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| CTAKES:Menu cTAKES 3.0 to Include |
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| CTAKES:Menu cTAKES 3.0 to Include |
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These instructions are under construction. |
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 3.0 Developer Guide.
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Step | Example |
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1. Open a command prompt and change to the cTAKES_HOME directory.
Windows: Linux: | Code Block |
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| cd /usr/bin/cTAKES-3.0
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| cTAKES_HOME must be your current directory unless you are skilled at setting paths on your machine. |
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2. Start the CAS Visual Debugger by running this command:
Windows: | Code Block |
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| bin\runctakesCVD.bat
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Linux: | Code Block |
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| bin/runctakesCVD.sh
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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
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| <cTAKES_HOME>/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml
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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 |
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CAS Index Repository \\
\* SofaIndex \[0\] \\
\* AnnotationIndex \[1\] \\ |
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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:
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| <cTAKES_HOME>/testdata/cdptest/testinput/plaintext/testpatient_plaintext_1.txt
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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. |
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.
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