Detecting role errors in the gene hierarchy of the NCI thesaurus

Cancer Informatics

Volumn 6, Issue , 2008, Pages 293-313

  Min, Hua ^a   Cohen, Barry ^b   Halper, Michael ^c   Oren, Marc ^b   Perl, Yehoshua ^b  

^a FOX CHASE CANCER CENTER   (United States)

^b University Heights   (United States)

^c KEAN UNIVERSITY   (United States)

Author keywords

Abstraction network; Auditing; Gene hierarchy; Gene terminology; National Cancer Institute Thesaurus (NCIT); Role error; Taxonomy

Indexed keywords

ARTICLE; CANCER RESEARCH; ERROR; GENE; HEALTH CARE ORGANIZATION; HUMAN; HUMAN GENOME PROJECT; MEDICAL INFORMATICS; NOMENCLATURE; NONHUMAN; QUALITY CONTROL; TAXONOMY; DRUG EFFICACY; GENOMICS; LINGUISTICS; NATIONAL HEALTH ORGANIZATION;

EID: 49649126844     PISSN: 11769351     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/cin.s440     Document Type: Article

References (30)

1. Baxevanis, A.D. 2003. The Molecular Biology Database Collection: 2003 update. Nucleic Acids Res., 31(1):1-12.
2. Brachman, R.J. and Levesque, H.J. 1984. The tractability of subsumption in frame based description languages, in 'Proc. AAAI-84', Austin, TX, pp. 34-7.
3. Brachman, R.J. and Schmolze, J. 1985. An overview of the KL-ONE knowledge representation system. Cognitive Science, 9(2):171-216.
4. College of American Pathologists. 2006. SNOMED Clinical Terms Reference Sets: Technical Specification (draft document).
5. Collins, F.S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R., Walters, L. et al. 1998. New goals for the U.S. human genome project: 1998-2003. Science, 282:682-9.
6. Covitz, P.A., Hartel, F.W., Schaefer, C., de Coronado, S., Fragoso, G., Sahni, H., Gustafson, S. and Buetow, K.H. 2003. caCORE: A common infrastructure for cancer informatics. Bioinformatics, 19(18):2404-12.
7. de Coronado, S., Haber, M.W., Sioutos, N., Tuttle, M.S. and Wright, L.W. 2004. NCI Thesaurus: Using science-based terminology to integrate cancer research results, in M. Fieschi, E. Coiera and Y.-C. Li, eds, Proc. Medinfo 2004, San Francisco, CA, pp. 33-7.
8. Dolin, R.H., Mattison, J.E., Cohn, S. et al. 2004. Kaiser Permanente's Convergent Medical Terminology, in M. Fieschi, E. Coiera and Y.-C. Li, eds, Proc. Medinfo 2004. San Francisco, CA, pp. 346-50.
9. Druss, B.G. and Marcus, S.C. 2005. Growth and decentralization of the medical literature: implications for evidence-based medicine. J. Med. Libr. Assoc., 93(4):499-501.
10. EMBL (2007 Sept. 5 (accessed)), EMBL Nucleotide Sequence Database. URL: http://www.ebi.ac.uk/embl
11. Entrez Gene (2008 Jan. 8 (accessed)), Entrez Gene. URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
12. GenBank (2007 Aug. 23 (accessed)), GenBank overview. URL: http://www.ncbi.nlm.nih.gov/Genbank
13. Golbeck, J., Fragoso, G., Hartel, F.W., Hendler, J., Parsia, B. and Oberthaler, J. 2003. The National Cancer Institute's thesaurus and ontology. Journal of Web Semantics, 1(1).
14. Hartel, F.W., de Coronado, S., Dionne, R., Fragoso, G. and Golbeck, J. 2005. Modeling a description logic vocabulary for cancer research. Journal of Biomedical Informatics, 38(2):114-29.
15. IHTSDO (2007 Dec. 31 (accessed)), IHTSDO: SNOMED CT. URL: http://www.ihtsdo.org/our-standards/snomed-ct
16. International Organization for Standardization. 2000. 'ISO 704:2000: Terminology work - Principles and methods'.
17. Karanjawala, Z.E. and Collins, F.S. 1998. Genetics in the context of medical practice. JAMA, 280(17):1533-4.
18. Lin, J.H. 1998. Divining and altering the future: Implications from the human genome project. Science, 282:15-32.
19. Lomax, J. and McCray, A.T. 2004. Mapping the Gene Ontology into the Unified Medical Language System. Comparative and Functional Genomics, 5(5):354-61.
20. Min, H., Perl, Y., Chen, Y., Halper, M., Geller, J. and Wang, Y. 2006. Auditing as part of the terminology design life cycle. JAMIA, 13(6):676-90.
21. Nardi, D. and Brachman, R.J. 2003. An introduction to description logics, in F. Baader, D. Calvanese, D. L. McGuinness, D. Nardi and P. F. Patel-Schneider, eds, The Description Logic Handbook: Theory, Implementation, and Applications, Cambridge University Press, Cambridge, UK., pp. 1-40.
22. NCICB. (2006 Dec. 21 (accessed)), NCICB: Enterprise Vocabulary Services (EVS). URL: http://ncicb.nci.nih.gov/NCICB./infrastructure/cacore_overview/ vocabulary
23. NCIT (2006 Dec. 21 (accessed)), NCI Terminology Browser. URL: http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do
24. OMIM (2008 Jan. 17 (accessed)), OMIM: Online Mendelian Inheritance in Man. URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim
25. Sarkar, I.N., Cantor, M.N., Gelman, R., Hartel, F.W. and Lussier, Y.A. 2003. Linking biomedical information and knowledge resources: GO and UMLS, in Proc. Pac. Symp Biocomputing, pp. 439-50.
26. Sioutos, N., de Coronado, S., Haber, M.W., Hartel, F.W., Shaiu, W.-L. and Wright, L.W. 2007. NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics, 40(1):30-43.
27. Smith, B., Ashburner, M., Rosse, C. et al. 2007. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25:1251-5.
28. The Gene Ontology Consortium. 2001. Creating the Gene Ontology resource: Design and implementation. Genome Research, 11:1425-33.
29. The Open Biomedical Ontologies (2008 Jan. 2 (accessed)), The Open Biomedical Ontologies. URL: http://www.obofoundry.org
30. Wang, Y., Halper, M., Min, H., Perl, Y., Chen, Y. and Spackman, K.A. 2007. Structural methodologies for auditing SNOMED. Journal of Biomedical Informatics, 40(5):561-81.