Structural group-based auditing of missing hierarchical relationships in UMLS

Journal of Biomedical Informatics

Volumn 42, Issue 3, 2009, Pages 452-467

  Chen, Yan ^a   Perl, Yehoshua ^b   Geller, James ^b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b NEW JERSEY INSTITUTE OF TECHNOLOGY   (United States)

^c Helen)   (United States)

Author keywords

Auditing; Hierarchical relationships; Partition; Refined semantic network; Refined semantic type; Semantic refinement; Semantic type assignment; UMLS

Indexed keywords

AUDITING; HIERARCHICAL RELATIONSHIPS; PARTITION; REFINED SEMANTIC NETWORK; REFINED SEMANTIC TYPE; SEMANTIC REFINEMENT; SEMANTIC TYPE ASSIGNMENT; UMLS;

REFINING; TERMINOLOGY;

SEMANTICS;

ARTICLE; CLASSIFICATION ALGORITHM; CONCEPT ANALYSIS; CONCEPT FORMATION; EXPERIMENTAL MODEL; HYPOTHESIS; KNOWLEDGE BASE; LINGUISTICS; MEDICAL INFORMATION SYSTEM; METHODOLOGY; NETWORK LEARNING; NOMENCLATURE; PRIORITY JOURNAL; RANDOM ERROR; SEMANTICS; VALIDATION PROCESS;

ALGORITHMS; MANAGEMENT AUDIT; UNIFIED MEDICAL LANGUAGE SYSTEM;

EID: 65649085898     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2008.08.006     Document Type: Article

References (50)

