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From "Coarr, Matt" <mco...@mitre.org>
Subject Re: Regarding Assertion Tagger
Date Thu, 15 Nov 2012 14:35:24 GMT
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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