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From build...@apache.org
Subject svn commit: r838281 - in /websites/staging/ctakes/trunk/content: ./ ctakes/3.0.0/user-guide-3.0.html
Date Tue, 13 Nov 2012 22:17:08 GMT
Author: buildbot
Date: Tue Nov 13 22:17:07 2012
New Revision: 838281

Log:
Staging update by buildbot for ctakes

Modified:
    websites/staging/ctakes/trunk/content/   (props changed)
    websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html

Propchange: websites/staging/ctakes/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Tue Nov 13 22:17:07 2012
@@ -1 +1 @@
-1408965
+1408988

Modified: websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html
==============================================================================
--- websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html (original)
+++ websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html Tue Nov 13 22:17:07
2012
@@ -84,124 +84,360 @@
   </div>
   <div id="contenta">
     <h1 id="ctakes-30-user-guide">cTAKES 3.0 User Guide</h1>
-<p>These instructions are for end users. With these instructions you can
-install cTAKES, configure it, and use it to process text (typically text
-associated with a medical record). If you were planning to expand,
-change, or modify the code within cTAKES, refer to the [cTAKES 2.5
-Developer Install Instructions][].</p>
-<p>These instructions will cover installation and a test of the main
-product including trained models for sentence detection and tagging
-parts of speech, dictionaries from a subset of the UMLS, a very small
-subset of the full LVG resource, etc. Optional components will also be
-described.</p>
-<p>Once you have finished installation of cTAKES, you will be able to see
-what cTAKES is capable of. Further exploitation of the software’s
-ability may require following a few additional steps involving what
-dictionaries are being used. These are the last steps in these
-instructions.</p>
+<p>These instructions are for end users. With these instructions you can install
+cTAKES, configure it, and use it to process text (typically text associated
+with a medical record). If you were planning to expand, change, or modify the
+code within cTAKES, refer to the <a href="/display/VKC/cTAKES+2.5+Developer+Install+Instructions">cTAKES
2.5 Developer Install
+Instructions</a>.</p>
+<p>These instructions will cover installation and a test of the main product
+including trained models for sentence detection and tagging parts of speech,
+dictionaries from a subset of the UMLS, a very small subset of the full LVG
+resource, etc. Optional components will also be described.</p>
+<p>Once you have finished installation of cTAKES, you will be able to see what
+cTAKES is capable of. Further exploitation of the software's ability may
+require following a few additional steps involving what dictionaries are being
+used. These are the last steps in these instructions.</p>
 <h2 id="prerequisites">Prerequisites</h2>
-<div class="table-wrap">
-<table class="confluenceTable">
-<tbody>
-<tr>
-<th class="confluenceTh">
-Step
-
-</th>
-<th class="confluenceTh">
-Example
-
-</th>
-</tr>
-<tr>
-<td class="confluenceTd">
-​1. Make sure you have Java 1.6 or higher. Most systems come with Java
-already installed. \
- Run this command to check your version. \
-
-<div class="code panel" style="border-width: 1px;">
-<div class="codeContent panelContent">
-~~~~ {.theme: .Confluence; .brush: .plain; .gutter: .false
-style="font-size:12px;"}
-java -version
-~~~~
-
-</div>
-
-<p></div>
-If you do not you can install Java from [java.com][].</p>
-<p></td>
-<td class="confluenceTd">
-<div class="code panel" style="border-width: 1px;">
-<div class="codeContent panelContent">
-~~~~ {.theme: .Confluence; .brush: .plain; .gutter: .false
-style="font-size:12px;"}
-C:>java -version
-java version "1.6.0_20"
-Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
-Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode, sharing)
-~~~~</p>
-<p></div>
-</div>
-</td>
-</tr>
-</tbody>
-</table>
-</div>
-Install cTAKES</p>
-<hr />
-<div class="table-wrap">
-<table class="confluenceTable">
-<tbody>
-<tr>
-<th class="confluenceTh">
-Step
-
-</th>
-<th class="confluenceTh">
-Example
-
-</th>
-</tr>
-<tr>
-<td class="confluenceTd">
-​1. Navigate to the [source downloads for a released version][] on
-SourceForge
-
-</td>
-<td class="confluenceTd">
-\
-
-</td>
-</tr>
-<tr>
-<td class="confluenceTd">
-​2. Download the **cTAKES-2.5.zip** file. \
- Save the file to a temporary location on your machine.
