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Section
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titleContents of this Page
Table of Contents
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Include Page
CTAKES:Menu cTAKES 3.0 to Include
CTAKES:Menu cTAKES 3.0 to Include

These instructions are for end users. With these instructions you can install Apache 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.

These instructions will cover installation and a test of the main product including trained models for sentence detection and tagging parts of speech, dictionaries from a subset of the UMLS, the LVG resource, etc. Optional components are described in the Component Use Guide.

Once you have finished installing cTAKES and its separately-bundled resources, you will be able to see what cTAKES is capable of. .

Prerequisites

...

Step

Example

1. Make sure you have Java 1.6 or higher. Most systems come with Java already installed.

Run this command to check your version.

Windows and Linux:

Code Block
languagenone
java -version

Windows:

Code Block
languagenone
C:\>java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode, sharing)

...


 Linux: 
 Code Block
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tbleeker@system:/$ java -version
java version "1.6.0_22"
OpenJDK Runtime Environment (IcedTea6 1.10.1) (6b22-1.10.1-0ubuntu1)
OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)

...
Install cTAKES
 Step 
 Example 
 1. Navigate to the cTAKES downloads page on the Apache site and download the binary package. Select a mirror site and press the Change button to modify the URL to your desired mirror location before doing the download or accept the default. 

 Windows: 
 Download the ZIP file. 
 Linux: 
 Use wget to obtain the *.TAR.GZ file. 
 wget <URL of the file from downloads> 

 Info
The download time will be commensurate with ~165MB of data.
 Windows: 
 Image Added
 Linux: 
 Code Block
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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
...
 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. This folder we will call <cTAKES_HOME>. You will need to refer to this directory later. 

 Windows: 
 Code Block
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C:\apache-ctakes-3.0.0-incubating

...
Linux: 
 Code Block
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/usr/local/apache-ctakes-3.0.0-incubating

...
 Windows: 
 Image Added
 Linux: 
 Code Block
languagenone
tar -xvf apache-ctakes-3.0.0-incubating-bin.tar.gz -C /usr/local 
...
 4. 
...
 Download 
...
cTAKES 
...
 3.0 
...
 Dictionaries 
...
 and 
...
 models
...
. 
...

 Info
Due to licensing considerations and easy of installability, one download from an external location was established with all the resources you will need. Licensing for these resources is found within the download.
Go to http://sourceforge.net/projects/ctakesresources/files/
...
 and 
...
 download 
...
 the 
...
 ZIP 
...
 file 
...
 with 
...
 a 
...
 matching 
...
 version 
...
 from 
...
 the 
...
 ctakesresources 
...
 project. 
...

 Download 
...
 time 
...
 will 
...
 be 
...
 commensurate 
...
 with 
...
 1GB 
...
 of 
...
 data. 
...

 Unzip 
...
 the 
...
 files 
...
 into 
...
 a 
...
 temporary 
...
 location. 
...
Windows
...
: 
...

 Code Block
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C:\temp\ctakes-resources-3.0.1\resources
...
Linux
...
: 
...

 Code Block
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/tmp/ctakes-resources-3.0.1/resources
...
 5. 
...
 Copy 
...
 (or 
...
 move) 
...
 the 
...
 resources 
...
 to 
...
 cTAKES_HOME. 
...

 Copy the contents of the temporary resources directory (and all sub-directories) 
...
 to 
...
 <cTAKES_HOME>/resources. 
...

 Info
There may be conflicts while taking this action. Overwrite the cTAKES_HOME files with those in the resources download.


 Windows: 
 Code Block
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xcopy /s C:\temp\ctakes-resources-3.0.1\resources C:\apache-ctakes-3.0.0-incubating\resources
...
Linux
...
: 
...

