Auditing description-logic-based medical terminological systems by detecting equivalent concept definitions

References 

1. de Keizer NF, Abu-Hanna A, Zwetsloot-Schonk JH. Understanding terminological systems. I. Terminology and typology. Methods Inform. Med. 2000;39(1):16–21
2. Rossi Mori A, Consorti F, Galeazzi E. Standards to support development of terminological systems for healthcare telematics. Methods Inform. Med. 1998;37(4–5):551–563
3. Cornelius Rosse JLV, Mejino . A reference ontology for biomedical informatics: the foundational model of anatomy. J. Biomed. Inform. 2003;36(6):478–500
   • MEDLINE
   • CrossRef
4. Harris MA, Clark J, Ireland A. The gene ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32(Database issue):D258–D261
5. Spackman KA. SNOMED CT milestones: endorsements are added to already-impressive standards credentials. Healthcare Inform. 2004;21(9):54, 56
6. Brown SH, Elkin PL, Rosenbloom ST. VA national drug file reference terminology: a cross-institutional content coverage study. In:  Fieschi M,  Coiera E,  Li J editor. Proceedings from Medinfo 2004, vol. 11. San Francisco, CA, USA. Amsterdam, The Netherlands: IOS Press; 2004;p. 477–481
7. Hartel FW, de Coronado S, Dionne R, Fragoso G, Golbeck J. Modeling a description logic vocabulary for cancer research. J. Biomed. Inform. 2005;38(2):114–129
   • MEDLINE
   • CrossRef
8. Cimino JJ. Desiderata for controlled medical vocabularies in the twenty-first century. Methods Inform. Med. 1998;37(4–5):394–403
9. Horridge M, Rector AL, Drummond N. OWL pizzas: common errors and common patterns from practical experience of teaching OWL-DL. In:  Motta E,  Shadbolt N,  Stutt A,  Gibbins N editor. European Knowledge Acquisition Workshop. Northamptonshire, UK: Springer Verlag; 2004;p. 63–81
10. Cornet R, Abu-Hanna A. Description logic-based methods for auditing frame-based medical terminological systems. Artif. Intell. Med. 2005;34(3):201–217
    • Abstract
    • Full Text
    • Full-Text PDF (317 KB)
    • CrossRef
11. Guarino N, Welty CA. Evaluating ontological decisions with OntoClean. Commun. ACM. 2002;45(2):61–65
12. Devanbu PT, Jones MA. The use of description logics in KBSE systems: experience report. In:  Fadini B,  Fadini B,  Osterweil L,  van Lamsweerde A editor. Proceedings of the 16th International Conference on Software Engineering. Sorrento, Italy. Los Alamitos, CA, USA: IEEE Computer Society Press; 1994;p. 23–35
13. Cimino JJ. Auditing the unified medical language system with semantic methods. J. Am. Med. Inform. Assoc. 1998;5(1):41–51
    • MEDLINE
    • CrossRef
14. Hole WT, Srinivasan S. Discovering missed synonymy in a large concept-oriented metathesaurus. In:  Marc Overhage J editors. Proceedings of the 2000 AMIA Annual Symposium. Los Angeles, CA, USA. Philadelphia, PA, USA: Hanley and Belfus Inc.; 2000;p. 354–358
15. Gu H, Perl Y, Elhanan G. Auditing concept categorizations in the UMLS. Artif. Intell. Med. 2004;31(1):29–44
    • Abstract
    • Full Text
    • Full-Text PDF (195 KB)
    • CrossRef
16. Geller J, Gu H, Perl Y, Halper M. Semantic refinement and error correction in large terminological knowledge bases. Data Knowledge Eng. 2003;45(1):1–32
17. Yeh I, Karp PD, Noy NF, Altman RB. Knowledge acquisition, consistency checking and concurrency control for gene ontology (GO). Bioinformatics. 2003;19(2):241–248
    • MEDLINE
    • CrossRef
18. Abu-Hanna A, Cornet R, de Keizer N, Crubezy M, Tu S. Protégé as a vehicle for developing medical terminological systems. Int. J. Hum. Comput. Stud. 2005;62(5):639–663
