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From blee...@apache.org
Subject svn commit: r1409953 - /incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
Date Thu, 15 Nov 2012 19:47:27 GMT
Author: bleeker
Date: Thu Nov 15 19:47:26 2012
New Revision: 1409953

URL: http://svn.apache.org/viewvc?rev=1409953&view=rev
Log:
CMS commit to ctakes by bleeker

Modified:
    incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext

Modified: incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext?rev=1409953&r1=1409952&r2=1409953&view=diff
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext (original)
+++ incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext Thu Nov 15 19:47:26
2012
@@ -49,14 +49,14 @@ java -version
 Save the file to a temporary location on your machine.
 
 3. Unzip the ZIP file into a directory that you want to be the cTAKES installed home directory.
-This directory we will call **cTAKES_HOME**. You will need to refer to this later. **Windows**:
<code>c:\cTAKES-3.0</code> **Linux**: <code>    /usr/bin/cTAKES-3.0</code>
 
+This directory we will call **&lt;cTAKES_HOME&gt;**. You will need to refer to this
later. **Windows**: <code>c:\cTAKES-3.0</code> **Linux**: <code>    /usr/bin/cTAKES-3.0</code>
 
 
 ## Process documents using cTAKES
 
 cTAKES allows you to use most components in two different ways:
 
   1. Using cTAKES CAS Visual Debugger (CVD) to view the results stored as XMI files or run
the annotators or
-  2. Using cTAKES collection processing engine (CPE) to process documents in cTAKES_HOME/testdata
directory
+  2. Using cTAKES collection processing engine (CPE) to process documents in &lt;cTAKES_HOME&gt;/testdata
directory
 
 ### CAS Visual Debugger (CVD)
 
@@ -64,20 +64,20 @@ The main purpose of the [CAS Visual Debu
 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.
 
-1. Open a command prompt and change to the cTAKES_HOME directory.  
+1. Open a command prompt and change to the &lt;cTAKES_HOME&gt; directory.  
 **Windows**: <code>cd \cTAKES-3.0</code> **Linux**: <code>cd /usr/bin/cTAKES-3.0</code>
 
 &nbsp;  
-**Note:** cTAKES_HOME must be your current directory unless you are skilled at setting
+**Note:** &lt;cTAKES_HOME&gt; must be your current directory unless you are skilled
at setting
 paths on your machine.
 
 2. Start the CAS Visual Debugger by running this command. The application may take a minute
to start on slower hardware:  
 **Windows**: <code>runctakesCVD.bat</code> **Linux**: <code>runctakesCVD.sh</code>
 
 3. An analysis engine (AE) needs to be loaded in order to process text.  
-Use the **Run** -> **Load AE** menu bar command. Navigate to the file: <code><cTAKES_HOME>/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</code>
Click **Open**.
+Use the **Run** -> **Load AE** menu bar command. Navigate to the file: <code>&lt;cTAKES_HOME&gt;/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</code>
Click **Open**.
 
 4. 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>&lt;cTAKES_HOME&gt;/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt</code>
 <pre>
 Dr. Nutritious
 &nbsp;
@@ -121,10 +121,10 @@ Text frame on the right.
 
 The [Collection Processing Engine (CPE) Configuration GUI](http://uima.apache.org/downloads/releaseDocs/2.2.2-incubating/docs/html/tools/tools.html#ugr.tools.cpe)
is for configuring components (aka analysis engine) to process documents (called a pipeline).
 
-1. Open a command prompt and change to the cTAKES_HOME directory.  
+1. Open a command prompt and change to the &lt;cTAKES_HOME&gt; directory.  
 **Windows**: <code>cd \cTAKES-3.0</code> **Linux**: <code>cd /usr/bin/cTAKES-3.0</code>
 
 &nbsp;  
-**Note:** cTAKES_HOME must be your current directory unless you are skilled at setting
+**Note:** &lt;cTAKES_HOME&gt; must be your current directory unless you are skilled
at setting
 paths on your machine.
 
 2. Start the Collection Processing Engine (CPE) by running this command. The application
may take a minute to start on slower hardware:  
@@ -133,7 +133,7 @@ paths on your machine.
 3. This will bring up the Collection Processing Engine Configurator. In the
 Menu bar click **File** > **Open CPE Descriptor**.
 
-4. Navigate to the file: <code><cTAKES_HOME>/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</code>
Click **Open**.
+4. Navigate to the file: <code>&lt;cTAKES_HOME&gt;/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml</code>
Click **Open**.
 