 Code Block
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cp /tmp/ctakes-resources-3.0.1/resources/* /usr/local/apache-ctakes-3.0.0-incubating/resources/*
...
Process documents using cTAKES
This version allows you to test most components bundled in cTAKES in two different ways:
  1. Using the bundled UIMA CAS Visual Debugger (CVD) to view the results stored as XCAS files or run the annotators
  2. Using the bundled UIMA Collection Processing Engine (CPE) to process documents in cTAKES_HOME/testdata 
...
  1.  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. 
 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
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cd \apache-ctakes-3.0.0-incubating

...
Linux:
 Code Block
languagenone
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
...
:
...
 Code Block
...
language
...
none
...
bin\runctakesCVD.bat

...
Linux:
 Code Block
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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. 
...


 You can also download a copy of the file from here
 Code Block
langnone
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 

 Code Block
languagenone
<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 \[1\] \\  
...
 Image Added
 5. From the menu bar, click Run -> Run AggregatePlaintextProcessor. 
 Image Added
 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. 
...
 Image Added
Collection Processing Engine (CPE)
 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
languagenone
cd \apache-ctakes-3.0.0-incubating

Linux:
 Code Block
languagenone
cd /usr/local/apache-ctakes-3.0.0-incubating
...


 2. Create a directory for some test data. 
 Windows:mkdir testdata 
 3. Download this sample file and place it into the testdata directory. 
 No example 
 4. Start the collection processing engine by running this command: 
 The application may take a minute to start on slower hardware. 
 Windows:
 Code Block
languagenone
bin\runctakesCPE.bat

...
Linux:
 Code Block
languagenone
bin/runctakesCPE.sh

...
 5. 
...
 This 
...
 will 
...
 bring 
...
 up 
...
 the 
...
 Collection 
...
 Processing 
...
 Engine 
...
 Configurator. 
...
 In 
...
 the 
...
 Menu 
...
 bar 
...
 click 
...
File
...
 >
...
Open 
...
 CPE 
...
Descriptor
 Image Added 
 6. Navigate to the file
 Code Block
langnone

<cTAKES_HOME>
  /desc
    /ctakes-clinical-pipeline
...


...
      /desc
        /collection_processing_engine
...

          /test1.xml
...



 Click 
...
Open
...
. 
...
 No 
...
example 
 7. 
...
 Change 
...
 the 
...
 Collection 
...
 reader 
...
 input 
...
 directory 
...
 to 
...
 testdata 
...
 and 
...
 the 
...
 CAS 
...
 Consumer 
...
 output 
...
 directory 
...
 to 
...
 testdata/output 
...
 in 
...
 the 
...
 CPE 
...
fields 
 45 
 8. Click the Play button (green/blue 
...
play 
...
 arrow
...
 near 
...
 the 
...
 bottom). 
...

