Issues in the Design of Medical Ontologies Used for Knowledge Sharing
Tóm tắt
Recent work in Medical Informatics is exploring the development and the use of formal ontologies as a way of specifying content-specific agreements for the sharing and reuse of knowledge among several computer systems. We describe the role of ontologies in supporting knowledge sharing activities in medicine Principles for the design of ontologies have been proposed, mainly in other domains: these principles include parsimony, clarity, representation of categories versus terms, and coherence. We analyze how and why these principles can or cannot be applied from case studies from medical systems. Regarding the fact that most of medical concepts are empirical, selected design decisions are discussed. An alternative representation choice consists in mapping principled general core ontologies and domain ontologies.
Tài liệu tham khảo
McCray, A. T., Scherrer, J. R., Safran, C., and Chute, C. G., Concepts, knowledge, and language in health-care information systems. Methods Inf. Med. 34:1/2, 1–4, 1995.
Guarino, N., Ontologies and knowledge bases: Towards a terminological clarification, In Towards Very Large Knowledge bases (N. J. I. Mars, ed. ), IOS Press, 1995 (Available at http://www.ladseb. pd. cnr. it/Infor/Ontology/Papers/OntologyPapers. html)
Gruber, T. R., A translation approach to portable ontology specifications. Knowledge Acquisition 5(2):199–220, 1993.
Chandrasekaran, B., Josephson, J. R., and Benjamins, V. R., Ontologies: what are they? Why do we need them? IEEE Intelligent Systems 14(1):20–26, 1999.
Rosch, E., Principles of categorization. In Cognition and Categorization, L. Erlbaum Associates, Hillsdale, NJ; 1978.
Musen, M. A., Dimensions of knowledge sharing and reuse. Comp. Biomed. Res. 25:435–467, 1994.
IEEE Standard Computer Dictionary: A Compilation of IEEE Standard Computer Glossaries, IEEE, 1990.
Staccini, P., Joubert, M., Fieschi, M., and Fieschi, D., Towards semantic integration within an existing medical information system. Medinfo 9 Pt 2:935–9, 1998.
Wiederhold, G., and Genesereth, M., The conceptual basis for mediation services. IEEE Expert 12(5):38–47, 1997.
Degoulet, P., Sauquet, D., Jaulent, M. C., Zapletal, E., and Lavril, M., Rationale and design considerations for a semantic mediator in health information systems. Methods Inf. Med. 37:518–26, 1998.
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G., Gene ontology: Tool for the unification of biology. Nat Genet. 25(1):25–9, 2000.
Giudicelli, V., and Lefranc, M. P., Ontology for immunogenetics: The IMGT-ONTOLOGY., Bioinformatics 15(12):1047–54, 1999.
Brigl, B., Ringleb, P., Steiner, T., Knaup, P., Hacke, W., and Haux, R., An integrated approach for a knowledge-based clinical workstation: architecture and experience. Methods Inf Med. 37(1):16–25, 1998.
Falasconi, S., Dazzi, L., Lanzola, G., Quaglini, S., Saracco, R., and Stefanelli, M., Towards cooperative patient management through organizational and medical ontologies. Methods Inf. Med. 37(4, 5):564–75, 1998.
Siregar, P., Sinteff, J. P., Chahine, M., and Lebeux, P., A cellular automata model of the heart and its coupling with a qualitative model. Comput Biomed. Res. 29(3):222–46, 1996.
Siregar, P., Sinteff, J. P., Julen, N., and Le Beux, P., An interactive 3D anisotropic cellular automata model of the heart. Comput. Biomed. Res. 31(5):323–47, 1998.
Reid, B., Meeting the information needs of an evidence-based world. Aust. Health Rev. 22(2):122–9, 1999.
Kaufman, C., Conway, S., and Gallagher, K. E., Health information resources: tradition and innovation in a medical school curriculum. Med. Ref. Serv. Q. 18(1):11–23, 1999.
Miller, N., Lacroix, E. M., and Backus, J. E., MEDLINEplus: Building and maintaining the National Library of Medicine's consumer health Web service. Bull. Med. Libr. Assoc. 88(1):11–7, 2000.
Bodenreider, O., Comment les usagers acc`edent `a l'information m´ edicale aux USA: l'exemple de Medlineplus. Communication Colloque CRISTAL'S Partage d'Information, Vannes, 16–17/09/99, ITBM to be published, 2000.
Breuker, Valente, A., Towards principled core ontologies. In Proceedings of the Tenth Knowledge Acquisition for Knowledge-Based Systems Workshop (KAW'96) (B. Gaines and M. Musen, eds. ) 1996.
Noy, N. F., and Hafner, C. D., The state of the art in ontology design. AI Magazine 18(3):53–74, 1999.
Gruber, T. R., Toward principles for the design of ontologies used for knowledge sharing. In Formal Ontology in Conceptual Analysis and Knowledge Representation (N. Guarino and R. Poli, eds. ), Kluwer Academic. http://www-ksl. stanford. edu/knowledge-sharing/papers/onto-design. rtf
Kayser, D., Ontologically yours, conceptual structures: Theory, tools and applications, lectures notes in artificial intelligence. Proceedings ICCS 98, 35–48, 1998.
