Artificial Intelligence in Medicine
Volume 46, Issue 2 , Pages 97-109 , June 2009

Using WordNet synonym substitution to enhance UMLS source integration

  • Kuo-Chuan Huang

      Affiliations

    • Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102-1982, USA
    • Corresponding Author InformationCorresponding author. Tel.: +1 973 596 3392; fax: +1 973 596 5777.
  • ,
  • James Geller

      Affiliations

    • Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102-1982, USA
  • ,
  • Michael Halper

      Affiliations

    • Department of Computer Science, Kean University, Union, NJ 07083-0411, USA
  • ,
  • Yehoshua Perl

      Affiliations

    • Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102-1982, USA
  • ,
  • Junchuan Xu

      Affiliations

    • Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102-1982, USA

Received 27 May 2008 ,Revised 15 August 2008 ,Accepted 9 November 2008.

References 

  1. Humphreys BL, Lindberg DAB, Schoolman HM, Barnett GO. The Unified Medical Language System: an informatics research collaboration. Journal of the American Medical Informatics Association. 1998;5(1):1–11
  2. SNOMED CT – Systematized Nomenclature of Medicine-Clinical Terms. Available from: http://www.ihtsdo.org/our-standards/snomed-ct/ [accessed 14 August 2008].
  3. LOINC – Logical Observations Identifiers, Names, Codes. Available from: http://www.nlm.nih.gov/research/umls/loinc_main.html [accessed 14 August 2008].
  4. NCI – National Cancer Institute. Available from: http://nci.nih.gov [accessed 14 August 2008].
  5. MeSH – Medical Subject Headings. Available from: http://www.nlm.nih.gov/mesh/meshhome.html [accessed 14 August 2008].
  6. MedDRA – Medical Dictionary for Regulatory Activities Terminology. Available from: http://meddramsso.com/ [accessed 14 August 2008].
  7. RxNorm – a standardized nomenclature for clinical drugs. Available from: http://www.nlm.nih.gov/research/umls/rxnorm/ [accessed 14 August 2008].
  8. Vocabularies in the UMLS Metathesaurus. Available from: http://www.nlm.nih.gov/research/umls/source_faq.html [accessed 14 August 2008].
  9. Schuyler PL, Hole WT, Tuttle MS, Sherertz DD. The UMLS Metathesaurus: representing different views of biomedical concepts. Bulletin of the Medical Library Association. 1993;81(2):217–222
  10. UMLS Release Notes and Problems. Available from: http://www.nlm.nih.gov/research/umls/release_notes.html [accessed 14 August 2008].
  11. Hole W, Srinivasan S. Discovering missed synonymy in a large concept-oriented metathesaurus. In: Overhage JM, editor. AMIA Annual Symp. 2000, Los Angeles, CA. p. 354–58.
  12. NLM Lexical Tools. Available from: http://lexsrv3.nlm.nih.gov/SPECIALIST/Projects/lvg/current/index.html [accessed 14 August 2008].
  13. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990;215(3):403–410
  14. Krauthammer M, Rzhetsky A, Morosov P, Friedman C. Using BLAST for identifying gene and protein names in journal articles. Journal of Functional and Evolutionary Genomics. 2000;259(1–2):245–252
  15. Gene Ontology Consortium – Gene Ontology. Available from: http://www.geneontology.org/ [accessed 14 August 2008].
  16. Lomax J, McCray AT. Mapping the gene ontology into the Unified Medical Language System. Comparative and Functional Genomics. 2004;5(5):354–361
  17. Huang K-C, Geller J, Halper M, Cimino JJ. Piecewise synonyms for enhanced UMLS source terminology integration. In: Teich JM, Suermondt J, Hripcsak G, editors. Proc. AMIA Annual Symp. 2007, Chicago, IL. p. 339–43.
  18. OMED – World Organisation of Digestive Endoscopy. Available from: http://www.omed.org/index.php/resources/ [accessed 14 August 2008].
  19. Miller GA. WordNet: a lexical database for English. Communications of the Association for Computing Machinery. 1995;38(11):39–41
  20. Tringali M, Hole WT, Srinivasan S. Integration of a standard gastrointestinal endoscopy. In: Kohane IS, editor. Proc. AMIA Annual Symp. 2002, San Antonio, TX. p. 801–05.
  21. WordNet 2.0. Available from: http://wordnet.princeton.edu/oldversions [accessed 14 August 2008].
  22. Johnson HL, Cohen K.B., Hunter L. A fault model for ontology mapping, alignment, and linking systems. In: Altman RB, et al., editors. Pacific Symposium on Biocomputing; 2007, Maui, HI. p. 233–44.
  23. ICPC – The International Classification of Primary Care. Available from: http://www.who.int/classifications/icd/adaptations/icpc2/en/index.html [accessed 14 August 2008].
  24. Mougin F, Burgun A, Bodenreider O. Using WordNet to improve the mapping of data elements to UMLS for data sources integration. In: Bates D, editor. Proc. AMIA Annual Symp. 2006, Washington, DC. p. 574–78.

PII: S0933-3657(08)00182-6

doi: 10.1016/j.artmed.2008.11.008

Artificial Intelligence in Medicine
Volume 46, Issue 2 , Pages 97-109 , June 2009