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Posted to commits@ctakes.apache.org by bu...@apache.org on 2012/11/15 23:17:32 UTC
svn commit: r838515 - in /websites/staging/ctakes/trunk/content: ./
ctakes/3.0.0/user-guide-3.0.html
Author: buildbot
Date: Thu Nov 15 22:17:32 2012
New Revision: 838515
Log:
Staging update by buildbot for ctakes
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websites/staging/ctakes/trunk/content/ (props changed)
websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html
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</ul>
</div>
<div id="contenta">
- <h1 id="this-page-is-under-construction">This page is under construction</h1>
-<h1 id="ctakes-30-user-guide">cTAKES 3.0 User Guide</h1>
-<p>cTAKES users are those who wish to use cTAKES as it is without code modifications.
-With these instructions you can install cTAKES, configure it, and use it to process text.
-cTAKES is built around analysis of text associated with a medical record. If you were planning to expand, change, or modify the
-code within cTAKES, refer to the <a href="/3.0.0/developer-guide-3.0">cTAKES 3.0 Developer Guide</a>.</p>
-<p>There are GUIs for the configuration and viewing of results, however, there are no summaries, statistics, or pretty graphs.
-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 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>
-<p>Further exploitation of the software's ability may require a few additional steps.
-For example, you may want to use a different dictionary in order to include vocabulary from your institution.</p>
-<h2 id="install-ctakes">Install cTAKES</h2>
-<ol>
-<li>Make sure you have <a href="http://www.java.com/en/download/faq/develop.xml">Java</a> 1.6 or higher. Many systems come with Java already
-installed. Run this command to check your version:
-<pre>
-java -version
-</pre></li>
-<li>
-<p>Download the <a href="NotYetAvailable"><strong>cTAKES-3.0.zip</strong></a> file.
-Save the file to a temporary location on your machine.</p>
-</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 />
-</p>
-</li>
-</ol>
-<h2 id="process-documents-using-ctakes">Process documents using cTAKES</h2>
-<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>
-</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>
-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 />
- <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. 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> -> <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>
-<pre>
-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.
-</pre></p>
-</li>
-<li>
-<p>From the menu bar, click <strong>Run</strong> -> <strong>Run AggregatePlaintextProcessor</strong>.
-You'll get a list of all the annotations in the Analysis Results frame.</p>
-</li>
-<li>
-<p>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 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></p>
-</li>
-<li>Then select <strong>edu.mayo.bmi.uima.core.type.textsem.EntityMention</strong> or
-<strong>edu.mayo.bmi.uima.core.type.textsem.EventMention.MedicationEventMention</strong>.<br />
-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.</li>
-</ol>
-<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 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 />
-<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
-paths on your machine.</p>
-</li>
-<li>
-<p>Start the Collection Processing Engine (CPE) by running this command. The application may take a minute to start on slower hardware:<br />
-<strong>Windows</strong>: <code>runctakesCPE.bat</code> <strong>Linux</strong>: <code>runctakesCPE.sh</code></p>
-</li>
-<li>
-<p>This will bring up the Collection Processing Engine Configurator. In the
-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>
-</li>
-<li>
-<p>Click the Play button (green/blue <strong>play arrow</strong> near the bottom).</p>
-</li>
-<li>
-<p>You should see that one document was processed. A collection of documents was processed, however,
-in this case, the collection only contained one just
-to show how to do it.<br />
-Close the results window.</p>
-</li>
-<li>
-<p>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.</p>
-</li>
-</ol>
-<h3 id="validate-cpe-results">Validate CPE Results</h3>
-<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 />
-</p>
-</li>
-<li>
-<p>To test the results, you will use a comparison tool that will help show that the
-results match expectations. Enter this command:
-<pre>
-java -cp cTAKES.jar edu.mayo.bmi.utils.xcas_comparison.Compare <First File> <Second File> <diff-html>
-</pre>
-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. For example:
-<strong>Windows</strong>:
-<pre>
-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
-</pre>
-<strong>Linux</strong>:
-<pre>
-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
-</pre>
-Copy and paste the example above, 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>
-</li>
-<li>
-<p>The resulting file will open for you. Look at the comparison to see the
-annotations resulting from this pipeline.
-<strong>Windows</strong>: <code>c:\stuff\diff-html.html</code> <strong>Linux</strong>: <code>/tmp/diff-html.html</code><br />
-</p>
-</li>
-</ol>
-<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>
-<table>
-<thead>
-<tr>
-<th>Annotator</th>
-<th>Description</th>
-<th>Abbreviated</th>
-<th>Example Analysis Engine (AE)</th>
-<th>Example Collection processing Engine (CPE)</th>
-<th>Example test data</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td>Clinical Document Pipeline</td>
-<td>the complete cTAKES pipeline to obtain majority of cTAKES annotations</td>
-<td>cdp</td>
-<td>cTAKES_HOME/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</td>
-<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>
-<h2 id="next-steps">Next Steps</h2>
-<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
-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><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>
-<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>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:</li>
-<li>Dictionary Lookup</li>
-<li>Clinical Documents pipeline</li>
-<li>Drug NER</li>
-<li>Side Effect</li>
-</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
-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&t=423">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=423</a></li>
-<li><a href="https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80&start=20#p1459">https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80&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="3.0.0/component-use-guide-3.0">cTAKES 3.0
-Component Use Guide</a>,
-particularly:</p>
-<ul>
-<li><a href="NotYet Available">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>
+ <h1 id="ctakes-30-user-guide">cTAKES 3.0 User Guide</h1>
+<p>Coming soon ...</p>
</div>
<div id="footera">