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
