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Step | Example |
|---|
1. If you do not have a UMLS username and password, you may request one at UMLS Terminology Services. | No example |
2. Edit the following files. Find the line in each script that runs java and add the ctakes.umlsuser and ctakes.umlspw parameters to the java command with your credentials. Make sure you substitute your actual ID and password if you cut and paste the example.
Windows: | Code Block |
|---|
| <cTAKES_HOME>\bin\runctakesCVD.bat
<cTAKES_HOME>\bin\runctakesCPE.bat
|
Linux: | Code Block |
|---|
| <cTAKES_HOME>/bin/runctakesCVD.sh
<cTAKES_HOME>/bin/runctakesCPE.sh
|
| | Code Block |
|---|
|
java -Dctakes.umlsuser=<YOUR_UMLS_ID_HERE> -Dctakes.umlspw=<YOUR_UMLS_PASSSWORD_HERE> -cp ...
|
For example, if your username and password were literally myusername and mypassword, you could insert them before the -cp option so the start of the java command would look like this: | Code Block |
|---|
java -Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword -cp ...
|
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Process documents using cTAKES
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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:
| Code Block |
|---|
| cd \apache-ctakes-3.2.1
|
Linux: | Code Block |
|---|
| cd /usr/local/apache-ctakes-3.2.1
|
|
2. Start the CAS Visual Debugger by running this command:
The application may take a minute to start on slower hardware. | Windows: | Code Block |
|---|
| bin\runctakesCVD.bat
|
Linux: | Code Block |
|---|
| 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.
You can also download a copy of the file from here | | Code Block |
|---|
| 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.
If you installed the UMLS resources, use | No Format |
|---|
AggregatePlaintextFastUMLSProcessor.xml |
in this step.
Use the Run-> Load AE menu bar command. Navigate to the file | Code Block |
|---|
| <cTAKES_HOME>
/desc
/ctakes-clinical-pipeline
/desc
/analysis_engine
/AggregatePlaintextFastUMLSProcessor.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: CAS Index Repository
* SofaIndex [0]
* AnnotationIndex [1]
| 
|
5. From the menu bar, click Run -> Run AggregatePlaintextFastUMLSProcessor. Note: If you would like to TEST some simple annotators to ensure it's working without UMLS, you can just load: /desc/ctakes-core/desc/analysis_egine/SentencesAndTokensAggregate.xml | 
|
6. You'll get a list of all the annotations for this clinical document in the Analysis Results frame. Annotations such as named entities, 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.typsystem.type.textsem.IdentifiedAnnotation
* org.apache.ctakes.typsystem.type.textsem.EventMention
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 disease/disorder 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.MedicationMention
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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Also, before you go on to process text in production, you will want to consider dictionaries and models. If you did not obtain the rights yet to the UMLS resources and models, you will want to do so. Be aware, the models have been trained on data that may not match your data well enough to be effective. In some cases you might want to modify the dictionaries and train models using your own data.