Lenoir, P., Roger, M. L., Frangeul, C., and Chales, G., R´ ealisation, d´eveloppement et maintenance de la base de donn´ees ADM. Med. Informatics 6(1):51–56, 1981.
Seka, L. P., Fresnel, A., Delamarre, D., Riou, C., Burgun, A., Pouliquen, B., Duvauferrier, R., and Le Beux, P., Computer assisted medical diagnosis using the Web. Int. J. Med. Inf. 47(1, 2):51–6, 1997.
Humphreys, B. L., McCray, A. T., and Cheh, M. L., Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary test. J. Am. Med. Inform. Assoc. 4(6):484–500, 1997.
McCray, A. T., and Browne, A. C., Discovering the modifiers in a terminology data set. J. Am. Med. Inform. Assoc. 1998 AMIA Annual Fall Symposium, 780–4, 1998.
Multilingual HYpertextual Thesaurus for Healthcare, http://zeus. eulogos. it/itb/
Rector, A. L., Gangemi, A., Galeazzi, E., Glowinski, A. J., and Rossi-Mori, A., The GALEN CORE model schemata for anatomy: towards a reusable application-independent model of medical concepts. Proceedings of MIE 94, 229–233, 1994.
Burgun, A., Denier, P., Bodenreider, O., Botti, G., Delamarre, D., Pouliquen, B., Oberlin, P., Leveque, J. M., Lukacs, B., Kohler, F., Fieschi, M., and Le Beux, P., A Web terminology server using UMLS for the description of medical procedures. J. Am. Med. Inform. Assoc. 4(5):356–63, 1997.
National Library of Medicine. UMLS Knowledge Sources (11th edition), National Library of Medicine, Bethesda, MD; 2000.
McCray, A. T., and Nelson, S. J., The representation of meaning in the UMLS. Methods Inf. Med. 34(1/2):193–201, 1995.
Bodenreider, O., Burgun, A., Botti, G., Fieschi, M., Le Beux, P., and Kohler, F., Evaluation of the Unified Medical Language System as a medical knowledge source. J. Am. Med. Inform. Assoc. 5(1):76–87, 1998.
Cimino, J. J., Auditing the Unified Medical Language System with semantic methods.J. Am. Med. Inform. Assoc. 5:41–51, 1998.
Rosch, E., Mervis, C., and Gray, W., Basic objects in natural categories. Cognitive Psychology 8:382–439, 1976.
Burgun, A., Botti, G., Bodenreider, O., Delamarre, D., Leveque, J. M., Lukacs, B., Mayeux, D., Bremond, M., Kohler, F., Fieschi, M., and Le Beux, P., Methodology for using the UMLS as a background knowledge for the description of surgical procedures. Int. J. Biomed. Comput. 43(3):189–202, 1996.
Zweigenbaum, P., Bachimont, B., Bouaud, J., Charlet, J., and Boisvieux, J. F., Issues in structuring and acquisition of an ontology for medical language understanding. Methods Inf. Med. 34(1/2):15–24, 1995.
Zweigenbaum, P., MENELAS:Anaccess system for medical records using natural language. Comput. Methods Programs Biomed. 45(1, 2):117–20, 1994.
Van Heijst, G., The role of ontologies in knowledge engineering, PhDthesis, University of Amsterdam, 1995.
Ribi`ere, M., Using viewpoints andCGfor the representation and management of a corporate memory in concurrent engineering. Proceedings of ICCS'98, Lecture Notes in Artificial Intelligence, 94–108, 1998.
Gruber, T. R., and Olsen, G. R., An ontology for engineering mathematics. Fourth International Conference on Principles of Knowledge Representation and Reasoning, (J. Doyle, P. Torasso, and E. Sandewall, eds. ), Germany, MorganKaufmann, 1994.http://www-ksl. stanford. edu/knowledgesharing/ papers/engmath. html
Rosse, C., Shapiro, L. G., and Brinckley, J. F., The digital anatomist model: Principles for defining and structuring its concept domain. J. Am. Med. Inform. Assoc. AMIA'98 Symp. Suppl. 820–824, 1998.
Rosse, C., Mejino, J. L., Modayur, B. R., Jakobovits, R., Hinshaw, K., and Brinkley, J. F., Motivation and organizational principles for anatomical knowledge representation: The Digital Anatomist Symbolic Knowledge Base. J. Am. Med. Inform. Assoc. 5:17–40, 1998.
Mejino, J. L. V., and Rosse, C., The potential of the Digital Anatomist Foundation Model for assuring consistency in UMLS sources. J. Am. Med. Inform. Assoc. 1998 AMIA Annual Fall Symp. 423–427, 1998.
Mejino, J. L., Jr., and Rosse, C., Conceptualization of anatomical spatial entities in the Digital Anatomist Foundational Model. J. Am. Med. Inform. Assoc. 1999 AMIA Annual Fall Symp. 112–6, 1999.
Sowa, J. F., Knowledge Representation: Logical, Philosophical and Computational Foundations, Brooks/Cole, Pacific Grove, CA; 2000.