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From blee...@apache.org
Subject svn commit: r1408960 - /incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
Date Tue, 13 Nov 2012 21:06:50 GMT
Author: bleeker
Date: Tue Nov 13 21:06:50 2012
New Revision: 1408960

URL: http://svn.apache.org/viewvc?rev=1408960&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=1408960&r1=1408959&r2=1408960&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 Tue Nov 13 21:06:50
2012
@@ -18,508 +18,4 @@ Notice:    Licensed to the Apache Softwa
 
 #cTAKES 3.0 User Guide
 
-These instructions are for end users. With these instructions you can install
-cTAKES, configure it, and use it to process text (typically text associated
-with a medical record). If you were planning to expand, change, or modify the
-code within cTAKES, refer to the [cTAKES 2.5 Developer Install
-Instructions](/display/VKC/cTAKES+2.5+Developer+Install+Instructions).
-
-These instructions will cover installation and a test of the main product
-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. Optional components will also be described.
-
-Once you have finished installation of cTAKES, you will be able to see what
-cTAKES is capable of. Further exploitation of the software's ability may
-require following a few additional steps involving what dictionaries are being
-used. These are the last steps in these instructions.
-
-## Prerequisites
-
-Step
-
-Example
-
-1. Make sure you have Java 1.6 or higher. Most systems come with Java already
-installed.
-
-Run this command to check your version.
-
-If you do not you can install Java from
-[java.com](http://www.java.com/en/download/faq/develop.xml).
-
-## Install cTAKES
-
-Step
-
-Example
-
-1. Navigate to the [source downloads for a released
-version](http://sourceforge.net/projects/ohnlp/files/cTAKES) on SourceForge
-
-  
-
-2. Download the **cTAKES-2.5.zip** file.
-
-Save the file to a temporary location on your machine.
-
-![screenshot illustrating step](/download/attachments/75014322/cTAKES-2.5
--download-progress.jpg?version=1&modificationDate=1336161194000)
-
-3. Unzip (extract the contents of) the compressed file you downloaded into a
-directory that you want to be the cTAKES install location.
-
-For example, **Windows**:
-
-  
-**Linux**:   
-
-  
-This folder we will call **<cTAKES_HOME>**. You will need to refer to the
-directory later.
-
-![screenshot illustrating step](/download/attachments/75014322/cTAKES-2.5-Extr
-acting.jpg?version=1&modificationDate=1336163791000)
-
-|
-
-## Process documents using cTAKES
-
-This version allows you to test most components bundled in cTAKES in two
-different ways:
-
-  1. Using cTAKES CAS Visual Debugger (CVD) to view the results stored as XCAS files or run
the annotators or
-  2. Using cTAKES collection processing engine (CPE) to process documents in cTAKES_HOME/testdata
directory
-
-### CAS Visual Debugger (CVD)
-
-Step
-
-Example
-
-1. Open a command prompt and change to the cTAKES_HOME directory.
-
-**Windows**:   
-
-  
-**Linux**:   
-
-![](/images/icons/emoticons/warning.png)
-
-**Note**  
-
-cTAKES_HOME 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:
-
-**Windows**:   
-
-  
-**Linux**:   
-
-  
-The application may take a minute to start on slower hardware.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav6ae43931
-208c6ae30f6e836859a2bb19.png?version=1&modificationDate=1334686366000)
-
-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
-
-Click **Open**.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav74c75ed2
-8c7c02f2be44fe41d0b65a16.png?version=1&modificationDate=1334686366000)
-
-4. 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.
-
-This example file can also be found in test data:
-
-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.
-
-3. From the menu bar, click **Run** -> **Run AggregatePlaintextProcessor**.
-
-  
-You'll get a list of all the annotations in the Analysis Results frame.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav2c25a00d
-f26e72f2c00fae8d12e5c3a5.png?version=1&modificationDate=1334686366000)
-
-4. Named entities are now recognized in this clinical document. Annotations of
-MedicationEventMention and EntityMention are created. To find one, in the
-**Analysis Results frame**, click on the key in front of:
-
-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
-
-
-  
-Then select **edu.mayo.bmi.uima.core.type.****textsem.****EntityMention** or *
-*edu.mayo.bmi.uima.core.type.****textsem.****EventMention.****Medication****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.
-
-![screenshot illustrating step](/download/attachments/75014322/worddavcfd76769
-7d1e58970d516f1312a8a6e4.png?version=1&modificationDate=1334686366000)
-
-### Collection processing engine (CPE)
-
-Step
-
-Example
-
-1. Open a command prompt and change to the cTAKES_HOME directory:
-
-**Windows**:   
-
-  
-**Linux**:   
-
-![](/images/icons/emoticons/warning.png)
