Abstract
GALEN seeks to provide re-usable terminology resources for clinical systems. The heart of GALEN is the Common Reference Model (CRM) formulated in a specialised description logic. The CRM is based on a set of principles that have evolved over the period of the project and illustrate key issues to be addressed by any large medical ontology. The principles on which the CRM is based are discussed followed by a more detailed look at the actual mechanisms employed. Finally the structure is compared with other biomedical ontologies in use or proposed.
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References
Artale, A., Franconi, E., Guarino, N.: Open problems for part-whole relations. In: International Workshop on Descripition Logics, Boston, MA (1996)
Artale, A., Franconi, E., Pazzi, L.: Part-whole relations in object-centered systems: An overview. Data and Knowledge Engineering 20, 347–383 (1996)
Bateman, J.A.: Upper modelling: A general organization of knowledge for natural language processing. USC/Information Sciences Institute (1989)
Bittner, T., Donnelly, M., Smith, B.: Individuals, Universals, collections: On the foundational relations of ontology. In: International Conference on Formal Ontology and Information Systems (FOIS 2004), Turin, Italy (2004)
Borgida, A.: Description logics in data management. IEEE Transactions on Knowledge and Data Engineering 7(5), 671–682 (1995)
Brachman, R., Levesque, H.: The tractability of subsumption in frame-based description languages. In: AAAI 1984. Morgan Kaufmann, San Francisco (1984)
Brachman, R.J., et al.: Living with Classic: When and how to use a KL-ONE-like language. In: Sowa, J. (ed.) Principles of Semantic Networks: Explorations in the representation of knowledge, pp. 401–456. Morgan Kaufmann, San Francisco (1991)
Brown, P., O’Neil, M., Price, C.: Semantic definition of disorders in Version 3 of the Read Codes. Methods of Information in Medicine 37, 415–419 (1998)
Casati, R., Varzi, A.C.: Parts and Places. In: Parts and Places: The Structurres of Spatial Representation. Clarendon Press, Oxford (1999)
Chute, C.: Clinical classification and terminology: Some history and current observations. Journal of the American Medical Informatics Association 7(3), 293–303 (2000)
Cimino, J.: Controlled Medical Vocabulary Construction: Methods from the Canon Group. Journal of the American Medical Informatics Association 1(3), 197–296 (1994)
Cimino, J.: Desiderata for controlled medical vocabularies in the twenty-first century. Methods of Information in Medicine 37(4-5), 394–403 (1998)
Degen, W., et al.: Formal Ontology in Information Systems (FOIS 2001) (2001)
Doyle, J., Patil, R.: Two theses of knowledge representation: Language restrictions, taxonomic classification and the utility of representation services. Artificial Intelligence 48, 261–297 (1991)
Etherington, D.: Formalising nonmonotonic reasoning systems. Artificial Intelligence 31, 41–85 (1987)
Evans, D.A., et al.: Position statement: Towards a medical concept representation language. Journal of the American Medical Informatics Association 1(3), 207–217 (1994)
Gangemi, A., Guarino, N., Masolo, C., Oltramari, A., Schneider, L.: Sweetening ontologies with DOLCE. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS, vol. 2473, p. 166. Springer, Heidelberg (2002)
Gruber, T.R.: Toward Principles for the Design of Ontologies Used for Knowledge Sharing. Knowledge Systems Laboratory, Stanford University (1993)
Guarino, N., Welty, C.: An overview of OntoClean. In: Staab, S., Studer, R. (eds.) Handbook of Ontologies, pp. 151–159. Springer, Heidelberg (2004)
Guarino, N., Welty, C.: Towards a methodology for ontology-based model engineering. In: ECOOP 2000 Workshop on Model Engineering, Cannes, France (2000)
Guha, R., Lenat, D.: Enabling agents to work together. Communications of the ACM 37, 127–142 (1994)
Haarslev, V., Moeller, R.: Expresive ABox reasoning with number restrictions, role hierarchies, and transitively closed roes. In: Proceedings of the Seventh International Conference on Knowledge Representation and Reasoning (KR 2000). Morgan Kaufmann, San Francisco (2000)