-
-</td>
-<td class="confluenceTd">
-![screenshot illustrating step][]
-
-</td>
-</tr>
-<tr>
-<td class="confluenceTd">
-​3. Unzip (extract the contents of) the compressed file you downloaded
-into a directory that you want to be the cTAKES install location. \
- For example, **Windows**: \
-
-<div class="code panel" style="border-width: 1px;">
-<div class="codeContent panelContent">
-~~~~ {.theme: .Confluence; .brush: .plain; .gutter: .false
-style="font-size:12px;"}
-c:\cTAKES-2.5
-~~~~
-
-  [cTAKES 2.5 Developer Install Instructions]: cTAKES%2B2.5%2BDeveloper%2BInstall%2BInstructions.html
-  [java.com]: http://www.java.com/en/download/faq/develop.xml
-  [source downloads for a released version]: http://sourceforge.net/projects/ohnlp/files/cTAKES
-  [screenshot illustrating step]: attachments/75014322/76808927.jpg
+<p>Step</p>
+<p>Example</p>
+<ol>
+<li>Make sure you have Java 1.6 or higher. Most systems come with Java already
+installed.</li>
+</ol>
+<p>Run this command to check your version.</p>
+<p>If you do not you can install Java from
+<a href="http://www.java.com/en/download/faq/develop.xml">java.com</a>.</p>
+<h2 id="install-ctakes">Install cTAKES</h2>
+<p>Step</p>
+<p>Example</p>
+<ol>
+<li>
+<p>Navigate to the <a href="http://sourceforge.net/projects/ohnlp/files/cTAKES">source
downloads for a released
+version</a> on SourceForge</p>
+</li>
+<li>
+<p>Download the <strong>cTAKES-2.5.zip</strong> file.</p>
+</li>
+</ol>
+<p>Save the file to a temporary location on your machine.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/cTAKES-2.5"
title="-download-progress.jpg?version=1&amp;modificationDate=1336161194000" /></p>
+<ol>
+<li>Unzip (extract the contents of) the compressed file you downloaded into a
+directory that you want to be the cTAKES install location.</li>
+</ol>
+<p>For example, <strong>Windows</strong>:</p>
+<p><strong>Linux</strong>: <br />
+</p>
+<p>This folder we will call <strong><cTAKES_HOME></strong>. You will
need to refer to the
+directory later.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/cTAKES-2.5-Extr"
title="acting.jpg?version=1&amp;modificationDate=1336163791000" /></p>
+<p>|</p>
+<h2 id="process-documents-using-ctakes">Process documents using cTAKES</h2>
+<p>This version allows you to test most components bundled in cTAKES in two
+different ways:</p>
+<ol>
+<li>Using cTAKES CAS Visual Debugger (CVD) to view the results stored as XCAS files
or run the annotators or</li>
+<li>Using cTAKES collection processing engine (CPE) to process documents in cTAKES_HOME/testdata
directory</li>
+</ol>
+<h3 id="cas-visual-debugger-cvd">CAS Visual Debugger (CVD)</h3>
+<p>Step</p>
+<p>Example</p>
+<ol>
+<li>Open a command prompt and change to the cTAKES_HOME directory.</li>
+</ol>
+<p><strong>Windows</strong>: <br />
+</p>
+<p><strong>Linux</strong>: <br />
+</p>
+<p><img alt="" src="/images/icons/emoticons/warning.png" /></p>
+<p><strong>Note</strong><br />
+</p>
+<p>cTAKES_HOME must be your current directory unless you are skilled at setting
+paths on your machine.</p>
+<ol>
+<li>Start the CAS Visual Debugger by running this command:</li>
+</ol>
+<p><strong>Windows</strong>: <br />
+</p>
+<p><strong>Linux</strong>: <br />
+</p>
+<p>The application may take a minute to start on slower hardware.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav6ae43931"
title="208c6ae30f6e836859a2bb19.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>An analysis engine (AE) needs to be loaded in order to process text.</li>
+</ol>
+<p>Use the <strong>Run</strong> -&gt; <strong>Load AE</strong>
menu bar command. Navigate to the file</p>
+<p>Click <strong>Open</strong>.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav74c75ed2"
