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Posted to commits@ctakes.apache.org by bu...@apache.org on 2012/11/15 20:54:08 UTC
svn commit: r838473 - in /websites/staging/ctakes/trunk/content: ./
ctakes/3.0.0/user-guide-3.0.html
Author: buildbot
Date: Thu Nov 15 19:54:07 2012
New Revision: 838473
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 Thu Nov 15 19:54:07 2012
@@ -1 +1 @@
-1409941
+1409954
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 Thu Nov 15 19:54:07 2012
@@ -112,7 +112,7 @@ Save the file to a temporary location on
</li>
<li>
<p>Unzip the ZIP file into a directory that you want to be the cTAKES installed home directory.
-This directory we will call <strong>cTAKES_HOME</strong>. You will need to refer to this later. <strong>Windows</strong>: <code>c:\cTAKES-3.0</code> <strong>Linux</strong>: <code> /usr/bin/cTAKES-3.0</code><br />
+This directory we will call <strong><cTAKES_HOME></strong>. You will need to refer to this later. <strong>Windows</strong>: <code>c:\cTAKES-3.0</code> <strong>Linux</strong>: <code> /usr/bin/cTAKES-3.0</code><br />
</p>
</li>
</ol>
@@ -120,7 +120,7 @@ This directory we will call <strong>cTAK
<p>cTAKES allows you to use most components in two different ways:</p>
<ol>
<li>Using cTAKES CAS Visual Debugger (CVD) to view the results stored as XMI files or run the annotators or</li>
-<li>Using cTAKES collection processing engine (CPE) to process documents in cTAKES_HOME/testdata directory</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>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>
@@ -128,10 +128,10 @@ is to let you browse all the data that i
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 />
+<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 />
<br />
-<strong>Note:</strong> cTAKES_HOME must be your current directory unless you are skilled at setting
+<strong>Note:</strong> <cTAKES_HOME> must be your current directory unless you are skilled at setting
paths on your machine.</p>
</li>
<li>
@@ -140,11 +140,11 @@ paths on your machine.</p>
</li>
<li>
<p>An analysis engine (AE) needs to be loaded in order to process text.<br />
-Use the <strong>Run</strong> -> <strong>Load AE</strong> menu bar command. Navigate to the file: <code><cTAKES_HOME>/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</code> Click <strong>Open</strong>.</p>
+Use the <strong>Run</strong> -> <strong>Load AE</strong> menu bar command. Navigate to the file: <code><cTAKES_HOME>/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</code> 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>
+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
@@ -191,10 +191,10 @@ Text frame on the right.</li>
<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>
-<p>Open a command prompt and change to the cTAKES_HOME directory.<br />
+<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 />
<br />
-<strong>Note:</strong> cTAKES_HOME must be your current directory unless you are skilled at setting
+<strong>Note:</strong> <cTAKES_HOME> must be your current directory unless you are skilled at setting
paths on your machine.</p>
</li>
<li>
@@ -206,7 +206,7 @@ paths on your machine.</p>
Menu bar click <strong>File</strong> > <strong>Open CPE Descriptor</strong>.</p>
</li>
<li>
-<p>Navigate to the file: <code><cTAKES_HOME>/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</code> Click <strong>Open</strong>.</p>
+<p>Navigate to the file: <code><cTAKES_HOME>/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</code> Click <strong>Open</strong>.</p>
</li>
<li>
<p>Click the Play button (green/blue <strong>play arrow</strong> near the bottom).</p>
@@ -225,7 +225,7 @@ was just a test you may click the <stron
<h3 id="validate-cpe-results">Validate CPE Results</h3>
<ol>
<li>
-<p>Open a command prompt and change to the cTAKES_HOME directory.<br />
+<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 />
