title: Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).
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.
authors.affiliation: Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Osborne
authors.forename: Simon
authors.initials: S
authors.lastname: Lin
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhu
authors.forename: Warren A
authors.initials: WA
authors.lastname: Kibbe
mesh_terms: D019295:Computational Biology / Q000706:statistics & numerical data*; D003627:Data Interpretation, Statistical; D016247:Information Storage and Retrieval / Q000706:statistics & numerical data; D016239:MEDLINE; D009323:Natural Language Processing; D012984:Software; D012985:Software Design; D017432:Unified Medical Language System