View - ResearchGate
View - ResearchGate View - ResearchGate
Mining Biomedical Data Using MMTx and UMLS 1613.3. DownloadingDownloading MMTx requires a login to the UMLSKS, which in turn requiresthe acceptance of a license agreement (see Note 1). The site for download ishttp://mmtx.nlm.nih.gov/Download/download.shtml, which is password protected.3.3.1. Downloading of MMTxAlthough MMTx is significantly smaller than the Metathesaurus, it is still almost2.5 GB in size when including the standard data sources. Therefore, the NLMrecommendation to use a fast Internet connection (and not a 802.11g wirelessconnection) should be taken seriously. The current version of MMTx as of July2006 is 2.4 MB. Both the smaller executable file (mmtx_V2.4.B_exec.jar) and thelarger data file (mmtx_V2.4.B_data.jar) should be downloaded and placed in thesame directory. The data file contains only the strict model of the Metathesaurus.3.3.2. Downloading Metathesaurus and Metamorphosys (Optional)Users interested in using MMTx with a custom data source or curious aboutthe “guts” of UMLS should install the Metathesaurus and Metamorphosys on alocal system. Download this by selecting “UMLS Knowledge Sources” fromthe download section of the UMLSKS (see Fig. 3). All the files for a releaseincluding the data files (the .nlm files), the checksum files (MD5 and CHK),and the installation program Metamorphosys (mmsys.zip) should be downloadedinto a single directory to a partition with at least 23 GB of space, preferably30 or more. In general, only a single release (ex., 2006AA) needs to bedownloaded, unless there is interest in changes in UMLS or its componentvocabularies over time. In most cases this is unlikely to be true.3.4. InstallationThe installation of both the MMTx and the UMLS requires Java to extract thejar files or to run Metamorphosys to set install the Metathesaurus. The latestrelease of MMTx has been tested with Java 1.4 and some trouble was encounteredrunning it with Java 1.5. It would be recommended that “java-version” berun on the command line to confirm that there is a compatible JVM before continuing.The JVM from Sun, Mac, and Blackdown are all known to work withUMLS. Installation of Java is beyond the scope of this chapter, but details can befound on the Sun website (http://www.java.com/en/download/manual.jsp).3.4.1. Installation of UMLS—MMTx ToolInstallation of UMLS is also relatively straightforward and full instructionscan be found at http://mmtx.nlm.nih.gov/install.shtml. For some notes on theinstallation process, see Note 2.
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Mining Biomedical Data Using MMTx and UMLS 1613.3. DownloadingDownloading MMTx requires a login to the UMLSKS, which in turn requiresthe acceptance of a license agreement (see Note 1). The site for download ishttp://mmtx.nlm.nih.gov/Download/download.shtml, which is password protected.3.3.1. Downloading of MMTxAlthough MMTx is significantly smaller than the Metathesaurus, it is still almost2.5 GB in size when including the standard data sources. Therefore, the NLMrecommendation to use a fast Internet connection (and not a 802.11g wirelessconnection) should be taken seriously. The current version of MMTx as of July2006 is 2.4 MB. Both the smaller executable file (mmtx_V2.4.B_exec.jar) and thelarger data file (mmtx_V2.4.B_data.jar) should be downloaded and placed in thesame directory. The data file contains only the strict model of the Metathesaurus.3.3.2. Downloading Metathesaurus and Metamorphosys (Optional)Users interested in using MMTx with a custom data source or curious aboutthe “guts” of UMLS should install the Metathesaurus and Metamorphosys on alocal system. Download this by selecting “UMLS Knowledge Sources” fromthe download section of the UMLSKS (see Fig. 3). All the files for a releaseincluding the data files (the .nlm files), the checksum files (MD5 and CHK),and the installation program Metamorphosys (mmsys.zip) should be downloadedinto a single directory to a partition with at least 23 GB of space, preferably30 or more. In general, only a single release (ex., 2006AA) needs to bedownloaded, unless there is interest in changes in UMLS or its componentvocabularies over time. In most cases this is unlikely to be true.3.4. InstallationThe installation of both the MMTx and the UMLS requires Java to extract thejar files or to run Metamorphosys to set install the Metathesaurus. The latestrelease of MMTx has been tested with Java 1.4 and some trouble was encounteredrunning it with Java 1.5. It would be recommended that “java-version” berun on the command line to confirm that there is a compatible JVM before continuing.The JVM from Sun, Mac, and Blackdown are all known to work withUMLS. Installation of Java is beyond the scope of this chapter, but details can befound on the Sun website (http://www.java.com/en/download/manual.jsp).3.4.1. Installation of UMLS—MMTx ToolInstallation of UMLS is also relatively straightforward and full instructionscan be found at http://mmtx.nlm.nih.gov/install.shtml. For some notes on theinstallation process, see Note 2.