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.
- Anatomical Structure
- Direct Part
- Anatomical Relation
- Anatomical Surface
- Reference Ontology
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Adult mouse anatomical dictionary browser.http://www.informatics.jax.org/searches/AMA form.shtml.
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.
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.
Aristotle. The categories.Harvard University Press, Cambridge, Mass., 1973.
A. Au, X. Li, and J.H. Gennari. Differences among cell structure ontologies: FMA, Goand CCO. In AMIA Symposium Proceedings, pages 16–20, 2006.
J. Bard, S.Y. Rhee, and M. Ashburner. An ontology for cell types. Genome Biology,6(R21), 2005.
J.B.L. Bard. Anatomics: the intersection of anatomy and bioinformatics. J Anat, pages1–16, 2005.
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.
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.
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.
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.
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.
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.
O. Bodenreider and S. Zhang. Comparing the representation of anatomy in the FMAand SNOMED CT. In AMIA Symposium Proceedings, pages 46–50, 2006.
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.
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.
M.B. Carpenter and J. Sutin. Human Neuroanatomy. Wilkins &Wilkins, Baltimore, 8th edition, 1983.
Cell type ontology.http://www.sanbi.ac.za/evoc/ontologies html/latest/celltype.html.
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 107
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.
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.
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.
Digital anatomist project - interactive atlases.http://www9.biostr.washington.edu/da.html.
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.
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.
Dorland’s medical dictionary.http://www.dorlands.com/.
Edinburgh developmental anatomy.http://www.ana.ed.ac.uk/anatomy/database/humat/.
D.W. Fawcett. Bloom and Fawcett Textbook of Histology. Chapman & Hall, NewYork,12th edition, 1994.
Federative Committee on Anatomical Terminology (FCAT). Terminologia Anatomica.Thieme, Stuttgart, 1998.
FMA in OWL-full format. Published on the Web.http://webrum.uni-mannheim.de/math/lski/release.html.
FMA open source.http://sig.biostr.washington.edu/cgi-bin/fma register.cgi.
Foundational Model Explorer.http://fme.biostr.washington.edu:8089/FME/index.html.
C. Golbreich, S. Zhang, and O. Bodenreider. The foundational model of anatomy inOWL: Experience and perspectives. Journal of Web Semantics, 4:181–195, 2006.
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.
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.
T.F. Hayamizu, M. Mangan, J.P. Corradi, J.A. Kadin, and M. Ringwald. Adult mouseanatomy dictionary. Genome Biology, 6(R29), 2005.
W.H. Hollinshead. Anatomy for surgeons, volume 1–3. Harper and Row, Philadelphia,3rd edition, 1982.
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.
IUPS Physionome Project - body systems.http://www.bioeng.auckland.ac.nz/physiome/anatomy.php.
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.
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.
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.
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.
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.
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.
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.
J.H. Martin. Neuroanatomy Text and Atlas. Appleton & Lange, Stamford, Connecticut,2nd edition, 1996.
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.
D. Marwede. RadiO. Personal Communication.
Medical Entities Dictionary.http://med.dmi.columbia.edu/.
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.
J.L.V. Mejino(Jr) and C. Rosse. Interactive radiology exercises.http://www9.biostr.washington.edu/hubio511/.
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.
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.
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.
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.
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 109
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.
C. Mungall. Personal Communication.
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.
S. Nelson. Personal Communication.
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.
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.
OBO - Open Biological Ontologies.htpp://obo.sourseforge.net.
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.
C. Rosse. Terminologia anatomica; considered from the perspective of next-generationknowledge sources. Clin. Anat., 14:120–133, 2001.
C. Rosse and P. Gaddum-Rosse. Hollinshead’s textbook of anatomy.Lippincott-Raven,Philadelphia, 5th edition, 1997.
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.
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.
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.
M.J. Schleiden. Beiträge zur Phytogenesis 1838. In Transactions in Sydenham Society,volume 12, London, 1838. Müller’s Archive 1838.
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.
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.
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.
B. Smith. Mereotopology: a theory of parts and boundaries. Data & Knowledge Engineering,20:287–303, 1996.
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.
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.
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.
B. Smith, A. Kumar, W. Ceusters, and C. Rosse. On carcinomas and other pathologicalenitities. Comp Funct Genom, 6:379–387, 2005.
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.
B. Smith and C. Rosse. The role of foundational relations in the alignment of biomedicalterminologies. In Proceedings of MedInfo, pages 444–448, 2004.
C.A. Sneiderman, T.C. Rindflesch, and C.A. Bean. Identification of anatomical terminologyin medical text. In AMIA Symposium Proceedings, pages 428–32, 1998.
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.
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.
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.
R. Trelease. Anatomical reasoning in the informatics age: Principles, ontologies andagendas. Anat Rec B New Anat., 289:72–84, 2006.
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.
Unified Medical Language System.http://www.nlm.nih.gov/research/umls/umlsmain.html.
Visible Human.http://www.nlm.nih.gov/research/visible/visible human.html.
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.
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.
L. Zhang, Y. Perl, M. Halper, and J. Geller. Designing metaschemas for the UMLSenriched semantic network. J Biomed Inform, 36:433–449, 2003.
S. Zhang and O. Bodenreider. Aligning representations of anatomy using lexical andstructural methods. In AMIA Symposium Proceedings, pages 753–757, 2003.
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 111
S. Zhang and O. Bodenreider. Law and order: Assessing and enforcing compliancewith ontological modeling principles. Computers in Biology and Medicine, 36:674–693,2006.
S. Zhang, O. Bodenreider, P. Mork, and P.A. Bernstein. Comparing two approaches foraligning representations of anatomy. Artificial Intelligence in Medicine, In press.
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© 2008 Albert Burger, Duncan Davidson, Richard Baldock
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Rosse, C., Mejino, J.L.V. (2008). The Foundational Model of Anatomy Ontology. In: Burger, A., Davidson, D., Baldock, R. (eds) Anatomy Ontologies for Bioinformatics. Computational Biology, vol 6. Springer, London. https://doi.org/10.1007/978-1-84628-885-2_4
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