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Mining Biomedical Data Using MMTx and UMLS 1694. Notes1. Registration and License Information: A complete description of the UMLS licenseagreement can be found here (http://www.nlm.nih.gov/research/umls/license.html).In general, one is free to use and incorporate UMLS as needed for research applicationsbut care should be taken when working with any of the particular vocabulariesin UMLS that are subject to their own licensing requirements. For instance theSNOMED vocabulary cannot be redistributed in commercial applications nor usedfor research outside the United States without a separate license agreement. TheUMLS license also has a minimal reporting requirement; licensees are required tofill out a short electronic report once a year.2. Installation of MMTx: After both the mmtx executable and the mmtx data file havebeen downloaded to the same directory, it is best to manually unjar both files.Problems have consistently been had with the installation script detecting andunjarring the data file.3. Command Line MMTx: No success has been had in handling tab delimited datawith MMTx, but “|” delimited data (the default) works just fine.4. Perl Expressions (-P) in grep: Require the presence of GNU grep (seehttp://www.gnu.org/software/grep/). Systems without GNU grep may not support it.References1. Aronson, A. R. (2001) Effective mapping of biomedical text to the UMLSMetathesaurus: the MetaMap program. Proc. AMIA Symp. 17–21.2. Smith, L., Rindflesch, T., and Wilbur, W. J. (2004) MedPost: a part-of-speech taggerfor bioMedical text. Bioinformatics 20(14), 2320–2321.3. Meystre, S. and Haug, P. J. (2005) Natural language processing to extract medicalproblems from electronic clinical documents: Performance evaluation. J. Biomed.Inform. 5, 5.4. Chapman, W. W., Fiszman, M., Dowling, J. N., Chapman, B. E., and Rindflesch, T.C.(2004) Identifying respiratory findings in emergency department reports forbiosurveillance using MetaMap. Medinfo 11(Pt 1), 487–491.5. Hofmann, O. and Schomburg, D. (2005) Concept-based annotation of enzymeclasses. Bioinformatics 21(9), 2059–2066.6. Meystre, S. and Haug, P. J. (2005) Evaluation of Medical Problem Extractionfrom Electronic Clinical Documents Using MetaMap Transfer (MMTx). Stud.Health Technol. Inform. 116, 823–828.7. Chapman, W. W., Bridewell, W., Hanbury, P., Cooper, G. F., and Buchanan, B. G.(2001) A simple algorithm for identifying negated findings and diseases in dischargesummaries. J. Biomed. Inform. 34(5), 301–310.