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Comment: explain where users who downloaded binary can get a copy of testpatient_plaintext_1.txt

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Step

Example

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

Note

It is best if <cTAKES_HOME> is your current directory. The scripts will change directories, so being home to run the command is best.


Windows:

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cd \apache-ctakes-3.0.0-incubating

Linux:

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cd /usr/local/apache-ctakes-3.0.0-incubating

2. Start the CAS Visual Debugger by running this command:
The application may take a minute to start on slower hardware.

Windows:

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bin\runctakesCVD.bat

Linux:

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bin/runctakesCVD.sh

3. Copy the example text from the next cell in this table and paste the contents into the Text section of CVD, replacing the text that is already there.

This file used to be in a binary distribution as well:
<cTAKES_HOME>/desc
Info

If you have been directed here as a developer the path to a copy of this file is here:

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<cTAKES_HOME>/ctakes-clinical-pipeline/src/testdata/plaintext/testpatient_plaintext_1.txt
Warning


You can also download a copy of the file from

https://svn.apache.org/repos/asf/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/src/test/testdatadata/plaintext/testpatient_plaintext_1.txt
Is it only in src now? Does it not exist?Image Added


Code Block
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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.

4. 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

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


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

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


5. From the menu bar, click Run -> Run AggregatePlaintextProcessor.


6. You'll get a list of all the annotations for this clinical document in the Analysis Results frame. Annotations such as concepts mentioned, division by sentence, etc from the pipeline are viewable. To see one, in the Analysis Results frame, click on the key in front of:

CAS Index Repository
* AnnotationIndex
 * uima.tcas.Annotation
  * org.apache.ctakes.medfacts.types.Concept

This will show an AnnotationIndex 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 like the concept of the problem Hyperlipidemia.

For a medication example select this

CAS Index Repository
* AnnotationIndex
 * uima.tcas.Annotation
  * org.apache.ctakes.typsystem.type.textsem.IdentifiedAnnotation
   * org.apache.ctakes.typsystem.type.textsem.EventMention
    * org.apache.ctakes.typsystem.type.textsem.MedicationEventMention

Now select items in the lower frame to see the text being annotated.

You may close the CAS Visual Debugger (CVD) application if you wish.


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