Hahn, U., Romacker, M., Schulz, S.: How knowledge drives understanding - matching medical ontologies with the needs of medical language processing. Artificial Intelligence in Medicine 15(1), 25–52 (1999)
Hahn, U., Schulz, S., Romacker, M.: Part-whole reasoning: a case study in medical ontology engineering. IEEE Intelligent Systems and their Applications 14(5), 59–67 (1999)
Hahn, U., Schulz, S., Romacker, M.: Partonomic reasoning as taxonomic reasoning in medicine. In: Proc. of the 16th National Conf. on Artificial Intelligence & 11th Innovative Applications of Artificial Intelligence (AAAI 1999/IAAI 1999). AAAI Press/MIT Press, Orlando FL (1999)
Hardiker, N.R., Rector, A.L.: Modeling nursing terminology using the GRAIL representation language. Journal of the American Medical Informatics Association 5, 120–128 (1998)
Horrocks, I.: Optimising Tableaux Decision Procedures for Description Logics, in Computer Science, p. 176. University of Manchester, Manchester (1997)
Horrocks, I.: Using an expressive description logic: FaCT or Fiction in Principles of Knowledge Representation and Reasoning. In: Proceedings of the Sixth International Conference on Knowledge Representation (KR 1998). Morgan Kaufmann, San Francisco (1998)
Horrocks, I., Sattler, U.: The decidability of SHIQ with complex role inclusion axioms. Artificial Intelligence 160(102), 79–104 (2004)
Kirby, J., Rector, A.L.: The PEN&PAD Data Entry System: From prototype to practical system. In: AMIA Fall Symposium. Hanley and Belfus, Inc., Washington DC (1996)
Lenat, D.B., Guha, R.V.: Building Large Knowledge-Based Systems: Representation and inference in the Cyc Project, p. 372. Addison-Wesley, Reading (1989)
Martin, R.F., et al.: Foundational Model of Neuroanatomy:Implications for the Human Brain Project. In: AMIA Fall Symposium, Washington DC (2001)
Masolo, C., et al.: WonderWeb Deliveable 18. WonderWeb consortium (2003)
Mejino, J.L.V., Rosse, C.: Conceptualization of anatomical spatial entities in the Digital Anatomist Foundational Model. Journal of the American Medical Informatics Association (1999 Annual Symposium Special Issue), 112–116 (1999)
Mork, P., Bernstein, P.: Adapting a generic match algorithm to align ontologies of human anatomy. In: 20th International Conference on Data Engineering, Boston. IEEE, Los Alamitos (2004)
Mork, P., Pottinger, R., Bernstein, P.: Challenges in precisely aligning models of human anatomy. In: Proceedings of Medinfo 2004. IMIA, San Francisco (2004)
Neal, P.J., Shapiro, L.G., Rosse, C.: The Digital Anatomist structural abstraction: a scheme for the spatial description lf anatomical entities. Journal of the American Medical Informatics Association (Fall Symposium Special Issue), 423–427 (1998)
Nowlan, W.A.: Clinical workstation: Identifying clinical requirements and understanding clinical information. International Journal of Bio-Medical Computing 34, 85–94 (1994)
O’Neil, M., Payne, C., Read, J.: Read Codes Version 3: A user led terminology. Methods of Information in Medicine 34, 187–192 (1995)
Odell, J.J.: Six different kinds of composition. Journal of Object Oriented Programming 5(8), 10–15 (1994)
Padgham, L., Lambrix, P.: A framework for part-of hierarchies in terminological logics. In: KR 1994 (1994)
Rector, A.: Analysis of propagation along transitive roles: Formalisation of the GALEN experience with medical ontologies. In: CEUR-Proceedings 53, 2002 International Workshop on Description Logics (DL 2002), Toulouse France, p. 53 (2002)
Rector, A.: Coordinating taxonomies: Key to re-usable concept representations. In: Wyatt, J.C., Stefanelli, M., Barahona, P. (eds.) AIME 1995. LNCS, vol. 934. Springer, Heidelberg (1995)
Rector, A.: Modularisation of domain ontologies Implemented in description logics and related formalisms including OWL. In: Knowledge Capture 2003, Sanibel Island, FL. ACM, New York (2003)
Rector, A.: Thesauri and formal classifications: Terminologies for people and machines. Methods of Information in Medicine 37(4-5), 501–509 (1998)
