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From build...@apache.org
Subject svn commit: r838276 - in /websites/staging/ctakes/trunk/content: ./ ctakes/3.0.0/user-guide-3.0.html
Date Tue, 13 Nov 2012 21:14:22 GMT
Author: buildbot
Date: Tue Nov 13 21:14:22 2012
New Revision: 838276

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 21:14:22 2012
@@ -1 +1 @@
-1408962
+1408965

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 21:14:22
2012
@@ -84,264 +84,124 @@
   </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|cTAKES%2B2.5%2BDeveloper%2BInstall%2BInstructions.html].</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>h2. Prerequisites</p>
-<p>Step</p>
-<p>Example</p>
-<ol>
-<li>Make sure you have Java 1.6 or higher. Most systems come with Java already installed.
\ Run this command to check your version. \</li>
-</ol>
-<p>java -version</p>
-<p>If you do not you can install Java from [java.com|http://www.java.com/en/download/faq/develop.xml].</p>
-<p>C:>java -version
+<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>
+<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>h2. Install cTAKES</p>
-<p>Step</p>
-<p>Example</p>
-<ol>
-<li>Navigate to the [source downloads for a released version|http://sourceforge.net/projects/ohnlp/files/cTAKES]
on SourceForge</li>
-</ol>
-<p>\</p>
-<ol>
-<li>Download the <em>cTAKES-2.5.zip</em> file. \ Save the file to a temporary
location on your machine.</li>
-</ol>
-<p>attachments/75014322/76808927.jpg</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. \ For example, <em>Windows</em>:
\</li>
-</ol>
-<p>c:\cTAKES-2.5</p>
-<p>\<em>Linux</em>: \</p>
-<p>/usr/bin/cTAKES-2.5</p>
-<p>\ This folder we will call <em><cTAKES_HOME></em>. You will need
to refer to the directory later.</p>
-<p>attachments/75014322/76808930.jpg\ |</p>
-<p>h2. Process documents using cTAKES</p>
-<p>This version allows you to test most components bundled in cTAKES in two different
ways:</p>
-<h1 id="using-ctakes-cas-visual-debugger-cvd-to-view-the-results-stored-as-xcas-files-or-run-the-annotators-or">Using
cTAKES CAS Visual Debugger (CVD) to view the results stored as XCAS files or run the annotators
or</h1>
-<h1 id="using-ctakes-collection-processing-engine-cpe-to-process-documents-in-ctakes_hometestdata-directory">Using
cTAKES collection processing engine (CPE) to process documents in cTAKES_HOME/testdata directory</h1>
-<p>h3. CAS Visual Debugger (CVD)</p>
-<p>Step</p>
-<p>Example</p>
-<ol>
-<li>Open a command prompt and change to the cTAKES_HOME directory. \<em>Windows</em>:
\</li>
-</ol>
-<p>cd \cTAKES-2.5</p>
-<p>\<em>Linux</em>: \</p>
-<p>cd /usr/bin/cTAKES-2.5images/icons/emoticons/warning.png<em>Note</em>\</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: \<em>Windows</em>:
\</li>
-</ol>
-<p>runctakesCVD.bat</p>
-<p>\<em>Linux</em>: \</p>
-<p>runctakesCVD.sh</p>
-<p>\ The application may take a minute to start on slower hardware.</p>
-<p>attachments/75014322/74941782.png</p>
-<ol>
-<li>An analysis engine (AE) needs to be loaded in order to process text. \ Use the
<em>Run</em> -&gt; <em>Load AE</em> menu bar command. Navigate
to the file</li>
-</ol>
-<p><cTAKES_HOME>/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</p>
-<p>Click <em>Open</em>.</p>
-<p>attachments/75014322/74941783.png</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. \ This example file can
also be found in test data:</li>
-</ol>
-<p><cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt</p>
-<p>Dr. Nutritious \\ Medical Nutrition Therapy for Hyperlipidemia \\ Referral from:
Julie Tester, RD, LD, CNSD \ Phone contact: (555) 555-1212 \ Height: 144 cm Current Weight:
45 kg Date of current weight: 02-29-2001 \ Admit Weight: 53 kg BMI: 18 kg/m2 \ Diet: General
\ Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity. \ Daily Protein
needs: 40 grams, assessed as 1.0 g/kg. \ Pt has been on a 3-day calorie count and has had
an average intake of 1100 calories. \ She was instructed to drink 2-3 cans of liquid supplement
to help promote weight gain. \ She agrees with the plan and has my number for further assessment.
