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:[email protected]] Sent: Friday, November 15, 2013 10:47 AM To: [email protected] 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