1. Humphreys B.L., Lindberg D.A.B., Schoolman H.M., and Barnett G.O. The Unified Medical Language System: an informatics research collaboration. JAMIA 5 1 (1998) 1-11
2. Schuyler P.L., Hole W.T., Tuttle M.S., and Sherertz D.D. The UMLS Metathesaurus: representing different views of biomedical concepts. Bull Med Libr Assoc 81 2 (1993) 217-222
3. US Dept. of Health and Human Services, National Institutes of Health, National Library of Medicine. Unified Medical Language System (UMLS) Available from: www.nlm.nih.gov/research/umls, 2008.
4. Cimino J.J. Auditing the Unified Medical Language System with semantic methods. JAMIA 5 (1998) 41-51
5. Cimino J.J., Min H., and Perl Y. Consistency across the hierarchies of the UMLS Semantic Network and Metathesaurus. JBI 36 6 (2003) 450-461
6. Chen Y., Perl Y., Geller J., and Cimino J.J. Analysis of a study of the users, uses and future agenda of the UMLS. JAMIA 14 2 (2007) 221-231
7. McCray AT, Hole WT. The scope and structure of the first version of the UMLS Semantic Network. In: Proc. Fourteenth Annual SCAMC, Institute of Electrical and Electronics Engineers, Los Alamitos, CA; 1990. p. 126-30.
8. McCray A.T. An upper-level ontology for the biomedical domain. Comp Funct Genomic 4 (2003) 80-84
9. McCray A.T., and Nelson S.J. The representation of meaning in the UMLS. Methods Inf Med 34 (1995) 193-201
10. Chen Y., Gu H., Perl Y., Geller J., and Halper M. Structural group-based auditing of UMLS semantic type assignments. JBI 42 (2009) 41-52
11. Geller J., Gu H., Perl Y., and Halper M. Semantic refinement and error correction in large terminological knowledge bases. Data Knowledge Eng 45 1 (2003) 1-32
12. Gu H., Perl Y., Geller J., Halper M., Liu L.M., and Cimino J.J. Representing the UMLS as an object-oriented database: modeling issues and advantages. JAMIA 7 1 (2000) 66-80
13. Cimino JJ. Battling Scylla and Charybdis: the search for redundancy and ambiguity in the 2001 UMLS Metathesaurus. In: Overhage JM, editor, Proc. 2001 AMIA Annual Symposium, 2001. p. 120-24.
14. Bodenreider O. Strength in numbers: exploring redundancy in hierarchical relations across biomedical terminologies. In: Proc. 2003 AMIA Annual Symposium, 2003. p. 101-5.
15. Bodenreider O. Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. In: Proc. AMIA Symposium, 2001. p. 57-61.
16. Mougin F, Bodenreider O. Approaches to eliminating cycles in the UMLS Metathesaurus: naive vs. formal. In Proc. 2005 AMIA Annual Symposium, 2005. p. 550-4.
17. Peng Y, Halper M, Perl Y, Geller J. Auditing the UMLS for redundant classifications. In: Proc. 2002 AMIA Annual Symposium, San Antonio, TX; 2002. p. 612-6.
18. Hole WT, Srinivasan S. Discovering missed synonymy in a large concept-oriented Metathesaurus. In: Overhage JM, editor, Proc. 2000 AMIA Annual Symposium, Los Angeles, CA; 2000. p. 354-8.
19. Schulze-Kremer S, Smith B, Kumar A. Revising the UMLS Semantic Network. In Proc. Medinfo2004, San Francisco, CA; 2004. p. 1700.
20. Zhang L., Perl Y., Geller J., Halper M., and Cimino J.J. An enriched UMLS Semantic Network with a multiple inheritance hierarchy. JAMIA 11 3 (2004) 195-206
21. Zhang L., Halper M., Perl Y., Geller J., and Cimino J.J. Relationship structures and semantic type assignments of the UMLS enriched semantic network. J Am Med Inform Assoc 12 6 (2005) 657-666
22. Min H., Perl Y., Chen Y., Halper M., Geller J., and Wang Y. Auditing as part of the terminology design life cycle. JAMIA 13 6 (2006) 676-690
23. Ceusters W, Smith B, Kumar A, Dhaen C. Mistakes in medical ontologies: where do they come from and how can they be detected? In: Pisanelli DM, editor, Ontologies in Medicine: Proc. Workshop on Medical Ontologies, Rome; 2003. p. 145-64.
24. Ceusters W, Smith B, Kumar A, Dhaen C. Ontology-based error detection in SNOMED-CT. In: Fieschi M, Coiera E, Li Y.-C, editors, Proc. Medinfo 2004, San Francisco, CA; 2004. p. 482-6.
25. Ceusters W., Smith B., and Goldberg L. A terminological and ontological analysis of the NCI Thesaurus. Methods Inf Med 44 (2005) 498-507
26. Ceusters W, Spackman KA, Smith B. Would SNOMED-CT benefit from realism-based ontology evolution? In: Teich JM, Suermondt J, Hripcsak G, editors, Proc. 2007 AMIA Annual Symposium, Chicago, IL; 2007. p. 105-9.
27. Wang Y., Halper M., Min H., Perl Y., Chen Y., and Spackman K.A. Structural methodologies for auditing SNOMED. J Biomed Inf 40 5 (2007) 561-581
28. Halper M, Wang Y, Min H, Chen Y, Hripcsak G, Perl Y, Spackman KA. Analysis of error concentrations in SNOMED. In: Teich JM, Suermondt J, Hripcsak G, editors, Proc. 2007 AMIA Annual Symposium, Chicago, IL; 2007. p. 314-8.
29. Bodenreider O, Smith B, Kumar A, Burgun A. Investigating subsumption in DL-based terminologies: a case study in SNOMED CT. In: Hahn U, Schulz S, Cornet R, editors, Proc. First Int'l Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), Whistler, Canada; 2004. p. 12-20.
30. In: Baader F., Calvanese D., McGuinness D.L., Nardi D., and Patel-Schneider P.F. (Eds). The description logic handbook: theory, implementation, and applications (2003), Cambridge University Press
31. Schlobach S., Huang Z., Cornet R., and Van Harmelen F. Debugging incoherent terminologies. J Autom Reasoning 39 (2007) 317-349
32. Cornet R., and Abu-Hanna A. Auditing description-logic-based medical terminological systems by detecting equivalent concept definitions. Int J Med Inf 77 5 (2008) 336-345
33. De Keizer N.F., Abu-Hanna A., Cornet R., Zwersloot-Schonk J.H., and Stoutenbeek C.P. Analysis and design of an ontology for intensive care diagnoses. Methods Inf Med 38 2 (1999) 102-112
34. Kohler J., Munn K., Rüegg A., Skusa A., and Smith B. Quality control for terms and definitions in ontologies and taxonomies. BMC Bioinformatics 7 (2006) 212
35. Kumar A, Smith B. The Unified Medical Language System and the Gene Ontology: some critical reflections. In: Günter A, Kruse R, Neumann B, editors, KI 2003, Advances in Artificial Intelligence, Lecture Notes in Artificial Intelligence 2821, Springer; 2003. p. 135-48.
36. Smith B, Williams J, Schulze-Kremer S. The ontology of the gene ontology. In: Musen MA, editor, Proc. 2003 AMIA Annual Symposium, Washington, DC; 2003. p. 609-13.
37. Smith B, Köhler J, Kumar A. On the application of formal principles to life science data: a case study in the Gene Ontology. In: Proc. DILS 2004 (Data Integration in the Life Sciences), Lecture Notes in Bioinformatics 2994, Springer; 2004. p. 79-94.
38. Kumar A, Smith B, Borgelt C. Dependence relationships between Gene Ontology terms based on TIGR Gene Product Annotations. In: Proc. third international workshop on computational terminology, 2004. p. 31-8.
39. Brachman R.J., and Schmolze J.G. An overview of the KL-ONE knowledge representation system. Cogn Sci (1985) 9
40. Schmolze J.G., and Lipkis T.A. Classification in the KL-ONE knowledge representation system. IJCAI 1 (1983) 330-331
41. Elke Angelika Rundensteiner. A classification algorithm for supporting object-oriented views. In: Proc. the third international conference on information and knowledge management, Gaithersburg, Maryland; 1994. p. 18-25.
42. Kaczmarek TS, Bates R, Robins G. Recent developments in NIKL. In: Proc. AAAI-86 Proceedings, 1986. p. 978-85.
43. Levesque H.J., and Brachman R. A fundamental tradeoff in knowledge representation and reasoning (1985), Morgan Kaufman Publishers, Los Altos, CA
44. Patel-Schneider P.F. Adding number restrictions to a four-valued terminological logic. AAAI (1988) 485-490
45. Peltason C, Nebel B, Luck KV, editor. Proc. of the international workshop on terminological logics. DFKI-D-91-13, 1991.
46. DBLP: description logic workshops. Available from: http://www.informatik.uni-trier.de/~ley/db/conf/dlog/index.html.
47. Nardi D, Brachman RJ. The description logic handbook: theory, implementation, and applications, an introduction to description logics. Cambridge University Press; 2003 [chapter 1].
48. Lomax J., and McCray A.T. Mapping the Gene Ontology into the Unified Medical Language System. Comp Funct Genomic 5 5 (2004) 345-361
49. Medical Subject Headings. Available from: http://www.nlm.nih.gov/mesh/.
50. National Cancer Insitute Thesaurus. http://www.nci.nih.gov/cancerinfo/terminologyresources.