Parts, Locations, and Holes — Formal Reasoning about Anatomical Structures

  • Stefan Schulz
  • Udo Hahn
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2101)


We propose an ontology engineering framework for the anatomy domain, focusing on mereotopological properties of parts, locations and empty spaces (holes). We develop and formally describe a basic ontology consisting of the mutually disjoint primitives solid object, hole and boundary. We embed the relations part-of and location-of into a parsimonious description logic (ALC) and emulate advanced reasoning across these relations — such as transitivity at the T-Box level — by taxonomic subsumption. Unlike common conceptualizations we do not distinguish between solids and the regions they occupy, as well as we allow solids to have holes as proper parts. Concrete examples from human anatomy are used to support our claims.


Description Logic Solid Object Formal Reasoning Cranial Cavity Basic 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.


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  1. 1.
    K. Campbell, A. Das, and Musen M. A logical foundation for representation of clinical data. JAMIA, 1(3):218–232, 1994.Google Scholar
  2. 2.
    R. Casati and A. Varzi. Holes and other Superficialities. MIT Press, 1994.Google Scholar
  3. 3.
    R. Casati and A. Varzi. Parts and Places. MIT Press, 1999.Google Scholar
  4. 4.
    D. Cruse. On the transitivity of the part-whole relation. J. of Linguistics, 15:29–38, 1979.CrossRefGoogle Scholar
  5. 5.
    FCAT. Terminologia Anatomica. Thieme-Verlag, 1998.Google Scholar
  6. 6.
    P. Gerstl and S. Pribbenow. Midwinters, end games and body parts: a classification of partwhole relations. International Journal of Human-Computer Studies, 43:865–889, 1995.CrossRefGoogle Scholar
  7. 7.
    U. Hahn, S. Schulz, and M. Romacker. Partonomic reasoning as taxonomic reasoning in medicine. In Proceedings of the AAAI’99, pages 271–276, 1999.Google Scholar
  8. 8.
    Udo Hahn, Martin Romacker, and Stefan Schulz. Discourse structures in medical reports-watch out! International Journal of Medical Informatics, 53(1):1–28, 1999.CrossRefGoogle Scholar
  9. 9.
    J. Mejino and C. Rosse. Conceptualization of anatomical spatial entities in the Digital Anatomist foundational model. In Proceedings of the AMIA’99, pages 112–116, 1999.Google Scholar
  10. 10.
    National Library of Medicine. Unified Medical Language System. Bethesda, MD: National Library of Medicine, 2001.Google Scholar
  11. 11.
    A. Rector, S. Bechhofer, C. Goble, I. Horrocks, W. Nowlan, and W. Solomon. The GRAIL concept modelling language for medical terminology. Artificial Intelligence in Medicine, 9:139–171, 1997.CrossRefGoogle Scholar
  12. 12.
    A. Rector, A. Gangemi, Galeazzi E., A. Glowinski, and Rossi-Mori A. The GALEN model schemata for anatomy. In Proceedings of the MIE’94, pages 229–233, 1994.Google Scholar
  13. 13.
    J. Rogers and A. Rector. GALEN’s model of parts and wholes: Experience and comparisons. In Proceedings of the AMIA 2000, pages 714–718, 2000.Google Scholar
  14. 14.
    C. Rosse, J. Mejino, B. Modayur, R. Jakobovits, K. Hinshaw, and J. Brinkley. Motivation and organizational principles for anatomical knowledge representation: The Digital Anatomist symbolic knowledge base. JAMIA, 5(1):17–40, 1998.Google Scholar
  15. 15.
    R. Schubert, K. Priesmeyer, H. Wulf, and K. Höhne. VOXEL-MAN(WEB) — Basistechnologie zur modellbasierten multimedialen Repräsentation von komplexen räumlichen Strukturen. Künstliche Intelligenz, 14(1):44–47, 2000.Google Scholar
  16. 16.
    S. Schulz and U. Hahn. Knowledge engineering by large-scale knowledge reuse: experience from the medical domain. In Proceedings of the KR 2000, pages 601–610, 2000.Google Scholar
  17. 17.
    S. Schulz, U. Hahn, and M. Romacker. Modeling anatomical spatial relations with description logics. In Proceedings of the AMIA 2000, pages 779–783, 2000.Google Scholar
  18. 18.
    K. Spackman and K. Campbell. Compositional concept representation using SNOMED: towards further convergence of clinical terminologies. In Proceedings of the AMIA 1998, pages 740–744, 1998.Google Scholar
  19. 19.
    A. Varzi. Parts, wholes, and part-whole relations: The prospects of mereotopology. Data & Knowledge Engineering, 20(3):259–268, 1996.zbMATHCrossRefGoogle Scholar
  20. 20.
    Morton Winston, Roger Chaffin, and Douglas J. Herrmann. A taxonomy of part-whole relationships. Cognitive Science, 11:417–444, 1987.CrossRefGoogle Scholar
  21. 21.
    W. Woods and J. Schmolze. The KL-ONE family. Computers & Mathematics with Applications, 23(2/5):133–177, 1992.zbMATHCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Stefan Schulz
    • 1
  • Udo Hahn
    • 2
  1. 1.Abteilung Medizinische InformatikUniversitätsklinikum FreiburgFreiburgGermany
  2. 2.Linguistische Informatik / ComputerlinguistikUniversität FreiburgGermany

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