title="8c7c02f2be44fe41d0b65a16.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>Copy the text in the example at the right (next cell) and paste the
+contents into the Text section of CVD, replacing the text that is already
+there.</li>
+</ol>
+<p>This example file can also be found in test data:</p>
+<p>Dr. Nutritious</p>
+<p>Medical Nutrition Therapy for Hyperlipidemia</p>
+<p>Referral from: Julie Tester, RD, LD, CNSD</p>
+<p>Phone contact: (555) 555-1212</p>
+<p>Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001</p>
+<p>Admit Weight: 53 kg BMI: 18 kg/m2</p>
+<p>Diet: General</p>
+<p>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</p>
+<p>Daily Protein needs: 40 grams, assessed as 1.0 g/kg.</p>
+<p>Pt has been on a 3-day calorie count and has had an average intake of 1100
+calories.</p>
+<p>She was instructed to drink 2-3 cans of liquid supplement to help promote
+weight gain.</p>
+<p>She agrees with the plan and has my number for further assessment. May want a
+Resting</p>
+<p>Metabolic Rate as well. She takes an aspirin a day for knee pain.</p>
+<ol>
+<li>From the menu bar, click <strong>Run</strong> -&gt; <strong>Run
AggregatePlaintextProcessor</strong>.</li>
+</ol>
+<p>You'll get a list of all the annotations in the Analysis Results frame.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav2c25a00d"
title="f26e72f2c00fae8d12e5c3a5.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>Named entities are now recognized in this clinical document. Annotations of
+MedicationEventMention and EntityMention are created. To find one, in the
+<strong>Analysis Results frame</strong>, click on the key in front of:</li>
+</ol>
+<p>AnnotationIndex</p>
+<p>uima.tcas.Annotation</p>
+<p>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</p>
+<p>edu.mayo.bmi.uima.core.type.textsem.EntityMention</p>
+<p>and</p>
+<p>edu.mayo.bmi.uima.core.type.textsem.EventMention</p>
+<p>edu.mayo.bmi.uima.core.type.textsem.EventMention.MedicationEventMention</p>
+<p>Then select <strong>edu.mayo.bmi.uima.core.type.<strong><em>*textsem.</em></strong>*EntityMention</strong>
or <em>
+</em>edu.mayo.bmi.uima.core.type.<strong><em>*textsem.</em></strong><em>EventMention.<strong><em>*Medication</em></strong></em>Ev
+entMention**.This will show an Annotation Index in the lower frame. Select any
+annotation in that lower frame and you will see the text discovered in the
+Text frame on the right. You may close CVD if you wish.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddavcfd76769"
title="7d1e58970d516f1312a8a6e4.png?version=1&amp;modificationDate=1334686366000" /></p>
+<h3 id="collection-processing-engine-cpe">Collection processing engine (CPE)</h3>
+<p>Step</p>
+<p>Example</p>
+<ol>
+<li>Open a command prompt and change to the cTAKES_HOME directory:</li>
+</ol>
+<p><strong>Windows</strong>: <br />
+</p>
+<p><strong>Linux</strong>: <br />
+</p>
+<p><img alt="" src="/images/icons/emoticons/warning.png" /></p>
+<p><strong>Note</strong><br />
+</p>
+<p>Note that cTAKES_HOME must be your current directory unless you are skilled at
+setting paths on your machine.</p>
+<ol>
+<li>Start the collection processing engine by running this command:</li>
+</ol>
+<p><strong>Windows</strong>: <br />
+</p>
+<p><strong>Linux</strong>: <br />
+</p>
+<p>The application may take a minute to start on slower hardware.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav6ae43931"
title="208c6ae30f6e836859a2bb19.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>This will bring up the Collection Processing Engine Configurator. In the
+Menu bar click <strong>File</strong> &gt; <strong>Open CPE Descriptor</strong></li>
+</ol>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddavdc5a7f71"
