NLP Virtual Machine Manual - University of California, San Diego
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1. Integrating Data for Analysis Anonymization and SHaring NLP Virtual Machine Manual Document Version 1 0 1 University of California San Diego Division of Biomedical Informatics NLP Virtual Machine Manual iDASH UC San Diego DBMI Table of Contents POT O UNE CONS O E E A E E E 3 l Instalino the VirtualBOK siisii aaa aeaa aE DEE aaea naaien 4 2 Tnstalline the NLP Virtal Machine i icsescnsavessavasssuscscncsisesuncucisseuusdasieavas sasursseuasaasancseutsusuesnadsinsans 4 3 Executing the NLP Virtual Machinen aieeaa aaa aa 6 de DEMO isisisi i E aa Ei aaa aiaa 8 EDS A U 8 MIS Doa EE a E A EEE aE 9 Mela Ap nsa a Ea 10 CEAL ES A E OO O E O ANE 11 ARC ra A R E AAA R 13 S Roron O Scanacon ERS 14 NLP Virtual Machine Manual iDASH UC San Diego DBMI About this Guide This virtual machine VM provided by iDASH has a suite of open source NLP tools installed eHOST an annotation interface for manually annotating text MetaMap a tool for indexing text to UMLS concepts cTAKES a UIMA based information extraction system MIST a suite of tools for identifying and redacting personally identifiable information PII in free text medical records Automated Retrieval Console ARC a tool for creating a classifier for text based on NLP derived features This guide will help you to learn about where to download and how to install this VM It also provides some demos on how to use the installed NLP tools To use the VM2. ova A dialog similar to the following will appear NLP Virtual Machine Manual iDASH UC San Diego DBMI Appliance to import Users ruilingliu Desktop NLP VM oval PA Appliance settings Description Configuration Virtual System 1 G3 Name NLP VM E Guest OS Type Ubuntu 64 bit CPU 1 RAM 2048 MB DvD M C4 USB Controller M P Sound Card M ICH AC97 jA Network Adapter v Intel PRO 1000 MT Desktop 82540EM _ Reinitialize the MAC address of all network cards Show Description Restore Defaults Go Back Import This presents the virtual machine described in NLP VM ova and allows you to change the virtual machine settings by double clicking on the description items Once you click on Import VirtualBox will copy the disk image and create a local virtual machine with the settings described in the dialog The imported virtual machine will show up in the Manager s list of virtual machines e080 Oracle VM VirtualBox Manager Z NLP VM pA a General Name NLP VM q Operating System Ubuntu 64 bit a System y Base Memory 2048 MB Boot Order Floppy CD DVD Hard Disk q Acceleration VT x AMD V Nested Paging Display Video Memory 12 MB Remote Desktop Server Disabled _ Video Capture Disabled J a Storage Controller IDE IDE Secondary Master CD DVD Empty Controller SATA q SATA Port 0 NLP VM disk2 vmdk Normal 25 00 GB bi ja A
3. workspace Workspace Lookin Jacke C demo_workspace c3 lib Folder name home nipym Desktop ehost bp 1 demo_workspace Files of Type Welcome to eHOST pri 5 Use the official document of eHOST and the demo data to explore the functions of eHOST http ehost knowtator com html start html NLP Virtual Machine Manual iDASH UC San Diego DBMI MIST 1 Open the terminal 2 Install the task The task has already been installed under the folder in the NLP VM home nlpvm Desktop MIST_2_0 src MAT 3 Start the UI by entering the command in the terminal bin MATWeb 4 Open your Firefox browser and a Ensure that popups are not blocked for localhost you can check this in the Firefox preferences window under the content tab b In the Firefox preferences window in the General tab ensure that Always ask me where to save files is selected 5 Navigate to http localhost 7801 MAT workbench MIST The MITRE Identification Scrubber Toolkit Mozilla Firefox MIST The MITRE Identification lt D File home nlpyvm Desktop MIST_2_0 static_doc html index html v E Google Q J A A MAT File Tabs view Reconciliation Help Logging is off press to start AMIA For users Tutorial 1 load and hand tag a document Tutorial 2 build a model Load document x Tutorial 3 automated tagging in the Ul Tutorial 4 view the Web demo Workflow mode Tutorial 5 use the command line
4. you will need your Unified Medical Language System UMLS username and password If you do not have one already go to the UTS website to request one The NLP VM and this manual were created and compiled by Ruiling Liu an intern at Division of Biomedical Informatics UC San Diego under the 2014 iDASH summer internship program NLP Virtual Machine Manual iDASH UC San Diego DBMI 1 Installing the VirtualBox 1 Download VirtualBox from https www virtualbox org wiki Downloads 2 Install the VirtualBox 2 Installing the NLP Virtual Machine 1 Download NLP virtual machine from http idash ucsd edu nlp umls vm 2 Open VirtualBox Oracle VM VirtualBox Manager Lad tes P v Details Snapshots New Settings Start Discard Welcome to VirtualBox The left part of this window is a list of all virtual machines on your computer The list is empty now because you haven t created any virtual machines yet In order to create a new virtual machine press the New button in the main tool bar located at the top of the window You can press the 36 key to get instant help or visit www virtualbox org for the latest information and news 3 Import the NLP Virtual Machine The downloaded NLP VM is a single archive file with the ova extension To import the NLP VM ova select File gt Import appliance from manager window In the file dialog that comes up navigate to the file NLP VM
