Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS)
Detailed instruction is described for mapping unstructured, free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Transfer (MMTx). MMTx can be used in applications including mining and inferring relationship between concepts in MEDLINE publications by transforming free text into computable concepts. MMTx is in general not designed to be an end-user program; therefore, a simple analysis is described using MMTx for users without any programming knowledge. In addition, two Java template files are provided for automated processing of the output from MMTx and users can adopt this with minimum Java program experience.
Key WordsAnalysis biomedical data mining MMTx NLP parsing UMLS
- 1.Aronson, A. R. (2001) Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc. AMIA Symp. 17–21.Google Scholar
- 3.Meystre, S. and Haug, P. J. (2005) Natural language processing to extract medical problems from electronic clinical documents: Performance evaluation. J. Biomed. Inform. 5, 5.Google Scholar
- 4.Chapman, W. W., Fiszman, M., Dowling, J. N., Chapman, B. E., and Rindflesch, T.C. (2004) Identifying respiratory findings in emergency department reports for biosurveillance using MetaMap. Medinfo 11(Pt 1), 487–491.Google Scholar