title="827d9e3ef9c3f0c241804365.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>Navigate to the file</li>
+</ol>
+<p>Click <strong>Open</strong>.</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav41b2878f"
title="e8e61ee02d2c07e89c106cdd.png?version=1&amp;modificationDate=1334686365000" /></p>
+<ol>
+<li>Click the Play button (green/blue <strong>play arrow</strong> near
the bottom).</li>
+</ol>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav9acbe68c"
title="6f920e134a8eb49db96025e7.png?version=1&amp;modificationDate=1334686365000" /></p>
+<ol>
+<li>You should see that one document was processed. You did process a
+collection of documents. In this case the collection only contained one just
+to show how to do it. Close the results window.</li>
+</ol>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav42012486"
title="af09ef9457b4022474979a83.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>Close the CPE application. You may be prompted to save changes. Since this
+was just a test you may click the <strong>No</strong> button.</li>
+</ol>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddav1c58ee84"
title="960f01830ce34429b3d96c3c.png?version=1&amp;modificationDate=1334686366000" /></p>
+<ol>
+<li>Open a new command prompt and change to the <cTAKES_HOME></li>
+</ol>
+<p>No example.</p>
+<ol>
+<li>To test the results there is a comparison tool that will help show that the
+results match expectations with the following syntax:</li>
+</ol>
+<p>Where: <strong><em><First File></em></strong> is the
first file to compare; <strong><em><Second File></em></strong>
is
+the second file to compare; <strong><em><diff-html></em></strong>
is where the results are written
+to</p>
+<p>Copy and paste the example at the right (next cell) which has had our example
+files already substituted into a command prompt to run. In this case we have
+shipped an example of what the output should be for you to compare against.</p>
+<p><strong>Windows</strong>:</p>
+<p><strong>Linux</strong>:</p>
+<ol>
+<li>The resulting file will open for you. Look at the comparison to see the
+annotations resulting from this pipeline.</li>
+</ol>
+<p><strong>Windows:</strong></p>
+<p><strong>Linux</strong>:</p>
+<p><img alt="screenshot illustrating step" src="/download/attachments/75014322/worddavefef1435"
title="06073a5a3d6c91cbbab2c686.png?version=1&amp;modificationDate=1334686366000" /></p>
+<p>Using the same CVD and CPE programs in the manner described above, you can
+test all the other components. The analysis engines and collection processing
+engines shipped with cTAKES for some of the annotators are described in the
+following table.</p>
+<p>Annotator</p>
+<p>Description</p>
+<p>Abbreviated</p>
+<p>Example Analysis Engine (AE)</p>
+<p>Example Collection processing Engine (CPE)</p>
+<p>Example test data</p>
+<p>Clinical Document Pipeline</p>
+<p>the complete cTAKES pipeline to obtain majority of cTAKES annotations</p>
+<p>cdp</p>
+<p>cTAKES_HOME/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</p>
+<p>cTAKES_HOME/testdata/cdptest</p>
+<p>Chunker</p>
+<p>obtain cTAKES chunking annotations</p>
+<p>chunker</p>
+<p>cTAKES_HOME/cTAKESdesc/chunkerdesc/analysis_engine/ChunkerAggregate.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/chunkerdesc/collection_processing_engine/ChunkerCPE.xml</p>
+<p>cTAKES_HOME/testdata/chunkertest</p>
+<p>Dependency Parser</p>
+<p>obtain dependency parsing tree</p>
+<p>dp</p>
+<p>cTAKES_HOME/cTAKESdesc/dpdesc/analysis_engine/ClearParserTokenizedInfPosAggreg
+ate.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/dpdesc/collection_processing_engine/ClearParserCPE.xml</p>
+<p>cTAKES_HOME/testdata/dptest</p>