May want a Resting \ Metabolic Rate as well. She takes an aspirin a day for knee pain.</p>
-<ol>
-<li>From the menu bar, click <em>Run</em> -&gt; <em>Run AggregatePlaintextProcessor</em>.
\\ You'll get a list of all the annotations in the Analysis Results frame.</li>
-</ol>
-<p>attachments/75014322/74941784.png</p>
-<ol>
-<li>Named entities are now recognized in this clinical document. Annotations of MedicationEventMention
and EntityMention are created. To find one, in the <em>Analysis Results frame</em>,
click on the key in front of: \ AnnotationIndex \ uima.tcas.Annotation \ edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation
\ edu.mayo.bmi.uima.core.type.textsem.EntityMention  \ and \ edu.mayo.bmi.uima.core.type.textsem.EventMention
\ edu.mayo.bmi.uima.core.type.textsem.EventMention.MedicationEventMention \   \\ Then select
<em>edu.mayo.bmi.uima.core.type.<strong>textsem.</strong>EntityMention</em>
or <em>edu.mayo.bmi.uima.core.type.<strong>textsem.</strong>EventMention.<strong>Medication</strong>EventMention</em>.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.</li>
-</ol>
-<p>attachments/75014322/74941785.png</p>
-<p>h3. Collection processing engine (CPE)</p>
-<p>Step</p>
-<p>Example</p>
-<ol>
-<li>Open a command prompt and change to the cTAKES_HOME directory: \<em>Windows</em>:
\</li>
-</ol>
-<p>cd C:\cTAKES2.5</p>
-<p>\<em>Linux</em>: \</p>
-<p>cd /usr/bin/cTAKES2.5images/icons/emoticons/warning.png<em>Note</em>\</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: \<em>Windows</em>:
\</li>
-</ol>
-<p>runctakesCPE.bat</p>
-<p>\<em>Linux</em>: \</p>
-<p>runctakesCPE.sh</p>
-<p>\ The application may take a minute to start on slower hardware.</p>
-<p>attachments/75014322/74941782.png</p>
-<ol>
-<li>This will bring up the Collection Processing Engine Configurator. In the Menu bar
click <em>File</em> &gt; <em>Open CPE Descriptor</em></li>
-</ol>
-<p>attachments/75014322/74941786.png</p>
-<ol>
-<li>Navigate to the file</li>
-</ol>
-<p><cTAKES_HOME>/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</p>
-<p>Click <em>Open</em>.</p>
-<p>attachments/75014322/74941773.png</p>
-<ol>
-<li>Click the Play button (green/blue <em>play arrow</em> near the bottom).</li>
-</ol>
-<p>attachments/75014322/74941774.png</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>attachments/75014322/74941775.png</p>
-<ol>
-<li>Close the CPE application. You may be prompted to save changes. Since this was
just a test you may click the <em>No</em> button.</li>
-</ol>
-<p>attachments/75014322/74941776.png</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>java -cp cTAKES.jar edu.mayo.bmi.utils.xcas_comparison.Compare
-<First File> <Second File> <diff-html></p>
-<p>Where: <em><em><First File></em></em> is the first
file to compare; <em><em><Second File></em></em> is the second
file to compare; <em><em><diff-html></em></em> is where the
results are written to \\ 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><em>Windows</em>:</p>
-<p>java -cp cTAKES.jar edu.mayo.bmi.utils.xcas_comparison.Compare ^
-"testdata\cdptest\testoutput\plaintext\sample_note_plaintext.xml" ^
-"testdata\cdptest\testsampleoutput\plaintext\sample_note_plaintext.xml" ^
-c:\stuff\diff-html.html</p>
-<p><em>Linux</em>:</p>
-<p>java edu.mayo.bmi.utils.xcas_comparison.Compare \
-"/usr/bin/cTAKES2.5/testdata/cdptest/testoutput/plaintext\sample_note_plaintext.xml" \
-"/usr/bin/cTAKES2.5/testdata/cdptest/testsampleoutput/plaintext/sample_note_plaintext.xml"
\
-/tmp/diff-html.html</p>
-<ol>
-<li>The resulting file will open for you. Look at the comparison to see the annotations
resulting from this pipeline. \<em>Windows:</em></li>
-</ol>
-<p>c:\stuff\diff-html.html</p>
-<p><em>Linux</em>:</p>
