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Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS)

  • John D. Osborne
  • Simon Lin
  • Lihua Julie Zhu
  • Warren A. Kibbe
Part of the Methods in Molecular Biology™ book series (MIMB, volume 408)

Abstract

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 Words

Analysis biomedical data mining MMTx NLP parsing UMLS 

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • John D. Osborne
    • 1
  • Simon Lin
    • 1
  • Lihua Julie Zhu
    • 1
  • Warren A. Kibbe
    • 1
  1. 1.Robert H. Lurie Cancer CenterNorthwestern UniversityChicago

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