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From Deepal Dhariwal <deepaldhari...@gmail.com>
Subject Re: Regarding Assertion Tagger
Date Thu, 15 Nov 2012 15:09:06 GMT
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 <mcoarr@mitre.org> 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" <deepaldhariwal@gmail.com> 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
> ><Pei.Chen@childrens.harvard.edu>wrote:
> >
> >> Fyi
> >> Also feel free to subscribe to the dev group.
> >>
> >> -----Original Message-----
> >> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> >> Sent: Wednesday, November 14, 2012 3:20 PM
> >> To: <ctakes-dev@incubator.apache.org>
> >> Cc: ctakes-users@incubator.apache.org; ctakes-dev@incubator.apache.org
> >> 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"
> >><deepaldhariwal@gmail.com>
> >> wrote:
> >>
> >> > ---------- Forwarded message ----------
> >> > From: Deepal Dhariwal <deepaldhariwal@gmail.com>
> >> > Date: Wed, Nov 14, 2012 at 8:37 AM
> >> > Subject: Regarding Assertion Tagger
> >> > To: ctakes-users@incubator.apache.org
> >> >
> >> >
> >> > 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
> >>
>
>

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