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162 Osborne et al.3.4.2. Installation of UMLS Metathesaurusand Metamorphosys (Optional)Although not required unless a user is planning to create a custom data set, itis recommended to install it anyway. Running Metamorphosys and seeing thelist of vocabularies in UMLS will give one a sense of the scale of UMLS andpotentially pointers to useful areas that might otherwise go undiscovered.Installation is relatively straightforward, for complete and up-to-date informationsee http://www.nlm.nih.gov/research/umls/meta6.html where the latestrequirements and instruction are detailed. There are only a couple of potentialproblems with installation. First, it is important that the checksum files be downloadedinto the same directory as the other files because Metamorphosys willneed to confirm that the downloaded files are intact. Second, one of the trickieraspects of Metamorphosys is that it is not always clear which vocabularies arebeing included and which are being excluded during source selection. Sourcesthat are highlighted in blue are selected for exclusion by default, not for inclusion.This is somewhat counterintuitive and because installation of UMLS cantake over an hour on some platforms, the radio buttons over the main menushould be checked to make sure the correct subset is selected. It is also worthwhileto save one’s configuration file because the selection of the subset ofUMLS to install tends to be fluid. It is often the case that the configuration chosenis not quite optimal (a source for inclusion or exclusion is often overlooked)so save the configuration to a file before beginning the subset process. Finally,the option to write the UMLS Metathesaurus as a database SQL script (eitherOracle or mySQL) is turned off, so if one wants to put UMLS into a relationaldatabase, then these options need to be selected before subsetting.3.5. Setup the Running EnvironmentIf not already present, copy all the input data to the host machine on whichMMTx has been installed. Everything can be run from a single directory.3.5.1. Formatting Input DataThis step should be done if the user is planning running MMTx from the commandline. If one is going to use the JAVA Application Programming Interface(Java API) to run and process MMTx (not recommended for non-programmer)then this input transformation step can be skipped because the programmer (notMMTx) will be responsible for parsing the input data.MMTx is extremely flexible in terms of the format of data it can accept. Itwill take in any free text, and MEDLINE data can be parsed directly by MMTxand so can particular fields in a text file delimited by arbitrary separators. For alisting on how to handle the data type, see Table 1. A user should be able to