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From digital paula <cybersat...@hotmail.com>
Subject RE: cTAKES Sectionizer: how to integrate it with clinical pipeline - Solved
Date Thu, 05 Dec 2013 01:58:46 GMT



Pei,
 Okay, the sectionizer is now integrated in the clinical pipeline and I did some preliminary
testing to confirm.  I added the CDASegmentAnnotator lines that you stated to the Aggregate
Descriptor and commented the simple annotator in the flow.  In addition, I also had to comment
out this in order for the Aggregate descriptor to save with no error:
<!--
<configurationParameter>

<name>SegmentID</name>

<description/>

<type>String</type>

<multiValued>false</multiValued>

<mandatory>false</mandatory>

<overrides>

<parameter>SimpleSegmentAnnotator/SegmentID</parameter>  

</overrides>

</configurationParameter>

-->
 
I didn't see it in the trunk so I  manually added the text file ccda_sections.txt taken from
the sandbox.    I added it under src/main/resources in ctakes-core:
org/apache/ctakes/core/sections/ccda_sections.txt
I tested on a few narratives and I'm attaching what returned using CVD tool for one of them.
   The segmentID was populated with segmentID:  1.3.6.1.4.1.19376.1.5.3.1.3.4.     I looked
in the ccda_sections.txt file and this was it: 1.3.6.1.4.1.19376.1.5.3.1.3.4,10164-2,HISTORY
OF PRESENT ILLNESS,brief history of physical illness,history of present illness,history of
the present illness
 I looked back in the narrative and the heading was:  HISTORY OF PRESENT ILLNESS: The patient.....
 
I just tested on a few narratives and though that hardly constitutes  testing because I need
to resolve a more urgent issue for my research but will return to this for full testing entailing
the application to all of my narratives.   However, from a preliminary perspective, it looks
good....only thing I'd like to see is the actual text as well for the segment heading as another
feature.  For example what displays is this:  
segmentID:  1.3.6.1.4.1.19376.1.5.3.1.3.4 
This would be good to have too:
segmentHeading:  HISTORY OF PRESENT ILLNESS: 
 
Thanks.  
 
Regards,
Paula

  > From: Pei.Chen@childrens.harvard.edu
> To: user@ctakes.apache.org
> Subject: RE: cTAKES Sectionizer:  how to integrate it with clinical pipeline
> Date: Tue, 3 Dec 2013 20:38:22 +0000
> 
> Paula,
> I moved the sectionizer to trunk now and added the xml descriptor for it.
> 
> In your Aggregate Descriptor, just add:
>     <delegateAnalysisEngine key="CDASegmentAnnotator">
>       <import location="../../../ctakes-core/desc/analysis_engine/CDASegmentAnnotator.xml"/>
>     </delegateAnalysisEngine>  
> .
> <node>CDASegmentAnnotator</node> 
> 
> If you would like to see it wired together via uimaFIT, check out the test case:
> ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java
> 
> Hope that helps.
> It might be even worthwhile defaulting to this instead of the SimpleSegment (since simple
segment does nothing more than span the entire document...)
> --Pei
> 
> 
> 
> From: digital paula [mailto:cybersation@hotmail.com] 
> Sent: Tuesday, December 03, 2013 1:51 PM
> To: user@ctakes.apache.org
> Subject: cTAKES Sectionizer: how to integrate it with clinical pipeline
> 
> Hi Pei,
>  
> Last week we discussed briefly the sectionizer and now that I have it loaded successfully
I just need to integrate it in the clinical pipeline.   
>  
> The sectionizer doesn't have a desc folder with associated XML descriptor and I understand
that things are moving towards UIMAfit so that's probably the reason why it doesn't.  Can
you provide some guidance on what you'd recommend for testing the sectionizer?  That is, should
I just create the XML Descriptor using one of the reference materials from the UIMA website
for creating descriptors or would you recommend  using UIMAfit?  If the latter, can you provide
assistance of how to integrate the sectionizer into the AggregatePlaintext AE using UIMAfit.
>  
> Thanks.
>  
> Regards,
> Paula

 		 	   		  
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