Hello Matt, Thanks for your reply. So currently my concept annotation produces properties are begin, end, concept type, concept Text, externalId, originalexternalID. However the annotation does not include polarity / conditional / uncertain. So shall I use Collection Processing Engine with AggregatePlainTextProcessor followed by AssertionMiniPipeLineAnalysis ? Further I am also trying Peripheral Artery Disease Spotter. However even that annotator returns only Document Annotation.
Thanks Deepal Dhariwal On Thu, Nov 15, 2012 at 9:35 AM, Coarr, Matt <[email protected]> wrote: > 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 > >> > >