-<p>/tmp/diff-html.html</p>
-<p>attachments/75014322/74941777.png</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/ClearParserTokenizedInfPosAggregate.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/DrugAggregatePlaintextProcesor.xml</p>
-<p>cTAKES_HOME/cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainText_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_TermSpotterAnnotatorTAE.xml</p>
-<p>cTAKES_HOME/cTAKESdesc/paddesc/collection_processing_engine/Radiology_Sample.xml</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_SmokingStatus_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.xml</p>
-<p>cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/SideEffectCPE.xml</p>
-<p>cTAKES_HOME/testdata/sideeffecttest</p>
-<p>h2. []Next Steps</p>
-<p>The [cTAKES 2.5 Component Use Guide|/display/VKC/cTAKES+2.5+Component+Use+Guide]
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>
-<p>h3. []Dictionaries</p>
-<p>h4. []Bundled UMLS Dictionaries</p>
-<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>images/icons/emoticons/warning.png<em>Note</em>\If you do not have a
UMLS username and password, you may request one at [UMLS Terminology Services|https://uts.nlm.nih.gov/license.html]</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><nameValuePair>
-<name>UMLSUser</name>
-<value>
-<string>YOUR_UMLS_USERNAME_HERE</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>UMLSPW</name>
-<value>
-<string>YOUR_UMLS_PASSWORD_HERE</string>
-</value>
-</nameValuePair></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.\ 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>
-<p>h4. []LVG</p>
-<p>We have successfully tested the 2008 release of the full [LVG|http://lexsrv2.nlm.nih.gov/LexSysGroup/Projects/lvg/current/docs/userDoc/tools/lvg.html]
data. In order to use this release of the full LVG data you should:</p>
-<h1 id="download-either-the-full-version-or-the-lite-version-from-nih-lexical-toolshttplexsrv2nlmnihgovlexsysgroupprojectslvg2008webdownloadhtml">Download
either the full version or the lite version from [NIH Lexical Tools|http://lexsrv2.nlm.nih.gov/LexSysGroup/Projects/lvg/2008/web/download.html]</h1>
-<h1 id="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">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.</h1>
-<h1 id="replace-the-directory-wzxhzdk28resourceslvgresourceslvgdatahsqldb-with-datahsqldb-from-your-extracted-download-replacing-the-entire-directory-is-appropriate">Replace
the directory <cTAKES_HOME>/resources/lvgresources/lvg/data/HSqlDb with data/HSqlDb
from your extracted download. Replacing the entire directory is appropriate.</h1>
-<h1 id="in-the-future-you-can-upgrade-to-later-versions-of-lvg-by-editing-the-wzxhzdk29resourceslvgresourceslvgdataconfiglvgproperties-file-replacing-lvg2008-with-the-name-of-the-new-release">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.</h1>
-<p>h4. []Building Your Own Dictionaries</p>
-<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>[https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=423]</li>
-<li>[https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&amp;t=80&amp;start=20#p1459]</li>
-</ul>
-<p>h3. []Models</p>
-<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 [cTAKES 2.5 Component Use Guide|/display/VKC/cTAKES+2.5+Component+Use+Guide],
particularly:</p>
-<ul>
-<li>[Training a sentence detector model|https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+-+Core#cTAKES2.5-Core-ToolsTrainingasentencedetectormodel]</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>
+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
   </div>
  
  <div id="footera">



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