Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine

IEEE Transactions on Information Technology in Biomedicine

Volumn 2, Issue 4, 1998, Pages 229-242

  Rector, Alan L ^b   Zanstra, Pieter E ^c   Solomon, W Daniel ^b   Rogers, Jeremy E ^b   Baud, Robert ^e   Ceusters, Werner ^a,f   Claassen, Wim ^c   Kirby, J ^g   Rodrigues, Jean Marie ^d   Mori, Angelo Rossi ^h   Van Der Haring, Egbert J ^c   Wagner, Judith ^e  

^a IEEE   (Belgium)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^d UNIVERSITÉ JEAN MONNET   (France)

^e GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^f Office Line Engineering   (Belgium)

^g Enterprise House   (United Kingdom)

^h CNR   (Italy)

Author keywords

Medical expert systems; Medical information systems; Terminology

Indexed keywords

ARTICLE; CLASSIFICATION; CLINICAL MEDICINE; GENERAL ASPECTS OF DISEASE; NOMENCLATURE;

CLINICAL MEDICINE; DISEASE; TERMINOLOGY;

EXPERT SYSTEMS; FORMAL LOGIC; HEALTH CARE; INFORMATION SCIENCE; NATURAL LANGUAGE PROCESSING SYSTEMS; TERMINOLOGY;

DESCRIPTION LOGICS; MEDICAL INFORMATION SYSTEMS; REUSABLE ONTOLOGY;

MEDICAL COMPUTING;

EID: 0032216446     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/4233.737578     Document Type: Article

References (61)

