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1. Open a command prompt and change to the cTAKES_HOME directory.
Windows:

cd \cTAKES-3.1

Linux:

cd /usr/bin/cTAKES-3.1

2. Start the CAS Visual Debugger by running this command:
Windows:

bin\runctakesCVD.bat

Linux:

bin/runctakesCVD.sh

The application may take a minute to start on slower hardware.

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

<cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml

Click Open.
Loading the analysis engine may take a minute. When the analysis engine has successfully loaded you should see a tree in the Analysis Results frame:

Wiki Markup
CAS Index Repository \\ \* SofaIndex \[0\] \\ \* AnnotationIndex \[1\] \\

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:

<cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt

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.

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:

CAS Index Repository
* AnnotationIndex
 * uima.tcas.Annotation
  * org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
   - org.apache.ctakes.typesystem.type.textsem.EntityMention

or

   * org.apache.ctakes.typesystem.type.textsem.EventMention
    - org.apache.ctakes.typesystem.type.textsem.EventMention.MedicationEventMention

Then select org.apache.ctakes.typesystem.type.textsem.EntityMention or
org.apache.ctakes.typesystem.type.textsem.EventMention.MedicationEventMention.
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 the CAS Visual Debugger (CVD) application if you wish.

1. Open a command prompt and change to the cTAKES_HOME directory:
Windows:

cd C:\cTAKES3.1

Linux:

cd /usr/bin/cTAKES3.1

2. Start the collection processing engine by running this command:
Windows:

bin\runctakesCPE.bat

Linux:

bin/runctakesCPE.sh

The application may take a minute to start on slower hardware.

3. This will bring up the Collection Processing Engine Configurator. In the Menu bar click File >Open CPE Descriptor

4. Navigate to the file

<cTAKES_HOME>/cTAKESdesc/cdpdesc/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml

Click Open.

5. Click the Play button (green/blue play arrow near the bottom).

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.

7. Close the CPE application. You may be prompted to save changes. Since this was just a test you may click the No button.

8. Open a new command prompt and change to the <cTAKES_HOME>

9. To test the results there is a comparison tool that will help show that the results match expectations with the following syntax:

java -cp cTAKESctakes-utils-3.0.0.jar eduorg.mayoapache.bmictakes.utils.xcas_comparison.Compare
<First File> <Second File> <diff-html>

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:

java -cp cTAKESctakes-utils-3.0.0.jar eduorg.mayoapache.bmictakes.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

Linux:

java edu.mayo.bmi. -cp ctakes-utils-3.0.0.jar org.apache.ctakes.utils.xcas_comparison.Compare \
"/usr/bin/cTAKES3.1/testdata/cdptest/testoutput/plaintext\sample_note_plaintext.xml" \
"/usr/bin/cTAKES3.1/testdata/cdptest/testsampleoutput/plaintext/sample_note_plaintext.xml" \
/tmp/diff-html.html

10. The resulting file will open for you. Look at the comparison to see the annotations resulting from this pipeline.
Windows:

c:\stuff\diff-html.html

Linux:

/tmp/diff-html.html

Clinical Document Pipeline

the complete cTAKES pipeline to obtain majority of cTAKES annotations

cdp

cTAKES_HOME/cTAKESdesc/cdpdescdesc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml

cTAKES_HOME/cTAKESdesc/cdpdesc/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml

cTAKES_HOME/testdata/cdptest

Chunker

obtain cTAKES chunking annotations

chunker

cTAKES_HOME/cTAKESdescdesc/chunkerdesc/analysis_enginectakes-chunker/desc/ChunkerAggregate.xml

cTAKES_HOME/cTAKESdescdesc/chunkerdesc/collection_processing_enginectakes-chunker/desc/ChunkerCPE.xml

cTAKES_HOME/testdata/chunkertest

Dependency Parser

obtain dependency parsing tree

dp

cTAKES_HOME/cTAKESdesc/dpdesc/desc/ctakes-dependency-parser/desc/analysis_engine/ClearParserTokenizedInfPosAggregateClearParserSRLTokenizedInfPosAggregate.xml

cTAKES_HOME/cTAKESdesc/dpdesc/desc/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserCPEClearParserTestCPE.xml

cTAKES_HOME/testdata/dptest

Drug NER

the annotator to obtain drug annotations

drugner

cTAKES_HOME/cTAKESdesc/drugnerdesc/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcesor.xml

cTAKES_HOME/cTAKESdesc/drugnerdescdesc/ctakes-drug-ner/desc/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/desc/ctakes-dictionary-lookup/desc/analysis_engine/TestAggregateTAE.xml

cTAKES_HOME/cTAKESdesc/lookupdesc/desc/ctakes-dictionary-lookup/desc/collection_processing_engine/LookupCPE.xml

cTAKES_HOME/testdata/lookuptest

PAD Term Spotter

identifying terms related to PAD

pad

cTAKES_HOME/cTAKESdesc/paddescdesc/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml

cTAKES_HOME/cTAKESdesc/paddesc/desc/ctakes-pad-term-spotter/desc/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/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml

cTAKES_HOME/cTAKESdesc/smokingdesc/desc/ctakes-smoking-status/desc/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/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml

cTAKES_HOME/cTAKESdesc/sideeffectdesc/collection_processing_engine/desc/ctakes-side-effect/desc/cpe/SideEffectCPE.xml

cTAKES_HOME/testdata/sideeffecttest