Summary
It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is_a’ and ‘part_of’. While this chapter is mainly concerned with the general issues of methodology, chapter 15, on ‘Spatial Representation and Reasoning’, will apply the methodology to the specific case of spatial relations. Although both chapters are self-contained, we recommend that they be seen as forming a unity.
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References
M. Donnelly, T. Bittner, and C. Rosse. A formal theory for spatial representation and reasoning in bio-medical ontologies. Artificial Intelligence in Medicine, 36(1):1–27, 2006.
N Guarino. Formal Ontology and Information Systems. In N Guarino (ed.), Proceedings of the 1st International Conference on Formal Ontologies in Information Systems, FOIS’98, IOS Press, Trento, 3-15, 1998.
I. Johansson. On the Transitivity of the Parthood Relations. In H. Hochberg and K. Mulligan (eds.), Relations and Predicates, 161-181, 2004.
C Rosse, JL Mejino, BR Modayur, R Jakobovits, KP Hinshaw, JF Brinkley. Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base. Journal of the American Medical Informatics Association, 5(1):17-40, 1998.
F de Saussure. Course In General Linguistics. McGraw-Hill, New York, 1965.
P. Simons. Parts, A Study in Ontology. Clarendon Press, Oxford, 1987.
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. Gnome Biology, 6(5):46, 2005.
B Smith, A Kumar, W Ceusters, C Rosse. On carcinomas and other pathological entities. Comparative and Functional Genomics, vol 6, 7-8, 379-387, 2005.
B Smith, W Kusnierczyk, D Schober, W Ceusters. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KRMED 2006, O. Bodenreider, ed., Proceedings of KR-MED, http://ceur-ws.org/Vol-222, 57-66, 2006.
B. Smith and C. Rosse. The Role of Foundational Relations in the Alignment of Biomedical Ontologies. In M. Fieschi, et al. (eds.), Medinfo 2004, IOS Press, Amsterdam, 444-448, 2004.
J Trier. Aufsätze und Vorträge zur Wortfeldtheorie. Berlin: DeGruyter, 1973.
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© 2008 Albert Burger, Duncan Davidson, Richard Baldock
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Neuhaus, F., Smith, B. (2008). Modelling Principles and Methodologies – Relations in Anatomical Ontologies. 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_14
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DOI: https://doi.org/10.1007/978-1-84628-885-2_14
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