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From build...@apache.org
Subject svn commit: r838376 - in /websites/staging/ctakes/trunk/content: ./ ctakes/3.0.0/user-guide-3.0.html
Date Wed, 14 Nov 2012 21:50:31 GMT
Author: buildbot
Date: Wed Nov 14 21:50:31 2012
New Revision: 838376

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 Wed Nov 14 21:50:31 2012
@@ -1 +1 @@
-1409356
+1409448

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 Wed Nov 14 21:50:31
2012
@@ -93,7 +93,7 @@ code within cTAKES, refer to the <a href
 The results are lots of annotations recorded in <a href="http://uima.apache.org/downloads/releaseDocs/2.1.0-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.xmi_emf">UIMA
XMI files</a>.
 You can see and sift through the results, but more processing is required to reap the benefits
of the annotations.
 The process that you set up to do these annotations is called a pipeline.</p>
-<p>These instructions will cover installation of cTAKES and a test of some components

+<p>These instructions will cover installation of cTAKES and test of some components

 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.</p>
@@ -123,75 +123,68 @@ This directory we will call <strong>cTAK
 <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><a href="http://uima.apache.org/downloads/releaseDocs/2.2.2-incubating/docs/html/tools/tools.html#ugr.tools.cvd">CAS
Visual Debugger (CVD)</a></p>
+<p>The main purpose of the <a href="http://uima.apache.org/downloads/releaseDocs/2.2.2-incubating/docs/html/tools/tools.html#ugr.tools.cvd">CAS
Visual Debugger (CVD)</a> 
+is to let you browse all the data that is created when you run an component over some text.

+Components are also called an "analysis engine" as they can be made up of multiple annotators.</p>
 <ol>
 <li>
 <p>Open a command prompt and change to the cTAKES_HOME directory.<br />
 <strong>Windows</strong>: <code>cd \cTAKES-3.0</code> <strong>Linux</strong>:
<code>cd /usr/bin/cTAKES-3.0</code><br />
+&nbsp;<br />
 <strong>Note:</strong> cTAKES_HOME must be your current directory unless you
are skilled at setting
 paths on your machine.</p>
 </li>
 <li>
-<p>Start the CAS Visual Debugger by running this command:</p>
+<p>Start the CAS Visual Debugger by running this command. The application may take
a minute to start on slower hardware:<br />
+<strong>Windows</strong>: <code>runctakesCVD.bat</code> <strong>Linux</strong>:
<code>runctakesCVD.sh</code></p>
+</li>
+<li>
+<p>An analysis engine (AE) needs to be loaded in order to process text.<br />
+Use the <strong>Run</strong> -&gt; <strong>Load AE</strong> menu
bar command. Navigate to the file. Click <strong>Open</strong>.</p>
+</li>
+<li>
+<p>Copy the text in this example 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: <code><cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt</code>
+<pre>
+Dr. Nutritious</p>
 </li>
 </ol>
-<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>
+<p>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.
+</pre>
+5. From the menu bar, click <strong>Run</strong> -&gt; <strong>Run
AggregatePlaintextProcessor</strong>.
+You'll get a list of all the annotations in the Analysis Results frame.</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
+<li>Named entities are now recognized in this clinical text. 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>
+<strong>Analysis Results frame</strong>, click on the keys in front of:
+<pre>
+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
+</pre></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>The <a href="http://uima.apache.org/downloads/releaseDocs/2.2.2-incubating/docs/html/tools/tools.html#ugr.tools.cpe">Collection
Processing Engine (CPE) Configuration GUI</a> is for configuring a pipeline to process
documents (called a pipeline).
-Step</p>
-<p>Example</p>
+<p>The <a href="http://uima.apache.org/downloads/releaseDocs/2.2.2-incubating/docs/html/tools/tools.html#ugr.tools.cpe">Collection
Processing Engine (CPE) Configuration GUI</a> is for configuring components (aka analysis
engine) to process documents (called a pipeline).</p>
 <ol>
 <li>Open a command prompt and change to the cTAKES_HOME directory:</li>
 </ol>



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