+<p>Drug NER</p>
+<p>the annotator to obtain drug annotations</p>
+<p>drugner</p>
+<p>cTAKES_HOME/cTAKESdesc/drugnerdesc/analysis_engine/DrugAggregatePlaintextProce
+sor.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainT
+ext_CPE.xml</p>
+<p>cTAKES_HOME/testdata/drugnertest</p>
+<p>Dictionary Lookup</p>
+<p>mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm</p>
+<p>lookup</p>
+<p>cTAKES_HOME/cTAKESdesc/lookupdesc/analysis_engine/TestAggregateTAE.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/lookupdesc/collection_processing_engine/LookupCPE.xml</p>
+<p>cTAKES_HOME/testdata/lookuptest</p>
+<p>PAD Term Spotter</p>
+<p>identifying terms related to PAD</p>
+<p>pad</p>
+<p>cTAKES_HOME/cTAKESdesc/paddesc/analysis_engine/Radiology_TermSpotterAnnotatorT
+AE.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/paddesc/collection_processing_engine/Radiology_Sample.x
+ml</p>
+<p>cTAKES_HOME/testdata/padtest</p>
+<p>Smoking Status</p>
+<p>the annotator to obtain document or patient-level smoking status</p>
+<p>smoking</p>
+<p>cTAKES_HOME/cTAKESdesc/smokingdesc/analysis_engine/SimulatedProdSmokingTAE.xml</p>
+<p>cTAKES_HOME/cTAKESdesc/smokingdesc/collection_processing_engine/Sample_Smoking
+Status_output_flatfile.xml</p>
+<p>cTAKES_HOME/testdata/smokingtest</p>
+<p>Side Effect</p>
+<p>the annotator to find side effect mentions and sentences from clinical
+documents</p>
+<p>sideeffect</p>
+<p>cTAKES_HOME/cTAKESdesc/sideeffectdesc/analysis_engine/SideEffectAggregateTAE.x
+ml</p>
+<p>cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/SideEffectC
+PE.xml</p>
+<p>cTAKES_HOME/testdata/sideeffecttest</p>
+<h2 id="next-steps">Next Steps</h2>
+<p>The <a href="/display/VKC/cTAKES+2.5+Component+Use+Guide">cTAKES 2.5 Component
Use
+Guide</a> will help you to
+understand in great detail each of the cTAKES components that have been
+installed. In some cases you can learn how to improve the components. However,
+before you go on to process text in production you will need to consider
+dictionaries and models.</p>
+<h3 id="dictionaries">Dictionaries</h3>
+<h4 id="bundled-umls-dictionaries">Bundled UMLS Dictionaries</h4>
+<p>cTAKES includes the complete UMLS (SNOMED-CT and RxNorm) dictionaries.</p>
+<ul>
+<li>An rxnorm_index database (a Lucene index) containing drug names from RxNorm</li>
+<li>A UMLS database (using two hsqldb tables) containing anatomical sites, procedures,
signs/symptoms, and disorders/diseases from SNOMED-CT (umls_ms_2011ab)</li>
+</ul>
+<p>To use them, you must have a UMLS username and password, and an Internet
+connection.</p>
+<p><img alt="" src="/images/icons/emoticons/warning.png" /></p>
+<p><strong>Note</strong><br />
+If you do not have a UMLS username and password, you may request one at <a href="https://uts.nlm.nih.gov/license.html">UMLS
+Terminology Services</a></p>
+<p>In order to use the UMLS dictionaries shipped with cTAKES you will need to do
+two things:</p>
+<p>(1) Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor
+files with your UMLS username and password.</p>
+<ul>
+<li>Dictionary Lookup: <cTAKES_HOME>/cTAKESdesc/lookupdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml</li>
+<li>(optional) Drug NER: <cTAKES_HOME>/cTAKESdesc/drugnerdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml</li>
+</ul>
+<p>The following shows where in the files you would make the changes. (Do not
+change the <configurationParameters> by the same name.)</p>
+<p>(2) Include the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within your
+aggregate Analysis Engine or switch to the ones provided by cTAKES. cTAKES has
+provided duplicates of shipped Analysis Engine descriptors, put UMLS in the