1. D. A. Evans, J. Cimino, W. R. Hersh, S. M. Huff, D. S. Bell, and The Canon Group, "Position Statement: Toward a medical concept representation language," J. Amer. Med. Inform. Assoc., vol. 1, pp. 207-217, 1994.
2. J. Cimino, "Controlled medical vocabulary construction: Methods from the Canon group," J. Amer. Med. Inform. Assoc., vol. 1, pp. 296-197, 1994.
3. _, "Desiderata for controlled medical vocabularies in the twentyfirst century," Meth. Inform. Med., 1997.
4. K. E. Campbell, A. K. Das, and M. A. Musen, "A logical foundation for representation of clinical data," J. Amer. Med. Inform. Assoc., vol. 1, pp. 218-232, 1994.
5. K. A. Spackman, K. E. Campbell, and R. A. Côté, A reference terminology for health care," J. Amer. Med. Inform. Assoc., Symposium Special Issue, pp. 640-644, 1997.
6. A. Rector, P. Zanstra, W. Solomon, and The GALEN Consortium, "GALEN: Terminology services for clinical information systems," in Health in the New Communications Age, M. Laires, M. Ladeira, and J. Christensen, Eds. Amsterdam, The Netherlands: IOS, 1995, pp. 90-100.
7. D. F. Sittig, "Grand challenges in medical informatics," J. Amer. Med. Inform. Assoc., vol. 1, pp. 412-113, 1994.
8. R. MacGregor, "The evolving technology of classification-based knowledge representation systems," in Principles of Semantic Networks: Explorations in the Representation of Knowledge, J. Sowa, Ed. San Mateo, CA: Morgan Kaufmann, 1991, pp. 385-400.
9. F. Baader, H.-J. Heinsohn, B. Hollunder, J. Muller, B. Nebel, W. Nutt, and H.-J. Profitlich, "Terminological knowledge representation: A proposal for a terminological logic," DKFI, Tech. Memo TM-90-04, 1991.
10. J. Sowa, Conceptual Structures: Knowledge Representation in Mind and Machine. New York: Wiley, 1985.
11. P. Zweigenbaum, B. Bachimont, J. Bouaud, and J. Charlet, "Issues in the structuring and acquisition of an ontology for medical language understanding," Meth. Inform. Med., vol. 34, pp. 15-24, 1995.
12. U. Hahn, M. Romacker, and S. Schulz, "How knowledge drives understanding-Matching medical ontologies with the needs of medical language processing," Artif. Intell. Med., 1998, in press.
13. R. Brachman and J. B. Schmölze, "An overview of the KL-ONE knowledge representation system," Cogn. Sei., vol. 9, pp. 171-216, 1985.
14. R. J. Brachman, D. L. McGuinness, P. F. Patel-Schneider, L. A. Resnick, and A. Borgida, "Living with classic: When and how to use a KL-ONElike language," in Principles of Semantic Networks: Explorations in the Representation of Knowledge, J. Sowa, Ed. San Mateo, CA: Morgan Kaufmann, 1991, pp. 401-456.
15. R. MacGregor, "Inside the LOOM description classifier," SIGART Bull., vol. 2, pp. 88-92, 1991.
16. B. Nebel, "Computational complexity of terminological reasoning in back," Artif. Intell, vol. 34, pp. 371-383, 1988.
17. N. Guarino and P. Giaretta, "Ontologies and knowledge bases: Toward a terminological clarification," in Toward Very Large Knowledge Bases, N. Mars, Ed. Amsterdam, The Netherlands: IOS, 1995, pp. 25-32.
18. W. Nowlan, S. Kay, A. Rector, B. Horan, and A. Wilson, "PEN&PAD: A multi-lingual patient care workstation based on a unified representation of the medical record and medical terminology," in Proc. Med. Inform. Europe (MIE'91). Vienna, Austria: Springer-Verlag, pp. 1043-1048.
19. J. Kirby and A. L. Rector, "The PEN&PAD data entry system: From prototype to practical system," in Proc. AMIA Fall Symp. Washington DC: Hanley and Belfus, 1996, pp. 709-713.
20. J. Rogers and A. L. Rector, "Terminological systems: Bridging the generation gap," J. Amer. Med. Inform. Assoc., AMIA Fall Symposium special issue, pp. 610-614, 1997.
21. J. Rogers, D. Solomon, A. Rector, and P. Zanstra, "From rubrics to dissections to GRAIL to classifications," in Proc. Med. Inform. Europe (MIE'97). Thessaloniki, Greece: IOS, pp. 241-245.
22. E. Galeazzi, A. Rossi Mori, F. Consorti, A. Errera, and P. Merialdo, "A cooperative methodology to build conceptual models in medicine," in Proc. Med. Inform. Europe'97. Porto Carras, Greece: IOS, pp. 280-284.
23. E. Galeazzi, A. Rossi Mori, F. Consorti, and A. Errera, "MEDITA: The reference methodology for cooperative production of dissections by terminological analysis," GALEN-IN-USE Int. Rep. GIU/MET-1/97 version 1.1, available from GALEN, 1997.
24. A. Rossi Mori, A. Gangemi, G. Steve, F. Consorti, and E. Galeazzi, "An ontological analysis of surgical deeds," in Proc. Artif. Intell. Med. Europe (AIME'97), Grenoble, France.
25. J. Cimino and P. D. Clayton, "Coping with changing controlled vocabularies," in Proc. 18th Annu. Symp. Comput. Applicat. Med. Care. Washington, DC/Philadelphia PA: Hanley and Belfus, 1994, pp. 135-139.
26. K. Campbell, S. Cohn, C. Chute, G. Rennels, and E. Shortliffe, "Galapagos: Computer-based support for evolution of a convergent medical terminology," in Proc. AMIA Fall Symp. Washington DC: Hanley and Belfus, 1996, pp. 269-273.
27. D. E. Oliver, Y. Shahar, E. H. Shortliffe, and M. A. Musen, "Representing change in controlled medical vocabularies," Artif. Intell. Med., 1998.
28. W. Solomon and H. Heathfield, "Conceptual modeling used to represent drug interactions," in Proc. 12th Int. Congr. Eur. Fed. Med. Inform., MIE'94, Lisbon, Portugal, 1994, pp. 186-190.
29. A. Rector, S. Bechhofer, C. Goble, I. Horrocks, W. Nowlan, and W. Solomon, "The GRAIL concept modeling language for medical terminology," Artif. Intell. Med., vol. 9, pp. 139-171, 1997.
30. J. Rogers and A. Rector, "The GALEN ontology," in Proc. Med. Inform. Eur. (MIE'96). Copenhagen, Denmark: IOS, 1996, pp. 174-178.
