Great. There is a redundant Negation step in one of final sub smoking desc xml's. Leave the Jira as a placeholder to clean up the smoking status desc's.
Sent from my iPhone > On Apr 20, 2015, at 1:11 PM, Tom Devel <[email protected]> wrote: > > Pei, > > I did what you recommended, I run a test input with this new pipeline and > did a diff with the clinical pipeline without the smoking status on the two > CAS files. It seems to do the trick, the Umls concept tags are still the > same, and there is now a new tag for the smoking status annotation, great! > > Before I create the Jira item, what do you mean with removing the last > NegEx? > > In AggregatePlaintextFastUMLSProcessor, the node of the NegationAnnotator > is commented out: > <!-- <node>NegationAnnotator</node> --> > > Did you mean this node? > > At the top of the file, there is an import for the NegationAnnotator: > <delegateAnalysisEngine key="NegationAnnotator">, but it is not commented > out and never run in the fixed flow. > > Am I correct that the negation detection in the clinical pipeline is now > performed by PolarityCleartkAnalysisEngine? > > Thanks, > Tom > >> On Sat, Apr 18, 2015 at 12:53 AM, Pei Chen <[email protected]> wrote: >> >> Tom, >> I would put it at the end of the pipeline (at a min, it should be behind >> sectionizer, sentence, tokenizer, lvg). I would remove >> ExternalBaseAggregateTAE >> as this simulates the sectionizer, sentence, tokenizer, lvg would would be >> redundant. I would also probably remove the last NegEx which could >> override the assertion values. >> >> Disclaimer: I did not test this yet. Feel free to open a Jira item if it >> works for you so it can be tracked. It seems kind of strange to have a >> descriptor xml define another xml descriptor to be loaded up via code >> again- I think this could be simplified. >> --Pei >> >>> On Thu, Apr 16, 2015 at 7:29 PM, Tom Devel <[email protected]> wrote: >>> >>> 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 >>