-
-**Note**  
-
-Note that cTAKES_HOME must be your current directory unless you are skilled at
-setting paths on your machine.
-
-2. Start the collection processing engine by running this command:
-
-**Windows**:   
-
-  
-**Linux**:   
-
-  
-The application may take a minute to start on slower hardware.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav6ae43931
-208c6ae30f6e836859a2bb19.png?version=1&modificationDate=1334686366000)
-
-3. This will bring up the Collection Processing Engine Configurator. In the
-Menu bar click **File** > **Open CPE Descriptor**
-
-![screenshot illustrating step](/download/attachments/75014322/worddavdc5a7f71
-827d9e3ef9c3f0c241804365.png?version=1&modificationDate=1334686366000)
-
-4. Navigate to the file
-
-Click **Open**.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav41b2878f
-e8e61ee02d2c07e89c106cdd.png?version=1&modificationDate=1334686365000)
-
-5. Click the Play button (green/blue **play arrow** near the bottom).
-
-![screenshot illustrating step](/download/attachments/75014322/worddav9acbe68c
-6f920e134a8eb49db96025e7.png?version=1&modificationDate=1334686365000)
-
-6. You should see that one document was processed. You did process a
-collection of documents. In this case the collection only contained one just
-to show how to do it. Close the results window.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav42012486
-af09ef9457b4022474979a83.png?version=1&modificationDate=1334686366000)
-
-7. Close the CPE application. You may be prompted to save changes. Since this
-was just a test you may click the **No** button.
-
-![screenshot illustrating step](/download/attachments/75014322/worddav1c58ee84
-960f01830ce34429b3d96c3c.png?version=1&modificationDate=1334686366000)
-
-8. Open a new command prompt and change to the <cTAKES_HOME>
-
-No example.
-
-9. To test the results there is a comparison tool that will help show that the
-results match expectations with the following syntax:
-
-Where: **_<First File>_** is the first file to compare; **_<Second File>_** is
-the second file to compare; **_<diff-html>_** is where the results are written
-to
-
-  
-Copy and paste the example at the right (next cell) 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.
-
-**Windows**:
-
-**Linux**:
-
-10. The resulting file will open for you. Look at the comparison to see the
-annotations resulting from this pipeline.
-
-**Windows:**
-
-**Linux**:
-
-![screenshot illustrating step](/download/attachments/75014322/worddavefef1435
-06073a5a3d6c91cbbab2c686.png?version=1&modificationDate=1334686366000)
-
-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.
-
-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
-
-## Next Steps
-
-The [cTAKES 2.5 Component Use
-Guide](/display/VKC/cTAKES+2.5+Component+Use+Guide) 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.
-
-### Dictionaries
-
-#### Bundled UMLS Dictionaries
-
-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)
-
-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)
-
-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
-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
-
-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
-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:
-
-  * Dictionary Lookup
-  * Clinical Documents pipeline
-  * Drug NER
-  * Side Effect
-
-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.
-
-You can, of course, modify your own aggregate Analysis Engine files and place
-the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within them.
-
-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.
-
-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.
-
-#### LVG
-
-We have successfully tested the 2008 release of the full [LVG](http://lexsrv2.
-nlm.nih.gov/LexSysGroup/Projects/lvg/current/docs/userDoc/tools/lvg.html)
-data. In order to use this release of the full LVG data you should:
-
-  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.
-
-#### Building Your Own Dictionaries
-
-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:
-
-  * [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)
-  * [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)
-
-### Models
-
-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 [cTAKES 2.5
-Component Use Guide](/display/VKC/cTAKES+2.5+Component+Use+Guide),
-particularly:
-
-  * [Training a sentence detector model](https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+-+Core#cTAKES2.5-Core-ToolsTrainingasentencedetectormodel)
-  * Training a Part of Speech (POS) tagger model (Building a model Obtaining training data)
-  * Creating a Part of Speech (POS) tag dictionary (Building a tag dictionary)
-  * Training a chunker model (Building a model - Prepare GENIA training data)
-  * Training a dependency parser (Dependency Parser)
\ No newline at end of file
+Coming soon ...
\ No newline at end of file



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