31. A. Rector, A. Gangemi, E. Galeazzi, A. Glowinski, and A. Rossi Mori, "The GALEN CORE model schemata for anatomy: Toward a re-usable application-independent model of medical concepts," in Proc. 12th Int. Congr. Eur. Fed. Med. Inform., MIE'94, Lisbon, Portugal, 1994, pp. 229-233.
32. I. Horrocks and A. Rector, "Using a description logic with concept inclusions," in Proc. Int. Description Logics Workshop (DL'96). Menlo Park, CA/Cambridge, MA: AAAI Press, pp. 132-135.
33. I. Horrocks, "Comparison of two terminological knowledge representation systems," M.Sc. thesis, Univ. Manchester, U.K., 1995.
34. I. Horrocks, A. Rector, and C. Goble, "A description logic based schema for the classification of medical data," in Proc. Knowledge Representation Meets Data Bases (KRDB '96), Budapest, Hungary, 1996, pp. 24-28.
35. I. Horrocks, "Optimising tableaux decision procedures for description logics," Ph.D. dissertation, Comput. Sei., Univ. Manchester, U.K., 1997, p. 176.
36. A. Rossi Mori and CEN Project Team PT003, "Medical informatics-Categorial structure of systems of concepts-Model of representation of semantics (ENV12264)," CEN TC251 WG2, ENV ENV 12264, 1995.
37. J. Bateman, B. Magnini, and G. Fabris, "The generalized upper model knowledge base: Organization and use," in Toward Very Large Knowedge Bases, N. Mars, Ed. Amsterdam, The Netherlands: IOS, 1995, pp. 60-72.
38. P. Zanstra, W. Claassen, and E. v. d. Haring, "A natural language generator in Rois," LINKS. [Online] Available at http://ehm.kun.nl/mi/project/rois/newsltr/Links2/Paper4/paper4.htm, 1997.
39. J. Wagner, A.-M. Rassinoux, R. Baud, and J.-R. Scherrer, "Generating noun phrases from a medical knowledge representation," in Proc. 12th Int. Congr. Eur. Fed. Med. Inform., MIE'94, Lisbon, Portugal, 1994, pp. 218-223.
40. W. A. Nowlan, "Clinical workstation: Identifying clinical requirements and understanding clinical information," Int. J. Biomed. Comput., vol. 34, pp. 85-94, 1994.
41. R. H. Baud, J.-M. Rodrigues, J. C. Wagner, A.-M. Rassinoux, C. Lovis, P. Rush, B. Trombert-Paviot, and J.-R. Scherrer, "Validation of concept representation using natural language generation," J. Amer. Med. Inform. Assoc., Fall Symp. suppl., p. 841, 1997.
42. Y. Shahar, A. K. Das, S. W. Tu, and M. A. Musen, "Knowledge-based temporal abstraction in clinical-management tasks," in Proc. AAAI'94 Spring Symp. Artif. Intell. Med., Stanford, CA.
43. F. Baader, "Augmenting concept languages by transitive closure of roles: An alternative to terminological cycles," in Proc. Int. Joint Conf. Artif. Intell. (IJCAI'91). San Mateo, CA: Morgan Kaufmann, pp. 446-151.
44. B. R. Gaines, M. L. Shaw, and J. B. Woodward, "Modeling as framework for knowledge acquisition methodologies and tools," Int. J. Intell. Syst., vol. 8, pp. 155-168, 1993.
45. World Health Organization, International Classification of Diseases, Geneva, Switzerland, 1989.
46. R. Côté and D. Rothwell, SNOMED-Intemational, Coll. Amer. Pathologists, Chicago, IL, 1993.
47. J. Read, "The read clinical classification," NHS Centre for Coding and Classification, Loughborough, U.K., 1993.
48. J. A. Bateman, "Upper modeling: A general organization of knowledge for natural language processing," USC/Information Sciences Institute, Penman Development Note, 1989.
49. W. Ceusters, J. Rogers, F. Consorti, and A. Rossi-Mori, "Syntacticsemantic tagging as a mediator between linguistic representations and formal modals: An exercise in linking SNOMED to GALEN," Artif. Intell. Med., 1998.
50. A. Rossi-Mori, F. Consorti, E. Galeazzi, and P. Merialdo, "A second generation of terminological systems is coming," in Proc. Med. Inform. Europe'97. Porto Carras, Greece: IOS, 1997, pp. 436-440.
51. D. B. Lenat and R. V. Guha, Building Large Knowledge-Based Sys-terns: Representation and Inference in the Cyc Project. Reading, MA: Addison-Wesley, 1989.
52. F. Giunchiglia and R. Sebastian!, "A SAT-based decision procedure for ALC," in Proc. Principles Know!. Representation Reasoning: Proc. 5th Int. Conf. (KR'96). Boston, MA: Morgan Kaufmann, pp. 304-314.
53. W. Ceusters and P. Spyns, "From natural language to formal language: When MultiTALE meets GALEN," in Proc. Med. Inform. Europe'97. Amsterdam, The Netherlands: IOS, pp. 396-400.
54. C. Lovis, R. Baud, P.-A. Michel, and J.-R. Scherre, "Morphosemantic decomposition and semantic representation to allow fast and efficient natural language recognition," J. Amer. Med. Inform. Assoc., Fall Symp. suppl., p. 873, 1997.
55. A.-M. Rassinoux, "Modeling just the important and relevant concepts in medical language understanding," Meth. Inform. Med., 1998, in press.
56. R. Baud, C. Lovis, L. Alpay, A.-M. Rassinoux, J.-R. Scherrer, A. Nowlan, and A. Rector, "Modeling for natural language understanding," in Proc. 17th Anna. Symp. Comput. Applicat. Med. Care (SCAMC'93). Washington, DC: McGraw-Hill, pp. 289-293.
57. H. Gu, Y. Perl, and J. Geller, "A methodology for partitioning a vocabulary hierarchy into trees," Artif. Intell. Med., to be published.
58. L. Padgham and P. Lambrix, "A framework for part-of hierarchies in terminological logics," in Proc. KR'94, 1994, pp. 485-596.
59. J. Bernauer and H. Goldberg, "Compositional classification based on conceptual graphs," in Proc. Artif. Intell. Med. Eur. (AIME'93), Munich, 1993.
60. J. Smart and M. Roux, "Medical knowledge representation for medical report analysis," in Proc. 5th Conf. Artif. Intell. Med. Eur. (AIME'95). Pavia, Italy: Springer, pp. 53-66.
61. E. Franconi, G. DeGiacomo, R. M. MacGregor, W. Nutt, C. A. Welty, and F. Sebastian!, in Proc. Int. Workshop on Descripion Logics (DL'98) Trento, Italy. [Online] Available at http://anemosyne.itc.it/1024/dl/dl98, 1998.