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From Tom Devel <deve...@gmail.com>
Subject Include the smoking status detection in AggregatePlaintextFastUMLSProcessor.xml
Date Thu, 16 Apr 2015 23:29:38 GMT
Hi,

I am using the smoking status AE from SimulatedProdSmokingTAE.xml, it works
fine, I can see the smoking status annotation in the CVD.

Now I would like to include the smoking status detection in the clinical
pipeline of AggregatePlaintextFastUMLSProcessor.xml, so that when I run the
clinincal pipeline, the smoking status will also be determined.

How can I do this?

I am thinking to just put the nodes from the fixed flow of
SimulatedProdSmokingTAE.xml into the fixed flow of
AggregatePlaintextFastUMLSProcessor.xml, is this the right approach?

If so, at which exact place in the clinical pipeline fixed flow should
these nodes be added?

Is there a preferred place (such as append after the last node or put
before the first node) ?

Can a wrong position or ordering of the smoking status nodes damage/corrupt
the rest of the annotations?

SimulatedProdSmokingTAE.xml contains these lines with the fixed flow:

<fixedFlow>
<node>ExternalBaseAggregateTAE</node>
<node>SentenceAdjuster</node>
<node>ClassifiableEntriesAnnotator</node>
</fixedFlow>

AggregatePlaintextFastUMLSProcessor.xml (3.2.2 from SVN) contains this
fixed flow:

<fixedFlow>
<node>SimpleSegmentAnnotator</node>
<node>SentenceDetectorAnnotator</node>
<node>TokenizerAnnotator</node>
<node>LvgAnnotator</node>
<node>ContextDependentTokenizerAnnotator</node>
<node>POSTagger</node>
<!-- <node>ClearPOSTagger</node>  -->
<node>Chunker</node>
<node>AdjustNounPhraseToIncludeFollowingNP</node>
<node>AdjustNounPhraseToIncludeFollowingPPNP</node>
<!--<node>LookupWindowAnnotator</node>-->
<node>DictionaryLookupAnnotatorDB</node>
<node>DrugNER</node>
<node>DependencyParser</node>
<node>SemanticRoleLabeler</node>
<node>ConstituencyParser</node>
<!-- <node>AssertionAnnotator</node> -->
<!-- <node>StatusAnnotator</node> -->
<!-- <node>NegationAnnotator</node> -->
<node>GenericCleartkAnalysisEngine</node>
<node>HistoryCleartkAnalysisEngine</node>
<node>PolarityCleartkAnalysisEngine</node>
<node>SubjectCleartkAnalysisEngine</node>
<node>UncertaintyCleartkAnalysisEngine</node>

<node>ExtractionPrepAnnotator</node>
</fixedFlow>

Thanks for any help or pointers,

Tom

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