 5. Click the Play button (green/blue **play arrow** near the bottom).
 
@@ -146,7 +146,7 @@ Close the results window.
 was just a test you may click the **No** button.
 
 ### Validate CPE Results
-1. Open a command prompt and change to the cTAKES_HOME directory.  
+1. Open a command prompt and change to the &lt;cTAKES_HOME&gt; directory.  
 **Windows**: <code>cd \cTAKES-3.0</code> **Linux**: <code>cd /usr/bin/cTAKES-3.0</code>
 
 
 2. To test the results, you will use a comparison tool that will help show that the
@@ -187,104 +187,17 @@ following table.
 |Annotator|Description|Abbreviated|Example Analysis Engine (AE)|Example Collection processing
Engine (CPE)|Example test data|
 |---------|-----------|-----------|----------------------------|------------------------------------------|-----------------|
 |Clinical Document Pipeline|the complete cTAKES pipeline to obtain majority of cTAKES annotations|cdp|cTAKES_HOME/cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml|cTAKES_HOME/cTAKESdesc/cdpdesc/collection_processing_engine/test_plaintext.xml|cTAKES_HOME/testdata/cdptest|
-
-Chunker
-
-obtain cTAKES chunking annotations
-
-chunker
-
-cTAKES_HOME/cTAKESdesc/chunkerdesc/analysis_engine/ChunkerAggregate.xml
-
-cTAKES_HOME/cTAKESdesc/chunkerdesc/collection_processing_engine/ChunkerCPE.xml
-
-cTAKES_HOME/testdata/chunkertest
-
-Dependency Parser
-
-obtain dependency parsing tree
-
-dp
-
-cTAKES_HOME/cTAKESdesc/dpdesc/analysis_engine/ClearParserTokenizedInfPosAggreg
-ate.xml
-
-cTAKES_HOME/cTAKESdesc/dpdesc/collection_processing_engine/ClearParserCPE.xml
-
-cTAKES_HOME/testdata/dptest
-
-Drug NER
-
-the annotator to obtain drug annotations
-
-drugner
-
-cTAKES_HOME/cTAKESdesc/drugnerdesc/analysis_engine/DrugAggregatePlaintextProce
-sor.xml
-
-cTAKES_HOME/cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainT
-ext_CPE.xml
-
-cTAKES_HOME/testdata/drugnertest
-
-Dictionary Lookup
-
-mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm
-
-lookup
-
-cTAKES_HOME/cTAKESdesc/lookupdesc/analysis_engine/TestAggregateTAE.xml
-
-cTAKES_HOME/cTAKESdesc/lookupdesc/collection_processing_engine/LookupCPE.xml
-
-cTAKES_HOME/testdata/lookuptest
-
-PAD Term Spotter
-
-identifying terms related to PAD
-
-pad
-
-cTAKES_HOME/cTAKESdesc/paddesc/analysis_engine/Radiology_TermSpotterAnnotatorT
-AE.xml
-
-cTAKES_HOME/cTAKESdesc/paddesc/collection_processing_engine/Radiology_Sample.x
-ml
-
-cTAKES_HOME/testdata/padtest
-
-Smoking Status
-
-the annotator to obtain document or patient-level smoking status
-
-smoking
-
-cTAKES_HOME/cTAKESdesc/smokingdesc/analysis_engine/SimulatedProdSmokingTAE.xml
-
-cTAKES_HOME/cTAKESdesc/smokingdesc/collection_processing_engine/Sample_Smoking
-Status_output_flatfile.xml
-
-cTAKES_HOME/testdata/smokingtest
-
-Side Effect
-
-the annotator to find side effect mentions and sentences from clinical
-documents
-
-sideeffect
-
-cTAKES_HOME/cTAKESdesc/sideeffectdesc/analysis_engine/SideEffectAggregateTAE.x
-ml
-
-cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/SideEffectC
-PE.xml
-
-cTAKES_HOME/testdata/sideeffecttest
+|Chunker|obtain cTAKES chunking annotations|chunker|cTAKES_HOME/cTAKESdesc/chunkerdesc/analysis_engine/ChunkerAggregate.xml|cTAKES_HOME/cTAKESdesc/chunkerdesc/collection_processing_engine/ChunkerCPE.xml|cTAKES_HOME/testdata/chunkertest|
+|Dependency Parser|obtain dependency parsing tree|dp|cTAKES_HOME/cTAKESdesc/dpdesc/analysis_engine/ClearParserTokenizedInfPosAggregate.xml|cTAKES_HOME/cTAKESdesc/dpdesc/collection_processing_engine/ClearParserCPE.xml|cTAKES_HOME/testdata/dptest|
+|Drug NER|the annotator to obtain drug annotations|drugner|cTAKES_HOME/cTAKESdesc/drugnerdesc/analysis_engine/DrugAggregatePlaintextProcesor.xml|cTAKES_HOME/cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainText_CPE.xml|cTAKES_HOME/testdata/drugnertest|
+|Dictionary Lookup|mapping cTAKES annotations to dictionaries (e.g., SNOMED_CT or RxNorm|lookup|cTAKES_HOME/cTAKESdesc/lookupdesc/analysis_engine/TestAggregateTAE.xml|cTAKES_HOME/cTAKESdesc/lookupdesc/collection_processing_engine/LookupCPE.xml|cTAKES_HOME/testdata/lookuptest|
+|PAD Term Spotter|identifying terms related to PAD|pad|cTAKES_HOME/cTAKESdesc/paddesc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml|vcTAKES_HOME/cTAKESdesc/paddesc/collection_processing_engine/Radiology_Sample.xml|cTAKES_HOME/testdata/padtest|
+|Smoking Status|the annotator to obtain document or patient-level smoking status|smoking|cTAKES_HOME/cTAKESdesc/smokingdesc/analysis_engine/SimulatedProdSmokingTAE.xml|cTAKES_HOME/cTAKESdesc/smokingdesc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml|cTAKES_HOME/testdata/smokingtest|
+|Side Effect|the annotator to find side effect mentions and sentences from clinical documents|sideeffect|cTAKES_HOME/cTAKESdesc/sideeffectdesc/analysis_engine/SideEffectAggregateTAE.xml|cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/SideEffectCPE.xml|cTAKES_HOME/testdata/sideeffecttest|
 