+name, and placed DictionaryLookupAnnotatorUMLS.xml within them for these
+components:</p>
+<ul>
+<li>Dictionary Lookup</li>
+<li>Clinical Documents pipeline</li>
+<li>Drug NER</li>
+<li>Side Effect</li>
+</ul>
+<p>So you simply need to switch to using those descriptors. For example, if you
+were using AggregateCdaProcessor.xml in the Clinical Documents pipeline you
+would switch to using AggregateCdaUMLSProcessor.xml instead and you will now
+hook into the complete dictionaries.</p>
+<p>You can, of course, modify your own aggregate Analysis Engine files and place
+the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within them.</p>
+<p>Since this is an in-memory database implementation, please be patient during
+the initial load as it could take approximately 20-30 seconds for the database
+to initialize.</p>
+<p>If you would like to go back to using the small sample dictionaries that do
+not require a UMLS username, use the DictionaryLookupAnnotator.xml (UMLS is
+not in the file name) Analyis Engine descriptor in your aggregate. Just
+removing your password from the DictionaryLookupAnnotatorUMLS.xml files will
+not switch you back to the small sample dictionaries.</p>
+<h4 id="lvg">LVG</h4>
+<p>We have successfully tested the 2008 release of the full <a href="http://lexsrv2.
+nlm.nih.gov/LexSysGroup/Projects/lvg/current/docs/userDoc/tools/lvg.html">LVG</a>
+data. In order to use this release of the full LVG data you should:</p>
+<ol>
+<li>Download either the full version or the lite version from <a href="http://lexsrv2.nlm.nih.gov/LexSysGroup/Projects/lvg/2008/web/download.html">NIH
Lexical Tools</a></li>
+<li>Extract the TGZ file that you downloaded with a tool like 7-zip (available online)
to a temporary directory. On some operating systems, like Windows, this may need to be done
in two steps, 1) to uncompress and 2) to unzip.</li>
+<li>Replace the directory <cTAKES_HOME>/resources/lvgresources/lvg/data/HSqlDb
with data/HSqlDb from your extracted download. Replacing the entire directory is appropriate.</li>
+<li>In the future, you can upgrade to later versions of LVG by editing the <cTAKES_HOME>/resources/lvgresources/lvg/data/config/lvg.properties
file, replacing "lvg2008" with the name of the new release.</li>
+</ol>
+<h4 id="building-your-own-dictionaries">Building Your Own Dictionaries</h4>
+<p>To install customized dictionaries for RxNorm, SNOMED-CT, or other
+vocabularies that are available through the UMLS, see the following posts on
+the cTAKES forums:</p>
+<ul>
+<li><a href="https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=423">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=423</a></li>
+<li><a href="https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=80&amp;start=20#p1459">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=80&amp;start=20#p1459</a></li>
+</ul>
+<h3 id="models">Models</h3>
+<p>Some models included in cTAKES may not represent your data distribution well.
+If you want to build or train your own models, please read the <a href="/display/VKC/cTAKES+2.5+Component+Use+Guide">cTAKES
2.5
+Component Use Guide</a>,
+particularly:</p>
+<ul>
+<li><a href="https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+-+Core#cTAKES2.5-Core-ToolsTrainingasentencedetectormodel">Training
a sentence detector model</a></li>
+<li>Training a Part of Speech (POS) tagger model (Building a model Obtaining training
data)</li>
+<li>Creating a Part of Speech (POS) tag dictionary (Building a tag dictionary)</li>
+<li>Training a chunker model (Building a model - Prepare GENIA training data)</li>
+<li>Training a dependency parser (Dependency Parser)</li>
+</ul>
   </div>
  
  <div id="footera">



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