 Info
What just happened? 
...
 You 
...
 placed 
...
 a 
...
 sample 
...
 CDA 
...
 document 
...
 into 
...
 the 
...
 input 
...
 of 
...
 a 
...
 pipeline. 
...
 The 
...
 pipeline 
...
 was 
...
 a 
...
 file 
...
 system 
...
 reader 
...
 that 
...
 will 
...
 process 
...
 all 
...
 files 
...
 in 
...
 a 
...
 directory. 
...
 The 
...
 processing 
...
 was 
...
 accomplished 
...
 by 
...
 the 
...
 chunker 
...
 cTAKES 
...
 component 
...
 (noted 
...
 by 
...
 the 
...
 descriptor 
...
 that 
...
 you 
...
 opened). 
...
 One 
...
 resulting 
...
 file 
...
 for 
...
 each 
...
 input 
...
 file 
...
 was 
...
 placed 
...
 into 
...
 the 
...
 output 
...
 directory. 
...
 This 
...
 output 
...
 file 
...
 is 
...
 an 
...
 XML 
...
 file 
...
 that 
...
 annotates 
...
 the 
...
 noun 
...
 phrases 
...
 and 
...
 verb 
...
 phrases.
...
 Image Added 
 9. 
...
 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. 
...
 44 
 10. 
...
 Close 
...
 the 
...
 CPE 
...
 application. 
...
 You 
...
 may 
...
 be 
...
 prompted 
...
 to 
...
 save 
...
 changes. 
...
 Since 
...
 this 
...
 was 
...
 just 
...
 a 
...
 test 
...
 you 
...
 may 
...
 click 
...
 the 
...
No
...
 button. 
...
 No 
...
example 
Using the same CVD and CPE programs in the manner described above, you can test all the other components. The analysis engines and collection processing engines shipped with cTAKES for some of the annotators are described in the following table.
 Annotator 
 Description 
 Abbreviated 
 Example Aggregate Analysis Engine (AE) 
 Example Collection processing Engine (CPE) 
 Clinical Document Pipeline 
 the complete cTAKES pipeline to obtain majority of cTAKES annotations 
 cdp 
 cTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml 
...
 cTAKES_HOME/desc/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml 
...
 Chunker 
 obtain cTAKES chunk annotations 
 chunker 
 NA 
 NA 
 Dependency Parser 
 obtain dependency parsing tree 
 dependency 
 cTAKES_HOME/desc/ctakes-dependency-parser/desc/analysis_engine/ClearParserSRLTokenizedInfPosAggregate.xml 
...
 cTAKES_HOME/desc/ctakes-dependency-parser/desc/collection_processing_engine/ClearParserTestCPE.xml 
...
 Drug 
...
 NER 
...
 the 
...
 annotator 
...
 to 
...
 obtain 
...
 drug 
...
 annotations 
...
 drugner 
 cTAKES_HOME/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcesor.xml 
...
 cTAKES_HOME/desc/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml 
...
 Dictionary 
...
 Lookup 
...
 mapping 
...
 cTAKES 
...
 annotations 
...
 to 
...
 dictionaries 
...
 (e.g., 
...
 SNOMED_CT 
...
 or 
...
 RxNorm 
...
 dictionary 
 cTAKES_HOME/desc/ctakes-dictionary-lookup/desc/analysis_engine/TestAggregateTAE.xml 
...
 NA 
 PAD Term Spotter 
 identifying terms related to PAD 
 padtermspotter 
 cTAKES_HOME/desc/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml 
...
 cTAKES_HOME/desc/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_Sample.xml 
...
 Relation 
...
 Extractor 
...
 annotate 
...
 certain 
...
 relations 
...
 between 
...
 certain 
...
 Event, 
...
 Entity, 
...
 and 
...
 Modifier 
...
 annotations 
...
 relation-extractor 
...
 cTAKES_HOME/desc/ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml 
...
 N/A 
...
 Smoking 
...
 Status 
...
 the 
...
 annotator 
...
 to 
...
 obtain 
...
 document 
...
 or 
...
 patient-level 
...
 smoking 
...
 status 
...
 smokingstatus 
 cTAKES_HOME/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml 
...
 cTAKES_HOME/desc/ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml 
...
 Side 
...
 Effect 
...
 the 
...
 annotator 
...
 to 
...
 find 
...
 side 
...
 effect 
...
 mentions 
...
 and 
...
 sentences 
...
 from 
...
 clinical 
...
 documents 
...
 sideeffect 
 cTAKES_HOME/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml 
...
 cTAKES_HOME/desc/ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml 
...

Next Steps
The cTAKES 3.0 
...
 Component 
...
 Use 
...
 Guide
...
 will 
...
 help 
...
 you 
...
 to 
...
 understand, 
...
 in 
...
 great 
...
 detail, 
...
 each 
...
 of 
...
 the 
...
 cTAKES 
...
 components 
...
 that 
...
 have 
...
 been 
...
 installed. 
...
 In 
...
 some 
...
 cases 
...
 you 
...
 can 
...
 learn 
...
 how 
...
 to 
...
 improve 
...
 the 
...
 components.
...
Also, 
...
 before 
...
 you 
...
 go 
...
 on 
...
 to 
...
 process 
...
 text 
...
 in 
...
 production 
...
 you 
...
 will 
...
 want 
...
 to 
...
 consider 
...
dictionaries
...
 and 
...
models
...
. 
...
 The 
...
 models 
...
 (within 
...
 the 
...
 separate 
...
 resources 
...
 download) 
...
 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
...
 on 
...
 your 
...
 own 
...
 data.