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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.
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Gene Function Analysis
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METHODS IN MOLECULAR BIOLOGYGene Fu
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PrefaceThis volume of Methods in Mo
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Prefaceixcolleagues demonstrate how
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xiiContentsPART III EXPERIMENTAL ME
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ICOMPUTATIONAL METHODS I
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4 BidautTable 1Input File Format Us
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6 BidautTable 2Folder Layout to Use
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8 Bidaut• alphaA: this is the num
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10 Bidautcomputing the maximum corr
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12 BidautFig. 3. The complete Clutr
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Table 3Some Identified Patterns (5,
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16 BidautFig. 4. This is a comparis
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18 BidautReferences1. Hughes, T. R.
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20 Kirov et al.way to associate gen
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22 Kirov et al.based on a study ass
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24 Kirov et al.1. Retrieve the gene
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26Fig. 1. Functional associations f
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28 Kirov et al.Fig. 2. Pathway anal
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30 Kirov et al.3. Gene symbols usag
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32 Kirov et al.9. OBO_Team, Open Bi
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3Estimating Gene Function With Leas
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Estimating Gene Function With LS-NM
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50 Gonye et al.activity and problem
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52 Gonye et al.Currently, PAINT can
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54 Gonye et al.dynamic nature of th
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Prediction Using PAINT 57represente
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Prediction Using PAINT 59In PAINT,
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Prediction Using PAINT 6114. On the
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Prediction Using PAINT 634.2. Size
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65Fig. 4. Localization of enrichmen
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Prediction Using PAINT 673. Okubo,
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5Prediction of Intrinsic Disorder a
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Prediction of ID and Its Use in Fun
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Table 1Summary of the Web Servers O
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IICOMPUTATIONAL METHODS II
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94 Crabtree et al.genomes, which is
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96 Crabtree et al.Fig. 2. Sybil pro
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98 Crabtree et al.Fig. 3. Computing
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100 Crabtree et al.3.1.5.1. FILTER
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102 Crabtree et al.3. For the sake
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104 Crabtree et al.Fig. 5. Best bid
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106 Crabtree et al.17. Some cluster
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108 Crabtree et al.19. Chado—The
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110 Dateproducts prevents the under
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112 DateDetails of these tasks are
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114 DateThis step creates additiona
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116 Date>hsapiens|gi|20093443 >hsap
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118 DateBLAST score from the match
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Table 1A Sample of Results From Pro
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122 DateFig. 1. A network of functi
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124 Datedescribed by Verjovsky Marc
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126 Dateor contracts put forth by t
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8Bioinformatics Tools for Modeling
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Modeling Transcription Factor Targe
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VISTA Program to search for TFBSs H
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Page 366: 174 Ho et al.allowing for cases whe
Page 370: 176 Ho et al.A different measure is
Page 374: 178 Ho et al.3.1.3. LA and Generali
Page 378: 180 Ho et al.The ECF-statistic can
Page 382: 182 Ho et al.In the special case of
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188 Ho et al.this section were not
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190 Ho et al.References1. Schena, M
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IIIEXPERIMENTAL METHODS
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194 Caldwell et al.for sequences th
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196 Caldwell et al.query because it
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198 Caldwell et al.Fig. 1. (A) Prot
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200 Caldwell et al.outside primer o
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202 Caldwell et al.5. Targeting scr
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204 Caldwell et al.will allow the s
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206 Caldwell et al.3.1.6. Plasmid P
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208 Caldwell et al.PCR amplify the
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210 Caldwell et al.8. Thawing cells
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212 Zhang et al.Going one step beyo
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214 Zhang et al.Fig. 2. Generation
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216 Zhang et al.Perform PCR cycles,
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218 Zhang et al.Fig. 4. Schematic m
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220 Zhang et al.Fig. 5. Replacement
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13Construction of Simple and Effici
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DNA Vector-Based shRNA-Expression S
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244 Hust et al.overcome by two appr
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246 Hust et al.Fig. 1. Schematic de
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248 Hust et al.interaction during p
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250 Hust et al.3.4. Titering1. Inoc
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252 Hust et al.10. Shortly before u
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254 Hust et al.activity by preservi
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15A Bacterial/Yeast Merged Two-Hybr
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Screening in Yeast With a Bacterial
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318 Thibodeau-Beganny and Joungbeen
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320 Thibodeau-Beganny and JoungFig.
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324 Thibodeau-Beganny and JoungTypi
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328 Thibodeau-Beganny and JoungPCR
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330 Thibodeau-Beganny and Joung16-1
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332 Thibodeau-Beganny and Joung2. P
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334 Thibodeau-Beganny and Joung11.
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336 IndexKknockin (gene knockin) 19
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