Versions Compared

Old Version 23

changes.mady.by.user Unknown User (bleeker)

Saved on

compared with

New Version 24

changes.mady.by.user Unknown User (bleeker)

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

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:

Step

Example

1. Navigate to the cTAKES downloads page for a released version on the Apache

 

2. Download the cTAKES-3.0.zip file.
Save the file to a temporary location on your machine.

Code Block
languagenone
c:\cTAKES-3.0

Linux:

Code Block
languagenone
/usr/bin/cTAKES-3.0
This folder we will call <cTAKES_HOME>. You will need to refer to the directory later.

site and download the binary package. Select a mirror site and press the Change button to modify the URL to your desired mirror location.

Windows:
Download the ZIP file.
Linux:
Take the link for the file you want and use wget to obtain the *.TAR.GZ file.

Code Block
wget http://people.apache.org/~chenpei/ctakes-3.0.0-incubating/rc5/target/apache-ctakes-3.0.0-incubating-bin.tar.gz


Warning

Need to replace the above line with the final location once cTAKES 3.0 is released.

Windows/Linux:
31

2. (Optional but recommended) Verify the downloaded files against a file signature to ensure you have the proper and complete file.

No example

3. Unzip the file you downloaded into a directory that you want to be the cTAKES install location. The compressed files contain a single directory at the top level.

Windows:

Code Block
languagenone
c:\apache-ctakes-3.0.0-incubating

Linux:

Code Block
languagenone
/apache-ctakes-3.0.0-incubating

This folder we will call <cTAKES_HOME>. You will need to refer to this directory later.

Windows:
33

Linux:

Code Block
Resolving people.apache.org... 140.211.11.9
Connecting to people.apache.org|140.211.11.9|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 763500777 (728M) [application/x-gzip]
Saving to: `apache-ctakes-3.0.0-incubating-bin.tar.gz'

13% [===========>                                     ] 106,548,331 1.13M/s eta 11m 9s


|

4. Download UMLS and model resources...


Warning

The location of these resources is not prepared yet. Replace this box with instructions.


| |

Process documents using cTAKES

This version allows you to test most components bundled in cTAKES in two different ways:

  1. Using cTAKES the bundled UIMA CAS Visual Debugger (CVD) to view the results stored as XCAS files or run the annotators or
  2. Using cTAKES collection processing engine the bundled UIMA Collection Processing Engine (CPE) to process documents in cTAKES_HOME/testdata directory

You will need a windowing environment on Linux to run these tools.

CAS Visual Debugger (CVD)

Step

Example

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

Code Block
languagenone
cd \cTAKES-3.0

Linux:

Code Block
languagenone
cd /usr/bin/cTAKES-3.0


Note
titleNote

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:

Code Block
languagenone
bin\runctakesCVD.bat

Linux:

Code Block
languagenone
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

Code Block
languagenone
<cTAKES_HOME>/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 \[1\] \\


4. 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 example file can also be found in test data:

Code Block
languagenone
<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.

...