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From digital paula <cybersat...@hotmail.com>
Subject RE: cTakes Assertion Component Question
Date Fri, 15 Nov 2013 16:46:41 GMT
Hi Pei,
 
Thanks for the response.   Yes, everything works as expected with what should be in IdentifiedAnnotation.
 For example,  take the text "Patient's father had adult onset diabetes. "   Under EventMention
polarity is 1, subject is family  member, confidence is 1, etc.   
 
In case attachments don't go through, this is what shows under AnnotationIndex:
AnnotationIndex[78]
     uima.tcas.DocumentationAnnotation[1]
     org.apache.ctakes.assertion.medfacts.types.Assertion[0]
     org.apache.ctakes.assertion.medfacts.types.Concept[4]
      ....
      ....
      org.apache.ctakes.typesystem.type.textsum.IdentifiedAnnotation[4]
      .....
 
What I'd like is to see this populated:
org.apache.ctakes.assertion.medfacts.types.Assertion[0] so I can see the results in AssertionType
and AssociatedConcept.
 
It appears for Concept as you can it's populated with four annotations:  org.apache.ctakes.assertion.medfacts.types.Concept[4]
but I'd like to see Assertion populated as well.    If you can see the attachment I expanded
on Concept and it shows a conceptType and conceptText  that's what I want to see for Assertion
but with it's associated features of AssertionType and  AssociatedConcept.  
 
Regards,
Paula
 
From: Pei.Chen@childrens.harvard.edu
To: user@ctakes.apache.org
Subject: RE: cTakes Assertion Component Question
Date: Fri, 15 Nov 2013 16:10:53 +0000









Hi Paula,
I believe those should be types (org.apache.ctakes.assertion.*)
 used internally by the assertion module.
What attributes do you see in IdentifiedAnnotation (along with their subclasses)?  I.e. there
should a field for ‘polarity’, ‘subject’, etc. that should get
 populated for diabetes.  Which should really be intended for downstream consumers…
 
--Pei
 
 



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


Sent: Friday, November 15, 2013 10:47 AM

To: user@ctakes.apache.org

Subject: cTakes Assertion Component Question


 

Hello again cTakes Community,

 

Okay I'm delving into the assertion component now:

https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion

 

I see that the AssertionAnnotation which is the assertionMiniPipelineAnalysisEngine was added
to the AggregatePlaintextUMLSProcessor descriptor as part of the install. 

 

1.  I typed the following text in the CVD gui:

"patient had elevated blood sugar but tests confirm no diabetes.  Patient's father had adult
onset diabetes. "

 

2.  Loaded and executed the AggregatePlaintextUMLSProcessor descriptor

 

3.  As stated in the Component Guide the output was in EntityMention and EventMention.   


 

The question that I have is that I see that there is also an Assertion type right before the
Concept type from the CVD gui.  The Concepts have annotations however there are no results
for Assertion.    I looked in the assertionAE and see that both Assertion
 and Concept type systems are there.  However,  in the capabilities section Assertion was
not listed so I just added it so it looks like this now:
<capabilities>
<capability>
<inputs>

<type
allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>

<type
allAnnotatorFeatures="true">org.apache.ctakes.assertion.medfacts.types.Concept</type>

<type
allAnnotatorFeatures="true">org.apache.ctakes.assertion.medfacts.types.Assertion</type>

<type
allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>

</inputs>



 

I reloaded and executed the AggregatePlaintextUMLSProcessor and still nothing showed up for
the Assertion annotations.  Is there something that I'm missing?   Concepts is populated but
I'd really like to see Assertion populated as well.

 

Thanks.

 

Regards,

Paula  


 		 	   		  
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