5. engine Input Browse No file selected and scorer Document type raw S Tutorial 6 workspaces Tutorial 7 the a experiment engine Memo optional Tutorial 8 hand annotation of complex annotation sets What you need to know about Annotations Tasks training and automated tagging File and workspace modes Cancel 6 Use the official document of MIST to explore the other functions of MIST file home nlpvm Desktop MIST_2_0 static_doc html index html NLP Virtual Machine Manual iDASH UC San Diego DBMI MetaMap 1 Open the terminal MetaMap requires the starting of two servers The Part of Speech Tagger and Word Sense Disambiguation WSD Servers Both servers will automatically run in the background when started They can be started and stopped as follows 2 Start the SKR Medpost Part of Speech Tagger Server by entering the command below in the terminal cd home nlpvm Desktop MetaMap public_mm sudo bin skrmedpostctl start sudo password for nlpvm is dbmi123 3 Start the Word Sense Disambiguation WSD Server by entering the command sudo bin wsdserverctl start 4 Using MetaMap echo lung cancer bin metamap11v2 I 5 Stop the SKR Medpost Part of Speech Tagger Server sudo bin skrmedpostctl stop 6 Stop the Word Sense Disambiguation WSD Server sudo bin wsdserverctl stop 7 Use the official document of MIST to explore the other functions of MetaMap
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7. http metamap nlm nih gov 10 NLP Virtual Machine Manual iDASH UC San Diego DBMI cTAKES 1 Open terminal 2 Enter the commands below in the terminal to open cTAKES cd home nlpvm Desktop apache ctakes 3 1 1 bin sh runctakesCPE sh Collection Processing Engine Configurator File View Help w Unstructured U Information Management MA Architecture An Apache Project Collection Reader Descriptor Analysis Engines Ada lt lt gt gt CAS Consumers Add lt lt gt gt Db a m nitialized 3 Enter the command below to open the CAS Visual Debugger CVD sh runctakesCVD sh 11 NLP Virtual Machine Manual iDASH UC San Diego DBMI CAS Visual Debugger CVD File Edit Run Tools Help Analysis Results CAS Index Repository FS List no selection 22 49 03 Ready No AE Loaded Cursor 0 4 Optional Add UMLS access rights a Ifyou do not have a UMLS username and password you may request one at UMLS Terminology Services b Edit the following files Find the line in each script that runs java and add the ctakes umlsuser and ctakes umlspw parameters to the java command with your credentials Make sure you substitute your actual ID and password if you cut and paste the example lt cTAKES_HOME gt bin runctakesCVD sh lt cTAKES_HOME gt bin runctakesCPE sh Java Command java Dctakes u
8. mlsuser lt YOUR_UMLS_ID_HERE gt Dctakes umlspw lt YOUR_UMLS_PASSSWORD_HERES gt cp 5 Use the official document of cTAKES to explore the functions of cTAKES https cwiki apache org confluence display CTAKES cTAKES 3 1 User Install Guid e 3bjsessionid 0F37630963F4482D9A9AD64578F9EICD cTAKES3 1UserInstallGuid e CollectionProcessingEngine CPE 12 NLP Virtual Machine Manual iDASH UC San Diego DBMI ARC 1 Open the terminal 2 Start the ARC program by entering the commands below cd home nlpvm Desktop ARC 2 0 cTAKES sh ARC sh 3 Select workspace Workspace Selector Select workspace folder by dragging below typing in box or pressing browse button Cancel 4 Click on Done MAVERIC ARC DIY Document Level Import document level classifications process the documents using cTAKES and build models using a feature blast 13 NLP Virtual Machine Manual iDASH UC San Diego DBMI 5 References 1 2 3 4 5 6 Oracle VM VirtualBox User Manual https www virtualbox org manual ch01 html intro installing eHOST User Guide https code google com p ehost cTAKES 3 1 User Install Guide https cwiki apache org confluence display CTAKES cTAKES 3 1 User Instal 1 Guide MetaMap http metamap nlm nih gov ARC 2 0 Installer with LVG and UMLS pre bundled https code google com p mavericarc The MITRE Identification Scrubber Toolkit http mist deid sourcefor
9. udio Host Driver CoreAudio _ Controller ICH AC97 ba P Network q Adapter 1 Intel PRO 1000 MT Desktop NAT oo Device Filters O 0 active NLP Virtual Machine Manual iDASH UC San Diego DBMI 3 Executing the NLP Virtual Machine 1 Click on Start to start the NLP virtual machine NLP VM Running Guest Session ubuntu 14 04 LTS JoPo QUe 4 2 Login the NLP VM The username for this NLP virtual machine is nlpvm and the password is dbmi123 3 Open the terminal Click on the icon in the top left corner of the desktop and then click on the terminal icon to open the terminal N L V M Le unnin g Ubuntu Desktop apache ctakes 3 oh w CherryPy 3 2 4 ooa ww ehostbp 1 MetaMap if a y NLP VM Running fji Applications Terminal Files amp Folders README txt NLP Virtual Machine Manual iDASH UC San Diego DBMI 4 Demo eHOST 1 Open terminal 2 Enter the command below in the terminal to open eHOST cd home nlpvm Desktop ehost bp 1 java jar eHOST jar 3 Click Brower button to navigate to the demo_workspace folder and click on Open The location of the demo_workspace is home nlpvm Desktop ehost bp 1 demo_workspace 4 Click on OK Result SYSTEM Sync E Editor Setting e Assignments parT WORKSPACE amp PROJECT Select a workspace Choose a workspace folder to save your annotation projects Projects in
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