscience. In A. G. Cohn and D. M. Mark, editors, Spatial Information Theory. Proceedings of COSIT 2005, Lecture Notes in Computer Science, pages 149–164, New York,2005. Springer.Google Scholar
  83. 83.
    B. Smith and C. Rosse. The role of foundational relations in the alignment of biomedicalterminologies. In Proceedings of MedInfo, pages 444–448, 2004.Google Scholar
  84. 84.
    C.A. Sneiderman, T.C. Rindflesch, and C.A. Bean. Identification of anatomical terminologyin medical text. In AMIA Symposium Proceedings, pages 428–32, 1998.Google Scholar
  85. 85.
    SNOMED.http://www.snomed.org/snomedct/index.html.Google Scholar
  86. 86.
    C.C. Teng, M.M. Austin-Seymour, J. Barker, I.J. Kalet, L.G. Shapiro, and M. Whipple.Head and neck lymph node region delineation with 3-D CT image registration. In AMIA Symposium Proceedings, pages 767–71, 2002.Google Scholar
  87. 87.
    R.S. Travillian, K. Diatchka, T.J. Judge, K.Wilamowska, and L.G. Shapiro. A graphicaluser interface for a comparative anatomy information system: design, implementationand usage scenarios. In AMIA Symposium Proceedings, pages 774–778, 2006.Google Scholar
  88. 88.
    R.S. Travillian, C. Rosse, and L.G. Shapiro. An approach to the anatomical correlation ofspecies through the foundational model of anatomy. In AMIA Symposium Proceedings,pages 669–673, 2003.Google Scholar
  89. 89.
    R. Trelease. Anatomical reasoning in the informatics age: Principles, ontologies andagendas. Anat Rec B New Anat., 289:72–84, 2006.Google Scholar
  90. 90.
    M. Tringali, W.T. Hole, and S. Srinivasan. Integration of a standard gastrointestinalendoscopy terminology in the UMLS metathesaurus. In AMIA Symposium Proceedings,pages 801–805, 2002.Google Scholar
  91. 91.
    Unified Medical Language System.http://www.nlm.nih.gov/research/umls/umlsmain.html.Google Scholar
  92. 92.
    Visible Human.http://www.nlm.nih.gov/research/visible/visible human.html.Google Scholar
  93. 93.
    P.L. Williams, L.H. Bannister, M.M. Berry, P. Collins, M. Dyson, J.E. Dussec, andM.W.J. Ferguson. Gray’s Anatomy. Churchill Livingstone, New York, 38th edition,1995.Google Scholar
  94. 94.
    WordNet.http://wordnet.princeton.edu/.Google Scholar
  95. 95.
    L. Zhang, Y. Perl, J. Geller, M. Halper, and J.J. Cimino. Enriching the structure of theUMLS semantic network. In AMIA Symposium Proceedings, pages 939–943, 2002.Google Scholar
  96. 96.
    L. Zhang, Y. Perl, M. Halper, and J. Geller. Designing metaschemas for the UMLSenriched semantic network. J Biomed Inform, 36:433–449, 2003.CrossRefGoogle Scholar
  97. 97.
    S. Zhang and O. Bodenreider. Aligning representations of anatomy using lexical andstructural methods. In AMIA Symposium Proceedings, pages 753–757, 2003.Google Scholar
  98. 98.
    S. Zhang and O. Bodenreider. Alignment of multiple ontologies of anatomy: Derivingindirect mappings from direct mappings to a reference. In AMIA Symposium Proceedings,pages 864–868, 2005.4 The Foundational Model of Anatomy Ontology 111Google Scholar
  99. 99.
    S. Zhang and O. Bodenreider. Law and order: Assessing and enforcing compliancewith ontological modeling principles. Computers in Biology and Medicine, 36:674–693,2006.CrossRefGoogle Scholar
  100. 100.
    S. Zhang, O. Bodenreider, P. Mork, and P.A. Bernstein. Comparing two approaches foraligning representations of anatomy. Artificial Intelligence in Medicine, In press.Google Scholar

Copyright information

© Albert Burger, Duncan Davidson, Richard Baldock 2008

Authors and Affiliations

  • Cornelius Rosse
  • José L. V. MejinoJr

There are no affiliations available

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