</p>
</li>
@@ -287,62 +287,66 @@ following table.</p>
<td>cTAKES_HOME/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</td>
<td>cTAKES_HOME/testdata/cdptest</td>
</tr>
+<tr>
+<td>Chunker</td>
+<td>obtain cTAKES chunking annotations</td>
+<td>chunker</td>
+<td>cTAKES_HOME/cTAKESdesc/chunkerdesc/analysis_engine/ChunkerAggregate.xml</td>
+<td>cTAKES_HOME/cTAKESdesc/chunkerdesc/collection_processing_engine/ChunkerCPE.xml</td>
+<td>cTAKES_HOME/testdata/chunkertest</td>
+</tr>
+<tr>
+<td>Dependency Parser</td>
+<td>obtain dependency parsing tree</td>
+<td>dp</td>
+<td>cTAKES_HOME/cTAKESdesc/dpdesc/analysis_engine/ClearParserTokenizedInfPosAggregate.xml</td>
+<td>cTAKES_HOME/cTAKESdesc/dpdesc/collection_processing_engine/ClearParserCPE.xml</td>
+<td>cTAKES_HOME/testdata/dptest</td>
+</tr>
+<tr>
+<td>Drug NER</td>
+<td>the annotator to obtain drug annotations</td>
+<td>drugner</td>
+<td>cTAKES_HOME/cTAKESdesc/drugnerdesc/analysis_engine/DrugAggregatePlaintextProcesor.xml</td>
+<td>cTAKES_HOME/cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainText_CPE.xml</td>
+<td>cTAKES_HOME/testdata/drugnertest</td>
+</tr>
+<tr>
+<td>Dictionary Lookup</td>
+<td>mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm</td>
+<td>lookup</td>
+<td>cTAKES_HOME/cTAKESdesc/lookupdesc/analysis_engine/TestAggregateTAE.xml</td>
+<td>cTAKES_HOME/cTAKESdesc/lookupdesc/collection_processing_engine/LookupCPE.xml</td>
+<td>cTAKES_HOME/testdata/lookuptest</td>
+</tr>
+<tr>
+<td>PAD Term Spotter</td>
+<td>identifying terms related to PAD</td>
+<td>pad</td>
+<td>cTAKES_HOME/cTAKESdesc/paddesc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml</td>
+<td>vcTAKES_HOME/cTAKESdesc/paddesc/collection_processing_engine/Radiology_Sample.xml</td>
+<td>cTAKES_HOME/testdata/padtest</td>
+</tr>
+<tr>
+<td>Smoking Status</td>
+<td>the annotator to obtain document or patient-level smoking status</td>
+<td>smoking</td>
+<td>cTAKES_HOME/cTAKESdesc/smokingdesc/analysis_engine/SimulatedProdSmokingTAE.xml</td>
+<td>cTAKES_HOME/cTAKESdesc/smokingdesc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml</td>
+<td>cTAKES_HOME/testdata/smokingtest</td>
+</tr>
+<tr>
+<td>Side Effect</td>
+<td>the annotator to find side effect mentions and sentences from clinical documents</td>
+<td>sideeffect</td>
+<td>cTAKES_HOME/cTAKESdesc/sideeffectdesc/analysis_engine/SideEffectAggregateTAE.xml</td>
+<td>cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/SideEffectCPE.xml</td>
+<td>cTAKES_HOME/testdata/sideeffecttest</td>
+</tr>
</tbody>
</table>
-<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
+<p>The <a href="3.0.0/component-use-guide-3.0">cTAKES 3.0 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
@@ -356,31 +360,45 @@ dictionaries and models.</p>
</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><strong>Note</strong>: 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
+<ol>
+<li>Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor
+files with your UMLS username and password.</li>
+<li>Dictionary Lookup: <cTAKES_HOME>/cTAKESdesc/lookupdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml</li>
+<li>(optional) Drug NER: <cTAKES_HOME>/cTAKESdesc/drugnerdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
+The following shows where in the files you would make the changes. (Do not
+change the <configurationParameters> by the same name.)
+<pre>
+<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>
+</pre></li>
+<li>
+<p>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>
+<li>
+<p>Dictionary Lookup</p>
+</li>
<li>Clinical Documents pipeline</li>
<li>Drug NER</li>
<li>Side Effect</li>
-</ul>
+</ol>
<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
@@ -402,8 +420,8 @@ data. In order to use this release of th
<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>
+<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