 ## Next Steps
 
-The [cTAKES 2.5 Component Use
-Guide](/display/VKC/cTAKES+2.5+Component+Use+Guide) will help you to
+The [cTAKES 3.0 Component Use Guide](3.0.0/component-use-guide-3.0) 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
@@ -296,31 +209,39 @@ dictionaries and models.
 
 cTAKES includes the complete UMLS (SNOMED-CT and RxNorm) dictionaries.
 
-  * An rxnorm_index database (a Lucene index) containing drug names from RxNorm
-  * A UMLS database (using two hsqldb tables) containing anatomical sites, procedures, signs/symptoms,
and disorders/diseases from SNOMED-CT (umls_ms_2011ab)
+* An rxnorm_index database (a Lucene index) containing drug names from RxNorm
+* A UMLS database (using two hsqldb tables) containing anatomical sites, procedures, signs/symptoms,
and disorders/diseases from SNOMED-CT (umls_ms_2011ab)
 
 To use them, you must have a UMLS username and password, and an Internet
 connection.
 
-![](/images/icons/emoticons/warning.png)
-
-**Note**  
-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)
+**Note**: 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).
 
 In order to use the UMLS dictionaries shipped with cTAKES you will need to do
 two things:
 
-(1) Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor
+1. Change the UMLSUser and UMLSPW &lt;nameValuePair&gt; strings in these descriptor
 files with your UMLS username and password.
-
-  * Dictionary Lookup: <cTAKES_HOME>/cTAKESdesc/lookupdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
-  * (optional) Drug NER: <cTAKES_HOME>/cTAKESdesc/drugnerdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
-
+ - Dictionary Lookup: &lt;cTAKES_HOME&gt;/cTAKESdesc/lookupdesc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
+ - (optional) Drug NER: &lt;cTAKES_HOME&gt;/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.)
-
-(2) Include the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within your
+change the &lt;configurationParameters&gt; 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>
+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
@@ -357,8 +278,8 @@ data. In order to use this release of th
 
   1. 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)
   2. 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.
-  3. Replace the directory <cTAKES_HOME>/resources/lvgresources/lvg/data/HSqlDb with
data/HSqlDb from your extracted download. Replacing the entire directory is appropriate.
-  4. 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.
+  3. Replace the directory &lt;cTAKES_HOME&gt;/resources/lvgresources/lvg/data/HSqlDb
with data/HSqlDb from your extracted download. Replacing the entire directory is appropriate.
+  4. In the future, you can upgrade to later versions of LVG by editing the &lt;cTAKES_HOME&gt;/resources/lvgresources/lvg/data/config/lvg.properties
file, replacing "lvg2008" with the name of the new release.
 
 #### Building Your Own Dictionaries
 



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