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From digital paula <cybersat...@hotmail.com>
Subject RE: cTAKES Sectionizer: how to integrate it with clinical pipeline - Solved
Date Tue, 10 Dec 2013 02:43:00 GMT
Pei, 
 
I added a couple more items 'PMH' for previous medical history,  'FH' for family history 
and 'SH' for social history.  
 
Regards,
Paula
 
From: Pei.Chen@childrens.harvard.edu
To: user@ctakes.apache.org
CC: user@ctakes.apache.org
Subject: Re: cTAKES Sectionizer:  how to integrate it with clinical pipeline - Solved
Date: Fri, 6 Dec 2013 13:50:41 +0000






Would be great if we you could share the header names/patterns from your data set if it's
not in the mappings file. 
Also side note, if you use the current DrugNER component, the sections to include for the
lookup needs to be added. 



Sent from my iPhone


On Dec 6, 2013, at 7:33 AM, "Miller, Timothy" <Timothy.Miller@childrens.harvard.edu>
wrote:






Glad you didn't encounter any issues. As far as getting it running there wasn't any particular
issue, my worry is just the 'unknown unknowns' as they say. I think for performance I have
one worry yet, especially if it is the default
 sectionizer -- does it fail gracefully and will it ever skip text? I think it should be ok
but that would be one thing it would be worth testing. So, Paula, what happens if you change
the spelling of a section header (i.e., introduce a typo)? And just out
 of curiosity, what kind of notes are you running it on? Any particular dataset?

Thanks

Tim



On 12/05/2013 09:04 PM, digital paula wrote:



Pei,   

 

I appreciate you mentioning the preferredText feature for getting section headings to render,
the first column in the mapping  file should suffice.

 

In a previous post, Tim stated that the sectionizer would be a huge benefit to the research
community once it's working or something along those lines.   What was the problem with getting
it to work?  I ask because I didn't encounter any issues during my preliminary
 testing.  All I did was an integration and minor configuration, as stated in my previous
post.   The reason why I'd like to know is so I'm cognizant of any known issues in case I
encounter them once I get back to using the sectionizer...should be in a few
 days. 

 

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 - Solved

Date: Thu, 5 Dec 2013 14:26:56 +0000





Paula,
Glad to hear it’s working for you.  Please feel free to let us know how it works out for
 you in your use case and dataset.
 
>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
Check out: 
http://svn.apache.org/r1547576 ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sections/ccda_sections.txt
  (with props)
 
>This would be good to have too: segmentHeading:  HISTORY OF PRESENT ILLNESS:

There is a field called Segment.preferredText.  Which should display the first text column
in the mappings file…




Thanks,
Pei
 



From:
 digital paula [mailto:cybersation@hotmail.com]


Sent: Wednesday, December 04, 2013 8:59 PM

To: 
user@ctakes.apache.org

Subject: RE: cTAKES Sectionizer: how to integrate it with clinical pipeline - Solved


 


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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