svn commit: r844143 - in /websites/staging/ctakes/trunk/content: ./ ctakes/3.0.0/user-guide-3.0.html

[bu...@apache.org]

Author: buildbot
Date: Fri Dec 28 17:01:45 2012
New Revision: 844143

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 Fri Dec 28 17:01:45 2012
@@ -1 +1 @@
-1426576
+1426583

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 Fri Dec 28 17:01:45 2012
@@ -97,50 +97,58 @@
 <p>If you plan to use the full LVG resource (recommended)</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 to a temporary directory. If you are on Windows, you can use a tool like 7-zip (available online). </li>
-<li>This may need to be done in two steps:
- 1) to uncompress and 2) to unzip.</li>
+<li>Extract the tgz file that you downloaded to a temporary directory. If you are on Windows, you can use a tool like 7-zip (available online). 
+    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>
 </ol>
 <p>If you plan to use the UMLS resources:</p>
 <ol>
 <li>
 <p>Download the UMLS resources from 
-http://sourceforge.net/projects/ctakesresources/files/</p>
+<a href="http://sourceforge.net/projects/ctakesresources/files/">http://sourceforge.net/projects/ctakesresources/files/</a></p>
 </li>
 <li>
 <p>Unpack the UMLS resources and add them to the resources directory</p>
 </li>
 <li>
 <p>Also either set/export env variables like this</p>
-</li>
-</ol>
 <p>export ctakes.umlsuser=[username], ctakes.umlspw=[password]</p>
 <p>or add the system properties to the java args</p>
 <p>-Dctakes.umlsuser=[username]  -Dctakes.umlspw=[password]</p>
+</li>
+</ol>
 <h2 id="usage">Usage</h2>
 <h3 id="to-run-a-basic-pipeline-without-the-umls-resources">To run a basic pipeline without the UMLS resources:</h3>
 <ol>
 <li>Run bin/runctakesCVD </li>
-<li>Load an AE (analysis engine)</li>
-</ol>
+<li>
+<p>Load an AE (analysis engine)</p>
 <p>Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor</p>
-<ul>
-<li>Enter note or other text</li>
+</li>
+<li>
+<p>Enter note or other text</p>
+</li>
 <li>Run analysis engine</li>
-</ul>
+</ol>
 <p>NOTE: The included example dictionary is very small. Try a sentence such as: 
-  Patient took aspirin for knee pain</p>
+    Patient took aspirin for knee pain</p>
 <h3 id="to-run-with-the-umls-resources">To run with the UMLS resources:</h3>
 <ol>
 <li>Run bin/runctakesCVD </li>
-<li>Load an AE (analysis engine)</li>
-</ol>
+<li>
+<p>Load an AE (analysis engine)</p>
 <p>Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor</p>
-<ul>
-<li>Enter note or other text</li>
+</li>
+<li>
+<p>Enter note or other text</p>
+</li>
 <li>Run analysis engine</li>
-</ul>
+</ol>
+<h3 id="to-process-multiple-files-at-once">To process multiple files at once:</h3>
+<ol>
+<li>Run bin/runctakesCPE </li>
+</ol>
   </div>
  
  <div id="footera">