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From Deepal Dhariwal <deepaldhari...@gmail.com>
Subject Re: Section Tagging Clinical Notes
Date Fri, 22 Feb 2013 17:58:20 GMT
Hello Chen,

Thanks a lot for informing. I'll follow the jira issue.

Further I had also doubt regarding the assertion annotator. I have been
using ctakes document processor on i2b2 data set. However even for terms
such as "no shortness of breath" , the assertion results are as follows:
confidence = 1.0
polarity = -1
uncertainty = 0
conditional = false
generic = false
subject = patient
entity = null

Kindly let me know how to detect negation using ctakes assertion annotator.
Identifying whether the condition is present or absent is important in my
work.

Regards
Deepal Dhariwal

On Fri, Feb 22, 2013 at 12:47 PM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

> Hi Deepal,
> Just an FYI:
> It looks like SectionSegmentAnnotator.java is in core, but the sample
> SectionSegmentAnnotator.xml descriptor is in ctakes-clinical-pipeline.
> https://issues.apache.org/jira/browse/CTAKES-169 has been opened to fix
> this.
>
> --Pei
>
> > -----Original Message-----
> > From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> > Sent: Saturday, February 16, 2013 6:01 PM
> > To: <ctakes-dev@incubator.apache.org>
> > Cc: ctakes-dev@incubator.apache.org; ctakes-user@incubator.apache.org
> > Subject: Re: Section Tagging Clinical Notes
> >
> > No. There should be one called SectionSegmentAnnotator.
> >
> > Sent from my iPhone
> >
> > On Feb 16, 2013, at 5:57 PM, "Deepal Dhariwal"
> > <deepaldhariwal@gmail.com> wrote:
> >
> > > Hello Pei,
> > >
> > > Thanks for your quick reply. Are you referring to Simple Segment
> > > Annotator from ctakes coredesc / analysis engine ?
> > > Reference:
> > > https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+-+Core#cTAKES25-Core-S
> > > impleSegmentAnnotatorxml
> > >
> > > Regards
> > > Deepal Dhariwal
> > >
> > >
> > > On Sat, Feb 16, 2013 at 5:23 PM, Chen, Pei
> > > <Pei.Chen@childrens.harvard.edu>wrote:
> > >
> > >> Hi Deepal,
> > >> Check out the SectionSegmentAnnotator from ctakes-core project which
> > >> was contributed by the MIT folks. There is a simple XML config for
> > >> heading names.
> > >>
> > >> --Pei
> > >>
> > >> On Feb 16, 2013, at 1:58 PM, "Deepal Dhariwal"
> > >> <deepaldhariwal@gmail.com>
> > >> wrote:
> > >>
> > >>> Hello all,
> > >>>
> > >>> I was looking at
> > >>> SecTag<
> > >> http://knowledgemap.mc.vanderbilt.edu/research/content/sectag-
> > tagging
> > >> -clinical-note-section-headers
> > >>>
> > >>> and
> > >>> I was wondering whether ctakes has a provision or are planning to
> > >>> have a Section Tag annotator. i.e. it annotates "History of Previous
> > >>> Illness", "Medications on Admission" as section headers in clinical
> > documents.
> > >>>
> > >>> Regards
> > >>> Deepal Dhariwal
> > >>
>

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