Hi Deepal, The Concept annotation is an internal temporary annotation used by the assertion module (created based on the combination of the entity mention and ontology concepts).
The assertion module does not produce new annotations. Instead it sets properties on the existing entity mention annotations (the properties are polarity, conditional, and uncertainty). Matt On 2012-11-15 07:44 , "Deepal Dhariwal" <[email protected]> wrote: >Hello Chen, > >Thanks for your reply. I tried AggregatePlainTextUMLSProcessor Analysis >Engine from cdpdesc. However it does not return assertion for presence of >medical concept. The org.mitre.medfacts.type.Concept returns begin, end >of >span, concept Type, concept Text and not whether the concept is >conditionally present or absent. >Thanks for log file. It is found in Tools -> View Log file. > >Regards >Deepal Dhariwal > >On Wed, Nov 14, 2012 at 4:59 PM, Chen, Pei ><[email protected]>wrote: > >> Fyi >> Also feel free to subscribe to the dev group. >> >> -----Original Message----- >> From: Chen, Pei [mailto:[email protected]] >> Sent: Wednesday, November 14, 2012 3:20 PM >> To: <[email protected]> >> Cc: [email protected]; [email protected] >> Subject: Re: Regarding Assertion Tagger >> >> Hi Deepal, >> I presume you are using v2.5. >> Did you know that the DefaultAggregatePipeline.xml from the cdp(clinical >> documents pipeline) folder should already have the negation/assertion >> module included for the identified annotations? >> >> Re:log in the CVD. There should be a menu option in the UIMA CVD >>view>log >> file. >> I hope that helps. >> >> Sent from my iPhone >> >> On Nov 14, 2012, at 9:09 PM, "Deepal Dhariwal" >><[email protected]> >> wrote: >> >> > ---------- Forwarded message ---------- >> > From: Deepal Dhariwal <[email protected]> >> > Date: Wed, Nov 14, 2012 at 8:37 AM >> > Subject: Regarding Assertion Tagger >> > To: [email protected] >> > >> > >> > Hello >> > I want to assert presence of medical terms using cTAKESdesc \ >> > assertiondesc \ AssertionAnalysisEngine. However when I load and >> > execute this analysis engine using cTakes CVD I am getting the >>following >> exception. >> > org.apache.uima.analysis_engine.AnalysisEngineProcessException: >> > Anootator processing failed. More detailed information is in the log >> file. >> > >> > Kindly let me know the cause of exception and the location where log >> > files are generated. >> > >> > Thanks >> > Deepal Dhariwal >>