Rector, A., et al.: The GRAIL concept modelling language for medical terminology. Artificial Intelligence in Medicine 9, 139–171 (1997)
Rector, A., et al.: Scale and Context: Issues in ontologies to link health- and bio-Informatics. In: AMIA Fall Symposium. Austin Texas, Hanley and Belfus, Philadelphia (2002)
Rector, A., et al.: Making sound re-usable terminology practical: The GALEN approach. In: Towards and Electronic Health Care Record, Europe 1998. Medical Records Institute, Newton Mass, London (1998)
Rector, A., et al.: A Terminology Server for Medical Language and Medical Information Systems. Methods of Information in Medicine 34, 147–157 (1995)
Rector, A., Taweel, A., Rogers, J.: Models and inference methods for clinical systems: A principled approach. In: Medinfo 2004. North Holland, San Francisco (2004)
Rector, A., et al.: GALEN: Terminology Services for Clinical Information Systems. In: Laires, M., Ladeira, M., Christensen, J. (eds.) Health in the New Communications Age, pp. 90–100. IOS Press, Amsterdam (1995)
Rector, A.L.: Clinical Terminology: Why is it so hard? Methods of Information in Medicine 38, 239–252 (1999)
Rector, A.L.: Defaults, context and knowledge: Alternatives for OWL-Indexed Knowledge bases. In: Pacific Symposium on Biocomputing (PSB-2004), Kona, Hawaii. World Scientific, Singapore (2004)
Rector, A.L.: The Interface between Information, Terminology, and Inference Models. In: Tenth World Conference on Medical and Health Informatics: Medinfo 2001, London, England (2001)
Rector, A.L., et al.: Interface of inference models with concept and medical record models. In: Artificial Intelligence in Medicine Europe (AIME), Cascais, Portugal. Springer, Heidelberg (2001)
Rector, A.L., et al.: Reconciling users’ needs and formal requirements: Issues in developing a re-usable ontology for medicine. IEEE Transactions on Information Technology in BioMedicine 2(4), 229–242 (1999)
Rodrigues, J.M., et al.: Galen-In-Use: An EU Project applied to the development of a new national coding system for surgical procedures: NCAM. In: Medical Informatics Europe 1997, Porto Carras, Greece. IOS Press, Amsterdam (1997)
Rogers, J., Rector, A.: The GALEN ontology. In: Medical Informatics Europe (MIE 1996), Copenhagen. IOS Press, Amsterdam (1996)
Rogers, J., Rector, A.: GALEN’s model of parts and wholes: Experience and comparisons. Journal of the American Medical Informatics Association (Fall symposium special issue), 819–823 (2000)
Rogers, J., et al.: From rubrics to dissections to GRAIL to classifications. In: Medical Informatics Europe (MIE 1997), Thesalonika, Greece. IOS Press, Amsterdam (1997)
Rogers, J.E.: Development of a methodology and an ontological schema for medical terminology. In: School of Medicine, Dentistry, Nursing and Pharmacy, p. 185. University of Manchester (2004)
Rogers, J.E., et al.: Validating clinical terminology structures: Integration and cross-validation of Read Thesaurus and GALEN. Journal of the American Medical Informatics Association (Fall Symposium Special Issue), 845–849 (1998)
Rosse, C., Shapiro, I.G., Brinkley, J.F.: The Digital Anatomist foundational model: Principles for defining and structuring its concept domain. Journal of the American Medical Informatics Association(1998 Fall Symposium Special issue), 820–824 (1998)
Schank, R.C., Abelson, R., Scripts, P.: Plans, Goals, and Understanding. Lawrence Erlbaum Associates, Hilsdale (1977)
Schulz, S., Hahn, U.: Mereotopological reasoning about parts and (w)holes in bio-ontologies. In: Formal Ontology in Information Systems (FOIS 2001). ACM, Ogunquit (2001)
Schulz, S., Hahn, U.: Parts, locations, and holes - Formal reasoning about anatomical structures. In: Quaglini, S., Barahona, P., Andreassen, S. (eds.) AIME 2001. LNCS, vol. 2101, p. 293. Springer, Heidelberg (2001)
Schulz, S., Hahn, U., Romacker, M.: Modeling anatomical spatial relations with description logics. In: AMIA Fall Symposium (AMIA 2000), Los Angeles, CA, Hanly & Belfus (2000)
