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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: cTakes Assertion Component Question
Date Fri, 15 Nov 2013 16:10:53 GMT
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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