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9Mining Biomedical Data Using MetaMap Transfer(MMTx) and the Unified Medical Language System(UMLS)John D. Osborne, Simon Lin, Lihua (Julie) Zhu, and Warren A. KibbeSummaryDetailed instruction is described for mapping unstructured, free text data into common biomedicalconcepts (drugs, diseases, anatomy, and so on) found in the Unified Medical LanguageSystem using MetaMap Transfer (MMTx). MMTx can be used in applications including miningand inferring relationship between concepts in MEDLINE publications by transforming free textinto 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. Inaddition, two Java template files are provided for automated processing of the output fromMMTx and users can adopt this with minimum Java program experience.Key Words: Analysis; biomedical; data mining; MMTx; NLP; parsing; UMLS.1. IntroductionThe explosion of biomedical information in electronic format has posed bothopportunities and challenges to researchers wishing to analyze that information.The easy accessibility and size of the information allow a wide range ofhypotheses to be tested and questions to be asked, but much of the data is in freetext format and consequently difficult to organize and compare. The field ofnatural language processing has a variety of tools to deal with these types ofproblems, one of which (MetaMap Transfer [MMTx]) (1) is of particular interestto biomedical researchers. MMTx is one of the tools used by the NationalLibrary of Medicine (NLM) to import medical and biological vocabularies into theUnified Medical Language System (UMLS) database. A total of 143 vocabulariesFrom: Methods in Molecular Biology, vol. 408: Gene Function AnalysisEdited by: M. Ochs © Humana Press Inc., Totowa, NJ153
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9Mining Biomedical Data Using MetaMap Transfer(MMTx) and the Unified Medical Language System(UMLS)John D. Osborne, Simon Lin, Lihua (Julie) Zhu, and Warren A. KibbeSummaryDetailed instruction is described for mapping unstructured, free text data into common biomedicalconcepts (drugs, diseases, anatomy, and so on) found in the Unified Medical LanguageSystem using MetaMap Transfer (MMTx). MMTx can be used in applications including miningand inferring relationship between concepts in MEDLINE publications by transforming free textinto 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. Inaddition, two Java template files are provided for automated processing of the output fromMMTx and users can adopt this with minimum Java program experience.Key Words: Analysis; biomedical; data mining; MMTx; NLP; parsing; UMLS.1. IntroductionThe explosion of biomedical information in electronic format has posed bothopportunities and challenges to researchers wishing to analyze that information.The easy accessibility and size of the information allow a wide range ofhypotheses to be tested and questions to be asked, but much of the data is in freetext format and consequently difficult to organize and compare. The field ofnatural language processing has a variety of tools to deal with these types ofproblems, one of which (MetaMap Transfer [MMTx]) (1) is of particular interestto biomedical researchers. MMTx is one of the tools used by the NationalLibrary of Medicine (NLM) to import medical and biological vocabularies into theUnified Medical Language System (UMLS) database. A total of 143 vocabulariesFrom: Methods in Molecular Biology, vol. 408: Gene Function AnalysisEdited by: M. Ochs © Humana Press Inc., Totowa, NJ153