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InformaticsforIntegratingBiologyandtheBedsidei2b2InstallationGuideNLPclinicalTextAnalysisandKnowledgeExtractionSystemDocumentVersion:1.
0I2b2SoftwareRelease:1.
6TableofContentsDocumentManagement3AboutthisGuide41.
Prerequisites51.
1RequiredSoftware51.
1.
1FirstRequiredSoftware51.
1.
2SecondRequiredSoftware52.
Install62.
1InstallingthecTAKESGUI62.
1.
1DownloadandExtractPackage62.
1.
2Verifyappisrunning62.
1.
3Runningatestexperiment72.
1.
4ConfiguringcustomInputandOutputDataSources82.
2Loadingtheontology9License10DocumentManagementRevisionNumberDateAuthorDescriptionofchange1.
004/12/12PeiJ.
ChenInitialDraftAboutthisGuideThisguideisintendedtowalkyouthroughtheinstallationofthecTAKESGUIandpopulatinganadditionalontologyforqueryingNLPconceptsviathewebclient.
ThisinstallationguideassumesyouarefamiliarwithJavaandTomcatServletContainers.
[Therewillbeaself-executablebundledwithJettyintheverynearfuture.
]IthasbeentestedonJava6,Tomcat5.
5/7.
0andi2b21.
6withMSSQL.
Itshouldworkonothersplatforms,butwehavenottestedandverifiedyet.
Note:ThecTAKESGUIwasdesignedtooutputthedatainthei2b2format.
However,itcanalsoberunasastand-aloneUIwherethedatacouldbeoutputtedtootherRDMSoritsembeddedDBwhereitcouldbequeriedviastandardSQL.
PrerequisitesRequiredSoftwareJava1.
6oraboveApacheTomcat5.
5oraboveFirstRequiredSoftwareIfyoudonotalreadyhavetheJavaRuntimeEnvironment,youcandownloaditat:(CurrentlytestedwithJRESE6)FollowtheinstallationinstructionsforinstallingJRE:http://java.
com/en/download/index.
jspSecondRequiredSoftwareIfyoudonotalreadyhaveaninstanceofTomcat,youcandownloadandinstallitat:(CurrentlytestedwithTomcat7.
0)FollowtheinstallationinstructionsforinstallingTomcat:http://tomcat.
apache.
org/Besuretomodifytheenvironmentvariablesinsetclasspath.
bator.
sh:set"JRE_HOME=%ProgramFiles%\Java\jre6"set"JAVA_OPTS=%JAVA_OPTS%-Xms500M-Xmx1024M"set"CLASSPATH=%CLASSPATH%;%CATALINA_HOME%\resources\cTAKES\dictionarylookup\lib\hsqldb_1_8_0_10.
jar"(Note:Thisisonlyneededforolderversionsoftomcatsuchas5.
5.
Laterversionsuchas7.
0willpickthisupfromthewebapp/WEB-INF/libautomatically.
)InstallInstallingthecTAKESGUIDownloadandExtractPackageUnpackthezipfilefrom[Addlinktodownloaddirectoryhere].
Withinthepackage,thereshouldbeawarfile(ctakes-gui-{version}.
war),andaresourcesfolder.
Steps:CopytheresourcesfolderintoyourTOMCAT_HOME/bin/resourcesdirectory(OrlocaltowhereverTomcatisbeingstartedfrom).
Besuretograntwriteaccesstotheresources(and/db)directorytopublicortheuserrunningtomcat.
Deploythectakes-gui-{version}.
wartothewebappsdirectoryasctakesgui.
warStartupTomcatbyexecutingTOMCAT_HOME/bin/startup.
batorstartup.
shVerifyappisrunningOncethewebapplicationhasbeensuccessfullydeployed,youshouldbeabletolaunchanewbrowserandpointittothehttp://{hostname}:{port}/ctakesgui.
Ifyoudonotgettheloginscreen,itismostlikelythatthewebappwasnotdeployedproperly.
ChecktheTOMCAT_HOME/logs/catalinalogfilesforanyerrors(ensurethatallthejars/libshavebeenincludedintheclasspath).
Forexample:RunningatestexperimentClickon'Loginwithadmin'CreateNewExperiment…EnterinaNameandDescriptionClickSaveandRunTherealreadyisatestdummynotebundledintheSamplei2b2inputdatabase.
Toverifythatthepipelinehassuccessfullybeenexecuted.
Clickontheresultslink,andyoushouldseethefullextractedresultsinagenericname-valuepairformat.
Note:Theappwasdesignedtobeexecutedasyncrously.
Feelfreetochecktheservletcontainerlogsforcurrentstatusofprocessing.
ConfiguringcustomInputandOutputDataSourcesClickonDataSourcesfromtheleftnavigationmenuCreateNeworModifytheexistingsampleDataSourceFillintherequiredinformationAfteryouhavesavedyoucustomdatasources,youcouldcreateanewexperimentandrunusingthemnow:Theoutputshouldberedirectedtothenewdestination.
VerifythecontentsofthedestinationtableviayourSQLclientofchoicesuchasMSSQLServerManagementStudioorOracleclient.
Note:MSSQL2005driversandhsqldbdrivershavebeenprebundled.
IfyourequireotherJDBCdrivers,besuretoincludethemintheWEB-INF/libortomcat'sclasspath.
LoadingtheontologyTomimicthesupportedontology,performandDBimporttotheontologytablefromthectakes-nlp-ontology.
csvfile[AddLinktofilehere].
Ifyourequirebuildingacustomontology,feelfreetousethei2b2relatedproject:https://community.
i2b2.
org/wiki/display/NCBO/NCBO+Ontology+ToolsWhichweusedtosubsetSNOMEDCT,RxNormtobuildtheOntologyusedfortheNLPtools.
Aftertheontologyhasbeenloadedandconfigured:Yourwebclientshouldlooklikethefollowing:License/**Copyright:(c)2012Children'sHospitalBoston**Exceptascontainedinthecopyrightnoticeabove,orasusedtoidentify*MFMERastheauthorofthissoftware,thetradenames,trademarks,service*marks,orproductnamesofthecopyrightholdershallnotbeusedin*advertising,promotionorotherwiseinconnectionwiththissoftwarewithout*priorwrittenauthorizationofthecopyrightholder.
**LicensedundertheApacheLicense,Version2.
0(the"License");*youmaynotusethisfileexceptincompliancewiththeLicense.
*YoumayobtainacopyoftheLicenseat**http://www.
apache.
org/licenses/LICENSE-2.
0**Unlessrequiredbyapplicablelaworagreedtoinwriting,software*distributedundertheLicenseisdistributedonan"ASIS"BASIS,*WITHOUTWARRANTIESORCONDITIONSOFANYKIND,eitherexpressorimplied.
*SeetheLicenseforthespecificlanguagegoverningpermissionsand*limitationsundertheLicense.
**/