Yu, There should be an attribute within any of the IdentifiedAnnotation(or Subclasses) called polarity. It's -1 if it's negated. For example:
- *polarity* = -1 - [image: Inline image 1] On Fri, Dec 12, 2014 at 4:17 PM, Liang, Yu <yu.li...@nyumc.org> wrote: > Last Question, thanks for your patience. > > Here is the result I run the AggregatePlaintextFastUMLSProcessor.xml by > using the real medical note. But I cannot find the negation result. > > > Yu Liang > > CHIBI > > > > > > On Dec 12, 2014, at 3:59 PM, Pei Chen <chen...@apache.org> wrote: > > Yes, Negation is handled by the new > <node>PolarityCleartkAnalysisEngine</node> > Within IdentifiedAnnotation, there should be a polarity() attribute that > should be populated. > > On Fri, Dec 12, 2014 at 3:55 PM, Liang, Yu <yu.li...@nyumc.org> wrote: > >> Thanks soooooooooo much!! Very Awesome ! I am not like a java person, so >> kind of totally lost. So I also see there includes NegationAnnotator, >> right? So don’t have to run NEcontext component?! >> Yu Liang >> >> CHIBI >> >> >> >> >> >> On Dec 12, 2014, at 3:51 PM, Pei Chen <chen...@apache.org> wrote: >> >> Hi Yu, >> That is correct. If you take a look at any of the 'Aggregate' >> examples, >> it should already have something like this defined in the xml 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>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> >> >> You should see the results in your CVD, look for >> **.IdentifiedAnnotation (Those are the Named Entities + Attributes that >> have been extracted and normalized to an UMLS CUI.) >> >> On Fri, Dec 12, 2014 at 3:45 PM, Liang, Yu <yu.li...@nyumc.org> wrote: >> >>> Thanks for your quick reply. So I am not quite sure if I understand >>> correctly, that is , if I ONLY run AggregatePlaintextFastUMLSProcessor.xml, >>> I don’t need to run the Segment, Sentence, Tokenizer, Chunker, dictionary >>> lookup in sequency? >>> Yu Liang >>> >>> CHIBI >>> >>> >>> >>> >>> >>> On Dec 12, 2014, at 3:40 PM, Pei Chen <chen...@apache.org> wrote: >>> >>> [+Dev] >>> Yu, >>> It's great that you have the AggregatePlaintextFastUMLSProcessor.xml >>> running. I presume it's returning IdentifiedAnnotations for you. >>> >>> Long answer: >>> The error "JCas type xyz is used in Java Code but not declared in XML" >>> is caused by the fact that the type system is not imported. Normally, this >>> could be fixed by adding in your primitive xml descriptor: >>> <typeSystemDescription> >>> <imports> >>> <import name="org.apache.ctakes.typesystem.types.TypeSystem"/> >>> </imports> >>> </typeSystemDescription> >>> But it should be already added in the SimpleSegmentAnnotator which is >>> part of the Aggregate examples. >>> The Dictionary lookup annotatorUMLS.xml was not intended to be used by >>> itself because it requires the other components such as Segment, Sentence, >>> Tokenizer, Chunker, etc. to work properly[1]. >>> >>> [1] >>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Component+Use+Guide#cTAKES3.2ComponentUseGuide-ComponentDependencies >>> >>> >>> On Fri, Dec 12, 2014 at 3:26 PM, Liang, Yu <yu.li...@nyumc.org> wrote: >>> >>>> I do have them, and I add them into the code where need the >>>> substitution. Loading is good, no error, and run >>>> AggregatePlaintextFastUMLSProcessor.xml with no error message. >>>> But when try to run other AE, like "dictionarylookupannotatorUMS.xml “ >>>> , the error is as in the previous email. Do you have any idea? >>>> Also, I tried to find the log file to check the detailed error info. >>>> it is weird that I click the “view log” from the pull-down menu, it says: >>>> “no /Users/yu/uima.log”. >>>> >>>> Yu Liang >>>> >>>> CHIBI >>>> >>>> >>>> >>>> >>>> >>>> On Dec 12, 2014, at 2:52 PM, Pei Chen <chen...@apache.org> wrote: >>>> >>>> Yu, >>>> Do you have an UMLS username and password so you can use the UMLS >>>> resources/dictionaries? (you can request a free one here: >>>> https://uts.nlm.nih.gov//license.html) >>>> >>>> I would suggest you use the AggregatePlaintextFastUMLSProcessor.xml >>>> >>>> >>>> On Fri, Dec 12, 2014 at 2:48 PM, Liang, Yu <yu.li...@nyumc.org> wrote: >>>> >>>>> Hi, >>>>> >>>>> I have a problem when using cTakes, our purpose is to annotate >>>>> medical notes using cTakes with build in UMLS dictionary. And It is fine >>>>> to >>>>> run the AggregatePlaintextProcessor.xml. >>>>> But when I try to run other analysis engine, always get this similar >>>>> error messages below. Could you help me out? Appreciate! This is one error >>>>> message after load and run AE called Dictionary lookup annotatorUMLS.xml. >>>>> Loading AE is good though. >>>>> Thanks again! Hope to hearing from you soon. Because I am in urgent to >>>>> use this and present my results. >>>>> >>>>> >>>>> <Screen Shot 2014-12-12 at 2.45.38 PM.png> >>>>> Yu Liang >>>>> >>>>> CHIBI >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> > >