19. Ceusters W, Smith B, Kumar A, Dhaen C. Mistakes in medical ontologies: where do they come from and how can they be detected?. Stud. Health Technol. Inform. 2004;102:145–163
    • MEDLINE
20. Ceusters W, Smith B, Kumar A, Dhaen C. Ontology-based error detection in SNOMED-CT^®. In:  Fieschi M,  Coiera E,  Li J editor. Proceedings from Medinfo 2004, vol. 11. San Francisco, CA, USA. Amsterdam, The Netherlands: IOS Press; 2004;p. 482–486
21. Van Buggenhout C, Ceusters W. A novel view on information content of concepts in a large ontology and a view on the structure and the quality of the ontology. Int. J. Med. Inform. 2005;74(2–4):125–132
    • Abstract
    • Full Text
    • Full-Text PDF (188 KB)
    • CrossRef
22. Simon J, Dos Santos M, Fielding J, Smith B. Formal ontology for natural language processing and the integration of biomedical databases. Int. J. Med. Inform. 2006;75(3–4):224–231
    • Abstract
    • Full Text
    • Full-Text PDF (105 KB)
    • CrossRef
23. Baader F, Calvanese D, McGuinness DL, Nardi D, Patel-Schneider PF. The Description Logic Handbook: Theory, Implementation, and Applications. Cambridge: University Press; 2003;
24. A.L. Rector, Coordinating taxonomies: key to reusable concept representations, in: P. Barahona, M. Stefanelli, J. Wyatt (Eds.), Proceedings of the Fifth Conference on Artificial Intelligence in Medicine in Europe, AIME, Pavia, Italy, Lecture Notes in Artificial Intelligence, Springer-Verlag, 1995, pp. 17–28.
25. Doyle J, Patil R. Two theses of knowledge representation: Language restrictions, taxonomic classifications, and the utility of representation services. Artif. Intell. 1991;48(3):261–298
26. Rector AL. Modularisation of domain ontologies implemented in description logics and related formalisms including OWL. In:  Gennari J,  Porter B editor. International Conference on Knowledge Capture. Sanibel, FL, USA. New York, USA: ACM Press; 2003;p. 121–128
27. Gu H, Perl Y, Geller J, Halper M, Singh M. A methodology for partitioning a vocabulary hierarchy into trees. Artif. Intell. Med. 1999;15(1):77–98
    • Abstract
    • Full Text
    • Full-Text PDF (399 KB)
    • CrossRef
28. Bodenreider O, Smith B, Kumar A, Burgun A. Investigating subsumption in DL-based terminologies: a case study in SNOMED CT. In:  Hahn U editors. KR 2004 Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004). Whistler, BC, Canada. AMIA; 2004;p. 12–20
29. de Keizer NF, Abu-Hanna A, Cornet R, Zwetsloot-Schonk JH, Stoutenbeek CP. Analysis and design of an ontology for intensive care diagnoses. Methods Inform. Med. 1999;38(2):102–112
30. P.F. Patel-Schneider, B. Swartout. Description-logic knowledge representation system specification from the KRSS group of the ARPA knowledge sharing effort. Technical Report, KRSS Group of the ARPA Knowledge Sharing Effort, November 1, 1993.
31. Cornet R, Abu-Hanna A. Using non-primitive concept definitions for improving DL-based knowledge bases. In:  Haarslev V,  Möller R editor. Proceedings of the 2004 International Workshop on Description Logics, DL2004, vol. 104. Whistler, Canada. Aachen, Germany: CEUR-WS; 2004;p. 138–147
32. N. F. Noy, W. E. Grosso, and M. A. Musen. Knowledge-acquisition interfaces for domain experts: an empirical evaluation of protégé-2000, in: S.-K. Chang (Ed.), Proceedings of the 12th International Conference on Software Engineering and Knowledge Engineering (SEKE2000), SMI Technical Report SMI-2000-0825, Chicago, IL, 2000, pp. 177–186.