UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text

Journal of Biomedical Informatics

Volumn 43, Issue 4, 2010, Pages 587-594

  Demner Fushman, Dina ^a   Mork, James G ^a   Shooshan, Sonya E ^a   Aronson, Alan R ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Clinical text; Content views; Indexing; Metathesaurus; Natural Language Processing; UMLS

Indexed keywords

BIOMEDICAL LITERATURE; CLINICAL APPLICATION; FREE TEXTS; MEDICAL TERMS; NATURAL LANGUAGE PROCESSING; TEXT CONTENT; UNIFIED MEDICAL LANGUAGE SYSTEMS;

AUTOMATIC INDEXING; COMPUTATIONAL LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS;

INDEXING (MATERIALS WORKING);

ARTICLE; CITATION ANALYSIS; DATA EXTRACTION; DOCUMENTATION; INFORMATION PROCESSING; LINGUISTICS; MEDICAL INFORMATICS; MEDICAL INFORMATION SYSTEM; MEDICAL LITERATURE; NATURAL LANGUAGE PROCESSING; PRIORITY JOURNAL; INFORMATION RETRIEVAL; PROCEDURES; PUBLICATION; STANDARDS; UNIFIED MEDICAL LANGUAGE SYSTEM;

INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PUBLICATIONS; UNIFIED MEDICAL LANGUAGE SYSTEM;

EID: 77954143867     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2010.02.005     Document Type: Article

References (25)

1. McCray A.T., Aronson A.R., Browne A.C., Rindflesch T.C., Razi A., Srinivasan S. UMLS knowledge for biomedical language processing. Bull Med Libr Assoc 1993, 81(2):184-194.
2. Johnson S.B. A semantic lexicon for medical language processing. J Am Med Inform Assoc 1999, 6(3):205-218.
3. Verspoor K. Towards a semantic lexicon for biological language processing. Comp Funct Genomics 2005, 6(1-2):61-66.
4. Overby C.L., Tarczy-Hornoch P., Demner-Fushman D. The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers. BMC Bioinformatics 2009, 10(Suppl. 9):S8.
5. Friedman C., Liu H., Shagina L., Johnson S., Hripcsak G. Evaluating the UMLS as a source of lexical knowledge for medical language processing. Proc AMIA Symp 2001, 189-193.
6. Liu H., Teller V., Friedman C. A multi-aspect comparison study of supervised word sense disambiguation. J Am Med Inform Assoc 2004, 11(4):320-331.
7. Schuemie M.J., Kors J.A., Mons B. Word sense disambiguation in the biomedical domain: an overview. J Comput Biol 2005, 12(5):554-565.
8. Xu H., Markatou M., Dimova R., Liu H., Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics 2006, 7:334.
9. Stevenson M., Guo Y., Gaizauskas R., Martinez D. Disambiguation of biomedical text using diverse sources of information. BMC Bioinformatics 2008, (9 Suppl. 11):S7.
10. Savova G.K., Coden A.R., Sominsky I.L., Johnson R., Ogren P.V., de Groen P.C., et al. Word sense disambiguation across two domains: biomedical literature and clinical notes. J Biomed Inform 2008, 41(6):1088-1100.
11. Alexopoulou D., Andreopoulos B., Dietze H., Doms A., Gandon F., Hakenberg J., et al. Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinformatics 2009, 10:28.
12. Humphrey S.M., Rogers W.J., Kilicoglu H., Demner-Fushman D., Rindflesch T.C. Word sense disambiguation by selecting the best semantic type based on journal descriptor indexing: preliminary experiment. J Am Soc Inf Sci Technol 2006, 57(1):96-113.
13. Aronson A.R. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp 2001, 17-21.
14. Mork JG, Aronson AR. Filtering the UMLS Metathesaurus for MetaMap: 2009 Edition. National Library of Medicine, Bethesda, MD. Available from: http://skr.nlm.nih.gov/papers/references/filtering09.pdf.
15. Shooshan SE, Mork JG, Aronson AR. Ambiguity in the UMLS Metathesaurus: 2009 Edition. National Library of Medicine, Bethesda, MD. Available from: http://skr.nlm.nih.gov/papers/references/ambiguity09.pdf.
16. Unified Medical Language System: Preface to the 2005AA Documentation. National Library of Medicine, Bethesda, MD. Available from: http://www.nlm.nih.gov/archive/20080407/research/umls/archive/2005AA/umlsdoc_preface.html.
17. Aronson A.R., Mork J.G., Neveol A., Shooshan S.E., Demner-Fushman D. Methodology for creating UMLS content views appropriate for biomedical natural language processing. Proc AMIA Symp 2008, 21-25.
18. Aronson A.R., Mork J.G., Gay C.W., Humphrey S.M., Rogers W.J. The NLM indexing initiative's medical text indexer. Stud Health Technol Inform 2004, 107(Pt. 1):268-272.
19. Demner-Fushman D., Lin J. Answering clinical questions with knowledge-based and statistical techniques. Comput Linguist 2007, 33(1):63-104.
20. Kingsland L.C., Prettyman M.F., Shooshan S.E. The NLM Gateway: a metasearch engine for disparate resources. Stud Health Technol Inform 2004, 107(Pt 1):52-56.
21. Sackett D.L., Straus S.E., Richardson W.S., Rosenberg W., Haynes R.B. Evidence-based medicine: how to practice and teach EBM 2000, Churchill Livingstone, Edinburgh, Scotland. 2nd ed.
22. McCray A.T., Burgun A., Bodenreider O. Aggregating UMLS semantic types for reducing conceptual complexity. Stud Health Technol Inform 2001, 84(Pt. 1):216-220.
23. Neamatullah I., Douglass M.M., Lehman L.W., Reisner A., Villarroel M., Long W.J., et al. Automated de-identification of free-text medical records. BMC Med Inform Decis Mak 2008, 8:32.
24. Saeed M., Lieu C., Raber G., Mark R.G. MIMIC II: a massive temporal ICU patient database to support research in intelligent patient monitoring. Comput Cardiol 2002, 29:641-644.
25. Richardson W.S., Wilson M.C., Nishikawa J., Hayward R.S. The well-built clinical question: a key to evidence-based decisions. ACP J Club 1995, 123(3):A12-A13.