Shahar, Y., et al.: A problem-solving architecture for managing temporal data and their abstractions. In: Workshop on Implementing Temporal Reasoning, AAAI 1992, San Jose, CA (1992)
Smith, B.: The basic tools of formal ontology. In: Formal Ontology in Information Systems (FOIS) (Frontiers in Artificial Intelligence and Applications). IOS Press, Amsterdam (1998)
Smith, B.: The logic of biological classification and the foundations of biomedical ontology. In: 10th International Conference in Logic Methodology and Philosophy of Science, Oviedo Spain. Elsevier-North-Holland (2004)
Solomon, W., Heathfield, H.: Conceptual modelling used to represent drug interactions. In: Twelfth International Congress of the European Federation for Medical Informatics, MIE 1994, Lisbon, Portugal (1994)
Solomon, W., et al.: A reference terminology for drugs. Journal of the American Medical Informatics Association (Fall Symposium Special Issue), 152–155 (1999)
Sowa, J.: Knowledge Representation. Morgan Kaufmann, San Francisco (1999)
Staab, S., Maedche, A.: Ontology engineering beyond the modeling of concepts and relations. In: ECAI 2000, 14th European Conference on Artificial Intelligence; Workshop on Applications of Ontologies and Problem Solving Methods (2000)
Stearns, M., et al.: SNOMED clinical terms: overview of the development process and project status. In: AMIA Fall Symposium (AMIA 2001), Henley & Belfus (2001)
The Gene Ontology Consortium, Creating the gene ontology resource: design and implementation. Genome Research 11, 1425–1433 (2001)
The Gene Ontology Consortium, Gene Ontology: tool for the unification of biology. Nature Genetics 25, 25–29 (2000)
Touretzky, D.: The Mathematics of Inheritance Systems. Morgan Kaufmann, Los Altos (1986)
Tuttle, M.S.: The position of the canon group: A reality check. Journal of the American Medical Informatics Association 1(3), 298–299 (1994)
United States Center for Health Statistics, International Classification of Diseases. In: Ninth Revision with Clinical Modifications. The Center, Washington (1980)
Uschold, M., Gruninger, M.: Ontologies: principles, methods and applications. Knowledge Engineering Review 11(2) (1996)
Varzi, A.C.: Mereological commitments. Dialectica 54, 283–305 (2000)
Welty, C., Guarino, N.: Supporting ontological analysis of taxonomic relationships. Data and Knowledge Engineering 39(1), 51–74 (2001)
Winston, M., Chaffin, R., Hermann, D.: A taxonomy of part-whole relations. Cognitive Science 11, 417–444 (1987)
Woods, W.: What’s important about knowledge representation? IEEE Computer 16, 22–29 (1983)
Wroe, C., Cimino, J.: Using openGALEN techniques to develop the HL7 drug formulation vocabulary. In: American Medical Informatics Association Fall Symposium(AMIA 2001) (2001)
Wroe, C., et al.: Inheritance of drug information. Journal of the American Medical Informatics Association (Annual Symposium Special Issue), 1158 (2000)
Zhang, S., Bodenreider, O.: Comparing associative concepts among equivalent concepts across ontologies. In: Medinfo 2004. IOS Press, San Francisco (2004)
Zhang, S., Bodenreider, O.: Investigating implicit knowledge in ontologies with application to the anatomical domain. In: Pacific Symposium on Bioinformatics (2004)
Zhang, S., Mork, P., Bodenreider, O.: Lessons learnned from aligning two representations of Anatomy. In: First international workshop on formal biomedical knowledge representation. Whistler, Canada (2004)
Zweigenbaum, P., et al.: Issues in the structuring and acquisition of an ontology for medical language understanding. Methods of Information in Medicine 34(1/2), 15–24 (1995)
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Rector, A., Rogers, J. (2006). Ontological and Practical Issues in Using a Description Logic to Represent Medical Concept Systems: Experience from GALEN. In: Barahona, P., Bry, F., Franconi, E., Henze, N., Sattler, U. (eds) Reasoning Web. Reasoning Web 2006. Lecture Notes in Computer Science, vol 4126. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11837787_9
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